bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep nutrients and soil fungal communities support tomato fruit yield and quality in dry farm management systems
Authors: Socolar Yvonne , Matta Tucker Javier , Fuentes Melanie Rodríguez , Andoko Bethany , Cook James , Hernández Cristóbal Cruz , Mazariegos-Anastassiou Cole , Mazariegos-Anastassiou Verónica , Schirmer Joel , Socolar Jacob B , Woodard Claire , Wong Darryl G , Bowles Timothy M 
Published: March 2024

Abstract
Changing climates are causing agricultural water shortages at unprecedented scales and magnitudes, especially in regions historically reliant on irrigation. Identifying and understanding systems of farming that allow continuity in agricultural operations in times of water scarcity are increasingly urgent needs. Vegetable dry farming relies on winter rains stored in soils to reduce irrigation to 0–2 events per season and has become prevalent on California’s Central Coast in recent decades. Until now, this system has been unexplored in scientific literature beyond extension publications, despite its promise as a model for low-water agriculture in arid regions. Dry farm management presents a unique challenge given that low water content restricts nutrient access in surface soils, which farmers typically target for fertility management. Managing soil nutrients at depth, as well as microorganisms that help plants access nutrients and alleviate water stress (e.g. arbuscular mycorrhizal fungi, or AMF) could be crucial to dry farm success. We engaged in a collaborative research design process with farmers managing seven commercial dry farm tomato fields to identify and answer three key management questions: 1. What are the depths at which nutrients influence harvest outcomes given low water content in surface soils?, 2. Are commercially available AMF inoculants effective at improving harvest outcomes?, and 3. How does the broader fungal community change in dry farm soils, and are those changes associated with harvest outcomes? Only soil nutrients below 60 cm depth were correlated with tomato yield and fruit quality. We identified a fungal class, Sordariomycetes, as a ‘signature’ fungal group in dry farm soils that distinguished them from irrigated management and correlated with positive fruit quality, while commercial AMF inoculation showed little benefit. These findings can inform management practices that optimize fruit yield and quality, and can guide farmers and policymakers alike in efforts to minimize agricultural water use.
Is Obesity Due to Overeating and Inactivity, or to a Defective Metabolic Rate? A Review
Authors: Shah Meena , Jeffery Robert W. 
Published: March 2024

Abstract
The cause of obesity could be overeating and inactivity, a defective metabolic rate, or a combination of these factors. This article investigates the causes of obesity by reviewing studies which have examined food intake, physical activity, basal metabolic rate (BMR), and thermogenesis in relation to obesity. Energy intake is at best weakly related to obesity. Fat intake may be a more important factor in the etiology of obesity. Post- and pre-obese individuals seem to have lower weight maintenance energy requirements than “normal.” Physical activity may be a function of obesity level with lower levels of activity in the highly obese. BMR is reduced in the post-obese and is suggestive of a predisposing factor for weight gain. Thermogenesis may be blunted in a significant number of obese individuals.
The Psychophysiology of Workload, Stress, and Health: Comparison Between the Sexes
Authors: Frankenhaeuser Marianne 
Published: March 2024

Abstract
A biopsychosocial framework is presented for the experimental study of interactions between environmental demands, stress, and health. Physiological responses to the psychosocial environment reflect the cognitive and emotional impact on the individual and serve as “early warnings” of long-term health risks. Research on the release of catecholamines and Cortisol in response to different psychosocial demands is interpreted in terms of the author's activity-affect model of stress. It is argued that neuroendocrine correlates (e.g. the catecholamine/cortisol ratio) of activity vs. passivity and positive vs. negative affect are potent determinants of health outcomes. The role of personal control as a mediator of positive affect is emphasized. A review of studies of catecholamine reactivity over the past two decades shows that sex differences have decreased markedly—an increasing proportion of women are reacting to achievement demands as strongly as men. The increasing similarity between the sexes on the physiological level reflects the increasing similarity in men's and women's roles. Possible adverse health consequences of women's multiple roles and heavy total workload are considered in the light of new epidemiological data. Special attention is given to potential health risks for women in managerial positions, who have a particularly heavy workload and tend to “unwind” slowly after work.
Nutritional Remedies: Reasonable and Questionable
Authors: Dwyer Johanna T. 
Published: March 2024

