Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic estimation of quantitative genetic parameters in wild admixed populations

Heritable genetic variation among free-living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a generalized linear mixed model known as the animal model. An underlying assumption of the standard animal model is that the study population is genetically unstructured, which is often unrealistic. In fact, admixture might be the norm rather than the exception in the wild, like in geographically structured populations, in the presence of (im)migration, or in re-introduction and conservation contexts. Unfortunately, animal model estimators may be biased in such cases. So-called genetic group animal models that account for genetically differentiated subpopulations have recently become popular, but methodology is currently only available for cases where relatedness among individuals can be estimated from pedigrees. To ensure that the animal model remains useful in future applications, there is a clear need to generalize genetic group animal models with heterogeneous VA to the case when exclusively genomic data is available. We therefore introduce such methodology for wild admixed systems by extending methods that were recently suggested in the context of plant breeding. Our extension relaxes the limiting assumptions that currently restrict their use to artificial breeding setups. We illustrate the usefulness of the extended genomic genetic groups animal model on a wild admixed population of house sparrows resident in an island system in Northern Norway, where genome-wide data on more than 180 000 single nucleotide polymorphisms (SNPs) is available to derive genomic relatedness. We compare our estimates of quantitative genetic parameters to those derived from a corresponding pedigree-based genetic groups animal model. The satisfactory agreement indicates that the new method works as expected. Our extension of the very popular animal model ensures that the upcoming challenges with increasing availability of genomic data for quantitative genetic studies of wild admixed populations can be handled. To make the method widely available to the scientific community, we offer guidance in the form of a tutorial including step-by-step instructions to facilitate implementation.
Comparison of NICE Guideline CG149 and the Sepsis Risk Calculator for the Management of Early-Onset Sepsis on the Postnatal Ward

Introduction: The NICE guideline CG149 has increased the number of well infants receiving antibiotics for suspected early-onset sepsis (EOS). The Kaiser Permanente sepsis risk calculator (SRC) has safely and dramatically reduced investigations and antibiotics for suspected EOS in the USA. This study evaluates the current management of suspected EOS against the NICE guideline CG149 and the SRC. Methods: This study is a prospective, multicentre, observational study across 13 neonatal units in London. Infants were born between June and August 2019 at ≥34 weeks gestation and commenced on antibiotics for suspected EOS and cared for on postnatal/transitional care wards. Data were prospectively recorded: risk factors, clinical indicators, investigations, and results. Outcome measures included the following: (1) incidence of EOS and (2) proportion of infants recommended for antibiotics by NICE versus theoretical application of SRC. Results: 1,066/8,856 (12%) infants on postnatal/transitional care wards received antibiotics, 7 of whom had a positive blood culture (group B Streptococcus = 6 and Escherichia coli = 1), making the EOS incidence 0.8/1,000 infants. Six hundred one infants had data for SRC analysis, which recommended “antibiotics” or “blood culture” for 130/601 (21.6%) infants using an EOS incidence of 0.5/1,000 versus 527/601 (87.7%) if NICE was applied. Conclusions: Currently, 12.0% of infants on postnatal/transitional care wards receive antibiotics for suspected EOS. The SRC could dramatically reduce antibiotic use, but further prospective studies are required to evaluate safety of SRC implementation.
Nests, eggs, clutch size, and nestlings of the Chestnut Seedeater (Sporophila cinnamomea), a vulnerable species of South America

ABSTRACT We present information on the nests, eggs, clutch size, and nestlings of the Chestnut Seedeater (Sporophila cinnamomea), a migratory, globally vulnerable species restricted to the natural grasslands of South America. Despite its vulnerability, there is currently a remarkable lack of basic information on this species. We searched for nests from October to March 2018–2019 and 2019–2020 at 2 grassland areas in southern Brazil and monitored a total of 98 nests of 50 different breeding pairs throughout this period. Birds placed their nests on shrubs, clumps, and herbaceous plants, 42–51 cm above humid or dry ground, or water. Nests were low cups built out of native grass stems, inflorescences, and rootlets, held together with spider webs. Nests measured 4.86 cm (SD 0.40) largest internal diameter, 4.17 cm (SD 0.37) smallest internal diameter, 6.31 cm (SD 0.57) largest external diameter, 5.42 cm (SD 0.51) smallest external diameter, 4.04 cm (SD 0.45) internal height, and 4.74 cm (SD 0.52) external height. Clutches had 1–3 eggs. Eggs were mostly ovate, with a whitish to light beige background mottled with blotches and spots of darker beige and brownish tints. The mean egg size was 16.15 mm (SD 1.07) by 12.11 mm (SD 0.34) (n = 23). Results are part of ongoing research in the southern Brazilian grasslands, which aims to fill the gaps in the knowledge of the breeding biology of Chestnut Seedeater and thereby contribute to its conservation.
Lumican silencing alleviates tumor necrosis factor-α-induced nucleus pulposus cell inflammation and senescence by inhibiting apoptosis signal regulating kinase 1/p38 signaling pathway via inactivating Fas ligand expression

