bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Practice Report From the Northern Dental Access Center: Offering Wraparound Services at a Community Dental Access Clinic to Improve Treatment Outcomes Among Rural Populations in Poverty
Authors: Larson Jeanne E. , Leider Jonathon P. , Knudson Alana 
Published: February 2018

Context:
Rural populations suffer significant adverse health outcomes without reliable access to dental care, including increased emergency department use for oral health. The Northern Dental Access Program (Northern Dental) serves more than 20 counties in Greater Minnesota and bordering states. Its population is generally poor and less healthy than the rest of the state, with high rates of Medicaid.

Approach:
Evaluation of Northern Dental focused primarily on utilization of dental and nondental wraparound/support services. First, descriptive analyses were conducted, including assessing the patient population, visit, and client counts over time. Measures include procedures performed, visits, unique clients, active client base (based on previous visits in 12, 18, or 24 months), treatment plan completion, and use of wraparound services.

Results:
Between 2009 and 2016, Northern Dental saw 20 367 unique clients. The staff performed more than 307 000 prevention and screening procedures, more than 55 000 fillings and restorations, and 20 000 oral surgery/endodontic procedures. Overall, 32% of patients (n = 6 626) completed their treatment plans. Bivariate comparisons suggested that those who were provided transportation assistance (5% of all patients) were more likely to complete their treatment than the overall patient population. Overall, in 2016, a total of 1 748 unduplicated clients worked with the staff more than 3 800 times to receive referrals and wraparound services. This represented about 27% of all clients seen in 2016 who had at least 1 clinical visit.

Discussion:
Evaluation of Northern Dental's practice and approach shows sustained growth over time in service provision to the Medicaid population in Greater Minnesota, high need for transportation assistance, and significant interest in wraparound services. Transportation assistance involved substantial outlays from Northern Dental but resulted in substantially higher reimbursement, billing, and treatment completion for patients.

Implications for Practice:
Wraparound services are typically supported through grants and charitable giving. Evidence like this can inform policy makers and insurance companies, making the case for reimbursing nonprofits that provide them.
Antibodies and the brain: antiribosomal P protein antibody and the clinical effects in patients with systemic lupus erythematosus
Authors: González Alfonso , Massardo Loreto 
Published: February 2018

Purpose of review
Analysis of antiribosomal P protein autoantibodies (anti-P) pathogenicity in diffuse brain manifestations of neuropsychiatric lupus, emphasizing cognitive dysfunction and the recently emerged role of cross-reacting neuronal surface P antigen (NSPA) in α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid and N-Methyl-d-Aspartate receptor glutamatergic transmission.

Recent findings
Circulating anti-P antibodies associate with executive planning dysfunction and attention impairments in lupus patients and perturb glutamatergic transmission through NSPA in mice hippocampus, translating into impaired synaptic plasticity and spatial memory. Planning impairment impacts quality of life.

Summary
In addition to the known association with lupus psychosis, new clinical and experimental evidence reveal a pathogenic role of anti-P antibodies in cognitive dysfunction, mechanistically explained by the anti-P interaction with NSPA as a target involved in glutamatergic synaptic plasticity.
AZIP1Separation-of-Function Allele Reveals that Meiotic Centromere Pairing Drives Meiotic Segregation of Achiasmate Chromosomes in Budding Yeast
Authors: Kurdzo Emily L. , Chuong Hoa H , Dawson Dean S. 
Published: February 2018

ABSTRACTIn meiosis I, homologous chromosomes segregate away from each other - the first of two rounds of chromosome segregation that allow the formation of haploid gametes. In prophase I, homologous partners become joined along their length by the synaptonemal complex (SC) and crossovers form between the homologs to generate links called chiasmata. The chiasmata allow the homologs to act as a single unit, called a bivalent, as the chromosomes attach to the microtubules that will ultimately pull them away from each other at anaphase I. Recent studies, in several organisms, have shown that when the SC disassembles at the end of prophase, residual SC proteins remain at the homologous centromeres providing an additional link between the homologs. In budding yeast, this centromere pairing is correlated with improved segregation of the paired partners in anaphase. However, the causal relationship of prophase centromere pairing and subsequent disjunction in anaphase has been difficult to demonstrate as has been the relationship between SC assembly and the assembly of the centromere pairing apparatus. Here, a series of in-frame deletion mutants of the SC component Zip1 were used to address these questions. The identification of separation-of-function alleles that disrupt centromere pairing, but not SC assembly, have made it possible to demonstrate that centromere pairing and SC assembly have mechanistically distinct features and that prophase centromere pairing function of Zip1 drives disjunction of the paired partners in anaphase I.AUTHOR SUMMARYThe generation of gametes requires the completion of a specialized cell división called meiosis. This division is unique in that it produces cells (gametes) with half the normal number of chromosomes (such that when two gametes fuse the normal chromosome number is restored). Chromosome number is reduced in meiosis by following a single round of chromosome duplication with two rounds of segregation. In the first round, meiosis I, homologous chromosomes first pair with each other, then attach to cellular cables, called microtubules, that pull them to opposite sides of the cell. It has long been known that the homologous partners become linked to each other by genetic recombination in a way that helps them behave as a single unit when they attach to the microtubules that will ultimately pull them apart. Recently, it was shown, in budding yeast and other organisms, that homologous partners can also pair at their centromeres. Here we show that this centromere pairing also contributes to proper segregation of the partners away from each other at meiosis I, and demonstrate that one protein involved in this process is able to participate in multiple mechanisms that help homologous chromosomes to pair with each other before being segregated in meiosis I.
Proper chromosome alignment depends on BRCA2 phosphorylation by PLK1
Authors: Ehlén Åsa , Martin Charlotte , Miron Simona , Julien Manon , Theillet François-Xavier , Ropars Virginie , Sessa Gaetana , Beaurepere Romane , Boucherit Virginie , Duchambon Patricia , El Marjou Ahmed , Zinn-Justin Sophie , Carreira Aura 
Published: February 2018

