bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMARCA4/BRG1 deficiency induces a targetable dependence on oxidative phosphorylation in clear cell renal cell carcinoma
Authors: Fang Ru , Wang Xiaotong , Wu Ruina , Pan Rui , Tian Miaomiao , Zhang Rusong , Wei Xue , Wang Xuan , Ye Shengbing , Li Feng , Xia Qiuyuan , Cheng Yang , Rao Qiu 
Published: January 2025

Abstract
The tumor suppressor gene SMARCA4, a critical component of the SWI/SNF chromatin remodeling complex, is frequently inactivated in various cancers, including clear cell renal cell carcinoma (ccRCC). Despite its significance, the role of SMARCA4 in ccRCC development and its potential therapeutic vulnerabilities have not been fully explored. Our research found that SMARCA4 deficiency was associated with poor prognosis and was observed in a subset of high-grade ccRCCs. Through functional assays, we determined that the suppression of SMARCA4 led to an increase in RCC cell proliferation. Further gene expression analysis unveiled that SMARCA4-deficient cells exhibit an upregulation of the oxidative phosphorylation (OXPHOS) pathway. Delving deeper, we combined RNA sequencing (RNA-Seq) and Assay for transposase-accessible chromatin with sequencing (ATAC-Seq) data to uncover that SMARCA4 plays a crucial role in modulating chromatin accessibility and the expression of genes essential for the respiratory electron transport chain. A significant finding from our study is that RCC cells and xenograft tumors lacking SMARCA4 demonstrated an increased sensitivity to the inhibition of the OXPHOS pathway by the novel small molecule IACS-010759. This sensitivity is attributed to the heightened energy demands and susceptibility to energy stress observed in SMARCA4-deficient cells, driven by their amplified biosynthetic requirements. The efficacy of IACS-010759 stems from its ability to induce energy deprivation, pinpointing OXPHOS inhibition as a promising therapeutic approach for targeting SMARCA4-mutant tumors. This strategy offers a novel avenue to address a currently unmet therapeutic need, highlighting the potential of OXPHOS inhibition in the treatment of cancers harboring SMARCA4 mutations.
Optimized genetic tools for neuroanatomical and functional mapping of the Aedes aegypti olfactory system
Authors: Shankar Shruti , Giraldo Diego , Tauxe Genevieve M , Spikol Emma D , Li Ming , Akbari Omar S , Wohl Margot P , McMeniman Conor J 
Published: January 2025

Abstract
The mosquito Aedes aegypti is an emerging model insect for invertebrate neurobiology. We detail the application of a dual transgenesis marker system that reports the nature of transgene integration with circular donor template for CRISPR–Cas9-mediated homology-directed repair at target mosquito chemoreceptor genes. Employing this approach, we demonstrate the establishment of cell-type-specific T2A-QF2 driver lines for the A. aegypti olfactory co-receptor genes Ir8a and orco via canonical homology-directed repair and the CO2 receptor complex gene Gr1 via noncanonical homology-directed repair involving duplication of the intended T2A-QF2 integration cassette separated by intervening donor plasmid sequence. Using Gr1+ olfactory sensory neurons as an example, we show that introgression of such T2A-QF2 driver and QUAS responder transgenes into a yellow cuticular pigmentation mutant strain facilitates transcuticular calcium imaging of CO2-evoked neural activity on the maxillary palps with enhanced sensitivity relative to wild-type mosquitoes enveloped by dark melanized cuticle. We further apply Cre-loxP excision to derive marker-free T2A-QF2 in-frame fusions to clearly map axonal projection patterns from olfactory sensory neurons expressing these 3 chemoreceptors into the A. aegypti antennal lobe devoid of background interference from 3xP3-based fluorescent transgenesis markers. The marker-free Gr1 T2A-QF2 driver facilitates clear recording of CO2-evoked responses in this central brain region using the genetically encoded calcium indicators GCaMP6s and CaMPARI2. Systematic application of these optimized methods to different chemoreceptors stands to enable mapping A. aegypti olfactory circuits at peripheral and central levels of olfactory coding at high resolution.
Estimating effective population size trajectories from time-series identity-by-descent segments
Authors: Huang Yilei , Carmi Shai , Ringbauer Harald 
Published: January 2025

