bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of prognosis, genome, microbiome, and microbial metabolome in different sites of colorectal cancer
Authors: Xi Yang , Yuefen Pan , Wei Wu , Quan Qi , Jing Zhuang , Jiamin Xu , Shuwen Han 
Published: October 2019

Abstract

Background
The colorectum includes ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. Different sites of colorectal cancer (CRC) are different in many aspects, including clinical symptoms, biological behaviour, and prognosis.

Purpose
This study aimed to analyse prognosis, genes, bacteria, fungi, and microbial metabolome in different sites of CRC.

Methods
The Surveillance, Epidemiology, and End Results (SEER) database and STAT were used to statistically describe and analyse the prognosis in different sites of CRC. RNA sequences of CRC from Broad Institute’s GDAC Firehose were re-annotated and reanalysed based on different sites using weighted gene co-expression network analysis (WGCNA). The Kaplan–Meier method was used to analyse the prognosis and Cytoscape was used to construct a drug-target network based on DGIdb databases. Bacterial 16S V3–V4 and fungal ITS V3–V4 ribosomal RNA genes of stool samples were sequenced. Gas chromatography/mass spectrometry (GS/MS) was performed to detect the microbial metabolites in stool samples. Bioinformatics analysis was performed to compare distinct gut microorganisms and microbial metabolites between rectal and sigmoid cancers.

Results
The prognosis in CRC with different sites is significantly different. The closer to the anus predicted longer survival time. The difference between genes and co-expression pairs in CRC with different sites were constructed. The relative abundance of 112 mRNAs and 26 lncRNAs correlated with the sites of CRC were listed. Nine differentially expressed genes at different sites of CRC were correlated with prognosis. A drug-gene interaction network contained 227 drug-gene pairs were built. The relative abundance of gut bacteria and gut fungus, and the content of microbe-related metabolites were statistically different between rectal and sigmoid cancers.

Conclusions
There are many differences in prognosis, genome, drug targets, gut microbiome, and microbial metabolome in different colorectal cancer sites. These findings may improve our understanding of the role of the CRC sites in personalized and precision medicine.
The clinical characteristics and molecular mechanism of pituitary adenoma associated with meningioma
Authors: Zhu Haibo , Miao Yazhou , Shen Yutao , Guo Jing , Xie Weiyan , Zhao Sida , Dong Wei , Zhang Yazhuo , Li Chuzhong 
Published: October 2019

Abstract

Background
Pituitary adenoma and meningioma are the most common benign tumors in the central nervous system. Pituitary adenoma associated with meningioma (PAM) is a rare disease and the clinical features and mechanisms of PAM are unclear.

Methods
We summarized the clinical data of 57 PAM patients and compared with sporadic pituitary adenoma (SPA) and sporadic meningioma (SM). 5 pituitary adenomas of PAM and 5 SPAs were performed ceRNA microarray. qRT-PCR, Western Blot, siMEN1 and rapamycin inhibition experiment were validated for ceRNA microarray.

Results
Clinical variable analyses revealed that significant correlations between PAM and female sex as well as older age when compared with SPA and significant correlations between PAM and transitional meningioma as well as older age when compared with SM. Additionally, the characteristics of PAM were significantly different for MEN1 patients. Functional experiments showed lower expression of MEN1 can upregulate mTOR signaling, in accordance with the result of ceRNA microarray. Rapamycin treatment promotes apoptosis in primary pituitary adenoma and meningioma cells of PAM.

Conclusions
MEN1 plays an important role in PAM by upregulating mTOR signaling pathway. Rapamycin represents a potential therapeutic strategy for PAM in the future.
Pharmacological and chemogenetic orexin/hypocretin intervention ameliorates Hipp-dependent memory impairment in the A53T mice model of Parkinson’s disease
Authors: Stanojlovic Milos , Pallais Jean Pierre , Lee Michael K. , Kotz Catherine M. 
Published: October 2019

