bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of synbiotic supplementation on energy and macronutrients homeostasis and muscle wasting of critical care patients: study protocol and a review of previous studies
Authors: Seifi Najmeh , Safarian Mohammad , Nematy Mohsen , Rezvani Reza , Khadem-Rezaian Majid , Sedaghat Alireza 
Published: February 2020

Abstract
Background
An extreme and persistent dysbiosis occurs among critically ill patients, regardless of the heterogeneity of disease. Dysbiosis in critically ill patients may make them prone to hospital-acquired infections, sepsis, multi-organ failure (MOF), energy homeostasis disturbance, muscle wasting, and cachexia. Modulation of gut microbiota through synbiotics can be considered as a potential treatment for muscle wasting and macronutrient homeostasis disturbances.

Methods
This is a prospective, single-center, double-blind, parallel randomized controlled trial with the aim to evaluate the effects of synbiotic supplementation on energy and macronutrient homeostasis and muscle wasting in critically ill patients. A total of 40 hemodynamically stable, adult, critically ill patients who receive enteral nutrition via a nasogasteric tube (NGT) in the 24–48 h after admission to critical care will be included in this study. Eligible patients will be randomly assigned to receive Lactocare (ZistTakhmir) capsules 500 mg every 12 h or a placebo capsule, which contains only the sterile maize starch and is similar to synbiotic capsules for 14 days. The synbiotic and placebo capsules will be given through the nasogastric tube, separately from gavage, after feeding.

Discussion
Gut microbiota modulation through synbiotics is proposed to improve clinical prognosis and reduce infectious complications, ventilator dependency, and length of ICU stay by improving energy and macronutrient homeostasis and reducing muscle protein catabolism.

Trial registration
Iranian Registry of Clinical Trials, IRCT20190227042857N1. Registered on 17 March 2019.
Effect of community active case-finding strategies for detection of tuberculosis in Cambodia: study protocol for a pragmatic cluster randomized controlled trial
Authors: Teo Alvin Kuo Jing , Prem Kiesha , Evdokimov Konstantin , Ork Chetra , Eng Sothearith , Tuot Sovannary , Chry Monyrath , Mao Tan Eang , Hsu Li Yang , Yi Siyan 
Published: February 2020

Abstract
Background
Cambodia has made notable progress in the fight against tuberculosis (TB). However, these gains are impeded by a significant proportion of undiagnosed cases. To effectively reach people with TB, active case-finding (ACF) strategies have been adopted by countries affected by the epidemic, including Cambodia, alongside passive case finding (PCF). Despite increased efforts to improve case detection, approximately 40% of TB cases in Cambodia remained undiagnosed in 2018. In Cambodia, several community-based TB ACF modalities have been implemented, but their effectiveness has yet to be systematically assessed.

Methods
This pragmatic cluster randomized controlled trial will be conducted between December 2019 and June 2021. We will randomize eight operational districts (clusters) in seven provinces (Kampong Cham, Kampong Thom, Prey Veng, Thbong Khmum, Kampong Chhnang, Kandal, and Kampong Speu) to either the control group (PCF) or the intervention groups (ACF using a seed-and-recruit model, ACF targeting household and neighborhood contacts, and ACF targeting persons aged ≥ 55 years using mobile screening units). The primary endpoints will be TB case notification rates, additionality, and cumulative yield of TB cases. The secondary endpoints include treatment outcomes, the number needed to screen to find one TB case, and cost-effectiveness outcome measures. We will analyze the primary and secondary endpoints by intention to treat. We will compare cluster and individual-level characteristics using Student’s t test and hierarchical or mixed-effect models to estimate the ratio of these means. The incremental cost-effectiveness ratio per disability-adjusted life year averted will also be considered as a benchmark to determine whether the interventions are cost-effective.