Abstract
Long, identical haplotypes shared between pairs of individuals, known as identity-by-descent (IBD) segments, result from recently shared co-ancestry. Various methods have been developed to utilize IBD sharing for demographic inference in contemporary DNA data. Recent methodological advances have extended the screening for IBD segments to ancient DNA (aDNA) data, making demographic inference based on IBD also possible for aDNA. However, aDNA data typically have varying sampling times, but most demographic inference methods for modern data assume that sampling is contemporaneous. Here, we present Ttne (Time-Transect Ne), which models time-transect sampling to infer recent effective population size trajectories. Using simulations, we show that utilizing IBD sharing in time series increased resolution to infer recent fluctuations in effective population sizes compared with methods that only use contemporaneous samples. To account for IBD detection errors common in empirical analyses, we implemented an approach to estimate and model IBD detection errors. Finally, we applied Ttne to two aDNA time transects: individuals associated with the Copper Age Corded Ware Culture and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records.
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation
Authors: Liu Chun , Zhang Jianyu , Xu Ranran , Lv Jinhui , Qiao Zhu , Bai Mingzhou , Zhao Shancen , Luo Lijuan , Liu Guodao , Liu Pandao 
Published: January 2025

Abstract

Background
Drought is a major limiting factor for plant survival and crop productivity. Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the molecular mechanisms driving its drought resistance remain largely unexplored.

Results
We present a chromosome-scale reference genome of S. angustifolia, which provides insights into its genome evolution and drought tolerance mechanisms. The assembled genome is 645.88 Mb in size, containing 319.98 Mb of repetitive sequences and 36,857 protein-coding genes. The high quality of this genome assembly is demonstrated by the presence of 99.26% BUSCO and a 19.49 long terminal repeat assembly index. Evolutionary analyses revealed that S. angustifolia shares a whole-genome duplication (WGD) event with other legumes but lacks recent WGD. Additionally, S. angustifolia has undergone gene expansion through tandem duplication approximately 12.31 million years ago. Through integrative multiomics analyses, we identified 4 gene families—namely, xanthoxin dehydrogenase, 2-hydroxyisoflavanone dehydratase, patatin-related phospholipase A, and stachyose synthetase—that underwent tandem duplication and were significantly upregulated under drought stress. These gene families contribute to the biosynthesis of abscisic acid, genistein, daidzein, jasmonic acid, and stachyose, thereby enhancing drought tolerance.

Conclusions
The genome assembly of S. angustifolia represents a significant advancement in understanding the genetic mechanisms underlying drought tolerance in this pioneer plant species. This genomic resource provides critical insights into the evolution of drought resistance and offers valuable genetic information for breeding programs aimed at improving drought resistance in crops.
Reconstructing a century of marine landings and fishing effort in Malaysia and Singapore
Authors: Ng Clement Z W , Jensen Olaf P , Ong Joyce J L 
Published: January 2025

Abstract
Marine capture fisheries are crucial for many coastal communities in Malaysia and Singapore. However, knowledge of the historical state of the marine fishing resources, particularly during the British colonial period, remains limited. We compiled annual species landing data and fishing metrics from colonial and contemporary fishery reports spanning 114 years, from 1907 to 2021. Our results revealed a steady increase in species landings over 90 years, peaking in 2016 before declining in recent years. Through three case studies, we highlight high colonial landings of fusiliers (Caesionidae) from Singapore, reflecting extensive fishing operations across Southeast Asia. Bayesian Change Point analyses also identified increases in lobster landings along the east coast of Peninsular Malaysia in the mid-1980s, with fishing operations expanding from Johor northward through Pahang and Terengganu. Granger-causality tests revealed significant associations between Indian mackerel landings and the number of powered fishing boats in Perlis and Kedah in western Peninsular Malaysia, with varying lag intervals among each state. While these results enhance our understanding of fisheries trends, spatial expansion of fisheries and technological changes complicate the interpretation of fishery trends. Our results suggest that the plateau in global fishery landings since the 1980s may also have already occurred in Southeast Asia.
Closure of ventricular septal defect in children with trisomy 18: perioperative events and long-term survival
Authors: Nemoto Shintaro , Kishi Kanta , Konishi Hayato , Suzuki Akiyo , Katsumata Takahiro , Ozaki Noriyasu , Odanaka Yutaka , Ashida Atsuko , Uchiyama Takamichi , Mine Kenji 
Published: January 2025

Abstract

OBJECTIVES
This retrospective study aimed to investigate the feasibility of surgical closure of ventricular septal defect in children with trisomy 18 by assessing perioperative events and long-term survival.

