bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do Parents Perceive the Initial Medical Consultation on their Child’s Developmental Disorder?
Authors: Hotopp Lena , Spindler Ulrike , Bach Vivien , Hornemann Frauke , Syrbe Steffen , Andreas Anna , Merkenschlager Andreas , Kiess Wieland , Bernhard Matthias , Bertsche Thilo , Neininger Martina , Bertsche Astrid 
Published: December 2017

Abstract
Background A developmental disorder of a child has a major impact on the affected families’ lives. However, data about the parents’ perception of the revealing of the diagnosis is scarce.
Patients and Methods Parents of children with developmental disorder treated as outpatients in a university hospital were interviewed about the initial medical consultation concerning the diagnosis of their child.
Results Parents of 210 children agreed to take part in the study. 35/210 (17%) had to be excluded from the study as they were not able to remember the initial medical consultation, or claimed there was either no initial medical consultation or they did not attend it. The diagnosis of developmental disorder was made in median 4 months (Q25/Q75: 0/12; min/max: 0/63) after the parents had noticed the first symptoms. According to the parents, options to support the development of the child were the most frequently addressed topic in the initial medical consultation (119/175, 68%). Some parents wished more empathy (19/175, 11%), and less medical terminology (12/175, 7%). 114/175 (65%) of parents rated the initial medical consultation as “very good” or “good”. After their initial medical consultation, 66/175 (38%) of the parents had open questions mainly concerning the prognosis of the disease. Sources of information that were used after the consultation were most often the treating physician (150/175, 86%) and the internet (133/175, 76%).
Conclusion Generally, parents perceive the initial medical consultation on the developmental disorder of their child well. Nevertheless, many parents state that they had unanswered questions after the consultation. The internet is one of the main sources parents use to answer those questions.
Von kalten und hitzigen Herzen
Authors: Mayer Arnold 
Published: December 2017

SummaryIn der Traditionellen Europäischen Medizin (TEM) wirkt das Herz als Regulationszentrum für das Lebensprinzip Sanguis und damit als Schlüsselorgan für das Ineinanderwirken von Soma und Psyche und die Verbreitung der Vitalkräfte. Stressoren beeinträchtigen immer auch das Herz bis hin zum Broken-Heart-Syndrom. Umgekehrt haben kardiale Störungen immer auch psychische Folgen. Die TEM kennt zahlreiche Phytotherapeutika zur Behandlung psychosomatischer Herzstörungen, beispielsweise das Kalte oder das Hitzige Herz.
Akutstationäre Versorgung – Routinedatenanalyse zum Sturzrisiko
Authors: Bretzke Pascal 
Published: December 2017

Jacobi L et al. Epidemiologie und Vorhersage des Sturzrisikos von Patienten in der akutstationären Versorgung: Analyse von Routinedaten eines
Universitätsklinikums. Z Evid Fortbild Qual Gesundh wesen 2017; 120: 9–15
Das Phänomen Sturz ist ein in allen Bereichen der Gesundheitsversorgung relevantes Problem. Stürze sind ein bedeutender Risikofaktor für
Frakturen, insbesondere bei älteren Menschen. Die patientenassoziierten Folgen sind diffizil und resultieren aus längeren
Behandlungszeiträumen, einer verminderten Lebensqualität oder einer vorzeitigen Mortalität. Ziel dieser Arbeit ist es,
versorgungsepidemiologische Daten zur Sturzhäufigkeit, Risikofaktoren und Güte eingesetzter Sturzrisikoassessments auszuwerten.
Stress im Erbgut
Authors: Sonnentag Marlies 
Published: December 2017

SummaryFaktoren wie Stress, Angst, Traumata und Mangelzustände wirken sich ebenso auf die Genaktivität aus wie positive soziale Bindungen, man spricht von Epigenetik. Zu den epigenetischen Belastungsfolgen zählen beschleunigte Alterung, erhöhte Stresssensitivität, aber auch Insulinresistenz, Tumorerkrankungen, Bindungs- und Gedächtnisstörungen. Die An- oder Abschaltung von DNA-Sequenzen ist vererbbar, aber unter günstigen Einflüssen reversibel.
The Combination of Fosfomycin, Metronidazole, and Recombinant Human Granulocyte-Macrophage Colony-Stimulating Factor is Stable in vitro and Has Maintained Antibacterial Activity
Authors: Fonnes Siv , Holzknecht Barbara , Gasbjerg Lærke , Weisser Johan , Hallberg Hanne , Arpi Magnus , Rosenberg Jacob 
Published: December 2017

