bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraoperative Ultrasound Navigation with Doppler Function to Guide Arteriovenous Malformation Resection: 3-Dimensional Operative Video
Authors: Dellaretti Marcos , Ronconi Daniel Espindola 
Published: March 2019

Abstract
Intraoperative ultrasound navigation was initially introduced in the neurosurgical field for brain tumor surgery and was then extended to arteriovenous malformation surgery with good success. This tool provides real-time intraoperative images.
1
Moreover, Doppler ultrasound permits early identification of feeding arteries and supplies the surgeon with a global impression of the flow dynamics.
2
A further use of doppler is to check for residual nidus. Other advantages are the capacity to identify intracerebral hemorrhage.
2

In this video, we demonstrate the case of a 15-yr-old patient who presented intracranial hemorrhage. Magnetic resonance imaging revealed the presence of left frontoparietal hematoma associated with an image suggestive of cerebral arteriovenous malformation (AVM). Arteriography confirmed the diagnosis of AVM fed by branches of the anterior cerebral and superficial drainage for the superior sagittal sinus.
The patient was placed in dorsal decubitus with his head turned to the right and a left parietal-frontal craniotomy was performed. After the dura mater was opened, cortical mapping was performed to locate the motor and sensory cortex. After the mapping, ultrasound with doppler was performed to locate the AVM and the hematoma and determine its relation to the motor and sensory cortex. At the end of the surgery, doppler ultrasound was used again to ensure complete resection of the AVM.
Intraoperative Ultrasound navigation with doppler is an inexpensive technology that can be used in the treatment of AVMs, especially in the subcortex, as it assists in locating the nidus and confirms its complete resection.
Calprotectin discriminates septic arthritis from pseudogout and rheumatoid arthritis
Authors: Baillet Athan , Trocmé Candice , Romand Xavier , Nguyen Chuong M.V. , Courtier Anais , Toussaint Bertrand , Gaudin Philippe , Epaulard Olivier 
Published: March 2019

Abstract

Objective
We aimed to determine whether calprotectin and α-defensins could discriminate septic from other inflammatory arthritides.

Methods
Synovial fluids with a predominance of neutrophils from patients with septic arthritis, pseudogout and RA were prospectively collected. Neutrophil-related proteins calprotectin and human neutrophil α-defensins levels were assessed in synovial fluids. Demographic parameters and biomarkers with P-value ⩽0.05 for differentiating septic from non-septic arthritis were included in a multivariable model. Multivariable logistic regression with stepwise selection was performed to build the final combined model.

Results
A total of 74 patients were included: septic arthritis (n = 26), pseudogout (n = 28) and RA (n = 20). Patients with septic arthritis were more likely to be male and young, and to display higher synovial neutrophil count. Calprotectin was significantly increased in patients with septic arthritis. The multivariable model included calprotectin, synovial fluid neutrophil count and gender. Calprotectin was the only biomarker that discriminated septic arthritis from non-septic inflammatory arthritides, with 76% sensitivity, 94% specificity and a positive likelihood ratio = 12.2 at the threshold for calprotectin of 150 mg/l.

Conclusion
Synovial fluid calprotectin is a relevant biomarker to discriminate septic arthritis from other inflammatory arthritides. This biomarker should be tested in an independent cohort.
BLT-Immune Humanized Mice as a Model for Nivolumab-Induced Immune-Mediated Adverse Events: Comparison of the NOG and NOG-EXL Strains
Authors: Weaver James L , Zadrozny Leah M , Gabrielson Kathleen , Semple Kenrick M , Shea Katherine I , Howard Kristina E 
Published: March 2019

