bluuebunny/crossref_metadata_2025_split huggingface dataset:
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data
Authors: Moreno-Mayar J Víctor , Korneliussen Thorfinn Sand , Dalal Jyoti , Renaud Gabriel , Albrechtsen Anders , Nielsen Rasmus , Malaspinas Anna-Sapfo 
Published: August 2019

AbstractMotivationThe presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.ResultsWe develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5 min, our method is applicable to large scale aDNA genomic studies.Availability and implementationThe method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.
Three-dimensional testicular organoids as novel in vitro models of testicular biology and toxicology
Authors: Sakib Sadman , Voigt Anna , Goldsmith Taylor , Dobrinski Ina 
Published: August 2019

AbstractOrganoids are three dimensional structures consisting of multiple cell types that recapitulate the cellular architecture and functionality of native organs. Over the last decade, the advent of organoid research has opened up many avenues for basic and translational studies. Following suit of other disciplines, research groups working in the field of male reproductive biology have started establishing and characterizing testicular organoids. The three-dimensional architectural and functional similarities of organoids to their tissue of origin facilitate study of complex cell interactions, tissue development and establishment of representative, scalable models for drug and toxicity screening. In this review, we discuss the current state of testicular organoid research, their advantages over conventional monolayer culture and their potential applications in the field of reproductive biology and toxicology.
Subsurface wavefields based on the generalized internal multiple imaging
Authors: Alkhalifah Tariq , Guo Qiang 
Published: August 2019

SUMMARY
Full Green’s functions between image points and the recording surface are crucial to constructing accurate subsurface wavefields and images beyond the single-scattering assumption. A direct approach to do so is offered by utilizing the recorded data combined with a background imaging velocity. The process includes extrapolating the recorded data back in time followed by a simple interferometric cross-correlation of the back-propagated wavefield with the recorded data. This interferometric step offers the opportunity to extract subsurface Green’s functions with first-order scattering forming the transmission component, and the second-order scattering becoming the leading scattering term. A cross-correlation of the resulting, assumed upgoing, wavefield with a forward modelled down going wavefield highlights the double-scattered reflectivity in a process referred to as the generalized internal multiple imaging (GIMI). The resulting image is vulnerable to cross-talk between different order multiples interacting with each other. Thus, we develop the adjoint GIMI operation that takes us from the image to the data, and use it to formulate a least-squares optimization problem to fit the image to the data. The result is reduced cross-talk and cleaner higher resolution multiscattered images. We also extract space extensions of the image, which offers the opportunity to evaluate the focusing capability of the velocity model, and formulate updates for that model based on double scattering. We show the features of this approach on the modified Marmousi model.
3-D fluid channel location from noise tremors using matched field processing
Authors: Umlauft J , Korn M 
Published: August 2019

SUMMARY
Presently ongoing geodynamic processes within the intracontinental lithospheric mantle give rise to different natural phenomena in the NW Bohemia/Vogtland region (Czech Republic, Germany), amongst others: earthquake swarms, mineral springs and degassing zones of mantle-derived fluids as well as highly concentrated CO2 (mofettes). Their interaction mechanisms and relations are not yet fully understood, but fluid pathways within the crust are assumed, that allow efficient fluid transport between the main hypocentral swarm quake region and the degassing areas at the surface. Here, we focus on the location of the presumed fluid channels as well as on the investigation of their near-surface spatio-temporal variability, targeting a depth of a few hundreds of metmetres. We applied a 3-D matched field processing (MFP) approach in the frequency band of 10–20 Hz considering the fluid flow as seismic noise source. Within three campaigns in 2015/2016, we recorded continuous seismic noise data on the Hartoušov Mofette Field within the Cheb Basin (NW Bohemia, CZ), which is a key site to study fluid flow as it is characterized by strong and continuous surface degassing of CO2. We used temporary arrays varying in extent (70-600 m aperture) and in the amount of stations (25–95 units). Assuming a homogeneous velocity model and applying conventional MFP phase-matching over a 3-D grid search, we located two channel-like structures beneath the test site, which could be traced down to a common source area down to 2000 m depth. We thereby evaluated the influence of amplitude normalization of the measured noise signal on the MFP location considering water-filled or dry mofette channels. Additionally, a spatio-temporal analysis using time windows with a length of 10 min during 5 hr of noise record shows variability of fluid flow activity in space and time and hence, its migration beneath the test site on a short timescale.
Density and Decline in the Founding of International NGOs in the United States
Authors: Bush Sarah Sunn , Hadden Jennifer 
Published: August 2019

