bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis of collagen fiber degradation by cathepsin K
Authors: Aguda Adeleke H. , Panwar Preety , Du Xin , Nguyen Nham T. , Brayer Gary D. , Brömme Dieter 
Published: November 2014

Significance
Fibrillar collagens constitute 90% of the organic bone matrix and are subjected either to physiological remodeling or excessive degradation during diseases such as osteoporosis. Cathepsin K is the critical collagenase in bone and represents a major antiresorptive drug target. Despite its critical role in bone remodeling, its mechanism of collagen degradation remained elusive. Here, we demonstrate that the degradation of fibrillar collagen requires the presence of a cathepsin K dimer bound at the surface of collagen fibers via glycosaminoglycans. Structural modifications of the protease dimerization site or the removal of collagen fiber-associated glycosaminoglycans specifically block fibrillar collagen degradation. The provided structure allows the development of a strategy to inhibit this highly relevant drug target in a substrate-specific manner.
Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors
Authors: Nayak Tapan K. , Bruhova Iva , Chakraborty Srirupa , Gupta Shaweta , Zheng Wenjun , Auerbach Anthony 
Published: November 2014

Significance
We present here energy measurements for agonist binding to adult and fetal neuromuscular junction acetylcholine receptors. We identify the chemical groups at the three functionally different types of transmitter binding site (αγ, αδ, and αε) that generate energy from the agonist for channel gating. We also predict the structural correlates of the energy differences from experiments and molecular dynamics simulations. This article is of general interest because it is the first time to our knowledge that single ligand-binding-site energies have been measured in any receptor. In addition, the results provide a rationale for understanding the required receptor subunit swap in synapse maturation (a long-standing and unsolved problem), as well as the structural basis for agonist efficacy.
Phylogenetic reconstruction of Bantu kinship challenges Main Sequence Theory of human social evolution
Authors: Opie Christopher , Shultz Susanne , Atkinson Quentin D. , Currie Thomas , Mace Ruth 
Published: November 2014

Significance
The agricultural revolution had a dramatic effect on all aspects of human society, but piecing together how humans lived as they spread farming practices worldwide remains difficult. In particular, the fundamental structures of human society, namely the way that property is inherited and the rules governing postmarriage residence, do not leave a clear trace in the archaeological record and, therefore, have been largely intractable. However, the recent availability of phylogenetic language trees coupled with new Bayesian statistical techniques makes it possible to reconstruct the ancestral state of Bantu kinship and reveals that inheritance and residence rules coevolved as farming spread throughout sub-Saharan Africa. Our results question current theory suggesting that residence rules are the primary driver of all other human social structures.
Timing the impact of literacy on visual processing
Authors: Pegado Felipe , Comerlato Enio , Ventura Fabricio , Jobert Antoinette , Nakamura Kimihiro , Buiatti Marco , Ventura Paulo , Dehaene-Lambertz Ghislaine , Kolinsky Régine , Morais José , Braga Lucia W. , Cohen Laurent , Dehaene Stanislas 
Published: November 2014

Significance
How does learning to read affect visual processing? We addressed this issue by scanning adults who could not attend school during childhood and either remained illiterate or acquired partial literacy during adulthood (ex-illiterates). By recording event-related brain responses, we obtained a high-temporal resolution description of how illiterate and literate adults differ in terms of early visual responses. The results show that learning to read dramatically enhances the magnitude, precision, and invariance of early visual coding, within 200 ms of stimulus onset, and also enhances later neural activity. Literacy effects were found not only for the expected category of expertise (letter strings), but also extended to other visual stimuli, confirming the benefits of literacy on early visual processing.
Global emissions of refrigerants HCFC-22 and HFC-134a: Unforeseen seasonal contributions
Authors: Xiang Bin , Patra Prabir K. , Montzka Stephen A. , Miller Scot M. , Elkins James W. , Moore Fred L. , Atlas Elliot L. , Miller Ben R. , Weiss Ray F. , Prinn Ronald G. , Wofsy Steven C. 
Published: November 2014

