bluuebunny/crossref_metadata_2025_split huggingface dataset:
A National Survey of the Prevalence and Impact of Cytomegalovirus Infection Among Hospitalized Patients With Ulcerative Colitis
Authors: Grossberg Laurie B. , Ezaz Ghideon , Grunwald Douglas , Cohen Jonah , Falchuk Kenneth R. , Feuerstein Joseph D. 
Published: November 2016

Goals:
To estimate the effect of cytomegalovirus (CMV) in patients with ulcerative colitis (UC), and compare these outcomes to patients with CMV without UC.

Background:
The impact of CMV infection in UC is not well understood.

Study:
We analyzed records from the Nationwide Inpatient Sample (NIS) of patients with UC and CMV between 2006 and 2012. Differences in outcomes were determined between patients with UC and CMV and those with UC without CMV. Secondary analysis compared outcomes of patients with UC and CMV to patients with CMV alone.

Results:
Patients with UC and CMV (n=145) had longer length of stay (16.31 vs. 5.52 d, P<0.0001), higher total charges ($111,835.50 vs. $39.895, P=0.001), and were less likely to be discharged home without services (50.0% vs. 81.83%, P<0.0001) compared with patients with UC without CMV (n=32,290). On regression analysis, CMV was significantly associated with higher total charges (P<0.01) and longer length of stay (P<0.01), but not for increased need for colorectal surgery. When comparing patients with UC and CMV to patients with CMV alone (n=14,960), patients with CMV alone had a higher Charlson Comorbidity Index and a trend toward higher in-hospital mortality.

Conclusions:
CMV infection in hospitalized patients with UC is associated with a longer length of stay, increased total charges, and fewer routine discharges, but not increased surgery or mortality. Patients with CMV alone had the worst outcomes of all groups suggesting that CMV in UC patients may not have the same negative impact as in other diseases.
Age-adapted Variation in Screening Interval of Fecal Immunochemical Test May Improve its Participation and Colonoscopy Acceptance
Authors: Kwak Min Seob , Cha Jae Myung , Yoon Jin Young , Jeon Jung Won , Shin Hyun Phil , Joo Kwang Ro , Lee Joung Il 
Published: November 2016

Goals:
We determined appropriate intervals for administering the fecal immunochemical test (FIT) and performance outcomes in an Asian national colorectal cancer (CRC) screening program.

Background:
The optimal interval for FIT in CRC screening is unclear, especially in Asian populations.

Study:
Between January 2009 and December 2015, 13,480 individuals aged 50 years or older with an initial negative FIT result underwent 2 rounds of FIT screening at intervals of 1 (annual group, 5333), 2 (biennial group, 7363), or 3 years (triennial group, 784). Positive rates of FIT, colonoscopy acceptance, colonoscopy findings, and detection rates for CRC and advanced neoplasia were compared according to FIT intervals.

Results:
The overall positivity rate of FIT in the second screening round was significantly higher in men and in older subjects than in the entire sample. Younger subjects were less likely to undergo annual FIT (36.0% vs. 46.4%, P<0.001). The colonoscopy acceptance rate was decreased in the biennial and triennial groups compared with an annual group among younger subjects (odds ratio, 0.56; 95% confidence interval, 0.33-0.95 for the biennial group vs. odds ratio, 0.19; 95% confidence interval, 0.03-1.37 for the triennial group). Detection rates for CRC and advanced neoplasia in the second round were significantly higher and accompanied by increased FIT screening intervals in older, but not younger subjects.

Conclusions:
Age-adapted variation in FIT screening intervals, such as annual screening for elderly subjects and biennial screening for younger subject, may improve FIT participation and colonoscopy acceptance.
Coffee consumption and risk of nonalcoholic fatty liver disease: a systematic review and meta-analysis
Authors: Wijarnpreecha Karn , Thongprayoon Charat , Ungprasert Patompong 
Published: November 2016

Background/objectives
Nonalcoholic fatty liver disease (NAFLD) is a worldwide public health concern. Coffee might have a protective effect against NAFLD. However, the results of previous reports are conflicting. Therefore, we carried out this meta-analysis to summarize all available data.

