bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quashing a suspected selection bias in galaxy samples having dynamically measured supermassive black holes
Authors: Sahu Nandini , Graham Alister W , Hon Dexter S-H 
Published: October 2022

ABSTRACT
Local early-type galaxies (ETGs) with directly measured black hole masses, Mbh, have been reported to represent a biased sample relative to the ETG population at large. Such galaxies with Spitzer Space Telescope imaging have been purported to possess velocity dispersions, σ, at least ∼0.1 dex larger for a given galaxy stellar mass, M*,gal, than is typically observed among thousands of ETGs imaged by the Sloan Digital Sky Survey (SDSS). This apparent offset led Shankar et al. to reduce the normalisation of the observed Mbh ∝ σ5 relation by at least ∼0.5 dex to give their ‘intrinsic relations’, including σ-based modifications to the observed Mbh–M*,gal relation. These modifications were based on the untested assumption that the stellar masses had been derived consistently between the two samples. Here, we provide the necessary check using galaxies common to the Spitzer Survey of Stellar Structure in Galaxies (S4G) and the SDSS. We find that the stellar masses of galaxies with and without directly measured black hole masses had appeared offset from each other due to the use of inconsistent stellar mass-to-light ratios, Υ*, for the optical and infrared data. We briefly discuss the ‘intrinsic relations’ and why some of these will at times appear to have had partial success when applied to data based on similarly inconsistent values ofΥ*. Finally, we reiterate the importance of the υ (lower-case Υ) term, which we previously introduced into the Mbh–M* relations to help avoid Υ*-related mismatches.
SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome
Authors: Piñero-Lambea Carlos , Garcia-Ramallo Eva , Miravet-Verde Samuel , Burgos Raul , Scarpa Margherita , Serrano Luis , Lluch-Senar Maria 
Published: October 2022

Abstract
The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a multi-recombinase engineering rationale combining oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We test this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombination machinery. Using SURE editing, we can seamlessly generate, in a single step, a wide variety of genome modifications at high efficiencies, including the largest possible deletion of this genome (30 Kb) and the targeted complementation of essential genes in the deletion of a region of interest. Additional steps can be taken to remove the selector plasmid from the edited area, to obtain markerless or even scarless edits. Of note, SURE editing is compatible with different site-specific recombinases for mediating transient plasmid integration. This battery of selector plasmids can be used to select different edits, regardless of the target sequence, which significantly reduces the cloning load associated to genome engineering projects. Given the proven functionality in several microorganisms of the machinery behind the SURE editing logic, this method is likely to represent a valuable advance for the synthetic biology field.
Two type I topoisomerases maintain DNA topology in human mitochondria
Authors: Menger Katja E , Chapman James , Díaz-Maldonado Héctor , Khazeem Mushtaq M , Deen Dasha , Erdinc Direnis , Casement John W , Di Leo Valeria , Pyle Angela , Rodríguez-Luis Alejandro , Cowell Ian G , Falkenberg Maria , Austin Caroline A , Nicholls Thomas J 
Published: October 2022

Abstract
Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.
HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Authors: Zeng Wanwen , Liu Qiao , Yin Qijin , Jiang Rui , Wong Wing Hung 
Published: October 2022

AbstractElucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains ∼262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.
Thyclotides, tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-21
Authors: Clausse Victor , Zheng Hongchao , Amarasekara Harsha , Kruhlak Michael , Appella Daniel H 
Published: October 2022

