bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crossing disciplinary boundaries: motivations, challenges, and enablers for early career marine researchers moving from natural to social sciences
Authors: Shellock R J , Cvitanovic C , Badullovich N , Catto D , DelBene J A , Duggan J , Karcher D B , Ostwald A , Tuohy P 
Published: December 2022

Abstract
Recent years have seen increasing calls to better document and understand the human dimensions of the marine and coastal environment and to incorporate this knowledge into decision-making. Human dimensions of the marine and coastal environment are best investigated through the application of marine social science. Individuals within marine social science are not solely “pure” social scientists, but rather are a diverse and interdisciplinary community, including many who have moved from the natural sciences to pursue a career in marine social science. This is particularly the case for early career researchers, with many moving from natural to social science earlier in their academic careers than their predecessors, and thus developing stronger interdisciplinary skills than previous generations of social scientists. In this perspective, we draw on our experiences, highlighting our main motivations for moving from natural to social science, the barriers we have faced and our top tips for early career researchers faced with similar opportunities and challenges. The ten tips include: “Work with like-minded researchers,” “Learn from and be inspired by academic heroes,” “Learn about and engage with research philosophy, positionality and reflexivity,” “Value your own skillset and perspective,” and “Be patient and kind to yourself.”
Discrete and continuum models for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes and tumour cells
Authors: Almeida Luís , Audebert Chloe , Leschiera Emma , Lorenzi Tommaso 
Published: December 2022

AbstractWe present an individual-based model for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes (CTLs) and tumour cells. In this model, every cell is viewed as an individual agent whose phenotypic state is modelled by a discrete variable. For tumour cells, this variable represents a parameterization of the antigen expression profiles, while for CTLs it represents a parameterization of the target antigens of T-cell receptors (TCRs). We formally derive the deterministic continuum limit of this individual-based model, which comprises a non-local partial differential equation for the phenotype distribution of tumour cells coupled with an integro-differential equation for the phenotype distribution of CTLs. The biologically relevant homogeneous steady-state solutions of the continuum model equations are found. The linear-stability analysis of these steady-state solutions is then carried out in order to identify possible conditions on the model parameters that may lead to different outcomes of immune competition and to the emergence of patterns of phenotypic coevolution between tumour cells and CTLs. We report on computational results of the individual-based model, and show that there is a good agreement between them and analytical and numerical results of the continuum model. These results shed light on the way in which different parameters affect the coevolutionary dynamics between tumour cells and CTLs. Moreover, they support the idea that TCR-tumour antigen binding affinity may be a good intervention target for immunotherapy and offer a theoretical basis for the development of anti-cancer therapy aiming at engineering TCRs so as to shape their affinity for cancer targets.
Simulating and Analyzing aggressive car-following behavior for testing autonomous vehicles
Authors: Tang Li , Gupta Abhishek , Liu Ziyi , Qiao Chunming , He Qing 
Published: December 2022

Abstract
In a mixed traffic flow, evaluating the operation safety of autonomous vehicles (AVs) is crucial under different aggressive car-following behavior of surrounding human driven-vehicles (HVs). To pursue this goal, this paper develops a machine-learning-based simulation method accompanied by a traditional car-following model. We integrate the unsupervised learning method, Approximate Bayesian computation, and Gipps car-following model to obtain different parameter distributions of the Gipps model. After utilizing the key parameter distribution, this paper employs a supervised learning method to predict the aggressive index of human-driven vehicles in each individual car-following event. Further, we verify the outputs of this simulation model with the NGSIM I-80 traffic dataset. After the validation, we develop an AV simulation study to analyze Avs’ performance in different aggressive HVs scenarios. The result indicates that the higher penetration rate of AV is essential for stabilizing AVs’ performance in terms of velocity and the probability of involving in a crash. Additionally, aggressive HV drivers significantly impact scenarios of low AV penetration rate regarding safety issues.
Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments
Authors: Wilson George D , Shaik Shabuddin 
Published: December 2022

