bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive Correlation Between Candida auris Skin-Colonization Burden and Environmental Contamination at a Ventilator-Capable Skilled Nursing Facility in Chicago
Authors: Sexton D Joseph , Bentz Meghan L , Welsh Rory M , Derado Gordana , Furin William , Rose Laura J , Noble-Wang Judith , Pacilli Massimo , McPherson Tristan D , Black Stephanie , Kemble Sarah K , Herzegh Owen , Ahmad Ausaf , Forsberg Kaitlin , Jackson Brendan , Litvintseva Anastasia P 
Published: May 2021

Abstract

Background
Candida auris is an emerging multidrug-resistant yeast that contaminates healthcare environments causing healthcare-associated outbreaks. The mechanisms facilitating contamination are not established.

Methods
C. auris was quantified in residents’ bilateral axillary/inguinal composite skin swabs and environmental samples during a point-prevalence survey at a ventilator-capable skilled-nursing facility (vSNF A) with documented high colonization prevalence. Environmental samples were collected from all doorknobs, windowsills and handrails of each bed in 12 rooms. C. auris concentrations were measured using culture and C. auris-specific quantitative polymerase chain reaction (qPCR) The relationship between C. auris concentrations in residents’ swabs and associated environmental samples were evaluated using Kendall’s tau-b (τ b) correlation coefficient.

Results
C. auris was detected in 70/100 tested environmental samples and 31/57 tested resident skin swabs. The mean C. auris concentration in skin swabs was 1.22 × 105 cells/mL by culture and 1.08 × 106 cells/mL by qPCR. C. auris was detected on all handrails of beds occupied by colonized residents, as well as 10/24 doorknobs and 9/12 windowsills. A positive correlation was identified between the concentrations of C. auris in skin swabs and associated handrail samples based on culture (τ b = 0.54, P = .0004) and qPCR (τ b = 0.66, P = 3.83e−6). Two uncolonized residents resided in beds contaminated with C. auris.

Conclusions
Colonized residents can have high C. auris burdens on their skin, which was positively related with contamination of their surrounding healthcare environment. These findings underscore the importance of hand hygiene, transmission-based precautions, and particularly environmental disinfection in preventing spread in healthcare facilities.
Influence of doctors’ perception on the diagnostic status of chronic kidney disease: results from 976 409 individuals with electronic health records in China
Authors: Wang Huai-Yu , Ding Guo-Hui , Lin Hongbo , Sun Xiaoyu , Yang Chao , Peng Suyuan , Wang Jinwei , Du Jian , Zhao Yu , Chen Zhengyue , Bao Beiyan , Kong Guilan , Zhang Luxia 
Published: May 2021

Abstract

Background
The diagnostic status of chronic kidney disease (CKD) and its underlying reasons provide evidence that can improve CKD management. However, the situation in developing countries remains under-investigated.

Methods
Adults with electronic health records (EHRs; 2008–19) in Yinzhou, China were included. The gold standard for CKD was defined as having persistently reduced estimated glomerular filtration rate (eGFR), albuminuria/proteinuria, haematuria or a history of CKD. CKD stages (G1–G5) were defined by eGFR. Clinical diagnosis of CKD in the real world setting was evaluated using International Classification of Diseases (ICD)-10 codes related to primary cause or stages of CKD. The specialty of doctors who administered the serum creatinine (SCr) tests and who made the primary-cause/CKD-staging diagnoses was analysed. The accuracy of CKD-staging codes was assessed.

Results
Altogether, 85 519 CKD patients were identified from 976 409 individuals with EHRs. Of them, 10 287 (12.0%) having persistent urinary abnormalities or labelled with CKD-related ICD codes did not receive SCr tests within 12 months before or after the urine tests. Among 75 147 patients who received SCr tests, 46 150 (61.4%) missed any CKD-related codes, 6857 (35.7%) were merely labelled with primary-cause codes, and only 2140 (2.9%) were labelled with CKD-staging codes. The majority of CKD patients (51.6–91.1%) received SCr tests from non-nephrologists, whereas CKD-staging diagnoses were mainly from nephrologists (52.3–64.8%). Only 3 of 42 general hospitals had nephrologists. The CKD-staging codes had high specificity (&gt;99.0%) but low sensitivity (G3–G4: &lt;10.0%).

