bluuebunny/crossref_metadata_2025_split huggingface dataset:
Curvature sensing amphipathic helix in the C-terminus of RTNLB13 is conserved in all endoplasmic reticulum shaping reticulons in Arabidopsis thaliana
Authors: Brooks Rhiannon L. , Mistry Chandni S. , Dixon Ann M. 
Published: March 2021

AbstractThe reticulon family of integral membrane proteins are conserved across all eukaryotes and typically localize to the endoplasmic reticulum (ER), where they are involved in generating highly-curved tubules. We recently demonstrated that Reticulon-like protein B13 (RTNLB13) from Arabidopsis thaliana contains a curvature-responsive amphipathic helix (APH) important for the proteins’ ability to induce curvature in the ER membrane, but incapable of generating curvature by itself. We suggested it acts as a feedback element, only folding/binding once a sufficient degree of curvature has been achieved, and stabilizes curvature without disrupting the bilayer. However, it remains unclear whether this is unique to RTNLB13 or is conserved across all reticulons—to date, experimental evidence has only been reported for two reticulons. Here we used biophysical methods to characterize a minimal library of putative APH peptides from across the 21 A. thaliana isoforms. We found that reticulons with the closest evolutionary relationship to RTNLB13 contain curvature-sensing APHs in the same location with sequence conservation. Our data reveal that a more distantly-related branch of reticulons developed a ~ 20-residue linker between the transmembrane domain and APH. This may facilitate functional flexibility as previous studies have linked these isoforms not only to ER remodeling but other cellular activities.
Proteomic blood profiling in mild, severe and critical COVID-19 patients
Authors: Patel Hamel , Ashton Nicholas J. , Dobson Richard J. B. , Andersson Lars-Magnus , Yilmaz Aylin , Blennow Kaj , Gisslen Magnus , Zetterberg Henrik 
Published: March 2021

AbstractThe recent SARS-CoV-2 pandemic manifests itself as a mild respiratory tract infection in most individuals, leading to COVID-19 disease. However, in some infected individuals, this can progress to severe pneumonia and acute respiratory distress syndrome (ARDS), leading to multi-organ failure and death. This study explores the proteomic differences between mild, severe, and critical COVID-19 positive patients to further understand the disease progression, identify proteins associated with disease severity, and identify potential therapeutic targets. Blood protein profiling was performed on 59 COVID-19 mild (n = 26), severe (n = 9) or critical (n = 24) cases and 28 controls using the OLINK inflammation, autoimmune, cardiovascular and neurology panels. Differential expression analysis was performed within and between disease groups to generate nine different analyses. From the 368 proteins measured per individual, more than 75% were observed to be significantly perturbed in COVID-19 cases. Six proteins (IL6, CKAP4, Gal-9, IL-1ra, LILRB4 and PD-L1) were identified to be associated with disease severity. The results have been made readily available through an interactive web-based application for instant data exploration and visualization, and can be accessed at https://phidatalab-shiny.rosalind.kcl.ac.uk/COVID19/. Our results demonstrate that dynamic changes in blood proteins associated with disease severity can potentially be used as early biomarkers to monitor disease severity in COVID-19 and serve as potential therapeutic targets.
Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Authors: Kang Hye-In , Lee Chae-Bin , Kwon Soon-Ho , Park Ji-Min , Kang Kyu-Suk , Shim Donghwan 
Published: March 2021

AbstractTilia species are valuable woody species due to their beautiful shape and role as honey trees. Somatic embryogenesis can be an alternative method for mass propagation of T. amurensis. However, the molecular mechanisms of T. amurensis somatic embryogenesis are yet to be known. Here, we conducted comparative transcriptional analysis during somatic embryogenesis of T. amurensis. RNA-Seq identified 1505 differentially expressed genes, including developmental regulatory genes. Auxin related genes such as YUC, AUX/IAA and ARF and signal transduction pathway related genes including LEA and SERK were differentially regulated during somatic embryogenesis. Also, B3 domain family (LEC2, FUS3), VAL and PKL, the regulatory transcription factors, were differentially expressed by somatic embryo developmental stages. Our results could provide plausible pathway of signaling somatic embryogenesis of T. amurensis, and serve an important resource for further studies in direct somatic embryogenesis in woody plants.
Systemic immunity markers associated with lymphocytes predict the survival benefit from paclitaxel plus bevacizumab in HER2 negative advanced breast cancer
Authors: Nakamoto Shogo , Ikeda Masahiko , Kubo Shinichiro , Yamamoto Mari , Yamashita Tetsumasa , Notsu Akifumi 
Published: March 2021

