bluuebunny/crossref_metadata_2025_split huggingface dataset:
ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data
Authors: Xiao Zhixia , Lam Hon-Ming 
Published: July 2022

AbstractMotivationSynteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region.ResultsWe developed ShinySyn, a Shiny/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-synteny to individual homologous genes.Availability and implementationThe source code and installation instructions for ShinySyn can be accessed via https://github.com/obenno/ShinySyn. A pre-built docker image is also available at https://hub.docker.com/r/obenno/shinysyn. The application can be used locally or seamlessly integrated into any Shiny application server.
Optical imaging detects metabolic signatures associated with oocyte quality
Authors: Tan Tiffany C Y , Brown Hannah M , Thompson Jeremy G , Mustafa Sanam , Dunning Kylie R 
Published: July 2022

AbstractOocyte developmental potential is intimately linked to metabolism. Existing approaches to measure metabolism in the cumulus oocyte complex (COC) do not provide information on the separate cumulus and oocyte compartments. Development of an assay that achieves this may lead to an accurate diagnostic for oocyte quality. Optical imaging of the autofluorescent cofactors reduced nicotinamide adenine dinucleotide (phosphate) [NAD(P)H] and flavin adenine dinucleotide (FAD) provides a spatially resolved indicator of metabolism via the optical redox ratio (FAD/[NAD(P)H + FAD]). This may provide an assessment of oocyte quality. Here, we determined whether the optical redox ratio is a robust methodology for measuring metabolism in the cumulus and oocyte compartments compared with oxygen consumption in the whole COC. We also determined whether optical imaging could detect metabolic differences associated with poor oocyte quality (etomoxir-treated). We used confocal microscopy to measure NAD(P)H and FAD, and extracellular flux to measure oxygen consumption. The optical redox ratio accurately reflected metabolism in the oocyte compartment when compared with oxygen consumption (whole COC). Etomoxir-treated COCs showed significantly lower levels of NAD(P)H and FAD compared to control. We further validated this approach using hyperspectral imaging, which is clinically compatible due to its low energy dose. This confirmed lower NAD(P)H and FAD in etomoxir-treated COCs. When comparing hyperspectral imaged vs non-imaged COCs, subsequent preimplantation development and post-transfer viability were comparable. Collectively, these results demonstrate that label-free optical imaging of metabolic cofactors is a safe and sensitive assay for measuring metabolism and has potential to assess oocyte developmental competence.
SARS-CoV-2 triggers pericyte-mediated cerebral capillary constriction
Authors: Hirunpattarasilp Chanawee , James Greg , Kwanthongdee Jaturon , Freitas Felipe , Huo Jiandong , Sethi Huma , Kittler Josef T , Owens Raymond J , McCoy Laura E , Attwell David 
Published: July 2022

Abstract
The SARS-CoV-2 receptor, ACE2, is found on pericytes, contractile cells enwrapping capillaries that regulate brain, heart and kidney blood flow. ACE2 converts vasoconstricting angiotensin II into vasodilating angiotensin-(1-7). In brain slices from hamster, which has an ACE2 sequence similar to human ACE2, angiotensin II evoked a small pericyte-mediated capillary constriction via AT1 receptors, but evoked a large constriction when the SARS-CoV-2 receptor binding domain (RBD, original Wuhan variant) was present. A mutated non-binding RBD did not potentiate constriction. A similar RBD-potentiated capillary constriction occurred in human cortical slices, and was evoked in hamster brain slices by pseudotyped virions expressing SARS-CoV-2 spike protein. This constriction reflects an RBD-induced decrease in the conversion of angiotensin II to angiotensin-(1-7) mediated by removal of ACE2 from the cell surface membrane and was mimicked by blocking ACE2. The clinically used drug losartan inhibited the RBD-potentiated constriction. Thus, AT1 receptor blockers could be protective in COVID-19 by preventing pericyte-mediated blood flow reductions in the brain, and perhaps the heart and kidney.
Expert insights on Malaysia’s residential solar-energy policies: shortcomings and recommendations
Authors: Lau Lin-Sea , Choong Yuen-Onn , Ching Suet-Ling , Wei Chooi-Yi , Senadjki Abdelhak , Choong Chee-Keong , Seow Ai-Na 
Published: July 2022

