bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pooling Sputum Samples for Efficient Mass Tuberculosis Screening in Prisons
Authors: dos Santos Paulo César Pereira , da Silva Santos Andrea , de Oliveira Roberto Dias , da Silva Bruna Oliveira , Soares Thiego Ramon , Martinez Leonardo , Verma Renu , Andrews Jason R , Croda Julio 
Published: September 2021

Abstract

Background
Although systematic tuberculosis screening in high-risk groups is recommended by the World Health Organization (WHO), implementation in prisons has been limited due to resource constraints. Whether Xpert Ultra sputum pooling could be a sensitive and efficient approach to mass screening in prisons is unknown.

Methods
In total, 1280 sputum samples were collected from incarcerated individuals in Brazil during mass screening and tested using Xpert G4. We selected samples for mixing in pools of 4, 8, 12, and 16, which were then tested using Ultra. In each pool, a single positive sample of differing Xpert mycobacterial loads was used. Additionally, 10 pools of 16 negative samples each were analyzed as controls. We then simulated tuberculosis screening at prevalences of 0.5–5% and calculated the cost per tuberculosis case detected at different sputum pooling sizes.

Results
The sensitivity and specificity of sputum pooling were high (sensitivity: 94%; 95% confidence interval [CI]: 88–98; specificity: 100%, 95% CI: 84–100). Sensitivity was greater in pools in which the positive sample had a high mycobacterial load compared to those that were very low (100% vs 88%). In settings with a higher tuberculosis prevalence, pools of 4 and 8 were more efficient than larger pool sizes. Larger pools decreased the costs by 87% at low prevalences, whereas smaller pools led to greater cost savings at higher prevalence at higher prevalences (57%).

Conclusions
Sputum pooling using Ultra was a sensitive strategy for tuberculosis screening. This approach was more efficient than individual testing across a broad range of simulated tuberculosis prevalence settings and could enable active case finding to be scaled while containing costs.
Accuracy of a Rapid Multiplex Polymerase Chain Reaction Plus a Chromogenic Phenotypic Test Algorithm for Detection of Extended-Spectrum β-Lactamase and Carbapenemase-Producing Gram-Negative Bacilli in Positive Blood Culture Bottles
Authors: Ong Sean Wei Xiang , Hon Pei Yun , Wee Sharon Syn Hui , Chia Jonathan Wei Zhong , Mendis Shehara , Izharuddin Ezlyn , Lin Ray Junhao , Chia Po Ying , Sim Rees Chin Swee , Chen Mark I-Cheng , Chow Angela , Yoong Joanne , Lye David Chien , Teng Christine B , Tambyah Paul Anantharajah , Banerjee Ritu , Patel Robin , De Partha Pratim , Vasoo Shawn 
Published: September 2021

Abstract
We studied the performance of an algorithm combining multiplex polymerase chain reaction with phenotypic detection of extended-spectrum β-lactamases and carbapenemases directly from positive blood culture bottles in patients with gram-negative bacteremia and found good concordance with routine cultures. Such an algorithm may be a tool to improve time to optimal therapy in patients with gram-negative bacteremia.
Pharmacokinetics and Efficacy of Human Hyperimmune Intravenous Immunoglobulin Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Adult Syrian Hamsters
Authors: Stauft Charles B , Tegenge Million , Khurana Surender , Lee Youri , Selvaraj Prabhuanand , Golding Hana , Wang Tony , Golding Basil 
Published: September 2021

Abstract

Background
After the failure of antibody therapies in treating hospitalized patients with coronavirus disease 2019 (COVID-19), we investigated the impact of viral replication on the pharmacokinetics and efficacy of a hyperimmune severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin (CoVIG) product in treating SARS-CoV-2 infection using an adult Syrian hamster model.

Methods
The CoVIG was manufactured from plasma donors who had recovered from COVID-19. The dose used (400 mg/kg) was based on the dose given in clinical trials to hospitalized patients with COVID-19. Hamsters were given a single dose of CoVIG 2 days after challenge with the SARS-CoV-2 virus (isolate NY/PV08410/2020), followed by sampling of blood, nasal, tracheal, and lung tissues at different time points. The blood samples were assayed for anti–SARS-CoV-2 spike binding and used to calculate pharmacokinetic (PK) parameters. Nasal wash, tracheal, and lung tissue samples were assayed for viral replication by polymerase chain reaction (subgenomic messenger RNA).

