bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coexisting Abnormal Esophageal Body Motility Predicts Clinical Symptoms and Bolus Transit in Patients With Esophagogastric Junction Outflow Obstruction (EGJOO)
Authors: Jodorkovsky Daniela , Wong Danny , Din Ryan , Sikavi Daniel R. , Lee Darren J.H. , Cai Jennifer X. , Lo Wai-Kit , Chan Walter W. 
Published: July 2020

Goal:
The goal of this study was to compare the clinical presentations of esophagogastric junction outflow obstruction (EGJOO) with coexisting abnormal esophageal body motility (EBM) to isolated EGJOO.

Background:
The clinical significance and management of EGJOO remain debated, as patients may have varied to no symptoms. The effect of coexisting abnormal EBM in EGJOO is unclear. We hypothesized that a concomitant EBM disorder is associated with clinical symptoms of EGJOO.

Study:
This was a retrospective cohort study of consecutive adults diagnosed with EGJOO on high-resolution impedance-manometry (HRIM) at 2 academic centers in March 2018 to September 2018. Patients with prior treatment for achalasia, foregut surgery, or evidence of obstruction were excluded. Subjects were divided into EGJOO with abnormal EBM per Chicago classification v3.0 and isolated EGJOO. Statistical analyses were performed using Fisher-exact or Student t test (univariate) and logistic or linear regression (multivariate).

Results:
Eighty-two patients (72% women, age 61.1±10.7 y) were included. Thirty-one (37.8%) had abnormal EBM, including 16 (19.5%) ineffective esophageal motility and 15 (18.2%) hypercontractile esophagus. Esophageal symptoms (heartburn, regurgitation, chest pain, dysphagia) were more prevalent among those with abnormal EBM (90.3% vs. 64.7%, P=0.01). On logistic regression adjusting for age, gender, body mass index, and opioid use, abnormal EBM remained predictive of esophageal symptoms (adjusted odds ratio [aOR] 7.51, P=0.007). On separate models constructed, HE was associated with chest pain (aOR 7.45, P=0.01) and regurgitation (aOR 4.06, P=0.046), while ineffective esophageal motility was predictive of heartburn (aOR 5.84, P=0.009) and decreased complete bolus transit (β-coefficient −0.177, P=0.04).

Conclusion:
Coexisting abnormal EBM is associated with esophageal symptoms and bolus transit in patients with EGJOO.
Outcomes and Predictors of Wound Healing among Patients with Complex Diabetic Foot Wounds Treated with a Dermal Regeneration Template (Integra)
Authors: Hicks Caitlin W. , Zhang George Q. , Canner Joseph K. , Mathioudakis Nestoras , Coon Devin , Sherman Ronald L. , Abularrage Christopher J. 
Published: July 2020

Background:
The utility of dermal regeneration templates for treating high-risk diabetic foot wounds is unclear. The authors report wound healing and major amputation outcomes among a cohort of diabetic patients with complex diabetic foot wounds treated in a multidisciplinary setting.

Methods:
All patients with complex diabetic foot wounds treated with a dermal regeneration template (March of 2013 to February of 2019) were captured in a prospective institutional database. Wound severity was classified according to the Society for Vascular Surgery Wound, Ischemia, and foot Infection (WIfI) classification system to determine limb salvage prognosis at baseline. Wound healing and major amputation rates were reported using Kaplan-Meier analyses. A stepwise Cox proportional hazards model was used to identify independent characteristics associated with wound healing.

Results:
Eighty-five patients with 107 complex diabetic foot wounds were treated (mean age, 61.2 ± 3.3 years; 63.5 percent male and 61.2 percent African American). Most diabetic foot wounds were high-risk (wound, ischemia, and foot infection stage 3 or 4, 93.5 percent), corresponding to a predicted 25 to 50 percent risk of major amputation at 1 year. Dermal regeneration template use resulted in successful wound granulation in 66.7 percent of cases, with a mean time to complete wound healing of 198 ± 18 days. Twelve- and 18-month wound healing rates were 79.0 ± 5.0 percent and 93.0 ± 3.3 percent, respectively. Major amputation was required in 11.2 percent of patients. Independent predictors of poor wound healing included lack of bone involvement, higher WIfI stage, and prior dermal regeneration template failure.

