bluuebunny/crossref_metadata_2025 huggingface dataset:
Infrared Thermography as a Diagnostic Tool for Peripheral Artery Disease
Authors: Ilo Arjaleena , Romsi Pekka , Mäkelä Jussi
Published: August 2020

OBJECTIVE

The prevalence of peripheral arterial disease (PAD) is increasing worldwide. The ankle-brachial index (ABI) is considered the criterion standard of noninvasive screening, but it does have limitations. The present study aimed to clarify the clinical diagnostic potential of infrared thermography (IRT) compared with conventional noninvasive measurements for PAD.

METHODS

Patients were divided into two groups: the healthy control group (n = 93) and the PAD group (n = 164). Control participants had an ABI 0.9 to 1.4 and no former PAD diagnosis. The PAD group was divided into three subgroups based on ABI classifications and two subgroups based on toe pressure measurements. Investigators performed IRT using a standardized protocol with temperature measurements at five different foot sites.

MAIN RESULTS

Differences in skin temperatures between feet were greater (P < .001) in the PAD group than in healthy controls. In general, mean foot temperatures were lower in the PAD group than in controls but did not differ significantly among PAD subgroups based on ABI classifications or toe pressure measurements.

CONCLUSIONS

Infrared thermography effectively distinguished temperature differences between feet and thus might be diagnostically useful. However, because normal skin surface temperature varies among individuals, IRT alone cannot be recommended for evaluating PAD. However, it does have potential to provide additional information about circulation, subclinical infections, and the severity of vascular disease.
Propensity Score Matching
Authors: Badhiwala Jetan H. , Karmur Brij S. , Wilson Jefferson R.
Published: August 2020

In using observational, nonrandomized data, there is often interest in studying the effect of a particular treatment on a specific outcome. However, the imbalance of potential confounding variables between the treatment groups can distort the relationship between treatment and outcome. Propensity score matching is one, increasingly utilized, method to help account for such imbalances, allowing for a more accurate estimation of the influence of treatment on outcome. In this paper, we provide the clinician with an overview of propensity score matching techniques and provide a practical example of how this has been used in clinical research relevant to spine surgery.
Spinal cannabinoid CB1 or CB2 receptors activation attenuates mechanical allodynia in streptozotocin-induced diabetic rats
Authors: Gonçalves Maryna Rodrigues , da Conceição Milena Santana , Jesus Carlos Henrique Alves , Gasparin Aléxia Thamara , Rosa Evelize Stacoviaki , da Cunha Joice Maria
Published: August 2020

Diabetes is a chronic disease associated with a high number of complications such as peripheral neuropathy, which causes sensorial disturbances and may lead to the development of diabetic neuropathic pain (DNP). The current treatment for DNP is just palliative and the drugs may cause severe adverse effects, leading to discontinuation of treatment. Thus, new therapeutic targets need to be urgently investigated. Studies have shown that cannabinoids have promising effects in the treatment of several pathological conditions, including chronic pain. Thus, we aimed to investigate the acute effect of the intrathecal injection of CB1 or CB2 cannabinoid receptor agonists N-(2-chloroethyl)-5Z, 8Z, 11Z, 14Z-eicosatetraenamide (ACEA) or JWH 133, respectively (10, 30 or 100 μg/rat) on the mechanical allodynia associated with experimental diabetes induced by streptozotocin (60 mg/kg; intraperitoneal) in rats. Cannabinoid receptor antagonists CB1 AM251 or CB2 AM630 (1 mg/kg) were given before treatment with respective agonists to confirm the involvement of cannabinoid CB1 or CB2 receptors. Rats with diabetes exhibited a significant reduction on the paw mechanical threshold 2 weeks after diabetes induction, having the maximum effect observed 4 weeks after the streptozotocin injection. This mechanical allodynia was significantly improved by intrathecal treatment with ACEA or JWH 133 (only at the higher dose of 100 μg). Pre-treatment with AM251 or AM630 significantly reverted the anti-allodynic effect of the ACEA or JWH 133, respectively. Considering the clinical challenge that the treatment of DPN represents, this study showed for the first time, that the intrathecal cannabinoid receptors agonists may represent an alternative for the treatment of DNP.
Effect of the Helping Babies Breathe Training Program
Authors: Hatamleh Reem , Abujilban Sanaa , Abuhammad Sawsan , Ariag Dalal Mohammad Ahmad , Joseph Rachel A.
Published: August 2020

