bluuebunny/crossref_metadata_2025_split huggingface dataset:
SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction
Authors: Uddin Mostofa Rafid , Mahbub Sazan , Rahman M Saifur , Bayzid Md Shamsuzzoha 
Published: May 2020

Abstract

Motivation
Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) for predicting the secondary structure (SS) of proteins are very expensive and time consuming. Therefore, developing efficient computational approaches for predicting the SS of protein is of utmost importance. Advances in developing highly accurate SS prediction methods have mostly been focused on 3-class (Q3) structure prediction. However, 8-class (Q8) resolution of SS contains more useful information and is much more challenging than the Q3 prediction.

Results
We present SAINT, a highly accurate method for Q8 structure prediction, which incorporates self-attention mechanism (a concept from natural language processing) with the Deep Inception-Inside-Inception network in order to effectively capture both the short- and long-range interactions among the amino acid residues. SAINT offers a more interpretable framework than the typical black-box deep neural network methods. Through an extensive evaluation study, we report the performance of SAINT in comparison with the existing best methods on a collection of benchmark datasets, namely, TEST2016, TEST2018, CASP12 and CASP13. Our results suggest that self-attention mechanism improves the prediction accuracy and outperforms the existing best alternate methods. SAINT is the first of its kind and offers the best known Q8 accuracy. Thus, we believe SAINT represents a major step toward the accurate and reliable prediction of SSs of proteins.

Availability and implementation
SAINT is freely available as an open-source project at https://github.com/SAINTProtein/SAINT.
18F-MK-6240 PET for early and late detection of neurofibrillary tangles
Authors: Pascoal Tharick A , Therriault Joseph , Benedet Andrea L , Savard Melissa , Lussier Firoza Z , Chamoun Mira , Tissot Cécile , Qureshi Muhammad Naveed Iqbal , Kang Min Su , Mathotaarachchi Sulantha , Stevenson Jenna , Hopewell Robert , Massarweh Gassan , Soucy Jean-Paul , Gauthier Serge , Rosa-Neto Pedro 
Published: May 2020

AbstractBraak stages of tau neurofibrillary tangle accumulation have been incorporated in the criteria for the neuropathological diagnosis of Alzheimer’s disease. It is expected that Braak staging using brain imaging can stratify living individuals according to their individual patterns of tau deposition, which may prove crucial for clinical trials and practice. However, previous studies using the first-generation tau PET agents have shown a low sensitivity to detect tau pathology in areas corresponding to early Braak histopathological stages (∼20% of cognitively unimpaired elderly with tau deposition in regions corresponding to Braak I–II), in contrast to ∼80–90% reported in post-mortem cohorts. Here, we tested whether the novel high affinity tau tangles tracer 18F-MK-6240 can better identify individuals in the early stages of tau accumulation. To this end, we studied 301 individuals (30 cognitively unimpaired young, 138 cognitively unimpaired elderly, 67 with mild cognitive impairment, 54 with Alzheimer’s disease dementia, and 12 with frontotemporal dementia) with amyloid-β 18F-NAV4694, tau 18F-MK-6240, MRI, and clinical assessments. 18F-MK-6240 standardized uptake value ratio images were acquired at 90–110 min after the tracer injection. 18F-MK-6240 discriminated Alzheimer’s disease dementia from mild cognitive impairment and frontotemporal dementia with high accuracy (∼85–100%). 18F-MK-6240 recapitulated topographical patterns consistent with the six hierarchical stages proposed by Braak in 98% of our population. Cognition and amyloid-β status explained most of the Braak stages variance (P &lt; 0.0001, R2 = 0.75). No single region of interest standardized uptake value ratio accurately segregated individuals into the six topographic Braak stages. Sixty-eight per cent of the cognitively unimpaired elderly amyloid-β-positive and 37% of the cognitively unimpaired elderly amyloid-β-negative subjects displayed tau deposition, at least in the transentorhinal cortex (Braak I). Tau deposition solely in the transentorhinal cortex was associated with an elevated prevalence of amyloid-β, neurodegeneration, and cognitive impairment (P &lt; 0.0001). 18F-MK-6240 deposition in regions corresponding to Braak IV–VI was associated with the highest prevalence of neurodegeneration, whereas in Braak V–VI regions with the highest prevalence of cognitive impairment. Our results suggest that the hierarchical six-stage Braak model using 18F-MK-6240 imaging provides an index of early and late tau accumulation as well as disease stage in preclinical and symptomatic individuals. Tau PET Braak staging using high affinity tracers has the potential to be incorporated in the diagnosis of living patients with Alzheimer’s disease in the near future.
Salience Network Atrophy Links Neuron Type-Specific Pathobiology to Loss of Empathy in Frontotemporal Dementia
Authors: Pasquini Lorenzo , Nana Alissa L , Toller Gianina , Brown Jesse A , Deng Jersey , Staffaroni Adam , Kim Eun-Joo , Hwang Ji-Hye L , Li Libo , Park Youngsoon , Gaus Stephanie E , Allen Isabel , Sturm Virginia E , Spina Salvatore , Grinberg Lea T , Rankin Katherine P , Kramer Joel H , Rosen Howard J , Miller Bruce L , Seeley William W 
Published: May 2020