Results
CoVIG-treated hamsters showed a reduction in viral replication in the lower respiratory tract, but minimal reduction in the upper respiratory tract, after challenge with SARS-CoV-2. Challenge resulted in altered PK parameters proportionate to viral replication, resulting in decreased area under the curve, accelerated clearance, and shorter half-life of CoVIG.

Conclusions
These data indicate that in the presence of actively replicating SARS-CoV-2 virus, PK parameters are altered and should trigger an adjustment in CoVIG dosing.
Diagnostic Stewardship in Clinical Microbiology, Essential Partner to Antimicrobial Stewardship
Authors: Sullivan Kaede V 
Published: September 2021

AbstractBackgroundDiagnostic stewardship is an important partner to antimicrobial stewardship.ContentDiagnostic stewardship focuses on ensuring correct diagnosis of infectious diseases while antimicrobial stewardship aims to optimize antimicrobial treatment. Both aim to improve patient outcomes. Diagnostic stewardship involves interventions that reduce testing in patients with low pretest probability, optimize a test’s likelihood ratio, and seek to warn providers when suboptimal test results might have been reported.ConclusionDiagnostic stewardship interventions have been described primarily in the areas of urinary tract infection, Clostridioides difficile infection, and bloodstream infection diagnosis. However, emerging areas include pneumonia and wound infections in addition to optimization of multiplexed panel-based testing.
Rare Correlated Coherent Association Rule Mining With CLS-MMS
Authors: Datta Subrata , Mali Kalyani , Ghosh Udit , Bose Subrata , Das Sourav , Ghosh Sourav 
Published: September 2021

AbstractThe study of coherent association rules based on propositional logic is an important area of association rule mining. Users may get a large number of itemsets for low minsup and lose valuable itemsets for high minsup. Mining without minsup may cause itemset explosions that contain spurious itemsets with low correlations and take a long time to mine. For mining coherence rules, existing approaches consider only the frequent itemsets, ignoring rare itemsets. Moreover, all items in the database are regarded equally important, which is not practical in real-world applications. By using the confidence-lift specified multiple minimum supports combined with propositional logic, we propose an efficient approach called rare correlated coherent association rule mining that addresses all of the problems stated above. We define and incorporate termination bound of support (${s}_{TB}$) and termination bound of dissociation (${d}_{TB}$) for early pruning of the candidate itemsets. In the proposed approach, support thresholds are automatically applied to the itemsets and coherent association rules are derived from the frequent and rare itemsets with high correlation and confidence. Experimental results obtained from real-life datasets show the effectiveness of the proposed approach in terms of itemsets and rule generation, correlation, confidence, runtime and scalability.
The Process of Developing a Disease Activity Index in Microscopic Colitis
Authors: Lesnovska Katarina Pihl , Münch Andreas , Bonderup Ole , Magro Fernando , Kupcinskas Juozas , Zabana Yamile , Tontini Gian Eugenio , Munck Lars Kristian , Guagnozzi Danila , Latella Giovanni , Fernandez-Banares Fernando , Miehlke Stephan , Madisch Ahmed , Wildt Signe , Hjortswang Henrik 
Published: September 2021

Abstract

Background and Aims
Patient-reported outcome measures [PROMs] aim to measure patients’ perception of how their disorder influences everyday functioning. The objective of this study was to develop a PROM to assess disease activity in microscopic colitis [MC] fulfilling the requirements of the Food and Drug Administration [FDA].

Methods
The European Microscopic Colitis Activity Index [E-MCAI] was developed in four steps. [1] A list of symptoms associated with active MC was created by a group of experts in the field. [2] Content validity of the symptoms was performed by experts [n = 14] and patients [n = 79] using the Content Validity Index. [3] Questions and response alternatives were created for each symptom, and validity of the E-MCAI was evaluated with cognitive interviews with patients [n = 7] and by the experts. [4] A pilot postal survey was performed to ensure usability.

Results
Seven of the symptoms related to active MC fulfilled the criteria for content validity and were included in the E-MCAI: stool consistency, stool frequency, stools at night, feel a need to pass more stools shortly after a bowel movement, urgent need to empty the bowel, leakage of stool and abdominal pain. The development and validation process resulted in the current version of the E-MCAI consisting of six questions related to MC.