The Helping Babies Breathe (HBB) training program trains providers in effective resuscitation of infants in developing countries. This study evaluated the effectiveness of the HBB training program on midwives' knowledge and skills in Northern Jordan. Using a nonequivalent control group design, 50 midwives (control, n = 25; experimental, n = 25) from 3 public hospitals in Northern Jordan were recruited and their knowledge and skills were evaluated before and after the training. The program has 3 aspects: 2 hours of teaching, 1 hour of testing, and 25 minutes of skills assessment per participant. The skills were tested individually for each participant, and they were reevaluated at 8 months after. The control and experimental groups significantly differed in posttest scores on knowledge, Objective Structured Clinical Examination A and B skills, and bag-mask application after adjusting for covariates. The HBB training program significantly enhanced knowledge of midwives in the experimental group (P < .05) and demonstrated skills. The HBB training program was helpful in improving midwives' knowledge and practices on immediate care of a newborn baby. Therefore, training midwives using the HBB training program can improve their knowledge and skills and thereby improve infant outcomes in Jordan.
Experience With Teduglutide in Pediatric Short Bowel Syndrome
Authors: Ramos Boluda Esther , Redecillas Ferreiro Susana , Manrique Moral Oscar , García Romero Ruth , Irastorza Terradillos Iñaki , Nuñez Ramos Raquel , Germán Díaz Marta , Polo Miquel Begoña , Vives Piñera Inmaculada , Alcolea Sánchez Alida , González Sacristán Rocío , Bautista Barea Marta , Moreno Villares Jose Manuel
Published: August 2020

Objectives:

The aim of the study was to describe the experience with teduglutide of several Spanish hospitals in pediatric patients with SBS (SBS).

Methods:

Seventeen pediatric patients with intestinal failure associated with SBS were treated with teduglutide. Patients received 0.05 mg · kg−1 · day−1 of subcutaneous teduglutide. Patients’ demographics and changes in parenteral nutrition (PN) needs, fecal losses, and citrulline level initially and at 3, 6, and 12 months were collected, as well as any adverse events.

Results:

Patients were receiving 55 ml · kg−1 · day−1 and 33 kcal · kg−1 · day−1 of parenteral supplementation on average at baseline (2 patients received only hydroelectrolytic solution). A total of 12/17 patients achieved parenteral independence: 3 patients after 3 months of treatment, 4 patients at 6 months, and 5 after 12 months. One patient discontinued treatment 1 year after the beginning as no changes in parenteral support or fecal losses were obtained. All others decreased their intravenous requirements by 50%. One patient suffered an episode of cholecystitis, and another one with a pre‐existing cardiac disease, developed a cardiac decompensation.

Conclusions:

Teduglutide seems to be a safe and effective treatment in the pediatric SBS population with better results than in the pivotal study as well as in the adult population.
Fructose Malabsorption in Chilean Children Undergoing Fructose Breath Test at a Tertiary Hospital
Authors: Alliende Francisco , Lucero Yalda , Jaime Francisca , Ríos Gloria , Arancibia María E. , Rodriguez Lorena
Published: August 2020

Fructose is a highly abundant carbohydrate in western diet and may induce bowel symptoms in children as in adults. The main objective of this study is to describe the frequency of fructose malabsorption (FM) in symptomatic patients 18 years or younger undergoing fructose breath test in a single tertiary center between 2013 and 2018, and to evaluate whether certain symptoms are related to positivity of the test. Out of 273 tests 183 (67%) were compatible with FM. The most frequent pretest symptom in the overall study population was bloating (83%), followed by abdominal pain (73%). Patients with positive test were younger than those with a negative test (median 5 vs 8 years, P < 0.001). In multivariate analysis, which included age, sex, and symptoms (diarrhea, abdominal pain, bloating, nausea), only age <6 years (odds ratio 2.93, 95% confidence interval 1.64–5.23) and absence of nausea (odds ratio = 3.32, 95% confidence interval 1.56–7.05) were associated with FM.
Outpatient Physical, Occupational, and Speech Therapy Synchronous Telemedicine
Authors: Tenforde Adam S. , Borgstrom Haylee , Polich Ginger , Steere Hannah , Davis Irene S. , Cotton Kester , O’Donnell Mary , Silver Julie K.
Published: August 2020

The COVID-19 pandemic transformed health care delivery, including rapid expansion of telehealth. Telerehabilitation, defined as therapy provided by physical therapy, occupational therapy, and speech and language pathology, was rapidly adopted with goals to provide access to care and limit contagion. The purpose of this brief report was to describe the feasibility of and satisfaction with telerehabilitation. A total of 205 participants completed online surveys after a telerehabilitation visit. Most commonly, participants were women (53.7%), 35–64 yrs old, and completed physical therapy (53.7%) for established visits of 30–44 mins in duration for primary impairments in sports, lower limb injuries, and pediatric neurology. Overall, high ratings (“excellent” or “very good” responses) were observed for all patient-centered outcome metrics (range, 93.7%–99%) and value in future telehealth visit (86.8%) across telerehabilitation visits. Women participated more frequently and provided higher ratings than male participants did. Other benefits included eliminating travel time, incorporating other health care advocates, and convenience delivering care in familiar environment to pediatric patients. Technology and elements of hands-on aspects of care were observed limitations. Recognizing reduced indirect costs of care that telerehabilitation may provide along with high patient satisfaction are reasons policy makers should adopt these services into future health care delivery models.
The Effect of Opioid Stewardship Interventions on Key Outcomes: A Systematic Review
Authors: Shoemaker-Hunt Sarah J. , Wyant Brandy E.
Published: August 2020

Objectives

We sought to identify potential patient safety practices to reduce high-risk opioid prescribing.

