bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of a multidrug-resistant worldwide-disseminated methicillin-resistant Staphylococcus epidermidis clone harbouring the cfr linezolid resistance gene in a French hospital with evidence of interspecies transfer to several Staphylococcus aureus lineages
Authors: Côrtes Marina Farrel , André Camille , Martins Simões Patricia , Corvec Stéphane , Caillon Jocelyne , Tristan Anne , Bes Michèle , Vandenesch François , Figueiredo Agnes Marie Sá , Dupieux Céline , Laurent Frédéric 
Published: March 2022

Abstract

Background
Resistance to linezolid has become a worldwide concern since it is one of the last-resort antibiotics to treat multidrug-resistant staphylococcal and enterococcal infections.

Objectives
We investigated staphylococcal infections caused by 16 cfr-positive linezolid-resistant Staphylococcus epidermidis and Staphylococcus aureus isolates in a French university hospital from 2015 to 2018.

Methods
Antimicrobial susceptibility of isolates was tested by broth microdilution and gradient strips. Genetic determinants of linezolid resistance (including cfr gene and 23S rRNA mutations) were assessed by PCR and WGS; the latter was also used to characterize the cfr-carrying plasmids in S. epidermidis and S. aureus, and to explore the clonal relationship of isolates.

Results
All linezolid-resistant staphylococcal isolates harboured the same cfr-carrying plasmid, sharing 99% identity with the previously described pSA737. The three S. aureus isolates belonged to different STs (ST8, ST72, ST2416); the 13 methicillin-resistant S. epidermidis (MRSE) belonged to ST2 and harboured both cfr and mutations in genes encoding 23S rRNA and ribosomal proteins. Phylogenetic analysis grouped the MRSE isolates into two clusters, one of which (n = 12 isolates) belonged to the recently reported multidrug-resistant worldwide-disseminated S. epidermidis lineages.

Conclusions
The results presented herein highlight the persistence and efficient spread of a cfr-carrying plasmid in a hospital related both to the dissemination of a multidrug-resistant S. epidermidis clone and the in vivo interspecies transfer of cfr between S. epidermidis and S. aureus. The emergence of linezolid-resistant strains should be closely monitored, and the mechanisms involved systematically explored in order to limit the spread of plasmid-mediated resistance.
Resolving the Cohenian paradox in judicial probability theory
Authors: Du Wenjing , Niu Zihan , Xiong Minghui 
Published: March 2022

Abstract
The Cohenian paradox is one of the main themes of judicial probability theory and one of the core topics discussed by the new evidence scholarship. To resolve this paradox, evidence scholars nowadays have proposed various solutions, including legal probabilism, judicial Bayesian decision theory and relative plausibility theory. These three solutions can be classified into two approaches, i.e. the probabilism and the explanationism. Among them, the former includes legal probabilism and judicial Bayesian decision theory, and the latter includes the relative plausibility theory. However, the two approaches have recently begun to converge and become more understandable to each other. For example, Welch (2020, Int. J. Evid. Proof, 24, 351–373) has recently defended and improved the relative plausibility theory by substantially improving it with the help of Bayesian decision theory. In this paper, by contrast, we attempt to defend the probabilistic approach—legal probabilism and Bayesian decision theory on the basis of relative plausibility theory.
Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases
Authors: Zivkovic Igor , Ivkovic Kate , Cvetesic Nevena , Marsavelski Aleksandra , Gruic-Sovulj Ita 
Published: March 2022

Abstract
Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. This ensures faithful protein synthesis and cellular fitness. Using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we demonstrated that the class I editing domain clears the non-cognate amino acids well-discriminated at the synthetic site with the same rates as the weakly-discriminated fidelity threats. This unveiled low selectivity suggests that evolutionary pressure to optimize the rates against the amino acids that jeopardize translational fidelity did not shape the editing site. Instead, we propose that editing was shaped to safeguard cognate aminoacyl-tRNAs against hydrolysis. Misediting is prevented by the residues that promote negative catalysis through destabilisation of the transition state comprising cognate amino acid. Such powerful design allows broad substrate acceptance of the editing domain along with its exquisite specificity in the cognate aminoacyl-tRNA rejection. Editing proceeds by direct substrate delivery to the editing domain (in cis pathway). However, we found that class I IleRS also releases misaminoacyl-tRNAIle and edits it in trans. This minor editing pathway was up to now recognized only for class II AARSs.
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion
Authors: Serna-Pujol Núria , Salinas-Pena Mónica , Mugianesi Francesca , Le Dily François , Marti-Renom Marc A , Jordan Albert 
Published: March 2022

