bluuebunny/crossref_metadata_2025_split huggingface dataset:
Healthcare Utilization Following Hemipelvectomy or Hip Disarticulation in the Military Health System
Authors: Wido Daniel , Harrington Colin J , Schulz Rebecca N , Jannace Kalyn C , Smith Douglas G , Pasquina Paul F 
Published: July 2023

ABSTRACT

Introduction
Amputations at the hip and pelvic level are often performed secondary to high-energy trauma or pelvic neoplasms and are frequently associated with a prolonged postoperative rehabilitation course that involves a multitude of health care providers. The purpose of this study was to examine the health care utilization of patients with hip- and pelvic-level amputations that received care in the U.S. Military Health System.

Materials and Methods
We performed a retrospective review of all patients who underwent a hip- or pelvic-level amputation in the Military Health System between 2001 and 2017. We compiled and reviewed all inpatient and outpatient encounters during three time points: (1) 3 months pre-amputation to 1 day pre-amputation, (2) the day of amputation through 12 months post-amputation, and (3) 13-24 months post-amputation. Health care utilization was defined as the average number of encounter days/admissions for each patient. Concomitant diagnoses following amputation including post-traumatic stress disorder, traumatic brain injury, anxiety, depression, and chronic pain were also recorded.

Results
A total of 106 individuals with hip- and pelvic-level amputations were analyzed (69 unilateral hip disarticulation, 6 bilateral hip disarticulations, 27 unilateral hemipelvectomy, 2 bilateral hemipelvectomies, and 2 patients with a hemipelvectomy and contralateral hip disarticulation). Combat trauma contributed to 61.3% (n = 65) of all amputations. During the time period of 3 months pre-amputation, patients had an average of 3.8 encounter days. Following amputation, health care utilization increased in both the year following amputation and the time period of 13-24 months post-amputation, averaging 170.8 and 77.4 encounter days, respectively. Patients with trauma-related amputations averaged more total encounter days compared to patients with disease-related amputations in the time period of 12 months following amputation (203.8 vs.106.7, P &lt; .001) and the time period of 13-24 months post-amputation (92.0 vs. 49.0, P = .005). PTSD (P = .02) and traumatic brain injuries (P &lt; .001) were more common following combat-related amputations.

Conclusions
This study highlights the increased health care resource demand following hip- and pelvic-level amputations in a military population, particularly for those patients who sustained combat-related trauma. Additionally, patients with combat-related amputations had significantly higher rates of concomitant PTSD and traumatic brain injury. Understanding the extensive needs of this unique patient population helps inform providers and policymakers on the requirements for providing high-quality care to combat casualties.
Wind-reprocessed transients from stellar-mass black hole Tidal Disruption Events
Authors: Kremer Kyle , Mockler Brenna , Piro Anthony L , Lombardi James C 
Published: July 2023

ABSTRACT
Tidal disruptions of stars by stellar-mass black holes are expected to occur frequently in dense star clusters. Building upon previous studies that performed hydrodynamic simulations of these encounters, we explore the formation and long-term evolution of the thick, super-Eddington accretion disks formed. We build a disk model that includes fallback of material from the tidal disruption, accretion onto the black hole, and disk mass losses through winds launched in association with the super-Eddington flow. We demonstrate that bright transients are expected when radiation from the central engine powered by accretion onto the black hole is reprocessed at large radii by the optically-thick disk wind. By combining hydrodynamic simulations of these disruption events with our disk + wind model, we compute light curves of these wind-reprocessed transients for a wide range of stellar masses and encounter penetration depths. We find typical peak bolometric luminosities of roughly $10^{41}\!-\!10^{44}\,$erg s−1 (depending mostly on accretion physics parameters) and temperatures of roughly $10^5\!-\!10^6\,$K, suggesting peak emission in the ultraviolet/blue bands. We predict all-sky surveys such as the Vera Rubin Observatory and ULTRASAT will detect up to thousands of these events per year in dense star clusters out to distances of several Gpc.
Nitrogen enrichment and clustered star formation at the dawn of the Galaxy
Authors: Belokurov Vasily , Kravtsov Andrey 
Published: July 2023

