bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twenty-five years of cyber threats in the news: a study of Swedish newspaper coverage (1995–2019)
Authors: Boholm Max 
Published: July 2021

AbstractThis paper explores how cyber threats are represented in Swedish newspapers. The sample comprises 1269 articles from three newspapers (Aftonbladet, Göteborgs-Posten, and Svenska Dagbladet) covering 25 years (1995–2019). The study provides a text-near and detailed analysis of the threats covered. The study analyzes these threats along several dimensions: their modality (e.g. unauthorized access or manipulation); to what extent ambiguous themes (e.g. attack, crime, and warfare) are specified in context; how cyber-threat coverage has changed over time; and the event orientation of the coverage, i.e. whether articles address topical events and, if so, which ones. There are five main findings. First, the Swedish newspaper cybersecurity discourse covers multiple threats; in total, 34 themes (present in at least 4% of articles) have been identified. Second, the representation of cyber threats varies in specificity. While generic themes such as attack and warfare are mostly specified in terms of their modality, they sometimes are not, leaving the representation vague. Third, this study, given its general approach, provides insights into media representations of particular cyber threats. For example, this study finds the meaning of “hacking” in the media to be more diversified and nuanced than previously assumed (e.g. as simply meaning “computer break-in”). Fourth, newspaper coverage of cyber threats has changed over time, in both quantity (i.e. the amount of coverage has increased) and quality, as three general trends have been observed: the state-ification and militarization of threats (i.e. increased attention to, e.g. nations and warfare as threats), the organization-ification of threats (i.e. increased attention to, e.g. government agencies and companies as threats), and the diversification and hyping of threats (i.e. cumulatively more threats are added to the cybersecurity discourse, although attention to particular threats is sometimes restricted in time). Finally, parallel to coverage of particular topical events (e.g. the “I love you” virus), newspaper representations of cyber threats largely exemplify “amplification without the event,” i.e. threats are covered without linking them to topical events, as is otherwise typical of news reports. The findings in relation to previous studies of cybersecurity discourse and the implications for informal learning and threat perception are discussed.
Mammographic features are associated with cardiometabolic disease risk and mortality
Authors: Grassmann Felix , Yang Haomin , Eriksson Mikael , Azam Shadi , Hall Per , Czene Kamila 
Published: July 2021

Abstract

Aims
In recent years, microcalcifications identified in routine mammograms were found to be associated with cardiometabolic disease in women. Here, we aimed to systematically evaluate the association of microcalcifications and other mammographic features with cardiometabolic disease risk and mortality in a large screening cohort and to understand a potential genetic contribution.

Methods and results
This study included 57 867 women from a prospective mammographic screening cohort in Sweden (KARMA) and 49 583 sisters. Cardiometabolic disease diagnoses and mortality and medication were extracted by linkage to Swedish population registries with virtually no missing data. In the cardiometabolic phenome-wide association study, we found that a higher number of microcalcifications were associated with increased risk for multiple cardiometabolic diseases, particularly in women with pre-existing cardiometabolic diseases. In contrast, dense breasts were associated with a lower incidence of cardiometabolic diseases. Importantly, we observed similar associations in sisters of KARMA women, indicating a potential genetic overlap between mammographic features and cardiometabolic traits. Finally, we observed that the presence of microcalcifications was associated with increased cardiometabolic mortality in women with pre-existing cardiometabolic diseases (hazard ratio and 95% confidence interval: 1.79 [1.24–2.58], P = 0.002) while we did not find such effects in women without cardiometabolic diseases.

Conclusions
We found that mammographic features are associated with cardiometabolic risk and mortality. Our results strengthen the notion that a combination of mammographic features and other breast cancer risk factors could be a novel and affordable tool to assess cardiometabolic health in women attending mammographic screening.
Sex differences in outcomes after coronary artery bypass grafting: a pooled analysis of individual patient data
Authors: Gaudino Mario , Di Franco Antonino , Alexander John H , Bakaeen Faisal , Egorova Natalia , Kurlansky Paul , Boening Andreas , Chikwe Joanna , Demetres Michelle , Devereaux Philip J , Diegeler Anno , Dimagli Arnaldo , Flather Marcus , Hameed Irbaz , Lamy Andre , Lawton Jennifer S , Reents Wilko , Robinson N Bryce , Audisio Katia , Rahouma Mohamed , Serruys Patrick W , Hara Hironori , Taggart David P , Girardi Leonard N , Fremes Stephen E , Benedetto Umberto 
Published: July 2021

