bluuebunny/crossref_metadata_2025_split huggingface dataset:
MIF -173 G > C (rs755622) Gene Polymorphism Modulates Tuberculosis Risk: Evidence from a Meta-analysis and Trial Sequential Analysis
Authors: Areeshi Mohammed Y. , Mandal Raju K. , Dar Sajad A. , Jawed Arshad , Wahid Mohd , Lohani Mohtashim , Panda Aditya K. , Mishra B. N. , Akhter Naseem , Haque Shafiul 
Published: November 2017

AbstractThe macrophage migration inhibitory factor (MIF) is a cytokine that plays an important role in inhibiting the growth of pathogenicMycobacterium tuberculosis(M.tb) and regulates immune responses againstM.tbpathogen.MIF-173 G > C gene polymorphism may affect immunity in an individual and leads to susceptibility to tuberculosis (TB). A large number of studies have investigated the relevance of this polymorphism with TB risk, but their results were inconclusive. To obtain a precise conclusion, a meta-analysis was performed by retrieving six eligible studies from Google Scholar, PubMed (Medline), and EMBASE online databases. Overall combined analysis suggested increased TB risk betweenMIF-173 G > C polymorphism and overall risk in four genetic models, i.e., allelic (C vs. G: p = 0.001; OR = 1.517, 95% CI = 1.312 to 1.753), homozygous (CC vs. GG: p = 0.026; OR = 1.874, 95% CI = 1.079 to 3.257), heterozygous (GC vs. GG: p = 0.001; OR = 1.542, 95% CI = 1.273 to 1.868) and dominant model (CC + GC vs. GG: p = 0.001; OR = 1.631, 95% CI = 1.362 to 1.955). Similarly, increased TB risk was observed in subgroup analysis of Asian ethnicity. No publication bias was observed. These results suggested thatMIF-173 G > C variant is a significant risk factor for TB in overall and in Asian populations, and can be used as prognostic marker for TB susceptibility.
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds
Authors: Grießmeier Victoria , Bremges Andreas , McHardy Alice C. , Gescher Johannes 
Published: November 2017

AbstractField denitrification beds containing polymeric plant material are increasingly used to eliminate nitrate from agricultural drainage water. They mirror a number of anoxic ecosystems. However, knowledge of the microbial composition, the interaction of microbial species, and the carbon degradation processes within these denitrification systems is sparse. This study revealed several new aspects of the carbon and nitrogen cycle, and these findings can be correlated with the dynamics of the microbial community composition and the activity of key species. Members of the order Pseudomonadales seem to be important players in denitrification at low nitrate concentrations, while a switch to higher nitrate concentrations seems to select for members of the orders Rhodocyclales and Rhizobiales. We observed that high nitrate loading rates lead to an unpredictable transition of the community’s activity from denitrification to dissimilatory reduction of nitrate to ammonium (DNRA). This transition is mirrored by an increase in transcripts of the nitrite reductase gene nrfAH and the increase correlates with the activity of members of the order Ignavibacteriales. Denitrification reactors sustained the development of an archaeal community consisting of members of the Bathyarchaeota and methanogens belonging to the Euryarchaeota. Unexpectedly, the activity of the methanogens positively correlated with the nitrate loading rates.
Cellular automaton models for time-correlated random walks: derivation and analysis
Authors: Nava-Sedeño J. M. , Hatzikirou H. , Klages R. , Deutsch A. 
Published: November 2017

AbstractMany diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory. For this purpose the reorientation probabilities are derived from velocity autocorrelation functions that are given a priori; in that respect our approach is “data-driven”. Particular examples we consider are velocity correlations that decay exponentially or as power laws, where the latter functions generate anomalous diffusion. The computational efficiency of cellular automata combined with our analytical results paves the way to explore the relevance of memory and anomalous diffusion for the dynamics of interacting cell populations, like confluent cell monolayers and cell clustering.
MiR-211 is essential for adult cone photoreceptor maintenance and visual function
Authors: Barbato Sara , Marrocco Elena , Intartaglia Daniela , Pizzo Mariateresa , Asteriti Sabrina , Naso Federica , Falanga Danila , Bhat Rajeshwari S. , Meola Nicola , Carissimo Annamaria , Karali Marianthi , Prosser Haydn M. , Cangiano Lorenzo , Surace Enrico Maria , Banfi Sandro , Conte Ivan 
Published: November 2017

AbstractMicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that play an important role in the control of fundamental biological processes in both physiological and pathological conditions. Their function in retinal cells is just beginning to be elucidated, and a few have been found to play a role in photoreceptor maintenance and function. MiR-211 is one of the most abundant miRNAs in the developing and adult eye. However, its role in controlling vertebrate visual system development, maintenance and function so far remain incompletely unexplored. Here, by targeted inactivation in a mouse model, we identify a critical role of miR-211 in cone photoreceptor function and survival. MiR-211 knockout (−/−) mice exhibited a progressive cone dystrophy accompanied by significant alterations in visual function. Transcriptome analysis of the retina from miR-211−/− mice during cone degeneration revealed significant alteration of pathways related to cell metabolism. Collectively, this study highlights for the first time the impact of miR-211 function in the retina and significantly contributes to unravelling the role of specific miRNAs in cone photoreceptor function and survival.
Tracking the Growth of Tense and Agreement in Children With Specific Language Impairment: Differences Between Measures of Accuracy, Diversity, and Productivity
Authors: Leonard Laurence B. , Haebig Eileen , Deevy Patricia , Brown Barbara 
Published: November 2017

Purpose
Composite measures of children's use of tense and agreement morphology differ in their emphasis on accuracy, diversity, or productivity, yet little is known about how these different measures change over time. An understanding of these differences is especially important for the study of children with specific language impairment, given these children's extraordinary difficulty with this aspect of grammar.

Method
We computed 3 types of composite scores from spontaneous speech samples obtained from 17 preschoolers with specific language impairment before, during, and after their participation in a language intervention study. These measures were the Finite Verb Morphology Composite (a measure of accuracy), the Tense Marker Total (a measure of diversity), and the Productivity Score (a measure of productivity).

Results
The 3 measures differed in their growth trajectories. Sample size did not alter the linear or quadratic nature of growth of any composite, although it did affect the absolute values found for the Tense Marker Total and Productivity Score.

Conclusion
Even when sample size is controlled, early growth can be seen in tense and agreement accuracy with relatively limited diversity and productivity, whereas later growth in diversity and productivity can occur with very little change in accuracy.
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
Authors: Ligon Thomas S , Fröhlich Fabian , Chiş Oana T , Banga Julio R , Balsa-Canto Eva , Hasenauer Jan 
Published: November 2017

Abstract

Motivation
Mathematical modeling using ordinary differential equations is used in systems biology to improve the understanding of dynamic biological processes. The parameters of ordinary differential equation models are usually estimated from experimental data. To analyze a priori the uniqueness of the solution of the estimation problem, structural identifiability analysis methods have been developed.

Results
We introduce GenSSI 2.0, an advancement of the software toolbox GenSSI (Generating Series for testing Structural Identifiability). GenSSI 2.0 is the first toolbox for structural identifiability analysis to implement Systems Biology Markup Language import, state/parameter transformations and multi-experiment structural identifiability analysis. In addition, GenSSI 2.0 supports a range of MATLAB versions and is computationally more efficient than its previous version, enabling the analysis of more complex models.

Availability and implementation
GenSSI 2.0 is an open-source MATLAB toolbox and available at https://github.com/genssi-developer/GenSSI.

Supplementary information
Supplementary data are available at Bioinformatics online.
Latin Rhetoric
Authors: Gaines Robert N. 
Published: November 2017