ABSTRACT
Anomalously high nitrogen-to-oxygen abundance ratios [N/O] are observed in globular clusters (GCs), among the field stars of the Milky Way (MW), and even in the gas in a z ≈ 11 galaxy. Using data from the APOGEE Data Release 17 and the Gaia Data Release 3, we present several independent lines of evidence that most of the MW’s high-[N/O] stars were born in situ in massive bound clusters during the early, pre-disc evolution of the Galaxy. Specifically, we show that distributions of metallicity [Fe/H], energy, the angular momentum Lz, and distance of the low-metallicity high-[N/O] stars match the corresponding distributions of stars of the Aurora population and of the in situ GCs. We also show that the fraction of in situ field high-[N/O] stars, fN/O, increases rapidly with decreasing metallicity. During epochs when metallicity evolves from $\rm [Fe/H]=-1.5$ to $\rm [Fe/H]=-0.9$, the Galaxy spins up and transitions from a turbulent Aurora state to a coherently rotating disc. This transformation is accompanied by many qualitative changes. In particular, we show that high N/O abundances similar to those observed in GN-z11 were common before the spin-up ($\rm [Fe/H]\lesssim -1.5$) when up to $\approx 50~{{\ \rm per\ cent}}-70~{{\ \rm per\ cent}}$ of the in situ stars formed in massive bound clusters. The dramatic drop of fN/O at $\rm [Fe/H]\gtrsim -0.9$ indicates that after the disc emerges the fraction of stars forming in massive bound clusters decreases by two orders of magnitude.
A model for GN-z11: top-heavy stellar initial mass functions in forming galactic nuclei and ultra-compact dwarfs
Authors: Bekki Kenji , Tsujimoto Takuji 
Published: July 2023

ABSTRACT
Recent JWST observations of the z = 10.6 galaxy GN-z11 have revealed a very high gas-phase nitrogen abundance (higher than four times the solar value), a very small half-light radius (≈60 pc), and a large stellar mass (Ms ≈ 109 M⊙) for its size. We consider that this object is a forming galactic nucleus or ultra-compact dwarf galaxy rather than a proto globular cluster, and thereby investigate the chemical abundance pattern using one-zone chemical evolution models. The principal results of the models are as follows. The observed log (N/O) &gt; −0.24, log (C/O) &gt; −0.78, and 12 + log (O/H) ≈ 7.8 can be self-consistently reproduced by the models both with very short star formation time-scales (&lt;107 yr) and with top-heavy stellar initial mass functions. The adopted assumption of no chemical enrichment by massive (m &gt; 25 M⊙) core collapse supernovae (CCSNe) is also important for the reproduction of high gas-phase log (N/O), because such CCSNe can decrease high log (N/O) of gas polluted by OB and Wolf–Rayet stars. GN-z11 can have a significant fraction (&gt;0.5) of nitrogen-rich ([N/Fe] &gt; 0.5) stars, which implies a possible link between nitrogen-rich stellar populations of the inner Galaxy and giant elliptical galaxies and high-z objects with high gas-phase log (N/O) like GN-z11.
Determinants of the Intensity of Bank-Firm Relationships: Evidence from Japan
Authors: Aoki Yasuharu 
Published: July 2023

Abstract
Focusing on the Japanese setting, this study investigates the standard firm characteristics that affect the intensity of bank-firm relationships (IBR) and how these characteristics relate to the decline in IBR. The regression results show that firm size, credit quality, investment opportunities, and ownership concentration are negatively associated with IBR, while firm age, pledgeability, and managerial ownership are positively associated. This study also finds that (1) an increase in credit quality, (2) a decrease in the positive impact of managerial ownership, and (3) an increase in the negative impact of ownership concentration cause the decline in IBR. (JEL G21, G32, L14)
Received March 15, 2023; editorial decision July 11, 2023 by Editor Isil Erel. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Symbolic and Transformative: Alignments Toward Feminicídio Legal Reform inside the Brazilian Police
Authors: Pamplona Roberta S 
Published: July 2023

