bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel SCCmec type XV (7A) and two pseudo-SCCmec variants in foodborne MRSA in China
Authors: Wang Wei , Hu Yue , Baker Michelle , Dottorini Tania , Li Hui , Dong Yinping , Bai Yao , Fanning Séamus , Li Fengqin 
Published: December 2021

Abstract

Background
Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 14 types. Novel SCCmec variants have been frequently detected from humans and animals but rarely from food.

Objectives
To characterize a novel SCCmec type and two SCCmec variants identified from food-associated MRSA in China.

Methods
Three MRSA (NV_1, NT_611 and NT_8) collected from retail foods in China were subjected to WGS and the SCCmec elements were determined.

Results
The novel SCCmecXV identified in NV_1 carried the mec gene complex class A (mecI-mecR1-mecA-IS431) and the ccr gene complex 7 (ccrA1B6), and a Tn558-mediated phenicol exporter gene fexA was detected in this SCCmecXV cassette. The pseudo-SCCmec elements ΨSCCmecNT_611 and ΨSCCmecNT_8 showed a truncated SCCmec pattern, carrying the class C2 mec gene complex but missing the ccr genes. The ΨSCCmecNT_611 element shared more similarities with those of Staphylococcus haemolyticus (AB478934.1) and carried a heavy metal resistance gene cluster cadD-cadX-arsC-arsB-arsR-copA. The ΨSCCmecNT_8 MRSA exhibited a highly resistant phenotype, showing the absence of a 19.3 kb segment compared with the reference SCCmecXII element (CP019945.1). Notably, a 46 kb region containing multiple transposons encoding antimicrobial or metal resistance genes flanked by IS431 or IS256 was identified ∼30 kb downstream from the mec gene complex in ΨSCCmecNT_8, which might explain such high resistance in MRSA NT_8.

Conclusions
Our finding of novel and pseudo-SCCmec elements reflected the ongoing intra/interspecies genetic rearrangements in staphylococci. Further study will be needed to investigate the biological significance and prevalence of those SCCmec variants along the food chain.
Acquired resistome and plasmid sequencing of mcr-1 carrying MDR Enterobacteriaceae from poultry and their relationship to STs associated with humans
Authors: Abou Fayad Antoine , El Azzi Maria , Sleiman Ahmad , Kassem Issmat I. , Bawazeer Reema A. , Okdah Liliane , Doumith Michel , Alghoribi Majed F. , Matar Ghassan M. 
Published: December 2021

Abstract

Objectives
To investigate the acquired resistome in 18 colistin-resistant Escherichia coli isolated from different poultry farms in Lebanon, analyse Inc plasmids associated with mcr and assess potential transmission to humans.

Methods
A total of 18 E. coli were recovered from poultry faeces collected from different poultry farms in Lebanon. Broth microdilution (BMD) assay was performed to determine the antimicrobial resistance profiles. WGS was used to identify the genetic determinants behind the resistance in these isolates.

Results
BMD results showed that all of the 18 isolates were colistin resistant. Furthermore, resistance to trimethoprim/sulfamethoxazole was the most recorded among the isolates and only one isolate was resistant to cefepime. Sequencing results showed that the isolates were distributed into seven different STs and that the most abundant was ST1140. The number of antimicrobial resistant determinants ranged from 4 to 21 among the 18 isolates, with tet(A) and floR being the most frequent. Moreover, a total of 15 different plasmid replicon types were identified. The mcr-1 gene was shown to be predominantly located on IncX4 plasmids. Additionally, two isolates harboured the IncI2-type self-conjugative plasmid.

Conclusions
The findings show that mcr and other important resistance determinants occur in MDR E. coli isolated poultry farms in Lebanon. The occurrence of mcr on mobile plasmids and the zoonotic potential and clinical relevance of some strains highlight a risk of transmission to humans.
Surgical treatment for extremity rhabdomyosarcoma: longitudinal national questionnaire survey in Japan
Authors: Nishida Yoshihiro , Kawai Akira 
Published: December 2021

Abstract

Background
Extremity rhabdomyosarcoma differs from other soft tissue sarcomas, being highly sensitive to chemotherapy and radiotherapy and having a high rate of metastasis to lymph nodes. Therefore, the treatment modality differs from that of other soft tissue sarcomas. The purpose of this study was to conduct a longitudinal questionnaire survey of orthopedic oncologists in charge of surgical treatment for extremity rhabdomyosarcoma in Japan to determine whether the treatment modality chosen here is in line with the international and national treatment ones.