SummaryThe BRCA2 tumor suppressor protein is involved in the maintenance of genome integrity through its role in homologous recombination. In mitosis, BRCA2 is phosphorylated by Polo-like kinase 1 (PLK1). Here we describe how this phosphorylation contributes to the control of mitosis. We identified two highly conserved phosphorylation sites at S193 and T207 of BRCA2. Phosphorylated-T207 is a bona fide docking site for PLK1 as illustrated by the crystal structure of the BRCA2 peptide bound to PLK1 Polo-box domain. We found that BRCA2 bound to PLK1 forms a complex with the phosphatase PP2A and phosphorylated-BUBR1. Reducing BRCA2 binding to PLK1, as observed in BRCA2 breast cancer variants S206C and T207A, alters the tetrameric complex resulting in misaligned chromosomes, faulty chromosome segregation and aneuploidy. We thus reveal a direct role of BRCA2 in the alignment of chromosomes, distinct from its DNA repair function, with important consequences on chromosome stability. These findings may explain in part the aneuploidy observed in BRCA2-mutated tumors.
THEA: A novel approach to gene identification in phage genomes
Authors: McNair Katelyn , Zhou Carol , Souza Brian , Edwards Robert A. 
Published: February 2018

AbstractMotivationCurrently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap, and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present THEA (The Algorithm), a novel method for gene calling specifically designed for phage genomes. While the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use graph theory to find the optimal path.ResultsWe compare THEA to other gene callers by annotating a set of 2,133 complete phage genomes from GenBank, using THEA and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with THEA predicting significantly more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and sequence read archive, and found that they are present at levels that suggest that these are functional protein coding genes.Availability and ImplementationThe source code and all files can be found at: https://github.com/deprekate/THEAContactKatelyn McNair: deprekate@gmail.com
Structural variation detection by proximity ligation from FFPE tumor tissue
Authors: Troll Chris , Putnam Nicholas H. , Hartley Paul D. , Rice Brandon , Blanchette Marco , Siddiqui Sameed , Ganbat Javkhlan-Ochir , Powers Martin P. , Kunder Christian A. , Bustamante Carlos D. , Zehnder James L. , Green Richard E. , Costa Helio A. 
Published: February 2018

AbstractThe clinical management and therapy of many solid tumor malignancies is dependent on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call “Fix-C”, which is similar in concept to Hi-C. Fix-C enables structural variation detection from fresh and archival FFPE samples. We applied this method to 15 clinical adenocarcinoma and sarcoma specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with FISH assays – the current clinical gold standard. Additionally, we are able to identify novel structural variation undetected by other methods and recover long-range chromatin configuration information from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material, and inform the development of targeted molecular diagnostic assays for patient care.
Primate MHC class I from Genomes
Authors: Olivieri D.N. , Gambón-Deza F. 
Published: February 2018

AbstractThe major histocompatibility complex (MHC) molecule plays a central role in the adaptive immunity of jawed vertebrates. Allelic variations have been studied extensively in some primate species, however a comprehensive description of the number of genes remains incomplete. Here, a bioinformatics program was developed to identify three MHC Class I exons (EX2, EX3 and EX4) from Whole Genome Sequencing (WGS) datasets. With this algorithm, MHC Class I exons sequences were extracted from 30 WGS datasets of primates, representatives of Apes, Old World and New World monkeys and prosimians. There is a high variability in the number of genes between species. From human WGS, six viable genes (HLA-A, -B, -C, -E, -F, and -G) and four pseudogene sequences (HLA-H, -J, -L, -V) are obtained. These genes serve to identify the phylogenetic clades of MHC-I in primates. The results indicate that human clades of HLA-A -B and -C were generated shortly after the separation of Old World monkeys. The clades pertaining to HLA-E, -H and -F are found in all primate families, except in Prosimians. In the clades defined by HLA-G, -L and -J, there are sequences from Old world monkeys. Specific clades are found in the four primate families. The evolution of these genes is consistent with birth and death processes having a high turnover rates.
ReadFilter - Filtering reads of interest for quicker downstream analysis
Authors: Lee Ng Kim , Johannesen Thor Bech , Østerlund Mark , Kiil Kristoffer , Andersen Paal Skytt , Stegger Marc 
Published: February 2018