AbstractAlthough paclitaxel plus bevacizumab (PB) therapy is an effective chemotherapeutic regimen for HER2-negative advanced breast cancer (ABC), predictive markers for its effectiveness remain undefined. We investigated the usefulness of systemic immunity markers associated with lymphocytes as predictive markers for PB therapy in patients with HER2-negative ABC. We retrospectively reviewed data from 114 patients with HER2-negative ABC who underwent PB therapy from November 2011 to December 2019. We calculated the absolute lymphocyte count (ALC), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and lymphocyte-to-monocyte ratio (LMR) as representative systemic immunity markers. The time to treatment failure (TTF) and overall survival (OS) of the patients with high ALC, low NLR, and high LMR were significantly longer compared with those of the patients with low ALC, high NLR, and low LMR. A multivariable analysis revealed that high ALC, low NLR, and low PLR were independent predictors for TTF and high ALC, low NLR, and high LMR were independent predictors for OS. Systemic immunity markers were significantly associated with longer TTF and OS in patients who underwent PB therapy and may represent predictive markers for PB therapy in patients with HER2-negative ABC.
Enhancing flotation separation of chalcopyrite and magnesium silicate minerals by surface synergism between PAAS and GA
Authors: Chen Zhiqiang , Wang Yanhong , Luo Liqun , Peng Tiefeng , Guo Feng , Zheng Mingyu 
Published: March 2021

AbstractSeparation effects of sodium polyacrylate (PAAS) and gum Arabic (GA) on flotation of chalcopyrite and magnesium silicate minerals using potassium butyl xanthate (PBX) as collector were investigated by micro-flotation experiments, zeta potential, Infrared spectral (IR), SEM–EDS, XPS analysis and copper sulphide ore beneficiation test. The micro-flotation experiments and zeta potential measurements showed that combined depressant consisting of PAAS and GA could efficiently reduce the recoveries of mixed minerals of serpentine and talc more than 25%, while that of chalcopyrite remained above 70% at pH 9.2. Infrared spectral (IR), SEM–EDS and XPS analysis showed that PAAS chemically reacted with Mg on the surface of serpentine, while GA adsorbed on talc surface mainly via physical interaction and hydrogen bond may also play a role. Surface synergism between PAAS and GA was investigated by turbidity test and its depression mechanism was proposed. The technology feasibility of using PAAS and GA to improve the copper sulphide ore flotation performance was verified through artificial mixed ore flotation and laboratory closed-flotation operation.
A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients
Authors: Xu Yuzi , Xu Fengqin , Lv Yiming , Wang Siyuan , Li Jia , Zhou Chuan , Jiang Jimin , Xie Binbin , He Fuming 
Published: March 2021

AbstractHead and neck squamous cell carcinoma (HNSCC) is one of the most malignant cancers with poor prognosis worldwide. Emerging evidence indicates that competing endogenous RNAs (ceRNAs) are involved in various diseases, however, the regulatory mechanisms of ceRNAs underlying HNSCC remain unclear. In this study, we retrieved differentially expressed long non-coding RNAs (DElncRNAs), messenger RNAs (DEmRNAs) and microRANs (DEmiRNAs) from The Cancer Genome Atlas database and constructed a ceRNA-based risk model in HNSCC by integrated bioinformatics approaches. Functional enrichment analyses showed that DEmRNAs might be involved in extracellular matrix related biological processes, and protein–protein interaction network further selected out prognostic genes, including MYL1 and ACTN2. Importantly, co-expressed RNAs identified by weighted co-expression gene network analysis constructed the ceRNA networks. Moreover, AC114730.3, AC136375.3, LAT and RYR3 were highly correlated to overall survival of HNSCC by Kaplan–Meier method and univariate Cox regression analysis, which were subsequently implemented multivariate Cox regression analysis to build the risk model. Our study provides a deeper understanding of ceRNAs on the regulatory mechanisms, which will facilitate the expansion of the roles on the ceRNAs in the tumorigenesis, development and treatment of HNSCC.
Immunomodulatory effect of Noni fruit and its isolates: insights into cell-mediated immune response and inhibition of LPS-induced THP-1 macrophage inflammation
Authors: Ezzat Marwa I. , Hassan Mariam , Abdelhalim Mai A. , EL-Desoky Ahmed M. , Mohamed Shanaz O. , Ezzat Shahira M. 
Published: March 2021

Immunomodulatory activity of Morinda citrifolia and its isolated compounds.
A Conceptual Framework for Understanding Speaking Dyspnea
Authors: Lansing Robert W. , Hoit Jeannette D. 
Published: March 2021

Purpose
A conceptual framework is proposed to better understand the experience of people who have dyspnea (breathing discomfort) when speaking: its nature, its physiological mechanisms, and its impacts on their lives.

