Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of alternative splicing in response to cold acclimation in fish

ABSTRACT Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes. Summary: Qualitative changes in gene expression, such as those mediated by alternative splicing of mRNAs, are involved in phenotypic plasticity in response to prolonged cold acclimation in ectothermic animals.
Talking across generations: Family communication about BRCA1 and BRCA2 genetic cancer risk

While family communication about a BRCA1 or BRCA2 (BRCA1/2) pathogenic variant can be a catalyst for the uptake of risk‐reducing measures in young adults, disseminating information within families and across generations is complex. This study aimed to explore how young adults and their families communicate about a BRCA1/2 pathogenic variant, from a family systems perspective. In‐depth family interviews and questionnaires (N = 67 individuals; 21 families) were completed at four metropolitan and regional genetic clinics in Australia. Data involved thematic analysis and interpretation based on family systems theory, including the use of standardized measures. Six key themes were identified and explored: (1) Responsibility to protect, (2) “It's a woman's problem,” (3) Family culture influences communication, (4) Adversarial growth and connection, (5) Key events can be relational turning points, and (6) Health professionals can help. Family identities were solidified through the incorporation of a pathogenic variant in family scripts, while members of the family who held differing views to their families expressed less agreeableness and openness to disseminate information. The collective family's experience and perspective toward a pathogenic variant can influence a young adult's decision‐making about genetic testing, risk‐management, and family planning. The utilization of family therapy skills in routine practice would be helpful in facilitating communication and the inclusion of standardized measures is beneficial to identify individuals needing ongoing psychological support. Understanding relationship difficulties that arise from family members holding divergent views can offer insight into future research inquiry and areas of further training and clinical support.
Influence of Physical and Musculoskeletal Factors on Occupational Injuries and Accidents in Korean Workers Based on Gender and Company Size

Though the overall incidence of occupational injuries and accidents has decreased, they continue to happen. Many associated factors are known and managing them with limited resources is difficult. This study evaluates related risk factors and prioritizes their management for reducing occupational injuries and accidents at the workplace. We used data from the 4th Korean Working Condition Survey conducted by the Korea Occupational Safety Health Research Institute from June to September 2014. A total of 14,381 persons (9776 men, 4605 women) were selected; t-test, chi-square test, and logistic regression analyses were performed to analyze data. The influence of physical (vibration, noise, abnormal temperature) and musculoskeletal (awkward posture, handling of heavy objects, repetitive tasks) factors was compared according to gender and company size. The risk of occupational injuries and accidents among men was related to musculoskeletal factors and vibration in companies with “under 50” employees and with awkward posture, vibration, and noise in companies with “50 or above” employees; however, among women in companies with “under 50” employees, it was associated with only vibration. Although we evaluated only a few risk factors, prioritizing them based on gender and company size has provided new valuable information.
Assessing Plantar Sensation in the Foot Using the Foot Roughness Discrimination Test (FoRDT): A Reliability and Validity Study in Stroke

The plantar foot represents a sensory dynamometric map and is essential for balance and gait control. Sensory impairments are common, yet often difficult to quantify in neurological conditions, particularly stroke. A functionally oriented and quantifiable assessment, the Foot Roughness Discrimination Test (FoRDT), was developed to address these shortcomings.
Psychometric properties of the cyberbullying triangulation questionnaire: A prevalence analysis through seven roles.

This study explores the psychometric properties of the Cyberbullying Triangulation Questionnaire (CTQ), which measures and triangulates the roles of cybervictimization, cyberaggression, and cyberbystanding. The study sample was composed of 5,036 Spanish students with a mean age of 14.19 years (SD = ±1.7; range = 10-23 years). Confirmatory factor analysis of the three correlated-factor model yielded a high goodness of fit. Reliability as measured by Omega coefficients was adequate (>0.94). The measurement model was invariant for the two age groups (10-14 years and 15-23 years). Cybervictimization and cyberaggression correlated with offline victimization and aggression (r = 0.49; p < 0.001; r = 0.57; p < 0.001, respectively). The results show that the most prevalent cyberbystanding subrole was that of the Defender of the Victim (54.6%), and that cyberaggression and cyberbystanding were more prevalent among male adolescents (p < 0.001). The lack of parental control over children's use of the mobile phone was associated with cyberaggression (p < 0.001).
Experimental Study on Drilling MDF with Tools Coated with TiAlN and ZrN

