bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disulfiram Ethanol Reaction with Alcohol-Based Hand Sanitizer: An Exploratory Study
Authors: Ghosh Abhishek , Mahintamani Tathagata , Balhara Y P S , Roub Fazl E , Basu Debashish , BN Subodh , Mattoo S K , Mishra Eepsita , Sharma Babita 
Published: September 2020

Abstract

Aims
We conducted a cross-sectional survey to estimate the prevalence and clinical manifestation of disulfiram ethanol reaction (DER) and isopropanol toxicity (IT) in patients with alcohol use disorders, on disulfiram. Alcohol-based hand rub contains either ethanol or isopropanol or both. COVID-19 pandemic has led to wide scale usage of sanitizers. Patients with alcohol use disorders, on disulfiram, might experience disulfiram ethanol like reactions with alcohol-based sanitizers.

Methods
We telephonically contacted 339 patients, prescribed disulfiram between January 2014 and March 2020. The assessment pertained to the last 3 months (i.e. third week of March to third week of June 2020).

Result
The sample consisted of middle-aged men with a mean 16 years of alcohol dependence. Among the 82 (24%) patients adherent to disulfiram, 42 (12.3%) were using alcohol-based hand rubs. Out of these, a total of eight patients (19%; 95% CI 9–33) had features suggestive of DER; four of whom also had features indicative of IT. Five patients (62.5%) had mild and self-limiting symptoms. Severe systemic reactions were experienced by three (37.5%). Severe reactions were observed with exposure to sanitizers in greater amounts, on moist skin or through inhalation.

Conclusion
Patients on disulfiram should be advised to use alternate methods of hand hygiene.
The night out task and scoring application: an ill-structured, open-ended clinic-based test representing cognitive capacities used in everyday situations
Authors: Schmitter-Edgecombe Maureen , Cunningham Reanne , McAlister Courtney , Arrotta Kayela , Weakley Alyssa 
Published: September 2020

Abstract

Objective
The night out task (NOT) was developed as a naturalistic, open-ended, multitasking measure that requires individuals to complete eight subtasks comparable to those encountered during real-world functioning (e.g., pack travel bag, prepare tea). We examined psychometric properties and administration feasibility of this direct observation measure within a clinic-like setting using a tablet-based coding application.

Method
A sample of 148 community-dwelling older adults (82% cognitively healthy; 18% mild cognitive impairment) and 57 younger adults completed the NOT along with other neurocognitive tests and questionnaires.

Results
Inter-rater reliability across NOT primary (i.e., time, accuracy, efficiency) and process-related (e.g., error-types, self-corrections) variables was mostly excellent. NOT primary measures showed expected patterns of convergent and discriminant validity with measures of cognition, demographics, and well-being. External validity was established by the NOT ability to distinguish between age and diagnostic (cognitively healthy vs. mild cognitive impairment) groups. Demonstrating incremental validity, the NOT primary variables (execution time in particular) were predictive of self-reported functional abilities and completion quality of in-home everyday tasks over and earlier variables such as demographics, cognition, and mobility.

Conclusions
These findings suggest that the NOT and its app interface, which allows for continuous logging of observations, are a feasible in-clinic measure to assess cognitive capacities important for real-world functioning. With further validation, the NOT may allow for earlier detection of functional difficulties. Understanding errors and strategies used during NOT performance could also have implications for individualized interventions.
VPTMdb: a viral posttranslational modification database
Authors: Xiang Yujia , Zou Quan , Zhao Lilin 
Published: September 2020