Abstract
This article reviews common, reasonable therapies and questionable nutritional remedies for diseases and conditions that have dietary implications. Standard and questionable dietary remedies are defined and distinguished from other types of therapies, such as experimental or investigational Reasons for concern about questionable remedies are summarized. Some of the possible causes of their popularity are briefly reviewed. Several disorders are discussed to illustrate general points and concerns about the use of unproven remedies in clinical practice. The article concludes with remarks about some collaborative efforts between nutritionists and behavior therapists that are likely to be helpful to patients.
Physiological Organization of Neurohormonal Responses to Psychosocial Stimuli: Implications for Health and Disease
Authors: Folkow Björn 
Published: March 2024

Abstract
In these days, when subcellular and molecular biology often seem to be the focus of biomedical attention, it is justified to stress how the highest centers of the brain can, via a number of differentiated neurohormonal patterns, readjust virtually all bodily functions–down to the subcellular and molecular levels of the organization. These response patterns, able to cope with a variety of environmental challenges even in anticipatory fashions, can– when intensely engaged–entirely dominate bodily functions and behavior. Further, several of them may, during prolonged or/and oft-repeated activations, even affect the structure of cells and organ systems as a consequence of the imposed alterations in functional load and by exerting growth-promoting influences via some hormones and nerve transmitters.
The more important of these age-old limbic–hypothalamic response patterns are outlined from a physiological point of view, with the main emphasis on the so-called “defense” and “defeat” reactions with respect to modes of induction, bodily expressions, and feedback effects on the brain. Both of these reactions appear to be of particular relevance for the gradual induction of some common “psychosomatic” disorders in modern man, evidently due to the abundance of psychosocial stimuli and the hectic pace which often characterize present-day affluent society. This situation is exemplified in the cardiovascular system, since the centrally-elicited neurohormonal influences seem to greatly contribute to the gradual induction of chronic high-pressure states as well as to atherosclerosis, particularly when predisposing genetic factors and other types of environmental influences are at hand.
Diabetes and Female Sexual Function: a Critical Review
Authors: Spector Ilana P. , Leiblum Sandra R. , Carey Michael P. , Rosen Raymond C. 
Published: March 2024

Abstract
The research which evaluates the prevalence and correlates of sexual dysfunction in female diabetics is reviewed. Results indicate that diabetic women experience hypoactive sexual desire, orgasmic dysfunction, and dyspareunia, but the prevalence rates do not appear to be significantly different from those of women in the general population. Female diabetics appear to report more arousal phase disorders than do non-diabetic controls in some studies. In a search for correlates of sexual dysfunction in diabetic females, researchers have examined neuropathy, micro- and macrovascular disease, age of onset of diabetes, duration of diabetes, and glucose control; however none of these variables are predictive of sexual difficulties. Psychosocial factors such as disease acceptance, marital satisfaction, and depression appear to correlate with sexual dysfunction and merit further study. Diabetic subtype may also predict degree of dysfunction. Methodological limitations include lack of physiological data to assess arousal, failure to examine samples with more severe diabetic complications, and neglect of menopausal status and obesity as critical variables.
Families and Health: the Negative Side of Social Ties
Authors: Burg Matthew M. , Seeman Teresa E. 
Published: March 2024

Abstract
Research on a range of illnesses has demonstrated a protective effect for social ties and social support, and has begun to address the potential mechanisms by which this effect is brought about. More recently, researchers examining the positive effects of social ties have also uncovered unexpected negative consequences. The supportive and non-supportive aspects of social relations are weakly correlated, indicating that both of these two domains of social experience need to be considered to understand the influence of family and other social ties on health. The purpose of this paper is to illustrate through selective examination of the literature how social support, particularly in the form of family ties, may increase risk for negative rather than positive health outcomes. In addition, we provide a framework for research to more fully elucidate this area.
Perceived Stress and Salivary Cortisol in Daily Life
Authors: van Eck Marleen M. , Nicolson Nancy A. 
Published: March 2024