Abstract
Checkpoint inhibitors represent a new class of therapeutics in the treatment of cancer that has demonstrated remarkable clinical effectiveness. However, some patients have experienced serious immune-mediated adverse effects including pneumonitis, hepatitis, colitis, nephritis, dermatitis, encephalitis, and adrenal or pituitary insufficiency. These adverse events were not predicted by nonclinical studies. To determine if bone marrow-liver-thymus (BLT) immune humanized mice could demonstrate these adverse effects, we studied the effect of nivolumab on 2 strains of BLT-humanized mice, NOD.Cg-Prkdcscid Il2rgtm1Sug/JicTac (NOG) and NOD.Cg-Prkdcscid Il2rgtm1Sug Tg(SV40/HTLV-IL3, CSF2)10-7Jic/JicTac (NOG-EXL). Mice were treated with 2.5, 5.0, or 10.0 mg/kg nivolumab or saline twice weekly for 28 days. BLT-NOG mice had significantly reduced survival compared with BLT-NOG-EXL mice. In spite of the difference in survival, both BLT-humanized strains showed adverse reactions similar to those reported in humans, including pneumonitis and hepatitis, with nephritis, dermatitis and adrenalitis also noted in some individuals. Additional histopathologic findings included pancreatic atrophy, myositis, and osteomyelitis in some animals. T-cell activation increased with concomitant loss of PD-1 detection. These findings show that BLT immune humanized mice can demonstrate immune-mediated adverse effects of antiPD1 therapy, and may represent a model that can be used to better understand toxicity of this class of drugs.
The Impact of Environmental Context on Intern Sign-Out Quality
Authors: Lee Soo-Hoon , Terndrup Christopher , Phan Phillip H. , Zaeh Sandra E. , Atsina Kwame , Minkove Nicole , Desai Sanjay V. 
Published: March 2019

Background
Resident duty-hour restrictions have led to more sign-out transitions, increasing the potential for preventable harm. An unfavorable environment is expected to exacerbate sign-out risks to patient safety.

Objective
The aim of the study was to evaluate the impact of noise, interruptions, long sign-outs, and sign-outs exceeding allotted time on sign-out quality.

Methods
Eight trained observers evaluated 620 evening patient sign-outs between interns for 40 weeknights between February and April 2015 at a large internal medicine training program. Quality of sign-out was measured three ways: information quality, scores from the Handoff CEX Tool, and peer evaluations.

Results
Noise had no impact on information quality. Interruptions negatively affected information quality (−0.10 < r < −0.15, P < 0.001) and Handoff CEX quality scores (−0.11 < r < −0.26, P < 0.001). Long sign-outs taking more than 1 hour negatively affected sign-out quality (−0.09 < r < −0.23, P < 0.05). Sign-outs exceeding allotted time negatively impacted peer evaluations (−0.11 < r < −0.22, P < 0.001).

Conclusions
Interruptions, long sign-outs, and sign-outs exceeding allotted time were related to lower sign-out quality. Improving the environment to reduce interruptions and training interns to manage their time during sign-outs may improve sign-out quality.
Sino-Nasal Anatomical Variations in Rhinogenic Headache Pathogenesis
Authors: Sollini Giacomo , Mazzola Francesco , Iandelli Andrea , Carobbio Andrea , Barbieri Andrea , Mora Renzo , Peretti Giorgio 
Published: March 2019

Abstract
Rhinogenic headache (RH) is a widespread pain syndrome but its pathogenesis and treatment are still unclear. Some authors recognize a correlation between RH and mucosal contact points or some other sinonasal anatomical variations. The authors conducted a retrospective case–control study to analyze the correlation between radiological findings and clinical symptoms.
One hundred-nineteen adults with Para-Nasal Sinuses Computed Tomography (PNS-CT) scans were included: 64 patients who have originally undergone PNS-CT scan as part of rhinogenic headache workup (Group A), and 55 controls in whom PNS-CT scans were obtained for other purposes (Group B). All subjects were asked to report their symptoms using a headache scoring system. PNS-CT scans of all subjects were analyzed for presence of mucosal contact points, middle turbinate concha bullosa (MTCB) and frontoethmoidal cells.
The most common anatomical abnormality found in our series was MTCB, reported in 60.9% of patients in Group A and 41.8% of those in Group B. A statistically significant prevalence was found in Group A compared to Group B regarding the presence of MTCB (P = 0.037) and Type II (P = 0.016) and Type III (P = 0.039) frontoethmoidal cells. No statistically significant difference (P >0.05) was found between Group A and Group B regarding the presence of mucosal contact points at each site.
Multiple anatomical variations in nasal and paranasal sinuses may cause a rhinogenic headache with different characteristics. Some of these, such as concha bullosa of middle turbinate or type II and III Kuhn cells, have shown a significant association with rhinogenic headache. No statistically significant association was found between presence of headache and mucosal contact points and type I and IV frontal cells. These findings can be very helpful for the surgeons that want to deal with the treatment of RH.
Kazantsev dynamo in turbulent compressible flows
Authors: Martins Afonso Marco , Mitra Dhrubaditya , Vincenzi Dario 
Published: March 2019