AbstractIt is now commonplace for scholars to note that the number of international nongovernmental organizations (INGOs) has exploded. But, in recent years, the growth rate of INGOs globally and in the United States has stagnated. We argue this stagnation can best be explained by changes in the environment in which INGOs work. Specifically, the now dense population environment discourages new INGOs from being founded, while also encouraging competition. Analysis of a new, comprehensive dataset on American INGOs between 1992 and 2012 supports the argument, as do case studies of trends within the environmental conservation and democracy assistance sectors. The analysis suggests that debates about INGO cooperation and competition overlook a key environmental factor that varies across and within populations of organizations: density. We draw out the implications of this approach for contemporary global governance.
Genetic parameters and genome-wide association study regarding feed efficiency and slaughter traits in Charolais cows
Authors: Martin Pauline , Taussat Sébastien , Vinet Aurélie , Krauss Daniel , Maupetit David , Renand Gilles 
Published: August 2019

Abstract
Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h2 = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.
miR-324-5p upregulation potentiates resistance to cisplatin by targeting FBXO11 signalling in non-small cell lung cancer cells
Authors: Ba Zhichang , Zhou Yufei , Yang Zhaoyang , Xu Jianyu , Zhang Xiushi 
Published: August 2019

Abstract
Dysregulation of microRNAs (miRNAs) plays a key role during the pathogenesis of chemoresistance in lung cancer (LCa). Previous study suggests that miR-324-5p may serve as a unique miRNA signature for LCa, but its role and the corresponding molecular basis remain largely explored. Herein, we report that miR-324-5p expression was significantly increased in cisplatin (CDDP)-resistant LCa tissues and cells, and this upregulation predicted a poor post-chemotherapy prognosis in LCa patients. miR-324-5p was further shown to impact CDDP response: Ectopic miR-324-5p expression in drug-naïve LCa cells was sufficient to attenuate sensitivity to CDDP and to confer more robust tumour growth in CDDP-challenged nude mice. Conversely, ablation of miR-324-5p expression in resistant cells effectively potentiated CDDP-suppressed cell growth in vitro and in vivo. Using multiple approaches, we further identified the tumour suppressor FBXO11 as the direct down-stream target of miR-324-5p. Stable expression of FBXO11 could abrogate the pro-survival effects of miR-324-5p in CDDP-challenged LCa cells. Together, these findings suggest that miR-324-5p upregulation mediates, at least partially, the CDDP resistance by directly targeting FBXO11 signalling in LCa cells. In-depth elucidation of the molecular basis underpinning miR-324-5p action bears potential implications for mechanism-based strategies to improve CDDP responses in LCa.
The intrinsic reddening of the Magellanic Clouds as traced by background galaxies – I. The bar and outskirts of the Small Magellanic Cloud
Authors: Bell Cameron P M , Cioni Maria-Rosa L , Wright A H , Rubele Stefano , Nidever David L , Tatton Ben L , van Loon Jacco Th , Ivanov Valentin D , Subramanian Smitha , Oliveira Joana M , de Grijs Richard , Pennock Clara M , Choi Yumi , Zaritsky Dennis , Olsen Knut , Niederhofer Florian , Choudhury Samyaday , Martínez-Delgado David , Muñoz Ricardo R 
Published: August 2019

ABSTRACT
We present a method to map the total intrinsic reddening of a foreground extinguishing medium via the analysis of spectral energy distributions (SEDs) of background galaxies. In this pilot study, we implement this technique in two distinct regions of the Small Magellanic Cloud (SMC) – the bar and the southern outskirts – using a combination of optical and near-infrared ugrizYJKs broad-band imaging. We adopt the lephare χ2-minimization SED-fitting routine and various samples of galaxies and/or quasi-stellar objects to investigate the intrinsic reddening. We find that only when we construct reddening maps using objects classified as galaxies with low levels of intrinsic reddening (i.e. ellipticals/lenticulars and early-type spirals), the resultant maps are consistent with previous literature determinations, i.e. the intrinsic reddening of the SMC bar is higher than that in the outer environs. We employ two sets of galaxy templates – one theoretical and one empirical – to test for template dependences in the resulting reddening maps and find that the theoretical templates imply systematically higher reddening values by up to 0.20 mag in E(B − V). A comparison with previous reddening maps, based on the stellar components of the SMC, typically shows reasonable agreement. There is, however, significant variation amongst the literature reddening maps as to the level of intrinsic reddening associated with the bar. Thus, it is difficult to unambiguously state that instances of significant discrepancies are the result of appreciable levels of dust not accounted for in some literature reddening maps or whether they reflect issues with our adopted methodology.
Tidal circularization of gaseous planets orbiting white dwarfs
Authors: Veras Dimitri , Fuller Jim 
Published: August 2019