Abstract
Each neurodegenerative syndrome reflects a stereotyped pattern of cellular, regional, and large-scale brain network degeneration. In behavioral variant of frontotemporal dementia (bvFTD), a disorder of social-emotional function, von Economo neurons (VENs), and fork cells are among the initial neuronal targets. These large layer 5 projection neurons are concentrated in the anterior cingulate and frontoinsular (FI) cortices, regions that anchor the salience network, a large-scale system linked to social-emotional function. Here, we studied patients with bvFTD, amyotrophic lateral sclerosis (ALS), or both, given that these syndromes share common pathobiological and genetic factors. Our goal was to determine how neuron type-specific TAR DNA-binding protein of 43 kDa (TDP-43) pathobiology relates to atrophy in specific brain structures and to loss of emotional empathy, a cardinal feature of bvFTD. We combined questionnaire-based empathy assessments, in vivo structural MR imaging, and quantitative histopathological data from 16 patients across the bvFTD/ALS spectrum. We show that TDP-43 pathobiology within right FI VENs and fork cells is associated with salience network atrophy spanning insular, medial frontal, and thalamic regions. Gray matter degeneration within these structures mediated loss of emotional empathy, suggesting a chain of influence linking the cellular, regional/network, and behavioral levels in producing signature bvFTD clinical features.
Atrial pacing and administration of nifekalant hydrochloride for unstable atrial fibrillation: a case report
Authors: Yakabe Daisuke , Araki Masahiro , Furukawa Kojiro , Nakamura Toshihiro 
Published: May 2020

Abstract

Background
Atrial fibrillation (AF) is a common arrhythmia in patients with hypertrophic cardiomyopathy (HCM) and can deteriorate haemodynamic status.

Case summary
We report a case of a 77-year-old woman with cardiogenic shock due to paroxysmal AF, complicated with HCM and aortic stenosis. Atrial fibrillation was successfully managed with temporary atrial pacing and administration of nifekalant hydrochloride without invasive mechanical circulatory support until surgery. Septal myectomy, aortic valve replacement, and pulmonary vein isolation were performed.

Discussion
This case suggests that atrial pacing and nifekalant may be safe and effective for rhythm control.
Primary extraskeletal chondroblastic osteosarcoma of the pericardium: a case report and literature review
Authors: Wang Qianqian , Wang Xiaojie , Zhu Qing , Gu Xinghua , Gao Peng , Chen Yuguo , Wu Xiaojuan , Li Chuanbao 
Published: May 2020

Abstract

Background
Primary extraskeletal chondroblastic osteosarcoma has very poor prognosis, especially in the elderly. The pericardium is an extremely rare site for this tumour.

