bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rational Design of a Protein Kinase A Nuclear-cytosol Translocation Reporter
Authors: Kim Allen K. , Wu Helen D. , Inoue Takanari 
Published: June 2020

AbstractProtein Kinase A (PKA) exists as a tetrameric holoenzyme which activates with increase of cAMP and plays an important role in many physiological processes including cardiac physiology, neuronal development, and adipocyte function. Although this kinase has been the subject of numerous biosensor designs, a single-fluorophore reporter that performs comparably to Förster resonance energy transfer (FRET) has not yet been reported. Here, we have used basic observations of electrostatic interactions in PKA substrate recognition mechanism and nucleus localization sequence motif to design a phosphorylation switch that shuttles between the cytosol and the nucleus, a strategy that should be generalizable to all basophilic kinases. The resulting reporter yielded comparable kinetics and dynamic range to the PKA FRET reporter, AKAR3EV. We also performed basic characterization and demonstrated its potential use in monitoring multiple signaling molecules inside cells using basic fluorescence microscopy. Due to the single-fluorophore nature of this reporter, we envision that this could find broad applications in studies involving single cell analysis of PKA activity.
High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project
Authors: Chen Yi-ran , Zheng Hui-min , Zhang Guo-xia , Chen Fang-lan , Chen Li-dan , Yang Zhi-cong 
Published: June 2020

AbstractOscillospira is a common yet rarely cultivated gut bacterial genus. Recently human gut microbiota studies have demonstrated its underlying significance for host health. However, little is known about Oscillospira-related host information and the links between Oscillospira and other members of the gut microbial community. To study the ecology of Oscillospira and gain insights into Oscillospira-related host physiological conditions, we analyzed data from the Guangdong Gut Microbiome Project, one of the largest gut microbiota database currently. Data of 6376 participants were analyzed. We studied the prevalence and relative abundance of Oscillospira as well as the profiles of associated microbial communities. We found that Oscillospira is closely related to human health because its abundance was positively correlated with microbial diversity, high density lipoprotein, and sleep time, and was inversely correlated with diastolic blood pressure, systolic blood pressure, fasting blood glucose, triglyceride, uric acid and Bristol stool type. Moreover, random forest analysis with five-fold cross validation showed Oscillospira could be a predictor of low BMI and constipation in the subset. Overall, in this study, we provide a basic understanding of Oscillospira-related microbiota profile and physiological parameters of the host. Our results indicate Oscillospira may play a role in aggravating constipation.
Bacterial community composition and potential pathogens along the Pinheiros River in the southeast of Brazil
Authors: Godoy Rafaela Garrido , Marcondes Marta Angela , Pessôa Rodrigo , Nascimento Andrezza , Victor Jefferson Russo , Duarte Alberto José da Silva , Clissa Patricia Bianca , Sanabani Sabri Saeed 
Published: June 2020

AbstractThe Pinheiros River in São Paulo, Brazil, crosses through the capital city and has its confluence with the River Tiete, which comprises several reservoirs along its course. Although Pinheiros River is considered one of the heaviest polluted rivers in Brazil, little is known about its bacterial composition, their metabolic functions or how these communities are affected by the physicochemical parameters of the river. In this study, we used the 16S rRNA gene Illumina MiSeq sequencing to profile the bacterial community from the water surface at 11 points along the course of the River. Taxonomical composition revealed an abundance of Proteobacteria phyla, followed by Firmicutes and Bacteroidetes, with a total of 233 classified bacterial families and 558 known bacterial genera. Among the 35 potentially pathogenic bacteria identified, Arcobacter was the most predominant genus. The disrupted physicochemical parameters detected in this study may possibly contribute to the composition and distribution of the bacterial community in the Pinheiros River. Predictive functional analysis suggests the River is abundant in motility genes, including bacterial chemotaxis and flagellar assembly. These results provide novel and detailed insights into the bacterial communities and putative function of the surface water in the Pinheiros River.
Prevalence and characterization of severe asthma in Hungary
Authors: Csoma Zsuzsanna , Gál Zsófia , Gézsi András , Herjavecz Irén , Szalai Csaba 
Published: June 2020