Abstract
Peptide nucleic acids (PNAs) are promising therapeutic molecules for gene modulation; however, they suffer from poor cell uptake. Delivery of PNAs into cells requires conjugation of the PNA to another large molecule, typically a cell-penetrating peptide or nanoparticle. In this study, we describe a new PNA-based molecule with cyclic tetrahydrofuran (THF) backbone modifications that in some cases considerably improve cell uptake. We refer to these THF-PNA oligomers as thyclotides. With THF groups at every position of the oligomer, the cell uptake of thyclotides targeted to miR-21 is enhanced compared with the corresponding unmodified PNA based on an aminoethylglycine backbone. An optimized thyclotide can efficiently enter cells without the use of cell-penetrating peptides, bind miR-21, its designated microRNA target, decrease expression of miR-21 and increase expression of three downstream targets (PTEN, Cdc25a and KRIT1). Using a plasmid with the PTEN-3′UTR coupled with luciferase, we further confirmed that a miR-21-targeted thyclotide prevents miR-21 from binding to its target RNA. Additionally, the thyclotide shows no cytotoxicity when administered at 200 times its active concentration. We propose that thyclotides be further explored as therapeutic candidates to modulate miRNA levels.
Measurement of Mobility and Physical Function in Patients Hospitalized With Hip Fracture: A Systematic Review of Instruments and Their Measurement Properties
Authors: Rix Alana , Lawrence Drew , Raper Eleanor , Calthorpe Sara , Holland Anne E , Kimmel Lara A 
Published: October 2022

AbstractObjectiveHip fractures are common and significantly impact mobility and physical function. Measurement of patient progress post hip fracture in the acute hospital setting is important to monitor early recovery and outcomes. The objective of this systematic review was to assess the measurement properties (reliability, validity, responsiveness), interpretability, and clinical utility of instruments used to measure mobility and physical function in patients with hip fracture in the acute hospital setting.MethodsThree databases (MEDLINE, Embase, and CINAHL) were searched. Studies reporting direct clinician assessment instruments to measure mobility or physical function in patients with hip fracture were included. Data were extracted by 2 reviewers, and the quality of each study was determined using the COnsensus-based Standards for the selection of health Measurement INstruments risk of bias checklist.ResultsSixty-eight studies were included with 19 measurement instruments identified. The most frequently used instruments were the Timed “Up & Go” Test (TUG) (19 studies), Barthel Index (BI) (18 studies), Cumulated Ambulation Score (CAS) (18 studies), and Functional Independence Measure (FIM) (14 studies). All 4 of these instruments demonstrated good predictive validity (clinical outcomes and mortality) and responsiveness over time (effect sizes 0.63–2.79). The BI and CAS also had good reliability (intraclass correlation coefficient [ICC] &gt;0.70). Floor effects were demonstrated for the TUG, CAS, and FIM (16%–60% of patients). The TUG, CAS, and BI all had good clinical utility.ConclusionDepending on the context (use by treating clinicians, research, benchmarking), 1 or a combination of the BI, CAS, and TUG provide robust measurement of mobility and physical function for patients with hip fracture in the acute hospital setting.ImpactThis study identified 3 instruments suitable for measuring mobility and physical function in hospitalized patients following hip fracture. This provides clinicians with tools to measure patient progress and benchmark across sites to improve patient outcomes.
Postoperative/postdischarge nausea and vomiting: evidence-based prevention and treatment
Authors: Schlesinger Tobias , Weibel Stephanie , Kranke Peter 
Published: October 2022

Purpose of review
Postoperative/postdischarge nausea and vomiting (PONV/PDNV) remains a relevant issue in perioperative care. Especially in outpatient surgery, PONV can prevent discharge or lead to unplanned readmission.

Recent findings
Evidence on prophylaxis and treatment of PONV is growing, but implementation remains poor.

Summary
A liberal, universal PONV management is now endorsed by the guidelines. Specific evidence concerning prevention and (at-home) treatment of PDNV is still scarce.
The Ideal Threshold of Hemoglobin A1C in Diabetic Patients Undergoing Elective Lumbar Decompression Surgery
Authors: Gupta Rishabh , Chanbour Hani , Roth Steven G. , O’Brien Alex , Davidson Claudia , Devin Clinton J. , Stephens Byron F. , Abtahi Amir M. , Zuckerman Scott L. 
Published: October 2022

Study Design:
Retrospective cohort study.

