bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unlocking the genetic diversity of Creole wheats
Authors: Vikram Prashant , Franco Jorge , Burgueño-Ferreira Juan , Li Huihui , Sehgal Deepmala , Saint Pierre Carolina , Ortiz Cynthia , Sneller Clay , Tattaris Maria , Guzman Carlos , Sansaloni Carolina Paola , Ellis Marc , Fuentes-Davila Guillermo , Reynolds Matthew , Sonder Kai , Singh Pawan , Payne Thomas , Wenzl Peter , Sharma Achla , Bains Navtej Singh , Singh Gyanendra Pratap , Crossa José , Singh Sukhwinder 
Published: March 2016

AbstractClimate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.
Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass
Authors: Chai Kian Piaw , Othman Noor Farhan Binti , Teh Aik-Hong , Ho Kok Lian , Chan Kok-Gan , Shamsir Mohd Shahir , Goh Kian Mau , Ng Chyan Leong 
Published: March 2016

AbstractA new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo and GtamyII), Bacillus aquimaris (BaqA) and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
Besser als der Markt
Authors: Schmidt Hartmut 
Published: March 2016

Die Stimmung an den Börsen bleibt nervös – doch die Aktien der deutschen Klinik- und Pflegeheimbetreiber konnten in den vergangenen Wochen Kursgewinne
verzeichnen. Als Überflieger entpuppten sich die Papiere von Euromed: Sie legten um 71 Prozent zu.
Preis für Innovatoren
Authors: Ghanaat Henrik 
Published: March 2016

IT wird im deutschen Gesundheitswesen immer wichtiger. KMA und der Branchenverband VHitG haben einen Preis für innovative IT-Experten und kreative IT-Lösungen ins Leben gerufen. Gewürdigt werden
Konzepte, die sich in der Praxis bewährt haben und anderen zum Vorbild dienen können.
Schutz vor Entscheidungen
Authors: Mühlnikel Ingrid 
Published: March 2016

Privatisierung ist nicht immer der Weisheit letzter Schluss. Das glaubt zumindest der neu gegründete
Interessenverband kommunaler Krankenhäuser. Weniger Einmischung durch die Politik soll kommunale Häuser wieder wettbewerbsfähig machen.
Personalkosten im Griff
Authors: Mühlnikel Ingrid 
Published: March 2016

Mit Beginn diesen Monats gilt der neue Tarifvertrag öffentlicher Dienst (TVöD).
Besonders für die Krankenhäuser verspricht er eine Reihe interessanter Neuerungen: flexible Arbeitszeiten, Regelungen zum Bereitschaftsdienst und leistungsbezogene Vergütung. Nur die Höhe der Einsparungen steht noch nicht fest.
Andere Länder, bessere Kurse
Authors: Schmidt Hartmut 
Published: March 2016

Deutsche Gesundheits-Aktien konnten in den vergangenen Jahren beträchtlich
zulegen. Dennoch schnitten sie schlechter ab als die Papiere der Konkurrenz aus dem Ausland. Schuld daran sind die rigideren Marktbedingungen hierzulande. Von einer internationalen Angleichung dürften die deutschen Anbieter stark profitieren.
Kapitalerhöhung erhöht Verkaufschance
Authors: Schmidt Hartmut 
Published: March 2016

Um die Bilanz zu entlasten, führte Maternus Ende des vergangenen Jahres eine Kapitalerhöhung durch. In der Folge stieg der Anteil des Großaktionärs WCM von
52 auf 76 Prozent. WCM hat damit wesentlich bessere Chancen, seine seit langem gehegten Verkaufspläne in die Tat umzusetzen.
Sparkommissar Ärzteschaft
Authors: Mühlnikel Ingrid 
Published: March 2016

Die Regierung hat ein neues Spargesetz beschlossen. Neben den altbewährten
Instrumenten wie Festbetragssenkungen und Preismoratorium, legt sich die Politik mit der Ärzteschaft an. Durch ein finanzielles Anreizsystem sollen sie zu einer sparsameren Verordnung von Medikamenten angehalten werden.
Der König der Kassen
Authors: Niermann Inga 
Published: March 2016

Wegen der neuen Wahltarife brauchen auch die Gesetzlichen Krankenkassen dringend Versicherungsmathematiker. Doch so begehrt sie sind: Eine Aktuar-Zusatzausbildung ist zu empfehlen. Sie erhöht die Chancen auf Festanstellung und Ve rantwortung:
Leitende Kräfte sind verpflichtet, die Zahlungsfähigkeit ihrer Kasse zu prüfen.
Wir kommen
Authors: Gaede Kirsten 
Published: March 2016