Abstract
Background Treatment of secondary peritonitis includes surgery and antimicrobial agents. Antimicrobial agents are often administered intravenously, however, the alternative route intraperitoneal administration could be considered. Investigations must be conducted prior to clinical application. Therefore, we aimed to investigate the combination of fosfomycin, metronidazole, and recombinant human granulocyte-macrophage colony-stimulating factor with regard to its chemical properties and the solution’s stability. In addition, the antibacterial effect of the mixed drug solution was compared with the effect of the individual antibacterial agents.
Methods The drugs were mixed to an aqueous solution. Basic chemical investigations of pH, precipitation, and calculated osmolarity of the drug combination were conducted. Fosfomycin and metronidazole’s chemical stability was investigated using High Pressure Liquid Chromatography-Mass Spectrometry. Microbiological investigations using the agar cup method were carried out to measure the antibacterial effect of fosfomycin and metronidazole.
Results The aqueous solution of the combination of the three drugs had a pH of 7.46–7.62, which was stable during 24 h, was without precipitation, and had a calculated osmolarity of 293 mOsm/l. High Pressure Liquid Chromatography-Mass Spectrometry found stable concentrations of fosfomycin and metronidazole both alone and in combination during 24 h. The antibacterial effect of the drug combination solution was similar to the antibacterial effects of fosfomycin and metronidazole alone.
Conclusion The drug combination had neutral and stable pH, was iso-osmotic, and had stable concentrations during 24 h of storage. The antibacterial effect of fosfomycin and metronidazole were not altered when the drugs were mixed.
Toward a unified theory of efficient, predictive, and sparse coding
Authors: Chalk Matthew , Marre Olivier , Tkačik Gašper 
Published: December 2017

SignificanceSensory neural circuits are thought to efficiently encode incoming signals. Several mathematical theories of neural coding formalize this notion, but it is unclear how these theories relate to each other and whether they are even fully consistent. Here we develop a unified framework that encompasses and extends previous proposals. We highlight key tradeoffs faced by sensory neurons; we show that trading off future prediction against efficiently encoding past inputs generates qualitatively different predictions for neural responses to natural visual stimulation. Our approach is a promising first step toward theoretically explaining the observed diversity of neural responses.
The dynamic properties of B4C/6061Al neutron absorber composites fabricated by power metallurgy
Authors: Chen Hongsheng , Wang Wenxian , Nie Huihui , Zhou Jun , Li Yuli , Zhang Peng 
Published: December 2017

The dynamic compression properties of B4C/6061Al neutron absorber composites (NACs) with three B4C volume fractions (20–40%), fabricated by power metallurgy, were studied. Compression tests were conducted at strain rates ranging from 760 to 1150 s−1, using a split Hopkinson pressure bar. The damage mechanism was studied through microstructural analysis. Results show that the B4C particles exhibited a uniform distribution in the 6061Al matrix. The NACs dynamic strength was found to improve with increasing quantities of B4C particles, and with strain rate. The damage mechanisms include particle fracture and interface debonding. Dislocation pile-up was observed at grain boundaries and at the interface between particles and the matrix. A constitutive model under dynamic compression was developed based on the Johnson–Cook model. This paper is part of a thematic issue on Nuclear Materials.
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data
Authors: Wei Lin , Jin Zhilin , Yang Shengjie , Xu Yanxun , Zhu Yitan , Ji Yuan 
Published: December 2017

Abstract

Motivation
The Cancer Genome Atlas (TCGA) program has produced huge amounts of cancer genomics data providing unprecedented opportunities for research. In 2014, we developed TCGA-Assembler, a software pipeline for retrieval and processing of public TCGA data. In 2016, TCGA data were transferred from the TCGA data portal to the Genomic Data Commons (GDCs), which is supported by a different set of data storage and retrieval mechanisms. In addition, new proteomics data of TCGA samples have been generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, which were not available for downloading through TCGA-Assembler. It is desirable to acquire and integrate data from both GDC and CPTAC.

