bluuebunny/crossref_metadata_2025_split huggingface dataset:
RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions
Authors: Whitford Whitney , Lehnert Klaus , Snell Russell G. , Jacobsen Jessie C. 
Published: November 2019

AbstractThe popularisation and decreased cost of genome resequencing has resulted in an increased use in molecular diagnostics. While there are a number of established and high quality bioinfomatic tools for identifying small genetic variants including single nucleotide variants and indels, currently there is no established standard for the detection of copy number variants (CNVs) from sequence data. The requirement for CNV detection from high throughput sequencing has resulted in the development of a large number of software packages. These tools typically utilise the sequence data characteristics: read depth, split reads, read pairs, and assembly-based techniques. However, the additional source of information from read balance (defined as relative proportion of reads of each allele at each position) has been underutilised in the existing applications. Here we present Read Balance Validator (RBV), a bioinformatic tool that uses read balance for prioritisation and validation of putative CNVs. The software simultaneously interrogates nominated regions for the presence of deletions or multiplications, and can differentiate larger CNVs from diploid regions. Additionally, the utility of RBV to test for inheritance of CNVs is demonstrated in this report. RBV is a CNV validation and prioritisation bioinformatic tool for both genome and exome sequencing available as a python package from https://github.com/whitneywhitford/RBV.
Unconventional secretion of α-Crystallin B requires the Autophagic pathway and is controlled by phosphorylation of its serine 59 residue
Authors: D’Agostino M. , Scerra G. , Cannata Serio M. , Caporaso M. G. , Bonatti S. , Renna M. 
Published: November 2019

Abstractα-Crystallin B (CRYAB or HspB5) is a chaperone member of the small heat-shock protein family that prevents aggregation of many cytosolic client proteins by means of its ATP-independent holdase activity. Surprisingly, several reports show that CRYAB exerts a protective role also extracellularly, and it has been recently demonstrated that CRYAB is secreted from human retinal pigment epithelial cells by an unconventional secretion pathway that involves multi-vesicular bodies. Here we show that autophagy is crucial for this unconventional secretion pathway and that phosphorylation at serine 59 residue regulates CRYAB secretion by inhibiting its recruitment to the autophagosomes. In addition, we found that autophagosomes containing CRYAB are not able to fuse with lysosomes. Therefore, CRYAB is capable to highjack and divert autophagosomes toward the exocytic pathway, inhibiting their canonical route leading to the lysosomal compartment. Potential implications of these findings in the context of disease-associated mutant proteins turn-over are discussed.
Non-Hermitian fractional quantum Hall states
Authors: Yoshida Tsuneya , Kudo Koji , Hatsugai Yasuhiro 
Published: November 2019

AbstractWe demonstrate the emergence of a topological ordered phase for non-Hermitian systems. Specifically, we elucidate that systems with non-Hermitian two-body interactions show a fractional quantum Hall (FQH) state. The non-Hermitian Hamiltonian is considered to be relevant to cold atoms with dissipation. We conclude the emergence of the non-Hermitian FQH state by the presence of the topological degeneracy and by the many-body Chern number for the ground state multiplet showing Ctot = 1. The robust topological degeneracy against non-Hermiticity arises from the manybody translational symmetry. Furthermore, we discover that the FQH state emerges without any repulsive interactions, which is attributed to a phenomenon reminiscent of the continuous quantum Zeno effect.
A polarization-independent blue phase liquid crystal on silicon with low operation voltage
Authors: Sun Changli , Lu Jiangang 
Published: November 2019

AbstractA polarization-independent blue phase liquid crystal on silicon (BPLCoS) device with low operation voltage for 2π phase depth is demonstrated. With optimized reflection structure and two reflection films, the incident light may experience multifold optical path and 2π phase depth can be obtained. For the polarization-independence, an inclined electric field made by periodical gradient voltage is applied on the blue phase liquid crystal (BPLC) to match the light propagation direction. With the structure, the operation voltage can be lowered to 5.5 V in simulation and 5.9 V in experiment for 2π phase modulation at 1550 nm. The proposed device shows great potential for communication and imaging systems.
Co-stimulation with IL-1β and TNF-α induces an inflammatory reactive astrocyte phenotype with neurosupportive characteristics in a human pluripotent stem cell model system
Authors: Hyvärinen Tanja , Hagman Sanna , Ristola Mervi , Sukki Lassi , Veijula Katariina , Kreutzer Joose , Kallio Pasi , Narkilahti Susanna 
Published: November 2019

