bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erbium Yttrium–Aluminum–Garnet Laser Versus Traditional Bur in the Extraction of Impacted Mandibular Third Molars: Analysis of Intra- and Postoperative Differences
Authors: Giovannacci Ilaria , Giunta Giovanna , Pedrazzi Giuseppe , Meleti Marco , Manfredi Maddalena , Migliario Mario , Brucoli Matteo , Greco Lucchina Alberta , Mortellaro Carmen , Vescovi Paolo 
Published: May 2018

Introduction:
Different osteotomy techniques have been proposed in order to improve postoperative course of impacted third molar extraction. The aim is to evaluate the possible advantages achieved with erbium yttrium–aluminum–garnet (Er:YAG) laser osteotomy compared with traditional burs.

Materials and Methods:
Seventy-six extractions were randomly classified into 2 groups according to osteotomy instrument: group 1 (G1)—Er:YAG laser: 35 patients; group 2 (G2)—traditional bur: 41 patients. Intraoperative parameters: total time, stitches number, and patient compliance. Postoperative: pain, health-related quality of life (HR-QoL), need for analgesics, edema, trismus, intra- and extraoral hematoma, and postoperative complications.

Results:
Mean time for G1 resulted 1069.4 seconds; for G2 1913.5 seconds (P < 0.0001). Mean number of stitches (P = 0.773) and patient compliance (P = 0.063) were not statistically different. Regarding pain, mean visual analog scale (VAS), and numeric rating scale (NRS) scores were lower in G1 than in G2. Statistically significant differences were highlighted at days 0, 1, and 3 with VAS scale and at days 0, 1, 3, and 7 with NRS scale. The HR-QoL scores resulted lower in G1 than in G2 (P < 0.0001). Mean facial swelling and trismus resulted statistically lower in G1 than in G2 at day 2 (P < 0.0001). Trismus resulted statistically lower in G1 than in G2 at days 2 (P < 0.0001) and 7 (P = 0.004). Two patients (5.71%) of subcutaneous emphysema was recorded in G1 and 2 patients (4.88%) of lip paresthesia in G2.

Conclusion:
Data confirm that the use of Er:YAG laser for osteotomy may achieve several advantages both technical and biological.
Endoscopically Assisted Transoral Gap Arthroplasty of the Temporomandibular Joint Ankylosis in a Pediatric Patient
Authors: Abdelazeem Mohamed Hazem , Erdogan Özgür , Awad Tarek Ahmed 
Published: May 2018

Abstract
Surgical management of temporomandibular joint (TMJ) ankylosis in children is often challenging and may result in various complications such as facial nerve injury and visible scar. In this clinical report, the authors present minimally invasive management of a 9-year-old boy with bilateral post-traumatic TMJ ankylosis. The ankylotic TMJs were addressed and gap arthoplasties were performed by endoscopically assisted transoral approach. The risk of facial nerve injury is minimized and facial scar was prevented by avoiding extraoral incision. Mandibular movements in 3 directions were satisfactory at 3rd postoperative month.
Cervical Tracheal Resection and Anastomosis for Postintubation Tracheal Stenosis
Authors: Kanlikama Muzaffer , Celenk Fatih , Gonuldas Burhanettin , Gulsen Secaattin 
Published: May 2018

Abstract
In this study the authors evaluated the outcomes of tracheal resection and anastomosis in postintubation tracheal stenosis. The authors also aimed to identify clinical and radiological factors associated with restenosis. Thirty-four consecutive patients were included in the study. Patients with subglottic stenosis who underwent procedures involving cricoid cartilage and patients with other etiologies were excluded from the study. Univariate analysis was performed to determine the risk factors for restenosis. Receiver operating characteristic (ROC) curves were generated for the diameter of the narrowest part of the trachea (Dst) and the distance between cricoid cartilage and stenosis (Dcs). Of the 34 patients, 31 (91.1%) patients were successfully decannulated. Nineteen (55.8%) patients had complications. After univariate analysis, Dst (P = 0.001), Dcs (P = 0.001), smoking (P = 0.007) and grade of the stenosis (P = 0.003) were significantly associated with restenosis. The sensitivity and specificity were 90.9% and 77.3%, respectively, when the cutoff value for Dst was 4 mm. Sensitivity and specificity were 72.7% and 100%, respectively, when the cutoff value for Dcs was 10 mm. Tracheal resection and anastomosis is an effective surgical method for treating postintubation tracheal stenosis. In our series, 91.1% of the patients with postintubation tracheal stenosis were successfully decannulated. Restenosis was the most common complication. The diameter of the narrowest part of the trachea (Dst), the distance between cricoid cartilage and stenosis (Dcs), smoking and grade of stenosis were significantly associated with restenosis.
Unpicking allosteric mechanisms of homo-oligomeric proteins by determining their successive ligand binding constants
Authors: Gruber Ranit , Horovitz Amnon 
Published: May 2018