Method
The components of the framework are presented in their natural order. They are a Speaking Domain (Speaking Activities and Speaking Variables), a Physiological Domain (Speech Breathing Variables and Physiological Mechanisms), a Perceptual Domain (Dyspnea), a Symptom Impact Domain (Emotional Responses, Immediate Behavioral Responses, and Long-Term Behavioral Response), and a Life Impact Domain (Short-Term Impacts and Long-Term Impacts).

Results
We discuss literature that most directly supports these components and includes findings from healthy people and those with disorders in whom speaking dyspnea was either evoked or measured. Caveats are noted where information is limited and further study is needed. A case example is provided to illustrate how to apply the framework.

Conclusions
This framework provides a broader view of the elements that contribute to the experience of speaking dyspnea. It is meant to guide researchers, clinicians, instructors, caregivers, and those for whom speaking dyspnea is a daily or even a life-long challenge.
An algorithm for fitting passive equivalent circuits for lumped parameter frequency dependent transmission line models
Authors: Challa Kiran Kumar , Gurrala Gurunath , Mukherjee Pritam 
Published: March 2021

AbstractAccurately fitting rational functions to the frequency response of modal impedances is crucial for including frequency dependency in lumped parameter models of transmission lines. Vector fitting is widely used for fitting rational functions to the frequency response of modal impedances and then an R‐L equivalent circuit is obtained from the rational functions. A single‐step method based on the properties of Foster equivalent circuit is proposed to directly fit an R‐L equivalent circuit to the frequency response of modal impedances. The positive peaks, negative peaks and the positive zero crossings of the slope change plot of the frequency response are found to provide a good approximation of zeros, poles and the flat region locations of the frequency response. An enhanced fitting algorithm is proposed based on these observations. A close enough fitting is achieved using the proposed method with less number of passive elements. Using the proposed model in EMTP‐RV, 400, 765, 1200 kV transmission lines and a 11‐bus 500 kV network are simulated for switching transients. The results are compared with the constant parameter cascaded ‐model and the Frequency‐dependent line model in EMTP‐RV. The switching transient results of the proposed model are found to be comparable to the Marti's model in EMTP‐RV.
An image encryption algorithm with a plaintext‐related quantisation scheme
Authors: Oravec Jakub , Ovseník Ľuboš , Papaj Ján 
Published: March 2021

AbstractThis paper describes an image encryption algorithm that utilises a plaintext‐related quantisation scheme. Various plaintext‐related approaches from other algorithms are presented and their properties are briefly discussed. Main advantage of the proposed solution is the achievement of a similar behaviour like that of more complex approaches with a plaintext‐related technique used in a rather simple step such as quantisation. This design should result in a favourable computational complexity of the whole algorithm. The properties of the proposal are evaluated by a number of commonly used numerical parameters. Also, the statistical properties of a pseudo‐random sequence that is quantised according to the plain image pixel intensities are investigated by tests from NIST 800‐22 suite. Obtained results are compared to values reported in related works and they imply that the proposed solution produces encrypted images with comparable statistical properties but authors' design is faster and more efficient.
MSR‐FAN: Multi‐scale residual feature‐aware network for crowd counting
Authors: Zhao Haoyu , Min Weidong , Wei Xin , Wang Qi , Fu Qiyan , Wei Zitai 
Published: March 2021