We consider the kinematic fluctuation dynamo problem in a flow that is random, white-in-time, with both solenoidal and potential components. This model is a generalization of the well-studied Kazantsev model. If both the solenoidal and potential parts have the same scaling exponent, then, as the compressibility of the flow increases, the growth rate decreases but remains positive. If the scaling exponents for the solenoidal and potential parts differ, in particular if they correspond to typical Kolmogorov and Burgers values, we again find that an increase in compressibility slows down the growth rate but does not turn it off. The slow down is, however, weaker and the critical magnetic Reynolds number is lower than when both the solenoidal and potential components display the Kolmogorov scaling. Intriguingly, we find that there exist cases, when the potential part is smoother than the solenoidal part, for which an increase in compressibility increases the growth rate. We also find that the critical value of the scaling exponent above which a dynamo is seen is unity irrespective of the compressibility. Finally, we realize that the dimension
d
= 3 is special, as for all other values of
d
the critical exponent is higher and depends on the compressibility.
Quantifying the efficiency and biases of forestSaccharomycessampling strategies
Authors: Boynton Primrose J. , Kowallik Vienna , Landermann Doreen , Stukenbrock Eva H. 
Published: March 2019

AbstractSaccharomycesyeasts are emerging as model organisms for ecology and evolution, and researchers need environmentalSaccharomycesisolates to test ecological and evolutionary hypotheses. However, methods for isolatingSaccharomycesfrom nature have not been standardized and isolation methods may influence the genotypes and phenotypes of studied strains. We compared the effectiveness and potential biases of an established enrichment culturing method against a newly developed direct plating method for isolating forest floorSaccharomycesspp. In a European forest, enrichment culturing was both less successful at isolatingS. paradoxusper sample collected and less labor intensive per isolatedS. paradoxuscolony than direct isolation. The two methods sampled similarS. paradoxusdiversity: the number of unique genotypes sampled (i.e., genotypic diversity) perS. paradoxusisolate and average growth rates ofS. paradoxusisolates did not differ between the two methods, and growth rate variances (i.e., phenotypic diversity) only differed in one of three tested environments. However, enrichment culturing did detect rareS. cerevisiaein the forest habitat, and also found twoS. paradoxusisolates with outlier phenotypes. Our results validate the historically common method of using enrichment culturing to isolate representative collections of environmentalSaccharomyces.We recommend that researchers choose aSaccharomycessampling method based on resources available for sampling and isolate screening. Researchers interested in discovering newSaccharomycesphenotypes or rareSaccharomycesspecies from natural environments may also have more success using enrichment culturing. We include step-by-step sampling protocols in the supplemental materials.
Improved HLA-based prediction of coeliac disease identifies two novel HLA risk modifiers, DQ6.2 and DQ7.3
Authors: Erlichster Michael , Bedo Justin , Skafidas Efstratios , Kwan Patrick , Kowalczyk Adam , Goudey Benjamin 
Published: March 2019