SignificanceHCFC-22 (CHClF2) and HFC-134a (CH2FCF3) are two major gases currently used worldwide in domestic and commercial refrigeration and air conditioning. HCFC-22 contributes to stratospheric ozone depletion, and both species are potent greenhouse gases. We find pronounced seasonal variations of global emissions for these two major refrigerants, with summer emissions two to three times higher than in winter. Thus results suggest that global emissions of these potent greenhouse gases might be mitigated by improved design and engineering of refrigeration systems and/or by reinforcing system service regulations.
Measuring missing heritability: Inferring the contribution of common variants
Authors: Golan David , Lander Eric S. , Rosset Saharon 
Published: November 2014

Significance
Studies have identified thousands of common genetic variants associated with hundreds of diseases. Yet, these common variants typically account for a minority of the heritability, a problem known as “missing heritability.” Geneticists recently proposed indirect methods for estimating the total heritability attributable to common variants, including those whose effects are too small to allow identification in current studies. Here, we show that these methods seriously underestimate the true heritability when applied to case–control studies of disease. We describe a method that provides unbiased estimates. Applying it to six diseases, we estimate that common variants explain an average of 60% of the heritability for these diseases. The framework also may be applied to case–control studies, extreme-phenotype studies, and other settings.
Trajectories of the ribosome as a Brownian nanomachine
Authors: Dashti Ali , Schwander Peter , Langlois Robert , Fung Russell , Li Wen , Hosseinizadeh Ahmad , Liao Hstau Y. , Pallesen Jesper , Sharma Gyanesh , Stupina Vera A. , Simon Anne E. , Dinman Jonathan D. , Frank Joachim , Ourmazd Abbas 
Published: November 2014

Significance
Many functions in the cell are performed by Brownian machines, macromolecular assemblies that use energy from the thermal environment for many of the conformational changes involved in their work cycles. Here we present a new approach capable of mapping the continuous motions of such nanomachines along their trajectories in the free-energy landscape and demonstrate this capability in the context of experimental cryogenic electron microscope snapshots of the ribosome, the nanomachine responsible for protein synthesis in all living organisms. We believe our approach constitutes a universal platform for the analysis of free-energy landscapes and conformational motions of molecular nanomachines and their dependencies on temperature, buffer conditions, and regulatory factors.
Elucidating severe urban haze formation in China
Authors: Guo Song , Hu Min , Zamora Misti L. , Peng Jianfei , Shang Dongjie , Zheng Jing , Du Zhuofei , Wu Zhijun , Shao Min , Zeng Limin , Molina Mario J. , Zhang Renyi 
Published: November 2014

Significance
We illustrate the similarity and difference in particulate matter (PM) formation between Beijing and other world regions. The periodic cycle of PM events in Beijing is regulated by meteorological conditions. While the particle chemical compositions in Beijing are similar to those commonly measured worldwide, efficient nucleation and growth over an extended period in Beijing are distinctive from the aerosol formation typically observed in other global areas. Gaseous emissions of volatile organic compounds and nitrogen oxides from urban transportation and sulfur dioxide from regional industry are responsible for large secondary PM formation, while primary emissions and regional transport of PM are insignificant. Reductions in emissions of the aerosol precursor gases from transportation and industry are essential to mediate severe haze pollution in China.
Brain–machine interface for eye movements
Authors: Graf Arnulf B. A. , Andersen Richard A. 
Published: November 2014

SignificanceWe developed a brain–machine interface (BMI) that records single cell activity from populations of neurons for decoding planned eye movements (i.e., saccades) without the animals executing them. The recordings were made from the lateral intraparietal area, an important cortical node in the primate saccade system. To our knowledge, this is the first BMI using neuronal populations to predict eye movements in a brain control task. Learning occurred during brain control trials, improving prediction performance by changing the response properties of single neurons. An eye movement BMI can assist patients locked-in from stroke or neurodegenerative disease who are unable to make any movements including eye movements.
Impact of ocean phytoplankton diversity on phosphate uptake
Authors: Lomas Michael W. , Bonachela Juan A. , Levin Simon A. , Martiny Adam C. 
Published: November 2014