Objective:
To evaluate the association of Hemoglobin A1C (HbA1c) with surgical site infection (SSI) and patient-reported outcomes (PROs), and to identify optimal HbA1c thresholds to minimize the risk of SSI and maximize PROs.

Summary of Background Data:
Diabetes mellitus has been associated with worsened outcomes following spine surgery. HbA1c, a surrogate of glycemic control, is an important assessment tool in diabetic patients.

Methods:
A single-center, retrospective cohort study using prospectively collected data was undertaken. Diabetic patients undergoing elective lumbar decompression surgery between October 2010 and May 2021 were included. HbA1c, demographics, comorbidities, and perioperative data were collected. Primary outcomes included: 1) SSI, and 2) PROs, including the Numeric Rating Scale (NRS)-back/leg pain and Oswestry Disability Index (ODI). Secondary outcomes included: complications, readmissions, and reoperations within 90-days postoperatively. The minimum clinically important difference (MCID) was set at a 30% improvement from baseline PROs.

Results:
Of 1819 patients who underwent lumbar decompression surgery, 368 patients had diabetes mellitus, and 177 had a documented preoperative HbA1c value. Of patients with available HbA1c values, the mean age was 62.5±12.3, the mean HbA1c value was 7.2±1.5%, and SSI occurred in 3 (1.7%) patients only, which prevented further analysis of SSI and HbA1c. A significant association was seen with a higher HbA1c and failure to achieve NRS-Back pain MCID30 [Odds ratio(OR)=0.53, 95% confidence interval(CI) 0.42–0.78;P=0.001] and ODI MCID30 (OR=0.58, 95%CI 0.44–0.77;P=0.001), but not NRS-Leg pain MCID30 (OR=1.29, 95%CI 0.86–1.93;P=0.208). ROC-curve analysis and Youden’s index revealed an HbA1c threshold of 7.8 for NRS-Back pain MCID30 (AUC=0.65,P<0.001) and 7.5 for ODI MCID30 (AUC=0.65,P=0.001).

Conclusions:
In diabetic patients undergoing elective lumbar decompression surgery, HbA1c levels above 7.8 and 7.5 were associated with less improvement of NRS-Back and ODI scores at 12-months postoperatively, respectively. To optimize PROs, We recommend a preoperative HbA1c of 7.5 or below for diabetic patients undergoing elective lumbar decompression surgery.
Association Between Tracheostomy and Functional, Neuropsychological, and Healthcare Utilization Outcomes in the RECOVER Cohort
Authors: Mehta Sangeeta , Brondani Anita , Tomlinson George , Chu Leslie , Burns Stacey , Matte Andrea , Cameron Jill I. , Friedrich Jan O. , Rudkowski Jill , Robles Priscila , Skrobik Yoanna , Herridge Margaret , Adhikari Neill K. J. ,   for the Canadian RECOVER Program Investigators and the Canadian Critical Care Trials Group (CCCTG)
Published: October 2022

OBJECTIVES:
Tracheostomy is commonly performed in critically ill patients requiring prolonged mechanical ventilation (MV). We evaluated the outcomes of tracheostomy in patients who received greater than or equal to 1 week MV and were followed for 1 year.

DESIGN:
In this secondary analysis of a prospective observational study, we compared outcomes in tracheostomy versus nontracheostomy patients. Outcomes post ICU included Functional Independence Measure (FIM) subscales, 6-Minute Walk Test (6MWT), Short Form 36 (SF36), Medical Research Council (MRC) Scale, pulmonary function tests (PFTs), Impact of Event Scale (IES), Beck Depression Inventory-II (BDI-II), and vital status and disposition.

SETTING:
Nine University affiliated ICUs in Canada.

PATIENTS:
Medical/surgical patients requiring MV for 7 or more days who were enrolled in the Towards RECOVER Study.

