bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin recruitment of OGG1 requires cohesin and mediator and is essential for efficient 8-oxoG removal
Authors: Lebraud Emilie , Pinna Guillaume , Siberchicot Capucine , Depagne Jordane , Busso Didier , Fantini Damiano , Irbah Lamya , Robeska Elena , Kratassiouk Gueorgui , Ravanat Jean-Luc , Epe Bernd , Radicella J Pablo , Campalans Anna
Published: July 2020

One of the most abundant DNA lesions induced by oxidative stress is the highly mutagenic 8-oxoguanine (8-oxoG), which is specifically recognized by 8-oxoguanine DNA glycosylase 1 (OGG1) to initiate its repair. How DNA glycosylases find small non-helix-distorting DNA lesions amongst millions of bases packaged in the chromatin-based architecture of the genome remains an open question. Here, we used a high-throughput siRNA screening to identify factors involved in the recognition of 8-oxoG by OGG1. We show that cohesin and mediator subunits are required for re-localization of OGG1 and other base excision repair factors to chromatin upon oxidative stress. The association of OGG1 with euchromatin is necessary for the removal of 8-oxoG. Mediator subunits CDK8 and MED12 bind to chromatin and interact with OGG1 in response to oxidative stress, suggesting they participate in the recruitment of the DNA glycosylase. The oxidative stress-induced association between the cohesin and mediator complexes and OGG1 reveals an unsuspected function of those complexes in the maintenance of genomic stability.
Video-Based Motion Analysis Use: A National Survey of Orthopedic Physical Therapists
Authors: Hensley Craig P , Millican Devyn , Hamilton Nida , Yang Amy , Lee Jungwha , Chang Alison H
Published: July 2020

Objectives

Motion analysis is performed by physical therapists to assess and improve movement. Two-dimensional video-based motion analysis (VBMA) is available for smartphones/tablets and requires little to no equipment or cost. Research on VBMA use in clinical practice is limited. The purpose of this study was to examine the current use of VBMA in orthopedic physical therapist practice.

Methods

Members of the Academy of Orthopaedic Physical Therapy completed an online survey. Questions examined frequency of VBMA use, reasons for use, facilitators/barriers, device/apps used, practice patterns, other certificates/degrees, and demographic information.

Results

Among the final analysis sample of 477 respondents, 228 (47.8%) use VBMA. Of 228 VBMA users, 91.2% reported using it for ≤25% of their caseload, and 57.9% reported using their personal device to capture movement. Reasons for using VBMA included visual feedback for patient education (91.7%), analysis of movement (91.2%), and assessment of progress (51.8%). Barriers to use included lack of device/equipment (48.8%), lack of space (48.6%), and time restraint (32.1%). Those with ≤20 years of clinical experience (odds ratio [OR] = 1.83, 95% CI = 1.21–2.76), residency training (OR = 2.49, 95% CI = 1.14–5.43), and fellowship training (OR = 2.97, 95% CI = 1.32–6.66), and those from the West region of the United States (OR = 1.66, 95% CI = 1.07–2.56) were more likely to use VBMA.

Conclusions

More than 50% of surveyed orthopedic physical therapists do not use VBMA in clinical practice. Future research should be directed toward assessing reliability and validity of VBMA use by smartphones, tablets, and apps and examining whether VBMA use enhances treatment outcomes. Data security, patient confidentiality, and integration into the electronic medical record should be addressed.

Impact

This study is the first to our knowledge to describe the use of VBMA in orthopedic physical therapist practice in the United States. It is the first step in understanding how VBMA is used and might be used to enhance clinical assessment and treatment outcomes.
CAMTA3 negatively regulates disease resistance through modulating immune response and extensive transcriptional reprogramming in cassava
Authors: Chang Yanli , Bai Yujing , Wei Yunxie , Shi Haitao
Published: July 2020

As one of the important crops in the world, cassava production is seriously threatened by Xanthomonas axonopodis pv. manihotis (Xam) all year round. Calmodulin-binding transcription activators (CAMTAs) play key roles in biotic stress and abiotic stress in plants, however, their roles in cassava remain elusive. In this study, six MeCAMTAs were identified, and MeCAMTA3 with the highest induction upon Xam infection was confirmed as a transcription factor that binds to the vCGCGb motif. MeCAMTA3 negatively regulates plant disease resistance against Xam. On the one hand, MeCAMTA3 negatively regulated endogenous salicylic acid and reactive oxygen species accumulation, pathogenesis-related genes MePRs’ transcripts and callose deposition during cassava-Xam interaction but not under control conditions. On the other hand, RNA sequencing showed extensive transcriptional reprogramming by MeCAMTA3, especially 18 genes with a vCGCGb motif in the promoter region in hormone signaling, antioxidant signaling and other disease resistance signaling. Notably, chromatin immunoprecipitation-polymerase chain reaction showed that eight of these genes might be directly regulated by MeCAMTA3 through transcriptional repression. In summary, MeCAMTA3 negatively regulates plant disease resistance against cassava bacterial blight through modulation of multiple immune responses during cassava-Xam interaction and extensive transcriptional reprogramming.
Adjunct treatment in snakebite envenoming: a systematic review of randomised controlled trials
Authors: Rodrigo Chaturaka , Gnanathasan Ariaranee
Published: July 2020

