bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation of Applied Linguistics in the Global South Context of Bangladesh: Researcher Agency, Imagination, and North-South Cooperation
Authors: Hamid M Obaidul , Sultana Shaila , Roshid Mohammod Moninoor 
Published: June 2024

AbstractThis article examines the transformation of applied linguistics knowledge production in the Global South taking postcolonial Bangladesh as a case. In the 1990s, one could not locate even a dozen applied linguistics articles in international journals authored by Bangladeshi researchers. However, in about two decades, Bangladeshi researchers can claim hundreds of journal articles, book chapters, monographs, and edited volumes. Drawing on bibliometric data and autoethnography, this article seeks to document a new dawn in applied linguistics research in Bangladesh complemented by researchers’ engagement in Southern epistemological thinking in a decolonial spirit. While demonstrating the role of researcher agency and imagination in this transformation, we also highlight the role of North-South interaction and collaboration. We argue that despite the hegemony of Eurocentric views underpinning language, epistemology and geopolitics of knowledge, there may be hope for Southern applied linguists to decolonize their research imagination and bring disciplinary changes in line with Southern perspectives to make the world a better place for the global community.
A global initiative on addressing bioinformatics’ grand challenges
Authors: Khan Asif M , Işık Esra Büşra , Tan Tin Wee 
Published: June 2024

Abstract
The Bioinformatics Grand Challenges Consortium (BGCC) is a collaborative effort to address the most pressing challenges in bioinformatics. Initially focusing on education and training, the consortium successfully defined seven key grand challenges and is actively developing actionable solutions for these challenges. Building on this foundation, the BGCC plans to broaden its focus to include additional grand challenges in emerging areas.
SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts
Authors: Ju Nianqiao , Liu Jiawei , He Qixin 
Published: June 2024

Abstract

Motivation
Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology.

Results
We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets.

Availability and Implementation
The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.
Acceleration of uterine 3D T2-weighted imaging by compressed SENSE—a multicentre study
Authors: Song Qingling , Ma Changjun , Tian Shifeng , Meng Xing , Chen Lihua , Wang Nan , Song Qingwei , Lu Shan , Liu Dengping , Gui Haiyan , Chen Honghao , Lin Liangjie , Xu Xiaofang , Wang Jiazheng , Liu Ailian 
Published: June 2024

Abstract

Objectives
To find the optimal acceleration factor (AF) of the compressed SENSE (CS) technique for uterine isotropic high-resolution 3D T2-weighted imaging (3D-ISO-T2WI).

Methods
A total of 91 female volunteers from the First Affiliated Hospital of Dalian Medical University, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, and The Fourth Hospital of Harbin were recruited. A total of 44 volunteers received uterus sagittal 3D-ISO-T2WI scans on 3.0T MRI device with different CS AFs (including SENSE3, CS3, CS4, CS5, CS6, and CS7), 51 received 3D-ISO-T2WI scans with different degrees of fat suppression (none, light, moderate, and severe), while 4 volunteers received both series of scans. Image quality was subjectively evaluated with a 3-point scoring system. Junction zone signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and myometrial SNR were also calculated. Intraclass correlation coefficients were used to analyse the consistency of the measurement results by 2 observers. Analysis of variance test or Friedman rank sum test was used to compare the differences in subjective scores, SNR, and CNR under different AFs/different degrees of fat suppression.

Results
Images by AFs of CS3, CS4, and CS5 had the highest SNR and CNR. Among them, CS5 had the shortest scan time. CS5 also had one of the highest subjective scores. There was no significant difference in SNR and CNR among images acquired with different degrees of fat suppression. Also, images with moderate fat suppression had the highest subjective scores.

Conclusion
The CS5 combined with moderate fat suppression is recommended for routine female pelvic 3D-ISO-T2WI scan.

Advances in knowledge
The CS5 has the highest image quality and has the shortest scan time, which is the best AF. Moderate fat suppression has the highest subjective scores. The CS5 and moderate fat suppression are the best combination for a female pelvic 3D-ISO-T2WI scan.
Early short-term hypoxia promotes epidermal cell migration by activating the CCL2-ERK1/2 pathway and epithelial–mesenchymal transition during wound healing
Authors: Jin Linbo , Zhou Shiqi , Zhao Shihan , Long Junhui , Huang Zhidan , Zhou Junli , Zhang Yiming 
Published: June 2024

