Feel free to discuss with Hypothesis.is
You can check out the new platform — which is essentially a short-form blog — by heading to www.DonaldJTrump.com/desk.
Apparently he's invented the idea of a microblog? And he's got a /desk page?
What comes next?
But let's be honest, he was posting these short status updates like this just a few days after he got kicked off of Twitter. He's just got a slightly better UI now.
How to Take Smart Notes
book to read
S. Y. Oh, et al., ACS Appl. Mater. Interfaces 10, 13729–13740
To add on wearable skin electronics, the created sweat glucose and pH sensors. The sensors were created out of carbon nanotubes combined with different polymers.
G. Schwartz, et al., Nat. Commun. 4, 1859
They have created a flexible pressure sensor which has the capability of non-invasive continuous radial artery pule monitoring. It is stated that this has the capability of being a breakthrough for wearable cardiovascular health monitoring.
H. C. Ko, et al., Nature 454, 748–753
They created an hemispherical optoelectronic device that can replicate the functions and characteristics of a human eye such as a wide field of view and low aberrations. This electronic device is based off of single-crystalline silicon and is compressible, which enables the hemispherical shape.
S. Choi, et al., Nat. Nanotechnol. 13, 1048–1056
Here, biocompatable and stretchable materials were tested for implant use. Gold coated silver nanowires within a polymer were tested to see its conductivity. Using this material they were able to fabricate wearable and implantable soft bioelectronic devices that can be conformally integrated with human skin.
J. A. Rogers, T. Someya, Y. Huang. Science 327, 1603–1607
They reviewed materials that maintain proper electronic properties while having the ability to be stretched, compressed, twisted, bent, and deformed. They discussed different applications for these technologies and possible commercialization.
T. Sekitani, et al.,Science 326, 1516–1519 (2009)
They used transistors with a floating gate embedded in hybrid dielectrics at a nanoscale of size, and created a flexible array of these floating gate transistors. They coupled this with a pressure sensitive rubber sheet, and the result was a matrix that was able to read mechanical pressure and store it as an image.
C. Choi, et al., Nat. Commun. 8,
They test a high density, hemispherical image sensor array comprised of an atomically small MoS2 heterostructure that has the capability of releasing strain. They deem this device to be capable of being a soft retinal implant capable of various imaging elements.
I. R. Minev, et al., Science 347, 159–163 (2015).
Stiff-neural implants have very rare compatibility with soft-neural tissues. Therefore an soft-neural implant was configured that is elastic like dura matter (the protective membrane of the spinal cord).
Y. M. Song, Yet al., Nature 497
An elastomeric camera was created in the likeness of ant and beetle eyes. These cameras have close to full hemispherical shapes, at around 160 degrees. This hopes to copy arthropods who have wide-angle field of view, low aberrations, high acuity to motion and an infinite depth of field which are all difficult to replicate.
1. W. Gao, et al., Nature 529, 509–514 (2016).
A self-healing system was created that was capable of automatically repair damage from repeating events. They used a coating-substrate (a substance on which an enzyme acts) to deliver healing agents to cracks within the polymer.
S. Xu, et al., Science 344, 70–74 (2014).
They created a thin, comfortable device that can be laminated or stuck to the skin of a person to allow for the monitoring of physiological monitoring for the user. Examples of this could be heart rate or blood pressure. This is also a wireless device.
D. H. Kim, et al., Nat. Mater
A non-invasive ultra-thin electronic interface was created what is capable of being mounted on tissue using a a protein called fibroin which can be obtained from silk. This protein is capable of being absorbed back into the tissue which results in the mounting of the device. These electronics are capable of neural mapping of the brain.
X. Yu, et al., Nature 575, 473–479 (2019).
They created a wireless, battery free, touch based electronic system that is capable of being placed onto the skin. This technology has the capability of communicating information through vibrations. They also have the capability of being used for VR.
Y. Chen, A. M. Kushner, G. A. Williams, Z. Guan, Nat. Chem
A multiple phase heat sensitive rubber like material was created. This substance is extremely tough and durable while also having the capability of self-healing.
D.-H. Kim, et al., Science 320, 507–511 (2008).
An easily foldable and stretchable circuit was created using silicon, a good semi-conductive metal. They combined the silicon with rubber like plastic material to help create the flexibility of the circuit.
Create an account using the sidebar on the right of the screen.
first note
Be sure to make notes while reading and write a little summary at the end. This will help greatly when you need to look back at the text.
I try to keep a note of what I read, which I probably would not do if I was not writing a blog
I've recently shifted into a frame of mind where I think that, if I'm reading something (something that isn't obviously news or entertainment), I should be making notes. If I'm not making notes, then I'm probably wasting my time reading that particular piece of content.
Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis
A flexible sensor device was created with the ability to analyze different elements/compounds found within sweat such as glucose and sodium while also monitoring skin temperature. All of this is fully integrated within the system so no outside analysis is needed.
One can now picture a future investigator in his laboratory. His hands are free, and he is not anchored. As he moves about and observes, he photographs and comments. Time is automatically recorded to tie the two records together. If he goes into the field, he may be connected by radio to his recorder. As he ponders over his notes in the evening, he again talks his comments into the record. His typed record, as well as his photographs, may both be in miniature, so that he projects them for examination.
This is one of the most important aspects of the essay. Noting that he is continuously talking about the work of a scientist, he stresses the act of recording, of looking at reality. This is radically different from what Ahrens claims in his book "How to take Smart Notes", in which there is not a single hint to the fact that you must look through the window and not just into previous works.
Preparatory remarks on the concept of an invisible hand: 1. The concept of an invisible hand plays a vital role in Karl’s analysis, even though Smith refers to it explicitly only twice in his two major books, once in The Wealth of Nations, and once in The Theory of Moral Sentiments(2005 [1759]). 2. While there is no generally agreed-upon definition of what is meant by an invisible hand, we shall employ the approach of Ullmann-Margalit (1978), which even Samuels (2011, 291) appears to regard as above reproach.
more positive-sounding term spontaneous order than the more mystical-sounding invisible hand. Others, however, prefer to use another term. ‘I prefer the term “unintended order” to the more familiar “spontaneous order” because the former conveys that the system of order was not anyone’s intentional design without suggesting, as “spontaneous” might, that there is no way to account for the creation of the system’ (Otteson 2002, 6; see also Otteson 2007, 21).
The importance of accountability is implied by introducing the term - "unintended order".
Hayek is thus informing us that the framework of our analysis should include institutions that are ‘The results of Human Action but not of Human Design’.