Conclusion:
Application of a dermal regeneration template to complex diabetic foot wounds at high risk for major amputation results in good wound healing and excellent limb salvage outcomes among diabetic patients treated in a multidisciplinary setting.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
High HIV Prevalence and Low HIV-Service Engagement Among Young Women Who Sell Sex: A Pooled Analysis Across 9 Sub-Saharan African Countries
Authors: Rucinski Katherine B. , Schwartz Sheree R. , Mishra Sharmistha , Phaswana-Mafuya Nancy , Diouf Daouda , Mothopeng Tampose , Kouanda Seni , Simplice Anato , Kouame Abo , Cham Bai , Tamoufe Ubald , Matse Sindy , Hausler Harry , Fouda Ghislaine , Pitche Vincent , Baral Stefan D. 
Published: July 2020

Background:
Epidemiological data are needed to characterize the age-specific HIV burden and engagement in HIV services among young, marginalized women in sub-Saharan Africa.

Setting:
Women aged ≥18 years who reported selling sex were recruited across 9 countries in Southern, Central, and West Africa through respondent driven sampling (N = 6592).

Methods:
Individual-level data were pooled and age-specific HIV prevalence and antiretroviral therapy (ART) coverage were estimated for each region using generalized linear mixed models. HIV-service engagement outcomes (prior HIV testing, HIV status awareness, and ART use) were compared among women living with HIV across age strata (18–19, 20–24, and ≥25 years) using generalized estimating equations.

Results:
By age 18%–19%, 45.4% [95% confidence interval (CI): 37.9 to 53.0], 5.8% (95% CI: 4.3 to 7.8), and 4.0% (95% CI: 2.9 to 5.4) of young women who sell sex were living with HIV in Southern, Central, and West Africa respectively. Prevalence sharply increased during early adulthood in all regions, but ART coverage was suboptimal across age groups. Compared with adult women ≥25, young women aged 18–19 were less likely to have previously tested for HIV [prevalence ratio (PR) 0.76; 95% CI: 0.72 to 0.80], less likely to already be aware of their HIV status (PR 0.48; 95% CI: 0.35 to 0.64), and less likely to be taking ART (PR 0.67; 95% CI: 0.59 to 0.75).

Conclusions:
HIV prevalence was already high by age 18–19 in this pooled analysis, demonstrating the need for prevention efforts that reach women who sell sex early in their adolescence. ART coverage remained low, with women in the youngest age group the least engaged in HIV-related services. Addressing barriers to HIV service delivery among young women who sell sex is central to a comprehensive HIV response.
Aspergillus fumigatus and pan-azole resistance: who should be concerned?
Authors: Wiederhold Nathan P. , Verweij Paul E. 
Published: July 2020

Purpose of review
Although clinical outcomes in the treatment of aspergillosis have markedly improved with the availability of newer triazoles, the development of resistance to these antifungals, especially in Aspergillus fumigatus, is a growing concern. The purpose of this review is to provide an update on azole resistance mechanisms and their epidemiology in A. fumigatus, the clinical implications of azole resistance, and to discuss future treatment options against azole-resistant aspergillosis.

Recent findings
Resistance may develop through either patient or environmental azole exposure. Environmental exposure is the most prevalent means of resistance development, and these isolates can cause disease in various at-risk groups, which now include those with influenza, and potentially COVID-19. Although current treatment options are limited, newer therapies are in clinical development. These include agents with novel mechanisms of action which have in vitro and in vivo activity against azole-resistant A. fumigatus.