Results
We develop TCGA-assembler 2 (TA2) to automatically download and integrate data from GDC and CPTAC. We make substantial improvement on the functionality of TA2 to enhance user experience and software performance. TA2 together with its previous version have helped more than 2000 researchers from 64 countries to access and utilize TCGA and CPTAC data in their research. Availability of TA2 will continue to allow existing and new users to conduct reproducible research based on TCGA and CPTAC data.

Availability and implementation
http://www.compgenome.org/TCGA-Assembler/ or https://github.com/compgenome365/TCGA-Assembler-2

Supplementary information
Supplementary data are available at Bioinformatics online.
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations
Authors: Jin Zhuxuan , Kang Jian , Yu Tianwei 
Published: December 2017

Abstract

Motivation
Metabolomics data generated from liquid chromatography-mass spectrometry platforms often contain missing values. Existing imputation methods do not consider underlying feature relations and the metabolic network information. As a result, the imputation results may not be optimal.

Results
We proposed an imputation algorithm that incorporates the existing metabolic network, adduct ion relations even for unknown compounds, as well as linear and nonlinear associations between feature intensities to build a feature-level network. The algorithm uses support vector regression for missing value imputation based on features in the neighborhood on the network. We compared our proposed method with methods being widely used. As judged by the normalized root mean squared error in real data-based simulations, our proposed methods can achieve better accuracy.

Availability and implementation
The R package is available at http://web1.sph.emory.edu/users/tyu8/MINMA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Personal Cancer Genome Reporter: variant interpretation report for precision oncology
Authors: Nakken Sigve , Fournous Ghislain , Vodák Daniel , Aasheim Lars Birger , Myklebost Ola , Hovig Eivind 
Published: December 2017

Abstract

Summary
Individual tumor genomes pose a major challenge for clinical interpretation due to their unique sets of acquired mutations. There is a general scarcity of tools that can (i) systematically interrogate cancer genomes in the context of diagnostic, prognostic, and therapeutic biomarkers, (ii) prioritize and highlight the most important findings and (iii) present the results in a format accessible to clinical experts. We have developed a stand-alone, open-source software package for somatic variant annotation that integrates a comprehensive set of knowledge resources related to tumor biology and therapeutic biomarkers, both at the gene and variant level. Our application generates a tiered report that will aid the interpretation of individual cancer genomes in a clinical setting.

Availability and implementation
The software is implemented in Python/R, and is freely available through Docker technology. Documentation, example reports, and installation instructions are accessible via the project GitHub page: https://github.com/sigven/pcgr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting Hospitalization and Outpatient Corticosteroid Use in Inflammatory Bowel Disease Patients Using Machine Learning
Authors: Waljee Akbar K , Lipson Rachel , Wiitala Wyndy L , Zhang Yiwei , Liu Boang , Zhu Ji , Wallace Beth , Govani Shail M , Stidham Ryan W , Hayward Rodney , Higgins Peter D R 
Published: December 2017

Abstract

Background
Inflammatory bowel disease (IBD) is a chronic disease characterized by unpredictable episodes of flares and periods of remission. Tools that accurately predict disease course would substantially aid therapeutic decision-making. This study aims to construct a model that accurately predicts the combined end point of outpatient corticosteroid use and hospitalizations as a surrogate for IBD flare.

Methods
Predictors evaluated included age, sex, race, use of corticosteroid-sparing immunosuppressive medications (immunomodulators and/or anti-TNF), longitudinal laboratory data, and number of previous IBD-related hospitalizations and outpatient corticosteroid prescriptions. We constructed models using logistic regression and machine learning methods (random forest [RF]) to predict the combined end point of hospitalization and/or corticosteroid use for IBD within 6 months.

Results
We identified 20,368 Veterans Health Administration patients with the first (index) IBD diagnosis between 2002 and 2009. Area under the receiver operating characteristic curve (AuROC) for the baseline logistic regression model was 0.68 (95% confidence interval [CI], 0.67–0.68). AuROC for the RF longitudinal model was 0.85 (95% CI, 0.84–0.85). AuROC for the RF longitudinal model using previous hospitalization or steroid use was 0.87 (95% CI, 0.87–0.88). The 5 leading independent risk factors for future hospitalization or steroid use were age, mean serum albumin, immunosuppressive medication use, and mean and highest platelet counts. Previous hospitalization and corticosteroid use were highly predictive when included in specified models.

