Miracle-dz/UniFAR-FTUs huggingface dataset:
DYNATE: Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree

Rare variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNATE (DYNamic Aggregation TEsting). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with controlled weighted false discovery rate. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared to existing methods. Importantly, DYNATE-identified regions have higher enrichment levels of disease-associated RVs. We applied DYNATE to an amyotrophic lateral sclerosis (ALS) study and identified a new gene, EPG5, harboringpossibly pathogenic mutations.
Full-Scale Testing of Open-Ended Steel Pipe Piles in Thick Varved Clayey Silt Deposits along the Delaware River in New Jersey

Although many studies have been done to investigate the axial behaviors of open-ended piles in sands, few studies have been reported for weak clayey silts. To develop reliable models for the design of open-ended steel-pipe piles driven into 29-m-thick varved clayey silt deposits, a series of full-scale field load tests including large-strain dynamic tests and static cyclic axial-compression-load tests was conducted on two groups of instrumented piles. Through analysis of the test data, soil parameters were back-calculated for estimation of pile capacities using the static-bearing-capacity formulas and cone-resistance-based methods. The comparisons between the calculated results and the field load test data demonstrated that the following considerations can be adopted in the design of static compression capacities of an open-ended pipe pile penetrating through thick varved clayey silts to end-bearing in dense cohesionless soils: (1) a fully plugged condition can be assumed, (2) cone resistance with an upper limit of 4,788 kPa (100 ksf) can be used for unit base resistance on the soil plug, and (3) exterior unit shaft resistance can be estimated using two-thirds of the total unit shaft resistance.
Antarctica; A Tale of Two Supercontinents?

On March 29, 1912, Captain Robert Falcon Scott and his companions, Dr. Edward A. Wilson and Lieutenant H. R. Bowers died in their tent during a blizzard on the Ross Ice Shelf in Antarctica from cold, exhaustion, and lack of nourishment. They were a mere 18 km from a supply depot they had cached months earlier, before their journey to the South Pole. They died disappointed men, having learned on their arrival at the pole that Roald Amundsen and his Norwegian party had beaten them to the long-sought goal by one month. During their return journey, despite full awareness of the seriousness of their situation, Scott and his men had taken time to "geologize" in the Transantarctic Mountains (Scott 1913). They man-hauled 16 kg of rock samples collected there towards civilization until they succumbed. The specimens were retrieved by the party that found their frozen remains the next summer. The accurate geologic positioning of Antarctica as the "keystone" of a southern supercontinent by Alex Du Toit in his reconstruction of 1937, following the early concepts of Taylor (1910) and Wegener (1912), would not have been on firm ground without the collections made on Scott's expeditions, and on the expedition of Ernest H. Shackleton that pioneered the route through the Transantarctic Mountains to the Polar Plateau in 1908 (Shackleton 1909). Specimens of the Glossopteris flora firmly linked Antarctica to the other southern continents, though full acceptance of the hypothesis of a Gondwana supercontinent by the scientific community
Anfibios y Reptiles de la Guajira Venezolana

Villalobos 11.5606 Normal 0 21 false false false MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:. 0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} Se presenta la lista de las especies de anfibios y reptiles de la Guajira venezolana, por medio de observaciones directas en campo, ejemplares depositados en los museos nacionales y referencias en la literatura. Ademas, se ubicaron las especies en biotopos para determinar la abundancia relativa por unidad ecologica. La lista de especies de la herpetofauna en la Guajira venezolana agrupa a 41 especies, 9 anfibios y 32 reptiles, lo que representa el 42,9% regional para anfibios y el 32,7% regional para reptiles. En general la peninsula de Paraguana, peninsula de Araya y la Guajira presentan menos del 7% de la herpetofauna nacional y referimos a la Guajira como el ecosistema seco venezolano con mayor numero de anfibios (9) y Paraguana corresponde al ecosistema seco con mayor numero de reptiles (38) para Venezuela. El biotopo que presento mayor abundancia relativa corresponde a la unidad vegetal de bosque deciduo con 81,3% para reptiles y 100% para anfibios. A su vez, las especies de anfibios que se encuentran en mayor numero de unidades ecologicas fueron Chaunus marinus , Leptodatylus Cf. wagneri , Pleurodema brachiops y Ceratophrys calcarata que ocupan las sabanas, espinar y el bosque deciduo. Entre los reptiles que se encontraron en la mayoria de los ambientes fueron Phimophis guianensis, Cnemidophorus lemniscatus lemniscatus , Ameiva ameiva y Anolis onca . El estatus de amenaza para los reptiles de la Guajira es de 21,9%, donde se incluyen a todas las especies de tortugas marinas
Trace Element and Sr, Nd, Pb and O Isotope Variations in Medium-K and High-K Volcanic Rocks from Merapi Volcano, Central Java, Indonesia: Evidence for the Involvement of Subducted Sediments in Sunda Arc Magma Genesis

