Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host‐associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual‐based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny‐informed and phylogeny‐independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny‐informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny‐independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β‐dispersion rather than β‐diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
Potential problems in the use of patient reported outcome measures (PROMs) and reporting of PROM data in sports science

To use an inadequate patient reported outcome measure (PROM) or use a PROM in an inappropriate way potentially influences the quality of measurement. The objectives of this study were to define potential inadequate uses of PROMs in sports research studies and estimate how often they occur. A consensus group consisting of medical researchers, statisticians, and psychometricians identified and defined potentially irregular applications of PROMs. Occurrence of these in 349 consecutive articles in sports medicine in which PROMs were used as primary outcomes was reviewed. In all, 14 different potential problems were defined, and one or several occurred in 172 of the articles (49%). These were as follows: using a PROM that was developed for a different patient group (100 cases), using two or more PROMs with identical questions (94), aggregation of domain sum scores (82), combinations of subjective and objective measures (27), using a PROM to diagnose or evaluate the individual patient (7), using a PROM for a single limb (3), recall bias (3), exclusion of domains or items (3), construction of a PROM for a specific occasion (2), categorization of the scale (2), and mixing different versions of a PROM (1). Adaption of scale scores (e. g., to percentage) when results are reported (144) carries a risk of miscalculation and distorted impression of results. Data related to uncertainty about completing the PROM and the handling of missing data were not provided in the manuscripts. In conclusion, potential problems in the use and reporting of PROMs are common in sports research, and this can influence the validity of reported results.
Novel perspective on contractile properties and intensity‐dependent verification of force–frequency relationship during neuromuscular electrical stimulation

The aims of the present study were: (a) to examine the effect of the stimulus intensity on force‐frequency and torque fluctuation–frequency relationships during Neuromuscular electrical stimulation; and (b) to identify a novel parameter that can be used to evaluate muscle contractile properties. Methods: Electrically elicited joint torque involving the quadriceps femoris muscle was recorded during neuromuscular electrical stimulation at two different stimulus intensities in 19 healthy men. Stimulation frequencies were set at 5–40 Hz with a duration of 10 s. Evoked joint torque was compared among all stimulation frequencies between the two stimulus intensities (68 and 113 V). The torque fluctuation at each stimulation frequency as the change in the contraction pattern was also compared between the intensities. Torque and torque fluctuation were normalized at each frequency by the largest torque or torque fluctuation, respectively. We extracted a novel parameter: the arrival point of tetanic contraction based on force‐frequency and torque fluctuation‐frequency curves. Results: There were significant differences in normalized torque at 5–25 and 40 Hz and in normalized torque fluctuation at 15–30 and 40 Hz between the two stimulus intensities. Extracted parameters showed no significant difference between the intensities. Conclusion: The results suggest that force–frequency relationships during neuromuscular electrical stimulation are influenced by the intensity of stimulation applied to the quadriceps femoris muscle. However, we consider that it is possible to simultaneously evaluate contractile properties using the novel parameter.
A picture is worth a thousand words: linking fibromyalgia pain widespreadness from digital pain drawings with pain catastrophizing and brain cross-network connectivity.

Pain catastrophizing is prominent in chronic pain conditions such as fibromyalgia, and has been proposed to contribute to the development of pain widespreadness. However, the brain mechanisms responsible for this association are unknown. We hypothesized that increased resting Salience Network (SLN) connectivity to nodes of the Default Mode Network (DMN), representing previously reported pain-linked cross-network enmeshment, would be associated with increased pain catastrophizing and widespreadness across body sites.We applied functional Magnetic Resonance Imaging (fMRI) and digital pain drawings (free-hand drawing over a body outline, analyzed using conventional software for multivoxel fMRI analysis) to investigate precisely-quantified measures of pain widespreadness and the associations between pain catastrophizing (Pain Catastrophizing Scale, PCS), resting brain network connectivity (Dual-regression Independent Component Analysis, 6-minute multiband accelerated fMRI), and pain widespreadness in fibromyalgia patients (N=79). Fibromyalgia patients reported pain in multiple body areas (most frequently the spinal region, from the lower back to the neck), with moderately high pain widespreadness (mean±SD: 26.1±24.1 percent of total body area), and high PCS scores (27.0±21.9, scale range: 0-52), which were positively correlated (r=0.26,p=0.02). A whole-brain regression analysis focused on SLN connectivity indicated that pain widespreadness was also positively associated with SLN connectivity to the Posterior Cingulate Cortex (PCC), a key node of the DMN. Moreover, we found that SLN-PCC connectivity statistically mediated the association between pain catastrophizing and pain widespreadness (p=0.01). In conclusion, we identified a putative brain mechanism underpinning the association between greater pain catastrophizing and a larger spatial extent of body pain in fibromyalgia, implicating a role for brain SLN-DMN cross-network enmeshment in mediating this association.
The Validated Features of Psychological Interventions for Weight Loss: An Integration

