bluuebunny/crossref_metadata_2025_split huggingface dataset:
HEART Failure? Episodes of Missed Major Cardiac Events When Applying the HEART Pathway to an Observation Unit Population
Authors: Tesson Alan , Abdo Rami , Kamath Aparna , Sutter Joanne , Cline Rachel , Hale Sarah L. , Bae Jonathan , Verma Lalit 
Published: May 2018

Objective:
The HEART Pathway risk prediction tool (HEART score plus serial troponin measures at 0 and 3 hours post-presentation) is used to identify low-risk patients with chest pain who may qualify for safe, early discharge. We calculated the percentage of patients in our observation unit that qualified as low risk using HEART Pathway, as well as their associated outcomes.

Methods:
We retrospectively reviewed charts on 966 consecutive patients admitted to our observation unit for chest pain (January 2015 to February 2016); HEART Pathway scores were retrospectively calculated and serial cardiac troponin values logged. The primary outcome was 42-day major adverse cardiac events (MACE), including acute myocardial infarction, urgent revascularization, and all-cause death.

Results:
The patients’ mean age was 59, 42% were male, 46% white, and 68 (7.7%) had MACE. HEART Pathway defined 384 patients as low risk (39.8%) and eligible for early discharge. Applying HEART Pathway would have missed 1.2% of patients with MACE; however, all adverse cardiac events occurred in patients with a HEART Pathway score of 3 (4 of 193, 2.1%) and none in those with a HEART Pathway score ≤2 (0 of 134).

Conclusions:
While the HEART Pathway identifies a pooled population at low risk for MACE, risk is not homogenous within this population. Patients with a score of 3 may have higher risk of 42-day MACE that may be unacceptable to some providers, while scores ≤2 saw no events. Caution is advised for those with HEART Pathway score of 3 until more data is available to accurately estimate risk.
Impact of Provider Participation in ACO Programs on Preventive Care Services, Patient Experiences, and Health Care Expenditures in US Adults Aged 18–64
Authors: Hong Young-Rock , Sonawane Kalyani , Larson Samantha , Mainous Arch G. , Marlow Nicole M. 
Published: May 2018

Background:
Little is known about the impact of accountable care organization (ACO) on US adults aged 18–64.

Objectives:
To examine whether having a usual source of care (USC) provider participating in an ACO affects receipt of preventive care services, patient experiences, and health care expenditures among nonelderly Americans.

Research Design:
A cross-sectional analysis of the 2015 Medical Organizations Survey linked with the Medical Expenditure Panel Survey.

Subjects:
Survey respondents aged 18–64 with an identified USC and continuous health insurance coverage during 2015.

Measures:
Preventative care services (routine checkup, flu vaccination, and cancer screening), patient experiences with health care (access to care, interaction quality with providers, and global satisfaction), and health care expenditures (total and out-of-pocket expenditures) for respondents with USC by ACO and non-ACO provider groups.

Results:
Among 1563, nonelderly Americans having a USC, we found that nearly 62.7% [95% confidence interval (CI), 58.6%–66.7%; representing 15,722,208 Americans] were cared for by ACO providers. Our analysis showed no significant differences in preventive care services or patient experiences between ACO and non-ACO groups. Adjusted mean total health expenditures were slightly higher for the ACO than non-ACO group [$7016 (95% CI, $4949–$9914) vs. $6796 (95% CI, $4724–$9892)]; however, this difference was not statistically significant (P=0.250).

Conclusions:
Our findings suggest that having a USC provider participating in an ACO is not associated with preventive care services use, patient experiences, or health care expenditures among a nonelderly population.
Seasonality of Common Pediatric Infectious Diseases
Authors: Lipsett Susan C. , Monuteaux Michael C. , Fine Andrew M. 
Published: May 2018

Background/Objective
Traditional sources cite seasonal patterns for common infectious diseases, often based on microbiologic data, but little is known about cyclical trends in clinically diagnosed infectious conditions in the emergency department (ED). We leveraged the publicly available Nationwide Emergency Department Sample database to measure the seasonality of the most common pediatric infectious diseases diagnosed in US EDs.

