bluuebunny/crossref_metadata_2025_split huggingface dataset:
Daniel Lindsay and TJ Martin, on LA92
Authors: MacDonald Scott 
Published: September 2024

Abstract
For LA92 (2017), Daniel Lindsay and TJ Martin scoured news archives and personal archives throughout the Los Angeles area to provide a complex, panoramic document of the widespread violent response to the exoneration of the police officers who were caught on video brutally beating Rodney King. Seeing what official news outlets did not show in 1992 demonstrates how fully commercial television news is committed to providing information without upsetting consumers. Lindsay and Martin have created an ongoing collaboration that allows them to produce engaging cinema in a wide variety of ways. Before they made LA92, they had made an Oscar-winning direct-cinema documentary about a white coach and a black high school football team working together in the Deep South (Undefeated, 2011), and they would go on to make Tina (2021), a biopic of Tina Turner during her later years as she looks back on her life.
Paul Cronin
Authors: MacDonald Scott 
Published: September 2024

Abstract
Paul Cronin is as likely to identify himself as a historian as a filmmaker, though he is both. His epic A Time to Stir—in a seven-and-a-half-hour version and a fifteen-and a half-hour version, both available via his website—documents the Columbia University rebellion of 1968, when students took over the campus to protest Columbia’s connections with the Vietnam War and the racial implications of the university’s decision to build a gym in a public park between the campus and Harlem. The combination of photo and cinema records of the events of that week and the memories of 700 veterans of the event interviewed for the project make A Time to Stir a fascinating addition to modern documentary and modern historical research. Cronin talks about the genesis of the project and its gradual evolution during more than a decade.
Analysis of sex-biased gene expression in a Eurasian admixed population
Authors: Cheng Shuangshuang , Ning Zhilin , Huang Ke , Yuan Yuan , Tan Xinjiang , Pan Yuwen , Zhang Rui , Tian Lei , Lu Yan , Wang Xiaoji , Lu Dongsheng , Yang Yajun , Guan Yaqun , Mamatyusupu Dolikun , Xu Shuhua 
Published: September 2024

Abstract
Sex-biased gene expression differs across human populations; however, the underlying genetic basis and molecular mechanisms remain largely unknown. Here, we explore the influence of ancestry on sex differences in the human transcriptome and its genetic effects on a Eurasian admixed population: Uyghurs living in Xinjiang (XJU), by analyzing whole-genome sequencing data and transcriptome data of 90 XJU and 40 unrelated Han Chinese individuals. We identified 302 sex-biased expressed genes and 174 sex-biased cis-expression quantitative loci (sb-cis-eQTLs) in XJU, which were enriched in innate immune-related functions, indicating sex differences in immunity. Notably, approximately one-quarter of the sb-cis-eQTLs showed a strong correlation with ancestry composition; i.e. populations of similar ancestry tended to show similar patterns of sex-biased gene expression. Our analysis further suggested that genetic admixture induced a moderate degree of sex-biased gene expression. Interestingly, analysis of chromosome interactions revealed that the X chromosome acted on autosomal immunity-associated genes, partially explaining the sex-biased phenotypic differences. Our work extends the knowledge of sex-biased gene expression from the perspective of genetic admixture and bridges the gap in the exploration of sex-biased phenotypes shaped by autosome and X-chromosome interactions. Notably, we demonstrated that sex chromosomes cannot fully explain sex differentiation in immune-related phenotypes.
GeneRaMeN enables integration, comparison, and meta-analysis of multiple ranked gene lists to identify consensus, unique, and correlated genes
Authors: Yousefi Meisam , See Wayne Ren , Aw-Yong Kam Leng , Lee Wai Suet , Yong Cythia Lingli , Fanusi Felic , Smith Gavin J D , Ooi Eng Eong , Li Shang , Ghosh Sujoy , Ooi Yaw Shin 
Published: September 2024