Advances in native mass spectrometry and single-molecule techniques have made it possible in recent years to determine the values of successive ligand binding constants for large multi-subunit proteins. Given these values, it is possible to distinguish between different allosteric mechanisms and, thus, obtain insights into how various bio-molecular machines work. Here, we describe for ring-shaped homo-oligomers, in particular, how the relationship between the values of successive ligand binding constants is diagnostic for concerted, sequential and probabilistic allosteric mechanisms.
This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
Molecular switch-like regulation in motor proteins
Authors: Tafoya Sara , Bustamante Carlos 
Published: May 2018

Motor proteins are powered by nucleotide hydrolysis and exert mechanical work to carry out many fundamental biological tasks. To ensure their correct and efficient performance, the motors' activities are allosterically regulated by additional factors that enhance or suppress their NTPase activity. Here, we review two highly conserved mechanisms of ATP hydrolysis activation and repression operating in motor proteins—the glutamate switch and the arginine finger—and their associated regulatory factors. We examine the implications of these regulatory mechanisms in proteins that are formed by multiple ATPase subunits. We argue that the regulatory mechanisms employed by motor proteins display features similar to those described in small GTPases, which require external regulatory elements, such as dissociation inhibitors, exchange factors and activating proteins, to switch the protein's function ‘on’ and ‘off'. Likewise, similar regulatory roles are taken on by the motor's substrate, additional binding factors, and even adjacent subunits in multimeric complexes. However, in motor proteins, more than one regulatory factor and the two mechanisms described here often underlie the machine's operation. Furthermore, ATPase regulation takes place throughout the motor's cycle, which enables a more complex function than the binary ‘active' and ‘inactive' states.
This article is part of a discussion meeting issue ‘Allostery and molecular machines'.
Interplay of self-association and conformational flexibility in regulating protein function
Authors: Garton Michael , MacKinnon Stephen S. , Malevanets Anatoly , Wodak Shoshana J. 
Published: May 2018

Many functional roles have been attributed to homodimers, the most common mode of protein self-association, notably in the regulation of enzymes, ion channels, transporters and transcription factors. Here we review findings that offer new insights into the different roles conformational flexibility plays in regulating homodimer function. Intertwined homodimers of two-domain proteins and their related family members display significant conformational flexibility, which translates into concerted motion between structural domains. This flexibility enables the corresponding proteins to regulate function across family members by modulating the spatial positions of key recognition surfaces of individual domains, to either maintain subunit interfaces, alter them or break them altogether, leading to a variety of functional consequences. Many proteins may exist as monomers but carry out their biological function as homodimers or higher-order oligomers. We present early evidence that in such systems homodimer formation primes the protein for its functional role. It does so by inducing elevated mobility in protein regions corresponding to the binding epitopes of functionally important ligands. In some systems this process acts as an allosteric response elicited by the self-association reaction itself. Our analysis furthermore suggests that the induced extra mobility likely facilitates ligand binding through the mechanism of conformational selection.This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
Haemophilus to meningococci transfer of beta-lactamase
Authors: Hong Eva , Deghmane Ala-Eddine , Taha Muhamed-Kheir 
Published: May 2018

