bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the Intensive Care Patient Experience With Virtual Reality—A Feasibility Study
Authors: Ong Triton L. , Ruppert Matthew M. , Akbar Maisha , Rashidi Parisa , Ozrazgat-Baslanti Tezcan , Bihorac Azra , Suvajdzic Marko
Published: June 2020

Objectives:

Patients’ stays in the ICU are often characterized by prolonged immobility, sedation, disrupted sleep, and extended periods of pain, which put ICU patients at greater risk for ICU-acquired weakness and delirium-related mortality. The aim of this study was to evaluate the feasibility and efficacy of using meditative virtual reality to improve the hospital experience of ICU patients.

Design:

Final report of prospective observational trial.

Setting:

Surgical and trauma ICUs of the University of Florida Health, an academic hospital.

Patients:

Fifty-nine nonintubated adult ICU patients without delirium at recruitment.

Interventions:

Patients were exposed to sessions of commercially available meditative virtual reality applications focused on calmness and relaxation, performed once daily for up to 7 days.

Measurements and Main Results:

Outcome measures included pain level, pain medication administration, anxiety, depression, sleep quality, heart rate, respiratory rate, blood pressure, delirium status, and patient ratings of the virtual reality system. Comparisons were made using paired t tests and mixed models. The virtual reality meditative intervention improved patients’ ICU experience with reduced levels of anxiety and depression; however, there was no evidence that virtual reality had significant effects on physiologic measures, pain, or sleep.

Conclusions:

The use of meditative virtual reality technology in the ICU was easily implemented and well-received by patients.
Electrocardiographic and Echocardiographic Findings in Ghanaian Female Soccer Players
Authors: Pambo Prince , Adu-Adadey Martin , Ankrah Patrina Takyi , Agbodzakey Hope , Scharhag Jürgen
Published: June 2020

Objective:

To examine the heart of Ghanaian adult and adolescent female soccer players using electrocardiography (ECG) and echocardiography (ECHO), and to describe typical ECG and ECHO findings in a cohort of west African female soccer players.

Design:

Cross-sectional study of ECG and ECHO performed as part of precompetition medical assessment for 3 national female football teams preparing for various Fédération Internationale de Football Association (FIFA) tournaments in 2016.

Setting:

Ghana National Football Association.

Participants:

Seventy-five female players playing for the National female football teams preparing for FIFA tournaments in 2016.

Interventions:

Precompetition medical assessment using ECGs and ECHOs.

Main Outcome Measure:

Number of athletes with abnormal ECG and ECHO findings using the International ECG Interpretation criteria.

Results:

Eight percent of the participants had T-wave inversions in lateral leads (V5–V6). Voltage criteria for left ventricular hypertrophy (LVH) were present in 35% of participants. A total of 2.7% of the players had LV wall thickness (LVWT) ≥12 mm with no player exceeding 13 mm. No player had LV cavity dimension greater than 60 mm.

Conclusion:

Ghanaian female soccer players seem to have a high prevalence of LVH and repolarization change. Although LVWT up to 12 mm might be normal in this cohort, deep T-wave inversions and LVWT ≥13 mm should always be further investigated and/or undergo a long-term follow.
Predictive Factors of Fall-Related Activity Avoidance in People With Parkinson Disease—A Longitudinal Study With a 3-Year Follow-up
Authors: Nilsson Maria H. , Jonasson Stina B. , Zijlstra G. A. Rixt
Published: June 2020

Background and Purpose:

Knowledge of predictive factors can foster the development of preventive approaches. This study examined how prevalence and severity of fall-related activity avoidance evolve over a 3-year period in people with Parkinson disease (PD). A specific aim was to identify predictive factors of fall-related activity avoidance (ie, modified Survey of Activities and Fear of Falling in the Elderly [mSAFFE] scores) after 3 years.

Methods:

The sample included 151 people with PD (mean [SD] age: 68 [8.8] years). The mSAFFE score was the dependent variable in multivariable linear regression analyses, with 17 potential predictors. On the basis of a collinearity check, 2 models studying various risk factors were developed. Model 1 included concerns about falling and model 2 walking difficulties.

Results:

After 3 years, more participants reported fall-related activity avoidance, that is, 34% versus 50% (P < 0.001). Regression model 1 explained 63% of the variance. The strongest predictive factor was concerns about falling (standardized regression coefficient, β = 0.589), followed by pain (β = 0.161), unsteadiness while turning (β = 0.137), and age (β = 0.136). These variables remained significant when adjusting for mSAFFE baseline scores.

In model 2 (explained 50% of the variance), the strongest predictive factor was perceived walking difficulties (β = 0.392), followed by age (β = 0.238), unsteadiness while turning (β = 0.198), and pain (β = 0.184). Unlike the other factors, walking difficulties were not significant when adjusting for mSAFFE baseline scores.

Discussion and Conclusions:

Fall-related activity avoidance increased over time in people with PD. If fall-related activity avoidance is to be targeted, this study suggests that interventions should address concerns about falling, pain, unsteadiness while turning, and walking difficulties.