Abstract
High-throughput experiments often produce ranked gene outputs, with forward genetic screening being a notable example. While there are various tools for analyzing individual datasets, those that perform comparative and meta-analytical examination of such ranked gene lists remain scarce. Here, we introduce Gene Rank Meta Analyzer (GeneRaMeN), an R Shiny tool utilizing rank statistics to facilitate the identification of consensus, unique, and correlated genes across multiple hit lists. We focused on two key topics to showcase GeneRaMeN: virus host factors and cancer dependencies. Using GeneRaMeN ‘Rank Aggregation’, we integrated 24 published and new flavivirus genetic screening datasets, including dengue, Japanese encephalitis, and Zika viruses. This meta-analysis yielded a consensus list of flavivirus host factors, elucidating the significant influence of cell line selection on screening outcomes. Similar analysis on 13 SARS-CoV-2 CRISPR screening datasets highlighted the pivotal role of meta-analysis in revealing redundant biological pathways exploited by the virus to enter human cells. Such redundancy was further underscored using GeneRaMeN’s ‘Rank Correlation’, where a strong negative correlation was observed for host factors implicated in one entry pathway versus the alternate route. Utilizing GeneRaMeN’s ‘Rank Uniqueness’, we analyzed human coronaviruses 229E, OC43, and SARS-CoV-2 datasets, identifying host factors uniquely associated with a defined subset of the screening datasets. Similar analyses were performed on over 1000 Cancer Dependency Map (DepMap) datasets spanning 19 human cancer types to reveal unique cancer vulnerabilities for each organ/tissue. GeneRaMeN, an efficient tool to integrate and maximize the usability of genetic screening datasets, is freely accessible via https://ysolab.shinyapps.io/GeneRaMeN.
Prolonged Time to Diagnosis of Crohn’s Disease in Patients With Perianal Fistulas Negatively Affects Long-Term Outcomes
Authors: Munster Liesbeth Jozefien , Pronk Aagje Johanna Martina , Mundt Marco William , Hompes Roel , Bemelman Willem Adrianus , van der Bilt Jarmila Dagmara Wendelien , Buskens Christianne Johanna 
Published: September 2024

Abstract

Background and Aim
This study aims to evaluate the effect of time to Crohn’s disease (CD) diagnosis on perianal fistula (PAF) outcomes in patients with a fistula as the first manifesting sign.

Methods
In this multicenter, retrospective study, CD patients with a PAF preceding CD diagnosis between November 2015 and June 2022 were included. The primary outcome parameter was the time to CD diagnosis and its correlation with long-term outcomes.

Results
In total, 126 patients with a PAF prior to CD diagnosis were identified. The median time to CD diagnosis was 15.0 months (IQR 3.8-47.3). A total of 49 patients (38.9%) had a clinically closed fistula of which 21 patients (42.9%) achieved radiological healing. Twenty-five patients (19.8%) underwent defunctioning, of which 9 patients (36.0%) needed proctectomy. Median time to CD diagnosis was shortest in patients with radiological healing (4.0 months, IQR 2.0-16.5) or clinical closure without radiological healing (11.0 months, IQR 3.0-47.8). In patients without fistula closure (n = 51), the median time to CD diagnosis was significantly longer compared to patients with fistula closure, 18.0 months vs 8.0 months (p = 0.031). In patients who needed defunctioning, the median time to diagnosis was more than twice as long compared to patients without defunctioning, 30.0 months vs 12.0 months (p = 0.054).

Conclusion
A prolonged time to CD diagnosis in patients with a PAF as a manifesting sign is associated with worse long-term outcomes. Patients in whom radiological healing could be achieved had the shortest time to CD diagnosis, emphasizing the relevance of increased clinical awareness of underlying CD in fistula patients.
Right ventricular free wall strain predicts transthyretin amyloidosis prognosis as well as biomarker-based staging systems
Authors: Istratoaie Sabina , Bourg Corentin , Lee K Charlotte , Marut Benjamin , Antonelli Jerome , L’official Guillaume , Wazzan Adrien Al , Donal Erwan 
Published: September 2024

Abstract

Aims
The diagnosis of transthyretin amyloidosis (ATTR) significantly impacts the management and prognosis of patients initially presenting with heart failure (HF). Despite recent advancements in treatment, prognosticating ATTR remains challenging. In this study, we aim to assess echocardiographic parameters associated with mid-term prognosis in patients with wild-type ATTR using a biomarker staging system as a reference point.