Methods
We searched the Nationwide Emergency Department Sample database to identify infectious diagnoses comprising at least 1% of all diagnosis codes ascribed to patients 21 years and younger in US EDs from 2009 to 2013. We used Fourier regression to examine seasonal trends in disease and calculated the peak-to-nadir ratio for each infectious condition.

Results
Over 20% of pediatric visits during the study period were for infectious conditions. Upper respiratory infection, otitis media, gastroenteritis, urinary tract infection/pyelonephritis, cellulitis/abscess, and pneumonia showed a seasonal pattern that matched trends found in prior regional or microbiologic-based studies. The strongest seasonal trend as measured by goodness of model fit was found in pneumonia (peak-to-nadir incidence ratio of 2.7), followed by otitis media (2.0), cellulitis/abscess (2.0), gastroenteritis (1.6), upper respiratory infection (3.2), and urinary tract infection/pyelonephritis (1.4). Pharyngitis did not show a strong seasonal trend.

Conclusions
Many of the most common pediatric infectious diseases diagnosed in US EDs exhibited seasonal patterns. Large administrative databases can be used to track seasonal disease patterns, with the advantage that they reflect clinician diagnosis beyond microbiologic confirmation. This methodology could aid in resource planning, infection control, and public health educational initiatives.
Comparison Between Ultrasonography and Galactography in Detecting Lesions in Patients With Pathologic Nipple Discharge
Authors: Jung Hyun Kyung , Park Young Mi , Baek Hye Jin , Choo Hye Jung , Kim Eun-Kyung , Kim Dong Wook , Lee Sun Joo , Lee Jin Hwa 
Published: May 2018

Purpose
This study aimed to compare the diagnostic performance of breast ultrasonography (US) with that of galactography in the detection of lesions in patients with pathologic nipple discharge.

Methods
We included 46 cases from 39 patients (all women; mean age, 44.0 years; range, 22–68 years) who had pathologic nipple discharge and underwent US and galactography between March 2004 and December 2012. Two radiologists retrospectively reviewed and compared the detectability of lesions on US and galactography images. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of US and galactography, and the area under the curve was compared between the 2 imaging modalities.

Results
A total of 35 cases were pathologically diagnosed. Out of 11 cases that completed a follow-up, none developed malignancies during the follow-up period (mean: 63.5 months; range: 34.8–125.7 months). The sensitivity, specificity, and positive and negative predictive values of US with respect to detectability of lesions were 75%, 42.9%, 11.1%, and 94.7%, respectively, and those of galactography were 100%, 38.1%, 13.3%, and 100%, respectively.

Conclusions
Galactography is more sensitive than US in the detection of lesions in patients with pathologic nipple discharge.
Ultrasound, Computed Tomography, and Magnetic Resonance Imaging in a Patient With Medullary Cystic Kidney Disease
Authors: Whang Gilbert , Tchelepi Hisham 
Published: May 2018

Abstract
Among the renal cystic diseases that result in end-stage renal disease, an important hereditary cause is medullary cystic kidney disease, which affects adults in an autosomal dominant pattern. It is characterized by progressive renal failure, tubulointerstitial fibrosis, and formation of small cysts in the renal medulla and corticomedullary junction. While the appearance of medullary/corticomedullary cysts may not be pathognomonic for medullary cystic kidney disease, encountering a patient with renal failure and medullary/corticomedullary cysts should prompt further investigation, given the implication of having the disease. Genetic testing can be used to identify potential renal donors as well as identify affected individuals in order to control risk factors for chronic renal disease that may mitigate the progression of the disease process. The treatment of choice is renal transplantation.
scVAE: Variational auto-encoders for single-cell gene expression data
Authors: Grønbech Christopher Heje , Vording Maximillian Fornitz , Timshel Pascal , Sønderby Casper Kaae , Pers Tune Hannes , Winther Ole 
Published: May 2018

