bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poly(U) polymerase activity in Caenorhabditis elegans regulates abundance and tailing of sRNA and mRNA
Authors: Kelley Leanne H , Caldas Ian V , Sullenberger Matthew T , Yongblah Kevin E , Niazi Adnan M , Iyer Anoop , Li Yini , Tran Patrick Minty , Valen Eivind , Ahmed-Braimah Yasir H , Maine Eleanor M 
Published: July 2024

Abstract
Terminal nucleotidyltransferases add nucleotides to the 3′ end of RNA to modify their stability and function. In Caenorhabditis elegans, the terminal uridyltransferases/poly(U) polymerases PUP-1 (aka CID-1, CDE-1), PUP-2, and PUP-3 affect germline identity, survival, and development. Here, we identify small RNA (sRNA) and mRNA targets of these PUPs and of a fourth predicted poly(U) polymerase, F43E2.1/PUP-4. Using genetic and RNA sequencing approaches, we identify RNA targets of each PUP and the U-tail frequency and length of those targets. At the whole organism level, PUP-1 is responsible for most sRNA U-tailing, and other PUPs contribute to modifying discrete subsets of sRNAs. Moreover, the expression of PUP-2, PUP-3, and especially PUP-4 limits uridylation on some sRNAs. The relationship between uridylation status and sRNA abundance suggests that U-tailing can have a negative or positive effect on abundance depending on context. sRNAs modified by PUP activity primarily target mRNAs that are ubiquitously expressed or most highly expressed in the germline. mRNA data obtained with a Nanopore-based method reveal that the addition of U-tails to nonadenylated mRNA is substantially reduced in the absence of PUP-3. Overall, this work identifies PUP RNA targets, defines the effect of uridylation loss on RNA abundance, and reveals the complexity of PUP regulation in C. elegans development.
Upscaling from mineral microstructures to tectonic macrostructures
Authors: Bercovici David , Girard Jennifer , Mulyukova Elvira 
Published: July 2024

SUMMARY
Earth’s plate tectonic behaviour arises from lithospheric ductile weakening and shear-localization. The ubiquity of mylonites at lithospheric shear zones is evidence that localization is caused by mineral grain size reduction. Most lithospheric mylonites are polymineralic, suggesting that the interaction between mineral phases by Zener pinning promotes grain size reduction and weakening. Yet this interaction only occurs where mineral phases mix at the grain scale. Phase mixing and its effect on microstructure and strength have been shown in deformation experiments and natural field samples. Our theory for the interaction between phase mixing (treated as a stress driven diffusion) with two-phase grain damage has been compared to lab experiments. But using processes at the tiny grain-scale embedded within the small hand-sample and lab scales to model large-scale lithospheric processes, requires an upscaling scheme that captures the physics from micro- to macrostructures. For example, weakening from grain-damage in zones of mixing can lead to banded viscosity structure at the small scale that manifests as viscous anisotropy at the large scale. Here we provide a new framework for self-consistently upscaling from microscopic (grain) scales, to mesoscopic (petrological heterogeneity) scales to macroscopic (tectonic) scales. The first upscaling step models phase mixing and grain size evolution in a small ‘mesoscopic’ lab-scale volume or ‘patch’, which is equivalent to a point in the macroscopic space. Within this mesoscale patch, stress driven diffusive mixing is described by an analytical solution for mineral phase fraction, provided a minimalist Fourier representation of phase fraction, and a transformation to the patch frame of reference as well as to the principal stress directions at that point. The orientation and volume fraction of mixed-phase regions can then be extracted from the analytical solution for phase fraction. The grain size and viscosity in the mixed bands are determined by two-phase grain-damage theory; the unmixed zone properties follow from mono-phase grain damage theory. The mesoscale banded viscosity field leads to a macroscale anisotropic viscosity at that point in space. But, the evolution of properties at each macroscale point involves tracking only a few quantities (phase fraction, grain sizes) rather than modelling each patch of mesoscale space as its own 2-D or 3-D system. For the final upscaling, the anisotropic viscosity field is used in a macroscale lithosphere flow model. We show an example of this scheme for a lithospheric Rayleigh–Taylor drip driven by ridge-push compressive stress, which can cause anisotropic weakening via grain mixing and damage that may help initiate subduction and passive margin collapse.
Development and validation of a community risk score for sexual and reproductive health in the United States
Authors: Lines Lisa M , Fowler Christina I , Kaganova Yevgeniya , Peacock Karen 
Published: July 2024