AbstractA new phreatoicidean isopod, Speonastes venkataramanigen., sp. nov. is described from Borra Cave in northeastern Andhra Pradesh, India. This new taxon has features seen in most phreatoicideans such as ventrally projecting pleonal pleurae, but also has features characteristic of the hypogean family Hypsimetopidae, such as an elongated pleotelson with a medially rotating uropod that has protopodal denticles or denticulate setae opposing the denticulate margin of the pleotelson, as well as the distal article of the antennula being minute and the penultimate article elongated and somewhat inflated. Robustness-tested phylogenetic analyses of character data from exemplars from nearly all phreatoicidean genera and four non-phreatoicidean outgroups finds that this species is the earliest derived member of Hypsimetopidae. These analyses have substantial implications for both relationships among Phreatoicidea, but within the family as well. The body form of the Phreatoicidea basal to the hypsimetopid clade resembles the form seen in fossils or by recent taxa such as CrenisopusWilson & Keable, 1999. Ancestors of Speonastesgen. nov. may have independently colonized India from those of the Nichollsia-Andhracoides clade. An early Mesozoic diversification of Hypsimetopidae and related taxa along continental rifts in eastern Gondwana between Antarctica, India, and Australia is one implication of the phylogeny. Although the caves of Andhra Pradesh and other Indian states have biologically unique and scientifically important taxa, India provides no protection for any cave. This exposes the fauna to negative impacts such as quarrying or illegal mining, over-exploitation of water resources, and damage from unconstrained tourist visitation.
Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines
Authors: Hamaya Yamato , Suzuki Ayako , Suzuki Yutaka , Tsuchihara Katsuya , Yamashita Riu 
Published: December 2022

Abstract

Background
Genome-wide landscape of alternative promoter use remains unknown. We determined expression profiles of promoters in 26 lung adenocarcinoma cell lines using the transcriptional start site-sequencing data and proposed an index ‘canonical promoter usage’ to quantify the diversity of alternative promoter usage.

Methods
Transcriptional start site-sequencing and other datasets were obtained from the DataBase of Transcriptional Start Sites. Transcriptional start site-sequencing read clusters were mapped onto RefGene to determine the promoters. Commonly used promoters were designated as canonical promoters. The sequence logos, CpG islands, DNA methylation and histone modifications of canonical and non-canonical promoters were examined. Canonical promoter usage was calculated by dividing ‘read counts of a canonical promoter’ by ‘read counts of all the units of promoters’ on each gene. The expressed genes were subjected to hierarchical clustering according to their canonical promoter usage.

Results
Among 104 455 promoters for 14 297 genes, 8659 canonical and 68 197 non-canonical promoters were identified. Corresponding to higher expression, canonical promoters showed core promoter sequences, higher CpG island positivity, less DNA methylation and higher transcription-promoting histone modifications. Gene ontology enrichment analysis revealed that the clusters with lower canonical promoter usage were related to signalling pathways, whereas clusters of tightly regulated genes with higher canonical promoter usage were related to housekeeping genes.

Conclusion
Canonical promoters were regulated by conventional transcriptional machinery, while non-canonical promoters would be targets of ‘leaky’ expression. Further investigation is warranted to analyse the correlation between alternative promoter usage and biological characteristics contributing to carcinogenesis.
Networking the Counterrevolution: The École Supérieure de Guerre, Transnational Military Collaboration, and Cold War Counterinsurgency, 1955–1975
Authors: Peterson Terrence G 
Published: December 2022

Abstract
Over the past several decades, scholars have devoted considerable attention to tracing the influence of French counterinsurgency practices developed in Indochina and Algeria on other militaries during the Cold War. This article builds on that literature to offer an explanation for why French counterrevolutionary knowledge circulated so broadly, and to connect the French military more concretely to an emerging literature on anticommunist internationalism. At the center of French efforts, this article argues, stood the Army’s École Supérieure de Guerre (ESG) in Paris, which trained growing numbers of high-ranking foreign officers after 1945. The ESG taught counterrevolutionary warfare directly, but as this article argues, it also helped constitute an audience abroad for such ideas by cultivating affective bonds, strategic preferences, and personal connections over the longer term. In tracing the partnerships cultivated through the ESG in this period, this article also illustrates the broader entanglements between counterinsurgency, international military cooperation, and professionalization at midcentury. For military partners seeking to professionalize their own forces, the attractiveness of French doctrines lay as much in the easily accessible set of materials, training, and expertise the French military offered as in their capacity to combat subversion. By tracing the transnational networks of exchange knit together by military academies in this period, this article concludes, scholars can better historicize the rise of counterinsurgency as a key paradigm of cold warfare.
Type 1 von Willebrand Disease in a Pediatric Patient Caused by a Novel Heterozygous Deletion of Exons 1 to 6 of the von Willebrand Factor Gene: A Case Report
Authors: Lapić Ivana , Radić Antolic Margareta , Rogić Dunja , Dejanović Bekić Sara , Coen Herak Désirée , Bilić Ernest , Zadro Renata 
Published: December 2022

