bluuebunny/crossref_metadata_2025_split huggingface dataset:
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor
Authors: Pallotta Simone , Cascianelli Silvia , Masseroli Marco 
Published: April 2022

AbstractBackgroundHeterogeneous omics data, increasingly collected through high-throughput technologies, can contain hidden answers to very important and still unsolved biomedical questions. Their integration and processing are crucial mostly for tertiary analysis of Next Generation Sequencing data, although suitable big data strategies still address mainly primary and secondary analysis. Hence, there is a pressing need for algorithms specifically designed to explore big omics datasets, capable of ensuring scalability and interoperability, possibly relying on high-performance computing infrastructures.ResultsWe propose RGMQL, a R/Bioconductor package conceived to provide a set of specialized functions to extract, combine, process and compare omics datasets and their metadata from different and differently localized sources. RGMQL is built over the GenoMetric Query Language (GMQL) data management and computational engine, and can leverage its open curated repository as well as its cloud-based resources, with the possibility of outsourcing computational tasks to GMQL remote services. Furthermore, it overcomes the limits of the GMQL declarative syntax, by guaranteeing a procedural approach in dealing with omics data within the R/Bioconductor environment. But mostly, it provides full interoperability with other packages of the R/Bioconductor framework and extensibility over the most used genomic data structures and processing functions.ConclusionsRGMQL is able to combine the query expressiveness and computational efficiency of GMQL with a complete processing flow in the R environment, being a fully integrated extension of the R/Bioconductor framework. Here we provide three fully reproducible example use cases of biological relevance that are particularly explanatory of its flexibility of use and interoperability with other R/Bioconductor packages. They show how RGMQL can easily scale up from local to parallel and cloud computing while it combines and analyzes heterogeneous omics data from local or remote datasets, both public and private, in a completely transparent way to the user.
A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota
Authors: Behzad Hayedeh , Ohyanagi Hajime , Alharbi Badr , Ibarra Martin , Alarawi Mohammed , Saito Yoshimoto , Duarte Carlos M. , Bajic Vladimir , Mineta Katsuhiko , Gojobori Takashi 
Published: April 2022

Abstract
Background
Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed “megacosm” to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters.

Results
We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month.

Conclusion
Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.
Elevated plasma Ninjurin-1 levels in atrial fibrillation is associated with atrial remodeling and thromboembolic risk
Authors: Fang Chen , Jiao Kaicheng , Zuo Kun , Yang Xinchun 
Published: April 2022

Abstract
Background
Nerve injury-induced protein 1 (Ninj1) is elevated in various inflammatory diseases. The soluble form of Ninj1 yield by matrix metalloproteinase cleavage is a secreted protein and inhibits cell adhesion and inflammation. However, the role of plasma Ninj1 in atrial fibrillation (AF) has not been reported. The present study aimed to investigate the correlation between plasma Ninj1 levels and AF.

Methods
A total of 96 AF patients [age 66.00 (60.00, 72.00) years, male 56 (58.33%)] and 51 controls without AF [age 65.00 (55.00, 68.00) years, male 21 (41.18%)] were enrolled in this study. Plasma Ninj1 concentrations were detected using enzyme-linked immunosorbent assay. Also, the clinical characteristics, left atrial volume index (LAVI), CHA2DS2-VASc score, and HAS-BLED score were evaluated.

Results
Plasma Ninj1 levels were significantly higher in patients with AF than in controls (P < 0.001). Plasma Ninj1 levels were positively correlated with LAVI (P = 0.019) and CHA2DS2-VASc score (P = 0.024). Logistic regression analysis confirmed that the Ninj1 plasma levels were associated with AF (P = 0.009). The receiver operating characteristic analysis showed that plasma Ninj1 had a predictive value for AF (P < 0.001).

