bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of a city-wide school-located influenza vaccination program in Oakland, California with respect to race and ethnicity: a matched cohort study
Authors: Nguyen Anna , Arnold Benjamin F. , Kennedy Chris J. , Mishra Kunal , Pokpongkiat Nolan , Seth Anmol , Djajadi Stephanie , Holbrook Kate , Pan Erica , Kirley Pam D. , Libby Tanya , Hubbard Alan E. , Reingold Arthur , Colford John M. , Benjamin-Chung Jade
Published: July 2021

Objectives

To evaluate the effectiveness of city-wide school-located influenza vaccination by race/ethnicity from 2014-2018.

Methods

We used multivariate matching to pair schools in the intervention district in Oakland, CA with schools in West Contra Costa County, CA, a comparison district. We estimated difference-in-differences (DIDs) in caregiver-reported influenza vaccination coverage and laboratory-confirmed influenza hospitalization incidence.

Results

Differences in influenza vaccination coverage in the intervention vs. comparison site were larger among White and Latino students than Asian/Pacific Islander (API), Black, and multiracial students. Concerns about vaccine effectiveness or safety were more common among Black and multiracial caregivers; logistical barriers to vaccination were more common among White, API, and Latinos. In both sites, hospitalization in 2017-18 was higher in Blacks vs. other races/ethnicities. All-age influenza hospitalization incidence was lower in the intervention site vs. comparison site among White/API individuals in 2016-17 and 2017-18 and Black older adults in 2017-18, but not in other groups.

Conclusions

SLIV was associated with higher vaccination coverage and lower influenza hospitalization, but associations varied by race/ethnicity. SLIV alone may be insufficient to ensure equitable health outcomes for influenza.
An Explainable Artificial Intelligence Approach for Predicting Cardiovascular Outcomes using Electronic Health Records
Authors: Wesołowski Sergiusz , Lemmon Gordon , Hernandez Edgar J. , Henrie Alex , Miller Thomas A. , Weyhrauch Derek , Puchalski Michael D. , Bray Bruce E. , Shah Rashmee U. , Deshmukh Vikrant G. , Delaney Rebecca , Yost H. Joseph , Eilbeck Karen , Tristani-Firouzi Martin , Yandell Mark
Published: July 2021

Understanding the conditionally-dependent clinical variables that drive cardiovascular health outcomes is a major challenge for precision medicine. Here, we deploy a recently developed massively scalable comorbidity discovery method called Poisson Binomial based Comorbidity discovery (PBC), to analyze Electronic Health Records (EHRs) from the University of Utah and Primary Children’s Hospital (over 1.6 million patients and 77 million visits) for comorbid diagnoses, procedures, and medications. Using explainable Artificial Intelligence (AI) methodologies, we then tease apart the intertwined, conditionally-dependent impacts of comorbid conditions and demography upon cardiovascular health, focusing on the key areas of heart transplant, sinoatrial node dysfunction and various forms of congenital heart disease. The resulting multimorbidity networks make possible wide-ranging explorations of the comorbid and demographic landscapes surrounding these cardiovascular outcomes, and can be distributed as web-based tools for further community-based outcomes research. The ability to transform enormous collections of EHRs into compact, portable tools devoid of Protected Health Information solves many of the legal, technological, and data-scientific challenges associated with large-scale EHR analyzes.
Early, intensive rehabilitation improves gross motor function after perinatal stroke: results of a randomized controlled trial
Authors: Hurd Caitlin , Livingstone Donna , Brunton Kelly , Smith Allison , Gorassini Monica , Watt Man-Joe , Andersen John , Kirton Adam , Yang Jaynie F.
Published: July 2021

Background

Perinatal stroke injures motor regions of the brain, compromising movement for life. Early, intensive, active interventions for the upper extremity are efficacious, but interventions for the lower extremity (LE) remain infrequent and understudied.

Objective

To determine the efficacy of ELEVATE – Engaging the Lower Extremity Via Active Therapy Early - on gross motor function, as compared to usual care.

Method

We conducted a single-blind, two-arm, randomized controlled trial (RCT), with the Immediate Group receiving the intervention while the Delay Group served as a three-month waitlist-control. A separate cohort living beyond commuting distance was trained by their parents with guidance from physical therapists. Participants were 8 months to 3 years old, with MRI-confirmed perinatal ischemic stroke and early signs of hemiparesis. The intervention was play-based, focused on weight-bearing, balance and walking for 1 hour/day, 4 days/week for 12 weeks. The primary outcome was the Gross Motor Function Measure-66 (GMFM-66). Secondary outcomes included steps and gait analyses. Final follow-up occurred at age four.

Results

Thirty-four children participated (25 RCT, 9 Parent-trained). The improvement in GMFM-66 over 12 weeks was greater for the Immediate than the Delay Group (average change 3.4 units higher) and greater in younger children. Average step counts reached 1370–3750 steps/session in the last week of training for all children. Parent-trained children also improved but with greater variability.

Conclusions

Early, activity-intensive LE therapy for young children with perinatal stroke is feasible and improves gross motor function in the short term. Longer term improvement may require additional bouts of intervention.