Abstract

Background
Due to vasculature injury and increased oxygen consumption, the early wound microenvironment is typically in a hypoxic state. We observed enhanced cell migration ability under early short-term hypoxia. CCL2 belongs to the CC chemokine family and was found to be increased in early hypoxic wounds and enriched in the extracellular signal-regulated kinase (ERK)1/2 pathway in our previous study. However, the underlying mechanism through which the CCL2-ERK1/2 pathway regulates wound healing under early short-term hypoxia remains unclear. Activation of epithelial–mesenchymal transition (EMT) is a key process in cancer cell metastasis, during which epithelial cells acquire the characteristics of mesenchymal cells and enhance cell motility and migration ability. However, the relationship between epithelial cell migration and EMT under early short-term hypoxia has yet to be explored.

Methods
HaCaT cells were cultured to verify the effect of early short-term hypoxia on migration through cell scratch assays. Lentiviruses with silenced or overexpressed CCL2 were used to explore the relationship between CCL2 and migration under short-term hypoxia. An acute full-thickness cutaneous wound rat model was established with the application of an ERK inhibitor to reveal the hidden role of the ERK1/2 pathway in the early stage of wound healing. The EMT process was verified in all the above experiments through western blotting.

Results
In our study, we found that short-term hypoxia promoted cell migration. Mechanistically, hypoxia promoted cell migration through mediating CCL2. Overexpression of CCL2 via lentivirus promoted cell migration, while silencing CCL2 via lentivirus inhibited cell migration and the production of related downstream proteins. In addition, we found that CCL2 was enriched in the ERK1/2 pathway, and the application of an ERK inhibitor in vivo and in vitro verified the upstream and downstream relationships between the CCL2 pathway and ERK1/2. Western blot results both in vivo and in vitro demonstrated that early short-term hypoxia promotes epidermal cell migration by activating the CCL2-ERK1/2 pathway and EMT during wound healing.

Conclusions
Our work demonstrated that hypoxia in the early stage serves as a stimulus for triggering wound healing through activating the CCL2-ERK1/2 pathway and EMT, which promote epidermal cell migration and accelerate wound closure. These findings provide additional detailed insights into the mechanism of wound healing and new targets for clinical treatment.
Quantum Cluster Algebras and 3D Integrability: Tetrahedron and 3D Reflection Equations
Authors: Inoue Rei , Kuniba Atsuo , Terashima Yuji 
Published: June 2024

Abstract
We construct a new solution to the tetrahedron equation and the three-dimensional (3D) reflection equation by extending the quantum cluster algebra approach by Sun and Yagi concerning the former. We consider the Fock–Goncharov quivers associated with the longest elements of the Weyl groups of type $A$ and $C$, and investigate the cluster transformations corresponding to changing a reduced expression into a “most distant” one. By devising a new realization of the quantum $y$-variables in terms of $q$-Weyl algebra, the solutions are extracted as the operators whose adjoint actions yield the cluster transformations of the quantum $y$-variables. Explicit formulas of their matrix elements are also derived for some typical representations.
In Search of Effective Corporate Grievance Mechanisms: Can Mandatory Due Diligence Laws be a Progressive Force?
Authors: Harrison James , Wielga Mark , Parejo Margarita 
Published: June 2024

Abstract
Mandatory human rights due diligence (mHRDD) laws are currently being proposed and/or implemented in countries around the world. Increasingly, these laws place obligations on corporations to establish or participate in corporate grievance mechanisms (CGMs). CGMs have the potential to ensure that rightsholders are empowered to hold corporations accountable for their human rights performance. But our limited knowledge of how CGMs operate indicates that many are not producing results that are valuable for workers and communities. CGM provisions in mHRDD laws in Germany and Norway, and draft laws produced in the European Union and Brazil are rudimentary and unlikely to produce better-performing CGMs. Analysis of Norwegian mHRDD corporate reporting identifies that many corporations fail to understand the basic elements of an effective CGM. The article therefore argues that requirements for CGMs in mHRDD laws will only be a progressive move if such laws also demand disclosure of information that empowers national authorities, as well as civil society actors and researchers, to scrutinize CGMs to ensure they are effective. Disclosure requirements must speak to three issues: (1) how accessible CGMs are, (2) the way complaints are handled, and (3) the remedies provided to rightsholders. If, as a result of scrutiny of this data, mHRDD laws can produce well-functioning CGMs, this could lead to rightsholder concerns becoming more central to due diligence processes, potentially addressing cosmetic compliance with due diligence obligations.
Ground beetle movement is deterred by habitat edges: a mark-release-recapture study on the effectiveness of border crops in an agricultural landscape
Authors: Anderson Magdeline E , Harman Rachel R , Kim Tania N 
Published: June 2024

