bluuebunny/crossref_metadata_2025_split huggingface dataset:
Daily mitochondrial dynamics in cone photoreceptors
Authors: Giarmarco Michelle M. , Brock Daniel C. , Robbings Brian M. , Cleghorn Whitney M. , Tsantilas Kristine A. , Kuch Kellie C. , Ge William , Rutter Kaitlyn M. , Parker Edward D. , Hurley James B. , Brockerhoff Susan E. 
Published: November 2020

Significance
Mitochondria are organelles that make cellular energy. In the retina, mitochondrial health is important for photoreceptor cell function and normal vision. Photoreceptors need more energy at night, but it is unclear how their mitochondria adapt to changing energy demands. We investigated zebrafish cone photoreceptor mitochondria throughout the day. At night cone mitochondria are smaller, more numerous, and more metabolically active. Material from mitochondria is also released from photoreceptors during nighttime, forming stalks and networks outside of the cell. In daytime, photoreceptor mitochondria associate with ER and autophagosomes, organelles that mediate mitochondrial turnover. These daily changes to mitochondrial structure may help photoreceptors adapt to metabolic demands of daytime and nighttime.
TREE1-EIN3–mediated transcriptional repression inhibits shoot growth in response to ethylene
Authors: Wang Likai , Ko Eun Esther , Tran Jaclyn , Qiao Hong 
Published: November 2020

Significance
Ethylene is an important plant hormone that is essential for many physiological and developmental processes such as apical hook formation, shoot and root growth, root nodulation, flower senescence, abscission, and fruit ripening. Transcriptional activation in the ethylene response has been well studied. However, the transcriptional repression in the ethylene response remains unclear. Here, by combined approaches of data analysis, molecular biology, and genetics, we found that a transcriptional repressor TREE1 interacts with EIN3 to regulate transcriptional repression, leading to an inhibition of shoot growth in response to ethylene. Our work provides insight into how the transcriptional activator can be tuned to repress downstream gene expression in hormone signals.
Resonant Raman scattering of core–shell GaN/AlN nanowires
Authors: Cros A , Cristóbal A García , Hestroffer K , Daudin B , Wang J , Demangeot F , Péchou R 
Published: November 2020

Abstract
We have analyzed the electron–phonon coupling in GaN/AlN core–shell nanowires by means of Raman scattering excited at various wavelengths in the ultraviolet spectral range (335, 325 and 300 nm) and as a function of the AlN shell thickness. The detailed analysis of the multi-phonon spectra evidences important differences with excitation energy. Under 325 and 300 nm excitation the Raman process is mediated by the allowed A
1(LO) phonon mode, where the atoms vibrate along the NW axis. Considering its selection rules, this mode is easily accessible in backscattering along the wurtzite c axis. Interestingly, for 335 nm excitation the scattering process is instead mediated by the E
1(LO) phonon mode, where atoms vibrate in the c-plane and that is forbidden in this configuration. This change is ascribed to the band anticrossing caused by the uniaxial strain imposed by the AlN shell and the proximity, at this particular excitation energy, of real electronic transitions separated by the energy of the longitudinal optical phonon modes. The energy and character of the electronic bands can be tuned by varying the AlN shell thickness, a degree of freedom unique to core–shell nanowires. The interpretation of the experimental results is supported by calculations of the electronic transitions of GaN under uniaxial strain performed within the framework of a k · p model.
Enhanced higher temperature irreversibility field and critical current density in MgB2 wires with Dy2O3 additions
Authors: Yang Y , Sumption M D , Rindfleisch M , Tomsic M , Collings E W 
Published: November 2020

