Miracle-dz/UniFAR-FTUs huggingface dataset:
Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation

Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non‐random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150–160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant‐native, native‐native and immigrant‐immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants’ offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non‐random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
Impact of Polypharmacy on Health-Related Quality of Life in Dialysis Patients

Introduction: Dialysis patients are often prescribed a large number of medications to improve metabolic control and manage coexisting comorbidities. However, some studies suggest that a large number of medications could also detrimentally affect patients’ health-related quality of life (HRQoL). Therefore, this study aims to provide insight in the association between the number of types of medications and HRQoL in dialysis patients. Methods: A multicentre cohort study was conducted among dialysis patients from Dutch dialysis centres 3 months after initiation of dialysis as part of the ongoing prospective DOMESTICO study. The number of types of medications, defined as the number of concomitantly prescribed types of drugs, was obtained from electronic patient records. Primary outcome was HRQoL measured with the Physical Component Summary (PCS) score and Mental Component Summary (MCS) score (range 0–100) of the Short Form 12. Secondary outcomes were number of symptoms (range 0–30) measured with the Dialysis Symptoms Index and self-rated health (range 0–100) measured with the EuroQol-5D-5L. Data were analysed using linear regression and adjusted for possible confounders, including comorbidity. Analyses for MCS and number of symptoms were performed after categorizing patients in tertiles according to their number of medications because assumptions of linearity were violated for these outcomes. Results: A total of 162 patients were included. Mean age of patients was 58 ± 17 years, 35% were female, and 80% underwent haemodialysis. The mean number of medications was 12.2 ± 4.5. Mean PCS and MCS were 36.6 ± 10.2 and 46.8 ± 10.0, respectively. The mean number of symptoms was 12.3 ± 6.9 and the mean self-rated health 60.1 ± 20.6. In adjusted analyses, PCS was 0.6 point lower for each additional medication (95% confidence interval [95% CI]: −0.9 to –0.2; p = 0.002). MCS was 4.9 point lower (95% CI: −8.8 to –1.0; p = 0.01) and 1.0 point lower (95% CI: −5.1–3.1; p = 0.63) for the highest and middle tertiles of medications, respectively, than for the lowest tertile. Patients in the highest tertile of medications reported 4.1 more symptoms than in the lowest tertile (95% CI: 1.5–6.6; p = 0.002), but no significant difference in the number of symptoms was observed between the middle and lowest tertiles. Self-rated health was 1.5 point lower for each medication (95% CI: −2.2 to –0.7; p < 0.001). Discussion/Conclusion: After adjustment for comorbidity and other confounders, a higher number of medications were associated with a lower PCS, MCS, and self-rated health in dialysis patients and with more symptoms.
Effects of selective breeding for voluntary exercise, chronic exercise, and their interaction on muscle attachment site morphology in house mice

Skeletal muscles attach to bone at their origins and insertions, and the interface where tendon meets bone is termed the attachment site or enthesis. Mechanical stresses at the muscle/tendon‐bone interface are proportional to the surface area of the bony attachment sites, such that a larger attachment site will distribute loads over a wider area. Muscles that are frequently active and/or are of larger size should cause attachment sites to hypertrophy (training effect); however, experimental studies of animals subjected to exercise have provided mixed results. To enhance our ability to detect training effects (a type of phenotypic plasticity), we studied a mouse model in which 4 replicate lines of High Runner (HR) mice have been selectively bred for 57 generations. Selection is based on the average number of wheel revolutions on days 5 & 6 of a 6‐day period of wheel access as young adults (6–8 weeks old). Four additional lines are bred without regard to running and serve as non‐selected controls (C). On average, mice from HR lines voluntarily run ~3 times more than C mice on a daily basis. For this study, we housed 50 females (half HR, half C) with wheels (Active group) and 50 (half HR, half C) without wheels (Sedentary group) for 12 weeks starting at weaning (~3 weeks old). We tested for evolved differences in muscle attachment site surface area between HR and C mice, plastic changes resulting from chronic exercise, and their interaction. We used a precise, highly repeatable method for quantifying the three‐dimensional (3D) surface area of four muscle attachment sites: the humerus deltoid tuberosity (the insertion point for the spinodeltoideus, superficial pectoralis, and acromiodeltoideus), the femoral third trochanter (the insertion point for the quadratus femoris), the femoral lesser trochanter (the insertion point for the iliacus muscle), and the femoral greater trochanter (insertion point for the middle gluteal muscles). In univariate analyses, with body mass as a covariate, mice in the Active group had significantly larger humerus deltoid tuberosities than Sedentary mice, with no significant difference between HR and C mice and no interaction between exercise treatment and linetype. These differences between Active and Sedentary mice were also apparent in the multivariate analyses. Surface areas of the femoral third trochanter, femoral lesser trochanter, and femoral greater trochanter were unaffected by either chronic wheel access or selective breeding. Our results, which used robust measurement protocols and relatively large sample sizes, demonstrate that muscle attachment site morphology can be (but is not always) affected by chronic exercise experienced during ontogeny. However, contrary to previous results for other aspects of long bone morphology, we did not find evidence for evolutionary coadaptation of muscle attachments with voluntary exercise behavior in the HR mice.
Rate of infant carrying impacts infant spontaneous motor tempo

