bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Inference of Population Structure for Ancestry Prediction and Correction of Stratification in the Presence of Relatedness
Authors: Conomos Matthew P. , Miller Michael B. , Thornton Timothy A. 
Published: March 2015

ABSTRACTPopulation structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model‐based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC‐AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC‐AiR utilizes genome‐screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC‐AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC‐AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC‐AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC‐AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness.
Temporal persistence of throughfall heterogeneity below and between the canopies of juvenile lodgepole pine (Pinus contorta)
Authors: Carlyle‐Moses D. E. , Lishman C. E. 
Published: March 2015

AbstractFrom May to October 2010, throughfall associated with 38 rainfall events in three below‐canopy zones (inner canopy, mid‐canopy and canopy periphery) of nine juvenile lodgepole pine trees and in open areas between canopies was measured along north, south, east and west transects radiating from each tree bole. Median cumulative throughfall (%) significantly differed among the canopy zones under differing rain depth classes and was negatively correlated with tree size metrics, but only for certain combinations of canopy zones and rain depth classes. Although median cumulative throughfall (%) was negatively correlated with canopy cover fraction when all below‐canopy gauges were considered, this relationship only held true for the inner‐canopy and mid‐canopy zones under relatively small rain depth classes. Additionally, cumulative throughfall (%) was often dependent on transect direction, with event throughfall showing a dependence on the direction of storm origin. Throughfall coefficient of variation (%) also varied by zone and was a function of not only rainfall depth but also other storm variables such as the maximum 30‐min rainfall intensity and the number and duration of intra‐storm breaks. Temporal persistence of throughfall was assessed using time stability plots and Spearman rank coefficients of rain event and depth class pairings for all gauges and by canopy zone, and the influence of temporal lag and meteorological variables on persistence was assessed. The implications of our findings on throughfall sampling and for future ecohydrological studies in juvenile lodgepole pine and similar stands are discussed. Copyright © 2015 John Wiley & Sons, Ltd.
Subsurface Drainage—What's Next?
Authors: Ayars James E. , Evans Robert G. 
Published: March 2015

AbstractField drainage is a critical component of agricultural production in both arid and humid regions, but field drainage is often neglected and mismanaged as an important water resource. Innovative approaches for the integrated design and management of irrigation and subsurface drainage systems have tremendous potential to improve yields to help meet the rapidly emerging food demands and decrease total freshwater diversions to agriculture. Although irrigation system design and management have evolved tremendously in the past few decades, the design methodology and management criteria for subsurface drainage have not changed in the last 50 years. Thus, all aspects of agricultural drainage require serious reconsideration and reevaluation to be able to meet emerging needs. This manuscript evaluates the current design criteria and practices and suggests viable alternatives for the improvement of subsurface agricultural drainage systems to meet the demands of modern agriculture. Drainage water treatment, reuse, and disposal are significant problems for agricultural drainage and various alternatives are presented. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
Curricular Reforms in Mexico
Authors: López‐Bonilla Guadalupe 
Published: March 2015

AbstractIn this article I present recent educational reforms implemented in Mexico and their implications for literacy instruction; in particular, I analyze changes to upper secondary education that seemingly want to promote the development of “disciplinary competences” among students enrolled in different educational tracks. The debates among the different stakeholders, the risks of poorly conceived policies, and the mediation role of participants involved in the enactment of such policies are finally discussed.
Post‐Translational Modifications of Histones in Human Sperm
Authors: Krejčí Jana , Stixová Lenka , Pagáčová Eva , Legartová Soňa , Kozubek Stanislav , Lochmanová Gabriela , Zdráhal Zbyněk , Sehnalová Petra , Dabravolski Siarhei , Hejátko Jan , Bártová Eva 
Published: March 2015