Methods
Questionnaire surveys were conducted in 2012 and 2019 to orthopedic oncologists of Japanese Orthopaedic Association and Japanese Musculoskeletal Oncology Group.

Results
Responses were obtained from 80 facilities and 76 facilities, respectively. Fewer than 50% of the facilities treated one or more patients a year in both years. Many facilities first performed diagnostic biopsy, but most did not perform pretreatment re-excision. The number of facilities that provided radiotherapy in addition to surgery increased significantly from 2012 to 2019 (P = 0.028), but it was still 21% in 2019. The number of facilities performing excision and lymph node dissection was 19% in both 2012 and 2019, which was a very low result without improvement. The departments responsible for follow-up have been changed to pediatrics and orthopedic oncology in tandem (P = 0.0004).

Conclusions
Radiotherapy and pathological evaluation of lymph nodes are important for improving the prognosis of patients with extremity rhabdomyosarcoma. It is necessary to continue and develop more efficient educational activities on the appropriate medical treatment modalities for extremity RMS.
Integration of Multiple Surveillance Systems to Track COVID-19 in the U.S. Army Population
Authors: Kebisek Julianna , Maule Alexis , Smith Jacob , Allman Matthew , Marquez Anthony , McCabe Ashleigh , Mafotsing Fopoussi Amelie , Gibson Kelly , Steelman Ryan , Superior Michael , Ambrose John 
Published: December 2021

ABSTRACT

Introduction
The coronavirus disease (COVID-19) pandemic presented unique challenges for surveillance of the military population, which include active component service members and their family members. Through integrating multiple Department of Defense surveillance systems, the Army Public Health Center can provide near real-time case counts to Army leadership on a daily basis.

Materials and Methods
The incidence of COVID-19 was tracked by incorporating data from the Disease Reporting System Internet, laboratory test results, Commanders’ Critical Incidence Reports, reports from the Centers for Disease Control and Prevention military liaison, and media reports. Cases were validated via a medical record review for all Army beneficiaries. Descriptive analyses were performed using Microsoft Excel and SAS 9.4 to measure demographic frequencies.

Results
In the first year of the pandemic from February 1, 2020 to February 28, 2021, a total of 96,315 COVID-19 cases were reported to the Disease Reporting System internet, the Army’s passive surveillance system, of which 95,429 (99%) were confirmed and 886 (1%) were probable. A total of 76 outbreak reports were submitted from 14 Army installations. The proportion of Army beneficiaries with severe illness was low: 2,271 (2.4%) individuals required hospitalization and 269 (0.3%) died. Installations in Texas reported the highest proportion of confirmed—not hospitalized cases (n = 19,246, 20.7%), confirmed—hospitalized cases (n = 1,037, 45.7%), and deaths (n = 137, 50.9%) as compared to other states with Army installations.

Conclusions
The pandemic has demonstrated the need for a robust public health enterprise with a focus on data collection, validation, and analysis, allowing leaders to make informed decisions that may impact the health of the Army.
An Education Intervention to Improve Knowledge of Post-Traumatic Stress Disorder Symptoms and Treatments Among U.S. Women Service Members and Veterans
Authors: Proctor Denise M , Emmons Kevin R , Scannell-Desch Elizabeth 
Published: December 2021

ABSTRACT

Introduction
Due to decades of prolonged combat operations, post-traumatic stress disorder (PTSD) is widely discussed and generally well conceptualized. The objective of this study was to determine if an educational program on the signs and symptoms of PTSD and an explanation of the current treatments utilized by the Veterans Administration is effective in increasing the knowledge levels of women service members and veterans, leading to seeking treatment.

