bluuebunny/crossref_metadata_2025_split huggingface dataset:
GoodFibes: An R Package for The Detection of Muscle Fibers from diceCT Scans
Authors: Arbour J H 
Published: August 2023

SynopsisContrast enhanced computed-tomography imaging like diffusible iodine-based contrast-enhanced computed tomography (diceCT) can provide detailed information on muscle architecture important to comparative analyses of functional morphology, using non-destructive approaches. However, manual segmentation of muscle fascicles/fibers is time-consuming, and automated approaches are at times inaccessible and unaffordable. Here, we introduce GoodFibes, an R package for reconstructing muscle architecture in 3D from diceCT image stacks. GoodFibes uses textural analysis of image grayscale values to track straight or curved fiber paths through a muscle image stack. Accessory functions provide quality checking, fiber merging, and 3D visualization and export capabilities. We demonstrate the utility and effectiveness of GoodFibes using two datasets, from an ant and bat diceCT scans. In both cases, GoodFibes provides reliable measurements of mean fiber length compared to traditional approaches, and is as effective as currently available software packages. This open-source, free to use software package will help to improve access to tools in the analysis of muscle fiber anatomy using diceCT scans. The flexible and transparent R-language environment allows other users to build on the functions described here and permits direct statistical analysis of the resulting fiber metrics. We hope that this will increase the number of comparative and evolutionary studies incorporating these rich and functionally important datasets.
Use of Real Time Clinical Video Telehealth to Home by primary care providers within the Veterans Health Administration during the first wave of the COVID-19 pandemic: variability across VA stations and with time
Authors: Sullivan Dennis H , Sawyer Linda M , Dawson Bonnie D , Dunlap Janette , Cigolle Christine T , Keller Hallie E , Burningham Zachary 
Published: August 2023

Abstract

Objective
Determine the extent to which use of Clinical Video Telehealth to Home (VT2H) for primary care licensed independent practitioner visits (PCLIPVs) varied over time and across the Veterans Health Administration (VA) during the first 18 months of the COVID pandemic, and if there was an association between VT2H usage and VA station characteristics.

Materials and Methods
All outpatient encounters (n = 12 143 456) for Veterans (n = 4 373 638) that had VA PCLIPVs during the period of observation were categorized as conducted by VT2H, in-person, or telephone. The change over time in the percentage of total PCLIPVs conducted by VT2H was plotted and associations between VA station characteristics and VT2H usage were analyzed using simple statistics and negative binomial regression.

Results
Between March 2020 and mid-August 2020, VT2H visits increased from &lt;2% to 13% of all VA PCLIPVs. However, VT2H usage varied substantively by VA station and declined system-wide to &lt;9% of PCLIPVs by July 2021. VA stations that serve a greater proportion of rural Veterans were found less likely to use VT2H.

Discussion
The VA was successful in increasing the use of VT2H for PCLIPVs during the first phase of the COVID pandemic. However, VT2H usage varied by VA station and over time. Beyond rurality, it is unknown what station characteristics may be responsible for the variance in VT2H use.

Conclusion
Future investigation is warranted to identify the unique practices employed by VA stations that were most successful in using VT2H for PCLIPVs and whether they can be effectively disseminated to other stations.
A national evaluation of adjuvant chemotherapy in pT4N0M0 colon cancer from the National Cancer Database
Authors: Reif de Paula Thais , Keller Deborah S 
Published: August 2023

Abstract

Background
T stage is a prognostic biomarker for overall survival in colon cancer and pathologic T4 disease is a high-risk characteristic. Adjuvant chemotherapy is recommended to improve overall survival in pT4N0M0, but compliance with guidelines is unknown. We aimed to evaluate adjuvant chemotherapy use and impact on overall survival in pT4N0M0 colon cancer.

Methods
The National Cancer Database was reviewed for pT4N0M0 colon adenocarcinomas undergoing curative surgical resection (2010-2017). Cases were stratified into no adjuvant chemotherapy and adjuvant chemotherapy cohorts. Moderated multiple regression assessed factors associated with no AC. Kaplan–Meier and Cox regression assessed overall survival in propensity-score matched cohorts. The main outcome measures were adjuvant chemotherapy use, factors associated with adjuvant chemotherapy, and impact on overall survival.