Abstract

Aims
Data suggest that women have worse outcomes than men after coronary artery bypass grafting (CABG), but results have been inconsistent across studies. Due to the large differences in baseline characteristics between sexes, suboptimal risk adjustment due to low-quality data may be the reason for the observed differences. To overcome this limitation, we undertook a systematic review and pooled analysis of high-quality individual patient data from large CABG trials to compare the adjusted outcomes of women and men.

Methods and results
The primary outcome was a composite of all-cause mortality, myocardial infarction (MI), stroke, and repeat revascularization (major adverse cardiac and cerebrovascular events, MACCE). The secondary outcome was all-cause mortality. Multivariable mixed-effect Cox regression was used. Four trials involving 13 193 patients (10 479 males; 2714 females) were included. Over 5 years of follow-up, women had a significantly higher risk of MACCE [adjusted hazard ratio (HR) 1.12, 95% confidence interval (CI) 1.04–1.21; P = 0.004] but similar mortality (adjusted HR 1.03, 95% CI 0.94–1.14; P = 0.51) compared to men. Women had higher incidence of MI (adjusted HR 1.30, 95% CI 1.11–1.52) and repeat revascularization (adjusted HR 1.22, 95% CI 1.04–1.43) but not stroke (adjusted HR 1.17, 95% CI 0.90–1.52). The difference in MACCE between sexes was not significant in patients 75 years and older. The use of off-pump surgery and multiple arterial grafting did not modify the difference between sexes.

Conclusions
Women have worse outcomes than men in the first 5 years after CABG. This difference is not significant in patients aged over 75 years and is not affected by the surgical technique.
Contemporary trends and in-hospital outcomes of catheter and stand-alone surgical ablation of atrial fibrillation
Authors: Ariss Robert W , Khan Minhas Abdul Mannan , Patel Neha J , Zafrullah Fnu , Bhavsar Krupa , Nazir Salik , Jneid Hani , Moukarbel George V 
Published: July 2021

Abstract

Aims
The contemporary trends in catheter ablation (CA) and surgical ablation (SA) utilization and surgical techniques [open vs. thoracoscopic, with or without left atrial appendage closure (LAAC)] are unclear. In addition, the in-hospital outcomes of stand-alone SA compared with CA are not well-described.

Methods and results
The National Inpatient Sample 2010–18 was queried for atrial fibrillation (AF) hospitalizations with CA or stand-alone SA. Complex samples multivariable logistic and linear regression models were used to compare the association between stand-alone SA vs. CA and the primary outcomes of in-hospital mortality and stroke. Of 180 243 hospitalizations included within the study, 167 242 were for CA and 13 000 were for stand-alone SA. Catheter ablation and stand-alone SA hospitalizations decreased throughout the study period (Ptrend &lt; 0.001). Surgical ablation had higher rates of in-hospital mortality [adjusted odds ratio (aOR) 2.26; 95% confidence interval (CI) 1.41–3.61; P = 0.001] and stroke (aOR 4.64; 95% CI 3.25–6.64; P &lt; 0.001) compared with CA. When examining different surgical approaches, thoracoscopic SA was associated with similar in-hospital mortality (aOR 1.53; 95% CI 0.60–3.89; P = 0.369) and similar risk of stroke (aOR 1.75; 95% CI 1.00–3.07; P = 0.051) compared with CA.

Conclusion
Stand-alone SA comprises a minority of AF ablation procedures and is associated with increased risk of mortality, stroke, and other in-hospital complications compared to CA. However, when a thoracoscopic approach was utilized, the risks of mortality and stroke appear to be reduced.
orthofisher: a broadly applicable tool for automated gene identification and retrieval
Authors: Steenwyk Jacob L , Rokas Antonis 
Published: July 2021

