bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor
Authors: Tian Yang , Lin Chien-Yuan , Park Joon-Hyun , Wu Chuan-Yin , Kakumanu Ramu , Pidatala Venkataramana R. , Vuu Khanh M. , Rodriguez Alberto , Shih Patrick M. , Baidoo Edward E. K. , Temple Stephen , Simmons Blake A. , Gladden John M. , Scheller Henrik V. , Eudes Aymerick 
Published: November 2021

Abstract
Background
The development of bioenergy crops with reduced recalcitrance to enzymatic degradation represents an important challenge to enable the sustainable production of advanced biofuels and bioproducts. Biomass recalcitrance is partly attributed to the complex structure of plant cell walls inside which cellulose microfibrils are protected by a network of hemicellulosic xylan chains that crosslink with each other or with lignin via ferulate (FA) bridges. Overexpression of the rice acyltransferase OsAT10 is an effective bioengineering strategy to lower the amount of FA involved in the formation of cell wall crosslinks and thereby reduce cell wall recalcitrance. The annual crop sorghum represents an attractive feedstock for bioenergy purposes considering its high biomass yields and low input requirements. Although we previously validated the OsAT10 engineering approach in the perennial bioenergy crop switchgrass, the effect of OsAT10 expression on biomass composition and digestibility in sorghum remains to be explored.

Results
We obtained eight independent sorghum (Sorghum bicolor (L.) Moench) transgenic lines with a single copy of a construct designed for OsAT10 expression. Consistent with the proposed role of OsAT10 in acylating arabinosyl residues on xylan with p-coumarate (pCA), a higher amount of p-coumaroyl-arabinose was released from the cell walls of these lines upon hydrolysis with trifluoroacetic acid. However, no major changes were observed regarding the total amount of pCA or FA esters released from cell walls upon mild alkaline hydrolysis. Certain diferulate (diFA) isomers identified in alkaline hydrolysates were increased in some transgenic lines. The amount of the main cell wall monosaccharides glucose, xylose, and arabinose was unaffected. The transgenic lines showed reduced lignin content and their biomass released higher yields of sugars after ionic liquid pretreatment followed by enzymatic saccharification.

Conclusions
Expression of OsAT10 in sorghum leads to an increase of xylan-bound pCA without reducing the overall content of cell wall FA esters. Nevertheless, the amount of total cell wall pCA remains unchanged indicating that most pCA is ester-linked to lignin. Unlike other engineered plants overexpressing OsAT10 or a phylogenetically related acyltransferase with similar putative function, the improvements of biomass saccharification efficiency in sorghum OsAT10 lines are likely the result of lignin reductions rather than reductions of cell wall-bound FA. These results also suggest a relationship between xylan-bound pCA and lignification in cell walls.
The association between FTO rs9939609 polymorphism and serum lipid profile in adult women
Authors: Jalili Vahideh , Mokhtari Zohreh , Rastgoo Samira , Hajipour Azadeh , Bourbour Fatemeh , Gholamalizadeh Maryam , Mosavi Jarrahi Alireza , JavadiKooshesh Sepehr , Moslem Alireza , Abdollahi Morteza , Doaei Saeid 
Published: November 2021

Abstract
Background
FTO gene is considered to play an important role in many metabolic diseases. Evidence from studies indicated the possible association between the FTO rs9939609 polymorphisms with serum lipid profile. Therefore, this study aimed to investigate the association of FTO rs9939609 polymorphism with lipid profile in Iranian women.

Methods
This cross-sectional study was carried out on 380 adult women. Information about age, height, weight, BMI, physical activity, and dietary intake were collected. The serum levels of Low Density Lipoprotein (LDL), High Density Lipoprotein (HDL), Triglyceride (TG), and total cholesterol were measured. The FTO gene was genotyped for rs9939609 polymorphism. The participants were divided into two groups of TT and AT/AA considering dominant model of FTO rs9939609 polymorphism.

Results
General characteristics of the participants with different FTO genotypes were not significantly different. The lower levels of HDL were observed in AT/AA genotypes compared to the TT wild type genotype of FTO rs9939609 polymorphism (P = 0.004). Adjustments of age, BMI, and physical activity did not change the results.