AbstractPurposeHuman Leukocyte Antigen (HLA) testing is useful in the clinical work-up of coeliac disease (CD), with high negative but low positive predictive value. We construct a genomic risk score (GRS) using HLA risk loci to improve CD prediction and guide exclusion criteria.MethodsImputed HLA genotypes for five European CD case-control GWAS (n>15,000) were used to construct and validate an HLA based risk models (HDQ15). Conditioning on this score, we identified novel HLA interactions which modified CD risk, and integrated these novel alleles into a new risk score (HDQ17).ResultsA GRS from HLA risk allele genotypes yields performance equivalent to a state-of-the-art GRS (GRS228) using 228 single nucleotide polymorphisms (SNPs) and significantly improves upon all previous HLA based risk models. Conditioning on this model, we find two novel associations, HLA-DQ6.2 and HLA-DQ7.3, that interact significantly with HLA-DQ2.5 (p = 2.51 × 10−9, 1.99 × 10−7 for DQ6.2 and DQ7.3 respectively). These epistatic interactions yield the best performing risk score (HDQ17) which retains performance when implemented using 6 tag SNPs. Using the HDQ17 model, the positive predictive value of CD testing in high risk populations increases from 17.5% to 27.1% while maintaining a negative predictive value above 99%.ConclusionOur proposed HLA-based GRS achieves state-of-the-art risk prediction, helps elucidate further risk factors and improves HLA typing exclusionary criteria, which may reduce the number of patients requiring unnecessary endoscopies.
CA1 pyramidal cells organize an episode by segmented and ordered events
Authors: Sun Chen , Yang Wannan , Martin Jared , Tonegawa Susumu 
Published: March 2019

ABSTRACTA prevailing view is that the brain represents episodic experience as the continuous moment to moment changes in the experience. Whether the brain also represents the same experience as a sequence of discretely segmented events, is unknown. Here, we report a hippocampal CA1 “chunking code”, tracking an episode as its discrete event subdivisions (“chunks”) and the sequential relationships between them. The chunking code is unaffected by unpredicted variations within the events, reflecting the code’s flexible nature by being organized around events as abstract units. The chunking code changes accordingly when relationships between events are disrupted or modified. The discrete chunking code and continuous spatial code are represented in the same cells, but in an orthogonal manner, and can be independently perturbed. Optogenetic inactivation of MEC inputs to CA1 disrupts the chunking but not spatial code. The chunking code may be fundamental for representing an episode, alongside codes tracking continuous changes.
Genetic drift in range expansions is very sensitive to density feedback in dispersal and growth
Authors: Birzu Gabriel , Matin Sakib , Hallatschek Oskar , Korolev Kirill S. 
Published: March 2019

AbstractTheory predicts rapid genetic drift in expanding populations due to the serial founder effect at the expansion front. Yet, many natural populations maintain high genetic diversity in the newly colonized regions. Here, we investigate whether density-dependent dispersal could provide a resolution of this paradox. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants from the diverse, high-density regions arrive at the expansion edge. When density-dependence is weak or negative, the effective population size of the front scales only logarithmically with the carrying capacity. The dependence, however, switches to a sublinear power law and then to a linear increase as the density-dependence becomes strongly positive. To understand these results, we introduce a unified framework that predicts how the strength of genetic drift depends on the density-dependence in both dispersal and growth. This theory reveals that the transitions between different regimes of diversity loss are controlled by a single, universal parameter: the ratio of the expansion velocity to the geometric mean of dispersal and growth rates at expansion edge. Importantly, our results suggest that positive density-dependence could dramatically alter evolution in expanding populations even when its contributions to the expansion velocity is small.
An R Implementation of Tumor-Stroma-Immune Transcriptome Deconvolution Pipeline using DeMixT
Authors: Cao Shaolong , Wang Zeya , Gao Fan , Chen Jingxiao , Zhang Feng , Frigo Daniel E. , Efstathiou Eleni , Kopetz Scott , Wang Wenyi 
Published: March 2019

