bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era
Authors: Špačková Anna , Vávra Ondřej , Raček Tomáš , Bazgier Václav , Sehnal David , Damborský Jiří , Svobodová Radka , Bednář David , Berka Karel 
Published: November 2023

Abstract
ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels—tunnels and pores—within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement the data obtained using original MOLE tool for detection and analysis of protein tunnels and pores. Secondly, we added tunnels starting from cofactors within the AlphaFill database to enlarge the scope of the database to protein models based on Uniprot. This has enlarged available channel annotations ∼4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. length and radius, and physico-chemical properties based on channel-lining amino acids. The stored data are interlinked with the available UniProt mutation annotation data. ChannelsDB 2.0 provides an excellent resource for deep analysis of the role of biomacromolecular tunnels and pores. The database is available free of charge: https://channelsdb2.biodata.ceitec.cz.
DriverDBv4: a multi-omics integration database for cancer driver gene research
Authors: Liu Chia-Hsin , Lai Yo-Liang , Shen Pei-Chun , Liu Hsiu-Cheng , Tsai Meng-Hsin , Wang Yu-De , Lin Wen-Jen , Chen Fang-Hsin , Li Chia-Yang , Wang Shu-Chi , Hung Mien-Chie , Cheng Wei-Chung 
Published: November 2023

Abstract
Advancements in high-throughput technology offer researchers an extensive range of multi-omics data that provide deep insights into the complex landscape of cancer biology. However, traditional statistical models and databases are inadequate to interpret these high-dimensional data within a multi-omics framework. To address this limitation, we introduce DriverDBv4, an updated iteration of the DriverDB cancer driver gene database (http://driverdb.bioinfomics.org/). This updated version offers several significant enhancements: (i) an increase in the number of cohorts from 33 to 70, encompassing approximately 24 000 samples; (ii) inclusion of proteomics data, augmenting the existing types of omics data and thus expanding the analytical scope; (iii) implementation of multiple multi-omics algorithms for identification of cancer drivers; (iv) new visualization features designed to succinctly summarize high-context data and redesigned existing sections to accommodate the increased volume of datasets and (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identification and subgroup expression analysis. DriverDBv4 facilitates comprehensive interpretation of multi-omics data across diverse cancer types, thereby enriching the understanding of cancer heterogeneity and aiding in the development of personalized clinical approaches. The database is designed to foster a more nuanced understanding of the multi-faceted nature of cancer.
StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination
Authors: Luo Yangyang , Guo Jingjing , Wen Jianguo , Zhao Weiling , Huang Kexin , Liu Yang , Wang Grant , Luo Ruihan , Niu Ting , Feng Yuzhou , Xu Haixia , Kim Pora , Zhou Xiaobo 
Published: November 2023

Abstract
StemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/. By utilizing single-cell RNA sequencing data, StemDriver has successfully assembled a comprehensive lineage map of hematopoiesis, capturing the entire continuum from the initial formation of hematopoietic stem cells to the fully developed mature cells. Extensive exploration and characterization were conducted on gene expression features corresponding to each lineage commitment. At the current version, StemDriver integrates data from 42 studies, encompassing a diverse range of 14 tissue types spanning from the embryonic phase to adulthood. In order to ensure uniformity and reliability, all data undergo a standardized pipeline, which includes quality data pre-processing, cell type annotation, differential gene expression analysis, identification of gene categories correlated with differentiation, analysis of highly variable genes along pseudo-time, and exploration of gene expression regulatory networks. In total, StemDriver assessed the function of 23 839 genes for human samples and 29 533 genes for mouse samples. Simultaneously, StemDriver also provided users with reference datasets and models for cell annotation. We believe that StemDriver will offer valuable assistance to research focused on cellular development and hematopoiesis.
PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs
Authors: Zeng Haonan , Zhang Wenjing , Lin Qing , Gao Yahui , Teng Jinyan , Xu Zhiting , Cai Xiaodian , Zhong Zhanming , Wu Jun , Liu Yuqiang , Diao Shuqi , Wei Chen , Gong Wentao , Pan Xiangchun , Li Zedong , Huang Xiaoyu , Chen Xifan , Du Jinshi ,   The PigGTEx Consortium, Zhao Fuping , Zhao Yunxiang , Ballester Maria , Crespo-Piazuelo Daniel , Amills Marcel , Clop Alex , Karlskov-Mortensen Peter , Fredholm Merete , Li Pinghua , Huang Ruihua , Tang Guoqing , Li Mingzhou , Liu Xiaohong , Chen Yaosheng , Zhang Qin , Li Jiaqi , Yuan Xiaolong , Ding Xiangdong , Fang Lingzhao , Zhang Zhe 
Published: November 2023