Abstract
Malaysia has a long way before achieving the 20% renewable-energy penetration by 2025. Currently, merely 2% of the country’s electricity is generated by renewable energy sources including solar power. Unlike the abundant literature about solar energy, qualitative studies that focus on experts’ opinions on the weaknesses of residential solar-energy policies have received less attention, particularly in the context of Malaysia. Understanding the flaws in the existing policies would lead to creating a better policy framework for solar-energy development. Thus, this study aims to identify the shortcomings of the current government initiatives and policies that deter solar photovoltaic adoption among households from experts’ perspectives. Experts also provide recommendations for better future policy design and implementation. This study employs a qualitative research approach (via semi-structured interviews) in collecting experts’ viewpoints. Key concerns emerging from the interviews include insufficient financial support, lack of awareness programmes and subsidized electricity tariffs. Also, interviewed experts suggest sufficient financial incentives, increased public awareness programmes and comprehensive legislation aimed at safeguarding consumer interests as a means to raising solar-energy adoption in the country. This underlines the need for policymakers to create public awareness, provide financial support and develop regulatory measures aimed at managing solar companies for the sake of solar development in Malaysia.
Clinical Outcomes in a Randomized Controlled Trial Comparing Point-of-Care With Standard Human Immunodeficiency Virus (HIV) Viral Load Monitoring in Nigeria
Authors: Chang Charlotte , Agbaji Oche , Mitruka Kiren , Olatunde Bola , Sule Halima , Dajel Titus , Zee Aaron , Ahmed Mukhtar L , Ahmed Isah , Okonkwo Prosper , Chaplin Beth , Kanki Phyllis 
Published: July 2022

Abstract

Background
Point-of-care (POC) viral load (VL) tests provide results within hours, enabling same-day treatment interventions. We assessed treatment outcomes with POC vs standard-of-care (SOC) VL monitoring.

Methods
We implemented a randomized controlled trial at an urban and rural hospital in Nigeria. Participants initiating antiretroviral therapy (ART) were randomized 1:1 for monitoring via the POC Cepheid Xpert or SOC Roche COBAS (v2.0) HIV-1 VL assays. Viral suppression (VS) and retention in care at 12 months were compared via intention-to-treat (ITT) and per-protocol (PP) analyses. Post-trial surveys for POC patients and healthcare workers (HCWs) evaluated acceptability.

Results
During April 2018–October 2019, 268 SOC and 273 POC patients enrolled in the trial. Viral suppression at &lt;1000 copies/mL at 12 months was 59.3% (162/273) for POC and 52.2% (140/268) for SOC (P = .096) in ITT analysis and 77.1% (158/205) for POC and 65.9% (137/208) for SOC (P = .012) in PP analysis. Retention was not significantly different in ITT analysis but was 85.9% for POC and 76.9% for SOC (P = .02) in PP analysis. The increased VS in the POC arm was attributable to improved retention and documentation of VL results. POC monitoring was preferred over SOC by 90.2% (147/163) of patients and 100% (15/15) of HCWs thought it facilitated patient care.

Conclusions
POC VL monitoring did not improve 12-month VS among those with results but did improve retention and VS documentation and was preferred by most patients and HCWs. Further research can inform best POC implementation conditions and approaches to optimize patient care.

Clinical Trials Registration
NCT03533868.
Centrality measures in interval-weighted networks
Authors: Alves Hélder , Brito Paula , Campos Pedro 
Published: July 2022

Abstract
Centrality measures are used in network science to assess the centrality of vertices or the position they occupy in a network. There are a large number of centrality measures according to some criterion. However, the generalizations of the most well-known centrality measures for weighted networks, degree centrality, closeness centrality and betweenness centrality have solely assumed the edge weights to be constants. This article proposes a methodology to generalize degree, closeness and betweenness centralities taking into account the variability of edge weights in the form of closed intervals (interval-weighted networks, IWN). We apply our centrality measures approach to two real-world IWN. The first is a commuter network in mainland Portugal, between the 23 NUTS 3 Regions. The second focuses on annual merchandise trade between 28 European countries, from 2003 to 2015.
Swimming performance of a pelagic species in the Yangtze River under different exposure modes of the total dissolved gas supersaturation
Authors: Ji Qianfeng , Li Kefeng , Wang Yuanming , Liang Ruifeng , Feng Jingjie , Li Ran , Zhu David Z 
Published: July 2022