Abstract
Identification and retrieval of genes of interest from genomic data are an essential step for many bioinformatic applications. We present orthofisher, a command-line tool for automated identification and retrieval of genes with high sequence similarity to a query profile Hidden Markov Model sequence alignment across a set of proteomes. Performance assessment of orthofisher revealed high accuracy and precision during single-copy orthologous gene identification. orthofisher may be useful for assessing gene annotation quality, identifying single-copy orthologous genes for phylogenomic analyses, estimating gene copy number, and other evolutionary analyses that rely on identification and retrieval of homologous genes from genomic data. orthofisher comes complete with comprehensive documentation (https://jlsteenwyk.com/orthofisher/), is freely available under the MIT license, and is available for download from GitHub (https://github.com/JLSteenwyk/orthofisher), PyPi (https://pypi.org/project/orthofisher/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/orthofisher).
The Identification of cDNAs That Affect the Mitosis-to-Interphase Transition in Schizosaccharomyces pombe, Including sbp1, Which Encodes a spi1p-GTP–Binding Protein
Authors: He Xiangwei , Hayashi Naoyuki , Walcott Nathan G , Azuma Yoshiaki , Patterson Thomas E , Bischoff F Ralf , Nishimoto Takeharu , Sazer Shelley 
Published: July 2021

AbstractPerturbations of the spi1p GTPase system in fission yeast, caused by mutation or overexpression of several regulatory proteins, result in a unique terminal phenotype that includes condensed chromosomes, a wide medial septum, and a fragmented nuclear envelope. To identify potential regulators or targets of the spi1p GTPase system, a screen for cDNAs whose overexpression results in this terminal phenotype was conducted, and seven clones that represent three genes, named med1, med2, and med3 (mitotic exit defect), were identified. Their genetic interaction with the spi1p GTPase system was established by showing that the spi1p guanine nucleotide exchange factor mutant pim1-d1ts was hypersensitive to their overexpression. med1 encodes a homologue of the human Ran-binding protein, RanBP1, and has been renamed sbp1 (spi1-binding protein). sbp1p binds to spi1p-GTP and costimulates the GTPase-activating protein (GAP)-catalyzed GTPase activity. Cells in which sbp1p is depleted or overproduced phenocopy cells in which the balance between spi1p-GTP and spi1p-GDP is perturbed by other means. Therefore, sbp1p mediates and/or regulates the essential functions of the spi1p GTPase system. med2 and med3 encode novel fission yeast proteins that, based on our phenotypic analyses, are likely to identify additional regulators or effectors of the spi1p GTPase system.
hyp Loci Control Cell Pattern Formation in the Vegetative Mycelium of Aspergillus nidulans
Authors: Kaminskyj Susan G W , Hamer John E 
Published: July 2021

Abstract
Aspergillus nidulans grows by apical extension of multinucleate cells called hyphae that are subdivided by the insertion of crosswalls called septa. Apical cells vary in length and number of nuclei, whereas subapical cells are typically 40 μm long with three to four nuclei. Apical cells have active mitotic cycles, whereas subapical cells are arrested for growth and mitosis until branch formation reinitiates tip growth and nuclear divisions. This multicellular growth pattern requires coordination between localized growth, nuclear division, and septation. We searched a temperature-sensitive mutant collection for strains with conditional defects in growth patterning and identified six mutants (designated hyp for hypercellular). The identified hyp mutations are nonlethal, recessive defects in five unlinked genes (hypA-hypE). Phenotypic analyses showed that these hyp mutants have aberrant patterns of septation and show defects in polarity establishment and tip growth, but they have normal nuclear division cycles and can complete the asexual growth cycle at restrictive temperature. Temperature shift analysis revealed that hypD and hypE play general roles in hyphal morphogenesis, since inactivation of these genes resulted in a general widening of apical and subapical cells. Interestingly, loss of hypA or hypB function lead to a cessation of apical cell growth but activated isotropic growth and mitosis in subapical cells. The inferred functions of hypA and hypB suggest a mechanism for coordinating apical growth, subapical cell arrest, and mitosis in A. nidulans.
Cohort Analysis of the Association of Delirium Severity With Cerebrospinal Fluid Amyloid-Tau-Neurodegeneration Pathologies
Authors: Parker Margaret , White Marissa , Casey Cameron , Kunkel David , Bo Amber , Blennow Kaj , Zetterberg Henrik , Pearce Robert A , Lennertz Richard , Sanders Robert D 
Published: July 2021