Abstract
Clarifying the nature of endocrine responses to chronic or intermittent stress in daily life requires repeated measurements of stress, hormone levels, and emotional states. In this study, 42 High Stress (HS) and 46 Low Stress (LS) subjects were selected on the basis of Perceived Stress Scale scores from a larger sample of male white-collar workers. Subjects completed self-reports [Experience Sampling Method (ESM)] and collected saliva samples for Cortisol determination ten times a day over five consecutive days, including three work and two non-work days. We test the hypothesis that high perceived stress is associated with elevated Cortisol.
The HS group scored higher than the LS group on measures of trait anxiety, depression, anger, and psychosomatic complaints, as well as on ESM measures of positive and negative affect and stressful daily events. Although negative affect was higher and stressful events more frequent on workdays than weekends (especially for HS subjects), no difference in workday vs. weekend Cortisol levels was found in the subsample of subjects with sufficient data. On workdays, HS subjects had higher mean Cortisol levels than LS subjects at each of the ten sampling times between 8 a.m. and 10 p.m. (repeated measures ANOVA, p &lt; .02). Mean workday Cortisol was correlated with higher trait anxiety, depression, and the low arousal dimension of ESM negative affect.
DNA-Testing for Heritable Breast Cancer Risks: Lessons from Traditional Genetic Counseling
Authors: Lerman Caryn , Audrain Janet , Croyle Robert T. 
Published: March 2024

Abstract
This article provides a brief overview of recent work in breast cancer genetics and addresses three areas of relevant behavioral medicine research: (a) understanding individuals' motivations to undergo genetic testing, (b) evaluating the impact of genetic testing on psychosocial outcomes, and (c) identifying moderators of the impact of genetic risk information. Recent studies show that levels of interest in genetic testing for breast cancer are high; however, most women who come forward lack understanding about inherited breast cancer risks and the benefits and limitations of genetic testing. Among those who participate in genetic testing for breast cancer, sociodemographic factors, psychological factors, and social/contextual factors may moderate their responses to genetic information. Before genetic testing for breast cancer is widely available, it is critical that prospective controlled trials be conducted to identify determinants of testing behavior, to elucidate the decision-making process, and to evaluate the behavioral and medical outcomes.
Application of graphite carbon black assisted-laser desorption ionization-mass spectrometry for soy sauce product discrimination
Authors: Tanaka Mitsuru , Arima Keishiro , Ide Haruna , Koshi Mariko , Ohno Naoto , Imamura Miho , Matsui Toshiro 
Published: March 2024

Abstract
In a previous study, we developed a novel analytical method to directly and simultaneously detect taste- and odor-active compounds using graphite carbon black (GCB)-assisted laser desorption ionization mass spectrometry (LDI-MS). In this study, we aimed to evaluate food quality using a variety of soy sauces using the method to discriminate each product. Graphite carbon black-laser desorption ionization-mass spectrometry allowed the provision of hundreds of MS peaks derived from soy sauces in both positive and negative modes without any tedious sample pretreatments. Principal component analysis using the obtained MS peaks clearly distinguished three soy sauce products based on the manufacturing countries (Japan, China, and India). Moreover, this method identified distinct MS peaks for discrimination, which significantly correlated with their quantitative amounts in the products. Thus, GCB-LDI-MS analysis was established as a simple and rapid technique for food analysis, illustrating the chemical patterns of food products.
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis
Authors: Wang Liang , Hong Chenyang , Song Jiangning , Yao Jianhua 
Published: March 2024

Abstract

Motivation
Cell-type clustering is a crucial first step for single-cell RNA-seq data analysis. However, existing clustering methods often provide different results on cluster assignments with respect to their own data pre-processing, choice of distance metrics, and strategies of feature extraction, thereby limiting their practical applications.

Results
We propose Cross-Tabulation Ensemble Clustering (CTEC) method that formulates two re-clustering strategies (distribution- and outlier-based) via cross-tabulation. Benchmarking experiments on five scRNA-Seq datasets illustrate that the proposed CTEC method offers significant improvements over the individual clustering methods. Moreover, CTEC-DB outperforms the state-of-the-art ensemble methods for single-cell data clustering, with 45.4% and 17.1% improvement over the single-cell aggregated from ensemble clustering method (SAFE) and the single-cell aggregated clustering via Mixture model ensemble method (SAME), respectively, on the two-method ensemble test.