AbstractCrowd counting aims to count the number of people in crowded scenes, which is important to the security systems, traffic control and so on. The existing methods typically using local features cannot properly handle the perspective distortion and the varying scales in congested scene images, and henceforth perform wrong people counting. To alleviate this issue, this study proposes a multi‐scale residual feature‐aware network (MSR‐FAN) that combines multi‐scale features using multiple receptive field sizes and learns the feature‐aware information on each image. The MSR‐FAN is trained end‐to‐end to generate high‐quality density map and evaluate the crowd number. The method consists of three parts. To handle the perspective changes problem, the first part, the direction‐based feature‐enhanced network, is designed to encode the perspective information in four directions based on the initial image feature. The second part, the proposed multi‐scale residual block module, gets the global information to handle the represent the regional feature better. This module explores features of different scales as well as reinforce the global feature. The third part, the feature‐aware block, is designed to extract the feature hidden in the different channels. Experiment results based on benchmark datasets show that the proposed approach outperforms the existing state‐of‐the‐art methods.
An optimized YOLO‐based object detection model for crop harvesting system
Authors: Junos Mohamad Haniff , Mohd Khairuddin Anis Salwa , Thannirmalai Subbiah , Dahari Mahidzal 
Published: March 2021

AbstractThe adoption of automated crop harvesting system based on machine vision may improve productivity and optimize the operational cost. The scope of this study is to obtain visual information at the plantation which is crucial in developing an intelligent automated crop harvesting system. This paper aims to develop an automatic detection system with high accuracy performance, low computational cost and lightweight model. Considering the advantages of YOLOv3 tiny, an optimized YOLOv3 tiny network namely YOLO‐P is proposed to detect and localize three objects at palm oil plantation which include fresh fruit bunch, grabber and palm tree under various environment conditions. The proposed YOLO‐P model incorporated lightweight backbone based on densely connected neural network, multi‐scale detection architecture and optimized anchor box size. The experimental results demonstrated that the proposed YOLO‐P model achieved good mean average precision and F1 score of 98.68% and 0.97 respectively. Besides, the proposed model performed faster training process and generated lightweight model of 76 MB. The proposed model was also tested to identify fresh fruit bunch of various maturities with accuracy of 98.91%. The comprehensive experimental results show that the proposed YOLO‐P model can effectively perform robust and accurate detection at the palm oil plantation.
Local dew-point temperature, water vapor pressure, and millimeter-wavelength opacity at the Sierra Negra volcano
Authors: Mendoza-Torres J. E. , Colín-Beltrán E. , Ferrusca D. , Contreras R. J. 
Published: March 2021

Aims. Some astronomical facilities are in operation at the Sierra Negra volcano (SNV), at ∼4.5 km over the sea level (o.s.l.) in Mexico. We asses whether it is possible to estimate the opacity for millimeter-wavelength observations based on the meteorological parameters at the site. A criterion for allowing astronomical observations at SNV depends on the atmospheric opacity at 225 GHz, which has to be τ225 ≤ 0.30 Nepers. The correlation of the opacity at SNV, measured with a radiometer at 225 GHz, τ225, with the local dew point temperature, TDP, the water vapor pressure, PH2O and the water vapor content (WVC) at SNV is studied with the aim to determine whether these parameters can be used to estimate the opacity at similar high-altitude locations for astronomical observations at millimeter wavelengths.
Methods. We used radiosonde data taken in various decades in Mexico City (MX) and Veracruz City (VR) to compute the WVC in 0.5 km altitude (h) intervals from 0 km for VR and from 2.0 km for MX to 9.5 km o.s.l. to study the altitude profile WVC(h) at SNV by interpolating data of MX and VR. We also fit exponential functions to observed WVC (WVCobs(h)), obtaining a fit WVC (WVCftd(h)). The WVCobs(h) and WVCftd(h) were integrated, from lower limits of hlow = 2.5–5.5 km to the upper limit of 9.5 km as a measure of the input of WVCobs(h ≥ hlow) to the precipitable water vapor.
Results. The largest differences between WVCobs and WVCftd values occur at low altitudes. The input of WVCobs(h) to the precitpitable water vapor for h ≥ 4.5 km ranges from 15% to 29%. At 4.5–5.0 km, the input is between 4% and 8%. This means that it is about a third of the WVC (h ≥ 4.5 km). The input above our limit (from 9.5–30.0 km) is estimated with WVCftd(h) and is found to be lower than 1%. The correlation of τ225 with TDP, PH2O, and WVCSNV takes values between 0.6 and 0.8. A functional relation is proposed based on simultaneous data taken in 2013–2015, according to which it is possible to estimate the opacity with the TDP, PH2O, or WVCSNV at the site.
Conclusions. With local meteorological parameters, it is possible to know whether the opacity meets the condition τ225 ≤ 0.30 Nepers, with an uncertainty of ±0.16 Nepers. The uncertainty is low for low opacities and increases with increasing opacity.
Anomalous Nernst effect in Pr0.5Sr0.5CoO3
Authors: Ghosh A. , Chanda A. , Mahendiran R. 
Published: March 2021

