bluuebunny/crossref_metadata_2025_split huggingface dataset:
head-bent resistant Hsc70 variants show reduced Hsp40 affinity and altered protein folding activity
Authors: Papsdorf Katharina , Sima Siyuan , Schmauder Lukas , Peter Sebastian , Renner Lisa , Hoffelner Patrica , Richter Klaus 
Published: August 2019

AbstractThe molecular chaperone Hsc70 performs essential tasks by folding proteins. Hsc70 is driven by the hydrolysis of ATP and tuned by the association with various co-chaperones. One such cofactor is the nematode nucleotide exchange factor UNC-23, whose mutation disrupts muscle attachment and induces a severe head-bent phenotype in C.elegans. Interestingly, four mutations in Hsc70 can suppress this phenotype, but the molecular mechanism underlying this suppression is unknown. Here we characterize these four suppressor variants, Hsc70 D233N, S321F, A379V and D384N. In vitro only Hsc70 S321F shows reduced stability and altered nucleotide interaction, but all mutations affect the ATPase stimulation. In particular, Hsc70 D233N and Hsc70 A379V show strongly reduced interactions with DNJ-12 and DNJ-13. Nucleotide exchange factor binding instead is barely influenced in Hsc70 D233N, A379V and D384N and their chaperone activity is preserved. Molecular dynamics simulations suggest that effects in Hsc70 S321F and Hsc70 A379V originate from steric clashes in the vicinity of the mutation site, while D233N disrupts a salt bridge that contributes to Hsc70’s nucleotide-induced conformational changes. In summary, the analyzed mutants show altered ATPase and refolding activity caused by changes in Hsp40 binding.
A linear mixed model approach to gene expression-tumor aneuploidy association studies
Authors: Yao Douglas W. , Balanis Nikolas G. , Eskin Eleazar , Graeber Thomas G. 
Published: August 2019

AbstractAneuploidy, defined as abnormal chromosome number or somatic DNA copy number, is a characteristic of many aggressive tumors and is thought to drive tumorigenesis. Gene expression-aneuploidy association studies have previously been conducted to explore cellular mechanisms associated with aneuploidy. However, in an observational setting, gene expression is influenced by many factors that can act as confounders between gene expression and aneuploidy, leading to spurious correlations between the two variables. These factors include known confounders such as sample purity or batch effect, as well as gene co-regulation which induces correlations between the expression of causal genes and non-causal genes. We use a linear mixed-effects model (LMM) to account for confounding effects of tumor purity and gene co-regulation on gene expression-aneuploidy associations. When applied to patient tumor data across diverse tumor types, we observe that the LMM both accounts for the impact of purity on aneuploidy measurements and identifies a new association between histone gene expression and aneuploidy.
Modelling of the tsunami from the December 22, 2018 lateral collapse of Anak Krakatau volcano in the Sunda Straits, Indonesia
Authors: Grilli Stephan T. , Tappin David R. , Carey Steven , Watt Sebastian F. L. , Ward Steve N. , Grilli Annette R. , Engwell Samantha L. , Zhang Cheng , Kirby James T. , Schambach Lauren , Muin Muslim 
Published: August 2019

