bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitability of Polygonal Soils in the Hyper‐Arid Atacama Desert After a Simulated Rain Experiment
Authors: Sager Christof , Airo Alessandro , Mangelsdorf Kai , Arens Felix L. , Karger Cornelia , Schulze‐Makuch Dirk 
Published: April 2023

AbstractIn the hyper‐arid Atacama Desert, microbial life thrives near its “dry limit” in scarcely distributed habitats. Fracture networks of salt‐poor sand wedges outlining salt‐cemented polygons on alluvial surfaces in the Yungay region (Chile) represent potential microbial habitats. The degree of soil habitability at the surface (0–5 cm depth) and subsurface (10–15 cm depth) of a polygon and adjacent sand wedge was assessed before and up to 42 days after a 20 mm simulated rain experiment through the abundance of phospholipid fatty acids (PLFAs). Mineralogical composition, salinity, pH, electrical and thermal conductivity, water content, and water activity were analyzed for their relevance to habitability. After wetting, the PLFA content exclusively increased steadily with time in the polygon subsurface indicating the growth of an indigenous bacterial community. This increased habitability is presumably related to the soil's ability to retain water for at least 6 weeks at this depth. The lack of a continuous growth signal at the surface is likely due to rapid desiccation. In the sand wedge subsurface, the increase in PLFA content is not continuous despite the water activity being >0.9. The reason for this remains unclear but indicates that not only water availability is relevant for habitability but also the here described soil heterogeneities might impact the detection of the microbial response. Yet, the increasing PLFA trend in the polygon subsurface emphasized its relevance as a saline microbial habitat in an otherwise hostile environment, which could have implications for the assessment of soil habitability on Mars.
Distinct Hydrologic Pathways Regulate Perennial Surface Water Dynamics in a Hyperarid Basin
Authors: McKnight S. V. , Boutt D. F. , Munk L. A. , Moran B. 
Published: April 2023

AbstractIn water‐stressed hyperarid basins, questions mount over the impacts of anthropogenic groundwater extraction and climate‐driven perturbations on groundwater‐surface water interactions and the resilience of ecosystem‐critical surface water. Coupling groundwater with surface water observations from Sentinel‐2 data provides an unprecedented opportunity to evaluate surface water connectivity with local aquifers following intense precipitation events in arid basins. Surface water area and groundwater level data were analyzed for trends following precipitation, including peak lag time, post‐peak recession rates, and changes in hydraulic gradients. Results indicate variable connectivity following large precipitation events between surface water change and groundwater level fluctuations in the upgradient freshwater aquifer, whereas the downgradient brine‐to‐brackish area of the aquifer indicated virtually no connectivity with the aquifer. Comparison between precipitation and surface water response indicate distinct responses based on the physical relationship of the surface water body with the brine‐to‐brackish area of the aquifer. Lumped parameter modeling of surface water inundation also constrains the possible hydrologic dynamics of the post‐precipitation response. While modeled influx to surface water seems primarily controlled by watershed hydraulics rather than direct hydraulic connectivity of the aquifers, the relationship between surface water and adjacent groundwater levels coupled with surface water area indicates that local aquifers are primarily connected to the surface water bodies through discharge via subsurface infiltration. Modeling results imply that the existence of brine‐adjacent surface water in arid basins relies on upgradient discharge from freshwater aquifers. Our results further support that marginal surface water systems can serve as a critical recharge mechanism to local aquifers.
Rapid detection of neurons in widefield calcium imaging datasets after training with synthetic data
Authors: Zhang Yuanlong , Zhang Guoxun , Han Xiaofei , Wu Jiamin , Li Ziwei , Li Xinyang , Xiao Guihua , Xie Hao , Fang Lu , Dai Qionghai 
Published: April 2023

