1. Last 7 days
    1. AbstractBackground Single-cell RNA-seq suffers from unwanted technical variation between cells, caused by its complex experiments and shallow sequencing depths. Many conventional normalization methods try to remove this variation by calculating the relative gene expression per cell. However, their choice of the Maximum Likelihood estimator is not ideal for this application.Results We present GTestimate, a new normalization method based on the Good-Turing estimator, which improves upon conventional normalization methods by accounting for unobserved genes. To validate GTestimate we developed a novel cell targeted PCR-amplification approach (cta-seq), which enables ultra-deep sequencing of single cells. Based on this data we show that the Good-Turing estimator improves relative gene expression estimation and cell-cell distance estimation. Finally, we use GTestimate’s compatibility with Seurat workflows to explore three common example data-sets and show how it can improve downstream results.Conclusion By choosing a more suitable estimator for the relative gene expression per cell, we were able to improve scRNA-seq normalization, with potentially large implications for downstream results. GTestimate is available as an easy-to-use R-package and compatible with a variety of workflows, which should enable widespread adoption.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giaf084), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 1: Gregory Schwartz

      In this manuscript, Fahrenberger et al. propose a new scRNA-seq normalization method to more accurately report UMI counts of individual cells. They specifically use a Good-Turing estimator, compared with a more commonly used Maximum Likelihood estimator, to adjust raw UMI counts. Using their own cta-seq, a cell targeted PCR-amplification strategy, as ground truth, they compare their estimator with a traditional size-corrected estimator. Furthermore, they illustrate downstream changes using their method, including changes to clustering results and spatial transcriptomic readouts. The manuscript was a clear read and presents an interesting alternative solution to an often overlooked, but important, problem. However, there are some aspects of the manuscript that need to be addressed. Some major content missing includes comparisons with more widely-used normalization methods throughout the manuscript, and better ground truth data sets in their downstream analysis. Specific comments are as follows:

      l. 34: To my knowledge, most groups do not use a single division by total UMI count as the only normalization. Seurat has NormalizeData, but also heavily promotes scTransform, a completely different method. Many use log transform (as I believe was done here), some use quantile transform, others use regression techniques etc. It was odd to see these standard normalizations missing in comparisons. The authors should use such standard procedures to demonstrate the superiority of GT.

      l. 42: Is there a justification for the successor function being applied within the frequency ((cg + 1) / total) instead of outside ((cg / total) + 1) as is expected with the Good-Turing estimation?

      Furthermore, there is typically a smoothing function for erratic N_cg values, which I would expect with single-cell data. In the methods there is a brief mention of linear smoothing, but that would imply that the GT equation is misleading and oversimplified. The actual equation should be included in the main text to avoid confusion.

      l. 58: Compared to 16,965 reads average per cell, what is the equivalent for the ultra-deep sequencing (not 23 million reads, as that is not 7.4 fold increase)?

      I am not entirely convinced on the use of cta-seq as a ground-truth for the cells, especially in comparison with ML. The authors should show that cta-seq has similar UMI and gene count distributions to more popular scRNA-seq technologies (e.g. 10x Chromium) or the application may be specific to cta-seq only.

      l. 110: Instead of using unknown classification data sets, there are existing cell-sorted data sets with ground truths (many even on the 10x website). The authors should use these data sets to compare downstream analysis.

      l. 125: The spatial transcriptomic results were very subjective, with no statistical hypotheses. The entire manuscript is missing any sort of statistics when comparing methods, which is a major flaw and should be rectified. Here specifically, the color scale stops at 3, but does this carry over to the relative differential expression? The claim is that it is constant, but if they are all greater than 3 then they must be quite variable, so it is surprising to see such a constant value of 0. Maybe the complete color scale should be shown on all figures to clarify this.

      From my understanding of the manuscript, the 18 cells for analysis and comparison were chosen based on a typical Seurat analysis. This technique introduces a range of biases into the comparison and makes the argument a bit circular.

      For a bias example, the top 2000 most variable genes were used, suggesting that entire classes of genes may be ignored even when highly or lowly expressed, such as housekeeping genes.

      There also appears to be many steps that were not entire justified outside of a "typical analysis", for example excluding a cluster in the analysis (just because it was not that large?), only selection 18 cells (why 6 from each cluster?), removing cells with less than 1000 expressed genes or over 8% mitochrondrial reads (this may be an issue, and removing specific cell types or proliferating cells, this should be a bivariate removal with justification). All of these filterings remove generalizeability of GT.

      Supplementary Figures in the text hyperlink to the main figures which is confusing. More importantly, the caption of Supplementary Figures read "Figure" rather than "Supplementary Figures".

    1. Neuroscience studies demonstrate this divergence, showing distinct brain activation patterns when patients receive identical personalized conversations from AI ver-sus human providers (Yun et al., 2021).

      Another important thing to note is that AI cannot connect and interact with another person as humans can with each other.

    2. For instance, AI demonstrates dermato-logical diagnostic accuracy through image analysis that matches or exceeds board-certified dermatologists (Leachman & Merlino, 2017).

      AI can be greater and smarter than humans, but with the drawback of also making mistakes that it must learn from first to not make again.

    3. AI’s advanced capacity to process medical data, text, images, and biological information has led to increasingly diverse and widespread healthcare applica-tions.

      AI has a great ability and range of applications as it can be used for such a wide variety of things effectively, especially in healthcare.

    4. However, most studies conceptual-ize efficiency and quality as isolated dimensions, rarely examining how AI assistance affects both dimensions simultaneously.

      People are not being brought to the light about how AI is negatively affecting the workplace, as AI has been glorified as this sort of do-no-wrong type of machine that can help you do what you need to get done with no drawbacks.

    5. Therefore, this study redirects scholarly attention from patient to physician behaviors, systematically examining AI’s effects on both workflow efficiency and clinical quality.

      The topic of the article along with the effects of AI in the workplace, along with clinical quality.

    1. What if your biggest competitive asset is not how fast AI helps you work, but how well you question what it produces?

      The idea that AI isn't all-knowing, but rather we should doubt it and apply ourselves as it was made by humans after all.

    2. Continuous engagement with AI-generated content leads workers to second-guess their instincts and over-rely on AI guidance, often without realizing it.

      Continuation of my previous point that AI is simply becoming problematic as we further its use and advancement.

