bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroepidemiology of the Seasonal Human Coronaviruses NL63, 229E, OC43 and HKU1 in France
Authors: De Thoisy Alix , Woudenberg Tom , Pelleau Stéphane , Donnadieu Françoise , Garcia Laura , Pinaud Laurie , Tondeur Laura , Meola Annalisa , Arowas Laurence , Clement Nathalie , Backovic Marija , Ungeheuer Marie-Noëlle , Fontanet Arnaud , White Michael ,   COVID-Oise and SeroPed study teams, Woudenberg Tom , Pelleau Stéphane , Pinaud Laurie , Tondeur Laura , Ungeheuer Marie-Noëlle , Fontanet Arnaud , White Michael , Pellerin Sandrine Fernandes , Guiheneuf Raphaël , Delamare Catherine , Marlet Karl Stefic and Julien , Brochot Etienne , Castelain Sandrine , Augereau Olivier , Sibilia Jean , Dubos François , Guen Christéle Gras-Le , Coste-Burel Marianne , Imbert-Marcille Berthe-Marie , Schweitzer Cyril , Gatin Amélie , Joulié Aline , Haas Hervé , Cantais Aymeric , Bertholon Frederique , Chinazzo-Vigouroux Marie-France , Duru Cécile , Koffi Aymar Davy 
Published: June 2023

Abstract

Background
The seasonal human coronaviruses (HCoV) NL63, 229E, OC43, and HKU1 are globally endemic, yet the majority of HCoV infections remain undiagnosed.

Methods
In a cross-sectional study, 2389 serum samples were collected from children and adults in France in 2020. In a longitudinal cohort study, 2520 samples were collected from 898 French individuals followed up between 2020 and 2021. Antibodies to HCoVs were measured using a bead-based multiplex assay.

Results
The rate of waning of anti-HCoV spike immunoglobulin G antibodies was estimated as 0.22–0.47 year−1 for children, and 0.13–0.27 year−1 for adults. Seroreversion was estimated as 0.31–1.37 year−1 in children and 0.19–0.72 year−1 in adults. The estimated seroconversion rate in children was consistent with 20%–39% of children being infected every year with each HCoV.

Conclusions
The high force of infection in children indicates that HCoVs may be responsible for a substantial proportion of fever episodes experienced by children.
Serum Response Factor Reduces Gene Expression Noise and Confers Cell State Stability
Authors: Zhang Jian , Wu Qiao , Hu Xiao , Wang Yadong , Lu Jun , Chakraborty Raja , Martin Kathleen A , Guo Shangqin 
Published: June 2023

Abstract
The role of serum response factor (Srf), a central mediator of actin dynamics and mechanical signaling, in cell identity regulation is debated to be either a stabilizer or a destabilizer. We investigated the role of Srf in cell fate stability using mouse pluripotent stem cells. Despite the fact that serum-containing cultures yield heterogeneous gene expression, deletion of Srf in mouse pluripotent stem cells leads to further exacerbated cell state heterogeneity. The exaggerated heterogeneity is detectible not only as increased lineage priming but also as the developmentally earlier 2C-like cell state. Thus, pluripotent cells explore more variety of cellular states in both directions of development surrounding naïve pluripotency, a behavior that is constrained by Srf. These results support that Srf functions as a cell state stabilizer, providing rationale for its functional modulation in cell fate intervention and engineering.
Sphingosine 1‐phosphate elicits a ROS‐mediated proinflammatory response in human endometrial stromal cells via ERK5 activation
Authors: Seidita Isabelle , Tusa Ignazia , Prisinzano Matteo , Menconi Alessio , Cencetti Francesca , Vannuccini Silvia , Castiglione Francesca , Bruni Paola , Petraglia Felice , Bernacchioni Caterina , Rovida Elisabetta , Donati Chiara 
Published: June 2023

AbstractEndometriosis is a chronic gynecological disease affecting ~10% women in the reproductive age characterized by the growth of endometrial glands and stroma outside the uterine cavity. The inflammatory process has a key role in the initiation and progression of the disorder. Currently, there are no available early diagnostic tests and therapy relies exclusively on symptomatic drugs, so that elucidation of the complex molecular mechanisms involved in the pathogenesis of endometriosis is an unmet need. The signaling of the bioactive sphingolipid sphingosine 1‐phosphate (S1P) is deeply dysregulated in endometriosis. S1P modulates a variety of fundamental cellular processes, including inflammation, neo‐angiogenesis, and immune responses acting mainly as ligand of a family of G‐protein‐coupled receptors named S1P receptors (S1PR), S1P1–5. Here, we demonstrated that the mitogen‐activated protein kinase ERK5, that is expressed in endometriotic lesions as determined by quantitative PCR, is activated by S1P in human endometrial stromal cells. S1P‐induced ERK5 activation was shown to be triggered by S1P1/3 receptors via a SFK/MEK5‐dependent axis. S1P‐induced ERK5 activation was, in turn, responsible for the increase of reactive oxygen species and proinflammatory cytokine expression in human endometrial stromal cells. The present findings indicate that the S1P signaling, via ERK5 activation, supports a proinflammatory response in the endometrium and establish the rationale for the exploitation of innovative therapeutic targets for endometriosis.
Laser-Assisted and Device-Assisted Filler Delivery: A Histologic Evaluation
Authors: Cervantes Jessica , Chang Yu-Feng , Dover Jeffrey S. , Hernandez Alvarez Angelica , Chung Hye Jin 
Published: June 2023