Availability and implementation
The source code of the benchmark in this work is available at the GitHub repository https://github.com/LWCHN/CTEC.git.
shinyExprPortal: a configurable ‘shiny’ portal for sharing analysis of molecular expression data
Authors: Henkin Rafael , Goldmann Katriona , Lewis Myles , Barnes Michael R 
Published: March 2024

Abstract

Motivation
The scale of omics research presents many obstacles to full sharing and access to analysis results. Current publication models impose limits on the number of pages and figures, requiring careful preparation and selection of content. At the same time, depositing data in open repositories significantly shifts the burden of access and reproduction to readers, who may include people who are not programmers or analysts.

Results
We introduce shinyExprPortal, an R package that implements omics web portals with minimal coding effort. The portals allow exploration of transcriptomic or proteomic expression data and phenotypes, showcasing results of various types of analysis including differential expression, co-expression and pathways analysis. The integration with bioinformatics workflows enables researchers to focus on their results and share findings using interactive and publication-quality plots.

Availability and implementation
The shinyExprPortal package is available to download and install from CRAN and https://github.com/C4TB/shinyExprPortal.
Ferns as facilitators of community recovery following biotic upheaval
Authors: Azevedo-Schmidt Lauren , Currano Ellen D , Dunn Regan E , Gjieli Elizabeth , Pittermann Jarmila , Sessa Emily , Gill Jacquelyn L 
Published: March 2024

Abstract
The competitive success of ferns has been foundational to hypotheses about terrestrial recolonization following biotic upheaval, from wildfires to the Cretaceous–Paleogene asteroid impact (66 million years ago). Rapid fern recolonization in primary successional environments has been hypothesized to be driven by ferns’ high spore production and wind dispersal, with an emphasis on their competitive advantages as so-called disaster taxa. We propose that a competition-based view of ferns is outdated and in need of reexamination in light of growing research documenting the importance of positive interactions (i.e., facilitation) between ferns and other species. Here, we integrate fossil and modern perspectives on fern ecology to propose that ferns act as facilitators of community assemblage following biotic upheaval by stabilizing substrates, enhancing soil properties, and mediating competition. Our reframing of ferns as facilitators has broad implications for both community ecology and ecosystem recovery dynamics, because of ferns’ global distribution and habitat diversity.
Effect of smoking cessation on psoriasis vulgaris, palmoplantar pustulosis and generalized pustular psoriasis
Authors: Kim Seong Rae , Choi Young-Geun , Jo Seong Jin 
Published: March 2024

Abstract

Background
Smoking is a known risk factor for psoriasis; however, the impact of smoking cessation on psoriasis has seldom been evaluated.

Objectives
We aimed to examine the effects of smoking cessation on the development of psoriasis vulgaris (PsV), palmoplantar pustulosis (PPP) and generalized pustular psoriasis (GPP).

Methods
Using the Korean National Health Insurance Service database, we retrospectively compiled a cohort of 5 784 973 participants without psoriasis, analysed their changes in smoking status from 2004 to 2007 and followed up new cases of psoriasis until 2021. The psoriasis risks were compared with those of sustained smokers, smoking quitters, sustained ex-smokers and never smokers using multivariate Cox proportional hazard models.

Results
The mean age of the participants was 47.1 years (SD 13.5) and 3 092 426 (53.5%) were male. During 77 990 688 person-years, 67 364 psoriasis cases were identified. Compared with sustained smokers, smoking quitters showed a reduced risk of developing psoriasis [adjusted hazard ratio (aHR) 0.91; 95% confidence interval (CI) 0.87–0.95], specifically PsV (aHR 0.92; 95% CI 0.88–0.97) and PPP (aHR 0.71; 95% CI 0.63–0.79). The reduction in risk due to smoking cessation was more prominent in sustained ex-smokers (psoriasis: aHR 0.77, 95% CI 0.74–0.79; PsV: aHR 0.76, 95% CI 0.73–0.79; PPP: aHR 0.56, 95% CI 0.51–0.61; GPP: aHR 0.64; 95% CI 0.52–0.78). When conducting sensitivity analyses to address the potential for changes in smoking habits after 2007, the results and trends were consistent with the main findings, and a more pronounced significance was observed.

