bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe Phenotype of Keratitis–Ichthyosis–Deafness Syndrome With Presumed Ocular Surface Squamous Neoplasia
Authors: Serrano-Ahumada Ana Silvia , Cortes-González Vianney , González-Huerta Luz María , Cuevas Sergio , Aguilar-Lozano Luis , Villanueva-Mendoza Cristina 
Published: October 2017

Purpose:
The aim of this study was to describe a case of severe keratitis–ichthyosis–deafness (KID) syndrome with ocular surface squamous neoplasia.

Methods:
The affected patient underwent complete ocular and systemic examinations. The molecular studies included polymerase chain reaction amplification and automated DNA sequencing of the complete gap junction beta-2 (GJB2) gene coding sequence.

Results:
A 30-year-old man presented with generalized erythro-hyperkeratosis and deafness and complaints of decreased visual acuity, tearing, and photophobia. Ophthalmic examination showed corneal erosion, vascularization, and a gray gelatinous lesion partially covering the right cornea, suggestive of squamous neoplasia. The clinical features were characteristic of KID syndrome. This diagnosis was confirmed with a DNA analysis showing the pathogenic variant p.D50N in the GJB2 gene. Presumed squamous neoplasia was treated with topical interferon α2b.

Conclusions:
KID syndrome is a very rare disease that has been reported with an incremental incidence of squamous cell carcinoma of the mucous membranes and skin (12%–15%). Here, we presented a case of severe systemic KID syndrome with ocular surface squamous neoplasia.
Epidemiology of Competition Injuries in Elite European Judo Athletes: A Prospective Cohort Study
Authors: Čierna Dušana , Štefanovský Miloš , Matejová Lenka , Lystad Reidar P. 
Published: October 2017

Objective:To determine the injury incidence rate (IIR) and injury pattern, and to identify risk factors for injury, among elite adult European judo athletes.Design:Prospective cohort study.Setting:The 2015 Under 23 European Judo Championships, Bratislava, Slovakia.Participants:All registered athletes (N = 295).Independent Variables:Sex, weight division, and fight outcome.Main Outcome Measures:Injury incidence rates were calculated per 1000 athlete-exposures (IIRAE) and per 1000 minutes of exposure (IIRME) with 95% confidence intervals (CI). Subgroups were compared by calculating the injury incidence rate ratio (RR) with a 95% CI.Results:The overall IIRAEand IIRMEwere 35.6 (95% CI, 22.8-53.0) and 10.9 (95% CI, 7.0-16.2), respectively. The most frequently injured anatomical region was the head/neck (41%), whereas the most common type of injury was contusion (33%). The risk of injury was almost 4 times greater for defeated athletes compared with winners [RRME3.80 (95% CI, 1.47-9.82)]. Athletes in middleweight divisions had a greater risk of injury compared with their lightweight [RRME3.58 (95% CI, 1.24-10.35)] and heavyweight [RRME2.34 (95% CI, 0.93-5.89)] counterparts. The risk of injury for women was not significantly different from their male counterparts [RRME1.33 (95% CI, 0.61-2.90)].Conclusions:Weight division (middle) and fight outcome (losing) are significant risk factors for injury. The IIR in elite adult judo competition is lower than that in taekwondo and karate. Future research is encouraged to investigate the actual severity of judo injuries, and to investigate potentially modifiable risk factors to mitigate the risk of injury in judo.
Abatacept Monotherapy Versus Abatacept Plus Methotrexate for Treatment-Refractory Rheumatoid Arthritis
Authors: Pascart Tristan , Philippe Peggy , Drumez Elodie , Deprez Xavier , Cortet Bernard , Duhamel Alain , Houvenagel Eric , Flipo René-Marc 
Published: October 2017

Background:
Methotrexate combination therapy improves abatacept efficacy as a first-line biologic agent for the treatment of rheumatoid arthritis, but it is unclear when abatacept is used later on, particularly after non–TNF inhibitor (TNFi) failure.

Study Question:
The objective of this study was to determine whether treatment response after non–TNFi inadequate response is different in patients with rheumatoid arthritis (RA) treated with abatacept in combination with or not with methotrexate.