Conclusions
Plasma Ninj1 levels were elevated in patients with AF, associated with left atrial enlargement and thromboembolic risk in AF.
Recommendations made by patients, caregivers, providers, and decision-makers to improve transitions in care for older adults with hip fracture: a qualitative study in Ontario, Canada
Authors: Cadel Lauren , Kuluski Kerry , Everall Amanda C. , Guilcher Sara J. T. 
Published: April 2022

AbstractBackgroundOlder adults frequently experience fall-related injuries, including hip fractures. Following a hip fracture, patients receive care across a number of settings and from multiple different providers. Transitions between providers and across settings have been noted as a vulnerable time, with potentially negative impacts. Currently, there is limited research on how to improve experiences with transitions in care following a hip fracture for older adults from the perspectives of those with lived experienced. The purpose of this study was to explore service recommendations made by patients, caregivers, healthcare providers, and decision-makers for improving transitions in care for older adults with hip fracture.MethodsThis descriptive qualitative study was part of a larger longitudinal qualitative multiple case study. Participants included older adults with hip fracture, caregivers supporting an individual with hip fracture, healthcare providers, and decision-makers. In-depth, semi-structured interviews were conducted with all participants, with patients and caregivers having the opportunity to participate in follow-up interviews as they transitioned out of hospital. All interviews were audio-recorded, transcribed verbatim, and analyzed thematically.ResultsA total of 47 participants took part in 65 interviews. We identified three main categories of recommendations: (1) hospital-based recommendations; (2) community-based recommendations; and (3) cross-sectoral based recommendations. Hospital-based recommendations focused on treating patients and families with respect, improving the consistency, frequency, and comprehensiveness of communication between hospital providers and between providers and families, and increasing staffing levels. Community-based recommendations included the early identification of at-risk individuals and providing preventative and educational programs. Cross-sectoral based recommendations were grounded in enhanced system navigation through communication and care navigators, particularly within primary and community care settings.ConclusionsOur findings highlighted the central role primary care can play in providing targeted, integrated services for older adults with hip fracture. The recommendations outlined have the potential to improve experiences with care transitions for older adults with hip fracture, and thus, addressing and acting on them should be a priority.
Evaluating the clinical impact of routine whole genome sequencing in tuberculosis treatment decisions and the issue of isoniazid mono-resistance
Authors: Park Mirae , Lalvani Ajit , Satta Giovanni , Kon Onn Min 
Published: April 2022

Abstract
Background
The UK has implemented routine use of whole genome sequencing (WGS) in TB diagnostics. The WHO recommends addition of a fluoroquinolone for isoniazid mono-resistance, so early detection may be of use. The aim of this study was to describe the clinical utility and impact of WGS on treatment decisions for TB in a low incidence high resource clinical setting. The clinical turnaround time (TAT) for WGS was analysed in comparison to TB PCR using Xpert MTB/RIF (Cepheid, Sunnyvale, CA) results where available and subsequent phenotypic drug susceptibility testing (DST) when required.

Methods
This was a retrospective analysis of TB cases from January 2018 to March 2019 in London. Susceptibility and TAT by WGS, phenotypic DST, TB PCR using Xpert MTB/RIF were correlated to drug changes in order to describe the utility of WGS on treatment decisions on isoniazid mono-resistance in a low incidence high resource setting.

Results
189 TB cases were identified; median age 44 years (IQR 28–60), m:f ratio 112:77, 7 with HIV and 6 with previous TB. 80/189 cases had a positive culture and WGS result. 50/80 were fully sensitive to 1st line treatment on WGS, and the rest required additional DST. 20/80 cases required drug changes; 12 were defined by WGS: 8 cases had isoniazid mono-resistance, 2 had MDR-TB, 1 had isoniazid and pyrazinamide resistance and 1 had ethambutol resistance. The median TAT for positive culture was 16 days (IQR 12.5–20.5); for WGS was 35 days (IQR 29.5–38.75) and for subsequent DST was 86 days (IQR 69.5–96.75), resulting in non-WHO regimens for a median of 50.5 days (IQR 28.0–65.0). 9/12 has TB PCRs (Xpert MTB/RIF), with a median TAT of 1 day.