Abstract
Border crops can increase beneficial insect biodiversity within agricultural fields by supplementing insects with food and nesting resources. However, the effectiveness of border crops relies on insect movement between adjacent habitats and some insects might consider habitat boundaries as barriers. Therefore, understanding insect movement between habitats is needed to determine the effectiveness of border crops for ecosystem services such as pest control within agricultural habitats. Our objective was to compare ground beetle (Coleoptera: Carabidae) movement across soybean plots that were bordered by corn and grassland habitat to determine whether habitat boundaries were considered barriers of movement to predatory beetles. Using a grid of pitfall traps within these habitats, we conducted a mark, release, and recapture experiment to track and evaluate ground beetle movement patterns. We found that ground beetles stayed in the habitat of their release and that movement between habitats, despite the type of bordering habitat or type of edge, was uncommon. We also found that long-distance movement was rare as most beetles moved less than 5 m (regardless of release or recaptured habitat) and movement was perpendicular to habitat edges. These results suggest that any edge habitat, including agricultural–agricultural boundaries and natural–agricultural boundaries, are likely barriers to ground beetle movement. Therefore, in order for border crops to be effective in pest management by ground beetles, making habitat edges more permeable, especially using techniques such as edge softening, could promote cross-habitat movement and ultimately contribute to natural pest control in agricultural systems.
Wakefield’s Harm-Based Critique of the Biostatistical Theory
Authors: Boorse Christopher 
Published: June 2024

Abstract
Jerome Wakefield criticizes my biostatistical analysis of the pathological—as statistically subnormal biological part-functional ability relative to species, sex, and age—for its lack of a harm clause. He first charges me with ignoring two general distinctions: biological versus medical pathology, and disease of a part versus disease of a whole organism. He then offers 10 counterexamples that, he says, are harmless dysfunctions but not medical disorders. Wakefield ends by arguing that we need a harm clause to explain American psychiatry’s 1973 decision to declassify homosexuality. I reply, first, that his two distinctions are philosophic fantasies alien to medical usage, invented only to save his own harmful-dysfunction analysis (HDA) from a host of obvious counterexamples. In any case, they do not coincide with the harmless/harmful distinction. In reality, medicine admits countless chronic diseases that are, contrary to Wakefield, subclinical for most of their course, as well as many kinds of typically harmless skin pathology. As for his 10 counterexamples, no medical source he cites describes them as he does. I argue that none of his examples contradicts the biostatistical analysis: all either are not part-dysfunctions (situs inversus, incompetent sperm, normal-flora infection) or are indeed classified as medical disorders (donated kidney, Typhoid Mary’s carrier status, latent tuberculosis or HIV, cherry angiomas). And if Wakefield’s HDA fits psychiatry, the fact that it does not fit medicine casts doubt on psychiatry’s status as a medical specialty.
(016) SALVAGE VAGINOPLASTY WITH SINGLE-PORT ROBOT ASSISTED TUBULARIZED URACHUS PERITONEAL HINGE FLAP: TECHNIQUE HIGHLIGHTS, OUTCOMES, AND AN EVIDENCE-BASED PROPOSAL FOR HOW AND WHEN TO USE (AND NOT USE!) PERITONEUM WITH VAGINOPLASTY
Authors: Sandhu S , Smith S , Mallavarapu S , Stelmar J , Yuan N , Gupta A , Kim H , Garcia M 
Published: June 2024

Abstract

Introduction
Vaginoplasty is a commonly performed genital gender affirming surgery. Currently there are two published techniques that describe using peritoneal tissue to contribute to the necessary tissue to line the neovaginal canal: The modified Davydov technique, first described in 2019 by Zhao et al, and the Tubularized Urachus-Peritoneal Hinge Flap, described by Garcia et al in 2022. Today many providers use the Davydov technique at time of primary vaginoplasty, while other providers argue that use of peritoneum is not necessary at the time of primary vaginoplasty. We use the urachus flap only for salvage surgery.

Objective
Herein, we report our technical innovations related to the urachus hinge flap, and our clinical outcomes at 1.5 years post-op. We also review the literature to determine whether there is evidence to support using peritoneum at time of primary vaginoplasty.