Clinical trial registratio

This study was registered at ClinicalTrials.gov (NCT01773369).
Waiting times, patient flow, and occupancy density in South African primary health care clinics: implications for infection prevention and control
Authors: Karat Aaron S , McCreesh Nicky , Baisley Kathy , Govender Indira , Kallon Idriss I , Kielmann Karina , MacGregor Hayley , Vassall Anna , Yates Tom A , Grant Alison D
Published: July 2021

Background

Transmission of respiratory pathogens, such asMycobacterium tuberculosisand severe acute respiratory syndrome coronavirus 2, is more likely during close, prolonged contact and when sharing a poorly ventilated space. In clinics in KwaZulu-Natal (KZN) and Western Cape (WC), South Africa, we estimated clinic visit duration, time spent indoors and outdoors, and occupancy density of waiting rooms.

Methods

We used unique barcodes to track attendees’ movements in 11 clinics in two provinces, multiple imputation to estimate missing arrival and departure times, and mixed-effects linear regression to examine associations with visit duration.

Results

2,903 attendees were included. Median visit duration was 2 hours 36 minutes (interquartile range [IQR] 01:36–3:43). Longer mean visit times were associated with being female (13.5 minutes longer than males; p<0.001) and attending with a baby (18.8 minutes longer than those without; p<0.01), and shorter mean times with later arrival (14.9 minutes shorter per hour after 0700; p<0.001) and attendance for tuberculosis or ante/postnatal care (24.8 and 32.6 minutes shorter, respectively, than HIV/acute care; p<0.01).

Overall, attendees spent more of their time indoors (median 95.6% [IQR 46–100]) than outdoors (2.5% [IQR 0–35]). Attendees at clinics with outdoor waiting areas spent a greater proportion (median 13.7% [IQR 1– 75]) of their time outdoors.

In two clinics in KZN (no appointment system), occupancy densities of ∼2.0 persons/m2were observed in smaller waiting rooms during busy periods. In one clinic in WC (appointment system), occupancy density did not exceed 1.0 persons/m2despite higher overall attendance.

Conclusions

Longer waiting times were associated with early arrival, being female, and attending with a young child. Attendees generally waited where they were asked to. Regular estimation of occupancy density (as patient flow proxy) may help staff assess for risk of infection transmission and guide intervention to reduce time spent in risky spaces.
Nutritional risk assessment using Malnutrition Universal Screening Tool (MUST) in COVID-19 patients: An observational study in a tertiary care hospital in Eastern India
Authors: Nag Sudeshna Maitra , Bhowmick Subhrojyoti , Bhowmick Sayantani , Deb Uttiya , Kundu Debarati , Ray Krishnangshu , Purkayastha Sujit Kar
Published: July 2021

Aims

To diagnose malnutrition, the nutritional status of each infected patient should be evaluated before starting general treatment. The role of Malnutrition Universal Screening Tool (MUST) in evaluating nutritional status of COVID-19 patients is still unknown. The aim of this study was to evaluate the use of MUST in assessment of nutritional status of COVID-19 patients.

Methods

We retrospectively analyzed the data of hospitalized COVID-19 patients above 18 years of age from July 25th to September 25th, 2020. All COVID-19 patients with a length of hospital stay greater than 24 hours underwent malnutrition screening and nutritional assessment based upon MUST. Demographic data, laboratory parameters and MUST score were retrieved from case files.

Results

Out of 106 COVID-19 patients included in the study, 68 (64%) were male and 38 (36%) were female. Number of deaths due to COVID-19 was 17 (16.03%). A total of 22 (20.75%) patients had MUST score of 2 and above. Analysis between MUST score and age group showed statistically significant result (p=0.012). MUST score according to clinical outcome at the end of hospitalization was also statistically significant (p<0.001).

Conclusion

Our results highlight a possible role of MUST as screening tool for malnutrition in COVID-19 patients.
Laboratory study to investigate the sensitivity and specificity of a diagnostic dressing to detect burn wound infection
Authors: Thet N.T. , Jenkins A.T.A. , Mercer-Chalmers J.D. , Coy K. , Booth S. , Collins D. , Bremner S. , Spickett-Jones F. , Greenwood R. , Young A.E.
Published: July 2021

Burn Wound Infection (BWI) is difficult to define and detect before it manifests with clear clinical symptoms. In this paper, an ex vivo study of a prototype BWI detecting wound dressing is reported. Consenting patients with burns were recruited from four burns services in the United Kingdom, their burn infection state recorded at time of recruitment and retrospectively following treatment. Their wound dressings were used as a source of inoculating bacteria to create an ex vivo biofilm model in the laboratory with reasonable fidelity to the original microbial state of their wound. The prototype infection detecting wound dressing, which responds to cytolytic toxins secreted by bacteria, was placed on the ex vivo biofilm and the response of the dressing correlated with the clinical decision on the patient’s wound infection state. The study illustrated a number of broader issues with clinical BWI diagnosis, notably the absence of objective diagnostic criteria: a ‘reference standard’ for BWI. The absence of such a reference standard made analysis of the relationship between the dressing response and BWI diagnosis challenging, however a point estimate of 68% sensitivity from the study suggests the potential future utility of using a sensor which detects secreted bacterial virulence factors to assist in BWI diagnosis.
Gastrodia-Uncaria Water Extract Inhibits Endoplasmic Reticulum Stress and Matrix Metalloproteinase in Protecting against Cerebral Ischemia
Authors: Yiu-Ting Choi Angus , Wen Xian Jia , Yi MA Sum , Zhixiu Lin , Wai Chan Chun
Published: July 2021