Abstract
A 6-year-old boy was referred to a hematologist due to excessive mucocutaneous bleeding. Diagnostic assessment for von Willebrand disease (VWD) was indicated and included both coagulation and genetic testing. Laboratory testing revealed proportionally decreased von Willebrand factor (VWF) glycoprotein Ib-binding activity (23.6%) compared to VWF antigen (24.7%), similarly decreased VWF collagen-binding activity (24.2%), and normally distributed VWF multimers, with decreased intensity of all fractions. Diagnosis of type 1 VWD was established. Genetic analysis by means of next-generation sequencing (NGS) of VWF and coagulation factor VIII genes did not identify any causative mutations. Additionally, multiplex ligation-dependent probe amplification (MLPA) of VWF gene exons revealed a heterozygous deletion of exons 1 to 6, which is reported in type 1 VWD for the first time. Application of MLPA was crucial for revealing the genetic basis of type 1 VWD in this case, which would have remained undetected if only NGS was used.
A high-resolution spectroscopic search for multiple populations in the 2 Gyr old cluster NGC 1846
Authors: Oh W S , Nordlander T , Da Costa G S , Mackey A D 
Published: December 2022

ABSTRACT
We present detailed C, O, Na, Mg, Si, Ca, Ti, V, Fe, Zr, Ba, and Eu abundance measurements for 20 red giant branch (RGB) stars in the Large Magellanic Cloud (LMC) star cluster NGC 1846 ([Fe/H] = −0.59). This cluster is 1.95 Gyr old and lies just below the supposed lower age limit (2 Gyr) for the presence of multiple populations in massive star clusters. Our measurements are based on high- and low-resolution VLT/FLAMES spectra combined with photometric data from Hubble Space Telescope (HST). Corrections for non-local thermodynamic equilibrium effects are also included for O, Na, Mg, Si, Ca, Fe, and Ba. Our results show that there is no evidence for multiple populations in this cluster based on the lack of any intrinsic star-to-star spread in the abundances of Na and O: We place 95  per cent confidence limits on the intrinsic dispersion for these elements of ≤0.07 and ≤0.09 dex, respectively. However, we do detect a significant spread in the carbon abundances, indicating varying evolutionary mixing occurring on the RGB that increases with luminosity. Overall, the general abundance patterns for NGC 1846 are similar to those seen in previous studies of intermediate-age LMC star clusters and field stars.
Clinical features and outcomes of spine surgery in patients with ankylosing spondylitis
Authors: Nakao Yuki , Sakuraba Koji , Harimaya Katsumi , Terada Kazuo , Kobara Nobuo , Kawaguchi Ken-Ichi , Hayashida Mitsumasa , Iida Keiichiro , Nakashima Yasuharu , Fukushi Jun-Ichi 
Published: December 2022

ABSTRACT

Objectives
The study aimed to comprehend the clinical features and outcomes of surgical treatments for spinal disorders in patients with ankylosing spondylitis (AS).

Methods
This retrospective study enrolled patients with AS who underwent spine surgery between 2000 and 2019 in our facility.

Results
Thirteen patients with AS underwent spine surgeries. The mean age was 56.2 years, and the mean disease duration was 25.1 years at the time of surgery. Nine patients had vertebral fracture, two had kyphotic deformity, and two had myelopathy due to the spinal ligament ossification. Fracture cases included five patients with secondary pseudarthrosis/delayed palsy due to conservative treatment failure. Spinal fixation was performed in all patients. Pedicle subtraction osteotomy for kyphosis and laminectomy for myelopathy were also conducted. All patients improved after surgeries. One patient with kyphotic deformity underwent additional surgery of bilateral hip prosthesis, which resulted in better spine alignment. Four cases of perioperative complications were observed.