Video Abstract available for more insights from the authors (see Video, Supplemental Digital Content 1, http://links.lww.com/JNPT/A310).
Improving Spatiotemporal Gait Asymmetry Has Limited Functional Benefit for Individuals Poststroke
Authors: Ryan Hannah P. , Husted Carty , Lewek Michael D.
Published: June 2020

Background and Purpose:

Prior literature suggests a relationship between spatiotemporal gait asymmetry and metabolic cost of walking, balance, endurance, quality of life, and physical activity in people with chronic stroke. Our purpose was to determine whether targeting spatiotemporal gait symmetry would concomitantly improve these measures.

Methods:

This study represents secondary outcome measures from a trial in which 48 participants with chronic stroke were randomized to groups that all targeted spatiotemporal gait asymmetry. Measures of balance, daily step count, endurance (6-minute walk test [6MWT), metabolic cost of walking, quality of life (Stroke Impact Scale [SIS]), and overground spatiotemporal asymmetries were collected 1 week prior to and following training. Separate analyses were performed for those who trained for spatial versus temporal asymmetry. The effect of time (pre/post) was examined for all measures and correlational analyses evaluated the potential relationships between changes in spatiotemporal asymmetry and all other measures.

Results:

Individuals who trained to target step length asymmetry improved balance, 6MWT distance, metabolic cost of walking, and SIS-Mobility. Individuals who trained to target stance time asymmetry improved balance, 6MWT distance, SIS-Mobility, and SIS-Global recovery scores. However, step length asymmetry improvements were only related to improved 6MWT distance (P = 0.025; r = −0.49). Stance time asymmetry improvements were only related to improved metabolic cost of walking (P = 0.031; r = 0.558).

Discussion and Conclusions:

Despite a targeted training approach and noted improvements in most measures, these changes did not appear to arise from improved spatiotemporal gait asymmetry. Furthermore, improvements in gait function observed in the laboratory setting did not appear to translate to increased community mobility.

Video Abstract available for more insights from the authors (see the Video, Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A316).
Pseudomonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica)
Authors: Jang Gwang Il , Lee Inae , Ha Tran Thu , Yoon Soo Jung , Hwang Yeon Ju , Yi Hana , Yun Sukyoung , Lee Won Sang , Hwang Chung Yeon
Published: June 2020

Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated SSM26Tand SSM44, were isolated from a sea surface microlayer sample from the Ross Sea, Antarctica. Analysis of the 16S rRNA gene sequences of strains SSM26Tand SSM44 revealed a clear affiliation with the genusPseudomonas. Based on the results of phylogenetic analysis, strains SSM26Tand SSM44 showed the closest phylogenetic relationship with the speciesPseudomonas sabulinigriKCTC 22137Twith the 16S rRNA gene sequence similarity level of 98.5 %. Strains SSM26Tand SSM44 grew optimally at 30 °C, pH 7.0–7.5 and 0.5–10.0 % NaCl (w/v). The major cellular fatty acids were C18 : 1 ω7c(31.3–34.9 %), C16 : 0(15.5–20.2 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 19.5–25.4 %) and C12 : 0(6.0–9.3 %). The genomic DNA G+C content of each strain was 56.2 mol%. Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strains SSM26Tand SSM44 constituted a single species that was clearly distinguishable from its phylogenetically close relatives. The combined phenotypic, chemotaxonomic, genomic and phylogenetic data also showed that strains SSM26Tand SSM44 could be distinguished from validly published members of the genusPseudomonas. Thus, these strains should be classified as representing a novel species in the genusPseudomonas, for which the namePseudomonas neustonicasp. nov. is proposed with the type strain SSM26T(=KCCM 43193T=JCM 31284T=PAMC 28426T) and a sister strain SSM44 (=KCCM 43194=JCM 31285=PAMC 28427).
Shewanella insulae sp. nov., isolated from a tidal flat
Authors: Park Sooyeon , Kim In Kyu , Kim Wonyong , Yoon Jung-Hoon
Published: June 2020

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M18T, was isolated from tidal-flat sediment collected from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M18T fell within the clade comprising the type strains of

Shewanella

species. Strain JBTF-M18T exhibited 16S rRNA gene sequence similarity values of 97.1–98.8 % to the type strains of

S. loihica

,

S. aquimarina

,

S. waksmanii

and

S. marisflavi

and of less than 96.9 % to the type strains of the other

Shewanella

species. The average nucleotide identity and digital DNA–DNA hybridization values between strain JBTF-M18T and the type strains of

S. waksmanii

and

S. loihica

were 72.0 and 89.5% and 18.9 and 38.1 %, respectively. DNA–DNA relatedness values between strain JBTF-M18T and the type strains of

S. aquimarina

and

S. marisflavi

were 14 and 19 %, respectively. The DNA G+C content of strain JBTF-M18T from genomic sequence data was 52.9 %. Strain JBTF-M18Tcontained MK-6 as the predominant menaquinone and Q-7 and Q-8 as the predominant ubiquinones. It had iso-C15 : 0, summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain JBTF-M18T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M18T is separated from recognized

Shewanella

species. On the basis of the data presented, strain JBTF-M18T is considered to represent a novel species of the genus