AbstractOn Dec. 22, 2018, at approximately 20:55–57 local time, Anak Krakatau volcano, located in the Sunda Straits of Indonesia, experienced a major lateral collapse during a period of eruptive activity that began in June. The collapse discharged volcaniclastic material into the 250 m deep caldera southwest of the volcano, which generated a tsunami with runups of up to 13 m on the adjacent coasts of Sumatra and Java. The tsunami caused at least 437 fatalities, the greatest number from a volcanically-induced tsunami since the catastrophic explosive eruption of Krakatau in 1883 and the sector collapse of Ritter Island in 1888. For the first time in over 100 years, the 2018 Anak Krakatau event provides an opportunity to study a major volcanically-generated tsunami that caused widespread loss of life and significant damage. Here, we present numerical simulations of the tsunami, with state-of the-art numerical models, based on a combined landslide-source and bathymetric dataset. We constrain the geometry and magnitude of the landslide source through analyses of pre- and post-event satellite images and aerial photography, which demonstrate that the primary landslide scar bisected the Anak Krakatau volcano, cutting behind the central vent and removing 50% of its subaerial extent. Estimated submarine collapse geometries result in a primary landslide volume range of 0.22–0.30 km3, which is used to initialize a tsunami generation and propagation model with two different landslide rheologies (granular and fluid). Observations of a single tsunami, with no subsequent waves, are consistent with our interpretation of landslide failure in a rapid, single phase of movement rather than a more piecemeal process, generating a tsunami which reached nearby coastlines within ~30 minutes. Both modelled rheologies successfully reproduce observed tsunami characteristics from post-event field survey results, tide gauge records, and eyewitness reports, suggesting our estimated landslide volume range is appropriate. This event highlights the significant hazard posed by relatively small-scale lateral volcanic collapses, which can occur en-masse, without any precursory signals, and are an efficient and unpredictable tsunami source. Our successful simulations demonstrate that current numerical models can accurately forecast tsunami hazards from these events. In cases such as Anak Krakatau’s, the absence of precursory warning signals together with the short travel time following tsunami initiation present a major challenge for mitigating tsunami coastal impact.
Pathophysiologic Characterization of a Novel Rabbit Model of Biliary Tract Infection-Derived Sepsis
Authors: Hu Liangshuo , Chai Yichao , Xi Rui , Zhu Haoyang , Wang Yue , Ren Fenggang , Zhang Jing , Xue Zhao , Zhang Hongke , Wu Rongqian , Lv Yi 
Published: August 2019

AbstractBiliary tract infection (BTI)-derived sepsis remains a serious problem with significant morbidity and mortality in the modern era of critical care management. Current animal models of BTI have relied mostly on injecting purified bacteria or their toxins into the biliary tract. These models do not fully reflect pathophysiology or disease processes of clinical cholangitis or cholecystitis. In the current study, we developed a novel model of BTI by performing cholecystocolonic anastomosis (CCA) in rabbits and characterized pathophysiologic changes in this model. This model is intended to mimic the clinical process of cholecystocolonic fistula with reflux cholangitis, a severe form of BTI. Adult male rabbits were subjected to BTI-derived sepsis through an anastomosis of the gall bladder to the colon (i.e., CCA). The animals were monitored for 7 days to record survival. In additional groups of animals, various bacterial, hemodynamic, histological and biochemical parameters were measured at 12, 24, 48 and 72 h after CCA. The anastomosis between the gallbladder and the colon required about 5–8 min to finish. The median survival time for rabbits after CCA was 96 h. The positive rates of bacterial culture at 72 h after CCA were 83.3% and 100% in the blood and liver, respectively. The most common microorganism was Escherichia coli followed by Enterococcus. Plasma Tumor Necrosis Factor-α (TNF-α), Lnterleukin-10 (IL-10), Lnterleukin-6 (IL-6), and High-mobility group box 1 protein (HMGB-1) levels were greatly elevated after CCA. The cardiac index and heart rate increased slightly at 12 h after CCA and then continued to decrease. Systemic hypotension developed 48 h after CCA. Histological studies showed reflux cholangitis with acute lung and kidney injury. Cholecystocolonic anastomosis produces polymicrobial sepsis in rabbits, which mimics many aspects of human BTI-derived sepsis. It is reproducible and easy to perform and may serve as an excellent model for future sepsis research.
Possible epigenetic regulatory effect of dysregulated circular RNAs in Alzheimer’s disease model
Authors: Lee Woo-Jin , Moon Jangsup , Jeon Daejong , Shin Yong-Won , Yoo Jung-Suk , Park Dong-Kyu , Lee Soon-Tae , Jung Keun-Hwa , Park Kyung-Il , Jung Ki-Young , Kim Manho , Lee Sang Kun , Chu Kon 
Published: August 2019

