bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impairment of the neurotrophic signaling hub B-Raf contributes to motoneuron degeneration in spinal muscular atrophy
Authors: Hensel Niko , Cieri Federica , Santonicola Pamela , Tapken Ines , Schüning Tobias , Taiana Michela , Pagliari Elisa , Joseph Antonia , Fischer Silke , Heidrich Natascha , Brinkmann Hella , Kubinski Sabrina , Bergmann Anke K. , Richter Manuela F. , Jung Klaus , Corti Stefania , Di Schiavi Elia , Claus Peter 
Published: April 2021

Significance
The mechanisms of neurodegeneration are important targets for future treatments of the devastating motoneuron disease spinal muscular atrophy (SMA). Here, we show an altered signaling network in SMA models and patient cells with a reduced B-Raf expression in the network center. B-Raf is crucial for motoneuron survival, and we present data that B-Raf restoration ameliorates motoneuron loss and symptoms in SMA models.
Circular swimming motility and disordered hyperuniform state in an algae system
Authors: Huang Mingji , Hu Wensi , Yang Siyuan , Liu Quan-Xing , Zhang H. P. 
Published: April 2021

Significance
Disordered hyperuniform materials suppress large-scale density fluctuations like crystals and remain locally isotropic as liquids. These materials possess unique properties, such as isotropic photonic gap, and have attracted the attention of scientists from many disciplines. Here we show that circularly swimming marine algae can robustly self-organize into disordered hyperuniform states through long-range hydrodynamic interactions at air–liquid interfaces. Important properties measured from hyperuniform states can be quantitatively reproduced by a numerical model whose main parameters are obtained experimentally. Our work clearly demonstrates the possibility to create disordered hyperuniform states via hydrodynamic interactions and highlights the importance of such interactions in active matter systems.
On Estimating Personality Traits of US Supreme Court Justices
Authors: Black Ryan C. , Owens Ryan J. , Wedeking Justin , Wohlfarth Patrick C. 
Published: April 2021

AbstractPsychological scholarship on personality is uniting with political science to redefine existing theories. This is clearly the case with research on judicial behavior and the US Supreme Court. But if this new approach is to survive and thrive, it must employ measures equal to the task. We show that Supreme Court Individual Personality Estimates, which seek to estimate justices’ personalities by examining their concurring opinions, suffer from a number of important methodological deficits that critically limit their usefulness. We briefly discuss what kinds of improved personality measures scholars should use instead and offer an improved set of estimates for one trait with an application that demonstrates our cautionary tale.
PN junction and band to band tunneling in carbon nanotube transistors at room temperature
Authors: Zeevi Gilad , Razin Alexey , Yaish Yuval E 
Published: April 2021

Abstract
We demonstrate band to band tunneling (BTBT) in a carbon nanotube (CNT) field effect transistor. We employ local electrostatic doping assisted by charged traps within the oxide to produce an intramolecular PN junction along the CNT. These characteristics apply for both metallic (m-CNTs) and semiconducting (SC-CNTs) CNTs. For m-CNTs we present a hysteretic transfer characteristic which originates from local electrostatic doping in the middle segment of the CNT. This controlled doping is reversible and results in formation and destruction of a PN junction along the CNT channel. For SC-CNTs we observe BTBT, and analysis based on the WKB approximation reveals a very narrow depletion region and high transmission probability at the optimal energy bands overlap. These results may assist in developing a non-volatile one-dimensional PN junction memory cell and designing a tunneling based field effect transistor.
Photonic devices based on thin-film lithium niobate on insulator
Authors: Yuan Shuai , Hu Changran , Pan An , Ding Yuedi , Wang Xuanhao , Qu Zhicheng , Wei Junjie , Liu Yuheng , Zeng Cheng , Xia Jinsong 
Published: April 2021