    3. One recent study found that in 40 per cent of tasks, knowledge workers —those who turn information into decisions or deliverables, like writers, analysts and designers —accepted AI outputs uncriticallywith zero scrutiny.

      If the workers accept the word of AI blindly, then the owners also accept the word of what the workers gave them, we will be in a world completely run by AI.

    4. One study found that users have a tendency to follow AI advice even when it contradicts their own judgment, resulting in a decline in confidence and autonomous decision-making.

      This is concerning, as the only thing we believe we can trust, we go against constantly because a chatbot or AI tells us otherwise.

    5. Such shifts can affect how people make decisions, calibrate trust and maintain psychological safety in AI-mediated environments.

      AI is far stronger than we realize, even affecting humans on a psychological level, weakening our abilities to think critically, making us more dependent on the AI, and making us lazier.

    6. Workers can end up deferring to AI as an authority despite its lack of lived experience, moral reasoning or contextual understanding.

      Just more of automation bias, as they would take AI as authority and omnipotent.

    7. One recent emerging studytracked professionals’ brain activity over four months and found that ChatGPT users exhibited 55 per cent less neural connectivity compared to those working unassisted. They struggled to remember the essays they just co-authored moments later, as well reduced creative engagement.

      Even the act of using AI consistently is actively weakening the neural connectivity of the brain.

    8. AI-generated outputs appear fluent and objective, they can be accepted uncritically, creating an inflated sense of confidenceand a dangerous illusion of competence.

      Essentially, automation bias as we believe it blindly without thought.

    9. Resilience has become something of a corporate buzzword, but genuine resilience can help organizations adapt to AI.

      We need to resist AI in a sort of way, as if we do not, it will eventually be our downfall.

    10. As we are starting to see, the drive for efficiency will not decide which firms are most successful; the ability to interpret and critically assess AI outputs will.

      This is how to truly use AI for good in the workplace, maximizing its abilities and usage.

    11. As researchers who study AI, psychology, human-computer interaction and ethics, we are deeply concerned with the hidden effects and consequences of AI use.

      Time and time again, AI is being perceived as a potential threat to mankind. The fact that we continue to pursue it could be our downfall, the vaulting ambition of our race.

    12. If people don’t set these defaults, tools like AI will instead.

      Incredibly short yet powerful on how AI will impact the job market and the lives of workers.

    13. Most organizational strategies focus on AI’s short-term efficiencies, such as automation, speed and cost saving.

      Companies, despite using AI for many minimal tasks, are not looking at the big picture as to how AI could be applied to more difficult and advanced tasks, whether it be drug synthesis or ideas for marketing.

    14. But in the rush to adopt AI, some organizations are overlooking the real impact it can have on workers and company culture.

      AI is impacting all of us immensely, both visibly and invisibly, from taking jobs from citizens to creating new jobs for others.

    1. Dickinson uses the Fly as a metaphor for the interruptions and uncertainties of death. In the lines, “There interposed a Fly With Blue uncertain stumbling Buzz” she shows how something small and ordinary can disrupt a profound, emotional moment, emphasizing the unpredictability and even the mundane reality present at the time of death.

  2. docdrop.org docdrop.org
    1. The maxim "less contact, less learning" succinctly summarizes the argu-ments supporting students' exposure to quality language models and in-struction. 42 fo·lea~n a°qanguage-we'tr,"'orre"'ftrrmflave-st1stained inter~1?t10ns \~t edueated-~ative-speakers--of-Englrnn, as \vellasgooct1angu_a~ i~s~~~l(-tion. Students can only learn the new language in the style to which they are exposed. If an English-language learner lives and talks daily with Eng-lish speakers in a boarding school in London, she will learn a very different kind of English and sound very different than if she had been immersed in a public school in Atlanta, Sidney, or Toronto. Likewise, someone hoping to improve their Spanish-speaking skills will sound very different ,1fter ,in extended study-abroad stay in Madrid, Mexico City, Santo Domingo, or Buenos Aires.

      “Less contact, less learning.” The key to learning a language lies not in mere classroom hours or memorized vocabulary, but in sustained interaction with high-quality language input. In other words, language proficiency is shaped within authentic contexts, not through isolated grammar drills. The example illustrates how different English or Spanish learning environments cultivate entirely distinct linguistic styles and pronunciation traits, revealing the social and contextual nature of language acquisition. From an educational perspective, this passage reminds teachers that language instruction cannot rely solely on textbooks or exams. Instead, educators should create rich communicative situations that allow students to truly “immerse” themselves in the language and culture. Simultaneously, it reflects the structural inequality faced by immigrant students in language learning—if they lack sustained interaction with native speakers, they are effectively deprived of the conditions necessary for language development.

    2. Clearly, if we are to expect newcomer students to learn English, as they and we would like them to, our schools need to do a better job of develop-ing educational contexts that will make it happen. Our focus at the begin-ning of the study was very student-centered; we considered the resources the students brought with them, the engagement they brought to the task, as well as the educational contexts they encountered. But while these fac-tors certainly contribute to language acquisition, the schools also play a fundamental role in whether students learn English. Our findings parallel those of Gary Orfield, Guadalupe Valdes, Laurie Olsen, and others who have insightfully described the intense physical and linguistic segregation that many newcomer immigrant students encounter. 54 While there have been some attempts to address the needs of students coming in at the ele-mentary level, there has been a lamentable and disconcerting absence of ef-forts to meet the needs of English-language learners arriving at the second-ary school level.55 This gap absolutely needs to be addressed if we wish to harness the energies of all of our newcomer students.

      Immigrant students require at least seven to ten years of high-quality learning environments to truly master “academic English,” yet current education policies demand they pass standardized tests within three years. This unrealistic expectation not only creates psychological pressure but also systematically produces “losers.” It reveals how U.S. education policies prioritize “measurable outcomes” over fairness and growth within the long-term learning process. This “time violence” exemplifies how the education system sacrifices marginalized groups under the logic of efficiency. When annotating this passage, one might reflect on whether educational assessment should shift toward “developmental support” rather than “elimination-based screening.”

    3. Today, immigration is once again a momentous social force, compelling Americans to face the challenge and opportunity of integrating and har-nessing the energy of the greatest number of immigrants in the nation's history. By 2005 there were well over 35 million immigrants in the United States-some 12.4 percent of the U.S. population.