Abstract
During flood discharges of upstream dams in the Yangtze River, the pelagic fish have a stress risk from total dissolved gas (TDG) supersaturation in the river water. This study took the silver carp as the object and systematically evaluated the effects of TDG supersaturation levels and exposure time on their critical swimming speed (Ucrit) at different temperatures. The external symptoms of gas bubble disease were found when TDG levels exceeded 130%. Both exposure time and TDG level did not significantly impact the Ucrit of fish under 6 days of non-lethal exposure (110%, 120%, 130% TDG) with lower or higher water temperature. Significant differences in Ucrit were found among different exposure times at 11.0 ± 1.0°C under 10 hours of lethal exposure (135%, 140%, 150% TDG) and the Ucrit reduced by 59.88%, 83.32%, and 92.40%, respectively. TDG level had a significant impact on the Ucrit at 21.0 ± 1.0°C when exposure time exceeded 8 hours. Ucrit at 21.0 ± 1.0°C water were significantly greater than those at 11.0 ± 1.0°C water where conditions had the same TDG supersaturation and exposure time. Differences in Ucrit between temperatures ranged from 3.24 to 6.12 BL/s under non-lethal exposure and from 6.38 to 13.88 BL/s under lethal exposure. The results of this study can provide a reference for fish conservation during flood discharge.
Patient-reported Outcomes: the ICHOM Standard Set for Inflammatory Bowel Disease in Real-life Practice Helps Quantify Deficits in Current Care
Authors: Wong Darren , Matini Lawrence , Kormilitzin Andrey , Kantschuster Ramona , Simadibrata Daniel Martin , Lyden Sara , Wilson Jean , Brain Oliver A , Palmer Rebecca , Ambrose Tim , Satsangi Jack , South Matthew , Geddes John , Bodger Keith , Travis Simon P L , Walsh Alissa 
Published: July 2022

Abstract

Background
Patient-reported outcome measures [PROMs] are key to documenting outcomes that matter most to patients and are increasingly important to commissioners of health care seeking value. We report the first series of the ICHOM Standard Set for Inflammatory Bowel Disease [IBD].

Methods
Patients treated for ulcerative colitis [UC] or Crohn’s disease [CD] in our centre were offered enrolment into the web-based TrueColours-IBD programme. Through this programme, e-mail prompts linking to validated questionnaires were sent for symptoms, quality of life, and ICHOM IBD outcomes.

Results
The first 1299 consecutive patients enrolled [779 UC, 520 CD] were studied with median 270 days of follow-up (interquartile range [IQR] 116, 504). 671 [52%] were female, mean age 42 years (standard deviation [sd] 16), mean body mass index [BMI] 26 [sd 5.3]. At registration, 483 [37%] were using advanced therapies. Median adherence to fortnightly quality of life reporting and quarterly outcomes was 100% [IQR 48, 100%] and 100% [IQR 75, 100%], respectively. In the previous 12 months, prednisolone use was reported by 229 [29%] patients with UC vs 81 [16%] with CD, p &lt;0.001; 202 [16%] for &lt;3 months; and 108 [8%] for &gt;3 months. An IBD-related intervention was reported by 174 [13%] patients, and 80 [6%] reported an unplanned hospital admission. There were high rates of fatigue [50%] and mood disturbance [23%].

Conclusions
Outcomes reported by patients illustrate the scale of the therapeutic deficit in current care. Proof of principle is demonstrated that PROM data can be collected continuously with little burden on health care professionals. This may become a metric for quality improvement programmes or to compare outcomes.
Longer leukocyte telomere length is associated with myeloid inflammation and increased mortality after transcatheter aortic valve replacement
Authors: Hoffmann Jedrzej , Tabata Noriaki , Mas-Peiro Silvia , Spyridopoulos Ioakim , Sinning Jan-Malte , Berkowitsch Alexander , Martin-Ruiz Carmen , Al-Kassou Baravan , Herrmann Eva , Dimmeler Stefanie , Zeiher Andreas M , Vasa-Nicotera Mariuca 
Published: July 2022

AbstractAimsInflammatory activation of leukocytes may limit prognosis of patients (pts) with severe aortic valve stenosis (AS) undergoing transcatheter aortic valve replacement (TAVR). Leukocyte telomere length (LTL) is a marker of proliferative capacity and inflammatory responsiveness but the impact of LTL on the prognosis in AS remains elusive. The aim of this study was to analyse the association of LTL with inflammatory markers and prognosis of pts undergoing TAVR.Methods and resultsLTL was analysed using quantitative real-time PCR in 285 consecutive pts (median age 82 years) undergoing TAVR and correlated with 18-month all-cause mortality. C-reactive protein was significantly elevated in pts with the longest LTL (P = 0.017), paralleled by increased procalcitonin (PCT) serum levels (P = 0.0006). This inflammatory reaction was accompanied by increased myeloid cells in the highest LTL tertile, mainly a rise in circulating neutrophils (P = 0.0025) and monocytes (P = 0.01). Multivariate analysis revealed LTL (HR 2.6, 95%CI 1.4–5.1,  P= 0.004) and PCT levels (HR 4.3, 95%CI 1.7–11.0, P = 0.003) as independent predictors of mortality.ConclusionsLonger LTL is associated with increased mortality after TAVR. This might be explained by enhanced proliferative capacity of cells resulting in myeloid and systemic inflammation. Our findings suggest that targeting the specific inflammation pathways could present a novel strategy to augment survival in selected patients with degenerative aortic stenosis.
Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes
Authors: Bo Jing , Xu Han , Lv Wenqi , Wang Cheng , He Shunping , Yang Liandong 
Published: July 2022