There is increasing use of wood-based composites in industry not only because of the shortage of solid wood, but above all for their better properties such as: strength, aesthetic appearance, etc., compared to wood. Medium density fiberboard (MDF) is a wood-based composite that is widely used in the furniture industry. The goal of the research conducted was to determine the effect of the type of coating on the drill cutting blades on the value of thrust force (Ft), cutting torque (Mc), cutting tool temperature (T) and surface roughness of the hole in drilling MDF panels. In the tests, three types of carbide drills (HW) were used: not coated, TiAlN coated and ZrN coated. The measurement of both the thrust force and the cutting torque was carried out using an industrial piezoelectric sensor. The temperature of the cutting tool in the drilling process was measured using an industrial temperature measurement system using a K-type thermocouple. It was found that the value of the maximum temperature of the tool in the drilling process depends not only on the cutting speed and feed rate, but also on the type of coating of the cutting tool. The value of both the cutting torque and the thrust force is significantly influenced by the value of the feed rate and the type of drill coating. The effect of varying plate density on the surface roughness of the hole and the variation of the value of the thrust force is also discussed. The results of the investigations were statistically analyzed using a multi-factorial analysis of variance (ANOVA).
Lupeol, the major compound of the dichloromethane extract of Millettia macrophylla Benth (Fabaceae), displays estrogenic effects in ovariectomized rats

The present work deals with the assessment of the in vitro and in vivo estrogenic effects of the triterpenoids (lupenone, lupeol, and stigmastenone) isolated from Millettia macrophylla extract. The in vitro estrogenicity was performed by a reporter gene assay and estrogen receptor‐α (ERα) target gene expression, whereas the in vivo estrogenicity was evaluated by a 3‐day uterotrophic assay in ovariectomized rats. As results, lupenone and lupeol did not transactivate ERα as well as ERβ of human embryonic kidney 293T (HEK293T) cells. However, lupeol seems to be antagonistic to estrogen (E2) only in HEK293T‐ERα (10−9 and 10−8 μM). Furthermore, lupeol slightly upregulated GREB1 gene expression at the concentration of 1 μM, suggesting a weak activation of endogenous ERα. In vivo, only lupeol at a dose of 1 mg/kg significantly increased the uterine wet weight (p < 0.05), uterine (p < 0.05), and vaginal (p < 0.01) epithelial heights. The concomitant administration of lupeol (1 mg/kg) with a pure antiestrogen fulvestrant abrogated its effects only in the vagina, whereas in combination with E2, lupeol exhibited a significant antiestrogen‐like effect in uterine wet weight and synergistic effects on endometrium. Lupeol has estrogenic effects that is partly through ERs transcriptional activity and does involve alternative mechanisms that are still to be uncovered.
Estimates of Within-Subject Biological Variation Derived from Pathology Databases: An Approach to Allow Assessment of the Effects of Age, Sex, Time between Sample Collections, and Analyte Concentration on Reference Change Values.

BACKGROUND Within-subject biological variation data (CVI) are used to establish quality requirements for assays and allow calculation of the reference change value (RCV) for quantitative clinical laboratory tests. The CVI is generally determined using a large number of samples from a small number of individuals under controlled conditions. The approach presented here is to use a small number of samples (n = 2) that have been collected for routine clinical purposes from a large number of individuals. METHODS Pairs of sequential results from adult patients were extracted from a routine pathology database for 29 common chemical and hematological tests. Using a statistical process to identify a central gaussian distribution in the ratios of the result pairs, the total result variation for individual results was determined for 26 tests. The CVI was then calculated by removing the effect of analytical variation. RESULTS This approach produced estimates of CVI that, for most of the analytes in this study, show good agreement with published values. The data demonstrated minimal effect of sex, age, or time between samples. Analyte concentration was shown to affect the distributions with first results more distant from the population mean more likely to be followed by a result closer to the mean. DISCUSSION The process described here has allowed rapid and simple production of CVI data. The technique requires no patient intervention and replicates the clinical environment, although it may not be universally applicable. Additionally, the effect of regression to the mean described here may allow better interpretation of sequential patient results.
Flowers of Astragalus membranaceus var. mongholicus as a Novel High Potential By-Product: Phytochemical Characterization and Antioxidant Activity