METHODS
From April 2008 to March 2024, 41 consecutive patients were referred to us for ventricular septal defect surgery. The defect was closed in 35 patients at the end (median age, 16 months; median body weight, 5.7 kg), 31 out of 37 patients after the preceding pulmonary artery banding according to our staged surgery policy and 4 patients without the banding. Sixty-five significant non-cardiac lesions existed concurrently, and 14 patients underwent tracheostomy before closure. The investigation was conducted by checking medical records and contacting the primary physician.

RESULTS
Four patients died during the inter-stage after banding to closure (10.8%). Two of them were awaiting closure. Concomitant surgeries, 15 right ventricular muscle resections, or 1 arch repair, were performed along with closure. Arrhythmia was the most common adverse event (51.4%). Three patients required extracorporeal membrane oxygenation support. Transient but severe hepatic injury occurred in 11 patients (31.4%). There were two hospital death (5.7%) due to severe respiratory insufficiency or fulminant sepsis. Five patients died after discharge, three pneumonia and two sudden death, resulting in a 5-year estimated survival of 79.5%. Three hepatoblastoma and one hepatoangioma developed, but complete remission was achieved in all patients.

CONCLUSIONS
Although further studies are mandatory, surgical closure of ventricular septal defect may be an effective treatment option even for children with trisomy 18.
Vancomycin-resistant Enterococcus prevalence and its association along the food chain: a systematic review and meta-analysis
Authors: Caddey Benjamin , Shaukat Waseem , Tang Karen L , Barkema Herman W 
Published: January 2025

Abstract

Background
Vancomycin-resistant Enterococcus (VRE) are present across the One Health continuum and pose a considerable risk for transmission along the food chain. This systematic review and meta-analysis estimates the prevalence of VRE colonization in livestock, food of animal origin, and in human populations.

Methods
Embase, MEDLINE and CAB Abstracts were searched for eligible literature. A total of 54 manuscripts passed inclusion criteria by providing prevalence estimates of VRE in a human population and at least one of either livestock or food. Random effects meta-analysis was conducted to determine prevalence estimates, and risk of bias in pooled estimates was assessed using funnel plots and Egger regression.

Results
Global pooled prevalence of VRE colonization was highest in poultry and poultry meat at 16% (95% CI: 6%–28%) and 15% (95% CI: 1%–39%), respectively. Human-associated VRE colonization was highest in livestock workers, with a pooled prevalence of 11% (95% CI: 2%–25%), and lowest in the general public at 2% (95% CI: 0%–3%). Meta-regression demonstrated that human VRE prevalence increased at a rate of 0.75% (95% CI: 0.46%–1.04%; P &lt; 0.001) per 1% increase in livestock VRE colonization.

Conclusions
This meta-analysis established a clear link of VRE across One Health sectors. VRE colonization is likely elevated for those in contact with colonized animals or contaminated food products. Quality of evidence in pooled prevalence estimates was limited by publication bias and heterogeneity. The results of this study enhance calls for a One Health approach for mitigating the global burden of priority antimicrobial resistance pathogens.
Assessing phenotypic effect of integrase strand-transfer inhibitor (INSTI)-based resistance substitutions associated with failures on cabotegravir
Authors: D’Antoni Michelle L , Falkard Brie , Andreatta Kristen , Cox Stephanie , Cohen Cal , Callebaut Christian 
Published: January 2025

Abstract

Objectives
International guidelines recommend integrase strand-transfer inhibitor (INSTI)-based regimens as initial and switch therapy in people with HIV. As novel INSTIs become available, understanding how emergence of resistance at virological failures and seroconversions affects subsequent treatment options is needed. For the latest approved INSTI, cabotegravir, resistance patterns comprising Q148K/R, N155H, R263K, G118R, E138A/K and G140A/S (alone or in combination) have been documented in virological failures and seroconversions. Here, the effect of these substitutions on antiviral activity of commercially approved INSTIs, bictegravir and elvitegravir, was assessed.