Abstract
Bulk samples of magnesium diboride (MgB2) doped with 0.5 wt% of the rare earth oxides (REOs) Nd2O3 and Dy2O3 (named B-ND and B-DY) prepared by standard powder processing, and wires of MgB2 doped with 0.5 wt% Dy2O3 (named W-DY) prepared by a commercial powder-in-tube processing were studied. Investigations included x-ray diffractometry, scanning- and transmission electron microscopy, magnetic measurement of superconducting transition temperature (T
c), magnetic and resistive measurements of upper critical field (B
c2) and irreversibility field (B
irr), as well as magnetic and transport measurements of critical current densities versus applied field (J
cm(B) and J
c(B), respectively). It was found that although the products of REO doping did not substitute into the MgB2 lattice, REO-based inclusions resided within grains and at grain boundaries. Curves of bulk pinning force density (F
p) versus reduced field (b = B/B
irr) showed that flux pinning was by predominantly by grain boundaries, not point defects. At all temperatures the F
p(b) of W-DY experienced enhancement by inclusion-induced grain boundary refinement but at higher temperatures F
p(b) was still further increased by a Dy2O3 additive-induced increase in B
irr of about 1 T at all temperatures up to 20 K (and beyond). It is noted that Dy2O3 increases B
irr and that it does so, not just at 4 K, but in the higher temperature regime. This important property, shared by a number of REOs and other oxides promises to extend the applications range of MgB2 conductors.
Stability of DC transport in HTS conductor with local critical current reduction
Authors: Gömöry Fedor , Šouc Ján 
Published: November 2020

Abstract
A common feature of commercially available conductors based on high-temperature superconducting compounds is the fluctuation of critical current along the length. Fortunately, the practice adopted by manufacturers nowadays is to supply the detailed I
c(x) data with the conductor. Compared to knowing just the average of critical current, this should also allow a much better prediction of the conductor performance. Statistical methods are suitable for this purpose in the case when the fluctuations are regular at the low end of critical current distribution. However, a different approach is necessary at the presence of ‘weak spots’ that drop out of any statistics. Because of the strong nonlinearity of the current–voltage curve, such a location could transform into a ‘hot spot’ at transporting direct current (DC), with an abrupt increase of temperature endangering the conductor operation. We present a set of analytical formulas including the prediction of the maximum DC that could be carried sustainably before the thermal runaway appears. It is necessary to know the cooling conditions as well as the properties of the conductor constituents and their architecture. A formula for the voltage appearing on a weak spot, and its dependence on the DC, is also proposed. For this purpose the result of previous theoretical work has been slightly modified after comparing it with numerical iterative computations and finite element modeling. We demonstrate that the derived model allows a powerful analysis of experimental data comprising an estimation of the weak spot parameters i.e. its critical current and the length of the defect zone.
Cognitive Fatigue Predicts Cognitive Failure in Multiple Sclerosis Patients and Healthy Controls: A Case-Control Study
Authors: Spiegelberg Nora , Breuer Svenja , Nielsen Jörn , Saliger Jochen , Montag Christian , Karbe Hans , Markett Sebastian 
Published: November 2020

AbstractObjectiveFatigue and cognitive deficits are frequent symptoms of multiple sclerosis (MS). However, the exact nature of their co-occurrence is not fully understood. We sought to determine the impact of cognitive and physical fatigue on subjective cognitive deficits in MS patients and healthy controls.MethodsSelf-reports of fatigue (FSMC), depression (CES-D), cognitive deficits (CFQ), and personality traits (NEO-FFI, ANPS) among 30 MS inpatients and 30 healthy controls were analyzed using hierarchical regression models. The frequency of cognitive mistakes was used as the dependent variable and the extent of cognitive and physical fatigue as the independent variable.ResultsCognitive fatigue was the only unique and significant predictor of cognitive mistakes in both groups, explaining 13.3% of additional variance in the MS group after correcting for age, mood, and physical fatigue. Physical fatigue had no significant impact on cognitive mistakes. While age had an impact on cognitive mistakes and depression in healthy controls, this association was not significant in MS patients. Depression was significantly correlated with cognitive mistakes and cognitive fatigue in MS patients.ConclusionsThe interplay of cognitive fatigue and subjective cognitive impairment can be generalized, with the exception of the variables of age and depression, which were shown to have differing impacts on cognitive mistakes in MS patients and healthy controls, respectively. Cognitive fatigue was linked to cognitive mistakes even after correcting for overlapping items in MS patients only. Future research should further investigate the link between cognitive fatigue and attention lapses in daily life by using various objective assessments.
Adaptive one-class Gaussian processes allow accurate prioritization of oncology drug targets
Authors: de Falco Antonio , Dezso Zoltan , Ceccarelli Francesco , Cerulo Luigi , Ciaramella Angelo , Ceccarelli Michele 
Published: November 2020