      American society has long harbored cultural anxieties and identity insecurities regarding immigration. The author notes that Americans' concerns over whether immigrants “are willing to learn English” are not a new phenomenon, but rather a recurring “political discourse” that resurfaces during periods of economic and social upheaval. At its core, this anxiety stems from fears about national identity and cultural purity. Learning English here is treated as a symbol measuring “loyalty” and “degree of Americanization,” rather than a matter of linguistic ability. This reflects how language is politically employed as an “assimilation tool,” maintaining the stability of social power structures by creating distinctions between “good immigrants” and “bad immigrants.” When annotating this passage, consider: Is learning English truly an educational goal, or an institutionalized social expectation?

    1. La palabra itacate proviene del náhuatl itacatl. El térmi-no refiere tanto a la provisión de alimentos que una personalleva a un viaje como al contenedor (caja, bolsa, mochila)en el que serán transportados

      @LIBSAN deberías recibir un correo con este comentario.

    1. . My parents tried to talk to my teacher about it, but it was kind of hard. They don’t really speak much English and my teacher wasn’t much of a help either. She cancelled a couple meetings with them and, you know, they were taking time off work to go, so they felt bad, like she wasn’t respecting their time. When they fi nally met she really scared them with stories about teachers being attacked by students and that she didn’t feel safe there. They ended up taking me out of school a couple weeks later.

      Parents struggled to communicate with teachers due to limited English proficiency. Hoping to understand the situation through face-to-face interaction, they were further marginalized by the teacher's negligence and fear-mongering narrative. The teacher's repeated cancellations not only reflect a disregard for immigrant families' time and effort but also reveal the system's implicit exclusion of non-native English-speaking parents. More alarmingly, when this teacher used the story of “students attacking teachers” to intimidate parents, she effectively transformed the educational space into a realm of distrust and fear, misleading parents into believing their children were unsafe at school. Ultimately, the student's forced withdrawal from school reveals how structural discrimination, through the accumulation of everyday interactions, quietly deprives immigrant families of educational opportunities. This narrative prompts reflection: true inclusive education occurs not only within the classroom but hinges on whether teachers are willing to listen to every family with respect and equality.

    2. What would be most benefi cial for the successful transitions of undocu-mented immigrant students are school structures and cultures that facilitate positive interactions between students, teachers, and staff, allowing those at all levels to develop school-based social capital and build relationships of trust so critical to their success. By investing in a baseline of support for all students, schools could develop support structures necessary to facilitate more targeted outreach to undocumented students. This is not only a social justice issue, but an economic imperative for the nation

      Institutional support and social capital play a pivotal role in the educational transition of undocumented immigrant students. The author argues that relying solely on individual teachers' compassion or students' personal efforts is insufficient; true change stems from systemic adjustments to school structures and cultures. When schools foster an atmosphere that encourages interaction, trust, and inclusion, the connections formed among students, teachers, and administrators create a “school-based social capital” that prevents undocumented students from remaining isolated. Notably, the author elevates this issue to the levels of social justice and economics, arguing that supporting undocumented students is not only a moral obligation but also vital to the nation's future development. This framing transcends narrow humanitarian perspectives on immigrant education, instead proposing a broader vision for structural reform. It reminds us that educational equity and societal prosperity are interdependent.

    3. Together with six siblings and her two parents, she came to the U.S. when she was just nine years old. Flor’s formative years were diffi cult and shaped in her a sense of ambivalence about the future. She realized from an early age that her lack of papers— papeles—would keep her from the good jobs she dreamed of as a child. She also felt like an outsider at school, internalizing a belief that no one was looking out for her—that she was on her own.

      Flor realized at a young age that “lack of papers” was not merely a legal issue but a form of enduring social exclusion, fostering a sense of “ambivalence” about her future. This internalized feeling of ‘invisibility’ led her to develop a survival strategy of “isolating herself” in school—believing she must face everything alone. This narrative reveals how immigrant status shapes one's self-perception and social positioning at a psychological level, while also exposing the profound impact of institutional exclusion (such as immigration restrictions) on educational opportunities and life aspirations. Flor's story is not an isolated case, but rather a microcosm of the struggles faced by countless undocumented students navigating the American education system.

    1. We see this coun-ter-narrative as a crucial element in the development of a systematic analysis of the racism, classism, and linguicism that permeate much of urban educa-tion as well as in the development of culturally relevant curricula

      Racism, classism, and linguicism are pervasive in urban education, and schools' overemphasis on “monolingual literacy standards” perpetuates these inequalities. By demonstrating how families and communities serve as children's “invisible classrooms,” the author calls on teachers to redefine their roles—not merely as knowledge transmitters, but as cultural bridge-builders. By acknowledging and leveraging students' home literacy experiences—such as religious practices, games, and bilingual storytelling—teachers can make education truly inclusive and socially just.

    2. We came to understand that there is a distinction between places as the actual locations while spaces are constructed by human actors who are, in turn, shaped by those spaces in fluid and reciprocal pro-cesses.

      This passage reveals the theoretical significance of the author's adoption of the “spatial turn”—she distinguishes between ‘place’ and “space.” Place refers to physical existence, while space is a product of social and cultural actions. In other words, literacy spaces are not naturally occurring; they are co-created by family members through daily interactions, language, objects, and emotions. For instance, Benny's bedroom or Miguel's library experience are not merely “places,” but learning “spaces” imbued with meaning through their engagement. This reminds educators that literacy development occurs not only in classrooms but also within children's daily lives. Those seemingly ordinary corners—the dining table, the church pew, the computer desk—are all vital educational settings.

    3. We planned to investigate both the places outside of school, in their homes and communities, where the two children and their families accessed literacy resources and the formal and informal literacy interactions that they con-structed there. In this way, we hoped to problematize the common privileging of school-centered literacy and education, challenge the discriminatory

      The author explicitly states that her research does not aim to replicate the conventional narrative of “resource scarcity in impoverished families,” but rather to construct a counter-narrative revealing how low-income Latino families proactively create literacy opportunities. The key term here is “agency”—meaning families and children are not passive recipients but active knowledge constructors. This perspective overturns the previous school-centered, standardized literacy view rooted in white middle-class norms. It also prompts us to rethink the true meaning of “educational equity”: equity does not mean having every child learn in the same way, but ensuring that every culture's learning methods are seen and respected.