Hayek notes that if we confine our arguments to the natural and artificial realms confusion is bound to ensure: ‘... one would describe a social institution as “natural” because it had never been deliberately designed, while another would describe the same institution as “artificial” because it resulted from human action’ (Hayek 1967, 130)
Preparatory remarks on the concept of an invisible hand: Suppose we identify an order in human affairs. On further investigation we ascertain that although the regularity came about as a result of human action, it did not arise from human deliberation. In other words, the order did not arise from human design. Under such conditions, says Ullmann-Margalit (1978, 263), we have an invisible hand explanation. She refers to this realm of things that results from human action but not from human design as a middle realm (1978, footnote 2) and cites Hayek (1966 and 1960) as her source. An example that comes most readily to the fore as an invisible hand explanation is the one associated with the creation of money (Ullmann-Margalit 1978, 264) or the emergence of language.
Long before there was the Internet, there was the commonplace book — a creative and intellectual ledger of fragmentary inspirations, which a writer would collect from other books and copy into a notebook, often alongside his or her reflections and riffs. These borrowed ideas are in dialogue with the writer’s own imagination and foment it into original thinking. Over long enough a period of time — years, decades, often a lifetime — the commonplace book, while composed primarily of copied passages, comes to radiate the singular sensibility of its keeper: beliefs are refined, ideas incubated, intellectual fixations fleshed out, and the outlines of a personhood revealed. (Brain Pickings is, in an unshakable sense, a commonplace book.)
Notions, Notes, Ideas and work notes
My equivalent, as best as I can tell, is:
resources written down with the context added of how I found them and why I was interested
I might also use Zotero to capture the original resource, with a few notes alongside it to explain why I kept it.
They can be linked to Ideas, Notes or Notions, or may give rise to them, but they serve a purpose firmly rooted in ongoing work. They are always placed within the context, and folder, of a specific project
Similar to how I've come to think of my "admin" or "operational" notes. They're instrumental in that they serve a purpose that is usually about moving some project forward.
We encourage people to use the daily notes and to brainstorm and brain dump, and just write all the things they’re thinking. I think that the first thing that we’re interested in is, how do you build systems so that it’s easy for you to take those and gradually refine them?
Conor is asking himself, how do you get people to take (daily) notes, and how do you get them to refine them.
One major advantage of Lotus Notes is that it allows all the major information organization techniques to be used in one information space: outlines, graphics, hypertext links, relational databases, free (rich) text, expanding/collapsing reports, collapsi ng rich text sections, tabbed notebooks (like wizards) and tables. In other words, Lotus Notes is a hodgepodge of every information organization technique Lotus could think of, all thrown into one quirky product. As such, it is phenomenally satisfying a nd phenomenally frustrating at the same time.
John Redmood claims that the advantage of Lotus Notes was that it brought together a wide range of information organization techniques: outlines, graphics, hypertext links, relational database, expanding/collapsing reports, collapsing rich text sections, tabbed notebooks and tables.
With Lotus Notes, I can combine a hierarchically organized outline view of the documents, with full text searching, hypertext links and traditiona l relational database like reports (for example, a sorted view of items to do).
What Lotus Notes allowed you to do is to combine a hierarchical organized overview, achieved through an outliner, with search, hyperlinks and relational-database-like reports. Lotus Notes also allowed you to organized different document formats (Word, emails, etc.)
o visualize the data in UCSC genome browser, clic
Provide trainees with a long period here to look at ucsc and play with it (time permitting)
Recovering exon info
So we have the original exon list, and we have a list of exon IDs, and the exon IDs on their own aren't very useful, so, let's find the exons in the original file which match these exon IDs
ount the number
Q: Ok, given last file, how would we figure this out? anyone know it in excel?
fall into that exon?
Again, numbers may be diff, compare with students
Find exons with the most SNPs
Q: What datasets do you have? How would you could about figuring this out? what information would you use?
Again open the UCSC Main - table brows
go back and do it again! It's the same thing over again
When the dataset is green
I usually just open the dataset and discuss what an exon is (genomic region w/ annotation.)
Now set the following parameters:
i'll read the parameters, but, they can check against the tutorial to be sure they're doing the right variables.
Rename your history
This is such an important step! So easy for students to get lost in their histories, remind them that it's normal, it happens to us, and life will be so much easier if they name things well.
Browse to your favourite
everyone should be logged into usegalaxy.eu by now
Background
Users can read if they like, but, not very important. Some people just really want to know the science, even though it's not relevant to what you're doing, which is learning how to manipulate the galaxy ui
We start with the question: In human chromosome 22, which exon has the highest number of single nucleotide polymorphisms (SNPs)?
Important to note for students, that they understand this central question
So I guess what @Rich-Harris is trying to say is that (sorry, I'm just logging it here for my own benefit)
The quickness of social media allows for forms of vitriol that do not exactly support thoughtful debate. We need to cherish the longer forms.
Course and Students
This study has a robust sample size that will be adequate for the statistical analyses. The experimental design is clear, with the manipulation of the independent variable as the grading format as handwritten or electronic.
Le rapport demande d’anonymiser le lycée d’origine et de lui substituer une mesure de l’écart entre les résultats du bac et la notation au contrôle continu, dispositif testé cette année pour le bac.
In Roam, each note becomes a node in your mind map, and there’s no central concept you have to start with. The map is fluid, with no hierarchy, no stacking, no linearity. It’s a giant knowledge web representing your notes and the connections between them.
Just like the brain works.
You should construct evergreen (permanent) notes based on concepts, not related to a source (e.g. a book) or an author.
Your mental models are compression functions. You make them more powerful by trying to use them on new information. Are you able to compress the new information with an already acquired function? Yes, then you've discovered an analogous concept across two different sources. Sort of? Then maybe there's an important difference, or maybe it's a clue that your compression function needs updating. And finally, no? Then perhaps this is an indication that you need to construct a new mental model – a new compression function.
Annotations—even inline marginalia which include your own writing—have very little informational value. They’re atomized; they don’t relate to each other; they don’t add up to anything; they’re ultra-compressed; they’re largely unedited. That’s fine: think of them as just a reminder. They say “hey, look at this passage,” with a few words of context to jog your memory about what the passage was about.Since you’re going to write lasting notes anyway, annotations need carry just enough information to recreate your mental context in that moment of reading. You wouldn’t want to rely on that long-term, since then you’d just have a huge pile of hooks you’d have to “follow” anytime you wanted to think about your experience with that book.
Classical marginalia in books, according to Andy Matuschok, have little informational value. They are not interlinked, they're very compressed and usually unedited. But that's okay.
Their purpose is to help you get back to the mental context you were in when you thought the passage was worth returning to.
Update 2020-01-14: I now store my outlines as Structure Zettel. For more information what a Structure Zettel is see this post.
An important update to this piece as Sascha's method evolved. Instead of using outlines to capture new notes, he started using structured notes.
