bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relationship Between Demographic Characteristics and Noninflammatory Complaints in Rheumatoid Arthritis Patients on Remission
Authors: Karatas Gulsah , Umay Ebru , Gurcay Eda 
Published: May 2019

Objectives
The aim of this study was to investigate the noninflammatory complaints in rheumatoid arthritis (RA) patients on remission and the relationship between these complaints and disease characteristics.

Methods
This is a medical records review study of 103 RA patients who sustained a remission period for at least 6 months. Clinical features and demographic characteristics of patients, such as laboratory parameters, current number of sensitive and swollen joints, pain level and Patient Global Assessment, previously used medications, and modified Health Assessment Questionnaire, were carefully recorded. Patients were divided into 2 groups according to the presence of noninflammatory complaints as patients with or without noninflammatory complaints (group 1, n = 56; group 2, n = 47, respectively).

Results
The most common complaints with a decreasing frequency were as follows: low back pain (n = 13 [23.2%]), degenerative knee pain (n = 11 [19.6%]), and widespread body pain due to fibromyalgia (n = 7 [12.5%]). The mean age and age at diagnosis were higher in group 1 than in those in group 2 (p = 0.039, and p = 0.014, respectively).

Conclusions
Noninflammatory complaints can be observed in about 50% of RA patients on remission. These complaints were more common in elderly patients with old-age disease onset. Therefore, while evaluating and treating this patient population, noninflammatory complaints and disease-specific parameters should be considered carefully in order to fully improve the clinical outcomes.
Ultrasonic Classification of Multicategory Thyroid Nodules Based on Logistic Regression
Authors: Zheng Yi , Xu Shangyan , Zheng Zhan , Wu Lili , Chen Lin , Zhan Weiwei 
Published: May 2019

Abstract
This study aims to screen out significant ultrasonic features to establish different predictive models of thyroid nodules based on logistic regression, with different indicators being included and nodular size being differentiated, and then compare them.
Ultrasonic features of 1906 thyroid nodules in 1761 patients who had undergone sonography and fine-needle aspiration or surgery in our hospital were retrospectively analyzed. According to nodule size and whether vascular or elastographic indicators being included or not, nodules were divided into 12 groups. By univariate and multivariate analysis, the significant sonographic features to diagnose nodules of each group were screened and compared. The logistic regression models were built, and the cutoff values were calculated. The diagnostic performance of newly established models was validated, and the best model was compared with the American College of Radiology Thyroid Imaging Reporting and Data System.
Significant features used to diagnose nodules in all models were hypoechoic, irregular margin, and microcalcification. Predominantly solid was an important indicator to differentiate benign and malignant macronodules. A taller-than-wide shape was a significant indicator of malignant micronodules. Strain elastographic character did show diagnostic value. The area under the curve of logistic regression models for malignant risk prediction were all higher than 0.7, and the best one was model 7, but the diagnostic performance was significantly reduced when models performed bivariate prediction.
The most valuable indicators of malignant thyroid nodules are hypoechoic, irregular margin, and microcalcification. New models are suitable for nodules of different sizes and with or without vascular or elastographic features being described.
The Value of Elasticity Contrast Index in the Differential Diagnosis of Thyroid Solid Nodules
Authors: Di Zhixin , Li Ziyao , Tian Jiawei , Wang Dongmo , Liu Li , Liu Cong 
Published: May 2019

Abstract

Objectives
To assess the clinical value of elasticity contrast index (ECI) in differentiating malignant thyroid nodules from benign ones.

Methods
Conventional ultrasound and elastography with pulsation of the carotid artery used as the compression source were retrospectively reviewed on 175 patients (143 females and 32 males; mean ± SD age, 45.17 ± 11.45 years) with 236 solid nodules (113 malignant and 123 benign). All nodules were confirmed by fine-needle aspiration or surgery to be accurately diagnosed. Elasticity contrast index values were computed and used to quantify local stiffness contrast within a nodule as determined with elastography. Elasticity contrast index values between the malignant and benign groups were compared and then related with pathological results. Diagnostic performance of this method was evaluated with use of the receiver operating characteristic curve.

Results
Mean ± SD ECI values for malignant thyroid nodules were significantly greater than those for benign nodules (3.67 ± 1.20 vs 1.80 ± 0.74, P < 0.01). Area under the receiver operating characteristic curve of ECI values was 0.907 (95% confidence interval, 0.867–0.948), and the best cutoff point was 2.16, leading to a sensitivity of 90.3%, specificity of 82.9%, positive predictive value of 83.7% and negative predictive value of 91.2%.