Abstract Many psychological inclinations, such as maladaptive beliefs, can diminish the capacity of individuals to manage their weight effectively and sustainably. Yet, interventions that purportedly address these psychological inclinations and improve weight management are not always beneficial. To be effective, these interventions should offer participants several choices, should be devoid of features that have not been validated in isolation, and should arrange the various activities in an efficient and effective sequence. Few if any programs fulfill these criteria. The aim of this paper was to construct an intervention that assimilates all the validated features of interventions that overcome the psychological impediments to weight loss. To achieve this goal, we blended a technique called intervention component analysis with thematic analysis. Specifically, we extracted refereed journal articles about weight loss from PsycInfo, distilled the practical recommendations from these articles, excluded recommendations that had not been validated in isolation of other features, integrated overlapping recommendations, and applied several principles to arrange these recommendations into the most effective sequence. This procedure generated an intervention that could comprise up to 43 features and activities, including self-affirmation to foster openness to change, anecdotes about dramatic improvements, ambitious rather than modest targets, an emphasis on strategies rather than targets, rewards for attempts, implementation intentions with partners, self-hypnosis, cognitive reframing, and distancing. If these features are unsuccessful, practices that demand more resources—such as group disclosure, virtual environments, motivational interviewing, and customized programs—were also recommended.
Effect of Momordica saponin- and Cyclocarya paliurus polysaccharide- enriched beverages on oxidative stress and fat accumulation in Caenorhabditis elegans.

BACKGROUND As an edible and medicinal herb in Chinese folk medicine, Cyclocarya paliurus (Batal.) Iljinskaja (C. paliurus) leaves are traditionally widely used in the treatment of metabolic disorders. The vegetable Momordica charantia L. (M. charantia) has been consumed worldwide for thousands of years as a traditional drug due to its activities against obesity and diabetes. In view of the therapeutic value of Momordica saponins (MS) and Cyclocarya paliurus polysaccharides (CPP), an independently developed MS- and CPP-containing beverage (MC) was evaluated for its efficacy in controlling oxidative stress and obesity in Caenorhabditis elegans (C. elegans). RESULTS First, we found that MC could promote the nuclear localization of DAF-16 and the translation of SOD-3. Further exploring its antioxidant properties, the oxidative stress byproducts reactive oxygen species (ROS), malondialdehyde (MDA) and nonesterified fatty acids (NEFAs) were significantly inhibited in C. elegans. Moreover, damage due to diseases related to oxidative stress (age pigments and neurodegenerative diseases) was alleviated. Furthermore, fat accumulation was significantly reduced in normal and high-fat models. Finally, the lipid-lowering effects of MC might involve reductions in the size and number of lipid droplets without impairing basic physiological functions in C. elegans. CONCLUSION These results provide promising data indicating MC as an innovative health beverage for the pharmacological management of oxidative stress and obesity. This article is protected by copyright. All rights reserved.
Multilayered non‐uniform atomic force microscope piezoelectric microcantilever control and vibration analysis considering different excitation based on the modified couple stress theory