Adjunct therapy in snakebite may be lifesaving if administered appropriately or can be harmful if non-judicious use leads to avoidable delays in administering antivenom. This systematic review analyses the evidence from randomised controlled trials (RCTs) on the efficacy of adjunct treatment administered with antivenom. PubMed, EMBASE, Scopus, Cochrane library and CINAHL were searched for RCTs enrolling patients with snakebite envenoming where a treatment other than antivenom has been assessed for its efficacy within the last 25 y. Fifteen studies met the inclusion criteria. The interventions assessed were categorised as adjunct therapies (heparin or fresh frozen plasma) to reverse haemotoxicity (three studies), antibiotics to prevent local infections (three studies), steroids to reduce local swelling (one study), premedication (adrenaline, steroids and antihistamines, either alone or in combination) to reduce hypersensitivity reactions to antivenom (five studies) and other interventions (three studies). Apart from a beneficial effect of low-dose adrenaline (1:1000, 0.25 ml administered subcutaneously) in preventing antivenom-induced hypersensitivities (OR: 0.54, 95% CI 0.32 to 0.93, two RCTs, 354 participants, moderate certainty evidence) in Sri Lanka, evidence for any other adjunct therapy is either non-existent or needs confirmation by larger better designed trials.
A Probabilistic Bio-Economic Assessment of the Global Consequences of Wheat Leaf Rust
Authors: Chai Yuan , Pardey Philip G. , Hurley Terrance M. , Senay Senait D. , Beddow Jason M.
Published: July 2020

This study provides a bio-economic assessment of the global climate suitability and probabilistic crop-loss estimates attributable to wheat leaf rust. We draw on a purpose-built, spatially explicit, ecoclimatic suitability model for wheat leaf rust to estimate that 94.4% of global wheat production is vulnerable to the disease. To reflect the spatiotemporal variation in leaf rust losses, we used a probabilistic approach to estimate a representative rust loss distribution based on long-term, state-level annual U.S. loss estimates. Applying variants of this representative loss distribution to selected wheat production areas in 15 epidemiological zones throughout the world, we project global annual average losses of 8.6 million metric tons of grain for the period 2000 to 2050 based on a conservative, baseline scenario, and 18.3 million metric tons based on a high-loss scenario; equivalent to economic losses ranging from $1.5 to $3.3 billion per year (2016 U.S. prices). Even the more conservative baseline estimate implies that a sustained, worldwide investment of $50.5 million per year in leaf rust research is economically justified.
Surgeons reaching satisfying outcomes without surgery: nasal dorsum skin cancer recurrence treated with electrochemotherapy
Authors: Pichi Barbara , Moretto Silvia , Petruzzi Gerardo , Zocchi Jacopo , Mazzola Francesco , Manciocco Valentina , Marchesi Paolo , Pellini Raul
Published: July 2020

Cutaneous squamous cell carcinoma of the head and neck district are generally treated with surgery. Surgery is the standard treatment in early stages and local advanced tumors, followed by adjuvant therapy, radiation or concurrent chemoradiation therapy. Local recurrence treatment depends on previous therapies, though radical surgery is often the first choice at the expense of anatomy preservation. We present the case of a patient with cutaneous squamous cell carcinoma of the nasal dorsum which relapsed after surgery and radiation therapy. The patient refused radical surgery and electrochemotherapy under general anesthesia was administered. After 6 months from treatment, the patient showed a complete clinical response. Electrochemotherapy could be considered as an alternative to surgery in small lesion when other approaches are refused.
Tracheostomy and Gastrostomy in Geriatric Trauma Associated With High Postdischarge Mortality
Authors: Boone Sherry M. , Collier Bryan R. , Faulks Emily R. , Locklear Tonja M. , Bower Katie L. , Lollar Daniel I. , Dhiman Nitasha , Nussbaum Michael S. , Hamill Mark E.
Published: July 2020

Objectives:

Identify 5-year mortality rates in trauma patients greater than 18 years old who undergo tracheostomy and/or gastrostomy tube placement.

Design:

Retrospective convenience sample with two cohorts.

Setting:

Academic level 1 trauma center.

Patients:

Hospitalized patients admitted to the trauma service from July 2008 to December 2012 who underwent tracheostomy and/or gastrostomy tube placement.

Interventions:

Patients were placed into two cohorts: adult 18–64 and geriatric greater than or equal to 65; mortality data were obtained from the National Death Index.

Measurements and Main Results:

The primary outcome was 5-year mortality of both cohorts as well as those admitted who did not receive tracheostomy or gastrostomy. Univariate analysis was performed using Fisher exact and Wilcoxon signed-rank tests. Kaplan-Meier curves were plotted to examine mortality up to 5 years after discharge.

Conclusions:

Five-year postdischarge mortality is significantly higher in geriatric patients undergoing tracheostomy and/or gastrostomy after traumatic injury. Fifty percent die within the first 28 weeks following discharge and 93% die within 2 years.
Effects of Telemedicine ICU Intervention on Care Standardization and Patient Outcomes: An Observational Study
Authors: Becker Christian D. , Fusaro Mario V. , Al Aseri Zohair , Millerman Konstantin , Scurlock Corey
Published: July 2020

Objectives:

Given the numerous recent changes in ICU practices and protocols, we sought to confirm whether favorable effects of telemedicine ICU interventions on ICU mortality and length of stay can be replicated by a more recent telemedicine ICU intervention.