Discussion
This study will build an evidence base to inform future scale-up, implementation, and sustainability of ACF strategies in Cambodia and other similar settings. Implementation of this study will also complement TB control strategies in Cambodia by conducting ACF in operational districts without active interventions to find TB cases currently. Those who are ill and might have TB will be promptly screened, diagnosed, and linked to care. Early diagnosis and treatment initiation will also benefit their community by interrupting transmission and prevent further infections. The experience gained from this project will inform future attempts in conducting pragmatic trials in low-resource settings.

Trial registration
ClinicalTrials.gov, NCT04094350. Registered on 18 September 2019.
New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
Authors: Campanaro Stefano , Treu Laura , Rodriguez-R Luis M. , Kovalovszki Adam , Ziels Ryan M. , Maus Irena , Zhu Xinyu , Kougias Panagiotis G. , Basile Arianna , Luo Gang , Schlüter Andreas , Konstantinidis Konstantinos T. , Angelidaki Irini 
Published: February 2020

Abstract
Background
Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.

Results
Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain.

Conclusions
The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
Molecular characterization of a Trichinella spiralis elastase-1 and its potential as a diagnostic antigen for trichinellosis
Authors: Hu Chen Xi , Jiang Peng , Yue Xin , Zeng Jie , Zhang Xin Zhuo , Song Yan Yan , Liu Ruo Dan , Zhang Xi , Wang Zhong Quan , Cui Jing 
Published: February 2020

Abstract
Background
Trichinella spiralis muscle larval (ML) excretion/secretion (ES) antigen is the most widely used diagnostic antigen of trichinellosis, but preparation of ES antigen requires collecting worms from infected animals, and detection of specific IgG against ML ES antigen may result in a false negative at the early stage of infection. The aim of the study was to characterize T. spiralis elastase-1 (TsEla) and to evaluate its potential as diagnostic antigen for trichinellosis.

Methods
The complete cDNA sequences of the TsEla gene were cloned and expressed, and recombinant (rTsEla) was purified. TsEla transcription and expression in different T. spiralis life-cycle stages was investigated by qPCR and western blotting, and its location in the nematodes was evaluated using an immunofluorescence assay (IFA). The antigenicity of rTsEla was investigated by western blotting analysis and ELISA. Anti-Trichinella IgG, IgM and IgE of experimentally infected mice and specific IgG antibodies of trichinellosis patients were assayed by rTsEla-ELISA and ES-ELISA.

Results
The results of the qPCR and western blotting showed that TsEla was expressed in various T. spiralis life stages. Natural TsEla was detected in the soluble proteins and ES proteins of different life stages. IFA revealed that TsEla was identified in the whole nematodes of various stages, especially in the cuticle, stichosome and genital primordium of the parasite. Serum anti-Trichinella IgM, IgG and IgE in infected mice was first detected by rTsEla-ELISA at 6, 10 and 12 days post-infection (dpi), and reached 100% at 8, 14 and 14 dpi, respectively. When rTsEla-ELISA and ES-ELISA were used to detect anti-Trichinella IgG in sera of trichinellosis patients, the sensitivity was 97.37% (37/38) and 89.74% (34/38) (P > 0.05), and the specificity was 99.10% (220/222) and 98.20% (218/222), respectively (P > 0.05). The rTsEla cross-reacted with only one serum sample out of 20 samples from paragonimiasis patients and 7 samples from clonorchiasis patients.

Conclusions
rTsEla is valuable to early diagnosis of trichinellosis and could be an alternative diagnostic antigen to the ML ES antigens.
Seasonal effect on fatigue, pain and dryness in primary Sjögren’s syndrome
Authors: Duret Pierre-Marie , Meyer Nicolas , Saraux Alain , Devauchelle-Pensec Valérie , Seror Raphaele , Le-Guern Véronique , Larroche Claire , Perdriger Aleth , Sibilia Jean , Guardiolle Vianney , Mariette Xavier , Gottenberg Jacques-Eric 
Published: February 2020

Abstract
Background
To assess the presence of a seasonal effect on fatigue, pain and dryness in primary Sjögren’s syndrome (pSS).