This bibliography is designed to provide a structured list of materials relevant to the study of Latin rhetoric in ancient times. In Rome, rhetoric was the art of making persuasive discourse, and its pursuit typically involved the mastery of rhetorical principles and the application of political speaking. Accordingly, the general subject of the bibliography is Latin rhetorical theory and oratorical practice. The period covered in the bibliography is 300 bce to 430 ce. These boundaries—at their outer extremes—are designed to include the earliest oration for which we have a date during the Roman republic (On King Pyrrhus by Appius Claudius Caecus, delivered around 280 bce) as well as the latest theory of Latin speaking that might be called ancient (Teaching Christianity by Saint Augustine, completed in 428 ce). The materials included in the bibliography are organized under headings, and these headings are ordered into three groups. In the first group there are four headings: General Overviews, Reference Works, Encyclopedias, and Handbooks and Companions. These headings cover materials of broad interest that allow users to orient themselves to Latin rhetorical scholarship and to answer questions—from simple to very complex—without consulting primary sources. In the second group there are three headings: Rhetorical Theory, Oratorical Discourse of the Republican Era, and Oratorical Discourse of the Imperial Era. Together these three headings organize a basic collection of the primary and secondary sources that make original research possible on Latin rhetoric. Subheadings under these headings are generally categories of authors or texts, and citations typically refer to Latin primary sources, modern language translations, and interpretive scholarship—including commentaries and scholarly books or essays—related to primary sources. This group of headings is designed principally for users who are undertaking research on Latin rhetoric. The final group of headings includes Rhetoric and Education, Rhetoric and Politics, Rhetoric and Literature, and Influence of Latin Rhetoric. These headings comprise scholarship on the interactions of Latin rhetoric with particular aspects of society and culture during ancient times and in subsequent eras. This group of headings offers aid to users who wish to explain historically situated events and artifacts that are related to, but lie outside the narrow sphere of, Latin rhetorical theory and oratory.
Five easy-to-master uses for point-of-care ultrasound
Authors: Fuller Fritz , Norman Francisco 
Published: November 2017

ABSTRACT
Clinicians are increasingly becoming familiar with the value of limited, focused point-of-care ultrasonography (POCUS) to help answer discrete clinical questions. Ultrasound education is being taught in medical schools and physician assistant (PA) and PA postgraduate programs nationwide. This article introduces five basic POC ultrasound scans that can easily be mastered by practicing PAs.
Publishing Trends in Otology and Neurotology
Authors: Boerner Ryan , Hatch Jonathan L. , Harruff Elizabeth , Nguyen Shaun A. , Rizk Habib G. , Meyer Ted A. , Lambert Paul R. , McRackan Theodore R. 
Published: November 2017

Objectives:
1) Describe publishing trends for otologic/neurotologic disorders over a 35-year span. 2) Compare trends in publishing with disease prevalence. 3) Evaluate changes in topic and journal specific ranking scores over time.

Methods:
PubMed searches were performed on 35 otologic/neurotologic disorders using medical subject headings (MeSH) terms from 1980 to 2015. Searches were limited in scope to the English language. A Mann–Kendall trend analysis evaluated changes in publication frequency as a discrete variable while correcting for total number of articles published per year. Scopus was used to identify SCImago Country and Journal Rank (SJR) indicator scores and weighted-averages used to calculate changes over time.

Results:
The total number of publications on the 35 topics increased from 853 in 1980 to a peak of 3,068 in 2013. Otitis media (τ = −0.799, p < 0.001) and Menière's disease (τ = −0.724, p < 0.001) showed strong decreasing publication trends. Temporal bone encephaloceles (τ = 0.743, p < 0.001) and cochlear implants (τ = 0.740, p < 0.001) showed strong increasing publication trends. Rapid rise in publications on superior canal dehiscence and vestibular migraine illustrate novel diagnoses. The weighted-average SJR score increased from 0.816 in 2000 to 1.160 in 2015 (p < 0.001).

Conclusion:
This study displays trends in the literature over the past 35 years that are often inconsistent with common disorders seen by otologists/neurotologists. Certain diagnoses that are currently being researched less commonly continue to impact patients with the same regularity. Quality of otologic/neurotologic literature has become more reputable with regards to SJR scores.
Diverse correlations between fibrosis-related factors and liver stiffness measurement by transient elastography in chronic hepatitis B
Authors: Lin Ziyu , Liang Jing , Zhu Jianyun , Hu Chaoxia , Gu Yurong , Lai Jing , Zheng Yubao , Gao Zhiliang 
Published: November 2017

Background
Several fibrosis-related factors influence liver stiffness measurements (LSM); however, these changes have not been investigated in the context of the various disease stages of chronic hepatitis B (CHB).

Aim
The aim of this study was to assess the correlations between fibrosis-related factors and LSM in different disease stages of CHB.