Den OPs mangelt es an Nachwuchs. Der Anteil junger Ärzte ist seit 1991 um etwa
40 Prozent gesunken. Der Bachelor-Studiengang Physician Assistent soll Abhilfe schaffen.
Noch ist er eine Rarität. Doch das wird sich ändern, denn die Nachfrage steigt – zum
Unmut der Pflegeverbände und der Gesellschaft für Chirurgie.
1.2 C—C Bond Formation by Hetarene C—H Activation
Authors: Nakao Y. 
Published: March 2016

AbstractHeteroaromatic compounds play key roles in pharmaceuticals, agrochemicals, and materials, and the development of efficient synthetic methods to access differently substituted hetarenes is therefore an important issue in organic synthesis. To circumvent the limitations associated with classical protocols to form hetaryl—carbon bonds, metal-catalyzed hetarene C—H activation followed by C—C bond-forming reactions has been developed extensively in recent decades. These transformations allow the construction of C—C bonds between hetaryl moieties and all the three differently hybridized carbons to result in alkylation, alkenylation, acylation, alkynylation, etc. of a diverse range of hetarenes irrespective of their electronic characters. This chapter deals with C—C bond formation by hetarene C—H activation achieved by transition-metal catalysis.
Kinesin-12 motors cooperate to suppress microtubule catastrophes and drive the formation of parallel microtubule bundles
Authors: Drechsler Hauke , McAinsh Andrew D. 
Published: March 2016

Significance
During cell division, molecular motors from the kinesin superfamily, in particular Kinesin-12 (Kif15) and Kinesin-5 (Eg5), play a crucial role in formation of the spindle—a bipolar microtubule array that is essential for accurate chromosome segregation. While Eg5 is well studied, the mechanism by which Kif15 maintains spindle bipolarity in the absence of Eg5 is unknown. In this work we reconstitute Kif15 motors on dynamic microtubules in vitro. We reveal that Kif15 is a multi-function motor that cross-links microtubules and drives transport of one along the other, which results in the formation of parallel microtubule bundles. Additionally, motors track the microtubule tips, maintaining them in a growing state, which can synchronize microtubule dynamics within a bundle.
Hierarchy and extremes in selections from pools of randomized proteins
Authors: Boyer Sébastien , Biswas Dipanwita , Kumar Soshee Ananda , Scaramozzino Natale , Nizak Clément , Rivoire Olivier 
Published: March 2016

Significance
Evolution by natural selection requires populations to be sufficiently diverse, but merely counting the number of different individuals provides a poor indication of the potential of a population to satisfy a new selective constraint. To achieve a more relevant characterization of this selective potential, we performed in vitro experiments of selection with populations of partially randomized proteins and analyzed the results quantitatively by high-throughput sequencing. We find that selective potentials in these populations follow simple statistical laws, which can be interpreted with extreme value theory (the mathematical theory of extreme events—here, the rare finding of a protein meeting the selective constraints). Our results provide an approach to quantitatively measure the selective potential of a population.
Sp5 and Sp8 recruit β-catenin and Tcf1-Lef1 to select enhancers to activate Wnt target gene transcription
Authors: Kennedy Mark W. , Chalamalasetty Ravindra B. , Thomas Sara , Garriock Robert J. , Jailwala Parthav , Yamaguchi Terry P. 
Published: March 2016

Significance
Deciphering the mechanisms that underlie stem cell growth and differentiation is key to understanding how embryos develop and will lead to important applications in regenerative medicine. Wnt proteins are powerful regulators of stem cells. We have determined that the Sp1-like transcription factors, Sp5 and Sp8, are components of the Wnt/β-catenin signaling pathway. Sp5/8 promote the differentiation of pluripotent progenitors into the multipotent mesoderm progenitors that largely generate the trunk musculoskeletal system. Unexpectedly, Sp5/8 functions to recruit the transcriptional coactivator β-catenin to select enhancers to stimulate expression of a subset of Wnt target genes. This study reveals a more refined level of Wnt/β-catenin target gene regulation and suggests previously unidentified ways to manipulate the expression of specific Wnt targets.
No difference in the competitive ability of introduced and native Trifolium provenances when grown with soil biota from their introduced and native ranges
Authors: Shelby Natasha , Hulme Philip E. , van der Putten Wim H. , McGinn Kevin J. , Weser Carolin , Duncan Richard P. 
Published: March 2016