Abstract
Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
Prognostic Value of Pretreatment Red Blood Cell Distribution Width in Patients With Esophageal Cancer Who Underwent Esophagectomy
Authors: Yoshida Naoya , Horinouchi Tomo , Eto Kojiro , Harada Kazuto , Sawayama Hiroshi , Imamura Yu , Iwatsuki Masaaki , Ishimoto Takatsugu , Baba Yoshifumi , Miyamoto Yuji , Watanabe Masayuki , Baba Hideo 
Published: March 2022

Objective:
This comprehensive analysis aimed to elucidate the mechanism underlying how high pretreatment red blood cell distribution width (RDW) reflects poor prognosis after esophagectomy for esophageal cancer.

Background:
Several cohort studies have reported that preoperative RDW might be a predictive marker for poor prognosis after esophagectomy; however, the underlying mechanism of this relationship has not been elucidated.

Methods:
This study included 626 patients with esophageal cancer who underwent esophagectomy between April 2005 and November 2020. A retrospective investigation of the association between pretreatment RDW and clinicopathological features, blood data, short-term outcomes, and prognosis was conducted using a prospectively entered institutional clinical database and the latest follow-up data.

Results:
Of 626 patients, 87 (13.9%) had a high pretreatment RDW. High RDW was significantly associated with several disadvantageous characteristics regarding performance status, the American Society of Anesthesiologists physical status, respiratory comorbidity, and nutritional status. Similarly, high RDW correlated with frequent postoperative morbidities (respiratory morbidity and reoperation; P = 0.022 and 0.034, respectively), decreased opportunities for adjuvant chemotherapy (P = 0.0062), and increased death from causes other than esophageal cancer (P = 0.046). Finally, RDW could be an independent predictor of survival after esophagectomy (hazard ratio, 1.47; 95% confidence interval, 1.009–2.148; P = 0.045).

Conclusion:
High pretreatment RDW reflected various adverse backgrounds and it could be a surrogate marker of poor prognosis in patients who have undergone esophagectomy for esophageal cancer.
Simulated Bundled Payments for 4 Common Surgical Approaches to Treat Degenerative Cervical Myelopathy
Authors: Jain Nikhil , Sharma Mayur , Wang Dengzhi , Ugiliweneza Beatrice , Drazin Doniel , Boakye Maxwell 
Published: March 2022

Study Design:
Retrospective cohort study.

Objective:
The aim was to compare 90-day and 2-year reimbursements for ≥2-level anterior cervical discectomy and fusion (mACDF), anterior cervical corpectomy and fusion (ACCF), posterior laminectomy and fusion (LF) and laminoplasty (LP) done for degenerative cervical myelopathy (DCM).

Summary of Background Data:
In DCM pathologies where there exists a clinical equipoise in approach selection, a randomized controlled trial found that an anterior approach did not significantly improve patient-reported outcomes over posterior approaches. In the era of value and bundled payments initiatives, cost profile of various approaches will form an important consideration for decision making.

Materials and Methods:
IBM MarketScan Research Database (2005–2018) was used to study beneficiaries (30–75 y) who underwent surgery (mACDF, ACCF, LF, LP) for DCM. Index hospital stay (operating room, surgeon, hospital services) and postdischarge inpatient, outpatient and prescription medication payments have been used to simulate 90-day and 2-year bundled payment amounts, along with their distribution for each procedure.

Results:
A total of 10,834 patients with median age of 54 years were included. The median 90-day payment was $46,094 (interquartile range: $34,243–$65,841) for all procedures, with LF being the highest ($64,542) and LP the lowest ($37,867). Index hospital was 62.4% (operating room: 46.6) and surgeon payments were 17.5% of the average 90-day bundle. There was significant difference in the index, 90-day and 2-year reimbursements and their distribution among procedures.