Design, Setting and Patients:

Observational before-after telemedicine ICU intervention study in seven adult ICUs in two hospitals. The study included 1,403 patients in the preintervention period (October 2014 to September 2015) and 14,874 patients in the postintervention period (January 2016 to December 2018).

Intervention:

Telemedicine ICU implementation.

Measurements and Main Results:

ICU and hospital mortality and length of stay, best practice adherence rates, and telemedicine ICU performance metrics. Unadjusted ICU and hospital mortality and lengths of stay were not statistically significantly different. Adjustment for Acute Physiology and Chronic Health Evaluation Version IVa score, ICU type, and ICU admission time via logistic regression yielded significantly lower ICU and hospital mortality odds ratios of 0.58 (95% CI, 0.45–0.74) and 0.66 (95% CI, 0.54–0.80), respectively. When adjusting for acuity by comparing observed-over-expected length of stay ratios through Acute Physiology and Chronic Health Evaluation IVa methodology, we found significantly lower ICU and hospital length of stay in the postintervention group. ICU mortality improvements were driven by nighttime ICU admissions (odds ratio 0.45 [95% CI, 0.33–0.61]) as compared to daytime ICU admissions (odds ratio 0.81 [95% CI, 0.55–1.20]), whereas hospital mortality improvements were seen in both subgroups but more prominently in nighttime ICU admissions (odds ratio 0.57 [95% CI, 0.44–0.74]) as compared to daytime ICU admissions (odds ratio 0.73 [95% CI, 0.55–0.97]), suggesting that telemedicine ICU intervention can effectively supplement low intensity bedside staffing hours (nighttime).

Conclusions:

In this pre-post observational study, telemedicine ICU intervention was associated with improvements in care standardization and decreases in ICU and hospital mortality and length of stay. The mortality benefits were mediated in part through telemedicine ICU supplementation of low intensity bedside staffing hours.
Case Report: A Rare Case of Silent Sinus Syndrome and Vertical Diplopia
Authors: Le Joan K.
Published: July 2020

SIGNIFICANCE

Silent sinus syndrome is classically a maxillary sinus disease characterized by transient and variable vertical diplopia, hypoglobus, and enophthalmos. Uncommon presentations may exist, and although rare, it should be considered when diagnostic testing is inconsistent with more common etiologies of diplopia.

PURPOSE

This study aimed to report an unusual presentation of silent sinus syndrome and review the thought process in diagnosing and managing this condition.

CASE REPORT

A 65-year-old white man presented to the eye clinic with left upper eyelid ptosis and intermittent vertical diplopia of 2-month onset. Clinical testing was variable, and initial differential diagnoses included a partial left pupil–sparing third nerve palsy involving the superior division, myasthenia gravis, and orbital disease. After extensive workup and review of his computed tomography images, the patient was diagnosed with severe chronic pansinusitis with an underlying condition known as silent sinus syndrome. He was referred to otorhinolaryngology for sinus decompression and oculoplastics for orbital reconstruction. While awaiting orbital reconstruction after decompression of multiple sinuses, he returned reporting a significant reduction in his diplopia.

CONCLUSIONS

Vertical diplopia is a common complaint in primary care optometry. It is important to delve into more rare etiologies when clinical, laboratory, and radiological studies do not support the more common diagnoses.
Intra–Right Ventricle Course of the Coronary Arteries on Computed Tomography Angiography
Authors: Tyczyński Paweł , Skowroński Jarosław , Opolski Maksymilian P. , Pręgowski Jerzy , Kępka Cezary , Kruk Mariusz , Orczykowski Michał , Łazarczyk Hubert , Witkowski Adam , Michałowska Ilona
Published: July 2020

Background

The clinical relevance and anatomic characteristics of intracavitary coronary arteries coursing within the right ventricle (RV) are largely unknown.

Objectives

The aim of our study was to assess the clinical and computed tomographic characteristics of patients diagnosed with intracavitary coronary arteries coursing within RV (intra-RV coronaries).

Methods

Electronic records from a single high-volume cardiac center were retrospectively screened for the presence of intra-RV coronaries among consecutive patients who underwent coronary computed tomography angiography (coronary CTA) from 2008 to 2019.

Results

Overall, 31,748 coronary CTA reports were evaluated, and 17 subjects with intra-RV coronaries were identified. None of these patients was referred for subsequent invasive coronary angiography. One patient underwent coronary artery bypass grafting, 1 patient had a history of percutaneous coronary intervention, and 1 patient had a concomitant coronary anomaly: left circumflex coronary artery originating from the right coronary artery. All of the involved coronaries (n = 17) were the left anterior descending coronary arteries (LADs). Typical segmental coronary course within RV was along the border between free RV wall and interventricular septum (beneath interventricular groove), often within trabeculae carneae of the RV. Only the midsegment and distal segment of the LAD traversed within the RV. The mean ± SD distance from the aorta to the coronary entrance into the RV was 74.5 ± 17.1 mm, whereas the mean ± SD intra-RV coronary length was 25.1 ± 14.0 mm.

Conclusions

Intra-RV course of the coronaries in an adult CTA population is an infrequent anatomical variant involving LAD. It may require additional attention during interventional and surgical interventions.
Patterns of Gray Matter Volume Alterations in Hemodialysis Patients With and Without Restless Legs Syndrome: Evidence From a Voxel-Based Morphometry Study
Authors: Wang Hao , Han Xue , Jin Mei , Zhang Peng , Wang Zheng , Lv Han , Ding He-yu , Zhang Zheng-yu , Zhao Peng-fei , Li Jing , Yang Zheng-han , Liu Wen-hu , Wang Zhen-chang
Published: July 2020

Purpose

The purpose of this study was to investigate the differences of gray matter volume (GMV) alteration patterns between hemodialysis with restless legs syndrome (HD-RLS) and hemodialysis without restless legs syndrome (HD-nRLS) patients using voxel-based morphometry.