AbstractBackground: Severe asthma (SA) database was established in Hungary to estimate the prevalence of SA and to define and analyze clinical phenotypes of the patients. Methods: SA questionnaires were sent out to 143 public pulmonary dispensaries specialized for diagnosing and caring pulmonary patients. Data of 520 SA patients were evaluated. Results: The prevalence of SA within the asthmatic population in Hungary was 0.89%. The mean age of patients were 56.4 ± 13.4 years, SA were more frequent in females (64%), the prevalence of allergy was 56.6%, 72.1% of patients had persistent airflow limitation (FEV1 < 80%), 37.9% severe airway obstruction (FEV1 ≤ 60%), 33.6% required systemic corticosteroid maintenance therapy, 21.5% had salicylate intolerance and 43.2% rhinosinusitis. A Bayesian dependency network was calculated which revealed several interdependencies between the characteristics. E.g. there was a strong association between salicylate intolerance and rhinosinusitis, more patients received regular systemic corticosteroid treatment who had salicylate intolerance and the proportion of salicylate intolerance was significantly higher in females. Conclusion: The prevalence of SA was determined in Hungary which was lower than in other studies. Using a Bayesian-based network analysis several interdependencies were revealed between patient characteristics.
High-glucose environment accelerates annulus fibrosus cell apoptosis by regulating endoplasmic reticulum stress
Authors: Pang Lianglong , Yang Keshi , Zhang Zhi 
Published: June 2020

AbstractDiabetes mellitus (DM) is an important risk factor of intervertebral disc degeneration. However, how DM affects annulus fibrosus (AF) biology remains unclear. The present study was aimed to investigate the effects and mechanism of high glucose on AF cell biology. Rat AF cells were cultured in baseline medium and culture medium with 0.2 M glucose. The inhibitor 4-PBA was added along with the high glucose culture medium to study the role of endoplasmic reticulum (ER) stress in this process. Compared with the control cells, high glucose significantly increased cell apoptosis ratio and caspase-3/9 activity, up-regulated mRNA/protein expression of Bax and caspase-3/cleaved caspase-3, but down-regulated mRNA/protein expression of Bcl-2. Moreover, high glucose increased mRNA and protein expression of CHOP, ATF-6 and GRP78. However, once ER stress was inhibited by the inhibitor 4-PBA in the high glucose group, cell apoptosis ratio and caspase-3/9 activity were decreased, mRNA/protein expression of Bax and caspase-3/cleaved caspase-3 was down-regulated, but mRNA/protein expression of Bcl-2 was up-regulated. In conclusion, high glucose condition can promote AF cell apoptosis through inducing ER stress. The present study helps us understand the mechanism of disc degeneration in DM patients.
Enhanced SMARCD1, a subunit of the SWI/SNF complex, promotes liver cancer growth through the mTOR pathway
Authors: Zhou Yongjie , Xu Qing , Tao Lv , Chen Yuwei , Shu Yuke , Wu Zhenru , Lu Changli , Shi Yujun , Bu Hong 
Published: June 2020

Abstract
The chromatin remodeling complex SWI/SNF regulates the accessibility of target genes to transcription factors and plays a critical role in the tumorigenesis of hepatocellular carcinoma (HCC). The SWI/SNF complex is assembled from approximately 15 subunits, and most of these subunits have distinct roles and are often aberrantly expressed in HCC. A comprehensive exploration of the expression and clinical significance of these subunits would be of great value. In the present study, we obtained the gene expression profile of each SWI/SNF subunit and the corresponding clinical information from The Cancer Genome Atlas (TCGA). We found that 14 out of the 15 SWI/SNF subunits were significantly increased in HCC tissues compared with paired normal liver tissues, and 11 subunits were significantly associated with overall survival (OS). We identified a four-gene prognostic signature including actin-like 6A (ACTL6A), AT-rich interaction domain 1A (ARID1A), SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily C member 1 (SMARCC1) and SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily D, member 1 (SMARCD1) that could effectively predict OS in HCC patients. Among the genes, SMARCD1 has the most prognostic value. We further conducted in vitro and in vivo experiments and revealed that SMARCD1 promotes liver cancer growth by activating the mTOR signaling pathway. In conclusion, our study has revealed that the expression of SWI/SNF complex subunits, especially SMARCD1, is highly associated with HCC development and acts as a promising prognostic predictor.
Construction of a statistical learning tool based on ordinary differential equations to model the digestive behaviour of ross chickens
Authors: Bloyet Nicolas , Flourent Hélène , Frénod Emmanuel , Handa Marouan , Moundoyi Harold , Phuong Thuy Vo Thi 
Published: June 2020