Abstract
Lithium niobate on insulator (LNOI) is rising as one of the most promising platforms for integrated photonics due to the high-index-contrast and excellent material properties of lithium niobate, such as wideband transparency from visible to mid-infrared, large electro-optic, piezoelectric, and second-order harmonic coefficients. The fast-developing micro- and nano-structuring techniques on LNOI have enabled various structure, devices, systems, and applications. In this contribution, we review the latest developments in this platform, including ultra-high speed electro-optic modulators, optical frequency combs, opto-electro-mechanical system on chip, second-harmonic generation in periodically poled LN waveguides, and efficient edge coupling for LNOI.
High-frequency characterization of high-speed modulators and photodetectors in a link with low-speed photonic sampling
Authors: Wang Mengke , Zhang Shangjian , Liu Zhao , Zhang Xuyan , He Yutong , Ma Yangxue , Zhang Yali , Zhang Zhiyao , Liu Yong 
Published: April 2021

Abstract
We propose a low-speed photonic sampling for independent high-frequency characterization of a Mach–Zehnder modulator (MZM) and a photodetector (PD) in an optical link. A low-speed mode-locked laser diode (MLLD) provides an ultra-wideband optical stimulus with scalable frequency range, working as the photonic sampling source of the link. The uneven spectrum lines of the MLLD are firstly characterized with symmetric modulation within the interesting frequency range. Then, the electro-optic modulated signals are down-converted to the first Nyquist frequency range, yielding the self-referenced extraction of modulation depth and half-wave voltage of the MZM without correcting the responsivity fluctuation of the PD in the link. Finally, the frequency responsivity of the PD is self-referenced measured under null modulation of the MZM. As frequency responses of the MZM and the PD can be independently obtained, our method allows self-referenced high-frequency measurement for a high-speed optical link. In the proof-of-concept experiment, a 96.9 MS/s MLLD is used for measuring a MZM and a PD within the frequency range up to 50 GHz. The consistency between our method and the conventional method verifies that the ultra-wideband and self-referenced high-frequency characterization of high-speed MZMs and PDs.
Combinations of photoinitiator and UV absorber for cell-based digital light processing (DLP) bioprinting
Authors: Huh JunTae , Moon Young-Wook , Park Jihoon , Atala Anthony , Yoo James J , Lee Sang Jin 
Published: April 2021

Abstract
Digital light processing (DLP) bioprinting, which provides predominant speed, resolution, and adaptability for fabricating complex cell-laden three-dimensional (3D) structures, requires a combination of photoinitiator (PI) and UV absorber (UA) that plays critical roles during the photo-polymerization of bioinks. However, the PI and UA combination has not been highlighted for cell-based DLP bioprinting. In this study, the most used PIs and UAs in cell-based bioprinting were compared to optimize a combination that can ensure the maximum DLP printability, while maintaining the cellular activities during the process. The crosslinking time and printability of PIs were assessed, which are critical in minimizing the cell damage by the UV exposure during the fabrication process. On the other hand, the UAs were evaluated based on their ability to prevent the over-curing of layers beyond the focal layer and the scattering of light, which are required for the desirable crosslinking of a hydrogel and high resolution (25–50 µms) to create a complex 3D cell-laden construct. Lastly, the cytotoxicity of PIs and UAs was assessed by measuring the cellular activity of 2D cultured and 3D bioprinted cells. The optimized PI and UA combination provided high initial cell viability (>90%) for up to 14 days in culture and could fabricate complex 3D structures like a perfusable heart-shaped construct with open vesicles and atriums. This combination can provide a potential starting condition when preparing the bioink for the cell-based DLP bioprinting in tissue engineering applications.
Evolution of texture and precipitates in Al–Cu–Li alloy during deformation and heat treatment and its effect on anisotropy
Authors: Yang Shengli , Liu Lele , Gao Fuyang , Xu Zhe , Song Dejun , Jiang Peng 
Published: April 2021