Significance
Nutrient uptake is a central property of ocean biogeochemistry, but our understanding of this process is based on laboratory cultures or bulk environmental studies. Thus, mathematical descriptions of nutrient uptake, at the heart of most biogeochemical models, must rely on this limited information. Hence, we have little knowledge of how natural phytoplankton populations vary in their abilities to take up key nutrients. Using advanced analytical techniques, this study provides the first comprehensive in situ quantification of nutrient uptake capabilities among dominant phytoplankton groups. Supported by a model that considers plastic ecological responses in an evolutionary context, this work further provides a fundamentally new framework for the integration of microbial diversity to describe and understand the controls of ocean nutrient assimilation.
Evaluation of Precision and Sample Sizes Using Standardized Sampling in Kansas Reservoirs
Authors: Koch Jeff D. , Neely Ben C. , Colvin Michael E. 
Published: November 2014

Abstract
We evaluated the precision of samples and the number of stock-length fish collected by means of standard methods used for sampling North American freshwater fishes from 2010 to 2013 in Kansas. Additionally, we used resampling procedures to determine the number of gear deployments needed to achieve a relative standard error (RSE) of 25% for the CPUE and collect 100 stock-length individuals. Median RSE of electrofishing samples was generally less than 25% for Largemouth Bass Micropterus salmoides in all sizes of reservoirs and for Channel Catfish Ictalurus punctatus in medium (251–1,000 acres) and large reservoirs (greater than 1,000 acres). The RSE estimates were generally &gt;25% for Bluegill Lepomis macrochirus and crappies Pomoxis spp. collected in trap nets and palmetto bass (female Striped Bass Morone saxatilis × male White Bass M. chrysops) and Walleye Sander vitreus sampled in gill nets. With few exceptions, 100 stock-length individuals of all target species (e.g., Largemouth Bass, Bluegill, crappies, palmetto bass, Channel Catfish, Walleye) were not sampled at current levels of effort. Resampling procedures indicated that fewer than 20 deployments were usually needed to obtain an RSE ≤ 25% and 100 stock-length fish for Largemouth Bass in smaller impoundments (i.e., &lt;250 acres); however, more than 20 deployments were needed in larger impoundments. The median effort needed to achieve an RSE ≤ 25% for Bluegills and crappies in trap nets varied and may exceed what some biologists find practical. Fewer gill-net deployments were needed to reach an RSE ≤ 25% for palmetto bass and Walleyes than to collect 100 stock-length fish. Our results indicate that more samples than are currently prescribed are generally needed to precisely sample sport fishes by means of standardized protocols in Kansas reservoirs. In some instances, obtaining precise samples may not be logistically feasible. In these situations, biologists should be aware of the potential shortcomings of sampling protocols and set objectives accordingly.
Received May 12, 2014; accepted August 23, 2014
Abandoned Agave sisalana fiber crop plantation in the Negev Desert, Israel as source of firewood for local Bedouins
Authors: Lev-Yadun Simcha 
Published: November 2014

Firewood is a vital energy source for cooking and heating in traditional societies worldwide. During the past century, increasing human populations have depleted many previously available resources, resulting in severe shortages of firewood in many regions, especially in arid zones. Here, I describe the use as a source of firewood for a local semi-nomadic Bedouin village of several dozen families and the fate of a 0.3 km2abandoned fiber-crop plantation ofAgave sisalanaPerr. which is more than 50 years old in the Negev Desert, Israel. The amount of firewood extracted in the last decade equals several thousand local wild shrubs, which, in the current vegetation density, grow in a radius of several square kilometers. Harvesting the plantation for about 20 years almost fully exploited the plantation. Because the Bedouins do not replant plants used only for firewood, this source is not sustainable despite its biological potential to be so. However, becauseAgaveare CAM (Crassulacean acid metabolism) plants, they can grow under very arid conditions, and because they are well defended from grazing by thorns and poisons, they may be planted as a source of firewood in various arid regions where other plants will not sustain.
Functional characterization of a member of alanine or glycine: cation symporter family in halotolerant cyanobacterium Aphanothece halophytica
Authors: Bualuang Aporn , Kageyama Hakuto , Tanaka Yoshito , Incharoensakdi Aran , Takabe Teruhiro 
Published: November 2014