AbstractMotivationModels for analysing and making relevant biological inferences from massive amounts of complex single-cell transcriptomic data typically require several individual data-processing steps, each with their own set of hyperparameter choices. With deep generative models one can work directly with count data, make likelihood-based model comparison, learn a latent representation of the cells and capture more of the variability in different cell populations.ResultsWe propose a novel method based on variational auto-encoders (VAEs) for analysis of single-cell RNA sequencing (scRNA-seq) data. It avoids data preprocessing by using raw count data as input and can robustly estimate the expected gene expression levels and a latent representation for each cell. We tested several count likelihood functions and a variant of the VAE that has a priori clustering in the latent space. We show for several scRNA-seq data sets that our method outperforms recently proposed scRNA-seq methods in clustering cells and that the resulting clusters reflect cell types.Availability and implementationOur method, called scVAE, is implemented in Python using the TensorFlow machine-learning library, and it is freely available at https://github.com/scvae/scvae.
Entrainment of circadian rhythms depends on firing rates and neuropeptide release of VIP SCN neurons
Authors: Mazuski Cristina , Abel John H. , Chen Samantha P. , Hermanstyne Tracey O. , Jones Jeff R. , Simon Tatiana , Doyle Francis J. , Herzog Erik D. 
Published: May 2018

SummaryThe mammalian suprachiasmatic nucleus (SCN) functions as a master circadian pacemaker, integrating environmental input to align physiological and behavioral rhythms to local time cues. Approximately 10% of SCN neurons express vasoactive intestinal polypeptide (VIP); however, it is unknown how firing activity of VIP neurons releases VIP to entrain circadian rhythms. To identify physiologically relevant firing patterns, we optically tagged VIP neurons and characterized spontaneous firing over three days. VIP neurons had circadian rhythms in firing rate and exhibited two classes of instantaneous firing activity. We next tested whether physiologically relevant firing affected circadian rhythms through VIP release. We found that VIP neuron stimulation with high, but not low, frequencies shifted gene expression rhythms in vitro through VIP signaling. In vivo, high frequency VIP neuron activation rapidly entrained circadian locomotor rhythms. Thus, increases in VIP neuronal firing frequency release VIP and entrain molecular and behavioral circadian rhythms.HighlightsMazuski et al. identified three classes of circadian SCN neurons based on their distinct firing patterns consistent over multiple daysThere are two distinct classes (tonic and irregular firing) of VIP SCN neurons.Stimulation of VIP SCN neurons at physiologically relevant frequencies phase shifts whole-SCN circadian rhythms in gene expression through VIP release. These effects are blocked with VIP antagonists.Firing of VIP SCN neurons entrains circadian rhythms in locomotor behavior in a frequency and time-of-day dependent manner.
Autolysin-Independent DNA Release inStreptococcus pneumoniae in vitroBiofilms
Authors: Domenech Mirian , García Ernesto 
Published: May 2018

ABSTRACTBiofilms are defined as layers of cells of microorganisms adhered to the surface of a substrate and embedded in an extracellular matrix and provide an appropriate environment for increased genetic exchange. Extracellular DNA (eDNA) is an essential component of the extracellular matrix of microbial biofilms, but the pathway(s) responsible for DNA release are largely unknown. Autolysis (either spontaneous or phage-induced) has been proposed the major event leading to the appearance of eDNA. The ‘suicidal tendency’ ofStreptococcus pneumoniaeis well-known, with lysis mainly caused by the triggering of LytA, the major autolytic amidase. However, the LytC lysozyme and CbpD (a possible murein hydrolase) have also been shown involved. The present work examines the relationship between eDNA, autolysins, and the formation and maintenance ofin vitropneumococcal biofilms, via fluorescent labelling combined with confocal laser scanning microscopy, plus genetic transformation experiments. Bacterial DNA release mechanisms other than those entailing lytic enzymes were shown to be involved by demonstrating that horizontal gene transfer in biofilms takes place even in the absence of detectable autolytic activity. It had been previously suggested that the quorum sensing systems ComABCDE and LuxS/AI-2 are involved in the production of eDNA as a response to the accumulation of quorum sensing signals, although our immunofluorescence results do not support this hypothesis. Evidence that the release of DNA is somehow linked to the production of extracellular vesicles byS. pneumoniaeis provided.
Using High Throughput DNA Sequencing to Evaluate the Accuracy of Serial Dilution Based Tests of Microbial Activities in Oil Pipelines
Authors: Khanipov K. , Golovko G. , Rojas M. , Pimenova M. , Albayrak L. , Chumakov S. , Duarte R. , Widger W.R. , Pickthall T. , Fofanov Y. 
Published: May 2018

