Miracle-dz/UniFAR-FTUs huggingface dataset:
Imputation of Variants from the 1000 Genomes Project Modestly Improves Known Associations and Can Identify Low-frequency Variant - Phenotype Associations Undetected by HapMap Based Imputation

Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF <5%) and rare variants (<1%)) can enhance previously identified associations and identify novel loci, we selected 93 quantitative circulating factors where data was available from the InCHIANTI population study. These phenotypes included cytokines, binding proteins, hormones, vitamins and ions. We selected these phenotypes because many have known strong genetic associations and are potentially important to help understand disease processes. We performed a genome-wide scan for these 93 phenotypes in InCHIANTI. We identified 21 signals and 33 signals that reached P<5×10−8 based on HapMap and 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P<5×10−11 respectively. Imputation of 1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P<5×10−8 in both analyses (17 of which represent well replicated signals in the NHGRI catalogue), six were captured by the same index SNP, five were nominally more strongly associated in 1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10−12). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.
‘Mexicans love red’ and other gentrification myths: Displacements and contestations in the gentrification of Pilsen, Chicago, USA

This article uses experiences from a decade-long community-based research project in the Pilsen neighbourhood of Chicago, a Mexican-American neighbourhood whose residents are both experiencing and resisting gentrification, to show how displacements and contestations evolve in conversation with each other in an iterative process we could call ‘actually existing’ gentrifications. I analyse a series of ‘moments’ in 13 years of research in Pilsen to illustrate the constantly shifting terrain of gentrification politics, covering not just housing affordability, but the nature of identity, democracy and belonging. As communities develop resistance strategies to gentrification, so too do city planners, policy makers and developers adapt to these community strategies to reframe their vision of the community. In highlighting both the success of community resistance in mitigating some of the worst effects of gentrification and the co-optation of some of these same strategies in the reframing of gentrification, my goal is to show that gentrification is rarely ever done or complete but is continuously enacted and resisted, challenging the idea that gentrification is somehow inevitable.
The Role of Leader’s Humility in Facilitating Frontline Employees’ Deep Acting and Turnover: The Moderating Role of Perceived Customer-Oriented Climate

Many cultures recognize humility as an important human virtue. However, there is scant research on a possible relationship between leader’s humility and employees’ emotional labor. The current study, based on strong-situation hypothesis, posits that within the service industry, leader’s humility could determine and facilitate employee’ deep acting and turnover. Moreover, the mediating effect of deep acting is moderated by employees’ perceptions of the organization’s customer-oriented climate. The study is based on self-reported and archival data of 157 frontline employees at a hospital in China. The results generally support the hypotheses. The theoretical and practical implications of these results are also discussed.
Levels of Germination Proteins in Bacillus subtilis Dormant, Superdormant, and Germinating Spores

Bacterial endospores exhibit extreme resistance to most conditions that rapidly kill other life forms, remaining viable in this dormant state for centuries or longer. While the majority of Bacillus subtilis dormant spores germinate rapidly in response to nutrient germinants, a small subpopulation termed superdormant spores are resistant to germination, potentially evading antibiotic and/or decontamination strategies. In an effort to better understand the underlying mechanisms of superdormancy, membrane-associated proteins were isolated from populations of B. subtilis dormant, superdormant, and germinated spores, and the relative abundance of 11 germination-related proteins was determined using multiple-reaction-monitoring liquid chromatography-mass spectrometry assays. GerAC, GerKC, and GerD were significantly less abundant in the membrane fractions obtained from superdormant spores than those derived from dormant spores. The amounts of YpeB, GerD, PrkC, GerAC, and GerKC recovered in membrane fractions decreased significantly during germination. Lipoproteins, as a protein class, decreased during spore germination, while YpeB appeared to be specifically degraded. Some protein abundance differences between membrane fractions of dormant and superdormant spores resemble protein changes that take place during germination, suggesting that the superdormant spore isolation procedure may have resulted in early, non-committal germination-associated changes. In addition to low levels of germinant receptor proteins, a deficiency in the GerD lipoprotein may contribute to heterogeneity of spore germination rates. Understanding the reasons for superdormancy may allow for better spore decontamination procedures.
Multistable Perception in Older Adults: Constructing a Whole from Fragments