Abstract
Feminism travels unevenly through state structures, and the state’s incorporation of feminist ideas remains controversial within feminist movements. This study uses the Brazilian Feminicídio Law, which increases punishment for gender-based homicides, as a case study to ask how law enforcement actors adopt a feminist legal reform. Data come from one year of in-depth fieldwork across police stations in a major Brazilian city and from newspaper articles. I show that state actors accept the feminist legal frame based on previous understandings of police practices. However, institutional divisions led them to develop different alignments toward the new legal reform. While police officers from the homicide division symbolically align toward feminicídio and do not aim to change police practices, officers from the women’s division perceive feminicídio as an opportunity to claim significant changes in police practices, revealing a transformative alignment. Struggles over legitimation and diverging professional beliefs and interests explain the two distinct responses.
Revisiting evidential presumptions of undue influence in Hong Kong
Authors: Cheng Yutong 
Published: July 2023

Abstract
The usefulness of evidential presumptions in establishing undue influence in equity has long been debated. This article revisits this debate in the Hong Kong context, arguing evidential presumptions are, in essence, of little use in establishing undue influence because there is no necessary causation between evidential presumptions and the establishment of undue influence. This article examines the fiduciary and evidentiary nature of the evidential presumptions and compares them as tools with tests of establishing undue influence throughout judicial history. Social implications behind evidential presumptions have been considered, aiming to adopt a flexible approach based on the maxim of equity.
XVIAmerican Literature: The Twentieth Century
Authors: Gifford James , Rudder Adam , Velásquez Antonio 
Published: July 2023

Abstract
This chapter has eight sections: 1. Poetry; 2. Fiction 1900–1945; 3. Fiction since 1945; 4. Genre Fiction; 5. Drama; 6. Comics; 7. African American Writing; 8. Native Writing; 9. Latino/a, Asian American, and General Ethnic Writing. Section 1 is by James Gifford; section 2 will resume next year; section 3 will resume next year; section 4 is by James Gifford; section 5 will resume next year; section 6 will resume next year; section 7 is by Adam Rudder; section 8 will resume next year; section 9 is by Antonio Velásquez.
Playing with FIRE: How an RXLR Oomycete Effector Fuels Disease by Hijacking 14-3-3 Proteins
Authors: Tiwari Manish , Lovelace Amelia H. 
Published: July 2023

The plant pathogen Phytophthora palmivora causes rot disease in several monocots and dicots. The plant 14-3-3 proteins are targets of different types of effector molecules secreted by the pathogens. An RXLR-type effector FIRE (14-3-3 interacting RXLR effector) and its target 14-3-3 proteins that localize to haustoria have been identified, pointing to a potential site of interaction. The pathogen hijacks the host 14-3-3 proteins through FIRE-mediated interaction and lowers the immunity for disease progression. The effector FIRE and 14-3-3 interaction deciphered in this study could pave the way for genetic modification of plants with altered 14-3-3 protein for broad host resistance.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
CytoPb: Segmentation-free and threshold-free analysis of highly multiplexed images of biological tissue
Authors: Barber Paul R , Dolcetti Luigi , Yeh Chen-An , Ng Tony 
Published: July 2023

AbstractWe present a novel method and code, CytoPb, for the analysis of multiplexed images that is segmentation-free and threshold-free and produces results that correlate well with existing methods but is faster to run, needs minimal training and removes subjectivity associated with the validation of single-cell segmentation and thresholding. In three data sets cell abundance measures correlate with previous methods (Pearson’s coef. >0.75). Neighbourhood analysis and cell-cell proximity are possible.
GAPiM: Discovering Genetic Variations on a Real Processing-in-Memory System
Authors: Abecassis Naomie , Gómez-Luna Juan , Mutlu Onur , Ginosar Ran , Moisson-Franckhauser Aphélie , Yavits Leonid 
Published: July 2023

AbstractVariant calling is a fundamental stage in genome analysis that identifies mutations (variations) in a sequenced genome relative to a known reference genome. Pair-HMM is a key part of the variant calling algorithm and its most compute-intensive part. In recent years, Processing-in-Memory (PiM) solutions, which consist of placing compute capabilities near/inside memory, have been proposed to speed up the genome analysis pipeline. We implement the Pair-HMM algorithm on a commercial PiM platform developed by UPMEM. We modify the Pair-HMM algorithm to make it more suitable for PiM execution with acceptable loss of accuracy. We evaluate our implementation on single chromosomes and whole genome sequencing datasets, demonstrating up to 2x speedup compared to existing CPU accelerations and up to 3x speedup compared to FPGA accelerations.
Directly selecting differentially expressed genes for single-cell clustering analyses
Authors: Chen Zihao , Wang Changhu , Huang Siyuan , Shi Yang , Xi Ruibin 
Published: July 2023