Abstract
Equitable access to sexual and reproductive health (SRH) care is key to reducing inequities in SRH outcomes. Publicly funded family-planning services are an important source of SRH care for people with social risk factors that impede their access. This study aimed to create a new index (Local Social Inequity in SRH [LSI-SRH]) to measure community-level risk of adverse SRH outcomes based on social determinants of health (SDoH). We evaluated the validity of the LSI-SRH scores in predicting adverse SRH outcomes and the need for publicly funded services. The data were drawn from more than 200 publicly available SDoH and SRH measures, including availability and potential need for publicly supported family planning from the Guttmacher Institute. The sample included 72 999 Census tracts (99.9%) in the 50 states and the District of Columbia. We used random forest regression to predict the LSI-SRH scores; 42 indicators were retained in the final model. The LSI-SRH model explained 81% of variance in the composite SRH outcome, outperforming 3 general SDoH indices. LSI-SRH scores could be a useful for measuring community-level SRH risk and guiding site placement and resource allocation.
Enablers and barriers to implementing cholera interventions in Nigeria: a community-based system dynamics approach
Authors: Elimian Kelly , Diaconu Karin , Ansah John , King Carina , Dewa Ozius , Yennan Sebastian , Gandi Benjamin , Forsberg Birger Carl , Ihekweazu Chikwe , Alfvén Tobias 
Published: July 2024

Abstract
Nigeria accounts for a substantial cholera burden globally, particularly in its northeast region, where insurgency is persistent and widespread. We used participatory group model building workshops to explore enablers and barriers to implementing known cholera interventions, including water, sanitation and hygiene, surveillance and laboratory, case management, community engagement, oral cholera vaccine, and leadership and coordination, as well as exploring leverage points for interventions and collaboration. The study engaged key cholera stakeholders in the northeastern States of Adamawa and Bauchi, as well as national stakeholders in Abuja. Adamawa and Bauchi States’ group modes building participants comprised 49 community members and 43 healthcare providers, while the 23 national participants comprised government ministry, department and agency staff, and development partners. Data were analysed thematically and validated via consultation with selected participants. The study identified four overarching themes regarding the enablers and barriers to implementing cholera interventions: (1) political will, (2) health system resources and structures, (3) community trust and culture, and (4) spill-over effect of COVID-19. Specifically, inadequate political will exerts its effect directly (e.g. limited funding for prepositioning essential cholera supplies) or indirectly (e.g. overlapping policies) on implementing cholera interventions. The healthcare system structure (e.g. centralization of cholera management in a State capital) and limited surveillance tools weaken the capacity to implement cholera interventions. Community trust emerges as integral to strengthening the healthcare system’s resilience in mitigating the impacts of cholera outbreaks. Lastly, the spill-over effects of COVID-19 helped promote interventions similar to cholera (e.g. water, sanitation and hygiene) and directly enhanced political will. In conclusion, the study offers insights into the complex barriers and enablers to implementing cholera interventions in Nigeria’s cholera-endemic settings. Strong political commitment, strengthening the healthcare system, building community trust and an effective public health system can enhance the implementation of cholera interventions in Nigeria.
Is ATP a signaling regulator for postharvest chilling tolerance in fruits?
Authors: Sati Hansika , Oberoi Harinder Singh , Pareek Sunil 
Published: July 2024

Abstract
Low-temperature storage is used to extend the shelf life of fruits, but prolonged storage at temperatures below tolerable levels may cause postharvest chilling injury (PCI) in sensitive commodities. This review aims to highlight adenosine triphosphate (ATP) activation and the interplay of extracellular ATP (eATP) and intracellular ATP (iATP) in fruits and to find out its significance in mitigating PCI. Various pathways, such as the Embden–Meyerhof–Parnas pathway, the tricarboxylic acid cycle, the pentose phosphate pathway, the γ-aminobutyric acid shunt pathway, and the cytochrome pathway, are studied critically to elucidate their role in continuous ATP supply and maintaining the membrane fluidity and integrity. This review summarizes the treatments helpful in modulating energy metabolism in fruit. Additionally, this work provides insights into the energy status in attenuating chilling tolerance. Moreover, it states the potential of nicotinamide adenine dinucleotide in mitigating PCI. Furthermore, it discusses the role of eATP and its receptor DORN1 in mitigating chilling stress.
Economic Sanctions and Food Consumption: Evidence from Iranian Households
Authors: RezaeeDaryakenari Babak , Asadzade Peyman , Thies Cameron G 
Published: July 2024

