bluuebunny/crossref_metadata_2025_split huggingface dataset:
Departures from Axisymmetric Balance Dynamics during Secondary Eyewall Formation
Authors: Abarca Sergio F. , Montgomery Michael T. 
Published: June 2014

Abstract
Departures from axisymmetric balance dynamics are quantified during a case of secondary eyewall formation. The case occurred in a three-dimensional mesoscale convection-permitting numerical simulation of a tropical cyclone, integrated from an initial weak mesoscale vortex in an idealized quiescent environment. The simulation exhibits a canonical eyewall replacement cycle. Departures from balance dynamics are quantified by comparing the azimuthally averaged secondary circulation and corresponding tangential wind tendencies of the mesoscale integration with those diagnosed as the axisymmetric balanced response of a vortex subject to diabatic and tangential momentum forcing. Balance dynamics is defined here, following the tropical cyclone literature, as those processes that maintain a vortex in axisymmetric thermal wind balance.
The dynamical and thermodynamical fields needed to characterize the background vortex for the Sawyer–Eliassen inversion are obtained by azimuthally averaging the relevant quantities in the mesoscale integration and by computing their corresponding balanced fields. Substantial differences between azimuthal averages and their homologous balance-derived fields are found in the boundary layer. These differences illustrate the inappropriateness of the balance assumption in this region of the vortex (where the secondary eyewall tangential wind maximum emerges). Although the balance model does broadly capture the sense of the forced transverse (overturning) circulation, the balance model is shown to significantly underestimate the inflow in the boundary layer. This difference translates to unexpected qualitative differences in the tangential wind tendency. The main finding is that balance dynamics does not capture the tangential wind spinup during the simulated secondary eyewall formation event.
The effect of multiple martensitic transformations on diffusion of Fe and Ni atoms in Fe-31.7%Ni-0.06%C alloy
Authors: Danilchenko Vitaliy E , Mazanko Vladimir F , Iakovlev Viktor E 
Published: June 2014

Abstract
Diffusion characteristics of iron and nickel atoms were investigated using radioactive isotopes method in phase-hardened metastable iron-nickel Fe-31.7%Ni-0.06%C alloy with nanofragmented structure. It has been found that diffusion mobility of nickel and iron atoms in reverted austenite of Fe-31.7%Ni-0.06%C alloy significantly increases as the result of multiple γ-α-γ martensitic transformations. The diffusion coefficients of nickel and iron in the austenite at 400°C corresponded to the stationary diffusion coefficients at the temperatures above 900°C. The revealed diffusion acceleration at low temperatures is caused by high-density dislocations and additional low-angle subboundaries of disoriented nanofragments of reverted austenite and deformation twin subboundaries formed during multiple γ-α-γ cycles.
Effect of ZnO:Cs2CO3 on the performance of organic photovoltaics
Authors: Kim Hyeong Pil , Yusoff Abd Rashid bin Mohd , Lee Hee Jae , Lee Seung Joo , Kim Hyo Min , Seo Gi Jun , Youn Jun Ho , Jang Jin 
Published: June 2014

Abstract
We demonstrate a new solution-processed electron transport layer (ETL), zinc oxide doped with cesium carbonate (ZnO:Cs2CO3), for achieving organic photovoltaics (OPVs) with good operational stability at ambient air. An OPV employing the ZnO:Cs2CO3 ETL exhibits a fill factor of 62%, an open circuit voltage of 0.90 V, and a short circuit current density of −6.14 mA/cm2 along with 3.43% power conversion efficiency. The device demonstrated air stability for a period over 4 weeks. In addition, we also studied the device structure dependence on the performance of organic photovoltaics. Thus, we conclude that ZnO:Cs2CO3 ETL could be employed in a suitable architecture to achieve high-performance OPV.
A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing
Authors: Korir Paul K , Roberts Lisa , Ramesar Raj , Seoighe Cathal 
Published: June 2014

AbstractBackgroundSubstantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci – sQTLs). Genetic variants that affect mRNA splicing intransare harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays.ResultsExon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factorPRPF8and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting approximately 20% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, rich, located towards the 5’ end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition.ConclusionsOur results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as atrans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. However, due to the small sample size available for this study, further studies are required to confirm the widespread impact of thisPRPF8mutation on mRNA splicing outside the retina.
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
Authors: Pop Mihai , Walker Alan W , Paulson Joseph , Lindsay Brianna , Antonio Martin , Hossain M Anowar , Oundo Joseph , Tamboura Boubou , Mai Volker , Astrovskaya Irina , Bravo Hector Corrada , Rance Richard , Stares Mark , Levine Myron M , Panchalingam Sandra , Kotloff Karen , Ikumapayi Usman N , Ebruke Chinelo , Adeyemi Mitchell , Ahmed Dilruba , Ahmed Firoz , Alam Meer Taifur , Amin Ruhul , Siddiqui Sabbir , Ochieng John B , Ouma Emmanuel , Juma Jane , Mailu Euince , Omore Richard , Morris J Glenn , Breiman Robert F , Saha Debasish , Parkhill Julian , Nataro James P , Stine O Colin 
Published: June 2014

Abstract
Background
Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.

Results
We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.

Conclusions
Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.
Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters
Authors: Quinodoz Mathieu , Gobet Cédric , Naef Felix , Gustafson Kyle B 
Published: June 2014

Abstract
Background
In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states.

Results
Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3.

Conclusions
We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.
Two new species of Begonia sect. Coelocentrum, B. guixiensis and B. longa, from Sino-Vietnamese limestone karsts
Authors: Peng Ching-I , Ku Shin-Ming , Yang Hsun-An , Leong Wai-Chao , Liu Yan , Nguyen Tien Hiep , Kono Yoshiko , Chung Kuo-Fang 
Published: June 2014

Abstract

Background
In our recent molecular phylogenetic study of Asian Begonia, two undescribed species, B. guixiensis sp. ined. (S. Guangxi, China) and B. longa sp. ined. (Vietnam), were sampled and placed within the strongly supported clade composed of Begonia sect. Coelocentrum and other co-distributed rhizomatous species in the Sino-Vietnamese limestone karsts. While Begonia sect. Coelocentrum has been recircumscribed based on the phylogenetic relationships, B. guixiensis sp. ined. and B. longa sp. ined. remain illegitimate names. In continuation of our studies in Asian Begonia, these two new species are described and illustrated.

Results

Begonia guixiensis resembles B. cylindrica in the peltate, subcoriaceous leaves, differing by the shape of ovary/fruit and the type of placentation. In aspect, B. longa bears a superficial resemblance to B. brevipedunculata in leaf shape in particular, differing by many other features such as the long internodes, shorter petioles and smaller leaves, longer peduncles and 3-locular ovary. The chromosome number of both new species is determined as 2n = 30.

Conclusion
A careful study of the literature, herbarium specimens and living plants, both in the wild and in cultivation in the experimental greenhouse, support the recognition of the two new species, which are described and illustrated herein.
Novel Pituitary Actions of TAC3 Gene Products in Fish Model: Receptor Specificity and Signal Transduction for Prolactin and Somatolactin α Regulation by Neurokinin B (NKB) and NKB-Related Peptide in Carp Pituitary Cells
Authors: Hu Guangfu , He Mulan , Ko Wendy K.W. , Lin Chengyuan , Wong Anderson O.L. 
Published: June 2014

AbstractTAC3 is a member of tachykinins, and its gene product neurokinin B (NKB) has recently emerged as a key regulator for LH through modulation of kisspeptin/GnRH system within the hypothalamus. In fish models, TAC3 not only encodes NKB but also a novel tachykinin-like peptide called NKB-related peptide (NKBRP), and the pituitary actions of these TAC3 gene products are still unknown. Using grass carp as a model, the direct effects and postreceptor signaling for the 2 TAC3 products were examined at the pituitary level. Grass carp TAC3 was cloned and confirmed to encode NKB and NKBRP similar to that of other fish species. In carp pituitary cells, NKB and NKBRP treatment did not affect LH release and gene expression but up-regulated prolactin (PRL) and somatolactin (SL)α secretion, protein production, and transcript expression. The stimulation by these 2 TAC3 gene products on PRL and SLα release and mRNA levels were mediated by pituitary NK2 and NK3 receptors, respectively. Apparently, NKB- and NKBRP-induced SLα secretion and transcript expression were caused by adenylate cyclase/cAMP/protein kinase A, phospholipase C/inositol 1,4,5-triphosphate/protein kinase C and Ca2+/calmodulin/Ca2+/calmodulin-dependent protein kinase II activation. The signal transduction for the corresponding responses on PRL release and mRNA expression were also similar, except that the protein kinase C component was not involved. These findings suggest that the 2 TAC3 gene products do not play a role in LH regulation at the pituitary level in carp species but may serve as novel stimulators for PRL and SLα synthesis and secretion via overlapping postreceptor signaling mechanisms coupled to NK2 and NK3 receptors, respectively.
Angiotensin II Type 2 Receptor Stimulation Improves Fatty Acid Ovarian Uptake and Hyperandrogenemia in an Obese Rat Model of Polycystic Ovary Syndrome
Authors: Leblanc Samuel , Battista Marie-Claude , Noll Christophe , Hallberg Anders , Gallo-Payet Nicole , Carpentier André C. , Vine Donna F. , Baillargeon Jean-Patrice 
Published: June 2014