    4. other important volumes were kept on a high shelf. As there were no book stores in his neighborhood, his grandmother took him to secondhand stores to purchase books, looking especially for ones with maps, one of his passions. Both boys owned a DS (dual-screen hand-held game console) and other elec-tronic toys and games

      This paragraph provides a vivid counterexample to the stereotype that low-income families lack educational resources or value literacy. The detailed descriptions of the boys’ homes—filled with books, newspapers, maps, magazines, and even technology like iPods and GPS devices—show how these families actively create literacy-rich environments that reflect their interests, cultures, and daily lives. I believe this approach is absolutely correct. My mother was also born in northern China, an area with scarce educational resources. Yet her mother relentlessly pushed every child in the family to study hard, sending them all to university. That's why I can now enjoy a quality education in a great city. In their eyes, education truly changed their destiny—all because of thoseold books sold one by one at street stalls.

    5. we focused on the strengths and resources of the children and their families, rather than their needs and alleged deficits as often described in the dominant discourse (Arzubiaga, Ceja, & Artiles, 2000). We knew that many Latino children had rich literacy lives—often invisible to teachers in urban schools or dismissed as irrelevant to school learning—and that they and their families possessed expertise and funds of knowledge (González, Moll, & Amanti, 2005; Long et al., 2007; Spencer et al., 2010) that could serve as the basis for a culturally relevant curriculum (Boardman et al., 2014; Gay, 2010)

      I believe diversity in education is crucial. As mentioned in the article, Latino children possess remarkable reading aptitude, yet this talent is often overlooked by teachers. In elementary school, I was a student with severe academic imbalances—I struggled immensely with math, consistently ranking near the bottom of the class. However, I possessed a natural aptitude for both English and Chinese. When given sufficient time to develop my ideas, my compositions were even selected by teachers to be read aloud to the entire class. Consequently, I always believed I had strengths during that time. Because the subjects I excelled in were valued by my teachers, I became even more motivated to study those particular subjects diligently.

    1. However, Arturo is failing as a reader in both English and Spanish. Ms. Stewart, Arturo’s English teacher, views him as a disengaged reader, not mak-ing progress, and not having the English vocabulary to engage with the chapter books that they are read-ing. Arturo is placed in the group with the lowest reading level. The stories they read are not complex, and the work in the group is mostly about vocabu-lary buildup. Ms. Stewart blames Arturo’s slow prog-ress on his Spanish. Similarly, Ms. Medina, Arturo’s Spanish teacher, believes that he does not have suf-ficient Spanish-language vocabulary to make sense of the Spanish-language chapter books. For Ms. Medina, raised and educated in Colombia through university, Arturo’s Spanish is simply deficient

      A shift in educators' perspectives can profoundly impact students' reading abilities. Initially, teachers evaluated Arturo's English and Spanish skills separately, concluding he “failed in both languages.” However, when educators began creating “cross-language spaces” in the classroom—allowing students to freely switch between English and Spanish for performances and discussions—Arturo demonstrated rich critical thinking and cultural insight. This transformation underscores the pivotal role of teacher attitudes in language education—students' “proficiency” is often not lacking, but obscured by narrow assessment methods. The author uses this case to remind us: educational equity lies not merely in offering bilingual programs, but in whether teachers can genuinely understand, respect, and enter students' linguistic worlds.

    2. I start with Paco, the 3-year-old bilingual child whose mother is a U.S.-born Latina woman and whose father is a U.S.-born white man. The mother grew up in a bilingual home, the father in a monolingual one, but he studied Spanish in high school. The family is comfortable in a translanguaging space, where their use of English and Spanish is unbounded, dynamic, and fluid and adapts to meet the communicative expectations of the many different people who enter the home.

      Paco's example vividly demonstrates the naturalness of multilingual practices in early childhood language development. While reading Jorge el Curioso, he freely mixed English and Spanish, using gestures and sounds to express the story—a behavior encouraged and praised in the home environment rather than corrected. This illustrates that language learning itself is multimodal, emotionally charged, and physically engaged, rather than a rigid accumulation of grammar rules. When annotating this passage, note the author's implicit critique: formal schooling often stifles such free expression, transforming children from “language creators” into “language conformists.” Paco's multilingual reading practice at home reminds us that authentic language education should center on comprehension and expression, not solely on linguistic correctness.

    3. In this article, I argue that the act of reading does not depend on the language of the written text or even on the concept of a named language such as English or Spanish. Rather, the act of reading is about readers assembling all their meaning-making resources and acting on them to read themselves.

      The process of reading does not depend on the “designation language” used in the text (such as English or Spanish), but rather on how readers utilize their entire linguistic repertoire to comprehend the text. This perspective challenges the assumption of “language compartmentalization” in traditional language education, proposing a more fluid and authentic approach to understanding. For Hispanic bilingual students, this cross-linguistic perspective holds profound significance, as it acknowledges their natural switching between two cultures and languages as a strength rather than a flaw. It also prompts reflection on the drawbacks of an educational system overly fixated on “linguistic purity”—where schools often view language mixing as “distraction,” when in fact it embodies the very essence of bilingual thinking and creativity.

    1. But told to whom? Who is the reader I’m addressing when I am writing in English?

      My question: I wonder how writers from countries in war can tell their true stories when they write in English, which is not their first language. Do they lose part of their real voice? Or maybe writing in English helps them reach more people and fight back against silence. Can writing in another language be a kind of power or it loses the originality of the story?

      This question makes me think about how translation and writing can change how stories are heard and understood.

    2. All the life squeezed out of them so that they fit into one headline. Sentences become coffins too small to contain all the multitudes of grief.

      Why this truth is important: This line tells a hard truth: that the news often makes stories of war and pain too small. When we read about people suffering, the headlines don’t show how big and real their pain is. The image of “sentences as coffins” means that sometimes writing can hide people’s emotions instead of showing them. It reminds me that we must use words carefully, because they can give life or take it away.

    3. To translate a text is to enter into the most intimate relationship with it possible. It is the translator’s body, almost more so than the translator’s mind, that is the vessel of transfer.

      Why it’s beautiful to me: This line feels beautiful because it turns the act of translation into something alive and human. Mounzer describes translation not as a mechanical task but as a relationship of empathy and feeling , almost like giving life to someone else’s experience inside your own body. As a reader, I find that image powerful because it shows that language connects people emotionally, and not just intellectually.

    1. void error_message(void); int get_month(void);

      この2つは関数のプロトタイプ宣言であり. 1つ目の関数は,戻り値を返さない,引数も受け取らない

    1. The girls rejected mainstream spaces where they often felt marginalized and isolated, such as the ‘Main Street,’ a popular place to sit during lunch, recess, and after school. ‘Main Street’ was a ‘big hallway’ with tall ceilings and many windows located near the main school entrance. It reflected the racial, ethnic, and class diversity of Maple High. It was packed with many groups of students who often sat together based on race, class, and/or gender.

