bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isomorphism Between Twisted q-Yangians and Affine ι Quantum Groups: Type AI
Authors: Lu Kang 
Published: November 2024

Abstract
By employing Gauss decomposition, we establish a direct and explicit isomorphism between the twisted $q$-Yangians (in R-matrix presentation) and affine $\imath $quantum groups (in current presentation) associated to symmetric pair of type AI introduced by Molev–Ragoucy–Sorba and Lu–Wang, respectively. As a corollary, we obtain a PBW-type basis for affine $\imath $quantum groups of type AI.
Characterization of blaNDM in two Escherichia coli ST1193 clinical isolates in the Gulf region
Authors: Tsui Clement Kin-Ming , Ben Abid Fatma , McElheny Christi Lee , Hamed Manal M , Perez-Lopez Andres , Omrani Ali S , Doi Yohei 
Published: November 2024

Abstract

Introduction
Escherichia coli ST1193 is an emerging high-risk clone associated with the production of plasmid-mediated CTX-type extended-spectrum β-lactamases. However, this clone has seldom been found to contain plasmids carrying carbapenemase genes. We report two epidemiologically unlinked multidrug-resistant (MDR) clinical isolates of E. coli ST1193 with plasmids harbouring NDM-type carbapenemase genes from the Gulf region.

Methods
The isolates were identified by MALDI-TOF MS and antibiotic susceptibility testing was performed using the VITEK 2/Phoenix system. A conjugation experiment was performed to assess the transferability of the resistance plasmids. Genomic DNA of both isolates was subject to Illumina sequencing; one isolate was also sequenced using Oxford Nanopore technology. Bioinformatics analyses were performed to detect antimicrobial resistance genes, and to annotate the genetic context of the NDM genes.

Results and Conclusions
Both isolates were resistant to carbapenems using phenotypic tests. Conjugation experiment confirmed that NDM-5-encoding plasmids of both strains could be transferred to the recipient cells. The completed NDM-5-encoding plasmid of E. coli isolate FQ71 was highly similar to several plasmids from ST410 isolates in the NCBI database. Genomic analysis revealed the presence of transposase genes and transposons in the flanking regions of the NDM genes in the plasmids. Since carbapenems constitute first-line agents for the treatment of serious infections caused by ESBL producers, E. coli ST1193 isolates co-producing ESBL and NDM-type carbapenemases represent a serious challenge for antimicrobial stewardship and infection control programmes.
Targetable molecular algorithm and training platform development for the treatment of non-small cell lung cancer
Authors: Bhuvaneshwar Krithika , Kim Chul , Parikh Kaushal , Reuss Joshua E , Bencheqroun Camelia , Agraharam Anvitha G , Munir Ayesha , Alaoui Adil , Gusev Yuriy , Veytsman Irina G 
Published: November 2024

Abstract

Background and Introduction
Over the last decade, treatment of patients with advanced non-small cell lung cancer (NSCLC) has become dependent on tissue and/or blood biomarkers to guide treatment decisions. Timely access to comprehensive biomarker and tumor signature information is crucial for diagnostic testing. With the rapid development and implementation of complex biomarker testing, comprehensive molecular profiling with in-depth analysis of DNA, RNA, and proteins can be easily performed. Initial data from the MedStar Health system showed considerable disparities in the use of next generation sequencing (NGS) between hospitals, and there is a clear need to improve education and understanding regarding which cases are appropriate for NGS, as well as the use of protocols to make those decisions in an expeditious manner.

Materials and Methods
Clinical pathways are systems-based tools that aim to create greater transparency around care decision making, therapeutic selection, and care delivery. They enhance quality and efficiency by reducing non-value-added intra-provider variability in care. We aimed to create a comprehensive clinical pathway system, the Targetable Molecular Algorithm (TMA), to increase the understanding and use of NGS in NSCLC by physicians in training, oncology nurse navigators, nurse practitioners, and general oncologists.

Discussion
We provide an overview of the implementation of the platform along with navigation guide. A realistic case study—a typical clinical workflow for a patient requiring NGS testing with an EGFR mutation—is also reviewed, demonstrating how the TMA platform can be applied. Additionally, we highlight the importance of the resource, and discuss its strengths, weaknesses, and potential future applications.