Conclusions
Compared with continuous smoking, smoking cessation was associated with a decreased risk of developing psoriasis. The risk-reducing effect of smoking cessation was more pronounced in those maintaining a smoke-free status. Smoking cessation and the maintenance of a smoke-free status should be encouraged to prevent the development of psoriasis and all other smoking-related diseases.
Morphological profiling in human neural progenitor cells classifies hits in a pilot drug screen for Alzheimer’s disease
Authors: McDiarmid Amina H , Gospodinova Katerina O , Elliott Richard J R , Dawson John C , Graham Rebecca E , El-Daher Marie-Therese , Anderson Susan M , Glen Sophie C , Glerup Simon , Carragher Neil O , Evans Kathryn L 
Published: March 2024

Abstract
Alzheimer’s disease accounts for 60–70% of dementia cases. Current treatments are inadequate and there is a need to develop new approaches to drug discovery. Recently, in cancer, morphological profiling has been used in combination with high-throughput screening of small-molecule libraries in human cells in vitro. To test feasibility of this approach for Alzheimer’s disease, we developed a cell morphology-based drug screen centred on the risk gene, SORL1 (which encodes the protein SORLA). Increased Alzheimer’s disease risk has been repeatedly linked to variants in SORL1, particularly those conferring loss or decreased expression of SORLA, and lower SORL1 levels are observed in post-mortem brain samples from individuals with Alzheimer’s disease. Consistent with its role in the endolysosomal pathway, SORL1 deletion is associated with enlarged endosomes in neural progenitor cells and neurons. We, therefore, hypothesized that multi-parametric, image-based cell phenotyping would identify features characteristic of SORL1 deletion. An automated morphological profiling method (Cell Painting) was adapted to neural progenitor cells and used to determine the phenotypic response of SORL1−/− neural progenitor cells to treatment with compounds from a small internationally approved drug library (TargetMol, 330 compounds). We detected distinct phenotypic signatures for SORL1−/− neural progenitor cells compared to isogenic wild-type controls. Furthermore, we identified 16 compounds (representing 14 drugs) that reversed the mutant morphological signatures in neural progenitor cells derived from three SORL1−/− induced pluripotent stem cell sub-clones. Network pharmacology analysis revealed the 16 compounds belonged to five mechanistic groups: 20S proteasome, aldehyde dehydrogenase, topoisomerase I and II, and DNA synthesis inhibitors. Enrichment analysis identified DNA synthesis/damage/repair, proteases/proteasome and metabolism as key pathways/biological processes. Prediction of novel targets revealed enrichment in pathways associated with neural cell function and Alzheimer’s disease. Overall, this work suggests that (i) a quantitative phenotypic metric can distinguish induced pluripotent stem cell-derived SORL1−/− neural progenitor cells from isogenic wild-type controls and (ii) phenotypic screening combined with multi-parametric high-content image analysis is a viable option for drug repurposing and discovery in this human neural cell model of Alzheimer’s disease.
Multiple Modernities in Civilizational Perspective: An Assessment of the Global Civilization(s) Initiative
Authors: Buzan Barry , Zhang Feng 
Published: March 2024

Abstract
This paper starts from the supposition that civilization is an important concept for thinking about world order, and one that is increasingly coming back into play in world politics. It opens with a close look at the Global Civilization Initiative (GCI): what does it say, what does it imply, about what is it silent, and what are its policy contexts? It offers the theory of Uneven and Combined Development (UCD) as a way of looking at multiple modernities in terms of civilizational pluralism. This is followed by a historical unfolding of UCD since the early 19th century, showing how it has generated both single and multiple modernities cast in civilizational terms. The penultimate section focuses on the risks and opportunities that a world order of civilizational pluralism would create specifically for China. The conclusions summarize the main points of argument, and set out a more detailed global vision of what the GCI might aim to achieve if played well.