Abstract
Delirium is associated with cognitive decline and subsequent dementia, and rises in plasma total tau (tTau) and neurofilament light (NfL), providing links to Amyloid-Tau-Neurodegeneration (ATN) pathophysiology. We investigated whether changes in delirium severity after surgery correlated with changes in cerebrospinal fluid (CSF) ATN biomarkers. Thirty-two thoracic vascular surgical patients were recruited into a prospective biomarker cohort study with assessment of delirium severity and incidence (NCT02926417). CSF (n = 54) and plasma (n = 118) samples were sent for biomarker analysis for tTau, phosphorylated tau-181 (pTau) (plasma n = 53), NfL, and amyloid-β 42/40 ratio (Ab42/40-ratio). The primary outcome was the correlation of preoperative to postoperative change in ATN biomarkers with the highest postoperative Delirium Rating Scale-98 score. CSF and plasma biomarkers all increased postoperatively (all p &lt; .05, n = 13 paired preoperative–postoperative samples). Delirium severity was associated with peak changes in CSF tTau (p = .007, r = .710) and pTau (p = .01, r = .667) but not NfL (p = .09, ρ = .491) or Ab42/40-ratio (p = .18, ρ = .394). Sensitivity analysis with exclusion of participants with putative spinal cord ischemia shifted the NfL result to significance (p &lt; .001, ρ = .847). Our data show that changes in tau and biomarkers of neurodegeneration in the CSF are associated with delirium severity. These data should be considered hypothesis-generating and future studies should identify if these changes are robust to confounding.
Racial-ethnic Disparities in Pain Intensity and Interference Among Middle-aged and Older U.S. Adults
Authors: Yang Yulin , Reid M Carrington , Grol-Prokopczyk Hanna , Pillemer Karl 
Published: July 2021

Abstract

Background
This study aims to better understand differing pain experiences across U.S. racial/ethnic subgroups by estimating racial-ethnic disparities in both pain intensity and domain-specific pain-related interference. To address this issue, we use a nationally representative sample of non-Hispanic White, non-Hispanic Black, and Hispanic adults ages 50+ who report recently experiencing pain.

Methods
Using data from the 2010 wave of the Health and Retirement Study (HRS; N = 684), we conducted a series of multivariate analyses to assess possible racial/ethnic disparities in pain intensity and 7 domains of pain interference, controlling for relevant sociodemographic variables and other health problems.

Results
Black and Hispanic participants reported higher pain intensity than White participants after controlling for socioeconomic status (SES) and other health conditions. Both Black and Hispanic individuals reported more domain-specific pain interference in bivariate analyses. In multivariate analyses, Black (vs White) participants reported significantly higher levels of pain interference with family–home responsibilities, occupation, sexual behavior, and daily self-care. We did not find significant Hispanic-White differences in the 7 pain interference domains, nor did we find Black-White differences in 3 domains (recreation, social activities, and essential activities).

Conclusions
Our findings highlight the need for using multidimensional measures of pain when assessing for possible pain disparities with respect to race/ethnicity. Future studies on pain interventions should consider contextualizing the pain experience across different racial subgroups to help pain patients with diverse needs, with the ultimate goal of reducing racial/ethnic disparities in pain.
“We Should Be at the Back of the Line”: A Frame Analysis of Old Age Within the Distribution Order of the COVID-19 Vaccine
Authors: Allen Laura D , Odziemczyk Idalina Z , Perek-Białas Jolanta , Ayalon Liat 
Published: July 2021

AbstractBackground and ObjectivesIn the fall of 2020, it became clear that the initial doses of the coronavirus disease 2019 (COVID-19) vaccine would be limited, and a priority order would be necessary. This article examines the perceptions of old age in the context of establishing a priority order for the COVID-19 vaccine from the perspective of online newspaper commenters. Two research questions are investigated: (a) How do commenters place older people in line for the COVID-19 vaccine? and (b) What frames and factors do commenters use as reasoning for their proposed position of older adults?Research Design and MethodsThis study involves a frame analysis of 440 online comments on an article published by The New York Times on December 1, 2020 about the U.S. recommendations for distributing the coronavirus vaccine.ResultsOlder adults were referenced as belonging to one of the 3 groups: older long-term care residents, older workers, and older adults retired and/or isolating at home. Two frames emerged from the data as criteria for prioritization: social contribution and vulnerability. Older commenters themselves frequently stated that they should be deprioritized so that others can be inoculated earlier.Discussion and ImplicationsThe findings may be interpreted as demonstrative of pervasive ageism throughout the pandemic; older commenters’ sacrificial remarks may reflect generativity, internalized ageism, social pressure from online forums, or some combination thereof.
DeepPhasePick: A method for detecting and picking seismic phases from local earthquakes based on highly optimized convolutional and recurrent deep neural networks
Authors: Soto Hugo , Schurr Bernd 
Published: July 2021