Conclusions
The E-MCAI was developed using the methods advocated by the FDA. The evaluation indicates good content validity. Further evaluation will be performed to achieve construct validity, reliability and responsiveness in future cross-sectional and longitudinal studies.
A scoping review of artificial intelligence applications in thoracic surgery
Authors: Seastedt Kenneth P , Moukheiber Dana , Mahindre Saurabh A , Thammineni Chaitanya , Rosen Darin T , Watkins Ammara A , Hashimoto Daniel A , Hoang Chuong D , Kpodonu Jacques , Celi Leo A 
Published: September 2021

Abstract

OBJECTIVES
Machine learning (ML) has great potential, but there are few examples of its implementation improving outcomes. The thoracic surgeon must be aware of pertinent ML literature and how to evaluate this field for the safe translation to patient care. This scoping review provides an introduction to ML applications specific to the thoracic surgeon. We review current applications, limitations and future directions.

METHODS
A search of the PubMed database was conducted with inclusion requirements being the use of an ML algorithm to analyse patient information relevant to a thoracic surgeon and contain sufficient details on the data used, ML methods and results. Twenty-two papers met the criteria and were reviewed using a methodological quality rubric.

RESULTS
ML demonstrated enhanced preoperative test accuracy, earlier pathological diagnosis, therapies to maximize survival and predictions of adverse events and survival after surgery. However, only 4 performed external validation. One demonstrated improved patient outcomes, nearly all failed to perform model calibration and one addressed fairness and bias with most not generalizable to different populations. There was a considerable variation to allow for reproducibility.

CONCLUSIONS
There is promise but also challenges for ML in thoracic surgery. The transparency of data and algorithm design and the systemic bias on which models are dependent remain issues to be addressed. Although there has yet to be widespread use in thoracic surgery, it is essential thoracic surgeons be at the forefront of the eventual safe introduction of ML to the clinic and operating room.
Impact of mild cognitive impairment on unplanned readmission in patients with coronary artery disease
Authors: Ishihara Kodai , Izawa Kazuhiro P , Kitamura Masahiro , Ogawa Masato , Shimogai Takayuki , Kanejima Yuji , Morisawa Tomoyuki , Shimizu Ikki 
Published: September 2021

Abstract

Aims
To investigate the effect of mild cognitive impairment (MCI) on unplanned readmission in patients with coronary artery disease (CAD).

Methods and results
From 2132 CAD patients, MCI was estimated with the Japanese version of the Montreal Cognitive Assessment (MoCA-J) in 243 non-dementia patients who met the study criteria. The primary outcome was unplanned hospital readmission after discharge. The incidence of MCI in this cohort was 33.3%, and 51 patients (21.0%) had unplanned readmission during a mean follow-up period of 418.6 ± 203.5 days. After adjusting for the covariates, MCI (hazard ratio, 2.28; 95% confidence interval: 1.09–4.76; P = 0.03) was independently associated with unplanned readmission in the multivariable Cox proportional hazard regression analysis. In the Kaplan–Meier analysis, the cumulative incidence of unplanned readmission for the MCI group was significantly higher than that for the non-MCI group (log-rank test, P &lt; 0.001). Even after exclusion of the patients readmitted within 30 days of discharge, the main results did not change (log-rank test, P &lt; 0.001).