MEASUREMENTS AND MAIN RESULTS:
Of 398 ICU survivors, 193 (48.5%) received tracheostomy, on median ICU day 14 (interquartile range [IQR], 8–0 d). Patients with tracheostomy were older, had similar severity of illness, had longer MV duration and ICU and hospital stays, and had higher risk of ICU readmission (odds ratio [OR], 1.9; 95% CI, 1.0–3.2) and hospital mortality (OR, 2.6; 95% CI, 1.1–6.1), but not 1-year mortality (hazard ratio, 1.41; 95% CI, 0.88–1.2). Over 1 year, tracheostomy patients had lower FIM-Total (7.7 points; 95% CI, 2.2–13.2); SF36, IES, and BDI-II were similar. From 3 months, tracheostomy patients had 12% lower 6MWT (p = 0.0008) and lower MRC score (3.4 points; p = 0.006). Most PFTs were 5–8% lower in the tracheostomy group. Tracheostomy patients had similar specialist visits (rate ratio, 0.63; 95% CI, 0.28–2.4) and hospital readmissions (OR, 0.82; 95% CI, 0.54–1.3) but were less likely to be at home at hospital discharge and 1 year.

CONCLUSIONS:
Patients who received tracheostomy had more ICU and hospital care and higher hospital mortality compared with patients who did not receive a tracheostomy. In 1 year follow-up, tracheostomy patients required a higher daily burden of care, expressed by FIM.
Benefits of international trauma rotation in South Africa: comparison with a trauma center in Tokyo
Authors: Nagao Tsuyoshi , Nakahara Shinji , Fujita Takashi , Sakamoto Tetsuya , Steyn Elmin 
Published: October 2022

Abstract
International rotations have been an option for young surgeons who face difficulties in obtaining sufficient trauma training in their own countries. One of the authors attended training in trauma surgery in South Africa for 6 months, where there are many trauma caseloads, and could experience the number of emergency operations equivalent to approximately 5 years in Japan. The rotation allows trainees to expose clinical practices intensively and to learn principles and theories of care under experienced academic surgeons. On the other hand, they could contribute to the host hospital as part of the workforce and by assisting young surgical residents. the development of a more systematic and formalized framework for staff exchange between developed and developing countries will provide mutual benefits to both sides.
Association between duration of return of spontaneous circulation and outcomes after out-of-hospital cardiac arrest
Authors: Lian Huixin , Xia Andong , Qin Xinyan , Tian Sijia , Kang Xuqin , Zhang Luxi , Niu Shengmei , Qin Fei , Zhang Jinjun 
Published: October 2022

Abstract

Background
Return of spontaneous circulation (ROSC) is a core outcome element of cardiopulmonary resuscitation (CPR); however, the definition or criterion of ROSC is disputed and varies in resuscitation for out-of-hospital cardiac arrest (OHCA).

Methods
This was a retrospective study of 126 patients with OHCA who achieved ROSC between January and December 2020. The probability of survival after OHCA related to CPR and ROSC duration was analyzed using the probability density function and empirical cumulative density functions.

Results
There were no significant differences between ROSC sustained until emergency department arrival and that sustained for at least 20 minutes in terms of the 24-hour survival rate (31.3% [31/99] vs. 35.7% [10/30]; P = 0.84), 30-day survival rate (23.2% [23/99] vs. 25.0% [7/30]; P = 0.99), or survival at 30 days with cerebral performance category (CPC) 1 and 2 (18.2% [18/99] vs. 10.7% [3/30]; P = 0.44). The Kolmogorov-Smirnov test values from the empirical cumulative density functions with ROSC sustained until hospital arrival and that sustained for at least 20 minutes were 0.44, 0.20, and 0.24 for CPC 1 or 2, CPC 3 or 4, and CPC 5, respectively.