Conclusions
Under-perception of CKD among doctors, rather than unsatisfactory health-seeking behaviour or low detection rates, was the main cause of under-diagnosis of CKD in China. Intensification of CKD education among doctors with different specialties might bring about immediate effective improvement in the diagnosis and awareness of CKD.
Agent-Based Autonomic Semantic Context-Aware Platform for Smart Health Monitoring and Disease Detection
Authors: Alti Adel , Laouamer Lamri 
Published: May 2021

Abstract
Nowadays, mobile applications have been widely used in various health and social domains. While there are large number of smart devices that connect and transmit their context data in free manner, these mobile applications have limitations regarding the increasing number of heterogeneous context data sent by devices, conducting the problem of identifying user-centric situations and providing services in real-time. Many smart mobile health systems were proposed to ensure context-aware personal health monitoring and diseases detection, while most of them are failed to ensure a right level of dynamicity and enough flexibility for assisting users everywhere, anytime, through widespread sensors and mobile devices. In fact, it becomes necessary to rethink a new way to minimize the response time combining competitive agents with semantic-based situation reasoning strategy. In this paper, we introduce a novel agent-based platform with three-layered ontology for the semantic description and parallel management of services selection approach dedicated to context-aware health mobile applications. In addition, we propose an innovative parallel services discovery and optimal selection process, which involved a set of filtered and classified semantic health multipath according to user’s context and preferences with consistent mobility of users and limited resources (low battery, processing capabilities, memory and others). Experimental results show the effectiveness of the proposed approach as it includes the semantic service information on cooperative agents. In addition, the proposed approach ensures fast response time and prolongs the continuity of the mobile application.
Improved Meet-in-the-Middle Attacks on Reduced-Round Tweakable Block Cipher Deoxys-BC
Authors: Li Manman , Chen Shaozhen 
Published: May 2021

Abstract
Deoxys-BC is an internal tweakable block cipher of the authenticated encryption algorithm Deoxys, which is a third-round finalist in the CAESAR competition. In this paper, we study the property of Deoxys-BC, such as the subtweakey difference cancelation and the freedom of the tweak. Combining the differential enumeration technique with these properties, the authors achieve the key-recovery attacks on Deoxys-BC under the meet-in-the-middle attack. As a result, we get an attack on 9-round Deoxys-BC-128-128 by constructing a 6-round meet-in-the-middle distinguisher with $2^{113}$ plaintext–tweak combinations, $2^{97}$ Deoxys-BC blocks and $2^{121.6}$ 9-round Deoxys-BC-128-128 encryptions. We also present an attack on 11-round Deoxys-BC-256-128 for the first time by constructing a 7-round meet-in-the-middle distinguisher with $2^{113}$ plaintext-tweak combinations, $2^{226}$ Deoxys-BC blocks and $2^{251}$ 11-round Deoxys-BC-256-128 encryptions.
Synthetic control method with convex hull restrictions: a Bayesian maximum a posteriori approach
Authors: Goh Gyuhyeong , Yu Jisang 
Published: May 2021

SummarySynthetic control methods have gained popularity among causal studies with observational data, particularly when estimating the impacts of the interventions implemented to a small number of large units. The synthetic control methods face two major challenges: (a) estimating weights for each donor to create a synthetic control and (b) providing statistical inferences. To overcome these challenges, we propose a Bayesian framework that implements the synthetic control method with the parallelly shiftable convex hull and provides a Bayesian inference, which is from the duality between a penalised least squares approach and a Bayesian maximum a posteriori (MAP) approach. Our approach differs from the recent Bayesian approach, which allow violating the convex hull restriction and face the potential extrapolation bias. Simulation results indicate that the proposed method leads to smaller biases compared to alternatives. We revisit Abadie and Gardeazabal (2003) by applying our proposed method.
Predicting the Location of Maple Habitat Under Warming Scenarios in Two Regions at the Northern Range in Canada
Authors: Jain Pratiksha , Khare Siddhartha , Sylvain Jean-Daniel , Raymond Patricia , Rossi Sergio 
Published: May 2021