AbstractIn single-cell RNA sequencing (scRNA-seq) studies, cell-types and their associated marker genes are often identified by clustering and differential expression gene (DEG) analysis. scRNA-seq data contain many genes not relevant to cell-types and gene selection procedures are needed for more accurate clustering. An ideal gene selection procedure should select all DEGs between cell-types for best cell-type identification. However, because cell-types are unknown, gene selection and DEG analysis are performed separately using different methods. Genes are selected using surrogate criteria not directly related with clustering, which often miss important genes or select unimportant genes. Clustering accuracy could be seriously influenced because of the inferior gene selection. DEGs are often detected by comparing different clusters, leading to many false DEGs due to the selection bias problem. In this paper, we present Festem, a unified method for gene selection and DEG analysis in scRNA-seq studies. Festem investigates gene’s clustering information based on the observation that marginal distributions of DEGs are mixtures of their different cell-type-conditional distributions, and can directly select the clustering-informative DEGs and avoid the selection bias problem. Extensive simulation and real data analyses show that Festem achieves high precision and recall for DEG detection, and enables more accurate clustering and cell-type identification. Applications to several scRNA-seq datasets demonstrate that Festem can identify cell-types that are often missed by other methods. In a large intrahepatic cholangiocarcinoma dataset, we identify CD8+ T cell-types and find that their marker genes are novel prognostic biomarkers.
Generating serum-based antibodies from tumor-exposed mice: a new potential strategy for cutaneous squamous cell carcinoma treatment
Authors: Liu Zheng 
Published: July 2023

AbstractCurrent cancer treatment strategies continue to face significant challenges, primarily due to tumor relapse, drug resistance, and low treatment efficiency. These issues arise because certain tumor cells adapt to the host immune microenvironment and evade the immune system. This study presents a new cancer immunotherapy strategy using serum-based antibodies from mice exposed to mouse cutaneous squamous cell carcinoma (mCSCC). The experiment was conducted in three stages. In the first stage, mCSCC cells were isolated and expanded cultured from DMBA/TPA-induced mCSCC. In the second stage, these expanded tumor cells were injected into healthy mice to stimulate the production of anti-tumor antibodies. In the final stage, therapeutic serum was extracted from these healthy mice and reintroduced into the tumor-bearing mice. An ELISA assay was utilized to analyze the levels of p53, Bcl-xL, NF-κB, and Bax. The results showed that the serum treatment not only reduced tumor volume but also reversed changes in p53, Bcl-xL, NF-κB, and Bax. In conclusion, this study developed a new immunotherapeutic strategy for treating mCSCC. However, further research is needed to fully comprehend the mechanism of this serum treatment.
Assessing the basal gene expression of cancer cell lines for in vitro transcriptomic toxicology screening
Authors: Black Michael B. , Efremenko Alina Y. , McMullen Patrick D. , Barutcu A. Rasim , Nong Andy 
Published: July 2023

ABSTRACTIn vitro toxicology has used immortalized cancer cell lines as model human systems for decades. However, these cell lines pose problems in designing toxicity testing programs as they inherently do not represent normal human biology. There is also a huge number of such cell lines to choose from, derived from human cancer cells from nearly every tissue. We explored the idea of using available basal gene expression data (NCI-60 cell line panel and Human GTEx tissue data) to determine if there was sufficient variability in cell line gene expression to group cell lines by relevance to specific human tissues. The transcriptomic analysis suggests that the variability in gene expression in cancer cell lines and in normal human tissue is minimal. The overall basal gene expression of cancer cells lines even overlapped normal human tissue gene expression. While some human tissues (e.g., lung) have basal expression profiles that do not appear to be like any cancer cell line, including cancers that may be derived from the same tissue, most human tissues show basal expression profiles comparable to several cancer cell lines. These results are important to address the genomic baseline and variability of cancer cell lines used for new approach methods of toxicity testing.
Sensitive remote homology search by local alignment of small positional embeddings from protein language models
Authors: Johnson Sean R. , Peshwa Meghana , Sun Zhiyi 
Published: July 2023