AbstractWidefield microscopy can provide optical access to multi-millimeter fields of view and thousands of neurons in mammalian brains at video rate. However, tissue scattering and background contamination results in signal deterioration, making the extraction of neuronal activity challenging, laborious and time consuming. Here we present our deep-learning-based widefield neuron finder (DeepWonder), which is trained by simulated functional recordings and effectively works on experimental data to achieve high-fidelity neuronal extraction. Equipped with systematic background contribution priors, DeepWonder conducts neuronal inference with an order-of-magnitude-faster speed and improved accuracy compared with alternative approaches. DeepWonder removes background contaminations and is computationally efficient. Specifically, DeepWonder accomplishes 50-fold signal-to-background ratio enhancement when processing terabytes-scale cortex-wide functional recordings, with over 14,000 neurons extracted in 17 h.
Evaluation of the biological activity of nanoemulsions fabricated by walnut oil (Juglans regia L.)
Authors: Khezri Somayeh , Karimian Sara , Yousefi Ehsan , Es‐haghi Ali 
Published: April 2023

AbstractHerbal medicines are currently attracting much attention as a potential cancer treatment. Juglans regia’s wide variety of anticancer actions have been demonstrated. The aim of this study is evaluating the cytotoxic and antioxidant effects of walnut oil (J. regia) nanoemulsion (WO‐NE) on CT26 colon cancer cell line. The dimensions and structure of the nanoemulsion were studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The 1,1‐Diphenyl‐2‐picrylhydrazyl (DPPH) technique was used to determine whether or not the nanoemulsions had any antioxidant properties. The cytotoxic effects of 3‐[4,5‐dimethylthiazol‐2‐yl‐2‐5‐[diphenyltetrazolium bromide] (MTT) on CT26 colon cancer cells and umbilical vein endothelial cells (HUVEC) as normal cells were measured. The DPPH experiment demonstrated that the manufactured nanoemulsion had the ability to scavenge free radicals in a dose‐dependent manner, with an IC50 of approximately 500 µg/mL. The WO‐NE were found to be toxic to both HUVEC and CT26 cancer cells, with an IC50 of 10 ± 2.6 µg/mL for the CT26 and 160 ± 7.1 µg/mL for the HUVEC after 24 h of incubation. For comparison the effects of walnut oil also have been investigated. Due to their antioxidant and anticancer capabilities, the WO‐NE synthesized here have been proposed for future study as potential anti‐tumour agents.
Facial involvement is reflective of patients’ global perception of vitiligo extent
Authors: Merhi Samar , Salameh Pascale , Abboud Mounya , Seneschal Julien , Eleftheriadou Viktoria  , Pane Isabelle , Tran Viet-Thi , Shourick Jason , Ezzedine Khaled  
Published: April 2023

Abstract

Background
The involvement of visible areas in vitiligo has been found to be correlated with increased psychiatric morbidity. Although multiple tools have been developed to assess vitiligo, no cutoff for improvement or worsening of vitiligo from a patient’s perspective has been established.

Objectives
To determine the minimal clinically important difference (MCID) of the Self-Assessment Vitiligo Extent Score (SA-VES) in patients with vitiligo and to evaluate, from the patient’s perspective, the importance of the change in the involvement of visible areas (face and hands) in patients’ overall perception of disease worsening or improving.

Methods
This was a cross-sectional study in the context of the ComPaRe e-cohort. Adult patients with vitiligo were invited to answer online questionnaires. They completed the SA-VES twice, 1 year apart. In addition, patients answered a 5-point Likert anchor question aimed at assessing their perception of the evolution of the extent of their vitiligo. The MCID was calculated using distribution- and anchor-based approaches. Using ordinal logistic regression, the change of vitiliginous lesions on the face or hands was compared to the overall extent of vitiligo (patches on all body areas).

Results
In total, 244 patients with vitiligo were included in the analyses; 20 (8%) were found to have an improvement in their vitiligo. The MCID in worsened patients was equal to a 1.3% body surface area [95% confidence interval (CI) 1.01–1.43] increase in the SA-VES. For participants with improved vitiligo, the MCID was equal to a decrease in total SA-VES of 1.3% (95% CI 0.867–1.697). Patients’ perceptions of change in their vitiligo was increased sevenfold when it affected the face vs. the rest of the body.