Shewanella

, for which the name Shewanella insulae sp. nov. is proposed. The type strain is JBTF-M18T (=KACC 19869T=NBRC 113583T).
Lysobacter profundi sp. nov., isolated from freshwater sediment and reclassification of Lysobacter panaciterrae as Luteimonas panaciterrae comb. nov.
Authors: Jin Chun-Zhi , Song Xiuli , Sung Yun Ju , Jin Feng-Jie , Li Taihua , Oh Hee-Mock , Lee Hyung-Gwan , Jin Long
Published: June 2020

A polyphasic taxonomic study was carried out on strains CHu50b-3-2T and CHu40b-3-1 isolated from a 67 cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of the strains were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of two strains with γ-Proteobacteria, which showed the highest pairwise sequence similarities to

Lysobacter hankyongensis

KTce-2T (96.5 %),

Lysobacter pocheonensis

Gsoil193T (96.3 %),

Lysobacter ginsengisoli

Gsoil 357T (96.1 %),

Lysobacter solanacearum

T20R-70T (96.1 %),

Lysobacter brunescens

KCTC 12130T (95.4 %) and

Lysobacter capsici

YC5194T (95.3 %). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus

Lysobacter

. The major fatty acids were identified as summed feature 9 (iso-C17 : 1
 ω9c and/or C18 : 1 10-methyl), iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The respiratory quinone was identified as ubiquinone Q-8. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was determined to be 66.8 mol% (genome) for strain CHu50b-3-2T and 66.4 mol% (HPLC) for strain CHu40b-3-1. Based on the combined genotypic and phenotypic data, we propose that strains CHu50b-3-2T and CHu40b-3-1 represent a novel species of the genus

Lysobacter

, for which the name Lysobacter profundi sp. nov. is proposed. The type strain is CHu50b-3-2T (=KCTC 72973T=CCTCC AB 2019129T). Besides

Lysobacter panaciterrae

Gsoil 068T formed a phylogenetic group together with strain

Luteimonas aquatica

RIB1-20T (EF626688) that is clearly separated from all other known

Lysobacter

strains. Based on the phylogenetic relationships together with fatty acid compositions,

Lysobacter panaciterrae

Gsoil 068T should be reclassified as a member of the genus Luteimonas: Luteimonas aquatica comb. nov. (type strain Gsoil 068T=KCTC 12601T=DSM 17927T).
Massilia arenosa sp. nov., isolated from the soil of a cultivated maize field
Authors: Raths Rachel , Peta Vincent , Bücking Heike
Published: June 2020

Strain MC02T, a Gram-stain-negative, rod-shaped bacterium, was isolated from field soil collected from California, USA. To examine if MC02Trepresents a novel species, we compared its colony morphology, 16S rRNA gene and whole genome sequence, and its metabolic phenotype using Biolog GenIII and MALDI-TOF analyses compared to reference strains. Based on 16S rRNA gene and whole genome sequencing, MC02Tbelongs to the genusMassiliaandMassilia agriK-3–1Tis the most similar strain with 96.97 % 16S rRNA gene sequence identity. MALDI-TOF analysis revealed thatMassilia aerilataDSM19289Tis the closest match, but the similarity score was much lower than the ≥1.7 threshold for a reliable identification at the genus level. The predominant fatty acids were summed feature 3 (C16 : 1⍵7cand/or C16 : 1⍵6c; 49.07 %) and C16 : 0(30.01 %). The genome is 5.02 Mbp and the G+C content is 66.2 mol%. Whole genome comparisons to the closest related strains revealed an average amino acid identity value of 67.4 %, an OrthoANI similarity of 77.1 %, and a DNA–DNA-hybridization probability ≥70 %, confirming that MC02Trepresents a novel species. Strain MC02Tcan grow at pH 6 but not at pH 5, and a salt concentration of ≥1 % inhibits its growth. In contrast to otherMassiliastrains, MC02Tcan utilize turanose, inosine andl-serine. The genome of MC02Tshows putative endophyte genes such as a nitrate reductase, several phosphatases, and biotin biosynthesis genes, 26 flagellar motility genes and 14 invasion and intracellular resistance genes. Based on its metabolic, physiological and genomic characteristics, we propose that strain MC02T(NRRL B-65554T=ATCC TSD-200T=LMG 31737T) represents a novel species of the genusMassiliawith the nameMassilia arenosasp. nov.
Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies
Authors: Gurney James , Azimi Sheyda , Brown Sam P. , Diggle Stephen P.
Published: June 2020

In the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing (QS) is a social trait that is exploitable by non-cooperating cheats. Previously it has been shown that by linking QS to the production of both public and private goods, cheats can be prevented from invading populations of cooperators and this was described by Dandekar et al. (Science 2012;338:264–266) as ‘a metabolic incentive to cooperate’. We hypothesized that

P. aeruginosa

could evolve novel cheating strategies to circumvent private goods metabolism by rewiring its combinatorial response to two QS signals (3O-C12-HSL and C4-HSL). We performed a selection experiment that cycled

