bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNES: single nucleus exome sequencing
Authors: Leung Marco L , Wang Yong , Waters Jill , Navin Nicholas E 
Published: March 2015

AbstractSingle-cell genome sequencing methods are challenged by poor physical coverage and high error rates, making it difficult to distinguish real biological variants from technical artifacts. To address this problem, we developed a method called SNES that combines flow-sorting of single G1/0 or G2/M nuclei, time-limited multiple-displacement-amplification, exome capture, and next-generation sequencing to generate high coverage (96%) data from single human cells. We validated our method in a fibroblast cell line, and show low allelic dropout and false-positive error rates, resulting in high detection efficiencies for single nucleotide variants (92%) and indels (85%) in single cells.
Evaluating intra- and inter-individual variation in the human placental transcriptome
Authors: Hughes David A , Kircher Martin , He Zhisong , Guo Song , Fairbrother Genevieve L , Moreno Carlos S , Khaitovich Philipp , Stoneking Mark 
Published: March 2015

Abstract
Background
Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta.

Results
We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection.

Conclusions
We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.
Characterization of a novel KCNQ1 mutation for type 1 long QT syndrome and assessment of the therapeutic potential of a novel IKs activator using patient-specific induced pluripotent stem cell-derived cardiomyocytes
Authors: Ma Dongrui , Wei Heming , Lu Jun , Huang Dou , Liu Zhenfeng , Loh Li Jun , Islam Omedul , Liew Reginald , Shim Winston , Cook Stuart A 
Published: March 2015

Abstract
Introduction
Type 1 long QT syndrome (LQT1) is a common type of cardiac channelopathy associated with loss-of-function mutations of KCNQ1. Currently there is a lack of drugs that target the defected slowly activating delayed rectifier potassium channel (IKs). With LQT1 patient-specific human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (hiPSC-CMs), we tested the effects of a selective IKs activator ML277 on reversing the disease phenotypes.

Methods
A LQT1 family with a novel heterozygous exon 7 deletion in the KCNQ1 gene was identified. Dermal fibroblasts from the proband and her healthy father were reprogrammed to hiPSCs and subsequently differentiated into hiPSC-CMs.

Results
Compared with the control, LQT1 patient hiPSC-CMs showed reduced levels of wild type KCNQ1 mRNA accompanied by multiple exon skipping mRNAs and a ~50% reduction of the full length Kv7.1 protein. Patient hiPSC-CMs showed reduced IKs current (tail current density at 30 mV: 0.33 ± 0.02 vs. 0.92 ± 0.21, P < 0.05) and prolonged action potential duration (APD) (APD 50 and APD90: 603.9 ± 39.2 vs. 319.3 ± 13.8 ms, P < 0.005; and 671.0 ± 41.1 vs. 372.9 ± 14.2 ms, P < 0.005). ML277, a small molecule recently identified to selectively activate KV7.1, reversed the decreased IKs and partially restored APDs in patient hiPSC-CMs.

Conclusions
From a LQT1 patient carrying a novel heterozygous exon7 deletion mutation of KCNQ1, we generated hiPSC-CMs that faithfully recapitulated the LQT1 phenotypes that are likely associated with haploinsufficiency and trafficking defect of KCNQ1/Kv7.1. The small molecule ML277 restored IKs function in hiPSC-CMs and could have therapeutic value for LQT1 patients.
Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites
Authors: Swindell William R , Sarkar Mrinal K , Stuart Philip E , Voorhees John J , Elder James T , Johnston Andrew , Gudjonsson Johann E 
Published: March 2015

AbstractBackgroundPsoriasis is a cytokine‐mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy.MethodsMeta‐analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically‐determined binding affinities of TFs and unconventional DNA‐binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs.ResultsPREs are recognized by IRF1, ISGF3, NF‐kappaB and multiple TFs with helix‐turn‐helix (homeo) or other all‐alpha‐helical (high‐mobility group) DNA‐binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine‐encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis‐activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF‐kappaB). Finally, we screened psoriasis‐associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele‐specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles.ConclusionsWe identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility.
Interferon-α inhibits CD4 T cell responses to interleukin-7 and interleukin-2 and selectively interferes with Akt signaling
Authors: Nguyen Thao P , Bazdar Doug A , Mudd Joseph C , Lederman Michael M , Harding Clifford V , Hardy Gareth A , Sieg Scott F 
Published: March 2015