Methods

We conducted a systematic review of the literature to identify opioid stewardship (OS) strategies implemented in primary care and other settings. Included studies evaluated an OS strategy or a multicomponent OS initiative to address potential harms of opioids and used experimental or quasi-experimental designs.

Results

We identified 14 studies and 1 systematic review that met inclusion criteria. Most studies examined multicomponent OS interventions, which often consisted of guideline-recommended clinical interventions or care processes (e.g., use urine drug screening, check Prescription Drug Monitoring Program), as well as implementation strategies (e.g., dashboards, audit and feedback). Most studies examined the effect of OS interventions on reducing the potential risks of opioids with judicious prescribing and guideline-concordant care (e.g., reduce inappropriate high opioid dosages, avoid co-prescribing opioids and benzodiazepines, use urine drug screening, treatment agreements).

Conclusions

The strength of the evidence is low to moderate that OS efforts decrease numbers of opioid prescriptions, proportion of patients on long-term opioids, or days’ supply. The strength of the evidence for OS initiatives producing significant reductions in opioid dosages was moderate. Future research is needed on the effectiveness of OS interventions, particularly studies with experimental designs and in diverse settings within the health care system.
System-Level Patient Safety Practices That Aim to Reduce Medication Errors Associated With Infusion Pumps: An Evidence Review
Authors: Bacon Olivia , Hoffman Lynn
Published: August 2020

Objectives

In this literature review, we discuss 2 system-level, nurse-targeted patient safety practices (PSPs) that aim to reduce medication errors associated with infusion pumps, including smart pumps. One practice focuses on implementing structured process changes and redesigning workflows to improve efficiencies with pump use. The other focuses on investing in initial and ongoing staff training on the correct use, maintenance, and monitoring of infusion pumps.

Methods

Two databases were searched for “infusion pumps” and related synonyms, along with relevant terms for each PSP. Articles were excluded if outcomes were not directly relevant to the PSP addressed in this review, the article was out of scope, or study design was insufficiently described.

Results

Limited research was found on best practices for reducing errors and improving infusion pump use through workflow and process changes, as well as education and training. Four studies reported medication administration errors, procedural errors, or deviations from hospital policy as clinical outcomes of workflow or process changes. Mixed results were found examining process outcomes related to pump handling. Education on the correct use of smart pumps was found to decrease medication errors and adverse drug events, and 2 studies found an increase in nurses’ adherence to using the medication safety software library as a result of education.

Conclusions

Standardization of process and integration of technology and workflows were found as facilitators. Type and content of education provided were identified as facilitators, whereas time and energy constraints on nurse educators can be barriers to implementing large hospital-wide education programs.
Squamous Cell Carcinoma Arising in Breast Implant Capsules
Authors: Goldberg Mytien Thi , Llaneras Jason , Willson Thomas D. , Boyd John Brain , Venegas Rose J. , Dauphine Christine , Kalantari Babak N.
Published: August 2020

Breast augmentation and reconstruction utilizing implants are among the most common plastic surgery procedures performed in the United States. A small proportion of these implants are removed each year. We report 2 cases where routine pathologic evaluation of capsulectomy specimens revealed squamous cell carcinoma associated with the breast implant capsule and discuss the possible pathogenesis of this unusual entity. Both patients had long-standing implants (>10 years) and presented with acute unilateral breast erythema and swelling. Intraoperatively, the capsules for both cases appeared thickened and calcified, containing extensive granulomatosis and keratinaceous debris invading into the chest wall. Extensive workup failed to find an occult primary. One patient died from a malignant pleural effusion secondary to tumor invasion during chemotherapy, and the second patient obtained stabilization of the mass after 5 weeks of chemotherapy but subsequently declined further surgical intervention. A thorough literature review was performed, and 5 similar reports were identified, involving 6 patients. All patients presented with similar clinical presentations as ours and had poor outcomes. The mean reporting age at diagnosis was 60 years, and the average time from initial implant to diagnosis was 25 years. Due to the small numbers of squamous cell carcinomas associated with breast implant capsules, the true association between the 2 is unknown. It is postulated that chronic inflammation/irritation from the breast implant and epithelialization of the capsule play a significant role in the disease process. This may represent a new entity of “chronic inflammatory capsular malignancies.” Increased awareness of this entity may allow for earlier suspicion, diagnosis, and management.
Anterolateral Thigh Flap With Vascularized Fascia Lata Associated With Thigh Flaps
Authors: Guiotto Martino , Watfa William , Raffoul Wassim , di Summa Pietro Giovanni
Published: August 2020

Radical surgical debridement after Fournier gangrene (FG) can totally change anatomical balance between structures and compromise urogenital function. This is particularly true when the suspensory ligament and the lower abdominal wall are involved, leading to erection and sexual intercourse dysfunction.

We present the case of a 48-year-old man, who underwent emergency debridement and split-thickness skin graft (STSG) of inferior abdominal wall, pubis, scrotal bag and penile shaft after Fournier gangrene.

