bluuebunny/crossref_metadata_2025_split huggingface dataset:
The appendicular osteology of the Early Jurassic theropod Piatnitzkysaurus floresi and its implications on the morphological disparity of non-coelurosaurian tetanurans
Authors: Pradelli Luciano A , Pol Diego , Ezcurra Martín D 
Published: January 2025

Abstract
Piatnitzkysaurus floresi is a theropod dinosaur from the Cañadón Asfalto Formation (Chubut Province, Argentina) and one of the few Early Jurassic tetanurans known worldwide. This species is known from two specimens and plays a key role in our understanding of the early evolution of tetanuran theropods. Nevertheless, the published information about its postcranium is limited to the original description of the 1980s and drawings in a few views. Here, we redescribe in detail the appendicular skeleton of Piatnitzkaysaurus and integrate new information into new phylogenetic and morphological disparity analyses focused on non-coelurosaurian tetanurans. Our results agree with recent studies that place Piatnitzkysauridae (including Condorraptor, Marshosaurus, Piatnitzkysaurus, and Xuanhanosaurus) as the earliest diverging group of Allosauroidea and within a monophyletic Carnosauria (Allosauroidea + Megalosauroidea). Morphological disparity analyses of the appendicular skeleton of non-coelurosaurian tetanurans show that the Jurassic species occupy a different morphospace from the Cretaceous species. Condorraptor and Piatnitzkysaurus are found within the morphospace occupied by the Middle Jurassic species from the Northern Hemisphere, which indicates the presence of similar body plans for the non-coelurosaurian tetanurans during the Early–Middle Jurassic worldwide. The new information about Piatnitzkysaurus improves our knowledge about the evolution of early tetanurans.
Potassium channel‐mediated NO‐induced vasodilation during maturation: Dominance of Kv7 channels
Authors: Shvetsova Anastasia A. , Gaynullina Dina K. , Winkler Peter , Wohlfart Paulus , Schubert Rudolf 
Published: January 2025

AbstractMaturation represents a process characterized by adaptive changes, particularly in the circulatory system. However, it is not known whether, in neonates, potassium channels contribute to NO‐induced vasorelaxation at all and, if so, which potassium channels these are. Therefore, this study tested the hypothesis that potassium channels mediate NO‐induced vasorelaxation in newborn rats. Young (10‐ to 15‐day‐old) and adult (2‐ to 3‐month‐old) male rats were studied using real‐time PCR, isometric myography, and the sharp microelectrode technique on saphenous arteries. We observed prominent mRNA expression of several distinct isoforms of potassium channel families known to potentially mediate SNP‐induced vasodilation. Further, in both adult and young rats, SNP can relax vessels independently of potassium channels. A solely potassium channel‐independent anticontractile effect of SNP was observed also when either Kir6, or Kir2, or Kv2 channels, respectively, were available in both adult and young rats. However, when Kv1 channels were available, a Kv1 channel‐dependent component contributed to the anticontractile effect of SNP in young rats. When BKCa channels were available, a BKCa channel‐dependent component contributed to the anticontractile effect of SNP in adult rats. A considerable Kv7 channel‐dependent component contributed to the anticontractile effect of SNP in both adult and young rats. Thus, the data of the present study show for the first time that potassium channels, even multiple ones, contribute to SNP‐induced vasorelaxation in newborn rats and that the potassium channels involved in SNP‐induced vasorelaxation change from Kv1/Kv7 channels to BKCa/Kv7 channels during postnatal development.
Estimating prevalence of opioid misuse in North Carolina counties from 2016-2021: An integrated abundance model approach
Authors: Kline David M. , White Brian N. , Lancaster Kathryn E. , Egan Kathleen L. , Murphy Eva , Miller William C. , Hepler Staci A. 
Published: January 2025

Background:
The overdose epidemic remains largely driven by opioids, but county-level prevalence of opioid misuse is unknown. Without this information, public health and policy responses are limited by a lack of knowledge on the scope of the problem.