Conclusions
A novel machine learning model substantially improved our ability to predict IBD-related hospitalization and outpatient steroid use. This model could be used at point of care to distinguish patients at high and low risk for disease flare, allowing individualized therapeutic management.
Plasma microRNA Profile Differentiates Crohn’s Colitis From Ulcerative Colitis
Authors: Netz Uri , Carter Jane , Eichenberger M Robert , Feagins Kayla , Galbraith Norman J , Dryden Gerald W , Pan Jianmin , Rai Shesh N , Galandiuk Susan 
Published: December 2017

AbstractBackgroundInflammatory bowel disease (IBD) is commonly divided into 2 entities: Crohn’s disease (CD) and ulcerative colitis (UC). Differentiating between these entities when dealing with IBD confined to the colon is important, especially when planning surgical treatment. Due to ambiguous histological or endoscopic findings, accurate diagnosis is not possible in up to 15% of cases. The aim of this study was to determine whether plasma microRNAs (miRNAs) can help differentiate Crohn’s colitis (CC) from ulcerative colitis.MethodsPatients with isolated CC and with UC were enrolled in our study from January 2010 to May 2016. Peripheral blood was collected, and total RNA was isolated from plasma. Screening was performed for 380 common miRNAs. miRNAs that were differentially expressed between these 2 groups were chosen, and their differential expression was confirmed using single miRNA assays in a larger sample size. A predictive model was generated using these data. Significantly differentially expressed miRNAs were then validated utilizing the predictive model to assess blinded data from the single assays.ResultsScreening was performed on 8 patients from each group. Seven differentially expressed miRNAs were chosen for single assay confirmation. Two miRNAs (miR-598, miR-642) were consistently different between the patient groups (P = 0.013, P = 0.005). Using blinded data, these 2 miRNAs were validated using the predictive model, achieving an overall accuracy of 75% (95% confidence interval, 40.7–92.9).ConclusionsWe identified 2 plasma miRNAs that differentiated CC from UC. Our data indicate the promise and feasibility of a plasma miRNA–based assay to distinguish between these 2 conditions.
Development and Validation of a Confocal Laser Endomicroscopy-Based Score for In Vivo Assessment of Mucosal Healing in Ulcerative Colitis Patients
Authors: Hundorfean Gheorghe , Chiriac Mircea T , Mihai Sidonia , Hartmann Arndt , Mudter Jonas , Neurath Markus F 
Published: December 2017

Abstract

Background
Endoscopic monitoring is fundamental for evaluating the therapeutic response in IBD, but a validated endomicroscopic mucosal healing (MH) score is not available to date. However, confocal laser endomicroscopy (CLE) might define MH more precisely than conventional endoscopy. The major aim was to establish and validate an MH score for ulcerative colitis (UC), based on CLE.

Methods
In an initial pilot study (n = 10), various CLE changes were analyzed for identification of reproducible criteria for establishing a CLE score. Four reproducible CLE criteria were implemented in a following validation study. Subsequently, active UC patients (n = 23, Mayo score ≥6) were prospectively included and underwent colonoscopy with CLE before and after 3 anti-TNF applications. Patients were clinically followed over a period of 3 years. The endomicroscopic MH score (eMHs; range, 0–4) was compared with histopathology and endoscopy scores from the same colonic location.

Results
The eMHs showed high sensitivity, specificity, and accuracy values (100% with 95% confidence interval [CI] of 15.81%–100%; 93.75% with 95% CI of 69.77%–99.84%, and 94.44%, respectively). The eMHs showed a good correlation with the histological Gupta score (rs = 0.82, P &lt; 0.0001) and the endoscopic Mayo subscore (rs = 0.81%, P &lt; 0.0001). Sixty percent of therapy responders presented an eMHs &lt;1, which translated into long-lasting clinical remission and reduced hospitalization, steroid, and surgery need.

Conclusions
CLE can accurately assess MH based on the newly developed and statistically validated eMHs in UC, and it is superior in predicting the long-lasting clinical outcome based on both descriptive and functional barrier imaging (NCT01417728).
Indeterminate QuantiFERON-TB Gold Increases Likelihood of Inflammatory Bowel Disease Treatment Delay and Hospitalization
Authors: Vajravelu Ravy K , Osterman Mark T , Aberra Faten N , Roy Jason A , Lichtenstein Gary R , Mamtani Ronac , Goldberg David S , Lewis James D , Scott Frank I 
Published: December 2017

Abstract

Background
QuantiFERON-TB Gold (QFTG) is a blood test used to diagnose latent tuberculosis infection (LTBI) prior to TNF-α inhibitor (anti-TNF) initiation. We sought to determine factors associated with indeterminate QFTG results in inflammatory bowel disease (IBD) patients and whether indeterminate results are associated with IBD-related morbidity.