ABSTRACT A recent study has reported that lumican (LUM) is expressed at a high level in the nucleus pulposus specimens from herniated lumbar disc, without description of the specific mechanism. This study was designed to investigate the function and mechanism of LUM in intervertebral disc degeneration (IDD). In this study, human nucleus pulposus cells (hNPCs) cells were challenged with tumor necrosis factor (TNF)-α to establish the IDD in vitro model. After LUM silencing, cell viability was detected using CCK-8 kit, and the expression of inflammatory factors was evaluated using RT-qPCR and ELISA. Flow cytometry and β-galactosidase staining were used to determine cell cycle and cell senescence. The expression of cycle and senescence-related proteins was evaluated with western blotting. Then, Fas ligand (FasL) was overexpressed and proteins in apoptosis signal regulating kinase 1 (ASK1)/p38 signaling were tested. Finally, GS-4997, an inhibitor of ASK1, was used to explore the regulatory effects of LUM on ASK1/p38 signaling in TNF-α-induced hNPCs. Results indicated that LUM expression was upregulated in TNF-α-challenged hNPCs. LUM gene interference mitigated TNF-α-induced inflammatory response, cell cycle arrest, and senescence of hNPCs. It was then found that LUM silencing could inhibit ASK1/p38 signaling in TNF-α-treated hNPCs, which was reversed by FasL overexpression. Additionally, ASK1/p38 participated in the mediation by LUM of TNF-α-induced inflammation, cell cycle arrest, and senescence of hNPCs. To conclude, interference with LUM effectively mitigated TNF-α-induced inflammatory response, cell cycle arrest, and cell senescence. Further experiments showed the involvement of ASK1/p38 pathway in LUM-mediated NP cell phenotypes through FasL.
Distribution, Dynamics, and Diversity of Questing Ticks in the Lower Midwest

Abstract We investigated the spatiotemporal patterns of medically important tick species in southcentral Indiana in 2018 and 2019. In recent decades, both Amblyomma americanum (Acari: Ixodidae) (Linnaeus) and Ixodes scapularis (Acari: Ixodidae) (Say) have been expanding their ranges into the Midwest. We report updates to the status of A. americanum, I. scapularis, and Dermacentor variabilis (Acari: Ixodidae) (Say) across 13 counties in southern and south-central Indiana. We found more northerly establishment of A. americanum and more widespread establishment of I. scapularis than previously reported in the literature. We also provide the first report of Amblyomma maculatum (Acari: Ixodidae) (Koch) in Indiana. Using negative binomial regression, we observed significant spatial variation among sampling sites in A. americanum adults and nymphs, D. variabilis adults, and I. scapularis nymphs. Further, we found higher densities of A. americanum nymphs and I. scapularis adults in more forested areas as opposed to less forested, more developed areas. We did not find significant interannual variation in tick densities for any species. More southern sites featured higher densities of A. americanum adults and nymphs, D. variabilis adults, and I. scapularis nymphs than more northern sites. Seasonally, we observed the highest peaks in tick activity in the spring and early summer, but I. scapularis adults were most common in the early spring and fall. Average adult A. americanum and adult D. variabilis densities were positively correlated at our sites. Our results reflect the northward expansion of A. americanum in the Lower Midwest, as well as the increasing geographic prevalence of I. scapularis in the region.
FG-LiquID

Contact-less liquid identification via wireless sensing has diverse potential applications in our daily life, such as identifying alcohol content in liquids, distinguishing spoiled and fresh milk, and even detecting water contamination. Recent works have verified the feasibility of utilizing mmWave radar to perform coarse-grained material identification, e.g., discriminating liquid and carpet. However, they do not fully exploit the sensing limits of mmWave in terms of fine-grained material classification. In this paper, we propose FG-LiquID, an accurate and robust system for fine-grained liquid identification. To achieve the desired fine granularity, FG-LiquID first focuses on the small but informative region of the mmWave spectrum, so as to extract the most discriminative features of liquids. Then we design a novel neural network, which uncovers and leverages the hidden signal patterns across multiple antennas on mmWave sensors. In this way, FG-LiquID learns to calibrate signals and finally eliminate the adverse effect of location interference caused by minor displacement/rotation of the liquid container, which ensures robust identification towards daily usage scenarios. Extensive experimental results using a custom-build prototype demonstrate that FG-LiquID can accurately distinguish 30 different liquids with an average accuracy of 97%, under 5 different scenarios. More importantly, it can discriminate quite similar liquids, such as liquors with the difference of only 1% alcohol concentration by volume.
REFRESH: A New Approach to Modeling Dimensional Biases in Perceptual Similarity and Categorization