Methods
This study consisted of two meta-analyses. The first meta-analysis included observational studies comparing the risk of NAFLD in patients who did and did not drink coffee. The second analysis included studies comparing the risk of liver fibrosis between NAFLD patients who did and did not drink coffee. Pooled risk ratios (RR) and 95% confidence interval (CI) were calculated.

Results
Out of 355 articles, five studies fulfilled our eligibility criteria and were included in the analysis. The risk of NAFLD in patients who drank coffee was significantly lower than that in patients who did not pooled RR 0.71 (95% CI, 0.60–0.85). We also found a significantly decreased risk of liver fibrosis among NAFLD patients who drank coffee compared with those who did not, with a pooled RR of 0.70 (95% CI, 0.60–0.82). However, it should be noted that the definition of regular coffee consumption varied between studies, which is the main limitation of this meta-analysis.

Conclusion
Our study found a significantly decreased risk of NAFLD among coffee drinkers and significantly decreased risk of liver fibrosis among patients with NAFLD who drank coffee on a regular basis. Whether consumption of coffee could be considered a preventative measure against NAFLD needs further investigations.
Identifying Children at Risk of Malignant Bordetella pertussis Infection
Authors: Ganeshalingham Anusha , McSharry Brent , Anderson Brian , Grant Cameron , Beca John 
Published: November 2016

Objective:
To identify factors associated with malignant pertussis.

Design:
A retrospective case notes review from January 2003 to August 2013. Area under the receiver-operator characteristic curve was used to determine how well vital sign and white cell characteristics within 48 hours of hospital presentation identified children with malignant pertussis.

Setting:
The national children’s hospital in Auckland, New Zealand.

Patients:
One hundred fifty-two children with pertussis.

Measurements and Main Results:
There were 152 children with confirmed pertussis identified, including 11 children with malignant pertussis. The area under the receiver-operator characteristic curve was 0.88 (95% CI, 0.78–0.97) for maximum heart rate. The optimal cut-point was 180 beats/min, which predicted malignant pertussis with a sensitivity of 73% and a specificity of 91%. The area under the receiver-operator characteristic curve was 0.92 (95% CI, 0.81–1.0) for absolute neutrophil count, 0.85 (95% CI, 0.71–0.99) for total WBC count, 0.80 (95% CI, 0.63–0.96) for neutrophil-to-lymphocyte ratio, and 0.77 (95% CI, 0.58–0.92) for absolute lymphocyte count. All children with malignant pertussis had one or more of heart rate greater than 180 beats/min, total WBC count greater than 25 × 109/L, and neutrophil-to-lymphocyte ratio greater than 1.0 with an area under the receiver-operator characteristic curve of 0.96 (95% CI, 0.91–1.0) for a multivariate model that included these three variables.

Conclusions:
Clinical predictors of malignant pertussis are identifiable within 48 hours of hospital presentation. Early recognition of children at risk of malignant pertussis may facilitate early referral to a PICU for advanced life support and selection for trials of investigational therapies.
Prognostic Value of Computed Tomography–Detected Extramural Venous Invasion to Predict Disease-Free Survival in Patients With Gastric Cancer
Authors: Kim Tae Un , Kim Suk , Lee Nam Kyung , Kim Hak Jin , Han Ga Jin , Lee Jun Woo , Baek Hyun Jung , Jeon Tae Yong , Kim Hyun Sung , Park Do Yoon 
Published: November 2016

Objective
This study aimed to investigate whether there is a correlation between the computed tomography–detected extramural venous invasion (ctEMVI) and disease-free survival (DFS) in patients with gastric cancer using pathologic lymphovascular invasion as a reference standard.