Merapi volcano (Central Java), located within the Quaternary volcanic front of the Sunda arc, is one of the most active volcanoes of the Indonesian archipelago. During the Holocene, Merapi erupted basalts and basaltic andesites of medium-K affinity during its earlier stages of activity and high-K compositions over the past 1900 years. Merapi lavas and pyroclastic rocks are characterized by enrichment in large ion lithophile elements (LILE) and light rare earth elements (LREE) relative to high field strength elements (HFSE) and higher Sr/Sr, Pb/Pb, Pb/Pb and Pb/Pb ratios and lower Nd/Nd ratios compared with Indian Ocean mid-ocean ridge basalt (MORB). Merapi high-K series rocks are enriched in LILE and LREE and slightly depleted in heavy REE (HREE) and HFSE compared with rocks from the medium-K series. The increase in K2O is accompanied by a marked increase in Sr/Sr and a general decrease in Nd/ Nd, but not by systematic variations in dO values. The low dO nature of the Merapi magmas, and the lack of any major shift in isotopic compositions along the evolutionary trend of the two individual series, precludes extensive crustal assimilation during magma ascent and differentiation, emphasizing the importance of subducted continental material in the genesis of Merapi magmas. The compositional contrast between medium-K and high-K series volcanics largely reflects variable contributions from subducted sediment to the mantle wedge, which was similar to a MORB-source mantle before any subduction-related modification. The temporal change in the K2O content of the magmas reflects compositional variation in the mantle wedge rather than intracrustal processes occurring within the shallow volcanic system.
Mechanism of interdecadal thermohaline circulation variability in a coupled ocean : Atmosphere GCM

Abstract Interdecadal variability of the Atlantic thermohaline circulation (THC) is studied in the third version of the Hadley Centre global coupled atmosphere–ocean sea-ice general circulation model (HadCM3). A diagnostic approach is used to elucidate the mechanism that governs the variability and its impacts on climate. An irregular and heavily damped THC oscillation with a period around 25 yr is identified. The oscillation appears to be forced by the atmosphere but the ocean is responsible for setting the time scale. Following a minimum in the THC, the mechanism for phase reversal involves the accumulation of cold water in the subpolar gyre, leading to an acceleration of the gyre circulation and the North Atlantic Current. This acceleration increases the transport of saline waters into the regions of active deep convection, raising the upper-ocean density and leading, after adjustment, to acceleration of the THC. The atmosphere stimulates this THC variability in two ways: 1) by forcing the subpolar gyr.
Explorer Characterisation and germline transmission of cultured avian primordial germ cells

Background: Avian primordial germ cells (PGCs) have significant potential to be used as a cell-based system for the study and preservation of avian germplasm, and the genetic modification of the avian genome. It was previously reported that PGCs from chicken embryos can be propagated in culture and contribute to the germ cell lineage of host birds. Principal Findings: We confirm these results by demonstrating that PGCs from a different layer breed of chickens can be propagated for extended periods in vitro. We demonstrate that intracellular signalling through PI3K and MEK is necessary for PGC growth. We carried out an initial characterisation of these cells. We find that cultured PGCs contain large lipid vacuoles, are glycogen rich, and express the stem cell marker, SSEA-1. These cells also express the germ cell-specific proteins CVH and CDH. Unexpectedly, using RT-PCR we show that cultured PGCs express the pluripotency genes c-Myc, cKlf4, cPouV, cSox2, and cNanog. Finally, we demonstrate that the cultured PGCs will migrate to and colonise the forming gonad of host embryos. Male PGCs will colonise the female gonad and enter meiosis, but are lost from the gonad during sexual development. In male hosts, cultured PGCs form functional gametes as demonstrated by the generation of viable offspring. Conclusions: The establishment of in vitro cultures of germline competent avian PGCs offers a unique system for the study of early germ cell differentiation and also a comparative system for mammalian germ cell development. Primary PGC lines will form the basis of an alternative technique for the preservation of avian germplasm and will be a valuable tool for transgenic technology, with both research and industrial applications. Citation: Macdonald J, Glover JD, Taylor L, Sang HM, McGrew MJ (2010) Characterisation and Germline Transmission of Cultured Avian Primordial Germ Cells. PLoS ONE 5(11): e15518. doi:10.1371/journal.pone. 0015518 Editor: David S. Milstone, Brigham and Women’s Hospital, United States of America Received August 7, 2010; Accepted October 11, 2010; Published November 29, 2010 Copyright: 2010 Macdonald et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research was supported by the Biotechnology and Biological Sciences Research Council, U.K. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mike.mcgrew@roslin.ed.ac.uk
Multiple Effects of Physical Activity on Molecular and Cognitive Signs of Brain Aging: Can Exercise Slow Neurodegeneration and Delay Alzheimer’s Disease? Authors