Methods
Data (date; visual analogue scales (VAS) for pain, fatigue and dryness) were extracted from three randomised placebo-controlled trials (RCTs) evaluating infliximab (TRIPSS; n = 103 patients), hydroxychloroquine (JOQUER; n = 120 patients) and rituximab (TEARS; n = 120 patients) and from the 5-year follow-up of the ASSESS prospective cohort (n = 395 patients). Data were analysed at each visit for each patient, according to the day, the month of the year and the season. Linear mixed models were used to take into account the repeated structure of the data and to analyse a potential cyclic effect.

Results
A total of 744, 584, 848 and 682 pain, fatigue and dryness VASs were collected on 632 subjects in spring, summer, fall and winter, respectively. No significant difference was observed in pain, fatigue and dryness, according to the month of the year or the season (all p values > 0.05).

Conclusion
In pSS, seasonality does not affect patient-reported outcomes (PROs) on fatigue, pain and dryness.
covRNA: discovering covariate associations in large-scale gene expression data
Authors: Urban Lara , Remmele Christian W. , Dittrich Marcus , Schwarz Roland F. , Müller Tobias 
Published: February 2020

AbstractObjectiveThe biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns.ResultsThe Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow.
Management of psoriasis-like rash associated with idelalisib monotherapy in a patient with refractory follicular lymphoma: a case report
Authors: Machan Salma , Plaza Carlos , Pérez-González Yosmar , Rodriguez-Pinilla Maria , Requena Luis , Cordoba Raul 
Published: February 2020

Abstract
Background
Follicular lymphoma is an indolent non-Hodgkin lymphoma that is most commonly diagnosed in elderly individuals. The majority of patients with follicular lymphoma present with advanced disease. Despite the recent advances in treatment, there remains a substantial unmet need for effective treatments for patients with relapsed/refractory follicular lymphoma. The PI3Kδ inhibitor idelalisib was approved by the European Medicines Agency in 2014 as a monotherapy for the treatment of adult patients with follicular lymphoma that is refractory to two prior lines of treatment. Real-world evidence from patients with follicular lymphoma treated with idelalisib indicates its utility in these patients.

Case presentation
This case report describes an 82-year-old, retired, white, female patient with refractory follicular lymphoma who achieved a partial response with idelalisib treatment. Despite experiencing two incidences of a psoriasis-like rash during idelalisib treatment that required effective management with topical steroids, the patient was able to restart treatment successfully and maintain a continued partial response.

Conclusions
The clinical relevance of the effective management of adverse events in this case demonstrates the opportunity to enable patients to remain on therapy, thereby maintaining long-term response and improving overall outcomes.
Indium-111-labeled CD166-targeted peptide as a potential nuclear imaging agent for detecting colorectal cancer stem-like cells in a xenograft mouse model
Authors: Guan Siao-Syun , Wu Cheng-Tien , Liao Tse-Zung , Luo Tsai-Yueh , Lin Kun-Liang , Liu Shing-Hwa 
Published: February 2020