AbstractAcer saccharum and Acer rubrum, two main maple species in North America, will be affected by ongoing global warming. Several studies predict a southern limit contraction but limited northward expansion of maple distribution for the future. We aimed to understand the main drivers of current maple distribution to quantify potential changes to maple habitat in this context. We identified the local conditions of maple stands and assessed the potential changes under warming scenarios. We selected two regions in Quebec, Canada, at the northern distribution of the species and applied probability distribution function and principal component analysis to identify the factors explaining the occurrence of maple compared with other forest species, croplands, and grasslands. Maple habitat was estimated under warming scenarios up to 2°C. We observed a lower density of maple stands in the north (7.76%), compared to the south (33.01%). Warming increased maple stands by 3.54 and 1.45% in the northernmost and southernmost regions, respectively, with the highest increases being estimated at the initial warming (+1.0°C). We conclude that maple of northern regions can benefit from local warming if precipitation does not become limiting. These changes could increase the potential for the regional maple industry and forest management.
Surgical treatment for a patient with immunoglobulin G4-related lung disease
Authors: Costa Rita , Maciel João , Fernandes Pedro , Pinho Paulo 
Published: May 2021

Abstract
Immunoglobulin G4-related disease (IgG4-RD) is an autoimmune fibroinflammatory disease, and isolated lung disease is a rare phenomenon. IgG4-RD frequently mimics primary pulmonary malignancy. It has been described in association with malignancies, including lung cancer, but it remains unclear if it increases the risk of malignancy. We report the case of a patient who had a left lower lobectomy after relapse while receiving corticotherapy. The pathological findings confirmed the diagnosis of IgG4-RD. After 2 months, the thoracic computerized tomography scan showed an important left pleural effusion that could be a consequence of the recent intervention or a relapse of IgG4-RD.
Rational Points on Solvable Curves over ℚ via Non-Abelian Chabauty
Authors: Ellenberg Jordan S , Hast Daniel Rayor 
Published: May 2021

Abstract
We study the Selmer varieties of smooth projective curves of genus at least two defined over $\mathbb{Q}$ which geometrically dominate a curve with CM Jacobian. We extend a result of Coates and Kim to show that Kim’s non-abelian Chabauty method applies to such a curve. By combining this with results of Bogomolov–Tschinkel and Poonen on unramified correspondences, we deduce that any cover of P$^1$ with solvable Galois group, and in particular any superelliptic curve over $\mathbb{Q}$, has only finitely many rational points over $\mathbb{Q}$.
The pharmacodynamics of minocycline alone and in combination with rifampicin against Staphylococcus aureus studied in an in vitro pharmacokinetic model of infection
Authors: Noel A R , Attwood M , Bowker K E , MacGowan A P 
Published: May 2021

Abstract

Background
Tetracyclines are widely used as oral therapy of MRSA infection, however, the pharmacodynamic underpinning is absent.

Objectives
We employed an in vitro pharmacokinetic model to study the pharmacodynamics of minocycline alone and in combination with rifampicin.

Methods
An exposure-ranging design was used to establish fAUC/MIC targets for static, −1 log drop and −2 log drop effects against Staphylococcus aureus for minocycline and in combination with rifampicin. We then simulated 7–10 day human dosing of minocycline and the combination.

Results
The minocycline fAUC/MIC for 24 h static effect and −1 log drop in bacterial load were 12.5 ± 7.1 and 23.3 ± 12.4. fAUC/MIC targets for static and −1 log drop were greater at 48 and 72 h. The addition of simulated free rifampicin associated with dosing 300 mg q12h reduced the 24 h minocycline fAUC/MICs. Simulations performed over 7–10 days exposure indicated that for minocycline standard human doses there was a 1–3 log reduction in viable count and no changes in population profiles. Addition of rifampicin resulted in larger reductions in staphylococcal load but emergence of resistance to rifampicin. There was no resistance to minocycline.

Conclusions
An fAUC/MIC minocycline target of 12–36 is appropriate for S. aureus. Addition of rifampicin decreases bacterial load but results in emergence of resistance to rifampicin. Unusually, there was no emergence of resistance to minocycline.
Redefining therapeutic success in HIV patients: an expert view
Authors: Antela Antonio , Rivero Antonio , Llibre Josep M , Moreno Santiago ,   the RET Group, Antela Antonio , Llibre Josep M , Moreno Santiago , Rivero Antonio , Alonso Montero Marta , Bernal Enrique , Ramos José Ramón Blanco , Castaño Manuel , Dalmau Juanola David , de la Fuente García Belén , Dueñas Carlos , Espinosa Nuria , Estrada Vicente , José Galindo Puerto María , García del Toro Miguel , González Juan , Górgolas Miguel , Hidalgo-Tenorio Carmen , Knobel Freu Hernando , Carlos López Bernaldo de Quirós Juan , Macías Sánchez Juan , Martín Ruíz Carlos , Martínez Chamorro Esteban , Masía Mar , Miguelez Máximo , Miralles Celia , Olalla Julián , Pascuet Esteban Ribera , Rodríguez-Vidigal Francisco , Rubio Rafael , Jesús Santos 
Published: May 2021