Conclusion
Mild cognitive impairment was independently associated with unplanned readmission after adjustment for many independent variables in CAD patients. In addition to its short-term effects, the adverse effects of MCI had a persistent, long-term impact on CAD patients. Assessment of cognitive function should be conducted by health professionals prior to hospital discharge and during follow-up. To prevent readmission of CAD patients, it will be necessary to support solutions to the problems that inhibit secondary prevention behaviours based on the assessment of the patients’ cognitive function.
Critical appraisal of technologies to assess electrical activity during atrial fibrillation: a position paper from the European Heart Rhythm Association and European Society of Cardiology Working Group on eCardiology in collaboration with the Heart Rhythm Society, Asia Pacific Heart Rhythm Society, Latin American Heart Rhythm Society and Computing in Cardiology
Authors: de Groot Natasja M S , Shah Dipen , Boyle Patrick M , Anter Elad , Clifford Gari D , Deisenhofer Isabel , Deneke Thomas , van Dessel Pascal , Doessel Olaf , Dilaveris Polychronis , Heinzel Frank R , Kapa Suraj , Lambiase Pier D , Lumens Joost , Platonov Pyotr G , Ngarmukos Tachapong , Martinez Juan Pablo , Sanchez Alejandro Olaya , Takahashi Yoshihide , Valdigem Bruno P , van der Veen Alle-Jan , Vernooy Kevin , Casado-Arroyo Ruben ,   ESC Scientific Document Group, De Potter Tom , Dinov Borislav , Kosiuk Jedrzej , Linz Dominik , Neubeck Lis , Svennberg Emma , Kim Young-Hoon , Wan Elaine , Lopez-Cabanillas Nestor , Locati Emanuela T , Macfarlane Peter 
Published: September 2021

Abstract
We aim to provide a critical appraisal of basic concepts underlying signal recording and processing technologies applied for (i) atrial fibrillation (AF) mapping to unravel AF mechanisms and/or identifying target sites for AF therapy and (ii) AF detection, to optimize usage of technologies, stimulate research aimed at closing knowledge gaps, and developing ideal AF recording and processing technologies. Recording and processing techniques for assessment of electrical activity during AF essential for diagnosis and guiding ablative therapy including body surface electrocardiograms (ECG) and endo- or epicardial electrograms (EGM) are evaluated. Discussion of (i) differences in uni-, bi-, and multi-polar (omnipolar/Laplacian) recording modes, (ii) impact of recording technologies on EGM morphology, (iii) global or local mapping using various types of EGM involving signal processing techniques including isochronal-, voltage- fractionation-, dipole density-, and rotor mapping, enabling derivation of parameters like atrial rate, entropy, conduction velocity/direction, (iv) value of epicardial and optical mapping, (v) AF detection by cardiac implantable electronic devices containing various detection algorithms applicable to stored EGMs, (vi) contribution of machine learning (ML) to further improvement of signals processing technologies. Recording and processing of EGM (or ECG) are the cornerstones of (body surface) mapping of AF. Currently available AF recording and processing technologies are mainly restricted to specific applications or have technological limitations. Improvements in AF mapping by obtaining highest fidelity source signals (e.g. catheter–electrode combinations) for signal processing (e.g. filtering, digitization, and noise elimination) is of utmost importance. Novel acquisition instruments (multi-polar catheters combined with improved physical modelling and ML techniques) will enable enhanced and automated interpretation of EGM recordings in the near future.
A novel hypermucoviscous Klebsiella pneumoniae ST3994-K2 clone belonging to Clonal Group 86
Authors: Cerdeira Louise , Nakamura-Silva Rafael , Oliveira-Silva Mariana , Sano Elder , Esposito Fernanda , Fuga Bruna , Moura Quézia , Miranda Carlos Eduardo Saraiva , Wyres Kelly , Lincopan Nilton , Pitondo-Silva André 
Published: September 2021

ABSTRACT
Emergent hypervirulent Klebsiella pneumoniae has been responsible for severe diseases, representing a serious threat to public health. We report the whole-genome sequencing of a novel ST3994-K2 clone, a single locus variant of ST86 K2, which is considered a worrying hypervirulent clone that emerged in several parts of the world. The strain K. pneumonia Kpi144 was isolated in 2013 from a blood culture of a 69-year-old male patient admitted to a tertiary hospital in Teresina, state of Piauí, northeastern Brazil. The strain was susceptible to 41 antibiotics tested, presented hypermucoviscous phenotype and a virulent behavior was observed in the Galleria mellonella infection model. Moreover, the virulome showed several virulence genes. To the best of our knowledge, this is the first worldwide report of a novel ST3994-K2 K. pneumoniae clone, an SLV of ST86 K2, which is considered a worrying virulent clone that has emerged in several parts of the world, including South America and Brazil.
Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets
Authors: Sanno Ryuto , Kataoka Kosuke , Hayakawa Shota , Ide Keigo , Nguyen Chuong N , Nguyen Thao P , Le Binh T N , Kim Oanh T P , Mineta Katsuhiko , Takeyama Haruko , Takeda Makio , Sato Toshiyuki , Suzuki Takeshi , Yura Kei , Asahi Toru 
Published: September 2021

