bluuebunny/crossref_metadata_2025_split huggingface dataset:
Row, Row, Row Your Boat: How to Not Find Weak Keys in Pilsung
Authors: Chuengsatiansup Chitchanok , Ronen Eyal , Rose Gregory G , Yarom Yuval 
Published: July 2022

AbstractThe Pilsung cipher is part of the North Korean Red Star operating system, which was leaked to the West in 2014. Initial analysis by Kryptos Logic reported a possibility of a class of weak keys due to the use of pseudo-random diffusion. Following this lead, we analyzed the cipher and identified a small class of such weak keys. We developed techniques for searching for a key that belongs to the class. After spending thousands of CPU hours, we found a supposedly weak key for a slightly weaker version of Pilsung, but the key did not behave as we expected. On further investigation we found out a crucial misunderstanding in a critical part of the cipher and that no such class of weak keys exists in Pilsung. Thus, this paper makes two main contributions to the art of cryptanalysis. First, it identifies and shows how to investigate a potential weakness in randomizing diffusion, which although does not exist in Pilsung, may affect future designs. Second, it highlights the need for early verification of results in order to identify errors before expending significant resources.
A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles
Authors: Lin Sheng-Jie , Yeh Wen-Chao , Chiu Yu-Wen , Chang Yung-Chun , Hsu Min-Huei , Chen Yi-Shin , Hsu Wen-Lian 
Published: July 2022

AbstractIn this research, we explored various state-of-the-art biomedical-specific pre-trained Bidirectional Encoder Representations from Transformers (BERT) models for the National Library of Medicine - Chemistry (NLM CHEM) and LitCovid tracks in the BioCreative VII Challenge, and propose a BERT-based ensemble learning approach to integrate the advantages of various models to improve the system’s performance. The experimental results of the NLM-CHEM track demonstrate that our method can achieve remarkable performance, with F1-scores of 85% and 91.8% in strict and approximate evaluations, respectively. Moreover, the proposed Medical Subject Headings identifier (MeSH ID) normalization algorithm is effective in entity normalization, which achieved a F1-score of about 80% in both strict and approximate evaluations. For the LitCovid track, the proposed method is also effective in detecting topics in the Coronavirus disease 2019 (COVID-19) literature, which outperformed the compared methods and achieve state-of-the-art performance in the LitCovid corpus.Database URL: https://www.ncbi.nlm.nih.gov/research/coronavirus/.
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
Authors: Summo Marilyne , Comte Aurore , Martin Guillaume , Perelle Pierrick , Weitz Eric M , Droc Gaëtan , Rouard Mathieu 
Published: July 2022

Abstract
In silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results of in silico chromosome painting. To facilitate data input generation, a script to execute analytical commands is provided and an interactive data curation mode is supported to ensure consistency of the automated procedure. GeMo contains preloaded datasets from published studies on crop domestication but can be applied to other purposes, such as breeding programs Although only applied so far on plants, GeMo can handle data from animals as well.
Database URL: https://gemo.southgreen.fr/
Cerebrovascular accidents in paediatric patients supported by the Berlin Heart EXCOR
Authors: Rohde Sofie , Sandica Eugen , Veen Kevin , Miera Oliver , Amodeo Antonio , Napoleone Carlo Pace , Özbaran Mustafa , Sliwka Joanna , Thiruchelvam Timothy , Zimpfer Daniel , Schubert Stephan , Bogers Ad J J C , de By Theo M M H 
Published: July 2022

Abstract

OBJECTIVES
Ventricular assist device support as a bridge to transplant or recovery is a well-established therapy in children on the cardiac transplant waiting list. The goal of this study was to investigate the incidence of and the associated factors for cerebrovascular accidents in paediatric patients supported by a Berlin Heart EXCOR.

METHODS
All patients &lt;19 years of age supported by a Berlin Heart EXCOR between January 2011 and January 2021 from the European Registry for Patients with Mechanical Circulatory Support were included.