      They perceive the “Main Street” corridor in the main building as representing the school's social hierarchy and aesthetic power center—a sphere to which they do not belong. This rejection is not merely an avoidance of campus social structures but a symbolic critique of society: they refuse to conform to mainstream definitions of ‘attractiveness’ or “popularity,” instead choosing self-defined communities. By actively withdrawing from mainstream spaces, they forge new meaning and security within the “non-mainstream.” This behavior reveals how adolescents express social identity and cultural resistance through seemingly simple “spatial choices” in everyday campus life.

    2. The girls also co-invented a pan-Asian fused language in which Japanese functioned as an Esperanto, an international language. It was their version of ‘language crossing’ (rampton, 1995), using a language that did not ‘belong’ to them. Early in my fieldwork, I was surprised to hear the students use some Japanese words among themselves. While there were no Japanese students or teachers at Maple High, the school offered Japanese as a general language course, and many of the girls took it. Those who had fairly high Japanese skills through taking classes and/or actively watching Japanese dramas, movies, and anime took an active role in using Japanese words such as ‘nani’ (what?), ‘genki?’ (how are you?), and ‘onegai’ (please) with their friends. As the only proximal native Japanese speaker, they happily used a mix of English and Japanese when communicating with me and asked me to teach them Japanese. I often saw the girls carry binders, notebooks, and post-it notes with Japanese words (e.g. their names in Japanese) on them. One day after school, Mino and her basement friends spent time together at a nearby mall writing words and drawing pictures on Meli’s arms, hands, and legs. Mino later showed me a picture she drew on Meli’s arm: a cute rabbit face, which she called an ‘Asian face,’ with the Japanese word ‘kawaii’ written above it

      These girls have created a hybrid language blending elements of Japanese, English, Tagalog, and even Korean to express intimacy and identity among themselves. This linguistic practice demonstrates that they are not passively absorbing mainstream English culture, but actively constructing a multi-layered “pan-Asian cultural identity.” Simultaneously, it reveals the power dynamics underlying language—their choice of Japanese partly stems from Japanese culture's elevated status in global trends. This “cultural borrowing” serves as both a means of self-expression and a reflection of global cultural inequalities. This complexity lies at the heart of the tension inherent in cultural hybridity.

    3. ‘We dominate the basement!’ Gina, a 15-year-old Chinese American girl, proudly proclaims. This article, based on two years of ethnographic fieldwork, examines how a group of Asian American1 immigrant high school girls (Filipina, Vietnamese, Chinese, and Indian) construct this basement into a community, which they name the ‘Basement Group.’ While this group comprises students with diverse backgrounds, I specifically focus on the perspectives, voices, and experiences of a group of Asian American girls who are its founders and core members

      The basement is not merely a physical space; it symbolizes how Asian girls marginalized by mainstream society reclaim agency in the “borderlands.” They reject mainstream social spaces like dining halls and hallways, choosing a dimly lit, overlooked place as their “home.” Phrases like “We rule the basement” express their pride and sense of control. This behavior reflects their resistance to and redefinition of power structures, revealing that belonging and strength can emerge even in seemingly excluded spaces. Marginality does not equate to weakness; it can foster new cultural creations and self-identity.

    4. Since the main goal of this study was to capture the experiences of Asian American girls, I did not include most of the other Basement Group students in my research. There may be gender, ethnic, and/or racial differences that are not reflected in this study. As an exception, I talked with Savannah and Meli, two Salvadoran immigrant girls who were close friends with the Asian American girls and part of the core members of the Basement Community. Their perspectives helped deepen my understanding of the experiences of the main participants

      The author focuses mainly on Asian American girls but includes insights from two Salvadoran immigrant girls to broaden the perspective. This shows an effort to include diverse voices and recognize that gender and ethnicity can shape school experiences in different ways.

    1. I give it most of the credit for the fact that ours isthe wealthiest, most technologically advanced, and most socially just soci-ety in human history, not to mention the fact that we have with ease be-come a military superpower .... The rest of the world is quite rightlyimpressed with us, and it is thus no accident that the United States ofAmerica has become the biggest single exporter of public law in the his-tory of humankind.

      I can't help but think that parts of this attitude expressed by Calabresi is debatable not just in light of the condition of the US in the present day, but even when he made these comments in 1998. Many would certainly disagree that the US is/was the "most socially just society in human history" nor was it the case that the US "with ease [became] a military superpower."

    Annotators

    1. Purpose and Problem Solved

      Overall, your understanding of the Finalizer seems inadequate. The purpose of a Finalizer is threefold: first, to convert EVM words to Circom words, second, to generate a circuit witness (which will be converted into a proof in the backend), and third, to analyze the chain of symbols and generate a permutation.

      I think this part needs to be rewritten.

    2. Raw placement data from execution can be inefficient (redundant wires, unused connections)

      Nothing to do with efficiency. We have to do this so that Circom can deal with the data values produced by the Synthesizer. If we could avoid this, the performance had been improved.

    3. Large circuits slow down proving time

      This is true but not in this case. Doing this splitting wires slows down the proving time, but we have to do.

    4. Purpose and Problem Solved The Finalizer bridges the gap between symbolic execution and concrete circuit generation: Problem 1: Symbolic → Concrete Conversion During execution, the Synthesizer works with symbolic pointers (e.g., StackPt, MemoryPt) The backend prover needs concrete numerical wire connections Solution: Finalizer converts all symbolic references into actual wire indices and constraint equations Problem 2: Circuit Optimization Raw placement data from execution can be inefficient (redundant wires, unused connections) Large circuits slow down proving time EVM uses 256-bit values but Circom's finite field is 254-bit (field overflow risk) Solution: PlacementRefactor optimizes wire sizes, removes unnecessary connections, and splits 256-bit values into two 128-bit limbs for field compatibility Problem 3: Backend Integration Frontend and backend use different data structures Backend needs standardized JSON format for circuit loading Solution: Permutation class generates JSON files that match backend's expected schema Problem 4: Witness Data Management Circuit needs both structure (permutation) and concrete values (witness) Witness data must align with circuit wire indices Solution: Generates permutation.json (structure) and placement-specific witness files

      I think this introduction can be moved to the "Execution Flow" section.

