bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria
Authors: Bombar Deniz , Heller Philip , Sanchez-Baracaldo Patricia , Carter Brandon J , Zehr Jonathan P 
Published: September 2014

Abstract
Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed ‘diazotrophs’) are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.
Unexpected structure for the N-terminal domain of hepatitis C virus envelope glycoprotein E1
Authors: El Omari Kamel , Iourin Oleg , Kadlec Jan , Sutton Geoff , Harlos Karl , Grimes Jonathan M. , Stuart David I. 
Published: September 2014

AbstractHepatitis C virus (HCV) infection remains a major health problem worldwide. HCV entry into host cells and membrane fusion are achieved by two envelope glycoproteins, E1 and E2. We report here the 3.5-Å resolution crystal structure of the N-terminal domain of the HCV E1 ectodomain, which reveals a complex network of covalently linked intertwined homodimers that do not harbour the expected truncated class II fusion protein fold.
Cyclic precipitation variation on the western Loess Plateau of China during the past four centuries
Authors: Tan Liangcheng , An Zhisheng , Huh Chih-An , Cai Yanjun , Shen Chuan-Chou , Shiau Liang-Jian , Yan Libin , Cheng Hai , Edwards R. Lawrence 
Published: September 2014

AbstractPrecipitation variation on the Loess Plateau (LP) of China is not only important for rain-fed agriculture in this environmentally sensitive region, but also critical for the water and life securities over the whole Yellow River basin. Here we reconstruct high resolution precipitation variation on the western LP during the past 370 years by using two replicated, annually-laminated stalagmites. Spatial analysis suggests that the reconstruction can be also representative for the whole LP region. The precipitation variations show a significant quasi-50 year periodicity during the last 370 years and have an important role in determining the runoff of the middle Yellow River. The main factor controlling the decadal scale variations and long-term trend in precipitation over this region is southerly water vapour transport associated with the Asian summer monsoon. The Pacific Decadal Oscillation is also an important influence on precipitation variation in this region, as it can affect the East Asian summer monsoon and the West Pacific Subtropical High.
Real Time Ligand-Induced Motion Mappings of AChBP and nAChR Using X-ray Single Molecule Tracking
Authors: Sekiguchi Hiroshi , Suzuki Yasuhito , Nishino Yuri , Kobayashi Suzuko , Shimoyama Yoshiko , Cai Weiyan , Nagata Kenji , Okada Masato , Ichiyanagi Kouhei , Ohta Noboru , Yagi Naoto , Miyazawa Atsuo , Kubo Tai , Sasaki Yuji C. 
Published: September 2014

AbstractWe observed the dynamic three-dimensional (3D) single molecule behaviour of acetylcholine-binding protein (AChBP) and nicotinic acetylcholine receptor (nAChR) using a single molecule tracking technique, diffracted X-ray tracking (DXT) with atomic scale and 100 μs time resolution. We found that the combined tilting and twisting motions of the proteins were enhanced upon acetylcholine (ACh) binding. We present the internal motion maps of AChBP and nAChR in the presence of either ACh or α-bungarotoxin (αBtx), with views from two rotational axes. Our findings indicate that specific motion patterns represented as biaxial angular motion maps are associated with channel function in real time and on an atomic scale.
Biogeographic variation in evergreen conifer needle longevity and impacts on boreal forest carbon cycle projections
Authors: Reich Peter B. , Rich Roy L. , Lu Xingjie , Wang Ying-Ping , Oleksyn Jacek 
Published: September 2014

SignificanceHow evergreen tree needle longevity varies from south to north in the boreal biome is poorly quantified and therefore ignored in vegetation and earth system models. This is problematic, because needle longevity translates directly into needle turnover rate and profoundly affects carbon cycling in both nature and computer models. Herein we present data for five widespread boreal conifers, including pines and spruces, from >125 sites along a 2,000-km gradient. For each species, individuals in colder, more northern environments had longer needle life span, highlighting its importance to evergreen ecological success. Incorporating biogeography of needle longevity into a global model improved predictions of forest productivity and carbon cycling and identified specific problems for models that ignore such variability.
Tectonic-driven climate change and the diversification of angiosperms
Authors: Chaboureau Anne-Claire , Sepulchre Pierre , Donnadieu Yannick , Franc Alain 
Published: September 2014

Significance
Angiosperm range expansion and diversification have been major biotic upheavals in the Earth history. Mechanisms involved in their successful diversification have mainly called upon intrinsic processes at the plant level, leaving the influence of the global tectonics poorly explored. We investigate evolution of paleogeography and climate and correlate it with the diversification of angiosperms by using a general circulation model. We show that Pangea breakup induced an important expansion of temperate zones during the late Cretaceous which was concomitant to the rise of angiosperms. We suggest that the breakup of Pangea led to the onset of new humid bioclimatic continents, which in turn may have provided new external conditions for ecological expansion of the angiosperms and their diversification.
Natural selection on thermal performance in a novel thermal environment
Authors: Logan Michael L. , Cox Robert M. , Calsbeek Ryan 
Published: September 2014