Stroke is the second leading cause of death in worldwide, in which cerebral ischemia accounts for 87% of all cases. The building up of endoplasmic reticulum stress in cerebral ischemia contributes to the disruption of blood brain barrier and neuronal cell death. The only FDA-approved drug, recombinant tissue plasminogen activator, is still of limited use due to the narrow window period and lack of neuroprotective effect. Therefore, it is necessary to explore alternative treatment on cerebral ischemia. Tianma-Gouteng decoction is a traditional Chinese Medicine prescription used to treat brain diseases in China. In this study, we investigated the neuroprotective effect of a water extract consisting of Gastrodia elata and Uncaria rhynchophylla, which are the two main herbs in the decoction. Cerebral ischemia was induced in rats using middle cerebral artery occlusion. GUW-treated rats have significantly reduced infarction volume and recovered neurological functions. The number of protein aggregates and caspase-12 positive cells were significantly inhibited. In vitro oxygen-glucose deprivation / reoxygenation stroke model demonstrated that the unfolded protein response proteins GRP78 and PDI were upregulated by GUW. Less ubiquitin puncta and normalized ubiquitin distribution indicated the reduction in endoplasmic reticulum stress. Furthermore, a lower Evan blue signal and MMPsense signal was observed, suggesting that GUW may preserve the blood brain barrier integrity through inhibiting MMP activity. Taken together, this suggested that GUW protected ischemic neurons and the blood brain barrier through inhibiting endoplasmic reticulum stress.
Herbarium specimens reveal herbivory patterns across the genus Cucurbita
Authors: Jenny Laura A. , Shapiro Lori R. , Davis Charles C. , Davies T. Jonathan , Pierce Naomi E. , Meineke Emily
Published: July 2021

PREMISE

Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for our understanding of variation in plant-insect ecological interactions and evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory over the entire geographic range where a plant-insect complex occurs is logistically difficult. Recently, new methods have been developed to use herbarium specimens to investigate patterns in plant-insect interactions across geographic areas, and during periods of accelerating anthropogenic change. Such investigations can provide insights into changes in herbivory intensity and phenology in plants that are of ecological and agricultural importance.

METHODS

Here, we analyze 274 pressed herbarium samples from all 14 species in the economically important plant genus Cucurbita (Cucurbitaceae) to investigate variation in herbivory damage. This collection is comprised of specimens of wild, undomesticated Cucurbita that were collected from across their native range in the Neotropics and subtropics, and Cucurbita cultivars that were collected from both within their native range and from locations where they have been introduced for agriculture in temperate Eastern North America.

RESULTS

We find that herbivory is common on individuals of all Cucurbita species collected from throughout their geographic ranges; however, estimates of herbivory varied considerably among individuals, with greater damage observed in specimens collected from unmanaged habitat. We also find evidence that mesophytic species accrue more insect damage than xerophytic species.

CONCLUSIONS

Our study demonstrates that herbarium specimens are a useful resource for understanding ecological interactions between domesticated crop plants and co-evolved insect herbivores.
Deep embeddings to comprehend and visualize microbiome protein space
Authors: Odrzywolek Krzysztof , Karwowska Zuzanna , Majta Jan , Byrski Aleksander , Milanowska-Zabel Kaja , Kosciolek Tomasz
Published: July 2021

Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.
Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer
Authors: Memon Danish , Rizvi Hira , Fromm George , Lihm Jayon , Schoenfeld Adam J. , Sauter Jennifer L. , Luo Jia , Chow Andrew , Bhanot Umesh K. , McCarthy Caroline , Ye Darwin , Vanderbilt Chad M. , Liu Cailian , Abu-Akeel Mohsen , Plodkowski Andrew J. , McGranahan Nicholas , Łuksza Marta , Greenbaum Benjamin D. , Merghoub Taha , Minn Andy J. , Beltrao Pedro , Schreiber Taylor H. , Miller Martin L. , Hellmann Matthew D.
Published: July 2021

