bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Incidence of and Risk Factors for Fluoroscopy-Guided Lumbar Puncture and Subsequent Persistent Low-Pressure Syndrome in Patients With Idiopathic Intracranial Hypertension
Authors: Lu Patricia , Goyal Manu , Huecker Julia B. , Gordon Mae O. , Van Stavern Gregory P. 
Published: September 2018

Background:
To explore the incidence of and potential risk factors for developing persistent low-pressure syndrome after lumbar puncture (LP) in patients with idiopathic intracranial hypertension (IIH), as measured by use of blood patches.

Methods:
A retrospective chart review was conducted of patients with definitively diagnosed IIH by clinical examination and LP, comparing them to patients with multiple sclerosis (MS) as controls who also received diagnostic LPs. Demographic, clinical, and radiological data were collected for each patient. The main outcome measure was the rate of post-LP blood patches in IIH patients compared with MS patients. Secondary outcome measures were the likelihood of undergoing an epidural blood patch related to age, body mass index, volume removed, opening pressure, the difference between opening and closing pressure, and the level of puncture within the IIH cohort.

Results:
One hundred four IIH patients and 149 MS patients were included in the study. Among IIH patients, 12/104 (11.5%) underwent an epidural blood patch after LP as compared to 8/149 (5.4%) of the MS control patients (P = 0.086). Within the IIH population, none of the clinical or LP parameters were significantly correlated with increased risk of needing a blood patch.

Conclusions:
The incidence of low-pressure syndrome, as measured by blood patches, is similar in IIH patients and MS controls. This suggests that having elevated intracranial pressure before an LP is not protective against developing postpuncture low-pressure syndrome, contrary to common assumptions.
Predictive Value of Midline Spikes on Pediatric EEG for Seizure and Developmental Outcome
Authors: Datta Anita N. , Wallbank Laura , Xu Qi , Wong Peter K. H. 
Published: September 2018

Purpose:
Midline spikes are epileptiform discharges localized to the midsagittal regions of the brain. Isolated midline spikes are rare, but more common in children. Our objective was to determine whether midline spikes are predictive of seizure characteristics and neurodevelopment.

Methods:
EEGs and clinical information of 123 children with isolated midline spikes, and EEG follow-up within 12 to 24 months, were reviewed and compared with controls.

Results:
Most children with midline spikes had seizures (91%), with an equal predisposition to focal or generalized seizure semiology. There was no difference between the midline spike and control groups in terms of neonatal complications, seizure characteristics (type, frequency, and etiology), and neurologic examination findings. In patients with abnormal neuro-maging, deep gray or white matter abnormalities were more frequent in the midline group (41% vs. 13%, P = 0.02). The midline group had a higher risk of development delay (DD) than controls (43% vs. 29%, odds ratio: 1.8, 95% CI [1.1–3.2], P = 0.03). A higher risk of DD was also noted in the midline group in those aged less than 4 years (52% vs. 26%, odds ratio: 3.1, 95% CI [1.0–9.2], P = 0.04) and in those without seizures (40% vs. 17%, odds ratio: 3.16, 95% CI [1.1–8.8], P = 0.03).

Conclusions:
This is the largest reported group of patients with midline spikes. Midline spikes have a strong association with seizures and DD. Our data suggest that midline spikes result from heterogeneous etiologies, are more common in young children, and are not benign.
Needle EMG of Thenar Muscles in Less Severe Carpal Tunnel Syndrome
Authors: Rubin Devon I. , Dimberg Elliot L. 
Published: September 2018

Introduction:
The value of needle electromyography (EMG) in thenar muscles in patients with less severe carpal tunnel syndrome is controversial.

Methods:
Patients referred for electrodiagnostic testing for carpal tunnel syndrome, in which nerve conduction study demonstrated median sensory nerve conduction study abnormalities and either normal median motor nerve conduction study or only prolonged median motor distal latencies (DLs) (with normal amplitudes) were prospectively studied. Patients with low-median compound muscle action potential amplitudes or any other EMG abnormality were excluded. Needle EMG of a thenar muscle was performed to assess for the presence and grade of fibrillation potentials and motor unit potential abnormalities. The frequency of abnormalities was recorded. Statistical comparison between patients with and without needle EMG abnormalities was performed.