Abstract
Persistent type I IFN production occurs during chronic viral infections, such as HIV disease. As type I IFNs have antiproliferative activity, it is possible that chronic exposure to these cytokines could adversely affect T cell homeostasis. We investigated the capacity of IFN-α to impair T cell proliferation induced by the homeostatic cytokine, IL-7, or another common γ-chain cytokine, IL-2, in cells from healthy human donors. We found that IL-7- or IL-2-induced proliferation of CD4+ T cells was partially inhibited in the presence of IFN-α. The CD4+ T cells that were exposed to IFN-α also displayed attenuated induction of IL-2 and CD40L following TCR stimulation. Analyses of signaling pathways indicated that IL-7 and IL-2 induced a delayed and sustained P-Akt signal that lasted for several days and was partially inhibited by IFN-α. In contrast, IL-7-induced P-STAT5 was not affected by IFN-α. Furthermore, IFN-α had no detectable effect on P-Akt that was induced by the chemokine SDF-1. Both inhibitors of P-Akt and P-STAT5 blocked IL-7-induced T cell proliferation, confirming that both signaling pathways are important for IL-7-induced T cell proliferation. These results demonstrate that IFN-α can selectively inhibit cytokine-induced P-Akt as a potential mechanism to disrupt homeostasis of T lymphocytes.
Acoustic models of orangutan hand-assisted alarm calls
Authors: de Boer Bart , Wich Serge A. , Hardus Madeleine E. , Lameira Adriano R. 
Published: March 2015

ABSTRACT
Orangutans produce alarm calls called kiss-squeaks, which they sometimes modify by putting a hand in front of their mouth. Through theoretical models and observational evidence, we show that using the hand when making a kiss-squeak alters the acoustics of the production in such a way that more formants per kilohertz are produced. Our theoretical models suggest that cylindrical wave propagation is created with the use of the hand and face as they act as a cylindrical extension of the lips. The use of cylindrical wave propagation in animal calls appears to be extremely rare, but is an effective way to lengthen the acoustic system; it causes the number of resonances per kilohertz to increase. This increase is associated with larger animals, and thus using the hand in kiss-squeak production may be effective in exaggerating the size of the producer. Using the hand appears to be a culturally learned behavior, and therefore orangutans may be able to associate the acoustic effect of using the hand with potentially more effective deterrence of predators.
Petrographic and Chemical Characterization of the Bonito Seam and its Beneficiation Products, South Santa Catarina Coalfield — Brazil
Authors: Simão Gustavo , Kalkreuth W. 
Published: March 2015

The Bonito seam has become recently a new exploration and exploitation target in the South Santa Catarina Coalfield, Brazil. The present study is a contribution to an understanding of the petrographical and chemical characteristics of the Bonito seam collected at three underground mine sites, followed by beneficiation tests using a density range from <1.6 to > 2.4 g/cm3. Seam Characteristics and Ash Fusibility Tests. Averaged ash yield is 58 wt.%, volatile matter content is 16 wt.%, and calorific value is 2910 cal/g. Vitrinite reflectance indicate high volatile B bituminous rank. Inertinite and vitrinite maceral groups are most abundant. Quartz, kaolinite and pyrite are the predominant minerals. The Free Swelling Index is 1. Ash Fusibility Tests indicated an initial deformation temperature at 1260 °C, and a flow temperature at 1473 °C. Beneficiation tests. In the beneficiated sample a gradual increase of ash yields with increasing density fraction occurs, whereas volatile matter, calorific values and fixed carbon decrease. Technological properties. High ash yields and low FSI values in the 1.6 and <1.6 g/cm3 density fractions, and the predominance of non-reactive components prevents the use of the Bonito seam in coke-making. The beneficiated samples showed, however, a high potential to be used in combustion.
Light-Dark-Light-Heavy: Reflections on an art–dance collaboration
Authors: Crickmay Chris 
Published: March 2015

Abstract
This article describes an interdisciplinary collaboration in the making of a new performance piece. In this work we explore visual and movement possibilities using a dancer carrying a single portable light – how the shifting qualities of space, light and shadow are created out of, and feed back into, bodily sensations of weight, breath, touch and momentum. The article raises issues concerning the making process in a collaborative practice where both partners work on equal terms and both are involved in all aspects of the work. An improvisational approach to making and performing the piece leads to the concept of ‘emergent form’ as opposed to a set choreography. The work exemplifies a ‘relational’ approach to performance, focusing on the interaction between the performer and her surroundings as a continuing dialogue within an integrated art–dance practice. Consistent with this interactive approach, the performance environment is conceived as a variable ‘kit of parts’, rather than a pre-determined set.
Somatic commonalities in the study of Budō and Zen
Authors: Doubleday Tony Shinro 
Published: March 2015