Results
Of 11 847 cases, 62.4% (n = 7391) received no adjuvant chemotherapy. With private insurance, comorbidities or income do not affect adjuvant chemotherapy use. Medicare cases with a Charlson–Deyo comorbidity index of 0 (odds ratio [OR] = 0.861, 95% confidence interval [CI] = 0.760 to 0.975; P = .019) and Medicare payors with high income (OR = 0.813, 95% CI = 0.690 to 0.959; P = .014) were associated with adjuvant chemotherapy. Medicaid Charlson–Deyo comorbidity index 0 (OR = 1.374, 95% CI = 1.125 to 1.679; P = .002) and uninsured Charlson–Deyo comorbidity index 0 (OR = 1.351, 95% CI = 1.120 to 1.629; P = .002) were associated with no adjuvant chemotherapy. Adjuvant chemotherapy was associated with improved 5-year overall survival (71.7% vs 56.4%; P &lt; .001; adjusted hazard ratio = 0.543, 95% CI = 0.499 to 0.590; P &lt; .001).

Conclusion
Although adjuvant chemotherapy is associated with improved overall survival, compliance is low. There is a complex relationship between payor, income, comorbidity, and adjuvant chemotherapy receipt. Medicare patients with no comorbidities or higher income have better adjuvant chemotherapy use. With private insurance, adjuvant chemotherapy compliance is not affected by comorbidities or income, whereas Medicaid and uninsured patients with no comorbidities have poor compliance. Future work could target these disparities for equitable care.
Legumain: a potential biomarker for atherosclerosis
Authors: Ke Bo-yi , Qin Yu-sheng , Cheng Lu , Wang Shu-zhi 
Published: August 2023

Abstract
Atherosclerosis is a lipid-driven chronic inflammatory disease that poses a serious threat to health. Legumain (LGMN), also known as asparagine endonuclease, is a new type of cysteine proteases that can specifically hydrolyze substrate molecules containing asparagine residues. It has anti-apoptotic effects in mammals and plays an antigen-presenting role in inflammatory response. Several studies have found that LGMN can activate multiple signal pathways to promote cell apoptosis and migration, inflammatory response, and the development of atherosclerosis. Importantly, LGMN exerts pro-atherogenic effects by participating in a variety of pathophysiological mechanisms of atherosclerosis, including vascular remodeling, inflammatory response, plaque stability, and the degradation of extracellular matrix. In the present review, we describe the LGMN distribution, structure, generation, and functional partners. Furthermore, we summarize the relationship between LGMN and atherosclerosis. Based on the relationship between LGMN and atherosclerosis, LGMN may be a potential biomarker for atherosclerosis.
Deep learning-based high-throughput detection of in vitro germination to assess pollen viability from microscopic images
Authors: Zhang Mengwei , Zhao Jianxiang , Hoshino Yoichiro 
Published: August 2023

Abstract
In vitro pollen germination is considered the most efficient method to assess pollen viability. The pollen germination frequency and pollen tube length, which are key indicators of pollen viability, should be accurately measured during in vitro culture. In this study, a Mask R-CNN model trained using microscopic images of tree peony (Paeonia suffruticosa) pollen has been proposed to rapidly detect the pollen germination rate and pollen tube length. To reduce the workload during image acquisition, images of synthesized crossed pollen tubes were added to the training dataset, significantly improving the model accuracy in recognizing crossed pollen tubes. At an Intersection over Union threshold of 50%, a mean average precision of 0.949 was achieved. The performance of the model was verified using 120 testing images. The R2 value of the linear regression model using detected pollen germination frequency against the ground truth was 0.909 and that using average pollen tube length was 0.958. Further, the model was successfully applied to two other plant species, indicating a good generalizability and potential to be applied widely.
Calbindin Has a Potential Spatiotemporal Correlation with Proliferation and Apoptosis in the Postnatal Rat Kidney
Authors: Mahmoud Sahar F , Elewa Yaser H , Nomir Ahmed G , Rashwan Ahmed M , Noreldin Ahmed E 
Published: August 2023