Methods:
Using an integrated abundance model, we estimate annual county-level prevalence of opioid misuse for counties in North Carolina from 2016 to 2021. The model integrates county-level observed counts of illicit opioid overdose deaths, people receiving prescriptions for buprenorphine, and people served by treatment programs. It also incorporates state-level survey estimates of misuse prevalence. County-level social and environmental covariates are also accounted for in the model. Data are integrated through a Bayesian hierarchical model to estimate posterior distributions of the parameters.

Results:
In general, the estimated prevalence of misuse was decreasing over the study period. Estimated prevalence was above average in the western and southeastern parts of the state. We also estimated that the proportion of people who misuse opioids who fatally overdosed increased sharply over the study period as the median estimated proportion in 2021 was more than 8 times greater than 2016. The proportion of people who misuse opioids who received buprenorphine and were served by treatment programs increased over the study period.

Conclusions:
Estimates from our integrated abundance model fill an important gap in public health knowledge about the local prevalence of people who misuse opioids and can be used to inform an adequate and equitable allocation of resources to communities across the state.
A quasi-experimental study of general practices’ referral to mammography in the post-trials treatment era
Authors: Lousdal Mette Lise , Lash Timothy L , Flanders W Dana , Brookhart M Alan , Kristiansen Ivar Sønbø , Vedsted Peter , Støvring Henrik 
Published: January 2025

Background:
Improvements in breast cancer therapy since the randomized controlled trials of mammography screening might have reduced the screening benefit. Most observational studies of mammography effectiveness would be confounded by these improvements and other factors. Using a design resistant to this confounding, we evaluated whether mammography in asymptomatic women reduces breast cancer mortality during the treatment era succeeding the trials.

Methods:
We designed a quasi-experimental cohort study in regions of Denmark without organized screening. We predicted the number of expected mammograms for each general practice based on observed numbers of mammograms and individual risk factors. Regardless of a woman’s individual exposure to mammography, we assigned her the ratio of observed to expected mammograms of her general practice as her instrumental variable. We employed this potential instrumental variable as mammography exposure status and followed women from January 1, 2006 until death, emigration, or December 31, 2014, whichever came first.

Results:
We included 169,197 women aged 50–66 from 738 general practices and without previous breast cancer as of January 1, 2006. Women affiliated with a practice referring more women than expected, compared with less, had a lower hazard of breast cancer death (hazard ratio 0.80, 95% confidence interval 0.68, 0.95). Negative control associations were near null, suggesting no confounding bias.

Conclusions:
This quasi-experimental study estimated a continued protective effect of mammography in women where most were presumably asymptomatic. In contrast to conventional observational studies, the use of practice referral ratio as an instrumental variable may avoid bias from uncontrolled confounding.
Point-of-Care Ultrasound of a Pediatric Mediastinal Mass
Authors: Greenwald Phoebe , Rabiner Joni E. 
Published: January 2025

Abstract
Point-of-care ultrasound may be used for identification of thoracic pathology, including mediastinal masses. In this case report, we describe the case of an otherwise healthy 17-year-old boy who presented with generalized pruritis. Point-of-care ultrasound was useful in identifying a complex cystic and solid mediastinal mass extending into the thoracic cavities as well as an associated pericardial effusion.
Genetic Analysis ofArabidopsisAutophagy-Related 8 Family Proteins
Reveals Their Redundant and Regulatory Roles in Plant Autophagy
Authors: Dong Kuntian , Deng Guiling , Liu Yilin , Wei Huan , Chen Kuo-En , Huang Xiner , Huang Wanying , Zheng Ping , Ueda Takashi , Vierstra Richard D. , Huang Xiao , Li Faqiang 
Published: January 2025