AbstractAstrocyte reactivation has been discovered to be an important contributor to several neurological diseases. In vitro models involving human astrocytes have the potential to reveal disease-specific mechanisms of these cells and to advance research on neuropathological conditions. Here, we induced a reactive phenotype in human induced pluripotent stem cell (hiPSC)-derived astrocytes and studied the inflammatory natures and effects of these cells on human neurons. Astrocytes responded to interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) treatment with a typical transition to polygonal morphology and a shift to an inflammatory phenotype characterized by altered gene and protein expression profiles. Astrocyte-secreted factors did not exert neurotoxic effects, whereas they transiently promoted the functional activity of neurons. Importantly, we engineered a novel microfluidic platform designed for investigating interactions between neuronal axons and reactive astrocytes that also enables the implementation of a controlled inflammatory environment. In this platform, selective stimulation of astrocytes resulted in an inflammatory niche that sustained axonal growth, further suggesting that treatment induces a reactive astrocyte phenotype with neurosupportive characteristics. Our findings show that hiPSC-derived astrocytes are suitable for modeling astrogliosis, and the developed in vitro platform provides promising novel tools for studying neuron-astrocyte crosstalk and human brain disease in a dish.
Sucrose intake lowers μ-opioid and dopamine D2/3 receptor availability in porcine brain
Authors: Winterdahl Michael , Noer Ove , Orlowski Dariusz , Schacht Anna C. , Jakobsen Steen , Alstrup Aage K. O. , Gjedde Albert , Landau Anne M. 
Published: November 2019

AbstractExcessive sucrose consumption elicits addiction-like craving that may underpin the obesity epidemic. Opioids and dopamine mediate the rewarding effects of drugs of abuse, and of natural rewards from stimuli such as palatable food. We investigated the effects of sucrose using PET imaging with [11C]carfentanil (μ-opioid receptor agonist) and [11C]raclopride (dopamine D2/3 receptor antagonist) in seven female anesthetized Göttingen minipigs. We then gave minipigs access to sucrose solution for one hour on 12 consecutive days and performed imaging again 24 hours after the final sucrose access. In a smaller sample of five minipigs, we performed an additional [11C]carfentanil PET session after the first sucrose exposure. We calculated voxel-wise binding potentials (BPND) using the cerebellum as a region of non-displaceable binding, analyzed differences with statistical non-parametric mapping, and performed a regional analysis. After 12 days of sucrose access, BPND of both tracers had declined significantly in striatum, nucleus accumbens, thalamus, amygdala, cingulate cortex and prefrontal cortex, consistent with down-regulation of receptor densities. After a single exposure to sucrose, we found decreased binding of [11C]carfentanil in nucleus accumbens and cingulate cortex, consistent with opioid release. The lower availability of opioid and dopamine receptors may explain the addictive potential associated with intake of sucrose.
An Evaluation of the Results of the Steroid and Non-steroidal Anti-inflammatory Drug Treatments in Subacute Thyroiditis in relation to Persistent Hypothyroidism and Recurrence
Authors: Sencar Muhammed Erkam , Calapkulu Murat , Sakiz Davut , Hepsen Sema , Kus Arif , Akhanli Pinar , Unsal Ilknur Ozturk , Kizilgul Muhammed , Ucan Bekir , Ozbek Mustafa , Cakal Erman 
Published: November 2019

AbstractSubacute thyroiditis (SAT) is an inflammatory thyroid disease. The main purpose of the treatment is to relieve pain and control the inflammatory process. The aim of the present study was to evaluate the therapeutic effects of steroid and non-steroidal anti-inflammatory drugs (NSAIDs) in SAT. Initial laboratory data, treatment response, and long-term results of 295 SAT patients treated with ibuprofen or methylprednisolone were evaluated. After the exclusion of 78 patients, evaluation was made of 126 patients treated with 1800 mg ibuprofen and 91 patients treated with 48 mg methylprednisolone. In 59.5% of 126 patients treated with ibuprofen, there was no adequate clinical response at the first control visit. In 54% of patients, the treatment was changed to steroids in mean 9.5 days. Symptomatic remission was achieved within two weeks in all patients treated with methylprednisolone. The total recurrence rate was 19.8%, and recurrences were observed more frequently in patients receiving only steroid therapy than in patients treated with NSAID only (23% vs. 10.5% p:0.04). Persistent hypothyroidism developed in 22.8% of patients treated only with ibuprofen and in 6.6% of patients treated with methylprednisolone only. Treatment with only ibuprofen (p:0.039) and positive thyroid peroxidase antibody (anti-TPO) (p:0.029) were determined as the main risk factors for permanent hypothyroidism. NSAID treatment is not as effective as steroid treatment in early clinical remission. Steroid treatment was detected as a protective factor against permanent hypothyroidism. Therefore, steroid therapy may be considered especially in anti-TPO positive SAT patients and patients with high-level acute phase reactants.
Thermosensitive PBP2a requires extracellular folding factors PrsA and HtrA1 for Staphylococcus aureus MRSA β-lactam resistance
Authors: Roch Mélanie , Lelong Emmanuelle , Panasenko Olesya O. , Sierra Roberto , Renzoni Adriana , Kelley William L. 
Published: November 2019