Atomic force microscope (AFM) is one of the most powerful tools for surface scanning, force measurement, and nano‐manipulation. To improve its performance, vibration and control of AFM micro‐cantilever (MC) should be studied. Hysteresis, as an undesired phenomenon affecting vibration amplitude and phase, is also another important issue to be examined. In this paper, vibration analysis and control of a ZnO non‐uniform multi‐layered piezoelectric MC has been investigated in non‐contact mode. A modified couple stress theory has been used to obtain the strain energy for modeling the MC. In order to control the amplitude, a sliding mode controller (SMC) has been utilized on AFM, due to its application in uncertain and nonlinear systems. For applying the control signal, two methods of piezo and base actuation are studied. The results are compared with proportional integral derivative (PID) control method and it is demonstrated that SMC method reduces the control input close to the surface and increases the accuracy near the surface. In addition to MC control, hysteresis amplitude and phase differences are investigated by applying the Prandtl–Ishlinskii model. Also, surface topography is studied with hysteresis. The simulations show backward phase difference and an increase in amplitude, accordingly.
Discovery of Amoebicidal Compounds by Combining Computational and Experimental Approaches

Pathogenic and opportunistic free-living amoebae such as Acanthamoeba spp. can cause keratitis (Acanthamoeba keratitis [AK]), which may ultimately lead to permanent visual impairment or blindness. Acanthamoeba can also cause rare but usually fatal granulomatous amoebic encephalitis (GAE). Current therapeutic options for AK require a lengthy treatment with nonspecific drugs that are often associated with adverse effects. ABSTRACT Pathogenic and opportunistic free-living amoebae such as Acanthamoeba spp. can cause keratitis (Acanthamoeba keratitis [AK]), which may ultimately lead to permanent visual impairment or blindness. Acanthamoeba can also cause rare but usually fatal granulomatous amoebic encephalitis (GAE). Current therapeutic options for AK require a lengthy treatment with nonspecific drugs that are often associated with adverse effects. Recent developments in the field led us to target cAMP pathways, specifically phosphodiesterase. Guided by computational tools, we targeted the Acanthamoeba phosphodiesterase RegA. Computational studies led to the construction and validation of a homology model followed by a virtual screening protocol guided by induced-fit docking and chemical scaffold analysis using our medicinal and biological chemistry (MBC) chemical library. Subsequently, 18 virtual screening hits were prioritized for further testing in vitro against Acanthamoeba castellanii, identifying amoebicidal hits containing piperidine and urea imidazole cores. Promising activities were confirmed in the resistant cyst form of the amoeba and in additional clinical Acanthamoeba strains, increasing their therapeutic potential. Mechanism-of-action studies revealed that these compounds produce apoptosis through reactive oxygen species (ROS)-mediated mitochondrial damage. These chemical families show promise for further optimization to produce effective antiacanthamoebal drugs.
Collaborative multicenter logistics delivery network optimization with resource sharing

Collaboration among logistics facilities in a multicenter logistics delivery network can significantly improve the utilization of logistics resources through resource sharing including logistics facilities, vehicles, and customer services. This study proposes and tests different resource sharing schemes to solve the optimization problem of a collaborative multicenter logistics delivery network based on resource sharing (CMCLDN-RS). The CMCLDN-RS problem aims to establish a collaborative mechanism of allocating logistics resources in a manner that improves the operational efficiency of a logistics network. A bi-objective optimization model is proposed with consideration of various resource sharing schemes in multiple service periods to minimize the total cost and number of vehicles. An adaptive grid particle swarm optimization (AGPSO) algorithm based on customer clustering is devised to solve the CMCLDN-RS problem and find Pareto optimal solutions. An effective elite iteration and selective endowment mechanism is designed for the algorithm to combine global and local search to improve search capabilities. The solution of CMCLDN-RS guarantees that cost savings are fairly allocated to the collaborative participants through a suitable profit allocation model. Compared with the computation performance of the existing nondominated sorting genetic algorithm-II and multi-objective evolutionary algorithm, AGPSO is more computationally efficient. An empirical case study in Chengdu, China suggests that the proposed collaborative mechanism with resource sharing can effectively reduce total operational costs and number of vehicles, thereby enhancing the operational efficiency of the logistics network.
Race and ethnic variation in college students’ allostatic regulation of racism-related stress