BACKGROUND
Lasers and devices are used to enhance transcutaneous delivery of fillers. However, little has been published on the histologic findings of this form of laser/device-assisted delivery to determine the optimal devices and fillers.

OBJECTIVE
To objectively evaluate the histological effects of laser-assisted and device-assisted filler delivery.

METHODS
Ex vivo human abdominoplasty skin samples were treated with fractional CO2 laser (ECO2, 120 μm tip, 120 mJ), fractional radiofrequency microneedling (FRMN, Genius, 1.5 mm, 20 mJ/pin), and microneedling (2.0 mm). Immediately after poly-l-lactic acid (PLLA), hyaluronic acid gel, calcium hydroxylapatite, and black tissue marking dye were topically applied. After treatment, biopsies were collected for histologic evaluation.

RESULTS
Histology revealed that PLLA and black dye were found in greatest abundance, hyaluronic acid was found to a lesser extent, and calcium hydroxylapatite was least found within channels created by fractional CO2 laser. Microneedling was effective only at delivering black dye, whereas FRMN failed to show significant channel formation or delivery of the studied products.

CONCLUSION
Among the devices and fillers studied, fractional CO2 laser and PLLA proved to be the most effective combination for laser/device-assisted filler delivery. Neither microneedling nor FRMN was effective as devices to enhance filler delivery.
Gastrointestinal failure, big data and intensive care
Authors: Singer Pierre , Robinson Eyal , Raphaeli Orit 
Published: June 2023

Purpose of review
Enteral feeding is the main route of administration of medical nutritional therapy in the critically ill. However, its failure is associated with increased complications. Machine learning and artificial intelligence have been used in intensive care to predict complications. The aim of this review is to explore the ability of machine learning to support decision making to ensure successful nutritional therapy.

Recent findings
Numerous conditions such as sepsis, acute kidney injury or indication for mechanical ventilation can be predicted using machine learning. Recently, machine learning has been applied to explore how gastrointestinal symptoms in addition to demographic parameters and severity scores, can accurately predict outcomes and successful administration of medical nutritional therapy.

Summary
With the rise of precision and personalized medicine for support of medical decisions, machine learning is gaining popularity in the field of intensive care, first not only to predict acute renal failure or indication for intubation but also to define the best parameters for recognizing gastrointestinal intolerance and to recognize patients intolerant to enteral feeding. Large data availability and improvement in data science will make machine learning an important tool to improve medical nutritional therapy.
Sex-based Disparities in Access to Liver Transplantation for Waitlisted Patients With Model for end-stage Liver Disease Score of 40
Authors: Cron David C. , Braun Hillary J. , Ascher Nancy L. , Yeh Heidi , Chang David C. , Adler Joel T. 
Published: June 2023

Objective:
To determine the association of sex with access to liver transplant among candidates with the highest possible model for end-stage liver disease score (MELD 40).

Background:
Women with end-stage liver disease are less likely than men to receive a liver transplant, due in part to MELD’s underestimation of renal dysfunction in women. The extent of the sex-based disparity among patients with high disease severity and equally high MELD scores is unclear.

Methods:
Using national transplant registry data, we compared liver offer acceptance (offers received at match MELD 40) and waitlist outcomes (transplant vs. death/de-listing) by sex for 7,654 waitlisted liver transplant candidates from 2009-2019 who reached MELD 40. Multivariable logistic and competing risks regression was used to estimate the association of sex with outcome and adjust for candidate and donor factors.

Results:
Women (N=3,019, 39.4%) spent equal time active at MELD 40 (median 5 vs. 5 days, P=0.28) but had lower offer acceptance (9.2% vs. 11.0%, P<0.01) compared to men (N=4,635, 60.6%). Adjusting for candidate/donor factors, offers to women were less likely accepted (OR=0.87, P<0.01). Adjusting for candidate factors, once they reached MELD 40, women were less likely transplanted (sub-distribution hazard ratio [SHR]=0.90, P<0.01) and more likely to die or be de-listed (SHR=1.14, P=0.02).