We report the anomalous Nernst effect (ANE) in polycrystalline metallic perovskite Pr0.5Sr0.5CoO3. The transverse Seebeck coefficient (Sxy) was measured at selected temperatures for magnetic fields up to H = 50 kOe and also as a function of temperature at two selected magnetic fields (H = 2 and 10 kOe). While Sxy increases linearly with H above the Curie temperature (TC ∼ 229 K), it changes non-linearly at low fields in the ferromagnetic state and exhibits hysteresis similar to magnetization. Linear extrapolation of the high field Sxy vs H graph to zero field gives Sxy = 0.46 µV/K at 175 K. It is found that the manganite counterpart Pr0.5Sr0.5MnO3 having a similar hole content exhibits much smaller Sxy than Pr0.5Sr0.5CoO3 in a field of 2 kOe. Our analysis suggests that the ANE in this sample is most likely due to asymmetric skew scattering of charge carriers.
Perfect Match Genomic Landscape strategy: Refinement and customization of reference genomes
Authors: Palacios-Flores Kim , García-Sotelo Jair , Castillo Alejandra , Uribe Carina , Morales Lucía , Boege Margareta , Dávila Guillermo , Flores Margarita , Palacios Rafael 
Published: March 2021

Significance
The accuracy of the nucleotide sequence of genomes is of utmost importance. The Perfect Match Genomic Landscape (PMGL) is a precise, sensitive, and nonstatistical strategy to detect genome variation. We used this strategy to refine reference genomes from microorganisms belonging to the three domains of life. Our studies show as well that the PMGL can be useful to detect variants in pathogen agents during a pandemic, and to isolate mutations generated during any desired stage of experimental evolution studies. We propose that the PMGL strategy could be the final step in the refinement of any haploid genome, independently of the methodology and algorithms used for its assembly.
Morphological complexity and rated writing proficiency
Authors: de la Torre García Nuria , Ainciburu María Cecilia , Buyse Kris 
Published: March 2021

Abstract
Linguistic complexity measures are used to describe second language (L2) performance and assess levels of
proficiency and development. Although morphology is considered crucial in L2 acquisition, morphological complexity has been
relatively neglected, hindering comprehensive views of grammatical complexity in L2. This article presents an application of a
recently proposed metric of morphological diversity, the Morphological Complexity Index (MCI), in an L2 Spanish corpus of 113
essays classified into four proficiency levels by expert evaluators. The aim of the study is to investigate the relationships of
MCI with subjectively rated proficiency and with other four quantitative measures of L2 complexity. Results indicate that
morphological complexity, as measured by MCI, does not vary significantly across proficiency levels in this corpus. The MCI shows
significant correlations with lexical but not with syntactic complexity measures. Findings are interpreted in the light of the
characteristics of the corpus and the acquisition of the Spanish verbal system.
Intra-specific variation of thermal performance, skin reflectance and body size partially co-vary with climate in a lizard
Authors: Aguado Sara , Clusella-Trullas Susana 
Published: March 2021

Abstract
Thermal adaptation theory posits that variation of thermal traits such as those affecting thermal budgets and the performance of ectotherms should be associated with climate gradients. Under a simple scenario, thermal traits should also co-vary to shape optimal thermal phenotypes under a particular climate. However, geographical variation and covariation of thermal traits can result from other sources of selection and a wide range of other mechanisms. Here, we explore variation and covariation of skin reflectance (melanization), body size and thermal performance traits among three populations of the lizard Cordylus cordylus, a species endemic to South Africa. We also examine relationships between skin reflectance and substrate reflectance, body size and crevice size to test alternative hypotheses. We found partial support for predictions of thermal adaptation to climate regimes for body size, melanization and chill-coma recovery time. Darker lizards also performed optimally at higher temperatures than lighter coloured lizards but there was limited individual covariation between morphological and performance traits. Despite partial support for thermal adaptation, the complex interactions between sex and body size and between substrate reflectance and size underlying skin reflectance emphasized the importance of testing multiple hypotheses when exploring drivers of thermal trait variation within species.