Abstract
Membrane proteins of amino acid–polyamine–organocation (APC) superfamily transport amino acids and amines across membranes and play important roles in the regulation of cellular processes. The alanine or glycine: cation symporter (AGCS) family belongs to APC superfamily and is found in prokaryotes, but its substrate specificity remains to be clarified. In this study, we found that a halotolerant cyanobacterium, Aphanothece halophytica has two putative ApagcS genes. The deduced amino acid sequence of one of genes, ApagcS1, exhibited high homology to Pseudomonas AgcS. The ApagcS1 gene was expressed in Escherichia coli JW4166 which is deficient in glycine uptake. Kinetics studies in JW4166 revealed that ApAgcS1 is a sodium-dependent glycine transporter. Competition experiments showed the significant inhibition by glutamine, asparagine, and glycine. The level of mRNA for ApagcS1 was induced by NaCl and nitrogen-deficient stresses. Uptake of glutamine by ApAgcS1 was also observed. Based on these data, the physiological role of ApAgcS1 was discussed.
Hypertension Control and Antihypertensive Therapy in Patients With Chronic Kidney Disease
Authors: Unni Sudhir , White Kellee , Goodman Michael , Ye Xiangyang , Mavros Panagiotis , Bash Lori D. , Brixner Diana 
Published: November 2014

BACKGROUND
Hypertension is a major risk factor in the progression of chronic kidney disease (CKD). Although hypertension is more prevalent and treated more often among CKD patients, it is less likely to be controlled. Current guidelines recommend the use of multiple antihypertensive agents to achieve optimal blood pressure (BP) control. However, BP control attained by number and type of antihypertensive therapy according to CKD stage has not been examined thoroughly.

STUDY DESIGN
Cross-sectional analysis of an electronic medical record (EMR) database.

SETTING AND PARTICIPANTS
A total of 115,608 patients with CKD (Stages 1–4) and diagnosed or treated hypertension in General Electric Centricity EMR from 1996 to 2012.

OUTCOME
BP control, based on JNC 7 guidelines, was defined as less than 130/80mm Hg.

MEASUREMENTS
BP and antihypertensive therapy use was obtained from the EMR. The Cockcroft–Gault equation was used to calculate estimated glomerular filtration rate and classify CKD stage.

RESULTS
Overall prevalence of BP control was 24.3%. BP control varied by CKD stage and number of antihypertensive therapy. In multivariable analysis, younger age was less likely to be associated with BP control, regardless of CKD stage. Multiple antihypertensive therapy use and BP control was strongest among CKD Stage 2 (odds ratio (OR): 1.41; 95% confidence interval (CI): 1.05, 1.90). Diuretic use was less likely to be associated with BP control among CKD Stage 1 (OR: 0.71; 95% CI: 0.59, 0.87) and 2 (OR: 0.78; 95% CI: 0.72, 0.85).

LIMITATIONS
Information on antihypertensive prescription fill data and adherence to medication regimens was unavailable.

CONCLUSIONS
This study highlighted the need to pay closer attention to achieving BP treatment goals for younger individuals with CKD. More research is needed to assess the extent to which specific combinations of antihypertensive drugs leads to adequate BP control.
DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
Authors: Jones Graham , Aydin Zeynep , Oxelman Bengt 
Published: November 2014

Abstract
Motivation: The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the sp tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space by requiring a guide tree and/or prior assignment of individuals to clusters or species.
Results: We present DISSECT, which explores the full space of possible clusterings of individuals and species tree topologies in a Bayesian framework. It uses an approximation to avoid the need for reversible-jump Markov Chain Monte Carlo, in the form of a prior that is a modification of the birth–death prior for the species tree. It incorporates a spike near zero in the density for node heights. The model has two extra parameters: one controls the degree of approximation and the second controls the prior distribution on the numbers of species. It is implemented as part of BEAST and requires only a few changes from a standard *BEAST analysis. The method is evaluated on simulated data and demonstrated on an empirical dataset. The method is shown to be insensitive to the degree of approximation, but quite sensitive to the second parameter, suggesting that large numbers of sequences are needed to draw firm conclusions.
Availability and implementation: http://tree.bio.ed.ac.uk/software/beast/, http://www.indriid.com/dissectinbeast.html.
Contact: bengt.oxelman@gu.se, www.indriid.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Bcl11b prevents the intrathymic development of innate CD8 T cells in a cell intrinsic manner
Authors: Hirose Satoshi , Touma Maki , Go Rieka , Katsuragi Yoshinori , Sakuraba Yoshiyuki , Gondo Yoichi , Abe Manabu , Sakimura Kenji , Mishima Yukio , Kominami Ryo 
Published: November 2014