Abstract
In viruses, posttranslational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for a better understanding of the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus–human interactions using comprehensive viral PTM datasets. To fill this gap, we developed the first comprehensive viral posttranslational modification database (VPTMdb) for collecting systematic information of PTMs in human viruses and infected host cells. The VPTMdb contains 1240 unique viral PTM sites with 8 modification types from 43 viruses (818 experimentally verified PTM sites manually extracted from 150 publications and 422 PTMs extracted from SwissProt) as well as 13 650 infected cells’ PTMs extracted from seven global proteomics experiments in six human viruses. The investigation of viral PTM sequences motifs showed that most viral PTMs have the consensus motifs with human proteins in phosphorylation and five cellular kinase families phosphorylate more than 10 viral species. The analysis of protein disordered regions presented that more than 50% glycosylation sites of double-strand DNA viruses are in the disordered regions, whereas single-strand RNA and retroviruses prefer ordered regions. Domain–domain interaction analysis indicating potential roles of viral PTMs play in infections. The findings should make an important contribution to the field of virus–human interaction. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylation sites. VPTMdb online web server (http://vptmdb.com:8787/VPTMdb/) was implemented for users to download viral PTM data and predict phosphorylation sites of interest.
Machine learning application identifies novel gene signatures from transcriptomic data of spontaneous canine hemangiosarcoma
Authors: Cheng Nuojin , Schulte Ashley J , Santosa Fadil , Kim Jong Hyuk 
Published: September 2020

Abstract
Angiosarcomas are soft-tissue sarcomas that form malignant vascular tissues. Angiosarcomas are very rare, and due to their aggressive behavior and high metastatic propensity, they have poor clinical outcomes. Hemangiosarcomas commonly occur in domestic dogs, and share pathological and clinical features with human angiosarcomas. Typical pathognomonic features of this tumor are irregular vascular channels that are filled with blood and are lined by a mixture of malignant and nonmalignant endothelial cells. The current gold standard is the histological diagnosis of angiosarcoma; however, microscopic evaluation may be complicated, particularly when tumor cells are undetectable due to the presence of excessive amounts of nontumor cells or when tissue specimens have insufficient tumor content. In this study, we implemented machine learning applications from next-generation transcriptomic data of canine hemangiosarcoma tumor samples (n = 76) and nonmalignant tissues (n = 10) to evaluate their training performance for diagnostic utility. The 10-fold cross-validation test and multiple feature selection methods were applied. We found that extra trees and random forest learning models were the best classifiers for hemangiosarcoma in our testing datasets. We also identified novel gene signatures using the mutual information and Monte Carlo feature selection method. The extra trees model revealed high classification accuracy for hemangiosarcoma in validation sets. We demonstrate that high-throughput sequencing data of canine hemangiosarcoma are trainable for machine learning applications. Furthermore, our approach enables us to identify novel gene signatures as reliable determinants of hemangiosarcoma, providing significant insights into the development of potential applications for this vascular malignancy.
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
Authors: Nieboer Marleen M. , de Ridder Jeroen 
Published: September 2020

Abstract

Motivation
Despite the fact that structural variants (SVs) play an important role in cancer, methods to predict their effect, especially for SVs in non-coding regions, are lacking, leaving them often overlooked in the clinic. Non-coding SVs may disrupt the boundaries of Topologically Associated Domains (TADs), thereby affecting interactions between genes and regulatory elements such as enhancers. However, it is not known when such alterations are pathogenic. Although machine learning techniques are a promising solution to answer this question, representing the large number of interactions that an SV can disrupt in a single feature matrix is not trivial.

Results
We introduce svMIL: a method to predict pathogenic TAD boundary-disrupting SV effects based on multiple instance learning, which circumvents the need for a traditional feature matrix by grouping SVs into bags that can contain any number of disruptions. We demonstrate that svMIL can predict SV pathogenicity, measured through same-sample gene expression aberration, for various cancer types. In addition, our approach reveals that somatic pathogenic SVs alter different regulatory interactions than somatic non-pathogenic SVs and germline SVs.

Availability and implementation
All code for svMIL is publicly available on GitHub: https://github.com/UMCUGenetics/svMIL.