Methods and results
We studied 182 consecutive patients with wild-type ATTR (91% male and median age 82 years) who were referred to our centre between 2016 and 2022. Using N-terminal pro-B-type natriuretic peptide and estimated glomerular filtration rate cut-offs, we classified patients into the following three stages: Stage I (101 patients, 55.5%), Stage II (53 patients, 29.0%), and Stage III disease (28 patients, 15.5%). We then compared traditional echocardiographic indices and markers of subclinical ventricular dysfunction [left ventricular (LV) global longitudinal strain, right ventricular (RV) free wall strain, and left atrial (LA) strain] among groups. Over a fixed follow-up period of 18 months, which included treatment with tafamidis 61 mg daily, 48 patients (26.4%) experienced the composite outcome of death or HF hospitalization. When compared with Stage I ATTR, the hazard ratio (HR) for death or hospitalization was 1.55 [95% confidence interval (CI) 0.62–3.86] for Stage II ATTR and 4.53 (95% CI 1.66–12.4, P = 0.0116) for Stage III ATTR. Among echocardiographic parameters, reduced RV free wall strrain (FWS) was independently associated with all-cause mortality or HF hospitalization after adjustment for the staging system (HR 2.03, 95% CI 1.07–3.85, P &lt; 0.05).

Conclusion
RV FWS should be routinely assessed for all patients with ATTR. It is an independent predictor of poor prognosis and provides additional value beyond biomarker staging systems.
Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol
Authors: Lori Martina , Kundel Dominika , Mäder Paul , Singh Akanksha , Patel Dharmendra , Sisodia Bhupendra Singh , Riar Amritbir , Krause Hans-Martin 
Published: September 2024

Abstract
The adverse effects of intensified cropland practices on soil quality and biodiversity become especially evident in India, where nearly 60% of land is dedicated to cultivation and almost 30% of soil is already degraded. Intensive agricultural practice significantly contributes to soil degradation, highlighting the crucial need for effective countermeasures to support sustainable development goals. A long-term experiment, established in the semi-arid Nimar Valley (India) in 2007, monitors the effect of organic and conventional management on the plant-soil system in a Vertisol. The focus of our study was to assess how organic and conventional farming systems affect biological and chemical soil quality indicators. Additionally, we followed the community structure of the soil microbiome throughout the vegetation phase under soya or cotton cultivation in the year 2019. We found that organic farming enhanced soil organic carbon and nitrogen content, increased microbial abundance and activity, and fostered distinct microbial communities associated with traits in nutrient mineralization. In contrast, conventional farming enhanced the abundance of bacteria involved in ammonium oxidation suggesting high nitrification and subsequent nitrogen losses with regular mineral fertilization. Our findings underscore the value of adopting organic farming approaches in semi-arid subtropical regions to rectify soil quality and minimize nitrogen losses.
An explanation for the sister repulsion phenomenon in Patterson's f-statistics
Authors: Atağ Gözde , Waldman Shamam , Carmi Shai , Somel Mehmet 
Published: September 2024

Abstract
Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern “sister repulsion”. We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.
Tracheobronchoplasty for severe tracheobronchomalacia: a case-series of patients with acute and chronic critical comorbidities
Authors: Herron Robert , Dhamija Ankit , Shumar Jenna , Kakuturu Jahnavi , Hayanga J W Awori , Lamb Jason , Toker Alper 
Published: September 2024

Abstract

OBJECTIVES
There are little data within the literature regarding tracheobronchoplasty in the setting of the acute and chronically ill, morbidly obese or ventilator-dependent patients with tracheobronchomalacia. Short- and long-term outcomes are studied.

