bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between cause of kidney failure and fracture incidence in a national US dialysis population cohort study
Authors: Ziolkowski Susan , Liu Sai , Montez-Rath Maria E , Denburg Michelle , Winkelmayer Wolfgang C , Chertow Glenn M , O'Shaughnessy Michelle M 
Published: September 2022

ABSTRACT

Background
Whether fracture rates, overall and by fracture site, vary by cause of kidney failure in patients receiving dialysis is unknown.

Methods
Using the US Renal Data System, we compared fracture rates across seven causes of kidney failure in patients who started dialysis between 1997 and 2014. We computed unadjusted and multivariable adjusted proportional sub-distribution hazard models, with fracture events (overall, and by site) as the outcome and immunoglobulin A nephropathy as the reference group. Kidney transplantation and death were competing events.

Results
Among 491 496 individuals, with a median follow-up of 2.0 (25%, 75% range 0.9–3.9) years, 62 954 (12.8%) experienced at least one fracture. Patients with diabetic nephropathy, vasculitis or autosomal polycystic kidney disease (ADPKD) had the highest (50, 46 and 40 per 1000 person-years, respectively), and patient with lupus nephritis had the lowest (20 per 1000 person-years) fracture rates. After multivariable adjustment, diabetic nephropathy [hazard ratio (HR) 1.43, 95% confidence interval 1.33–1.53], ADPKD (HR 1.37, 1.26–1.48), vasculitis (HR 1.22, 1.09–1.34), membranous nephropathy (HR 1.16, 1.02–1.30) and focal segmental glomerulosclerosis (FSGS) (HR 1.13, 1.02–1.24) were associated with a significantly higher, and lupus nephritis with a significantly lower (HR 0.85, 0.71–0.98) fracture hazard. The hazards for upper extremity and lower leg fractures were significantly higher in diabetic nephropathy, ADPKD, FSGS and membranous nephropathy, while the hazard for vertebral fracture was significantly higher in vasculitis. Our findings were limited by the lack of data on medication use and whether fractures were traumatic or non-traumatic, among other factors.

Conclusions
Fracture risk, overall and by fracture site, varies by cause of end-stage kidney disease. Future work to determine underlying pathogenic mechanisms contributing to differential risks might inform more tailored treatment strategies. Our study was limited by lack of data regarding numerous potential confounders or mediators including medications and measures or bone biomarkers.
COTTONOMICS: a comprehensive cotton multi-omics database
Authors: Dai Fan , Chen Jiedan , Zhang Ziqian , Liu Fengjun , Li Jun , Zhao Ting , Hu Yan , Zhang Tianzhen , Fang Lei 
Published: September 2022

Abstract
The rapid advancement of sequencing technology, including next-generation sequencing (NGS), has greatly improved sequencing efficiency and decreased cost. Consequently, huge amounts of genomic, transcriptomic and epigenetic data concerning cotton species have been generated and released. These large-scale data provide immense opportunities for the study of cotton genomic structure and evolution, population genetic diversity and genome-wide mining of excellent genes for important traits. However, the complexity of NGS data also causes distress, as it cannot be utilized easily. Here, we presented the cotton omics data platform COTTONOMICS (http://cotton.zju.edu.cn/), an easily accessible web database that integrates 32.5 TB of omics data including seven assembled genomes, resequencing data from 1180 allotetraploid cotton accessions and RNA-sequencing (RNA-seq), small RNA-sequencing (smRNA-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), DNase hypersensitive sites sequencing (DNase-seq) and Bisulfite sequencing (BS-seq). COTTONOMICS allows users to employ various search scenarios and retrieve information concerning the cotton genomes, genomic variation (Single nucleotide polymorphisms (SNPs) and Insertion and Deletion (InDels)), gene expression, smRNA expression, epigenetic regulation and quantitative trait locus (QTLs). The user-friendly web interface offers a variety of modules for storing, retrieving, analyzing and visualizing cotton multi-omics data to diverse ends, thereby enabling users to decipher cotton population genetics and identify potential novel genes that influence agronomically beneficial traits.
Database URL: http://cotton.zju.edu.cn
Hybrid nanofluids flow and heat transfer in cavities: a technological review
Authors: Scott Temiloluwa O , Ewim Daniel R E , Eloka-Eboka Andrew C 
Published: September 2022

