bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influences on limited antimicrobial use in small-scale freshwater aquaculture farms in central Thailand
Authors: Alhusein Nour , Chantong Boonrat , Suwanpakdee Sarin , Wiratsudakul Anuwat , Gould Virginia C. , Wichuwaranan Kantima , Poonsawad Kornrawan , Montrivade Varapon , Charoenboon Nutcha , Sringernyuang Luechai , Avison Matthew B. , Lambert Helen , Sakcamduang Walasinee , Buller Henry , Reyher Kristen K. 
Published: February 2024

AbstractRecent years have shown substantial growth both in the scale and the spread of freshwater aquaculture in Thailand, raising concerns about potential widespread antimicrobial use. This mixed-methods study used surveys and qualitative interviews to examine conditions of freshwater aquaculture farming in central Thailand in relation to animal health, disease management and patterns of antimicrobial use. Freshwater aquaculture in this area of Thailand was largely a domestic venture operated as a source of additional household income to increase financial security. Aquaculture was often integrated with other types of farming; initial outlay was reduced by repurposing unused crops, food, or animal manure (e.g. chicken droppings and pig dung) to fertilise aquaculture ponds. Among farmers representing twenty farms who were surveyed during 2019, only six farmers said they used antimicrobials. These included oxytetracycline, enrofloxacin, norfloxacin, ciprofloxacin and sulphonamides. Farmers doubted the benefits of using antimicrobials to treat aquatic animals; some believed antimicrobials stunted growth. The high cost of medicines and prohibitive regulations also discouraged antimicrobial use. Farmers linked disease occurrence to changes in the weather, the emergence of new diseases and variable water quality. They relied on farm management practices to maintain the health of their aquatic animals, using lime and salt to maintain and improve water quality and pH and to disinfect aquaculture pools. Farmers also reported obtaining juvenile fish and shrimp selectively from farms known to produce healthy stock. Specialised veterinary services for aquatic farming were rare, so farmers relied on their own experimentation with medicines, peer advice and recommendations of shopkeepers who sold both aquatic feed and medicines. This study unexpectedly reveals limited use of antimicrobials linked to socio-economic and ecological features of small-scale family aquaculture farms.
Recurrent and Concurrent Prediction of Longitudinal Progression of Stargardt Atrophy and Geographic Atrophy
Authors: Mishra Zubin , Wang Ziyuan , Xu Emily , Xu Sophia , Majid Iyad , Sadda SriniVas R. , Hu Zhihong Jewel 
Published: February 2024

AbstractStargardt disease and age-related macular degeneration are the leading causes of blindness in the juvenile and geriatric populations, respectively. The formation of atrophic regions of the macula is a hallmark of the end-stages of both diseases. The progression of these diseases is tracked using various imaging modalities, two of the most common being fundus autofluorescence (FAF) imaging and spectral-domain optical coherence tomography (SD-OCT). This study seeks to investigate the use of longitudinal FAF and SD-OCT imaging (month 0, month 6, month 12, and month 18) data for the predictive modelling of future atrophy in Stargardt and geographic atrophy. To achieve such an objective, we develop a set of novel deep convolutional neural networks enhanced with recurrent network units for longitudinal prediction and concurrent learning of ensemble network units (termed ReConNet) which take advantage of improved retinal layer features beyond the mean intensity features. Using FAF images, the neural network presented in this paper achieved mean (± standard deviation, SD) and median Dice coefficients of 0.895 (± 0.086) and 0.922 for Stargardt atrophy, and 0.864 (± 0.113) and 0.893 for geographic atrophy. Using SD-OCT images for Stargardt atrophy, the neural network achieved mean and median Dice coefficients of 0.882 (± 0.101) and 0.906, respectively. When predicting only the interval growth of the atrophic lesions with FAF images, mean (± SD) and median Dice coefficients of 0.557 (± 0.094) and 0.559 were achieved for Stargardt atrophy, and 0.612 (± 0.089) and 0.601 for geographic atrophy. The prediction performance in OCT images is comparably good to that using FAF which opens a new, more efficient, and practical door in the assessment of atrophy progression for clinical trials and retina clinics, beyond widely used FAF. These results are highly encouraging for a high-performance interval growth prediction when more frequent or longer-term longitudinal data are available in our clinics. This is a pressing task for our next step in ongoing research.
Prevalence of falls in the last weeks of life and relationship between falls, independence, and quality of dying: A secondary analysis of a large prospective cohort study
Authors: Otani Hiroyuki , Shimoinaba Junichi , Kashiwagi Hideyuki , Morita Tatsuya , Maeda Isseki , Yokomichi Naosuke , Hamano Jun , Yamaguchi Takashi , Mori Masanori 
Published: February 2024