Methods

Twenty-three HD-RLS patients, 27 HD-nRLS patients, and 27 age-, sex-, and education-matched healthy controls were included in this study. One-way analysis of covariance and post hoc analyses were used to assess differences in GMV, demographics, and clinical data among the 3 groups. Pearson correlation analysis was conducted between altered GMV in the HD-RLS group and clinical data.

Results

Compared with HD-nRLS patients, HD-RLS patients showed decreased GMV in the left primary motor cortex (false discovery rate corrected,P< 0.05). Compared with the healthy controls, both HD subgroups (ie, those with and without RLS) exhibited consistent GMV changes, including decreased GMV in the bilateral anterior cingulate and paracingulate gyrus and left middle temporal gyrus (false discovery rate corrected,P< 0.05). The GMV values in the left precentral gyrus were negatively correlated with the RLS rating scores (r= 0.2138,P= 0.0263).

Conclusions

This abnormal decreased GMV in the sensorimotor cortex provides evidence for a sensory processing disorder in RLS that may be involved in the pathogenesis of RLS in HD patients.
Coronary Sinus Diameter to Inferior Vena Cava Diameter Ratio in the Diagnosis of Cardiac Tamponade: A Novel Approach
Authors: Ozcan Cetin Elif Hande , Cetin Mehmet Serkan , Könte Hasan Can , Tak Bahar Tekin , Ekizler Firdevs Aysenur , Ozcan Fırat , Cay Serkan , Ozeke Ozcan , Akcay Burak , Topaloglu Serkan , Aras Dursun
Published: July 2020

Background

In cardiac tamponade, coronary sinus (CS) as an intrapericardial structure can be easily compressed, whereas inferior vena cava (IVC) dilates. This inverse relationship may augment their roles in the evaluation of tamponade imaging.

Aim

We assessed the usefulness of computerized tomographic measures of CS diameter and also CS/IVC ratio to predict tamponade in clinically stable patients with large pericardial effusion.

Methods

Sixty-six clinically stable patients who had large pericardial effusions were included. Coronary sinus diameter was measured from the point at 1 cm proximal to the CS ostium. Inferior vena cava diameter was measured from the segment between its right atrial orifice and hepatic vein.

Results

Patients with tamponade had smaller CS diameter and CS/IVC ratio. After adjusting with other parameters, only either CS diameter or CS/IVC ratio predicted tamponade, respectively. (Nagelkerke r
2 value for CS was 53.7% and 72.1% for CS/IVC ratio). In Receiver Operating Characteristic Curve analysis, a cutoff value of 6.85 mm for CS diameter had 82.6% sensitivity and 83.7% specificity and a cutoff value of 27% for CS/IVC ratio had 87.0% sensitivity and 86.0% specificity for predicting cardiac tamponade.

Conclusions

The tomographic measures of both the CS diameter and the CS/IVC ratio predicted tamponade in clinically stable patients with large pericardial effusion. Compared with CS diameter, CS/IVC ratio seemed to be a more powerful predictor of tamponade.
Foot stiffening during the push-off phase of human walking is linked to active muscle contraction, and not the windlass mechanism
Authors: Farris Dominic James , Birch Jonathon , Kelly Luke
Published: July 2020

The rigidity of the human foot is often described as a feature of our evolution for upright walking and is bolstered by a thick plantar aponeurosis that connects the heel to the toes. Previous descriptions of human foot function consider stretch of the plantar aponeurosis via toe extension (windlass mechanism) to stiffen the foot as it is levered against the ground for push-off during walking. In this study, we applied controlled loading to human feet
in vivo
, and studied foot function during the push-off phase of walking, with the aim of carefully testing how the foot is tensioned during contact with the ground. Both experimental paradigms revealed that plantar aponeurosis strain via the ‘windlass mechanism' could not explain the tensioning and stiffening of the foot that is observed with increased foot-ground contact forces and push-off effort. Instead, electromyographic recordings suggested that active contractions of ankle plantar flexors provide the source of tension in the plantar aponeurosis. Furthermore, plantar intrinsic foot muscles were also contributing to the developed tension along the plantar aspect of the foot. We conclude that active muscular contraction, not the passive windlass mechanism, is the foot's primary source of rigidity for push-off against the ground during bipedal walking.
Hansschlegelia quercus sp. nov., a novel methylotrophic bacterium isolated from oak buds
Authors: Agafonova Nadezhda V. , Kaparullina Elena N. , Grouzdev Denis S. , Doronina Nina V.
Published: July 2020