ABSTRACT
The urgent and indispensable need to develop new methods of enhancing heat transfer efficiency to improve energy devices’ performance cannot be overlooked in this era of green energy and sustainable technologies. Nanofluids research has proliferated in the past decade, and reports indicate that nanofluids can be used for heat transfer applications in engineering and in general and/or commercial industries. Nanofluid is the dispersion of nanoparticles with high thermal conductivity in common working fluids. Nevertheless, a growing area of research in recent years has involved using two or more nanoparticles in a base fluid, known as hybrid nanofluids. Studies show that hybrid nanofluids exhibited better thermal and rheological characteristics than mono nanofluids. In addition, many researchers have reported on the thermal-fluid behaviors of nanofluids in comparison with hybrid nanofluids on natural convection in cavity flows. This review discusses hybrid nanofluids preparation, stability analysis and characterization, thermal properties and heat transfer characteristics in cavities. Furthermore, hybrid nanofluids demonstrated better heat transfer characteristics than mono nanofluids or conventional fluids even if more research is needed in terms of hybrid nanofluids preparation, stability, characterization and applications.
Combined Use of Flubromazepam and Stimulants: Blood and Oral Fluid Concentrations and Impact on Driving Ability
Authors: Wille Sarah M R , Bouazzati Malika , Rubbens Jari , Di Fazio Vincent , Samyn Nele 
Published: September 2022

Abstract
“Designer” benzodiazepines (DBZDs) are becoming increasingly available in Europe, with the European Monitoring Centre of Drugs and Drug Addiction currently monitoring ∼30 new benzodiazepines. The following driving under the influence of drug (DUID) case describes the oral fluid (OF) and blood concentrations, as well as the observed effects after the combined use of stimulants and flubromazepam. Both OF, collected via the Intercept i2 collector (Immunalysis, Pomona, CA, USA), and blood (collected in containers with various stabilizers) were screened using a liquid chromatographic (LC) time-of-flight (TOF) mass spectrometric (MS-MS) method. In addition, various LC–MS-MS methods in multi-reaction monitoring mode were applied for confirmation and quantification. The OF and blood samples were taken 2 h 25 min and 9 h 19 min after the accident, respectively. OF contained 789 ng/mL amphetamine, 5,173 ng/mL MDMA, 168 ng/mL benzoylecgonine, 492 ng/mL cocaine, 134 ng/mL 4-methylmethcathinone (4-MMC) and traces of flubromazepam (less than limit of quantification (LLOQ); 2 ng/mL). The sodium-fluoride blood samples contained 19 ng/mL amphetamine, 284 ng/mL MDMA, 20 ng/mL MDA, 38 ng/mL benzoylecgonine, 4 ng/mL methylecgonine, 161 ng/mL flubromazepam and traces of 4-MMC (&lt;LLOQ; 2.5 ng/mL). The driver was observed to have an irregular speed driving pattern and could not keep his lane. He demonstrated the following effects after the accident: bloodshot eyes, red face, sweating, fatigue, disorientation in time and space and mental confusion. Even 24 h after the accident, the driver was confused, disoriented, had red spots on his face and could not keep his balance. The effects of flubromazepam combined with several stimulants are demonstrated. Moreover, this case illustrates well the pros and cons of the different biological matrices applied in a DUID context. Differences between the biological matrices are not only observed concerning the ease/practicality of (on-site) collection, but also in the final drug detectability due to the large variations in OF/blood drug concentration ratios and metabolism/elimination rates as a result of the different chemical entities of the compounds.
The family pictures of our neighbours: investigating the mass function and dynamical parameters of nearby open clusters
Authors: Ebrahimi H , Sollima A , Haghi H 
Published: September 2022

ABSTRACT
We determine the mass functions (MFs) and the dynamical parameters of 15 nearby open clusters (OCs), using the unprecedented data set of the Gaia Early Data Release 3. We select the members of each cluster by combining the photometric (colour and magnitude) and astrometric (parallax and proper motions) parameters of stars, minimizing the contamination from Galactic field interlopers. By comparing the observed distribution of stars along the cluster main sequence with the best-fitting synthetic population, we find the present-day MF and the binary fraction of the OCs, along with their dynamical parameters like mass, half-mass radius, and half-mass relaxation time. We found that the global present-day MF of OCs are consistent with a single power-law function, F(m) ∝ mα, with slopes −3 &lt; α &lt; −0.6 including both subsolar, 0.2 &lt; m/M⊙ &lt; 1, and supersolar mass regimes. A significant correlation between the MF slope and the ratio of age to half-mass relaxation time is evidenced, similarly to the same conclusion already observed among Galactic globular clusters. However, OCs evolve along different tracks in comparison with the globular clusters, possibly indicating primordial differences in their initial mass function (IMF). The comparison with Monte Carlo simulations suggests that all the analysed OCs could be born with an IMF with slope αIMF &lt; −2.3. We also show that the less evolved OCs have an MF consistent with that of the solar neighbourhood, indicating a possible connection between the dissolution of OCs and the formation of the Galactic disc.
Evaluating the efficacy of sonification for signal detection in univariate, evenly sampled light curves using astronify
Authors: Tucker Brown J , Harrison C M , Zanella A , Trayford J 
Published: September 2022