Methods
Antiviral testing was performed using person-derived clinical isolates (n = 52) with viral profiles similar to cabotegravir INSTI resistance patterns; susceptibility to cabotegravir, bictegravir and elvitegravir was measured using a phenotypic assay. Substitution patterns from isolates included triple [Q148K/H/R + E138A/K + G140A/C/S (n = 16)], double [Q148R + E138K (n = 3); Q148H/R + G140A/S (n = 24)] and single [N155H (n = 6); Q148R (n = 3)] resistance-associated mutations (RAMs).

Results
IC50 fold changes (FCs) for triple RAMs were the highest, at 47.0, 7.59 and &gt;144 for cabotegravir, bictegravir and elvitegravir, respectively. For cabotegravir, bictegravir and elvitegravir, respectively, mean IC50 FCs were 9.5, 2.5 and &gt;144 for double RAMs; and 3.3, 1.4 and &gt;65 for single RAMs. When considering clinical/biological assay cut-offs, 54% (28/52) of isolates were susceptible to bictegravir, 40% (21/52) were partially susceptible and 6% (3/52) were resistant; for elvitegravir, 100% of isolates were resistant. Cabotegravir cut-offs were not available at the time of reporting.

Conclusions
Overall, clinical isolates with RAM patterns similar to clinically observed cabotegravir INSTI resistance showed meaningful increases in IC50 FCs, suggesting that cabotegravir-associated resistance may negatively affect efficacy of bictegravir- and elvitegravir-based regimens.
Compulsory dispute settlement system under the BBNJ agreement: some considerations on future constraints
Authors: Cho Hoon , Lee Changyoul 
Published: January 2025

Abstract
The newly adopted BBNJ Agreement introduces UNCLOS Part XV as its Part IX, which regulates a compulsory dispute settlement mechanism to resolve disputes related to the Agreement. Given that this Agreement is the third implementing agreement of UNCLOS, it may be the default approach to adhering to the Part XV system rather than taking other measures. However, this article contends that specific functions should be expected for Part IX of the Agreement, especially in ensuring State parties’ compliance with obligations under the BBNJ Agreement for pursuing its common goals and objectives. Rather than taking an overly optimistic approach, this article explores some of the challenges that the Part XV system is likely to face in future disputes over the BBNJ Agreement. In addition, other institutional arrangements within the BBNJ Agreement that will supplement the compulsory system of the Agreement to fulfil its function are looked into.
Media consolidation and news content quality
Authors: Garz Marcel , Ots Mart 
Published: January 2025

Abstract
News organizations have been under financial pressure to streamline their activities for decades. Critics argue that this pressure undermines the quality of news, posing a severe threat to democracy. However, the effects of media consolidation on news quality are theoretically ambiguous and empirical evidence is scarce. To address this gap, we study the case of the Swedish newspaper industry between 2014 and 2022, a period where more than half of the country’s newspapers changed their owners. We collect over 2 million articles from 108 newspapers and apply state-of-the-art computational methods to create theoretically grounded, fine-grained measures of news content quality. Our results indicate that mergers are associated with slight increases in content quality. However, we also find evidence of content homogenization, as merging newspapers tend to slightly decrease their provision of local news, while relying more on content shared with co-owned newspapers.
Oxidative and nitrative DNA damage induced by industrial chemicals in relation to carcinogenesis
Authors: Hiraku Yusuke 
Published: January 2025