RESULTS
In total, 230 patients were included. A total of 140 (60.9%) patients had a diagnosis of dilated cardiomyopathy. 46 patients (20.0%) sustained 55 cerebrovascular accidents, with 70.9% of the episodes within 90 days after the ventricular assist device was implanted. The event rate of cerebrovascular accidents was highest in the first era (0.75). Pump thrombosis and secondary need for a right ventricular assist device were found to be associated with a cerebrovascular accident (hazard ratio 1.998, P = 0.040; hazard ratio 11.300, P = 0.037). At the 1-year follow-up, 44.4% of the patients had received a transplant, 13.1% were weaned after recovery and 24.5% had died. Event rates for mortality showed a significantly decreasing trend.

CONCLUSIONS
Paediatric ventricular assist device support is associated with important adverse events, especially in the early phase after the device is implanted. Pump thrombosis and the need for a secondary right ventricular assist device are associated with cerebrovascular accidents. Furthermore, an encouragingly high rate of recovery in this patient population was shown, and death rates declined. More complete input of data into the registry, especially concerning anticoagulation protocols, would improve the data.
Health literacy and prognosis of heart failure: a prospective propensity-matched study in the community
Authors: Gomez Rocio , Andrey Jose L , Puerto Jose L , Romero Sotero P , Pedrosa Maria J , Rosety-Rodriguez Manuel , Gomez Francisco 
Published: July 2022

AbstractAimsHealth literacy (HL), the ability to obtain and understand health information, is critical to self-care in chronic disorders. A low HL is common among these patients and has been associated with a worse prognosis. Nevertheless, the relationship between HL and the prognosis of heart failure (HF) with reduced (HFrEF) vs. preserved (HFpEF) ejection fraction remains unsettled. To analyse the relationship between HL and the prognosis of patients with incident HFrEF and HFpEF.Methods and resultsProspective study over 10 years (2010–19) on 6444 patients diagnosed with incident HF. The main outcomes were mortality, hospitalizations, and visits to emergency services. The independent relationship between HL and the prognosis, stratifying patients for cardiovascular comorbidity after propensity score-matching was analysed.After matching 5355 HF patients, 1785 with low HL (874 with HFrEF and 911 with HFpEF) vs. 3570 with adequate HL (1748 with HFrEF and 1822 with HFpEF), during a median follow-up of 5.41 years, 3874 patients died (72.3%) and 3699 patients were hospitalized (69.1%). After adjustment for potential confounders, an adequate HL was associated with a lower all-cause and cardiovascular mortality, less hospitalizations, and less 30-day readmissions [relative risk (RR) for HF &lt;0.72 (0.66–0.86), RR for HFrEF &lt;0.69 (0.63–0.95), and RR for HFpEF &lt;0.62 (0.55–0.88), P &lt; 0.001 in all cases], both for patients with HFrEF and HFpEF. Analyses of recurrent hospitalizations gave larger HL effects than time-to-first-event analyses.ConclusionsIn this propensity-matched study, a low HL is associated with a worse prognosis of patients with incident HFrEF and HFpEF.
Trade and traders in Plantation Ulster, c.1600–c.1650
Authors: Roulston William , Scott Brendan 
Published: July 2022

Abstract
The Ulster Plantation of the early seventeenth century introduced to that province not only new markets and marketplaces, but also a new community interested in buying and selling the goods now on offer there. The Ulster port books for 1612–15 not only offer a great deal of information regarding the products being bought and sold in the province, but also provide us with the names and activities of the merchants and the captains entrusted with the transportation of these goods. This essay investigates the traders themselves, their activities and the conditions under which they operated during this unsettled period.
Updated variant curation expert panel criteria and pathogenicity classifications for 251 variants for RYR1-related malignant hyperthermia susceptibility
Authors: Johnston Jennifer J , Dirksen Robert T , Girard Thierry , Hopkins Phil M , Kraeva Natalia , Ognoon Mungunsukh , Radenbaugh K Bailey , Riazi Sheila , Robinson Rachel L , Saddic, III Louis A , Sambuughin Nyamkhishig , Saxena Richa , Shepherd Sarah , Stowell Kathryn , Weber James , Yoo Seeley , Rosenberg Henry , Biesecker Leslie G 
Published: July 2022