Abstracts
Despite scholarly consensus on the harmful effects of economic sanctions on civilians, there is little micro-level empirical research on how and to what extent economic sanctions affect the food consumption of citizens in sanctioned countries. One of the methodological barriers to studying the micro-level dynamics of sanctions is the limited availability of reliable data in sanctioned countries, which are often governed by authoritarian leaders. Our study leverages an original dataset comprising approximately 1 million observations related to the income and expenses of Iranian households from 1991 to 2021. We assess the impact of economic sanctions on individual food consumption at the national level and among distinct demographic segments. To illustrate how and to what extent international sanctions affected citizens' eating habits, we pay particular attention to 2012–2015 and 2018–2021, when Iran was subject to the most severe sanctions. Our findings demonstrate that while all segments of society feel the effects of economic coercion, low-income citizens' food consumption is more likely to deteriorate due to sanctions. Nonetheless, the geographical impact of sanctions presents a mixed picture, with rural and urban areas each exhibiting specific vulnerabilities to certain food items. We discuss the implications of our findings for sanctions policy and human rights.
CTC-177, a novel drug–Fc conjugate, shows promise as an immunoprophylactic agent against multidrug-resistant Gram-negative bacterial infections
Authors: Lovey Arianne , Lee Annie , Yu Allison , Krel Mila , Wang Mingming , Paderu Padmaja , Brady Thomas , Hough Grayson , Zhao Qiping , Balkovec James M , Perlin David S , Zhao Yanan 
Published: July 2024

Abstract

Background
The widespread emergence of antibiotic resistance including MDR in Gram-negative bacterial pathogens poses a critical challenge to the current antimicrobial armamentarium.

Objectives
To create a novel drug–Fc conjugate (DFC) that can be delivered at sustained and prolonged levels while simultaneously activating the host immune response to combat MDR Gram-negative infections.

Methods
The Cloudbreak™ platform was used to develop DFCs consisting of a targeting moiety (TM) (a polymyxin-derived dimer) attached via a non-cleavable linker to an effector moiety (EM) (the Fc domain of human IgG1). In vitro activities of the DFCs were assessed by MIC testing. Neutropenic mouse models of thigh infection, septicaemia and pneumonia were used to evaluate in vivo efficacy. Pharmacokinetics were evaluated in mice and cynomolgus monkeys.

Results
A single prophylactic dose of our lead DFC, CTC-177, resulted in significantly decreased bacterial burdens and reduced inflammation comparable to daily treatment with colistin in septicaemia and pneumonia mouse models. Furthermore, CTC-177 prophylaxis was able to restore colistin efficacy in colistin-resistant septicaemia, reducing bacterial burdens beyond the limit of detection. Finally, CTC-177 displayed a long terminal half-life of over 24 and 65 h in mice and cynomolgus monkeys, respectively.

Conclusions
These data support the continued development of Cloudbreak™ DFCs as broad-spectrum prophylactic agents against Gram-negative infections.
Development and initial validation of a data quality evaluation tool in obstetrics real-world data through HL7-FHIR interoperable Bayesian networks and expert rules
Authors: Coutinho-Almeida João , Saez Carlos , Correia Ricardo , Rodrigues Pedro Pereira 
Published: July 2024

Abstract

Background
The increasing prevalence of electronic health records (EHRs) in healthcare systems globally has underscored the importance of data quality for clinical decision-making and research, particularly in obstetrics. High-quality data is vital for an accurate representation of patient populations and to avoid erroneous healthcare decisions. However, existing studies have highlighted significant challenges in EHR data quality, necessitating innovative tools and methodologies for effective data quality assessment and improvement.