Patients and methods
Patients with mild CHB (n=305) and cirrhotic hepatitis B (cirrhotic HB) (n=137) were compared with determine the relationship between LSM and fibrosis-related factors including parameters of liver inflammation [aminotransferase (ALT), aspartate transaminase (AST), total bilirubin (Tbil)], albumin, globulin, peripheral blood cells (neutrophil granulocytes, red blood cells, platelets), abdominal ultrasound B-scan parameters including right liver thickness, portal vein inradium, diameter of spleen (DS), thickness of spleen (TS), and splenic vein inradium (SV).

Results
In patients with mild CHB, LSM was correlated strongly with ALT (r=0.3534, P<0.0001), AST (r=0.3976, P<0.0001), and ALT+AST (r=0.3760, P<0.0001). LSM was correlated closely with Tbil (r=0.2237, P<0.0001), albumin (r=−0.3126, P<0.0001), albumin/globulin (r=−0.3086, P<0.0001), SV (r=0.3317, P<0.0001), DS (r=0.4157, P<0.0001), and spleen volume (DS×TS) (r=−0.4399, P<0.0001). Red blood cells were correlated negatively with LSM in both mild CHB and cirrhotic HB patients (r=−0.1981, P=0.0203; r=−0.1593, P=0.0053). LSM was not correlated with age, peripheral blood cell parameters, right liver thickness, portal vein inradium, or TS in mild CHB or cirrhosis HB patients. However, in patients with cirrhotic HB, LSM values were not correlated significantly with other fibrosis-related factors, except for Tbil (r=0.2272, P=0.0076).

Conclusion
Our findings suggest that the magnitude of these correlations differs significantly between mild CHB and cirrhotic HB patients.
The Great Mimicker
Authors: Amaratunga Thelina , Millo Noam , Gordon Vallerie , Blcamumpaka Cyrille , Yan Yi , Sparkes Stephanie , Goubran Ashraf 
Published: November 2017

Abstract
Meig syndrome is the triad of benign ovarian tumor, ascites, and pleural effusion. Pseudo-Meig syndrome mimics the Meig syndrome triad; however, in pseudo-Meig syndrome, the ovarian tumor usually represents a primary malignancy or metastases. Differentiating Meig from pseudo-Meig syndrome is challenging both clinically and with diagnostic imaging but is important because prognoses for these distinct entities are drastically different. Evidence-based sonographic prediction models are valuable because they can aid in this distinction. Here, we present the first reported case of pseudo-Meig syndrome secondary to large, bilateral Krukenberg tumors of unknown origin, in a gravid 30-year-old woman at 24 weeks' gestation, discovered initially by ultrasound.
Cranioplasty With Mandibular Outer Cortex Bone Grafts
Authors: Sun Jiaming , Chen Hongbo , Wang Jiecong 
Published: November 2017

Background:
Autologous bone grafts are still the best materials for calvarial reconstruction. In the past, rib, iliac crest, and cranial bone have been used for the reconstruction of the calvarial defects. However, the use of mandibular outer cortex bone graft in calvarial defects reconstruction is poorly reported in literature. This study focused on using the mandibular outer cortex bone grafts for calvarial defects.

Methods:
From October 2004 to July 2016, there were a total of 13 patients in this study who underwent cranioplasty with mandibular outer cortex bone grafts to reconstruction calvarial defects. All the patients were followed up for at least 6 months.

Results:
The majority of the patients were satisfied with the reconstructive outcome.

Conclusion:
The authors consider the mandibular outer cortex bone graft can achieve excellent esthetic results in selected cranioplasty reconstructions.
Facial Anthropometric Evaluation of Unilateral Cleft Lip and Palate Patients: Infancy Through Adolescence
Authors: Dehghani Mahboobe , Jahanbin Arezoo , Omidkhoda Maryam , Entezari Mostafa , Shadkam Elaheh 
Published: November 2017

Introduction:
Craniofacial anthropometric studies measure the differences in humans’ craniofacial dimensions. The aim of this study was to determine facial anthropometric dimensions of newborn to 12-year-old girls with nonsyndromic unilateral cleft lip and palate (UCLP).