Abstract
Autophagy, a critical process for the vacuolar degradation of proteins and
organelles, is governed by multiple conserved autophagy-related (ATG) proteins.
The central component of the ATG machinery is the ubiquitin-like protein ATG8,
which is essential for multiple steps of the autophagy process, including
phagophore expansion, autophagosome closure, trafficking and fusion with the
lysosome/vacuole, and selective cargo recruitment. Currently, our understanding
of the roles of ATG8 in plant autophagy and the functional specialization of
ATG8 family members is limited due to genetic redundancy. To assess the roles
ofATG8genes in plant autophagy, here we used
CRISPR/Cas9 technology to systematically knockout theArabidopsis
ATG8genes. By analyzing
theatg8mutants, we found that in contrast to
mammalian ATG8s, in which the LC3s and GABARAP subfamilies play distinct roles
in the autophagic process,ArabidopsisATG8s perform an
overlapping function in controlling autophagic flux. Combinatorial mutations of
Clade I and Clade II ATG8s resulted in severely impaired autophagy under
nutrient-starved conditions. Furthermore, we found that RABG3 proteins, members
of the RAB7/RABG GTPase family, interact with ATG8s through AIM-LDS interfaces,
and that such interaction is essential for the association of RABG3 proteins
with the autophagosomal membrane and probably for the fusion of autophagosome
with the vacuole, but is not required for endosomal trafficking. With the
collection of multiple high-orderatg8mutants
generated in this study, we now provide a venue to study the roles
ofATG8genes in canonical autophagy and
non-canonical autophagy inArabidopsis.
Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starvingBacillus subtilis
Authors: Zhang Yujia , Palma Cristina S.D. , Chen Zhuo , Zarazúa-Osorio Brenda , Fujita Masaya , Igoshin Oleg 
Published: January 2025

AbstractIn starvingBacillus subtilisbacteria, the initiation of two survival programs – biofilm formation and sporulation – is both controlled by the same phosphorylated master regulator Spo0A∼P. Its gene,spo0A, is transcribed from two promoters, Pvand Ps, that are respectively regulated by RNAP holoenzymes bearing σAand σH. Notably, transcription is directly autoregulated by Spo0A∼P binding sites known as 0A1, 0A2, and 0A3 box, located in between the two promoters. It remains unclear whether, at the onset of starvation, these boxes activate or repressspo0Aexpression, and whether the Spo0A∼P transcriptional feedback plays a role in the increase inspo0Aexpression. Based on the experimental data of the promoter activities under systematic perturbation of the promoter architecture, we developed a biophysical model of transcription regulation ofspo0Aby Spo0A∼P binding to each of the 0A boxes. The model predicts that Spo0A∼P binding to its boxes does not affect the RNA polymerase recruitment to the promoters but instead affects the transcriptional initiation rate. Moreover, the effects of Spo0A∼P binding to 0A boxes are mainly repressive and saturated early at the onset of starvation. Therefore, the increase inspo0Aexpression is mainly driven by the increase in RNAP holoenzyme levels. Additionally, we reveal that Spo0A∼P affinity to 0A boxes is strongest at 0A3 and weakest at 0A2 and that there are attractive forces between the occupied 0A boxes. Our findings, in addition to clarifying how the sporulation master regulator is controlled, offer a framework to predict regulatory outcomes of complex gene-regulatory mechanisms.ImportanceCell differentiation is often critical for survival. In bacteria, differentiation decisions are controlled by transcriptional master regulators under transcriptional feedback control. Therefore, understanding how master regulators are transcriptionally regulated is required to understand differentiation. However, in many cases, underlying regulation is complex with multiple transcription factor binding sites and multiple promoters, making it challenging to dissect the exact mechanisms. Here, we address this problem for theB. subtilismaster regulator Spo0A. Using a biophysical model, we quantitatively characterize the effect of individual transcription factor binding sites on eachspo0Apromoter. Further, the model allows to identify the specific transcription step that is affected by transcription factor binding. Such model is promising for the quantitative study of a wide range of master regulators involved in transcriptional feedback.
Hybrid sequencing reveals the genome of aChrysochromulina parvavirus and highlight its distinct replication strategy
Authors: Nash Delaney , Palermo Christine N. , Inamoto Ichiro , Charles Trevor C. , Nissimov Jozef I. , Short Steven M. 
Published: January 2025