Five months after the emergency procedure, bilateral medial thigh flaps recreated the scrotal compartment, whereas a pedicled composite anterolateral thigh flap including fascia lata could cover the lower abdominal wall and rebuilt the penile suspensory ligament (PSL).

Healing was uneventful and the patient returned to a normal sexual life with satisfactory erection and intercourse.

Composite and/or chimeric anterolateral thigh fascia lata flaps have been previously used as a reliable option for complex defects, including tendon and ligaments. We describe here, the first case in the literature of a penile suspensory ligament reconstruction.
Reversed Palmaris Longus Muscle With Median Nerve Compression Symptoms
Authors: Demir Can İlker , Yaşar Emrah Kağan , Dursun Buket , Alagöz Murat Şahin
Published: August 2020

Background

The palmaris longus (PL) is one of the most anatomically variable muscles in the body. Although these variations are often asymptomatic, symptoms related to nerve compression can sometimes be encountered. If treatment is indicated, correct diagnosis is important for successful management. In cases of upper extremity nerve compression, variations of the PL should be included in the differential diagnosis. We report a case of reversed PL (RPL) with symptoms of median nerve compression and review the literature, emphasizing the rare and challenging character of these lesions.

Methods

The literature review was performed using Google Scholar and PubMed databases. Keywords were “reversed palmaris longus,” “reversed palmaris longus median nerve compression,” “anomolous palmaris longus muscle,” and “symptomatic palmaris longus.” Only clinical RPL muscle cases with at least one of the symptoms of paresthesia and pain in the median nerve sensory area or swelling on the wrist were included.

Results

In the literature review, 21 publications including 30 patients, matched the search criteria between 1973 and 2018 and were evaluated.

Conclusion

In carpal tunnel syndrome, in cases with atypical presentation, RPL should be considered in the differential diagnosis.
Effect of pimavanserin on anxious depression in patients with major depression and an inadequate response to previous therapy: secondary analysis of the clarity study
Authors: Papakostas George I. , Fava Maurizio , Freeman Marlene P. , Shelton Richard C. , Thase Michael E. , Jha Manish K. , Trivedi Madhukar H. , Dirks Bryan , Liu Keith , Stankovic Srdjan
Published: August 2020

In a post hoc analysis, the effect of pimavanserin on anxious depression was determined from CLARITY, a randomized, double-blind, placebo-controlled study in patients with major depression and an inadequate response to previous therapy. Patients were randomized in a 3:1 ratio to placebo or pimavanserin 34 mg daily added to ongoing antidepressant therapy. At 5 weeks, placebo nonresponders were rerandomized to placebo or pimavanserin for an additional 5 weeks. Mean change from baseline to week 5 for the Hamilton depression rating scale (HAMD) anxiety/somatization (AS) factor was examined for all patients and those with a score ≥7 at baseline. Least squares (LS) mean [standard error (SE)] difference between placebo and pimavanserin for the AS factor score was −1.5 (0.41) [95% confidence interval (CI) −2.4 to −0.7; P = 0.0003; effect size: 0.634]. Among patients with an AS factor score ≥7 at baseline, LS mean (SE) difference was −2.2 (0.66) (95% CI −3.5 to −0.9; P = 0.0013; effect size: 0.781). Response rates (≥50% reduction in HAMD-17 from baseline) were 22.4 and 55.2% (P = 0.0012) and remission rates (HAMD-17 total score <7) were 5.3 and 24.1% (P = 0.0047), respectively, with placebo and pimavanserin among patients with a baseline AS factor score ≥7. Among patients with anxious major depressive disorder at baseline, adjunctive pimavanserin was associated with a significant improvement.
Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)
Authors: Neuzil-Bunesova Vera , Lugli Gabriele Andrea , Modrackova Nikol , Makovska Marie , Mrazek Jakub , Mekadim Chahrazed , Musilova Sarka , Svobodova Ivona , Spanek Roman , Ventura Marco , Killer Jiri
Published: August 2020

A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were

Bifidobacterium animalis

subsp.

animalis

ATCC 25527T,

Bifidobacterium animalis

subsp.

lactis

DSM 10140T and

Bifidobacterium anseris

LMG 30189T, belonging to the

Bifidobacterium pseudolongum

phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the

B. pseudolongum

phylogenetic group were in the concatenated range of 83.08–88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the

B. pseudolongum

phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).
Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands
Authors: Wasai-Hara Sawa , Minamisawa Kiwamu , Cloutier Sylvie , Bromfield Eden S. P.
Published: August 2020

The taxonomic status of two previously characterized

Bradyrhizobium

strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus

Bradyrhizobium

with

Bradyrhizobium betae

as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described

Bradyrhizobium

species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.
Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)
Authors: Ouyabe Michel , Tanaka Naoto , Shiwa Yuh , Fujita Nobuyuki , Kikuno Hidehiko , Babil Pachakkil , Shiwachi Hironobu
Published: August 2020

This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus

Rhizobium

, S-93T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with

Rhizobium miluonense

CCBAU 41251T,

Rhizobium hainanense

I66T,

Rhizobium multihospitium

HAMBI 2975T,

Rhizobium freirei

PRF 81T and

Rhizobium tropici

CIAT 899T being their closest species. Their bacterial fatty acid profile, with major components of C19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus

Rhizobium

. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for

R. multihospitium

HAMBI 2975T,

R. tropici

CIAT 899T,

R. hainanense

CCBAU 57015T,

R. miluonense

HAMBI 2971T and

R. freirei

PRF 81T, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93T (=NRIC 0988T=NBRC 114257T=DSM 110498T).
Trebonia kvetii gen. nov., sp. nov., an acidophilic actinobacterium, and proposal of the new actinobacterial family Treboniaceae fam. nov.
Authors: Rapoport Daria , Sagova-Mareckova Marketa , Sedláček Ivo , Provaznik Jan , Králová Stanislava , Pavlinic Dinko , Benes Vladimir , Kopecky Jan
Published: August 2020

A novel actinobacterial strain, designated 15TR583T, was isolated from a waterlogged acidic soil collected near the town of Trebon, Czech Republic, and was subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that the organism forms an individual line of descent related to the orderStreptosporangiales, classActinomycetia. The strain shared highest 16S rRNA gene sequence similarity, yet of only 92.8%, withActinocorallia aureaIFO 14752T. The strain grew in white colonies of aerobic, Gram-stain-positive, unbranching substrate mycelium bearing single spores at hyphae tips. The major fatty acids (>10%) were iso-C16 : 0, C16 : 0, iso-C17 : 1ω9 and 10-methyl-C17 : 0. The fatty acid pattern differed from all patterns currently described for actinobacterial genera. The organism contained as major menaquinones MK9(H6) and MK9(H8), which differentiated it from other actinobacterial families. Polar lipids were composed of six unidentified glycolipids, an unidentified phosphoglycolipid, two unidentified phospholipids and two unidentified aminolipids. Whole-cell sugars contained galactose, xylose and arabinose as major components. The peptidoglycan type was A1γmeso-diaminopimelic acid. The genomic DNA G+C content was 69.7 mol%. The distinct phylogenetic position and unusual combination of chemotaxonomic characteristics justify the proposal ofTreboniagen. nov., with the type speciesTrebonia kvetiisp. nov. (type strain 15TR583T=CCM 8942T=DSM 109105T), withinTreboniaceaefam. nov.
MIMIC in the OMOP Common Data Model
Authors: Paris Nicolas , Parrot Adrien
Published: August 2020

Objectives

In the era of big data, the intensive care unit (ICU) is very likely to benefit from real-time computer analysis and modeling based on close patient monitoring and Electronic Health Record data. MIMIC is the first open access database in the ICU domain. Many studies have shown that common data models (CDMs) improve database searching by allowing code, tools and experience to be shared. OMOP-CDM is spreading all over the world. The objective was to evaluate the difficulty to transform MIMIC into an OMOP (MIMIC-OMOP) database and the benefits of this transformation for analysts.

Material & Method

A documented, tested, versioned, exemplified and open repository has been set up to support the transformation and improvement of the MIMIC community’s source code. The resulting data set was evaluated over a 48-hour datathon.

Result

With an investment of 2 people for 500 hours, 64% of the data items of the 26 MIMIC tables have been standardized into the OMOP CDM and 78% of the source concepts mapped to reference terminologies. The model proved its ability to support community contributions and was well received during the datathon with 160 participants and 15,000 requests executed with a maximum duration of one minute.

Conclusion

The resulting MIMIC-OMOP dataset is the first MIMIC-OMOP dataset available free of charge with real disidentified data ready for replicable intensive care research. This approach can be generalized to any medical field.
The effect of smoking on COVID-19 symptom severity: Systematic review and meta-analysis
Authors: Gülsen Askin , Yigitbas Burcu Arpinar , Uslu Berat , Drömann Daniel , Kilinc Oguz
Published: August 2020

Background

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SAR2-COV-2), and was first identified in Wuhan, China in December of 2019, but quickly spread to the rest of the world, causing a pandemic. While some studies have found no link between smoking status and severe COVID-19, others demonstrated a significant one. The present study aimed to determine the relationship between smoking and clinical COVID-19 severity via a systematic meta-analysis approach.

Methods

We searched the Google Scholar, PubMed, Scopus, Web of Science, and Embase databases to identify clinical studies suitable for inclusion in this meta-analysis. Studies reporting smoking status and comparing non-severe and severe patients were included. Non-severe cases were described as mild, common type, non-intensive care unit (ICU) treatment, survivors, and severe cases as critical, need for ICU, refractory, and non-survivors.

Results

A total of 16 articles detailing 11322 COVID-19 patients were included. Our meta-analysis revealed a relationship between a history of smoking and severe COVID-19 cases (OR=2.17; 95% CI: 1.37–3.46; P <.001). Additionally, we found an association between the current smoking status and severe COVID-19 (OR=1.51; 95% CI: 1.12–2.05; P <.008). In 10.7% (978/9067) of non-smokers, COVID-19 was severe, while in active smokers, severe COVID-19 occurred in 21.2% (65/305) of cases.