Conclusions
However, the significant association between FTO genotype and the HDL level was disappeared after further adjustments for dietary intake. Further studies are warranted to identify the underlying mechanisms of the possible association between FTO gene and serum lipid profile.
Machine learning-based CT radiomics approach for predicting WHO/ISUP nuclear grade of clear cell renal cell carcinoma: an exploratory and comparative study
Authors: Xv Yingjie , Lv Fajin , Guo Haoming , Zhou Xiang , Tan Hao , Xiao Mingzhao , Zheng Yineng 
Published: November 2021

AbstractPurposeTo investigate the predictive performance of machine learning-based CT radiomics for differentiating between low- and high-nuclear grade of clear cell renal cell carcinomas (CCRCCs).MethodsThis retrospective study enrolled 406 patients with pathologically confirmed low- and high-nuclear grade of CCRCCs according to the WHO/ISUP grading system, which were divided into the training and testing cohorts. Radiomics features were extracted from nephrographic-phase CT images using PyRadiomics. A support vector machine (SVM) combined with three feature selection algorithms such as least absolute shrinkage and selection operator (LASSO), recursive feature elimination (RFE), and ReliefF was performed to determine the most suitable classification model, respectively. Clinicoradiological, radiomics, and combined models were constructed using the radiological and clinical characteristics with significant differences between the groups, selected radiomics features, and a combination of both, respectively. Model performance was evaluated by receiver operating characteristic (ROC) curve, calibration curve, and decision curve analyses.ResultsSVM-ReliefF algorithm outperformed SVM-LASSO and SVM-RFE in distinguishing low- from high-grade CCRCCs. The combined model showed better prediction performance than the clinicoradiological and radiomics models (p < 0.05, DeLong test), which achieved the highest efficacy, with an area under the ROC curve (AUC) value of 0.887 (95% confidence interval [CI] 0.798–0.952), 0.859 (95% CI 0.748–0.935), and 0.828 (95% CI 0.731–0.929) in the training, validation, and testing cohorts, respectively. The calibration and decision curves also indicated the favorable performance of the combined model.ConclusionA combined model incorporating the radiomics features and clinicoradiological characteristics can better predict the WHO/ISUP nuclear grade of CCRCC preoperatively, thus providing effective and noninvasive assessment.
Cell therapy as a treatment of secondary lymphedema: a systematic review and meta-analysis
Authors: Lafuente Hector , Jaunarena Ibon , Ansuategui Eukene , Lekuona Arantza , Izeta Ander 
Published: November 2021

AbstractBackgroundLymphedema, the accumulation of interstitial fluid caused by poor lymphatic drainage, is a progressive and permanent disease with no curative treatment. Several studies have evaluated cell-based therapies in secondary lymphedema, but no meta-analysis has been performed to assess their efficacy.MethodsWe conducted a systematic review and meta-analysis of all available preclinical and clinical studies, with assessment of their quality and risk of bias.ResultsA total of 20 articles using diverse cell types were selected for analysis, including six clinical trials and 14 pre-clinical studies in three species. The meta-analysis showed a positive effect of cell-based therapies on relevant disease outcomes (quantification of edema, density of lymphatic capillaries, evaluation of the lymphatic flow, and tissue fibrosis). No significant publication bias was observed.ConclusionCell-based therapies have the potential to improve secondary lymphedema. The underlying mechanisms remain unclear. Due to relevant heterogeneity between studies, further randomized controlled and blinded studies are required to substantiate the use of these novel therapies in clinical practice.
Sex and gender considerations in reporting guidelines for health research: a systematic review
Authors: Gogovor Amédé , Zomahoun Hervé Tchala Vignon , Ekanmian Giraud , Adisso Évèhouénou Lionel , Deom Tardif Alèxe , Khadhraoui Lobna , Rheault Nathalie , Moher David , Légaré France 
Published: November 2021

Abstract
Background
Despite growing recognition of the importance of sex and gender considerations in health research, they are rarely integrated into research design and reporting. We sought to assess the integration of sex, as a biological attribute, and gender, as a socially constructed identity, in published reporting guidelines.