AbstractWe report the detection in France of a beta-lactamase producing invasive meningococcal isolate. Whole genome sequencing of the isolate revealed ROB-1 type beta-lactamase that is frequently encountered in Haemophilus influenzae suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci with no reports from more than two decades. This report is worrying as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.
Comparative Proteomics Reveals Characteristic Proteins on Praziquantel-resistance inSchistosoma mansoni
Authors: Pinto-Almeida António , Mendes Tiago , Ferreira Pedro , Belo Silvana , Freitas Anibal Fernanda de , Allegretti Silmara Marques , Carrilho Emanuel , Afonso Ana 
Published: May 2018

AbstractThe extensive use of Praziquantel (PZQ), the only drug available to treat schistosomiasis, has brought concern about the emergence of PZQ-resistance/tolerance bySchistosomaspp., thus reaffirming an urge for the development of new treatment alternatives. Therefore, it is imperative and urgent to study this phenomenon trying to understand what is involved in its occurrence. Studies ofSchistosomaspp. genome, transcriptome and proteome are crucial to better understand this situation. By stepwise drug pressure from a fully susceptible parasite strain, our group selected aS. mansonivariant strain stably resistant to PZQ and isogenic to its fully susceptible parental counterpart, except for the genetic determinants of PZQ-resistance phenotype. Based on this, the objective of this study was to compare the proteomes of both strains, identifying proteins from male and female adult worms of PZQ-resistant and PZQ-susceptible strains, exposed and not exposed to PZQ, which were separated by high-resolution two-dimensional electrophoresis and sequenced by high throughput LC-MS/MS. Likewise, this work is extremely relevant since for the first time the proteome of aS. mansoniPZQ-resistant strain is studied and compared to the proteome of the respectiveS. mansoniPZQ-susceptible strain. This study identified 60S. mansoniproteins, some of which differentially expressed in either strain, which may putatively be involved in the PZQ-resistance phenomenon. This information represents substantial progress towards deciphering the worm proteome. Furthermore, these data may constitute an informative source for further investigations into PZQ-resistance and increase the possibility of identifying proteins related to this condition, possibly contributing to avoid or decrease the likelihood of development and spread of PZQ-resistance. This is an innovative study that opens doors to PZQ-resistance surveys, contributing to discover a solution to PZQ-resistance problem, as suggests new potential targets for study.
RsmV a small non-coding regulatory RNA in Pseudomonas aeruginosa that sequesters RsmA and RsmF from target mRNAs
Authors: Janssen Kayley H. , Diaz Manisha R. , Gode Cindy J. , Wolfgang Matthew C. , Yahr Timothy L. 
Published: May 2018

ABSTRACTThe Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm post-transcriptional regulatory system plays an important role in the inverse control of phenotypes associated with acute and chronic virulence. RsmA and RsmF are RNA-binding proteins that interact with target mRNAs to control gene expression at the post-transcriptional level. Previous work found that RsmA activity is controlled by at least three small, non-coding regulatory RNAs (RsmW, RsmY, and RsmZ). In this study, we took an in-silico approach to identify additional sRNAs that might function in the sequestration of RsmA and/or RsmF and identified RsmV, a 192 nt transcript with four predicted RsmA/RsmF consensus binding sites. RsmV is capable of sequestering RsmA and RsmF in vivo to activate translation of tssA1, a component of the T6SS, and to inhibit T3SS gene expression. Each of the predicted RsmA/RsmF consensus binding sites contribute to RsmV activity. Electrophoretic mobility shifts assays show that RsmF binds RsmV with >10-fold higher affinity than RsmY and RsmZ. Gene expression studies revealed that the temporal expression pattern of RsmV differs from RsmW, RsmY, and RsmZ. These findings suggest that each sRNA may play distinct roles in controlling RsmA and RsmF activity.IMPORTANCEThe role of RsmF in post-transcriptional control of gene expression remains enigmatic. While numerous rsmA-dependent phenotypes are more pronounced in an rsmAF double mutant, deletion of rsmF alone has only modest effects. Understanding mechanisms that control RsmF activity will provide insight into additional roles for RsmF. In the current study we identify RsmV as an sRNA that controls RsmA and RsmF activity, and show that RsmV, RsmW, RsmY, and RsmZ are differentially expressed during growth.
Adipose tissue in health and disease through the lens of its building blocks
Authors: Lenz Michael , Arts Ilja C.W. , Peeters Ralf L.M. , de Kok Theo M. , Ertaylan Gökhan 
Published: May 2018