Abstract
If Bcl11b activity is compromised, CD4+CD8+ double-positive (DP) thymocytes produce a greatly increased fraction of innate CD8+ single-positive (SP) cells highly producing IFN-γ, which are also increased in mice deficient of genes such as Itk, Id3 and NF-κB1 that affect TCR signaling. Of interest, the increase in the former two is due to the bystander effect of IL-4 that is secreted by promyelocytic leukemia zinc finger-expressing NKT and γδT cells whereas the increase in the latter is cell intrinsic. Bcl11b zinc-finger proteins play key roles in T cell development and T cell-mediated immune response likely through TCR signaling. We examined thymocytes at and after the DP stage in Bcl11bF/S826GCD4cre, Bcl11bF/+CD4cre and Bcl11b+/S826G mice, carrying the allele that substituted serine for glycine at the position of 826. Here we show that Bcl11b impairment leads to an increase in the population of TCRαβhighCD44highCD122high innate CD8SP thymocytes, together with two different developmental abnormalities: impaired positive and negative selection accompanying a reduction in the number of CD8SP cells, and developmental arrest of NKT cells at multiple steps. The innate CD8SP thymocytes express Eomes and secrete IFN-γ after stimulation with PMA and ionomycin, and in this case their increase is not due to a bystander effect of IL-4 but cell intrinsic. Those results indicate that Bcl11b regulates development of different thymocyte subsets at multiple stages and prevents an excess of innate CD8SP thymocytes.
First Report of Phakopsora pachyrhizi on Soybean in Costa Rica
Authors: Murillo-Williams A. , Esker P. , Allen T. , Stone C. , Frederick R. 
Published: November 2014

Phakopsora meibomiae (Arthur) Arthur has been reported to occur in several legume species in the tropical regions of Central and South America. In Costa Rica, this pathogen was initially reported as P. pachyrhizi Sydow (1); however, to our knowledge, P. pachyrhizi has not been detected in Costa Rica. In routine evaluations of a 0.2-ha field planted with soybean (Glycine max (L.) Merr var. CIGRAS 06) in La Garita, Alajuela, Costa Rica, symptoms similar to Asian soybean rust were observed in December 2012 and January 2013. Soybean plants were at growth stages R4 to R5 when these symptoms were observed, which included yellow spots on leaves with brown spots on the abaxial surface. Further evaluations at growth stage R5 to R6 indicated that the spots had coalesced, turned grayish-brown, and caused substantial defoliation. Microscopic examination of symptomatic leaves showed the presence of uredinia and urediniospores on the lower surface of the leaf. While initial symptoms were on the southern side of the field, a substantial area of the field was infected at the second evaluation. Infected leaves were submitted to the USDA-ARS Foreign Disease-Weed Science Research Unit under the appropriate USDA-Animal Plant Health Inspection Service permit for molecular characterization and identification. Urediniospores were collected by washing infected leaves with sterile water and then pelleted by centrifugation. DNA was extracted from urediniospore pellets and excised leaf pieces using a DNeasy Plant Mini Kit (Qiagen, Germantown, MD), and eight samples were amplified in real-time polymerase chain reaction (PCR) with P. pachyrhizi-specific primers Ppm1 and Ppa2 but not with the P. meibomiae-specific primers Ppm1 and Pme2 (2). Nucleotide sequence alignment of the internal transcribed spacer (ITS) regions 1 and 2 that were amplified by PCR using the primers Ppa1 and Ppa2 further confirmed the identification as P. pachyrhizi. To the best of our knowledge, this is the first known confirmation of soybean rust, caused by P. pachyrhizi in Costa Rica. CIGRAS-06 is the only soybean variety bred in the country as well as one of the very few varieties available for growers. Given that breeding for disease resistance is not a short-term option for P. pachyrhizi, alternative disease management strategies will have to be developed. References: (1) K. R. Bromfield. Soybean Rust, Monograph No. 11. APS Press, St. Paul, MN, 1984. (2) R. D. Frederick et al. Phytopathology 92:217, 2002.