Methods
We conducted a systematic review of published reporting guidelines listed on the EQUATOR website (www.equator-nework.org) from inception until December 2018. We selected all reporting guidelines (original and extensions) listed in the EQUATOR library. We used EndNote Citation Software to build a database of the statements of each guideline identified as a "full bibliographic reference" and retrieved the full texts. Reviewers independently extracted the data on use of sex and gender terms from the checklist/abstract/main text of guidelines. Data were analyzed using descriptive statistics and narrative synthesis.

Results
A total of 407 reporting guidelines were included; they were published between 1995 and 2018. Of the 407 guidelines, 235 (57.7%) mentioned at least one of the sex- and gender-related words. In the checklist of the reporting guidelines (n = 363), “sex” and “gender” were mentioned in 50 (13.8%) and 40 (11%), respectively. Only one reporting guideline met our criteria (nonbinary, appropriate categorization, and non-interchangeability) for correct use of sex and gender concepts. Trends in the use of "sex" and "gender" in the checklists showed that the use of “sex” only started in 2003, while “gender” has been in use since 1996.

Conclusions
We assessed the integration of sex and gender in reporting guidelines based on the use of sex- and gender-related words. Our findings showed a low use and integration of sex and gender concepts and their incorrect use. Authors of reporting guidelines should reduce this gap for a better use of research knowledge.
Trial registration PROSPERO no. CRD42019136491.
Deleting qseC downregulates virulence and promotes cross-protection in Pasteurella multocida
Authors: Yang Yang , Hu Pei , Gao Lixu , Yuan Xiang , Hardwidge Philip R. , Li Tian , Li Pan , He Fang , Peng Yuanyi , Li Nengzhang 
Published: November 2021

AbstractQseC, a histidine sensor kinase of the QseBC two-component system, acts as a global regulator of bacterial stress resistance, biofilm formation, and virulence. The function of QseC in some bacteria is well understood, but not inPasteurella multocida. We found that deletingqseCinP. multocidaserotype A:L3 significantly down-regulated bacterial virulence. The mutant had significantly reduced capsule production but increased resistance to oxidative stress and osmotic pressure. DeletingqseCled to a significant increase inqseBexpression. Transcriptome sequencing analysis showed that 1245 genes were regulated byqseC, primarily those genes involved in capsule and LPS biosynthesis and export, biofilm formation, and iron uptake/utilization, as well as several immuno-protection related genes includingompA,ptfA,plpB,vacJ, andsodA. In addition to presenting strong immune protection againstP. multocidaserotypes A:L1 and A:L3 infection, live ΔqseCalso exhibited protection againstP. multocidaserotype B:L2 and serotype F:L3 infection in a mouse model. The results indicate that QseC regulates capsular production and virulence inP. multocida. Furthermore, theqseCmutant can be used as an attenuated vaccine againstP. multocidastrains of multiple serotypes.
RETRACTED ARTICLE: Real-time detection of aerobics posture based on strain sensor
Authors: Zhu Shanshan 
Published: November 2021

AbstractThe Internet of Things is a network that realizes the intelligent connection between things. It is another major industry after the computer industry and the Internet industry. It is also a collection of computer technology, communication technology, sensor technology, storage technology, and many other leading technologies in an integrated industry, the application industry is very wide. This article mainly introduces the real-time detection of aerobics posture based on strain sensors. This paper proposes a real-time detection method of motion posture based on strain sensors, using flexible rods to simulate the joints of aerobics athletes. Through the survey of the motion posture by the strain sensor, the relevant data and parameters are collected, and then the data are processed, and the data are finally transmitted to the terminal. Since the stress of a specific point on the surface of the flexible rod is proportional to the curve of that point, strain gauges can be used to detect curve changes at multiple points in real time and draw the change curve on the computer. The experimental structure of this paper shows that the use of BP neural network to process the measurement data improves the accuracy of real-time detection. The error distance between the sampling point and the actual value is less than 0.3 cm. In addition, through the real-time detection of the motion posture, it can be concluded that good Body posture is the basic requirement of aerobics, and it is of great significance to improve the effect of improving the quality of movement and artistic expression.
A multichannel learning-based approach for sound source separation in reverberant environments
Authors: Chen You-Siang , Lin Zi-Jie , Bai Mingsian R. 
Published: November 2021