METHODS
The series represents 12 tracheobronchomalacia patients with American Society of Anesthesiologists (ASA) physical status scores of 3–5. Candidacy was based on bronchoscopic findings during spontaneous respirations with &gt;90% collapse of the trachea and both mainstem bronchi. We used dynamic computed tomography scan as an adjunct in those not mechanically ventilated. Our operative approach was a complete portal robotic approach for those outpatients (wheelchair dependent) and right thoracotomy for those who were already mechanically ventilated with 100% fraction of inspired oxygen with high pressure. Extracorporeal support was used in 2 patients.

RESULTS
Patients who underwent robotic repair were discharged without complications. Two patients who were critically ill and required extracorporeal support for their surgeries were separated from extracorporeal membrane oxygenation on postoperative day 2. Three patients died at the follow-up. In 1 patient, the prolene mesh migrated into trachea and caused obstruction of the trachea and required removal with endobronchial techniques.

CONCLUSIONS
The repair of tracheobronchomalacia in patients with multiple comorbidities and with severe life-threatening problems in or outside the intensive care unit may have improvement due to the ability to wean from positive pressure ventilation. Surgical technique and the utilization of mesh support in tracheobronchoplasty operations may need to be debated due to duration of the surgery in patients with severe comorbidities.
Digital identity: an approach to its nature, concept, and functionalities
Authors: Robles-Carrillo Margarita 
Published: September 2024

Abstract
Digital identity is a basic component of the knowledge economy and society. It is the key for accessing the digital world and for carrying out commercial, economic, or any kind of transactions and communications. Far from being a merely digital version of the physical identity, digital identity is a singular and complex construct which poses three main dilemmas that provide the framework for its analysis. The first arises from the context in which it is located, the digital ecosystem, that changes its scope and nature. The second, conceptual, is a consequence of the lack of agreement about its definition but also of the different legal framework derived from it. A third dilemma, functional, is due to the fact that digital identity can fulfil different, even contradictory, functionalities. An analysis of these dilemmas can contribute to a better understanding of this category leading to a proposal for its definition and legal framework.
A coupled steady thermo-electromagnetic problem in axisymmetric geometries. Mathematical and numerical analysis
Authors: Gómez Dolores , López-Rodríguez Bibiana , Salgado Pilar , Venegas Pablo 
Published: September 2024

Abstract
This paper focuses on the analysis of a steady thermo-electromagnetic problem related to the modeling of induction heating processes. Taking advantage of the cylindrical symmetry, the original three-dimensional problem can be reduced to a two-dimensional one on a meridional section, provided that the current density has only the azimuthal component. A variational formulation is presented in appropriately weighted Sobolev spaces, and the existence of a solution is established by employing a fixed-point argument. Furthermore, uniqueness and additional regularity results are proved under reasonable assumptions on the physical coefficients. A finite element approximation combined with a fixed-point iteration scheme is proposed for the numerical solution of the problem. A priori error estimates are obtained to quantify the accuracy of the approximation. Finally, numerical results are reported to validate the theoretical estimates and assess the performance of the method in a physical application.
Character Sheaves on Reductive Lie Algebras in Positive Characteristic
Authors: Zhou Tong 
Published: September 2024

Abstract
We prove a microlocal characterisation of character sheaves on a reductive Lie algebra over an algebraically closed field of sufficiently large positive characteristic: a perverse irreducible $G$-equivariant sheaf is a character sheaf if and only if it has nilpotent singular support and is quasi-admissible. We also present geometric proofs, in positive characteristic, of the equivalence between being admissible and being a character sheaf, and various characterisations of cuspidal sheaves, following the work of Mirković.
Evaluation of rifle cartridge and shot placement for euthanizing feral swine (Sus scrofa) in traps
Authors: Lavelle Michael J , Snow Nathan P , Brown Vienna R , Bodenchuk Michael J , Cook Seth M , VerCauteren Kurt C 
Published: September 2024