Significance
Tropical ectotherms are considered especially vulnerable to climate change because they have narrow thermal tolerance ranges, such that even small increases in environmental temperature are likely to be detrimental. Although evolutionary adaptation may prevent extinction, it is unclear whether climate change generates selection on thermal physiology in nature or whether the strength of this selection is sufficient for rapid evolution to occur. When we transplanted lizards from their preferred habitat to a warmer and more thermally variable site, strong natural selection favored individuals that ran faster at warmer temperatures and across a broader range of temperatures. If thermal performance traits are heritable, some tropical species may be capable of rapid evolutionary adaptation to changing climates.
Neural and cognitive characteristics of extraordinary altruists
Authors: Marsh Abigail A. , Stoycos Sarah A. , Brethel-Haurwitz Kristin M. , Robinson Paul , VanMeter John W. , Cardinale Elise M. 
Published: September 2014

Significance
Altruism, and particularly costly altruism toward strangers, such as altruistic kidney donation, represents a puzzling phenomenon for many fields of science, including evolutionary biology, psychology, and economics. How can such behavior be explained? The propensity to engage in costly altruism varies widely and may be genetically mediated, but little is known about the neural mechanisms that support it. We used structural and functional brain imaging to compare extraordinary altruists, specifically altruistic kidney donors, and controls. Altruists exhibited variations in neural anatomy and functioning that represent the inverse of patterns previously observed in psychopaths, who are unusually callous and antisocial. These findings suggest extraordinary altruism represents one end of a caring continuum and is supported by neural mechanisms that underlie social and emotional responsiveness.
Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity
Authors: An Na , Fleming Aaron M. , Middleton Eric G. , Burrows Cynthia J. 
Published: September 2014

Significance
The bacterial protein α-hemolysin (α-HL) can form a mushroom-shaped ion channel by self-assembling across a lipid bilayer, allowing capture of a single DNA molecule inside its nanometer-scale vestibule in an electric field. Interactions between the protein nanocavity and DNA molecules generate characteristic current signals that reveal structural information. We harnessed such analytical power to investigate various G-quadruplex conformations adopted by the human telomeric sequence, namely hybrid, basket, and propeller folds that are formed under different physical conditions. Results presented here demonstrate the ability of α-HL to distinguish these G-quadruplexes based on their overall shapes and sizes and also to monitor their unraveling kinetics at different locations in the protein channel, expanding the applicability of the nanopore technology.
Effects of relaxation of gluten network on rehydration kinetics of pasta
Authors: Ogawa Takenobu , Hasegawa Ayako , Adachi Shuji 
Published: September 2014

Abstract
The aim of this study was to investigate the effects of the relaxation of the gluten network on pasta rehydration kinetics. The moisture content of pasta, under conditions where the effects of the diffusion of water on the moisture content were negligible, was estimated by extrapolating the average moisture content of pasta of various diameters to 0 mm. The moisture content of imaginary, infinitely thin pasta did not reach equilibrium even after 1 h of rehydration. The rehydration of pasta made of only gluten was also measured. The rate constants estimated by the Long and Richman equation for both the pasta indicated that the rehydration kinetics of infinitely thin pasta were similar to those of gluten pasta. These results suggest that the swelling of starch by fast gelatinization was restricted by the honeycomb structural network of gluten and the relaxation of the gluten network controlled pasta rehydration kinetics.
Anti-obese and anti-diabetic effects of a mixture of daidzin and glycitin on C57BL/6J mice fed with a high-fat diet
Authors: Zang Yanqing , Igarashi Kiharu , Yu Changqing 
Published: September 2014

Abstract
We investigated the effects of a mixture of daidzin and glycitin, which are the glycoside-form isoflavones of daidzein and glycitein, respectively, on body weight, lipid levels, diabetic markers, and metabolism in a high-fat diet (HF) fed C57BL/6J mice for 92 days. The mice were divided into basic diet group (CON), HF group, and HF companied with the isoflavone mixture group (HFISO). Results showed that mice in HFISO had a significantly lower body weight and adipose tissue compared to HF group. Blood glucose, serum HbA1c, and serum insulin also showed lower levels in HFISO group. In addition, higher hepatic GSH level and lower serum 8-hydroxy-2′-deoxyguanosine (8-OHdG) level were found in HFISO group mice. This suggests that the regulation of oxidative stress by daidzin and glycitin was closely related to the suppression of adipose tissue and the progression of diabetes.
JAMM: a peak finder for joint analysis of NGS replicates
Authors: Ibrahim Mahmoud M. , Lacadie Scott A. , Ohler Uwe 
Published: September 2014