AbstractBackgroundHighly specialized cells work in synergy forming tissues to perform functions required for the survival of organisms. Understanding this tissue-specific cellular heterogeneity and homeostasis is essential to comprehend the development of diseases within the tissue and also for developing regenerative therapies. Cellular subpopulations in the adipose tissue have been related to disease development, but efforts towards characterizing the adipose tissue cell type composition are limited due to lack of robust cell surface markers, limited access to tissue samples, and the labor-intensive process required to identify them.ResultsWe propose a framework, identifying cellular heterogeneity while providing state-of-the-art cellular markers for each cell type present in tissues using transcriptomics level analysis. We validate our approach with an independent dataset and present the most comprehensive study of adipose tissue cell type composition to date, determining the relative amounts of 21 different cell types in 779 adipose tissue samples detailing differences across four adipose tissue depots, between genders, across ranges of BMI and in different stages of type-2 diabetes. We also highlight the heterogeneity in reported marker-based studies of adipose tissue cell type composition and provide novel cellular markers to distinguish different cell types within the adipose tissue.ConclusionsOur study provides a systematic framework for studying cell type composition in a given tissue and valuable insights into adipose tissue cell type heterogeneity in health and disease.
The landscape and diagnostic potential of T and B cell repertoire in Immunoglobulin A Nephropathy
Authors: Huang Chen , Li Xuemei , Wu Jinghua , Zhang Wei , Sun Shiren , Lin Liya , Wang Xie , Li Hongmei , Wu Xiaolei , Zhang Peng , Xu Guoshuang , Wan Hanmin , Liu Hongbao , Liu Yuzhen , Chen Dapeng , Zhuo Li , Yang Huanming , Wang Jian , Wang Ling , Liu Xiao 
Published: May 2018

AbstractImmunoglobulin A Nephropathy (IgAN) is the most common glomerulonephritis worldwide. In IgAN, immune complex deposite in glomerular mesangium, which induce inflammation and affect the kidney’s normal functions. However, the exact pathogenesis of IgAN is still incompletely understood. Further, in current practice the clinical diagnosis relies on needle biopsy on renal tissue. Therefore, a non-invasive method for clinical diagnosis and prognosis surveillance of the disease is in high demand. In this paper, we investigated both the T cell receptor bata chain (TCRB) and immunoglobulin heavy chain (IGH) repertoire of kidney infiltrating and circulating lymphocytes of IgAN patients by immune repertoire high throughput sequencing. We found that the features of TCRB and IGH in the renal tissues were remarkably different from that in blood, including a decreased repertoire diversity and increased IgA and IgG frequency, and more activated B cells. The CDR3 length of PBMC TCRB and IGH in patients is significantly shorter than that in healthy controls, which is the result of both VDJ rearrangement and clone selection. We also found that the IgA1 frequency in the PBMC of IgAN is significant higher than that in other Nephropathy (NIgAN) and healthy control, which is consistent with the previous reports on the level of IgA1 producing B cells and serum IgA1. Significantly, we identified a set of IgAN disease related TCRB and IGH CDR3s, which can be used to distinguish IgAN from NIgAN and healthy controls from the blood with high accuracy. These results indicated that TCRB and IGH repertoire can potentially serve as non-invasive biomarkers for IgAN diagnosis. The characteristics of kidney infiltrating and circulating lymphocytes repertoire shed light on IgAN detection, treatment and surveillance.
Pathways to Consumers’ Minds: Using Machine Learning and Multiple EEG Metrics to Increase Preference Prediction Above and Beyond Traditional Measurements
Authors: Hakim Adam , Klorfeld Shira , Sela Tal , Friedman Doron , Shabat-Simon Maytal , Levy Dino J 
Published: May 2018