Case summary
A 67-year-old man presented with a large pericardial effusion and an intrapericardial mass. His past medical history of pulmonary tuberculosis led us to initially suspect tuberculous pericarditis. Primary extraskeletal chondroblastic osteosarcoma arising from the pericardium was diagnosed by the pathologist after surgery. The patient suffered severe intraoperative blood loss and surgical trauma. He went into shock and died a few hours after surgery.

Discussion
Extraskeletal chondroblastic osteosarcoma is a very rare tumour with a grim prognosis. Clinical manifestations frequently are not specific and can be explained by associated pathology. In this report, we describe an unusual case of primary extraskeletal chondroblastic osteosarcoma located in the pericardium and present a review of the literature.
Pathogenesis of Influenza A(H7N9) Virus in Aged Nonhuman Primates
Authors: Fukuyama Satoshi , Iwatsuki-Horimoto Kiyoko , Kiso Maki , Nakajima Noriko , Gregg Robert W , Katsura Hiroaki , Tomita Yuriko , Maemura Tadashi , da Silva Lopes Tiago Jose , Watanabe Tokiko , Shoemaker Jason E , Hasegawa Hideki , Yamayoshi Seiya , Kawaoka Yoshihiro 
Published: May 2020

Abstract
The avian influenza A(H7N9) virus has caused high mortality rates in humans, especially in the elderly; however, little is known about the mechanistic basis for this. In the current study, we used nonhuman primates to evaluate the effect of aging on the pathogenicity of A(H7N9) virus. We observed that A(H7N9) virus infection of aged animals (defined as age 20–26 years) caused more severe symptoms than infection of young animals (defined as age 2–3 years). In aged animals, lung inflammation was weak and virus infection was sustained. Although cytokine and chemokine expression in the lungs of most aged animals was lower than that in the lungs of young animals, 1 aged animal showed severe symptoms and dysregulated proinflammatory cytokine and chemokine production. These results suggest that attenuated or dysregulated immune responses in aged animals are responsible for the severe symptoms observed among elderly patients infected with A(H7N9) virus.
Influence of Storage Conditions on SARS-CoV-2 Nucleic Acid Detection in Throat Swabs
Authors: Li Lin , Li Xiao , Guo Zhendong , Wang Zhongyi , Zhang Ke , Li Chao , Wang Changjun , Zhang Shoufeng 
Published: May 2020

Abstract
The detection of SARS-CoV-2 infection is the premise of quarantine. In many countries or areas, samples need to be shipped or inactivated before SARS-CoV-2 testing. In this study, we checked the influence of sample storage conditions on SARS-CoV-2 nucleic acid testing results, including sample inactivation time, storage temperature, and storage time. All of these conditions caused an increase in the cycle threshold values of the nucleic acid tests and led to the misclassification of at least 10.2% of positive cases as negative or suspected. The results highlight the importance of immediate testing of samples for SARS-CoV-2 nucleic acid detection.
Binary evolution leading to the formation of the very massive neutron star in the J0740+6620 binary system
Authors: Echeveste M , Novarino M L , Benvenuto O G , De Vito M A 
Published: May 2020

ABSTRACT
We study the evolution of close binary systems in order to account for the existence of the recently observed binary system containing the most massive millisecond pulsar ever detected, PSR J0740+6620, and its ultra-cool helium white dwarf companion. In order to find a progenitor for this object we compute the evolution of several binary systems composed by a neutron star and a normal donor star employing our stellar code. We assume conservative mass transfer. We also explore the effects of irradiation feedback on the system. We find that irradiated models also provide adequate models for the millisecond pulsar and its companion, so both irradiated and non irradiated systems are good progenitors for PSR J0740+6620. Finally, we obtain a binary system that evolves and accounts for the observational data of the system composed by PSR J0740+6620 (i.e. orbital period, mass, effective temperature and inferred metallicity of the companion, and mass of the neutron star) in a time scale smaller than the age of the Universe. In order to reach an effective temperature as low as observed, the donor star should have an helium envelope as demanded by observations.
Structure of two G-quadruplexes in equilibrium in the KRAS promoter
Authors: Marquevielle Julien , Robert Coralie , Lagrabette Olivier , Wahid Mona , Bourdoncle Anne , Xodo Luigi E , Mergny Jean-Louis , Salgado Gilmar F 
Published: May 2020