Abstract
The ClinGen malignant hyperthermia susceptibility (MHS) variant curation expert panel specified the American College of Medical Genetics and Genomics/Association of Molecular Pathologists (ACMG/AMP) criteria for RYR1-related MHS and a pilot analysis of 84 variants was published. We have now classified an additional 251 variants for RYR1-related MHS according to current ClinGen standards and updated the criteria where necessary. Criterion PS4 was modified such that individuals with multiple RYR1 variants classified as pathogenic (P), likely pathogenic (LP), or variant of uncertain significance (VUS) were not considered as providing evidence for pathogenicity. Criteria PS1 and PM5 were revised to consider LP variants at the same amino-acid residue as providing evidence for pathogenicity at reduced strength. Finally, PM1 was revised such that if PS1 or PM5 are used PM1, if applicable, should be downgraded to supporting. Of the 251 RYR1 variants, 42 were classified as P/LP, 16 as B/LB, and 193 as VUS. The primary driver of 175 VUS classifications was insufficient evidence supporting pathogenicity, rather than evidence against pathogenicity. Functional data supporting PS3/BS3 was identified for only 13 variants. Based on the posterior probabilities of pathogenicity and variant frequencies in gnomAD, we estimated the prevalence of individuals with RYR1-related MHS pathogenic variants to be between 1/300 and 1/1075, considerably higher than current estimates. We have updated ACMG/AMP criteria for RYR1-related MHS and classified 251 variants. We suggest that prioritization of functional studies is needed to resolve the large number of VUS classifications and allow for appropriate risk assessment. RYR1-related MHS pathogenic variants are likely to be more common than currently appreciated.
Immunomodulatory functions of the circ_001678/miRNA-326/ZEB1 axis in non-small cell lung cancer via the regulation of PD-1/PD-L1 pathway
Authors: Tian Qi , Wu Tong , Zhang Xiudi , Xu Ke , Yin Xiaobo , Wang Xiaojie , Shi Shanshan , Wang Ping , Gao Liming , Xu Shufeng , Liu Xinyan 
Published: July 2022

Abstract
High-throughput circular RNA (circRNA) sequencing identified circRNA_001678 (circ_001678) as an upregulated circRNA in non-small cell lung cancer (NSCLC) tissues. Hence, the current study sought to investigate the function and the underlying mechanism of circRNA_001678 in immune escape of NSCLC. Briefly, commercially purchased NSCLC cell lines were adopted for in vitro experiment to evaluate the effects of circ_001678 over-expression or knockdown on cell biological functions, including proliferation, migration and invasive abilities. In addition, the effects of circ_001678 on the in vivo tumorigenicity ability were evaluated for verification. Accordingly, we uncovered that circ_001678 over-expression augmented NSCLC progression in vitro and enhanced tumorigenicity ability in vivo. The interaction between circ_001678 and miR-326 predicted online was verified by means of luciferase and RNA pull-down assays. Furthermore, circ_001678 could sponge miR-326 to up-regulate ZEB1. On the other hand, the tumor-promoting effects of circ_001678 could be inhibited by anti-PD-L1/PD-1 treatment. Mechanistically, circ_001678 led to the activation of the PD-1/PD-L1 pathway to promote CD8+ T cell apoptosis, thereby inducing NSCLC cell immune escape via regulation of the miR-326/ZEB1 axis. To conclude, our findings revealed that circ_001678 sponges miR-326 to up-regulate ZEB1 expression and induce the PD-1/PD-L1 pathway-dependent immune escape, thereby promoting the malignant progression of NSCLC.
Is modularity robust to misfits? A formal test
Authors: Fang Christina , Kim Ji-hyun Jason 
Published: July 2022

Abstract
In this paper, we ask—is the power of modularity robust to a potential misfit between organizations and their underlying technical systems? We design a computational model to systematically explore the role of misfits, building on prior models using the numerical NK paradigm. We find that the impact of misfits is either neutral or even performance-enhancing when the organizations carry out a decentralized search while coordinating and evaluating the alternatives at the organizational level. This is good news for the theoretical efficacy of modularity—the benefits of modular search do not have to be contingent upon a precise understanding of the underlying technical dependencies. The reason is that in decentralized and hierarchical systems, there exists a tension between (i) the exploration and generation of alternatives and (ii) the exercise of restraint and control. The latter is important to implement only those alternatives that have an overall positive impact on the organization, by limiting the downside of radical experiments.
Interpretation of Mendelian randomization using a single measure of an exposure that varies over time
Authors: Morris Tim T , Heron Jon , Sanderson Eleanor C M , Davey Smith George , Didelez Vanessa , Tilling Kate 
Published: July 2022

Abstract

Background
Mendelian randomization (MR) is a powerful tool through which the causal effects of modifiable exposures on outcomes can be estimated from observational data. Most exposures vary throughout the life course, but MR is commonly applied to one measurement of an exposure (e.g. weight measured once between ages 40 and 60 years). It has been argued that MR provides biased causal effect estimates when applied to one measure of an exposure that varies over time.

