bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of hay feeding method, supplement moisture, or access time on intake and waste by beef cows
Authors: Jaderborg Jeffery P , Bird Scott L , Crawford Grant I , Walker Ryon S , DiCostanzo Alfredo
Published: May 2021

Experiments were performed to determine the effects of feeding method and hay processing (Experiment 1), energy supplement moisture content and feeding method (Experiment 2), and access time to hay (Experiment 3) on cow body weight (BW), dry matter intake (DMI), and hay or energy supplement intake and waste. Experiment 1 was designed as a 4 × 4 Latin Square using 48 multiparous, late-gestating, Angus cows (626 kg initial BW). Cows were stratified by age and BW into four treatment groups (n = 12 cows/group); treatment groups were then initially assigned randomly to treatments in a sequence of preset Latin Square periods. In Experiment 1, round bales were processed and delivered on the pen surface or in a bunk, or left unprocessed and delivered in a hay ring or rolled out on the pen surface. Experiment 2 was designed as a 6 × 6 Latin Square utilizing 54 multiparous, late-gestating, Angus cows (616 kg initial BW). Cows were stratified by age and BW into treatment groups (n = 9 cows/group); treatment groups were then initially assigned randomly to treatments in a sequence of preset Latin Square periods. In Experiment 2, corn screenings (CS) or wet beet pulp (BP) were fed in a structure (inverted tire or bunk) or BP only on the pen surface. Experiment 3 was designed as a replicated 3 × 3 Latin Square utilizing 24 multiparous, late-gestating, Angus cows (584 kg initial BW). Cows were stratified by age and BW into treatment groups (n = 8 cows/group); treatment groups were then initially assigned randomly to treatments in a sequence of preset Latin Square periods. In Experiment 3, cows were permitted access to round-bales in a hay ring for 6, 14, or 24 h. In Experiment 1, hay DMI was not affected (P ≥ 0.579). Hay waste was greater (P ≤ 0.007) when hay, processed or not, was fed on the pen surface. In Experiment 2, hay DMI was greatest (P ≤ 0.011) for cows fed no supplement and those fed CS in a bunk. Feeding BP in a bunk led to the greatest (P ≤ 0.003) hay waste. In Experiment 3, cows permitted 6-h access consumed and wasted less (P < 0.001) hay compared with those permitted longer access; BW was unaffected (P ≥ 0.870). In these experiments, cows fed hay on the pen surface, processed or not, achieved similar DMI as those fed in a ring or bunk, but wasted more hay. Delivering BP in a bunk or on the pen surface increased hay and supplement waste, respectively. Controlling access to hay reduced DMI and waste while maintaining cow BW.
Acceptability of digital health interventions: embracing the complexity
Authors: Perski Olga , Short Camille E
Published: May 2021

Acceptability is a core concept in digital health. Available frameworks have not clearly articulated why and how researchers, practitioners and policy makers may wish to study the concept of acceptability. Here, we aim to discuss (i) the ways in which acceptability might differ from closely related concepts, including user engagement; (ii) the utility of the concept of acceptability in digital health research and practice; (iii) social and cultural norms that influence acceptability; and (iv) pragmatic means of measuring acceptability, within and beyond the research process. Our intention is not to offer solutions to these open questions but to initiate a debate within the digital health community. We conducted a narrative review of theoretical and empirical examples from the literature. First, we argue that acceptability may usefully be considered an emergent property of a complex, adaptive system of interacting components (e.g., affective attitude, beliefs), which in turn influences (and is influenced by) user engagement. Second, acceptability is important due to its ability to predict and explain key outcomes of interest, including user engagement and intervention effectiveness. Third, precisely what people find acceptable is deeply contextualized and interlinked with prevailing social and cultural norms. Understanding and designing for such norms (e.g., through drawing on principles of user centered design) is therefore key. Finally, there is a lack of standard acceptability measures and thresholds. Star ratings coupled with free-text responses may provide a pragmatic means of capturing acceptability. Acceptability is a multifaceted concept, which may usefully be studied with a complexity science lens.
The importance of community and culture for the recruitment, engagement, and retention of Chinese American immigrants in health interventions
Authors: Tsai William , Zhang Liwei , Park James S , Tan Yi-Ling , Kwon Simona C
Published: May 2021