Objective
This article addresses the critical need for data quality evaluation in obstetrics by developing a novel tool. The tool utilizes Health Level 7 (HL7) Fast Healthcare Interoperable Resources (FHIR) standards in conjunction with Bayesian Networks and expert rules, offering a novel approach to assessing data quality in real-world obstetrics data.

Methods
A harmonized framework focusing on completeness, plausibility, and conformance underpins our methodology. We employed Bayesian networks for advanced probabilistic modeling, integrated outlier detection methods, and a rule-based system grounded in domain-specific knowledge. The development and validation of the tool were based on obstetrics data from 9 Portuguese hospitals, spanning the years 2019-2020.

Results
The developed tool demonstrated strong potential for identifying data quality issues in obstetrics EHRs. Bayesian networks used in the tool showed high performance for various features with area under the receiver operating characteristic curve (AUROC) between 75% and 97%. The tool’s infrastructure and interoperable format as a FHIR Application Programming Interface (API) enables a possible deployment of a real-time data quality assessment in obstetrics settings. Our initial assessments show promised, even when compared with physicians’ assessment of real records, the tool can reach AUROC of 88%, depending on the threshold defined.

Discussion
Our results also show that obstetrics clinical records are difficult to assess in terms of quality and assessments like ours could benefit from more categorical approaches of ranking between bad and good quality.

Conclusion
This study contributes significantly to the field of EHR data quality assessment, with a specific focus on obstetrics. The combination of HL7-FHIR interoperability, machine learning techniques, and expert knowledge presents a robust, adaptable solution to the challenges of healthcare data quality. Future research should explore tailored data quality evaluations for different healthcare contexts, as well as further validation of the tool capabilities, enhancing the tool’s utility across diverse medical domains.
Cholecalciferol and Ergocalciferol Replacement in Critically Injured Burn Patients: An Observational Cohort Study
Authors: Vanderwyk Kees , Young Sierra , Louie Erin , Wong Kristi , La Force Jessica , Alexander Molly , Sen Soman , Duby Jeremiah J 
Published: July 2024

Abstract
Vitamin D deficiency appears to be more prevalent than previously considered in the adult critically ill population, specifically burn-injured patients. No definitive regimen has been shown to restore vitamin D (25(OH)D) levels more effectively to therapeutic levels in the burn-injured population. The purpose of this study was to investigate the effects of either ergocalciferol (D2, 50 000 IU weekly) or cholecalciferol (D3, 6000 IU daily) in adults with burns ≥10% TBSA. This retrospective, observational study (2020-2022) included patients with vitamin D insufficiency (&lt;30 ng/mL) who received replacement and monitoring with weekly vitamin D levels. Patients on dialysis or those with a hospital length of stay less than 2 weeks were excluded. Forty-five patients treated with ergocalciferol and 99 patients with cholecalciferol were included in the study. Patients treated with cholecalciferol were more likely to achieve 25(OH)D levels greater than 30 ng/mL compared to ergocalciferol over a 42-day period (HR 23.56, [95% CI, 12.57-44.16], P &lt; .0001). A higher proportion of patients in the cholecalciferol group achieved vitamin D greater than 20 ng/mL (HR 6.37, [95% CI, 4.20-9.66], P &lt; .0001). The adjusted hazard ratios (D3 vs D2) for achieving 25(OH)D levels &gt; 30 ng/mL and &gt; 20 ng/mL were and 23.94 (95% CI 5.09-427.6, P = .0019) and 7.32 (95% CI, 3.83-15.52, P &lt; .0001) respectively, after controlling for TBSA and initial 25(OH)D. Cholecalciferol appears to be a more effective agent than ergocalciferol for correcting vitamin D deficiency and insufficiency in patients with burn injuries.
Extended flexible sigmoidoscopy using water exchange facilitates a complete colon examination without sedation in participants undergoing average risk colorectal cancer screening: results from a randomized trial
Authors: Bak Adrian , Parker Brent , Perini Rafael , Aulakh Arshbir , Oliveira Caio , Richardson Wes , Hirschkorn Peter , Sullivan Barry , Recsky Magda , Orlando Tess , Leung Felix 
Published: July 2024