Western countries are experiencing aging populations and increased longevity; thus the incidence of dementia and Alzheimer's disease (AD) in these countries is projected to soar. In the absence of a therapeutic drug, non-pharmacological preventative approaches are being investigated. One of these approaches is regular participation in physical activity or exercise. This paper reviews studies that have explored the relationship between physical activity and cognitive function, cognitive decline, AD/dementia risk and AD-associated biomarkers and processes. There is now strong evidence that links regular physical activity or exercise to higher cognitive function, decreased cognitive decline and reduced risk of AD or dementia. Nevertheless, these associations require further investigation, more specifically with interventional studies that include long follow-up periods. In particular, relatively little is known about the underlying mechanism(s) of the associations between physical activity and AD neuropathology; clearly this is an area in need of further research, particularly in human populations. While benefits of physical activity or exercise are clearly recognised, there is a need to clarify how much physical activity provides the greatest benefit and also whether people of different genotypes require tailored exercise regimes.
The psychosocial and behavioral impact of familial adenomatous polyposis

Purpose Familial adenomatous polyposis (FAP) is characterized by the development of multiple adenomas in the colorectum that can lead to colorectal cancer. The purpose of this study was to document the impact of FAP on health ‐ related quality of life (HRQL) and on practical aspects of daily life. Methods Participants were 525 individuals (response rate 64%) from 145 families at high ‐ risk for FAP. A battery of self ‐ report questionnaires was used to assess generic (SF ‐ 36 Health Survey) and condition ‐ specific (
First Record of Mesotheriidae in the Late Oligocene of Mendoza Province, Argentina

The present paper deals with the description of the first remains of the Family Mesotheriidae in the Quebrada Fiera locality. The fauna from Quebrada Fiera comes from sediments nowadays considered to represent the base of the Agua de la Piedra Formation. The recovered faunal assemblage includes typical elements of the Deseadan Age (late Oligocene), shared with both Patagonian and lower latitude associations (e.g., Salla, Bolivia). A unique specimen of Mesotheriidae has been recovered after several field seasons since 2006. It is a palatal portion in two fragments, one bearing the I1 and the other with left P4-M2 and right M1-2. Morfological and metrical features of this material reveal a taxon much closer to the Patagonian mesotheriid species Trachytherus spegazzinianus than to the Bolivian taxa, T. alloxus and T. subandinus, and it is determined as Trachytherus cf. T. spegazzinianus. Its presence in Mendoza fills a gap in the expected geographical distribution of this mesotheriid, as it was also recorded in the Bolivian site of Lacayani. The scanty record of mesotheriids in Quebrada Fiera contrasts with Salla and Patagonian localities.
Can Labor Regulation Hinder Economic Performance ? Evidence from India

This paper investigates whether the industrial relations climate in Indian states has affected the pattern of manufacturing growth in the period 1958-92. We show that states which ammended the Industrial Disputes Act in a pro-worker direction experienced lowered output, employment, investment and productivity in registered or formal manufacturing. In contrast, output in unregistered or informal manufacturing increased. Regulating in a pro-worker direction was also associated with increases in urban poverty. This suggests that attempts to redress the balance of power between capital and labor can end up hurting the
Kin groups and reciprocity : A model of credit transactions in Ghana

This paper studies kinship band networks as capital market institutions. Membership in a community where individuals are dynastically linked has two effects on informal credit transactions. First, the non-anonymity of the dynastic link allows to sanction the defaulters' offspring and induce compliance even in short-term interactions (social enforcement). Second, preferential agreements can arise in which kin members condition their behavior on the characteristics of a player's predecessor, e.g., lend to the children of rich players, because they expect that others will do the same with their offspring (reciprocity). These effects are incorporated in an overlapping generations repayment game with endogenous matching between lenders and borrowers and tested using household-level data from Ghana. I wish to thank two anonymous referees, Abhijit Banerjee and Debraj Ray for their invaluable comments and suggestions. I also benefitted from the inputs of excellent research assistance. I am indebted to the Ghana Statistical service for making the data available to me and to Harold Coulombe for sharing information on the panel. Financial support from the Harvard-MIT RTG in Positive Political Economy, from CNR-ISFSE and from Bocconi University is gratefully acknowledged. The usual disclaimer applies. Ahwe-wo-da-bi ba na wahwe no.
Gosses Bluff - a latest Jurassic impact structure, central Australia. Part 1: geological structure, stratigraphy, and origin