Summary
Azole-resistant A. fumigatus is an emerging threat that hampers our ability to successfully treat patients with aspergillosis. Certain geographic regions and patient populations appear to be at increased risk for this pathogen. As new patient groups are increasingly recognized to be at increased risk for invasive aspergillosis, studies to define the epidemiology and management of azole-resistant A. fumigatus are critically needed. While treatment options are currently limited, new agents under clinical development may offer hope.
EEG Findings and Releases From Hospital for Patients With Anti-NMDA Receptor Encephalitis
Authors: Gómez Ávila Felipe Alberto , González-Aragón Maricarmen Fernández , Avellán Álvaro Moreno , San-Juan Daniel 
Published: July 2020

Purpose:
Anti-N-methyl-D-aspartate receptor encephalitis is produced by an autoimmune reaction against macromolecular structures that form ionotropic receptors for glutamic acid NR2A and NR2B subunits. Other important findings are the multiple clinical and paraclinical manifestations, among which the EEG stands out. We characterized EEG patterns and their association with functional disability and hospitalization time in patients with anti-N-methyl-D-aspartate receptor encephalitis admitted in our center.

Methods:
We performed a retrospective cohort study that included patients with anti-N-methyl-D-aspartate receptor encephalitis. We recorded the clinical and sociodemographic characteristics and initial scalp EEG data. Functional disability was evaluated at admission and follow-up using the modified Rankin scale.

Results:
Forty-five patients aged 15 to 80 years were included. An abnormal EEG was reported in 92.5% of patients. We identified six EEG patterns. The mean hospitalization time was 3.2 (±2.4) months. The higher modified Rankin scale at admission and the absence of parietal or temporal epileptiform activity were associated with more prolonged hospitalization, hazard ratio of 0.338 for each modified Rankin scale level (95% confidence interval 0.174–0.658, P = 0.001), 14.5, P = 0.017, and hazard ratio of 5.6, P = 0.009, respectively.

Conclusions:
EEGs are frequently abnormal in patients with anti-N-methyl-D-aspartate receptor encephalitis. The lower modified Rankin scale at admission and the absence of some focal epileptiform activity may be associated with shorter hospitalizations.
SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility
Authors: Jokela Pia , Jääskeläinen Anu E , Jarva Hanna , Holma Tanja , Ahava Maarit J , Mannonen Laura , Lappalainen Maija , Kurkela Satu , Loginov Raisa 
Published: July 2020

AbstractRapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS-CoV-2 and Mobidiag Novodiag® Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag® test in tertiary care emergency departments was assessed. In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert®, whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag®. Rapid SARS-CoV-2 testing with Novodiag® was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag® and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag® and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag®, but positive with the reference method with late Ct values. On average, a test result using Novodiag® was available nearly 8 hours earlier than that obtained with the large-scale PCR tests. While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting.
An Agent Based Modeling of COVID-19: Validation, Analysis, and Recommendations
Authors: Shamil Md. Salman , Farheen Farhanaz , Ibtehaz Nabil , Khan Irtesam Mahmud , Rahman M. Sohel 
Published: July 2020

AbstractThe Coronavirus disease 2019 (COVID-19) has resulted in an ongoing pandemic worldwide. Countries have adopted Non-pharmaceutical Interventions (NPI) to slow down the spread. This study proposes an Agent Based Model that simulates the spread of COVID-19 among the inhabitants of a city. The Agent Based Model can be accommodated for any location by integrating parameters specific to the city. The simulation gives the number of daily confirmed cases. Considering each person as an agent susceptible to COVID-19, the model causes infected individuals to transmit the disease via various actions performed every hour. The model is validated by comparing the simulation to the real data of Ford county, Kansas, USA. Different interventions including contact tracing are applied on a scaled down version of New York city, USA and the parameters that lead to a controlled epidemic are determined. Our experiments suggest that contact tracing via smartphones with more than 60% of the population owning a smartphone combined with a city-wide lock-down results in the effective reproduction number (Rt) to fall below 1 within three weeks of intervention. In the case of 75% or more smartphone users, new infections are eliminated and the spread is contained within three months of intervention. Contact tracing accompanied with early lock-down can suppress the epidemic growth of COVID-19 completely with sufficient smartphone owners. In places where it is difficult to ensure a high percentage of smartphone ownership, tracing only emergency service providers during a lock-down can go a long way to contain the spread. No particular funding was available for this project.
Universal rules of life: Metabolic rates, biological times and the equal fitness paradigm
Authors: Burger Joseph Robert , Hou Chen , Hall Charles A.S , Brown James H. 
Published: July 2020