Conclusions:
Even among candidates with high disease severity and equally high MELD scores, women have reduced access to liver transplant and worse outcomes compared to men. Policies addressing this disparity should consider factors beyond MELD score adjustments alone.
Production of antigenically stable enterovirus A71 virus-like particles in Pichia pastoris as a vaccine candidate
Authors: Kingston Natalie J. , Snowden Joseph S. , Martyna Agnieszka , Shegdar Mona , Grehan Keith , Tedcastle Alison , Pegg Elaine , Fox Helen , Macadam Andrew J. , Martin Javier , Hogle James M. , Rowlands David J. , Stonehouse Nicola J. 
Published: June 2023

Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation.
We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilized virus-like particles (VLPs) in Pichia pastoris.
The stabilized VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilization, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralize virus in vitro. Therefore, anti-EVA71 neutralizing antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responses in vivo remains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies.
Social Determinants of Health and Fatal Crashes Involving US Geriatric and Non-Geriatric Road Users
Authors: Adeyemi Oluwaseun , DiMaggio Charles , Grudzen Corita , Konda Sanjit , Rogers Erin , Goldfeld Keith , Blecker Saul , Chodosh Joshua 
Published: June 2023

AbstractIntroductionSocial determinants of health (SDoH), defined as nonmedical factors that impact health outcomes, have been associated with fatal crash occurrences. Road users who live in communities with negative SDoH may be at increased risk of crash-related mortality, and the risks may be further heightened among geriatric road users and in rural areas. We evaluated the relationship between the county-level measure of SDoH and county-level fatal crash counts among geriatric and non-geriatric road users living in rural, suburban, and urban areas.MethodsFor this ecological study, we pooled data from Fatality Analysis Reporting System (2018 to 2020) and the U.S. Census Bureau (2019 data) and limited our analyses to the 3,108 contiguous US counties. The outcome measures were county-level fatal crash counts involving (1) geriatric (65 years and older) road users (2) non-geriatric road users, and (2) the general population. The predictor variable was the Multidimensional Deprivation Index (MDI), a score that measures the five domains of SDoH - economic quality, healthcare access, education, community, and neighborhood quality. We defined the MDI as a three-level categorical variable: at or below the national average, within two-fold of the national average, and higher than two-fold of the national average. We controlled for county-level demographics and crash characteristics. We performed a Bayesian spatial Poisson regression analysis using Integrated Nested Laplace Approximations and reported the crash fatality rate ratios (plus 95% Credible Intervals (CrI)).ResultsThe median (Q1, Q3) standardized mortality rate ratios among geriatric and non-geriatric road users were 1.3 (0.6, 2.5) and 1.6 (0.9, 2.7), respectively. A total of 283 (9.1%) and 806 (15.9%) counties were classified as very highly deprived and highly deprived, respectively. Clusters of counties with high deprivation rates were identified in the Southern states. Counties classified as very highly deprived and highly deprived had 40% (95% CrI: 1.24 – 1.57) and 25% (95% CrI: 1.17 – 1.34) increased geriatric fatality crash rate ratios and this pattern of association persisted in suburban and urban areas. Also, counties classified as very highly deprived and highly deprived had 42% (95% CI: 1.27 – 1.58) and 32% (95% CI: 1.23 – 1.38) increased fatality crash rate ratios among all road users and this pattern persisted in suburban and urban areas. Counties with more than four-fold increased fatality rate ratios were located commonly in Texas, Oklahoma, Nevada, and Utah.ConclusionDespite older adults being less frequent road users, county-level deprivation measures of the SDoH are equally associated with geriatric and non-geriatric crash-related fatal rate ratios. Policies that improve county-level SDoH may reduce the county-level fatal rate ratios equally among geriatric and non-geriatric road users.
Crop modeling suggests limited transpiration would increase yield of sorghum across drought-prone regions of the United States
Authors: Raymundo Rubí , Mclean Greg , Sexton-Bowser Sarah , Morris Geoffrey 
Published: June 2023