Novel aerobic, restricted facultatively methylotrophic bacteria were isolated from buds of English oak (Quercus roburL.; strain DubT) and northern red oak (Quercus rubraL.; strain KrD). The isolates were Gram-negative, asporogenous, motile short rods that multiplied by binary fisson. They utilized methanol, methylamine and a few polycarbon compounds as carbon and energy sources. Optimal growth occurred at 25 °C and pH 7.5. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phoshatidylglycerol. The major cellular fatty acids of cells were C18 : 1 ω7c, 11-methyl C18 : 1 ω7cand C16 : 0. The major ubiquinone was Q-10. Analysis of 16S rRNA gene sequences showed that the strains were closely related to the members of the genusHansschlegelia:Hansschlegelia zhihuaiaeS113T(97.5–98.0 %),Hansschlegelia plantiphilaS1T(97.4–97.6 %) andHansschlegelia beijingensisPG04T(97.0–97.2 %). The 16S rRNA gene sequence similarity between strains DubTand KrD was 99.7 %, and the DNA–DNA hybridization (DDH) result between the strains was 85 %. The ANI and the DDH values between strain DubTandH. zhihuaiaeS113Twere 80.1 and 21.5  %, respectively. Genome sequencing of the strain DubTrevealed a genome size of 3.57 Mbp and a G+C content of 67.0 mol%. Based on the results of the phenotypic, chemotaxonomic and genotypic analyses, it is proposed that the isolates be assigned to the genusHansschlegeliaasHansschlegelia quercussp. nov. with the type strain DubT(=VKM B-3284T=CCUG 73648T=JCM 33463T).
A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a
Authors: Firth Andrew E.
Published: July 2020

Identification of the full complement of genes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high-throughput experimental approaches – such as ribosome profiling – cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV-2 and related viruses (subgenus Sarbecovirus) and correlating the results with the conserved presence of an open reading frame (ORF) and a plausible translation mechanism, a putative new gene – ORF3c – was identified. ORF3c overlaps ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection. ORF3c is conserved across the subgenus Sarbecovirus, and encodes a 40–41 amino acid predicted transmembrane protein.
Increased serum levels of soluble TNF-α receptor is associated with mortality of ICU COVID-19 patients
Authors: Mortaz Esmaeil , Tabarsi Payam , Jamaati Hamidreza , Roofchayee Neda Dalil , K.Dezfuli Neda , Hashemian Seyed Mohamadreza , Moniri Afshin , Marjani Majid , Malkmohammad Majid , Mansouri Davood , Varahram Mohammad , Folkerts Gert , Adcock Ian M
Published: July 2020

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has spread to almost 100 countries, infected over 10M patients and resulted in 505K deaths worldwide as of 30thJune 2020. The major clinical feature of severe COVID-19 requiring ventilation is acute Respiratory Distress Syndrome (ARDS) with multi-functional failure as a result of a cytokine storm with increased serum levels of cytokines such as TNF-α and IL-6 being reported. TNF-α levels are increased during the cytokine storm in very ill patients and soluble receptors for IL-6 and IL-2 are present in the blood of COVID-19 patients,

Objectives

To elucidate the involvement of serum levels of soluble TNF-Receptor of severe and mild COVID-19 patients to determine for severity of disease.

Method

We recruited16 severe COVID-19 patients in the ICU on ventilator support and 26 milder COVID-19 patients who were hospitalised but not within the intensive care unit (ICU) between March-May 2020 at the Masih Daneshvari Hospital Tehran, Iran. After harvesting of whole blood the serum was isolated and soluble TNF-Receptor levels measured by ELISA.

Results

Serum levels of the usually inhibitory soluble TNF-α receptor 1 (sTNFαR1) were significantly elevated in severe COVID-19 patients at admission to ICU. High serum levels of sTNFαR1 were associated with mortality of severe COVID-19 patients treated within ICU.

Conclusions

This pilot study demonstrates for role of STNF-αR1 receptor in severity of disease. Future studies should examine whether lower levels of systemic sTNFαR1 at admission may indicate a better disease outcome.
Association between epidemic dynamics of Covid-19 infection and ABO blood group types
Authors: Liu Yuefei , Häussinger Lisa , Steinacker Jürgen M. , Dinse-Lambracht Alexander
Published: July 2020

Background

Covid-19 pandemic is the most critical challenge nowadays for the manhood, and the infection and death cases are still speedily increasing. Since there are no available vaccine and specifically effective treatment, to break the infectious way of the pandemic remains the unique measure to efficiently combat Covid-19 infection. Understanding factors that affect the Covid-19 infection can help make better balance between activity restriction and infection dynamics. This study sought to investigate association between Covid-19 infection and blood type distribution.

Methods

The big data provided by World Health Organization and Johns Hopkins University were taken to assess epidemic dynamics of Covid-19 infection. Growth rate and doubling time of infection and death cases, reproductive number, infection and death cases in the mid-exponential phase were analyzed in relation to blood type distribution.

Results

Growth rate of infection and death cases correlated significantly to blood type A proportion of the population positively while to blood type B proportion negatively. In comparison with lower blood type A population (< 30%) people with higher blood type A (≥ 30%) had more infection and death cases in the early exponential phase, higher growth rates, and shorter case doubling time for infection and death.

Discussion

Covid-19 infection is significantly associated with blood type distribution and people with blood type A are more susceptible to Covid-19 infection and have higher epidemic dynamics and higher case fatality rate. The results of this study provide important and useful information for fighting Covid-19 pandemic.
Association between health-related hope and adherence to prescribed treatment in CKD patients: multicenter cross-sectional study
Authors: Kurita Noriaki , Wakita Takafumi , Ishibashi Yoshitaka , Fujimoto Shino , Yazawa Masahiko , Suzuki Tomo , Koitabashi Kenichiro , Yanagi Mai , Kawarazaki Hiroo , Green Joseph , Fukuhara Shunichi , Shibagaki Yugo
Published: July 2020

Background

In chronic kidney disease (CKD), patients’ adherence to prescriptions for diet and for medications might depend on the degree to which they have hope that they will enjoy life, and that hope could vary with the stage of CKD. The aims of this study were to quantify both the association of CKD stage with health-related hope (HR-Hope), and the association of that hope with psychological and physiological manifestations of adherence.