I suspect the reason for this is that a system with atomic notes and structured notes is more clear cut than a system that relies on work-in-progress outlines. The main difference being that a structured note will contain only notes and not some floating, un-evolved ideas.
Instead of having a task like “write an outline of the first chapter,” you have a task like “find notes which seem relevant.” Each step feels doable. This is an executable strategy (see Executable strategy).
Whereas Dr. Sönke Ahrens in How to Make Smart Notes seemed to be saying that the writing of a permanent note (~evergreen note) is a unit of knowledge work with predictable effort & time investment (as well as searching for relevant notes), Andy emphasizes only the note searching activity in this context.
Ericsson claims (2016, p. 98) that there is no deliberate practice possible for knowledge work because there are no objective criteria (so, poor feedback), because the skills aren’t clearly defined, and because techniques for focused skill improvement in these domains aren’t known.
According to Ericsson deliberate practice for knowledge work is not possible because the criteria are not objective (you don't know if you're doing well).
This collides with Dr. Sönke Ahrens' contention that note taking, specifically elaboration, instantiates two feedback loop. One feedback loop in that you can see whether you're capturing the essence of what you're trying to make a note on and a second feedback loop in that you can see whether your note is not only an accurate description of the original idea, but also a complete one.
Put differently, note taking instantiates two feedback loops. One for precision and one for recall.
By contrast, when we’re working on a large work-in-progress manuscript, we’re juggling many ideas in various states of completion. Different parts of the document are at different levels of fidelity. The document is large enough that it’s easy to lose one’s place or to forget where other relevant points are when one returns. Starting and stopping work for the day feel like heavy tasks, drawing heavily on working memory.
One key difference between working with atomic, evergreen notes compared to a draft manuscript is that the ideas in the manuscript are at different levels of evolution / fidelity. The ideas in the evergreen notes are all evolved components.
Instead, nurture the wild idea and let it develop over time by incrementally writing Evergreen notes about small facets of the idea.
If you cannot tackle a subject head on, tackle it obliquely by writing evergreen notes about facets of the idea.
This is an interesting way of reducing the scope of, say, an essay, without sacrificing quality. Instead of writing the whole thing, just write an atomic piece about one of the concepts you need for the larger piece.
The issue of the different layers is similar. If you chose software that doesn’t deal with those layers in a sophisticated way, you will not reap the benefits in the long term. Your archive will note work as a whole. I think that this is one of the reasons why many retreat to project-centered solutions, curating one set of notes for each book, for example. The problems that come with big and organic (= dynamic and living) systems is avoided. But so is the opportunity to create something that is greater than you.
Interesting point where the author compares the barrier that is created between the editing and the writing mode in a wiki (which makes it more cumbersome to continue lines of thought) to the barriers that appear when you're not using the right software or conventions to structure your knowledge items, as well as to structure your knowledge items' structure.
After a while, I did not only have structure notes that structure content notes, I also had structure notes that mainly structured sets of structure notes. They became my top level structure notes because they began to float on the top of my archive, so to say.
After the need for a layer of Hub Notes a new need may emerge: to better organize the Hub Notes themselves. At this point you may want to introduce structure notes that structure sets of structured notes.
Structure notes share a similarity to tags: Both point to sets of notes. Structure notes just add another element. They are sets with added structure. This added structure provides a better overview and adds to the utility of the archive.
Structure notes or Hub Notes are similar to tags (or pages in Roam) in that they point to a collection of other notes (or pages in Roam). The only difference being that structure notes contain within themselves a structure which provides hierarchy and context.
But after a while, you won’t be able to keep up. When I search for tags I get a couple hundred of notes. I have to review them to connect a note to some of them, or get a grasp of what I wrote and thought about a specific topic. Naturally, a need to organize the archive arises at this point. I can’t remember how many notes I had when I experienced this. I introduced hub-like notes when I had between 500 and 700 notes.1 I gave myself an overview of the most important notes on that topic.
There seems to be an inflection point where your initial approach to organizing your Zettelkasten starts to fail (perhaps 500-700 notes). You'll simply have too many tags to choose from.
At this point hub-like notes will be the next stage in the evolution of your Zettelkasten organization.
Est-ce que je peux évaluer les élèves et attribuer des notes durant cette période ?Il s’agit de prévoir des séquences compatibles avec des enseignements à distance et d’adapter le travail demandé aux élèves aux contraintes des ENT. Les travaux demandés s’appuient plus spécifiquement sur des compétences variées adossées au travail autonome.
5. Bosiger YJ, McCormick M. Temporal links in daily activity patterns between coral reef predators and their prey. PLoS One 2014; 9:e111723. doi: 10.1371/journal.pone.0111723 PMID: 25354096
The timing of activity for two predators (rockcod and dottyback, both reef fishes), and their common prey (the lemon damselfish) was compared. The behavior of the prey fish was determined to be a compromise between ideal times for efficient food capture and predator avoidance, with a particularly strong avoidance of the rockcod.
For the present study on blacktip reef sharks, considering the influence of prey activity allowed researchers to explore if factors other than temperature were driving the behavior of sharks.
7. Sims DW, Wearmouth VJ, Southall EJ, Hill JM, Moore P, Rawlinson K, et al. Hunt warm, rest cool: bioenergetic strategy underlying diel vertical migration of a benthic shark. J Anim Ecol 2006; 75:176–190. PMID: 16903055
This previous study of temperature-related shark behavior sought to study the feeding movements of dogfish: a relatively small shark that lives on the bottom of shallow marine environments. Researchers found that dogfish "avoided warmer water even when it was associated with greater food availability" showing a strong preference for colder waters when given the chance.
The similar title of this paper ("Hunt warm, rest cool...") with that of the present study (."..Hunt Warm, Rest Warmer?) suggests that Dr. Papastamatiou and colleagues used the dogfish study as an important source of inspiration for their own study on blacktip reef sharks.
(http://aa.usno.navy.mil/data/docs/MoonFraction.php)
This link does not seem to work, but the data resources of the United States Naval Observatory Astronomical Applications Department can be found at this website.
Release Notes for Ally for LMS
Release notes for Ally
Ruelas_C_OIP
Implementing Accessibility in a Digital Print
LO
Address the design of a variety of instructional media while effectively designing and testing for accessibility
Types of Impairments and Disabilities
Preview of a digital print
Developing a design plan
Give me some specifics on Dyslexia, cognitive disabilities, etc.
recommending listing Step 1 of X, Why is this easier for a person with disabilities?
cool cool i know how to add alt text
Designing Plan Considerations:
Visual - images with alt text
Motor/Mobility - use mouse-free
Auditory - add close captioning
Learning - Add visual cues and dyslexic font
4 kinds of notes
Organizing them are critical in notes. To do so you need a central system. So far, this is how it works with me:
Literature Notes - Use either Kindle (while reading a book)
Fleeting Notes - Custom Shortcuts (while on the phone) , custom Keyboard Maestro script (while on the mac). Also RoamResearch to see connection between ideas!