AbstractAs circular RNAs (circRNAs) regulates the effect of micro RNAs (miRNAs), circRNA–miRNA-mRNA network might be implicated in various disease pathogenesis. Therefore, we evaluated the dysregulated circRNAs in the Tg2576 mouse Alzheimer’s disease (AD) model, their possible regulatory effects on downstream target mRNAs, and their pathomechanistic role during the disease progression. The microarray-based circRNA expression analysis at seven- and twelve-months of ages (7 M and 12 M) returned 101 dysregulated circRNAs at 7 M (55 up-regulated and 46 down-regulated) and twelve dysregulated circRNAs at 12 M (five up-regulated and seven down-regulated). For each dysregulated circRNA, potential target miRNAs and their downstream target mRNAs were searched. Dysregulation of circRNAs was associated with increased frequency of relevant dysregulation of their downstream target mRNAs. Those differentially expressed circRNA–miRNA-mRNA regulatory network included 2,275 networks (876 for up-regulated circRNAs and 1,399 for down-regulated circRNAs) at 7 M and 38 networks (25 for up-regulated circRNAs and 13 for down-regulated circRNAs) at 12 M. Gene ontology (GO) and pathway analyses demonstrated that the dysregulated mRNAs in those networks represent the AD pathomechanism at each disease stage. We concluded that the dysregulated circRNAs might involve in the AD pathogenesis by modulating disease relevant mRNAs via circRNA–miRNA-mRNA regulatory networks.
Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean
Authors: Yu Anmin , Li Fei , Xu Wei , Wang Zaiqing , Sun Chao , Han Bing , Wang Yue , Wang Bo , Cheng Xiaomao , Liu Aizhong 
Published: August 2019

AbstractCastor bean (Ricinus communisL., Euphorbiaceae) is a critical biodiesel crop and its seed derivatives have important industrial applications. Due to lack of a high-density genetic map, the breeding and genetic improvement of castor bean has been largely restricted. In this study, based on a recombinant inbred line (RIL) population consisting of 200 individuals, we generated 8,896 high-quality genomic SNP markers and constructed a high-resolution genetic map with 10 linkage groups (LGs), spanning 1,852.33 centiMorgan (cM). Based on the genetic map, 996 scaffolds from the draft reference genome were anchored onto 10 pseudo-chromosomes, covering 84.43% of the castor bean genome. Furthermore, the quality of the pseudo-chromosome scale assembly genome was confirmed via genome collinearity analysis within the castor bean genome as well as between castor bean and cassava. Our results provide new evidence that the phylogenetic position of castor bean is relatively solitary from other taxa in the Euphorbiaceae family. Based on the genetic map, we identified 16 QTLs that control seed size and weight (covering 851 candidate genes). The findings will be helpful for further research into potential new mechanisms controlling seed size and weight in castor bean. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits, as well as the accelerated molecular breeding of castor bean in a cost-effective pattern.
Doping of ZnO inorganic-organic nanohybrids with metal elements
Authors: Zhang Y. , Apostoluk A. , Theron C. , Cornier T. , Canut B. , Daniele S. , Masenelli B. 
Published: August 2019

AbstractWe present a general and in-depth study of the effect of dopants in hybrid inorganic/organic ZnO/PAA (polyacrylic acid) nanocomposites. These dopants vary as much by their ionic size, as by their electronic valence and some of them have been used in ZnO due to their known magnetic and/or optical properties. The chemical nature of the dopants controls their ability to incorporate into ZnO crystal lattice. Three concentrations (0.1%, 1% and 5%) of dopants were studied in order to compare the effect of the concentration with the results obtained previously in the literature. Our results confirm in the first place the trend observed in the literature, that increase in dopant concentration leads to quenching of visible luminescence for ZnO nanocrystals obtained by very different processes. However, the degradation of photoluminescence quantum yield (PL QY) is not inevitable in our nanocomposites. At low doping concentration for some dopants with a small or comparable ionic radius than Zn2+, PL QY can be maintained or even improved, making it possible to tune the visible emission spectrum between 2.17 eV and 2.46 eV. This opens up the prospect of synthesizing phosphors without rare earth for white LEDs, whose spectrum can be tuned to render warm or cold white light, by a chemical synthesis process with a low environmental impact.
A neutrophil-centric view of chemotaxis
Authors: Michael Melina , Vermeren Sonja 
Published: August 2019