Methods:
Patients treated with abatacept monotherapy or in combination with methotrexate after non–TNFi failure were included.

Results:
Data from 46 patients aged 56 years [49–61] with 12 years [8–16] of disease duration were examined. Rituximab was the treatment used in the previous line for 75.0% of the combination therapy group (15/20) and 34.6% (9/26) in the monotherapy group. At 12 months, 38.5% (10/26) of patients were in good-to-moderate EULAR response in the monotherapy group compared with 25.0% (5/20) in the combination therapy group (P = 0.33). Treatment persistence at 12 months was 61.5% (16/26) in the monotherapy group and 35.0% (7/20) in the combination therapy group (P = 0.07).

Conclusions:
Adding methotrexate to abatacept did not improve treatment response in patients with RA after non–TNFi inadequate response.
Procalcitonin and MR-Proadrenomedullin Combination with SOFA and qSOFA Scores for Sepsis Diagnosis and Prognosis: A Diagnostic Algorithm
Authors: Spoto Silvia , Cella Eleonora , de Cesaris Marina , Locorriere Luciana , Mazzaroppi Silvia , Nobile Edoardo , Lanotte Arcangela M. , Pedicino Lucia , Fogolari Marta , Costantino Sebastiano , Dicuonzo Giordano , Ciccozzi Massimo , Angeletti Silvia 
Published: October 2017

ABSTRACT

Purpose:
The third Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defined sepsis as an organ dysfunction consequent to infection. A Sequential Organ Failure Assessment (SOFA) score at least 2 identifies sepsis. In this study, procalcitonin (PCT) and midregional pro-adrenomedullin (MR-proADM) were evaluated along with SOFA and quick SOFA (qSOFA) scores in patients with sepsis or septic shock.

Methods:
A total of 109 septic patients and 50 patients with noninfectious disease admitted at the Department of Internal Medicine and General Surgery of the University Hospital Campus Bio-Medico of Rome were enrolled. PCT and MR-proADM were measured with immunoluminometric assays (Brahms, Hennigsdorf, Germany). Data were analyzed with receiver-operating characteristic (ROC) curve analysis, likelihood ratios, and Mann–Whitney U test using MedCalc 11.6.1.0 package.

Results:
At ROC curve analysis, PCT showed the highest area under the curve and positive likelihood ratio values of 27.42 in sepsis and 43.62 in septic shock. MR-proADM and SOFA score showed a comparable performance. In septic shock, lactate showed the most accurate diagnostic ability. In sepsis, the best combination was PCT with MR-proADM with a posttest probability of 0.988. Based upon these results, an algorithm for sepsis and septic shock diagnosis has been developed. MR-proADM, SOFA, and qSOFA scores significantly discriminated survivors from nonsurvivors.

Conclusions:
PCT and MR-proADM test combination represent a good tool in sepsis diagnosis and prognosis suggesting their inclusion in the diagnostic algorithm besides SOFA and qSOFA scores. Furthermore, MR-proADM as marker of organ dysfunction, with a turn around time of about 30 min, has the advantage to be more objective and rapid than SOFA score.
Insights Into the Therapeutic Effect of Responsive Neurostimulation Assessed With Scalp EEG Recording: A Case Report
Authors: Bruzzone Maria Jose , Issa Naoum , Rose Sandra , Warnke Peter , Towle Vernon L. , Tao James X. , Wu Shasha 
Published: October 2017