Chinese Americans experience cancer health disparities throughout the entire cancer continuum. Yet, they remain underrepresented in health research in part due to barriers in recruitment, engagement, and retention. This paper describes the strategies that we devised, by drawing upon our experiences with conducting two culturally sensitive cancer intervention studies, to help researchers improve their recruitment and retention rates of Chinese Americans in health research and address the gap in knowledge on intervention research with this population. The first study assessed the efficacy, adoption, and impact of an intervention, delivered by community health workers, to improve adherence to recommended stomach cancer prevention guidelines for at-risk Chinese Americans. The second study evaluated the feasibility and preliminary efficacy of a culturally adapted version of the Expressive Helping intervention for Chinese American cancer patients and survivors. Our main recruitment strategies revolved around building community relationships, developing culturally sensitive materials, and establishing good first impressions with participants. Our main engagement and retention strategies focused on attending to cultural sensitivity, fostering relationships, and using technology. Harnessing the community’s inherent strengths and prioritizing cultural understanding is crucial for culturally sensitive health research with Chinese Americans.
Costing a population health management approach for participant recruitment to a diabetes prevention study
Authors: Michaud Tzeyu L , Wilson Kathryn , Silva Fabiana , Almeida Fabio , Katula Jeff , Estabrooks Paul
Published: May 2021

Limited research has reported the economic feasibility—from both a research and practice perspective—of efforts to recruit and enroll an intended audience in evidence-based approaches for disease prevention. We aimed to retrospectively assess and estimate the costs of a population health management (PHM) approach to identify, engage, and enroll patients in a Type 1 Hybrid Effectiveness-Implementation (HEI), diabetes-prevention trial. We used activity-based costing to estimate the recruitment costs of a PHM approach integrated within an HEI trial. We took the perspective of a healthcare system that may adopt, and possibly sustain, the strategy in the typical practice. We also estimated replication costs based on how the strategy could be applied in healthcare systems interested in referring patients to a local diabetes prevention program from a payer perspective. The total recruitment and enrollment costs were $360,424 to accrue 599 participants over approximately 15 months. The average cost per screened and enrolled participant was $263 and $620, respectively. Translating to the typical settings, total recruitment costs for replication were estimated as $193,971 (range: $43,827–$210,721). Sensitivity and scenario analysis results indicated replication costs would be approximately $283–$444 per patient enrolled if glucose testing was necessary, based on the Medicare-covered services. From a private payer perspective, and without glucose testing, per-participant assessed costs were estimated at $31. A PHM approach can be used to accrue a large number of participants in a short period of time for an HEI trial, at a comparable cost per participant.
Beyond Hours Worked and Dollars Earned: Multidimensional EQ, Retirement Trajectories and Health in Later Life
Authors: Andrea Sarah B , Eisenberg-Guyot Jerzy , Oddo Vanessa M , Peckham Trevor , Jacoby Daniel , Hajat Anjum
Published: May 2021

The working lives of Americans have become less stable over the past several decades and older adults may be particularly vulnerable to these changes in employment quality (EQ). We aimed to develop a multidimensional indicator of EQ among older adults and identify EQ and retirement trajectories in the United States. Using longitudinal data on employment stability, material rewards, workers’ rights, working-time arrangements, unionization, and interpersonal power relations from the Health and Retirement Study (HRS), we used principal component analysis to construct an EQ score. Then, we used sequence analysis to identify late-career EQ trajectories (age 50–70 years; N = 11,958 respondents), overall and by sociodemographics (race, gender, educational attainment, marital status). We subsequently examined the sociodemographic, employment, and health profiles of these trajectories. We identified 10 EQ trajectories; the most prevalent trajectories were Minimally Attached and Wealthy (13.9%) and Good EQ to Well-off Retirement (13.7%), however, 42% of respondents were classified into suboptimal trajectories. Those in suboptimal trajectories were disproportionately women, people of color, and less-educated. Individuals in the Poor EQ to Delayed and Poor Retirement and Unattached and Poor clusters self-reported the greatest prevalence of poor health and depression, while individuals in the Wealthy Business Owners and Great EQ to Well-off Retirement clusters self-reported the lowest prevalence of poor health and depression at baseline. Trajectories were substantially constrained for women of color. Although our study demonstrates EQ is inequitably distributed in later life, labor organizing and policy change may afford opportunities to improve EQ and retirement among marginalized populations.
Risk assessment for long and short range airborne transmission of SARS-CoV-2, indoors and outdoors, using carbon dioxide measurements
Authors: Poydenot Florian , Abdourahamane Ismael , Caplain Elsa , Der Samuel , Haiech Jacques , Jallon Antoine , Khoutami Inés , Loucif Amir , Marinov Emil , Andreotti Bruno
Published: May 2021