Results and Conclusion
This new and innovative pathway system will make decision-making easier for clinicians trying to understand the appropriate tests and treatment algorithms for their patients. Our aim is to increase the appropriate and timely use of NGS among health-system providers with the hope that this system will empower physicians to provide better care by providing a quick, simple, user-friendly tool for comprehensive patient care.
A landmark federal interagency collaboration to promote data science in health care: Million Veteran Program-Computational Health Analytics for Medical Precision to Improve Outcomes Now
Authors: Justice Amy C , McMahon Benjamin , Madduri Ravi , Crivelli Silvia , Damrauer Scott , Cho Kelly , Ramoni Rachel , Muralidhar Sumitra 
Published: November 2024

Abstract

Objectives
In 2016, the Department of Veterans Affairs (VA) and the Department of Energy (DOE) established an Interagency Agreement (IAA), the Million Veteran Program-Computational Health Analytics for Medical Precision to Improve Outcomes Now (MVP-CHAMPION) research collaboration.

Materials and Methods
Oversight fell under the VA Office of Research Development (VA ORD) and DOE headquarters. An Executive Committee and 2 senior scientific liaisons work with VA and DOE leadership to optimize efforts in the service of shared scientific goals. The program supported centralized data management and genomic analysis including creation of a scalable approach to cataloging phenotypes. Cross-cutting methods including natural language processing, image processing, and reusable code were developed.

Results
The 79.6 million dollar collaboration has supported centralized data management and genomic analysis including a scalable approach to cataloging phenotypes and launched over 10 collaborative scientific projects in health conditions highly prevalent in veterans. A ground-breaking analysis on the Summit and Andes supercomputers at the Oak Ridge National Laboratory (ORNL) of the genetic underpinnings of over 2000 health conditions across 44 million genetic variants which resulted in the identification of 38 270 independent genetic variants associating with one or more health traits. Of these, over 2000 identified associations were unique to non-European ancestry. Cross-cutting methods have advanced state-of-the-art artificial intelligence (AI) including large language natural language processing and a system biology study focused on opioid addiction awarded the 2018 Gordon Bell Prize for outstanding achievement in high-performance computing. The collaboration has completed work in prostate cancer, suicide prevention, and cardiovascular disease, and cross-cutting data science. Predictive models developed in these projects are being tested for application in clinical management.

Discussion
Eight new projects were launched in 2023, taking advantage of the momentum generated by the previous collaboration. A major challenge has been limitations in the scope of appropriated funds at DOE which cannot currently be used for health research.

Conclusion
Extensive multidisciplinary interactions take time to establish and are essential to continued progress. New funding models for maintaining high-performance computing infrastructure at the ORNL and for supporting continued collaboration by joint VA-DOE research teams are needed.
Exploring optimal folic acid supplementation levels for lactating-pregnant rabbit does with different litter size
Authors: Song Bing , Yu Lin , Liu Xiaoxiao , Goswami Naqash , Gong Ruiguang , Ren Zhanjun 
Published: November 2024