P. aeruginosa

between public and private goods growth media and evolved an isolate that rewired its control of cooperative protease expression from a synergistic (AND-gate) response to dual-signal input to a 3O-C12-HSL-only response. We show that this isolate circumvents metabolic incentives to cooperate and acts as a combinatorial signalling cheat, with higher fitness in competition with its ancestor. Our results show three important principles: first, combinatorial QS allows for diverse social strategies to emerge; second, restrictions levied by private goods are not sufficient to explain the maintenance of cooperation in natural populations; and third, modifying combinatorial QS responses could result in important physiological outcomes in bacterial populations.
Association Between ACEIs or ARBs Use and Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-analysis
Authors: Diaz-Arocutipa Carlos , Saucedo-Chinchay Jose , Hernandez Adrian V.
Published: June 2020

Importance

There is a controversy regarding whether or not to continue angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) in patients with coronavirus disease 2019 (COVID-19).

Objective

To evaluate the association between ACEIs or ARBs use and clinical outcomes in COVID-19 patients.

Data Sources

Systematic search of the PubMed, Embase, Scopus, Web of Science, and Cochrane Central Register of Controlled Trials from database inception to May 31, 2020. We also searched the preprint servers medRxiv and SSNR for additional studies.

Study Selection

Observational studies and randomized controlled trials reporting the effect of ACEIs or ARBs use on clinical outcomes of adult patients with COVID-19.

Data Extraction and Synthesis

Risk of bias of observational studies were evaluated using the Newcastle-Ottawa Scale. Meta-analyses were performed using a random-effects models and effects expressed as Odds ratios (OR) and mean differences with their 95% confidence interval (95%CI). If available, adjusted effects were pooled.

Main Outcomes and Measures

The primary outcome was all-cause mortality and secondary outcomes were COVID-19 severity, hospital discharge, hospitalization, intensive care unit admission, mechanical ventilation, length of hospital stay, and troponin, creatinine, procalcitonin, C-reactive protein (CRP), interleukin-6 (IL-6), and D-dimer levels.

Results

40 studies (21 cross-sectional, two case-control, and 17 cohorts) involving 50615 patients were included. ACEIs or ARBs use was not associated with all-cause mortality overall (OR 1.11, 95%CI 0.77-1.60, p=0.56), in subgroups by study design and using adjusted effects. ACEI or ARB use was independently associated with lower COVID-19 severity (aOR 0.56, 95%CI 0.37-0.87, p<0.01). No significant associations were found between ACEIs or ARBs use and hospital discharge, hospitalization, mechanical ventilation, length of hospital stay, and biomarkers.

Conclusions and Relevance

ACEIs or ARBs use was not associated with higher all-cause mortality in COVID-19. However, ACEI or ARB use was independently associated with lower COVID-19 severity. Our results support the current international guidelines to continue the use of ACEIs and ARBs in COVID-19 patients with hypertension.

Key points

Question

What is the association between angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin receptor blockers (ARBs) use and clinical outcomes in coronavirus disease 2019 (COVID-19) patients?

Findings

In this systematic review and meta-analysis of 40 observational studies, the use of ACEIs or ARBs was not associated with higher all-cause mortality in COVID-19 patients. Additionally, ACEIs or ARBs use was independently associated with lower COVID-19 severity.

Meaning

These results support the current international guidelines to continue the use of ACEIs and ARBs in COVID-19 patients with hypertension.
Drug-Drug interactions between COVID-19 treatments and antipsychotics drugs: integrated evidence from 4 databases and a systematic review
Authors: Oda Plasencia-García Beatriz , Gonzalo Rodriguez-Menendez , Isabel Rico-Rangel María , Ana Rubio-Garcia , Jaime Torelló-Iserte , Benedicto Crespo-Facorro
Published: June 2020

Relevance

Management of symptoms like anxiety, delirium and agitation cannot be neglected in COVID-19 patients. Antipsychotics are usually used for the pharmacological management of delirium, and confusion and behavioral disturbances. The selection of concomitant COVID-19 medications and antipsychotics should be evidence-based and closely monitored

Objective

To systematically review evidence-based available on drug-drug interactions between COVID-19 treatments and antipsychotics.

Evidence Review

Three databases were consulted: (a) Lexicomp® Drug Interactions, (b) Micromedex® Solutions Drugs Interactions, (c) Liverpool © Drug Interaction Group for COVID-19 therapies. To acquire more information on QT prolongation and TdP, the CredibleMeds® QTDrugs List was searched. Based on the information collected, the authors made a recommendation agreed to by consensus. In addition, a systematic review was conducted to find the clinical outcomes of drug-drug interactions between COVID-19 treatments and antipsychotics

Results

The main interaction between COVID-19 drugs and antipsychotics are the risk of QT prolongation and TdP, and CYP interactions. Remdesivir, favipiravir, baricinitib, and anakinra can be used concomitantly with antipsychotics with no risk of drug-drug interaction (except for hematological risk with clozapine and baricinitib). Tocilizumab is rather safe to use in combination with antipsychotics, although it can restore the activity of CYP3A4 and therefore its substrate metabolism may increase. The most demanding COVID-19 treatments for co-administration with antipsychotics are chloroquine, hydroxychloroquine, azithromycin (all prolong QT interval) and lopinavir / ritonavir (CYP interaction and risk of QT prolongation).