ABSTRACT
Sonification is the technique of representing data with sound, with potential applications in astronomy research for aiding discovery and accessibility. Several astronomy-focused sonification tools have been developed; however, efficacy testing is extremely limited. We performed testing of astronify, a prototype tool for sonification functionality within the Barbara A. Mikulski Archive for Space Telescopes. We created synthetic light curves containing zero, one, or two transit-like signals with a range of signal-to-noise ratios (SNRs = 3–100) and applied the default mapping of brightness to pitch. We performed remote testing, asking participants to count signals when presented with light curves as a sonification, visual plot, or combination of both. We obtained 192 responses, of which 118 self-classified as experts in astronomy and data analysis. For high SNRs (=30 and 100), experts and non-experts performed well with sonified data (85–100 per cent successful signal counting). At low SNRs (=3 and 5), both groups were consistent with guessing with sonifications. At medium SNRs (=7 and 10), experts performed no better than non-experts with sonifications but significantly better (factor of ∼2–3) with visuals. We infer that sonification training, like that experienced by experts for visual data inspection, will be important if this sonification method is to be useful for moderate SNR signal detection within astronomical archives and broader research. None the less, we show that even a very simple, and non-optimized, sonification approach allows users to identify high SNR signals. A more optimized approach, for which we present ideas, would likely yield higher success for lower SNR signals.
Oral Polio Vaccine to Mitigate the Risk of Illness and Mortality During the Coronavirus Disease 2019 Pandemic: A Cluster-Randomized Trial in Guinea-Bissau
Authors: Fisker Ane B , Martins Justiniano S D , Nanque Line M , Jensen Andreas M , Ca Elsi J C , Nielsen Sebastian , Martins Cesario L , Rodrigues Amabelia 
Published: September 2022

Abstract

Background
Oral polio vaccine (OPV) may improve resistance to non-polio-infections. We tested whether OPV reduced the risk of illness and mortality before coronavirus disease 2019 (COVID-19) vaccines were available.

Methods
During the early COVID-19 pandemic, houses in urban Guinea-Bissau were randomized 1:1 to intervention or control. Residents aged 50+ years were invited to participate. Participants received bivalent OPV (single dose) or nothing. Rates of mortality, admissions, and consultation for infections (primary composite outcome) during 6 months of follow-up were compared in Cox proportional hazards models adjusted for age and residential area. Secondary outcomes included mortality, admissions, consultations, and symptoms of infection.

Results
We followed 3726 participants (OPV, 1580; control, 2146) and registered 66 deaths, 97 admissions, and 298 consultations for infections. OPV did not reduce the risk of the composite outcome overall (hazard ratio [HR] = 0.97; 95% confidence interval [CI], .79–1.18). OPV reduced the risk in males (HR = 0.71; 95% CI, .51–.98) but not in females (HR = 1.18; 95% CI, .91–1.52) (P for same effect = .02). OPV also reduced the risk in Bacillus Calmette-Guérin scar-positive (HR = 0.70; 95% CI, .49–.99) but not in scar-negative participants (HR = 1.13; 95% CI, .89–1.45) (P = .03). OPV had no overall significant effect on mortality (HR = 0.96; 95% CI, .59–1.55), admissions (HR = 0.76; 95% CI, .49–1.17) or recorded consultations (HR = 0.99; 95% CI, .79–1.25), but the OPV group reported more episodes with symptoms of infection (6050 episodes; HR = 1.10 [95% CI, 1.03–1.17]).