    1. Generate

      "Utilize a combination of subcircuits to derive a new symbol to represent the true value in the EVM memory, ​​from existing symbols in MemoryPt."

    1. This technique can get up to 108 ideas from six participants in just 30 minutes, and it’s great if you want to encourage every participant to generate ideas – especially if your team is predominantly introverts.

      I'm curious about the quality vs. quantity trade-off here. While 108 ideas in 30 minutes sounds impressive, I wonder if this rapid-fire approach actually leads to more superficial thinking?

    2. Ask participants to focus on generating bad ideas only. They should consider everything that couldn’t work before you ask them “What can we do to make these ideas work better?”

      Curious. If it's not whimsical or impulsive or taken for granted, it will also be tough to generate bad ideas, and often good ideas may come around through those bad ideas.

    1. Most industries have an orthodoxy – a set of deeply-held, unspoken beliefs that everyone follows when it comes to “how we do things around here.”

      This concept really resonates with me because it explains why breakthrough innovations often come from outsiders to an industry.

    2. First, create a statement that clearly defines what your creative objective is.

      Totally agree! Whether we’re brainstorming ideas or designing a course, it’s so important to fully understand the objective before moving forward.

    3. Next, randomly combine one word from each list and spend time brainstorming around the mini-story they suggest.

      I really like how this strategy pushes people to think outside the box. But I do have concerns about how efficient it is because it depends on “randomly combining” ideas.

    4. Next, randomly combine one word from each list and spend time brainstorming around the mini-story they suggest.

      I love how this strategy pushes people to think outside the box. But I do have concerns about how efficient it is because it depends on "randomly combining" ideas.

    5. Semantic intuition is a technique that can inject fresh energy into a group that is starting to feel brain dead toward the end of a brainstorming session, according to Mattimore. It prompts participants to create new ideas by having them combine several categories of key words to create a name for a new idea – even though they have no idea what the newly-named idea IS yet. The first step is to select the three categories of words that are related to your challenge. For a consumer product, Mattimore suggests that three possibilities would be places in a store, kinds of promotional appeals and benefits of the product or needs of the customer. Next, generate variations on each of these category words. Next, randomly combine one word from each list and spend time brainstorming around the mini-story they suggest. Mattimore points out there are no “rules” to using this technique. Don’t be afraid to let the keyword prompts take you far afield from them. And don’t be concerned if you generated an idea that only uses two of the three words. The point of semantic intuition is simply to get you to think differently.

      This is very useful, especially for a group project when we are ideating together. It would be playful, which helps to reengage.

    6. This technique works surprisingly well because it tends to mentally disarm brainstorming participants.

      Not sure this is very effective in a rgeular setting where people dont feel pressured. Maybe use this and ask: "Whats the worst idea for our business? What can we do to fail as soon as possible?" Then turn it around.

    7. Next, pick three of the most interesting words in the opportunity statement and generate creative alternatives for each of them. Mattimore recommends using words that represent the 5W’s and H – who, what, when, where, why and how – of your challenge. Once you have generated your three lists of alternative words, place them in a table, with the original words at the top of each column and the alternatives you have brainstormed arranged in columns below them.

      Structured and randomized. It is easy to follow and sparks surprizing and creative results. Try it out!

    1. Be sure not to put this off. Theabove is what has to be communicated

      This is a very straightforward but very accurate and effective letter. He makes all the best arguments, pointing out that the English are either openly selling drugs out of their enormous greed, or are either too unwilling or inefficient to control what their own traders are doing. Its funny how clearly it is just a kindly worded diss. He's pretty much saying that the English can either stop being evil or otherwise China will not give them awesome stuff.

    2. This is the source fromwhich your country has become known for its wealth

      Wow, basically saying the Chinese gave the British their bag. Its so funny how in documents like these people are just throwing shade and talking smack.

    3. enowned for his competencein administering fiscal matters and public works, and his skill at governance.

      Likely also a philosopher / political philosopher. China had a very unique focus on the learning and philosophy of governance. I should consult my reading from PS10, but as I recall there was a rich history of political philosophy and development. Confucius himself was a statesman. Even the Dao which advocates for a solitary life gives governing advice. That is all to say that the Chinese had a rich history of political philosophy as well as great respect for good statesmen. There was a very different, service oriented, attitude which contrasts with the European binary of government by tyrant or republic.

    Annotators

    1. The term ‘judicial review’ describes the power of courts to declare legislation or actionsof the executive in violation of the constitution.

      DEFINITION

    2. Semi-presidential systems are particularly problematicwhen, in a multi-party system, divided minority governments result, in which neither theparty of the president nor of the prime minister enjoys a majority in the legislature.

      ARGUES THAT semi-presidential systems are particularly problematic when in a multi-party system, divided minority govs are created

    3. hough the President is by far the stronger of the two offices, the Presidentand Prime Minister to some degree share executive power.

      president stronger than PM but they to some degree share executive power

    4. the South African President is actually selected by the parliament rather thanby direct election,®”

      South African president selected by the parliament rather than by direct election

    5. England has a bicameral legislature, consisting of the House of Commons andthe House of Lords.

      England= bicameral legislature, House of Commons and House of Lords

    6. Many Latin American presidents hadthe power of ‘line-item veto’,44 and greater independent authority to appoint federal andstate officials.

      Reason: Many latin american presidents had the power of line-item veto and greater independent authority to appoint federal and state officials

    7. presidency and reduced authority in the legislature and courts.

      Reason: Scholars noticed that latin american cons provided greater powers in the office of the presidency and reduced authority in the legislature and courts

    8. There are a variety of differenttheories for why this might be so, but a dominant one is the idea that when the presidentdoes not enjoy the support of a majority of the legislature

      the reasons for troubled democracy in Latin America could be that when the president does NOT enjoy the support of the majority of the legislature, it can lead to constituional breakdown

    9. Observers divide most constitutional systems into presidential (typified by the UnitedStates), parliamentary (typified by the United Kingdom), and semi-presidential (typifiedby France).

      Constitutional System Types:

      1) Presidential 2) Parliamentary 3) Semi-Presidential

    10. Accordingly, he argued that the powers of government should be divided amongdifferent persons or bodies, which would act as a check on each other.

      Montesquieu's argument

    11. despotic.

      A despotism is a government in which a single ruler governs without laws or constraints, according to their own will.