Conclusion
Myelopathy was newly found as the aetiology requiring surgery in patients with AS. This summarized case series could help physicians to identify patients with surgically treatable spinal disorders among patients with AS.
Bispecific antibodies—effects of point mutations on CH3-CH3 interface stability
Authors: Pomarici Nancy D , Fernández-Quintero Monica L , Quoika Patrick K , Waibl Franz , Bujotzek Alexander , Georges Guy , Liedl Klaus R 
Published: December 2022

Abstract
A new format of therapeutic proteins is bispecific antibodies, in which two different heavy chains heterodimerize to obtain two different binding sites. Therefore, it is crucial to understand and optimize the third constant domain (CH3-CH3) interface to favor heterodimerization over homodimerization, and to preserve the physicochemical properties, as thermal stability. Here, we use molecular dynamics simulations to investigate the dissociation process of 19 CH3-CH3 crystal structures that differ from each other in few point mutations. We describe the dissociation of the dimeric interface as a two-steps mechanism. As confirmed by a Markov state model, apart from the bound and the dissociated state, we observe an additional intermediate state, which corresponds to an encounter complex. The analysis of the interdomain contacts reveals key residues that stabilize the interface. We expect that our results will improve the understanding of the CH3-CH3 interface interactions and thus advance the developability and design of new antibodies formats.
Editing Aspergillus terreus using the CRISPR-Cas9 system
Authors: Shih Sra-Yh , Mortensen Uffe Hasbro , Chang Fang-Rong , Tsai HsinYuan 
Published: December 2022

Abstract
CRISPR-Cas9 technology has been utilized in different organisms for targeted mutagenesis, offering a fast, precise and cheap approach to speed up molecular breeding and study of gene function. Until now, many researchers have established the demonstration of applying the CRISPR/Cas9 system to various fungal model species. However, there are very few guidelines available for CRISPR/Cas9 genome editing in Aspergillus terreus. In this study, we present CRISPR/Cas9 genome editing in A. terreus. To optimize the guide ribonucleic acid (gRNA) expression, we constructed a modified single-guide ribonucleic acid (sgRNA)/Cas9 expression plasmid. By co-transforming an sgRNA/Cas9 expression plasmid along with maker-free donor deoxyribonucleic acid (DNA), we precisely disrupted the lovB and lovR genes, respectively, and created targeted gene insertion (lovF gene) and iterative gene editing in A. terreus (lovF and lovR genes). Furthermore, co-delivering two sgRNA/Cas9 expression plasmids resulted in precise gene deletion (with donor DNA) in the ku70 and pyrG genes, respectively, and efficient removal of the DNA between the two gRNA targeting sites (no donor DNA) in the pyrG gene. Our results showed that the CRISPR/Cas9 system is a powerful tool for precise genome editing in A. terreus, and our approach provides a great potential for manipulating targeted genes and contributions to gene functional study of A. terreus.
Medical Counseling on Sexual Enrichment Aids: Women’s Preferences and Medical Practitioner Expertise
Authors: Collar Amanda L. , Brakey Heidi Rishel , Fuentes Jesus E. , Frietze Kathryn M. 
Published: December 2022

(Abstracted from Obstet Gynecol 2022;140:489–498)
Use of sexual enrichment aids such as sex toys is increasing among sexually active women. Nearly 80% of women aged 18 to 35 years reported previous use.
Activating transcription factor 4 protects mice against sepsis-induced intestinal injury by regulating gut-resident macrophages differentiation
Authors: Wen Zhenliang , Chen Dechang , Xiong Xi , Shao Lujing , Tang Xiaomeng , Shen Xuan , Zhang Sheng , Huang Sisi , Zhang Lidi , Chen Yizhu , Zhang Yucai , Wang Chunxia , Liu Jiao 
Published: December 2022

Abstract

Background:
Gut-resident macrophages (gMacs) supplemented by monocytes-to-gMacs differentiation play a critical role in maintaining intestinal homeostasis. Activating transcription factor 4 (ATF4) is involved in immune cell differentiation. We therefore set out to investigate the role of ATF4-regulated monocytes-to-gMacs differentiation in sepsis-induced intestinal injury.

