bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptoms, Viral Loads, and Rebound Among COVID-19 Outpatients Treated With Nirmatrelvir/Ritonavir Compared With Propensity Score–Matched Untreated Individuals
Authors: Smith-Jeffcoat Sarah E , Biddle Jessica E , Talbot H Keipp , Morrissey Kerry Grace , Stockwell Melissa S , Maldonado Yvonne , McLean Huong Q , Ellingson Katherine D , Bowman Natalie M , Asturias Edwin , Mellis Alexandra M , Johnson Sheroi , Kirking Hannah L , Rolfes Melissa A R , Olivo Vanessa , Merrill Lori , Battan-Wraith Steph , Sano Ellen , McLaren Son H , Vargas Celibell Y , Goodman Sara , Sarnquist Clea C , Govindaranjan Prasanthi , Petrie Joshua G , Belongia Edward A , Ledezma Karla , Pryor Kathleen , Lutrick Karen , Bullock Ayla , Yang Amy , Haehnel Quenla , Rao Suchitra , Zhu Yuwei , Schmitz Jonathan , Hart Kimberly , Grijalva Carlos G , Salvatore Phillip P 
Published: November 2023

Abstract

Background
Nirmatrelvir/ritonavir (N/R) reduces severe outcomes from coronavirus disease 2019 (COVID-19); however, rebound after treatment has been reported. We compared symptom and viral dynamics in individuals with COVID-19 who completed N/R treatment and similar untreated individuals.

Methods
We identified symptomatic participants who tested severe acute respiratory syndrome coronavirus 2–positive and were N/R eligible from a COVID-19 household transmission study. Index cases from ambulatory settings and their households contacts were enrolled. We collected daily symptoms, medication use, and respiratory specimens for quantitative polymerase chain reaction for 10 days during March 2022—May 2023. Participants who completed N/R treatment (treated) were propensity score matched to untreated participants. We compared symptom rebound, viral load (VL) rebound, average daily symptoms, and average daily VL by treatment status measured after N/R treatment completion or 7 days after symptom onset if untreated.

Results
Treated (n = 130) and untreated participants (n = 241) had similar baseline characteristics. After treatment completion, treated participants had greater occurrence of symptom rebound (32% vs 20%; P = .009) and VL rebound (27% vs 7%; P &lt; .001). Average daily symptoms were lower among treated participants without symptom rebound (1.0 vs 1.6; P &lt; .01) but not statistically lower with symptom rebound (3.0 vs 3.4; P = .5). Treated participants had lower average daily VLs without VL rebound (0.9 vs 2.6; P &lt; .01) but not statistically lower with VL rebound (4.8 vs 5.1; P = .7).

Conclusions
Individuals who completed N/R treatment experienced fewer symptoms and lower VL but rebound occured more often compared with untreated individuals. Providers should prescribe N/R, when indicated, and communicate rebound risk to patients.
Political Memoir, Celebrity, and the Reclamation of Feminism: Gendered Self-representation in Julia Gillard’sMy Storyand Hillary Clinton’sWhat Happened
Authors: Taylor Anthea 
Published: November 2023

AbstractOffering a close textual analysis of My Story (2014), the memoir of Australia’s first woman Prime Minister, Julia Gillard, and What Happened (2017), by the 2016 US Democratic Presidential nominee, Hillary Clinton, this article explores their attempts—as is becoming common for celebrities—to use the memoir form to attempt to regain some control over their public personas and their feminisms. Focusing on the kind of feminist selves they seek to bring into being through these memoirs, this article examines the rhetorical strategies they each deploy to disrupt the dominant gendered narratives that came to circulate during their time in power and beyond.
Long-term outcomes of bioprosthetic valves in the mitral position a systematic review of studies published over the last 20 years
Authors: Koulouroudias Marinos , Di Mauro Michele , Lorusso Roberto 
Published: November 2023

Abstract

OBJECTIVES
Although the use of bioprostheses for mitral valve replacement (bMVR) is on the rise, their long-term durability is not well described. Defining bMVR durability will be instrumental in setting the standard against which the performance of transcatheter mitral replacement is to be judged against. The authors of this systematic review aimed to identify, assess the quality and review the outcomes in studies reporting on long-term outcomes after bMVR published over the last 20 years.

METHODS
Medline, Embase and Cochrane CENTRAL were searched for studies that have reported outcomes beyond a minimum of 5 years of follow-up after bMVR. Cohort characteristics, definitions of structural valve deterioration (SVD) and outcomes were summarized. The risk of bias in included studies was assessed using the Cochrane QUIPS tool.