Materials and Methods
The design of this study was a quantitative pretest/posttest interventional study. The educational program was conducted at a Senior Citizen Center. The population was a purposive sample of 44 women service members and veterans from a military base in New Jersey. A 25-item PTSD Knowledge Questionnaire developed for the earlier Web-Based Post-traumatic Stress Disorder Education for Military Family Members (2012) study was used as the pretest and posttest.

Results
The knowledge level of PTSD among women service members and veterans who participated in this study was significantly higher after completing the educational program with 43% indicating that they would seek mental health care.

Conclusions
Women service members and veterans were ill-informed on the signs, symptoms, and treatment options of PTSD. If the results of this survey are an indicator of the knowledge level of women service members in broader populations, there is a need to restructure how those who are at risk of developing PTSD are educated. Through better educational programs, women and men could seek care with increasingly favorable long-term outcomes.
Faraday depolarization and induced circular polarization by multipath propagation with application to FRBs
Authors: Beniamini Paz , Kumar Pawan , Narayan Ramesh 
Published: December 2021

ABSTRACT
We describe how the observed polarization properties of an astronomical object are related to its intrinsic polarization properties and the finite temporal and spectral resolutions of the observing device. Moreover, we discuss the effect that a scattering screen, with non-zero magnetic field, between the source and observer has on the observed polarization properties. We show that the polarization properties are determined by the ratio of observing bandwidth and coherence bandwidth of the scattering screen and the ratio of temporal resolution of the instrument and the variability time of screen, as long as the length over which the Faraday rotation induced by the screen changes by ∼π is smaller than the size of the screen visible to the observer. We describe the conditions under which a source that is 100 per cent linearly polarized intrinsically might be observed as partially depolarized, and how the source’s temporal variability can be distinguished from the temporal variability induced by the scattering screen. In general, linearly polarized waves passing through a magnetized scattering screen can develop a significant circular polarization. We apply the work to the observed polarization properties of a few fast radio bursts (FRBs), and outline potential applications to pulsars.
miRetrieve—an R package and web application for miRNA text mining
Authors: Friedrich Julian , Hammes Hans-Peter , Krenning Guido 
Published: December 2021

Abstract
microRNAs (miRNAs) regulate gene expression and thereby influence biological processes in health and disease. As a consequence, miRNAs are intensely studied and literature on miRNAs has been constantly growing. While this growing body of literature reflects the interest in miRNAs, it generates a challenge to maintain an overview, and the comparison of miRNAs that may function across diverse disease fields is complex due to this large number of relevant publications. To address these challenges, we designed miRetrieve, an R package and web application that provides an overview on miRNAs. By text mining, miRetrieve can characterize and compare miRNAs within specific disease fields and across disease areas. This overview provides focus and facilitates the generation of new hypotheses. Here, we explain how miRetrieve works and how it is used. Furthermore, we demonstrate its applicability in an exemplary case study and discuss its advantages and disadvantages.
Extent of MGMT promoter methylation modifies the effect of temozolomide on overall survival in patients with glioblastoma: a regional cohort study
Authors: Poon Michael T C , Keni Shivank , Vimalan Vineeth , Ip Chak , Smith Colin , Erridge Sara , Weir Christopher J , Brennan Paul M 
Published: December 2021

Abstract

Background
MGMT methylation in glioblastoma predicts response to temozolomide but dichotomizing methylation status may mask the true prognostic value of quantitative MGMT methylation. This study evaluated whether extent of MGMT methylation interacts with the effect of temozolomide on overall survival.

Methods
We included consecutive glioblastoma patients aged ≥16 years diagnosed (April 2012–May 2020) at a neuro-oncology center. All patients had quantitative MGMT methylation measured using pyrosequencing. Those with MGMT methylated tumors were stratified into high and low methylation groups based on a cut-off using Youden index on 2-year survival. Our accelerated failure time survival models included extent of MGMT methylation, age, postoperative Karnofsky performance score, extent of resection, temozolomide regimen, and radiotherapy.