Abstract
Polycystic ovary syndrome (PCOS) is mainly defined by hyperandrogenism but is also characterized by insulin resistance (IR). Studies showed that overexposure of nonadipose tissues to nonesterified fatty acids (NEFA) may explain both IR and hyperandrogenism. Recent studies indicate that treatment with an angiotensin II type 2 receptor (AT2R)-selective agonist improves diet-induced IR. We thus hypothesized that PCOS hyperandrogenism is triggered by ovarian NEFA overexposure and is improved after treatment with an AT2R agonist. Experiments were conducted in 12-week-old female JCR:LA-cp/cp rats, which are characterized by visceral obesity, IR, hyperandrogenism, and polycystic ovaries. Control JCR:LA +/? rats have a normal phenotype. Rats were treated for 8 days with saline or the selective AT2R agonist C21/M24 and then assessed for: 1) fasting testosterone, NEFA, and insulin levels; and 2) an iv 14(R,S)-[18F]fluoro-6-thia-heptadecanoic acid test to determine NEFA ovarian tissue uptake (Km). Compared with controls, saline-treated PCOS/cp rats displayed higher insulin (100 vs 5.6 μU/mL), testosterone (0.12 vs 0.04 nmol/L), NEFA (0.98 vs 0.48 mmol/L), and Km (20.7 vs 12.9 nmol/g·min) (all P &lt; .0001). In PCOS/cp rats, C21/M24 did not significantly improve insulin or NEFA but normalized testosterone (P = .004) and Km (P = .009), which were strongly correlated together in all PCOS/cp rats (ρ = 0.74, P = .009). In conclusion, in an obese PCOS rat model, ovarian NEFA uptake and testosterone levels are strongly associated and are both significantly reduced after short-term C21/M24 therapy. These findings provide new information on the role of NEFA in PCOS hyperandrogenemia and suggest a potential role for AT2R agonists in the treatment of PCOS.
ROS1 Signaling Regulates Epithelial Differentiation in the Epididymis
Authors: Jun Hyun Jung , Roy Jeremy , Smith Tegan B. , Wood Levi B. , Lane Keara , Woolfenden Steve , Punko Diana , Bronson Roderick T. , Haigis Kevin M. , Breton Sylvie , Charest Al 
Published: June 2014

AbstractThe initial segment (IS) of the epididymis plays an essential role in male fertility. The IS epithelium is undifferentiated and nonfunctional at birth. Prior to puberty, the epithelium undergoes differentiation that leads to the formation of a fully functional organ. However, the mechanistic details of this program are not well understood. To explore this further, we used genetic engineering to create a kinase dead allele of the ROS1 receptor tyrosine kinase in mice and studied the effects of ROS1 tyrosine kinase activity on the differentiation of the IS epithelium. We show that the expression and activation of ROS1 coincides with the onset of differentiation and is exclusively located in the IS of the maturing and adult mouse epididymides. Here we demonstrate that the differentiation of the IS is dependent on the kinase activity of ROS1 and its downstream effector MEK1/2-ERK1/2 signaling axis. Using genetic engineering, we show that germ line ablation of ROS1 kinase activity leads to a failure of the IS epithelium to differentiate, and as a consequence sperm maturation and infertility were dramatically perturbed. Pharmacological inhibition of ROS1 kinase activity in the developing epididymis, however, only delayed differentiation transiently and did not result in infertility. Our results demonstrate that ROS1 kinase activity and the ensuing MEK1/2-ERK1/2 signaling are necessary for the postnatal development of the IS epithelium and that a sustained ablation of ROS1 kinase activity within the critical window of terminal differentiation abrogate the function of the epididymis and leads to sterility.
mRNA-Seq Reveals Novel Molecular Mechanisms and a Robust Fingerprint in Graves' Disease
Authors: Yin Xiaoming , Sachidanandam Ravi , Morshed Syed , Latif Rauf , Shi Ruijin , Davies Terry F. 
Published: June 2014

Abstract

Context:
The immune response in autoimmune thyroid disease has been shown to occur primarily within the thyroid gland in which the most abundant antigens can be found. A variety of capture molecules are known to be expressed by thyroid epithelial cells and serve to attract and help retain an intrathyroidal immune infiltrate.