AbstractIn this paper, a multichannel learning-based network is proposed for sound source separation in reverberant field. The network can be divided into two parts according to the training strategies. In the first stage, time-dilated convolutional blocks are trained to estimate the array weights for beamforming the multichannel microphone signals. Next, the output of the network is processed by a weight-and-sum operation that is reformulated to handle real-valued data in the frequency domain. In the second stage, a U-net model is concatenated to the beamforming network to serve as a non-linear mapping filter for joint separation and dereverberation. The scale invariant mean square error (SI-MSE) that is a frequency-domain modification from the scale invariant signal-to-noise ratio (SI-SNR) is used as the objective function for training. Furthermore, the combined network is also trained with the speech segments filtered by a great variety of room impulse responses. Simulations are conducted for comprehensive multisource scenarios of various subtending angles of sources and reverberation times. The proposed network is compared with several baseline approaches in terms of objective evaluation matrices. The results have demonstrated the excellent performance of the proposed network in dereverberation and separation, as compared to baseline methods.
Positive solutions for eigenvalue problems of fractional q-difference equation with ϕ-Laplacian
Authors: Wang Jufang , Yu Changlong , Zhang Boya , Wang Si 
Published: November 2021

AbstractThe aim of this paper is to investigate the boundary value problem of a fractional q-difference equation with ϕ-Laplacian, where ϕ-Laplacian is a generalized p-Laplacian operator. We obtain the existence and nonexistence of positive solutions in terms of different eigenvalue intervals for this problem by means of the Green function and Guo–Krasnoselskii fixed point theorem on cones. Finally, we give some examples to illustrate the use of our results.
A price-aware congestion control protocol for cloud services
Authors: Sun Xiaocui , Wang Zhijun , Wu Yunxiang , Che Hao , Jiang Hong 
Published: November 2021

AbstractIn current infrastructure-as-a service (IaaS) cloud services, customers are charged for the usage of computing/storage resources only, but not the network resource. The difficulty lies in the fact that it is nontrivial to allocate network resource to individual customers effectively, especially for short-lived flows, in terms of both performance and cost, due to highly dynamic environments by flows generated by all customers. To tackle this challenge, in this paper, we propose an end-to-end Price-Aware Congestion Control Protocol (PACCP) for cloud services. PACCP is a network utility maximization (NUM) based optimal congestion control protocol. It supports three different classes of services (CoSes), i.e., best effort service (BE), differentiated service (DS), and minimum rate guaranteed (MRG) service. In PACCP, the desired CoS or rate allocation for a given flow is enabled by properly setting a pair of control parameters, i.e., a minimum guaranteed rate and a utility weight, which in turn, determines the price paid by the user of the flow. Two pricing models, i.e., a coarse-grained VM-Based Pricing model (VBP) and a fine-grained Flow-Based Pricing model (FBP), are proposed. The optimality of PACCP is verified by both large scale simulation and small testbed implementation. The price-performance consistency of PACCP are evaluated using real datacenter workloads. The results demonstrate that PACCP provides minimum rate guarantee, high bandwidth utilization and fair rate allocation, commensurate with the pricing models.
Clonal spread of carbapenem-resistant Klebsiella pneumoniae among patients at admission and discharge at a Vietnamese neonatal intensive care unit
Authors: Berglund Björn , Hoang Ngoc Thi Bich , Lundberg Ludwig , Le Ngai Kien , Tärnberg Maria , Nilsson Maud , Bornefall Elin , Khu Dung Thi Khanh , Welander Jenny , Le Hai Thanh , Olson Linus , Dien Tran Minh , Nilsson Lennart E. , Larsson Mattias , Hanberger Håkan 
Published: November 2021

Abstract
Background
The increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is a growing problem globally, particularly in low- to middle-income countries (LMICs). Previous studies have shown high rates of CRE colonisation among patients at hospitals in LMICs, with increased risk of hospital-acquired infections.