Summary
Seismic phase detection, identification and first-onset picking are basic but essential routines to analyse earthquake data. As both the number of seismic stations, globally and regionally, and the number of experiments greatly increase due to ever greater availability of instrumentation, automated data processing becomes more and more essential. E.g., for modern seismic experiments involving 100s to even 1,000s instruments, conventional human analyst-based identification and picking of seismic phases is becoming unfeasible, and the introduction of automatic algorithms mandatory. In this paper, we introduce DeepPhasePick, an automatic two-stage method that detects and picks P and S seismic phases from local earthquakes. The method is entirely based on highly optimized deep neural networks, consisting of a first stage that detects the phases using a convolutional neural network, and a second stage that uses two recurrent neural networks to pick both phases. Detection is performed on three-component seismograms. P- and S-picking is then conducted on the vertical and the two-horizontal components, respectively. Systematic hyperparameter optimization was applied to select the best model architectures and to define both the filter applied to preprocess the seismic data as well as the characteristics of the window sample used to feed the models. We trained DeepPhasePick using seismic records extracted from two sets of manually-picked event waveforms originating from northern Chile (∼39,000 records for detection and ∼36,000 records for picking). In different tectonic regimes, DeepPhasePick demonstrated the ability to both detect P and S phases from local earthquakes with high accuracy, as well as predict P- and S-phase time onsets with an analyst level of precision. DeepPhasePick additionally computes onset uncertainties based on the Monte Carlo Dropout technique as an approximation of Bayesian inference. This information can then further feed an associator algorithm in an earthquake location procedure.
Recording earthquakes for tomographic imaging of the mantle beneath the South Pacific by autonomous MERMAID floats
Authors: Simon Joel D , Simons Frederik J , Irving Jessica C E 
Published: July 2021

SUMMARYWe present the first 16 months of data returned from a mobile array of 16 freely floating diving instruments, named mermaid for Mobile Earthquake Recording in Marine Areas by Independent Divers, launched in French Polynesia in late 2018. Our 16 are a subset of the 50 mermaid deployed over a number of cruises in this vast and understudied oceanic province as part of the collaborative South Pacific Plume Imaging and Modeling (SPPIM) project, under the aegis of the international EarthScope-Oceans consortium. Our objective is the hydroacoustic recording, from within the oceanic water column, of the seismic wavefield generated by earthquakes worldwide, and the nearly real-time transmission by satellite of these data, collected above and in the periphery of the South Pacific Superswell. This region, characterized by anomalously elevated oceanic crust and myriad seamounts, is believed to be the surface expression of deeply rooted mantle upwellings. Tomographically imaging Earth’s mantle under the South Pacific with data from these novel instruments requires a careful examination of the earthquake-to-mermaid traveltimes of the high-frequency P-wave detections within the windows selected for reporting by the discrimination algorithms on board. We discuss a workflow suitable for a fast-growing mobile sensor database to pick the relevant arrivals, match them to known earthquakes in global earthquake catalogues, calculate their traveltime residuals with respect to global seismic reference models, characterize their quality and estimate their uncertainty. We detail seismicity rates as recorded by mermaid over 16 months, quantify the completeness of our catalogue and discuss magnitude–distance relations of detectability for our network. The projected lifespan of an individual mermaid is 5 yr, allowing us to estimate the final size of the data set that will be available for future study. To prove their utility for seismic tomography we compare mermaid data quality against ‘traditional’ land seismometers and their low-cost Raspberry Shake counterparts, using waveforms recovered from instrumented island stations in the geographic neighbourhood of our floats. Finally, we provide the first analyses of traveltime anomalies for the new ray paths sampling the mantle under the South Pacific.