Conclusions
In line with previous studies, OPV had beneficial nonspecific effects in males.
Natural Language Processing and Machine Learning to Identify People Who Inject Drugs in Electronic Health Records
Authors: Goodman-Meza David , Tang Amber , Aryanfar Babak , Vazquez Sergio , Gordon Adam J , Goto Michihiko , Goetz Matthew Bidwell , Shoptaw Steven , Bui Alex A T 
Published: September 2022

Abstract

Background
Improving the identification of people who inject drugs (PWID) in electronic medical records can improve clinical decision making, risk assessment and mitigation, and health service research. Identification of PWID currently consists of heterogeneous, nonspecific International Classification of Diseases (ICD) codes as proxies. Natural language processing (NLP) and machine learning (ML) methods may have better diagnostic metrics than nonspecific ICD codes for identifying PWID.

Methods
We manually reviewed 1000 records of patients diagnosed with Staphylococcus aureus bacteremia admitted to Veterans Health Administration hospitals from 2003 through 2014. The manual review was the reference standard. We developed and trained NLP/ML algorithms with and without regular expression filters for negation (NegEx) and compared these with 11 proxy combinations of ICD codes to identify PWID. Data were split 70% for training and 30% for testing. We calculated diagnostic metrics and estimated 95% confidence intervals (CIs) by bootstrapping the hold-out test set. Best models were determined by best F-score, a summary of sensitivity and positive predictive value.

Results
Random forest with and without NegEx were the best-performing NLP/ML algorithms in the training set. Random forest with NegEx outperformed all ICD-based algorithms. F-score for the best NLP/ML algorithm was 0.905 (95% CI, .786–.967) and 0.592 (95% CI, .550–.632) for the best ICD-based algorithm. The NLP/ML algorithm had a sensitivity of 92.6% and specificity of 95.4%.

Conclusions
NLP/ML outperformed ICD-based coding algorithms at identifying PWID in electronic health records. NLP/ML models should be considered in identifying cohorts of PWID to improve clinical decision making, health services research, and administrative surveillance.
Contribution of zooplankton nutrient recycling and effects on phytoplankton size structure in a hypereutrophic reservoir
Authors: Butts Tyler J , Moody Eric K , Wilkinson Grace M 
Published: September 2022

AbstractConsumer nutrient recycling influences aquatic ecosystem functioning by altering the movement and transformation of nutrients. In hypereutrophic reservoirs, zooplankton nutrient recycling has been considered negligible due to high concentrations of available nutrients. A comparative analysis ( Moody and Wilkinson, 2019) found that zooplankton communities in hypereutrophic lakes are dominated by nitrogen (N)-rich species, which the authors hypothesized would increase phosphorus (P) availability through excretion. However, zooplankton nutrient recycling likely varies over the course of a growing season due to changes in biomass, community composition and grazing pressure on phytoplankton. We quantified zooplankton, phytoplankton and nutrient concentration dynamics during the summer of 2019 in a temperate, hypereutrophic reservoir. We found that the estimated contribution of zooplankton excretion to the dissolved nutrient pool on a given day was equivalent to a substantial proportion (21–39%) of the dissolved inorganic P standing stock in early summer when P concentrations were low and limiting phytoplankton growth. Further, we found evidence that zooplankton affected phytoplankton size distributions through selective grazing of smaller phytoplankton cells likely affecting nutrient uptake and storage by phytoplankton. Overall, our results demonstrate zooplankton excretion in hypereutrophic reservoirs likely helped drive springtime phytoplankton dynamics through nutrient recycling while grazing influenced phytoplankton size distributions.
The Risk of Implicit Guarantees: Evidence from Shadow Banks in China
Authors: Huang Ji , Huang Zongbo , Shao Xiang 
Published: September 2022

Abstract
We study how risks spill over from shadow banking activities to traditional banks through implicit guarantees. Using data on wealth management products (WMPs), China’s largest shadow banking component, we find that banks with higher interbank borrowing rates strategically provide stronger implicit guarantees to their issued WMPs. Extending implicit guarantees builds bank reputations and reduces rollover costs while exposing banks to losses from shadow banking activities. Our findings thus suggest a bank-specific approach to assessing the risk of implicit guarantees based on transparent and real-time interbank rates.
Diagnostic Reference Levels for Common CT Examinations: Results from a Statewide dose Survey
Authors: Jusoh Irwan Iskandar , Abdullah Kamarul Amin , Ali Mohd Hanafi 
Published: September 2022