Conclusions
Changes in the facial SA-VES were highly correlated with patients’ impressions of the extent of vitiligo.
A happy accident: a novel turfgrass reference genome
Authors: Phillips Alyssa R , Seetharam Arun S , Albert Patrice S , AuBuchon-Elder Taylor , Birchler James A , Buckler Edward S , Gillespie Lynn J , Hufford Matthew B , Llaca Victor , Romay Maria Cinta , Soreng Robert J , Kellogg Elizabeth A , Ross-Ibarra Jeffrey 
Published: April 2023

Abstract
Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
A Bayesian two-stage group sequential scheme for ordinal endpoints
Authors: Zhong Chengxue , Miao Hongyu , Pan Haitao 
Published: April 2023

AbstractOrdinal endpoints are common in clinical studies. For example, many clinical trials for evaluating COVID-19 infection therapies have adopted an ordinal scale as recommended by the World Health Organization. Despite their importance in clinical studies, design methods for ordinal endpoints are limited; in practice, a dichotomized approach is often used for simplicity. Here, we introduce a Bayesian group sequential scheme to assess ordinal endpoints, which considers a proportional-odds (PO) model, a nonproportional-odds (NPO) model, and a PO/NPO-switch model to handle various scenarios. Extensive simulations are conducted to demonstrate desirable performance, and the R package BayesOrdDesign has been made publicly available.
Enslaved Litigants, Emotions, and a Shifting Legal Landscape in Cauca, Colombia (1825–1831)
Authors: Pérez-Villa Ángela 
Published: April 2023

Abstract
This article reconstructs judicial practice in Cauca, Republic of Colombia, through the close reading of two criminal court cases involving enslaved litigants during the early transition from colony to independent state. In 1825, the enactment of laws that created new courts, judgeships, and procedures aimed to restructure and strengthen judicial practice in a nascent republic convulsed by internal division, which would disintegrate politically in 1831. Enslaved people—who had a long engagement with the law since colonial times—litigated in this context of political and judicial transformation in cases about adultery, theft, murder, vagrancy, cruelty, and freedom. This article sheds light on how these litigants were caught in the tensions that emerged between low- and high-ranking legal authorities over conflicting understandings of the role of religious thinking and the use of emotions in the adjudication of criminal cases and their appeals. In addition to drawing from the rich scholarship on slavery and the law in Latin America, this article broadly addresses recent calls from Latin America-based scholars to nourish national historiographies by inserting “the emotional” into the analytical framework. Through this approach, enslaved litigants appear moving through an uneven judicial apparatus in which authorities tried balancing their desire to uphold new procedural rules to create a secular legal sphere on the one hand and their personal religious convictions and status as enslavers on the other.
Pharmacological Interventions for the Prevention of Antipsychotic-Induced Weight Gain in People With Schizophrenia: A Cochrane Systematic Review and Meta-Analysis
Authors: Agarwal Sri Mahavir , Stogios Nicolette , Faulkner Guy E J , Hahn Margaret 
Published: April 2023

Abstract
Patients with schizophrenia are burdened by higher rates of obesity, cardiovascular disease and reduced life expectancy than the general population. In addition to illness, genetic and lifestyle factors, the associated weight gain and metabolic adverse effects of antipsychotic (AP) medications are known to exacerbate and accelerate these cardiometabolic problems significantly. Given the detrimental consequences of weight gain and other metabolic disturbances, there is an urgent need for safe and effective strategies to manage these issues as early on as possible. This review summarizes the literature of adjunctive pharmacological interventions aimed at preventing AP-induced weight gain.
The challenge of medication adherence to reduce cardiovascular risk in primary care: a mixed design multi-center study in underserved populations
Authors: Puschel K , Gonzalez K , Varas J , Sateler J , Aravena H , Greig D , Escalona G , Palominos M , Rioseco A , Cea A , Thompson B 
Published: April 2023