Conclusions

We urge to development of evidence-based guidelines that can help clinicians decide the safest treatment combination and monitoring necessary for each particular patient. The selection of concomitant COVID-19 medications and antipsychotics should be evidence-based and closely monitored.
Policy Implications of an Approximate Linear Infection Model for SARS-CoV-2
Authors: McCarthy John E. , Dumas Bob A.
Published: June 2020

We propose a linear model of infection probability, and prove that this is a good approximation to a more refined model in which we assume infections come from a series of independent risks. We argue that the linearity assumption makes interpreting and using the model much easier, without significantly diminishing the reliability of the model.
Postural constraints recruit shorter-timescale processes into the non-Gaussian cascade processes
Authors: Furmanek Mariusz P. , Mangalam Madhur , Kelty-Stephen Damian G. , Juras Grzegorz
Published: June 2020

Healthy human postural sway exhibits strong intermittency, reflecting a richly interactive foundation of postural control. From a linear perspective, intermittent fluctuations might be interpreted as engagement and disengagement of complementary control processes at distinct timescales or from a nonlinear perspective, as cascade-like interactions across many timescales at once. The diverse control processes entailed by cascade-like multiplicative dynamics suggest specific non-Gaussian distributional properties at different timescales. Multiscale probability density function (PDF) analysis showed that when standing quietly while balancing a sand-filled tube with the two arms elicited non-Gaussianity profiles showing a negative-quadratic crossover between short and long timescales. A more stringent task of balancing a water-filled tube elicited simpler monotonic decreases in non-Gaussianity, that is, a positive-quadratic cancellation of the negative-quadratic crossover. Multiple known indices of postural sway governed the appearance or disappearance of the crossover. Finally, both tasks elicited lognormal distributions over progressively larger timescales. These results provide the first evidence that more stringent postural constraints recruit shorter-timescale processes into the non-Gaussian cascade processes, that indices of postural sway moderate this recruitment, and that more stringent postural constraints show stronger statistical hallmarks of cascade structure.
Phenotype-guided subpopulation identification from single-cell sequencing data
Authors: Sun Duanchen , Guan Xiangnan , Moran Amy E. , Qian David Z. , Schedin Pepper , Adey Andrew , Spellman Paul T. , Xia Zheng
Published: June 2020

Single-cell sequencing yields novel discoveries by distinguishing cell types, states and lineages within the context of heterogeneous tissues. However, interpreting complex single-cell data from highly heterogeneous cell populations remains challenging. Currently, most existing single-cell data analyses focus on cell type clusters defined by unsupervised clustering methods, which cannot directly link cell clusters with specific biological and clinical phenotypes. Here we present Scissor, a novel approach that utilizes disease phenotypes to identify cell subpopulations from single-cell data that most highly correlate with a given phenotype. This “phenotype-to-cell within a single step” strategy enables the utilization of a large amount of clinical information that has been collected for bulk assays to identify the most highly phenotype-associated cell subpopulations. When applied to a lung cancer single-cell RNA-seq (scRNA-seq) dataset, Scissor identified a subset of cells exhibiting high hypoxia activities, which predicted worse survival outcomes in lung cancer patients. Furthermore, in a melanoma scRNA-seq dataset, Scissor discerned a T cell subpopulation with lowPDCD1/CTLA4and highTCF7expressions, which is associated with a favorable immunotherapy response. Thus, Scissor provides a novel framework to identify the biologically and clinically relevant cell subpopulations from single-cell assays by leveraging the wealth of phenotypes and bulk-omics datasets.
Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution
Authors: Velu P. , Craney A. , Ruggiero P. , Sipley J. , Cong L. , Hissong Erika M. , Loda M. , Westblade L. F. , Cushing M. , Rennert H.
Published: June 2020

An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital system following the emergency use authority (EUA) guidance issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=124) using newly designed dual-target rRT-PCR (altona RealStar® SARS-CoV-2 Reagent) for detecting of SARS-CoV-2 in upper respiratory and lower respiratory tract specimens, including bronchoalveolar lavage and tracheal aspirates. Accuracy testing demonstrated excellent assay agreement between expected and observed values. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 tests from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Our findings demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarizes clinical data from early in the epidemic in New York City.
Genome-Wide Sequencing as a First-Tier Screening Test for Short Tandem Repeat Expansions
Authors: Rajan-Babu Indhu-Shree , Peng Junran , Chiu Readman ,   IMAGINE Study,   CAUSES Study, Mohajeri Arezoo , Dolzhenko Egor , Eberle Michael A. , Birol Inanc , Friedman Jan M.
Published: June 2020

Short tandem repeat (STR) expansions cause several neurological and neuromuscular disorders. Screening for STR expansions in genome-wide (exome and genome) sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate genetic counselling of patients with repeat expansion disorders. We assessed the performance of lobSTR, HipSTR, RepeatSeq, ExpansionHunter, TREDPARSE, GangSTR, STRetch, and exSTRa – bioinformatics tools that have been developed to detect and/or genotype STR expansions – on experimental and simulated genome sequence data with known STR expansions aligned using two different aligners, Isaac and BWA. We then adjusted the parameter settings to optimize the sensitivity and specificity of the STR tools and fed the optimized results into a machine-learning decision tree classifier to determine the best combination of tools to detect full mutation expansions with high diagnostic sensitivity and specificity. The decision tree model supported using ExpansionHunter’s full mutation calls with those of either STRetch or exSTRa for detection of full mutations with precision, recall, and F1-score of 90%, 100%, and 95%, respectively.