AbstractObjectiveTo determine the frequency of falls and their serious complications in palliative care units (PCUs), as well as explore the complex interplay between falls, independence, and quality of dying.MethodsA secondary analysis of a large prospective cohort study of 23 PCUs in Japan was conducted from January 2017 to June 2018. Palliative care specialist physicians recorded whether patients experienced falls, serious complications from falls, activities that led to falls, independence (workability in the last days and use of indwelling urinary catheter), and Good Death Scale.ResultsOf the 1,633 patients evaluated, 9.2% (95% Confidence interval [95% CI 7.8 to 11]) experienced falls within 30 days prior to death. The patients who fell were mostly men, had eastern cooperative oncology group performance status 3 on admission, a longer estimated prognosis on admission, and delirium during hospitalization. Serious falls causing fractures or intracranial hemorrhages were rare (0.3% [95% CI 0.038 to 0.57]). The most common reason for falls was the need to use the toilet. The Good Death Scale and indwelling urinary catheter use were not significantly associated with falls.ConclusionFalls occur in approximately 10% of patients in PCUs, but serious complications are rare. The relationship between falls, independence, and quality of dying is complex; that is, a fall may not be necessarily bad, if it is the result of respect for the patient’s independence. Healthcare providers need to consider fall prevention while supporting patients’ desire to move on their own to maintain independence.WHAT IS ALREADY KNOWN ON THIS TOPICFalls are a major healthcare concern because of their potential to cause physical harm, emotional distress, and increased healthcare costs.Although many studies have investigated falls in acute care settings and the elderly population, there is a lack of literature specifically focusing on falls in the unique context of palliative care units.WHAT THIS STUDY ADDSFalls occur in only approximately 10% of patients, and only five cases (0.3%) of serious events were due to falls in palliative care units (PCUs).Independence and quality of dying are not significantly compromised by falls.HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYAlthough fall prevention is considered a priority, healthcare providers should support patients’ desires to move on their own to maintain independence.It may be possible to maintain independence and quality of dying even for patients who have fallen.
Experiences of faculty and scientists with disabilities at academic institutions in the United States
Authors: Castro Franz , Cerilli Caroline , Hu Luanjiao , Iezzoni Lisa , Varadaraj Varshini , Swenor Bonnielin K. 
Published: February 2024

IntroductionPeople with disabilities are underrepresented in higher education, facing systematic obstacles such as inaccessible institutions and difficulties in obtaining accommodations. This qualitative study aims to shed light on barriers to accessibility and disability inclusion in STEM and research institutions through confidential qualitative interviews with disabled faculty and scientists.MethodsWe recruited participants (via virtual flyers) working in the United States (U.S.) as research faculty or scientists that applied for grant funding (last five years), and self-identified as having a disability. Interviews (n=35) were conducted via semi-structured one-on-one live interviews or written interviews to accommodate participants’ needs. Data were analyzed by two study members using content analysis to identify themes and codes until saturation was reached.ResultsThemes included identity/visibility, career trajectories, accessibility, accommodations, bias, representation, and inclusion. Some participants reported not disclosing their disabilities at work or during hiring processes due to fear of negative perceptions from peers or potential employers. Experiences around stigma and bias were noted both in professional relationships and when interacting with disability service offices, underscoring difficulties and delays in processes to secure accommodations. Respondents highlighted the issues of lack of disability inclusion and low representation of people with disabilities in academia, elevating the importance of self-advocacy, and of role models and mentors in shaping career pathways for future researchers with disabilities.ConclusionFaculty with disabilities encounter systematic barriers at academic institutions, and lack of acknowledgement and research on these experiences has held back institutional and policy changes. To reduce disparities for disabled faculty, academic leadership must allocate resources to address ableism, create more inclusive environments, and raise standards beyond ADA compliance.
Cohort study of cardiovascular safety of different COVID-19 vaccination doses among 46 million English adults
Authors: Ip Samantha , North Teri-Louise , Torabi Fatemeh , Li Yangfan , Abbasizanjani Hoda , Akbari Ashley , Horne Elsie , Denholm Rachel , Keene Spencer , Denaxas Spiros , Banerjee Amitava , Khunti Kamlesh , Sudlow Cathie , Whiteley William N , Sterne Jonathan A C , Wood Angela M , Walker Venexia 
Published: February 2024