ABSTRACTWe examined the levels and distribution of post‐translationally modified histones and protamines in human sperm. Using western blot immunoassay, immunofluorescence, mass spectrometry (MS), and FLIM‐FRET approaches, we analyzed the status of histone modifications and the protamine P2. Among individual samples, we observed variability in the levels of H3K9me1, H3K9me2, H3K27me3, H3K36me3, and H3K79me1, but the level of acetylated (ac) histones H4 was relatively stable in the sperm head fractions, as demonstrated by western blot analysis. Sperm heads with lower levels of P2 exhibited lower levels of H3K9ac, H3K9me1, H3K27me3, H3K36me3, and H3K79me1. A very strong correlation was observed between the levels of P2 and H3K9me2. FLIM‐FRET analysis additionally revealed that acetylated histones H4 are not only parts of sperm chromatin but also appear in a non‐integrated form. Intriguingly, H4ac and H3K27me3 were detected in sperm tail fractions via western blot analysis. An appearance of specific histone H3 and H4 acetylation and H3 methylation in sperm tail fractions was also confirmed by both LC‐MS/MS and MALDI‐TOF MS analysis. Taken together, these data indicate that particular post‐translational modifications of histones are uniquely distributed in human sperm, and this distribution varies among individuals and among the sperm of a single individual. J. Cell. Biochem. 116: 2195–2209, 2015. © 2015 Wiley Periodicals, Inc.
Perceived Burdensomeness and Thwarted Belongingness Predict Excessive Reassurance Seeking Among Clinical Outpatients
Authors: Hames Jennifer L. , Chiurliza Bruno , Podlogar Matthew C. , Smith April R. , Selby Edward A. , Anestis Michael D. , Joiner Thomas E. 
Published: March 2015

ObjectiveThe current study aimed to investigate whether perceived burdensomeness and thwarted belongingness (i.e., suicide risk factors) were associated with excessive reassurance seeking (a behavior linked to rejection). It was predicted that perceived burdensomeness and thwarted belongingness would predict higher levels of excessive reassurance seeking, controlling for depressive symptoms and global functioning.MethodA cross‐sectional sample of 415 clinical outpatients (62% female; mean age = 28) was examined.ResultsPerceived burdensomeness and thwarted belongingness significantly predicted excessive reassurance seeking, controlling for depressive symptoms and global functioning.ConclusionsPerceived burdensomeness and thwarted belongingness predicted excessive reassurance seeking, suggesting that it would be beneficial for clinicians to assess for and target excessive reassurance seeking among individuals experiencing perceived burdensomeness and thwarted belongingness so that excessive reassurance seeking does not elicit interpersonal rejection.
Single‐dose evaluation of safety, tolerability and pharmacokinetics of newly formulated hydromorphone immediate‐release and hydrophilic matrix extended‐release tablets in healthy Japanese subjects without co‐administration of an opioid antagonist
Authors: Toyama Kaoru , Uchida Naoki , Ishizuka Hitoshi , Sambe Takehiko , Kobayashi Shinichi 
Published: March 2015

AbstractThis single dose, open‐label study investigated the safety, tolerability and pharmacokinetics of single oral doses of newly formulated immediate‐release (IR) and hydrophilic matrix extended‐release (ER) hydromorphone tablets in healthy Japanese subjects without co‐administration of an opioid antagonist under fasting and fed conditions. Plasma and urinary concentrations of hydromorphone and metabolites were measured by liquid‐chromatography tandem mass‐spectroscopy. Following administration of the ER tablet, plasma concentrations of hydromorphone slowly increased with a median tmax of 5.0 h and the Cmax decreased to 37% of the IR tablet, while the AUC0‐inf was comparable with that of the IR tablet when administered at the same dose. The degree of fluctuation in the plasma concentration for the ER tablet was much lower than that of the IR tablet and certain levels of plasma concentrations were maintained after 24 h of ER dosing. The AUC0‐inf and Cmax increased with food for both IR and ER tablets. The AUC0‐inf of hydromorphone‐3‐glucoside was one‐tenth of that of hydromorphone‐3‐glucuronide. A single oral administration of the hydromorphone tablets would be well‐tolerated in healthy Japanese subjects despite a lack of co‐administration of an opioid antagonist and the newly developed ER hydromorphone tablets may have the appropriate PK characteristics for once‐daily dosing.
Mouse brain magnetic resonance microscopy: Applications in Alzheimer disease
Authors: Lin Lan , Fu Zhenrong , Xu Xiaoting , Wu Shuicai 
Published: March 2015