Abstract
Neutrophils are key players of the innate immune system, that are involved in coordinating the initiation, propagation and resolution of inflammation. Accurate neutrophil migration (chemotaxis) to sites of inflammation in response to gradients of chemoattractants is pivotal to these roles. Binding of chemoattractants to dedicated G-protein-coupled receptors (GPCRs) initiates downstream signalling events that promote neutrophil polarisation, a prerequisite for directional migration. We provide a brief summary of some of the recent insights into signalling events and feedback loops that serve to initiate and maintain neutrophil polarisation. This is followed by a discussion of recent developments in the understanding of in vivo neutrophil chemotaxis, a process that is frequently referred to as ‘recruitment’ or ‘trafficking’. Here, we summarise neutrophil mobilisation from and homing to the bone marrow, and briefly discuss the role of glucosaminoglycan-immobilised chemoattractants and their corresponding receptors in the regulation of neutrophil extravasation and neutrophil swarming. We furthermore touch on some of the most recent insights into the roles of atypical chemokine receptors (ACKRs) in neutrophil recruitment, and discuss neutrophil reverse (transendothelial) migration together with potential function(s) in the dissemination and/or resolution of inflammation.
Reading Outcomes for Individuals With Histories of Suspected Childhood Apraxia of Speech
Authors: Miller Gabrielle J. , Lewis Barbara , Benchek Penelope , Freebairn Lisa , Tag Jessica , Budge Karlie , Iyengar Sudha K. , Voss-Hoynes Heather , Taylor H. Gerry , Stein Catherine 
Published: August 2019

Purpose
The primary aims of this study were to examine the speech-language correlates of decoding difficulties in children with histories of suspected childhood apraxia of speech (sCAS) and to identify predictors of low-proficiency reading levels.

Method

Participants were school-age children and adolescents, 7–18 years of age, diagnosed with sCAS (
n
= 40) or speech sound disorder but no sCAS (SSD-no sCAS;
n
= 119). The sCAS and SSD-no sCAS reading groups were compared on measures of performance IQ, oral language, phonological awareness, rapid automatic naming, diadochokinetic rates, single word articulation, and multisyllable and nonsense word repetition. Logistic regression analyses were employed to identify predictors of low-proficiency reading in the sCAS and SSD-no sCAS groups.

Results
Sixty-five percent of the participants with sCAS compared to 24% of those with SSD-no sCAS were classified as low-proficiency readers based on nonsense and single word decoding. Analysis failed to reveal significant differences in reading, oral language, or phonological awareness between low-proficiency readers with sCAS and low-proficiency readers with SSD-no sCAS. Oral language and phonological awareness skills were the best predictors of reading level for all participants, followed by performance on multisyllabic word repetition and diadochokinetic rate.

Conclusions
The language and phonological awareness deficits of children with sCAS are related to their risks for reading failure. To a lesser degree, motor speech deficits and speech sound production also increase risks for reading difficulties. The findings justify early intervention for this subset of children.
A Retrospective Study of Long-Term Improvement on the Boston Naming Test
Authors: Sachs Alyssa , Rising Kindle , Beeson Pélagie M. 
Published: August 2019

Purpose

Lexical retrieval impairment is a universal characteristic of aphasia and a common treatment focus. Although naming improvement is well documented, there is limited information to shape expectations regarding long-term recovery. This was the motivation for a retrospective study of longitudinal data on the Boston Naming Test (BNT;
Kaplan, Goodglass, & Weintraub, 1983
,
2000
).

Method
BNT scores were analyzed from a heterogeneous cohort of 42 individuals with anomia associated with a range of aphasia types. The data were collected over the course of 20 years from individuals who had participated in treatment and received at least 2 BNT administrations. A linear mixed model was implemented to evaluate effects of initial BNT score, time postonset, and demographic variables. For those over 55 years of age, BNT change was evaluated relative to data from the Mayo Clinic's Older Americans Normative Studies.

Results
There was a significant average improvement of +7.67 points on the BNT in individuals followed for an average of 2 years. Overall, the average rate of improvement was +5.84 points per year, in contrast to a decline of 0.23 points per year in a healthy adult cohort from the Mayo Clinic's Older Americans Normative Studies. Naming recovery was approximately linear, with significant main effects of initial BNT score (i.e., initial severity) and time postonset; the greatest changes were noted in those whose initial severity was moderate.