Methods:
In this cross-sectional analytical study, data was collected from 65 infant to 12-year old girls with UCLP. Digital frontal and profile facial photographs were transferred to a computer and desired anthropometric landmarks were traced on each image. Fifteen anthropometric parameters were measured which were the angles of facial, nasofacial, nasomental, Z, nasolabial, inclination of nasal base and labial fissure, nasal deviation, mentocervical, facial convexity and also ratios of nasal prominence relative to nasal height, middle to lower facial third, upper lip to lower lip height, columellar length relative to upper lip, and incisal show relative to incisal width. Pearson coefficient and linear regression were used for statistical analysis.

Results:
Upper lip to lower lip height ratio and angles of nasofacial, nasolabial, and facial convexity decreased with the age of the patients. In contrast, nasomental angle and the ratios of columellar length to upper lip length, middle facial height to lower facial height, and incisal show relative to incisal width increased. Other parameters studied did not appear to have any significant correlation with age.

Conclusion:
In the girls with UCLP, various craniofacial dimensions have different growth rates with some parts growing slower than others. Some of the parameters studied were significantly correlated with age, thus growth-related curves and equations were obtained and presented.
All-Resolutions Inference for Brain Imaging
Authors: Rosenblatt Jonathan D. , Finos Livio , Weeda Wouter D. , Solari Aldo , Goeman Jelle J. 
Published: November 2017

AbstractThe most prevalent approach to activation localization in neuroimaging is to identify brain regions as contiguous supra-threshold clusters, check their significance using random field theory, and correct for the multiple clusters being tested. Besides recent criticism on the validity of the random field assumption, a spatial specificity paradox remains: the larger the detected cluster, the less we know about the location of activation within that cluster. This is because cluster inference implies “there exists at least one voxel with an evoked response in the cluster”, and not that “all the voxels in the cluster have an evoked response”. Inference on voxels within selected clusters is considered bad practice, due to the voxel-wise false positive rate inflation associated with this circular inference. Here, we propose a remedy to the spatial specificity paradox. By applying recent results from the multiple testing statistical literature, we are able to quantify the proportion of truly active voxels within selected clusters, an approach we call All-Resolutions Inference (ARI). If this proportion is high, the paradox vanishes. If it is low, we can further “drill down” from the cluster level to sub-regions, and even to individual voxels, in order to pinpoint the origin of the activation. In fact, ARI allows inference on the proportion of activation in all voxel sets, no matter how large or small, however these have been selected, all from the same data. We use two fMRI datasets to demonstrate the non-triviality of the spatial specificity paradox, and its resolution using ARI. One of these datasets is large enough for us to split it and validate the ARI estimates. The conservatism of ARI inference permits circularity without losing error guarantees, while still returning informative estimates.
Uncoupling Intraflagellar Transport and Primary Cilia Formation Demonstrates Deep Integration of IFT in Hedgehog Signaling
Authors: Eguether Thibaut , Cordelieres Fabrice P , Pazour Gregory J 
Published: November 2017

AbstractThe vertebrate hedgehog pathway is organized in primary cilia and hedgehog components relocate into or out of cilia during signaling. Defects in intraflagellar transport (IFT) typically disrupt ciliary assembly and attenuate hedgehog signaling. Determining if IFT drives the movement of hedgehog components is difficult due to the requirement of IFT for building cilia. Unlike most IFT proteins, IFT27 is dispensable for cilia formation but affects hedgehog signaling similar to other IFTs allowing us to examine its role in the dynamics of signaling. Activating signaling at points along the pathway inIft27mutant cells showed that IFT is extensively involved in the pathway. Similar analysis ofBbsmutant cells showed that BBS proteins participate at many levels of signaling but are not needed to concentrate Gli transcription factors at the ciliary tip. Our analysis showed that smoothened delivery to cilia does not require IFT27, but the role of other IFTs is not known. Using a rapamycin-induced dimerization system to stop IFT after ciliary assembly was complete we show that smoothened delivery to cilia is IFT independent.AbbreviationsMEFsmouse embryonic fibroblastsSAGsmoothen agonistIFTintraflagellar transportFKBPFK506 Binding Protein 12FRBFKBP12-rapamycin binding