Abstract
The aim of this study was to investigate the current radiation doses for CT examinations throughout a state in Malaysia and, based on this data, to propose local diagnostic reference levels (DRLs) for the most common CT examinations. A study was conducted in three of the four hospitals that have provided CT services throughout the state. A survey booklet was designed to facilitate collection of pertinent CT scan data. The following information were extracted and recorded for each study: tube voltage, tube current, number of scans phases, CT dose index volume (CTDIvol) and dose length product (DLP). Proposed local DRLs of CT brain and thorax were up to 12% lower than the current national DRLs. However, an increase of DLP (median value) for CT abdomen was also found as compared to the 75th percentile of national DRLs. Therefore, considerable optimisation should be made to achieve a better dose reduction.
MRI of Cerebrovascular Injury Associated With COVID-19 and Non-COVID-19 Acute Respiratory Distress Syndrome: A Matched Case-Control Study
Authors: Shoskes Aaron , Huang Merry , Gedansky Aron , Hassett Catherine , Buletko A. Blake , Duggal Abhijit , Uchino Ken , Cho Sung-Min 
Published: September 2022

OBJECTIVES:
Cerebrovascular injury associated with COVID-19 has been recognized, but the mechanisms remain uncertain. Acute respiratory distress syndrome (ARDS) is a severe pulmonary injury, which is associated with both ischemic and hemorrhagic stroke. It remains unclear if cerebrovascular injuries associated with severe COVID-19 are unique to COVID-19 or a consequence of severe respiratory disease or its treatment. The frequency and patterns of cerebrovascular injury on brain MRI were compared among patients with COVID-19 ARDS and non-COVID-19 ARDS.

DESIGN:
A case-control study.

SETTING:
A tertiary academic hospital system

PATIENTS:
Adult patients (>18 yr) with COVID-19 ARDS (March 2020 to July 2021) and non-COVID-19 ARDS (January 2010-October 2018) who underwent brain MRI during their index hospitalization.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Cerebrovascular injury on MRI included cerebral ischemia (ischemic infarct or hypoxic ischemic brain injury) and intracranial hemorrhage (intraparenchymal, subarachnoid, or subdural, and cerebral microbleed [CMB]).
Twenty-six patients with COVID-19 ARDS and sixty-six patients with non-COVID ARDS underwent brain MRI during the index hospitalization, resulting in 23 age- and sex-matched pairs. The frequency of overall cerebrovascular injury (57% vs 61%), cerebral ischemia (35% vs 43%), intracranial hemorrhage (43% vs 48%), and CMB (52% vs 41%) between COVID-19 ARDS and non-COVID-19 ARDS patients was similar (all p values >0.05). However, four of 26 patients (15%) with COVID-19 and no patients with non-COVID-19 ARDS had disseminated leukoencephalopathy with underlying CMBs, an imaging pattern that has previously been reported in patients with COVID-19.

CONCLUSIONS:
In a case-control study of selected ARDS patients with brain MRI, the frequencies of ischemic and hemorrhagic cerebrovascular injuries were similar between COVID-19 versus non-COVID-19 ARDS patients. However, the MRI pattern of disseminated hemorrhagic leukoencephalopathy was unique to the COVID-19 ARDS patients in this cohort.
Prognostic factors in primary central nervous system lymphoma
Authors: Morales-Martinez Andrea , Nichelli Lucia , Hernandez-Verdin Isaias , Houillier Caroline , Alentorn Agustí , Hoang-Xuan Khê 
Published: September 2022

Purpose of review
Primary central nervous system lymphoma (PCNSL) is a rare and aggressive extranodal diffuse large B cell lymphoma. Despite its apparent immunopathological homogeneity, PCNSL displays a wide variability in outcome. Identifying prognostic factors is of importance for patient stratification and clinical decision-making. The purpose of this review is to focus on the clinical, neuroradiological and biological variables correlated with the prognosis at the time of diagnosis in immunocompetent patients.

Recent findings
Age and performance status remain the most consistent clinical prognostic factors. The current literature suggests that neurocognitive dysfunction is an independent predictor of poor outcome. Cumulating data support the prognostic value of increased interleukin-10 level in the cerebrospinal fluid (CSF), in addition to its interest as a diagnostic biomarker. Advances in neuroimaging and in omics have identified several semi-quantitative radiological features (apparent diffusion restriction measures, dynamic contrast-enhanced perfusion MRI (pMRI) pattern and 18F-fluorodeoxyglucose metabolism) and molecular genetic alterations with prognostic impact in PCNSL.

Summary
Validation of new biologic and neuroimaging markers in prospective studies is required before integrating future prognostic scoring systems. In the era of radiomic, large clinicoradiological and molecular databases are needed to develop multimodal artificial intelligence algorithms for the prediction of accurate outcome.