Abstract

Motivation
The cost of drug development has dramatically increased in the last decades, with the number new drugs approved per billion US dollars spent on R&D halving every year or less. The selection and prioritization of targets is one the most influential decisions in drug discovery. Here we present a Gaussian Process model for the prioritization of drug targets cast as a problem of learning with only positive and unlabeled examples.

Results
Since the absence of negative samples does not allow standard methods for automatic selection of hyperparameters, we propose a novel approach for hyperparameter selection of the kernel in One Class Gaussian Processes. We compare our methods with state-of-the-art approaches on benchmark datasets and then show its application to druggability prediction of oncology drugs. Our score reaches an AUC 0.90 on a set of clinical trial targets starting from a small training set of 102 validated oncology targets. Our score recovers the majority of known drug targets and can be used to identify novel set of proteins as drug target candidates.

Availability and implementation
The matrix of features for each protein is available at: https://bit.ly/3iLgZTa. Source code implemented in Python is freely available for download at https://github.com/AntonioDeFalco/Adaptive-OCGP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cultural Processes Shaping Stop-and-Check Practices and Interaction Dynamics in a Large Dutch City: Police Vulnerabilities, Thought Styles and Rituals
Authors: Brown Patrick , van Eijk Nathalie 
Published: November 2020

AbstractExisting scholarship on police decision-making notes the importance of categories and ‘governing mentalities’ in shaping front-line discretionary practices. Much of this work explores categories of race and ethnicity. Important questions remain regarding how micro-level practices connect to organizational dynamics and why ethnic profiling endures despite attempts to counter such practices. Drawing on critical approaches to uncertainty and risk, not least Mary Douglas’s cultural theory, we analyse data drawn from an ethnographic study of police work in a large city in the Netherlands. Our analysis emphasizes the multiple lines of accountability that render officers vulnerable in different ways, officers’ combining of different rationalities of decision-making and the influence of everyday rituals that cultivate and reinforce particular organizational thought styles and discretionary practices.
Quantitative Polyunsaturated Fatty Acid Analysis of Chia Seed Oil by High-Performance Liquid Chromatography
Authors: Liu Bingbing , Yan Weidong 
Published: November 2020

Abstract
Alpha-linolenic acid (ALA) and linoleic acid (LA), abundant in chia seed oil, are useful polyunsaturated fatty acids (PUFA) with numerous health benefits. The objectives of the present study were to explore the optimum extraction condition of chia seed oil and the possibilities of direct analysis of ALA and LA in chia seed oil by reversed-phase high-performance liquid chromatography with ultraviolet detection (RP-HPLC-UV). The optimized chia seed oil extraction condition was set by the usage of Soxhlet extrator with hexane as a solvent, with the solvent to solid ratio of 8 and the extraction time of 8 h. Prior to HPLC-UV analysis, the oil was saponified in order to get the free fatty acids for detection. The results showed that the proposed HPLC-UV method allowed the quantification of ALA and LA in chia seed oil. The method was simple, rapid (within 18 min) and sensitive (limit of detection 0.006 mg/mL for ALA and 0.02 mg/mL for LA) and precise (RSD ≤ 2%). Thus, the proposed experimental designs were shown to offer considerable advantages over traditional derivatization approaches in the ALA and LA analyses.
Scottish Women’s Poetry: Introduction
Authors: Jones Carole , Mcculloch Fiona 
Published: November 2020