Abstract
This article explores the central place of body-mind practice in the Japanese martial arts, known as Budō, and the Sōtō Zen sect of Buddhism, as I have encountered them in Europe. Drawing on my experiences from the study of Budō and Zen, my purpose is to explore a body-mind synthesis in subjective–objective experience, as described by the medieval Japanese Zen master Eihei Dōgen and the philosopher Yasuo Yuasa, which I find to be the fertile shared ground of these two systems of self-cultivation. It is ground that is, I think, all too easily overlooked and left fallow, but which it has been my good fortune to encounter in the training methods of the Tetsushinkan dōjō, in east London.
The presence of absences: Unconscious performances and muscle memories in Pilates
Authors: Holmes Sarah W. 
Published: March 2015

Abstract
This article synthesizes the scholarly areas of dance studies, somatic research and kinaesiology, to illustrate how Pilates history continuously overlooks values culturally transmitted from body-to-body through Pilates practice. In this process, I suggest that not all embodied memories have liberatory effects. This could be potentially problematic, especially with respect to the historical marginalization and invisiblization of non-white bodies. I maintain by making the goal of Pilates an ‘unconscious’ and therefore unreflective performance of its exercise, it perpetuates specific cultural and behavioural values.
Die Arbeitsgemeinschaft der Regionalbibliotheken in der Sektion 4 des dbv – Bericht für die Jahre 2013/2014
Authors: Freifrau Hiller von Gaertringen Julia 
Published: March 2015

Zusammenfassung:
Der Bericht informiert über die Tätigkeit der Arbeitsgemeinschaft der Regionalbibliotheken in der Sektion 4 des Deutschen Bibliotheksverbands (dbv) in den Jahren 2013 und 2014.
Öffentliche Bibliotheken als Agenten der Beruflichen Aus- und Weiterbildung
Authors: Hermann Elisa 
Published: March 2015

Zusammenfassung:
Dieser Artikel befasst sich mit den für berufliche Aus- und Weiterbildung spezifischen Zielgruppen. Näher betrachtet werden die Zufriedenheit mit den Bibliotheksangeboten sowie mögliche Dienstleistungen zur Steigerung der Attraktivität und damit der Rolle der Öffentlichen Bibliotheken Berlins als Bildungsagenten nach dem Besuch der allgemeinbildenden Schule.
Potentiometric measurement of urinary iodine concentration in patients with thyroid diseases with and without previous exposure to non-radioactive iodine
Authors: Giovacchini Giampiero , Giovanella Luca , Haldemann Andreas , Staub Uwe , Füchsel Frank G. , Koch Peter 
Published: March 2015

AbstractExtensive application of measurement of urinary iodine concentration (UIC) in several benign and malignant thyroid diseases could profit by the availability of rapid and inexpensive measuring techniques. Aim of this study was to apply a simple and inexpensive commercially available potentiometric method for the quantification of UIC based on iodine-specific ion-selective electrodes (ISE) in patients with thyroid diseases.This retrospective study included patients with differentiated thyroid cancer (n=286) and patients with hyperthyroidism of different etiologies (n=203). Within the whole sample (n=489) 20 patients had previously (1 week–6 months) been exposed to iodine overload, either from contrast media (n=8) or amiodarone (n=12).: In patients not exposed to iodine, the histogram showed that the distribution of UIC violated normality. The peak of the curve occurred between 5.0 μmol/L and 6.0 μmol/L. Variability was sizeable (percent coefficient of variation, %CV: 66%, 95% confidence interval: 1.48–18.72 μmol/L). The group of exposed patients could be easily distinguished from not exposed patients (median UIC: 47.5 μmol/L vs. 5.42 μmol/L). UIC was significantly correlated to urinary creatinine concentration, but normalization to urinary creatinine increased the inter-subject variability of UIC (%CV=96% vs. 66%). In test-retest studies (n=25) the intra-class correlation coefficient was 0.73 for UIC, 0.82 for creatinine and 0.64 for the UIC: creatinine ratio.Iodine-specific ISE-based potentiometric methods can be successfully applied as an alternative to existing methods in patients with thyroid diseases. The promising characteristics of the method need to be confirmed in future larger prospective studies.
Transversal Oxide-Metal Thermoelectric Device for Low-Power Energy Harvesting
Authors: Dreßler Christian , Bochmann Arne , Schulz Thomas , Reimann Timmy , Töpfer Jörg , Teichert Steffen 
Published: March 2015

Abstract
The concepts of dual leg, unileg and transversal oxide thermoelectric harvesting devices were compared with regard to the dimensionless figure of merit calculated from published data on common dual leg oxide thermoelectric generators. The analysis shows that the application of the transversal thermoelectric effect does not significantly reduce the expected electrical output power density of thermoelectric devices utilizing thermoelectric oxides. At the same time, the transversal device layout is simple in comparison to the common dual leg device. A transversal thermoelectric harvester consisting of a tilted multilayer stack La1.97Sr0.03CuO4/Ag was prepared and analyzed in detail. Simulations using the finite elements method were performed to verify the results. Based on this data, the electrical power density of the transversal oxide-metal device is estimated to be in the range of currently published data on oxide dual leg devices, thus allowing energy harvesting for low power applications.
Study on Dynamics and Constraints of the Employment in the Serbian SMEs During a Crisis
Authors: Predić Biljana , Stefanović Suzana , Stošić Danijela 
Published: March 2015