ABSTRACTUsing longitudinal health records from 45.7 million adults in England followed for a year, our study compared the incidence of thrombotic and cardiovascular complications after first, second and booster doses of brands and combinations of COVID-19 vaccines used during the first two years of the UK vaccination program with the incidence before or without the corresponding vaccination. The incidence of common arterial thrombotic events (mainly acute myocardial infarction and ischaemic stroke) was generally lower after each vaccine dose, brand and combination. Similarly, the incidence of common venous thrombotic events, (mainly pulmonary embolism and lower limb deep venous thrombosis) was lower after vaccination. There was a higher incidence of previously reported rare harms after vaccination: vaccine-induced thrombotic thrombocytopenia after first ChAdOx1 vaccination, and myocarditis and pericarditis after first, second and transiently after booster mRNA vaccination (BNT-162b2 and mRNA-1273). These findings support the wide uptake of future COVID-19 vaccination programs.
Active Mutual Conjoint Estimation of Multiple Contrast Sensitivity Functions
Authors: Marticorena Dom CP , Wong Quinn Wai , Browning Jake , Wilbur Ken , Davey Pinakin , Seitz Aaron R. , Gardner Jacob R. , Barbour Dennis L. 
Published: February 2024

AbstractRecent advances in nonparametric Contrast Sensitivity Function (CSF) estimation have yielded a new tradeoff between accuracy and efficiency not available to classical parametric estimators. An additional advantage of this new framework is the ability to independently tune multiple aspects of the estimator to seek further improvements. Machine Learning CSF (MLCSF) estimation with Gaussian processes allows for design optimization in the kernel, acquisition function and underlying task representation, to name a few. This paper describes a novel kernel for CSF estimation that is more flexible than a kernel based on strictly functional forms. Despite being more flexible, it can result in a more efficient estimator. Further, trial selection for data acquisition that is generalized beyond pure information gain can also improve estimator quality. Finally, introducing latent variable representations underlying general CSF shapes can enable simultaneous estimation of multiple CSFs, such as from different eyes, eccentricities or luminances. The conditions under which the new procedures perform better than previous nonparametric estimation procedures are presented and quantified.PrecisMachine learning contrast sensitivity function estimation is improved by incorporation of additional information about the nature of the underlying and data from other eyes.
PheWAS analysis on large-scale biobank data with PheTK
Authors: Tran Tam C. , Schlueter David J. , Zeng Chenjie , Mo Huan , Carroll Robert J. , Denny Joshua C. 
Published: February 2024

ABSTRACTSummaryWith the rapid growth of genetic data linked to electronic health record data in huge cohorts, large-scale phenome-wide association study (PheWAS), have become powerful discovery tools in biomedical research. PheWAS is an analysis method to study phenotype associations utilizing longitudinal electronic health record (EHR) data. Previous PheWAS packages were developed mostly in the days of smaller biobanks and with earlier PheWAS approaches. PheTK was designed to simplify analysis and efficiently handle biobank-scale data. PheTK uses multithreading and supports a full PheWAS workflow including extraction of data from OMOP databases and Hail matrix tables as well as PheWAS analysis for both phecode version 1.2 and phecodeX. Benchmarking results showed PheTK took 64% less time than the R PheWAS package to complete the same workflow. PheTK can be run locally or on cloud platforms such as theAll of UsResearcher Workbench (All of Us) or the UK Biobank (UKB) Research Analysis Platform (RAP).Availability and implementationThe PheTK package is freely available on the Python Package Index (PyPi) and on GitHub under GNU Public License (GPL-3) athttps://github.com/nhgritctran/PheTK. It is implemented in Python and platform independent. The demonstration workspace forAll of Uswill be made available in the future as a featured workspace.ContactPheTK@mail.nih.gov
Tricuspid Valve Annulus Size by Echocardiography: Predictor of Cardiac Limitation in Pediatric Pectus Excavatum
Authors: Chang James , Eubanks James , Jancelewicz Tim , Joshi Vijaya , Martinez Hugo , Shah Samir , Paton Elizabeth , Philip Ranjit 
Published: February 2024