A quantitative analysis of the viral transmission risk in public spaces allows us to identify the dominant mechanisms that a proactive public health policy can act upon to reduce risk, and to evaluate the reduction of risk that can be obtained. The contribution of public spaces to the propagation of SARS-CoV-2 can be reduced to a level necessary for a declining epidemic, i.e. an overall reproduction rate below one. Here, we revisit the quantitative assessment of indoor and outdoor transmission risk. We show that the long-range aerosol transmission is controlled by the flow rate of fresh air and by the mask filtering quality, and is quantitatively related to the CO2 concentration, regardless the room volume and the number of people. The short-range airborne transmission is investigated experimentally using dedicated dispersion experiments performed in two shopping malls. Exhaled aerosols are dispersed by turbulent draughts in a cone, leading to a concentration inversely proportional to the squared distance and to the flow velocity. We show that the average infection dose, called the viral quantum, can be determined from epidemiological data in a manner consistent with biological experimental data. The results provide quantitative guidance useful for making rational public health policy decisions to prevent the dominant routes of viral transmission through reinforced ventilation, air purification, mechanical dispersion using fans, and incentivizing the wearing of correctly fitted, quality facial masks (surgical masks, possibly covered by another fabric mask, or non-medical FFP2 masks). Taken together, such measures significantly reduce the airborne transmission risk of SARS-CoV-2.
Cancer risk perception and knowledge and physician communication behaviors: specific influences on cervical cancer and colorectal cancer screening in women 50-65 years old
Authors: Harper Diane M , Tariq Madiha , Alhawli Asraa , Syed Nadia , Patel Minal R , Resnicow Ken
Published: May 2021

Background

Women 50-65 years old have the lowest cervical and colorectal cancer (CRC) screening rates amongst ages recommended for screening. The primary aim of this work is to determine how cancer risk perceptions and provider communication behaviors, in addition to known demographic factors, influence the uptake of both cervical and CRC screening or a single screen among women in southeast Michigan.

Methods

14 health services and communication behavior questions were adapted from the Health Information National Trends Survey (HINTS) and administered to a multiethnic sample of adults in southeast Michigan. The outcome variable was self-reported up to date cervical and/or CRC screening as defined by the United States Preventive Services Task Force (USPSTF). Demographic and cancer risk/communication behavior responses of the four screening status categories (both tests, one test, no tests) were analyzed with multinomial regression for all comparisons.

Results

Of the 394 respondents, 54% were up to date for both cervical and CRC screening, 21% were up to date with only cervical cancer screening and 12% were up to date for only CRC screening. Of the 14 risk perception and communication behaviors only, Did your primary care physician (PCP) involve you in the decisions about your health care as much as you wanted? was significantly associated with women having both screens compared to only cervical cancer screening (aOR 1.67 (95% CI: 1.08, 2.57). The control variables included in the model, also significant, were MENA and Black races compared to white women and age.

Conclusions

Screening behavior for both cancers is different than a single screen and associated with the woman’s perception of the physician involving her in her care as much as she wanted. In addition, educational programs are needed for MENA women.
Evidence-to-decision frameworks: a review and analysis to inform decision-making for environmental health interventions
Authors: Norris Susan L. , Aung Max T. , Chartres Nicholas , Woodruff Tracey J.
Published: May 2021

Background

Evidence-to-decision (EtD) frameworks provide a structured and transparent approach for groups of experts to use when formulating recommendations or making decisions. While extensively used for clinical and public health recommendations, EtD frameworks are not in widespread use in environmental health.

Objectives

This review sought to identify, compare and contrast key EtD frameworks for decisions or recommendations on interventions used in clinical medicine, public health or environmental health. Our goal was to identify best practices and guidance which will be used to inform the development of an EtD framework for formulating recommendations regarding interventions to prevent or mitigate the harmful effects of exposure to substances in the environment.

Methods

We identified a convenience sample of EtD frameworks used by a range of organizations. We searched Medline for systematic reviews of EtD frameworks used in clinical medicine, and public or environmental health. In a qualitative manner, we summarized the decision criteria in the selected frameworks and in the reviews.

Results

Fourteen key organizations provided 18 EtD frameworks; most frameworks focused on clinical medicine or public health interventions; four focused on environmental health and three on economic considerations. Only one framework was based on an underlying conceptual model, and rarely was a systematic review of potential criteria performed during the frameworks development. GRADE encompasses a set of closely related frameworks for different types of decisions. Harms of interventions were examined in all frameworks and benefits in all but one. Other criteria included certainty of the body of evidence (15 frameworks), resource considerations (15), feasibility (13), equity (12), values (11), acceptability (11), and human rights (2). There was variation in how specific criteria were defined. The five identified systematic reviews reported a similar spectrum of EtD criteria.

Discussion

The EtD frameworks examined encompassed similar criteria, with tailoring to specific audience needs. However, there is variation in development processes, terminology, level of detail provided and presentation of the criteria. Existing frameworks are a useful starting point for development of one tailored to decision-making in environmental health.
Multi-site Evaluation of SARS-CoV-2 Spike Mutation Detection Using a Multiplex Real-time RT-PCR Assay
Authors: Bier Carolin , Edelmann Anke , Theil Kathrin , Schwarzer Rolf , Deichner Maria , Gessner Andre , Hiergeist Andreas , Rentschler Ute , Gohl Peter , Kuchta Alison , Manohar Chitra , Santini Chris , Duncan Dana , Canchola Jesse , Sun Jingtao , Spier Gene , Simon Christian
Published: May 2021

Background

SARS-CoV-2 causes COVID-19, which can be fatal and is responsible for a global pandemic. Variants with increased transmissibility or the potential to evade immunity have emerged and represent a threat to global pandemic control. Variants of concern (VOC) can be identified by sequencing of viral RNA, or by more rapid methods for detection of subsets of signature mutations.