AbstractHere we review and extend the equal fitness paradigm (EFP) as an important step in developing and testing a synthetic theory of ecology and evolution based on energy and metabolism. The EFP states that all organisms are equally fit at steady state, because they allocate the same quantity of energy, ~22.4 kJ/g/generation to production of offspring. On the one hand, the EFP may seem tautological, because equal fitness is necessary for the origin and persistence of biodiversity. On the other hand, the EFP reflects universal laws of life: how biological metabolism – the uptake, transformation and allocation of energy – links ecological and evolutionary patterns and processes across levels of organization from: i) structure and function of individual organisms, ii) life history and dynamics of populations, iii) interactions and coevolution of species in ecosystems. The physics and biology of metabolism have facilitated the evolution of millions of species with idiosyncratic anatomy, physiology, behavior and ecology but also with many shared traits and tradeoffs that reflect the single origin and universal rules of life.
Ketamine increases activity of a fronto-striatal projection that regulates compulsive behavior
Authors: Davis Gwynne L. , Minerva Adelaide R. , Lario Argentina , Rodriguez Carolyn I. , Gunaydin Lisa A. 
Published: July 2020

AbstractObsessive-Compulsive Disorder (OCD), characterized by intrusive thoughts (obsessions) and repetitive behaviors (compulsions), is associated with dysfunction in fronto-striatal circuits. There are currently no fastacting pharmacological treatments for OCD. However, recent clinical studies demonstrated that an intravenous infusion of ketamine rapidly reduces OCD symptoms. To probe mechanisms underlying ketamine’s therapeutic effect on OCD-like behaviors, we used the SAPAP3 knockout (KO) mouse model of compulsive grooming. Here we recapitulate the fast-acting therapeutic effect of ketamine on compulsive behavior, and show that ketamine increases activity of dorsomedial prefrontal neurons projecting to the dorsomedial striatum in KO mice. Optogenetically mimicking this increase in fronto-striatal activity rescued compulsive grooming behavior in KO mice. Conversely, inhibiting this circuit in wild-type mice increased grooming. These studies demonstrate that ketamine increases activity in a fronto-striatal circuit that causally controls compulsive grooming behavior, suggesting this circuit may be important for ketamine’s therapeutic effects in OCD.
SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities
Authors: Gramm Marie , Pérez-Palma Eduardo , Schumacher-Bass Sarah , Dalton Jarrod , Leu Costin , Blank-enberg Daniel , Lal Dennis 
Published: July 2020

AbstractLiterature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on words from abstracts and/or other text. SimText can be used for (i) data generation: text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis of data using unsupervised learning techniques and visualization in a Shiny web application.Availability and ImplementationWe developed SimText as an open-source R software and integrated it into Galaxy, an online data analysis platform. A command line version of the toolset is available for download from GitHub athttps://github.com/mgramm1/simtext.
Changes in insulin resistance do not occur in parallel with changes in mitochondrial content and function in male rats
Authors: Genders Amanda J , Kuang Jujiao , Marin Evelyn C , Saner Nicholas J , Botella Javier , Jacques Macsue , McConell Glenn K , Andrade-Souza Victor A , Chagolla Javier , Bishop David J 
Published: July 2020