The root of Astragalus membranaceus var. mongholicus is one of the most popular herbal medicines worldwide. In order to increase the yield of underground roots of A. membranaceus var. mongholicus, its flowers (AMF) have often been removed in their flowering stage, which produces the flowers as waste being discarded. To explore its phytochemicals and potential value for utilization, the antioxidant activities of extracts from AMF were evaluated by a free radical scavenging assay and reducing power assay. The total phenols and flavonoids, as well as the individual compounds, in different extracts of AMF were also investigated. The results showed that the extract ME obtained from AMF through macroporous resins separation exhibited strong antioxidant activities, which were close to those of positive control BHT. ME was rich in phenolic acids and flavonoids, and the contents reached 108.42 mg gallic acid equivalents/g and 265.70 mg rutin equivalents/g, respectively. A total of 31 compounds, including four phenolic acids, nineteen flavonoids, three isoflavones, two pterocarpans, and three saponins, were identified using UPLC-QTOF-MS in ME. Quantitative analysis of sixteen components in the extracts of AMF showed that flavonoids were the predominant constituents, especially for the compounds of hyperoside, rutin, and isorhamnetin-3-O-β-d-glucoside.
Functions of the right DLPFC and right TPJ in proposers and responders in the ultimatum game

Abstract Recent studies explored a network of brain regions involved in economic decision making. The present study focuses on two of those regions, each relevant for specific and distinct functions in economic decision making: the right temporoparietal junction (rTPJ) and the right dorsolateral prefrontal cortex (rDLPFC). In two experiments using transcranial direct current stimulation, we explored two proposed functions of these areas in bargaining situations using the ultimatum game (UG): understanding the others perspective and integration of fairness norms. Participants first took the role of the proposer and then the role of the responder. We showed that stimulation of the rTPJ only affected the proposer condition. Interestingly, inhibition of the rTPJ led to fairer offers, which strengthens the view that the role of the rTPJ in bargaining situations is to differentiate one's own from the other's perspective. Furthermore, we argue that the rDLPFC is most likely involved in suppressing self‐interest when a person is confronted with a direct reward but does not play a role in long‐term reward anticipation or integrating social fairness norms. We conclude that self‐interest inhibition is shown only in responders, and that perspective taking seems to be a necessary specifically for proposers in the UG.
Weather-driven malaria transmission model with gonotrophic and sporogonic cycles

ABSTRACT Malaria is mainly a tropical disease and its transmission cycle is heavily influenced by environment: The life-cycles of the Anopheles mosquito vector and Plasmodium parasite are both strongly affected by ambient temperature, while suitable aquatic habitat is necessary for immature mosquito development. Therefore, how global warming may affect malaria burden is an active question, and we develop a new ordinary differential equations-based malaria transmission model that explicitly considers the temperature-dependent Anopheles gonotrophic and Plasmodium sporogonic cycles. Mosquito dynamics are coupled to infection among a human population with symptomatic and asymptomatic disease carriers, as well as temporary immunity. We also explore the effect of incorporating diurnal temperature variations upon transmission. Rigorous analysis of the model show that the non-trivial disease-free equilibrium is locally-asymptotically stable when the associated reproduction number is less than unity (this equilibrium is globally-asymptotically for a special case with no density-dependent larval and disease-induced host mortality). Numerical simulations of the model, for the case where the ambient temperature is held constant, suggest a nonlinear, hyperbolic relationship between the reproduction number and clinical malaria burden. Moreover, malaria burden peaks at 29.5 C when daily ambient temperature is held constant, but this peak decreases with increasing daily temperature variation, to about 23–25 C. Malaria burden also varies nonlinearly with temperature, such that small temperature changes influent disease mainly at marginal temperatures, suggesting that in areas where malaria is highly endemic, any response to global warming may be highly nonlinear and most typically minimal, while in areas of more marginal malaria potential (such as the East African highlands), increasing temperatures may translate nearly linearly into increased disease potential. Finally, we observe that while explicitly modelling the stages of the Plasmodium sporogonic cycle is essential, explicitly including the stages of the Anopheles gonotrophic cycle is of minimal importance.
Are Reading Interventions for English Language Learners Effective? A Meta-Analysis

Despite concerted efforts to improve the reading skills of English language learners (ELLs), it remains unclear if the interventions they have been receiving produce any positive results. Thus, the purpose of this meta-analysis was to examine how effective reading interventions are in improving ELLs’ reading skills and what factors may influence their effectiveness. Twenty-six studies with reported outcomes for pretest and posttest were selected, and four moderators (group size, intensity of intervention, students’ risk status, and type of intervention) were coded. The results of random-effects analyses showed that the reading interventions had a large effect on ELLs’ reading accuracy (d = 1.221) and reading fluency (d = 0.802) and a moderate effect on reading comprehension (d = 0.499). In addition, for real-word reading accuracy, intervention groups composed of more than five students were less effective than groups composed of two to five students, and longer intervention sessions were less effective than shorter ones. Overall, our findings suggest that reading interventions have positive effects on ELLs’ reading skills, and they should not be delayed until these students have reached a certain level of oral English proficiency.
Mast Cells Are a Marked Source for Complement C3 Products That Associate with Increased CD11b-Positive Cells in Keratinocyte Skin Carcinomas