AbstractBackgroundCardiovascular disease is a leading cause of death in Latin America. Internationally, low medication adherence is associated with 15% to 40% of excess cardiovascular deaths. In Latin America, the magnitude of low medication adherence and the factors associated with it, are not well known, especially among socially vulnerable populations. The aim of this study is to estimate the magnitude and associated factors of low medication adherence in a socially vulnerable population with high cardiovascular risk in Chile.MethodsThe study is based on a mixed-methods design. It included a multicenter cross-sectional design of a randomly selected clinical population of 900 participants, and a qualitative design based on the analytical framework model, that included patients and health team members, from three primary care clinics in Chile.ResultsOnly 24.6% from the 886 (out of 900) patients who completed the study had “high” medication adherence, 24.9% had “regular,” and 50.4% had “low” adherence. Depression was the main factor associated with regular and low adherence combined (OR: 2.12; 95%CI:1.55-2.89). Confusion and tiredness were identified as barriers for adherence. Main facilitators reported by patients included better understanding of the medications, and availability of reminders. Clearer information and family support were identified by team members as initiators for improving adherence.ConclusionLow medication adherence is highly prevalent among patients with high cardiovascular risk in a low-income population in Chile. Quantitatively, depression was a significant risk factor for regular and low adherence; qualitatively, confusion and tiredness were identified as barriers. Clearer information and family support are identified as potential facilitators.What is new?▪Cardiovascular disease is a growing epidemic in Latin America▪Low medication adherence is a significant risk factor for cardiovascular diseaseWhat are de clinical implications?▪Low medication adherence is highly prevalent in socially vulnerable populations of high cardiovascular risk in Chile.▪Depression increased the risk of low medication adherence by more than two times in high-risk populations and is associated with the perception of confusion and tiredness in this group of patients.▪Primary care teams recognize the relevance of providing clearer information, reminder systems and developing family support strategies for improving medication adherence.
Disrupted maturation of white matter microstructure after concussion contributes to internalizing behavior problems in female children
Authors: Nishat Eman , Scratch Shannon E , Ameis Stephanie H , Wheeler Anne L 
Published: April 2023

1.AbstractSome children that experience a concussion exhibit long-lasting emotional and behavioral problems post-injury, with greater rates of persistent problems in females. Establishing the contribution of (1) pre-existing behavioral problems and (2) disrupted maturation of the brain’s vulnerable white matter, to long-lasting behavioral problems has been a challenge due to a lack of pre-injury behavioral and imaging data. From the Adolescent Brain Cognitive Development Cohort, this study examined 204 11-12-year-old children who experienced a concussion after baseline data collection at age 9-10-years-old. Internalizing and externalizing behavioral problems were assessed with the Child Behavior Checklist. In 99 of these children with MRI data available, white matter microstructure was characterized in deep and superficial white matter by neurite density from restriction spectrum image modeling of diffusion MRI. Linear regressions modeled 1) post-concussion behavior symptoms controlling for pre-injury behavior, 2) the impact of concussion on white matter maturation, and 3) the contribution of deviations in white matter maturation to post-concussion behavior symptoms. When controlling for preinjury scores, post-injury internalizing and externalizing scores were higher in female but not male children with concussion compared to children with no concussion. Group comparisons of change in neurite density over two years reflecting white matter maturation demonstrated an age-dependent effect whereby younger female children had less change in neurite density over time than younger children with no concussion. In female children with concussion, less change in superficial white matter neurite density over time was associated with more internalizing behavior problems. These results suggest that in female children, concussions are associated with behavior problems beyond those that exist pre-injury, and injury to the brain’s vulnerable white matter may be a biological substrate underlying persistent internalizing behaviors.
Multimodal anatomical mapping of subcortical regions in Marmoset monkeys using high-resolution MRI and matched histology with multiple stains
Authors: Saleem Kadharbatcha S , Avram Alexandru V , Yen Cecil Chern-Chyi , Magdoom Kulam Najmudeen , Schram Vincent , Basser Peter J 
Published: April 2023