Although cancer immunotherapy with PD-(L)1 blockade is now routine treatment for patients with lung cancer, remarkably little is known about acquired resistance. We examined 1,201 patients with NSCLC treated with PD-(L)1 blockade to clinically characterize acquired resistance, finding it to be common (occurring in more than 60% of initial responders), with persistent but diminishing risk over time, and with distinct metastatic and survival patterns compared to primary resistance. To examine the molecular phenotype and potential mechanisms of acquired resistance, we performed whole transcriptome and exome tumor profiling in a subset of NSCLC patients (n=29) with acquired resistance. Systematic immunogenomic analysis revealed that tumors with acquired resistance generally had enriched signals of inflammation (including IFNγ signaling and inferred CD8+ T cells) and could be separated into IFNγ upregulated and stable subsets. IFNγ upregulated tumors had putative routes of resistance with signatures of dysfunctional interferon signaling and mutations in antigen presentation genes. Transcriptomic profiling of cancer cells from a murine model of acquired resistance to PD-(L)1 blockade also showed evidence of dysfunctional interferon signaling and acquired insensitivity to in vitro interferon gamma treatment. In summary, we characterized clinical and molecular features of acquired resistance to PD-(L)1 blockade in NSCLC and found evidence of ongoing but dysfunctional IFN response. The persistently inflamed, rather than excluded or deserted, tumor microenvironment of acquired resistance informs therapeutic strategies to effectively reprogram and reverse acquired resistance.
skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation
Authors: Turner Stephen D. , Nagraj V. P. , Scholz Matthew , Jessa Shakeel , Acevedo Carlos , Ge Jianye , Woerner August E. , Budowle Bruce
Published: July 2021

Motivation

SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream processing and manipulation. A dedicated software package that consistently and intuitively implements this analysis functionality is needed.

Results

Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data.

Availability

The skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.
Democratizing Data-Independent Acquisition Proteomics Analysis on Public Cloud Infrastructures Via The Galaxy Framework
Authors: Fahrner Matthias , Föll Melanie Christine , Grüning Björn , Bernt Matthias , Röst Hannes , Schilling Oliver
Published: July 2021

Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging due to the high complexity and large data and sample size, which require specialized software and large computing infrastructures. Most available open-source DIA software necessitate basic programming skills and cover only a fraction of the analysis steps, often yielding a complex of multiple software tools, severely limiting usability and reproducibility. To overcome this hurdle, we have integrated a suite of DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their usage on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate usability of the all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided, to further increase access for the proteomics community.
Structure insights, thermodynamic profiles, dsDNA melting activity, and liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid N-terminal domain binding to DNA
Authors: Caruso Icaro Putinhon , dos Santos Almeida Vitor , Juliani do Amaral Mariana , de Andrade Guilherme Caldas , de Araújo Gabriela Rocha , de Araújo Talita Stelling , de Azevedo Jéssica Moreira , Barbosa Glauce Moreno , Bartkevihi Leonardo , Bezerra Peter Reis , dos Santos Cabral Katia Maria , Lourenço Isabella Otênio , Malizia-Motta Clara L. F. , de Luna Marques Aline , Mebus-Antunes Nathane Cunha , Neves-Martins Thais Cristtina , de Sá Jéssica Maróstica , Sanches Karoline , Santana-Silva Marcos Caique , Vasconcelos Ariana Azevedo , da Silva Almeida Marcius , de Amorim Gisele Cardoso , Anobom Cristiane Dinis , Da Poian Andrea T. , Gomes-Neto Francisco , Pinheiro Anderson S. , Almeida Fabio C. L.
Published: July 2021

The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD), either with or without the SR-rich motif (SR), upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on specificity for N-NTD/N-NTD-SR interaction with TRS, including an unfavorable energetic contribution to binding along with hydrogen bonds between the triple-thymidine (TTT) motif in the dsTRS and β-sheet II due to the defined position and orientation of the DNA duplex, a well-defined pattern (ΔH > 0 and ΔS > 0 for ssTRS, and ΔH < 0 and ΔS < 0 for dsTRS) for the thermodynamic profile of binding, and a preference for TRS in the formation of liquid condensates when compared to a non-specific sequence. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity.
Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2,3-dioxygenase axis
Authors: Priyadarshini Medha , Navarro Guadalupe , Reiman Derek J , Sharma Anukriti , Xu Kai , Lednovich Kristen , Manzella Christopher R , Khan Md Wasim , Wicksteed Barton , Chlipala George E , Sanzyal Barbara , Bernabe Beatriz Penalver , Maki Pauline M , Gill Ravinder K , Gilbert Jack , Dai Yang , Layden Brian T
Published: July 2021

Background and aims

Normal gestation involves reprogramming of maternal gut microbiome (GM) that may contribute to maternal metabolic changes by unclear mechanisms. This study aimed to understand the mechanistic underpinnings of GM – maternal metabolism interaction.

Methods

The GM and plasma metabolome of CD1, NIH-Swiss and C57BL/6J mice were analyzed using 16S rRNA sequencing and untargeted LC-MS throughout gestation and postpartum. Pharmacologic and genetic knockout mouse models were used to identify the role of indoleamine 2,3-dioxygenase (IDO1) in pregnancy-associated insulin resistance (IR). Involvement of gestational GM in the process was studied using fecal microbial transplants (FMT).