Methods
This nested case-control study included IBD patients who underwent QFTG testing. Cases were patients with indeterminate QFTG and controls were those with negative QFTG. The association of demographic and clinical data with indeterminate QFTG result was assessed using logistic regression. We examined the clinical impact of indeterminate QFTG results on risk of hospitalization and delay in anti-TNF initiation using inverse probability-of-treatment weighting (IPTW) regression.

Results
We identified 411 patients with QFTG testing (320 negative, 80 indeterminate, and 11 positive results). No patient with an indeterminate result subsequently had LTBI. Systemic corticosteroid use (OR, 4.4; 95% CI, 2.0–9.6) and hospitalization at the time of QFTG (OR, 3.8; 95% CI, 1.9–7.7) were associated with indeterminate QFTG, while immunomodulator use was nearly statistically significant (OR, 3.1; 95% CI, 0.9–9.8) and anti-TNF use was not (OR, 0.9; 95% CI, 0.2–4.6). After IPTW adjustment, indeterminate QFTG was associated with a 23.1% (95% CI, 8.2%–37.9%) greater probability of delay in anti-TNF initiation beyond 30 days and an 11.9% (95% CI, 0.6%–23.1%) greater probability of hospitalization within 60 days.

Conclusions
Systemic corticosteroid use and hospitalization were associated with an indeterminate QFTG result. Indeterminate QFTG results were associated with delayed anti-TNF initiation and subsequent hospitalization.
10.1093/ibd/izx019_video1 izx019.video1 5732754519001
IBD Serology and Disease Outcomes in African Americans With Crohn’s Disease
Authors: Bertha Madeline , Vasantharoopan Arthi , Kumar Archana , Bruce Beau B , Prince Jarod , Hofmekler Tatyana , Okou David , Chopra Pankaj , Wang Gabriel , Sauer Cary , Landers Carol J , Hussain Sunny Z , Cross Raymond K , Baldassano Robert N , Kappelman Michael D , Katz Jeffrey , Alexander Jonathan S , Kirschner Barbara S , Moulton Dedrick E , Osuntokun Bankole O , Patel Ashish , Saeed Shehzad , Klapproth Jan-Michael A , Dhere Tanvi A , Dubinsky Marla C , McGovern Dermot , Kugathasan Subra 
Published: December 2017

Abstract

Backgrounds
Recent studies have identified the role of serologic markers in characterizing disease phenotype, location, complications, and severity among Northern Europeans (NE) with Crohn’s disease (CD). However, very little is known about the role of serology in CD among African Americans (AA). Our study explored the relationship between serology and disease phenotype in AA with CD, while controlling for genetic ancestry.

Methods
AAs with CD were enrolled as participants through multicenter collaborative efforts. Serological levels of IgA anti-Saccharomyces cervisiae antibody (ASCA), IgG ASCA, E. coli outermembrane porin C, anti-CBir1, and ANCA were measured using enzyme-linked immunosorbent assays. Genotyping was performed using Illumina immunochip technology; an admixture rate was calculated for each subject. Multiple imputation by chained equations was performed to account for data missing at random. Logistic regression was used to calculate adjusted odds ratio (OR) for associations between serological markers and both complicated disease and disease requiring surgery.

Results
A total of 358 patients were included in the analysis. The majority of our patients had inflammatory, noncomplicated disease (58.4%), perianal disease (55.7%), and documented colonic inflammation (86.8%). On multivariable analysis, both IgG ASCA and OmpC were associated with complicated disease (OR, 2.67; 95% CI, 1.67–4.28; OR, 2.23; 95% CI, 1.41–3.53, respectively) and disease requiring surgery (OR, 2.51; 95% CI, 1.49–4.22; OR, 3.57; 95% CI, 2.12–6.00). NE admixture to the African genome did not have any associations or interactions in relation to clinical outcome.

Conclusions
Our study comprises the largest cohort of AAs with CD. The utility of serological markers for the prognosis of CD in NE applies equally to AA populations.