Methods

We developed a multiplex, real-time RT-PCR assay (cobas®SARS-CoV-2 Variant Set 1) for the qualitative detection and differentiation of three key SARS-CoV-2 mutations in the viral spike protein: del 69-70, E484K and N501Y. Analytical sensitivity and accuracy were evaluated at three testing sites using clinical specimens from patients infected with SARS-CoV-2 variants belonging to several different lineages, including B.1.1.7, B.1.351, and P.1.

Results

The limit of detection for E484K was between 180 and 620 IU/mL for the three different isolates tested. For N501Y, the LOD was between 270 and 720 IU/mL (five isolates), while for del 69-70, it was 80 - 92 IU/mL (two isolates). Valid test results were obtained with all clinical specimens that were positive using routine diagnostic tests. Compared to sequencing (Sanger and next-generation), test results were 100% concordant at all three loci; no false positive or false negative results were observed.

Conclusions

Data collected at three independent laboratories indicates excellent performance and concordance of cobas®SARS-CoV-2 Variant Set 1 with sequencing. New sets of primers and probes that target additional loci can be rapidly deployed in response to the identification of other emerging variants.
Identifying Cases of Shoulder Injury Related to Vaccine Administration (SIRVA) Using Natural Language Processing
Authors: Zheng Chengyi , Duffy Jonathan , Liu In-Lu Amy , Sy Lina S. , Navarro Ronald A. , Kim Sunhea S. , Ryan Denison , Chen Wansu , Qian Lei , Mercado Cheryl , Jacobsen Steven J.
Published: May 2021

Background

Shoulder injury related to vaccine administration (SIRVA) accounts for more than half of all claims received by the National Vaccine Injury Compensation Program. However, there is a lack of population-based studies due to the challenge of identifying SIRVA cases in large health care databases.

Objective

To develop a natural language processing (NLP) method to identify SIRVA cases from clinical notes.

Methods

We conducted the study among members of a large integrated health care organization who were vaccinated between 04/1/2016 and 12/31/2017 and had subsequent diagnosis codes indicative of shoulder injury. Based on a training dataset with a chart review reference standard of 164 individuals, we developed an NLP algorithm to extract shoulder disorder information, including prior vaccination, anatomic location, temporality and causality. The algorithm identified three groups of positive SIRVA cases (definite, probable and possible) based on the strength of evidence. We compared NLP results to a chart review reference standard of 100 vaccinated individuals. We then applied the final automated NLP algorithm to a broader cohort of vaccinated individuals with a shoulder injury diagnosis code and performed manual chart confirmation on a random sample of NLP-identified definite cases and all NLP-identified probable and possible cases.

Results

In the validation sample, the NLP algorithm had 100% accuracy for identifying 4 SIRVA cases and 96 individuals without SIRVA. In the broader cohort of 53,585 individuals, the NLP algorithm identified 291 definite, 124 probable, and 52 possible SIRVA cases. The chart-confirmation rates for these groups were 95.3%, 67.7% and 18.9%, respectively.

Conclusions

The algorithm performed with high sensitivity and reasonable specificity in identifying positive SIRVA cases. The NLP algorithm can potentially be used in future population-based studies to identify this rare adverse event, avoiding labor-intensive chart review validation.
Influenza A M2 recruits M1 to the plasma membrane: a fluorescence fluctuation microscopy study
Authors: Petrich Annett , Dunsing Valentin , Bobone Sara , Chiantia Salvatore
Published: May 2021

Influenza A virus (IAV) is a respiratory pathogen that causes seasonal epidemics with significant mortality. One of the most abundant proteins in IAV particles is the matrix protein 1 (M1), which is essential for the virus structural stability. M1 organizes virion assembly and budding at the plasma membrane (PM), where it interacts with other viral components. The recruitment of M1 to the PM as well as its interaction with the other viral envelope proteins (hemagglutinin (HA), neuraminidase, matrix protein 2 (M2)) is controversially discussed in previous studies. Therefore, we used fluorescence fluctuation microscopy techniques (i.e., scanning fluorescence cross-correlation spectroscopy and Number and Brightness) to quantify the oligomeric state of M1 and its interactions with other viral proteins in co-transfected as well as infected cells. Our results indicate that M1 is recruited to the PM by M2, as a consequence of the strong interaction between the two proteins. In contrast, only a weak interaction between M1 and HA was observed. M1-HA interaction occurred only in the case that M1 was already bound to the PM. We therefore conclude that M2 initiates the assembly of IAV by recruiting M1 to the PM, possibly allowing its further interaction with other viral proteins.