AbstractChrysochromulina parva(C. parva) is a eukaryotic freshwater haptophyte algae found in lakes and rivers worldwide. It is known to be infected by viruses, yet knowledge of the diversity and activity of these viruses is still very limited. Based on sequences of PCR-amplifiedpolBgene fragments,Chrysochromulina parvavirus BQ1 (CpV-BQ1) was the first known lytic agent ofC. parva, and was considered a member of the virus familyPhycodnaviridae,orderAlgavirales. However, the genome of a differentC. parva-infecting virus (CpV-BQ2, orTethysvirus ontarioense) from another virus family, theMesomimiviridae, orderImitervirales,was the first sequenced. Here, we report the complete genome sequence of the putative phycodnavirus CpV-BQ1, accessionPQ783904. The complete CpV-BQ1 genome sequence is 165,454 bp with a GC content of 32.32% and it encodes 193 open reading frames. Phylogenetic analyses of several virus hallmark genes including the DNA polymerase (polB), the late gene transcription factor (VLTF-3), and the putative A32-like virion packaging ATPase (Viral A32) all demonstrate that CpV-BQ1 is most closely related to other viruses in the phylumMegaviriceteswithin the orderAlgavirales, familyPhycodnaviridae.
mzQuality: A tool for quality monitoring and reporting of targeted mass spectrometry measurements
Authors: van der Peet Marielle , Maas Pascal , Wegrzyn Agnieszka , Lamont Lieke , Fleming Ronan , Harms Amy , Hankemeier Thomas , Kindt Alida 
Published: January 2025

AbstractAnalyzing metabolites using mass spectrometry can offer valuable insight into an individual’s health or disease status. However, various sources of experimental variation can affect the data, making robust quality control essential. In this context, we introduce mzQuality, a user-friendly software tool designed to evaluate and correct technical variations in mass spectrometry-based metabolomics data. MzQuality offers key quality control features, such as batch correction, outlier identification, and analysis of signal-to-noise ratios. It supports any peak-integrated processed data independent of vendor software and does not require the user to have any programming skills. We demonstrate the functionality of mzQuality with a data set of 419 samples measured across six batches, in which mzQuality effectively minimized experimental variation, ensuring the data’s readiness for statistical analysis and biological interpretation. With customizable settings, mzQuality can be seamlessly integrated into research workflows to produce more accurate and reproducible metabolomics data.
Multi-scale simulations of membrane adhesion mediated by CD47-SIRPαcomplexes
Authors: Hou Ruihan , Ren Shuanglong , Wang Rong , Różycki Bartosz , Hu Jinglei 
Published: January 2025

AbstractAdhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and lignad proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multi-scale approach to study membrane adhesion mediated by the CD47-SIRPαbinding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 µm on time scales ranging from 0.1 ns all the way up to about 20 s. The multi-scale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRPαand membrane-mediated cooperativity of the CD47-SIRPαbinding as well as fluctuation-induced interactions between the CD47-SIRPαcomplexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.
Regionally specific resting-state beta neural power predicts brain injury and symptom recovery in adolescents with concussion: a longitudinal study
Authors: Edgar J. Christopher , Blaskey Lisa , Chen Yuhan , Podolak Olivia E. , Murray Drayton L. , McNamee Marybeth , Konka Kimberly , Berman Jeffrey I. , Roberts Timothy P.L. , Huang Mingxiong , Arbogast Kristy B. , Master Christina L. 
Published: January 2025