Conclusions
Elasticity contrast index values can serve as a useful parameter in the differential diagnosis of solid thyroid nodules. With the use of ECI values, objective quantitative information on the tumor stiffness can be achieved to improve diagnostic confidence.
Geomimetic approaches in the design and synthesis of metal-organic frameworks
Authors: Huskić Igor , Friščić Tomislav 
Published: May 2019

The recent discovery of minerals with metal-organic framework (MOF) structures has challenged the view of MOFs as purely synthetic materials. At the same time, the application of geo-inspired synthetic methodologies, such as accelerated ageing and pseudomorphic replication, has enabled a cleaner, more environmentally friendly synthesis of MOFs from mineral-like feedstocks, as well as the assembly of materials with structure controlled at both micro- and meso-scales. These almost concomitant developments have highlighted the previously unknown relationships between geology and MOF chemistry. Here, we outline examples of MOF structures found in minerals, and note geologically inspired approaches to MOF synthesis, as a means to highlight how the emergent geomimetic concepts in MOF chemistry can lead to advances in the design and synthesis of MOFs.
This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
Flexibility of network materials and the Rigid Unit Mode model: a personal perspective
Authors: Dove Martin T. 
Published: May 2019

The Rigid Unit Mode model was initially developed to understand the origin of displacive phase transitions in network silicate structures. Here, we review the successes of the model, and consider how it might apply to a wider range of network structures.
This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacteria via Dynamic RNA Nanotechnology
Authors: Hanewich-Hollatz Mikhail H. , Chen Zhewei , Huang Jining , Hochrein Lisa M. , Pierce Niles A. 
Published: May 2019

ABSTRACTA guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering diverse modes of synthetic regulation (edit, silence, induce, bind). However, the fact that gRNAs are constitutively active places limitations on the ability to confine gRNA activity to a desired location and time. To achieve programmable control over the scope of gRNA activity, here we apply principles from dynamic RNA nanotechnology to engineer conditional guide RNAs (cgRNAs) whose activity is dependent on the presence or absence of an RNA trigger. These cgRNAs are programmable at two levels, with the trigger-binding sequence controlling the scope of the effector activity and the target-binding sequence determining the subject of the effector activity. We demonstrate molecular mechanisms for both constitutively active cgRNAs that are conditionally inactivated by an RNA trigger (ON→OFF logic) and constitutively inactive cgRNAs that are conditionally activated by an RNA trigger (OFF→ON logic). For each mechanism, automated sequence design is performed using the reaction pathway designer within NUPACK to design an orthogonal library of three cgRNAs that respond to different RNA triggers. In E. coli expressing cgRNAs, triggers, and silencing dCas9 as the protein effector, we observe programmable conditional gene silencing with a median dynamic range of ≈6-fold for an ON→OFF “terminator switch” mechanism, ≈15-fold for an ON→OFF “splinted switch” mechanism, and ≈3.6-fold for an OFF→ON “toehold switch” mechanism; the median crosstalk within each cgRNA library is <2%, <2%, and ≈20% for the three mechanisms. By providing programmable control over both the scope and target of protein effector function, cgRNA regulators offer a promising platform for synthetic biology.
Prediction of specific TCR-peptide binding from large dictionaries of TCR-peptide pairs
Authors: Springer Ido , Besser Hanan , Tickotsky-Moskovitz Nili , Dvorkin Shirit , Louzoun Yoram 
Published: May 2019

AbstractCurrent sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents tools are based on conserved motifs and are applied to peptides with many known binding TCRs.Given any TCR and peptide, we employ new NLP-based methods to predict whether they bind. We combined large-scale TCR-peptide dictionaries with deep learning methods to produce ERGO (pEptide tcR matchinG predictiOn), a highly specific and generic TCR-peptide binding predictor.A set of standard tests are defined for the performance of peptide-TCR binding, including the detection of TCRs binding to a given peptide/antigen, choosing among a set of candidate peptides for a given TCR and determining whether any pair of TCR-peptide bind. ERGO significantly outperforms current methods in these tests even when not trained specifically for each test.The software implementation and data sets are available at https://github.com/louzounlab/ERGO
Persistent features of intermittent transcription
Authors: Wilkinson Michael , Darmanis Spyros , Pisco Angela Oliveira , Huber Greg 
Published: May 2019