ABSTRACTOver the past two decades, various Alzheimer's disease (AD) trangenetic mice models harboring genes with mutation known to cause familial AD have been created. Today, high‐resolution magnetic resonance microscopy (MRM) technology is being widely used in the study of AD mouse models. It has greatly facilitated and advanced our knowledge of AD. In this review, most of the attention is paid to fundamental of MRM, the construction of standard mouse MRM brain template and atlas, the detection of amyloid plaques, following up on brain atrophy and the future applications of MRM in transgenic AD mice. It is believed that future testing of potential drugs in mouse models with MRM will greatly improve the predictability of drug effect in preclinical trials. Microsc. Res. Tech. 78:416–424, 2015. © 2015 Wiley Periodicals, Inc.
Which Factors Drive the Regional Expansion of Microfinance Institutions? Evidence from Peru
Authors: Vanroose Annabel 
Published: March 2015

AbstractThis paper analyses the location decisions and geographical expansion of microfinance institutions (MFIs) across Peru. To this end, econometric analyses are performed on a self‐constructed dataset that covers MFI presence and expansion in the 1832 districts of Peru, and this for 39 MFIs and 13 commercial banks over the period 2001–2008. The paper shows that Peruvian MFIs have expanded considerably during the last decade. MFIs especially increase access in districts with higher levels of development and therefore seem to follow principally a commercial logic. Districts with banks have also a higher probability of an MFI opening. Copyright © 2015 John Wiley & Sons, Ltd.
Three‐dimensional virtual histology of silurian osteostracan scales revealed by synchrotron radiation microtomography
Authors: Qu Qingming , Blom Henning , Sanchez Sophie , Ahlberg Per 
Published: March 2015

ABSTRACTWe used propagation phase contrast X‐ray synchrotron microtomography to study the three‐dimensional (3D) histology of scales of two osteostracans, Tremataspis and Oeselaspis, members of a jawless vertebrate group often cited as the sister group of jawed vertebrates. 3D‐models of the canal systems and other internal structures are assembled based on the virtual thin section datasets and compared with previous models based on real thin sections. The primary homology framework of the canal systems in the two taxa is revised and new histological details are revealed based on the results of this work. There is no separation of vascular canals and lower mesh canals in the Tremataspis scale, contrary to previous results. The secondary upper mesh canals have a limited distribution to the anterior region of the Tremataspis scale. The upper and lower mesh canal systems of Tremataspis have different geometries, inferred to reflect different developmental origins: we interpret the upper system as a probable epithelial invagination, the lower system as entirely vascular. Oeselaspis has no equivalent of the upper mesh canal system. The upper mesh canal system of Tremataspis may have been sensory in function. In Oeselaspis, numerous polyp‐shaped structures opening from the canal system onto the surface of the scale resemble the innervation tracts for neuromast organs. The growth of the Oeselaspis scale proceeds by addition of small odontodes containing unmineralized lacunae, which may further mineralize and become more compact. Our results highlight that 3D‐histological investigation on scales and other dermal skeletons of osteostracans is necessary to fully appreciate the diversity of skeletal histologies in the group. Traditional 3D‐models based on thin sections alone are not reliable and should no longer be used as the basis for homology assessments or functional hypotheses. J. Morphol. 276:873–888, 2015. © 2015 Wiley Periodicals, Inc.
Off‐resonance saturation ratio obtained with ultrashort echo time‐magnetization transfer techniques is sensitive to changes in static tensile loading of tendons and degeneration
Authors: Chang Eric Y. , Du Jiang , Biswas Reni , Statum Sheronda , Pauli Chantal , Bae Won C. , Chung Christine B. 
Published: March 2015