Conclusion

Active smoking and a history of smoking are clearly associated with severe COVID-19. The SARS-COV-2 epidemic should serve as an impetus for patients and those at risk to maintain good health practices and discontinue smoking.
Evaluation of commercially available immuno-magnetic agglutination and enzyme-linked immunosorbent assays for rapid point-of-care diagnostics of COVID-19
Authors: Moeller Maria Engel , Fock Jeppe , Pah Pearlyn , Veras Antia De La Campa , Bade Melanie , Donolato Marco , Israelsen Simone Bastrup , Eugen-Olsen Jesper , Benfield Thomas , Engsig Frederik Neess
Published: August 2020

Introduction

Coronavirus Disease 2019 (COVID-19) is caused bysevere acute respiratory coronavirus-2(SARS-CoV-2). Fast, accurate and simple blood-based assays for quantification of anti-SARS-CoV-2 antibodies are urgently needed to identify infected individuals and keep track of the spread of disease.

Methods

The study included 35 plasma samples from 22 individuals with confirmed COVID-19 by real time reverse-transcriptase-polymerase-chain-reaction and 40 non-COVID-19 plasma samples. Anti-SARS-CoV-2 IgM/lgA or IgG antibodies were detected by a microfluidic quantitative immunomagnetic assay (IMA) (ViroTrack Sero COVID IgM+lgA /IgG Ab, Blusense Diagnostics, Denmark) and by enzyme-linked immunosorbent assay ((ELISA) (Eurolmmun Medizinische Labordiagnostika, Germany).

Results

Of the 35 plasma samples from the COVID-19 patients, 29 (82.9%) were positive for IgA/IgM or IgG by IMA and 29 samples (82.9%) were positive by ELISA. Sensitivity for only one sample per patient was 68% for IgA+IgM and 73% IgG by IMA and 73% by ELISA. For samples collected 14 days after symptom onset, the sensitivity of both IMA and ELISA was around 90%. Specificity of the IMA reached 100% compared to 95% for ELISA IgA and 97.5% for ELISA IgG.

Conclusion

IMA for COVID-19 is a rapid simple-to-use point of care test with sensitivity and specificity similar to a commercial ELISA.
A pilot study to see any Change of the Nasal and Oropharyngeal Microbiota with Prolonged Use of Medical Masks during the COVID-19 Outbreak
Authors: Roy Sayak , Majumder Pampi , Bhattacharya Kingshuk
Published: August 2020

Background

The outbreak of coronavirus disease 2019 (COVID-19) has played havoc on the healthcare system and society. Many international guidelines have put forward various measures to control the spread and, using various quality masks seems to be the most important amongst them. This was a cross-sectional pilot study to see any alterations in the bacterial flora of the nasal and the oropharyngeal (OP) microbiota with the use of medical masks over prolonged periods during this COVID-19 outbreak.

Methods

Nasal and oropharyngeal swabs were collected using proper international guidelines from 30 healthy healthcare workers matching pre-set inclusion criteria, who gave written informed consent. The swabs were used for gram stain as well as culture and sensitivity analysis using standard methods.

Results

In general, we found that the oropharyngeal microflora harboured a more diverse population of bacteria (n=13) than the nasal microflora (n=5). The predominant bacterial flora was found to Staphylococcus epidermidis in the nasal cavity and Streptococcus viridans in the oropharyngeal cavity. There was no growth in 8 (26.68%) samples of oropharynx and 3 (10%) of nasal samples, with one patient having no growth in both the samples. The commonest resistant antibiotic from both the cavity cultures was benzylpenicillin (nasal flora 80% and OP flora 47.37%).

Conclusion

This small pilot study has shown a reassuring aspect of no change in the typical bacterial microflora species of the nasal and OP cavity with prolonged use of medical masks. This is the first study to show this convincing evidence during the COVID-19 outbreak and also in healthy healthcare workers who have to wear masks over long durations.
IL-6 and IL-10 as predictors of disease severity in COVID-19 patients: results from meta-analysis and regression
Authors: Dhar Sujan K , Vishnupriyan K , Damodar Sharat , Gujar Shashi , Das Manjula
Published: August 2020

Aims

SARS-CoV-2, an infectious agent behind the ongoing COVID-19 pandemic, induces high levels of cytokines such as IL-1, IL-2, IL-4, IL-6, IL-10, TNF-α, IFN-γ etc in infected individuals which contribute towards the underlying disease patho-physiology. Nonetheless, exact association and contribution of every cytokine towards COVID-19 pathology remains poorly understood. Delineation of the role of the cytokines during COVID-19 holds the key of efficient patient management in clinics. This study performed a comprehensive meta-analysis to establish association between induced cytokines and COVID-19 disease severity to help in prognosis and clinical care.

Main methods

Scientific literature was searched to identify 13 cytokines (IL-1β, IL-2, IL-2R, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12, IL-17, TNF-α and IFN-γ) from 18 clinical studies. Standardized mean difference (SMD) for selected 6 cytokines IL-2, IL-4, IL-6, IL-10, TNF-α and IFN-γ between severe and non-severe COVID-19 patient groups were summarized using random effects model. A classifier was built using logistic regression model with cytokines having significant SMD as covariates.