ABSTRACTBreeding sorghum for drought adaptation is pivotal to secure crop production in drought-prone regions. Limited transpiration (LT) restricts water demand at high vapor pressure deficit, saving water for use in critical periods later in the growing season. Here we evaluated the hypothesis that LT would increase sorghum grain yield in the United States. We used a process-based crop model, APSIM, which simulates interactions of genotype, environment, and management (G × E × M). In this study, the G component includes the LT trait (GT) and maturity group (GM), the E component entails water deficit patterns, and the M component represents different planting dates. Simulations were conducted over 33 years (1986-2018) for representative locations across the US sorghum belt (Kansas, Texas, and Colorado) for three planting dates and maturity groups. The interaction of GTx E indicated a higher impact of LT sorghum on grain for LD, MD, and ED (8%), than on WW environments (4%). Thus significant impacts of LT can be achieved in western regions of the sorghum belt. Otherwise, the lack of interaction of GT× GM× M suggested that an LT sorghum would increase yield by around 8% across maturity groups and planting dates. Although the interaction GM× M revealed that specific combinations are better suited across geographical regions. Overall, the findings suggest that breeding for LT would increase sorghum yield in the drought-prone areas of the US without tradeoffs.
Dysregulated Pulmonary Inflammatory Responses Exacerbate the Outcome of Secondary Aspergillosis Following Influenza
Authors: Lee Chrono K. , Oliveira Lorena V. N. , Akalin Ali , Specht Charles A. , Lourenco Diana , Gomez Christina L. , Ramirez-Ortiz Zaida G. , Wang Jennifer P. , Levitz Stuart M. 
Published: June 2023

AbstractInhalation of airborne conidia of the ubiquitous fungusAspergillus fumigatuscommonly occurs but invasive aspergillosis is rare except in profoundly immunocompromised persons. Severe influenza predisposes patients to invasive pulmonary aspergillosis by mechanisms that are poorly defined. Using a post-influenza aspergillosis model, we found that superinfected mice had 100% mortality when challenged withA. fumigatusconidia on days 2 and 5 (early stages) of influenza A virus infection but 100% survival when challenged on days 8 and 14 (late stages). Influenza-infected mice superinfected withA. fumigatushad increased levels of the pro-inflammatory cytokines and chemokines IL-6, TNFα, IFNβ, IL-12p70, IL-1α, IL-1β, CXCL1, G-CSF, MIP-1α, MIP-1β, RANTES and MCP-1. Surprisingly, on histopathological analysis, superinfected mice did not have greater lung inflammation compared with mice infected with influenza alone. Mice infected with influenza had dampened neutrophil recruitment to the lungs following subsequent challenge withA. fumigatus, but only if the fungal challenge was executed during the early stages of influenza infection. However, influenza infection did not have a major effect on neutrophil phagocytosis and killing ofA. fumigatusconidia. Moreover, minimal germination of conidia was seen on histopathology even in the superinfected mice. Taken together, our data suggest that the high mortality rate seen in mice during the early stages of influenza-associated pulmonary aspergillosis is multifactorial, with a greater contribution from dysregulated inflammation than microbial growth.ImportanceSevere influenza is a risk factor for fatal invasive pulmonary aspergillosis; however, the mechanistic basis for the lethality is unclear. Utilizing an influenza-associated pulmonary aspergillosis (IAPA) model, we found that mice infected with influenza A virus followed byA. fumigatushad 100% mortality when superinfected during the early stages of influenza but survived at later stages. While superinfected mice had dysregulated pulmonary inflammatory responses compared to controls, they had neither increased inflammation nor extensive fungal growth. Although influenza-infected mice had dampened neutrophil recruitment to the lungs following subsequent challenge withA. fumigatus, influenza did not affect the ability of neutrophils to clear the fungi. Our data suggest that the lethality seen in our model IAPA is multifactorial with dysregulated inflammation being a greater contributor than uncontrollable microbial growth. If confirmed in humans, our findings provide a rationale for clinical studies of adjuvant anti-inflammatory agents in the treatment of IAPA.
NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research
Authors: Mitchell Keith G. , Gong Belvin , Hunter Samuel S. , Burkart-Waco Diana , Gavira-O’Neill Clara E. , Templeton Kayla M. , Goethel Madeline E. , Bzymek Malgorzata , MacNiven Leah M. , Murray Karl D. , Settles Matthew L. , Froenicke Lutz , Trimmer James S. 
Published: June 2023

AbstractThe Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Authors: Larivière Delphine , Abueg Linelle , Brajuka Nadolina , Gallardo-Alba Cristóbal , Grüning Bjorn , Ko Byung June , Ostrovsky Alex , Palmada-Flores Marc , Pickett Brandon D. , Rabbani Keon , Balacco Jennifer R. , Chaisson Mark , Cheng Haoyu , Collins Joanna , Denisova Alexandra , Fedrigo Olivier , Gallo Guido Roberto , Giani Alice Maria , Gooder Grenville MacDonald , Jain Nivesh , Johnson Cassidy , Kim Heebal , Lee Chul , Marques-Bonet Tomas , O’Toole Brian , Rhie Arang , Secomandi Simona , Sozzoni Marcella , Tilley Tatiana , Uliano-Silva Marcela , van den Beek Marius , Waterhouse Robert M. , Phillippy Adam M. , Jarvis Erich D. , Schatz Michael C. , Nekrutenko Anton , Formenti Giulio 
Published: June 2023

AbstractImprovements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ∼500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).