We used this pipeline to screen the BWA-aligned exome or genome sequence data of 306 families of children with suspected genetic disorders for pathogenic expansions of known disease STR loci. We identified 27 samples, 17 with an apparent full-mutation expansion of theAR,ATXN1,ATXN2,ATXN8,DMPK,FXN,HTT, orTBPlocus, nine with an intermediate or premutation allele in theFMR1locus, and one with a borderline allele in theATXN2locus. We report the concordance between our bioinformatics findings and the clinical PCR results in a subset of these samples. Implementation of our bioinformatics workflow can improve the detection of disease STR expansions in exome and genome sequence diagnostics and enhance clinical outcomes for patients with repeat expansion disorders.
Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype
Authors: Gaurav Shubham , Pandey Shambhavi , Puvar Apurvasinh , Shah Tejas , Joshi Madhvi , Joshi Chaitanya , Kumar Sachin
Published: June 2020

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. Studies on SARS-CoV-2 are being carried out at an unprecedented rate to tackle this threat. Genomics studies, in particular, are indispensable to elucidate the dynamic nature of the RNA genome of SARS-CoV-2. RNA viruses are marked by their unique ability to undergo high rates of mutation in their genome, much more frequently than their hosts, which diversifies their strengths qualifying them to elude host immune response and amplify drug resistance. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. In addition to multiple point mutations, we found a remarkable similarity between relatively common mutations of 36-nucleotide deletion in ORF8 of SARS-CoV-2. Our results corroborate with the earlier reported 29-nucleotide deletion in SARS, which was frequent during the early stage of human-to-human transmission. The results will be useful to understand the biology of SARS-CoV-2 and itsattenuation for vaccine development.
Bioengineering a light-responsive encapsulin nanoreactor: a potential tool for photodynamic therapy
Authors: Diaz Dennis , Vidal Xavier , Sunna Anwar , Care Andrew
Published: June 2020

Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as ‘nanoreactors’ for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision is lacking. We report the construction of a light-responsive encapsulin nanoreactor for “on-demand” production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-Singlet Oxygen Generator (miniSOG), a biological photosensitizer that is activated by blue-light to generate ROS, primarily singlet oxygen (1O2). We established that the nanocompartments stably encased miniSOG, and in response to blue-light were able to mediate the photoconversion of molecular oxygen into ROS. Using anin vitromodel of lung cancer, ROS generated by the nanoreactor was shown to trigger photosensitized oxidation reactions that exerted a toxic effect on tumour cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.
Feasibility and visualization of deep learning detection and classification of inferior vena cava filters
Authors: Park Brian J. , Sotirchos Vlasios S. , Adleberg Jason , Stavropoulos S. William , Cook Tessa S. , Hunt Stephen J.
Published: June 2020

Purpose

This study assesses the feasibility of deep learning detection and classification of 3 retrievable inferior vena cava filters with similar radiographic appearances and emphasizes the importance of visualization methods to confirm proper detection and classification.

Materials and Methods

The fast.ai library with ResNet-34 architecture was used to train a deep learning classification model. A total of 442 fluoroscopic images (N=144 patients) from inferior vena cava filter placement or removal were collected. Following image preprocessing, the training set included 382 images (110 Celect, 149 Denali, 123 Günther Tulip), of which 80% were used for training and 20% for validation. Data augmentation was performed for regularization. A random test set of 60 images (20 images of each filter type), not included in the training or validation set, was used for evaluation. Total accuracy and receiver operating characteristic area under the curve were used to evaluate performance. Feature heatmaps were visualized using guided backpropagation and gradient-weighted class activation mapping.

Results

The overall accuracy was 80.2% with mean receiver operating characteristic area under the curve of 0.96 for the validation set (N=76), and 85.0% with mean receiver operating characteristic area under the curve of 0.94 for the test set (N=60). Two visualization methods were used to assess correct filter detection and classification.