AbstractMicrobial activities have detrimental effects on industrial infrastructure. If not controlled, microbial presence can result in corrosion, biofilm formation, and product degradation. Serial dilution tests are routinely used for evaluating presence and abundance of microorganisms by diluting samples and culturing microbes in specific media designed to support microorganisms with particular properties, such as sulfate reduction.A high-throughput sequencing approach was used to evaluate changes in microbial composition during four standard serial dilution tests. Analysis of 159 isolates revealed significant differences in the microbial compositions of sequential serial dilution titers and identified several cases where: (a) bacteria known to have a detrimental metabolic function (such as acid production) were lost in the serial dilution medium designed to test for this function; (b) bacteria virtually absent in the original sample became dominant in the serial dilution medium. These observations raise concerns regarding the accuracy and overall usefulness of serial dilution tests.
Quasi-periodic patterns contribute to functional connectivity in the brain
Authors: Abbas Anzar , Belloy Michaël , Kashyap Amrit , Billings Jacob , Nezafati Maysam , Schumacher Eric , Keilholz Shella 
Published: May 2018

AbstractFunctional connectivity is widely used to study the coordination of activity between brain regions over time. Functional connectivity in the default mode and task positive networks is particularly important for normal brain function. However, the processes that give rise to functional connectivity in the brain are not fully understood. It has been postulated that low-frequency neural activity plays a key role in establishing the functional architecture of the brain. Quasi-periodic patterns (QPPs) are a reliably observable form of low-frequency neural activity that involve the default mode and task positive networks. Here, QPPs from resting-state and working memory task-performing individuals were acquired. The spatiotemporal pattern, strength, and frequency of the QPPs between the two groups were compared and the contribution of QPPs to functional connectivity in the brain was measured. In task-performing individuals, the spatiotemporal pattern of the QPP changes, particularly in task-relevant regions, and the QPP tends to occur with greater strength and frequency. Differences in the QPPs between the two groups could partially account for the variance in functional connectivity between resting-state and task-performing individuals. The QPPs contribute strongly to connectivity in the default mode and task positive networks and to the strength of anti-correlation seen between the two networks. Many of the connections affected by QPPs are also disrupted during several neurological disorders. These findings contribute to understanding the dynamic neural processes that give rise to functional connectivity in the brain and how they may be disrupted during disease.HighlightsQuasi-periodic patterns (QPPs) of low-frequency activity contribute to functional connectivityThe spatiotemporal pattern of QPPs differs between resting-state and task-performing individualsQPPs account for significant functional connectivity in the DMN and TPN during rest and task performanceChanges in functional connectivity in these networks may reflect differences in QPPs
Hyd ubiquitinates the NF-κB co-factor Akirin to activate an effective immune response in Drosophila
Authors: Cammarata-Mouchtouris Alexandre , Nguyen Xuan-Hung , Bonnay François , Goto Akira , Orian Amir , Fauvarque Marie-Odile , Boutros Michael , Reichhart Jean-Marc , Matt Nicolas 
Published: May 2018