Abstract
Feral swine are a highly destructive invasive species around the globe. Wildlife managers commonly trap and euthanize feral swine with firearms to reduce their adverse impacts. The utility of euthanizing domestic swine with firearms has been considered when emergency situations arise such as in the event of a foreign animal disease outbreak in domestic swine. Similarly, the rapid depopulation of domestic swine facilities became necessary when the COVID-19 pandemic disrupted pork production in 2020. Evaluation of the effects of caliber, cartridge, size of feral swine, and shot placement on effectiveness and safety of the method is needed. We collected data from feral swine euthanized in traps on how those variables influenced the effectiveness in time to death and number of shots required and safety risks based on the occurrence of bullet pass-through (i.e., bullet exiting the pig). We tested 3 cartridges of 2 calibers (0.22 long rifle, 0.22 Winchester magnum rimfire, and 0.308 Winchester) delivered from a rifle with 3 shot placements targeting the brain. From 570 euthanization events, we calculated an average time to death of 100.06 (SD = 29.24) s, with larger feral swine taking slightly longer. Most feral swine (73%) were euthanized with a single shot but averaged 1.28 (SD = 0.48) shots overall. Safety risks from pass-through shots were more common when using the 0.308 Winchester cartridge, and when rear and side shot placements were used. Overall, we recommend a 0.22 long rifle cartridge and frontal shot placement as an effective and safe option for euthanizing feral swine in traps, and likely for domestic swine of similar size and shot distances.
Colour polymorphism is prevalent on islands but shows no association with range size in web-building spiders
Authors: Salgado-Roa Fabian C , Stuart-Fox Devi , White Thomas E , Medina Iliana 
Published: September 2024

Abstract
One of the most evident sources of phenotypic diversity within a population is colouration, as exemplified by colour polymorphism. This is relevant to a greater extent in animals with visually biased sensory systems. There is substantial evidence suggesting that different colour morphs can access a broader range of habitats or niches, leading to larger geographic range sizes. However, this hypothesis has been tested in few lineages, comprising species where colour is likely to be involved in sexual selection. Furthermore, some available evidence considers geographical variation as polymorphism, thus limiting our comprehension of how sympatric colour polymorphism can influence a species’ geographic range. Through an extensive systematic literature review and a comparative analysis, we examined the relationship between colour polymorphism and range size or niche breadth in web-building spiders. We identified 140 colour polymorphic spider species, belonging mainly to the families Araneidae and Theridiidae. We found no evidence that colour polymorphic species differ significantly from non-polymorphic species in terms of range size and niche breadth, after accounting for phylogenetic relationships and other covariates. However, we did observe that colour polymorphic species were more likely to be found on islands compared to non-polymorphic species. Overall, our results indicate that the association between colour polymorphism and geographic range size may not exist among web-building spiders, or be as pronounced as in other lineages. This suggests that the strength of the association between colour polymorphism and ecological success might depend on the ecological role that colouration plays in each clade.
A case of rare obstructive jaundice induced by concealed displacement of T-tube
Authors: Yangjun Gu , Qingqing Fang , Zhitao Chen , Qiyong Li 
Published: September 2024

Abstract
We present the case of a 32-year-old woman who was ultimately diagnosed with obstructive jaundice. She exhibited persist jaundice, liver dysfunction with normal drainage of T-tube (400–500 ml per day), and normal stools. Prior to her admission to our department, she had undergone a cholecystectomy and T-tube placement following common bile duct exploration for cholelithiasis. Although her serum bilirubin levels initially decreased post-surgery, it rose sharply after T-tube cholangiography. The diagnosis remained unclear until we performed endoscopic retrograde cholangiopancreatography (ERCP), which revealed that the obstructive jaundice was induced by improper T-tube placement. There were few such presentations reported before, and it’s particularly unusual to encounter jaundice following T-tube placement. Moreover, diagnosing and treating this condition can be challenging when T-tube drainage appears normal. Thus, our case report provides a unique contribution to the literature on obstructive jaundice.