Conclusions

A deep learning model can be used to automatically detect and accurately classify inferior vena cava filters on radiographic images. Visualization techniques should be utilized to ensure deep learning models function as intended.
Assessing the Impact of Imputation on the Interpretations of Prediction Models: A Case Study on Mortality Prediction for Patients with Acute Myocardial Infarction
Authors: Payrovnaziri Seyedeh Neelufar , Xing Aiwen , Salman Shaeke , Liu Xiuwen , Bian Jiang , He Zhe
Published: June 2020

Acute myocardial infarction poses significant health risks and financial burden on healthcare and families. Prediction of mortality risk among AMI patients using rich electronic health record (EHR) data can potentially save lives and healthcare costs. Nevertheless, EHR-based prediction models usually use a missing data imputation method without considering its impact on the performance and interpretability of the model, hampering its real-world applicability in the healthcare setting. This study examines the impact of different methods for imputing missing values in EHR data on both the performance and the interpretations of predictive models. Our results showed that a small standard deviation in root mean squared error across different runs of an imputation method does not necessarily imply a small standard deviation in the prediction models’ performance and interpretation. We also showed that the level of missingness and the imputation method used can have a significant impact on the interpretation of the models.
Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system
Authors: Cantuti-Castelvetri Ludovico , Ojha Ravi , Pedro Liliana D. , Djannatian Minou , Franz Jonas , Kuivanen Suvi , Kallio Katri , Kaya Tuğberk , Anastasina Maria , Smura Teemu , Levanov Lev , Szirovicza Leonora , Tobi Allan , Kallio-Kokko Hannimari , Österlund Pamela , Joensuu Merja , Meunier Frédéric A. , Butcher Sarah , Winkler Martin Sebastian , Mollenhauer Brit , Helenius Ari , Gokce Ozgun , Teesalu Tambet , Hepojoki Jussi , Vapalahti Olli , Stadelmann Christine , Balistreri Giuseppe , Simons Mikael
Published: June 2020

The causative agent of the current pandemic and coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1. Understanding how SARS-CoV-2 enters and spreads within human organs is crucial for developing strategies to prevent viral dissemination. For many viruses, tissue tropism is determined by the availability of virus receptors on the surface of host cells2. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as a host receptor, yet, their tropisms differ3-5. Here, we found that the cellular receptor neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, which was inhibited by a monoclonal blocking antibody against the extracellular b1b2 domain of NRP1. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial cells and in the epithelial cells facing the nasal cavity. Neuropathological analysis of human COVID-19 autopsies revealed SARS-CoV-2 infected NRP1-positive cells in the olfactory epithelium and bulb. In the olfactory bulb infection was detected particularly within NRP1-positive endothelial cells of small capillaries and medium-sized vessels. Studies in mice demonstrated, after intranasal application, NRP1-mediated transport of virus-sized particles into the central nervous system. Thus, NRP1 could explain the enhanced tropism and spreading of SARS-CoV-2.
IP-MS Analysis of ESX-5 and ESX-1 Substrates Enables Mycobacterial Species Identification
Authors: Shu Qingbo , Rajagopal Meena , Fan Jia , Zhan Lingpeng , Kong Xiangxing , He Yifan , Rotcheewaphan Suwatchareeporn , Lyon Christopher J. , Sha Wei , Zelazny Adrian M. , Hu Tony
Published: June 2020

Pulmonary disease resulting from non-tuberculous mycobacteria (NTM) infection has emerged as an increasingly prevalent clinical entity in the past two to three decades, but there are no standardized, commercial assays available for the molecular diagnosis of NTM infections from clinical samples. Herein we discuss the development of an assay that employs immunoprecipitation coupled with mass spectrometry (IP-MS) to rapidly and accurately discriminate prevalent slow-growing mycobacterial species (i.e.,M. aviumandM. intracellulare, M. kansasii, M. gordonae, M. marinumandM. tuberculosis) during early growth in mycobacterial growth indicator tube (MGIT) cultures. This IP-MS assay employs antibodies specific for conserved tryptic peptides of M. tuberculosis EsxN (AQAASLEAEHQAIVR) and CFP-10 (TQIDQVESTAGSLQGQWR) to capture and identify specific mycobacterial species and allows species-specific mycobacterium identification at the first sign of MGIT culture positivity.
Design of an online spectrometer for the diagnosis of free-electron lasers
Authors: Zhang Ximing , Guo Zhi , Meng Xiangyu , Chen Jiahua , Ji Zhan , Jin Zuanming , Zhang Xiangzhi , Wang Yong , Tai Renzhong
Published: June 2020

A self-amplified spontaneous emission free-electron laser (FEL) is under construction at the Shanghai Soft X-ray Free-Electron Facility. Therefore, it is necessary to develop a suitable diagnostic tool capable of resolving the natural emission band of each FEL pulse. Thus, an online spectrometer with a plane mirror and plane variable-line-spacing grating at grazing incidence to monitor each single FEL pulse during the propagation of FEL radiation has been designed and is presented in this work. The method of ray tracing is used for monitoring incident radiation in order to understand spectral characteristics, and SHADOW, an X-ray optics simulation tool, and SRW, an X-ray optics wavefront tool, are applied to study the resolving power and focusing properties of the grating. The designed resolving power is ∼3 × 104 at 620 eV. Meanwhile, the effect of the actual slope error of mirrors on the ray-tracing results is also discussed. In order to provide further optimization for the choice of grating, a comparison of resolving powers between 2000 lines mm−1 and 3000 lines mm−1 gratings at different energies is analyzed in detail and radiation damage of mirrors as well as parameters such as the first-order diffraction angle β, the exit-arm length r
2, and the tilt angle θ between the focal plane and the diffraction arm are studied and optimized. This work has provided comprehensive designing methods and detailed data for the design of diagnostic spectrometers in soft X-ray FELs and will be favorable to the design of other similar instruments.
Investigation of third-order nonlinear dynamical X-ray diffraction based on a new exact solution
Authors: Balyan Minas K.
Published: June 2020