Much categorization behavior can be explained by family resemblance: New items are classified by comparison with previously learned exemplars. However, categorization behavior also shows a variety of dimensional biases, where the underlying space has so-called “separable” dimensions: Ease of learning categories depends on how the stimuli align with the separable dimensions of the space. For example, if a set of objects of various sizes and colors can be accurately categorized using a single separable dimension (e.g., size), then category learning will be fast, while if the category is determined by both dimensions, learning will be slow. To capture these dimensional biases, almost all models of categorization supplement family resemblance with either rule-based systems or selective attention to separable dimensions. But these models do not explain how separable dimensions initially arise; they are presumed to be unexplained psychological primitives. We develop, instead, a pure family resemblance version of the Rational Model of Categorization (RMC), which we term the Rational Exclusively Family RESemblance Hierarchy (REFRESH), which does not presuppose any separable dimensions in the space of stimuli. REFRESH infers how the stimuli are clustered and uses a hierarchical prior to learn expectations about the variability of clusters across categories. We first demonstrate the dimensional alignment of natural-category features and then show how through a lifetime of categorization experience REFRESH will learn prior expectations that clusters of stimuli will align with separable dimensions. REFRESH captures the key dimensional biases and also explains their stimulus-dependence and how they are learned and develop.
Sleep-disordered breathing and risk of lung cancer: a meta-analysis longitudinal follow-up studies

Consensus remains lack regarding whether sleep-disordered breathing (SDB) is an independent risk factor for lung cancer. We therefore conducted a meta-analysis to clarify the relationship of SDB and lung cancer. Longitudinal follow-up studies investigating the association between SDB and incidence of lung cancer were included by search of electronic databases including PubMed, Embase, and Cochrane’s Library. A random-effects model was adopted to combine the results. Seven studies were included. Pooled results showed that presence of SDB was independently associated with higher incidence of lung cancer [adjusted risk ratio (RR): 1.28; 95% confidence interval (CI), 1.11–1.47; P < 0.001; I2 = 37%]. Sensitivity analysis limited to studies with adjustment of smoking showed consistent results (three studies, RR: 1.34; 95% CI, 1.22–1.48; P < 0.001; I2 = 8%). Subgroup analysis suggested that the association between SDB and higher risk of lung cancer was not significantly affected by study characteristics such as study design, source of population, sample size, evaluation methods for SDB, follow-up duration, methods for validation of lung cancer, or score of study quality (P values for subgroup difference all >0.05). No significant publication bias was observed (P for Egger’s regression test = 0.258). These results suggested that SDB may be an independent risk factor of lung cancer in adult population. Intensive screening and prevention of lung cancer in subjects with SDB should be considered.
Friction and Mechanical Properties of AFM-Scan-Induced Ripples in Polymer Films

When compliant samples such as polymer films are scanned with an atomic force microscope (AFM) in contact mode, a periodic ripple pattern can be induced on the sample. In the present paper, friction and mechanical properties of such ripple structures on films of polystyrene (PS) and poly-n-(butyl methacrylate) (PnBMA) are investigated. Force volume measurements allow a quantitative analysis of the elastic moduli with nanometer resolution, showing a contrast in mechanical response between bundles and troughs. Additionally, analysis of the lateral cantilever deflection when scanning on pre-machined ripples shows a clear correlation between friction and the sample topography. Those results support the theory of crack propagation and the formation of voids as a mechanism responsible for the formation of ripples. This paper also shows the limits of the presented measuring methods for soft, compliant, and small structures. Special care must be taken to ensure that the analysis is not affected by artefacts.
Study of the corrosion-inhibiting activity of the green materials of the Posidonia oceanica leaves’ ethanolic extract based on PVP in corrosive media (1 M of HCl)