RESULTS
Twenty-one studies, including 15 833 patients, were identified. Sixty-four percent of all implants were porcine and the remaining bovine pericardial. Freedom from SVD at 10 years ranged from 58.9% to 100% and at 15 years from 58.3% to 93%. Freedom from reoperation ranged from 65% to 98.7% at 10 years and 78.5% to 91% at 15 years. Information on native valve pathology or dominant haemodynamic lesion was missing in 25% and 66% of studies, respectively. Reports of postoperative echocardiography were lacking, despite the heavy reliance on echocardiography for SVD diagnosis.

CONCLUSIONS
There is considerable variability in reporting bMVR long-term outcomes. As such, it is difficult to generate an unbiased, generalizable understanding of long- term outcomes after bMVR across the spectrum of mitral disease phenotypes.
Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil
Authors: Doherty Stacey J , Busby Ryan R , Baker Christopher C M , Barbato Robyn A 
Published: November 2023

Abstract
In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.
Diagnosis of gastrointestinal infections: comparison between traditional microbiology and a commercial syndromic molecular-based panel
Authors: Ligero-López Jorge , García-Rodríguez Julio , Ruiz-Carrascoso Guillermo 
Published: November 2023

Abstract
Traditional diagnosis of infectious gastroenteritis is based on culture, microscopy and antigen detection. The development of gastrointestinal syndromic panels based on molecular techniques have allowed rapid and simultaneous identification of multiple pathogens. The objective was to evaluate the implementation of Allplex™ Gastrointestinal Panel Assays (AGPA): Allplex™ GI-Virus, Allplex™ GI-Bacteria (I) and Allplex™ GI-Parasite by comparing with traditional diagnosis. A retrospective comparative study was conducted at Hospital Universitario La Paz, between the first year of implementation of the AGPA (April 1, 2018 to March 31, 2019) and the results obtained during the previous year with traditional methods (April 1, 2017 to March 31, 2018). With the implementation of AGPA we obtained an increase in the detection of rotavirus and adenovirus, being statistically significant for rotavirus ([CI95%:3.60–6.79]; P &lt; 0.05) and an increase in the positivity rates of all the bacteria tested, with the exception of Salmonella spp. ([CI95%:3.60–6.79]; P &lt; 0.05). Comparing the bacteria recovered by culture, we obtained an increase in the case of Shigella spp. cultivation during the AGPA period. Regarding protozoa, we achieved a significant increase in the positivity rates for Cryptosporidium spp. ([CI95%:1.98–3.01] P &lt; 0.05), Giardia intestinalis ([CI95%:3.94–5.25]; P &lt; 0.05) and Blastocystis spp. ([CI95%:9.44–11.36]; P &lt; 0.05). There was an improvement in report turnaround time when comparing molecular diagnosis to bacterial culture and concentration plus microscopy for parasites; but not compared with antigen detection. The molecular diagnosis approach with AGPA were more sensitive and had a faster turnaround time for some targets, and in our setting, enabled an increased diagnostic capacity for viruses and protozoa.
Improved semantic segmentation network using normal vector guidance for LiDAR point clouds
Authors: Kim Minsung , Oh Inyoung , Yun Dongho , Ko Kwanghee 
Published: November 2023

Abstract
As Light Detection and Ranging (LiDAR) sensors become increasingly prevalent in the field of autonomous driving, the need for accurate semantic segmentation of three-dimensional points grows accordingly. To address this challenge, we propose a novel network model that enhances segmentation performance by utilizing normal vector information. Firstly, we present a method to improve the accuracy of normal estimation by using the intensity and reflection angles of the light emitted from the LiDAR sensor. Secondly, we introduce a novel local feature aggregation module that integrates normal vector information into the network to improve the performance of local feature extraction. The normal information is closely related to the local structure of the shape of an object, which helps the network to associate unique features with corresponding objects. We propose four different structures for local feature aggregation, evaluate them, and choose the one that shows the best performance. Experiments using the SemanticKITTI dataset demonstrate that the proposed architecture outperforms both the baseline models, RandLA-Net, and other existing methods, achieving mean intersection over union of 57.9%. Furthermore, it shows highly competitive performance compared with RandLA-Net for small and dynamic objects in a real road environment. For example, it yielded 95.2% for cars, 47.4% for bicycles, 41.0% for motorcycles, 57.4% for bicycles, and 53.2% for pedestrians.
PathBank 2.0—the pathway database for model organism metabolomics
Authors: Wishart David S , Kruger Ray , Sivakumaran Aadhavya , Harford Karxena , Sanford Selena , Doshi Rahil , Khetarpal Nitya , Fatokun Omolola , Doucet Daphnee , Zubkowski Ashley , Jackson Hayley , Sykes Gina , Ramirez-Gaona Miguel , Marcu Ana , Li Carin , Yee Kristen , Garros Christiana , Rayat Dorsa Yahya , Coleongco Jeanne , Nandyala Tharuni , Gautam Vasuk , Oler Eponine 
Published: November 2023