BackgroundTo determine if off‐saturation ratio (OSR) measured with the ultrashort echo time magnetization transfer (UTE‐MT) sequence could differentiate between tendons under different states of tensile load and to compare these changes between normal versus degenerated tendons.MethodsFourteen tendons were imaged at 3 Tesla before and during the application of 0.5–1 kg tension. A two‐dimensional (2D) ‐UTE‐MT sequence with 1.5, 3, and 5 kHz frequency offsets was used on nine tendons and a 3D‐UTE‐MT sequence with 1.5 kHz frequency offset was used on five tendons. OSR was calculated and compared for each condition. Histologic correlation was performed using light microscopy.ResultsIn general, OSR increased after the application of tension. Mean increase of 2D OSR was 0.035 (95% confidence interval [CI], 0.013–0.056) at 1.5 kHz offset (P < 0.01), 0.031 (95% CI, 0.023–0.040) at 3 kHz offset (P < 0.01), and 0.013 (95% CI, −0.013–0.027) at 5 kHz offset (P = 0.07) from pre‐ to posttension states. Mean increase of 3D OSR was 0.026 (95% CI, 0.008–0.044) at a 1.5 kHz offset (P = 0.02) from pre‐ to posttension states. Mean decrease of 2D OSR at 1.5 kHz offset was 0.074–0.087 when comparing normal versus degenerated tendons (P < 0.01).ConclusionOSR as measured with 2D or 3D UTE‐MT sequences can detect the changes in hydration seen when tendons are placed under two different states of tensile load, but these changes are smaller than those encountered when comparing between normal versus pathologic tendons. Lower off‐resonance saturation frequencies (3 kHz or less) are more sensitive to these changes than higher off‐resonance saturation frequencies.J. Magn. Reson. Imaging 2015. J. Magn. Reson. Imaging 2015;42:1064–1071.
Self‐Compassion as a Prospective Predictor of PTSD Symptom Severity Among Trauma‐Exposed U.S. Iraq and Afghanistan War Veterans
Authors: Hiraoka Regina , Meyer Eric C. , Kimbrel Nathan A. , DeBeer Bryann B. , Gulliver Suzy Bird , Morissette Sandra B. 
Published: March 2015

AbstractU.S. combat veterans of the Iraq and Afghanistan wars have elevated rates of posttraumatic stress disorder (PTSD) compared to the general population. Self‐compassion, characterized by self‐kindness, a sense of common humanity when faced with suffering, and mindful awareness of suffering, is a potentially modifiable factor implicated in the development and maintenance of PTSD. We examined the concurrent and prospective relationship between self‐compassion and PTSD symptom severity after accounting for level of combat exposure and baseline PTSD severity in 115 Iraq and Afghanistan war veterans exposed to 1 or more traumatic events during deployment. PTSD symptoms were assessed using the Clinician Administered PTSD Scale for DSM‐IV (CAPS‐IV) at baseline and 12 months (n =101). Self‐compassion and combat exposure were assessed at baseline via self‐report. Self‐compassion was associated with baseline PTSD symptoms after accounting for combat exposure (β = −.59; p < .001; ΔR2 = .34; f2 = .67; large effect) and predicted 12‐month PTSD symptom severity after accounting for combat exposure and baseline PTSD severity (β = −.24; p = .008; ΔR2 = .03; f2 = .08; small effect). Findings suggest that interventions that increase self‐compassion may be beneficial for treating chronic PTSD symptoms among some Iraq and Afghanistan war veterans.
Critical Incident History Questionnaire Replication: Frequency and Severity of Trauma Exposure Among Officers From Small and Midsize Police Agencies
Authors: Chopko Brian A. , Palmieri Patrick A. , Adams Richard E. 
Published: March 2015

Frequency and severity of trauma exposure are thought to influence posttraumatic reactions. Weiss et al.’s Critical Incident History Questionnaire (CIHQ; 2010) measures these variables among law enforcement officers; they reported findings using a sample of officers from large urban departments. We noted the need for replication studies utilizing samples from smaller and rural police agencies. The purpose of this study was to replicate the CIHQ findings from Weiss et al. using a sample (N = 193) of officers from small and midsize police departments and officers whose duties include policing rural and isolated jurisdictions. Frequency and severity findings were similar to those reported by Weiss et al. (2010). Regarding frequency, the present study found the critical incident exposure mean score was 188.5, compared to 168.5 from Weiss et al. (2010). Making a mistake that kills or injures a colleague had the highest mean nomothetic severity rating in both studies. Among the various variables examined in this study, PTSD symptoms demonstrated the strongest association with the exposure indices, based on Spearman rank correlations (r = .26–.46).
Vascular considerations in foot and ankle free tissue transfer: Analysis of 231 free flaps
Authors: Cho Eugenia H. , Garcia Ryan M. , Pien Irene , Kuchibhatla Maragatha , Levinson Howard , Erdmann Detlev , Levin L. Scott , Hollenbeck Scott T. 
Published: March 2015