AbstractStaphylococcus aureus is a major human pathogen and represents a clinical challenge because of widespread antibiotic resistance. Methicillin resistant Staphylococcus aureus (MRSA) is particularly problematic and originates by the horizontal acquisition of mecA encoding PBP2a, an extracellular membrane anchored transpeptidase, which confers resistance to β-lactam antibiotics by allosteric gating of its active site channel. Herein, we show that dual disruption of PrsA, a lipoprotein chaperone displaying anti-aggregation activity, together with HtrA1, a membrane anchored chaperone/serine protease, resulted in severe and synergistic attenuation of PBP2a folding that restores sensitivity to β-lactams such as oxacillin. Purified PBP2a has a pronounced unfolding transition initiating at physiological temperatures that leads to irreversible precipitation and complete loss of activity. The concordance of genetic and biochemical data highlights the necessity for extracellular protein folding factors governing MRSA β-lactam resistance. Targeting the PBP2a folding pathway represents a particularly attractive adjuvant strategy to combat antibiotic resistance.
Polarimetric imaging mode of VLT/SPHERE/IRDIS
Authors: van Holstein R. G. , Girard J. H. , de Boer J. , Snik F. , Milli J. , Stam D. M. , Ginski C. , Mouillet D. , Wahhaj Z. , Schmid H. M. , Keller C. U. , Langlois M. , Dohlen K. , Vigan A. , Pohl A. , Carbillet M. , Fantinel D. , Maurel D. , Origné A. , Petit C. , Ramos J. , Rigal F. , Sevin A. , Boccaletti A. , Le Coroller H. , Dominik C. , Henning T. , Lagadec E. , Ménard F. , Turatto M. , Udry S. , Chauvin G. , Feldt M. , Beuzit J.-L. 
Published: November 2019

Context. Circumstellar disks and self-luminous giant exoplanets or companion brown dwarfs can be characterized through direct-imaging polarimetry at near-infrared wavelengths. SPHERE/IRDIS at the Very Large Telescope has the capabilities to perform such measurements, but uncalibrated instrumental polarization effects limit the attainable polarimetric accuracy.
Aims. We aim to characterize and correct the instrumental polarization effects of the complete optical system, that is, the telescope and SPHERE/IRDIS.
Methods. We created a detailed Mueller matrix model in the broadband filters Y, J, H, and Ks and calibrated the model using measurements with SPHERE’s internal light source and observations of two unpolarized stars. We developed a data-reduction method that uses the model to correct for the instrumental polarization effects, and applied it to observations of the circumstellar disk of T Cha.
Results. The instrumental polarization is almost exclusively produced by the telescope and SPHERE’s first mirror and varies with telescope altitude angle. The crosstalk primarily originates from the image derotator (K-mirror). At some orientations, the derotator causes severe loss of signal (> 90% loss in the H- and Ks-band) and strongly offsets the angle of linear polarization. With our correction method we reach, in all filters, a total polarimetric accuracy of ≲0.1% in the degree of linear polarization and an accuracy of a few degrees in angle of linear polarization.
Conclusions. The correction method enables us to accurately measure the polarized intensity and angle of linear polarization of circumstellar disks, and is a vital tool for detecting spatially unresolved (inner) disks and measuring the polarization of substellar companions. We have incorporated the correction method in a highly-automated end-to-end data-reduction pipeline called IRDAP, which we made publicly available online.
Einfluss einer lokalen Insufflation von befeuchtetem und erwärmtem CO2 auf die Wundoberflächen- und Körperkerntemperatur sowie auf die Wundheilung in der offenen Kolorektalchirurgie
Authors: Kalev Georgi , Egglseder Thomas , Marquardt Christoph , Schiedeck Thomas 
Published: November 2019