Abstract
The protein calbindin-D28k modulates calcium reabsorption in the kidney. Here, we aimed to study the influence of proliferation and apoptosis in different compartments of the kidney on the developmental function of calbindin. Using immunohistochemistry, we investigated the postnatal development of rats’ kidneys by using calbindin, proliferative cell nuclear antigen (PCNA), and apoptotic single-stranded DNA (ssDNA). In the neonatal stage (1-day and 1-week-old rats), calbindin showed a positive reaction in the distal convoluted tubule (DCT), a short nephron segment between the macula densa, collecting ducts, and tubules. Moreover, the localization of calbindin was restricted to immature nephrons and mesenchymal tissues. Furthermore, PCNA immunoreactivity was moderate in early-developed podocytes with no reactivity in other renal tubules. The ssDNA immunoreactivity was moderate in the undifferentiated nephron. Then, in the mature stage (3 and 6 weeks old), there was an intense calbindin reaction in DCT but a moderate reaction to PCNA and ssDNA in podocytes. A more intense calbindin reactivity was found in the adult stage (2- and 3-month-old rats) in DCT and collecting tubules. Therefore, in this study, calbindin localization showed an inverse relationship with PCNA and ssDNA of the nephron compartments, which might reflect the efficiency of bone-building and muscle contraction during animal development.
3D X-ray Histology for the Investigation of Temporal Lobe Epilepsy in a Mouse Model
Authors: Rodgers Griffin , Bikis Christos , Janz Philipp , Tanner Christine , Schulz Georg , Thalmann Peter , Haas Carola A , Müller Bert 
Published: August 2023

Abstract
The most common form of epilepsy among adults is mesial temporal lobe epilepsy (mTLE), with seizures often originating in the hippocampus due to abnormal electrical activity. The gold standard for the histopathological analysis of mTLE is histology, which is a two-dimensional technique. To fill this gap, we propose complementary three-dimensional (3D) X-ray histology. Herein, we used synchrotron radiation-based phase-contrast microtomography with 1.6 μm-wide voxels for the post mortem visualization of tissue microstructure in an intrahippocampal-kainate mouse model for mTLE. We demonstrated that the 3D X-ray histology of unstained, unsectioned, paraffin-embedded brain hemispheres can identify hippocampal sclerosis through the loss of pyramidal neurons in the first and third regions of the Cornu ammonis as well as granule cell dispersion within the dentate gyrus. Morphology and density changes during epileptogenesis were quantified by segmentations from a deep convolutional neural network. Compared to control mice, the total dentate gyrus volume doubled and the granular layer volume quadrupled 21 days after injecting kainate. Subsequent sectioning of the same mouse brains allowed for benchmarking 3D X-ray histology against well-established histochemical and immunofluorescence stainings. Thus, 3D X-ray histology is a complementary neuroimaging tool to unlock the third dimension for the cellular-resolution histopathological analysis of mTLE.
Hunting for the candidates of misclassified sources in LSP BL Lacs using machine learning
Authors: Kang Shi-Ju , Zheng Yong-Gang , Wu Qingwen 
Published: August 2023

ABSTRACT
An equivalent–width-based classification may cause the erroneous judgement to the flat spectrum radio quasars (FSRQs) and BL Lacerate objects (BL Lac) due to the diluting the line features by dramatic variations in the jet continuum flux. To help address the issue, this work explores the possible intrinsic classification on the basis of a random forest supervised machine learning algorithm. In order to do so, we compile a sample of 1680 Fermi blazars that have both gamma-rays and radio-frequencies data available from the 4LAC-DR2 catalogue, which includes 1352 training and validation samples and 328 forecast samples. By studying the results for all of the different combinations of 23 characteristic parameters, we found that there are 178 optimal parameter combinations (OPCs) with the highest accuracy (≃98.89 per cent). Using the combined classification results from the nine combinations of these OPCs to the 328 forecast samples, we predict that there are 113 true BL Lacs (TBLs) and 157 false BL Lacs (FBLs) that are possible intrinsically FSRQs misclassified as BL Lacs. The FBLs show a clear separation from TBLs and FSRQs in the gamma-ray photon spectral index, Γph, and X-band radio flux, logFR, plot. Phenomenally, existence a BL Lac to FSRQ (B-to-F) transition zone is suggested, where the FBLs are in the stage of transition from BL Lacs to FSRQs. Comparing the LSP changing-look blazars (CLBs) reported in the literatures, the majority of LSP CLBs are located at the B-to-F zone. We argue that the FBLs located at B-to-F transition zone are the most likely candidates of CLBs.
CO-CHANGES – I. IRAM 30-m CO observations of molecular gas in the sombrero galaxy
Authors: Jiang Yan , Li Jiang-Tao , Gao Yu , Bregman Joel N , Ji Li , Jiang Xue-Jian , Tan Qing-Hua , Wang Jian-Fa , Wang Q Daniel , Yang Yang 
Published: August 2023