Conclusions
These findings indicate a positive prognosis for naming improvement over time regardless of demographic factors and provide estimates for clinical predictions for those who seek rehabilitation during the chronic phase.
Fault resilient multi‐terminal high voltage direct current systems using distributed corrective power dispatch
Authors: Mojallal Aslan , Lotfifard Saeed , Azimi Seyed Mohammad 
Published: August 2019

A distributed secondary layer control scheme for multi‐terminal high voltage direct current (MTDC) transmission systems is proposed. The proposed control scheme is achieved via solving a multi‐objective optimization problem. The objectives are defined such that: (i) the power losses of the system are minimized and (ii) the resiliency of the system in facing large disturbances and faults is enhanced. The second objective prevents the constant power converters to change their intended operating mode to avoid over‐voltages. Hence, the proposed scheme enhances the power commitment of such buses despite the occurrence of faults and large disturbances in the system. The proposed secondary controller is implemented in a distributed architecture using optimality condition decomposition. By employing the distributed scheme, the computational burden of the secondary level control is decreased and the autonomy of each zone in the MTDC grid is increased. The CIGRE B4 MTDC test system is employed to demonstrate the effectiveness of the proposed method. PSCAD and MATLAB are used to perform the simulations for the case studies. The simulation results verify that the proposed method enhances the resiliency of the MTDC systems by avoiding undesirable change of operations mode of constant power converters while decreasing losses of the system.
Kernel-phase detection limits
Authors: Ceau A. , Mary D. , Greenbaum A. , Martinache F. , Sivaramakrishnan A. , Laugier R. , N’Diaye M. 
Published: August 2019

Context. The James Webb Space Telescope (JWST) will offer high angular resolution observing capability in the near-infrared with masking interferometry on the Near-Infrared Imager and Slitless Spectrograph (NIRISS), and coronagraphic imaging on the Near-Infrared Camera (NIRCam) and the Mid-Infrared Instrument (MIRI). Full-aperture kernel-phase-based interferometry complements these observing modes by allowing us to probe for companions at small angular resolution while preserving the telescope throughput.
Aims. Our goal is to derive both theoretical and operational contrast-detection limits for the kernel-phase analysis of JWST NIRISS full-pupil observations using tools from hypothesis testing theory. The study is immediately applied to observations of faint brown dwarfs with this instrument, but the tools and methods introduced here are applicable in a wide variety of contexts.
Methods. We construct a statistically independent set of observable quantities from a collection of aberration-robust kernel phases. Three detection tests based on these observable quantities are designed and analysed, all having the property of guaranteeing a constant false-alarm rate for phase aberrations smaller than about one radian. One of these tests, the likelihood ratio or Neyman-Pearson test, provides a theoretical performance bound for any detection test.
Results. The operational detection method considered here is shown to exhibit only marginal power loss with respect to the theoretical bound. In principle, for the test set to a false-alarm probability of 1%, companions at contrasts reaching 103 and separations of 200 mas around objects of magnitude 14.1 are detectable with a probability of 68%. For the brightest objects observable using the full pupil of JWST and NIRISS, contrasts of up to 104 at separations of 200 mas could ultimately be achieved, barring significant wavefront drift. We also provide a statistical analysis of the uncertainties affecting the contrasts and separations that are estimated for the detected companions.
Conclusions. The proposed detection method is close to the ultimate bound and offers guarantees on the probability of making a false detection for binaries, as well as on the error bars for the estimated parameters of the binaries that will be detected by JWST NIRISS. This method is not only applicable to JWST NIRISS but to any imaging system with adequate sampling.
Update Allergologie im Kindesalter
Authors: Wagner Nicola , Sticherling Michael 
Published: August 2019

ZusammenfassungAllergologische Erkrankungen im Kindesalter manifestieren sich mit diversen Symptomen. Das zunehmend breitere Spektrum verfügbarer spezifischer IgE auf rekombinante Allergene verbessert die Diagnostik und die Beurteilung ätiologischer Zusammenhänge einer allergologischen Symptomatik. Nahrungsmittelassoziierte Allergien und Intoleranzen nehmen zu und erfordern, insbesondere im Kindesalter, eine rasche Aufklärung des auslösenden Allergens. Die Empfehlungen zur allergologischen Diagnostik bei Arzneimittelallergie-/unverträglichkeit stehen als deutsche SK2-Leitlinie zur Verfügung. Ekzematöse Hautveränderungen können neben Atopie-assoziierten Ekzemreaktionen auch auf Kontaktallergien zurückzuführen sein, weshalb auch neue Kontaktallergene, wie Isobornylacrylat, in kontinuierlich messenden Glukosesensoren, differenzialdiagnostisch bedacht werden sollten.