AbstractBackgroundThe severity of pectus excavatum (PEX) as measured by Haller index (HI) does not always correlate with symptoms of aerobic capacity. Transthoracic echocardiograms (TTE) are generally reported as normal which may influence the pediatrician’s decision to refer for corrective surgery. The aim of this study was to find a reproducible TTE marker as an indicator of right ventricular compression and compare it to severity of PEX and cardiopulmonary exercise test (CPET) indices.MethodsThe study included patients aged 10-19 years with an institution-based protocol for preoperative PEX evaluation with TTE, chest computed tomography (CT) for HI, and CPET from 2015-2021. We divided the patients into two groups, mild/moderate PEX (HI 2-3.5) and severe PEX (HI > 3.5). Tricuspid valve annulus size (TVAS) was compared between the groups as well as with other CPET and TTE indices using Student’s t-test. Spearman’s rank correlation coefficient was used to evaluate correlations between the severity of PEX by HI with the TTE and CPET parameters.ResultsOf the 124 patients, 82 (66.1%) had severe PEX and 42 (33.9%) had mild/moderate PEX. The mean TVAS z-scores in the mild/moderate PEX group was -1.98(SD 0.51) and -2.24 (SD 0.71) in the severe PEX group (p 0.046). There was a negative correlation between the TVAS z-score and the severity of PEX but this was not statistically significant (r = -0.154, p = 0.087). There was no significant difference in peak oxygen uptake (peak VO2) or left ventricular ejection fraction between the severity groups. However, the TVAS z-score positively correlated with peak VO2(median 43 ml/kg/min, r = 0.023, p = 0.01), peak VO2percent predicted (median 86%, r = 0.19, p = 0.04), and O2pulse (median 12.7 ml/beat, r = 0.20, p = 0.025), and negatively correlated with VE/VCO2(median 29, r = -0.23, p = 0.01).ConclusionThe severity of PEX by HI does not factor in the location of cardiac compression and may not always reflect the degree of cardiac limitation. The Tricuspid valve annulus size is a good TTE indicator of cardiopulmonary compromise from PEX. A TVAS z score <-2 is a good predictor of cardiac compromise in pediatric PEX. This may provide additional functional parameters in the decision-making process for corrective surgery.
Phosphoketolase and KDPG aldolase metabolism modulate photosynthetic carbon yield in cyanobacteria
Authors: Xie Ningdong , Sharma Chetna , Rusche Katherine , Wang Xin 
Published: February 2024

AbstractCyanobacteria contribute to roughly a quarter of global net carbon fixation. During diel light/dark growth, dark respiration significantly lowers the overall photosynthetic carbon yield in cyanobacteria and other phototrophs. Currently, it is unclear how respiratory pathways participate in allocating carbon resources at night to optimize dark survival and support daytime photosynthesis. Here we show in the cyanobacteriumSynechococcus elongatusPCC 7942 that phosphoketolase is orchestrated in an integrative respiratory network in the dark to best allocate carbon resource for amino acid synthesis and prepare for photosynthesis reinitiation upon photoinduction. We further show that the respiratory Entner-Doudoroff (ED) pathway inS. elongatusis incomplete, with its key enzyme 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase serving to modulate daytime photosynthesis through an alternative oxaloacetate decarboxylation activity. This activity allows for the bypassing of the tricarboxylic acid (TCA) cycle when ATP/NADPH consumption for biosynthesis is excessive and imbalanced relative to their production by light reactions, thereby preventing relative NADPH accumulation and ensuring optimal photosynthetic carbon yield. Optimizing these metabolic processes offers new opportunities to enhance photosynthetic carbon yield in cyanobacteria and other photosynthetic organisms under diel light/dark cycles.
Compensatory mutations potentiate constructive neutral evolution by gene duplication
Authors: Després Philippe C , Dubé Alexandre K , Grenier Jordan , Picard Marie-Ève , Shi Rong , Landry Christian R 
Published: February 2024

AbstractProtein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.One sentence summaryCompensatory deleterious mutations entangle gene duplicates
Instantaneous change in hyphal diameter in basidiomycete fungi
Authors: Mazheika Igor , Voronko Oxana , Kolomiets Oxana , Kamzolkina Olga 
Published: February 2024

ABSTRACTUnder certain conditions, fungi can rapidly change the size of their cells. For example, it is known that the cells of many yeast species under hyperosmosis instantly and reversibly shrink entirely, without plasmolysis, with a decrease in volume of up to 70%. There is evidence that filamentous fungi can also instantly change the diameter of their unspecialized hyphae. This property is fundamental but requires detailed study. In this large-scale study (involving more than 50,000 cells measured) using light microscopy, the ability of three unrelated basidiomycete species to rapidly change the diameter of their hyphae under various factors was analyzed. It was found that all three fungi respond similarly to moderate hyperosmotic shock or detergent treatment, shrinking by an average of 12–14% in diameter. However, inhibitors of actin assembly can cause either expansion or shrinkage of hyphae or have no effect on a fungus. These results, along with previously established features of the macroinvagination systems of the plasma membrane in basidiomycetes, are important for understanding the complex structural-protective physiological mechanisms responsible for the survival and continuous functioning of fungal cells in unstable environmental conditions.