Being able to monitor and forecast farm animal performances is a strategic problem in the agronomy industry. We use a Data-Model Coupling approach to build a biomimetic Statistical Learning tool taking into account some aspects of the biological dynamics of the animal body. The objective is to build a tool which is able to assimilate data about daily feed consumption and measured performances.
The model encompasses several sub-models corresponding to compartments and permitting to mimic a kinetic process divided into several steps. Each sub-model contains parameters which can be learnt by using an optimization algorithm and data.
The goal of the ﬁrst application of the model on ﬁeld data was to simulate and predict the growth of chickens.
An experiment was performed during 70 days to collect every day the feed consumption and the weight gain of a male and a female chickens. After the learning of the model parameters, the model shows a very good approximation of the chicken’s weight evolution over time.
Soziale Distanz: Wenn die protektiven Effekte sozialer Nähe
eingeschränkt sind
Authors: Ditzen Beate 
Published: June 2020

Liebe Kolleginnen und Kollegen,das letztmonatige Editorial in der PPmP von Martina de Zwaan und Stephan Herpertz war
betitelt mit „So etwas haben wir noch nie erlebt!“. Nun sind wir
schon einen Monat länger weltweit mit der Corona-Krise beschäftigt
und in den betroffenen Ländern wurden mehr oder weniger umfassende
Maßnahmen zum „social distancing“ getroffen, um die
Verbreitung des Virus SARS-CoV-2 zu bremsen.
Automatic Alignment of Cranial CT Examinations to the Anterior Commissure/Posterior Commissure (ACPC) Reference Plane for Reliable Interpretation and Quality Assurance
Authors: Rubbert Christian , Turowski Bernd , Caspers Julian 
Published: June 2020

Alignment of cranial CT scans (cCTs) to a common reference plane simplifies anatomical-landmark-based orientation and eases follow-up assessment of intracranial findings. We developed and open sourced a fully automated system, which aligns cCTs to the Anterior Commissure/Posterior Commissure (ACPC) line and exports the results to the PACS. FMRIB’s Linear Image Registration Tool (FLIRT) with an ACPC-aligned atlas is used in the alignment step. Five mm mean slabs are generated with the top non-air slice as the starting point. For evaluation, 301 trauma cCTs from the CQ500 dataset were processed. In visual comparison with the respective ACPC-aligned atlas, all were successfully aligned. Image quality (IQ) and ease of identification of the central sulcus (CS) were rated on a Likert scale (5 = excellent IQ/immediate CS identification). The median IQ was 4 (range: 2–4) in the original series and 5 (range: 4–5) in the ACPC-aligned series (p < 0.0001). The CS was more easily identified after fatbACPC (original scans: 4 (range: 2–5); ACPC-aligned: 5 (range: 4–5); p < 0.0001). The mean rotation to achieve alignment was |X| = 6.4 ± 5.2° ([–X,+X] = –26.8°–24.2°), |Y| = 2.1 ± 1.7° ([-Y,+Y] = –8.7°–9.8°), and |Z| = 3.1 ± 2.4° ([–Z,+Z] = –14.3°–12.5°). The developed system can robustly and automatically align cCTs to the ACPC line. Degrees of deviation from the ideal alignment could be used for quality assurance.
Key Points:

Citation Format
Avaliação das propriedades histológicas de enxertos meniscais humanos armazenados em banco de tecido
Authors: Netto Alfredo dos Santos , Antebi Uri , Morais Carolina Esteves de , Sementilli Leonardo , Severino Nilson Roberto , Cury Ricardo de Paula Leite 
Published: June 2020