AbstractWhole-genome sequencing is becoming the method of choice but provides redundant data for many tasks. ReadFilter (https://github.com/ssi-dk/serum_readfilter) is offered as a way to improve run time of these tasks by rapidly filtering reads against user-specified sequences in order to work with a small fraction of original reads while maintaining accuracy. This can noticeably reduce mapping time and substantially reduce de novo assembly time.
A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
Authors: Pflueger Christian , Tan Dennis , Swain Tessa , Nguyen Trung , Pflueger Jahnvi , Nefzger Christian , Polo Jose M. , Ford Ethan , Lister Ryan 
Published: February 2018

Abstract:DNA methylation is a covalent modification of the genome that plays important roles in genome regulation and vertebrate development. Although detection of this modification in the genome has been possible for several decades, the ability to deliberately and specifically manipulate local DNA methylation states in the genome has been extremely limited. Consequently, this has impeded the direct determination of the consequence of DNA methylation on transcriptional regulation and transcription factor binding in the native chromatin context. Thus, highly specific targeted epigenome editing tools are needed to address this outstanding question. Recent adaptations of genome editing technologies, such as the fusion of the DNMT3A methyltransferase catalytic domain to catalytically inactive Cas9 (dC9-D3A), have aimed to provide new tools for altering DNA methylation at desired loci. Here, we performed a deeper analysis of the performance of these tools, revealing consistent off-target binding events and DNA methylation deposition in the genome, limiting the capacity of these tools to unambiguously assess the functional consequences of DNA methylation. To address this, we developed a modular dCas9-SunTag (dC9Sun-D3A) system that can recruit multiple DNMT3A catalytic domains to a target site for editing DNA-methylation. dC9Sun-D3A is tunable, specific and exhibits much higher induction of DNA methylation at target sites than the dC9-D3A direct fusion protein. Importantly, genome-wide characterization of dC9Sun-D3A binding sites and DNA methylation revealed minimal off-target protein binding and induction of DNA methylation with dC9Sun-D3A, compared to pervasive off-target binding and methylation by the dC9-D3A direct fusion construct. Furthermore, we used dC9Sun-D3A to test the impact of DNA methylation upon the DNA binding of CTCF and NRF1 upon targeted methylation of their core binding sites, demonstrating the binding sensitivity of these proteins to DNA methylation in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the lowest amount of off-target DNA methylation reported to date, allowing accurate functional determination of the role of DNA methylation at single loci.
pyseer: a comprehensive tool for microbial pangenome-wide association studies
Authors: Lees John A , Galardini Marco , Bentley Stephen D , Weiser Jeffrey N , Corander Jukka 
Published: February 2018

AbstractSummaryGenome-wide association studies (GWAS) in microbes face different challenges to eukaryotes and have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.Availability and Implementationpyseer is written in python and is freely available at https://github.com/mgalardini/pyseer, or can be installed through pip. Documentation and a tutorial are available at http://pyseer.readthedocs.io.Contactjohn.lees@nyumc.org and marco@ebi.ac.ukSupplementary informationSupplementary data are available online.
Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide
Authors: Ruderfer Douglas M. , Walsh Colin G. , Aguirre Matthew W. , Tanigawa Yosuke , Ribeiro Jessica D. , Franklin Joseph C. , Rivas Manuel A. 
Published: February 2018