AbstractA basic aim of marketing research is to predict consumers’ preferences and the success of marketing campaigns in the general population. However, traditional behavioral measurements have various limitations, calling for novel measurements to improve predictive power. In this study, we use neural signals measured with electroencephalography (EEG) in order to overcome these limitations. We record the EEG signals of subjects, as they watched commercials of six food products. We introduce a novel approach in which instead of using one type of EEG measure, we combine several measures, and use state-of-the-art machine learning algorithms to predict subjects’ individual future preferences over the products and the commercials’ population success, as measured by their YouTube metrics. As a benchmark, we acquired measurements of the commercials’ effectiveness using a standard questionnaire commonly used in marketing research. We reached 68.5% accuracy in predicting between the most and least preferred items and a lower than chance RMSE score for predicting the rank order preferences of all six products. We also predicted the commercials’ population success better than chance. Most importantly, we demonstrate for the first time, that for all of our predictions, the EEG measurements increased the prediction power of the questionnaires. Our analyses methods and results show great promise for utilizing EEG measures by managers, marketing practitioners, and researchers, as a valuable tool for predicting subjects’ preferences and marketing campaigns’ success.
Glioblastoma recurrence and the role of MGMT promoter methylation
Authors: Storey Katie , Leder Kevin , Hawkins-Daarud Andrea , Swanson Kristin , Ahmed Atique U. , Rockne Russell C. , Foo Jasmine 
Published: May 2018

AbstractTumor recurrence in glioblastoma multiforme (GBM) is often attributed to acquired resistance to the standard chemotherapeutic agent temozolomide (TMZ). Promoter methylation of the DNA repair gene MGMT has been associated with sensitivity to TMZ, while increased expression of MGMT has been associated with TMZ resistance. Clinical studies have observed a downward shift in MGMT methylation percentage from primary to recurrent stage tumors. However, the evolutionary processes driving this shift, and more generally the emergence and growth of TMZ-resistant tumor subpopulations, are still poorly understood. Here we develop a mathematical model, parameterized using clinical and experimental data, to investigate the role of MGMT methylation in TMZ resistance during the standard treatment regimen for GBM (surgery, chemotherapy and radiation). We first find that the observed downward shift in MGMT promoter methylation status between detection and recurrence cannot be explained solely by evolutionary selection. Next, our model suggests that TMZ has an inhibitory effect on maintenance methylation of MGMT after cell division. Finally, incorporating this inhibitory effect, we study the optimal number of TMZ doses per adjuvant cycle for GBM patients with high and low levels of MGMT methylation at diagnosis.
Min-Redundancy and Max-Relevance Multi-view Feature Selection for Predicting Ovarian Cancer Survival using Multi-omics Data
Authors: EL-Manzalawy Yasser , Hsieh Tsung-Yu , Shivakumar Manu , Kim Dokyoon , Honavar Vasant 
Published: May 2018

AbstractBackgroundLarge-scale collaborative precision medicine initiatives (e.g., The Cancer Genome Atlas (TCGA)) are yielding rich multi-omics data. Integrative analyses of the resulting multi-omics data, such as somatic mutation, copy number alteration (CNA), DNA methylation, miRNA, gene expression, and protein expression, offer the tantalizing possibilities of realizing the potential of precision medicine in cancer prevention, diagnosis, and treatment by substantially improving our understanding of underlying mechanisms as well as the discovery of novel biomarkers for different types of cancers. However, such analyses present a number of challenges, including the heterogeneity of data types, and the extreme high-dimensionality of omics data.MethodsIn this study, we propose a novel framework for integrating multi-omics data based on multi-view feature selection, an emerging research problem in machine learning research. We also present a novel multi-view feature selection algorithm, MRMR-mv, which adapts the well-known Min-Redundancy and Maximum-Relevance (MRMR) single-view feature selection algorithm for the multi-view settings.ResultsWe report results of experiments on the task of building a predictive model of cancer survival from an ovarian cancer multi-omics dataset derived from the TCGA database. Our results suggest that multi-view models for predicting ovarian cancer survival outperform both view-specific models (i.e., models trained and tested using one multi-omics data source) and models based on two baseline data fusion methods.ConclusionsOur results demonstrate the potential of multi-view feature selection in integrative analyses and predictive modeling from multi-omics data.