Methods
We retrospectively reviewed 153 patients with gastric cancer who underwent computed tomography during 1 year. Differences in pathological findings between the ctEMVI-positive and ctEMVI-negative groups were analyzed. Disease-free survival was estimated using the Kaplan-Meier method. Factors affecting DFS were analyzed with the Cox proportional hazard model.

Results
The ctEMVI-positive group was correlated more with lymphovascular invasion (P = 0.008). The 1- and 2-year DFS rates were 92% and 80%, respectively, in the ctEMVI-negative group, but 77% and 54%, respectively, in the ctEMVI-positive group. A multivariate analysis revealed that tumor size, ctEMVI, and pathological stage remained associated with DFS (Ps = 0.037, 0.015, and 0.002, respectively).

Conclusions
The ctEMVI was an independent prognostic factor for worse DFS in patients with gastric cancer.
The Effect of Patient Diameter on the Dual-Energy Ratio of Selected Contrast-Producing Elements
Authors: Lambert Jack W. , FitzGerald Paul F. , Edic Peter M. , Sun Yuxin , Bonitatibus Peter J. , Colborn Robert E. , Yeh Benjamin M. 
Published: November 2016

Objectives
The aim of this study was to assess whether the low- to high-kVp computed tomography (CT) number ratio at dual-energy CT is affected by changes in patient diameter.

Methods
Seven contrast-producing elements were housed sequentially within an abdomen phantom. Fat rings enlarged the phantom diameter from 26 to 44 cm. The phantom was scanned using single-energy CT at tube potentials of 80 and 140 kVp and rapid-kVp-switching dual-energy CT.

Results
CT numbers decreased proportionally (∼20% CT number reduction for smallest to largest phantom diameters) for low- and high-energy acquisitions but resulted in consistent dual-energy ratios for each contrast element. For 17 of 21 material pair combinations, the dual-energy ratio ranges of the two elements did not overlap, implying that discrimination should remain possible for these material pairs at all patient sizes.

Conclusions
The dual-energy ratio for different contrast materials is largely unaffected by changes in phantom diameter. This should allow for robust separation of most contrast material combinations irrespective of patient size.
Antagonistic interactions in the zebrafish midline prior to the emergence of asymmetric gene expression are important for left–right patterning
Authors: Burdine Rebecca D. , Grimes Daniel T. 
Published: November 2016

Left–right (L-R) asymmetry of the internal organs of vertebrates is presaged by domains of asymmetric gene expression in the lateral plate mesoderm (LPM) during somitogenesis. Ciliated L-R coordinators (LRCs) are critical for biasing the initiation of asymmetrically expressed genes, such asnodalandpitx2, to the left LPM. Other midline structures, including the notochord and floorplate, are then required to maintain these asymmetries. Here we report an unexpected role for the zebrafish EGF-CFC geneone-eyed pinhead(oep) in the midline to promotepitx2expression in the LPM. Late zygoticoep(LZoep) mutants have strongly reduced or absentpitx2expression in the LPM, but this expression can be rescued to strong levels by restoringoepin midline structures only. Furthermore, removing midline structures from LZoepembryos can rescuepitx2expression in the LPM, suggesting the midline is a source of an LPMpitx2repressor that is itself inhibited byoep. Reducinglefty1activity in LZoepembryos mimics removal of the midline, implicatinglefty1in the midline-derived repression. Together, this suggests a model where Oep in the midline functions to overcome a midline-derived repressor, involvinglefty1, to allow for the expression of left side-specific genes in the LPM.This article is part of the themed issue ‘Provocative questions in left–right asymmetry’.
Heterotaxy inCaenorhabditis: widespread natural variation in left–right arrangement of the major organs
Authors: Alcorn Melissa R. , Callander Davon C. , López-Santos Agustín , Torres Cleuren Yamila N. , Birsoy Bilge , Joshi Pradeep M. , Santure Anna W. , Rothman Joel H. 
Published: November 2016

Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematodeCaenorhabditis elegansis known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristicCaenorhabditisspecies. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal.This article is part of the themed issue ‘Provocative questions in left–right asymmetry’.
Predicting brain-age from multimodal imaging data captures cognitive impairment
Authors: Liem Franziskus , Varoquaux Gaël , Kynast Jana , Beyer Frauke , Kharabian Masouleh Shahrzad , Huntenburg Julia M. , Lampe Leonie , Rahim Mehdi , Abraham Alexandre , Craddock R. Cameron , Riedel-Heller Steffi , Luck Tobias , Loeffler Markus , Schroeter Matthias L. , Witte Anja Veronica , Villringer Arno , Margulies Daniel S. 
Published: November 2016

AbstractThe disparity between the chronological age of an individual and their brain-age measured based on biological information has the potential to offer clinically-relevant biomarkers of neurological syndromes that emerge late in the lifespan. While prior brain-age prediction studies have relied exclusively on either structural or functional brain data, here we investigate how multimodal brainimaging data improves age prediction. Using cortical anatomy and whole-brain functional connectivity on a large adult lifespan sample (N = 2354, age 19-82), we found that multimodal data improves brain-based age prediction, resulting in a mean absolute prediction error of 4.29 years. Furthermore, we found that the discrepancy between predicted age and chronological age captures cognitive impairment. Importantly, the brain-age measure was robust to confounding effects: head motion did not drive brain-based age prediction and our models generalized reasonably to an independent dataset acquired at a different site (N = 475). Generalization performance was increased by training models on a larger and more heterogeneous dataset. The robustness of multimodal brain-age prediction to confounds, generalizability across sites, and sensitivity to clinically-relevant impairments, suggests promising future application to the early prediction of neurocognitive disorders.HighlightsBrain-based age prediction is improved with multimodal neuroimaging data.Participants with cognitive impairment show increased brain aging.Age prediction models are robust to motion and generalize to independent datasets from other sites.
Software tools for visualizing Hi-C data
Authors: Yardımcı Galip Gürkan , Noble William Stafford 
Published: November 2016

AbstractRecently developed, high-throughput assays for measuring the three-dimensional configuration of DNA in the nucleus have provided unprecedented insights into the relationship between DNA 3D configuration and function. However, accurate interpretation of data from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using a standard genome browser. In particular, an effective Hi-C visualization tool must provide a variety of visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review a number of such software tools that have been described recently in the literature, focusing on tools that do not require programming expertise on the part of the user. In particular, we describe HiBrowse, Juicebox, my5C, the 3D Genome Browser, and the Epigenome Browser, outlining their complementary functionalities and highlighting which types of visualization tasks each tool is best designed to handle.
Cracking the Barcodes of Fullerene-Like Cortical Microcolumns
Authors: Tozzi Arturo , Peters James F. , Ori Ottorino 
Published: November 2016

ABSTRACTArtificial neural systems and nervous graph theoretical analysis rely upon the stance that the neural code is endowed in logic circuits,e.g., spatio-temporal sequences of ON/OFF spiking neurons. Nevertheless, this assumption does not fully explain complex brain functions. Here we show how nervous activity, other than logic circuits, could instead depend on topological transformations and symmetry constraints occurring at the micro-level of the cortical microcolumn,i.e., the embryological, anatomical and functional basic unit of the brain. Tubular microcolumns can be flattened in guise of a fullerene-like two-dimensional lattices, equipped with about 80 nodes, standing for pyramidal neurons, where neural computations take place. We show how the countless possible combinations of activated neurons embedded in the lattice resemble a barcode. Different assemblies of firing neurons might stand for diverse codes, each one responsible for a single mental activity. A two-dimensional fullerene-like lattice not just simulates the real microcolumn’s microcircuitry, but also allows us to build artificial networks equipped with robustness, plasticity and fastness, because they are grounded on simple topological changes corresponding to pyramidal neurons’ activation.
A Canonical Neural Mechanism for Behavioral Variability
Authors: Darshan Ran , Wood William E. , Peters Susan , Leblois Arthur , Hansel David 
Published: November 2016