Abstract
The lactation-pregnancy overlap in the industrialized 49-d breeding model increases nutritional demands for lactating-pregnant rabbit does. This study examined the effects of folic acid (FA) on the production performance and intestinal microflora of does with different litter sizes (LS, or number of kits). A total of 144 third-parity Hyplus does, aged 11 mo and weighing approximately 5.00 ± 0.07 kg, were divided into 4 treatment groups: control group (basal diet) and FA groups (basal diet + 15, 30, and 45 mg/kg FA). Does with LS of 5, 7, and 9 were selected after weaning. Our findings revealed that 1) Increased FA supplementation initially increased and then decreased the pre-lactation body weight of 21-d-old kits and prolactin (PRL) level of lactating does, while showing an inverse trend for estrogen (E) level of does. Increased LS significantly (P &lt; 0.05) correlated with reduced milk yield of does. There was a significant (P &lt; 0.05) interaction between FA and LS affecting PRL, E, growth hormone levels of does, and the pre-lactation body weight of 21-d-old kits; 2) Increased FA supplementation initially increased and then decreased the post-lactation body weight of 21-d-old and 35-d-old kits, elevated plasma FA (PFA) level of lactating-pregnant does, and significantly (P &lt; 0.05) impacted the pregnancy rate of does. Increased LS was associated with reduced post-lactation body weight in 21-d-old and 35-d-old kits (P &lt; 0.05). There was a significant (P &lt; 0.05) interaction between FA and LS affecting plasma insulin-like growth factor-1 (IGF-1), homocysteine (HCY), PFA levels of does, the post-lactation body weight of 21-d-old kits, and weaning body weight of 35-d-old kits; and 3) FA supplementation promoted the growth of Ruminococcaceae and Rikenellaceae_RC9_gut_group in the feces of lactating-pregnant does, as well as the proliferation of Lachnospiraceae_NK4A136_group in the feces of pregnant does, suggesting enhanced anti-inflammatory properties and improved crude fiber breakdown. In summary, FA supplementation improved conception rates, regulated lactation-related hormone synthesis and secretion, increased body weight of 21-d-old kits, and enhanced intestinal anti-inflammatory functions.
Cost-effectiveness of radiofrequency echographic multi-spectrometry for the diagnosis of osteoporosis in the United States
Authors: Reginster Jean-Yves , Silverman Stuart L , Alokail Majed , Al-Daghri Nasser , Hiligsmann Mickael 
Published: November 2024

Abstract
Radiofrequency echographic multi-spectrometry (REMS) is an innovative, non-ionizing diagnostic technique that has shown high accuracy and precision, making it a promising alternative to DXA for osteoporosis diagnosis in clinical settings. With economic considerations playing an increasingly crucial role in healthcare decisions, this study aims to evaluate the cost-effectiveness and economic impact of improved osteoporosis diagnosis using REMS followed by treatment in the United States. A microsimulation-based Markov model was constructed to estimate the cost per quality-adjusted life year (QALY) gained (in US$2022) for REMS followed by treatment vs no diagnosis and treatment in US women aged 50 yr and older with osteoporosis. Women were categorized as high risk (receiving alendronate monotherapy for 5 yr) or very high risk (receiving an 18-mo course of anabolic treatment, abaloparatide, followed by 5 yr of alendronate). The study evaluated 2 medication adherence scenarios: one assuming full adherence to treatment and the other reflecting real-world adherence. The results indicate that REMS followed by treatment is associated with improved health outcomes, including more QALYs and fewer fractures, and reduced fracture-related costs compared to no diagnosis and treatment. The incremental cost-effectiveness ratio of REMS was estimated at $33 891 and $49 198 per QALY gained, under the full adherence and real-world adherence scenarios, respectively. These values are below the US cost-effectiveness threshold of $100 000 per QALY. Moreover, a 5% increase in the diagnosis and treatment of women over 50 yr at high and very high risk of fractures using REMS is projected to save approximately 30 000 life yr, 43 500 QALYs, and prevent 100 000 fractures over a lifetime under real-world medication adherence. In conclusion, this study suggests that REMS is a cost-effective strategy for the diagnosis and management of osteoporosis in US women, offering substantial potential economic benefits and improved health outcomes.
Three-dimensional hullform reconstruction from two-dimensional drawings based on image processing techniques
Authors: Park Jun-Su , Ham Seung-Ho 
Published: November 2024

Abstract
Repair shipyards sometimes need three-dimensional geometry for repairs and retrofits. However, they often create models manually from two-dimensional drawings provided by ship owners. In this case, human error leads to inaccuracies, making the process time-consuming and laborious. Therefore, there is a need for research on efficient three-dimensional hullform reconstruction from two-dimensional drawings. This study proposed a method to automatically extract points from two-dimensional lines and visualize them in three dimensions. The proposed method consists of three steps. The first step is a point extraction through image processing, which uses a starting point search algorithm to access overlapping or intersection lines and extracts the points on the lines in the drawing by searching for paths between the starting point and the end point entered by the user. The second step is the transformation of the extracted data, which transforms the points based on pixel coordinate into 3D points through coordinate transformation and scaling by utilizing the stored line data and three-dimensional coordinate information. The last step is to visualize the transformed data as a real three-dimensional model with point visualization. This study demonstrates that the proposed method can be effectively utilized by detecting two-dimensional lines and reconstructing the hullform in three dimensions.
A genome assembly for the California endemic liverwort Calasterella californica
Authors: González-Ramírez Ixchel S , Escalona Merly , Miller Courtney , Chumchim Noravit , Marimuthu Mohan P A , Nguyen Oanh , Song Michael J , Mishler Brent D 
Published: November 2024