Abstract
Species of infraorder Gryllidea, or crickets, are useful invertebrate models for studying developmental biology and neuroscience. They have also attracted attention as alternative protein sources for human food and animal feed. Mitochondrial genomic information on related invertebrates, such as katydids, and locusts, has recently become available in attempt to clarify the controversial classification schemes, although robust phylogenetic relationships with emphasis on crickets remain elusive. Here, we report newly sequenced complete mitochondrial genomes of crickets to study their phylogeny, genomic rearrangements, and adaptive evolution. First, we conducted de novo assembly of mitochondrial genomes from eight cricket species and annotated protein-coding genes and transfer and ribosomal RNAs using automatic annotations and manual curation. Next, by combining newly described protein-coding genes with public data of the complete Gryllidea genomes and gene annotations, we performed phylogenetic analysis and found gene order rearrangements in several branches. We further analyzed genetic signatures of selection in ant-loving crickets (Myrmecophilidae), which are small wingless crickets that inhabit ant nests. Three distinct approaches revealed two positively selected sites in the cox1 gene in these crickets. Protein 3D structural analyses suggested that these selected sites could influence the interaction of respiratory complex proteins, conferring benefits to ant-loving crickets with a unique ecological niche and morphology. These findings enhance our understanding of the genetic basis of cricket evolution without relying on estimates based on a limited number of molecular markers.
Comparison of Multiple Lapse Time Window Analysis and Qopen to determine intrinsic and scattering attenuation
Authors: van Laaten M , Eulenfeld T , Wegler U 
Published: September 2021

SUMMARYThis study compares the results of Multiple Lapse Time Windows Analysis (MLTWA) and full envelope inversion (Qopen) to determine intrinsic and scattering attenuation of the crust using the region around the central part of the Leipzig–Regensburg fault zone in Germany as an example. We use 18 of the region’s strongest earthquakes from 2008 to 2019 with a magnitude between 1.4 and 3.0 in the frequency band range between 3 and 34 Hz. The determined attenuation values of both methods are similar within their error bars. The inverse quality factors of the shear wave are relatively low compared to other regions, with values of 3.2 × 10−4 to 8.7 × 10−4 for $Q^{-1}_{i}$ and 1.4 × 10−4 to 2.8 × 10−4 for $Q^{-1}_{sc}$, respectively. As a by-product of Qopen, we also obtain the energy site amplification of the stations used in the inversion as well as source displacement spectra and moment magnitudes of the inverted earthquakes. Several combinations of inversion parameters were tested for MLTWA, with $Q^{-1}_{i}$ and $Q^{-1}_{sc}$ providing the lowest trade-off. Likewise, we investigated the influence of window length on the results of Qopen. We found a dependency of the results on the length, if the windows are shorter than 30 s. For longer time windows, the dependence disappears, and the result becomes independent of window length..
Predictors of social distancing compliance in an Australian sample
Authors: Thacker J , Sturman D , Auton J 
Published: September 2021

Abstract
Pandemics are associated with high rates of morbidity and mortality, and the coronavirus disease (COVID-19) pandemic has been the most fatal coronavirus outbreak of the 21st century. To reduce person-to-person transmission, interventions such as social distancing have been recommended; however, it is anticipated that 80% compliance is required to control the outbreak. A questionnaire was used to assess the factors related to compliance with social distancing restrictions using a modified version of the Theory of Planned Behavior (TPB) that included participants’ understanding of restrictions. The questionnaire included 18 vignettes (violating, non-violating and ambiguous) to assess participants’ knowledge of the social distancing restrictions and intentions to violate them. Participants were also presented the social distancing restrictions relevant at the time of completion and they were asked to consider the restrictions when anticipating their behavior in the vignettes. In line with the predictions of the TPB, intentions to adhere to restrictions and perceived behavioral control predicted participants’ self-reported behaviors. Further, attitudes (ATT) toward social distancing restrictions and knowledge of the restrictions predicted intentions to adhere to them. Public health messaging should aim to increase the understanding of the restrictions, e.g. through the use of example scenarios of permitted and prohibited behaviors. This would be particularly beneficial when changes are implemented to promote the understanding of the restrictions and positive ATT toward them.