Summary:
The responsive neurostimulation system (RNS) is the first closed-loop neurostimulator approved as an adjunctive treatment for adults with medically refractory focal epilepsy from no more than two seizure foci. In addition to its therapeutic effect, it provides chronic intracranial EEG recordings, with limited storage capacity. Long-term monitoring with scalp EEG recordings can provide additional information regarding seizure patterns, the efficacy of RNS stimulation in aborting individual seizures, and the net effect of RNS on seizure control. We present a 34-year-old woman with medically intractable right temporoparietal lobe epilepsy who failed two resective epilepsy surgeries and MR-guided laser interstitial thermal therapy (MRgLITT), after which RNS was implanted. Long-term scalp EEG performed 16 months after implantation showed continuous right hemisphere slowing and right temporal sharp waves. In addition, RNS stimulation produced bursts of high-voltage, broad-field, surface-negative activity, which allowed correlation of RNS stimulation with scalp EEG patterns. Twenty-seven seizures were captured. Responsive neurostimulation system stimulation did not abort any of the seizures recorded on the scalp EEG. However, the frequency of seizures doubled after RNS stimulation was discontinued and returned to baseline once it was turned back on. This observation supports the neuromodulation effect of RNS.
Medical Error Avoidance in Intraoperative Neurophysiological Monitoring: The Communication Imperative
Authors: Skinner Stan , Holdefer Robert , McAuliffe John J. , Sala Francesco 
Published: October 2017

Summary:
Error avoidance in medicine follows similar rules that apply within the design and operation of other complex systems. The error-reduction concepts that best fit the conduct of testing during intraoperative neuromonitoring are forgiving design (reversibility of signal loss to avoid/prevent injury) and system redundancy (reduction of false reports by the multiplication of the error rate of tests independently assessing the same structure). However, error reduction in intraoperative neuromonitoring is complicated by the dichotomous roles (and biases) of the neurophysiologist (test recording and interpretation) and surgeon (intervention). This “interventional cascade” can be given as follows: test → interpretation → communication → intervention → outcome. Observational and controlled trials within operating rooms demonstrate that optimized communication, collaboration, and situational awareness result in fewer errors. Well-functioning operating room collaboration depends on familiarity and trust among colleagues. Checklists represent one method to initially enhance communication and avoid obvious errors. All intraoperative neuromonitoring supervisors should strive to use sufficient means to secure situational awareness and trusted communication/collaboration. Face-to-face audiovisual teleconnections may help repair deficiencies when a particular practice model disallows personal operating room availability. All supervising intraoperative neurophysiologists need to reject an insular or deferential or distant mindset.
Peer-Led Team Learning Improves Minority Student Retention in STEM Majors
Authors: Sloane Jeremy D. , Snyder Julia J. , Wiles Jason R. 
Published: October 2017

AbstractThe President’s Council of Advisors on Science and Technology issued a report in 2012 calling for a drastic increase in the number of STEM graduates produced in our country over the following decade if we are to remain economically competitive globally (PCAST, 2012). The report cited the disparity between the diversity among the general public versus that of the STEM professional community and recommended measures to ensure that the women and members of underrepresented racial groups, who together comprise 70% of college graduates but only 45% of college STEM graduates, would become better represented in those fields. This call for action echoed calls by the National Academy of Sciences to expand underrepresented minority participation in STEM at the college level (NAS, 2011). In the following study, we examined whether participation in the Peer-Led Team Learning (PLTL) model in introductory biology influenced the rates of recruitment into STEM and retention in STEM for underrepresented minority (URM) students and for non-URM students. Chi-square analyses reveal that there are significant gaps in STEM recruitment and retention rates between URM and non-URM students, but when these students participate in the PLTL model, no differences in STEM recruitment or retention rates were observed. Additionally, we found that STEM retention rates were significantly improved for URM students who engaged in PLTL.
An alignment method for nucleic acid sequences against annotated genomes
Authors: Deforche Koen 
Published: October 2017