Visual perception is constructive in nature; that is, a coherent whole is generated from ambiguous fragments that are encountered in dynamic visual scenes. Creating this coherent whole from fragmented sensory inputs requires one to detect, identify, distinguish and organize sensory input. The organization of fragments into a coherent whole is facilitated by the continuous interactions between lower level sensory inputs and higher order processes. However, age-related declines are found in both neural structures and cognitive processes (e.g., attention and inhibition). The impact of these declines on the constructive nature of visual processing was the focus of this study. Here we asked younger adults, young-old (65–79 years), and old-old adults (80+ years) to view a multistable figure (i.e., Necker cube) under four conditions (free, priming, volition, and adaptation) and report, via a button press, when percepts spontaneously changed. The oldest-olds, unlike young-olds and younger adults, were influenced by priming, had less visual stability during volition and showed less ability to adapt to multistable stimuli. These results suggest that the ability to construct a coherent whole from fragments declines with age. More specifically, vision is constructed differently in the old-olds, which might influence environmental interpretations and navigational abilities in this age group.
Keeping us grounded: academic staff perceptions of service user and carer involvement in health and social work training

Abstract Academic staff perceptions of the value and purpose of service user and carer (SUAC) involvement within a health and social work faculty in an English university were explored in this co-produced qualitative study. Relevant research findings over the past two decades were reviewed and two SUAC researchers, plus an academic member of staff, designed the study based around 15 semi-structured telephone interviews. Findings were that staff were very positive about the benefits brought by SUAC involvement, in respect of their own grounding, knowledge, and continuing professional development (CPD), these findings not having previously been reflected in the literature. Barriers to involvement of SUACs were found to be negligible compared to those found in recent literature, and the input of SUACs appeared to be embraced by academic staff. This changing picture has emerged at a time when managerialism and marketisation affect the working conditions of staff. In times of increasing workloads, this study suggested that academics find SUAC involvement both supportive and constructively challenging. SUACs were perceived to bring fresh interdisciplinary knowledge and challenges to staff value bases alongside constructs of professionalism that staff may not be able to access elsewhere. The encouragement of interdisciplinary ways of thinking was noted to have been a serendipitous consequence of SUACs from different backgrounds inputting on courses across the faculty. Recommendations are to better ensure consistency in the use of SUACs in terms of resourcing, support and development if such involvement is to be meaningful rather than marginalised and de-valued.
The relationships among high school STEM learning experiences, expectations, and mathematics and science efficacy and the likelihood of majoring in STEM in college

ABSTRACT This study examines college students’ science, technology, engineering, and mathematics (STEM) choices as they relate to high school experiences, parent, teacher, and self-expectations, and mathematics and science efficacy. Participants were 2246 graduates of a STEM-focused public Harmony Public Schools in Texas, Harmony Public Schools (HPS). Descriptive analyses indicated that the overall percentage of HPS graduates who chose a STEM major in college was greater than Texas state and national averages. Logistic regression analyses revealed that males and Asian students are more likely to choose a STEM major in college than females and non-Asian students, respectively. Moreover, students whose parents had a college degree in the U.S. are more likely to major in STEM fields than those who did not. Furthermore, males with higher mathematics efficacy and females with higher science efficacy are more likely to choose a STEM major than their counterparts with lower mathematics and science efficacy.
Predictors of Virological Response to a Combination Therapy with Pegylated Interferon Plus Ribavirin Including Virus and Host Factors

A combination therapy with pegylated interferon (PEG-IFN) plus ribavirin (RBV) has made it possible to achieve a sustained virological response (SVR) of 50% in refractory cases with genotype 1b and high levels of plasma HCVRNA. Several factors including virus mutation and host factors such as age, gender, fibrosis of the liver, lipid metabolism, innate immunity, and single nucleotide polymorphism (SNPs) are reported to be correlated to therapeutic effects. However, it is difficult to determine which factor is the most important predictor for an individual patient. Data mining analysis is useful for combining all these together to predict the therapeutic effects. It is important to analyze blood tests and to predict therapeutic effects prior to initiating treatment. Since new anti-HCV agents are under development, it will be necessary in the future to select the patients who have a high possibility of achieving SVR if treatment is performed with standard regimen.
The Distribution of Pressures in a Supernova-driven Interstellar Medium. I. Magnetized Medium