AbstractMild traumatic brain injury (mTBI) is common in adolescents. Magnetoencephalography (MEG) studies (primarily reporting on adult males) have demonstrated abnormal resting-state (RS) brain activity in mTBI. The present study sought to identify RS abnormalities in male and female adolescents with mTBI (no previous mTBI and no previous DSM-5 diagnosis) identified from an outpatient specialty care concussion program setting as a basis for evaluating potential clinical utility. Visit 1 MEG RS data were obtained from 46 adolescents with mTBI (mean age: 15.4 years, 25 females) within 4 months of a mTBI (mTBI acute to sub-acute period) as well as from 34 typically developing (TD) controls (mean age: 14.8 years; 17 females) identified from the local community. Visit 2 RS data (follow-up ∼4.3 months after Visit 1; mTBI sub-chronic period) were obtained from 36 mTBI (19 females) and 29 TD (14 females) of those participants. Source-space RS neural activity was examined from 4 to 56 Hz. Visit 1 t-tests showed that group differences were largest in the beta range (16-30 Hz; mTBI < TD), with Visit 2 whole-brain linear mixed model (LMM) analyses examining beta-band group differences as a function of Visit. A main effect of Group indicated Visit 1 and 2 beta-band group differences in midline superior frontal gyrus, right temporal pole, and right central sulcus (all mTBI < TD). The group effects were large (Cohen’sdvalues 0.75 to 1.31). Of clinical significance in the mTBI group, a decrease in mTBI symptoms from Visit 1 to 2 was associated with an increase in beta power in 4 other brain regions. Present findings suggest that RS beta power has potential as a measure and perhaps as a mechanism of clinical recovery in adolescents with mTBI.
3D dynamic multiscale force and shape analysis ofin-vivoelastic stress sensors
Authors: Jurado Alejandro , Isensee Jonas , Hofemeier Arne , Krüger Lea Johanna , Wittkowski Raphael , Golestanian Ramin , Bittihn Philip , Betz Timo 
Published: January 2025

AbstractThe measurement of stresses and forces at the tissue level has proven to be an indispensable tool for the understanding of complex biological phenomena such as cancer invasion, embryo development or wound healing. One of the most versatile tools for force inference at the cell and tissue level are elastic force sensors, whose biocompatibility and tunable material properties make them suitable for many different experimental scenarios. The evaluation of those forces, however, is still a bottleneck due to the numerical methods seen in literature until now, which are usually slow and render low experimental yield. Here we present Bead-Buddy, a ready-to-use platform for the evaluation of deformation and stresses from fluorescently labelled sensors within seconds. The strengths of BeadBuddy lie in the pre-computed analytical solutions of the elastic problem, the abstraction of data into Spherical Harmonics, and a simple user interface that creates a smooth workflow for force inference.Abstract Figure
Extrachromosomal circular DNA promotes inflammation and hepatocellular carcinoma development
Authors: Chan Lap Kwan , Shan Juanjuan , Rodriguez-Fos Elias , Healy Marc Eamonn , Leary Peter , Parrotta Rossella , Desboeufs Nina , Semere Gabriel , Wittstruck Nadine , Henssen Anton G. , Weber Achim 
Published: January 2025

AbstractTwo decades after the initial report on increased micronuclei in human chronic liver disease (CLD) and hepatocellular carcinoma (HCC), their role in HCC development is still poorly understood. Here we show that micronuclei in hepatocytes trigger hepatic immune response and promote HCC development via an increased level of extrachromosomal circular DNA (eccDNA). Livers from a CLD model (Mcl1Δhepmice) show increased micronuclei in parallel to eccDNA. Circular sequencing confirms higher eccDNA levels in micronuclei compared to primary nuclei. We developed nuclei-segregated DNA fiber (NuSeF) assay to show that micronuclei are more susceptible to replication stress, showing increased replication fork slowing. By comparing different murine liver disease models, high eccDNA is correlated with increased tumor incidence. EccDNA is a strong immunostimulant and promotes a crosstalk between hepatocytes and immune cells through the cGAS-STING pathway. Deletion ofSting1inMcl1Δhepmice reduces immune cell chemotaxis, as well as tumor incidence. Our findings suggest that eccDNA from micronuclei mediates inflammation-driven liver carcinogenesis in CLD.