AbstractSubcortical nuclei and other deep brain structures play essential roles in regulating the central and peripheral nervous systems. However, many of these nuclei and their subregions are challenging to identify and delineate in conventional MRI due to their small size, hidden location, and often subtle contrasts compared to neighboring regions. To address these limitations, we scanned the whole brain of the marmoset monkeys inex vivousing a clinically feasible diffusion MRI method, called the mean apparent propagator (MAP)-MRI, along with T2W and MTR (T1-like contrast) images acquired at 7 Tesla. Additionally, we registered these multimodal MRI volumes to the high-resolution images of matched whole-brain histology sections with seven different stains obtained from the same brain specimens. At high spatial resolution, the microstructural parameters and fiber orientation distribution functions derived with MAP-MRI can distinguish the subregions of many subcortical and deep brain structures, including fiber tracts of different sizes and orientations. The good correlation with multiple but distinct histological stains from the same brain serves as a thorough validation of the structures identified with MAP-MRI and other MRI parameters. Moreover, the anatomical details of deep brain structures found in the volumes of MAP-MRI parameters are not visible in conventional T1W or T2W images. The high-resolution mapping using novel MRI contrasts, combined and correlated with histology, can elucidate structures that were previously invisible radiologically. Thus, this multimodal approach offers a roadmap toward identifying salient brain areasin vivoin future neuroradiological studies. It also provides a useful anatomical standard reference for the region definition of subcortical targets and the generation of a 3D digital template atlas for the marmoset brain research (Saleem et al., 2023). Additionally, we conducted a cross-species comparison between marmoset and macaque monkeys using results from our previous studies (Saleem et al., 2021). We found that the two species had distinct patterns of iron distribution in subregions of the basal ganglia, red nucleus, and deep cerebellar nuclei, confirmed with T2W MRI and histology.
Nucleolar structure connects with global nuclear organization
Authors: Wang Chen , Ma Hanhui , Baserga Susan J. , Pederson Thoru , Huang Sui 
Published: April 2023

AbstractThe nucleolus is a multi-functional nuclear body. To tease out the roles of nucleolar structure without resorting to multi-action drugs, we knocked down RNA polymerase I subunit RPA194 in HeLa cells by siRNA. Loss of RPA194 resulted in nucleolar structural segregation and effects on both nucleolus-proximal and distal nuclear components. The perinucleolar compartment was disrupted, centromere-nucleolus interactions were significantly reduced, and the intranuclear locations of specific genomic loci were altered. Moreover, Cajal bodies, distal from nucleoli, underwent morphological and compositional changes. To distinguish whether these global reorganizations are the results of nucleolar structural disruption or inhibition of ribosome synthesis, the pre-ribosomal RNA processing factor, UTP4, was also knocked down, which did not lead to nucleolar segregation, nor the intranuclear effects seen with RPA195A knockdown, demonstrating that they do not arise from a cessation of ribosome synthesis. These findings point to a commutative system that links nucleolar structure to the maintenance and spatial organization of certain nuclear bodies and genomic loci.
RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses
Authors: Cruz-León Sergio , Assenza Salvatore , Poblete Simón , Guzman Horacio V. 
Published: April 2023

AbstractMultiscale simulations have broadened our understanding of RNA structure and function. Various methodologies have enabled the quantification of electrostatic and mechanical interactions of RNA at the nanometer scale. Atom-by-atom simulations, coarse-grained strategies, and continuum models of RNA and its environment provide physical insight and allow to interpret diverse experiments in a systematic way. In this chapter, we present and discuss recent advances in a set of methods to study nucleic acids at different scales. In particular, we introduce details of their parameterization, recent applications, and current limitations. We discuss the interaction of the proteinacous virus capsid, RNA with substrates, compare the properties of RNA and DNA and their interaction with the environment, and analyze the application of these methods to reconstruct the structure of the virus genome structure. Finally, the last lines are dedicated to future developments and challenges ahead.