Objective:
To explore the entire repertoire of expressed genes in human thyroid tissue, we have deep sequenced the transcriptome (referred to as mRNA-Seq).

Design and Patients:
We applied mRNA-Seq to thyroid tissue from nine patients with Graves' disease subjected to total thyroidectomy and compared the data with 12 samples of normal thyroid tissue obtained from patients having a thyroid nodule removed. The expression for each gene was calculated from the sequencing data by taking the median of the coverage across the length of the gene. The expression levels were quantile normalized and a gene signature was derived from these.

Results:
On comparison of expression levels in tissues derived from Graves' patients and controls, there was clear evidence for overexpression of the antigen presentation pathway consisting of HLA and associated genes. We also found a robust disease signature and discovered active innate and adaptive immune signaling networks.

Conclusions:
These data reveal an active immune defense system in Graves' disease, which involves novel molecular mechanisms in its pathogenesis and development.
Synthesis of High-purity Vaterite from Calcium Sulfate and Ammonium Carbonate
Authors: Zhao Jingcai , Song Xingfu , Sun Ze , Chen Bo , Yu Jianguo 
Published: June 2014

Abstract
High-purity calcium carbonate of vaterite type was directly obtained from calcium sulfate and ammonium carbonate in ammonium sulfate matrix. This matrix can successfully break the limitations of reactant concentration, temperature, and stirring speed on vaterite. An orthogonal experiment combined with back propagation neural network was then performed to optimize the impurity in vaterite. Under the optimum conditions, 99.9% vaterite was obtained.
How do eubacterial organisms manage aggregation-prone proteome?
Authors: Das Roy Rishi , Bhardwaj Manju , Bhatnagar Vasudha , Chakraborty Kausik , Dash Debasis 
Published: June 2014

Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC) nucleotides ranges from 20% to 70%. It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed that proteins encoded by GC-poor organisms are more prone to aggregation than proteins encoded by GC-rich organisms. To test this proposition using a genome-wide approach, we classified different eubacterial proteomes in terms of their aggregation propensity and chaperone-dependence using multiple machine learning models. In contrast to the expected decrease in protein aggregation with an increase in GC richness, we found that the aggregation propensity of proteomes increases with GC content. A similar and even more significant correlation was obtained with the GroEL-dependence of proteomes: GC-poor proteomes have evolved to be less dependent on GroEL than GC-rich proteomes. We thus propose that a decrease in eubacterial GC content may have been selected in organisms facing proteostasis problems.
On the taxonomic status of the enigmatic Phycolepidoziaceae (Marchantiophyta: Jungermanniales) with description of a new species,Phycolepidozia indica
Authors: Gradstein S. Robbert , Laenen Benjamin , Frahm Jan-Peter , Schwarz Uwe , Crandall-Stotler Barbara J. , Engel John J. , Von Konrat Matthew , Stotler Raymond E. , Shaw Blanka , Shaw A. Jonathan 
Published: June 2014

AbstractThe monospecific Phycolepidoziaceae with the single neotropical speciesPhycolepidoziaexigua is a highly specialized leafy liverwort without vegetative leaves. The extreme reduction of morphological and anatomical characters ofPhycolepidoziahas caused uncertainties as to the systematic position of the genus and family. In 2012, a second species ofPhycolepidoziawas detected in the Western Ghats, South India. The Indian plant differs from P. exigua in several respects and is described here as P. (subg.Metaphycolepidozia)indicaGradst., J.‐P.Frahm & U.Schwarz. Differences include the massive stem of P.indica, the larger perianth with a crenate, 3‐lobed mouth, and the epidermis of the capsule wall made up of non‐tiered cells with nodular thickenings on both longitudinal and transverse walls. A phylogenetic analysis using four different chloroplast regions (psbA, psbT, rps4, rbcL) ofP. indicaand putatively related groups shows thatPhycolepidoziais nested within the leafy liverwort family Cephaloziellaceae. Consequently, Phycolepidoziaceae is placed in the synonymy of Cephaloziellaceae. The discovery ofP. indicaadds a further example to the list of amphi‐Pacific tropical disjunctions in bryophytes.