Results

Significant variation in gut microbial alpha diversity occurred throughout pregnancy. Enrichment in gut bacterial taxa was mouse strain and pregnancy time-point specific, with species enriched at gestation day 15/19 (G15/19), a point of heightened IR, distinct from those enriched pre- or post- pregnancy. Untargeted and targeted metabolomics revealed elevated plasma kynurenine at G15/19 in all three mouse strains. IDO1, the rate limiting enzyme for kynurenine production, had increased intestinal expression at G15, which was associated with mild systemic and gut inflammation. Pharmacologic and genetic inhibition of IDO1 inhibited kynurenine levels and reversed pregnancy-associated IR. FMT revealed that IDO1 induction and local kynurenine levels effects on IR derive from the GM in both mouse and human pregnancy.

Conclusions

GM changes accompanying pregnancy shift IDO1-dependent tryptophan metabolism toward kynurenine production, intestinal inflammation and gestational IR, a phenotype reversed by genetic deletion or inhibition of IDO1.
Transfer of learned cognitive flexibility to novel stimuli and task sets
Authors: Wen Tanya , Geddert Raphael M. , Madlon-Kay Seth , Egner Tobias
Published: July 2021

Adaptive behavior requires learning about the structure of one’s environment to derive optimal action policies, and previous studies have documented transfer of such structural knowledge to bias choices in new environments. Here, we asked whether people could also acquire and transfer more abstract knowledge across different task environments, specifically expectations about cognitive control demands. Over three experiments, participants performed a probabilistic card-sorting task in environments of either a low or high volatility of task rule changes (requiring low or high cognitive flexibility respectively) before transitioning to a medium-volatility environment. Using reinforcement learning modeling, we consistently found that previous exposure to high task rule volatilities led to faster adaptation to rule changes in the subsequent transfer phase. These transfers of expectations about cognitive flexibility demands were both task- (Experiment 2) and stimulus- (Experiment 3) independent, thus demonstrating the formation and generalization of environmental structure knowledge to guide cognitive control.

Statement of Relevance

We investigated whether structural knowledge of one task environment can be transferred to guide cognitive control strategies in new environments. Past research has found that while learning generally improves subsequent performance, it does so only for the learned task (“near transfer”) and has little or no generalizability to novel task rules and stimuli (“far transfer”). However, recent studies suggest that learning more abstract, structural task features (e.g., cognitive maps) allows for that knowledge to be applied to new environments. Here, we took a critical additional step and showed that people can acquire and transfer expectations about cognitive control demands (specifically cognitive flexibility) across different task environments. To our knowledge, this is the first demonstration of people’s ability to extract and re-use cognitive control learning parameters that transcend specific stimuli and tasks. This transfer of learned cognitive flexibility is particularly noteworthy because such flexibility is impaired in several common psychiatric conditions.
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps
Authors: Sharma Sudip , Kumar Sudhir
Published: July 2021

Felsenstein’s bootstrap resampling approach, applied in thousands of research articles, imposes a high computational burden for very long sequence alignments. We show that the bootstrapping of a collection of little subsamples, coupled with median bagging of subsample confidence limits, produces accurate bootstrap confidence for phylogenetic relationships in a fraction of time and memory. The little bootstraps approach will enhance rigor, efficiency, and parallelization of big data phylogenomic analyses.
Retrosplenial cortex is necessary for spatial and non-spatial latent learning in mice
Authors: Bottura de Barros Ana Carolina , Baruchin Liad J. , Panayi Marios C. , Nyberg Nils , Samborska Veronika , Mealing Mitchell T. , Akam Thomas , Kwag Jeehyun , Bannerman David M. , Kohl Michael M.
Published: July 2021

Latent learning occurs when associations are formed between stimuli in the absence of explicit reinforcement. Traditionally, latent learning in rodents has been associated with the creation internal models of space. However, increasing evidence points to roles of internal models also in non-spatial decision making. Whether the same brain structures and processes support the creation of spatially-anchored or non-spatial internal models via latent learning, is an open question. To address this question, we developed a novel operant box task that allows to test spatial and non-spatial versions of a flavour-based sensory preconditioning paradigm. We probed the role of the retrosplenial cortex, a brain area associated with spatial cognition and subjective value representation, in this task using precise, closed-loop optogenetic silencing during different task phases. We show that the retrosplenial cortex is necessary for both spatial and non-spatial latent learning in mice. We further demonstrate that the requirement of retrosplenial cortex is limited to the preconditioning phase of the task. Our results provide insight into the specific role of the retrosplenial cortex in latent learning, demonstrate that latent learning plays a general part in the creation of internal models, independent of spatial anchors, and provide a novel avenue for studying model-based decision making.
Csp1, A Cold-Shock Protein Homolog in Xylella fastidiosa Influences Pili Formation, Stress Response, and Gene Expression
Authors: Wei Wei , Sawyer Teresa , Burbank Lindsey P.
Published: July 2021