Observations have suggested substantial departures from pressure equilibrium in the interstellar medium (ISM) in the plane of the Galaxy, even on scales under 50 pc. Nevertheless, multiphase models of the ISM assume at least locally isobaric gas. The pressure then determines the density reached by gas cooling to stable thermal equilibrium. We use numerical models of the magnetized ISM to examine the consequences of supernova driving for interstellar pressures. In this paper we examine a (200 pc)3 periodic domain threaded by magnetic fields. Individual parcels of gas at different pressures reach widely varying points on the thermal equilibrium curve: no unique set of phases is found but rather a dynamically determined continuum of densities and temperatures. A substantial fraction of the gas remains entirely out of thermal equilibrium. Our results appear consistent with observations of interstellar pressures. They also suggest that the high pressures observed in molecular clouds may be due to ram pressures in addition to gravitational forces. Much of the gas in our model lies far from equipartition between thermal and magnetic pressures, with ratios ranging from 0.1 to 104 and ratios of uniform to fluctuating magnetic field of 0.5-1. Our models show broad pressure probability distribution functions with log-normal functional forms produced by both shocks and rarefaction waves rather than power-law distributions produced by isolated supernova remnants. The width of the distribution can be described quantitatively by a formula derived from the work of Padoan, Nordlund, & Jones.
Default ne in Child Mandarin Chinese

Transcripts of children acquiring Mandarin Chinese reveal errors in the morphological realization of inchoative aspect. Where an adult would use a sentence-final particle le, children will often either omit it, or substitute a different marker (ne). We analyze the overuse of ne in child Mandarin as a retreat to a default form that results from an impoverished syntactic representation. We compare the actual proportions of S-le successes, ne errors, and omission errors across fine-grained developmental stages by estimating the number of inchoative “attempts,” based on the frequency of adult usage of S-le from the same transcripts. We propose an Optimality Theoretic account in which constraints requiring syntactic realization of the features of the intended meaning “float” in the ranking over constraints that require economy of syntactic structure. These partial rankings characterize a set of alternative grammars that the child uses in production. Finally, we compare these results to similar results from the acquisition of French and of Catalan, all of which display a coexistence of competing grammars, retreats to a default form, and constraints requiring economy of structure, despite obvious differences in the morphological richness of the three languages.
Managing Stovepiped Organisations - A Comparison of Public and Private Organisations

Stovepiped systems and difficulties associated with managing cross-functional boundaries are problems that are hindering the successful implementation of customercentred systems and processes within public organisations. The present study covers public organisations, and discusses and analyses the results in relation to those from a previous study in the banking sector. While problems with stovepiped systems and departments have, in general, been solved in the banking sector, the results from the interviewed public organisations confirm that the stovepipe problem is still evident and that cross-functional collaboration, processes, customer focus and integration of services and channels all require additional improvement or development. The present study concludes that the goals with the highest priority for leaders in public organisations are not those associated with customer relations and that the political level rates higher than the customers’ demands. The public organisations are following a similar path to that of the private sector, but there are differences in both the time-frame and ability to implement changes due to weaker incentives for customer related work, and additionally, a larger organisational inertia of both culture and collaboration to overcome. Similarities are found in IT organisations and projects, and in the views regarding business organisations and the necessity for an enterprise architecture.
50 Hz Electromagnetic Field Produced Changes in FTIR Spectroscopy Associated with Mitochondrial Transmembrane Potential Reduction in Neuronal-Like SH-SY5Y Cells

SH-SY5Y neuroblastoma cells were used as an experimental model to study the effects of 50 Hz electromagnetic field, in the range from 50 µT to 1.4 mT. Fourier transform infrared spectroscopy analysis evidenced a reduction in intensity of the amide A band and a slight increase of vibration bands at 2921 cm−1 and 2853 cm−1 corresponding to methylene groups. A further increase of the magnetic field intensity of exposure up to 0.8 mT and 1.4 mT produced a clear increase in intensity of CH2 vibration bands. Moreover, it has been observed some alterations in the amide I region, such as a shifted peak of the amide I band to a smaller wavenumber, probably due to protein conformational changes. These results suggested that exposure to extremely low electromagnetic fields influenced lipid components of cellular membrane and the N–H in-plane bending and C–N stretching vibrations of peptide linkages, modifying the secondary structures of α-helix and β-sheet contents and producing unfolding process in cell membrane proteins. The observed changes after exposure to 50 Hz electromagnetic field higher than 0.8 mT were associated with a significant reduction of cell viability and reduced mitochondrial transmembrane potential.
Does it pay to be proactive? Testing proactiveness and the joint effect of internal and external collaboration on key account manager performance