Resumo
Objetivos Avaliar e comparar as características histológicas de meniscos frescos e meniscos congelados armazenados em banco de tecidos por 1 mês e por 5 anos.
Métodos Foi feito um estudo histológico com enxertos meniscais. Avaliamos 10 meniscos, sendo 2 que ficaram armazenados sob congelamento por 5 anos, 4 armazenados congelados por 1 mês, e 4 frescos, recém captados. Foram feitos cortes histológicos corados com hematoxilina e eosina e Tricrômico de Masson, para avaliação das propriedades histológicas.
Resultados Os meniscos congelados por 1 mês apresentaram preservação parcial da estrutura das fibras colágenas, sem degeneração hidrópica significativa do tecido. Nos meniscos congelados por 5 anos, observamos dissociação evidente das fibras colágenas, com presença de múltiplos focos de degeneração hidrópica.
Discussão Encontramos degeneração bem mais significativa nos meniscos armazenados por 5 anos, o que indica que o longo período de congelamento leva à progressão significativa da degeneração do tecido. Isto pode sugerir que o período de 5 anos, considerado período máximo que o enxerto pode permanecer armazenado antes de ser transplantado, é um período muito longo.
Conclusão Nos enxertos armazenados por 1 mês, existiu apenas discreta alteração degenerativa das fibras colágenas, enquanto que nos meniscos com 5 anos de congelamento foi observada degeneração significativa do tecido. Tibiais
Giant Retroperitoneal Sarcoma: A Case Report and Review of Literature
Authors: Saad Melissa K. , Fiani Elias , Abdullah Ali , Saikaly Elias 
Published: June 2020

AbstractLiposarcomas are neoplasms of mesodermal origin derived from adipose tissue representing 10 to 14% of all soft tissue sarcomas, with the most frequent subtype being liposarcoma. Given that the retroperitoneum is a large space in which the retroperitoneal liposarcoma can grow asymptomatically up until a mass effect develop. Hence, patients usually present late with symptoms with possible invasion to nearby structures. These tumors are known to reach significantly large dimension, despite their poor vascularization and can grow to enormous size, the average diameter of the tumor is 20 to 25 cm with a weight of 15 to 20 kg. Surgery with en-bloc resection of the tumor and adherent nearby structures, with intact capsule, remains the gold standard in surgical management of retroperitoneal sarcomas. Herein, we present a case of 52 year old male patient with a huge 48 cm right-sided retroperitoneal liposarcoma, managed surgically by en bloc excision of the tumor, right kidney, right ureter, right adrenal gland, and the right colon.
Common genetic susceptibility loci link PFAPA syndrome, Behçet’s disease, and recurrent aphthous stomatitis
Authors: Manthiram Kalpana , Preite Silvia , Dedeoglu Fatma , Demir Selcan , Ozen Seza , Edwards Kathryn M. , Lapidus Sivia , Katz Alexander E. ,   The Genomic Ascertainment Cohort, Feder Henry M. , Lawton Maranda , Licameli Greg R. , Wright Peter F. , Le Julie , Barron Karyl S. , Ombrello Amanda K. , Barham Beverly , Romeo Tina , Jones Anne , Srinivasalu Hemalatha , Mudd Pamela A. , DeBiasi Roberta L. , Gül Ahmet , Marshall Gary S. , Jones Olcay Y. , Chandrasekharappa Settara C. , Stepanovskiy Yuriy , Ferguson Polly J. , Schwartzberg Pamela L. , Remmers Elaine F. , Kastner Daniel L. , Ascher David P. , Biesecker Leslie G. , Chan Priscilla , Conrads Thomas P. , Johnston Jennifer J. , Katz Alexander E. , Lewis Katie L. , Maxwell G. Larry , Paschall Justin , Shiferaw Henoke , Wolfsberg Tyra G. , Wong Wendy S.W. , Zhang Suiyuan 
Published: June 2020

SignificanceIn this report we identify genetic susceptibility variants for periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome, the most common periodic fever syndrome in children. PFAPA shares risk loci atIL12A,STAT4, IL10, andCCR1-CCR3with Behçet’s disease and recurrent aphthous stomatitis, defining a family of Behçet’s spectrum disorders. DifferentialHLAassociations along this spectrum may determine where individual phenotypes fall among the Behçet’s spectrum disorders.
Formulaicity without expressed multiword units
Authors: Tao Hongyin 
Published: June 2020

Abstract
In this chapter, I investigate three types of formulaic structure that can be
characterized as underspecified with elliptical materials and lacking the
kind of expressed multiword units as typically conceived. The elliptical or
source structures are shown to manifest in different unit sizes: (a) simple
constituents such as modifiers/quantifiers, (b) phrasal units of various
types, and (c) larger clausal units or complex turn-constructional units and
the use of conjunctions. As elliptical forms of formulaic expressions are
found at multiple levels of linguistic structure, this chapter raises a
range of theoretical questions concerning formulaicity, including the
prevailing conceptualization of formulaic language or fixed expression,
proportions of prefabricated constructions in human language, mechanisms of
storage and retrieval, as well as cross-linguistic properties of formulaic
language.
Study of the possibilities with combinations of circularly and linearly polarized light for attosecond delay investigations
Authors: Sörngård J , Dahlström J M , Lindroth E 
Published: June 2020