AbstractParkinson’s disease (PD), classically defined as a progressive motor disorder accompanied with dopaminergic neuron loss and presence of Lewy bodies, is the second most common neurodegenerative disease. PD also has various non-classical symptoms, including cognitive impairments. In addition, inflammation and astrogliosis are recognized as an integral part of PD pathology. The hippocampus (Hipp) is a brain region involved in cognition and memory, and the neuropeptide orexin has been shown to enhance learning and memory. Previous studies show impairments in Hipp-dependent memory in a transgenic mouse model of Parkinson’s disease (A53T mice), and we hypothesized that increasing orexin tone will reverse this. To test this, we subjected 3, 5, and 7-month old A53T mice to a Barnes maze and a contextual object recognition test to determine Hipp dependent memory. Inflammation and astrogliosis markers in the Hipp were assessed by immuno-fluorescence densitometry. The data show that early cognitive impairment is coupled with an increase in expression of inflammatory and astrogliosis markers. Next, in two separate experiments, mice were given intra-hippocampal injections of orexin or chemogenetic viral injections of an orexin neuron specific Designer Receptor Exclusively Activated by Designer Drug (DREADD). For the pharmacological approach mice were intracranially treated with orexin A, whereas the chemogenetic approach utilized clozapine N-oxide (CNO). Both pharmacological orexin A intervention as well as chemogenetic activation of orexin neurons ameliorated Hipp-dependent early memory impairment observed in A53T mice. This study implicates orexin in PD-associated cognitive impairment and suggests that exogenous orexin treatment and/or manipulation of endogenous orexin levels may be a potential strategy for addressing early cognitive loss in PD.
Safety and tolerability of Meningococcus B vaccine in patients with chronical medical conditions (CMC)
Authors: Nicolosi L. , Rizzo C. , Gattinara G. Castelli , Mirante N. , Bellelli E. , Bianchini C. , Pansini V. , Villani A. 
Published: October 2019

Abstract

Background
Invasive meningococcal disease is a serious global health threat in the world; in 2016, the European Centre for Disease Control and Prevention reported 3280 confirmed cases (including 304 deaths) of Invasive Meningococcal Diseases in Europe. In Italy, in 2017 were reported 200 cases 41% of which due to menB serogroup. From January 2013 the European Medicines Agency (EMA) has authorized the marketing of the meningococcal B vaccine 4CMenB.

Methods
The study aimed to evaluate and complement the safety profile of 4CMenB in high risk children accessing the vaccine service of the Bambino Gesù Children’s Hospital. All individuals aged six weeks or more receiving the meningococcal 4CMenB (Bexsero®) vaccine that approached the vaccine Centre at the Bambino Gesù Children’s Hospital in Rome, were asked to participate. All parents or caregivers of vaccinated individuals in the study period, were recruited and requested to answer to a questionnaire on adverse events following immunization (AEFI) observed after 7 days, starting from the date of vaccination.

Results
During the study period (October 2016–October 2017), we collected 157 completed questionnaires (out of 200 distributed). Of those 132 were first doses and 25 were booster administered doses. The median age of the study population was 4.5 years (range 0.29 to 26.8 years), the majority of subjects were high-risk individuals (64%) with chronic health conditions. Overall, 311 adverse events were reported in the 7 days after vaccine administration. In particular 147 events (47%) after administration of first dose and 58 (19%) after the booster doses. A large majority of those events, were of little clinical importance and concentrated in the 24 h after vaccine administration. No hospitalizations or Emergency Department access were reported.

Conclusions
Results of our study demonstrated that the Bexsero® vaccine is almost well tolerated, with a low incidence of severe AEFIs. Our results also shown that the occurrence of AEFIs is similar within healthy and high risk children.
Adaptive mechanical ventilation with automated minimization of mechanical power—a pilot randomized cross-over study
Authors: Becher Tobias , Adelmeier Anna , Frerichs Inéz , Weiler Norbert , Schädler Dirk 
Published: October 2019

AbstractBackgroundAdaptive mechanical ventilation automatically adjusts respiratory rate (RR) and tidal volume (VT) to deliver the clinically desired minute ventilation, selecting RR andVTbased on Otis’ equation on least work of breathing. However, the resultingVTmay be relatively high, especially in patients with more compliant lungs. Therefore, a new mode of adaptive ventilation (adaptive ventilation mode 2, AVM2) was developed which automatically minimizes inspiratory power with the aim of ensuring lung-protective combinations ofVTand RR. The aim of this study was to investigate whether AVM2 reducesVT, mechanical power, and driving pressure (ΔPstat) and provides similar gas exchange when compared to adaptive mechanical ventilation based on Otis’ equation.MethodsA prospective randomized cross-over study was performed in 20 critically ill patients on controlled mechanical ventilation, including 10 patients with acute respiratory distress syndrome (ARDS). Each patient underwent 1 h of mechanical ventilation with AVM2 and 1 h of adaptive mechanical ventilation according to Otis’ equation (adaptive ventilation mode, AVM). At the end of each phase, we collected data onVT, mechanical power, ΔP, PaO2/FiO2ratio, PaCO2, pH, and hemodynamics.ResultsComparing adaptive mechanical ventilation with AVM2 to the approach based on Otis’ equation (AVM), we found a significant reduction inVTboth in the whole study population (7.2 ± 0.9 vs. 8.2 ± 0.6 ml/kg,p <  0.0001) and in the subgroup of patients with ARDS (6.6 ± 0.8 ml/kg with AVM2 vs. 7.9 ± 0.5 ml/kg with AVM,p <  0.0001). Similar reductions were observed for ΔPstat(whole study population: 11.5 ± 1.6 cmH2O with AVM2 vs. 12.6 ± 2.5 cmH2O with AVM,p <  0.0001; patients with ARDS: 11.8 ± 1.7 cmH2O with AVM2 and 13.3 ± 2.7 cmH2O with AVM,p = 0.0044) and total mechanical power (16.8 ± 3.9 J/min with AVM2 vs. 18.6 ± 4.6 J/min with AVM,p = 0.0024; ARDS: 15.6 ± 3.2 J/min with AVM2 vs. 17.5 ± 4.1 J/min with AVM,p = 0.0023). There was a small decrease in PaO2/FiO2(270 ± 98 vs. 291 ± 102 mmHg with AVM,p = 0.03; ARDS: 194 ± 55 vs. 218 ± 61 with AVM,p = 0.008) and no differences in PaCO2, pH, and hemodynamics.ConclusionsAdaptive mechanical ventilation with automated minimization of inspiratory power may lead to more lung-protective ventilator settings when compared with adaptive mechanical ventilation according to Otis’ equation.Trial registrationThe study was registered at the German Clinical Trials Register (DRKS00013540) on December 1, 2017, before including the first patient.
Neuropsychological management of multiple sclerosis: evaluation of a supervised and customized cognitive rehabilitation program for self-used at home (SEPIA): protocol for a randomized controlled trial
Authors: Harand Caroline , Daniel France , Mondou Audrey , Chevanne Damien , Creveuil Christian , Defer Gilles 
Published: October 2019