Abstract
KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conformations of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nuclease Hypersensitive Element (NHE) region. We have determined the structure of the two major stable conformers that 32R can adopt and which display slow equilibrium (&gt;ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3′ end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.
A powder method for the high-efficacy evaluation of electro-optic crystals
Authors: Xu Feng , Zhang Ge , Luo Min , Peng Guang , Chen Yu , Yan Tao , Ye Ning 
Published: May 2020

Abstract
The electro-optic crystal holds great promise for extensive applications in optoelectronics and optical communication. However, the discovery of novel electro-optic crystals is sporadic due to the difficulties of large-sized crystal growth for electro-optic coefficient measurement. Herein, to address this issue, a high-efficacy evaluation method using accessible powder samples is proposed in which the second-harmonic-generation effect, infrared reflectance spectrum and Raman spectrum are introduced to predict the magnitude of the electro-optic coefficient. The calculated electro-optic coefficients of numerous reported electro-optic crystals through this approach give universal agreement to the experimental values, evidencing the validity of the strategy. Based on this method, CsLiMoO4 is screened as a novel potential electro-optic crystal and a high-quality crystal is grown by the Czochralski technique for electro-optic coefficient measurement using the half-wave voltage method, the result of which is also comparable to the calculated value. Consequently, the evaluation strategy presented here will pave a new way to explore promising electro-optic crystals efficiently.
Correlation Between Chest CT Findings and Clinical Features of 211 COVID-19 Suspected Patients in Wuhan, China
Authors: Song Songlin , Wu Feihong , Liu Yiming , Jiang Hongwei , Xiong Fu , Guo Xiaopeng , Zhang Hongsen , Zheng Chuansheng , Yang Fan 
Published: May 2020

AbstractBackgroundChest computed tomography (CT) has been widely used to assess pulmonary involvement in COVID-19. We aimed to investigate the correlation between chest CT and clinical features in COVID-19 suspected patients with or without fever.MethodsWe retrospectively enrolled 211 COVID-19 suspected patients who underwent both chest CT and reverse transcription polymerase chain reaction in Wuhan, China. The performance of CT in patients with relevant onset of symptoms, with fever (n = 141) and without fever (n = 70), was assessed respectively.ResultsThe sensitivity of CT for COVID-19 was 97.3%, with area under the curve (AUC) of 0.71 (95% confidence interval [CI], 0.66–0.76). There were 141 suspected patients with fever and 70 without fever. In the fever group, 4 variables were screened to establish the basic model: age, monocyte, red blood cell, and hypertension. The AUC of the basic model was 0.72 (95% CI, 0.63–0.81), while the AUC of the CT-aided model was 0.77 (95% CI, 0.68–0.85), a significant difference (P &lt; .05). In the nonfever group, only dry cough was screened out to establish the basic model. The AUC was 0.76 (95% CI, 0.64–0.88), which was not significantly different than the CT-aided model (P = .08).ConclusionsChest CT has a high sensitivity in patients with COVID-19, and it can improve diagnostic accuracy for COVID-19 suspected patients with fever during the initial screen, whereas its value for nonfever patients remains questionable.
Life Stressors: Elevations and Disparities Among Older Adults with Pain
Authors: Brennan Penny L 
Published: May 2020

Abstract

Objective
To examine stressor elevations among older adults with pain, and gender and race disparities in the dual burdens of late-life pain and stressors.

Design
Cross-sectional.

Setting
Community.

Subjects
Participants in the Longitudinal Late-Life Health study (LLLH; N = 1,884) and the Health and Retirement Study (HRS; N = 7,704).

Methods
Pain and stressor measures were harmonized across the LLLH and HRS samples. Analyses of covariance were conducted to determine the effects of older adults’ pain, gender, race, and interactions between these factors, on their stressors in nine separate life domains, and in stressors overall.