AbstractMotivationBiological sequence alignment is fundamental to their further interpretation. Current alignment algorithms typically align either nucleic acid or amino acid sequences. Using only nucleic acid sequence similarity, divergent sequences cannot be aligned reliably because of the limited alphabet and genetic saturation. To align divergent coding nucleic acid sequences, one can align using the translated amino acid sequences. This requires the detection of the correct open reading frame, is prone to eventual frame shift errors, and typically requires the treatment of genes separately. It was our motivation to design a nucleic acid sequence alignment algorithm to align a nucleic acid sequence against a (reference) genome sequence, that works equally well for similar and divergent sequences, and produces an optimal alignment considering simultaneously the alignment of all annotated coding sequences.ResultsWe define agenome alignment scorefor evaluating the quality of an alignment of a nucleic acid query sequence against a reference genome sequence, for which coding sequence features have been annotated (for example in a GenBank record). The genome alignment score combines the a ne gap score for the nucleic acid sequence with an a ne gap score for all amino acid alignments resulting from coding sequences in open reading frames contained within the query sequence. We present a Dynamic Programming algorithm to compute the optimal global or local alignment using this genomic alignment score and provide a formal proof of correctness. This algorithm allows the alignment of nucleic acid sequences from closely related and highly divergent sequences within the same software and using the same parameters, automatically correcting any eventual frame shift errors and produces at the same time the aligned translated amino acid sequences of all relevant coding sequence features.AvailabilityThe software is available as a web application athttp://www.genomedetective.com/app/agaand as command-line application athttps://github.com/emweb/aga
Pneumococcal phenotype and interaction with nontypeableHaemophilus influenzaeas determinants of otitis media progression
Authors: Lewnard Joseph A. , Givon-Lavi Noga , Tähtinen Paula A. , Dagan Ron 
Published: October 2017

ABSTRACTBackgroundAll-cause otitis media (OM) incidence has declined in numerous settings following introduction of pneumococcal conjugate vaccines (PCVs) despite increases in carriage of non-vaccine pneumococcal serotypes escaping immune pressure. To understand the basis for declining incidence, we assessed the intrinsic capacity of pneumococcal serotypes to cause OM independently and in polymicrobial infections involving nontypeableHaemophilus influenzae(NTHi) using samples obtained from middle ear fluid and nasopharyngeal cultures before PCV7/13 rollout.MethodsData included OM episodes (11,811) submitted for cultures during a 10-year prospective study in southern Israel and nasopharyngeal samples (1588) from unvaccinated asymptomatic children in the same population. We compared pneumococcal serotype diversity across carriage and disease isolates with and without NTHi co-isolation. We also measured associations between pneumococcal phenotype and rate of progression from colonization to OM in the presence and absence of NTHi.ResultsWhereas pneumococcal serotype diversity in single-species OM is lower than in single-species colonization, serotype diversity does not differ significantly between colonization and OM in mixed-species episodes. Serotypes differed roughly 100-fold in progression rates, and these differences were attenuated in polymicrobial episodes. Vaccine-serotype pneumococci had higher rates of progression than non-vaccine serotypes. While serotype invasiveness was a weak predictor of OM progression rate, efficient capsular metabolic properties—traditionally thought to serve as an advantage in colonization—predicted an enhanced rate of progression to complex OM.ConclusionsThe lower capacity of non-vaccine serotypes to cause OM may partially account for reductions in all-cause OM incidence despite serotype replacement in carriage following rollout of PCVs.
Transcriptomic Dynamics of a non-coding trinucleotide repeat expansion disorder SCA12 in iPSC derived neuronal cells: signatures of interferon induced response
Authors: Kumar Deepak , Dhapola Parashar , Hussain Ashaq , Kutum Rintu , Srivastava Achal K. , Mukerji Mitali , Mukherjee Odity , Faruq Mohammed 
Published: October 2017