Results:
One-hundred two patients were included (50 with normal median motor DLs and 52 with abnormal DLs). Minimal or equivocal thenar needle EMG abnormalities were found in 12% of subjects with normal DLs. In patients with abnormal DLs, 32.6% had abnormalities, 15.4% with a mild degree of fibrillation potentials, and 25.0% with mild motor unit potential abnormalities. Patients with abnormal DLs and needle EMG abnormalities had significantly lower compound muscle action potential amplitudes compared to those without needle EMG changes.

Conclusions:
Patients with carpal tunnel syndrome with no involvement of the median motor nerve conduction study are unlikely to demonstrate prominent abnormalities on needle EMG of thenar muscles, and needle EMG of the thenar muscles is not necessary. However, in patients with carpal tunnel syndrome in which the median motor DL is prolonged but compound muscle action potential amplitudes are absolutely normal, needle EMG should be considered, as it may provide value in indicating some axonal loss despite a normal median compound muscle action potential amplitude.
Efficient generation of endogenous fluorescent reporters by Nested CRISPR in Caenorhabditis elegans
Authors: Vicencio Jeremy , Martínez-Fernández Adrian , Serrat Xènia , Cerón Julián 
Published: September 2018

AbstractCRISPR-based genome editing methods in model organisms are evolving at an extraordinary speed. Whereas the generation of deletion or missense mutants is quite straightforward, the production of endogenous fluorescent reporters is still inefficient. The use of plasmids with selection markers is an effective methodology, but often requires laborious and complicated cloning steps. We have established a cloning-free ribonucleoprotein-driven Nested CRISPR method that robustly produces endogenous fluorescent reporters. This methodology is based on the division of the GFP and mCherry sequences in three fragments. In the first step we use ssDNA donors (≤200 bp) to insert 5’ and 3’ fragments in the place of interest. In the second step, we use these sequences as homology regions for Homology Directed Repair (HDR) with a dsDNA donor (PCR product, ≈700 bp) including the middle fragment, thus completing the fluorescent protein sequence. This method is advantageous because the first step with ssDNA donors is known to be very efficient, and the second step, uses universal reagents, including validated PCR products and crRNAs, to create fluorescent reporters reaching reliable editing efficiencies as high as 40%. We have also used Nested CRISPR in a non-essential gene to produce a deletion mutant in the first step and a transcriptional reporter in the second step.In the search of modifications to optimize the method, we tested synthetic sgRNAs, but we did not observe a significant increase in the efficacy compared to independently adding tracrRNA and crRNA to the injection mix. Conveniently, we also found that both steps of Nested CRISPR could be performed in a single injection. Finally, we discuss the utility of Nested CRISPR for targeted insertion of long DNA fragments in other systems and prospects of this method in the future.
Using Google Trends to Examine the Spatio-Temporal Incidence and Behavioral Patterns of Dengue Disease: A Case Study in Metropolitan Manila, Philippines
Authors: Ho Howell T. , Carvajal Thaddeus M. , Bautista John Robert , Capistrano Jayson Dale R. , Viacrusis Katherine M. , Hernandez Lara Fides T. , Watanabe Kozo 
Published: September 2018