AbstractAccurately detecting distant evolutionary relationships between proteins remains an ongoing challenge in bioinformatics. Search methods based on primary sequence struggle to accurately detect homology between sequences with less than 20% amino acid identity. Profile- and structure-based strategies extend sensitive search capabilities into this twilight zone of sequence similarity but require slow pre-processing steps. Recently, whole-protein and positional embeddings from deep neural networks have shown promise for providing sensitive sequence comparison and annotation at long evolutionary distances. Embeddings are generally faster to compute than profiles and predicted structures but still suffer several drawbacks related to the ability of whole-protein embeddings to discriminate domain-level homology, and the database size and search speed of methods using positional embeddings. In this work, we show that low-dimensionality positional embeddings can be used directly in speed-optimized local search algorithms. As a proof of concept, we use the ESM2 3B model to convert primary sequences directly into the 3Di alphabet or amino acid profiles and use these embeddings as input to the highly optimized Foldseek, HMMER3, and HH-suite search algorithms. Our results suggest that positional embeddings as small as a single byte can provide sufficient information for dramatically improved sensitivity over amino acid sequence searches without sacrificing search speed.
Mcadet: a feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection
Authors: Cui Saishi , Nassiri Sina , Zakeri Issa 
Published: July 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) data analysis faces numerous challenges, including high sparsity, a high-dimensional feature space, technical biases, and biological noise. These challenges hinder downstream analysis, necessitating the use of feature selection methods to address technical biases, identify informative genes, and reduce data dimensionality. However, existing methods for selecting highly variable genes (HVGs) exhibit limited overlap and inconsistent clustering performance across benchmark datasets. Moreover, these methods often struggle to accurately select HVGs from fine-resolution scRNA-seq datasets and rare cell types, raising concerns about the reliability of their results. To overcome these limitations, we propose a novel feature selection framework for unique molecular identifiers (UMIs) scRNA-seq data called Mcadet. Mcadet integrates Multiple Correspondence Analysis (MCA), graph-based community detection, and a novel statistical testing approach. To assess the effectiveness of Mcadet, we conducted extensive evaluations using both simulated and real-world data, employing unbiased metrics for comparison. Our results demonstrate the superior performance of Mcadet in the selection of HVGs in scenarios involving fine-resolution scRNA-seq datasets and datasets containing rare cell populations. By addressing the challenges of feature selection in scRNA-seq analysis, Mcadet provides a valuable tool for improving the reliability and accuracy of downstream analyses in single-cell transcriptomics.
Early life lipid overload in Native American myopathy is phenocopied bystac3knock out in zebrafish
Authors: Donaka Rajashekar , Zheng Houfeng , Karasik David 
Published: July 2023

AbstractUnderstanding the early stages of human congenital myopathies is critical for proposing strategies for improving skeletal muscle performance by the functional integrity of cytoskeleton. SH3 and cysteine-rich domain 3 (Stac3) is a protein involved in nutrient sensing, and is an essential component of the excitation-contraction (EC) coupling machinery for Ca2+releasing. A mutation inSTAC3causes debilitating Native American myopathy (NAM) in humans, and loss of this gene in mice and zebrafish resulted in death in early life. Previously, NAM patients demonstrated increased lipids in skeletal muscle biopsy. However, elevated neutral lipids could alter muscle function in NAM disease via EC coupling apparatus is yet undiscovered in early development.Here, using a CRISPR/Cas9 inducedstac3knockout (KO) zebrafish model, we determined that loss ofstac3led to muscle weakness, as evidenced by delayed larval hatching. We observed decreased whole-body Ca2+level at 5 days post-fertilization (dpf) and defects in the skeletal muscle cytoskeleton, i.e., F-actin and slow muscle fibers at 5 and 7 dpf. Homozygous larvae exhibited elevated neutral lipid levels at 5 dpf, which persisted beyond 7 dpf. Myogenesis regulators such asmyoDandmyf5, were significantly altered instac3-/-larvae at 5 dpf, thus a progressive death of the KO larva by 11 dpf.In summary, the presented findings suggest thatstac3-/-can serve as a non-mammalian model to identify lipid-lowering molecules for refining muscle function in NAM patients.