Permanent Notes - Not yet made... Maybe I can use TiddlyWiki? or Notion?
Project Notes - Devonthink
And I sync all of them to the central notes folder present in document folder in the mac which is indexed by Devonthink.
I guess this annotation itself is a literature notes.
Short feedback loops
Making an Anki note can be considered as making a permanent note as well
he use of a learning analytics tool is always aligned with assessment regimes, which are in turn grounded in epistemological assumptions and pedagogical practices.
Assessment that is grounded in epistemological assumptions on what is knowing and how to know, and pedagogical practices (how to teach?).
I am an avid reader, but I’m always struggling to memorize my learnings. I guess, that's why I started to write down my notes of books I enjoyed to read.
Context notes are used as a map to a series of notes. A context note that outlines a more complex concept or broader subject, using links to other notes in the process. For example, while I’m reading a book, I build an outline of the things I find relevant, based on my highlights and notes of the book. Each of the outline’s items links to a separate note explaining the idea in more detail, and usually contains the highlighted text of the book.
Each note is also given tags for classification. Good tagging helps with accuracy when searching. The method’s recommendation is to use tags for objects, and not for subjects4. In the same note, I write down the ideas I had in mind when highlighting the paragraph, or any connection that comes to mind during this process.
It works!
Note stuff in a textarea element. The text will be stored on localstorage.
La prise de notes est essentielle à la mémorisation et nécessite un entrainement régulier. Dans le cadre de l'enseignement à distance cela peut être un avantage
Il n’est pas possible d’entraîner la mémoire de travail pour en améliorer la performance. En revanche, les autres aptitudes concernées peuvent faire l’objet d’un entraînement.
A défaut de muscler la mémoire, on peut s'entrainer à prendre des notes.
Toutefois avec la popularité croissante des cours en ligne, l’apprenant peut faire une pause à tout moment pour prendre des notes.
Le fait de suivre des cours en ligne peut être un avantage.
Le mode de présentation a aussi un impact
La mémorisation ne dépend pas que de celui qui prend des notes
Open source note taking software article
Please share your most important points from this chapter for our collaborative study notes.
She felt out of place.
Ей было не по себе.
for starters orders
сигналов стартеров
Of course, we've had our ups and downs
Конечно, у нас бывало то лучше, то хуже
processed kind
консервированный
Jean put the ruler down on the conveyor belt.
Джин положила линейку на конвейер. (Прим.: В западных супермаркетах для экономии времени несколько покупателей выгружают продукты на конвейер одновременно. Для того, чтобы кассир видела, где граница, покупатели кладут пластиковую линейку яркого цвета между своими и чужими покупками.)
Think of all the oriental foods you can get into
Как подумаешь, каких только ни бывает восточных продуктов
her individual yoghurt seemed to say it all
казалось, что её единственная упаковка йогурта говорит сама за себя.
a gross offish fingers
оптовая закупка рыбных палочек
You can always tell a person by their shopping
Всегда можно определить, что за человек перед тобой, по его покупкам
when I turned up?
когда я бы вдруг пришла?
a see-through tray of tomatoes which fell casualty to the rest.
прозрачный лоток с помидорами, придавленный другими покупками.
the quick till
касса-экспресс
Jean felt her patience beginning to itch.
Джин чувствовала, что её терпение заканчивается.
giving an accompaniment of nods and headshaking at the appropriate parts.
в такт словам то кивала, то качала головой.
why I should have to put up with her at family occasions.
с какой стати я должна мириться с её присутствием на семейных праздниках.
RSA ANIMATE: Drive: The surprising truth about what motivates us
Notes from Video -Group of students and gave them a set of challenges- to incentivize their performance 3 levels of rewards- High, middle, and lower levels of rewards -mechanical skills- bonuses worked as expected- higher pay brought better performance -rudimentary cognitive skills- larger reward led to poorer performance-rewards don't work that way once you get to rudimentary cognitive skills- defies laws of behavioral physics -did the experiment in india- small rewards (2 weeks salary) medium rewards (1 months salary) highest reward (2 months salary)- Higher incentive led to worse performance -replicated over and over again- simple straight forward tasks- rewards work
Understanding by Design
Notes
they are not meant to be substituted for a recollection that may fail. They constitute, rather, a material and a framework for exercises to be carried out frequently: reading, rereading, meditating, conversing with oneself and with others.
Looking at one's academic notes in this sense, what if students were taught from a young age to view their notes and note taking as a continuous process which required frequent study and conversation? Even in college, students often only refer to notes as a means of remembering a specific fact, statement or concept.
Artificial Neural Networks
三大板块：Hopfield 网络+ 监督学习+非监督学习
Create a note by selecting some text and clicking the butto
Här skriver jag "note" alltså en annotering, kommentarer och feedback till studenten.
followed by failure to interbreed when partial connection between the oceans was reestablished
Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.
Hence, pairs P5-C5 and P6-C6 probably separated during the period of marked shoaling and environmental divergence preceding final closure.
P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.
1. E. Mayr, Animal Species and Evolution (Harvard Univ. Press, Cambridge, 1963).
This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.
D. S. Jordan, Am. Nat. 42, 73 (1908)
Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.
J. A. Coyne and H. A. Orr, Evolution 43, 362 (1989). W. R. Rice, ibid., p. 223.
The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)
D. L. Swofford, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1; (Illinois Natural History Survey, Champaign, IL, 1993).
The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)
J. H. Gillespie, The Causes of Molecular Evolution (Oxford Univ. Press, New York, 1991).
The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)
Genetic divergence before final closure may have been facilitated by changing oceanographic conditions
Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)
J. E. K. Byrnes, L. Gamfeldt, F. Isbell, J. S. Lefcheck, J. N. Griffin, A. Hector, B. J. Cardinale, D. U. Hooper, L. E. Dee, J. E. Duffy, Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions. Methods Ecol. Evol. 5, 111–124 (2014).
Byrne's review focuses on the impacts of assemblage diversity on ecosystem functions.
This study acknowledges the impact of diversity on resource utilization and thus productivity, however the focus is on the characterization of multi-functionality.
C. Fissore, J. Espeleta, E. A. Nater, S. E. Hobbie, P. B. Reich, Limited potential for terrestrial carbon sequestration to offset fossil-fuel emissions in the upper midwestern US. Front. Ecol. Environ. 8, 409–413 (2010).
Fissore's review argues that carbon sequester by forests in the mid-west can not off set fossil fuel based carbon dioxide emissions. The study compares hypothetical scenarios necessary to offset significant proportions of the carbon dioxide emissions by converting landscapes into carbon sequestering species.