Methods

This was a cross-sectional study involving 461 adult CKD patients, some of whom were receiving dialysis. The main exposure was HR-Hope, measured using a recently-developed 18-item scale. The outcomes were perceived burden of fluid restriction and of diet restriction, measured using the KDQOL, and physiological manifestations of adherence (systolic and diastolic blood pressure [BP], and serum phosphorus and potassium levels).

General linear models and generalized ordered logit models were fit.

Results

Participants at non-dialysis stage 4 and those at stage 5 had lower HR-Hope scores than did those at stage 2 or 3 (combined). Those at non-dialysis stage 5 had the lowest scores. HR-Hope scores of participants at stage 5D were similar to those of participants at stage 4, but they were lower than the scores of participants at stage 2 or 3 (combined). Higher HR-Hope scores were associated with lower perceived burdens of fluid restriction and of diet restriction (adjusted ORs per ten-point difference were 0.82 and 0.84, respectively). Higher HR-Hope scores were associated with lower systolic BP (adjusted mean difference in systolic BP per ten-point difference in HR-Hope scores was -1.87 mmHg). In contrast, HR-Hope scores were not associated with diastolic BP, serum phosphorus levels, or serum potassium levels.

Conclusions

Among CKD patients, HR-Hope is associated with disease stage, with psychological burden, and with some physiological manifestations of adherence.
Work-related and Personal Predictors of COVID-19 Transmission
Authors: Anand Paul , Allen Heidi , Ferrer Robert , Gold Natalie , Gonzales Martinez Rolando Manuel , Kontopantelis Evan , Krause Melanie , Vergunst Francis
Published: July 2020

The paper provides new evidence from a survey of 2000 individuals in the US and UK related to predictors of Covid-19 transmission. Specifically, it investigates work and personal predictors of transmission experience reported by respondents using regression models to better understand possible transmission pathways and mechanisms in the community. Three themes emerge from the analysis. Firstly, transport roles and travelling practices are significant predictors of infection. Secondly, evidence from the US especially shows union membership, consultation over safety measures and the need to use public transport to get to work are also significant predictors. This is interpreted as evidence of the role of deprivation and of reactive workplace consultations. Thirdly and finally, there is some, often weaker, evidence that income, car-owership, use of a shared kitchen, university degree type, risk-aversion, extraversion and height are predictors of transmission. The comparative nature of the evidence indicates that the less uniformly stringent nature of the US lockdown provides more information about both structural and individual factors that predict transmission. The evidence about height is discussed in the context of the aerosol transmission debate. The paper concludes that both structural and individual factors must be taken into account when predicting transmission or designing effective public health measures and messages to prevent or contain transmission.

JEL Codes

I1 I12 I14 I18
Climate & BCG: Effects on COVID-19 Death Growth Rates
Authors: Finlay Chris , Bassett Bruce A.
Published: July 2020

Multiple studies have suggested the spread of COVID-19 is affected by factors such as climate, BCG vaccinations, pollution and blood type. We perform a joint study of these factors using the death growth rates of 40 regions worldwide with both machine learning and Bayesian methods. We find weak, non-significant (< 3σ) evidence for temperature and relative humidity as factors in the spread of COVID-19 but little or no evidence for BCG vaccination prevalence or PM2.5 pollution. The only variable detected at a statistically significant level (>3σ) is the rate of positive COVID-19 tests, with higher positive rates correlating with higher daily growth of deaths.
Analysis of COVID-19 cases and associated ventilator requirement in Indian States
Authors: Dhanya V , Anitha R , Kishan Ashwini Kumar , Sumathi S R , Roy Amrit
Published: July 2020

Analysis of COVID-19 cases and prediction of quantity of associated ventilator requirement is very relevant during this pandemic. This paper presents a method for predictive estimation of ventilator requirement for COVID-19 patients in Indian states. It uses ARIMA (Autoregressive Integrated Moving Average) model for predicting the future cumulative cases and daily fatality. Taking cue from this, ventilator requirement is estimated for each state. State wise estimation of ventilator is important because public healthcare system in India is managed at state level. Dataset on Novel Corona Disease 2019 in India from Kaggle website is used in this work.
Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity
Authors: Montague Zachary , Lv Huibin , Otwinowski Jakub , DeWitt William S. , Isacchini Giulio , Yip Garrick K. , Ng Wilson W. , Tsang Owen Tak-Yin , Yuan Meng , Liu Hejun , Wilson Ian A. , Peiris J. S. Malik , Wu Nicholas C. , Nourmohammad Armita , Mok Chris Ka Pun
Published: July 2020