Abstract
To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.
Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species
Authors: Nosková Adéla , Li Chao , Wang Xiaolong , Leonard Alexander S , Pausch Hubert , Kadri Naveen Kumar 
Published: November 2023

Abstract
The branch point sequence is a degenerate intronic heptamer required for the assembly of the spliceosome during pre-mRNA splicing. Disruption of this motif may promote alternative splicing and eventually cause phenotype variation. Despite its functional relevance, the branch point sequence is not included in most genome annotations. Here, we predict branch point sequences in 30 plant and animal species and attempt to quantify their evolutionary constraints using public variant databases. We find an implausible variant distribution in the databases from 16 of 30 examined species. Comparative analysis of variants from whole-genome sequencing shows that variants submitted from exome sequencing or false positive variants are widespread in public databases and cause these irregularities. We then investigate evolutionary constraint with largely unbiased public variant databases in 14 species and find that the fourth and sixth position of the branch point sequence are more constrained than coding nucleotides. Our findings show that public variant databases should be scrutinized for possible biases before they qualify to analyze evolutionary constraint.
Economics as intervention: Expert struggles over quantitative easing at the Bank of England
Authors: Cassar Dylan 
Published: November 2023

Abstract
How does a technocratic entity, such as a central bank, craft a key policy intervention when faced with limits to established frameworks of governance? This article explores the Bank of England’s turn to unconventional policy in 2009 drawing on a set of eighteen in-depth interviews with former members of the Monetary Policy Committee, Executive team, and staff economists, and a corpus of documents. Adopting Goffman’s ‘framing analysis’, it argues that the limits to established governance led to the temporary replacement of the New Keynesian frame with a Monetarist frame, as a result of expert struggles, with consequential outcomes on the policy intervention. As the backstage dissensus spilled over onto the frontstage, manifesting as limits to knowledge, the Bank’s ‘expert authority’ was threatened. The Bank engaged in ‘manufactured consensus’—a backstage compromise between competing frames forged into a frontstage consensus via a hybrid frame—which proved to be a fragile strategy. By throwing light on the backstage–frontstage relations of technocratic organizations, I claim that an intervention may be shaped both by internal processes as well as by the ways in which the organization seeks to handle the external demands to which those very same internal processes may give rise.
Variations in gender identity and sexual orientation of university students
Authors: Yoshida Tomoko , Matsubara Keiko , Ogata-Kawata Hiroko , Miyado Mami , Ishiwata Keisuke , Nakabayashi Kazuhiko , Hata Kenichiro , Kageyama Ikuko , Tamaoka Satoshi , Shimada Yukiko , Fukami Maki , Sasaki Shoko 
Published: November 2023

Abstract

Background
Previous studies have shown that a small percentage of people in the general population have atypical gender identity and/or sexual orientation.

Aim
This study aimed to explore variations in gender identity and sexual orientation in university students and determine genetic factors associated with these variations.

Methods
Deviations from complete gender congruence and exclusive heterosexual orientation in 736 Japanese university students were quantitatively assessed with self-assessment questionnaires. Next, we conducted genetic tests for 80 participants who showed relatively low gender identity scores and/or atypical sexual orientation. These genetic tests consisted of repeat number analysis of the androgen receptor gene (AR) and a SKAT-O: an optimal unified sequence kernel association test, which is an exome-based rare variant association study. The results of the genetic tests were compared with the Japanese reference data and the results of our 637 control samples.

Outcomes
We calculated the gender identity and sexual orientation scores of all participants and analyzed the molecular data of 80 selected participants.

Results
The gender identity scores of 736 participants were broadly distributed: only ~15% of natal males and ~5% of natal females had the maximum score that corresponds to complete gender congruence. The sexual orientation scores also varied: ~80% of natal males and ~60% of natal females showed exclusive heterosexual orientation. We found no association between gender characteristics and AR repeat numbers. The SKAT-O showed that rare damaging variants of TDRP and 3 other genes were more common in the 80 participants than in the control group.

Clinical Implications
Our data support the view that gender is a phenotypic continuum rather than a binary trait.