Results
There were 414 patients. Optimal cut-off point using Youden index was 25.9% MGMT methylation. The number of patients in the unmethylated, low and high methylation groups was 223 (53.9%), 81 (19.6%), and 110 (26.6%), respectively. In the adjusted model, high (hazard ratio [HR] 0.60, 95% confidence intervals [CI] 0.46–0.79, P = 0.005) and low (HR 0.67, 95% CI 0.50–0.89, P &lt; 0.001) methylation groups had better survival compared to unmethylated group. There was no evidence for interaction between MGMT methylation and completed temozolomide regimen (interaction term for low methylation P = 0.097; high methylation P = 0.071). This suggests no strong effect of MGMT status on survival in patients completing temozolomide regimen. In patients not completing the temozolomide regimen, higher MGMT methylation predicted better survival (interaction terms P &lt; 0.001).

Conclusions
Quantitative MGMT methylation may provide additional prognostic value. This is important when assessing clinical and research therapies.
Increased Moxifloxacin Dosing Among Patients With Multidrug-Resistant Tuberculosis With Low-Level Resistance to Moxifloxacin Did Not Improve Treatment Outcomes in a Tertiary Care Center in Mumbai, India
Authors: Tornheim Jeffrey A , Udwadia Zarir F , Arora Prerna R , Gajjar Ishita , Sharma Samridhi , Karane Megha , Sawant Namrata , Kharat Nisha , Blum Alexander J , Shivakumar Shri Vijay Bala Yogendra , Gupte Akshay N , Gupte Nikhil , Mullerpattan Jai B , Pinto Lancelot M , Ashavaid Tester F , Gupta Amita , Rodrigues Camilla 
Published: December 2021

Abstract

Background
Mycobacterium tuberculosis (Mtb) strains resistant to isoniazid and rifampin (multidrug-resistant tuberculosis [MDR-TB]) are increasingly reported worldwide, requiring renewed focus on the nuances of drug resistance. Patients with low-level moxifloxacin resistance may benefit from higher doses, but limited clinical data on this strategy are available.

Methods
We conducted a 5-year observational cohort study of MDR-TB patients at a tertiary care center in India. Participants with Mtb isolates resistant to isoniazid, rifampin, and moxifloxacin (at the 0.5 µg/mL threshold) were analyzed according to receipt of high-dose moxifloxacin (600 mg daily) as part of a susceptibility-guided treatment regimen. Univariable and multivariable Cox proportional hazard models assessed the relationship between high-dose moxifloxacin and unfavorable treatment outcomes.

Results
Of 354 participants with MDR-TB resistant to moxifloxacin, 291 (82.2%) received high-dose moxifloxacin. The majority experienced good treatment outcomes (200 [56.5%]), which was similar between groups (56.7% vs 54.0%, P = .74). Unfavorable outcomes were associated with greater extent of radiographic disease, lower initial body mass index, and concurrent treatment with fewer drugs with confirmed phenotypic susceptibility. Treatment with high-dose moxifloxacin was not associated with improved outcomes in either unadjusted (hazard ratio [HR], 1.2 [95% confidence interval {CI}, .6–2.4]) or adjusted (HR, 0.8 [95% CI, .5–1.4]) models but was associated with joint pain (HR, 3.2 [95% CI, 1.2–8.8]).

Conclusions
In a large observational cohort, adding high-dose (600 mg) moxifloxacin to a drug susceptibility test–based treatment regimen for MDR-TB was associated with increased treatment-associated side effects without improving overall outcomes and should be avoided for empiric treatment of moxifloxacin-resistant MDR-TB.
Contemporary Clinical and Molecular Epidemiology of Vancomycin-Resistant Enterococcal Bacteremia: A Prospective Multicenter Cohort Study (VENOUS I)
Authors: Contreras German A , Munita Jose M , Simar Shelby , Luterbach Courtney , Dinh An Q , Rydell Kirsten , Sahasrabhojane Pranoti V , Rios Rafael , Diaz Lorena , Reyes Katherine , Zervos Marcus , Misikir Helina M , Sanchez-Petitto Gabriela , Liu Catherine , Doi Yohei , Abbo Lilian M , Shimose Luis , Seifert Harald , Gudiol Carlota , Barberis Fernanda , Pedroza Claudia , Aitken Samuel L , Shelburne Samuel A , van Duin David , Tran Truc T , Hanson Blake M , Arias Cesar A 
Published: December 2021

Abstract

Background
Vancomycin-resistant enterococci (VRE) are major therapeutic challenges. Prospective contemporary data characterizing the clinical and molecular epidemiology of VRE bloodstream infections (BSIs) are lacking.