R. F. Follett, Soil management concepts and carbon sequestration in cropland soils. Soil Tillage Res. 61, 77–92 (2001).
Follett discusses the role organic soils play in the movement of carbon dioxide from the atmosphere to the soil. This review characterizes terrestrial soils as carbon sinks which is important for crop management.
P. B. Reich, D. Tilman, S. Naeem, D. S. Ellsworth, J. Knops, J. Craine, D. Wedin, J. Trost, Species and functional group diversity independently influence biomass accumulation and its response to CO2 and N. Proc. Natl. Acad. Sci. U.S.A. 101, 10101–10106 (2004).
Reich compares the role of CO2 and N on species richness and functional group diversity.
This study compares the roles of functional group diversity and species richness has on biomass accumulation in an elevated carbon dioxide and nitrogen environment.
R. Sedjo, B. Sohngen, Carbon sequestration in forests and soils, in Annual Review of Resource Economics, G. C. Rausser, Ed. (Annual Reviews, Palo Alto, 2012), vol. 4, pp. 126–143
Sejo discusses the role species richness plays in effecting economic value.
This review puts emphasis on the role of biodiversity on marginal economic value represented as carbon storage for conservation efforts.
D. A. Fornara, D. Tilman, Plant functional composition influences rates of soil carbon and nitrogen accumulation. J. Ecol. 96, 314–322 (2008).
Fornara reviews the mechanisms that control carbon and nitrogen accumulation in soils.
The review covers the relationships between biodiversity and carbon and nitrogen accumulation in soils, with an emphasis on the c3 and c4 grasses.
T. L. Daniels, Integrating forest carbon sequestration into a cap-and-trade program to reduce net CO2 emissions. J. Am. Plann. Assoc. 76, 463–475 (2010).
Daniels reviews the role forests play in reducing atmospheric carbon dioxide levels. His focus however is primarily advocating for including carbon sequester by forests into management plans or a cap-and-trade program.
A. D. Barnosky, N. Matzke, S. Tomiya, G. O. U. Wogan, B. Swartz, T. B. Quental, C. Marshall, J. L. McGuire, E. L. Lindsey, K. C. Maguire, B. Mersey, E. A. Ferrer, Has the Earth's sixth mass extinction already arrived? Nature 471, 51–57 (2011).
Barnosky discusses the events known as mass extinctions and compares the rates of extinction for these events to modern rates of extinction. PB
Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2.
Each additional degree of species richness is worth less than the previous degree of richness in terms of economic value. Therefore, the economic value does not increase in direct proportion with the species richness, although they are correlated.
SC
B. J. Cardinale, K. L. Matulich, D. U. Hooper, J. E. Byrnes, E. Duffy, L. Gamfeldt, P. Balvanera, M. I. O'Connor, A. Gonzalez, The functional role of producer diversity in ecosystems. Am. J. Bot. 98, 572–592 (2011).
Cardinale reviews the roles of primary producer biodiversity with respect to ecological processes critical to the functionality and health of terrestrial and marine ecosystems. PB
predicted secondary structure
Villordo and peers (2015) studied the cycle of how mosquito viruses could quickly adapt to different human host environments. The changes in RNA structures were examined in the dengue virus during host adaptation. The researchers discovered that the 3’UTR of RNA is modified during host adaptation, such as duplicating the structure to accommodate for beneficial mutations.
Musashi-1
Sakakibara and peers studied the Musashi-1 protein within a mouse and associated the protein with neural development. Musashi-1 was found to be highly enriched within the central nervous system of mammalian cells, regulate stem cell translation, and can differentiate into neurons through regulation.
interferes specifically with fetal brain development
Li and others (2016) hypothesized that ZIKV can infect not only developing neuronal stem cells, but also adult brain cells. The results seen were that adults can be affected by the ZIKV. The adult would need to be triply deficient in the regulatory factor for interferon to allow the virus to take hold of the stem cells in the brain.
interferes specifically with fetal brain development
Li and others (2016) hypothesized that ZIKV can infect not only developing neuronal stem cells, but also adult brain cells. The results seen were that adults can be affected by the ZIKV. The adult would need to be triply deficient in the regulatory factor for interferon to allow the virus to take hold of the stem cells in the brain.
effect on fetal neurodevelopment
Cugola et al., (2016) found that ZIKV infects fetuses, causes intrauterine growth restriction (IUGR), and causes signs of microcephaly in mice. Data demonstrated that the infection of ZIKV into human brain organoids reduced proliferation and disrupted cortical layers. This indicates that ZIKV is able to cross the placenta and cause microcephaly by inducing apoptosis in cortical progenitor cells.
it in-creases hyperexcitability in Abprecursor protein(APP) transgenic mice
Side effects of phosphorylation
n-hibition of p38aand p38bimproves Ab-induced
inhibition may have a short term positive effect
Accordingly, the depletion of tau prevents Abtoxicity in AD models (7–9). Ab-induced neuronalnetwork and synaptic dysfunction is associatedwith aberrant glutamatergic synaptic transmis-sion (10).N-methyl-D-aspartate (NMDA)–typeglutamatergic receptors (NRs) drive glutamate-induced neuronal excitotoxicity (11)andmediateAbtoxicity by downstream responses that pro-mote neuronal dysfunction (12
The steps that tau tangles interfere with in the transmittance of signals in the brain.
Aberrant tau phosphorylation is the firststep in a cascade leading to its deposition and tocognitive dysfunction (4,5). Abis thought to trig-ger toxic events, including tau phosphorylation
steps and relevance to Alzheimer's disea
Long-term nutrient enrichment decouples predator and prey production
This article discusses the effect the addition of nutrients has on an aquatic ecosystem. Originally the author hypothesized an increase of energy transfer from prey to predators because of the increase of nutrients. However, this did not occur because the increase in nutrient led to an increase of predator resistant prey.
Stream nutrient enrichment has a greater effect on coarse than on fine benthic organic matter
This article discusses how an increase in nutrients affects the levels of coarse and fine organic litter. It was observed that there were higher levels of fine organic material which led to an increase in bacteria. However, in the stream with no nutrients added to it, there was an increase in both fungal and bacterial communities.
Nutrient enrichment alters storage and fluxes of detritus in a headwater stream ecosystem
This article demonstrates how the addition of nitrogen and phosphorus led to an increase in the production of fine organic compound by more than 300%. The article also mentions that this increase in fine organic compound will have an effect on the entire ecosystem in that area in the long term.
Multiple trophic levels of a forest stream linked to terrestrial litter inputs
This article discusses the importance of terrestrial litter on an aquatic ecosystem. It was observed that organisms that lived in the stream that was being tested were affected the most by the absence of litter and the same effects could be observed throughout the entire ecosystem. However, terrestrial fauna was not affected meaning that it got its carbon from another source.