Abstract
The evolution of increased competitive ability (EICA) hypothesis could explain why some introduced plant species perform better outside their native ranges. The EICA hypothesis proposes that introduced plants escape specialist pathogens or herbivores leading to selection for resources to be reallocated away from defence and towards greater competitive ability. We tested the hypothesis that escape from soil-borne enemies has led to increased competitive ability in three non-agricultural Trifolium (Fabaceae) species native to Europe that were introduced to New Zealand in the 19th century. Trifolium performance is intimately tied to rhizosphere biota. Thus, we grew plants from one introduced (New Zealand) and two native (Spain and the UK) provenances for each of three species in pots inoculated with soil microbiota collected from the rhizosphere beneath conspecifics in the introduced and native ranges. Plants were grown singly and in competition with conspecifics from a different provenance in order to compare competitive ability in the presence of different microbial communities. In contrast to the predictions of the EICA hypothesis, we found no difference in the competitive ability of introduced and native provenances when grown with soil microbiota from either the native or introduced range. Although plants from introduced provenances of two species grew more slowly than native provenances in native-range soils, as predicted by the EICA hypothesis, plants from the introduced provenance were no less competitive than native conspecifics. Overall, the growth rate of plants grown singly was a poor predictor of their competitive ability, highlighting the importance of directly quantifying plant performance in competitive scenarios, rather than relying on surrogate measures such as growth rate.
IL-15 boosts the function and migration of human terminally differentiated CD8+ T cells by inducing a unique gene signature
Authors: Setoguchi Ruka 
Published: March 2016

Abstract
Human CCR7lowCD45RAhigh effector memory CD8+ T cells (terminally differentiated TEMRA) are reportedly a functionally compromised population with characteristics of cellular senescence when examined ex vivo. Although their frequencies are increased in elderly subjects in association with declined immune competence, however, it remains unclear whether their impaired functions can be reversed so that they contribute to immune responses in vivo. Here, I show that, in contrast to TCR stimulation, stimulation of TEMRA with IL-15 induced a unique transcriptional signature, promoted IFN-γ production and cell cycle entry, and reduced chemotaxis toward sphingosine-1-phosphate (S1P). TEMRA preferentially accumulated in non-lymphoid tissues when transferred into IL-15-treated NOD.SCID.γc-deficient mice compared with non-treated mice. This accumulation was impaired by S1P receptor 1 over-expression. These results suggest that TEMRA act as functional effector T cells in non-lymphoid tissues when IL-15 is abundant and that IL-15 treatment may be beneficial in enhancing vaccine efficacy in elderly people.
Alignments of radio galaxies in deep radio imaging of ELAIS N1
Authors: Taylor A. R. , Jagannathan P. 
Published: March 2016

Abstract
We present a study of the distribution of radio jet position angles of radio galaxies over an area of 1 square degree in the ELAIS N1 field. ELAIS N1 was observed with the Giant Metrewave Radio Telescope at 612 MHz to an rms noise level of 10 μJy and angular resolution of 6 arcsec × 5 arcsec. The image contains 65 resolved radio galaxy jets. The spatial distribution reveals a prominent alignment of jet position angles along a ‘filament’ of about 1°. We examine the possibility that the apparent alignment arises from an underlying random distribution and find that the probability of chance alignment is less than 0.1 per cent. An angular covariance analysis of the data indicates the presence of spatially coherence in position angles on scales &gt;0 $_{.}^{\circ}$5. This angular scales translates to a comoving scale of &gt;20 Mpc at a redshift of 1. The implied alignment of the spin axes of massive black holes that give rise to the radio jets suggest the presence of large-scale spatial coherence in angular momentum. Our results reinforce prior evidence for large-scale spatial alignments of quasar optical polarization position angles.
Shedding of Hepatitis C Virus in Semen of Human Immunodeficiency Virus-Infected Men
Authors: Turner Samuel S. , Gianella Sara , Yip Marcus J-S. , van Seggelen Wouter O. , Gillies Robert D. , Foster Andrew L. , Barbati Zachary R. , Smith Davey M. , Fierer Daniel S. 
Published: March 2016