Conclusion
WGS clearly has a substantial role in our routine UK clinical settings with faster turnaround times in comparison to phenotypic DST. However, the majority of treatment changes defined by WGS were related to isoniazid resistance and given the 1 month TAT for WGS, it would be preferable to identify isoniazid resistance more quickly. Therefore if resources allow, diagnostic pathways should be optimised by parallel use of WGS and new molecular tests to rapidly identify isoniazid resistance in addition to rifampicin resistance and to minimise delays in starting WHO isoniazid resistance treatment.
The effect of a full-time infection control nursing service in the prevention of multidrug-resistant organism in the orthopedic ward
Authors: Yang Yun , Tang Ting-ting , Lin Ji , Gan Chun-lan , Huang Wen-zhi , Fang Yue 
Published: April 2022

Abstract
Background
Our aim was to evaluate the effect of setting up a full-time infection control nursing service on reducing the prevalence of multidrug-resistant organism (MDRO) in the orthopedic ward.

Methods
From January 2015 to March 2019, routine prevention and control measures were taken for patients infected/colonized with MDRO in this ward, which was set as the pre-intervention period. The intervention period was from April 2019 to June 2021. The study was designed to evaluate whether the establishment of a full-time infection control nursing service could reduce the positive density of MDRO in the hospital by using an interrupted time-series model of a quasi experimental study.

Results
There were 11,759 patients during pre-intervention period and 8142 patients during intervention period. The total number of MDRO isolated before intervention was 177, of which 145 were obtained in hospital and 32 were brought in from outside hospital. The total number of MDRO isolated after intervention was 47, of which 29 were obtained in hospital and 18 were brought in from outside hospital. Before intervention, the positive density of MDRO in the orthopedic ward showed an increasing trend (β1 = 0.02, P = 0.003). After intervention, the positive density of MDRO showed a downward trend (β3 = − 0.05, P = 0.018).

Conclusions
The establishment of the full-time infection control nursing service in the orthopedic ward can effectively reduce the nosocomial prevalence of MDRO.
Optimizing Prehospital Stroke Systems of Care-Reacting to Changing Paradigms (OPUS-REACH): a pragmatic registry of large vessel occlusion stroke patients to create evidence-based stroke systems of care and eliminate disparities in access to stroke care
Authors: Isenberg Derek L. , Henry Kevin A. , Sigal Adam , Deaner Traci , Nomura Jason T. , Murphy Kathleen A. , Cooney Derek , Wojcik Susan , Brandler Ethan S. , Kuc Alexander , Carroll Gerard , Kraus Chadd K. , Shahan Judy B. , Herres Joseph , Ackerman Daniel , Gentile Nina T. 
Published: April 2022

Abstract
Background
Large vessel occlusion (LVO) strokes are best treated with rapid endovascular therapy (EVT). There are two routes that LVO stroke patients can take to EVT therapy when transported by EMS: primary transport (ambulance transports directly to an endovascular stroke center (ESC) or secondary transport (EMS transports to a non-ESC then transfers for EVT). There is no clear evidence which path to care results in better functional outcomes for LVO stroke patients. To find this answer, an analysis of a large, real-world population of LVO stroke patients must be performed.

Methods
A pragmatic registry of LVO stroke patients from nine health systems across the United States. The nine health systems span urban and rural populations as well as the spectrum of socioeconomic statuses. We will use univariate and multivariate analysis to explore the relationships between type of EMS transport, socioeconomic factors, and LVO stroke outcomes. We will use geographic information systems and spatial analysis to examine the complex movements of patients in time and space. To detect an 8% difference between groups, with a 3:1 patient ratio of primary to secondary transports, 95% confidence and 80% power, we will need approximately 1600 patients.
The primary outcome is the patients with modified Rankin Scale (mRS) ≤ 2 at 90 days. Subgroup analyses include patients who receive intravenous thrombolysis and duration of stroke systems. Secondary analyses include socioeconomic factors associated with poor outcomes after LVO stroke.