Rhythm production is a critical component of human interaction, not least forming the basis of our musicality. Infants demonstrate a spontaneous motor tempo (SMT), or natural rate of rhythmic movement. Here, we ask whether infant SMT is influenced by the rate of locomotion infants experience when being carried. Ten-month-old, non-walking infants were tested using a free drumming procedure before and after 10 min of being carried by an experimenter walking at a slower (98 BPM) or faster (138 BPM) than average tempo. We find that infant SMT is differentially impacted by carrying experience dependent on the tempo at which they were carried: infants in the slow-walked group exhibited a slower SMT from pre-test to post-test, while infants in the fast-walked group showed a faster SMT from pre-test to post-test. Heart rate data suggest that this effect is not due to a general change in the state of arousal. We argue that being carried during caregiver locomotion is a predominant experience for infants throughout the first years of life, and as a source of regular, vestibular, information, may at least partially form the basis of their sense of rhythm.
Dynamic EMT: a multi‐tool for tumor progression

The process of epithelial–mesenchymal transition (EMT) is fundamental for embryonic morphogenesis. Cells undergoing it lose epithelial characteristics and integrity, acquire mesenchymal features, and become motile. In cancer, this program is hijacked to confer essential changes in morphology and motility that fuel invasion. In addition, EMT is increasingly understood to orchestrate a large variety of complementary cancer features, such as tumor cell stemness, tumorigenicity, resistance to therapy and adaptation to changes in the microenvironment. In this review, we summarize recent findings related to these various classical and non‐classical functions, and introduce EMT as a true tumorigenic multi‐tool, involved in many aspects of cancer. We suggest that therapeutic targeting of the EMT process will—if acknowledging these complexities—be a possibility to concurrently interfere with tumor progression on many levels.
Does piriformis muscle syndrome impair postural balance? A case control study

Abstract Background and purpose While patients with musculoskeletal disorders reported postural balance impairments, it is unknown whether patients with piriformis muscle syndrome (PMS) may exhibit postural balance disorders compared to controls. The aim was to compare postural balance in patients with PMS to controls in static and dynamic conditions. Material and methods Twelve patients with PMS and twelve controls were enrolled. Static postural balance was assessed by calculating the symmetry index (SI) in the unipedal posture. To measure vision contribution, the Romberg index (RI) was computed. Dynamic postural balance was evaluated with the Timed up and go test (TUGT). Besides, inter-limb strength asymmetry (SA), pain and the short form-36 (SF-36) were assessed. Results The PMS group (PMSG) exhibited significant (p < 0.001) higher SI in eyes opened (EO) and eyes closed (EC) conditions compared to the control group (CG). Besides, PMSG had significant higher RI (p < 0.05), TUGT scores (p < 0.001), SA values (p < 0.05), pain intensity (p < 0.001), and worse SF-36 scores on all physical health (p < 0.05) and psychological health (only in vitality and mental health [p < 0.05]), compared to CG. Conclusion Our data revealed impaired static and dynamic postural balance, and reduced quality of life in PMSG compared to CG. Postural balance impairments could explain the poor quality of life, which are likely due to the higher SA and higher pain intensity. Clinicians and physiotherapists should consider postural balance disorders while designing rehabilitation programs in these patients.
Core Elements of Family Therapy for Adolescent Behavioral Health Problems: Validity Generalization in Community Settings

ABSTRACT Objective The core elements of family therapy for adolescent mental health and substance use problems, originally distilled from high-fidelity sessions conducted by expert clinicians, were tested for validity generalization when delivered by community therapists in routine settings. Method The study sampled recorded sessions from 161 cases participating in one of three treatment pools: implementation trial of Functional Family Therapy (98 sessions/50 cases/22 therapists), adaptation trial of Multisystemic Therapy (115 sessions/59 cases/2 therapists), and naturalistic trial of non-manualized family therapy in usual care (107 sessions/52 cases/21 therapists). Adolescents were identified as 60% male and 40% female with an average age of 15.4 years; 49% were Latinx, 27% White Non-Latinx, 15% African American, 3% another race/ethnicity, 6% race/ethnicity unknown. Session recordings (n = 320) were randomly selected for each case and coded for 21 discrete family therapy techniques. Archived data of one-year clinical outcomes were gathered. Results Confirmatory factor analyses replicated the factor structure from the original distillation study, retaining all four clinically coherent treatment modules comprised of all 21 techniques: Interactional Change (ICC = .77, Cronbach’s α = .81); Relational Reframe (ICC = .75, α = .81); Adolescent Engagement (ICC = .72, α = .78); Relational Emphasis (ICC = .76, α = .80). Exploratory analyses found that greater use of core techniques predicted symptom improvements in one treatment pool. Conclusions Core techniques of family therapy distilled from manualized treatments for adolescent behavioral health problems showed strong evidence of validity generalization, and initial evidence of links to client outcomes, in community settings.
T Cell Epitope Prediction and Its Application to Immunotherapy