Abstract
PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.
ELM—the Eukaryotic Linear Motif resource—2024 update
Authors: Kumar Manjeet , Michael Sushama , Alvarado-Valverde Jesús , Zeke András , Lazar Tamas , Glavina Juliana , Nagy-Kanta Eszter , Donagh Juan Mac , Kalman Zsofia E , Pascarelli Stefano , Palopoli Nicolas , Dobson László , Suarez Carmen Florencia , Van Roey Kim , Krystkowiak Izabella , Griffin Juan Esteban , Nagpal Anurag , Bhardwaj Rajesh , Diella Francesca , Mészáros Bálint , Dean Kellie , Davey Norman E , Pancsa Rita , Chemes Lucía B , Gibson Toby J 
Published: November 2023

Abstract
Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant, especially when considering post-translational modifications. As well as being found throughout the cell as part of regulatory processes, SLiMs are extensively mimicked by intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource is a representative (not comprehensive) database. The ELM entries are created by a growing community of skilled annotators and provide an introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances in areas ranging from innate immunity to both protein and RNA degradation systems. In total, 39 classes of newly annotated motifs have been added, and another 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publications and including &gt;700 links to experimentally determined 3D structures. In a recent development, the InterPro protein module resource now also includes ELM data. ELM is available at: http://elm.eu.org.
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Authors: Rauluseviciute Ieva , Riudavets-Puig Rafael , Blanc-Mathieu Romain , Castro-Mondragon Jaime A , Ferenc Katalin , Kumar Vipin , Lemma Roza Berhanu , Lucas Jérémy , Chèneby Jeanne , Baranasic Damir , Khan Aziz , Fornes Oriol , Gundersen Sveinung , Johansen Morten , Hovig Eivind , Lenhard Boris , Sandelin Albin , Wasserman Wyeth W , Parcy François , Mathelier Anthony 
Published: November 2023

Abstract
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Pan-cancer analysis of promoter activity quantitative trait loci
Authors: Li Ran , Wan Dongyi , Liang Junnan , Liang Huifang , Huang Haohao , Li Ganxun 
Published: November 2023

Abstract
Altered promoter activity has been generally observed in diverse biological processes, including tumorigenesis. Accumulating evidence suggests that employing a quantitative trait locus mapping approach is effective in comprehending the genetic basis of promoter activity. By utilizing genotype data from The Cancer Genome Atlas and calculating corresponding promoter activity values using proActiv, we systematically evaluated the impact of genetic variants on promoter activity and identified &gt;1.0 million promoter activity quantitative trait loci (paQTLs) as both cis- and trans-acting. Additionally, leveraging data from the genome-wide association study (GWAS) catalog, we discovered &gt;1.3 million paQTLs that overlap with known GWAS linkage disequilibrium regions. Remarkably, ∼9324 paQTLs exhibited significant associations with patient prognosis. Moreover, investigating the impact of promoter activity on &gt;1000 imputed antitumor therapy responses among pan-cancer patients revealed &gt;43 000 million significant associations. Furthermore, ∼25 000 significant associations were identified between promoter activity and immune cell abundance. Finally, a user-friendly data portal, Pancan-paQTL (https://www.hbpding.com/PancanPaQTL/), was constructed for users to browse, search and download data of interest. Pancan-paQTL serves as a comprehensive multidimensional database, enabling functional and clinical investigations into genetic variants associated with promoter activity, drug responses and immune infiltration across multiple cancer types.
MOS4-associated complex contributes to proper splicing and suppression of ER stress under long-term heat stress in Arabidopsis
Authors: Endo Naoya , Tsukimoto Ryo , Isono Kazuho , Hosoi Akito , Yamaguchi Ryo , Tanaka Keisuke , Iuchi Satoshi , Yotsui Izumi , Sakata Yoichi , Taji Teruaki 
Published: November 2023