ABSTRACT
Molecular gas plays a critical role in explaining the quiescence of star formation (SF) in massive isolated spiral galaxies, which could be a result of either the low molecular gas content and/or the low SF efficiency. We present IRAM 30-m observations of the CO lines in the Sombrero galaxy (NGC 4594), the most massive spiral at $d\lesssim 30\rm ~Mpc$. We detect at least one of the three CO lines covered by our observations in all 13 observed positions located at the galactic nucleus and along an $\sim 25\rm ~kpc$-diameter dusty ring. The total extrapolated molecular gas mass of the galaxy is $M_{\rm H_2}\approx 4\times 10^{8}\rm ~M_\odot$. The measured maximum CO gas rotation velocity of $\approx 381\rm ~km~s^{-1}$ suggests that NGC 4594 locates in a dark matter halo with a mass $M_{\rm 200}\gtrsim 10^{13}\rm ~M_\odot$. Comparing to other galaxy samples, NGC 4594 is extremely gas poor and SF inactive, but the SF efficiency is apparently not inconsistent with that predicted by the Kennicutt–Schmidt law, so there is no evidence of enhanced SF quenching in this extremely massive spiral with a huge bulge. We also calculate the predicted gas supply rate from various sources to replenish the cold gas consumed in SF, and find that the galaxy must experience a starburst stage at high redshift, then the leftover or recycled gas provides SF fuels to maintain the gradual growth of the galactic disc at a gentle rate.
Inhibition of Wnt activity improves peri-implantation development of somatic cell nuclear transfer embryos
Authors: Li Yanhe , Zheng Caihong , Liu Yingdong , He Jincan , Zhang Qiang , Zhang Yalin , Kou Xiaochen , Zhao Yanhong , Liu Kuisheng , Bai Dandan , Jia Yanping , Han Xiaoxiao , Sheng Yifan , Yin Jiqing , Wang Hong , Gao Shuai , Liu Wenqiang , Gao Shaorong 
Published: August 2023

ABSTRACT
Somatic cell nuclear transfer (SCNT) can reprogram differentiated somatic cells into totipotency. Although pre-implantation development of SCNT embryos has greatly improved, most SCNT blastocysts are still arrested at the peri-implantation stage, and the underlying mechanism remains elusive. Here, we develop a 3D in vitro culture system for SCNT peri-implantation embryos and discover that persistent Wnt signals block the naïve-to-primed pluripotency transition of epiblasts with aberrant H3K27me3 occupancy, which in turn leads to defects in epiblast transformation events and subsequent implantation failure. Strikingly, manipulating Wnt signals can attenuate the pluripotency transition and H3K27me3 deposition defects in epiblasts and achieve up to a 9-fold increase in cloning efficiency. Finally, single-cell RNA-seq analysis reveals that Wnt inhibition markedly enhances the lineage developmental trajectories of SCNT blastocysts during peri-implantation development. Overall, these findings reveal diminished potentials of SCNT blastocysts for lineage specification and validate a critical peri-implantation barrier for SCNT embryos.
Continuous-Time Games with Imperfect and Abrupt Information
Authors: Bernard Benjamin 
Published: August 2023