      Principle: Fear — subjects obey out of terror of punishment.

      There are no formal checks on power, and the ruler is above the law.

      Example: Absolute autocracies or tyrannies (Montesquieu often cited the Ottoman Empire as an example).

    12. monarchical,

      A monarchy is a government in which a single person (the monarch) rules, but according to fixed and established laws.

      Principle: Honor — the motivation of nobles to serve the king and maintain hierarchy.

      The monarch’s power is limited by tradition, law, or institutions (like courts or parliaments).

      Example: France under Louis XIV, or Britain under a constitutional monarchy

    13. republican (either democratic or aristocratic),

      A republic is a government in which the people (or a portion of them) hold sovereign power. It can take two main forms:

      Democratic republic: Power is held by the whole people — citizens rule directly or through elected representatives.

      Principle: Virtue (citizens’ love of equality and the common good).

      Example: Ancient Athens or modern democracies.

      Aristocratic republic: Power is held by a select group of citizens — often the nobility or elite.

      Principle: Moderation (restraint and fairness among the ruling class).

      Example: The Roman Republic, Venice.

    14. That Actalso strengthened judicial independence by requiring that judges should remain in officeduring good behavior and could only be removed by parliament.!

      The Act strengthened judicial independence by requiring that judges should remain in office during good behavior and could only be removed by parliament

    15. The English Bill of Rights Act of 1689 established someof the central principles of Britain's constitutional monarchy by declaring that ‘thepretended power of suspending the laws or the execution of laws by regal authoritywithout consent of Parliament is illegal’ and that parliamentary consent was required toraise revenue or maintain a standing army.

      English Bill of Rights Act of 1689- established -pretended power of suspending laws or execution of laws without consent of parliament was illegal, this ultimately gave parliament a lot of power

    16. The constitutional struggles between the king and parliament in England in theseventeenth century gave rise to the related, but distinct, idea of a functional separationof powers, which is the core of the modern doctrine.

      Constitutional struggle between king & parliament in England in the 17th century gave rise to the idea of a functional separation of powers

    17. the idea that dividingpower will inhibit government action and therefore tyranny; the idea that different typesof government bodies are more or less competent at certain tasks; and the idea thatcertain allocations of authority will help ensure democratic legitimacy for governmentpolicies.

      Arguments for why separation of powers is considered normatively desirable: 1) idea that dividing power will inhibit gov action and therefore tyranny 2) the idea that different types of gov bodies are more or less competent at certain tasks 3) the idea that certain allocations of authority will help ensure democratic legitimacy for government policies

    1. This... this line is chilling. Palantir, Curtis Yarvin, etc. It also ignores that Jim Crow wasn't passed by the majority public opinion. It was enacted into law by a small group of elected officials elected by the majority of the white voting public. Most people don't vote, and in many areas, the population that wasn't White was greater or equal to the White population, but still didn't have a say. The system is not actually the majority opinion. Additionally, information is still filtered by someone, with all their biases, and the biases they built into the computer

    Annotators

    1. Eachdaughter cell represents one outcome of all possible combi-nations of maternal and paternal chromosomes.

      ex. 1 pair of homologs (2 inherited chromosomes) = 2 possible daughter cell combinations. as shown by 2^n, where n= the number of homolog pairs.

    Annotators

    1. One strategy discussed in this WHO report is using an ethical framework. There are two types:

      1. procedural ethical framework: covers who decides and how to make a decision
      2. substantive ethical framework: covers what to decide, based on earlier consensus
    2. Ethical frameworks must generally be tailored to the ethicalissues and challenges at hand. Hence, although they mayappeal to similar ethical principles, there are likely to bedifferent ethical frameworks for questions related to publichealth surveillance and for individual treatment decisions

      The process of assigning or tailoring ethical principles to situations sounds complicated and almost like it needs its own selection framework...!

    3. This is another case of a moral con-flict – between the freedom to relocate and associate freelyand the need to improve the health of some of the mostvulnerable people.

      An interesting example of ethical conflict in public health that I hadn't considered - the tension between allowing free movement of people across borders and keeping skilled workers local.

    4. Whileaccess to good health may be thought to be a vitally impor-tant ethical principle, it remains unavailable to most peo-ple.

      I agree that this is true. I've only highlighted the sentence because it's both sobering and depressing to read in 2025.

    5. Research ethics committees perform the important roleof assessing the potential risks and benefits involved inresearch. In some cases, such committees may decidethat the risks of the study are not justified by the poten-tial benefits and decide not to allow the research to goahead.

      These committees act as an ethical check on upcoming research. However, who makes up these ethics committees and what safeguards are in place to prevent conflicts of interest and other issues?

    1. The monks and scholars at these monasteries used a new writing system called Carolingian Miniscule that, unlike earlier script, began using lower-case letters, spaces between words, and punctuation. This allowed them to transcribe three or four pages in a day, rather than just one. As a result, over a thousand volumes survive using the new technique, versus just fifty from the previous Merovingian system.

      This is also very interesting. I cannot believe that over a thousand volumes survive.

    1. The money used along the Silk Road included Abbasid gold dinars, Tang silver ingots, and Samanid (Bukhara) silver dirhams. Copper coins were not used in long-distance trade because they were too heavy.

      I did not know this. I guess, coins are heavy and if there is a long ride ahead, you do not want yourself or the animals to tire very fast.

    1. "House of Wisdom" where  Muhammad al-Khwarizmi published a book on mathematics now known as "Algebra"

      This is interesting. Is it the Algebra we know of today? I wonder how much it changed if it did.

    1. My own personal experience of civic engagement was volunteering and helping to start an afterschool ecology program at PS 126’s urban farm in Manhattan on the Lower East Side.

      Q- why would someone decide to do something like this without knowing the possible outcome.

    2. Understanding from across communities and participation by residents across different communities, encourages more participation, raising levels of equity and inclusion.

      L- love the involvement of the community.

    3. Communities are made up of individuals and each individual comes from a unique background, maybe a different country, perhaps speaks and feels comfortable in different languages, has their own level of education, family status, and more.

      L- I love how this shows us how different but alike we all are.

    4. Active participation can be measured with the help of a survey or questionnaires given to students. These tools can determine how often they get involved within their community and provide a sample of what types of activities they involve themselves in that meet the requirement of civic engagement. Multiple choice questions can be used to gauge a student’s level of active participation and there’s the option of adding open ended questions which will provide more information since a student would have to think back to any prior experience they may have had. Providing open ended questions allows a student to open up and get a closer look and understanding if they know what active participation means.  Another option could be to study a focus group of students as this can show if there are any similarities between them about how they view active participation. This could be used to get a sense of how students are thinking about active participation.