Abstract
Al–Li alloy offersa great advantage over traditional alloys and it is the ideal material for today’s aerospace industry. Therefore, here we examined the Al–Cu–Li alloy as the third generation of Al–Li alloy. Deformation and heat treatment on the texture and precipitate type and distribution of Al–Cu–Li alloy were studied by mechanical properties test, XRD, and TEM analysis. The effect of texture and precipitate on the plane anisotropy of yield strength was discussed. The results showed thatBrass texture was mainly formed in the deformation process. On the one hand, increasethe pass deformation or cross rolling,the total volume fraction of the texture (S{123}〈634〉, G{011}〈100〉, {011}〈011〉) was increased, which lowered thesheet anisotropy. While on the other hand, the δ′ phase precipitated rapidly during solution treatment and easily caused a coplanar slip, increasing plane anisotropy. However, owing to the difference distribution of the aged precipitated T1 on the two group of {111} habit plane, the strengthening effect of the Al–Cu–Li alloy sheet was weak at 45° direction, but stronger atthe rolling direction (0°) and transverse direction (90°).
A study of the permeation and water-structuring behavioural properties of PEG modified hydrated silk fibroin membranes
Authors: Mann Aisling , Lydon Fiona , Tighe Brian J , Suzuki Shuko , Chirila Traian V 
Published: April 2021

Abstract
The potential of naturally occurring substances as a source of biomedical materials is well-recognised and is being increasingly exploited. Silk fibroin membranes derived from Bombyx mori silk cocoons exemplify this, for example as substrata for the growth of ocular cells with the aim of generating biomaterial-cell constructs for tissue engineering. This study investigated the transport properties of selected silk fibroin membranes under conditions that allowed equilibrium hydration of the membranes to be maintained. The behaviour of natural fibroin membranes was compared with fibroin membranes that have been chemically modified with poly(ethylene glycol). The permeation of the smaller hydrated sodium ion was higher than that of the hydrated calcium ion for all three ethanol treated membranes investigated. The PEG and HRP-modified C membrane, which had the highest water content at 59.6 ± 1.5% exhibited the highest permeation of the three membranes at 95.7 ± 2.8 × 10–8 cm2 s−1 compared with 17.9 ± 0.9 × 10–8 cm2 s−1 and 8.7 ± 1.7 × 10–8 cm2 s−1 for membranes A and B respectively for the NaCl permeant. Poly(ethylene glycol) was used to increase permeability while exploiting the crosslinking capabilities of horseradish peroxidase to increase the compressive strength of the membrane. Importantly, we have established that the permeation behaviour of water-soluble permeants with hydrated radii in the sub-nanometer range is analogous to that of conventional hydrogel polymers.
Advanced fuzzy cognitive maps: state-space and rule-based methodology for coronary artery disease detection
Authors: Apostolopoulos Ioannis D , Groumpos Peter P , Apostolopoulos Dimitris J 
Published: April 2021

Abstract
According to the World Health Organization, 50% of deaths in European Union are caused by Cardiovascular Diseases (CVD), while 80% of premature heart diseases and strokes can be prevented. In this study, a Computer-Aided Diagnostic model for a precise diagnosis of Coronary Artery Disease (CAD) is proposed. The methodology is based on State Space Advanced Fuzzy Cognitive Maps (AFCMs), an evolution of the traditional Fuzzy Cognitive Maps. Also, a rule-based mechanism is incorporated, to further increase the knowledge of the proposed system and the interpretability of the decision mechanism. The proposed method is evaluated utilizing a CAD dataset from the Department of Nuclear Medicine of the University Hospital of Patras, in Greece. Several experiments are conducted to define the optimal parameters of the proposed AFCM. Furthermore, the proposed AFCM is compared with the traditional FCM approach and the literature. The experiments highlight the effectiveness of the AFCM approach, obtaining 85.47% accuracy in CAD diagnosis, showing an improvement of +7% over the traditional approach. It is demonstrated that the AFCM approach in developing Fuzzy Cognitive Maps outperforms the conventional approach, while it constitutes a reliable method for the diagnosis of Coronary Artery Disease.
New features in the surface plasmon induced photon drag effect in noble metal thin films
Authors: Khichar Vivek , Sharma Suresh C , Hozhabri Nader 
Published: April 2021