AbstractSuicide accounts for nearly 800,000 deaths per year worldwide with rates of both deaths and attempts rising. Family studies have estimated substantial heritability of suicidal behavior; however, collecting the sample sizes necessary for successful genetic studies has remained a challenge. We utilized two different approaches in independent datasets to characterize the contribution of common genetic variation to suicide attempt. The first is a patient reported suicide attempt phenotype from genotyped samples in the UK Biobank (337,199 participants, 2,433 cases). The second leveraged electronic health record (EHR) data from the Vanderbilt University Medical Center (VUMC, 2.8 million patients, 3,250 cases) and machine learning to derive probabilities of attempting suicide in 24,546 genotyped patients. We identified significant and comparable heritability estimates of suicide attempt from both the patient reported phenotype in the UK Biobank (h2SNP = 0.035, p = 7.12×10−4) and the clinically predicted phenotype from VUMC (h2SNP = 0.046, p = 1.51×10−2). A significant genetic overlap was demonstrated between the two measures of suicide attempt in these independent samples through polygenic risk score analysis (t = 4.02, p = 5.75×10−5) and genetic correlation (rg = 1.073, SE = 0.36, p = 0.003). Finally, we show significant but incomplete genetic correlation of suicide attempt with insomnia (rg = 0.34 - 0.81) as well as several psychiatric disorders (rg = 0.26 - 0.79). This work demonstrates the contribution of common genetic variation to suicide attempt. It points to a genetic underpinning to clinically predicted risk of attempting suicide that is similar to the genetic profile from a patient reported outcome. Lastly, it presents an approach for using EHR data and clinical prediction to generate quantitative measures from binary phenotypes that improved power for our genetic study.
Biochemical Characterization of RecBCD Enzyme from An AntarcticPseudomonasSpecies and Identification of Its Cognate Chi (χ) Sequence
Authors: Pavankumar Theetha L. , Sinha Anurag Kumar , Ray Malay K. 
Published: February 2018

ABSTRACTPseudomonas syringaeLz4W RecBCD enzyme, RecBCDPs, is a trimeric protein complex comprised of RecC, RecB, and RecD subunits. RecBCD enzyme is essential forP. syringaegrowth at low temperature, and it protects cells from low temperature induced replication arrest. In this study, we show that the RecBCDPsenzyme displays distinct biochemical behaviors. UnlikeE. coliRecBCD enzyme, the RecD subunit is indispensable for RecBCDPsfunction. The RecD motor activity is essential for the Chi-like fragments production inP. syringae, highlighting a distinct role forP. syringaeRecD subunit in DNA repair and recombination process. Further, the ssDNA-dependent endonuclease activity is notably absent in RecBCDPsenzyme. Here, we demonstrate that the RecBCDPsenzyme recognizes a unique octameric DNA sequence, 5′-GCTGGCGC-3′ (ChiPs) that attenuates nuclease activity of the enzyme when it enters dsDNA from the 3′-end. We propose that the reduced translocation activities manifested by motor-defective mutants cause cold sensitivity inP. syrinage; emphasizing the importance of DNA processing and recombination functions in rescuing low temperature induced replication fork arrest.Abbreviations:ATPAdenosine triphosphateDSBdouble-strand break‘ChiCrossover hotspot instigatorNi-NTANitrio tri-acetic acidTLCthin layer chromatographyMMCmitomycin CUV lightUltra violetABMAntarctic bacterial mediumLBLuria-Bertani medium
A mechanism for the proliferative control of tissue mechanics in the absence of growth
Authors: Wu Min , Mani Madhav 
Published: February 2018

AbstractDuring the development of a multicellular organism, cells coordinate their activities to generate mechanical forces, which in turn drives tissue deformation and eventually defines the shape of the adult tissue. Broadly speaking, it is recognized that mechanical forces can be generated through differential growth and the activity of the cytoskeleton. Based on quantitative analyses of live imaging of theDrosophiladorsal thorax, we suggest a novel mechanism that can generate contractile forces within the plane of an epithelia - via cell proliferation in the absence of growth. Utilizing force inference techniques, we demonstrate that it is not the gradient of junction tension but the divergence of junction-tension associated stresses that induces the area constriction of the proliferating tissue. Using the vertex model simulations, we show that the local averaged stresses can be roughly elevated by a fold ofp2 per cell division without growth. Moreover, this mechanism is robust to disordered cell shapes and the division anisotropy, but can be dominated by growth. In competition with growth, we identify the parameter regime where this mechanism is effective and suggest experiments to test this new mechanism.
Associations between organisational factors, TQM and competitive advantage
Authors: Ferdousi Farhana , Baird Kevin , Munir Rahat , Su Sophia 
Published: February 2018

PurposeThe purpose of this paper is to examine the association between the extent of adoption of TQM, using Kaynak’s (2003) core TQM practices (quality data and reporting, supplier quality management, product/service design, process management) model and competitive advantage. In addition, the study examines the antecedent role of organisational-related factors (intensity of market competition, information technology (IT), expert systems and the supplier evaluation programme) in respect to the extent of adoption of TQM.Design/methodology/approachA survey was conducted of 673 business units of garment organisations in a developing country, Bangladesh.FindingsThe findings indicate that the extent of adoption of TQM practices was positively associated with competitive advantage. In addition, two organisational-related factors (intensity of market competition and IT) were positively associated with the extent of adoption of TQM.Practical implicationsThe findings provide an insight into the ability of TQM to facilitate competitive advantage in developing countries. Practitioners are also provided with an insight into which organisational factors facilitate the adoption of TQM practices.Originality/valueThe findings provide an important insight into the use and value of TQM practices in developing countries.