AbstractDengue is a major public health concern and an economic burden in the Philippines. Despite the country’s improved dengue surveillance, it still suffers from various setbacks and therefore needs to be complemented with alternative approaches. Previous studies have demonstrated the potential of internet-based surveillance such as Google Dengue Trends (GDT) in supplementing current epidemiological methods for predicting future dengue outbreaks and patterns. With this, our study aims to assess the temporal relationship of GDT and dengue incidence in Metropolitan Manila from previous years and examine web search behavior of the population towards the disease. The study collated and organized the population statistics and reported dengue cases in Metropolitan Manila from respective government agencies to calculate the spatial and temporal dengue incidence. The relative search volume of the term ‘dengue’ and top dengue-related search queries in Metropolitan Manila were obtained and organized from the Google trends platform. Data processing of GDT and dengue incidence was performed by conducting an ‘adjustment’ procedure and subsequently used for correlation and cross-correlation analyses. Moreover, a thematic analysis was employed on the top dengue-related search queries. Results revealed a high temporal relationship between GDT and dengue incidence when either one of the variables is adjusted. Cross-correlation showed that there is delayed effect (1-2 weeks) of GDT to dengue incidence, demonstrating its potential in predicting future dengue outbreaks and patterns in Metropolitan Manila. Thematic analysis of dengue-related search queries indicated 5 categories namely; (a) dengue, (b) sign and symptoms of dengue, (c) treatment and prevention, (d) mosquito and (e) other diseases where the majority of the search queries was ‘signs and symptoms’ which indicate the health-seeking behavior of the population towards the disease.
Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
Authors: Iacobucci Claudio , Piotrowski Christine , Aebersold Ruedi , Amaral Bruno C. , Andrews Philip , Borchers Christoph , Brodie Nicolas I. , Bruce James E. , Chaignepain Stéphane , Chavez Juan D. , Claverol Stéphane , Cox Jürgen , Degliesposti Gianluca , Dong Meng-Qiu , Edinger Nufar , Emanuelsson Cecilia , Gay Marina , Götze Michael , Gozzo Fabio C. , Gutierrez Craig , Haupt Caroline , Heck Albert J. R. , Herzog Franz , Huang Lan , Hoopmann Michael R. , Kalisman Nir , Klykov Oleg , Kukačka Zdeněk , Liu Fan , MacCoss Michael J. , Mechtler Karl , Mesika Ravit , Moritz Robert L. , Nagaraj Nagarjuna , Nesati Victor , Ninnis Robert , Novák Petr , O’Reilly Francis J , Pelzing Matthias , Petrotchenko Evgeniy , Piersimoni Lolita , Plasencia Manolo , Pukala Tara , Rand Kasper D. , Rappsilber Juri , Reichmann Dana , Sailer Caroline , Sarnowski Chris P. , Scheltema Richard A. , Schmidt Carla , Schriemer David C. , Shi Yi , Skehel J. Mark , Slavin Moriya , Sobott Frank , Solis-Mezarino Victor , Stephanowitz Heike , Stengel Florian , Stieger Christian E. , Trnka Michael , Vilaseca Marta , Viner Rosa , Xiang Yufei , Yilmaz Sule , Zelter Alex , Ziemianowicz Daniel , Leitner Alexander , Sinz Andrea 
Published: September 2018

AbstractThe number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has largely increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats that are generally accepted in the field and that have shown to lead to high-quality results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. From the results obtained, common protocols will be established. Our study serves as basis for establishing best practice guidelines in the field for conducting cross-linking experiments, performing data analysis, and reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.
The dorsolateral striatum regulates habits by way of performance vigor when actions are initiated
Authors: Crego Adam C.G. , Štoček Fabián , Marchuk Alec G. , Carmichael James E. , van der Meer Matthijs A.A. , Smith Kyle S. 
Published: September 2018

AbstractDespite clear evidence linking basal ganglia control to habits, it remains unclear through what mechanisms this control occurs. Here, we demonstrate that a key function of the dorsolateral striatum (DLS) is to regulate the vigor of a learned behavior at the moment of initiation in a habit-promoting manner. Shifts in vigor by phasic DLS perturbations coincide closely with how outcome-insensitive (i.e., habitual) the behaviors are in both response-based and cue-based task situations. Surprisingly, the control over habit strength by way of changes in vigor occurs without consistent changes in accuracy, suggesting that mechanisms controlling habit and vigor are dissociable from performance governed task rules. Finally, we show that increased DLS activity improves vigor preferentially when learned outcome values are stable, while reduced DLS activity dampens vigor preferentially when outcome values change. These data indicate that improving action vigor could be a principle route by which the basal ganglia facilitate habits.
CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data
Authors: Harmancı Akdes Serin , Harmanci Arif O. , Zhou Xiaobo 
Published: September 2018