Abstract
This paper studies two-player games in continuous time with imperfect public monitoring, in which information may arrive both gradually and continuously, governed by a Brownian motion, and abruptly and discontinuously, according to Poisson processes. For this general class of two-player games, we characterize the equilibrium payoff set via a convergent sequence of differential equations. The differential equations characterize the optimal trade-off between value burnt through incentives related to Poisson information and the noisiness of incentives related to Brownian information. In the presence of abrupt information, the boundary of the equilibrium payoff set may not be smooth outside the set of static Nash payoffs. Equilibrium strategies that attain extremal payoff pairs as well as their intertemporal incentives are elicitable from the limiting solution. The characterization is new even when information arrives through Poisson events only.
Health-related quality of life, remission and low lupus disease activity state in patients with systemic lupus erythematosus
Authors: Thibault Thomas , Rajillah Abdessamad , Bourredjem Abderrahmane , Corneloup Marie , Maurier François , Wahl Denis , Muller Geraldine , Aumaitre Olivier , Sève Pascal , Blaison Gilles , Besancenot Jean-François , Martin Thierry , Magy-Bertrand Nadine , Samson Maxime , Arnaud Laurent , Amoura Zahir , Devilliers Hervé ,   the EQUAL Study Group, Besancenot Jean-François , Bielefeld Philip , Berthier Sabine , Audia Sylvain , Lorcerie Bernard , Bonnotte Bernard , Samson Maxime , Vinit Julien , Ruault Sabine Meaux , Gil Helder , Broussolle Christiane , Varron Loig , Le Roux Karine , Zuily Stephane , Kaminsky Pierre , Mohamed Shirine , Muller Daniela Ibba , de Korwin Jean-Dominique , Guichard Jean-François , Marianetti Paola , Imbert Gaelle Guettrot 
Published: August 2023

Abstract

Objectives
To measure the association between SLE remission and scores of patients-reported outcome (PRO) measures.

Methods
We performed a prospective cohort study of SLE patients with a 2-year follow-up, using Lupus Patient-Reported Outcome (LupusPRO), Lupus Quality of Life (LupusQoL), Systemic Lupus Erythematosus Quality of Life (SLEQOL) and 36-item Short Form (SF-36) questionnaires. Remission was defined as remission off treatment (ROFT) and remission on treatment (RONT) according to the definitions of remission in SLE consensus. Mixed models accounting for repeated measures were used to compare groups as follow: ROFT and RONT vs no remission and lupus low disease activity state (LLDAS) vs no LLDAS.

Results
A total of 1478 medical visits and 2547 PRO questionnaires were collected during the follow-up from the 336 recruited patients. A between-group difference in PRO scores reaching at least 5 points on a 0–100 scale was obtained in the following domains: lupus symptoms (LLDAS: +5 points on the 0–100 scale, RONT: +9, ROFT: +5), lupus medication (LLDAS: +5, RONT: +8, ROFT: +9), pain vitality (LLDAS: +6, RONT: +9, ROFT: +6) of LupusPRO; role emotional (LLDAS: +5, RONT: +8), role physical (RONT: +7 and ROFT: +7), bodily pain (RONT: +6), mental health (RONT: +5) and social functioning (RONT: +6) of SF-36. In contrast, a between-group difference reaching at least 5 points was not achieved for any of the LupusQoL and SLEQOL domains.

Conclusions
RONT, ROFT and LLDAS were associated with significant and clinically relevant higher QoL in most PRO domains of the LupusPRO (disease specific) and SF-36 (generic) questionnaires, but not with LupusQoL and SLEQOL disease-specific questionnaires.
The Protestants’ Dilemma: When Cultural Mismatches Shape Deliberate Action
Authors: Tien Grace 
Published: August 2023

Abstract
Drawing from an ethnographic study and 63 interviews of Protestant professionals in the workplace, this article develops a conceptualization of how a cultural mismatch—defined here as a moral conflict between actors’ beliefs and values and their contextual norms and practices—catalyzes actors to strategically and deliberately shape future lines of action. In this study, a range of Protestant executives, professionals, and workers in China experience a cultural mismatch and respond in a number of ways. This study builds on accounts of culture in action to argue that when actors’ values and beliefs conflict with their organizational context, such cultural mismatches can shape action in not only unconscious, automatic ways or as post hoc justifications, as much of the extant scholarship has emphasized, but can also deliberately shape future lines of irrational, strategic, and creative action.
How Important Is Budding Speciation for Comparative Studies?
Authors: Caetano Daniel S , Quental Tiago B 
Published: August 2023

Abstract
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.