Conclusion:
In a national cohort of patients undergoing surgery for DCM, LP had the lowest complication rate, and simulated bundled reimbursements at 90 days and 2 years postoperatively. The lowest quartile 90-day payment for LF was more expensive than median amounts for mACDF, ACCF, and LP. If surgeons encounter scenarios of clinical equipoise in practice, LP is likely to result in maximum value as it is on an average 70% less expensive than LF over 90 days.
ASSESSMENT OF FLUORESCEIN ANGIOGRAPHY NONPERFUSION IN EYES WITH DIABETIC RETINOPATHY USING ULTRAWIDE FIELD RETINAL IMAGING
Authors: Silva Paolo S. , Liu Danni , Glassman Adam R. , Aiello Lloyd P. , Grover Sandeep , Kingsley Ronald M. , Melia Michele , Sun Jennifer K. ,   for the DRCR Retina Network
Published: March 2022

Purpose:
Evaluate association of retinal nonperfusion (NP) on ultrawide field (UWF) fluorescein angiography (FA) with diabetic retinopathy (DR) severity and predominantly peripheral lesions (PPL).

Methods:
Multicenter observational study, 652 eyes (361 participants) having nonproliferative DR (NPDR) without center-involved diabetic macular edema in at least one eye. Baseline 200° UWF-color and UWF-FA images were graded by a central reading center for color-PPL and FA-PPL, respectively. UWF-FA was graded for NP index within concentric zones: posterior pole (<10 mm from fovea), midperiphery (10–15 mm), and far periphery (>15 mm).

Results:
Baseline Early Treatment Diabetic Retinopathy Study DR severity was 31.7% no DR/mild NPDR, 24.1% moderate NPDR, 14.0% moderately severe NPDR, 25.6% severe/very severe NPDR, and 4.6% proliferative DR. Worse DR severity was associated with increased NP index overall (P = 0.002), in the posterior pole (P < 0.001), midperiphery (P < 0.001), and far periphery (P = 0.03). On average, 29.6% of imaged retinal NP was in the posterior pole, 33.7% in midperiphery, and 36.7% in far periphery. Increased NP index was associated with FA-PPL (P < 0.001) but not with color-PPL (P = 0.65).

Conclusion:
Approximately, 70% of NP in diabetic eyes is located outside the posterior pole. Increased NP is associated with the presence of FA-PPL, suggesting UWF-FA may better predict future DR worsening than UWF-color alone.
REGIONAL SCLERAL THICKNESS AS A RISK FACTOR FOR CENTRAL SEROUS CHORIORETINOPATHY
Authors: Spaide Richard F. , Fisher Yale L. , Ngo Wei Kiong , Barbazetto Irene 
Published: March 2022

Purpose:
To evaluate regional sclera thicknesses as possible risk factors for central serous chorioretinopathy (CSC).

Methods:
Patients with CSC and controls were evaluated with contact B-scan ultrasonography using a 20 Mhz concentric phased array ultrasound unit and enhanced depth imaging optical coherence tomography to measure the scleral thickness at the equator and posterior pole. The resultant data were evaluated using univariate analysis and generalized estimating equations.

Results:
There were 40 patients with CSC with a mean age of 58 years and 23 controls with a mean age of 60.7 years (P = 0.31). The mean subfoveal scleral thicknesses were 1.3 mm in the CSC group and 0.86 mm in the control group (P < 0.001). The mean equatorial scleral thickness was 0.61 mm in the CSC group and 0.42 mm in the control group (P < 0.001). Using generalized estimating equations, the equatorial scleral thickness (P = 0.001), posterior scleral thickness (P < 0.001), and subfoveal choroidal thickness (P = 0.032) were independent predictors of CSC. Once these variables were entered into the equation, neither sex nor age were significant predictors. Generalized estimating equation analysis showed that equatorial, but not posterior, scleral thickness was a significant predictor of subfoveal choroidal thickness.