Third-order nonlinear two-wave dynamical X-ray diffraction in a crystal is considered. For the Laue symmetrical case of diffraction a new exact solution is obtained. The solution is presented via Jacobi elliptic functions. Two input free parameters are essential: the deviation parameter from the Bragg exact angle and the intensity of the incident wave. It is shown that the behavior of the field inside the crystal is determined by the sign of a certain combination of these parameters. For negative and positive signs of this combination, the wavefield is periodic and the nonlinear Pendellösung effect takes place. For the nonlinear Pendellösung distance the appropriate expressions are obtained. When the above-mentioned combination is zero, the behavior of the field can be periodic as well as non-periodic and the solution is presented by elementary functions. In the nonperiodic case, the nonlinear case Pendellösung distance tends to infinity. The wavefield diffracts and propagates in a medium, whose susceptibility is modulated by the amplitudes of the wavefields. The behavior of the wavefield can be described also by an effective deviation from the Bragg exact angle. This deviation is also a function of the wavefields.
Explanatory Q&A recommendation algorithm in community question answering
Authors: Li Ming , Li Ying , Xu YingCheng , Wang Li
Published: June 2020

Purpose

In community question answering (CQA), people who answer questions assume readers have mastered the content in the answers. Nevertheless, some readers cannot understand all content. Thus, there is a need for further explanation of the concepts that appear in the answers. Moreover, the large number of question and answer (Q&A) documents make manual retrieval difficult. This paper aims to alleviate these issues for CQA websites.

Design/methodology/approach

In the paper, an algorithm for recommending explanatory Q&A documents is proposed. Q&A documents are modeled with the biterm topic model (BTM) (Yan et al., 2013). Then, the growing neural gas (GNG) algorithm (Fritzke, 1995) is used to cluster Q&A documents. To train multiple classifiers, three features are extracted from the Q&A categories. Thereafter, an ensemble classification model is constructed to identify the explanatory relationships. Finally, the explanatory Q&A documents are recommended.

Findings

The GNG algorithm shows good clustering performance. The ensemble classification model performs better than other classifiers. The both effect and quality scores of explanatory Q&A recommendations are high. These scores indicate the practicality and good performance of the proposed recommendation algorithm.

Research limitations/implications

The proposed algorithm alleviates information overload in CQA from the new perspective of recommending explanatory knowledge. It provides new insight into research on recommendations in CQA. Moreover, in practice, CQA websites can use it to help retrieve Q&A documents and facilitate understanding of their contents. However, the algorithm is for the general recommendation of Q&A documents which does not consider individual personalized characteristics. In future work, personalized recommendations will be evaluated.

Originality/value

A novel explanatory Q&A recommendation algorithm is proposed for CQA to alleviate the burden of manual retrieval and Q&A overload. The novel GNG clustering algorithm and ensemble classification model provide a more accurate way to identify explanatory Q&A documents. The method of ranking the explanatory Q&A documents improves the effectiveness and quality of the recommendation. The proposed algorithm improves the accuracy and efficiency of retrieving explanatory Q&A documents. It assists users in grasping answers easily.
Do new-generation construction professionals be provided what they desire at work? A study on work values and supplies–values fit
Authors: Song Ziyang , Yang Fan , Boezeman Edwin J. , Li Xiaodong
Published: June 2020

Purpose

The declining attractiveness of construction industry to the new-generation onsite construction professionals (OCPs) in China can be the result of insufficient supply of what they desire at work. There is a lack of studies that make clear the work values of this cohort and the fit between their work value preferences and job supplies. Therefore, the purpose of this study is to address this issue.

Design/methodology/approach

This study focused on Chinese new-generation OCPs. Work values and job supplies were measured by two rounds of questionnaire surveys. Factor analysis was implemented to identify work value types. Paired samplest-test, independent samplest-test and one-way ANOVA were performed to figure out work value preferences and degree of supplies–values (S-V) fit and compare them across subgroups.

Findings

Intrinsic, “good time”, work-team-related, altruistic/prestigious and extrinsic work value types were identified. Chinese new-generation OCPs most valued work-team-related and intrinsic work aspects, while significant insufficient supply was relevant to intrinsic, extrinsic and “good time” aspects. Work value preferences and S-V fit showed significant differences among subgroups of gender, growth background, work rank and project type.

Practical implications

The results provide insights for construction companies to practice work-value-based human resource management toward new-generation OCPs and make targeted measures to address the misfit between supplies and values experienced by these OCPs.

Originality/value

This study for the first time examined work values of Chinese new-generation OCPs. It opens a new perspective for research based on S-V fit theory that focused on industry level. The effects of demographic and professional variables on the work values and the degree of S-V fit were revealed. This study thus contributes to the extant literature of work values and S-V fit.