Key findings

Out of 13 cytokines, IL-6 and IL-10 showed statistically significant SMD across the studies synthesized. Classifier with mean values of both IL-6 and IL-10 as covariates performed well with accuracy of ~ 92% that was significantly higher than accuracy reported in literature with IL-6 and IL-10 as individual covariates.

Significance

Simple panel proposed by us with only two cytokine markers can be used as predictors for fast diagnosis of patients with higher risk of COVID-19 disease deterioration and thus can be managed well for a favourable prognosis.
Effects of SARS-CoV-2 Mutations on Protein Structures and Intraviral Protein-Protein Interactions
Authors: Wu Siqi , Tian Chang , Liu Panpan , Guo Dongjie , Zheng Wei , Huang Xiaoqiang , Zhang Yang , Liu Lijun
Published: August 2020

Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has infected ten millions of people across the globe, and massive mutations in virus genome have occurred during the rapid spread of this novel coronavirus. Variance in protein sequence might lead to change in protein structure and interaction, then further affect the viral physiological characteristics, which could bring tremendous influence on the pandemic. In this study, we investigated 18 non-synonymous mutations in SARS-CoV-2 genome which incidence rates were all ≥1% as of July 15th, 2020, then modeled the mutated protein structures and compared them with the reference ones. The results showed that four types of mutations could cause dramatic changes in protein structures (RMSD ≥5.0 Å), which were Q57H and G251V in open reading frames 3a (ORF3a), S194L and R203K/G204R in nucleocapsid (N). Next, we found that these mutations could affect the binding affinity of intraviral protein interactions. In addition, the hot spots within these docking complexes were altered, among which the mutation Q57H was involved in both Orf3a-Orf8 and Orf3a-S protein interactions. Besides, these mutations were widely distributed all over the world, and their occurrences fluctuated as time went on. Notably, the incidences of R203K/G204R in N and Q57H in Orf3a were both over 50% in some countries. Overall, our findings suggest that SARS-CoV-2 mutations can change viral protein structure, binding affinity and hot spots of the interface, thereby may have impacts on SARS-CoV-2 transmission, diagnosis and treatment of COVID-19.
High titers of multiple antibody isotypes against the SARS-CoV-2 spike receptor-binding domain and nucleoprotein associate with better neutralization
Authors: Noval Maria G. , Kaczmarek Maria E. , Koide Akiko , Rodriguez-Rodriguez Bruno A. , Louie Ping , Tada Takuya , Hattori Takamitsu , Panchenko Tatyana , Romero Larizbeth A. , Teng Kai Wen , Bazley Andrew , Vries Maren de , Samanovic Marie I. , Weiser Jeffrey N. , Aifantis Ioannis , Cangiarella Joan , Mulligan Mark J. , Desvignes Ludovic , Dittmann Meike , Landau Nathaniel R. , Aguero-Rosenfeld Maria , Koide Shohei , Stapleford Kenneth A.
Published: August 2020

Understanding antibody responses to SARS-CoV-2 is indispensable for the development of containment measures to overcome the current COVID-19 pandemic. Here, we determine the ability of sera from 101 recovered healthcare workers to neutralize both authentic SARS-CoV-2 and SARS-CoV-2 pseudotyped virus and address their antibody titers against SARS-CoV-2 nucleoprotein and spike receptor-binding domain. Interestingly, the majority of individuals have low neutralization capacity and only 6% of the healthcare workers showed high neutralizing titers against both authentic SARS-CoV-2 virus and the pseudotyped virus. We found the antibody response to SARS-CoV-2 infection generates antigen-specific isotypes as well as a diverse combination of antibody isotypes, with high titers of IgG, IgM and IgA against both antigens correlating with neutralization capacity. Importantly, we found that neutralization correlated with antibody titers as quantified by ELISA. This suggests that an ELISA assay can be used to determine seroneutralization potential. Altogether, our work provides a snapshot of the SARS-CoV-2 neutralizing antibody response in recovered healthcare workers and provides evidence that possessing multiple antibody isotypes may play an important role in SARS-CoV-2 neutralization.
Susceptibility of swine cells and domestic pigs to SARS-CoV-2
Authors: Meekins David A. , Morozov Igor , Trujillo Jessie D. , Gaudreault Natasha N. , Bold Dashzeveg , Artiaga Bianca L. , Indran Sabarish V. , Kwon Taeyong , Balaraman Velmurugan , Madden Daniel W. , Feldmann Heinz , Henningson Jamie , Ma Wenjun , Balasuriya Udeni B. R. , Richt Juergen A.
Published: August 2020