Supplementary information
Supplementary data are available at Bioinformatics online.
FastSK: fast sequence analysis with gapped string kernels
Authors: Blakely Derrick , Collins Eamon , Singh Ritambhara , Norton Andrew , Lanchantin Jack , Qi Yanjun 
Published: September 2020

AbstractMotivationGapped k-mer kernels with support vector machines (gkm-SVMs) have achieved strong predictive performance on regulatory DNA sequences on modestly sized training sets. However, existing gkm-SVM algorithms suffer from slow kernel computation time, as they depend exponentially on the sub-sequence feature length, number of mismatch positions, and the task’s alphabet size.ResultsIn this work, we introduce a fast and scalable algorithm for calculating gapped k-mer string kernels. Our method, named FastSK, uses a simplified kernel formulation that decomposes the kernel calculation into a set of independent counting operations over the possible mismatch positions. This simplified decomposition allows us to devise a fast Monte Carlo approximation that rapidly converges. FastSK can scale to much greater feature lengths, allows us to consider more mismatches, and is performant on a variety of sequence analysis tasks. On multiple DNA transcription factor binding site prediction datasets, FastSK consistently matches or outperforms the state-of-the-art gkmSVM-2.0 algorithms in area under the ROC curve, while achieving average speedups in kernel computation of ∼100× and speedups of ∼800× for large feature lengths. We further show that FastSK outperforms character-level recurrent and convolutional neural networks while achieving low variance. We then extend FastSK to 7 English-language medical named entity recognition datasets and 10 protein remote homology detection datasets. FastSK consistently matches or outperforms these baselines.Availability and implementationOur algorithm is available as a Python package and as C++ source code at https://github.com/QData/FastSKSupplementary informationSupplementary data are available at Bioinformatics online.
UHPLC for quality evaluation of genuine and illegal medicines containing sildenafil citrate and tadalafil
Authors: Reis Naialy Fernandes Araújo , Silva Luiz Felipe Gomes , Souza Mateus Araújo Castro e , Fialho Sílvia Ligório , Souza Moreira Carolina Paula , Oliveira Andrade Marcus Vinicius , Paula Washington Xavier , Gloria Maria Beatriz Abreu , Pianetti Gerson Antônio , Fernandes Christian 
Published: September 2020

Abstract
One of the highest incidences of illegal drug products is related to phosphodiesterase-5 inhibitors, used in treatment of erectile dysfunction, including those containing sildenafil citrate and tadalafil. In this context, comprehensive evaluation of the quality of genuine and illegal medicines was performed. A simple and rapid ultra-high performance liquid chromatography (UHPLC-UV) method to quantify sildenafil and tadalafil in the presence of six degradation products was developed and validated. Sildenafil and tadalafil were submitted to forced degradation. The separation was carried out on a Kinetex C18 (50 × 2.1 mm; 1.7 μm) column with mobile phase composed of acetonitrile and aqueous triethylamine solution. The calibration curves were linear in the range of 14–126 μg mL−1 for sildenafil citrate and 4–36 μg mL−1 for tadalafil and the method proved to be selective, precise, accurate and robust. Sildenafil degraded in oxidative media, whereas tadalafil degraded in acidic, alkaline and oxidative environment. The chemical structures and the mechanisms for the formation of the main degradation products were proposed by UHPLC coupled to tandem mass spectrometry. The UHPLC-UV method was applied in the pharmaceutical analysis of genuine and seized medicines. Some of them did not meet quality standards, mainly due to contents below specifications and the large variation on contents between units within a batch.
Impact of white blood cell count on clinical outcomes in patients treated with aspirin-free ticagrelor monotherapy after percutaneous coronary intervention: insights from the GLOBAL LEADERS trial
Authors: Ono Masafumi , Tomaniak Mariusz , Koenig Wolfgang , Khamis Ramzi , de Silva Ranil , Chichareon Ply , Kawashima Hideyuki , Hara Hironori , Gao Chao , Wang Rutao , Huber Kurt , Vrolix Mathias , Jasionowicz Pawel , Wykrzykowska Joanna J , Piek Jan J , Jüni Peter , Hamm Christian , Steg Philippe Gabriel , Windecker Stephan , Onuma Yoshinobu , Storey Robert F , Serruys Patrick W 
Published: September 2020

Abstract

Aims
The aim of this study was to investigate the efficacy and safety of ticagrelor monotherapy in patients undergoing percutaneous coronary intervention (PCI) stratified according to the baseline white blood cell (WBC) count.