AbstractBackgroundCancer stem cells (CSCs) are involved in drug resistance, metastasis, and relapse of cancers, which can significantly affect tumor therapy. Hence, to develop specifically therapeutic target probe at CSCs for improvement of survival and quality of life of cancer patients is urgently needed. The CD166 protein has been suggested to be involved in colorectal cancer (CRC) tumorigenesis and to be considered a marker for colorectal CSCs (CRCSCs) detection. In this study, therefore, we attend to apply a nuclear imaging agent probe, Glycine18-Cystine-linked CD166-targeted peptides (CD166tp-G18C), to detect the changes of CD166 level in a CRC xenograft mouse model.ResultsWe isolated the CD166-positive cells from the HCT15 CRC cell line (CD166+HCT15) and evaluated their morphology and ability of clone formation, migration, protein expression, and drug resistance. The CD166-positive HCT15 cells display the CSCs characteristics. We discovered and designed a CD166-targeted peptide (CD166tp-G18C) as a targeted probe of CRC stem-like cell for cell binding assay. The CD166tp-G18C confirmed the CD166 protein targeting ability in CD166+HCT15 cells. The diethylenetriaminopentaacetic acid (DTPA)-conjugated CD166tp-G18C further was labeled with indium-111 (111In-DTPA-CD166tp-G18C) as nuclear imaging agent for imaging and bio-distribution analysis in vivo. Finally, we observed that the111In-DTPA-CD166tp-G18C was significantly enhanced in tumor tissues of CD166+HCT15 xenograft mice as compared to the non-CD166tp-G18C control.ConclusionsOur results indicated that the indium-111-labeled CD166tp-G18C may be served as a powerful tool for colorectal CSCs nuclear imaging in the CRC patients.
Adaptive filtering and analysis of EEG signals in the time-frequency domain based on the local entropy
Authors: Madhale Jadav Guruprasad , Lerga Jonatan , Štajduhar Ivan 
Published: February 2020

AbstractThe brain dynamics in the electroencephalogram (EEG) data are often challenging to interpret, specially when the signal is a combination of desired brain dynamics and noise. Thus, in an EEG signal, anything other than the desired electrical activity, which is produced due to coordinated electrochemical process, can be considered as unwanted or noise. To make brain dynamics more analyzable, it is necessary to remove noise in the temporal location of interest, as well as to denoise data from a specific spatial location. In this paper, we propose a novel method for noisy EEG analysis with accompanying toolbox which includes adaptive, data-driven noise removal technique based on the improved intersection of confidence interval (ICI)-based algorithm. Next, a local entropy-based method for EEG data analysis was designed and included in the toolbox. As shown in the paper, the relative intersection of confidence interval (RICI) procedure retains the dominant dipole activity projected on electrodes, while the local (short-term) Rényi entropy-based analysis of the EEG representation in the time-frequency domain is efficient in detecting the presence of P300 event-related potential (ERP) at specific electrodes. Namely, the P300 are detected as sharp drop of entropy in the temporal domain that enabled accurate calculation of the index of the noise class for the EEG signals.
Existence of extremal solutions for discontinuous Stieltjes differential equations
Authors: López Pouso Rodrigo , Márquez Albés Ignacio 
Published: February 2020

AbstractStieltjes differential equations, which contain equations with impulses and equations on time scales as particular cases, simply consist in replacing usual derivatives by derivatives with respect to a nondecreasing function. In this paper we prove new results for the existence of extremal solutions for discontinuous Stieltjes differential equations. In particular, we prove that the pointwise infimum of upper solutions of a Stieltjes differential equation is the minimal solution under certain hypotheses. These results can be adapted to the context of both difference equations and impulsive differential equations.
Global exponential stability of delayed inertial competitive neural networks
Authors: Shi Min , Guo Juan , Fang Xianwen , Huang Chuangxia 
Published: February 2020

AbstractIn this paper, the exponential stability for a class of delayed competitive neural networks is studied. By applying the inequality technique and non-reduced-order approach, some novel and useful criteria of global exponential stability for the addressed network model are established. Moreover, a numerical example is presented to show the feasibility and effectiveness of the theoretical results.
Dynamic correlation pattern amongst alternative energy market for diversification opportunities
Authors: Rehman Mobeen Ur 
Published: February 2020