Lakes and reservoirs as regulators of carbon cycling and climate.
This article mentions the that the rate at which inland water sources release carbon dioxide is equivalent to the rate at which carbon is absorbed by the ocean. Methane is also being release in higher levels from lakes which are beginning to thaw because of increasing temperatures from global warming.
Continental-scale effects of nutrient pollution on stream ecosystem functioning
This experiment was a pan-European research of more than 100 streams in multiple European countries. It helped determine the importance of litter breakdown and states that countries should begin to consider the importance of regulating nutrient levels in aquatic ecosystems.
Ecosystem metabolism and turnover of organic carbon along a blackwater river continuum
This article discusses the respiration rate of an aquatic ecosystem and uses it to determine patterns of activity found within a river during different seasons. It was observed that there were higher levels of respiration when there were was more organic carbon in the river.
Nutrient co-limitation of primary producer communities
This article focuses on how nutrients affect the growth of primary producers. The factors that were observed to have the highest effects on the ecosystems were nitrogen and phosphorus levels.
Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem
This article discusses how the addition of nutrients in an aquatic ecosystem affects secondary production. It was noted that there was an increase in secondary consumers most likely caused because of an increase in prey. There was also an increase of secondary consumer predators. It is mentioned that the increase of nutrients in the two years the survey was done resulted in positive effects for the secondary consumers, however, this might eventually change as the carbon levels in the ecosystem begin to decline because of the higher nutrient levels.
Human influences on nitrogen removal in lakes
This article discusses how human practices have led to a increase of nitrogen levels in lakes. The article also mentions that an increase of phosphorus in lakes resulted in the extraction of higher levels of nitrogen. However, the author also states that laws pertaining to the concentration of phosphorus in aquatic habitats should not be removed or relaxed because phosphorus can also have a negative effect on an ecosystem if found in high concentrations.
Min, K.-T. and Benzer, S. (1997). Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death. Proc. Natl. Acad. Sci. USA 94, 10792-10796.
Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.
GG
Teixeira, L., Ferreira, A. and Ashburner, M. (2008). The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol. 6, e2.
The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.
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Ponton, F., Wilson, K., Holmes, A., Raubenheimer, D., Robinson, K. L. and Simpson, S. J. (2015). Macronutrients mediate the functional relationship between Drosophila and Wolbachia. Proc. Biol. Sci. 282, 20142029.
Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.
GG
Serbus, L. R., White, P. M., Silva, J. P., Rabe, A., Teixeira, L., Albertson, R. and Sullivan, W. (2015). The impact of host diet on Wolbachia titer in Drosophila. PLoS Pathog. 11, e1004777.
Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.
GG
Mouton, L., Henri, H., Charif, D., Bouletreau, M. and Vavre, F. (2007). Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis. Biol. Lett. 3, 210-213. Musselman, L. P., Fink, J. L., Narzinski, K., Ramachandran, P. V., Hathiramani, S. S., Cagan, R. L. and Baranski, T. J. (2011). A high-sugar diet produces obesity and insulin resistance in wild-type Drosophila. Dis. Model. Mech. 4, 842-849.
Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.
GG
Wang, M. and Wang, C. (1993). Characterization of glucose transport system in Drosophila Kc cells. FEBS Lett. 317,241-244.
Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.
GG
Dale, C. and Moran, N. A. (2006). Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453-465
While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.
GG
Christensen, S., Pérez Dulzaides, R., Hedrick, V. E., Momtaz, A. J. M. Z., Nakayasu, E. S., Paul, L. N. and Serbus, L. R. (2016). Wolbachia endosymbionts modify Drosophila ovary protein levels in a context-dependent manner. Appl. Environ. Microbiol. 82, 5354-5363
Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophilaovaries are modified by Wolbachia.
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Bordenstein, S. R. and Bordenstein, S. R. (2011). Temperature affects the tripartite interactions between bacteriophage WO, Wolbachia, and cytoplasmic incompatibility. PLoS ONE 6, e29106. Boyle, L., O'Neill, S. L., Robertson, H. M. and Karr, T. L. (1993). Interspecific and intraspecific horizontal transfer of Wolbachia in Drosophila. Science 260, 1796-1799.
Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.
Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.
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Caragata, E. P., Rancès, E., Hedges, L. M., Gofton, A. W., Johnson, K. N., O'Neill, S. L. and McGraw, E. A. (2013).Dietary cholesterol modulates pathogen blocking by Wolbachia. PLoS Pathog. 9, e1003459.
Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.
GG
D. S. Jordan, Am. Nat. 42, 73 (1908)
Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.
E. Mayr, Animal Species and Evolution (Harvard Univ. Press, Cambridge, 1963).
This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.
Hence, pairs P5-C5 and P6-C6 probably separated during the period of marked shoaling and environmental divergence preceding final closure.
P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.
followed by failure to interbreed when partial connection between the oceans was reestablished
Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.
J. A. Coyne and H. A. Orr, Evolution 43, 362 (1989). W. R. Rice, ibid., p. 223.
The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)
D. L. Swofford, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1; (Illinois Natural History Survey, Champaign, IL, 1993).
The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)
J. H. Gillespie, The Causes of Molecular Evolution (Oxford Univ. Press, New York, 1991).
The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)
Genetic divergence before final closure may have been facilitated by changing oceanographic conditions
Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)
one of the most valuable fish species on the planet (8)
Very open ended statement, what did they consider in order to determine its value?
M. Nei, Genetics 89, 583 (1978)
Nei found the average heterozygosity and genetic distance from a small number of individuals.This paper explains how biases arise in calculations when small samples are used. However, this paper establishes an average that reduces bias. (JP)
R. W. Rubinoff and 1. Rubinoff, Evolution 25, 88 (1971)
This paper, through studying 3 different species of Bathygobius, found that morphological divergence is not correlated with reproductive isolation. Their experiment was testing the extent in which these 3 species had evolved reproductive isolation in the Isthmus of Panama. (JP)
4. E. Bermingham and H. A. Lessios, Proc. Nati. Acad. Sci. U.S.A. 90, 2734 (1993).
This source demonstrates that mitochondrial DNA is able to provide fairly accurate estimates of times since separation of a species in a 3 million year range. Here they also used organisms from the Isthmus of Panama and gel electrophoresis to deduce the time of speciation. (JP)
A. T. Vawter, R. Rosenblatt, G. C. Gorman, Evolution 34, 705 (1980)
The authors of this paper found that, through parsimony analysis of the sequence divergence estimates and of sequence polymorphisms of the Holarctic fish's mtDNA, different Holarctic fish species arose from a geographical event that occurred during the beginning of the mid-Pliocene period.