Methods and results
This is a post hoc analysis of the GLOBAL LEADERS trial, a multi-centre, open-label, randomized all-comer trial in patients undergoing PCI, comparing the experimental strategy (23-month ticagrelor monotherapy following 1-month dual anti-platelet therapy [DAPT]) with the reference strategy (12-month aspirin monotherapy following 12-month DAPT). Patients were stratified into two WBC groups, either &lt; or ≥median WBC count of 7.8 × 109 cells/L (lower or higher WBC group, respectively). The primary endpoint was a composite of all-cause mortality or new Q-wave myocardial infarction at 2 years. Of 14 576 patients included in the present study, 7212 patients (49.5%) were classified as the lower WBC group, who had a significantly lower risk of both ischaemic and bleeding outcomes at 2 years. At 2 years, the experimental strategy was associated with a significant lower incidence of the primary endpoint compared with the reference strategy in the lower WBC group [2.8% vs. 4.2%; hazard ratio (HR): 0.67; 95% confidence interval (CI): 0.52–0.86] but not in the higher WBC group (4.8% vs. 4.7%; HR: 1.01; 95% CI: 0.82–1.25; Pinteraction=0.013). There were no significant differences in the risks of Bleeding Academic Research Consortium type 3 or 5 bleeding between two anti-platelet strategies regardless of the WBC groups.

Conclusion
Increased WBC counts, which may reflect degree of inflammation, at the time of index procedure may attenuate the anti-ischaemic benefits of ticagrelor monotherapy observed in patients with lower WBC counts.
Eternal rest, perpetual light and the Last Judgement: Antoine Brumel’s Dies irae in the early Requiem tradition
Authors: Rothenberg David J 
Published: September 2020

Abstract
Antoine Brumel’s Missa pro defunctis is one of the earliest polyphonic Requiem settings, and the first by several decades to include the sequence, Dies irae. Whereas most chants in the Mass for the Dead were set c.1500 to the low-pitched, highly consonant polyphony that denoted mourning and penitence at the time, the Dies irae is a musical portrayal of the Last Judgement that might seem to demand more vivid polyphonic treatment. And yet Brumel’s setting, a grand alternatim movement, responds more to the formal regularity of the chant than to its text, which describes a terrifying scene much like what is seen in contemporaneous visual depictions of the Last Judgement. Indeed, Brumel’s most striking rhetorical moment comes not in the frightening early verses of the sequence but in its concluding plea to Christ that the dead be granted peace. Analysis of Brumel’s Dies irae in the context of his Missa pro defunctis, therefore, shows that early Requiem compositions, even at their most terrifying, serve first and foremost as functional pleas to God that the deceased be granted eternal rest and perpetual light.
Significance of post-pacing intervals shorter than tachycardia cycle length for successful catheter ablation of atypical flutter
Authors: Dall’Aglio Pietro Bernardo , Johner Nicolas , Namdar Mehdi , Shah Dipen C 
Published: September 2020

Abstract

Aims
During entrainment mapping of macro-reentrant tachycardias, the time difference (dPPI) between post-pacing interval (PPI) and tachycardia cycle length (TCL) is thought to be a function of the distance of the pacing site to the re-entry circuit and dPPI &lt; 30 ms is considered within the re-entry circuit. This study assessed the importance of PPI &lt; TCL as a successful target for atypical flutter ablation.

Methods and results
A total of 177 ablation procedures were investigated. Surface electrocardiograms (ECGs) were evaluated and combined activation and entrainment mapping were performed to choose ablation sites. Each entrainment sequence immediately preceding static radiofrequency delivery at the same site was analysed. A total of 545 entrainment sequences were analysed. dPPI &lt; 0 ms was observed in 45.3% (247/545) sequences. Ablation resulted in tachycardia termination more often at sites with dPPI &lt; 0 (27.8% vs. 14.5%, P &lt; 0.001) and with a progressively increasingly inverse correlation between dPPI duration and ablation success [odds ratio (OR): 0.974; 95% confidence interval (CI) 0.960–0.988; P &lt; 0.001]. Tachycardia termination or cycle length prolongation also occurred more often at sites with dPPI &lt; 0 (50.6% vs. 33.2%, P &lt; 0.001) and with a similar inverse correlation with dPPI duration (OR: 0.972; 95% CI 0.960–0.984; P &lt; 0.001). Twelve-lead synchronous isoelectric intervals were observed in 64.4% (163/253) flutter ECGs and were associated with a dPPI &lt; 0 (75.3% vs. 55.8%, P &lt; 0.001).