Abstract
We study light–matter interactions leading to the generation of photon drag voltage under surface plasmon resonance conditions in noble metal thin films and observe important effects, which provide opportunity for condensed matter theorists to critically evaluate theoretical models. The drag voltage originates from a force that arises because of the transfer of momentum from incident light to electrons. This transfer of photon momentum leads to an electric current, which in turn results in the generation of drag voltage. The effect is particularly enhanced under surface plasmon resonance conditions and thereby reinforces the interaction between light and collective oscillations of the surface charges. We observe relatively high voltages with a nonlinear dependence on laser intensity. In disagreement with previous results, we do not observe a reversal in the sign of the voltage when the direction of the incident laser momentum is reversed. Qualitative analyses of the data show that the hydrodynamic model of laser-induced drag voltage does not work: the hydrodynamic model predicts voltages that are nine orders of magnitude lower than our measurements. However, there is reasonable consistency between the results of the measurements and numerical simulations.
Inversion of incomplete spectral data using support information with an application to magnetic resonance imaging
Authors: de Leeuw den Bouter Merel L , van den Berg Peter M , Remis Rob F 
Published: April 2021

Abstract
In this paper we discuss an imaging method when the object has known support and its spatial Fourier transform is only known on a certain k-space undersampled pattern. The simple conjugate gradient least squares algorithm applied to the corresponding truncated Fourier transform equation produces reconstructions that are basically of a similar quality as reconstructions obtained by solving a standard compressed sensing problem in which support information is not taken into account. Connections with previous one-dimensional approaches are highlighted and the performance of the method for two- and three-dimensional simulated and measured incomplete spectral data sets is illustrated. Possible extensions of the method are also briefly discussed.
Practical selection of representative sets of RNA-seq samples using a hierarchical approach
Authors: Tung Laura H , Kingsford Carl 
Published: April 2021

Abstract

Motivation
Despite numerous RNA-seq samples available at large databases, most RNA-seq analysis tools are evaluated on a limited number of RNA-seq samples. This drives a need for methods to select a representative subset from all available RNA-seq samples to facilitate comprehensive, unbiased evaluation of bioinformatics tools. In sequence-based approaches for representative set selection (e.g. a k-mer counting approach that selects a subset based on k-mer similarities between RNA-seq samples), because of the large numbers of available RNA-seq samples and of k-mers/sequences in each sample, computing the full similarity matrix using k-mers/sequences for the entire set of RNA-seq samples in a large database (e.g. the SRA) has memory and runtime challenges; this makes direct representative set selection infeasible with limited computing resources.

Results
We developed a novel computational method called ‘hierarchical representative set selection’ to handle this challenge. Hierarchical representative set selection is a divide-and-conquer-like algorithm that breaks representative set selection into sub-selections and hierarchically selects representative samples through multiple levels. We demonstrate that hierarchical representative set selection can achieve summarization quality close to that of direct representative set selection, while largely reducing runtime and memory requirements of computing the full similarity matrix (up to 8.4× runtime reduction and 5.35× memory reduction for 10 000 and 12 000 samples respectively that could be practically run with direct subset selection). We show that hierarchical representative set selection substantially outperforms random sampling on the entire SRA set of RNA-seq samples, making it a practical solution to representative set selection on large databases like the SRA.

Availability and implementation
The code is available at https://github.com/Kingsford-Group/hierrepsetselection and https://github.com/Kingsford-Group/jellyfishsim.

Supplementary information
Supplementary data are available at Bioinformatics online.
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes
Authors: Hu Fengyuan , Lu Jia , Matheson Louise S , Díaz-Muñoz Manuel D , Saveliev Alexander , Xu Jinbo , Turner Martin 
Published: April 2021

Abstract

Motivation
The annotation of small open reading frames (smORFs) of &lt;100 codons (&lt;300 nucleotides) is challenging due to the large number of such sequences in the genome.

Results
In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Four novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions.

Availability and implementation
Freely available on the web at https://github.com/boboppie/ORFLine.

Supplementary information
Supplementary data are available at Bioinformatics online.
Slow-transit constipation and criteria for colectomy: a cross-sectional study of 1568 patients
Authors: Chaichanavichkij P , Vollebregt P F , Tee S Z Y , Scott S M , Knowles C H 
Published: April 2021

Abstract

Background
Colectomy remains a treatment option for a minority of patients with slow-transit constipation (STC) refractory to conservative treatment. However careful patient selection is essential to maximize benefits and minimize risk of adverse outcome. This study determined the proportion of patients with chronic constipation that would meet criteria for colectomy based on recent European graded practice recommendations derived by expert consensus.