Methods
We propose an approach that emphasizes the liability that causes the entire exposure trajectory. We demonstrate this approach using simulations and an applied example.

Results
We show that rather than estimating the direct or total causal effect of changing the exposure value at a given time, MR estimates the causal effect of changing the underlying liability for the exposure, scaled to the effect of the liability on the exposure at that time. As such, results from MR conducted at different time points are expected to differ (unless the effect of the liability on exposure is constant over time), as we illustrate by estimating the effect of body mass index measured at different ages on systolic blood pressure.

Conclusion
Univariable MR results should not be interpreted as time-point-specific direct or total causal effects, but as the effect of changing the liability for the exposure. Estimates of how the effects of a genetic variant on an exposure vary over time, together with biological knowledge that provides evidence regarding likely effective exposure periods, are required to interpret time-point-specific causal effects.
Mortality among twin individuals exposed to loss of a co-twin
Authors: Song Huan , Shang Yanan , Fang Fang , Almqvist Catarina , Pedersen Nancy L , Magnusson Patrik K E , Larsson Henrik , Valdimarsdóttir Unnur A 
Published: July 2022

Abstract

Background
Although the death of a child, sibling or spouse has been associated with elevated risk of mortality, less is known about the survival of twin siblings exposed to a co-twin loss.

Methods
In a Swedish population-based sibling-matched cohort, we compared the mortality of 5548 twin individuals who lost their co-twin between 1932 and 2011 with that of 27 740 age-matched and sex-matched twin individuals without such a loss and 6772 full siblings of these exposed twin individuals. Cox regression models were used to estimate the hazard ratios (HRs) of all-cause and cause-specific mortality.

Results
We found increased risk of all-cause mortality among twin individuals exposed to a co-twin loss compared with matched unexposed twin individuals (HR = 1.30, 95% CI: 1.18–1.43) and their full siblings (HR = 1.10, 95% CI: 0.96–1.27) after adjusting for multiple covariates. The all-cause mortality risk was greater for loss of a co-twin due to unnatural deaths (HR = 1.54, 95% CI: 1.17–2.03) than natural deaths (HR = 1.26, 95% CI: 1.14–1.40). For cause-specific mortality, co-twin loss was associated with a higher risk of unnatural deaths both among twin individuals who lost their co-twin due to unnatural deaths (HR = 1.98, 95% CI: 1.27–3.10) and those whose loss was due to natural deaths (HR = 1.48, 95% CI: 1.07–2.06). The risk elevations were generally stronger for loss of a monozygotic co-twin than loss of a dizygotic co-twin.

Conclusion
Loss of a co-twin, especially a monozygotic co-twin, was associated with increased mortality, particularly of unnatural causes, among the surviving twin individuals. The excess mortality is likely attributable to both shared disease susceptibility within the twin pair and the adverse health sequelae of bereavement.
Long-term exposure to low-level air pollution, genetic susceptibility and risk of dementia
Authors: Ma Hao , Li Xiang , Zhou Tao , Wang Mengying , Heianza Yoriko , Qi Lu 
Published: July 2022

Abstract

Background
We aimed to assess the association between low-level air pollution and the risk of dementia, and examine the modification effect by genetic susceptibility on the relationship.

Methods
A total of 164 447 participants who were free of dementia at baseline and aged ≥60 years were included. Annual average concentrations of particulate matter (PM) with diameters of ≤2.5 μm (PM2.5), between 2.5 and 10 μm (PMcoarse), PM2.5 absorbance and nitrogen dioxides (NO2) were evaluated using the Land Use Regression models. Cox proportional hazards regression was used to estimate the association between air pollutants and incident dementia.