Abstract
Plants are often exposed not only to short-term (S-) but also to long-term (L-)heat stress over several consecutive days. A few Arabidopsis mutants defective in L-heat tolerance have been identified, but the molecular mechanisms are less understood for this tolerance than for S-heat stress tolerance. To elucidate the mechanisms of the former, we used a forward genetic screen for sensitive to long-term heat (sloh) mutants and isolated sloh3 and sloh63. The mutants were hypersensitive to L- but not to S-heat stress, and sloh63 was also hypersensitive to salt stress. We identified the causal genes, SLOH3 and SLOH63, both of which encoded splicing-related components of the MOS4-associated complex (MAC). This complex is widely conserved in eukaryotes and has been suggested to interact with spliceosomes. Both genes were induced by L-heat stress in a time-dependent manner, and some abnormal splicing events were observed in both mutants under L-heat stress. In addition, endoplasmic reticulum (ER) stress and subsequent unfolded protein response occurred in both mutants under L-heat stress and were especially prominent in sloh63, suggesting that enhanced ER stress is due to the salt hypersensitivity of sloh63. Splicing inhibitor pladienolide B led to concentration-dependent disturbance of splicing, decreased L-heat tolerance, and enhanced ER stress. These findings suggest that maintenance of precise mRNA splicing under L-heat stress by the MAC is important for L-heat tolerance and suppressing ER stress in Arabidopsis.
Frequent asymmetric migrations suppress natural selection in spatially structured populations
Authors: Abbara Alia , Bitbol Anne-Florence 
Published: November 2023

Abstract
Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, evolutionary graph theory has shown that some graphs can amplify or suppress natural selection, in a way that depends on microscopic update rules. We propose a model of spatially structured populations on graphs directly inspired by batch culture experiments, alternating within-deme growth on nodes and migration-dilution steps, and yielding successive bottlenecks. This setting bridges models from evolutionary graph theory with Wright–Fisher models. Using a branching process approach, we show that spatial structure with frequent migrations can only yield suppression of natural selection. More precisely, in this regime, circulation graphs, where the total incoming migration flow equals the total outgoing one in each deme, do not impact fixation probability, while all other graphs strictly suppress selection. Suppression becomes stronger as the asymmetry between incoming and outgoing migrations grows. Amplification of natural selection can nevertheless exist in a restricted regime of rare migrations and very small fitness advantages, where we recover the predictions of evolutionary graph theory for the star graph.
Oleic acid stimulation of amino acid uptake in primary human trophoblast cells is mediated by phosphatidic acid and mTOR signaling
Authors: Silva Elena , Ferchaud‐Roucher Véronique , Kramer Anita , Madi Lana , Pantham Priyadarshini , Chassen Stephanie , Jansson Thomas , Powell Theresa L. 
Published: November 2023

AbstractNormal fetal development is critically dependent on optimal nutrient supply by the placenta, and placental amino acid transport has been demonstrated to be positively associated with fetal growth. Mechanistic target of rapamycin (mTOR) is a positive regulator of placental amino acid transporters, such as System A. Oleic acid (OA) has been previously shown to have a stimulatory role on placental mTOR signaling and System A amino acid uptake in primary human trophoblast (PHT) cells. We investigated the mechanistic link between OA and System A activity in PHT. We found that inhibition of mTOR complex 1 or 2, using small interfering RNA to knock down raptor or rictor, prevented OA‐stimulated System A amino acid transport indicating the interaction of OA with mTOR. Phosphatidic acid (PA) is a key intermediary for phospholipid biosynthesis and a known regulator of the mTOR pathway; however, phospholipid biosynthetic pathways have not been extensively studied in placenta. We identified placental isoforms of acyl transferase enzymes involved in de novo phospholipid synthesis. Silencing of 1‐acylglycerol‐3‐phosphate‐O‐acyltransferase‐4, an enzyme in this pathway, prevented OA mediated stimulation of mTOR and System A amino acid transport. These data indicate that OA stimulates mTOR and amino acid transport in PHT cells mediated through de novo synthesis of PA. We speculate that fatty acids in the maternal circulation, such as OA, regulate placental functions critical for fetal growth by interaction with mTOR and that late pregnancy hyperlipidemia may be critical for increasing nutrient transfer to the fetus.