Conclusion:
Scleral thicknesses of the posterior and equatorial portions of the eye were found to be significant predictors of CSC, consistent with what was proposed in the theory of venous overload choroidopathy. Direct measurement by high resolution ultrasonography provides independent information about specific regions of the sclera and also avoids making speculative assumptions derived from anterior segment measurements.
NINE-YEAR PROGRESSION OF PENTOSAN MACULOPATHY WITH MULTIMODAL RETINAL IMAGING
Authors: Santina Ahmad , Fogel-Levin Miri , Abraham Neda , Sarraf David 
Published: March 2022

Background/Purpose:
The purpose of this study was to describe the characteristic pattern of progression of pentosan polysulfate (PPS) maculopathy with multimodal retinal imaging in two patients, including one with over 9 years of follow-up.

Methods:
Two patients with PPS maculopathy were sequentially evaluated with near-infrared reflectance (NIR) and optical coherence tomography.

Results:
Near-infrared reflectance showed characteristic centrifugal progression of the parafoveal hyperreflective lesions toward the vascular arcades with the development of hyporeflective areas in both cases. Optical coherence tomography demonstrated focal retinal pigment epithelium (RPE) thickening that corresponded to the hyperreflective lesions on NIR. On subsequent optical coherence tomography scans, the hyperreflective areas resolved with the development of ellipsoid zone attenuation, RPE disruption, and atrophy, which colocalized with hyporeflectivity on NIR.

Conclusion:
This report describes the progression of pentosan polysulfate maculopathy over almost 10 years of PPS treatment and highlights the importance of NIR as a tool for the diagnosis and monitoring of PPS maculopathy. Pentosan polysulfate lesions present as areas of focal RPE thickening with ensuing development of ellipsoid zone loss and RPE drop-out. The pathophysiology of PPS toxicity is unknown and may either result from primary RPE or choroidal toxicity.
Patterns of Adherence to a Dapivirine Vaginal Ring for HIV-1 Prevention Among South African Women in a Phase III Randomized Controlled Trial
Authors: Browne Erica N. , Brown Elizabeth R. , Palanee-Phillips Thesla , Reddy Krishnaveni , Naidoo Logashvari , Jeenarain Nitesha , Nair Gonasagrie , Husnik Marla J. , Singh Devika , Scheckter Rachel , Soto-Torres Lydia , Baeten Jared M. , van der Straten Ariane ,   On behalf of the MTN-020/ASPIRE Study Team
Published: March 2022

Background:
Persistent use of HIV prevention methods can be a challenge, particularly for some younger women. The long-acting, discreet, woman-centric dapivirine vaginal ring offers promise as a prevention method with less user burden, which could support continued use. We assessed dapivirine vaginal ring use to understand adherence patterns and identify characteristics influencing patterns.

Setting:
Participants enrolled in South Africa in the MTN-020/ASPIRE randomized placebo-controlled trial.

Methods:
We used group-based trajectory modeling to identify clusters of participants with similar longitudinal patterns of adherence in the last year of participation and potential predictors of group membership. Women with at least 1 year of follow-up were included (n = 626).

Results:
Five adherence patterns were identified: (1) consistently high, 34%, (2) consistently moderate, 34%, (3) consistently low, 16%, (4) decreasing, 9%, and (5) increasing, 7%. Women younger than 22 years [adjusted odds ratio (AOR) 1.8, 95% confidence interval (CI): 1.0 to 3.0], using an intrauterine device (AOR 3.3, 95% CI: 1.4 to 7.8) or oral contraceptives (AOR 3.9, 95% CI: 1.7 to 8.9), experiencing menses (AOR 1.8, 95% CI: 1.1 to 3.0), and who reported inconsistent condom use (AOR 1.8, 95% CI: 1.0 to 3.3) were more likely to be classified as consistently low compared to consistently high (referent).