      I- found it interesting how they take note of participation

    5. It was a lot of physical labor but it was a collaborative day which saw everyone work together to achieve success.

      S- I found this surprising because when most people encounter difficulty they tend to give up

    1. The ways of your culture are familiar to you, often so deeply ingrained that they come naturally. Culture itself feels like home.

      Reading about how this paragraph describes culture reminds of the word ethnocentrism we talked about in class. In a way, ethnocentrism and culture can be distinguishable to people growing up in a isolated place.

    2. Dominant ideas about work, gender, marriage, parenting, hospitality, and status all shape the places we call home.

      Houses are built to accommodate all of human needs. All these factors make everything about our homes unique to each family that inhabits it.

    3. In Bourdieu’s analysis, the Kabyle house was divided into two realms: a dark, low realm associated with animals and natural activities (sleeping, sex, childbirth, and death) and a lighter, higher realm associated with humans and cultural activities (weaving, cooking, brides, and guests).

      This is very interesting, these ideas are very similar to how we view our living room, and bedrooms.

    4. With the loom and the hearth, the main area of human activity in the house was associated with the work of women.

      Women worked mostly in the house during this time period so it makes sense they occupied the nicest parts.

    1. An academic coach/advisor uses GenAI to draft a tailored study plan for a student struggling in STEM courses. Then, the coach reviews and edits the plan to ensure fit. They also two strategies appropriate for the student, which GenAI missed, and have worked well for other STEM students.

      I think last sentence is missing words or was edited but no longer makes sense

    1. Who it’s for (students, faculty, staff) What the task is (announcement, summary, email, syllabus)

      Learning flow could benefit from switching these. To me it seems more natural to say who am I , what ma I building, who am I building it for and reading that in this section seems natural to read it that way to reinforce that order of operations.

      I typically would say, I am < insert who I am here > building a < insert task here > for < insert audience here >

    1. Ruha Benjamin: ‘We definitely can’t wait for Silicon Valley to become more diverse’

      @lajulia ahor me da curiosidad saber si puedo citar a alguien en un comentario de Hypothesis. De paso si no conoces a Ruha Benjamin acabo de conocerla y me parece que tiene cosas muy interesantes!

    1. You have free access to Microsoft Copilot through the university's Microsoft 365 subscription

      Link or Resources section to take users to these resources would be good!

    1. eLife Assessment

      The authors present a set of wrappers around previously developed software and machine-learning toolkits, and demonstrate their use in identifying endogenous sterols binding to a GPCR. The resulting pipeline is potentially useful for molecular pharmacology researchers due to its accessibility and ease of use. However, the evidence supporting the GPCR-related findings remains incomplete, as the machine-learning model shows indications of overfitting, and no direct ligand-binding assays are provided for validation.

    2. Reviewer #1 (Public review):

      This is a re-review following an author revision. I will go point-by-point in response to my original critiques and the authors' responses. I appreciate the authors taking the time to thoughtfully respond to the reviewer critiques.

      Query 1. Based on the authors' description of their contribution to the algorithm design, it sounds like a hyperparameter search wrapped around existing software tools. I think that the use of their own language to describe these modules is confusing to potential users as well as unintentionally hides the contributions of the original LigBuilder developers. The authors should just explain the protocol plainly using language that refers specifically to the established software tools. Whether they use LigBuilder or something else, at the end of the day the description is a protocol for a specific use of an existing software rather than the creation of a new toolkit.

      Query 2. I see. Correct me if I am mistaken, but it seems as though the authors are proposing using the Authenticator to identify the best distributions of compounds based on an in silico oracle (in this case, Vina score), and train to discriminate them. This is similar to training QSAR models to predict docking scores, such as in the manuscript I shared during the first round of review. In principle, one could perform this in successive rounds to create molecules that are increasingly composed of features that yield higher docking scores. This is an established idea that the authors demonstrate in a narrow context, but it also raises concern that one is just enriching for compounds with e.g., an abundance of hydrogen bond donors and acceptors. Regarding points (4) and (5), it is unclear to me how the authors perform train/test splits on unlabeled data with supervised machine learning approaches in this setting. This seems akin to a Y-scramble sanity check. Finally, regarding the discussion on the use of experimental data or FEP calculations for the determination of HABs and LABs, I appreciate the authors' point; however, the concern here is that in the absence of any true oracle the models will just learn to identify and/or generate compounds that exploit limitations of docking scores. Again, please correct me if I am mistaken. It is unclear to me how this advances previous literature in CADD outside of the specific context of incorporating some ideas into a GPCR-Gprotein framework.

      Query 3. The authors mention that the hyperparameters for the ML models are just the package defaults in the absence of specification by the user. I would be helpful to know specifically what the the hyperparameters were for the benchmarks in this study; however, I think a deeper concern is still that these models are almost certainly far overparameterized given the limited training data used for the models. It is unclear why the authors did not just build a random forest classifier to discriminate their HABs and LABs using ligand- or protein-ligand interaction fingerprints or related ideas.

      Query 4. It is good, and expected, that increasing the fraction of the training set size in a random split validation all the way to 100% would allow the model to perfectly discriminate HABs and LABs. This does not demonstrate that the model has significant enrichment in prospective screening, particularly compared to simpler methods. The concern remains that these models are overparameterized and insufficiently validated. The authors did not perform any scaffold splits or other out-of-distribution analysis.

      Query 5. The authors contend that Gcoupler uniquely enables training models when data is scarce and ultra-large screening libraries are unavailable. Today, it is rather straightforward to dock a minimum of thousands of compounds. Using tools such as QuickVina2-GPU (https://pubs.acs.org/doi/10.1021/acs.jcim.2c01504), it is possible to quite readily dock millions in a day with a single GPU and obtain the AutoDock Vina score. GPU-acclerated Vina has been combined with cavity detection tools likely multiple times, including here (https://arxiv.org/abs/2506.20043). There are multiple cavity detection tools, including the ones the authors use in their protocol.

      Query 6. The authors contend that the simulations are converged, but they elected not to demonstrate stability in the predicting MM/GBSA binding energies with block averaging across the trajectory. This could have been done through the existing trajectories without additional simulation.