Abstract
Thanks to advances in the field over the years, HIV/AIDS has now become a manageable chronic condition. Nevertheless, a new set of HIV-associated complications has emerged, related in part to the accelerated ageing observed in people living with HIV/AIDS, the cumulative toxicities from exposure to antiretroviral drugs over decades and emerging comorbidities. As a result, HIV/AIDS can still have a negative impact on patients’ quality of life (QoL). In this scenario, it is reasonable to believe that the concept of therapeutic success, traditionally associated with CD4 cell count restoration and HIV RNA plasma viral load suppression and the absence of drug resistances, needs to be redefined to include other factors that reach beyond antiretroviral efficacy. With this in mind, a group of experts initiated and coordinated the RET Project, and this group, using the available evidence and their clinical experience in the field, has proposed new criteria to redefine treatment success in HIV, arranged into five main concepts: rapid initiation, efficacy, simplicity, safety, and QoL. An extensive review of the literature was performed for each category, and results were discussed by a total of 32 clinicians with experience in HIV/AIDS (4 coordinators + 28 additional experts). This article summarizes the conclusions of these experts and presents the most updated overview on the five topics, along with a discussion of the experts’ main concerns, conclusions and/or recommendations on the most controversial issues.
Seeking an optimal dosing regimen for OZ439/DSM265 combination therapy for treating uncomplicated falciparum malaria
Authors: Dini Saber , Zaloumis Sophie G. , Price David J. , Gobeau Nathalie , Kümmel Anne , Cherkaoui Mohammed , Moehrle Joerg J. , McCarthy James S. , Simpson Julie A. 
Published: May 2021

Abstract

Background
The efficacy of artemisinin-based combination therapies (ACTs), the first-line treatments for uncomplicated falciparum malaria, has been declining in malaria-endemic countries due to the emergence of malaria parasites resistant to these compounds. Novel alternative therapies are needed urgently to prevent the likely surge in morbidity and mortality due to failing ACTs.

Objectives
This study investigates the efficacy of the combination of two novel drugs, OZ439 and DSM265, using a biologically informed within-host mathematical model.

Methods
A within-host model was developed, which accounts for the differential killing of these compounds against different stages of the parasite’s life cycle and accommodates the pharmacodynamic interaction between the drugs. Data of healthy volunteers infected with falciparum malaria collected from four trials (three that administered OZ439 and DSM265 alone, and the fourth a combination of OZ439 and DSM265) were analysed. Model parameters were estimated in a hierarchical Bayesian framework.

Results
The posterior predictive simulations of our model predicted that 800 mg of OZ439 combined with 450 mg of DSM265, which are within the safe and tolerable dose range, can provide above 90% cure rates 42 days after drug administration.

Conclusions
Our results show that the combination of OZ439 and DSM265 can be a promising alternative to replace ACTs. Our model can be used to inform future Phase 2 and 3 clinical trials of OZ439/DSM265, fast-tracking the deployment of this combination therapy in the regions where ACTs are failing. The dosing regimens that are shown to be efficacious and within safe and tolerable limits are suggested for future investigations.
More than Just Contaminants: Frequency and Characterization of Polymicrobial Blood Cultures from a Central Clinical Microbiology Laboratory Serving a Large Healthcare System
Authors: Mitchell Kaitlin F , Yarbrough Melanie L , Burnham Carey-Ann D 
Published: May 2021

Abstract

Background
Polymicrobial blood stream infection is often considered uncommon, and corresponding cultures may be assumed to represent contamination. Here we characterized the prevalence and epidemiology of these cultures submitted to a central clinical microbiology laboratory.

Methods
Blood cultures from 2017 to 2018 (n = 104 547) were evaluated. Polymicrobial blood cultures were defined by the presence of more than one organism in a blood culture set (set = one aerobic and one anaerobic bottle). Data were stratified by patient location and characteristics of the microbiota detected.