Bacterial cold shock-domain proteins (CSPs) are conserved nucleic acid binding chaperones that play important roles in stress adaptation and pathogenesis. Csp1 is a temperature-independent cold shock protein homolog in Xylella fastidiosa, a bacterial plant pathogen of grapevine and other economically important crops. Csp1 contributes to stress tolerance and virulence in X. fastidiosa. However, besides general single stranded nucleic acid binding activity, little is known about the specific function(s) of this protein. To further investigate the role(s) of Csp1, we compared phenotypic differences between wild type and a csp1 deletion mutant (Δcsp1). We observed decreases in cellular aggregation and surface attachment with the Δcsp1 strain compared to the wild type. Transmission electron microscopy imaging revealed that Δcsp1 had reduced pili compared to the wild type and complemented strains. The Δcsp1 strain also showed reduced survival after long term growth, in vitro. Since Csp1 binds DNA and RNA, its influence on gene expression was also investigated. Long-read Nanopore RNA-Seq analysis of wild type and Δcsp1 revealed changes in expression of several genes important for attachment and biofilm formation in Δcsp1. One gene of intertest, pilA1, encodes a type IV pili subunit protein and was up regulated in Δcsp1. Deleting pilA1 increased surface attachment in vitro and reduced virulence in grapevines. X. fastidiosa virulence depends on bacterial attachment to host tissue and movement within and between xylem vessels. Our results show Csp1 may play a role in both virulence and stress tolerance by influencing expression of genes important for biofilm formation.

Importance

Xylella fastidiosa is a major threat to the worldwide agriculture industry (1, 2). Despite its global importance, many aspects of X. fastidiosa biology and pathogenicity are poorly understood. There are currently few effective solutions to suppress X. fastidiosa disease development or eliminate bacteria from infected plants(3). Recently, disease epidemics due to X. fastidiosa have greatly expanded(2, 4, 5), exacerbating the need for better disease prevention and control strategies. Our studies show that Csp1 is involved in X. fastidiosa virulence and stress tolerance. Understanding how Csp1 influences pathogenesis and bacteria survival can aide in developing novel pathogen and disease control strategies. We also streamlined a bioinformatics protocol to process and analyze long read Nanopore bacterial RNA-Seq data, which has previously not been reported for X. fastidiosa.
Pich, an ATP-dependent chromatin remodeling protein, transcriptionally co-regulates oxidative stress response
Authors: Dutta Anindita , Das Apurba , Bisht Deepa , Arya Vijendra , Muthuswami Rohini
Published: July 2021

Cells respond to oxidative stress by elevating the levels of antioxidants, signaling, and transcriptional regulation often implemented by chromatin remodeling proteins. The study presented in this paper shows that the expression of PICH, an ATP-dependent chromatin remodeler, is upregulated during oxidative stress in HeLa cells. We also show that PICH regulates the expression of Nrf2, a transcription factor regulating antioxidant response, both in the absence and presence of oxidative stress. In turn, Nrf2 regulates the expression of PICH in the presence of oxidative stress. Both PICH and Nrf2 together regulate the expression of antioxidant genes and this transcriptional regulation is dependent on the ATPase activity of PICH. In addition, H3K27ac modification also plays a role in activating transcription in the presence of oxidative stress. Co-immunoprecipitation experiments show that PICH and Nrf2 interact with H3K27ac in the presence of oxidative stress. Mechanistically, PICH recognizes ARE sequences present on its target genes and introduces a conformational change to the DNA sequences leading us to hypothesize that PICH regulates transcription by remodeling DNA. PICH ablation leads to reduced expression of Nrf2 and impaired antioxidant response leading to increased ROS content, thus, showing PICH is essential for the cell to respond to oxidative stress.
CD8+ T cell signature in acute SARS-CoV-2 infection identifies memory precursors
Authors: Adamo Sarah , Michler Jan , Zurbuchen Yves , Cervia Carlo , Taeschler Patrick , Raeber Miro E. , Sain Simona Baghai , Nilsson Jakob , Moor Andreas E. , Boyman Onur
Published: July 2021

Immunological memory is a hallmark of adaptive immunity and facilitates an accelerated and enhanced immune response upon re-infection with the same pathogen1,2. Since the outbreak of the ongoing coronavirus disease 19 (COVID-19) pandemic, a key question has focused on whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells stimulated during acute infection give rise to long-lived memory T cells3. Using spectral flow cytometry combined with cellular indexing of transcriptomes and T cell receptor (TCR) sequencing we longitudinally characterize individual SARS-CoV-2-specific CD8+ T cells of COVID-19 patients from acute infection to one year into recovery and find a distinct signature identifying long-lived memory CD8+ T cells. SARS-CoV-2-specific memory CD8+ T cells persisting one year after acute infection re-express CD45RA and interleukin-7 receptor α (CD127), upregulate T cell factor-1 (TCF1), and maintain low CCR7, thus resembling CD45RA+ effector-memory T (TEMRA) cells. Tracking individual clones of SARS-CoV-2-specific CD8+ T cells, we reveal that an interferon signature marks clones giving rise to long-lived cells, whereas prolonged proliferation and mammalian target of rapamycin (mTOR) signaling are associated with clone contraction and disappearance. Collectively, we identify a transcriptional signature differentiating short-from long-lived memory CD8+ T cells following an acute virus infection in humans.
E-cadherin regulates the stability and transcriptional activity of β-catenin in embryonic stem cells
Authors: Bhattacharyya Sinjini , Mote Ridim D. , Freimer Jacob W. , Singh Surya Bansi , Arumugam Sandhya , Narayana Yadavalli V. , Rajan Raghav , Subramanyam Deepa
Published: July 2021