The authors of this paper cited this source because this source conducts a similar study in deducing a time frame in which speciation of the Holarctic fish occurred. (JP)
H. A. Lessios, Nature 280, 599 (1979)
This source published in 1979 to Nature tests the reliability of the molecular clock hypothesis by using Panamanian sea urchins. The author argues that the molecular clock hypothesis is not tenable or supportable. (JP)
McCauley, D.J., Young, H.S., Dunbar, R.B., Estes, J.A., Semmens, B.X., and Micheli, F. (2012). Assessing the effects of large mobile predators on ecosystem connectivity. Ecol. Appl. 22, 1711–1717.
This study states that sharks in the Palmyra Atoll find food in other habitats.
-RKL
Heithaus, M.R., Frid, A., Wirsing, A.J., and Worm, B. (2008). Predicting ecological consequences of marine top predator declines. Trends Ecol. Evol. 23, 202–210.
The study explains how the effects of a high cost/ low reward way of life may affect an ecosystem -M.A.S
Brown, J.H., Gillooly, J.F., Allen, A.P., Savage, V.M., and West, G.B. (2004). Toward a metabolic theory of ecology. Ecology 85, 1771–1789.
Explains the metabolic equation used in the study -M.A.S.
What is annotation as a genre? I think what he observed in the annotations was a wide range of reader responses, some highly engaging, others less clearly so.
This question seems like it should be more specific to disciplines. What is annotation in the legal world? How about for scientists? For beginning readers?
If I'm annotating a text to make meaning, that's different than if I'm a prof annotating a historical text to provide relevant background. The two notes have only their "noteness" in common, I'd say.
Unfortunately Evernote stopped its syncing service. Only a pay-account can use syncing across more than two devices. This made it useless for millions of users, who are now forced to export their notes and look for a more contemporary, user-loyal alternative.
Headrick, Daniel R. 2000. When Information Came of Age: Technologies of Knowledge in the Age of Reason and Revolution, 1700-1850. Oxford University Press.
Notes (American spelling).
Frequency
Frequency of the note A_x: $$f(A_x) = 440 \cdot 2^{x - 4}$$
Inverse (octave x of the note A_x from frequency f): $$x = \log_2{\frac{f}{440}} + 4 = \log_2{f} + 4 - \log_2{440}$$
64hz-131072hz
Approximately C2–A12
H. Wang, M. A. Winnik, I. Manners, Synthesis and self-assembly of poly(ferrocenyldimethylsilane- b -2-vinylpyridine) diblock copolymers. Macromolecules 40, 3784 (2007).
In this paper, the authors developed a new class of diblock copolymers that have a metal-containing hydrophobic block (PFS) and an organic hydrophilic block (P2VP): PFS = poly(ferrocenyldimethylsilane) and P2VP = poly(2-vinylpyridine). The authors of this publication discovered the ability to obtain spherical and cylindrical morphologies simply by using different alcohols. Having established the ability to obtain cylindrical micelles using the PFS-b-P2VP block copolymer system in isopropyl alcohol, the authors modified their approach in the current study to obtain supermicelles.
P. A. Rupar, G. Cambridge, M. A. Winnik, I. Manners, Reversible cross-linking of polyisoprene coronas in micelles, block comicelles, and hierarchical micelle architectures using Pt(0)–olefin coordination. J. Am. Chem. Soc. 133, 16947 (2011).
This paper established that Karstedt's catalysts ability to cross-link the double bonds in polyisoprene in the absences of silicon-containing molecules. Besides acquiring a variety of morphologies, the authors also investigated their ability to use Karstedt's catalyst to synthesize reversible polymer gel networks.
X. S. Wanget al., Shell-cross-linked cylindrical polyisoprene- b -polyferrocenylsilane (PI- b -PFS) block copolymer micelles: One-dimensional (1D) organometallic nanocylinders. J. Am. Chem. Soc. 129, 5630 (2007).
This reference investigates the development of 1D nano-structures through the use of cross-linked cylindrical micelles. This paper highlights possible applications for these 1D nanomaterials such as microfluidics.
R. K. O’Reilly, C. J. Hawker, K. L. Wooley, Cross-linked block copolymer micelles: functional nanostructures of great potential and versatility. Chem. Soc. Rev. 35, 1068 (2006).
This review paper describes the uses and progress made in the field of cross-linked micelles. Concepts covered include stabilization as well chemical modification and functionalization.
W. Zhanget al., Supramolecular linear heterojunction composed of graphite-like semiconducting nanotubular segments. Science 334, 340 (2011).
References: This paper describes the synthesis of semiconducting nanotubes through a process similar to CDSA by connecting dissimilar junctions, referred to as heterojuntions, to study the behaviors of photocarriers.
Z.-X. Du, J.-T. Xu, Z.-Q. Fan, Micellar morphologies of poly(ε-caprolactone)- b -poly(ethylene oxide) block copolymers in water with a crystalline core. Macromolecules 40, 7633 (2007).
This paper describes the use of a biodegradable polymer in order to obtain a variety of micelle morphologies. A concept referred to as tethering density is used in this paper to explain unexpected morphologies.
Schmelz, M. Karg, T. Hellweg, H. Schmalz, General pathway toward crystalline-core micelles with tunable morphology and corona segregation. ACS Nano 5, 9523 (2011).
This paper uses triblock copolymers to synthesize cylindrical and spherical micelles. By carefully controlling crystallization, the authors were able to control the micellar morphology in a highly selective fashion.
T. Gädt, N. S. Ieong, G. Cambridge, M. A. Winnik, I. Manners, Complex and hierarchical micelle architectures from diblock copolymers using living, crystallization-driven polymerizations. Nat. Mater. 8, 144 (2009).
This paper utilizes CDSA to synthesize noncylindrical block co-micelles. The authors utilized plateletlike micelle and cylindrical micelles in order to form scarflike architectures using platelet-cylindrical and cylindrical-cylindrical connections.
X. S. Wanget al., Cylindrical block copolymer micelles and co-micelles of controlled length and architecture. Science 317, 644 (2007)
This paper describes the discovery of CDSA. The authors draw a comparison to living polymerization and explain the phenomenon of epitaxial crystallization-induced co-micellization
Y. Xia, B. D. Olsen, J. A. Kornfield, R. H. Grubbs, Efficient synthesis of narrowly dispersed brush copolymers and study of their assemblies: The importance of side chain arrangement. J. Am. Chem. Soc. 131, 18525 (2009).
This reference describes the synthesis of brush block and random copolymers. The polymers are referred to as a "brush" because pendant groups are dangling off the main chain. The brush polymers synthesized were amphiphilic and demonstrated self-assembly.
Walther, M. Drechsler, A. H. E. Müller, Structures of amphiphilic Janus discs in aqueous media. Soft Matter 5, 385 (2009).