AbstractMotivation: Although peak finding in next-generation sequencing (NGS) datasets has been addressed extensively, there is no consensus on how to analyze and process biological replicates. Furthermore, most peak finders do not focus on accurate determination of enrichment site widths and are not widely applicable to different types of datasets.Results: We developed JAMM ( J oint A nalysis of NGS replicates via M ixture M odel clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM’s replicate integration improves peak spatial resolution, sorting and peak finding accuracy.Availability and implementation: JAMM is available for free and can run on Linux machines through the command line: http://code.google.com/p/jamm-peak-finderContact : mahmoud.ibrahim@mdc-berlin.de or uwe.ohler@mdc-berlin.de .Supplementary information: Supplementary data are available at Bioinformatics online.
Postoperative Hyperoxia (60%) Worsens Hepatic Injury in Mice
Authors: Zangl Quirin , Martignoni André , Jackson Sharon H. , Ohta Akio , Klaunberg Brenda , Kaufmann Ines , Lukashev Dimitry , Ward Jerrold M. , Sitkovsky Michail , Thiel Manfred , Choukèr Alexander 
Published: September 2014

Abstract

Background:
Liver damage by ischemia and reperfusion injury is a risk factor for morbidity and mortality after liver surgery. Postoperative oxygen treatment is routinely applied in the postanesthesia and intensive care unit after liver surgery. The risks of aggravating the injury by increasing inspiratory oxygen from 21 to 60% in the postoperative period were investigated in mice.

Methods:
Parameters of liver injury were compared after induction of hepatic ischemia–reperfusion injury, by clamping the left liver lobe for 45 min, and reperfusion for 24 h either under normoxic (21% oxygen) or hyperoxic (60% oxygen) conditions (n = 22 per group). The extent of tissue injury and oxidative responses was analyzed in the presence or absence of polymorphonuclear leukocytes, functional Kupffer cells, and the p47phox unit of the nicotinamide adenine dinucleotide phosphate oxidase (n = 6 to 11 per group).

Results:
Compared with postoperative normoxic conditions, hyperoxia increased cell damage (glutamate-pyruvate transaminase: 1,870 [±968 SD] vs. 60% 2,981 [±1,038 SD], 21 vs. 60% oxygen, in U/l as mean ± SD; P < 0.01), liver weights (341 ± 52 vs. 383 ± 44, 21 vs. 60% oxygen, in mg as mean ± SD; P = 0.02), damage scores (1.9 ± 0.8 vs. 3.1 ± 1.0, 21 vs. 60% oxygen, score as mean ± SD; P = 0.02), and reactive oxygen species (15.0 ± 12.0 vs. 30.4 ± 19.2, 21 vs. 60% oxygen, in μmol/l as mean ± SD; P < 0.05). The aggravation of the tissue damaging effects as a result of hyperoxia was not seen in mice with depletions of polymorphonuclear leukocytes or Kupffer cells, or with nonfunctioning nicotinamide adenine dinucleotide phosphate oxidase.

Conclusion:
Liver injury after ischemia was significantly aggravated by hyperoxia as a consequence of immune cell-mediated oxidative burst. Further studies are needed to elucidate whether routine delivery of high inspirational oxygen concentrations postoperatively should be limited.
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mousePeromyscus eremicus
Authors: MacManes Matthew D. , Eisen Michael B. 
Published: September 2014

AbstractAs a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal,Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of theP.eremicustranscriptome. We assay four tissues (kidney, liver, brain, testes) from a single individual and supplement this with population level renal transcriptome sequencing from 15 additional animals. We identified a set of transcripts undergoing both purifying and balancing selection based on estimates of Tajima’s D. In addition, we used the branch-site test to identify a transcript – Slc2a9, likely related to desert osmoregulation – undergoing enhanced selection inP.eremicusrelative to a set of related non-desert rodents.
Co‐infection of Scedosporium apiospermum and Mycobacterium chelonae in an immunocompetent host
Authors: Kim Ji Seok , Choi Misoo , Nam Chan Hee , Kim Jee Young , Hong Seung Phil , Kim Myung Hwa , Park Byung Cheol 
Published: September 2014