Strength and Limitations
This study quantitatively assessed the gender characteristics of a large cohort of university students. Moreover, we conducted systematic screening for genetic factors associated with gender variations. The weaknesses of the study were the limited analytic power of the questionnaires, the relatively small sample for molecular analyses, and incomplete clinical information and relatively advanced ages of the control group.

Conclusion
This study revealed significant variations in gender identity and sexual orientation in university students, which may be partly associated with variants in TDRP or other genes.
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains
Authors: Renner Susanne S , Scherz Mark D , Schoch Conrad L , Gottschling Marc , Vences Miguel 
Published: November 2023

Abstract
Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen’s type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.
Social Protection and Foundational Cognitive Skills during Adolescence: Evidence from a Large Public Works Program
Authors: Freund Richard , Favara Marta , Porter Catherine , Behrman Jere 
Published: November 2023

Abstract
Many low- and middle-income countries have introduced public works programs (PWPs) to fight poverty. This paper provides the first evidence that children from families who benefit from PWPs show increased foundational cognitive skills. The results, based on unique tablet-based data collected as part of a long-standing longitudinal survey, show positive associations between participation in the Productive Safety Net Programme (PSNP) in Ethiopia during childhood with long-term memory and implicit learning, and suggestive evidence for working memory. These associations appear to be strongest for children whose households were still PSNP participants in the year of data collection. Evidence suggests that the association with implicit learning may be operating partially through children's time reallocation away from unpaid labor responsibilities, while the association with long-term memory may in part be due to the program's success in remediating nutritional deficits caused by early-life rainfall shocks.
Reconstruction of Complex Anterior Chest Wall Defects: The Lasagna Technique
Authors: Baccarani Alessio , Filosso Pierluigi , Marra Caterina , De Maria Federico , Blessent Claudio Gio Francesco , Ruggiero Ciro , Pappalardo Marco , Pedone Antonio , De Santis Giorgio 
Published: November 2023

Background:
Sternal tumors are rare, comprising only 0.94% of all bone tumors, with the majority being sarcomas. An extensive composite defect is often the result of surgical resection. Reconstruction of this anatomical area is a challenge for plastic surgeons. Reconstruction must fulfil two different tasks: restoration of soft tissues and stabilization of the chest wall. Both are well defined, and many techniques have been historically proposed.

Methods:
We present the case of a 66-year-old man affected by sternal metastasis of lung non-small cell carcinoma with sarcomatoid features. After wide tumor resection, a large defect was created.

Results:
The patient underwent a complex multilayer reconstruction that combined multiple techniques: Gore DualMesh to reconstruct the pericardial plane and protect the heart muscle, omental flap to facilitate integration of the mesh, titanium bars to recreate chest wall stability, and bilateral pectoralis muscle flaps to cover hardware. This multilayer reconstruction was named the “lasagna technique.”

Conclusions:
Due to the rarity of primary malignancies of the sternum, it is difficult to standardize a therapeutic approach. For this reason, it is necessary to customize the surgical treatment by combining several techniques and materials. Our lasagna technique may be considered a valuable option in treating these complex reconstructive cases.
Hair Transplantation in the United States: A Population-based Survey of Female and Male Pattern Baldness
Authors: Knoedler Leonard , Ruppel Felix , Kauke-Navarro Martin , Obed Doha , Wu Mengfan , Prantl Lukas , Broer P. Niclas , Panayi Adriana C. , Knoedler Samuel 
Published: November 2023

Background:
Androgenetic alopecia, the most common type of hair loss, can impair the patient’s overall mental health. Although there are pharmaceutical and surgical treatments available, little is known about the public standpoint toward hair transplantation (HT).

Methods:
A sample of individuals living in the United States (n = 1000; male and female participants were equally distributed) was asked to fill out the questionnaire. The online survey was conducted in June 2022.

Results:
Most participants (42%; n = 416) were between 41 and 60 years of age. Study participants frequently reported that, with their hair loss progressing, they would not feel attractive anymore (n = 400; 40%), nor as confident as before (n = 330; 33%). Although women with minimal hair loss were willing to spend a median price of $4000 [interquartile range (IQ) IQR $1000–$5000], women with extensive hair loss were willing to spend significantly more (median = $5000; IQR $3600–$6375; P = 0.011). This was reproducible in men (P = 0.033). Although significantly fewer women considered undergoing HT (430 women versus 447 men; P < 0.001), female participants were willing to pay more for their HT compared with men (P = 0.039).