AbstractThis introduction to the Scottish Women’s Poetry special issue presents a brief overview of the current critical field, sets out the rationale behind the special issue as going some way to initiate a redressing of the critical neglect of twenty-first-century Scottish women poets, and addresses the significance of the terms of engagement before going on to introduce the essays. It argues for the special issue as a step toward encouraging greater critical engagement with Scottish women’s poetry and exploration of the diverse strands of practice in the field.
Left atrial mechanics for secondary prevention from embolic stroke of undetermined source
Authors: Sade Leyla Elif , Keskin Suzan , Can Ufuk , Çolak Ayşe , Yüce Deniz , Çiftçi Orçun , Özin Bülent , Müderrisoğlu Haldun 
Published: November 2020

Abstract

Aims
Anticoagulation is not justified unless atrial fibrillation (AF) is detected in cryptogenic stroke (CS) patients. We sought to explore whether left atrial (LA) remodelling is associated with embolic stroke of undetermined source (ESUS).

Methods and results
In this prospective study, we evaluated consecutively 186 patients in sinus rhythm who presented with an acute ischaemic stroke (embolic and non-embolic) and sex- and age-matched controls. We performed continuous electrocardiogram (ECG) monitoring to capture paroxysmal AF episodes as recommended by the guidelines. After 12 months of follow-up, continuous ECG monitoring was repeated in patients with undetected AF episodes. We quantified LA reservoir and contraction strain (LASr and LASct) by speckle-tracking, LA volumes by 3D echocardiography. Out of 186 patients, 149 were enrolled after comprehensive investigation for the source of ischaemic stroke and divided into other cause (OC) (n = 52) and CS (n = 97) groups. CS patients were also subdivided into AF (n = 39) and ESUS (n = 58) groups. Among CS patients, LA strain predicted AF independently from CHARGE-AF score and LA volume indices. ESUS group, despite no captured AF, had significantly worse LA metrics than OC and control groups. AF group had the worst LA metrics. Moreover, LASr predicted both CS (embolic stroke with and without AF) and ESUS (embolic stroke with no detected AF) independently from LAVImax and CHA2DS2-VASc score. LASr &gt;26% yielded 86% sensitivity, 92% specificity, 92% positive, and 86% negative predictive values for the identification of ESUS (areas under curve: 0.915, P &lt; 0.0001, 95% confidence interval: 0.86–0.97).

Conclusion
Echocardiographic quantification of LA remodelling has great potential for secondary prevention from ESUS.
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Authors: Lee Alexandra J , Park YoSon , Doing Georgia , Hogan Deborah A , Greene Casey S 
Published: November 2020

Abstract

Motivation
In the past two decades, scientists in different laboratories have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, or "batch effects," may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to extract true underlying biological patterns. As more integrative analysis methods arise and data collections get bigger, we must determine how technical variability affects our ability to detect desired patterns when many experiments are combined.

Objective
We sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprising data aggregated across multiple experiments.

Method
We developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability.

Results
The signal from a baseline compendium was obscured when the number of added sources of variability was small. Applying statistical correction methods rescued the underlying signal in these cases. However, as the number of sources of variability increased, it became easier to detect the original signal even without correction. In fact, statistical correction reduced our power to detect the underlying signal.

Conclusion
When combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces our ability to extract underlying patterns.
New interpretation of the spreading evolution of the Knipovich Ridge derived from aeromagnetic data
Authors: Dumais M-A , Gernigon L , Olesen O , Johansen S E , Brönner M 
Published: November 2020

SUMMARYInsights into the spreading evolution of the Knipovich Ridge and development of the Fram Strait are revealed from a recent aeromagnetic survey. As an ultraslow spreading ridge in an oblique system located between the Svalbard–Barents Sea and the Northeast Greenland rifted margins, the dynamics of the Knipovich Ridge opening has long been debated. Its 90° bend with the Mohns Ridge, rare in plate tectonics, affects the evolution of the Fram Strait and motivates the study of crustal deformation with this distinctive configuration. We identified magnetic isochrons on either side of the present-day Knipovich Ridge. These magnetic observations considerably reduce the mapped extent of the oceanic domain and question the present understanding of the conjugate rifted margins. Our analysis reveals a failed spreading system before a major spreading reorganization of the Fram Strait gateway around magnetic chron C6 (circa 20 Ma).
From 9 to 91: health promotion through the life-course—illuminating the inner child
Authors: Sjöblom Margareta , Jacobsson Lars , Öhrling Kerstin , Kostenius Catrine 
Published: November 2020

