bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential inhibitors for the novel coronavirus (SARS-CoV-2)
Authors: Han Yanqiang , Wang Zhilong , Ren Jiahao , Wei Zhiyun , Li Jinjin
Published: August 2020

The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition.
TRTools: a toolkit for genome-wide analysis of tandem repeats
Authors: Mousavi Nima , Margoliash Jonathan , Pusarla Neha , Saini Shubham , Yanicky Richard , Gymrek Melissa
Published: August 2020

A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.

Availability and implementation

TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.

Supplementary information

Supplementary data are available at Bioinformatics online.
Diversity in leading and laggard regions: living standards, residual income and regional policy
Authors: Calafati Luca , Froud Julie , Haslam Colin , Johal Sukhdev , Williams Karel
Published: August 2020

This article develops a Foundational Economy contribution to debate about regional inequalities by presenting new calculations of household income after the costs of three essential items (housing, transport and utilities). These residual income measures illustrate the diversity of living standards within and between English and Welsh regions. The analysis shows a mosaic of variation in residual income and wealth accumulation driven by the variability of housing costs in four different tenure groups (outright owners, mortgage payers, private renters and social renters). The article argues that GVA averages and descriptors like “left behind” are a poor guide to differences within and between regions; they also misdirect policy towards “levelling up” the apparently unsuccessful places without directly addressing the quality of and access to essential services. From a foundational point of view, regional policy needs to focus on access to housing at reasonable cost for all income and tenure groups in every region.
Barriers to Psychosocial Support and Quality of Life for Patients With Inflammatory Bowel Disease: A Survey Study
Authors: Lawrence Rebecca , Choudhary Cuckoo
Published: August 2020

Background

Psychological comorbidities are common among people with inflammatory bowel disease (IBD) and are associated with worse disease outcomes. Evidence-based psychotherapy is an effective means to increase psychosocial support. This study aimed to identify the barriers to attending psychotherapy.

Methods

This electronic survey study included a demographic, quality of life, and barriers to psychotherapy questionnaire. Quality of life was assessed using the Short Inflammatory Bowel Disease Questionnaire (SIBDQ). Barriers were assessed using the Perceived Barriers to Psychological Treatments scale (PBPT). Linear regression was used to identify participant characteristics associated with higher PBPT scores.

Results

One hundred eighty-seven participants completed the study. Fifty-eight percent of participants had ≥1 significant barrier. Time (28%), knowledge about the availability of services (25%), and cost (19%) were the most common barriers. Least common were stigma (14%), lack of motivation (12%), and emotional concerns (7%). Lower SIBDQ scores, being male, not being full-time employed, having Crohn disease, and being in disease remission were associated with higher PBPT scores.

Conclusions

Knowledge about the availability of services, time constraints, and cost are the leading barriers to psychotherapy among people with IBD. Care providers should develop a network of psychotherapists available to those with IBD. Being male and not being full-time employed may be risk factors for greater barriers. Further research is needed on barriers among groups underrepresented in this study and on novel psychotherapy solutions, like telehealth and low-cost options.
Utilization of diagnostic resources and costs in patients with suspected cardiac chest pain
Authors: Vester Marijke P M , Eindhoven Daniëlle C , Bonten Tobias N , Wagenaar Holger , Holthuis Hendrik J , Schalij Martin J , de Grooth Greetje J , van Dijkman Paul R M
Published: August 2020

Aims

Non-acute chest pain is a common complaint and can be caused by various conditions. With the rising healthcare expenditures of today, it is necessary to use our healthcare resources effectively. This study aims to give insight into the diagnostic effort and costs for patients with non-acute chest pain.

Methods and results

Financial data of patients without a cardiac history from four hospitals (January 2012–October 2018), who were registered with the national diagnostic code ‘no cardiac pathology’ (ICD-10 Z13.6), ‘chest wall syndrome’ (ICD-10 R07.4), or ‘stable angina pectoris’ (ICD-10 I20.9) were extracted. In total, 74 091 patients were included for analysis and divided into the following final diagnosis groups: no cardiac pathology: N = 19 688 (age 53 ± 18), 46% male; chest wall syndrome: N = 40 858 (age 56 ± 15), 45% male; and stable angina pectoris (AP): N = 13 545 (age 67 ± 11), 61% male. A total of approximately €142.7 million was spent during diagnostic work-up. The total expenditure during diagnostic effort was €1.97, €8.13, and €10.7 million, respectively for no cardiac pathology, chest wall syndrome, and stable AP per year. After 8 years of follow-up, ≥95% of the patients diagnosed with no cardiac pathology or chest wall syndrome had an (cardiac) ischaemic-free survival.