ABSTRACT
A gas giant planet which survives the giant branch stages of evolution at a distance of many au and then is subsequently perturbed sufficiently close to a white dwarf will experience orbital shrinkage and circularization due to star–planet tides. The circularization time-scale, when combined with a known white dwarf cooling age, can place coupled constraints on the scattering epoch as well as the active tidal mechanisms. Here, we explore this coupling across the entire plausible parameter phase space by computing orbit shrinkage and potential self-disruption due to chaotic f-mode excitation and heating in planets on orbits with eccentricities near unity, followed by weakly dissipative equilibrium tides. We find that chaotic f-mode evolution activates only for orbital pericentres which are within twice the white dwarf Roche radius, and easily restructures or destroys ice giants but not gas giants. This type of internal thermal destruction provides an additional potential source of white dwarf metal pollution. Subsequent tidal evolution for the surviving planets is dominated by non-chaotic equilibrium and dynamical tides which may be well-constrained by observations of giant planets around white dwarfs at early cooling ages.
Obstetric Management and Maternal Outcomes of Childbirth Among Patients With Chiari Malformation Type I
Authors: Wilkinson D Andrew , Johnson Kyle , Castaneda Peris R , Nadel Jeffrey L , Garton Hugh J L , Muraszko Karin M , Maher Cormac O 
Published: August 2019

Abstract

BACKGROUND
A range of opinions exist in the literature regarding obstetric management of pregnant women with Chiari malformation type I (CM-I).

OBJECTIVE
To examine obstetrical practices and outcomes with childbirth of women with CM-I.

METHODS
We examined insurance claims data from a large, privately insured health care network and identified admissions for childbirth from 2004 to 2014. Women with a diagnosis of CM-I as well as normal controls were analyzed for demographic characteristics, type of obstetric management, and complications of childbirth.

RESULTS
We identified 866 patients with CM-I diagnosis who had 1048 hospitalizations for delivery, including 103 deliveries to 83 patients who underwent performance of CM-I decompression (CMD) either before or after childbirth. Among 400 births that occurred after CM-I diagnosis, rates of caesarean section (C-section) were higher (42.3% vs 36.2%, OR 1.29, 95% CI 1.00-1.66, P = .05) and rates of epidural analgesia were lower (45.3% vs 55.4%, OR 0.67, 95% CI 0.52-0.85, P = .001) compared to 648 births before CM-I diagnosis. The rate of serious maternal morbidity was similar among deliveries to women with CM-I diagnosis (both before and after delivery) compared to 11 000 normal controls.

CONCLUSION
A diagnosis of CM-I prior to delivery is associated with a higher rate of C-section and a lower rate of epidural analgesia. Rates of serious maternal morbidity among women with CM-I were similar to those for normal controls. The data suggest a predelivery diagnosis of CM-I may influence obstetric decisions despite no evidence of substantially increased delivery risk in this group.
Logging Season Affects Hardwood Reproduction
Authors: Tubbs Carl H. , Reid Bruce D. 
Published: August 2019

Abstract
The Rochester District of the Green Mountain National Forest has kept records of regeneration following clearcut and shelterwood harvesting since 1969. These records offered the opportunity to evaluate the effects of summer and winter harvesting on regeneration. Season of logging did not affect the number of stands with adequate stocking but winter logging resulted in somewhat better stocking of sugar maple and yellow and paper birch than summer logging. Shelterwoods were better stocked with sugar maple than clearcuts, which on average were better stocked with the birches. The year of cut seemed to have the greatest influence on the relative proportion of birches and sugar maple after clearcutting. Citation: Northern Journal of Applied Forestry, April 1984 NJ 1:5-7.
Reforestation of Mined Land in the Northeastern and North-Central U.S
Authors: Davidson Walter H. , Hutnik Russell J. , Parr Delbert E. 
Published: August 2019