Abstract

Background
Cognitive and mood disorders negatively impact daily life in patients with multiple sclerosis (MS). Pharmacological treatments did not demonstrate any effect on cognition compared with cognitive rehabilitation (CR). However, if CR programs offer promising results on cognition, they are less consistent concerning mood and quality of life (QoL). In this context, we designed a randomized controlled trial to evaluate the efficacy of an innovative computerized CR program, conducted at home, on QoL. Secondary objectives will estimate the improvement, or the stabilization over time, of patients’ cognitive performances and their emotional affects.

Methods
Forty MS patients (relapsing-remitting or secondary progressive forms) who have cognitive impairment will be recruited for the trial (called SEPIA-NCT03471338) and randomly assigned to either the experimental group or the control group. Patients randomly assigned in the experimental group will perform a home-based CR program with psychological support during eight consecutive weeks. CR will be based on computerized cognitive exercises from the PRESCO® software developed by HAPPYneuron©. Training sessions (three sessions of 45 min per week) will consist of short exercises evaluating a broad range of cognitive domains and will be personalized for each patient (tracking tool and supervised guidance). The control group, designed to control for non-specific elements of the intervention, will receive only psychological support consisting of various issues related to MS, such as everyday cognitive-related difficulties or management of emotions. QoL, assessed by the MUSIQOL (Multiple Sclerosis International Quality Of Life) questionnaire, will be evaluated three times (at baseline and after 1 week and 25 weeks after home-based intervention) as well as secondary outcomes measuring self-esteem, cognition, depression, anxiety, metacognition, fatigue, and sleep quality. Given the expected MUSIQOL variation, the inclusion of 20 patients per group (alpha risk 5% and power 80%) will be required.

Discussion
Evidence suggests that computerized programs may be a practice option for CR for people with MS, but there is a paucity of studies evaluating QoL. We hope that this innovative program will highlight such benefits over time in patients’ daily life. In the future, such programs will allow a wider range of available therapeutic options for MS patients with cognitive impairment and for practitioners in charge of their care.

Trial registration
ClinicalTrials.gov identifier: NCT03471338. Retrospectively registered on 25 April 2018. https://clinicaltrials.gov/ct2/show/NCT03471338?term=NCT03471338&cond=Multiple+Sclerosis&draw=2&rank=1.
Reliability of crowdsourcing as a method for collecting emotions labels on pictures
Authors: Korovina Olga , Baez Marcos , Casati Fabio 
Published: October 2019

AbstractObjectiveIn this paper we study if and under what conditions crowdsourcing can be used as a reliable method for collecting high-quality emotion labels on pictures. To this end, we run a set of crowdsourcing experiments on the widely used IAPS dataset, using the Self-Assessment Manikin (SAM) emotion collection instrument, in order to rate pictures on valence, arousal and dominance, and explore the consistency of crowdsourced results across multiple runs (reliability) and the level of agreement with the gold labels (quality). In doing so, we explored the impact of targeting populations of different level of reputation (and cost) and collecting varying numbers of ratings per picture.ResultsThe results tell us that crowdsourcing can be a reliable method, reaching excellent levels of reliability and agreement with only 3 ratings per picture for valence and 8 per arousal, with only marginal difference between target populations. Results for dominance were very poor, echoing previous studies on the data collection instrument used. We also observed that specific types of content generate diverging opinions in participants (leading to higher variability or multimodal distributions), which remain consistent across pictures of the same theme. These can inform the data collection and exploitation of crowdsourced emotion datasets.
Costing for universal health coverage: insight into essential economic data from three provinces in Cambodia
Authors: Jacobs Bart , Hui Kelvin , Lo Veasnakiry , Thiede Michael , Appelt Bernd , Flessa Steffen 
Published: October 2019