Abstract
We present calculations on the atomic delay in photoionzation obtained with different combinations of linearly and circularly polarized light, and show how a tensor operator approach can be used to readily obtain results for any combination from a single calculation of the radial integrals. We find that for certain choices of polarization and detection geometry a single time-delay measurement is enough to extract the atomic delay since the relative phase in a RABBIT type measurement will be imprinted on the photo electron anisotropy. We show further that the full angular dependence can be qualitatively understood from a plane wave analysis. The results are illustrated by many-body calculations of two-photon above threshold ionization on argon.
Design of a dual-port, side-incident microwave probe for detection of in-pipe damage
Authors: Chen Guanren , Katagiri Takuya , Yusa Noritaka , Hashizume Hidetoshi 
Published: June 2020

Abstract
This study reports on a dual-port, side-incident microwave probe dedicated to the non-destructive inspection of metal pipes. Two types of side-incident probes (LJ and JL) are proposed to emit TM01- and TM02-mode microwaves into the pipe under test, and each type of probe has two ports used to inspect in two opposite directions. Numerical simulations are conducted to study the dimensional parameters affecting the transmission characteristics of the probe and optimize the probe to obtain better mode purity and transmission directivity. The simulation results also suggest that the optimal probe dimensions for one inner pipe diameter can be applied to another diameter by multiplying the dimensions by a factor that is determined by the ratio of two diameters. Two LJ-type, side-incident probes, one with an inner diameter of 19 mm and one of 39 mm, are fabricated according to the simulation results. Experimental verification is subsequently carried out to test the detection directivity of the probes by detecting the short pipes with partially milled damage situated on both sides of both probes. Experimental results show that the proposed dual-port, side-incident probe can effectively detect the in-pipe damage on either side of the probe using the corresponding port and thus realize the directional pipe inspection. Furthermore, this method shows a potential to be applied to various inner pipe diameters.
A measuring method for micro force based on MEMS planar torsional spring
Authors: Wu Jian , Liu Tonggang , Wang Kesheng , Sørby Knut 
Published: June 2020

Abstract
In order to measure the micro force in a micro-nano device, a new measuring method for micro force is introduced. In this paper, a measuring system based on a micro-electro-mechanical systems (MEMS) planar torsional spring is presented, which contains a support block, MEMS planar torsional spring, a support arm, and a laser displacement detection system. The micro force has been obtained by measuring the moving distance of the light spot which is reflected by the MEMS planar torsional spring. The spring sample has been prepared with laser processing technology, and the stiffness is obtained by theoretical calculation, simulation, and calibration. The results show that the torsional stiffness of the MEMS planar torsional spring is 3.7181 Nm rad−1. The measurement system has a measuring range of ±159 mN. The maximum error of mean in repeated measurement is 1.25% of the reference value, and the repeatability standard deviation is a maximum 4.44% of the reference value.
Alkali-cation-incorporated and functionalized iron oxide nanoparticles for methyl blue removal/decomposition
Authors: Singh N Joseph , Wareppam Boris , Ghosh Subrata , Sahu B Prasad , AjiKumar P K , Singh H Premjit , Chakraborty Soumee , Pati S S , Oliveira A C , Barg Suelen , Garg V K , Singh L Herojit 
Published: June 2020

Abstract
Enhancing the rate of decomposition or removal of organic dye by designing novel nanostructures is a subject of intensive research aimed at improving waste-water treatment in the textile and pharmaceutical industries. Despite radical progress in this challenging area using iron-based nanostructures, enhancing stability and dye adsorption performance is highly desirable. In the present manuscript alkali cations are incorporated into iron oxide nanoparticles (IONPs) to tailor their structural and magnetic properties and to magnify methyl blue (MB) removal/decomposition capability. The process automatically functionalizes the IONPs without any additional steps. The plausible mechanisms proposed for IONPs incubated in alkali chloride and hydroxide solutions are based on structural investigation and correlated with the removal/adsorption capabilities. The MB adsorption kinetics of the incubated IONPs is elucidated by the pseudo second-order reaction model. Not only are the functional groups of –OH and –Cl attached to the surface of the NPs, the present investigation also reveals that the presence of alkali cations significantly influences the MB adsorption kinetics and correlates with the cation content and atomic polarizability.