Discussion
Using the data obtained from the OPUS-REACH registry, we will develop evidence based algorithms for prehospital transport of LVO stroke patients. Unlike prior research, the OPUS-REACH registry contains patient-level data spanning from EMS dispatch to ninety day functional outcomes. We expect that we will find modifiable factors and socioeconomic disparities associated with poor outcomes in LVO stroke. OPUS-REACH with its breadth of locations, detailed patient records, and multidisciplinary researchers will design the optimal prehospital stroke system of care for LVO stroke patients.
Utility of prognostic nutritional index and systemic immune-inflammation index in oral cancer treatment
Authors: Kubota Kosei , Ito Ryohei , Narita Norihiko , Tanaka Yusuke , Furudate Ken , Akiyama Natsumi , Chih Chuang Hao , Komatsu Shotaro , Kobayashi Wataru 
Published: April 2022

AbstractPurposeThis study aimed to evaluate the utility of inflammation-based prognostic scores (IBPS) and systemic immune-inflammation index (SII) in the treatment of oral cancer patients.MethodsFor the 183 patients enrolled in this study, IBPS and SII were calculated from peripheral blood samples obtained before and after treatment and at the time of relapse. We examined overall survival (OS) and disease-free survival (DFS) using previously reported cut-off values for IBPS. Cut-off values of neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), and prognostic nutritional index (PNI) were analyzed as NLR 1.79, PLR 114.97, LMR 5, and PNI 52.44. The cut-off value for SII was set at 569. OS and DFS were analyzed by Kaplan–Meier methods using the cutoff of each IBPS and SII. Univariate analysis and multivariate analysis using Cox proportional hazards were performed for OS and DFS.ResultsKaplan–Meier methods showed the high-PNI group showed good prognosis including OS and DFS, while the high-SII group displayed poor DFS. Univariate analysis showed that pre-treatment high PNI and low SII were significantly associated with better prognosis. Multivariate analysis identified pre-treatment PNI as independently associated with OS. For DFS, univariate analysis using Cox proportional hazards modeling showed that pre-treatment high NLR and high SII were significantly associated with worse prognosis, while high PNI was significantly associated with better prognosis. Multivariate analysis identified pre-treatment PNI and SII as independently associated with DFS. Parameters of PNI and SII components were compared between pre-treatment, post-treatment and at relapse in the high- and low-PNI groups. PNI was predominantly decreased in both high- and low-PNI groups at post-treatment and at relapse compared to pre-treatment. This trend was also observed for albumin.ConclusionsHigher pre-treatment PNI was associated with better OS, while lower pre-treatment PNI and higher treatment SII were associated with poorer DFS in oral cancer patients. Our data indicated that PNI and SII might offer useful biomarkers for gauging prognosis and the efficacy of conventional therapies.
Implementation of novel and conventional outbreak control measures in managing COVID-19 outbreaks in a large UK prison
Authors: Coleman Paul C. , Pailing Adam , Roy Anjana , O’Moore Éamonn , Chandan Joht Singh , Lumby Victoria , Newton Paul , Taylor Anna , Robinson Esther , Swindells Jonathon , Dowle Sarah , Gajraj Roger 
Published: April 2022

Abstract
Background
Outbreak control measures during COVID-19 outbreaks in a large UK prison consisted of standard (e.g., self-isolation) and novel measures, including establishment of: (i) reverse cohorting units for accommodating new prison admissions; (ii) protective isolation unit for isolating symptomatic prisoners, and (iii) a shielding unit to protect medically vulnerable prisoners.

Methods
Single-centre prospective longitudinal study (outbreak control study), implementing novel and traditional outbreak control measures to prevent a SARS-COV-2 outbreak. The prison held 977 prisoners and employed 910 staff at that start of the outbreak.