This paper describes the synthesis of amphiphilic Janus discs using a block terpolymer (three distinct blocks comprised of three distinct monomers). Two different size discs were made where, depending on size, the manner in which the hydrophobic side is "protected" from water can vary. The smaller discs are stabilized by the long hydrophilic polymer chains, protruding out of one side and shielding the hydrophobic side against water. The larger discs undergo aggregation as well as bending to again shield the hydrophobic side from the water by flipping over one part of the structure.
J. Dupont, G. Liu, ABC triblock copolymer hamburger-like micelles, segmented cylinders, and Janus particles. Soft Matter 6, 3654 (2010).
This reference is an example where triblock copolymers were photo-crosslinked to create Janus particles which were classified as "hamburger-like" micelles.
Walther, A. H. E. Müller, Janus particles. Soft Matter 4, 663 (2008)
This review paper discusses a class of noncentrosymmetric nanoparticles referred to as the Janus particle. These particles are rather challenging to synthesize because two different chemistries are present on the surface of the particle.
H. Cui, Z. Chen, S. Zhong, K. L. Wooley, D. J. Pochan, Block copolymer assembly via kinetic control. Science 317, 647 (2007).
This paper utilized charged polymers as well as metal cations and a variety of solvents to kinetically trap unique micelle morphologies. The self-assembly systems were forced down a specific pathway in order to form morphologies that would not have typically occurred without assistance.
L. Zhang, A. Eisenberg, Multiple morphologies of “crew-cut” aggregates of polystyrene-b-poly(acrylic acid) block copolymers. Science 268, 1728 (1995).
This paper was one of the first papers to establish the ability to form micelles of different morphologies (beyond just spherical) for systems using amphiphilic block copolymers
J. F. Soderholm, S. L. Bird, P. Kalab, Y. Sampathkumar, K. Hasegawa, M. Uehara-Bingen, K. Weis, R. Heald, Importazole, a small molecule inhibitor of the transport receptor importin-β. ACS Chem. Biol. 6, 700–708 (2011).
Importazole is a small molecule inhibitor of the transport receptor importin-β. This inhibitor was identified by a screening assay developed by the authors of this paper.
A. J. Firestone, J. S. Weinger, M. Maldonado, K. Barlan, L. D. Langston, M. O’Donnell, V. I. Gelfand, T. M. Kapoor, J. K. Chen, Small-molecule inhibitors of the AAA+ ATPase motor cytoplasmic dynein. Nature 484, 125–129 (2012). doi:10.1038/nature10936 pmid:22425997
This work reported the discovery of ciliobrevins, the first specific small-molecule antagonists of cytoplasmic dynein.
K. V. Butler, J. Kalin, C. Brochier, G. Vistoli, B. Langley, A. P. Kozikowski, Rational design and simple chemistry yield a superior, neuroprotective HDAC6 inhibitor, tubastatin A. J. Am. Chem. Soc. 132, 10842–10846 (2010). doi:10.1021/ja102758v pmid:20614936
This paper reported the development of Tubastatin A, a potent and selective HDAC6 inhibitor.
H. Ouyang, Y. O. Ali, M. Ravichandran, A. Dong, W. Qiu, F. MacKenzie, S. Dhe-Paganon, C. H. Arrowsmith, R. G. Zhai, Protein aggregates are recruited to aggresome by histone deacetylase 6 via unanchored ubiquitin C termini. J. Biol. Chem. 287, 2317–2327 (2012).
This work suggested a novel ubiquitin-mediated signaling pathway, where the exposure of ubiquitin C termini within protein aggregates enables HDAC6 recognition and transport to the aggresome. The authors found that the ubiquitin-binding domain (ZnF-UBP) of HDAC6, instead of recognizing protein aggregates by binding directly to polyubiquitinated proteins, binds exclusively to the unanchored C-terminal diglycine motif of ubiquitin.
Y. Zhang, B. Gilquin, S. Khochbin, P. Matthias, Two catalytic domains are required for protein deacetylation. J. Biol. Chem. 281, 2401–2404 (2006).
In this report, the authors showed that both HDAC domains are required for the intact deacetylase activity of HDAC-6.
Y. Zhang, S. Kwon, T. Yamaguchi, F. Cubizolles, S. Rousseaux, M. Kneissel, C. Cao, N. Li, H. L. Cheng, K. Chua, D. Lombard, A. Mizeracki, G. Matthias, F. W. Alt, S. Khochbin, P. Matthias, Mice lacking histone deacetylase 6 have hyperacetylated tubulin but are viable and develop normally. Mol. Cell. Biol. 28, 1688–1701 (2008). doi:10.1128/MCB.01154-06 pmid:18180281
In this study, the author generated HDAC6 knock out mice and investigated the in vivo functions of HDAC6 and the relevance of tubulin acetylation/deacetylation. they observed that HDAC6-deficient mice are viable and fertile and show hyperacetylated tubulin in most tissues.They concluded that mice survive well without HDAC6 and that tubulin hyperacetylation is not detrimental to normal mammalian development.
I. Kemler, G. Whittaker, A. Helenius, Nuclear import of microinjected influenza virus ribonucleoproteins. Virology 202, 1028–1033 (1994).
This work showed that when influenza virus ribonucleoproteins (vRNPs), devoid of M1, were introduced into the cytoplasm of cells by microinjection, they were found to be imported into the nucleus, and the RNA was transcribed. Their uptake into the nucleus was ATP-dependent, inhibited by antibodies to the nuclear pore complex, unaffected by the prior acidification of the vRNPs, and not inhibited by an anti-virurs, called amantadine. These experiments demonstrated that for productive infection, all the early stages of the viral entry pathway can be bypassed.
anerjee, Y. Yamauchi, A. Helenius, P. Horvath, High-content analysis of sequential events during the early phase of influenza A virus infection. PLOS ONE 8, e68450 (2013).
This study provides a powerful high-throughput platform to understand the host cell processes. The authors developed quantitative, imaging-based assays to dissect seven consecutive steps in the early phases of IAV infection in tissue culture cells.
K. S. Matlin, H. Reggio, A. Helenius, K. Simons, Infectious entry pathway of influenza virus in a canine kidney cell line. J. Cell Biol. 91, 601–613 (1981).
This work investigated the cell fusion process of representatives of 3 families of enveloped viruses. it was discovered that hemagglutinin plays a role for the influenza in the low-pH-dependent membrane fusion activity. Low-pH-induced fusion is a widespread property of enveloped animal viruses and that it may play a role in the infective process.
L. H. Pinto, L. J. Holsinger, R. A. Lamb, Influenza virus M2 protein has ion channel activity. Cell 69, 517–528 (1992).
The authors of this paper identified the ion channel activity of M2.