Abstract Since the corrosion protection of mild steel samples in corrosive media (1 M of hydrochloric acid [HCl]) was cheap and successful, the ethanol extract of Posidonia oceanica leaves based on polyvinylpyrrolidone (P. oceanica/PVP) was analyzed using the weight reduction, the open circuit potential, and the potentiodynamic polarization methods. The obtained results explained that the productivity of hindrance increments had the greatest restraint efficiency of ∼81% at 1,000 ppm, as the concentration of the extract increased. Liable for adsorption as a thin layer on the surface of mild steel to protect it, the creation of kaolin-traced phenolic and polysaccharide compounds was confirmed by the Fourier transform infrared spectroscopy analysis. A scanning electron microscope was used to evaluate the inhibitive action of P. oceanica/PVP against steel in corrosive media and the change in surface morphology was considered. It is presumed that the ethanol removed from the Posidonia oceanica leaves can fill in as a compelling consumption inhibitor for gentle steel in HCL solution (1 M).
The use of variable delay multipulse chemical exchange saturation transfer for separately assessing different CEST pools in the human brain at 7T

Current challenges of in vivo CEST imaging include overlapping signals from different pools. The overlap arises from closely resonating pools and/or the broad magnetization transfer contrast (MTC) from macromolecules. This study aimed to evaluate the feasibility of variable delay multipulse (VDMP) CEST to separately assess solute pools with different chemical exchange rates in the human brain in vivo, while mitigating the MTC.
Factors contributing to gender inequities in physical activity and campus recreation facility use

Abstract Objective: Examine college women’s perceptions of factors contributing to gender inequities in physical activity and campus recreational facility use. Methods: Semi-structured interviews were conducted with female undergraduate students at a large university located in the Northeast of the United States. Qualitative data were analyzed using thematic analyses using the socio-ecological model as a conceptual framework. Results: Women (N = 18; 6 non-Hispanic White, 5 Black, 7 Asian American; 20.6 ± 1.2 years old) cited intrapersonal, interpersonal, and environmental factors impacting their physical activity and campus recreation facility use due to their gender. Built environmental factors included facility proximity, facility layout and equipment, and crowdedness. Male peers impacted women by making them feel uncomfortable/intimidated and harassed. Intrapersonal factors included a perceived lack of skills/competence/knowledge, lack of confidence, and self-consciousness. Conclusions: Findings demonstrate the need for institutions to implement and enforce policies that achieve a cultural shift in the social environment to provide equitable physical activity participation opportunities.
Optimal echocardiographic assessment of myocardial dysfunction for arrhythmic risk stratification in phospholamban mutation carriers

Abstract Aims Phospholamban (PLN) p.Arg14del mutation carriers are at risk of developing malignant ventricular arrhythmias (VAs) and/or heart failure. Currently, left ventricular ejection fraction (LVEF) plays an important role in risk assessment for VA in these individuals. We aimed to study the incremental prognostic value of left ventricular mechanical dispersion (LVMD) by echocardiographic deformation imaging for prediction of sustained VA in PLN p.Arg14del mutation carriers. Methods and results We included 243 PLN p.Arg14del mutation carriers, which were classified into three groups according to the ‘45/45’ rule: (i) normal left ventricular (LV) function, defined as preserved LVEF ≥45% with normal LVMD ≤45 ms (n = 139), (ii) mechanical LV dysfunction, defined as preserved LVEF ≥45% with abnormal LVMD >45 ms (n = 63), and (iii) overt LV dysfunction, defined as reduced LVEF <45% (n = 41). During a median follow-up of 3.3 (interquartile range 1.8–6.0) years, sustained VA occurred in 35 individuals. The negative predictive value of having normal LV function at baseline was 99% [95% confidence interval (CI): 92–100%] for developing sustained VA. The positive predictive value of mechanical LV dysfunction was 20% (95% CI: 15–27%). Mechanical LV dysfunction was an independent predictor of sustained VA in multivariable analysis [hazard ratio adjusted for VA history: 20.48 (95% CI: 2.57–162.84)]. Conclusion LVMD has incremental prognostic value on top of LVEF in PLN p.Arg14del mutation carriers, particularly in those with preserved LVEF. The ‘45/45’ rule is a practical approach to echocardiographic risk stratification in this challenging group of patients. This approach may also have added value in other diseases where LVEF deterioration is a relative late marker of myocardial dysfunction.
Variations of the bridge quiver for domestic string algebras

In the computation of some representation-theoretic numerical invariants of domestic string algebras, a finite combinatorial gadget introduced by Schröer– the bridge quiver whose vertices are (representatives of cyclic permutations of) bands and whose arrows are certain band-free strings–has been used extensively. There is a natural but ill-behaved partial binary operation, ○, on the larger set of weak bridges such that bridges are precisely the ○-irreducibles. With the goal of computing hammocks up to isomorphism in a later work we equip an even larger set of weak arch bridges with another partial binary operation, ○H , to obtain a finite category. Each weak arch bridge admits a unique ○H-factorization into arch bridges, i.e., the ○H-irreducibles.