COVID-19 patients show varying severity of the disease ranging from asymptomatic to requiring intensive care. Although a number of SARS-CoV-2 specific monoclonal antibodies have been identified, we still lack an understanding of the overall landscape of B-cell receptor (BCR) repertoires in COVID-19 patients. Here, we used high-throughput sequencing of bulk and plasma B-cells collected over multiple time points during infection to characterize signatures of B-cell response to SARS-CoV-2 in 19 patients. Using principled statistical approaches, we determined differential features of BCRs associated with different disease severity. We identified 38 significantly expanded clonal lineages shared among patients as candidates for specific responses to SARS-CoV-2. Using single-cell sequencing, we verified reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identified natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in a number of patients. Our results provide important insights for development of rational therapies and vaccines against COVID-19.
Asthma in COVID-19: An extra chain fitting around the neck?
Authors: Hussein Mohammad Hosny , Toraih Eman Ali , Attia Abdallah S , Youssef Mohanad , Omar Mahmoud , Burley Nicholas , Zhang Allen D. , Roos Jackson , Houghton August , Aniemeka Nedum , Shama Mohamed Ahmed , Duchesne Juan , Kandil Emad
Published: July 2020

Introduction

The novel coronavirus disease 2019 (COVID-19) has rapidly spread across the globe, overwhelming healthcare systems and depleting resources. The infection has a wide spectrum of presentations, and pre-existing comorbidities have been found to have a dramatic effect on the disease course and prognosis. We sought to analyze the effect of asthma on the disease progression and outcomes of COVID-19 patients.

Methods

We conducted a multi-center retrospective study of positively confirmed COVID-19 patients from multiple hospitals in Louisiana. Demographics, medical history, comorbidities, clinical presentation, daily laboratory values, complications, and outcomes data were collected and analyzed. The primary outcome of interest was in-hospital mortality. Secondary outcomes were Intensive Care Unit (ICU) admission, risk of intubation, duration of mechanical ventilation, and length of hospital stay.

Results

A total of 502 COVID-19 patients (72 asthma and 430 non-asthma cohorts) were included in the study. The frequency of asthma in hospitalized cohorts was 14.3%, higher than the national prevalence of asthma (7.7%). Univariate analysis revealed that asthma patients were more likely to be obese (75% vs 54.2%,p=0.001), with higher frequency of intubation (40.3% vs 27.8%,p= 0.036), and required longer duration of hospitalization (15.1±12.5 vs 11.5±10.6,p=0.015). After adjustment, multivariable analysis showed that asthmatic patients were not associated with higher risk of ICU admission (OR=1.81, 95%CI=0.98-3.09,p=0.06), endotracheal intubation (OR=1.77, 95%CI=0.99-3.04,p=0.06) or complications (OR=1.37, 95%CI=0.82-2.31,p=0.23). Asthmatic patients were not associated with higher odds of prolonged hospital length of stay (OR=1.48, 95%CI=0.82-2.66, p=0.20) or with the duration of ICU stay (OR=0.76, 95%CI=0.28-2.02,p=0.58). Kaplan-Meier curve showed no significant difference in overall survival of the two groups (p=0.65).

Conclusion

Despite the increased prevalence of hospitalization in asthmatic COVID-19 patients compared to the general population, after adjustment for other variables, it was neither associated with increased severity nor worse outcomes.
Consistent Consideration of RNA Structural Alignments Improves Prediction Accuracy of RNA Secondary Structures
Authors: Tagashira Masaki
Published: July 2020

The probabilistic consideration of the global pairwise sequence alignment of two RNAs tied with their global single secondary structures, or global pairwise structural alignment, is known to predict more accurately global single secondary structures of unaligned homologs by discriminating between conserved local single secondary structures and those not conserved. However, conducting rigorously this consideration is computationally impractical and thus has been done to decompose global pairwise structural alignments into their independent components, i.e. global pairwise sequence alignments and single secondary structures, by conventional methods. ConsHomfold and ConsAlifold, which predict the global single and consensus secondary structures of unaligned and aligned homologs considering consistently preferable (or sparse) global pairwise structural alignments on probability respectively, were developed and implemented in this study. These methods demonstrate the best trade-off of prediction accuracy while exhibiting comparable running time compared to conventional methods. ConsHomfold and ConsAlifold optionally report novel types of loop accessibility, which are useful for the analysis of sequences and secondary structures. These accessibilities are average on sparse global pairwise structural alignment and can be computed to extend the novel inside-outside algorithm proposed in this study that computes pair alignment probabilities on this alignment.
SmartPeak automates targeted and quantitative metabolomics data processing
Authors: Kutuzova Svetlana , Colaianni Pasquale , Röst Hannes , Sachsenberg Timo , Alka Oliver , Kohlbacher Oliver , Burla Bo , Torta Federico , Schrübbers Lars , Kristensen Mette , Nielsen Lars , Herrgård Markus J. , McCloskey Douglas
Published: July 2020

SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments.

Highlights

Novel algorithms for retention time alignment, calibration curve fitting, and peak integration

Enables reproducibility by reducing operator bias and ensuring high QC/QA

Automated pipeline for high throughput targeted and/or quantitative metabolomics, lipidomics, and fluxomics data processing from multiple analytical instruments

Manually curated data set of LC-MS/MS, GC-MS, and HPLC integrated peaks for further algorithm development and benchmarking
Prediction of Direct Carbon Emissions of Chinese Provincial Residents under Artificial Neural Networks in Deep Learning Environment
Authors: Hui Jin
Published: July 2020