T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for epitope prediction, with a particular focus on tools aimed at identifying neoepitopes, i.e. cancer-specific peptides and their potential for use in immunotherapy for cancer treatment. This review will cover how these tools work, what kind of data they use, as well as pros and cons in their respective applications.
Loneliness and Cyberloafing in the Time of COVID-19: A Psychological Perspective

Abstract Background The COVID-19 pandemic, which has affected the entire world, has driven countries into economic, social, and political uncertainty and has forced quite significant changes, especially in areas such as health, work, education, and social security. Social changes that are occurring as a result of the crisis include the restructuring of businesses and working styles and the shaping of work life along the new-normal axis. Many psychosocial risks such as conflict management, organisational relationships, communications problems, job satisfaction, stress, productivity, and performance are being redefined as the nature of jobs, job descriptions, employee competence, and ways of working are being recreated for a virtual environment. The importance of concepts related to work psychology such as loneliness, cyberloafing, digital mobbing, emotional resilience, psychological resilience, compassion, self-compassion, conscious awareness, design of habits, coping with loneliness, and coping with crisis is becoming apparent. Research aims The aim of this study is to examine cyberloafing and loneliness with its changing structure in terms of work psychology. In addition, the researchers and their results on cyberloafing and loneliness are discussed in terms of both sociodemographic factors and some variables of work life. Methodology The research method of critical analysis of literature on the subject of cyberloafing and loneliness was applied in this study. Common findings of secondary research were used in terms of work psychology. Findings The concepts of loneliness and cyberloafing, which have been evaluated in relation to different sociodemographic and work-life factors and whose mutual relations have been the subject of a very limited number of studies, are examined more intensively in the context of personal and organisational factors applicable to the technology-intensive future.
Broadband Internet and Income Inequality

Abstract Digital technologies like the Internet can affect income inequality through increased demand for employment in manual and abstract jobs and reduced demand for employment in routine jobs. In this paper, we combine city-level income distribution and jobs data with broadband data from France to investigate the impact of broadband Internet access on income inequality. Using an instrumental variable estimation strategy, we find that broadband Internet reduces income inequality through increased employment in manual jobs. These effects increase with the availability of skilled workers and are significant in cities with a large service sector or high-speed Internet access. Further, the diffusion of broadband Internet comes with relatively greater benefits in low-income cities compared to high-income cities. Several robustness checks support these findings.
In Situ Flame Temperature Measurements Using a Mid-Infrared Two-Line H2O Laser-Absorption Thermometry

ABSTRACT A mid-infrared two-line thermometry based on H2O absorption was developed for in situ and sensitive temperature measurements of laminar flames. The H2O absorption lines in v3 fundamental band were systematically investigated and a new promising line pair (4029.52 cm–1 and 4030.73 cm–1) was selected to achieve strong absorption line-strength and high-temperature sensitivity over the temperature range of 1000–3000 K. This line pair was readily assessed by a single current scan of a distributed feedback laser near 2.5 μm. The scanned-wavelength laser absorption strategy was adopted for temperature measurements for both laminar sooting and non-sooting flames. This optical sensor was applied in measuring various flame conditions including CH4/air and C2H4/air premixed flames (Ф = 0.8–1.2), C2H4/air sooting flames (Ф = 1.78–2.38), and partially premixed flames. Our measurements were in good agreement with thermocouple measurements for all the flame conditions. In addition, numerical simulations using the detailed chemical kinetic mechanisms (CH4 flame: GRI 3.0, C2H4 flame: USC 2.0) were conducted to validate the experimental results.
Dose rate correction for a silicon diode detector array