Conclusion

The diagnostic expenditure and clinical effort to ascertain non-cardiac chest pain are high. We should define what we as society find acceptable as ‘assurance costs’ with an increasing pressure on the healthcare system and costs.
Textbook analysis: the case of the first Nicaraguan ELT series
Authors: Tórrez Nahúm Misael , Lund Ragnhild Elisabeth
Published: August 2020

Nicaragua published its first series of textbooks for the teaching of English in public secondary schools in 2016. This article reports on an investigation of the first three textbooks belonging to this series. The aim was to see how the textbooks follow up the Nicaraguan national curriculum, which emphasizes the need for learners to develop communication skills. We discuss the approaches with reference to principles of communicative language teaching and Nation’s four strands for a well-balanced language course. We identify significant discrepancies between the three books and, thus, a lack of progression in the course. The investigation is also an example of the affordances of our analytical tool for textbook analysis.
Impact of cardiovascular risk factors and genetics on 10-year absolute risk of dementia: risk charts for targeted prevention
Authors: Juul Rasmussen Ida , Rasmussen Katrine Laura , Nordestgaard Børge G , Tybjærg-Hansen Anne , Frikke-Schmidt Ruth
Published: August 2020

Aims

Dementia is a major global challenge for health and social care in aging populations. A third of all dementia may be preventable due to cardiovascular risk factors. Intensive multi-domain intervention trials targeting primarily cardiovascular risk factors show improved cognitive function in people at risk. Such interventions will, however, be expensive to implement in all individuals at risk and will represent unrealistic economic tasks for most societies. Therefore, a risk score identifying high-risk individuals is warranted.

Methods and results

In 61 664 individuals from two prospective cohorts of the Danish general population, we generated 10-year absolute risk scores for all-cause dementia from cardiovascular risk factors and genetics. In both sexes, 10-year absolute risk of all-cause dementia increased with increasing age, number of apolipoprotein E (APOE) ɛ4 alleles, number of genome-wide association studies (GWAS) risk alleles, and cardiovascular risk factors. The highest 10-year absolute risks of all-cause dementia seen in smoking women with diabetes, low education, APOE ɛ44 genotype, and 22–31 GWAS risk alleles were 6%, 23%, 48%, and 66% in those aged 50–59, 60–69, 70–79, and 80–100, respectively. Corresponding values for men were 5%, 19%, 42%, and 60%, respectively.

Conclusion

Ten-year absolute risk of all-cause dementia increased with age, APOE ɛ4 alleles, GWAS risk alleles, diabetes, low education, and smoking in both women and men. Ten-year absolute risk charts for dementia will facilitate identification of high-risk individuals, those who likely will benefit the most from an early intervention against cardiovascular risk factors.
Infanticide vs. inherited cardiac arrhythmias
Authors: Brohus Malene , Arsov Todor , Wallace David A , Jensen Helene Halkjær , Nyegaard Mette , Crotti Lia , Adamski Marcin , Zhang Yafei , Field Matt A , Athanasopoulos Vicki , Baró Isabelle , Ribeiro de Oliveira-Mendes Bárbara B , Redon Richard , Charpentier Flavien , Raju Hariharan , DiSilvestre Deborah , Wei Jinhong , Wang Ruiwu , Rafehi Haloom , Kaspi Antony , Bahlo Melanie , Dick Ivy E , Chen Sui Rong Wayne , Cook Matthew C , Vinuesa Carola G , Overgaard Michael Toft , Schwartz Peter J
Published: August 2020

Aims

In 2003, an Australian woman was convicted by a jury of smothering and killing her four children over a 10-year period. Each child died suddenly and unexpectedly during a sleep period, at ages ranging from 19 days to 18 months. In 2019 we were asked to investigate if a genetic cause could explain the children’s deaths as part of an inquiry into the mother’s convictions.

Methods and results

Whole genomes or exomes of the mother and her four children were sequenced. Functional analysis of a novel CALM2 variant was performed by measuring Ca2+-binding affinity, interaction with calcium channels and channel function. We found two children had a novel calmodulin variant (CALM2 G114R) that was inherited maternally. Three genes (CALM1-3) encode identical calmodulin proteins. A variant in the corresponding residue of CALM3 (G114W) was recently reported in a child who died suddenly at age 4 and a sibling who suffered a cardiac arrest at age 5. We show that CALM2 G114R impairs calmodulin's ability to bind calcium and regulate two pivotal calcium channels (CaV1.2 and RyR2) involved in cardiac excitation contraction coupling. The deleterious effects of G114R are similar to those produced by G114W and N98S, which are considered arrhythmogenic and cause sudden cardiac death in children.