The emergence of SARS-CoV-2 has resulted in an ongoing global pandemic with significant morbidity, mortality, and economic consequences. The susceptibility of different animal species to SARS-CoV-2 is of concern due to the potential for interspecies transmission, and the requirement for pre-clinical animal models to develop effective countermeasures. In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. SARS-CoV-2 was able to replicate in two different porcine cell lines with cytopathic effects. Interestingly, none of the SARS-CoV-2-inoculated pigs showed evidence of clinical signs, viral replication or SARS-CoV-2-specific antibody responses. Moreover, none of the sentinel pigs displayed markers of SARS-CoV-2 infection. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Pigs are therefore unlikely to be significant carriers of SARS-CoV-2 and are not a suitable pre-clinical animal model to study SARS-CoV-2 pathogenesis or efficacy of respective vaccines or therapeutics.
THE INFLAMMATORY MICROENVIRONMENT IN SCREEN-DETECTED PREMALIGANT ADENOMATOUS POLYPS: EARLY RESULTS FROM THE INTEGRATED TECHNOLOGIES FOR IMPROVED POLYP SURVEILLANCE (INCISE) PROJECT
Authors: Mansouri David , McSorley Stephen T , Park James H , Orange Clare , Horgan Paul G , McMillan Donald C , Edwards Joanne
Published: August 2020

Introduction

Around 40% of patients who attend for colonoscopy following a positive stool screening test have adenomatous polyps. Identifying which patients have a higher propensity for malignant transformation is currently poorly understood. The aim of the present study was to assess whether the type and intensity of inflammatory infiltrate differs between high-grade (HGD) and low-grade dysplastic (LGD) screen detected adenomas.

Methods

A representative sample of 207 polyps from 134 individuals were included from a database of all patients with adenomas detected through the first round of the Scottish Bowel Screening Programme (SBoSP) in NHS GG&C (April 2009 to April 2011).

Inflammatory cell phenotype infiltrate was assessed by immunohistochemistry for CD3+, CD8+, CD45+ and CD68+ in a semi-quantitative manner at 20x resolution. Immune-cell infiltrate was graded as absent, weak, moderate or strong.

Patient and polyp characteristics and inflammatory infiltrate were then compared between HGD and LGD polyps.

Results

CD3+ infiltrate was significantly higher in HGD polyps compared to LGD polyps (74% vs 69%, p<0.05). CD8+ infiltrate was significantly higher in HGD polyps compared to LGD polyps (36% vs 13%, p<0.001) where as CD45+ infiltrate was not significantly different(69% vs 64%, p=0.401). There was no significant difference in CD68+ infiltrate (p=0.540) or total inflammatory cell infiltrate (calculated from CD3+ and CD68+) (p=0.226).

Conclusions

This study reports an increase in CD3+ and CD8+ infiltrate with progression from LGD to HGD in colonic adenomas. It may therefore have a use in the prognostic stratification and treatment of dysplastic polyps.
Pathway for Enhanced Recovery after Spinal Surgery-A Systematic Review of Evidence for use of Individual Components
Authors: Licina Ana , Silvers Andrew , Laughlin Harry , Russell Jeremy , Wan Crispin
Published: August 2020

Background

Enhanced recovery in spinal surgery (ERSS) has shown promising improvements in clinical and economical outcomes. We have proposed an ERSS pathway based on societal recommendations and qualitative reviews. We aimed to delineate the clinical efficacy of individual pathway components in ERSS through a systematic narrative review.

Methods

We included systematic reviews and meta-analysis, randomized controlled trials, non-randomized controlled studies, and observational studies in adults and pediatric patients evaluating any one of the 22 pre-defined care components. Our primary outcomes included all-cause mortality, morbidity outcomes (e.g., pulmonary, cardiac, renal, surgical complications), patient-reported outcomes and experiences (e.g., pain, quality of care experience), and health services outcomes (e.g., length of stay and costs). We searched the following databases (1990 onwards)

MEDLINE, EMBASE, and Cochrane Library (Cochrane Database of Systematic Reviews and CENTRAL). Two reviewers independently screened all citations, full-text articles, and abstracted data. A narrative synthesis was provided. Where applicable, we constructed Evidence Profile (EP) tables for each individual element. Due to clinical and methodological heterogeneity, we did not conduct a meta-analyses. Confidence in cumulative evidence for each component of the pathway was classified according to the GRADE system.

Results

We identified 5423 relevant studies excluding duplicates as relating to the 22 pre-defined components of enhanced recovery in spinal surgery. We included 664 studies in the systematic review. We found specific evidence within the context of spinal surgery for 14/22 proposed components. Evidence was summarized in EP tables for 12/22 components. We performed thematic synthesis without EP for 6/22 elements. We identified appropriate societal guidelines for the remainder of the components.

Discussion

We identified the following components with high quality of evidence as per GRADE system: pre-emptive analgesia, peri-operative blood conservation (antifibrinolytic use), surgical site preparation and antibiotic prophylaxis. There was moderate level of evidence for implementation of prehabilitation, minimally invasive surgery, multimodal perioperative analgesia, intravenous lignocaine and ketamine use as well as early mobilization. This review allows for the first formalized evidence-based unified protocol in the field of ERSS.

Further studies validating the multimodal ERSS framework are essential to guide the future evolution of care in patients undergoing spinal surgery.