In a survey of key account managers, we examine how internal and external collaboration individually and jointly affect performance. We shed light on the role of proactiveness in generating these effects. Using a social exchange theory lens, we consider how managing a portfolio of relationships through collaboration, both inside and outside of the organization, plays an important role in key account manager performance. Using data collected from key account managers across a range of industries, this study finds that proactive key account managers have higher levels of collaboration and performance. We find however that only the joint effect of internal and external collaboration positively affects performance. Interestingly, there were no direct effects. This study extends our understanding of the nature of collaboration in business-to-business relationships. Drawing on these findings, we discuss several theoretical and managerial implications.
Faster Thalamocortical Processing for Dark than Light Visual Targets

ON and OFF visual pathways originate in the retina at the synapse between photoreceptor and bipolar cells. OFF bipolar cells are shorter in length and use receptors with faster kinetics than ON bipolar cells and, therefore, process information faster. Here, we demonstrate that this temporal advantage is maintained through thalamocortical processing, with OFF visual responses reaching cortex ∼3–6 ms before ON visual responses. Faster OFF visual responses could be demonstrated in recordings from large populations of cat thalamic neurons representing the center of vision (both X and Y) and from subpopulations making connection with the same cortical orientation column. While the OFF temporal advantage diminished as visual responses reached their peak, the integral of the impulse response was greater in OFF than ON neurons. Given the stimulus preferences from OFF and ON channels, our results indicate that darks are processed faster than lights in the thalamocortical pathway.
Combination Proximal Pulmonary Artery Coiling and Distal Embolization Induces Chronic Elevations in Pulmonary Artery Pressure in Swine

Pulmonary hypertension (PH) is associated with aberrant vascular remodeling and right ventricular (RV) dysfunction that contribute to early mortality. Large animal models that recapitulate human PH are essential for mechanistic studies and evaluating novel therapies; however, these models are not readily accessible to the field owing to the need for advanced surgical techniques or hypoxia. In this study, we present a novel swine model that develops cardiopulmonary hemodynamics and structural changes characteristic of chronic PH. This percutaneous model was created in swine (n=6) by combining distal embolization of dextran beads with selective coiling of the lobar pulmonary arteries (2 procedures per lung over 4 weeks). As controls, findings from this model were compared with those from a standard weekly distal embolization model (n=6) and sham animals (n=4). Survival with the combined embolization model was 100%. At 8 weeks after the index procedure, combined embolization procedure animals had increased mean pulmonary artery pressure (mPA) and pulmonary vascular resistance (PVR) compared to the controls with no effect on left heart or systemic pressures. RV remodeling and RV dysfunction were also present with a decrease in the RV ejection fraction, increase in the myocardial performance index, impaired longitudinal function, as well as cardiomyocyte hypertrophy, and interstitial fibrosis, which were not present in the controls. Pulmonary vascular remodeling occurred in both embolization models, although only the combination embolization model had a decrease in pulmonary capacitance. Taken together, these cardiopulmonary hemodynamic and structural findings identify the novel combination embolization swine model as a valuable tool for future studies of chronic PH.
Subimage sensitive eigenvalue spectra for image comparison Can one hear what ’ s painted on a drum ?

This publication is a contribution to basic research in image comparison using eigenvalue spectra as features. The differential-geometric approach of eigenvalue spectrum-based descriptors is naturally applicable to shape data, but so far little work has been done to transfer it to the setting of image data painted on a rectangle or general curved surface. We present a new semi-global feature descriptor that also contains information about geometry of shapes visible in the image. This may not only improve the performance of the resulting distance measures, but may even enable us to approach the partial matching problem using eigenvalue spectra, which were previously only considered as global feature descriptors. We introduce some concepts that are useful in designing and understanding the behaviour of similar fingerprinting algorithms for images (and surfaces) and discuss some preliminary results.
Estimation of Ocean Current Velocity near Incheon using Radarsat-1 SAR and HF-radar Data

This paper presents the results of the ocean surface current velocity estimation using 6 Radarsat-1 SAR images acquired in west coastal area near Incheon. We extracted the surface velocity from SAR images based on the Doppler shift approach in which the azimuth frequency shift is related to the motion of surface target in the radar direction. The Doppler shift was measured by the difference between the Doppler centroid estimated in the range-compressed, azimuth-frequency domain and the nominal Doppler centroid used during the SAR focusing process. The extracted SAR current velocities were statistically compared with the current velocities from the high frequency (HF) radar in terms of averages, standard deviations, and root mean square errors. The problem of the unreliable nominal Doppler centroid for the estimation of the SAR current velocity was corrected by subtracting the difference of averages between SAR and HF-radar current velocities from the SAR current velocity. The corrected SAR current velocity inherits the average of HF-radar data while maintaining high-resolution nature of the original SAR data.