AbstractHere we report statistical studies of single-cell mRNA counts from cells derived from different tissues of adult mice. By examining correlations between mRNA gene counts we find strong evidence that when genes are only observed in a small fraction of cells, this is as a consequence of intermittent transcription rather than of expression only in specialized cell types. Count statistics are used to estimate a peak transcription level for each gene, and a probability for the gene to be active in any given cell. We find that the peak transcription levels are approximately constant across different tissue types, but the gene expression probabilities may be markedly different. Both these quantities have very wide ranges of values, with a probability density function well approximated by a power law.Author summaryUsing evidence from single-cell mRNA counts, we argue that the expression of many genes in individual mouse cells is highly intermittent. Comparing cells from different tissues, we find that the peak activity of a given gene is approximately the same in all tissue types, whereas the probability of a gene being active can differ markedly.
Population history and genetic adaptation of the Fulani nomads: Inferences from genome-wide data and the lactase persistence trait
Authors: Vicente Mário , Priehodová Edita , Diallo Issa , Podgorná Eliska , Poloni Estella S. , Černý Viktor , Schlebusch Carina M. 
Published: May 2019

AbstractHuman population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. Our findings further suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first Genome Wide Association study (GWAS) of the lactase persistence trait. We also further explored signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.
TEMPO: Detecting Pathway-Specific Temporal Dysregulation of Gene Expression in Disease
Authors: Pietras Christopher Michael , Ocitti Faith , Slonim Donna K. 
Published: May 2019

AbstractWhile many transcriptional profiling experiments measure dynamic processes that change over time, few include enough time points to adequately capture temporal changes in expression. This is especially true for data from human subjects, for which relevant samples may be hard to obtain, and for developmental processes where dynamics are critically important. Although most expression data sets sample at a single time point, it is possible to use accompanying temporal information to create a virtual time series by combining data from different individuals.We introduce TEMPO, a pathway-based outlier detection approach for finding pathways showing significant temporal changes in expression patterns from such combined data. We present findings from applications to existing microarray and RNA-seq data sets. TEMPO identifies temporal dysregulation of biologically relevant pathways in patients with autism spectrum disorders, Huntington’s disease, Alzheimer’s disease, and COPD. Its findings are distinct from those of standard temporal or gene set analysis methodologies.Overall, our experiments demonstrate that there is enough signal to overcome the noise inherent in such virtual time series, and that a temporal pathway approach can identify new functional, temporal, or developmental processes associated with specific phenotypes.AvailabilityAn R package implementing this method and full results tables are available at bcb.cs.tufts.edu/tempo/.
IQGAP2 acts as a tumor suppressor in breast cancer and its reduced expression promotes cancer growth and metastasis by MEK/ERK signalling pathways
Authors: Kumar Dinesh , Hassan Md. Khurshidul , Pattanaik Niharika , Mohapatra Nachiketa , Dixit Manjusha 
Published: May 2019

AbstractIQGAP2 is a member of IQGAPs scaffolding protein family. It has been reported as a tumor suppressor in various cancers, as well as, an oncogene in some cancers, suggesting organ specific role. Need to identify therapeutic targets which function in ER/PR independent way, prompted us to explore role of IQGAP2 in molecular mechanism in breast cancer, which was completely unknown. In vitro studies in estrogen receptor positive breast cancer cell line (MCF7) showed that low IQGAP2 expression results in increased cell proliferation, migration and invasion of cells whereas an opposite effect was observed with ectopic expression of IQGAP2. Triple negative breast cancer cell line (MDA-MB-468), with IQGAP2 depletion showed similar effect, supporting its role in ER/PR independent manner. Furthermore, we found that reduced IQGAP2 expression induces the expression of EMT markers; twist and N-cadherin and decreases the expression of MET marker, E-cadherin via the MEK/ERK pathway but not via AKT pathway. Validation of findings in patients showed a reduced IQGAP2 expression in breast cancer tissues compared to normal tissue. Patients with low levels of IQGAP2 showed correlation with higher tumor stage. Our results suggest that IQGAP2 acts as a tumor suppressor and its down regulation results in cell growth, cell invasion and EMT through the MEK/ERK signalling pathways and it hence may be a potential therapeutic target in breast cancer.
Presence of a family history and excessive pressure on the first toe pad during walking in female subjects with pincer nails
Authors: Makino Koji , Ogawa Youichi , Kanagawa Takaiki , Matsuzawa Miyuki , Yamamoto Saori , Yamada Kazuki , Shimada Shinji , Kawamura Tatsuyoshi , Terada Hidetsugu 
Published: May 2019