Abstract
Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca, pik3cg, vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1, ednrb, and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments.
Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish,Atherinomorus stipes
Authors: Drown Melissa K , DeLiberto Amanda N , Flack Nicole , Doyle Meghan , Westover Alexander G , Proefrock John C , Heilshorn Sandra , D’Alessandro Evan , Crawford Douglas L , Faulk Christopher , Oleksiak Marjorie F 
Published: July 2022

AbstractGenetic data from nonmodel species can inform ecology and physiology, giving insight into a species’ distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). These fish are found in shallow coastal waters and are frequently included in ecological models because they serve as abundant prey for commercially and ecologically important species. Despite their importance in sub-tropical and tropical ecosystems, little is known about their population connectivity and genetic diversity. Our A. stipes genome assembly is about 1.2 Gb with comparable repetitive element content (∼47%), number of protein duplication events, and DNA methylation patterns to other teleost fish species. Among five sampled populations spanning 43 km of South Florida and the Florida Keys, we find little population structure suggesting high population connectivity.
A role for the Saccharomyces cerevisiae Rtt109 histone acetyltransferase in R-loop homeostasis and associated genome instability
Authors: Cañas Juan Carlos , García-Rubio María Luisa , García Alicia , Antequera Francisco , Gómez-González Belén , Aguilera Andrés 
Published: July 2022

Abstract
The stability of the genome is occasionally challenged by the formation of DNA–RNA hybrids and R-loops, which can be influenced by the chromatin context. This is mainly due to the fact that DNA–RNA hybrids hamper the progression of replication forks, leading to fork stalling and, ultimately, DNA breaks. Through a specific screening of chromatin modifiers performed in the yeast Saccharomyces cerevisiae, we have found that the Rtt109 histone acetyltransferase is involved in several steps of R-loop-metabolism and their associated genetic instability. On the one hand, Rtt109 prevents DNA–RNA hybridization by the acetylation of histone H3 lysines 14 and 23 and, on the other hand, it is involved in the repair of replication-born DNA breaks, such as those that can be caused by R-loops, by acetylating lysines 14 and 56. In addition, Rtt109 loss renders cells highly sensitive to replication stress in combination with R-loop-accumulating THO-complex mutants. Our data evidence that the chromatin context simultaneously influences the occurrence of DNA–RNA hybrid-associated DNA damage and its repair, adding complexity to the source of R-loop-associated genetic instability.
A Model of Care to Improve Survival of Older Trauma Patients: Geriatrics Comanagement
Authors: Neupane Iva , Mujahid Nadia , Zhou Eric P , Filipe Goncalves Monteiro Joao , Lueckel Stephanie , Cizginer Sevdenur , Yildiz Ferhat , Raza Sakeena , Singh Mriganka , Gravenstein Stefan , McNicoll Lynn 
Published: July 2022

Abstract

Background
Trauma patients older than 80 years of age have higher mortality rates compared to younger peers. No studies have investigated the effectiveness of geriatrics comanagement on mortality in general trauma.

Methods
A retrospective cohort study from 2015 to 2016 comparing overall and inpatient mortality in a geriatrics trauma comanagement (GTC) program versus usual care (UC). Demographic and outcome measures were obtained from the trauma registry at an 11-bed trauma critical care unit within a 719-bed Level 1 Trauma Center. One thousand five hundred and seventy two patients, 80 years and older, with an admitting trauma diagnosis were evaluated. Primary outcome was in-hospital mortality and overall mortality (defined as inpatient death or discharge to hospice). Secondary outcomes included hospital length of stay (LOS), Intensive Care Unit (ICU) LOS, discharge location, and medical complications.

Results
Three hundred and forty six patients (22%) were placed in the GTC program. Overall mortality was lower in the GTC (4.9%) when compared with UC (11.9%), representing a 57% reduction (95% odds ratio [OR] confidence interval [CI] 0.24–0.75, p value = .0028). There was a 7.42% hospital mortality rate in the UC group compared to 2.6% in the GTC group (95% CI 0.21–0.92, p value = .0285), representing a 56% decrease in in-hospital mortality. GTC patients had a longer mean LOS (6.4 days vs 5.3 days, p value &lt; .0001). More GTC patients were sent to inpatient rehabilitation facilities or skilled nursing facilities (80% vs 60%, p value &lt; .0001).

Conclusion
Geriatrics trauma comanagement of trauma patients above the age of 80 may reduce mortality and deserves formal study.