AbstractThe deconvolution of transcriptomic data from heterogeneous tissues in cancer studies remains challenging. Available software faces difficulties for accurately estimating both component-specific proportions and expression profiles for individual samples. To address these challenges, we present a new R-implementation pipeline for the more accurate and efficient transcriptome deconvolution of high dimensional data from mixtures of more than two components. The pipeline utilizes the computationally efficient DeMixT R-package with OpenMP and additional cancer-specific biological information to perform three-component deconvolution without requiring data from the immune profiles. It enables a wide application of DeMixT to gene expression datasets available from cancer consortium such as the Cancer Genome Atlas (TCGA) projects, where, other than the mixed tumor samples, a handful of normal samples are profiled in multiple cancer types. We have applied this pipeline to two TCGA datasets in colorectal adenocarcinoma (COAD) and prostate adenocarcinoma (PRAD). In COAD, we found varying distributions of immune proportions across the Consensus Molecular Subtypes, from the highest to the lowest being CMS1, CMS3, CMS4 and CMS2. In PRAD, we found the immune proportions are associated with progression-free survival (p<0.01) and negatively correlated with Gleason scores (p<0.001). Our DeMixT-centered analysis protocol opens up new opportunities to investigate the tumor-stroma-immune microenvironment, by providing both proportions and component-specific expressions, and thus better define the underlying biology of cancer progression.Availability and implementation: An R package, scripts and data are available: https://github.com/wwylab/DeMixTallmaterials.
MicroRNA-138 negatively regulates the hypoxia-inducible factor 1α to suppress melanoma growth and metastasis
Authors: Qiu Haijiang , Chen Fangchao , Chen Minjun 
Published: March 2019

ABSTRACTMelanoma with rapid progression towards metastasis becomes the deadliest form of skin cancer. However, the mechanism of melanoma growth and metastasis is still unclear. Here, we found that miRNA-138 was low expression and hypoxia-inducible factor 1α (HIF1α) was high expression in the patient’s melanoma tissue, and they had a significant negative correlation (r = -0.937, P < 0.001). Patients with miRNA-138low/HIF1αhigh signature were predominant in late stage. Further, bioinformatic analysis demonstrated that miRNA-138 directly targeted HIF1α. We found that the introduction of miRNA-138 mimics to A375 cells could reduced HIF1α mRNA expression, and suppressed the cell proliferation, migration and invasion. Overexpression of miRNA-138 or inhibition of HIF1α significantly suppressed the growth and metastasis of melanoma in vivo. Our study demonstrates the role and clinical relevance of miRNA-138 and HIF1α in melanoma cell growth and metastasis, providing a novel therapeutic target for suppression of melanoma growth and metastasis.
How helpful are the protein-protein interaction databases and which ones?
Authors: Bajpai Akhilesh Kumar , Davuluri Sravanthi , Tiwary Kriti , Narayanan Sithalechumi , Oguru Sailaja , Basavaraju Kavyashree , Dayalan Deena , Thirumurugan Kavitha , Acharya Kshitish K 
Published: March 2019

AbstractProtein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs. But in absence of systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among such protein interaction databases and tools. In fact, a comprehensive list of such bioinformatics resources has not been reported so far. For the first time, we compiled 375 PPI resources, short-listed and performed preliminary comparison of 125 important ones (both lists available publicly at startbioinfo.com), and then systematically compared human PPIs from 16 carefully-selected databases. General features have been first compared in detail. The coverage of ‘experimentally verified’ vs. all PPIs, as well as those significant in case of disease-associated and other types of genes among the chosen databases has been compared quantitatively. This has been done in two ways: outputs manually obtained using web-interfaces, and all interactions downloaded from the databases. For the first approach, PPIs obtained in response to gene queries using the web interfaces were compared. As a query set, 108 genes associated with different tissues (specific to kidney, testis, and uterus, and ubiquitous) or diseases (breast cancer, lung cancer, Alzheimer’s, cystic fibrosis, diabetes, and cardiomyopathy) were chosen. PPI-coverage for well-studied genes was also compared with that of less-studied ones. For the second approach, the back-end-data from the databases was downloaded and compared. Based on the results, we recommend the use of STRING and UniHI for retrieving the majority of ‘experimentally verified’ protein interactions, and hPRINT and STRING for obtaining maximum number of ‘total’ (experimentally verified as well as predicted) PPIs. The analysis of experimentally verified PPIs found exclusively in each database revealed that STRING contributed about 71% of exclusive hits. Overall, hPRINT, STRING and IID together retrieved ~94% of ‘total’ protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types. The results also indicate that the database usage frequency may not correlate with their advantages, thereby justifying the need for more frequent studies of this nature.
HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations
Authors: Drayman Nir , Patel Parthiv , Vistain Luke , Tay Savaş 
Published: March 2019

ABSTRACTViral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that they cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming involves the recruitment of beta-catenin to the host nucleus and viral replication compartments and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.