Abstract
Calasterella californica belongs to a monotypic genus of liverworts endemic to the west coast of North America, primarily distributed in California. This dioicous species occurs in a variety of ecosystems from deserts to redwood forests; little is known about how this species is adapted to live in those seemingly contrasting environments. In this paper, we report on the assembly of the nuclear genome of C. californica. As part of the California Conservation Genomics Project (CCGP), we used Pacific Biosciences HiFi long-read sequencing data to produce a de novo assembly that consists of 772 contigs, with a total length of 517 Mbp and a BUSCO complete score of 95%. Calasterella californica is only the sixth species of liverworts—a group with more than 7,200 described species—to have a nuclear reference genome. The availability of this reference genome will facilitate the study of the unique features of C. californica and other liverworts, pave the road towards a comparative understanding of liverwort genomes, and add an important starting point for studies of the geographic variation of this species within the CCGP project.
The invasive spongy moth, Lymantria dispar japonica (Lepidoptera: Erebidae) in South Korea
Authors: Jeong Na Ra , Inoue Maki N , Lee Sang-Bin , Nam Youngwoo , Lee Wonhoon 
Published: November 2024

Abstract
Lymantria dispar japonica (Lepidoptera: Erebidae), commonly known as the spongy moth, is predominant and widely distributed in Japan. However, between 2021 and 2023, L. d. japonica was simultaneously discovered in several regions of South Korea. Lymantria dispar japonica was distinguished from Lymantria dispar asiatica on the basis of adult forewing length and wing patterns and their genetic distance ranged from 0.065% to 0.588% in the COI gene. Here, we provide a description of this subspecies and details of its sampling locations. The discovery of L. d. japonica is of great importance to the forests of South Korea. Therefore, this study presents an opportunity to investigate new strategies for advancing the efforts to detect and eliminate threats related to this pest in the future.
Role of the basic leucine zipper transcription factor BATF2 in modulating immune responses and inflammation in health and disease
Authors: van der Geest Rick , Lee Janet S 
Published: November 2024

Abstract
BATF2 is a transcription factor known to exhibit tumor-suppressive activity in cancer cells. Within recent years, however, BATF2 has also emerged as an important transcriptional regulator of the immune system. Through its immunomodulatory function, BATF2 has been implicated in a variety of (patho)physiological processes, including host defense against infection, antitumor immunity, and maintenance of tissue inflammatory homeostasis. Below, we discuss recent literature that has provided insight into the role of BATF2 as a transcriptional regulator of immune responses in health and disease, including the cell types that express BATF2, the different diseases in which the immunomodulatory effects of BATF2 have been shown to play a role, and the molecular mechanisms through which BATF2 is thought to exert those effects. In doing so, we highlight that the immunological effects of BATF2 are highly context dependent, and we point out the overlap between the mechanisms of action of BATF2 in infectious and noninfectious diseases. We also discuss areas of interest for future research, the clinical relevance of better understanding BATF2 function, and potential strategies for therapeutic modulation of BATF2.
Development of a pharmacokinetic/pharmacodynamic evaluation model for osteomyelitis and usefulness of tedizolid as an alternative to vancomycin against MRSA osteomyelitis
Authors: Liu Xiaoxi , Enoki Yuki , Taguchi Kazuaki , Matsumoto Kazuaki 
Published: November 2024

Abstract

Objectives
This study aimed to develop a suitable osteomyelitis model for pharmacokinetic/pharmacodynamic (PK/PD) evaluation and to investigate the target PK/PD values of vancomycin and tedizolid against methicillin-resistant Staphylococcus aureus (MRSA) osteomyelitis.