Abstract
This paper reviews the state of the art of surface mine reclamation for forestry in Pennsylvania, Maryland, West Virginia, Ohio, Indiana, and Illinois. Legislative constraints, socioeconomic issues, factors limiting the success of reforestation efforts, post-mining land-use trends, species options, and establishment techniques are discussed. Sources of assistance to landowners or managers are given and major publications on reclamation methods are cited. Information provided in the paper also applies to coal mining states adjacent to those listed above. Citation: Northern Journal of Applied Forestry, April 1984 NJ 1:7-12.
Guides for Estimating Forest Stand Losses to Gypsy Moth
Authors: Gansner David A. , Herrick Owen W. 
Published: August 2019

Abstract
People who have to make decisions about cost-effective management for gypsy moth need help in predicting and evaluating its effects. Field plot data collected during recent outbreaks in Pennsylvania are being used to develop guides for predicting forest stand losses to the pest Presented here are some of the more useful products of that effort to date. Easy-to-measure data for forest characteristics such as species composition and crown condition can be collected and applied in models that estimate potential stand and tree mortality and changes in timber value. North. J. Appl. For. 2:21-23, June 1984.
Survey of Black Walnut Canker in Plantations in Five Central States
Authors: Carlson Jane Cummings , Mielke Manfred E. , Appleby James E. , Hatcher Roy , Hayes Edward M. , Luley Christopher J. , O'Brien Joseph G. , Rugg David J. 
Published: August 2019

Abstract
A survey was conducted to determine the incidence of an annual stem canker of plantation-grown black walnut in Illinois, Iowa, Minnesota, Missouri, and Wisconsin. Regionwide, walnut canker was observed in 84% of the 183 plantations surveyed, and 9.7% of the 19,340 trees examined were cankered. Canker incidence was significantly higher on bottomland sites (12.2%) than on upland sites (7.2%). Fusarium solani was the Fusarium sp. most frequently isolated from cankers. Regionwide, 30% of the cankers were associated with wounds; pruning wounds were the most frequently observed wounds associated with cankers. Only 1.6% of the cankers were associated with signs of attack by ambrosia beetles. Minimizing wounding may reduce the chances of canker formation. North. J. Appl. For. 10(1):10-13.
Establishing Equitable Contract Rates for Timber Harvesting Using Deterministic Simulation
Authors: Howard Andrew F. , Tanz Jordan S. 
Published: August 2019

Abstract
Deterministic simulation was used in a case study of a logging contractor working in south central British Columbia. A comparison of simulated and actual contract rates for five tracts showed substantial differences. Cashflow shortfalls and surpluses arising from the disparity betweensimulated costs and revenue generated from logging were appreciable. The findings suggest that deterministic simulation may provide a means for establishing equitable contract rates for harvesting individual tracts of timber. North. J. Appl. For. 10(1): 5-7.
Performance of Northern Red Oak Planting Stock
Authors: Zaczek James J. , Steiner Kim C. , Bowersox Todd W. 
Published: August 2019

Abstract
Northern red oak planting trials were established in three clearcuts in Pennsylvania to evaluate field performance in relation to type of planting stock (1-0, 2-0, 1-1, 2-1, containerized direct-seeded) and other treatments (undercutting in the nursery, top-clipping at planting time, hormone treatment of roots). All treatments were planted simultaneously, and most employed the same genetic material. After 3 yr in the field, seedlings that had been grown for 2 yr in 7.9-1 pots were tallest and had the best survival, but this stock was expensive to produce and difficult to plant. The 2-0 bareroot stock performed best among remaining treatments, especially if the seedlings had been undercut in the nursery. Undercutting was not beneficial to the performance of 1-0 seedlings. Top-clipping and a hormone treatment had little effect on performance. Seedlings from direct-seeding were as tall as those from 1-0 stock. The advantage of 2-0 stock over 1-0 stock was partly, but not entirely, attributable to its larger size. North. J. Appl. For. 10(3):105-111.
Testing the Accuracy of White Spruce Total-Tree Volume Equations
Authors: Rauscher H. Michael , Harding R. Bruce 
Published: August 2019

Abstract
Sixteen equations developed for predicting the volume of white spruce were tested for accuracy on plantation-grown trees in the upper Great Lakes region. Ten equations were found biased and six unbiased; of the six unbiased equations, only three were also precise. Precise tree volume equations can predict to within 13% to 15% of the actual volumes as estimated by stem analyses. North. J. Appl. For. 10(3): 112-116.