It is aimed to deepen the understanding of the consumption carbon emissions of Chinese provinces, establish an accurate and feasible carbon emission prediction model, develop an urban low-carbon economy, and ensure the sustainable development of Chinese cities. Through the national statistical data information, based on the artificial neural network model, mathematical statistics and deep learning methods are used to learn and analyze the carbon emission data of various provinces in China from 1999 to 2019. The neural network toolbox in Matlab is used to program separately to realize the prediction of carbon emissions by different neural network models. After comparing and analyzing the accuracy and prediction performance, the optimal model for the prediction effect is selected. Finally, based on ArcGIS Engine (Arc Geographic Information Science Engine) and C#.NET platform, the call to Matlab neural network toolbox is realized. The selected model is embedded in the prediction system to complete the development of the entire system. The results show that the carbon emissions of residents in the north are distinctly higher than those in the south. Also, with the passage of time, the rate of carbon emissions continues to accelerate. Compared with other models, Elman neural network has higher accuracy and smaller error in carbon emission prediction. Compared to BP (Back Propagation) neural network, the accuracy is improved by 55.93%, and the prediction performance is improved by 19.48%. The prediction results show that China is expected to reach the peak of carbon emissions from 2027 to 2032. This investigation will provide a theoretical basis to control and plan carbon emissions from Chinese urban residents.
Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites
Authors: Stewart Lindsay B. , Diaz-Ingelmo Ofelia , Claessens Antoine , Abugri James , Pearson Richard D. , Goncalves Sonia , Drury Eleanor , Kwiatkowski Dominic P. , Awandare Gordon A. , Conway David J.
Published: July 2020

Pathogen multiplication rate is theoretically an important determinant of virulence, although often poorly understood. We show intrinsic multiplication rate variation of the major human malaria parasitePlasmodium falciparumto be associated with blood-stage infection intensity. A panel of clinical isolates from a highly endemic West African population was analysed repeatedly during five months of continuous culture, showing a range of exponential multiplication rates at all timepoints tested, mean rates increasing over time. All isolates had different genome sequences, many containing within-isolate diversity that decreased over time, but increases in multiplication rates were not primarily attributable to genomic selection. New mutants, including premature stop codons emerging in a few isolates, did not attain sufficiently high frequencies to substantially affect overall multiplication rates. Significantly, multiplication rate variation at each of the cultured timepoints robustly correlated with parasite levels in patients at clinical presentation, indicating parasite control of multiplication that contributes to virulence.
CB1R Regulates Soluble Leptin Receptor Levels via CHOP, Contributing to Hepatic Leptin Resistance
Authors: Drori Adi , Gammal Asaad , Azar Shahar , Hinden Liad , Hadar Rivka , Wesley Daniel , Nemirovski Alina , Szanda Gergő , Salton Maayan , Tirosh Boaz , Tam Joseph
Published: July 2020

The soluble isoform of leptin receptor (sOb-R), secreted by the liver, regulates leptin bioavailability and bioactivity. Its reduced levels in diet-induced obesity (DIO) contributes to hyperleptinemia and leptin resistance, effects that are known to be regulated by the endocannabinoid (eCB)/CB1R system. Here we show that pharmacological activation/blockade as well as genetic overexpression/deletion of hepatic CB1R modulates sOb-R levels and consequently hepatic leptin resistance. Interestingly, peripheral CB1R blockade failed to reverse DIO-induced reduction of sOb-R levels, fat mass, dyslipidemia, and hepatic steatosis in mice lacking C/EBP homologous protein (CHOP), whereas direct activation of CB1R in hepatocytes reduced sOb-R levels in a CHOP-dependent manner. Moreover, CHOP stimulation increased sOb-R expression and release via a direct regulation of its promoter, while CHOP deletion reduced leptin sensitivity. Our findings highlight a novel molecular aspect by which the hepatic eCB/CB1R system involves in the development of hepatic leptin resistance by regulating sOb-R levels via CHOP.

Here we describe a novel molecular aspect by which the hepatic endocannabinoid/CB1R system contributes to hepatic leptin resistance by regulating soluble leptin receptor levels via CHOP.
Classification of ovarian cancer cell lines using transcriptional profiles defines the five major pathological subtypes
Authors: Barnes B. M. , Nelson L. , Tighe A. , Morgan R. D. , McGrail J. , Taylor S. S.
Published: July 2020

Epithelial ovarian cancer (EOC) is a heterogenous disease consisting of five major pathologically distinct subtypes: High-grade serous ovarian carcinoma (HGSOC), low-grade serous (LGS), endometrioid, clear cell and mucinous carcinoma. Although HGSOC is the most prevalent subtype, representing approximately 75% of cases, a 2013 landmark study from Domckeet al., found that many frequently used ovarian cancer cell lines were not genetically representative of HGSOC tissue samples from The Cancer Genome Atlas. Although this work subsequently identified several rarely used cell lines to be highly suitable as HGSOC models, cell line selection for ovarian cancer research does not appear to have altered substantially in recent years. Here, we find that application of non-negative matrix factorisation (NMF) to the transcriptional profiles of 45 commonly used ovarian cancer cell lines exquisitely clusters them into five distinct classes, representative of the five main subtypes of EOC. This methodology was in strong agreement with Domckeet al., in identification of cell lines most representative of HGSOC. Furthermore, this robust classification of cell lines, including some previously not annotated or miss-annotated in the literature, now informs selection of the most appropriate models for all five pathological subtypes of ovarian cancer. Furthermore, using machine learning algorithms trained using the classification of the current cell lines, we are able provide a methodology for future classification of novel EOC cell lines.