AbstractRNA sequencing experiments generate large amounts of information about expression levels of genes. Although they are mainly used for quantifying expression levels, they contain much more biologically important information such as copy number variants (CNV). Here, we propose CaSpER, a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data. CaSpER performs smoothing of the genome-wide RNA sequencing signal profiles in different multiscale resolutions, identifying CNV events at different length scales. CaSpER also employs a novel methodology for generation of genome-wide B-allele frequency (BAF) signal profile from the reads and utilizes it in multiscale fashion for correction of CNV calls. The shift in allelic signal is used to quantify the loss-of-heterozygosity (LOH) which is valuable for CNV identification. CaSpER uses Hidden Markov Models (HMM) to assign copy number states to regions. The multiscale nature of CaSpER enables comprehensive analysis of focal and large-scale CNVs and LOH segments. CaSpER performs well in accuracy compared to gold standard SNP genotyping arrays. In particular, analysis of single cell Glioblastoma (GBM) RNA sequencing data with CaSpER reveals novel mutually exclusive and co-occurring CNV sub-clones at different length scales. Moreover, CaSpER discovers gene expression signatures of CNV sub-clones, performs gene ontology (GO) enrichment analysis and identifies potential therapeutic targets for the sub-clones. CaSpER increases the utility of RNA-sequencing datasets and complements other tools for complete characterization and visualization of the genomic and transcriptomic landscape of single cell and bulk RNA sequencing data, especially in cancer research.
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
Authors: Collado-Torres L , Burke EE , Peterson A , Shin JH , Straub RE , Rajpurohit A , Semick SA , Ulrich WS , BrainSeq Consortium , Valencia C , Tao R , Deep-Soboslay A , Hyde TM , Kleinman JE , Weinberger DR , Jaffe AE 
Published: September 2018

AbstractRecent large-scale genomics efforts have better characterized the molecular correlates of schizophrenia in postmortem human neocortex, but not hippocampus which is a brain region prominently implicated in its pathogenesis. Here in the second phase of the BrainSeq Consortium (Phase II), we have generated RiboZero RNA-seq data for 900 samples across both the dorsolateral prefrontal cortex (DLPFC) and the hippocampus (HIPPO) for 551 individuals (286 affected by schizophrenia disorder: SCZD). We identify substantial regional differences in gene expression, in both pre- and post-natal life, and find widespread differences in how genes are regulated across development. By extending quality surrogate variable analysis (qSVA) to multiple brain regions, we identified 48 and 245 differentially expressed genes (DEG) by SCZD diagnosis (FDR<5%) in HIPPO and DLPFC, respectively, with surprisingly minimal overlap in DEG between the two brain regions. We further identified 205,618 brain region-dependent eQTLs (FDR<1%) and found that 124 GWAS risk loci contain eQTLs in at least one of the regions. We also identify potential molecular correlates of in vivo evidence of altered prefrontal-hippocampal functional coherence in schizophrenia. These results underscore the complexity and regional heterogeneity of the transcriptional correlates of schizophrenia, and suggest future schizophrenia therapeutics may need to target molecular pathologies localized to specific brain regions.
A bacterial DNA repair pathway specific to a natural antibiotic
Authors: Burby Peter E. , Simmons Lyle A. 
Published: September 2018