Abstract
Objectives: Many chemicals have been used for industrial purposes, and some of them are carcinogenic to humans. However, the molecular mechanisms of their carcinogenetic effects have not been well understood. Reactive oxygen species are generated from industrial chemicals and contribute to carcinogenesis. Particles and fibers are accumulated in respiratory systems by inhalation exposure and cause chronic inflammation. Under inflammatory conditions, reactive nitrogen species are generated from inflammatory and epithelial cells. These species cause oxidative and nitrative DNA damage, leading to carcinogenesis. We carried out experiments on DNA damage induced by various industrial chemicals and investigated their molecular mechanisms.
Methods: We examined oxidative DNA damage induced by industrial chemicals using DNA fragments derived from human cancer-relevant genes by polyacrylamide gel electrophoresis. Using immunohistochemistry and immunocytochemistry we also examined the formation of 8-nitroguanine (8-nitroG), a DNA lesion formed under inflammatory conditions, in lung tissues and cultured cells exposed to industrial chemicals.
Results: Benzene and o-toluidine metabolites caused oxidative damage to DNA fragments in the presence of Cu(II). H2O2 and Cu(I) were generated during oxidation of these chemicals and involved in DNA damage. 8-NitroG formation was observed in lung tissues of asbestos-exposed mice and humans. Carbon nanomaterials and indium compounds induced 8-nitroG formation in human lung epithelial cells via the release of damage-associated molecular patterns from exposed cells.
Conclusions: Various industrial chemicals are considered to induce carcinogenesis by causing oxidative and nitrative DNA damage. These findings provide an insight into risk assessment of industrial chemicals and prevention of carcinogenesis in workplaces.
Residual Symptoms and Quality of Life After Treated Lyme Neuroborreliosis: Case-Control Study (QoLYME)
Authors: Foret Julie , Paren Anne-Julie , Zayet Souheil , Chirouze Catherine , Gendrin Vincent , Bouiller Kevin , Klopfenstein Timothée 
Published: January 2025

Abstract

Background
Earlier studies revealed that 10%–50% of patients reported remaining complaints after treatment for Lyme neuroborreliosis (LNB). The aim of our study was to assess symptoms and quality of life in patients with diagnosed and treated LNB and to compare them with findings in the general population.

Methods
Adults with LNB receiving adequate antibiotics were included between 2015 and 2021 in 2 tertiary hospitals. Two controls without Lyme borreliosis history were included for each case patient, matched by age and geographic area. All participants were interviewed to answer a standardized questionnaire. Fatigue was assessed by the Fatigue Severity Scale (FSS) and quality of life by the 12-Item Short Form Survey, including physical component summary (PCS) and mental component summary (MCS) scores.

Results
Fifty-three patients and 104 controls were included. The mean age (SD) was 62 (13) years in both groups; 66% were male in the LNB group and 44% in the control group (P = .01). Fatigue (68% vs 48%, respectively; P = .02), memory disorders (60% vs 38%; P &lt; .01), and attention disorders (32% vs 17%; P = .05) were significantly more frequent in the LNB group than in controls. In multivariable analysis, no association was found between LNB and FSS scores (odds ratio, 1.6 [95% confidence interval, .9–3.0]; P = .15) or between LNB and MCS scores (0.8 [.4–1.5]; P = .45); however, patients with LNB had lower PCS scores (0.5 [.3–.9]; P = .03).

Conclusions
Several symptoms were similar in patients with LNB and controls. Quality of life was slightly impaired in patients with LNB and PCS scores were lower, but there were no differences in MCS or FSS scores. Reassurance and specific rehabilitation measures could be provided to these patients.
An application of matching algorithms to generalize small-area estimates of chronic pain prevalence to neighbourhoods across England
Authors: Quinn L , Yu D , Lynch M , Jordan K P , Wilkie R , Peat G 
Published: January 2025

Abstract

Background
Local decision-makers lack granular data on the prevalence of chronic pain in their populations. We applied matching methods to generalize estimates from one local survey in England to other neighborhoods across the country with a similar sociodemographic composition.

Methods
We used propensity score matching to match lower-layer super output areas (LSOA) across England with 230 surveyed LSOAs in North Staffordshire by age, sex, ethnicity, deprivation, and rurality. LSOA-specific crude prevalence of chronic pain and high-impact chronic pain in adults aged 35+ years were estimated and mapped for matched LSOAs.

Results
Satisfactory matching was achieved for 24 871 of 31 580 LSOAs (79%). The 6709 LSOAs identified as either “off common support” or unmatched were principally inner-city neighborhoods with younger, more ethnically diverse populations. LSOA-specific estimates of chronic pain and high impact chronic pain ranged from 14% to 52% and from 4% to 31% respectively. Integrated Care Board estimates ranged from 27% to 38% and from 10% to 18%, respectively. Estimates for England were 31.9% and 12.6%, respectively.

Conclusions
Using matching methods we have produced the first detailed map of the distribution of chronic pain in England but with several strong assumptions. Our estimates highlight substantial variation in prevalence within ICBs.