Conclusions:
Most South African women successfully persisted with a moderate or high level of use. Encouraging ring replacement with completion of menses may help to decrease concerns about hygiene and improve persistence. Associations between contraception and persistent low adherence suggest efforts may be needed to ensure contraceptive method choice does not interfere with ring use.
Youth violence prevention can be enhanced by geospatial analysis of trauma registry data
Authors: Doucet Jay J. , Godat Laura N. , Berndtson Allison E. , Liepert Amy E. , Weaver Jessica L. , Smith Alan M. , Kobayashi Leslie M. , Biffl Walter L. , Costantini Todd W. 
Published: March 2022

BACKGROUND
Geographic information systems (GIS) have been used to understand relationships between trauma mechanisms, locations, and social determinants for injury prevention. We hypothesized that GIS analysis of trauma center registry data for assault patients aged 14 years to 29 years with census tract data would identify geospatial and structural determinants of youth violence.

METHODS
Admissions to a Level I trauma center from 2010 to 2019 were retrospectively reviewed to identify assaults in those 14 years to 29 years. Prisoners were excluded. Home and injury scene addresses were geocoded. Cluster analysis was performed with the Moran I test for spatial autocorrelation. Census tract comparisons were done using American Communities Survey (ACS) data by t-test and linear regression.

RESULTS
There were 1,608 admissions, 1,517 (92.4%) had complete addresses and were included in the analysis. Mean age was 23 ± 3.8 years, mean ISS was 7.5 ± 6.2, there were 11 (0.7%) in-hospital deaths. Clusters in six areas of the trauma catchment were identified with a Moran I value of 0.24 (Z score = 17.4, p < 0.001). Linear regression of American Communities Survey demographics showed predictors of assault were unemployment (odds ratio, 4.5; 95% confidence interval, 2.7–6.4; p < 0.001), Spanish spoken at home (odds ratio, 6.6; 95% confidence interval, 3.4–9.8; p < 0.001) and poverty level (odds ratio, 1.9; 95% confidence interval, 1.1–2.7; p < 0.001). Education level of less than high school diploma, single parent households and race were not significant predictors.

CONCLUSION
GIS analysis of registry data can identify high-risk areas for youth violence and correlated social and structural determinants. Violence prevention efforts can be better targeted geographically and socioeconomically with better understanding of these risk factors.

LEVEL OF EVIDENCE
Prognostic/Epidemiological; Level III.
The Utility of Noninvasive PET/CT Myocardial Perfusion Imaging in Adult Liver Transplant Candidates
Authors: Tincopa Monica A. , Weinberg Richard L. , Sengupta Shreya , Slivnick Jeremy , Corbett James , Sonnenday Christopher J. , Fontana Robert J. , Sharma Pratima 
Published: March 2022

Background.
The optimal cardiovascular (CV) risk stratification in liver transplant (LT) candidates remains unclear. The aim of this study was to evaluate concordance of findings between dobutamine stress echocardiography (DSE), positron emission tomography/computed tomography myocardial perfusion imaging (PET/CT MPI), and left heart catheterization in adult LT candidates.

Methods.
Data on 234 consecutive adult LT candidates from February 2015 to June 2018 with PET/CT MPI were reviewed. Adverse CV outcomes were adjudicated via chart review by a board-certified cardiologist.

Results.
Median age was 60.8, body mass index 30.2 kg/m2, and model of end-stage liver disease–sodium 14; 61% were male, and 54% had diabetes. Thirty-seven percent had nonalcoholic steatohepatitis and 29% alcohol-related liver disease. Sixty-five percent of patients had a DSE, of which 41% were nondiagnostic. No factors were independently associated with having a nondiagnostic DSE. The median global myocardial flow reserve correlated positively with hemoglobin and negatively with model of end-stage liver disease–sodium, age, ejection fraction, and body mass index. Moderate/high-risk MPIs were associated with older age and known CV disease. In patients with 2 cardiac testing modalities, findings were concordant in 87%. Eleven of 53 LT recipients experienced an adverse CV outcome, but no independent predictors were identified for this outcome.

Conclusions.
Results of different cardiac risk-stratification modalities were concordant across modalities the majority of the time in LT candidates, although these findings were not independently correlated with risk of post-LT CV outcomes. Given the high rates of nondiagnostic DSEs in this population, PET/CT MPI may be the preferred CV risk-stratification modality in older patients and those with known CV disease.