Methods:
Sepsis was induced in C57BL/6 wild type (WT) mice and Atf4-knockdown (Atf4

+/−) mice by cecal ligation and puncture or administration of lipopolysaccharide (LPS). Colon, peripheral blood mononuclear cells, sera, lung, liver, and mesenteric lymph nodes were collected for flow cytometry, hematoxylin and eosin staining, immunohistochemistry, quantitative reverse transcription polymerase chain reaction, and enzyme-linked immunosorbent assay, respectively.

Results:
CD64, CD11b, Ly6C, major histocompatibility complex-II (MHC-II), CX3CR1, Ly6G, and SSC were identified as optimal primary markers for detecting the process of monocytes-to-gMacs differentiation in the colon of WT mice. Monocytes-to-gMacs differentiation was impaired in the colon during sepsis and was associated with decreased expression of ATF4 in P1 (Ly6Chi monocytes), the precursor cells of gMacs. Atf4 knockdown exacerbated the impairment of monocytes-to-gMacs differentiation in response to LPS, resulting in a significant reduction of gMacs in the colon. Furthermore, compared with WT mice, Atf4

+/−
mice exhibited higher pathology scores, increased expression of inflammatory factor genes (TNF-α, IL-1β), suppressed expression of CD31 and vascular endothelial-cadherin in the colon, and increased translocation of intestinal bacteria to lymph nodes and lungs following exposure to LPS. However, the aggravation of sepsis-induced intestinal injury resulting from Atf4 knockdown was not caused by the enhanced inflammatory effect of Ly6Chi monocytes and gMacs.

Conclusion:
ATF4, as a novel regulator of monocytes-to-gMacs differentiation, plays a critical role in protecting mice against sepsis-induced intestinal injury, suggesting that ATF4 might be a potential therapeutic target for sepsis treatment.
Considerations for genetic testing in individuals with autosomal dominant polycystic kidney disease
Authors: Noce Elyssa M. 
Published: December 2022

ABSTRACT
Autosomal dominant polycystic kidney disease (ADPKD) is a systemic, irreversible, genetic condition caused by mutations in the PKD1 and PKD2 genes, and the most common form of inherited kidney disease in the United States, affecting more than 600,000 individuals. Because the condition is autosomal dominant, there is a 50% chance that each child of an affected adult will also have the pathogenic genetic mutation. PKD1 mutation accounts for approximately 85% of ADPKD cases and is characterized by an earlier onset of disease with more rapid progression, whereas PKD2 mutation accounts for the remaining 15% of cases and is characterized by a less severe and less rapid disease course. Genetic testing is not consistently used in the management of individuals with ADPKD, although it can provide invaluable information regarding disease progression and prognosis. Genetic data are necessary to effectively communicate disease progression with patients, use current prognostic calculators, and play a role in family planning. Increasing clinician knowledge in primary care and nephrology providers will contribute to improved care for individuals affected by ADPKD.
Social Vulnerability Index and Surgical Management of Abnormal Uterine Bleeding in Reproductive-Age Women
Authors: Fakas Steliana , Lu Anjanique Mariquit Rosete , Shahani Disha , Blitz Matthew J. , Rodriguez-Ayala Gianni 
Published: December 2022

(Abstracted from J Minim Invasive Gynecol 2022;29:1104–1109)
Abnormal uterine bleeding (AUB) is common and affects 10% to 50% of reproductive-age women. A large number of nonmedical factors in the social and physical environment have a strong effect on health outcomes in patients with AUB and other disorders/diseases.
Linzagolix With and Without Hormonal Add-Back Therapy for the Treatment of Symptomatic Uterine Fibroids: Two Randomized, Placebo-Controlled, Phase 3 Trials
Authors: Donnez Jacques , Taylor Hugh S. , Stewart Elizabeth A. , Bradley Linda , Marsh Erica , Archer David , Al-Hendy Ayman , Petraglia Felice , Watts Nelson , Gotteland Jean-Pierre , Bestel Elke , Terrill Paul , Loumaye Ernest , Humberstone Andrew , Garner Elizabeth 
Published: December 2022

(Abstracted from Lancet 2022;400:896–907)
Uterine fibroids occur in 50% to 60% of women and are symptomatic in 30% of patients by causing abnormal uterine bleeding and pelvic pressure. Treatment of uterine fibroids involves surgical and radiological interventions, as well as progestogens and other medical therapies.