AbstractA 75‐year‐old man presented with multiple, scaly, erythematous, grouped papules, nodules and plaques with tenderness ranging from the right forearm to hand dorsum and the right lower leg for 2–3 months. Five months prior to presentation, the patient had received an antibiotic skin test on his right forearm. Lesions appeared approximately 2–3 months after the antibiotic skin test, slowly progressing without clinical improvement. Culture for fungus on the right forearm revealed growth of Scedosporium apiospermum. The tissue acid‐fast bacilli (AFB) culture for the right forearm and right leg revealed growth of non‐tuberculous mycobacteria which was Mycobacterium chelonae, and subsequent tissue polymerase chain reaction of both sites reported positive signs of M. chelonae. On diastase periodic acid‐Schiff stain of the biopsy specimen of the right forearm, fungal hyphae were found while rod‐shaped bacilli could be seen in AFB stain for the biopsy specimen of the right leg. The patient was treated with oral clarithromycin and ciprofloxacin along with an oral antifungal agent for 13 weeks. After the treatment, the lesions subsided and left a scar. We report a rare case of co‐infection of S. apiospermum and M. chelonae in an immunocompetent host.
Case series of volar juvenile xanthogranuloma: Clinical observation of a peripheral rim of hyperkeratosis
Authors: Mervak Julie , Amadi Ugochukwu , Khandpur Ritika , Ha Lan Thanh T. , Hristov Alexandra , Do Thy Thy , Maier Lisa , Wang Frank 
Published: September 2014

AbstractJuvenile xanthogranuloma is a benign histiocytic tumor predominantly occurring in children as yellowish papules on the head and trunk. Presentations on the volar surfaces are rare and may cause diagnostic confusion with pyogenic granuloma, eccrine poroma and digital fibrokeratoma. We report two patients with unusual presentations of solitary juvenile xanthogranuloma on the palm or sole. Both had lesions lacking the classic yellowish color and demonstrating a well‐defined, peripheral hyperkeratotic rim. Histopathological evaluation revealed prominent orthokeratosis corresponding to the rim. Additional histological features, including dermal histiocytes and Touton giant cells, were consistent with the diagnosis of juvenile xanthogranuloma. Given the unusual locations and colors of the lesions, we conclude that histopathological evaluation is central to diagnosing volar juvenile xanthogranuloma. We additionally suggest that juvenile xanthogranuloma should be included in the differential diagnoses of volar lesions displaying a peripheral hyperkeratotic rim.
Sustained costs of growth and the trajectory of recovery
Authors: Perez Kestrel O. , Munch Stephan B. 
Published: September 2014

Summary

Large body size is associated with many fitness advantages. Despite this, most species do not grow at their physiological maximum, suggesting costs to rapid growth. There are now many empirical examples of trade‐offs with growth.

Despite the ubiquity of physiological delays, few studies have evaluated the duration over which growth costs occur. To address this question, we measured swimming ability in growth‐manipulated Atlantic silversides (Menidia menidia). Fish were manipulated to grow at their maximum for 2 weeks and then were put on restricted rations, so they grew slowly. We then compared swimming ability with fish that had always grown slowly.

Fast‐grown fish had significantly poorer swimming ability and continued to show a prolonged cost of this early period of rapid growth. We found that fish fully recovered normal swimming ability after ˜1 month of growing slowly. Most surprisingly, the trajectory of recovery was not monotonic; performance actually decreased before it improved.

We conclude with a suggestion to develop a better understanding of the mechanisms linking growth to performance trade‐offs. Our results suggest that reduced swimming performance following fast growth is unlikely to be completely explained by bioenergetic constraints. Additionally, there is need for more nuanced life‐history theory that incorporates prolonged growth costs to increase accuracy of growth rate prediction.
Signal detectability of marine electromagnetic methods in the exploration of resistive targets
Authors: Goldman Mark , Mogilatov Vladimir , Haroon Amir , Levi Eldad , Tezkan Bülent 
Published: September 2014

ABSTRACTWe compare selected marine electromagnetic methods for sensitivity to the presence of relatively thin resistive targets (e.g., hydrocarbons, gas hydrates, fresh groundwater, etc.). The study includes the conventional controlled‐source electromagnetic method, the recently introduced transient electromagnetic prospecting with vertical electric lines method, and the novel marine circular electric dipole method, which is still in the stage of theoretical development. The comparison is based on general physical considerations, analytical (mainly asymptotic) analysis, and rigorous one‐dimensional and multidimensional forward modelling. It is shown that transient electromagnetic prospecting with vertical electric lines and marine circular electric dipole methods represent an alternative to the conventional controlled‐source electromagnetic method at shallow sea, where the latter becomes less efficient due to the air‐wave phenomenon. Since both former methods are essentially short‐offset time‐domain techniques, they exhibit a much better lateral resolution than the controlled‐source electromagnetic method in both shallow sea and deep sea. The greatest shortcoming of the transient electromagnetic prospecting with vertical electric lines and marine circular electric dipole methods comes from the difficulties in accurately assembling the transmitter antenna within the marine environment. This makes these methods significantly less practical than the controlled‐source electromagnetic method. Consequently, the controlled‐source electromagnetic method remains the leading marine electromagnetic technique in the exploration of large resistive targets in deep sea. However, exploring laterally small targets in deep sea and both small and large targets in shallow sea might require the use of the less practical transient electromagnetic prospecting with vertical electric lines and/or marine circular electric dipole method as a desirable alternative to the controlled‐source electromagnetic method.