E-CADHERIN is abundantly expressed in embryonic stem cells (ESCs) and plays an important role in the maintenance of cell-cell adhesions. However, the exact function of this molecule beyond cell adhesion, in the context of cell fate decisions is largely unknown. Using mouse ESCs (mESCs), we demonstrate that E-CADHERIN and β- CATENIN interact at the membrane and continue to do so upon internalization within the cell. Knockout of the gene encoding E-CADHERIN, Cdh1, in mESCs resulted in a failure to form tight colonies, accompanied by altered expression of differentiation markers, and retention of pluripotency factor expression during differentiation. Interestingly, Cdh1-/- mESCs showed a dramatic reduction in β-CATENIN levels. Transcriptional profiling of Cdh1-/- mESCs displayed a significant alteration in the expression of a subset of β-CATENIN targets, in a cell-state dependent manner. While treatment with a pharmacological inhibitor against GSK3β could rescue levels of β-CATENIN in Cdh1-/- mESCs, expression of downstream targets were altered in a context-dependent manner, indicating an additional layer of regulation within this subset. Together, our results reveal the existence of a cell-state-dependent regulation of β-CATENIN and its transcriptional targets in an E-CADHERIN dependent manner. Our findings hint at hitherto unknown roles played by E- CADHERIN in regulating the activity of β-CATENIN in ESCs.

Significance Statement

Are cell adhesions only responsible for maintaining tissue architecture, or do they also regulate cell fate decisions during early embryonic stages by modulating the output of specific signalling pathways? In this study, we study the role of E- CADHERIN, a crucial component of cell-cell adhesions in the context of mouse embryonic stem cells (mESCs). We find that E-CADHERIN regulates the stability and activity of β-CATENIN in mESCs through physical interactions. However, the loss of E-CADHERIN affected the expression of only a subset of downstream targets of β-CATENIN in a cell-state dependent manner. This study highlights a critical cross-talk between molecules involved in cell-cell adhesion and the underlying signalling network critical for establishing cell fate during early mammalian development.
Cryo-EM structure of the NLRP3 decamer bound to the cytokine release inhibitory drug CRID3
Authors: Hochheiser Inga V. , Pilsl Michael , Hagelueken Gregor , Moecking Jonas , Marleaux Michael , Brinkschulte Rebecca , Latz Eicke , Engel Christoph , Geyer Matthias
Published: July 2021

NLRP3 is an intracellular sensor protein whose activation by a broad spectrum of exogenous and endogenous stimuli leads to inflammasome formation and pyroptosis. The mechanisms leading to NLRP3 activation and the way how antagonistic small molecules function remain poorly understood. Here we report the cryo-electron microscopy structures of full-length NLRP3 in its native form and complexed with the inhibitor CRID3 (also named MCC950). Inactive, ADP-bound NLRP3 is a decamer composed of homodimers of intertwined LRR domains that assemble back-to-back as pentamers with the NACHT domain located at the apical axis of this spherical structure. Molecular contacts between the concave sites of two opposing LRRs are mediated by an acidic loop extending from an LRR transition segment. Binding of CRID3 significantly stabilizes the NACHT and LRR domains relative to each other, allowing structural resolution of 3.9-4.2 Å. CRID3 binds into a cleft, connecting four subdomains of the NACHT with the transition LRR. Its central sulfonylurea group interacts with the Walker A motif of the NLRP3 nucleotide-binding domain and is sandwiched between two arginines from opposing sites, explaining the specificity of NLRP3 for this chemical entity. With the determination of the binding site of this lead therapeutic, specific targeting of NLRP3 for the treatment of autoinflammatory and autoimmune diseases and rational drug optimization are within reach.
The Murine Neuronal Receptor NgR1 Is Dispensable for Reovirus Pathogenesis
Authors: Aravamudhan Pavithra , Guzman-Cardozo Camila , Urbanek Kelly , Welsh Olivia , Konopka-Anstadt Jennifer , Sutherland Danica M. , Dermody Terence S.
Published: July 2021

Engagement of host receptors is essential for viruses to enter target cells and initiate infection. Expression patterns of receptors in turn dictate host and tissue tropism and disease pathogenesis during infection. Mammalian orthoreovirus (reovirus) displays serotype-dependent patterns of tropism in the murine central nervous system (CNS) that are dictated by viral attachment protein σ1. However, the receptor that mediates reovirus CNS tropism is unknown. Two proteinaceous receptors have been identified for reovirus, junctional adhesion molecule-A (JAM-A) and Nogo 66 receptor 1 (NgR1). Engagement of JAM-A is required for reovirus hematogenous dissemination but is dispensable for neural spread. To determine whether NgR1 functions in reovirus neuropathogenesis, we compared virus replication and disease following inoculation of wild-type (WT) and NgR1-/- mice. Genetic ablation of NgR1 did not alter replication of neurotropic reovirus strain T3SA- in the intestine and transmission to the brain following peroral inoculation. Viral titers in neural tissues following intramuscular inoculation, which provides access to neural dissemination routes, also were comparable in WT and NgR1-/- mice, suggesting that NgR1 is dispensable for reovirus neural spread to the CNS. The absence of both NgR1 and JAM-A also did not alter replication, neural tropism, and virulence of T3SA- following direct intracranial inoculation. In agreement with these findings, we found that the human but not the murine homolog of NgR1 functions as a receptor and confers efficient reovirus binding and infection of nonsusceptible cells in vitro. These results eliminate functions for JAM-A and NgR1 in shaping CNS tropism in mice and suggest that other receptors, yet to be identified, support this function.