Zusammenfassung
Hintergrund Eine perioperative Hypothermie kann die Ursache vieler schwerwiegender Komplikationen, insbesondere Wundinfektionen, darstellen. Diese Arbeit untersucht den Einfluss einer lokalen Insufflation von angewärmtem, angefeuchtetem Kohlendioxid (feucht-warm-CO2) während offener Kolorektalchirurgie auf die Körperkern- und Wundoberflächentemperatur sowie die Rate an Wundheilungsstörungen (WHS).
Methode Zwischen 02/2018 und 07/2019 wurden 50 Patienten zur offenen Resektion bei Kolon- oder Rektumkarzinom rekrutiert und in eine Kontroll- (n = 25) sowie in eine Experimentalgruppe (n = 25) randomisiert. In der Experimentalgruppe wurde eine Vorrichtung zur Insufflation von feucht-warm-CO2 in die Operationswunde verwendet. Erfasst wurden die Körperkern- sowie die Wundoberflächentemperatur. Das Serum-IL-6 wurde im Verlauf sequenziell bestimmt. Die klinische Beobachtung der Wundheilung reichte bis zum 30. postoperativen Tag.
Ergebnisse In der Kontrollgruppe lag die Körperkerntemperatur im Median (1. Quartil/3. Quartil) zu Beginn des Eingriffs bei 36,2 °C (36/36,4 °C) und am OP-Ende bei 36,2 °C (35,9/36,45 °C), während sie in der Experimentalgruppe initial bei 36,2 °C (35,7/36,4 °C) und am OP-Ende bei 36,4 °C (36/36,7 °C) lag. Hier ergab sich kein statistisch signifikanter Unterschied (p = 0,08). Die mittlere Wundoberflächentemperatur sank in der Kontrollgruppe von 32,8 °C (Median; 31,85/34,05 °C) auf 30,7 °C (Median; 29,85/32,15 °C) ab. In der Experimentalgruppe war ein Rückgang von 31,9 °C (Median; 30,25/32,95 °C) auf 31,6 °C (Median; 30,25/31,85 °C) zu verzeichnen. Dies bedeutet einen statistisch signifikanten Unterschied (p = 0,000475). Die Dynamik des Serum-IL-6 ergab keinen signifikanten Unterschied (p = 0,66; p = 0,88; p = 0,88). In der Kontrollgruppe traten bei 8 Patienten eine oberflächliche WHS sowie 2 Anastomoseninsuffizienzen (AI) auf, während in der Experimentalgruppe 5-mal eine WHS sowie eine AI beobachtet wurde. Die Unterschiede waren für alle WHS nicht signifikant (p = 0,42).
Schlussfolgerung Die bereits etablierten Maßnahmen zur Vorbeugung der perioperativen Hypothermie bei elektiven Eingriffen können als ausreichend erachtet werden. Die lokale Wundoberflächentemperatur bleibt dabei allerdings unbeeinflusst. Die Verwendung von intraoperativer Gasinsufflation mit feucht-warm-CO2 kann zur Aufrechterhaltung der lokalen Normothermie beitragen. Größere Studien sollten die Frage nach einer signifikanten Wirkung dieses Verfahrens auf die postoperative Wundheilung beantworten.
Postoperative Venous Thromboembolism after Neurotologic Surgery
Authors: Ali Noor-E-Seher , Alyono Jennifer C. , Song Yohan , Kouhi Ali , Blevins Nikolas H. 
Published: November 2019

Abstract
Objective This study aimed to determine the incidence of postoperative venous thromboembolism (VTE) in adults undergoing neurotologic surgery at a single center.
Methods The records of adults undergoing neurotologic surgery from August 2009 to December 2016 at a tertiary care hospital were reviewed for VTE within 30 postoperative days. Particular attention was focused on postoperative diagnosis codes, imaging, and a keyword search of postoperative notes. Caprini risk scores were calculated.
Results Among 387 patients, 5 experienced postoperative VTE including 3 cases of pulmonary embolism (PE) and 2 cases of isolated deep vein thrombosis (DVT). All patients were given sequential compression devices perioperatively, and none received preoperative chemoprophylaxis. Patients with Caprini score > 8 had a significantly higher rate of VTE compared with those < 8 (12.5 vs. 1%, p = 0.004). Receiver operating characteristic analysis revealed the Caprini risk assessment model to be a fair predictor of VTE, with a C-statistic of 0.70 (95% confidence interval [CI]: 0.49–0.92).
Conclusion While no specific validated VTE risk stratification scheme has been widely accepted for patients undergoing neurotologic surgery, the Caprini score appears to be a useful predictor of risk. The benefits of chemoprophylaxis should be balanced with the risks of intraoperative bleeding, as well as the potential for postoperative intracranial hemorrhage.
On the partial productivity of constructions
Authors: Tian Zhen 
Published: November 2019