Results
In both the LLLH and HRS samples, older adults with painful conditions (joint, back, headache, chest pain), more numerous painful conditions, more severe pain, and more pain interference had elevated stressors in all life domains, compared with older adults without or with less serious pain. Pain was more prevalent among women and nonwhites than men and whites. Stressor exposure was higher for men than women in most life domains; it was higher for nonwhites than whites in all life domains. For certain types of pain and life domains, pain and gender, as well as pain and race, interacted to predict stressor elevations.

Conclusions
Late-life pain is associated with elevations in stressors, and there are gender and race disparities in the dual burdens of heightened pain and elevated stressors in later life. Pain and stressors are not consistently more strongly linked among older women than older men, or among older nonwhite than older white persons.
The effects of phenanthrene exposure on Treg and Th17 cells related cytokines in female rats
Authors: Ma Haitao , Guo Huizhen , Zhang Wenwen , Hu Fengjing , Huang Yushan , Zeng Yong , Liu Yang , Li Chengyun , Wang Junling 
Published: May 2020

Abstract
Phenanthrene (Phe) female rat model was established to explore the mechanism of Phe on immune impairment. The rats were randomly divided into three groups, including control (C), low (L), and high (H) groups. Phe was supplied to L and H groups at the dose of 180 and 900 mg/kg orally at first day and with the dose of 90 and 450 mg/kg by intraperitoneal injection at the last 2 days. The C group was enriched with the same volume of corn oil. The liver tissue was collected. Then, the protein and mRNA expressions of interleukin (IL)-35 and the concentration IL-17 were detected to evaluate the function of regulatory T cells (Treg cells) and T helper 17 cells (Th17 cells). In addition, IL-1β and interferon-γ (IFN-γ) were analyzed to evaluate the immune impairment. The results showed that the protein and mRNA expressions of IL-35 decreased significantly in H groups (P &lt; 0.05). Meanwhile, there were significant increases in IL-17, IFN-γ and IL-1β in the liver of H group (P &lt; 0.05). This study demonstrated that Phe exposure might be associated with the immune impairment via changing inflammatory mediators including IL-35 and IL-17 in female rats.
Prevalence and clinical manifestations of dengue in older patients in Bangkok Hospital for Tropical Diseases, Thailand
Authors: Chhong Lay Ngeab , Poovorawan Kittiyod , Hanboonkunupakarn Borimas , Phumratanaprapin Weerapong , Soonthornworasiri Ngamphol , Kittitrakul Chatporn , Nontprasert Apichart , Pukrittayakamee Sasithon 
Published: May 2020

Abstract

Background
The global incidence of dengue has increased with the ageing population. We examined the prevalence, clinical manifestations and risk factors associated with dengue severity among older patients.

Methods
A retrospective cohort study was conducted at a hospital in Thailand from 2013 to 2018. Data were collected from patient records. Older patients were those aged ≥60 y, whereas adult patients were aged at least 18 y but younger than 60 y.

Results
In total, 1822 patients were included in the study. The prevalence of older dengue was 7.96%. Older dengue patients were at a higher risk of developing dengue haemorrhagic fever (DHF) than adult dengue patients (40.69% vs 30.71%). Haematuria was significantly more frequent in older patients (24.82% vs 3.58%), whereas other clinical manifestations had similar frequencies between the groups. Multivariate logistic regression indicated that hypertension (adjusted OR [aOR]=3.549, 95% CI 1.498 to 8.407) and abdominal pain (aOR=10.904, 95% CI 1.037 to 114.710) were significantly associated with DHF among older patients.

Conclusions
Dengue is common in older adults, who also have a higher incidence of developing DHF. Older patients with dengue and comorbid hypertension and abdominal pain should be monitored for their increasing risk of DHF.
Dix-seq: An integrated pipeline for fast amplicon data analysis
Authors: wei Yongjun , Ren Tianqi , Zhang Lei 
Published: May 2020

AbstractThe amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.