Abstract By using immunohistochemistry and antibodies that identify complement C3c (in C3 and C3b) or CD11b receptor, we report that the proportion C3c+ mast cells and the number of CD11b+ cells are increased in basal cell carcinoma (BCC). Instead, only CD11b+ cells are increased in squamous cell carcinoma/Bowen’s disease, and only slightly so in actinic keratosis. Only C3c+ mast cells are increased in psoriasis. Furthermore, C3c+ mast cells correlated positively with CD11b+ cells, and iC3b immunoreactivity was detected around tryptase+ mast cells. Therefore, mast cells may convey immunoregulatory signals through C3, C3b, and iC3b to CD11b+ cells, especially in BCC.
The neurological and psychological phenotype of adult patients with early‐treated phenylketonuria: A systematic review

Newborn screening for phenylketonuria (PKU) and early introduction of dietary therapy has been remarkably successful in preventing the severe neurological features of PKU, including mental retardation and epilepsy. However, concerns remain that long‐term outcome is still suboptimal, particularly in adult patients who are no longer on strict phenylalanine‐restricted diets. With our systematic literature review we aimed to describe the neurological phenotype of adults with early‐treated phenylketonuria (ETPKU). The literature search covered the period from 1 January 1990 up to 16 April 2018, using the NLM MEDLINE controlled vocabulary. Of the 643 records initially identified, 83 were included in the analysis. The most commonly reported neurological signs were tremor and hyperreflexia. The overall quality of life (QoL) of ETPKU adults was good or comparable to control populations, and there was no evidence for a significant incidence of psychiatric disease or social difficulties. Neuroimaging revealed that brain abnormalities are present in ETPKU adults, but their clinical significance remains unclear. Generally, intelligence quotient (IQ) appears normal but specific deficits in neuropsychological and social functioning were reported in early‐treated adults compared with healthy individuals. However, accurately defining the prevalence of these deficits is complicated by the lack of standardized neuropsychological tests. Future research should employ standardized neurological, neuropsychological, and neuroimaging protocols, and consider other techniques such as advanced imaging analyses and the recently validated PKU‐specific QoL questionnaire, to precisely define the nature of the impairments within the adult ETPKU population and how these relate to metabolic control throughout life.
Effective connectivity changes in LSD-induced altered states of consciousness in humans

Significance Lysergic acid diethylamide (LSD) is a psychedelic drug that reliably induces an altered state of consciousness. Interest in psychedelic compounds is growing due to their remarkable potential for understanding altered neural states and potential clinical applications. However, there are major knowledge gaps regarding LSD’s neuropharmacology. Using cutting-edge neuroimaging methods we investigated directed connectivity between cortico–striato–thalamo-cortical (CSTC) regions after administration of LSD together with the specific role of the serotonin 2A receptor. Our results provide evidence that LSD alters directed connectivity within CSTC pathways in humans, suggesting that a disintegration of information processing within these loops is underlying the psychedelic state. These results inform the neurobiology of altered states of consciousness with critical implications for rational development of novel treatments. Psychedelics exert unique effects on human consciousness. The thalamic filter model suggests that core effects of psychedelics may result from gating deficits, based on a disintegration of information processing within cortico–striato–thalamo-cortical (CSTC) feedback loops. To test this hypothesis, we characterized changes in directed (effective) connectivity between selected CTSC regions after acute administration of lysergic acid diethylamide (LSD), and after pretreatment with Ketanserin (a selective serotonin 2A receptor antagonist) plus LSD in a double-blind, randomized, placebo-controlled, cross-over study in 25 healthy participants. We used spectral dynamic causal modeling (DCM) for resting-state fMRI data. Fully connected DCM models were specified for each treatment condition to investigate the connectivity between the following areas: thalamus, ventral striatum, posterior cingulate cortex, and temporal cortex. Our results confirm major predictions proposed in the CSTC model and provide evidence that LSD alters effective connectivity within CSTC pathways that have been implicated in the gating of sensory and sensorimotor information to the cortex. In particular, LSD increased effective connectivity from the thalamus to the posterior cingulate cortex in a way that depended on serotonin 2A receptor activation, and decreased effective connectivity from the ventral striatum to the thalamus independently of serotonin 2A receptor activation. Together, these results advance our mechanistic understanding of the action of psychedelics in health and disease. This is important for the development of new pharmacological therapeutics and also increases our understanding of the mechanisms underlying the potential clinical efficacy of psychedelics.