Results
The adjusted hazard ratio (HR) of dementia for a 5-μg/m3 increase in NO2 was 1.09 (95% CI, 1.05–1.14); the adjusted HR of dementia for a 1-μg/m3 increase in PM2.5 was 1.10 (1.04–1.17). Such significant associations were present even within concentration ranges well below the present World Health Organization, US and European annual mean limit values. In addition, higher PM2.5 absorbance, a marker closely related to motorized traffic, was associated with higher risk of dementia. We found the risk of dementia associated with a combination of air pollutants (NO2 or PM2.5) and high genetic susceptibility (APOE-ε4 alleles or overall genetic susceptibility) was greater than the addition of the risk associated with each individual factor, indicating significant interactions on an additive scale (all P-interaction &lt; 0.05).

Conclusion
Long-term exposure to PM2.5 or NO2, even at relatively low levels, is associated with a higher risk of dementia. Air pollution may additively interact with the genetic susceptibility on dementia risk.
The influence of adverse drug effects on health-related quality of life in chronic obstructive pulmonary disease patients
Authors: Altawalbeh Shoroq M , Almomani Basima A , Alefan Qais , Mohammad Momany Suleiman , Al-Share Qusai Y 
Published: July 2022

AbstractObjectivesChronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Concerns have been raised about the influence of adverse drug effects on patient’s health-related quality of life (HRQoL) in COPD patients. This study aimed to evaluate the impact of COPD treatment-related adverse effects on HRQoL in COPD patients.MethodsIn a cross-sectional study, COPD patients aged 40 years or older were identified and interviewed during their hospital visits. The EuroQol 5 Dimension 5 Level (EQ-5D-5L) questionnaire was used for evaluating HRQoL. Potential treatment adverse effects were evaluated as experienced by participants during the last 2 weeks preceding the interview. The intensity of adverse effects was reported in the following categories: never, mild, moderate and severe. Multivariable linear regression model was performed to evaluate the influence of adverse drug effects on utility scores as an indicator of HRQoL.Key findingsA total of 203 patients diagnosed with COPD were recruited in the current study. The mean utility score of the study sample was 0.68 (SD = 0.36). Moderate-severe constipation, moderate-severe confusion, mild urinary hesitation, moderate-severe urinary hesitation, moderate-severe dry eyes and moderate-severe drowsiness were significant predictors/determinants for the average utility scores (coefficients were −0.099, −0.191, −0.111, −0.157 and −0.144, respectively). In addition, having higher COPD Assessment Test scores and severe disease was negatively associated with average utility scores (coefficients were −0.287 and −0.124, respectively).ConclusionsHigher intensity of COPD treatment-related adverse effects has a negative influence on HRQoL in COPD patients. Anticholinergic drug effects are of concern in COPD adults’ population.
Swedish community pharmacy employees’ knowledge and experience of substandard and falsified medical products: a cross-sectional descriptive survey
Authors: Persson A , Troein M , Lundin S , Midlöv P , Lenander C 
Published: July 2022

Abstract

Objectives
Substandard and falsified medical products are, according to the World Health Organization, a global threat to public health. To evaluate if community pharmacy employees can guide the public to safer medication purchases, their knowledge and experience about SF medical products was examined.

Methods
A digital questionnaire was distributed to the five dominating pharmacy companies in Sweden, representing 97% of the community pharmacies (1391/1433), giving the theoretical possibility of reaching 6200 employees. Three companies published a link to the questionnaire on their intranets, one distributed the link via e-mail to the responsible pharmacist for quality and knowledge, respectively. The fifth company did not pass on, due to technical problems. Employees aged 18 years or older with customer contact were invited to participate.

Key findings
The questionnaire was available for 74% of all community pharmacies (1067/1433), having approximately 4900 employees with customer contact. The response rate was 5% (228/4900). Of the respondents, 89% were pharmacists (203/228), 84% were women (191/228) and 43% were 35-49 years (98/228). The respondents worked in pharmacies of different size, located both in rural and urban areas. The definition of substandard and falsified medical products was known by 182 of the 228 respondents (80%) and the main source of knowledge was media (61%, 111/228). The common European logo for authorized online pharmacies was not recognized by 74% (169/228).

Conclusions
For pharmacy employees to guide the public to safer medication purchases, knowledge about substandard and falsified medical products needs to be enhanced specially about legal international e-commerce.