Results
Of all blood culture sets, 14 600 (14.0%) were positive. Among these, 1651 sets (11.3% of positive cultures; 1.6% of total cultures) were polymicrobial. Most cultures (85.2%) grew two microorganisms; the greatest number of microorganisms in a culture was 6. The most common microorganism pairs were (a) two coagulase-negative staphylococci (CoNS), (b) Corynebacterium and CoNS, and (c) S. aureus and CoNS. Microorganisms in polymicrobial cultures represented microbiota from skin (46.1%), the gastrointestinal (GI) tract (33.9%), strict anaerobes (1.4%), and “other” microorganisms (18.6%). Most cultures with GI microbiota originated from an adult academic medical center compared to community or pediatric settings (40.5% of polymicrobial cultures vs 27.2% and 25.8%, P &lt; 0.0001). Within the academic medical center, patients in an intensive care unit (ICU) or who had bone marrow transplants (BMT) had more cultures suggestive of GI microbiota compared to those from the emergency department (ED) (50.8% and 52.8% vs 31.2%, P &lt; 0.0001).

Conclusions
Polymicrobial blood cultures are common in a variety of healthcare settings and the recovered microorganisms can be clinically relevant.
Identifying and prioritizing benefits and risks of using privacy-enhancing software through participatory design: a nominal group technique study with patients living with chronic conditions
Authors: Giannouchos Theodoros V , Ferdinand Alva O , Ilangovan Gurudev , Ragan Eric , Nowell W Benjamin , Kum Hye-Chung , Schmit Cason D 
Published: May 2021

Abstract

Objective
While patients often contribute data for research, they want researchers to protect their data. As part of a participatory design of privacy-enhancing software, this study explored patients’ perceptions of privacy protection in research using their healthcare data.

Materials and Methods
We conducted 4 focus groups with 27 patients on privacy-enhancing software using the nominal group technique. We provided participants with an open source software prototype to demonstrate privacy-enhancing features and elicit privacy concerns. Participants generated ideas on benefits, risks, and needed additional information. Following a thematic analysis of the results, we deployed an online questionnaire to identify consensus across all 4 groups. Participants were asked to rank-order benefits and risks. Themes around “needed additional information” were rated by perceived importance on a 5-point Likert scale.

Results
Participants considered “allowance for minimum disclosure” and “comprehensive privacy protection that is not currently available” as the most important benefits when using the privacy-enhancing prototype software. The most concerning perceived risks were “additional checks needed beyond the software to ensure privacy protection” and the “potential of misuse by authorized users.” Participants indicated a desire for additional information with 6 of the 11 themes receiving a median participant rating of “very necessary” and rated “information on the data custodian” as “essential.”

Conclusions
Patients recognize not only the benefits of privacy-enhancing software, but also inherent risks. Patients desire information about how their data are used and protected. Effective patient engagement, communication, and transparency in research may improve patients’ comfort levels, alleviate patients’ concerns, and thus promote ethical research.
Machine learning for initial insulin estimation in hospitalized patients
Authors: Nguyen Minh , Jankovic Ivana , Kalesinskas Laurynas , Baiocchi Michael , Chen Jonathan H 
Published: May 2021

Abstract

Objective
The study sought to determine whether machine learning can predict initial inpatient total daily dose (TDD) of insulin from electronic health records more accurately than existing guideline-based dosing recommendations.

Materials and Methods
Using electronic health records from a tertiary academic center between 2008 and 2020 of 16,848 inpatients receiving subcutaneous insulin who achieved target blood glucose control of 100-180 mg/dL on a calendar day, we trained an ensemble machine learning algorithm consisting of regularized regression, random forest, and gradient boosted tree models for 2-stage TDD prediction. We evaluated the ability to predict patients requiring more than 6 units TDD and their point-value TDDs to achieve target glucose control.

Results
The method achieves an area under the receiver-operating characteristic curve of 0.85 (95% confidence interval [CI], 0.84-0.87) and area under the precision-recall curve of 0.65 (95% CI, 0.64-0.67) for classifying patients who require more than 6 units TDD. For patients requiring more than 6 units TDD, the mean absolute percent error in dose prediction based on standard clinical calculators using patient weight is in the range of 136%-329%, while the regression model based on weight improves to 60% (95% CI, 57%-63%), and the full ensemble model further improves to 51% (95% CI, 48%-54%).

Discussion
Owingto the narrow therapeutic window and wide individual variability, insulin dosing requires adaptive and predictive approaches that can be supported through data-driven analytic tools.

Conclusions
Machine learning approaches based on readily available electronic medical records can discriminate which inpatients will require more than 6 units TDD and estimate individual doses more accurately than standard guidelines and practices.