Lay Summary
Colon cancer is a leading cause of cancer deaths. Leading guidelines recommend flexible sigmoidoscopy (FS) every 10 years as a screening option for average-risk people. One area of progress involves a method called water exchange (WE). This is useful for cancer screening. We performed a randomized controlled trial on 90 average-risk individuals aged 50-74. They were tested with 2 methods: unsedated extended FS using either WE or the standard method of gas insufflation (GAS). Both methods showed similar success in examining the whole colon. More participants were satisfied with WE than GAS. Both groups felt little pain. Our study shows that modern methods, especially using WE, are effective and safe. They may remove the need for sedation, making it easier to include in large-scale screening programs.
Modified crayfish optimization algorithm with adaptive spiral elite greedy opposition-based learning and search-hide strategy for global optimization
Authors: Li Guanghui , Zhang Taihua , Tsai Chieh-Yuan , Lu Yao , Yang Jun , Yao Liguo 
Published: July 2024

Abstract
Crayfish optimization algorithm (COA) is a novel bionic metaheuristic algorithm with high convergence speed and solution accuracy. However, in some complex optimization problems and real application scenarios, the performance of COA is not satisfactory. In order to overcome the challenges encountered by COA, such as being stuck in the local optimal and insufficient search range, this paper proposes four improvement strategies: search-hide, adaptive spiral elite greedy opposition-based learning, competition-elimination, and chaos mutation. To evaluate the convergence accuracy, speed, and robustness of the modified crayfish optimization algorithm (MCOA), some simulation comparison experiments of 10 algorithms are conducted. Experimental results show that the MCOA achieved the minor Friedman test value in 23 test functions, CEC2014 and CEC2020, and achieved average superiority rates of 80.97%, 72.59%, and 71.11% in the WT, respectively. In addition, MCOA shows high applicability and progressiveness in five engineering problems in actual industrial field. Moreover, MCOA achieved 80% and 100% superiority rate against COA on CEC2020 and the fixed-dimension function of 23 benchmark test functions. Finally, MCOA owns better convergence and population diversity.
Asian Mus musculus: subspecies divergence, genetic diversity, and historical biogeography
Authors: Amir Afzali Yaser 
Published: July 2024

Abstract
The House Mouse, Mus musculus, is a model organism that has greatly contributed to evolutionary research. Despite its significance, there remain gaps in our understanding of its phylogeography and population genetic structure in Asian regions. This comprehensive study aims to elucidate the evolutionary history, genetic diversity, and distribution patterns of M. musculus. A diverse data set of 281 M. musculus samples was collected from across Asia, covering 101 localities in 19 countries. Phylogenetic analysis using Cytochrome b and D-Loop region unveiled well-supported lineages. These lineages correspond to: M. m. musculus, M. m. domesticus, M. m. castaneus, and M. m. bactrianus. Also, validity of M. m. bactrianus was questioned. The analysis suggests a monophyletic origin of these subspecies approximately 0.59 million years ago (Mya), followed by 2 main lineages—one consisting of M. m. domesticus (~0.59 Mya) and the other comprising M. m. castaneus, M. m. bactrianus, and M. m. musculus (~0.56 Mya). Genetic diversity varied among subspecies, with M. m. domesticus exhibiting the highest diversity due to its extensive global distribution and M. m. bactrianus exhibiting the lowest diversity due to restriction in southwest Asia. Pairwise genetic distances and Fst values confirmed significant genetic differentiation among the subspecies, underlining their historical isolation. Additionally, a Mantel test indicated that geographical distance played a pivotal role in shaping genetic differentiation. Demographic analysis revealed evidence of population expansions in M. m. domesticus, M. m. musculus, and M. m. castaneus, while M. m. bactrianus showed characteristics of neutral selection and genetic drift. Species distribution modeling, assessing both Current Conditions and the Last Glacial Maximum, indicated habitat shifts and losses during glacial periods, particularly in the eastern and northern regions of Asia. However, each subspecies displayed unique responses to climatic changes, reflecting their distinct ecological adaptations. Historical biogeography analysis pointed to complex origins and a network of dispersal and vicariance events that led to the contemporary distribution of subspecies. Deserts and xeric shrublands emerged as critical areas for diversification and speciation. This study contributes to our understanding of the phylogeography and population genetics of M. musculus in Asia, highlighting the significance of geographical factors and climatic fluctuations in shaping its evolutionary history and genetic diversity.