Statement of Significance

Influenza A virus (IAV) is a pathogen responsible for epidemics and occasional pandemics and, therefore, a significant burden on health systems. To develop innovative therapeutic approaches, a deeper understanding of the viral replication cycle is needed. For example, during the formation of new virions in infected cells, several viral components must assemble at the plasma membrane, but the molecular interactions involved in this process are not clearly understood. In this work, we use quantitative fluorescence microscopy methods to monitor the interplay between several viral proteins in live cell models. Our results underline the importance of the interactions between two specific proteins (M1 and M2) and shed light on the first steps in IAV assembly.
Multiple mechanisms for overcoming lethal over-initiation of DNA replication
Authors: Anderson Mary E. , Smith Janet L. , Grossman Alan D.
Published: May 2021

DNA replication is a highly regulated process that is primarily controlled at the step of initiation. In the gram-positive bacteriumBacillus subtilisthe replication initiator DnaA, is regulated by YabA, which inhibits cooperative binding at the origin. Mutants lacking YabA have increased and asynchronous initiation. We found that under conditions of rapid growth, thednaA1mutation that causes replication over-initiation, was synthetic lethal with a deletion ofyabA. We isolated several classes of suppressors of the lethal phenotype of the ΔyabA dnaA1double mutant. Some suppressors (dnaC, cshA) caused a decrease in replication initiation. Others (relA, nrdR) stimulate replication elongation. One class of suppressors decreased levels of the replicative helicase, DnaC, thereby limiting replication initiation. We found that decreased levels of helicase were sufficient to decrease replication initiation under fast growth conditions. Our results highlight the multiple mechanisms cells use to regulate DNA replication.
Extracting spatial networks from capture-recapture data reveal structured habitat use within a marine mammal’s spatial range
Authors: Bonnell Tyler R. , Michaud Robert , Dupuch Angélique , Lesage Véronique , Chion Clément
Published: May 2021

Estimating the impacts of anthropogenic disturbances requires an understanding of the habitat use patterns of individuals within a population. This is especially the case when disturbances are localized within a population’s spatial range, as variation in habitat-use within a population can drastically alter the distribution of impacts.

Here, we illustrate the potential for multilevel multinomial models to generate spatial networks from capture-recapture data, a common data source use in wildlife studies to monitor population dynamics and habitat use. These spatial networks capture which regions of a population’s spatial distribution share similar/dissimilar individual usage patterns, and can be especially useful for detecting structured habitat use within the population’s spatial range.

Using simulations and 18 years of capture-recapture data from St. Lawrence Estuary (SLE) beluga, we show that this approach can successfully estimate the magnitude of similarities/dissimilarities in individual usage patterns across sectors, and identify sectors that share similar individual usage patterns that differ from other sectors, i.e., structured habitat use. In the case of SLE beluga, this method identified multiple clusters of individuals, each preferentially using restricted areas within their summer range of the SLE.

Synthesis and applications.Multilevel multinomial models can be effective at estimating spatial structure in habitat use within wildlife populations sampled by capture-recapture of individuals. Our finding of a structured habitat use within the SLE beluga summer range has direct implications for estimating individual exposures to localized stressors, such as underwater noise from shipping or other activities.
Single Nuclei Sequencing of Human Putamen Oligodendrocytes Reveals Altered Heterogeneity and Disease-Associated Changes in Parkinson’s Disease and Multiple System Atrophy
Authors: Teeple Erin , Joshi Pooja , Pande Rahul , Huang Yinyin , Karambe Akshat , Latta-Mahieu Martine , Sardi S. Pablo , Cedazo-Minguez Angel , Klinger Katherine W. , Flores-Morales Amilcar , Madden Stephen L. , Rajpal Deepak , Kumar Dinesh
Published: May 2021

The role of oligodendrocytes in neurodegenerative diseases remains incompletely understood and largely unexplored at the single cell level. We profiled 87,086 single nuclei from human brain putamen region for healthy control, Parkinson’s Disease (PD), and Multiple System Atrophy (MSA). Oligodendrocyte lineage cells were the dominant cell-type in the putamen with oligodendrocyte subpopulations clustered by transcriptomic variation found to exhibit diverse functional enrichment patterns, and this oligodendrocyte heterogeneity was altered in a disease-specific way. Among profiled oligodendrocyte subpopulations, differences in expression of SNCA, HAPLN2, MAPT, APP, and OPALIN were observed for PD and MSA compared with healthy controls. Intriguingly, greater activation of unfolded protein response pathway gene expression was observed in PD nuclei versus MSA. Using network analysis, we then identified specific PD- and MSA-correlated gene co-expression modules enriched with disease relevant pathways; the PD-correlated module was significantly enriched for Parkinson’s Disease GWAS loci (p = 0.01046). Our analysis provides a broader understanding of oligodendrocyte heterogeneity and reveals distinctive oligodendrocyte pathological alterations associated with PD and MSA which may suggest potential novel therapeutic targets and new strategies for disease modification.
Subpopulations of neurons in lOFC encode previous and current rewards at time of choice
Authors: Hocker David , Brody Carlos D. , Savin Cristina , Constantinople Christine M
Published: May 2021