Abstract
Small and medium sized-enterprises (SMEs) are often seen as a sector important for job creation. About 2/3 of the overall employment is provided by this sector, both in the EU and in the Republic of Serbia. There is evidence that SMEs are responsible for the most part of the net employment growth. The SMEs sector in Serbia is identified as sector which can absorb a part of the unemployment generated by the large scale enterprises’ (LSEs) restructuring and privatization. Today, the unemployment rate in Serbia is high above the average unemployment rate in the EU. The question is whether the SMEs sector can absorb that unemployment, or is this sector more influenced by the crisis, relative to the LSEs. The aim of this paper is to examine the employment contribution of the SMEs in the Republic of Serbia. Furthermore, the paper will deal with the impact of the crisis on the SMEs’ employment, efficiency and their investment activities. The problems that are identified by SMEs, and that lead to rising unemployment in this sector over the past few years will be considered and analyzed.
Microstructural Changes of a Creep-Damaged Nickel-Based K002 Superalloy Containing Hf Element under Different HIP Temperatures
Authors: Wang Xiaomeng , Zhou Yu , Dong Jian , Wang Tianyou , Zhao Zihua , Zhang Zheng 
Published: March 2015

AbstractEffects of hot isostatic pressing (HIP) temperature on the microstructural evolution of a nickel-based K002 superalloy containing Hf element after long-term service were investigated using three different soaking temperatures during HIP. The degraded γ′ precipitates represented coarse and irregular morphology after long-term service. These γ′ precipitates still were of coarse and irregular shape, but the size and volume fraction of γ′ precipitates were markedly reduced under HIP condition of 1,190°C/200 MPa/4 h, indicating that the γ′ precipitates were experiencing a dissolution process. Meanwhile, the concentrically oriented N-type γ′ rafting structure around the cavities was formed. With HIP temperature increase to 1,220°C and 1,250°C, the small-sized, cubic and regular γ′ precipitates were re-precipitated, and the concentrically oriented γ′ structure vanished. The unstable morphology induced by the nucleation and growth of γ matrix was found near the creep cavities, indicating that the solute atoms diffused inward the creep-induced cavities during HIP. However, at HIP temperature of 1,220°C and 1,250°C, a large number of blocky MC(2)-type carbides containing amounts of Hf elements were precipitated, demonstrating that HIP treatment at higher temperatures can result in the formation of a large number of blocky MC(2)-type carbides.
Tag questions across Irish English and British English: A corpus analysis of form and function
Authors: Barron Anne , Pandarova Irina , Muderack Karoline 
Published: March 2015

Abstract
The present study, situated in the area of variational pragmatics, contrasts tag question (TQ) use in Ireland and Great Britain using spoken data from the Irish and British components of the International Corpus of English (ICE). Analysis is on the formal and functional level and also investigates form-functional relationships. Findings reveal many similarities in the use of TQs across the varieties. They also point, however, to a lower use of TQs in Irish English and in a range of variety-preferential features on both the formal and functional levels. The paper shows how an in-depth analysis of form-function relations together with a fine-tuned investigation of sub-functions gives an insight into formal preferences.
La pena di morte per ľ"assassinio" del bue aratore (a proposito di Varrò rust. 2,5,3-4 e Colum. 6, praef. 7)
Authors: Bellandi Franco 
Published: March 2015

Abstract
This essay is focused on a difficult passage in Varrò, rust. 2,5,3-4, which is quoted, explained and partially corrected by Columella (6 praef. 7). Both passages are for us a valuable source of information about the capital sentence inflicted, in a very early age, on the person who caused the death of the ploughing ox. However, a contradiction or apory can be observed in the attitude of the two authors. On the one hand - as admirers of the mos maiorum - they seem to praise the innocence and the restraint of the ancients, who showed so much respect for so beneficent an animal. On the other hand, in their roles as instructors of the most efficient farming techniques, they are keen on the profits assured by the raising of farm animals, and discuss without embarrassment the slaughter of oxen (either sacrificial or simply commercial) and the eating of beef. In Greece, the Attic Bouphonia, with all their functional ambiguities, marked the transition from the age of the bloodless sacrifice - praised and placed forever in the archives of history - to the "modern" age of slaughter; on the contrary, Roman culture lacked a similar rite that could somehow reconcile the two antithetical ideas, the ancient taboo about the slaying of domestic animals and the actual killing as performed in historical times.