SummaryA life-course perspective is according to the World Health Organization about increasing the effectiveness of health promotion interventions at all ages. This targets the needs of human beings throughout their life. Descriptions of the phenomenon of the inner child invite the possibility that it may be of help when promoting health throughout the life-course. The aim was to describe and understand schoolchildren’s, adults and older person’s experiences of childhood in connection to health and well-being in the present and through the life-course, illuminating the inner child. The research strategy used was a secondary analysis of the original transcribed data from three Swedish studies investigating new questions. In total, 53 individuals aged 9–91, 20 school children, 20 adults and 13 older persons were interviewed about childhood experiences. The schoolchildren were invited to create a drawing, and to narrate about it during the interview. The main question in the secondary analysis was ‘How do the participants’ narrations about childhood experiences illuminate the inner child, useful for health promotion through the life-course?’ The findings showed the importance of a secure atmosphere and trusting relationships, indicating that experiences during childhood can help us to adapt and pass along life lessons across generations. There were narratives about play as an activity where they learned to promote a healthy childhood, struggle for independence and learning how to be responsible when growing up. Dimensions of mental, social and existential well-being can be seen as examples of the inner child’s role in health promotion through the life-course.
Risk Factors for Cytomegalovirus Reactivation and Association With Outcomes in Critically Ill Adults With Sepsis: A Pooled Analysis of Prospective Studies
Authors: Imlay Hannah , Dasgupta Sayan , Boeckh Michael , Stapleton Renee D , Rubenfeld Gordon D , Chen Ying , Limaye Ajit P 
Published: November 2020

Abstract
We performed multivariable analysis of potential risk factors (including cytomegalovirus [CMV] reactivation) for clinical outcomes by day 28 (death or continued hospitalization, ventilator-free days, intensive care unit (ICU)-free days, hospital-free days) from pooled cohorts of 2 previous prospective studies of CMV-seropositive adults with sepsis. CMV reactivation at any level, &gt;100 IU/mL, &gt;1000 IU/mL, peak viral load, and area under the curve were independently associated with the clinical outcomes. We identified the potential effect size of CMV on outcomes that could be used as end points for future interventional trials of CMV prevention using antiviral prophylaxis in ICU patients with sepsis.
Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites
Authors: Digan William , Névéol Aurélie , Neuraz Antoine , Wack Maxime , Baudoin David , Burgun Anita , Rance Bastien 
Published: November 2020

Abstract

Background
The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to handle the reproducibility bottleneck.

Objective
To evaluate if WMS and other bioinformatics practices could impact the reproducibility of clinical NLP frameworks.

Materials and Methods
Based on the literature across multiple researcho fields (NLP, bioinformatics and clinical informatics) we selected articles which (1) review reproducibility practices and (2) highlight a set of rules or guidelines to ensure tool or pipeline reproducibility. We aggregate insight from the literature to define reproducibility recommendations. Finally, we assess the compliance of 7 NLP frameworks to the recommendations.

Results
We identified 40 reproducibility features from 8 selected articles. Frameworks based on WMS match more than 50% of features (26 features for LAPPS Grid, 22 features for OpenMinted) compared to 18 features for current clinical NLP framework (cTakes, CLAMP) and 17 features for GATE, ScispaCy, and Textflows.

Discussion
34 recommendations are endorsed by at least 2 articles from our selection. Overall, 15 features were adopted by every NLP Framework. Nevertheless, frameworks based on WMS had a better compliance with the features.

Conclusion
NLP frameworks could benefit from lessons learned from the bioinformatics field (eg, public repositories of curated tools and workflows or use of containers for shareability) to enhance the reproducibility in a clinical setting.