One Sentence SummaryUpon microbial infection in Drosophila, the E3-ubiquitin ligase Hyd ubiquitinylates the NF-κB co-factor Akirin for its efficient binding to the NF-κB factor Relish and subsequent activation of immune effectors genes.ABSTRACTThe Drosophila IMD pathway is activated upon microbial challenge with Gramnegative bacteria to trigger the innate immune response. In order to decipher this NF-κB signaling pathway, we undertook an ex-vivo RNAi screen targeting specifically E3 ubiquitin ligases and identified the HECT E3 ubiquitin ligase Hyperplastic Discs “Hyd” as a new actor of the IMD pathway. We showed that Hyd targets the NF-κB cofactor of Akirin. The K63-polyubiquitination chains deposited by Hyd decorate Akirin for its efficient binding to the NF-κB transcription factor Relish. We showed that this Hyd-mediated interaction is critical to activate immune-induced genes that depend on both Relish and Akirin, but is dispensable for those that depend solely on Relish. Therefore Hyd is key in operating a NF-κB transcriptional selectivity downstream of the IMD pathway. Drosophila depleted for Hyd or Akirin failed to express the full set of immune-induced anti-microbial peptide coding genes and succumbed to immune challenges. We showed further that Ubr5, the mammalian homolog of Hyd, is also required downstream of the NF-κB pathway for the IL1β-mediated IL6 activation. This study links the action of a E3-ubiquitin ligase to the activation of immune effector genes, deepening our understanding of the involvement of ubiquitination in inflammation and identifying a potential target for the control of inflammatory diseases.
Parasite intensity is driven by temperature in a wild bird
Authors: Mennerat Adèle , Charmantier Anne , Perret Philippe , Hurtrez-Boussès Sylvie , Lambrechts Marcel M. 
Published: May 2018

AbstractIncreasing awareness that parasitism is an essential component of nearly all aspects of ecosystem functioning, as well as a driver of biodiversity, has led to rising interest in the consequences of climate change in terms of parasitism and disease spread. Yet empirical knowledge on the extent and ways in which climatic factors affect parasite prevalence and intensities remains scarce. In an 18-year, multi-site, correlative study we investigated the contributions of weather variables and other factors to spatio-temporal variation in infestation by blowfly parasitic larvae (Protocalliphoraspp.) in nests of Corsican blue tits (Cyanistes caeruleus). We found that ambient temperature during the nestling stage is strongly and positively related to parasite load (number of parasites per chick), both across broods when controlling for year, and across years. In addition, annual mean parasite load also increased with minimal spring temperature, and decreased with increasing average temperature in the previous summer. There was no indication of a dependence of parasite dynamics on host dynamics in this system, likely due in part to the wide host range of blowflies that do not solely rely on blue tit hosts. This suggests a major effect of temperature during the blowfly life cycle, with potential implications for blowfly – host interactions across their geographical range as climate keeps warming up. Finally, given that ambient temperature increases throughout the breeding season and that blowflies negatively affect survival and recruitment of blue tits, these results also mean that parasites, along with caterpillar availability, can drive selection for breeding date in this system.
Genome-Scale CRISPR Screening Identifies Novel Human Pluripotent Gene Networks
Authors: Ihry Robert J. , Salick Max R. , Ho Daniel J. , Sondey Marie , Kommineni Sravya , Paula Steven , Raymond Joe , Frias Elizabeth , Worringer Kathleen A. , Russ Carsten , Reece-Hoyes John , Altshuler Bob , Randhawa Ranjit , Yang Zinger , McAllister Gregory , Hoffman Gregory R. , Dolmetsch Ricardo , Kaykas Ajamete 
Published: May 2018

ABSTRACTHuman pluripotent stem cells (hPSCs) generate a wide variety of disease-relevant cells that can be used to improve the translation of preclinical research. Despite the potential of hPSCs, their use for genetic screening has been limited because of technical challenges. We developed a renewable Cas9/sgRNA-hPSC library where loss-of-function mutations can be induced at will. Our inducible-mutant hPSC library can be used for an unlimited number of genome-wide screens. We screened for novel genes involved in 3 of the fundamental properties of hPSCs: Their ability to self-renew/survive, their capacity to differentiate into somatic cells, and their inability to survive as single-cell clones. We identified a plethora of novel genes with unidentified roles in hPSCs. These results are available as a resource for the community to increase the understanding of both human development and genetics. In the future, our stem cell library approach will be a powerful tool to identify disease-modifying genes.VISUAL ABSTRACT