AbstractPincer nails (PN) are defined as a transverse overcurvature of the nail plate. Although there have been advancements in therapeutic approaches, the precise underlying mechanisms for the development of PN are still not fully understood. Currently, PN are assumed to develop due to lack of upward mechanical force on the toes. We developed a novel wireless device to observe detailed gait motion. We analyzed trends of gait motion in healthy individuals without PN, healthy individuals with PN without a family history of PN, and healthy individuals with PN and a family history of PN. We found that a family history of PN is an independent risk factor for PN, irrespective of gait motion. Moreover, healthy individuals with PN but without a family history of PN exhibit strong and concentrated pressure on the first toe pad during walking. In sum, a family history of PN and excess upward mechanical forces on the first toe pad during walking may be risk factors for the development of PN.
A test of trophic and functional island biogeography theory with the avifauna of a continental archipelago
Authors: Ross Samuel R. P.‐J. , Friedman Nicholas R. , Janicki Julia , Economo Evan P. 
Published: May 2019

Abstract

The classical MacArthur–Wilson theory of island biogeography (TIB) emphasizes the role of island area and isolation in determining island biotas, but is neutral with respect to species differences that could affect community assembly and persistence. Recent extensions of island biogeography theory address how functional differences among species may lead to non‐random community assembly processes and different diversity–area scaling patterns. First, the trophic TIB considers how diversity scaling varies across trophic position in a community, with species at higher trophic levels being most strongly influenced by island area. Second, further extensions have predicted how trait distributions, and hence functional diversity, should scale with area. Trait‐based theory predicts richness‐corrected functional diversity should be low on small islands but converge to null on larger islands. Conversely, competitive assembly predicts high diversity on small islands converging to null with increasing size.

However, despite mounting interest in diversity–area relationships across different dimensions of diversity, these predictions derived from theory have not been extensively tested across taxa and island systems.

Here, we develop and test predictions of the trophic TIB and extensions to functional traits, by examining the diversity–area relationship across multiple trophic ranks and dimensions of avian biodiversity in the Ryūkyū archipelago of Japan.

We find evidence for a positive species– and phylogenetic diversity–area relationship, but functional diversity was not strongly affected by island area. Counter to the trophic TIB, we found no differences in the slopes of species–area relationships among trophic ranks, although slopes varied among trophic guilds at the same rank. We revealed differential assembly of trophic ranks, with evidence of trait‐based assembly of intermediate predators but otherwise neutral community assembly.

Our results suggest that niche space differs among trophic guilds of birds, but that differences are mostly not predicted by current extensions of island biogeography theory. While predicted patterns do not fit the empirical data well in this case, the development of such theory provides a useful framework to analyse island patterns from new perspectives. The application of empirical datasets such as ours should help provide a basis for developing further iterations of island biogeography theory.
Negative frequency‐dependent foraging behaviour in a generalist herbivore (Alces alces) and its stabilizing influence on food web dynamics
Authors: Hoy Sarah R. , Vucetich John A. , Liu Rongsong , DeAngelis Don L. , Peterson Rolf O. , Vucetich Leah M. , Henderson John J. 
Published: May 2019

AbstractResource selection is widely appreciated to be context‐dependent and shaped by both biological and abiotic factors. However, few studies have empirically assessed the extent to which selective foraging behaviour is dynamic and varies in response to environmental conditions for free‐ranging animal populations.Here, we assessed the extent that forage selection fluctuated in response to different environmental conditions for a free‐ranging herbivore, moose (Alces alces), in Isle Royale National Park, over a 10‐year period. More precisely, we assessed how moose selection for coniferous versus deciduous forage in winter varied between geographic regions and in relation to (a) the relative frequency of forage types in the environment (e.g. frequency‐dependent foraging behaviour), (b) moose abundance, (c) predation rate (by grey wolves) and (d) snow depth. These factors are potentially important for their influence on the energetics of foraging. We also built a series of food‐chain models to assess the influence of dynamic foraging strategies on the stability of food webs.Our analysis indicates that moose exhibited negative frequency dependence, by selectively exploiting rare resources. Frequency‐dependent foraging was further mediated by density‐dependent processes, which are likely to be predation, moose abundance or some combination of both. In particular, frequency dependence was weaker in years when predation risk was high (i.e. when the ratio of moose to wolves was relatively low). Selection for conifers was also slightly weaker during deep snow years.The food‐chain analysis indicates that the type of frequency‐dependent foraging strategy exhibited by herbivores had important consequences for the stability of ecological communities. In particular, the dynamic foraging strategy that we observed in the empirical analysis (i.e. negative frequency dependence being mediated by density‐dependent processes) was associated with more stable food web dynamics compared to fixed foraging strategies.The results of this study indicated that forage selection is a complex ecological process, varying in response to both biological (predation and moose density) and abiotic factors (snow depth) and over relatively small spatial scales (between regions). This study also provides a useful framework for assessing the influence of other aspects of foraging behaviour on the stability of food web dynamics.