Methods
An osteomyelitis model was established by implanting an MRSA-exposed sterilized suture in the tibia of normal mice and mice with cyclophosphamide-induced neutropenia. The suitability of the osteomyelitis mouse model for PK/PD evaluation was assessed using vancomycin as an indicator. The target PK/PD values for tedizolid were determined using this model.

Key findings
In neutropenic mice, to achieve a static effect and 1 log10 kill against MRSA, the ratios of the area under the free drug concentration–time curve for 24 h to the minimum inhibitory concentration (fAUC24/MIC) of vancomycin were 91.29 and 430.03, respectively, confirming the validity of the osteomyelitis model for PK/PD evaluation. In immunocompetent mice, the target fAUC24/MIC values of tedizolid for achieving a static effect and 1 log10 kill against MRSA were 2.40 and 49.20, respectively. Additionally, only a 0.28 log10 kill was achieved in neutropenic mice with 20 times the human equivalent dose of tedizolid.

Conclusions
In patients with restored immunity, tedizolid can potentially be used as an alternative to intravenous vancomycin therapy.
Atypical presentation of Wilms’ tumor in an adult: a case report and diagnostic considerations
Authors: Aaboudech Taha Yassine , Derqaoui Sabrine , Znati Kaoutar , Zouaidia Fouad , Ibrahimi Ahmed , Mzouri Khalid , Nouini Yassine , Bernoussi Zakia , Jahid Ahmed 
Published: November 2024

Abstract
Wilms’ tumor (WT), while common in pediatric populations, is exceedingly rare in adults, accounting for only 0.5% of renal neoplasms. This report describes a 44-year-old patient diagnosed with stage II WT in the left kidney who underwent a radical nephrectomy, illustrating the diagnostic challenges encountered in adult cases. The patient’s symptoms and radiological findings were non-specific, complicating early detection. Histopathological analysis revealed a mixed-type tumor with a 60% blastemal component. Accurate histopathological evaluation is crucial for determining prognosis and guiding treatment. This case is rare due to its early-stage (stage II) diagnosis in an adult, which is almost unheard of in the literature, where most adult WT are advanced. This highlights the critical need for heightened clinical suspicion, early diagnostic efforts, and pivotal surgery-based treatment to improve outcomes in such rare cases.
A novel, double Limberg flap repair for recurrent pilonidal sinus disease
Authors: Leung Emily , Finlayson Andrew 
Published: November 2024

Abstract
Pilonidal sinuses are chronic inflammation and/or infection of the intergluteal region. Recurrent disease is common and is a source of significant morbidity for affected patients. We present a case of an eighteen-year-old male with extensive recurrent pilonidal disease. A novel technique of a double Limberg flap repair was used, with the vertical axes of each flap positioned to optimise wound tension. The cranio-caudal length of the disease in the natal cleft would have resulted in a large amount of excised normal tissue laterally if a single Limberg flap was considered. To avoid this, we used two Limberg flaps over the craniocaudal length to minimise the laterally excised tissue. The patient made an uneventful recovery with no recurrence at 3 months follow-up. This technique demonstrates the flexibility of the Limberg flap, and that a double flap may be successfully used in extensive disease.
Squamous cell carcinoma arising from anal fistula in an HIV-positive individual: a case report
Authors: Yang Jie , Zhang Liman , Wang Qiang , Wang Lili 
Published: November 2024

Abstract
Chronic anal fistula represents a prevalent form of perianal disease that frequently originates from perianal infection. Specifically, perianal abscesses that are inadequately or improperly treated are susceptible to the development of chronic anal fistulas. In HIV-infected individuals, an impaired immune system significantly diminishes the body’s capacity to combat infections and inflammation, thereby complicating the healing process of anal fistulas. Moreover, the impact of HIV on tissue repair results in a markedly prolonged healing process for wounds and tissue damage in these patients, exacerbating the difficulty in anal fistula resolution. Chronic anal fistulas that remain untreated for extended periods not only severely impair the patient’s quality of life but also pose an increased risk of malignant transformation.