Conclusion
Return of spontaneous circulation is a core outcome element of CPR. It should be defined as sustained for at least 20 minutes or until arrival at the emergency department and as a basic standard for evaluating resuscitation success after OHCA.
Facial microbial flora in bearded versus nonbearded men in the operating room setting: A single-center cross-sectional STROBE-compliant observational study
Authors: El Edelbi Mostapha , Hassanieh Joelle , Malaeb Nancy , Abou Fayad Antoine , Jaafar Rola F. , Sleiman Ahmad , Abedelrahim Abdelkader , Kanafani Zeina , Matar Ghassan M. , Zaghal Ahmad 
Published: October 2022

Beards are controversial in the operating room setting because of the possible retention and shedding of pathogens. Surgical site infection poses a significant burden on healthcare systems. All male healthcare workers who entered the operating room were approached to participate in the study. Four facial swab samples were anonymously collected and a hygiene practice questionnaire was administered. Sample A was taken from the upper and lower lips, sample B from cheeks, and samples C and D were collected by 20 and 40 cm shedding below the face. Colony-forming units (CFUs) and minimum inhibitory concentrations (MICs) of meropenem resistance were determined for samples A and B. Random samples from A, B, C, and D, in addition to meropenem-resistant isolates were cultured with chlorohexidine. Sixty-one bearded and 19 nonbearded healthcare workers participated in the study. 98% were positive for bacterial growth with CFU ranging between 30 × 104 and 200 × 106 CFU/mL. Bacterial growth was significantly higher in bearded participants (P < .05). Eighteen (27.1%) isolates were resistant to meropenem; of these which 14 (77.8%) were from bearded participants, this was not statistically significant. Chlorohexidine was effective in inhibiting the growth of all strains including the meropenem-resistant isolates. Bearded men in the operating room had a significantly higher facial bacterial load. Larger-scale resistance studies are needed to address facial bacterial resistance among healthcare workers in the operating room.
This study aimed to estimate the facial microbial load and identify strains and antimicrobial resistance profiles in bearded versus nonbearded male healthcare workers in the operating room of a tertiary hospital in the Middle East.
Trend and prediction of citations on the topic of neuromuscular junctions in 100 top-cited articles since 2001 using a temporal bar graph: A bibliometric analysis
Authors: Wu Jian-Wei , Yan Yu-Hua , Chien Tsair-Wei , Chou Willy 
Published: October 2022

Background:
A neuromuscular junction (NMJ) (or myoneural junction) is a chemical synapse between a motor neuron (MN) and a muscle fiber. Although numerous articles have been published, no such analyses on trend or prediction of citations in NMJ were characterized using the temporal bar graph (TBG). This study is to identify the most dominant entities in the 100 top-cited articles in NMJ (T100MNJ for short) since 2001; to verify the improved TBG that is viable for trend analysis; and to investigate whether medical subject headings (MeSH terms) can be used to predict article citations.

Methods:
We downloaded T100MNJ from the PubMed database by searching the string (“NMJ” [MeSH Major Topic] AND (“2001” [Date - Modification]: “2021” [Date - Modification])) and matching citations to each article. Cluster analysis of citations was performed to select the most cited entities (e.g., authors, research institutes, affiliated countries, journals, and MeSH terms) in T100MNJ using social network analysis. The trend analysis was displayed using TBG with two major features of burst spot and trend development. Next, we examined the MeSH prediction effect on article citations using its correlation coefficients (CC) when the mean citations in MeSH terms were collected in 100 top-cited articles related to NMJ (T100NMJs).

Results:
The most dominant entities (i.e., country, journal, MesH term, and article in T100NMJ) in citations were the US (with impact factor [IF] = 142.2 = 10237/72), neuron (with IF = 151.3 = 3630/24), metabolism (with IF = 133.02), and article authored by Wagh et al from Germany in 2006 (with 342 citing articles). The improved TBG was demonstrated to highlight the citation evolution using burst spots, trend development, and line-chart plots. MeSH terms were evident in the prediction power on the number of article citations (CC = 0.40, t = 4.34).

Conclusion:
Two major breakthroughs were made by developing the improved TBG applied to bibliographical studies and the prediction of article citations using the impact factor of MeSH terms in T100NMJ. These visualizations of improved TBG and scatter plots in trend, and prediction analyses are recommended for future academic pursuits and applications in other disciplines.