AbstractLast couple of decades witnessed recognition of energy markets as investment commodities which led interest of the international investment community. We investigate the potential of globally diverse alternative energy markets for optimal returns by analysing their correlation pattern. Our study employs daily data spanning from January 2006 to December 2017. To estimate pair-wise return co-movement, we employ rolling window multiple wavelet correlation based on decomposed returns using maximal overlap discrete wavelet transformation to infer implications for both short- and long-run investors. We witness maximum diversification between developed (World, Developed, EU, G7) and emerging (BRIC, Emerging) markets. Most of these combinations exhibit no traces of contagion during the financially and economically turbulent periods. Finally, we use non-linear causality test to highlight increased integration between our sampled alternative energy indices after financial and economic crises periods. Our results carry implications for short- and long-run investors as well as for policy makers.
Applying micro-computed tomography (micro-CT) and Raman spectroscopy for non-invasive characterization of coating and coating pigments on ancient Chinese papers
Authors: Li Tao , Liu Chuang , Wang Dongmei 
Published: February 2020

Abstract
The coating technique, supposedly invented by Chinese papermakers no later than the 3rd century AD, greatly improved paper sheets’ qualities of color, texture, writability, and printability. Alongside the dispersal of papermaking and surface-treatment techniques beyond China, coated papers were manufactured and used in many other regions of the world. Understanding the manufacture of coated papers, therefore, is crucial for perceiving how surface treatments were developed to meet the need for paper with enhanced properties. However, the characterization of coating and coating pigments on ancient Chinese papers has long remained an unsolved issue, and previous studies on this topic have often produced inconclusive results. To explore a non-invasive methodology that can more reliably characterize coated papers and the coating pigment on them, this article presents the results of a pilot study that applied micro-computed tomography (micro-CT) and Raman spectroscopy to samples of three Qing Dynasty (1644–1911 AD) papers and two handmade papers manufactured in China in the 1990s. Micro-CT revealed the coating layer(s) on Lajian (waxed coated paper) and Lengjinjian (gold-dusted paper) of the Qing Dynasty and characterized the modern raw xuan and bamboo papers as uncoated. Raman spectroscopy, together with handheld X-ray fluorescence analysis, identified the mineral-based pigment in the coating layer, suggesting the use of lead white or kaolin as the coating pigment. Additionally, Raman analysis confirmed the use of other mineral pigments (red lead and cinnabar), beeswax, and organic dyes (gamboge, kermesic acid, and possibly purpurin) in the manufacture of Lajian and Lengjinjian papers. The combination of micro-CT and Raman spectroscopy, it is therefore suggested, is a practical, more reliable approach for non-invasive investigation of coating and coating pigments on ancient Chinese paper specimens.
Non-contact visual control of personalized hand prostheses/exoskeletons by tracking using augmented reality glasses
Authors: Hazubski Simon , Hoppe Harald , Otte Andreas 
Published: February 2020

AbstractA new concept for robust non-invasive optical activation of motorized hand prostheses by simple and non-contact commands is presented. In addition, a novel approach for aiding hand amputees is shown, outlining significant progress in thinking worth testing. In this, personalized 3D-printed artificial flexible hands are combined with commercially available motorized exoskeletons, as they are used e.g. in tetraplegics.
The prevalence, characteristics and outcome of seizure in tuberculous meningitis
Authors: Abdulaziz Ammar Taha Abdullah , Li Jinmei , Zhou Dong 
Published: February 2020

AbstractSeizures are a common finding in patients with tuberculous meningitis (TBM), and associate with four times increased risk of death and neurological disability, especially in children. It has been reported that brain inflammation, diffuse neuronal injury, and reactive gliosis may all contribute to the pathogenesis of seizures in TBM. Early seizure onset may be associated with meningeal irritation and cerebral oedema; while, the late seizures are usually due to infarction, hydrocephalus, tuberculoma and paradoxical response. Moreover, recurrent uncontrolled seizures can evolve to status epileptics resulting in an increased risk of chronic epilepsy and poor prognosis. Therefore, this review aimed to assess the frequency of seizures in patients with TBM, and discuss the etiologies, mechanisms, and characteristics of seizures in TBM. Besides, we have searched the literature to identify the prognostic factors for chronic epilepsy after TBM.