IMPORTANCE

The CNS presents a range of barriers to pathogen invasion. Yet neurotropic viruses have evolved strategies to breach these barriers and establish infection by engagement of host factors that allow navigation to the CNS and neural cell entry. Human NgR1 was identified as a reovirus receptor in an RNA interference screen and is expressed in CNS neurons in a pattern overlapping with reovirus tropism. Using mice genetically lacking NgR1 expression, and following different routes of inoculation, we discovered that murine NgR1 is dispensable for reovirus dissemination to the CNS, tropism and replication in the brain, and resultant disease. Concordant with these results, expression of human but not murine NgR1 confers reovirus binding and infection of nonsusceptible cells in vitro. These results point to species-specific use of alternate receptors by reovirus. A detailed understanding of species- and tissue-specific factors that dictate viral tropism will inform development of interventions and targeted gene delivery and therapeutic viral vectors.
Limited accessibility of nitrogen supplied as amino acids, amides, and amines as energy sources for marine Thaumarchaeota
Authors: Damashek Julian , Bayer Barbara , Herndl Gerhard J. , Wallsgrove Natalie J. , Allen Tamara , Popp Brian N. , Hollibaugh James T.
Published: July 2021

Genomic and physiological evidence from some strains of ammonia-oxidizing Thaumarchaeota demonstrate their additional ability to oxidize nitrogen (N) supplied as urea or cyanate, fueling conjecture about their ability to conserve energy by directly oxidizing reduced N from other dissolved organic nitrogen (DON) compounds. Similarly, field studies have shown rapid oxidation of polyamine-N in the ocean, but it is unclear whether Thaumarchaeota oxidize polyamine-N directly or whether heterotrophic DON remineralization is required. We tested growth of two marine Nitrosopumilus isolates on DON compounds including polyamines, amino acids, primary amines, and amides as their sole energy source. Though axenic cultures only consumed N supplied as ammonium or urea, there was rapid but inconsistent oxidation of N from the polyamine putrescine when cultures included a heterotrophic bacterium. Surprisingly, axenic cultures oxidized 15N-putrescine during growth on ammonia, suggesting co-metabolism or accelerated breakdown of putrescine by reactive metabolic byproducts. Nitric oxide, hydrogen peroxide, or peroxynitrite did not oxidize putrescine in sterile seawater. These data suggest that the N in common DON molecules is not directly accessible to marine Thaumarchaeota, with thaumarchaeal oxidation (and presumably assimilation) of DON-N requiring initial heterotrophic remineralization. However, reactive byproducts or enzymatic co-metabolism may facilitate limited thaumarchaeal DON-N oxidation.
Structure and lipid-mediated remodelling mechanism of the Na+/H+exchanger NHA2
Authors: Matsuoka Rei , Fudim Roman , Jung Sukkyeong , Zhang Chenou , Bazzone Andre , Chatzikyriakidou Yurie , Nomura Norimichi , Iwata So , Orellana Laura , Beckstein Oliver , Drew David
Published: July 2021

Na+/H+exchangers catalyse an ion-exchange activity that is carried out in most, if not all cells. SLC9B2, also known as NHA2, correlates with the long-sought after sodium/lithium (Na+/Li+) exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite its functional importance, structural information and the molecular basis of its ion-exchange mechanism have been lacking. Here, we report the cryo EM structures ofbisonNHA2 in detergent and in nanodiscs at 3.0 and 3.5 Å resolution, respectively. NHA2 shares closest structural similarity to the bacterial electrogenic Na+/H+antiporter NapA, rather than other mammalian SLC9A members. Nevertheless, SSM-based electrophysiology results with NHA2 show the catalysis of electroneutral rather than electrogenic ion exchange, and the ion-binding site is quite distinctive, with a tryptophan-arginine- glutamate triad separated from the well-established ion-binding aspartates. These triad residues fine-tune ion binding specificity, as demonstrated by a salt-bridge swap mutant that converts NHA2 into a Li+-specific transporter. Strikingly, an additional N-terminal helix in NHA2 establishes a unique homodimer with a large ∼ 25 Å intracellular gap between protomers. In the presence of phosphatidylinositol lipids, the N-terminal helix rearranges and closes this gap. We confirm that dimerization of NHA2 is required for activityin vivo, and propose that the N- terminal helix has evolved as a lipid-mediated remodelling switch for regulation of transport activity.