ABSTRACTThe ability to generate variable movements is essential for learning and adjusting complex behaviors. This variability has been linked to the temporal irregularity of neuronal activity in the central nervous system. However, how neuronal irregularity actually translates into behavioral variability is unclear. Here we combine modeling, electrophysiological and behavioral studies to address this issue. We demonstrate that a model circuit comprising topographically organized and strongly recurrent neural networks can autonomously generate irregular motor behaviors. Simultaneous recordings of neurons in singing finches reveal that neural correlations increase across the circuit driving song variability, in agreement with the model predictions. Analyzing behavioral data, we find remarkable similarities in the babbling statistics of 5-6 month-old human infants and juveniles from three songbird species, and show that our model naturally accounts for these ‘universal’ statistics.
A synthetic oligo library and sequencing approach reveals an insulation mechanism encoded within bacterial σ54promoters
Authors: Levy Lior , Anavy Leon , Solomon Oz , Cohen Roni , Brunwasser-Meirom Michal , Ohayon Shilo , Atar Orna , Goldberg Sarah , Yakhini Zohar , Amit Roee 
Published: November 2016

SummaryWe use an oligonucleotide library of over 10000 variants together with a synthetic biology approach to identify an insulation mechanism encoded within a subset of σ54promoters. Insulation manifests itself as dramatically reduced protein expression for a downstream gene that may be expressed by transcriptional read-through. The insulation we observe is strongly associated with the presence of short CT-rich motifs (3-5 bp), positioned within 25 bp upstream of the Shine-Dalgarno (SD) motif of the silenced gene. We hypothesize that insulation is effected by binding of the RBS to the upstream CT-rich motif. We provide evidence to support this hypothesis using mutations to the CT-rich motif and gene expression measurements on multiple sequence variants. Modelling is also consistent with this hypothesis. We show that the strength of the silencing, effected by insulation, depends on the location and number of CT-rich motifs encoded within the promoters. Finally, we show that inE.colithese insulator sequences are preferentially encoded within σ54promoters as compared to other promoter types, suggesting a regulatory role for these sequences in natural contexts. Our findings suggest that context-related regulatory effects may often be due to sequence-specific interactions encoded sparsely by short motifs that are not easily detected by lower throughput studies. Such short sequence-specific phenomena can be uncovered with a focused OL design that filters out the sequence noise, as exemplified herein.
On the transdiagnostic nature of peripheral biomarkers in major psychiatric disorders: a systematic review
Authors: Pinto Jairo V. , Moulin Thiago C. , Amaral Olavo B. 
Published: November 2016

ABSTRACTThe search for biomarkers has been one of the leading endeavors in biological psychiatry; nevertheless, in spite of hundreds of publications, it has yet to make an impact in clinical practice. To study how biomarker research has progressed over the years, we performed a systematic review of the literature to evaluate (a) the most studied peripheral molecular markers in major psychiatric disorders, (b) the main features of studies in which they are proposed as biomarkers and (c) whether their patterns of variation are similar across disorders. Out of the six molecules most commonly present as keywords in articles studying plasmatic markers of schizophrenia, major depressive disorder or bipolar disorder, five (BDNF, TNF-alpha, IL-6, C-reactive protein and cortisol) were the same across the three diagnoses. An analysis of the literature on these molecules showed that, while 65% of studies were cross-sectional and 66% compared biomarker levels between patients and controls in specific disorders, only 10% presented an objective measure of diagnostic or prognostic efficacy. Meta-analyses showed that variation in the levels of these molecules was robust across studies, but also similar among disorders, suggesting them to reflect transdiagnostic systemic consequences of psychiatric illness rather than diagnostic markers. Based on this, we discuss how current publication practices have led to research fragmentation across diagnoses, and what steps can be taken in order to increase clinical translation in the field.