Significance Racial resentment, antiimmigration sentiment, and hate crimes, including on college campuses, have increased recently. Although African American (70%) and Hispanic/Latinx people (56%) report considerable discrimination exposure, there remains a critical need for research examining the pathways through which racism-related stress affects health. Here, we developed an ecological, intensive longitudinal design leveraging an independent biosignal of stress arousal collected from a wearable sensor. Our method documents both increased simultaneous negative emotion and stress arousal among African American, Latinx, and African students in response to racism-related stress. These findings provide support for allostasis-based theories of mental and physical health via a naturalistic assessment of emotional and physiological responding to real-life social experiences. Racism-related stress is thought to contribute to widespread race/ethnic health inequities via negative emotion and allostatic stress process up-regulation. Although prior studies document race-related stress and health correlations, due to methodological and technical limitations, they have been unable to directly test the stress-reactivity hypothesis in situ. Guided by theories of constructed emotion and allostasis, we developed a protocol using wearable sensors and daily surveys that allowed us to operationalize and time-couple self-reported racism-related experiences, negative emotions, and an independent biosignal of emotional arousal. We used data from 100 diverse young adults at a predominantly White college campus to assess racism-related stress reactivity using electrodermal activity (EDA), a biosignal of sympathetic nervous system activity. We find that racism-related experiences predict both increased negative emotion risk and heightened EDA, consistent with the proposed allostatic model of health and disease. Specific patterns varied across race/ethnic groups. For example, discrimination and rumination were associated with negative emotion for African American students, but only interpersonal discrimination predicted increased arousal via EDA. The pattern of results was more general for Latinx students, for whom interpersonal discrimination, vicarious racism exposure, and rumination significantly modulated arousal. As with Latinx students, African students were particularly responsive to vicarious racism while 1.5 generation Black students were generally not responsive to racism-related experiences. Overall, these findings provide support for allostasis-based theories of mental and physical health via a naturalistic assessment of the emotional and sympathetic nervous system responding to real-life social experiences.
Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation

Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell‐, tissue‐ and structure‐level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here, we examine whether traits that are integrated at the phenotypic level also exhibit a shared genetic basis (e.g. pleiotropy). We micro‐CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium and ventricle, respectively) from an F5 hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric from asymmetric components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.
Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic

Triple-negative breast cancer (TNBC) presents a marked diversity at the molecular level, which promotes a clinical heterogeneity that further complicates treatment. We performed a detailed whole exome sequencing profile of 29 Mexican patients with long follow-up TNBC to identify genomic alterations associated with overall survival (OS), disease-free survival (DFS), and pathologic complete response (PCR), with the aim to define their role as molecular predictive factors of treatment response and prognosis. We detected 31 driver genes with pathogenic mutations in TP53 (53%), BRCA1/2 (27%), CDKN1B (9%), PIK3CA (9%), and PTEN (9%), and 16 operative mutational signatures. Moreover, tumors with mutations in BRCA1/2 showed a trend of sensitivity to platinum salts. We found an association between deficiency in DNA repair and surveillance genes and DFS. Across all analyzed tumors we consistently found a heterogeneous molecular complexity in terms of allelic composition and operative mutational processes, which hampered the definition of molecular traits with clinical utility. This work contributes to the elucidation of the global molecular alterations of TNBC by providing accurate genomic data that may help forthcoming studies to improve treatment and survival. This is the first study that integrates genomic alterations with a long follow-up of clinical variables in a Latin American population that is an underrepresented ethnicity in most of the genomic studies.
Mouse Age Matters: How Age Affects the Murine Plasma Metabolome

A large part of metabolomics research relies on experiments involving mouse models, which are usually 6 to 20 weeks of age. However, in this age range mice undergo dramatic developmental changes. Even small age differences may lead to different metabolomes, which in turn could increase inter-sample variability and impair the reproducibility and comparability of metabolomics results. In order to learn more about the variability of the murine plasma metabolome, we analyzed male and female C57BL/6J, C57BL/6NTac, 129S1/SvImJ, and C3HeB/FeJ mice at 6, 10, 14, and 20 weeks of age, using targeted metabolomics (BIOCRATES AbsoluteIDQ™ p150 Kit). Our analysis revealed high variability of the murine plasma metabolome during adolescence and early adulthood. A general age range with minimal variability, and thus a stable metabolome, could not be identified. Age-related metabolomic changes as well as the metabolite profiles at specific ages differed markedly between mouse strains. This observation illustrates the fact that the developmental timing in mice is strain specific. We therefore stress the importance of deliberate strain choice, as well as consistency and precise documentation of animal age, in metabolomics studies.