1

Studies of neural dynamics in lateral orbitofrontal cortex (lOFC) have shown that subsets of neurons that encode distinct aspects of behavior, such as value, may project to common downstream targets. However, it is unclear whether reward history, which may subserve lOFC’s well-documented role in learning, is represented by functional subpopulations in lOFC. Previously, we analyzed neural recordings from rats performing a value-based decision-making task, and we documented trial-by-trial learning that required lOFC (Constantinopleet al., 2019). Here we characterize functional subpopulations of lOFC neurons during behavior, including their encoding of task variables. We found five distinct clusters of lOFC neurons, either based on clustering of their trial-averaged peristimulus time histograms (PSTHs), or a feature space defined by their average conditional firing rates aligned to different task variables. We observed weak encoding of reward attributes, but stronger encoding of reward history, the animal’s left or right choice, and reward receipt across all clusters. Only one cluster, however, encoded the animal’s reward history at the time shortly preceding the choice, suggesting a possible role in integrating previous and current trial outcomes at the time of choice. This cluster also exhibits qualitatively similar responses to identified corticostriatal projection neurons in a recent study (Hirokawaet al., 2019), and suggests a possible role for subpopulations of lOFC neurons in mediating trial-by-trial learning.
Palbociclib-mediated cell cycle arrest can occur in the absence of the CDK inhibitors p21 and p27
Authors: Pennycook Betheney R. , Barr Alexis R.
Published: May 2021

The use of CDK4/6 inhibitors in the treatment of a wide range of cancers is an area of ongoing investigation. Despite their increasing clinical use, there is limited understanding of the determinants of sensitivity and resistance to these drugs. Recent data has cast doubt on how CDK4/6 inhibitors arrest proliferation, provoking renewed interest in the role(s) of CDK4/6 in driving cell proliferation. As the use of CDK4/6 inhibitors in cancer therapies becomes more prominent, an understanding of their effect on the cell cycle becomes more urgent. Here, we investigate the mechanism of action of CDK4/6 inhibitors in promoting cell cycle arrest. Two main models explain how CDK4/6 inhibitors cause G1 cell cycle arrest, which differ in their dependence on the CDK inhibitor proteins p21 and p27. We have used live and fixed single-cell quantitative imaging, with inducible degradation systems, to address the roles of p21 and p27 in the mechanism of action of CDK4/6 inhibitors. We find that CDK4/6 inhibitors can initiate and maintain a cell cycle arrest without p21 or p27. This work clarifies our current understanding of the mechanism of action of CDK4/6 inhibitors and has implications for cancer treatment and patient stratification.
Self-assembly of tessellated tissue sheets by growth and collision
Authors: Heinrich Matthew A. , Alert Ricard , Wolf Abraham E. , Košmrlj Andrej , Cohen Daniel J.
Published: May 2021

Tissues do not exist in isolation–they interact with other tissues within and across organs. While cell-cell interactions have been intensely investigated, less is known about tissue-tissue interactions. Here, we studied collisions between monolayer tissues with different geometries, cell densities, and cell types. First, we determine rules for tissue shape changes during binary collisions and describe complex cell migration at tri-tissue boundaries. Next, we demonstrate that genetically identical tissues displace each other based solely on cell density gradients, and present a physical model of tissue interactions that allows us to estimate the bulk modulus of the tissues from collision dynamics. Finally, we introduce TissEllate, a design tool for self-assembling complex tessellations from arrays of many tissues, and we use cell sheet engineering techniques to transfer these composite tissues like cellular films. Overall, our work provides insight into the mechanics of tissue collisions, harnessing them to engineer tissue composites as designable living materials.
Ca2+-mediated higher-order assembly of b0,+AT–rBAT is a key step for system b0,+biogenesis and cystinuria
Authors: Lee Yongchan , Wiriyasermkul Pattama , Moriyama Satomi , Mills Deryck J. , Kühlbrandt Werner , Nagamori Shushi
Published: May 2021

Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, which causes recurrent kidney stones and occasionally severe kidney failure. Mutations of the two responsible proteins, rBAT and b0,+AT, which comprise system b0,+, are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Although recent structural insights into human b0,+AT–rBAT suggested a model for transport-inactivating mutations, the mechanisms by which type I mutations trigger trafficking deficiencies are not well understood. Here, using electron cryo-microscopy and biochemistry, we discover that Ca2+-mediated higher-order assembly of system b0,+is the key to its trafficking on the cell surface. We show that Ca2+stabilizes the interface between two rBAT molecules to mediate super-dimerization, and this in turn facilitates the N-glycan maturation of system b0,+. A common cystinuria mutant T216M and mutations that disrupt the Ca2+site in rBAT cause the loss of higher-order assemblies, resulting in protein trafficking deficiency. Mutations at the super-dimer interface reproduce the mis-trafficking phenotype, demonstrating that super-dimerization is essential for cellular function. Cell-based transport assays confirmed the importance of the Ca2+site and super-dimerization, and additionally suggested which residues are involved in cationic amino acid recognition. Taken together, our results provide the molecular basis of type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and trafficking diseases in general.
Fixel-Based Analysis and Free Water Corrected DTI Evaluation of HIV Associated Neurocognitive Disorders
Authors: Finkelstein Alan , Faiyaz Abrar , Weber Miriam T. , Qiu Xing , Uddin Md Nasir , Zhong Jianhui , Schifitto Giovanni
Published: May 2021

White matter damage is a consistent finding in HIV infected (HIV+) individuals. Previous studies have evaluated WM fiber tract specific brain regions in HIV-associated neurocognitive disorders using diffusion tensor imaging (DTI). However, DTI might lack an accurate biological interpretation, and the technique suffers from several limitations. Here, we sought to evaluate Fixel-based analysis (FBA) and free water corrected DTI (fwcDTI) metrics between HIV+ and HIV uninfected (HIV−) individuals, and their relationships with blood markers and cognitive scores. We also compared the specificity of both MRI metrics in their ability to distinguish between individuals with and without cognitive impairment using machine learning classifiers. Using 94 age-matched participants, we found that whole brain FBA was significantly reduced (up to 15%) in various fiber bundles. Tract based special statistics (TBSS) of fwcDTI metrics revealed decreased fractional anisotropy FAT(by 1-2%) in HIV+ compared to HIV− individuals in areas consistent with those observed in FBA, but these were not significant. An adaptive boosting classifier reliably distinguished between cognitively normal patients and those with cognitive impairment with 80% precision and 78% recall. Therefore, FBA may serve as a potential in-vivo biomarker for evaluating and monitoring axonal degeneration in HIV+ patients at risk for neurocognitive impairment.
Generalizing predictions to unseen sequencing profiles via deep generative models
Authors: Oh Min , Zhang Liqing
Published: May 2021

Predictive models trained on sequencing profiles often fail to achieve expected performance when externally validated on unseen profiles. While many factors such as batch effects, small data sets, and technical errors contribute to the gap between source and unseen data distributions, it is a challenging problem to generalize the predictive models across studies without any prior knowledge of the unseen data distribution. Here, this study proposes DeepBioGen, a sequencing profile augmentation procedure that characterizes visual patterns of sequencing profiles, generates realistic profiles based on a deep generative model capturing the patterns, and generalizes the subsequent classifiers. DeepBioGen outperforms other methods in terms of enhancing the generalizability of the prediction models on unseen data. The generalized classifiers surpass the state-of-the-art method, evaluated on RNA sequencing tumor expression profiles for anti-PD1 therapy response prediction and WGS human gut microbiome profiles for type 2 diabetes diagnosis.
DeepGeni: Deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy
Authors: Oh Min , Zhang Liqing
Published: May 2021

Recent studies revealed that gut microbiota modulates the response to cancer immunotherapy and fecal microbiota transplantation has clinical benefit in melanoma patients during the treatment. Understanding microbiota affecting individual response is crucial to advance precision oncology. However, it is challenging to identify the key microbial taxa with limited data as statistical and machine learning models often lose their generalizability. In this study, DeepGeni, a deep generalized interpretable autoencoder, is proposed to improve the generalizability and interpretability of microbiome profiles by augmenting data and by introducing interpretable links in the autoencoder. DeepGeni-based machine learning classifier outperforms state-of-the-art classifier in the microbiome-driven prediction of responsiveness of melanoma patients treated with immune checkpoint inhibitors. DeepGeni-based machine learning classifier outperforms state-of-the-art classifier in the microbiome-driven responsiveness prediction of melanoma patients treated with immune checkpoint inhibitors. Also, the interpretable links of DeepGeni elucidate the most informative microbiota associated with cancer immunotherapy response.
Active Surveillance Characterizes Human Intratumoral T Cell Exhaustion
Authors: You Ran , Artichoker Jordan , Fries Adam , Edwards Austin , Combes Alexis , Reeder Gabriella , Samad Bushra , Krummel Matthew F.
Published: May 2021