AbstractSpinocerebellar ataxia type-12 (SCA12) is a neurological disorder that exhibits a unique progressive tremor/ataxia syndrome induced by triplet (CAG) repeat expansion in 5’ UTR ofPPP2R2B. SCA12 is one of the most prominent SCA-subtype in India and till date no appropriate disease models have been described. Our aim was to establish human iPSC derived neuronal cell lines of SCA12 and study transcriptomic level alterations induced by CAG expansion. For translational application, peripheral blood transcriptomics of SCA12 patients was also performed. Lymphoblastoid cell lines of three SCA12 patients were reprogrammed to iPSCs and then re-differentiated into pan-neuronal lineage. RNA-sequencing based comparative transcriptomics was performed for disease and control cell lineages. Microarray based transcriptomic profiling of peripheral blood of SCA12 patients was performed in a case/control (n=15/9) design. We have successfully created human neuronal cell lines of SCA12 patient as exhibited by their molecular profiling. Differential expression analysis of RNA-Seq data has shown enrichment for type-I interferon signaling and other relevant cellular processes in SCA12-neurons. At the splice-isoform level, we observed an upregulation of expanded CAG containing non-coding transcript ofPPP2R2B. Peripheral blood transcriptomics analysis and targeted validation of RNA-Seq data has allowed us to identify inflammatory signatures as potential markers of molecular pathology in SCA12. Our study has allowed us to establish first iPSC based neuronal cell lines of SCA12. We have identified pro-inflammatory signatures in SCA12-neurons suggestive of a dsRNA mediated activation of interferon signaling and that corroborates with the emerging evidence of neuronal atrophy due to neuro-inflammation in common neurodegenerative diseases. This study involved development of an iPSCs derived neuronal cells of SCA12 and look through signatures of neurodegeneration by whole RNA sequencing. This model sheds light upon key role of RNA mediated induced response in Interferon signaling for neurodegeneration.
Identification and characterization ofGypsophila paniculatacolor morphs in Sleeping Bear Dunes National Lakeshore, MI, USA
Authors: Yang Marisa L. , Rice Emma , Leimbach-Maus Hailee , Partridge Charlyn G. 
Published: October 2017

AbstractBackgroundGypsophila paniculata(baby’s breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby’s breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby’s breath in order to assess whether alternative management strategies should be employed to control these populations.MethodsWe sequenced two chloroplast regions, rbcL and matK, and one nuclear region, ITS2, from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to the reference sequences from otherGypsophilaspecies obtained from the Barcode of Life (BOLD) and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after five-months of growth.ResultsPhylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong toG. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs.DiscussionBased upon these results, we propose that the two color morphs are variants ofG. paniculata. Given the significant difference in the number of green-yellow morphs produced from the seeds of each morph type, we also suggest that this color difference has some genetic basis. We propose that current management continue to treat the two color morphs in a similar manner in terms of removal to prevent the further spread of this species.
Parental allele-specific genome architecture and transcription during the cell cycle
Authors: Chen Haiming , Liu Sijia , Seaman Laura , Najarian Cyrus , Wu Weisheng , Ljungman Mats , Higgins Gerald , Hero Alfred , Wicha Max , Rajapakse Indika 
Published: October 2017

AbstractA normal human somatic cell inherits two haploid genomes. Individual chromosomes of each pair have distinct parental origins and parental alleles are known to unequally contribute to cellular function. We integrated chromosome conformation (form) and gene transcription (function) analyses to dissect the dynamics of the maternal and paternal genomes in lymphoblastoid cells during the cell cycle. We found a distinct set of homologous alleles with very different activity often located close to boundaries of euchromatin and heterochromatin domains. We also identified a set of allele-biased topologically associating domains (TADs) that were small sized and had higher gene density. Thousands of genes show allelically biased expression (ABE) with false discovery rate < 0.05, and 98% of them have no allelic switching during G1, S, and G2/M phases. A subset of ABE genes are preferentially localized near TAD boundaries, enriched with chromatin organization transcription factor binding sites, and contained higher number of sequence variants in CCCTC-binding factor sites. Our results extend previous findings of sequence variation as a basis for unequal functional parental genomes. Investigation of haplotype-resolved form-function dynamics may further our understanding of phenotypic traits, genetic diseases, vulnerability to complex disorders, and the development of cancers.
Sexual lineage specific DNA methylation regulates Arabidopsis meiosis
Authors: Walker James , Gao Hongbo , Zhang Jingyi , Aldridge Billy , Vickers Martin , Higgins James D. , Feng Xiaoqi 
Published: October 2017

SUMMARYDNA methylation controls eukaryotic gene expression and is extensively reprogrammed to regulate animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive, gene-targeted RNA-directed DNA methylation (RdDM) activity in theArabidopsis thalianamale sexual lineage that regulates gene expression in meiocytes. Loss of sexual lineage-specific RdDM causes mis-splicing of theMPS1/PRD2gene, thereby disrupting meiosis. Our results establish a regulatory paradigm in whichde novomethylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.