The productive schema of a grammatical construction allows speakers to produce creative utterances. However, the fact that constructions tend to be partially but not fully productive has puzzled scholars for decades. This chapter analyzes the partial productivity of a highly productive construction – the Chinese zhe Existential Construction, in particular the collostructional strength (Stefanowitsch and Gries 2003) between verbs and this construction. Findings suggest that there is a blending of scenes in the use of transitive verbs in this construction and the semantic constraints limiting new instances lie in the relative salience of the following participant roles in verb semantics – theme, patient and location. Verbs with the profiled role of agent or experiencer are not compatible with this construction.
Cheater, cheater, pumpkin eater: the Dark Triad, attitudes towards doping, and cheating behaviour among athletes
Authors: Nicholls Adam R. , Madigan Daniel J. , Duncan Lindsay , Hallward Laura , Lazuras Lambros , Bingham Kevin , Fairs Lucas R. W. 
Published: November 2019

ABSTRACTWe examined the relationships between the Dark Triad personality traits (Machiavellianism, narcissism, and psychopathy), attitudes towards doping, and cheating behaviour among athletes. One‐hundred and sixty‐four athletes completed a completed a matrix solving task within a specific time limit. Participants were told they would receive a financial reward for the total number matrices they could solve, but only 13 of the 20 matrices were solvable. This provided the incentive and opportunity for the athletes to cheat. Following this, athletes completed two questionnaires, which assessed the Dark Triad and their attitudes towards doping. All three Dark Triad personality traits correlated positively with attitudes towards doping and cheating behaviour. Regression analyses revealed that psychopathy and narcissism positively predicted attitudes towards doping, and narcissism emerged as a positive predictor of cheating behaviour. Attitudes towards doping correlated positively with cheating behaviour. The Dark Triad appears to be important in relation to both attitudes towards doping and cheating behaviour among athletes. In addition, our findings illustrate that favourable attitudes towards doping are linked with actual cheating among athletes. National Anti‐Doping Organizations, sports federations, and coaches could assess athletes’ Dark Triad scores and attitudes towards doping in order to identify who may be more likely to cheat.
Recent advances in flexible photodetectors based on 1D nanostructures
Authors: Yip Senpo , Shen Lifan , Ho Johnny C 
Published: November 2019

Abstract
Semiconductor nanowires have demonstrated excellent electronic and optoelectronic properties. When integrated into photodetectors, excellent device performance can be easily attained. Apart from the exceptional performance, these nanowires can also enable robust and mechanically flexible photodetectors for various advanced utilizations that the rigid counterparts cannot perform. These unique applications include personal healthcare, next-generation robotics and many others. In this review, we would first discuss the nanowire fabrication techniques as well as the assembly methods of constructing large-scale nanowire arrays. Then, the recent development of flexible photodetectors based on these different nanowire material systems is evaluated in detail. At the same time, we also introduce some recent advancement that allows individual photodetectors to integrate into a more complex system for advanced deployment. Finally, a short conclusion and outlook of challenges faced in the future of the community is presented.
Diagnosis of physics learning difficulties of X MIA grade students of SMA Negeri 3 Pinrang
Authors: Yusuf M , Ali M S , Yani A 
Published: November 2019

Abstract
This research is a descriptive quantitative research which aims to determine the level of physics learning difficulties of students and factor causing of physics learning difficulties of X MIA grade students of SMA Negeri 3 Pinrang. Subject in this research is X MIA grade students of SMA Negeri 3 Pinrang of Academic Year 2017/2018 which amounted to 204 students. The level data of physics learning difficulty of students is obtained from diagnostic test result of students. The factors data that causing students have learning difficulty of physics, obtained from semi-open questionnaire sheet filled by students and it’s continued by semi structured interview. Based on the results of data analysis, level of physics learning difficulties on material of newton’s law was in the very high category with an average score of diagnostic test of students in the amount of 9,59. The difficulties experienced by students in solving diagnostic tests consist of: linguistic knowledge with percentage of difficulty level is 52,81% at the high category, schematic knowledge with percentage of difficulty level of 87,59% at the very high category, and algorithmic knowledge with percentage of difficulty level of 93,09% at the very high category. Difficulties experienced of students are caused by factor of health, intelligence, community environment, study habits, and study time.