Methods
The Vancomycin-Resistant Enterococcal BSI Outcomes Study (VENOUS I) is a prospective observational cohort of adult patients with enterococcal BSI in 11 US hospitals. We included patients with Enterococcus faecalis or Enterococcus faecium BSI with ≥1 follow-up blood culture(s) within 7 days and availability of isolate(s) for further characterization. The primary study outcome was in-hospital mortality. Secondary outcomes were mortality at days 4, 7, 10, 12, and 15 after index blood culture. A desirability of outcome ranking was constructed to assess the association of vancomycin resistance with outcomes. All index isolates were subjected to whole genome sequencing.

Results
Forty-two of 232 (18%) patients died in hospital and 39 (17%) exhibited microbiological failure (lack of clearance in the first 4 days). Neutropenia (hazard ratio [HR], 3.13), microbiological failure (HR, 2.4), VRE BSI (HR, 2.13), use of urinary catheter (HR, 1.85), and Pitt BSI score ≥2 (HR, 1.83) were significant predictors of in-hospital mortality. Microbiological failure was the strongest predictor of in-hospital mortality in patients with E faecium bacteremia (HR, 5.03). The impact of vancomycin resistance on mortality in our cohort changed throughout the course of hospitalization. Enterococcus faecalis sequence type 6 was a predominant multidrug-resistant lineage, whereas a heterogeneous genomic population of E faecium was identified.

Conclusions
Failure of early eradication of VRE from the bloodstream is a major factor associated with poor outcomes.
Ultrathin metal–organic framework nanosheets and devices
Authors: Meiyazhagan AshokKumar 
Published: December 2021

Abstract
A few recent findings on ultrathin two-dimensional (2D) metal–organic frameworks (MOFs) were discussed in this spotlight review. MOFs are a class of materials with intriguing properties for possible applications in several fields ranging from catalysis to sensors and functional devices. To date, several synthesis strategies have been explored to derive crystalline 2D MOF structures. However, most synthetic strategies to obtain such materials remain underexplored. This highlighted review evaluated select synthesis strategies focused on deriving micron-sized 2D MOF crystals, emphasizing their rich chemistries. More importantly, the possibility of integrating the synthesized ultrathin 2D crystalline MOFs into the functional device and their electrical conductivity measurements is reviewed. Overall, this review provides the most recent outcomes in the ultrathin 2D MOF community and its influence on electronic devices.
Thin-film growth of MAX phases as functional materials
Authors: Biswas Abhijit , Natu Varun , Puthirath Anand B 
Published: December 2021

Abstract
Layered nanolaminate ternary carbides, nitrides and carbonitrides with general formula Mn+1AXn or MAX (n = 1, 2, or 3, M is an early transition metal, A is mostly group 13 or 14 element and X is C and/or N) has revolutionized the world of nanomaterials, due to the coexistence of both ceramic and metallic nature, giving rise to exceptional mechanical, thermal, electrical, chemical properties and wide range of applications. Although several solid-state bulk synthesis methods have been developed to produce a variety of MAX phases, however, for certain applications, the growth of MAX phases, especially in its high-quality epitaxial thin-films form is of increasing interest. Here, we summarize the progress made thus far in epitaxial growth and property evaluation of MAX phase thin films grown by various deposition techniques. We also address the important future research directions to be made in terms of thin-film growth. Overall, in the future, high-quality single-phase epitaxial thin-film growth and engineering of chemically diverse MAX phases may open up interesting new avenues for next-generation technology.