AbstractBackgroundKnowledge of the costs of health services improves health facility management and aids in health financing for universal health coverage. Because of resource requirements that are often not present in low- and middle-income countries, costing exercises are rare and infrequent. Here we report findings from the initial phase of establishing a routine costing system for health services implemented in three provinces in Cambodia.MethodsData was collected for the 2016 financial year from 20 health centres (including four with beds) and five hospitals (three district hospitals and two provincial hospitals). The costs to the providers for health centres were calculated using step-down allocations for selected costing units, including preventive and curative services, delivery, and patient contact, while for hospitals this was complemented with bed-day and inpatient day per department. Costs were compared by type of facility and between provinces.ResultsAll required information was not readily available at health facilities and had to be recovered from various sources. Costs per outpatient consultation at health centres varied between provinces (from US$2.33 to US$4.89), as well as within provinces. Generally, costs were inversely correlated with the quantity of service output. Costs per contact were higher at health centres with beds than health centres without beds (US$4.59, compared to US$3.00). Conversely, costs for delivery were lower in health centres with beds (US$128.7, compared to US$413.7), mainly because of low performing health centres without beds. Costs per inpatient-day varied from US$27.61 to US$55.87 and were most expensive at the lowest level hospital.ConclusionsEstablishing a routine health service costing system appears feasible if recording and accounting procedures are improved. Information on service costs by health facility level can provide useful information to optimise the use of available financial and human resources.
Attribute development and level selection for a discrete choice experiment to elicit the preferences of health care providers for capitation payment mechanism in Kenya
Authors: Obadha Melvin , Barasa Edwine , Kazungu Jacob , Abiiro Gilbert Abotisem , Chuma Jane 
Published: October 2019

AbstractBackgroundStated preference elicitation methods such as discrete choice experiments (DCEs) are now widely used in the health domain. However, the “quality” of health-related DCEs has come under criticism due to the lack of rigour in conducting and reporting some aspects of the design process such as attribute and level development. Superficially selecting attributes and levels and vaguely reporting the process might result in misspecification of attributes which may, in turn, bias the study and misinform policy. To address these concerns, we meticulously conducted and report our systematic attribute development and level selection process for a DCE to elicit the preferences of health care providers for the attributes of a capitation payment mechanism in Kenya.MethodologyWe used a four-stage process proposed by Helter and Boehler to conduct and report the attribute development and level selection process. The process entailed raw data collection, data reduction, removing inappropriate attributes, and wording of attributes. Raw data was collected through a literature review and a qualitative study. Data was reduced to a long list of attributes which were then screened for appropriateness by a panel of experts. The resulting attributes and levels were worded and pretested in a pilot study. Revisions were made and a final list of attributes and levels decided.ResultsThe literature review unearthed seven attributes of provider payment mechanisms while the qualitative study uncovered 10 capitation attributes. Then, inappropriate attributes were removed using criteria such as salience, correlation, plausibility, and capability of being traded. The resulting five attributes were worded appropriately and pretested in a pilot study with 31 respondents. The pilot study results were used to make revisions. Finally, four attributes were established for the DCE, namely, payment schedule, timeliness of payments, capitation rate per individual per year, and services to be paid by the capitation rate.ConclusionBy rigorously conducting and reporting the process of attribute development and level selection of our DCE,we improved transparency and helped researchers judge the quality.
Online non-negative discriminative dictionary learning for tracking
Authors: Wang Weisong , Yang Fei , Zhang Hongzhi 
Published: October 2019

AbstractIn this paper, online non-negative discriminative dictionary learning for tracking is proposed, which combines the advantages of the global dictionary learning model and the class-specific dictionary learning model. The previous algorithm based on general dictionary learning does not take into account the inter-class relations between classes and make full use of tag information. In order to improve the classification ability of dictionaries, the class correlation was proposed to guide the learning of discriminant dictionaries, which makes full use of the correlation and difference between the atomic classes of dictionaries and introduces the tag information of the categories to improve the discriminant ability of dictionaries. For this purpose, the Huber loss function and the Fisher weight coefficient is used in the discriminative term to improve computational efficiency. In addition, non-negative constraints is added on dictionaries to enhance the performance. The OTB50 and OTB100 datasets are used to evaluate our tracker and compare with related algorithm. The experimental results show that our method performs much better than the tracking method compared in this paper.
On a weak solution matching up with the double degenerate parabolic equation
Authors: Weng Sujun 
Published: October 2019

Abstract
The well-posedness of weak solutions to a double degenerate evolutionary $p(x)$
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