SummaryAll organisms possess several DNA repair pathways to maintain the integrity of their genetic material. Although there are several DNA repair pathways that are well understood, we recently identified several genes inBacillus subtilisthat are important for surviving treatment with drugs that damage DNA. Here, we report a drug specific DNA repair pathway inB. subtilis. We identified genes coding for a previously uncharacterized helicase and exonuclease,mrfAandmrfB, respectively. Deletion ofmrfAandmrfBresulted in sensitivity to the DNA damaging agent mitomycin C, but not other types of DNA damage. We found that MrfAB operate independently of canonical nucleotide excision repair, forming a novel excision repair pathway in bacteria. A phylogenetic analysis demonstrates that MrfAB homologs are present in diverse bacterial phyla, and a cross-complementation assay shows that MrfAB function is conserved in closely related species. Mitomycin C is a natural antibiotic that is produced by the soil dwelling bacteriumStreptomyces lavendulae, andB. subtilisis also a soil dwelling organism. The specificity of the ΔmrfABphenotype suggests that MrfAB have been adapted as a countermeasure to mitomycin producing bacteria.Abbreviated SummaryBacteria possess DNA repair pathways to maintain the integrity of their genetic material. The helicase MrfA and the exonuclease MrfB are part of a mitomycin C specific DNA repair pathway inBacillus subtilis. Despite being present in many bacterial species, MrfAB activity in repairing MMC damaged DNA appears to be restricted to closely related species, suggesting that these proteins have likely been adapted to the specific needs of each bacterium.
Macroscale estimates of species abundance reveal evolutionary drivers of biodiversity
Authors: Fukaya Keiichi , Kusumoto Buntarou , Shiono Takayuki , Fujinuma Junichi , Kubota Yasuhiro 
Published: September 2018

AbstractEvolutionary processes underpin the biodiversity on the planet. Theories advocate that the form of the species abundance distribution (SAD), presented by the number of individuals for each species within an ecological community, is intimately linked to speciation modes such as point mutation and random fission. This prediction has rarely been, however, verified empirically; the fact that species abundance data can be obtained only from local communities critically limits our ability to infer the role of macroevolution in shaping ecological patterns. Here, we developed a novel statistical model to estimate macroscale SADs, the hidden macroecological property, by integrating spatially replicated multispecies detection-nondetection observations and the data on species geographic distributions. We determined abundance of 1,248 woody plant species at a 10 km grid square resolution over East Asian islands across subtropical to temperate biomes, which produced a metacommunity (i.e. species pool) SAD in four insular ecoregions along with its absolute size. The metacommunity SADs indicated lognormal-like distributions, which were well explained by the unified neutral theory of biodiversity and biogeography (UNTB) with protracted speciation, a mode of speciation intermediate between point mutation and random fission. Furthermore, the analyses yielded an estimate of speciation rate in each region that highlighted the importance of geographic characteristics in macroevolutionary processes and predicted the average species lifetime that was congruent with previous estimates. The estimation of macroscale SADs plays a remarkable role in revealing evolutionary diversification of regional species pools.
Automated, predictive, and interpretable inference of C. elegans escape dynamics
Authors: Daniels Bryan C. , Ryu William S. , Nemenman Ilya 
Published: September 2018

AbstractThe roundworm C. elegans exhibits robust escape behavior in response to rapidly rising temperature. The behavior lasts for a few seconds, shows history dependence, involves both sensory and motor systems, and is too complicated to model mechanistically using currently available knowledge. Instead we model the process phenomenologically, and we use the Sir Isaac dynamical inference platform to infer the model in a fully automated fashion directly from experimental data. The inferred model requires incorporation of an unobserved dynamical variable, and is biologically interpretable. The model makes accurate predictions about the dynamics of the worm behavior, and it can be used to characterize the functional logic of the dynamical system underlying the escape response. This work illustrates the power of modern artificial intelligence to aid in discovery of accurate and interpretable models of complex natural systems.
A Reptilian Endogenous Foamy Virus Sheds Light on the Early Evolution of Retroviruses
Authors: Wei Xiaoman , Chen Yicong , Duan Guangqian , Holmes Edward C. , Cui Jie 
Published: September 2018

AbstractEndogenous retroviruses (ERVs) can be thought of as host genomic fossils of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFV) have previously been discovered in mammals, amphibians and fish. Here we report a novel endogenous foamy virus, named SpuEFV, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that SpuEFV has likely co-diverged with its host over a period of many millions of years. The discovery of SpuEFV fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.