Methods
Retrospective application of graded practice recommendations was undertaken on a prospectively maintained data set of consecutive adult patients with chronic constipation who underwent whole-gut transit studies using radio-opaque markers. Primary analysis applied contraindications achieving high level of expert consensus (normal whole-gut transit as an absolute contraindication and faecal incontinence as a relative contraindication for colectomy). Secondary analysis applied contraindications with less certain consensus.

Results
Primary analysis of 1568 patients undergoing a whole-gut transit study between January 2004 and March 2016 found 208 (13.3 per cent) met published criteria to be selected for colectomy, with 974 excluded for normal whole-gut transit and 386 for faecal incontinence. Secondary analysis demonstrated high prevalence of other relative contraindications to colectomy: 165 concomitant upper gastrointestinal symptoms, 216 abdominal pain (including 126 irritable bowel syndrome), and 446 evacuation disorder. The majority of patients (416 of 594) had two or more relative contraindications. If these patients were excluded, only 26 (1.7 per cent) chronically constipated patients retrospectively met selection criteria for colectomy.

Conclusions
The retrospective application of selection criteria is a limitation. However, the data highlight the high prevalence of factors associated with poor postoperative outcome and provide further caution to surgeons undertaking colectomy for STC.
A case report: adenosine triggered myocardial infarction during myocardial perfusion stress test imaging in a diabetic patient
Authors: de Mulder Maarten , van Gameren Menno , van Asperen Eric A , Meuwissen Martijn 
Published: April 2021

Abstract

Background
Myocardial perfusion imaging (MPI) using single-photon emission computed tomography (SPECT) can in general be used safely in daily clinical practice. However, under the right circumstances, it can lead to serious complications.

Case summary
A 68-year-old female patient with diabetes and a history of inferior ST-elevation myocardial infarction 8 years earlier, visited our outpatient clinic with atypical chest discomfort. In order to assess whether this is due to myocardial ischaemia, MPI-SPECT was ordered. As it was suspected she would not achieve sufficient exercise levels, pharmacologic stress using adenosine was arranged. During the scan, she developed acute myocardial infarction. Subsequent urgent coronary angiography demonstrated a subtotal stenosis in the proximal left anterior descending coronary artery which was successfully stented. She was still free from angina 4 months later.

Discussion
The combination of a reduced systemic and coronary perfusion pressure in the presence of an exhausted coronary autoregulation, may be a starting point for local geometrical changes that initiate the classic cascade of thrombus formation and acute occlusion of coronary arteries during MPI-SPECT. This illustrates the need for continuous patient and electrocardiogram monitoring.
Neonatal arrhythmias in Turner syndrome: a case report and review of the literature
Authors: Choi Yeyoon , Hoffman Jodi , Alarcon Lizzeth , Pfau Jennifer , Bolourchi Meena 
Published: April 2021

AbstractBackgroundWhile left-sided congenital heart defects have been well described in females with Turner syndrome (45, X), the literature is scarce regarding arrhythmias in this patient population.Case summaryA full-term neonate referred to cardiology was found to have a non-apex forming left ventricle and partial anomalous pulmonary venous return. During the echocardiogram, she developed atrial flutter, followed by orthodromic reentrant supraventricular tachycardia (SVT). She was started on propranolol and eventually switched to sotalol due to breakthrough SVT. A genetics evaluation revealed Turner syndrome with complete monosomy X (45, X). The patient is now 18 months old and has not had any further arrhythmias.DiscussionWe present a rare case of atrial flutter followed by supraventricular tachycardia in a neonate with Turner syndrome and left-sided heart defects. This case highlights the importance of early and precise investigation of cardiac abnormalities in neonatal patients, especially among females with Turner syndrome given their relatively higher risk of cardiovascular disease compared to the general population.