Abstract Purpose A signal dependence on dose rate was reported for the ArcCHECK array due to recombination processes within the diodes. The purpose of our work was to quantify the necessary correction and apply them to quality assurance measurements. Methods Static 10 × 10 cm2 6‐MV fields delivered by a linear accelerator were applied to the detector array while decreasing the average dose rate, that is, the pulse frequency, from 500 to 30 MU/min. An ion chamber was placed inside the ArcCHECK cavity as a reference. Furthermore, the instantaneous dose rate dependence (DRD) was studied. The position of the detector was adjusted to change the dose‐per‐pulse, varying the distance between the focus and the diode closest to the focus between 69.6 and 359.6 cm. Reference measurements were performed with an ion chamber placed inside a PMMA slab phantom at the same source‐to‐detector distances (SDDs). Exponential saturation functions were fitted to the data, with different parameters to account for two generations of ArcCHECK detectors (types 2 and 3) and both DRDs. Corrections were applied to 12 volumetric modulated arc therapy plans. Results The sensitivity decreased by up to 2.8% with a decrease in average dose rate and by 9% with a decrease in instantaneous dose rate. Correcting the average DRD, the mean gamma pass rates (2%/2‐mm criterion) of the treatment plans were improved by 5 percentage points (PP) for diode type 3 and 0.4 PP for type 2. Correcting the instantaneous DRD, the improvement was 8.4 PP for type 3 and 0.9 PP for type 2. Conclusions The instantaneous DRD was identified as the prevailing effect on the diode sensitivity. We developed and validated a method to correct this behavior. The number of falsely not passed treatment plans could be considerably reduced.
Evaluation of commercially available high-throughput SARS-CoV-2 serological assays for serosurveillance and related applications

SARS-CoV-2 serosurveys can estimate cumulative incidence for monitoring epidemics but require characterization of employed serological assays performance to inform testing algorithm development and interpretation of results. We conducted a multi-laboratory evaluation of 21 commercial high-throughput SARS-CoV-2 serological assays using blinded panels of 1,000 highly-characterized blood-donor specimens. Assays demonstrated a range of sensitivities (96%-63%), specificities (99%-96%) and precision (IIC 0.55-0.99). Durability of antibody detection in longitudinal samples was dependent on assay format and immunoglobulin target, with anti-spike, direct, or total Ig assays demonstrating more stable, or increasing reactivity over time than anti-nucleocapsid, indirect, or IgG assays. Assays with high sensitivity, specificity and durable antibody detection are ideal for serosurveillance. Less sensitive assays demonstrating waning reactivity are appropriate for other applications, including characterizing antibody responses after infection and vaccination, and detection of anamnestic boosting by reinfections and vaccine breakthrough infections. Assay performance must be evaluated in the context of the intended use.
Population Pharmacokinetics, Exposure-Response, and Probability of Target Attainment Analyses for Tedizolid in Adolescent Patients with Acute Bacterial Skin and Skin Structure Infections

Tedizolid phosphate is an oxazolidinone antibacterial agent approved for the treatment of Gram-positive acute bacterial skin and skin structure infections (ABSSSIs) in patients aged ≥12 years. To support the use of tedizolid phosphate in adolescents with ABSSSIs, a population pharmacokinetic (PK) model, developed using adult and pediatric data, was updated to include PK data from a phase 3 clinical trial (PN012) that evaluated the safety and efficacy of once-daily oral or intravenous 200-mg tedizolid phosphate treatment in adolescents (12 to <18 years) with ABSSSIs, along with emerging data from a phase 1 trial (PN013) in children (2 to <12 years). ABSTRACT Tedizolid phosphate is an oxazolidinone antibacterial agent approved for the treatment of Gram-positive acute bacterial skin and skin structure infections (ABSSSIs) in patients aged ≥12 years. To support the use of tedizolid phosphate in adolescents with ABSSSIs, a population pharmacokinetic (PK) model, developed using adult and pediatric data, was updated to include PK data from a phase 3 clinical trial (PN012) that evaluated the safety and efficacy of once-daily oral or intravenous 200-mg tedizolid phosphate treatment in adolescents (12 to <18 years) with ABSSSIs, along with emerging data from a phase 1 trial (PN013) in children (2 to <12 years). Updated PK parameter estimates remained similar to those of the previous model. Body weight was a statistically significant covariate on clearance and volume parameters, with no clinically meaningful effects on exposure in adolescents. Tedizolid exposures in adolescents from PN012 were slightly higher with largely overlapped area under the concentration-time curve distribution compared with adults from previous phase 2 and 3 trials. The probability of PK/pharmacodynamic target attainment at the MIC susceptibility breakpoint of 0.5 μg/ml for Staphylococcus and Streptococcus sp. was 100%. As most participants from the PN012 trial were cured, no significant exposure-efficacy relationship was identified. Tedizolid exposures were similar between participants with and without a safety event from PN012; no clear relationship was detected between exposure and safety. Despite lower body weight and higher exposures in adolescents, safety profiles in adolescents were similar those in adults. These results support the 200-mg, once-daily intravenous or oral dose of tedizolid phosphate in adolescents with ABSSSIs.