tag=1 data=Gosses Bluff - a latest Jurassic impact structure, central Australia. Part 1: geological structure, stratigraphy, and origin. by D.J. Milton, A.Y. Glikson & R. Brett tag=2 data=Milton, D.J.%Glikson, A.Y. %Brett, R. tag=3 data=AGSO Journal of Australian Geology & Geophysics, tag=4 data=16 tag=5 data=4 tag=6 data=1996 tag=7 data=453-486. tag=8 data=MINES & MINERALS tag=10 data=Evidence for an extraterrestrial impact. tag=13 data=IND
Institutional Repository Motivational predictors of physical education students ' effort , exercise intentions , and leisure-time physical activity : a multilevel linear growth analysis

Grounded in self-determination theory (Deci & Ryan, 2000), the present study explored whether Physical Education (PE) students’ psychological needs and their motivational regulations towards PE, predicted mean differences and changes in effort in PE, exercise intentions and leisure-time physical activity (LTPA) over the course of one UK school trimester. One-hundred and seventyeight students (69% male) aged between 11 and 16 years completed a multi-section questionnaire at the beginning, middle and end of a school trimester. Multilevel growth models revealed that students’ perceived competence and self-determined regulations were the most consistent predictors of the outcome variables at the withinand between-person levels. The results of this work add to the extant SDT-based literature by examining change in PE students’ motivational regulations and psychological needs, as well as underscoring the importance of disaggregating withinand between-student effects.
BRIDGE PIER SCOUR IN GRAVEL BED RIVERS

ABSTRACT This paper presents a critical note on the practice being followed in India for estimating the design scour depth around bridge piers founded in the gravel bed rivers. Limitations of the provisions existing in the engineering codes of Indian practice are illustrated through examples and the methods recently developed through scientific investigations for estimation of the scour depth are described. A new relationship is proposed for the Lacey's silt factor estimation in gravel bed rivers. The discharge intensity based Lacey-Inglis procedure when used in conjunction with the relation for estimation of the silt factor proposed herein is expected to produce realistic estimates for the scour depth around bridge piers founded in the gravel bed rivers.
Cognitive Neuroscience and Robotics: A Mutually Beneficial Joining of Forces

— This paper describes an ongoing interdisciplinary collaboration between robotics and human cognitive neuroscience research. We argue such research is beneficial to both disciplines and can be viewed a win-win. Not only it is important to understand the human factors in human-robot interaction, collaborations with robotics can also help cognitive scientists answer questions about human brain and behavior, and take steps toward understanding how the human brain enables some of our most important skills such as action understanding, social cognition, empathy, and communication.
Biportal Endoscopic Approach for Lumbar Degenerative Disease in the Ambulatory Outpatient vs Inpatient Setting: A Comparative Study

Background Biportal spinal endoscopy is increasingly utilized for lumbar disc herniations and lumbar stenosis. The objective was to investigate the safety and effectiveness of the technique in the outpatient vs inpatient setting. Methods This is a comparative study of consecutive patients who underwent biportal spinal endoscopy by a single surgeon at a single institution. Demographics, surgical complications, and patient-reported outcomes were prospectively collected and retrospectively analyzed. Statistics were calculated among treatment groups using unpaired t test and χ 2 analysis where appropriate. Statistical significance was determined as P < 0.05. Results Eighty-four patients were included, 58 (69.0%) as outpatient, 26 (31.0%) as inpatient. Mean follow-up was 7.5 months. Statistically significant differences in age, American Society of Anesthesiologists classification, and Charleston Comorbidity Index scores were reported between cohorts, with younger and healthier patients undergoing outpatient surgery (P < 0.0001). Outpatients were more likely to have discectomies while inpatients were more likely to have decompressions for stenosis. No significant differences in postoperative complications were found between groups. Both cohorts demonstrated significant improvement in visual analog scale (VAS) back and leg pain scores and Oswestry Disability Index scores (P < 0.001). Outpatients had significantly lower postoperative VAS back pain (P = 0.001) and Oswestry Disability Index scores (P = 0.004) at 5–8 weeks compared with inpatients, but there was no significant difference for VAS leg pain scores at all time points between the cohorts. Conclusions Early results demonstrate that biportal spinal endoscopy can safely and effectively be performed in both inpatient and outpatient settings. Clinical Relevance Outpatient biportal spinal endoscopy can be performed successfully in well selected patients, which may reduce the financial burden of spine surgery to the U.S. healthcare system. Level of Evidence 3.