AbstractBackground.  The epidemic of sexually transmitted hepatitis C virus (HCV) infection among human immunodeficiency virus (HIV)-infected men who have sex with men (MSM) has been documented for over a decade. Despite this, there is no consensus as to the risk factors for sexual acquisition of HCV in these men.Methods.  We obtained paired semen and blood samples at 2-week intervals from HIV-infected MSM with recent and chronic HCV infection and quantified HCV in semen.Results.  Hepatitis C virus was quantified in 59 semen specimens from 33 men. Hepatitis C virus was shed in 16 (27%) of semen specimens from 11 (33%) of the men. Median HCV viral load (VL) in semen was 1.49 log10 IU/mL. Hepatitis C virus VL in blood was significantly higher at the time of HCV shedding in semen than when HCV shedding in semen was not detected (P = .002). Furthermore, there was a significant correlation between the HCV VL in blood and semen overall (rs = 0.41; P = .001), and in the subgroup with recent HCV infection (rs = 0.37; P = .02), but not in the subgroup with chronic HCV infection (rs = 0.34; P = .1).Conclusions.  One third of HIV-infected MSM coinfected with HCV shed HCV into their semen. Based on the HCV VL in semen in this study, an average ejaculate would deliver up to 6630 IU of virus into the rectum of the receptive partner. Therefore, our data strongly support that condoms should be used during anal intercourse among MSM to prevent transmission of HCV.
Infectious Diseases (ID) Learning Unit: How Rapidly to Evaluate for Active Tuberculosis Disease in Low-Prevalence Settings
Authors: Chida Natasha , Shah Maunank 
Published: March 2016

Abstract
With declining tuberculosis (TB) incidence in low-prevalence settings, many clinicians are likely unaware that the approach to diagnosing active TB is evolving with newer technologies. Rapid molecular assays are commercially available, and more are likely to enter the market in the coming years. These tests, such as the Xpert MTB/RIF, which can detect TB and drug-resistance in 2 hours, are increasingly used in settings with higher TB prevalence; however, uptake has been slower in low-prevalence settings. Newer algorithms incorporating rapid TB diagnostics have the ability to alter current clinical and infection control practice patterns. In this learning unit, we review current and newly available tests for the detection of active TB disease and their usage in low-prevalence settings.
Combining multiple tools outperforms individual methods in gene set enrichment analyses
Authors: Alhamdoosh Monther , Ng Milica , Wilson Nicholas J. , Sheridan Julie M. , Huynh Huy , Wilson Michael J. , Ritchie Matthew E. 
Published: March 2016

AbstractGene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular data set. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions.Results:The ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. redEGSEA’s gene set database contains around 25,000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse data sets and, based on biologists' feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes.Availability and Implementation:EGSEA is available as an R package athttp://www.bioconductor.org/packages/EGSEA/. The gene sets collections are available in the R package EGSEAdata fromhttp://www.bioconductor.org/packages/EGSEA/.
Exploratory analysis and error modeling of a sequencing technology
Authors: Inouye Michael , Small Kerrin S. , Teo Yik Y. , Li Heng , Whiteford Nava , Skelly Tom , Abnizova Irina , Turner Daniel J. , Deloukas Panos , Kwiatkowski Dominic P. , Brown Clive G. , Clark Taane G. 
Published: March 2016

AbstractNext generation DNA sequencing methods have created an unprecedented leap in sequence data generation, thus novel computational tools and statistical models are required to optimize and assess the resulting data. In this report, we explore underlying causes of error for the Illumina Genome Analyzer (IGA) sequencing technology and attempt to quantify their effects using a human bacterial artificial chromosome sequenced to 60,000 fold coverage. Seven potential error predictors are considered:Phredscore, read entropy, tile coordinates, local tile density, base position within read, nucleotide call, and lane. With these parameters, logistic regression and log-linear models are constructed and used to show that each of the potential predictors contributes to error (P<1×10−4). With this additional information, we apply the logistic model and achieve a 3% improvement in both the sensitivity and specificity to detect IGA errors. Further, we demonstrate that these modeling approaches can be used as a feedback loop to inform laboratory methods and identify specific machine or run bias.
Metabolic adaptations in a range expanding arthropod
Authors: Van Petegem Katrien H. P. , Renault David , Stoks Robby , Bonte Dries 
Published: March 2016

SummaryDespite an increasing number of studies documenting life-history evolution during range expansions or shifts, we lack a mechanistic understanding of the underlying physiological processes. In this explorative study, we used a metabolomics approach to study physiological changes associated with the recent range expansion of the two-spotted spider mite (Tetranychus urticae). Mite populations were sampled along a latitudinal gradient from range core to edge and reared under benign common garden conditions for two generations. Using Gas Chromatography-Mass Spectrometry (GC-MS), we obtained metabolic population profiles, which showed a gradual differentiation along the latitudinal gradient, indicating (epi)genetic changes in the metabolome in association with range expansion. These changes seemed not related with shifts in the mites’ energetic metabolism, but rather with differential use of amino acids. Particularly, more dispersive northern populations showed lowered concentrations of several essential and non-essential amino acids, suggesting a potential downregulation of metabolic pathways associated with protein synthesis.