AbstractAims/hypothesisTo investigate if there is a causal relationship between changes in insulin resistance and mitochondrial respiratory function and content in rats fed a high fat diet (HFD) with or without concurrent exercise training. We hypothesised that provision of a high fat diet (HFD) would increase insulin resistance and decrease mitochondrial characteristics (content and function), and that exercise training would improve both mitochondrial characteristics and insulin resistance in rats fed a HFD.MethodsMale Wistar rats were given either a chow diet or a high fat diet (HFD) for 12 weeks. After 4 weeks of the dietary intervention, half of the rats in each group began eight weeks of interval training.In vivoglucose and insulin tolerance was assessed, as wasex vivoglucose uptake in epitrochlearis muscle. Mitochondrial respiratory function was assessed in permeabilised soleus and white gastrocnemius (WG) muscles. Mitochondrial content was determined by measurement of citrate synthase (CS) activity and protein expression of components of the electron transport system (ETS).ResultsHFD rats had impaired glucose and insulin tolerance. HFD did not change CS activity in the soleus; however, it did increase CS activity in WG (Chow 5.9 ± 0.5, HFD 7.2 ± 0.7 mol h-1kg protein-1). Protein expression of components of the ETS and mitochondrial respiratory function (WG Chow 65.2 ± 8.4, HFD 88.6 ± 8.7 pmol O2 s-1mg-1) were also increased by HFD. Exercise training improved glucose and insulin tolerance in the HFD rats. Exercise training did not alter CS activity in either muscle. Mitochondrial respiratory function was increased with exercise training in the chow fed animals in soleus muscle, but not in WG. This exercise effect was absent in the HFD animals. Mitochondrial characteristics did not consistently correlate with insulin or glucose tolerance.Conclusions/interpretationHFD induced insulin resistance, but it did not negatively affect any of the measured mitochondrial characteristics. Exercise training improved insulin resistance, but without changes in mitochondrial respiration and content. The lack of an association between mitochondrial characteristics and insulin resistance was reinforced by the absence of strong correlations between these measures. Our results suggest that defects in mitochondrial respiration and content are not responsible for insulin resistance in HFD rats.
EnterococcalPrgU mitigates PrgB overexpression toxicity by binding to intergenic RNA downstream of the PQpromoter
Authors: Lassinantti Lena , Camacho Martha I , Erickson Rebecca J B , Willett Julia L E , De Lay Nicholas R. , ter Beek Josy , Dunny Gary M , Christie Peter J , Berntsson Ronnie P-A 
Published: July 2020

AbstractEfficient horizontal gene transfer of the conjugative plasmid pCF10 fromEnterococcus faecalisdepends on the sex pheromone cCF10, which induces the expression of the Type 4 Secretion System (T4SS) genes controlled by the PQpromoter. The pheromone responsive PQpromoter is strictly regulated to prevent overproduction of theprgQoperon, which contains the T4SS, and to limit the cell toxicity caused by overproduction of PrgB, a T4SS adhesin involved in cellular aggregation. PrgU plays an important role in regulating this toxicity by decreasing PrgB production. PrgU has an RNA-binding fold, prompting us to test whether PrgU exerts its regulatory control through binding ofprgQtranscripts. With a combination oflacZreporter fusion, northern blot, and RNAseq analyses, we provide evidence that PrgU binds a specific RNA sequence within the intergenic region (IGR), ca 400 bp downstream of the PQpromoter. PrgU-IGR binding reduces levels of downstream transcripts, with the strongest decrease seen forprgBmessages. Consistent with these findings, we determined that pCF10-carrying cells expressingprgUdecreased transcript levels more rapidly than isogenic cells deleted ofprgU. Finally, purified PrgU bound RNAin vitro, but without sequence specificity, suggesting that PrgU requires a specific RNA structure or one or more host factors to bind its RNA targetin vivo. Together, our results support a working model where PrgU binding to the IGR serves to recruit RNase(s) for targeted degradation of downstream transcripts.ImportanceBacteria utilize Type 4 Secretion Systems (T4SS) to efficiently transfer DNA from donor to recipient cells, thereby spreading genes encoding for antibiotic resistance as well as various virulence factors. The conjugative plasmid pCF10 fromEnterococcus faecalis, originally isolated from clinical isolates, serves as a model system for these processes in Gram-positive bacteria. It is very important to strictly regulate the expression of the T4SS proteins for the bacteria, as some of these proteins are highly toxic to the cell. Here, we identify the mechanism by which PrgU performs its delicate fine tuning of the expression levels. AsprgUgenes are present in various conjugative plasmids and transposons, this provides an important new insight into the bacterial repertoire of regulation mechanisms of these clinically important systems.