Intratumoral T cells that might otherwise control tumors are often identified in an ‘exhausted’ state, defined by specific epigenetic modifications as well as upregulation of genes such as CD38, CTLA-4 and PD-1. While the term might imply inactivity, there has been little study of this state at the phenotypic level in tumors to understand the extent of their incapacitation. Starting with the observation that T cells move more quickly through mouse tumors as residence time increases and they progress towards exhaustion, we elaborated a non-stimulatory live-biopsy method for real-time study of T cell behaviors within individual patient tumors. Using two-photon microscopy, we studied native CD8 T cells interacting with APCs and with cancer cells in different micro-niches of human tumors, finding that T cell speed was variable by region and by patient, was independent of T cell density and was inversely correlated with local tumor density. Across a range of tumor types, we found a strong relationship between CD8 T cell motility and exhausted T cell state that corresponds to observations made in mouse models where exhausted T cells move faster. While this is a small study, it demonstrates at least two types of T cell dynamic states in individual human tumors and supports the existence of an active program in ‘exhausted’ T cells that extends beyond incapacitating them.
Notch-Induced Endoplasmic Reticulum-Associated Degradation Governs Thymocyte β−Selection
Authors: Liu Xia , Yu Jingjing , Xu Longyong , Umphred-Wilson Katharine , Peng Fanglue , Ding Yao , Barton Brendan M , Lv Xiangdong , Zhao Michael Y , Sun Shengyi , Hong Yuning , Qi Ling , Adoro Stanley , Chen Xi
Published: May 2021

Signals from the pre-T cell receptor and Notch coordinately instructβ-selection of CD4−CD8−double negative (DN) thymocytes to generateαβT cells in the thymus. However, how these signals ensure a high-fidelity proteome and safeguard the clonal diversification of the pre- selection TCR repertoire given the considerable translational activity imposed byβ-selection is largely unknown. Here, we identify the endoplasmic reticulum (ER)-associated degradation (ERAD) machinery as a critical proteostasis checkpoint duringβ-selection. Expression of the SEL1L-HRD1 complex, the most conserved branch of ERAD, is directly regulated by the transcriptional activity of the Notch intracellular domain. Deletion ofSel1limpaired DN3 to DN4 thymocyte transition and severely impairedαβT cell development. Mechanistically,Sel1ldeficiency induced unresolved ER stress that triggered thymocyte apoptosis through the PERK pathway. Accordingly, genetically inactivating PERK rescued T cell development fromSel1l- deficient thymocytes. Our study reveals a critical developmental signal controlled proteostasis mechanism that enforces T cell development to ensure a healthy adaptive immunity.
Panacea: a hyperpromiscuous antitoxin protein domain for the neutralisation of diverse toxin domains
Authors: Kurata Tatsuaki , Saha Chayan Kumar , Buttress Jessica A. , Mets Toomas , Brodiazhenko Tetiana , Turnbull Kathryn J. , Awoyomi Ololade F. , Oliveira Sofia Raquel Alves , Jimmy Steffi , Ernits Karin , Delannoy Maxence , Persson Karina , Tenson Tanel , Strahl Henrik , Hauryliuk Vasili , Atkinson Gemma C.
Published: May 2021

Toxin-Antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids, as well as bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets, and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analysed the conservation of genomic neighbourhoods using our computational tool FlaGs (for Flanking Genes), which allows high-throughput detection of TA-like operons. Focussing on the widespread but poorly experimentally characterised antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have renamed the domain to Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralised TA pairs. While the majority of validated PanA-neutralised toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises replication and translation, as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralisation mechanisms employed by Type II TA systems. Finally, through directed evolution we have selected PanA variants that can neutralise non-cognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain.

Significance

Toxin-antitoxin systems are enigmatic and diverse elements of bacterial and bacteriophage genomes. We have uncovered remarkable versatility of an antitoxin protein domain, that has evolved to neutralise dozens of different toxin domains. We find that antitoxins carrying this domain – Panacea – form complexes with their cognate toxins, indicating a direct neutralisation mechanism, and that Panacea can be evolved to neutralise a non-cognate and non-homologous toxin with just two amino acid substitutions. This raises the possibility that this domain could be an adaptable universal, or semi-universal protein neutraliser with significant biotechnological and medical potential.
A Comprehensive Human Embryogenesis Reference Tool using Single-Cell RNA-Sequencing Data
Authors: Zhao Cheng , Plaza Reyes Alvaro , Schell John Paul , Weltner Jere , Ortega Nicolás M. , Zheng Yi , Björklund Åsa K. , Baqué-Vidal Laura , Sokka Joonas , Torokovic Ras , Cox Brian , Rossant Janet , Fu Jianping , Petropoulos Sophie , Lanner Fredrik
Published: May 2021

Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to theirin vivocounterparts. To authenticate human embryo models, single-cell RNA-sequencing has been utilised for unbiased transcriptional profiling. However, a well-organised and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Herein, we developed such a reference, through integration of six published human datasets covering developmental stages from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and non-human primate datasets. Using stabilised UMAP we constructed a web tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined several recent human embryo models, highlighting the risk of misannotation when relevant references are lacking.