Conclusion
When combined with activation mapping, a negative dPPI is a more effective parameter for identifying a target for successful ablation compared to a dPPI = 0–30 ms. Its occurrence is associated with a critical small narrow slow-conducting isthmus at the target site.
Selective Gene Loss of Visual and Olfactory Guanylyl Cyclase Genes Following the Two Rounds of Vertebrate-Specific Whole-Genome Duplications
Authors: Gesemann Matthias , Neuhauss Stephan C F 
Published: September 2020

AbstractPhotoreceptors convey visual information and come in two flavors; dim-light and bright-light dedicated rod and cones. Both cell types feature highly specialized phototransduction cascades that convert photonic energy into intracellular signals. Although a substantial amount of phototransduction gene ohnologs are expressed either in rods or cones, visual guanylyl cyclases (GCs) involved in the calcium (Ca2+) dependent feedback regulation of phototransduction are neither rod nor cone specific. The co-existence of visual GCs in both photoreceptor types suggests that specialization of these ohnologs occurred despite their overlapping expression.Here, we analyze gene retention and inactivation patterns of vertebrate visual and closely related olfactory GCs following two rounds (2R) of vertebrate-specific whole-genome duplication events (2R WGD). Although eutherians generally use two visual and one olfactory GC, independent inactivation occurred in some lineages. Sauropsids (birds, lizards, snakes, turtles, and crocodiles) generally have only one visual GC (GC-E). Additionally, turtles (testodes) also lost the olfactory GC (GC-D). Pseudogenization in mammals occurred in specific species/families likely according to functional needs (i.e., many species with reduced vision only have GC-E). Likewise, some species not relying on scent marks lack GC-D, the olfactory GC enzyme. Interestingly, in the case of fish, no species can be found with fewer than three (two visual and one olfactory) genes and the teleost-specific 3R WGD can increase this number to up to five. This suggests that vision in fish now requires at least two visual GCs.
Dancing With Dementia: Exploring the Embodied Dimensions of Creativity and Social Engagement
Authors: Kontos Pia , Grigorovich Alisa , Kosurko An , Bar Rachel J , Herron Rachel V , Menec Verena H , Skinner Mark W 
Published: September 2020

AbstractBackground and ObjectivesDance is increasingly being implemented in residential long-term care to improve health and function. However, little research has explored the potential of dance to enhance social inclusion by supporting embodied self-expression, creativity, and social engagement of persons living with dementia and their families.Research Design and MethodsThis was a qualitative sequential multiphase study of Sharing Dance Seniors, a dance program that includes a suite of remotely streamed dance sessions that are delivered weekly to participants in long-term care and community settings. Our analysis focused on the participation of 67 persons living with dementia and 15 family carers in residential long-term care homes in Manitoba, Canada. Data included participant observation, video recordings, focus groups, and interviews; all data were analyzed thematically.ResultsWe identified 2 themes: playfulness and sociability. Playfulness refers to the ways that the participants let go of what is “real” and became immersed in the narrative of a particular dance, often adding their own style. Sociability captures the ways in which the narrative approach of the Sharing Dance Seniors program encourages connectivity/intersubjectivity between participants and their community; participants co-constructed and collaboratively animated the narrative of the dances.Discussion and ImplicationsOur findings highlight the playful and imaginative nature of how persons living with dementia engage with dance and demonstrate how this has the potential to challenge the stigma associated with dementia and support social inclusion. This underscores the urgent need to make dance programs such as Sharing Dance Seniors more widely accessible to persons living with dementia everywhere.