Methods
We review our single-port robot assisted urachus hinge flap technique to augment neovaginal depth after primary vaginoplasty complicated by loss of vaginal depth. We also review technical innovations to maximize neovaginal depth with primary vaginoplasty using only penile and scrotal skin. We present our literature review, and posit a theory that explains why, regardless of PV technique, mean neovaginal depth is 11-13 cm in all series.

Results
Our mean neovaginal depth after our salvage urachus hinge flap technique is 12.5 cm (range 11-14.2) at 409 days post-op. This is comparable to the Davydov PV technique. With primary vaginoplasty using only penile and scrotal skin, our mean depth is 12.5 cm, which is &gt; other series using only penile/scrotal skn, and comparable to series that also use peritoneum. We use video to show how, with the Davydov technique, rectum and bowel are pulled deep into the pelvis post-op, which increases risk of bowel injury at time of salvage surgery with intestine.

Conclusions
By the techniques described herein, in our hands, with primary vaginoplasty using only penile and scrotal skin we achieve vaginal depth comparable to techniques that augment with peritoneum. We suggest that peritoneum is rarely to never necessary at primary vaginoplasty, and should be reserved for use as a salvage surgery if and when it is needed. We also suggest that the urachus flap is a safer alternative to the Davydov technique if and when PV fails and salvage intestinal vaginoplasty must be undertaken.

Disclosure
No.
RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin
Authors: Palek Matous , Palkova Natalie ,   consortium CZECANCA, Cerna Marta , Horackova Klara , Hovhannisyan Milena , Janatova Marketa , Jelinkova Sandra , Nehasil Petr , Soukupova Jana , Stastna Barbora , Zemankova Petra , Foretova Lenka , Machackova Eva , Krutilkova Vera , Tavandzis Spiros , Cerna Leona , Chvojka Stepan , Koudova Monika , Havranek Ondrej , Novotny Jan , Vesela Kamila , Vocka Michal , Hruskova Lucie , Michalovska Renata , Schwetzova Denisa , Vlckova Zdenka , Cerna Monika , Hejnalova Marketa , Jedlickova Nikol , Subrt Ivan , Zavoral Tomas , Kosarova Marcela , Vacinova Gabriela , Janikova Maria , Kratochvilova Romana , Curtisova Vaclava , Vrtel Radek , Scheinost Ondrej , Duskova Petra , Stranecky Viktor , Kleiblova Petra , Kleibl Zdenek , Macurek Libor 
Published: June 2024

Abstract
RAD18 is an E3 ubiquitin ligase that prevents replication fork collapse by promoting DNA translesion synthesis and template switching. Besides this classical role, RAD18 has been implicated in homologous recombination; however, this function is incompletely understood. Here, we show that RAD18 is recruited to DNA lesions by monoubiquitination of histone H2A at K15 and counteracts accumulation of 53BP1. Super-resolution microscopy revealed that RAD18 localizes to the proximity of DNA double strand breaks and limits the distribution of 53BP1 to the peripheral chromatin nanodomains. Whereas auto-ubiquitination of RAD18 mediated by RAD6 inhibits its recruitment to DNA breaks, interaction with SLF1 promotes RAD18 accumulation at DNA breaks in the post-replicative chromatin by recognition of histone H4K20me0. Surprisingly, suppression of 53BP1 function by RAD18 is not involved in homologous recombination and rather leads to reduction of non-homologous end joining. Instead, we provide evidence that RAD18 promotes HR repair by recruiting the SMC5/6 complex to DNA breaks. Finally, we identified several new loss-of-function mutations in RAD18 in cancer patients suggesting that RAD18 could be involved in cancer development.
ENL reads histone β-hydroxybutyrylation to modulate gene transcription
Authors: Chen Chen , Chen Cong , Wang Aiyuan , Jiang Zixin , Zhao Fei , Li Yanan , Han Yue , Niu Ziping , Tian Shanshan , Bai Xue , Zhang Kai , Zhai Guijin 
Published: June 2024

Abstract
Histone modifications are typically recognized by chromatin-binding protein modules (referred to as ‘readers’) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap should be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark, and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation led to the suppressed expression of genes such MYC that drive cell proliferation. Together, our work offered a chemoproteomics approach and identified ENL as a novel histone β-hydroxybutyrylation effector that regulates gene transcription, providing new insight into the regulation mechanism and function of histone Kbhb.
Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome
Authors: Wang Shuai , Jiang Yiqi , Che Lijia , Wang Ruo Han , Li Shuai Cheng 
Published: June 2024

Abstract
Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%—verified by Nanopore data—across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.