ObjectiveSuccessful foot and ankle soft tissue reconstruction is dependent on a clear understanding of the vascular supply to the foot. The aim of this study was to identify risk factors for reconstructive failure following foot and ankle free tissue transfer.MethodsThe authors retrospectively reviewed their 17‐year institutional experience with 231 foot and ankle free flaps performed in 225 patients to determine predictors of postoperative foot ischemia and flap failure. Postoperative foot ischemia was defined as ischemia resulting in tissue necrosis, separate from the reconstruction site.ResultsSix (3%) patients developed postoperative foot ischemia, and 28 (12%) patients experienced flap failure. Chronic ulceration (P = 0.02) and an elevated preoperative platelet count (P = 0.04) were independent predictors of foot ischemia. The presence of diabetes was predictive of flap failure (P = 0.05). Flap failure rates were higher in the setting of an abnormal preoperative angiogram (P = 0.04), although the type and number of occluded arteries did not influence outcome. Foot ischemia was more frequent following surgical revascularization in conjunction with free tissue transfer and the use of the distal arterial bypass graft for flap anastomosis (P < 0.01). Overall, no differences were observed in foot ischemia (P = 0.17) and flap failure (P = 0.75) rates when the flap anastomosis was performed to the diseased artery noted on angiography, compared with an unobstructed native tibial artery.ConclusionsFoot and ankle free tissue transfer may be performed with a low incidence of foot ischemia. Patients with diabetes, chronic ulceration, and an elevated preoperative platelet count are at higher risk for reconstructive failure. © 2015 Wiley Periodicals, Inc. Microsurgery 36:276–283, 2016.
Prevalence and triage of first‐contact complaints on pelvic floor dysfunctions in female patients at a Pelvic Care Centre
Authors: Berghmans Bary , Nieman Fred , Leue C. , Weemhoff M. , Breukink S. , van Koeveringe G. 
Published: March 2015

Aims(i) To describe and analyse pelvic floor dysfunction symptoms in women referred to a Pelvic Care Centre (PCC). (ii) To describe the triage process of the same patients based on response to a first‐contact interview.MethodsTriage started with a telephone interview using previously constructed questions, asking for seven types of PF complaints during the preceding 6 months. If present, complaint severity was registered on a 0–10 scale. Next, these first‐contact complaints were used to describe patient case mix profiles using cross‐tabular analysis. Later on, at first PCC visit, an intake questionnaire containing questions on specific PF health problem(s) was filled out. This procedure contributed to a firm baseline characterization of the individual patient profile and a clinically valid allocation to structured, predefined assessment, and treatment.ResultsFrom 2005 to 2013, 4473 first‐time patients (mean age 56.9 (SD 16.2) have been referred to the PCC. Most frequently mentioned complaints: voiding dysfunction (59.5%), urinary incontinence (46.6%), prolapse (41.1%), fecal incontinence (15.1%), constipation (12.6%), and sexual problems (4.6%). A first appointment to a single specialist was determined in 3.110 (69.5%) patients, in 1.192 (26.7%) consultation of >1 specialist. Data analysis revealed higher‐order interactions between PF complaints, suggesting patient profile complexity and patient population heterogeneity.ConclusionsMore than one out of four PCC patients showed multifactorial problems, needing >1 specialist. PF complaints either turned out to stand alone or cluster with others, or even to strengthen, weaken, nullify, or inverse relationships. Neurourol. Urodynam. 35:503–508, 2016. © 2015 Wiley Periodicals, Inc.