Conclusions:
Individuals living in the United States consider hair loss to impair their attractiveness and regard HT as a valuable therapeutic option. More affordable and gender-specific HT should be subject to future research work.
Umbilical Complications That Require Surgical Intervention after Gynecologic Laparoscopic Surgery
Authors: Sano Risa , Oka Aiko , Hirata Eri , Ochiai Hiroko 
Published: November 2023

Background:
In laparoscopic surgery, the trocar is often inserted through the umbilicus because of the ease of insertion and inconspicuous postoperative scar formation. However, postoperative complications that require plastic surgical intervention may occur to the umbilicus.

Methods:
We reviewed 14 patients who received plastic surgery for umbilical issues following gynecologic laparoscopic surgery in our department from January 2015 to September 2021.

Results:
Most complications requiring umbilical surgery post gynecologic laparoscopic surgery include local infections, scar contractures, ectopic endometriosis, and umbilical necrosis. Mass resection and umbilical formation procedures were performed under general or local anesthesia. After a follow-up period of 6 months following surgery, no incidences of tumor development or recurrence of infection were seen, and the hypertrophic scar at the wound site gradually healed after the complete removal of the tumor and adequate suturing. Pathologically, 90% of the cases with keloid-like collagen disorder had concomitant inflammatory diseases such as epidermal cysts and abscesses.

Conclusions:
The majority of umbilical complications associated with laparoscopic surgery were predicted to be due to implantation of epithelial and tumor components during laparoscopic surgery and delayed postoperative inflammation. Therefore, it is necessary to educate surgeons about general measures of local infection control and careful surgical manipulation to prevent umbilical problems associated with laparoscopic surgery.
Identifying the Best Reduction Point for Zygomatic Arch Fractures Using Surface Markers
Authors: Abdelazeem Mohamed H. , Nadershah Mohammed 
Published: November 2023

This study aimed to describe a straightforward and efficient surgical technique for identifying the ideal point of reduction in isolated zygomatic arch fractures using preoperative radiopaque markers. In addition, a retrospective review of patient outcomes associated with this technique was conducted. The collected data encompassed demographics, injury side, mechanism of injury, time of injury, and classification of the isolated arch fracture. Measured outcomes included radiographic anatomic reduction, clinical facial symmetry, surgical operating time, and maximum interincisal mouth opening. Descriptive statistics were computed for each study variable. A total of 12 patients (10 males and 2 females) with an average age of 39.25 years (range: 26–60 y) were included in the study. The mechanisms of injury comprised road traffic accidents (6 patients, 50%), sports-related injuries (2 patients, 16.7%), occupational injuries (2 patients, 16.7%), and falls (2 patients, 16.7%). On average, patients presented 3 days after the injury (range: 1–14 d). The fracture classification according to Reyes and colleagues categorized 10 patients (83.3%) as type 4 and 2 patients (16.7%) as type 2. Coronoid impingement was observed in half of the patients (50%). The average surgical time was 15.4 minutes (range: 12–19 min). All patients exhibited optimal radiographic anatomic reduction, clinical facial symmetry, and maximum interincisal opening. In conclusion, this study demonstrates that the described technique is a simple and effective method for identifying the optimal reduction point in isolated zygomatic arch fractures.
Orbital Roof Decompression and Transposition of Orbital Contents for Treatment of Orbital Deviation Associated With Fibrous Dysplasia
Authors: Nuri Takashi , Kawabata Erina , Ueda Koichi 
Published: November 2023

A 25-year-old male was admitted to our institute complaining of caudal deviation of orbit. Surgery was performed through a coronal incision, a subtarsal incision, and a lynch incision. The periosteum of the orbital roof was raised, and the supraorbital wall was shaved cephalad in reference to the nonaffected side. Then the periosteum was incised from the inferior margin of the orbit to the medial and lateral palpebral ligaments, and the periosteum of the orbital floor was raised until the inferior orbital fissure. After the circumferential intraorbital periosteal detachment, the orbital contents could be readily moved cephalad ward. The outer table of the calvarial bone was transplanted to the orbital floor, and the palpebral ligaments were fixed 5 mm cranially. In the 5-year follow-up, the patient’s visual function was normal, and no recurrence of fibrous dysplasia was observed.