Methods
We isolated carbapenem-resistant Klebsiella pneumoniae (CRKP) from faecal samples collected in 2017 from patients at admission and discharge at a Vietnamese neonatal intensive care unit (NICU). 126 CRKP were whole-genome sequenced. The phylogenetic relationship between the isolates and between clinical CRKP isolates collected in 2012–2018 at the same hospital were investigated.

Results
NDM-type carbapenemase-(61%) and KPC-2-encoding genes (41%) were the most common carbapenem resistance genes observed among the admission and discharge isolates. Most isolates (56%) belonged to three distinct clonal clusters of ST15, carrying blaKPC-2, blaNDM-1 and blaNDM-4, respectively. Each cluster also comprised clinical isolates from blood collected at the study hospital. The most dominant ST15 clone was shown to be related to isolates collected from the same hospital as far back as in 2012.

Conclusions
Highly resistant CRKP were found colonising admission and discharge patients at a Vietnamese NICU, emphasising the importance of continued monitoring. Whole-genome sequencing revealed a population of CRKP consisting mostly of ST15 isolates in three clonally related clusters, each related to blood isolates collected from the same hospital. Furthermore, clinical isolates collected from previous years (dating back to 2012) were shown to likely be clonally descended from ST15 isolates in the largest cluster, suggesting a successful hospital strain which can colonise inpatients.
Tensile Performance, Lap-Splice Length and Behavior of Concretes Confined by Prefabricated C-FRCM System
Authors: Choi Donguk , Vachirapanyakun Sorrasak , Ochirbud Munckhtuvshin , Naidangjav Undram , Ha Sangsu , Kim Youngho 
Published: November 2021

AbstractResults of an experimental study aimed to evaluate tensile performance, lap-splice length of carbon fabric-reinforced cementitious matrix system (C-FRCM), and performance of concretes confined by C-FRCM are presented. Green high-strength mortar was used in this study which actively utilized recycled fine aggregate and fine waste glass powder to partially substitute cementitious binder. Test plans were developed in due consideration of prefabricated C-FRCM for strengthening concrete columns: 14 tensile tests, 12 lap-splice tests, and 6 uniaxial compression tests of plain concrete specimens confined by C-FRCM were performed. Test variable for the tensile test was number of fabric layers (one or two layers). Nominal strength of the C-FRCM with two fabric layers was 11.0 MPa while it was 7.4 MPa with one fabric layer in tension. Full strength of the carbon fabric was developed in all tensile tests while the C-FRCM with two fabric layers (with axial fiber amount = 0.59% by vol.) showed pseudo-ductile behavior. From the lap-splice tests in direct tension, an increased lap-splice length was required for the double fabrics over that for the single fabrics. The required splice length was about 170 mm for the single fabrics and it was about 310 mm for the double fabrics. Plain concrete cylinders and prismatic specimens were laterally confined by C-FRCM and subjected to uniaxial compression. All test results showed strain-softening behavior. Compressive strength increased by 10–41% while ductility also increased by 6–45% indicating applicability of the prefabricated type C-FRCM in the future.
Efficient parallel derivation of short distinguishing sequences for nondeterministic finite state machines using MapReduce
Authors: Elghadyry Bilal , Ouardi Faissal , Lotfi Zineb , Verel Sébastien 
Published: November 2021

AbstractDistinguishing sequences are widely used in finite state machine-based conformance testing to solve the state identification problem. In this paper, we address the scalability issue encountered while deriving distinguishing sequences from complete observable nondeterministic finite state machines by introducing a massively parallel MapReduce version of the well-known Exact Algorithm. To the best of our knowledge, this is the first study to tackle this task using the MapReduce approach. First, we give a concise overview of the well-known Exact Algorithm for deriving distinguishing sequences from nondeterministic finite state machines. Second, we propose a parallel algorithm for this problem using the MapReduce approach and analyze its communication cost using Afrati et al. model. Furthermore, we conduct a variety of intensive and comparative experiments on a wide range of finite state machine classes to demonstrate that our proposed solution is efficient and scalable.