Results
120 probable and 25 confirmed cases among prisoners and staff were recorded between March and June 2020 during the first outbreak. Over 50% of initial cases among prisoners were on the two wings associated with the index case.
During the second outbreak, 182 confirmed cases were recorded after probable reintroduction from a staff member. Widespread testing identified 145 asymptomatic prisoners, 16.9% of the total prisoner cases. The cohorting units prevented re-infection from new prison admissions and the shielding unit had no COVID-19 infections linked to either outbreak.

Conclusions
Identifying and isolating infected prisoners, cohorting new admissions and shielding vulnerable individuals helped prevent uncontrollable spread of SARS-COV-2. These novel and cost-effective approaches can be implemented in correctional facilities globally.
Associations between motorized transport access, out-of-home activities, and life-space mobility in older adults in Japan
Authors: Tran Yen , Hashimoto Naohisa , Ando Takafumi , Sato Toshihisa , Konishi Naoki , Takeda Yuji , Akamatsu Motoyuki 
Published: April 2022

Abstract
Background
Motorized transport access and out-of-home activities are two potential correlates of Life-space mobility (LSM), a common research topic in mobility studies of older adults. These correlates remain mostly unexplored in previous literature and relating them with LSM can reveal directions for improving the LSM of older adults.

Methods
The associations between motorized transport access, out-of-home activities, and LSM were examined using data from 1,333 older adults (mean age = 70.63) living in 15 cities and towns in Japan. LSM was assessed using composite life-space assessment (LSA) scores. Motorized transport access was measured using dummies showing whether a person had car access (divided into five levels) and used public transport (bus and railway), and out-of-home activities were measured using the number of various activities that were conducted during the most recent weekday and weekend day. Generalized linear models were used to assess the associations.

Results
The sample was dominated by males (74.42%), with more than half of the sample had their own cars. On average, each respondent had four activities during two survey days, and shopping was the most common activity. The results showed that owning a car and using railway, as well as various activities were associated with increased composite LSA scores, whereas no cars or only shared cars in home were associated with decreased composite LSA scores. However, these associations differed between males and females.

Conclusions
In this study, different levels of motorized transport access and different types of out-of-home activities were found to associate differently with composite LSA scores. Based on these findings, we suggest that policymakers should provide more transport access, pay more attention to the LSM of older adults with high clinics/hospital activities, and trigger more shopping and daily leisure activities for older adults to improve the LSM of this population.
Safety of chronic hypertonic bicarbonate inhalation in a cigarette smoke-induced airway irritation guinea pig model
Authors: Csekő Kata , Hargitai Dóra , Draskóczi Lilla , Kéri Adrienn , Jaikumpun Pongsiri , Kerémi Beáta , Helyes Zsuzsanna , Zsembery Ákos 
Published: April 2022

AbstractBackgroundCystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are often associated with airway fluid acidification. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene leads to impaired bicarbonate secretion contributing to CF airway pathology. Chronic cigarette smoke (CS) -the major cause of COPD- is reported to induce acquired CFTR dysfunction underlying airway acidification and inflammation. We hypothesize that bicarbonate-containing aerosols could be beneficial for patients with CFTR dysfunctions. Thus, we investigated the safety of hypertonic sodium bicarbonate (NaHCO3) inhalation in CS-exposed guinea pigs.MethodsAnimals were divided into groups inhaling hypertonic NaCl (8.4%) or hypertonic NaHCO3(8.4%) aerosol for 8 weeks. Subgroups from each treatment groups were further exposed to CS. Respiratory functions were measured at 0 and after 2, 4, 6 and 8 weeks. After 8 weeks blood tests and pulmonary histopathological assessment were performed.ResultsNeither smoking nor NaHCO3-inhalation affected body weight, arterial and urine pH, or histopathology significantly. NaHCO3-inhalation did not worsen respiratory parameters. Moreover, it normalized the CS-induced transient alterations in frequency, peak inspiratory flow, inspiratory and expiratory times.ConclusionLong-term NaHCO3-inhalation is safe in chronic CS-exposed guinea pigs. Our data suggest that bicarbonate-containing aerosols might be carefully applied to CF patients.