Conclusion

A novel functional calmodulin variant (G114R) predicted to cause idiopathic ventricular fibrillation, catecholaminergic polymorphic ventricular tachycardia, or mild long QT syndrome was present in two children. A fatal arrhythmic event may have been triggered by their intercurrent infections. Thus, calmodulinopathy emerges as a reasonable explanation for a natural cause of their deaths.
Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps
Authors: Franzetti A , Pittino F , Gandolfi I , Azzoni R S , Diolaiuti G , Smiraglia C , Pelfini M , Compostella C , Turchetti B , Buzzini P , Ambrosini R
Published: August 2020

In this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.
The hydrogen threshold of obligately methyl-reducing methanogens
Authors: Feldewert Christopher , Lang Kristina , Brune Andreas
Published: August 2020

Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.
The earthquake arrest zone
Authors: Ke Chun-Yu , McLaskey Gregory C , Kammer David S
Published: August 2020

Earthquake ruptures are generally considered to be cracks that propagate as fracture or frictional slip on pre-existing faults. Crack models have been used to describe the spatial distribution of fault offset and the associated static stress changes along a fault, and have implications for friction evolution and the underlying physics of rupture processes. However, field measurements that could help refine idealized crack models are rare. Here, we describe large-scale laboratory earthquake experiments, where all rupture processes were contained within a 3-m long saw-cut granite fault, and we propose an analytical crack model that fits our measurements. Similar to natural earthquakes, laboratory measurements show coseismic slip that gradually tapers near the rupture tips. Measured stress changes show roughly constant stress drop in the centre of the ruptured region, a maximum stress increase near the rupture tips and a smooth transition in between, in a region we describe as the earthquake arrest zone. The proposed model generalizes the widely used elliptical crack model by adding gradually tapered slip at the ends of the rupture. Different from the cohesive zone described by fracture mechanics, we propose that the transition in stress changes and the corresponding linear taper observed in the earthquake arrest zone are the result of rupture termination conditions primarily controlled by the initial stress distribution. It is the heterogeneous initial stress distribution that controls the arrest of laboratory earthquakes, and the features of static stress changes. We also performed dynamic rupture simulations that confirm how arrest conditions can affect slip taper and static stress changes. If applicable to larger natural earthquakes, this distinction between an earthquake arrest zone (that depends on stress conditions) and a cohesive zone (that depends primarily on strength evolution) has important implications for how seismic observations of earthquake fracture energy should be interpreted.
Gene expression profiles complement the analysis of genomic modifiers of the clinical onset of Huntington disease
Authors: Wright Galen E B , Caron Nicholas S , Ng Bernard , Casal Lorenzo , Casazza William , Xu Xiaohong , Ooi Jolene , Pouladi Mahmoud A , Mostafavi Sara , Ross Colin J D , Hayden Michael R
Published: August 2020

Huntington disease (HD) is a neurodegenerative disorder that is caused by a CAG repeat expansion in HTT. The length of this repeat, however, only explains a proportion of the variability in age of onset in patients. Genome-wide association studies have identified modifiers that contribute toward a proportion of the observed variance. By incorporating tissue-specific transcriptomic information with these results, additional modifiers can be identified. We performed a transcriptome-wide association study assessing heritable differences in genetically determined expression in diverse tissues, with genome-wide data from over 4000 patients. Functional validation of prioritized genes was undertaken in isogenic HD stem cells and patient brains. Enrichment analyses were performed with biologically relevant gene sets to identify the core pathways. HD-associated gene coexpression modules were assessed for associations with neurological phenotypes in an independent cohort and to guide drug repurposing analyses. Transcriptomic analyses identified genes that were associated with age of HD onset and displayed colocalization with gene expression signals in brain tissue (FAN1, GPR161, PMS2, SUMF2), with supporting evidence from functional experiments. This included genes involved in DNA repair, as well as novel-candidate modifier genes that have been associated with other neurological conditions. Further, cortical coexpression modules were also associated with cognitive decline and HD-related traits in a longitudinal cohort. In summary, the combination of population-scale gene expression information with HD patient genomic data identified novel modifier genes for the disorder. Further, these analyses expanded the pathways potentially involved in modifying HD onset and prioritized candidate therapeutics for future study.
SAY NO to mild ovarian stimulation for all poor responders: it is time to realize that not all poor responders are the same
Authors: Polyzos N P , Popovic-Todorovic B
Published: August 2020

Over the last 25 years, a vast body of literature has been published evaluating different treatment modalities for the management of poor ovarian responders. Despite the evidence that maximizing ovarian response can improve the chances of live born babies in poor responders, there are still voices suggesting that all poor responders are the same, irrespective of their age and their actual ovarian reserve. This has resulted in the suggestion of adopting a mild ovarian stimulation approach for all poor responders, based on the results of several trials which failed to identity differences when comparing mild and more intense stimulation in predicted poor responders. The current article analyzes in detail these studies and discusses the shortcomings in terms of type of population included, outcomes and settings performed, which may actually be responsible for the belief that only mild stimulation should be used. In the era of individualization in medicine, it must be realized that there are subgroups of predicted poor responders who will benefit from an individual rather than ‘one fits all’ mild stimulation approach and thus we should provide the same standard of treatment for all our poor responder patients.
Spacetime Positive Mass Theorems for Initial Data Sets with Non-Compact Boundary
Authors: Almaraz Sérgio , de Lima Levi Lopes , Mari Luciano
Published: August 2020

In this paper, we define an energy-momentum vector at the spatial infinity of either asymptotically flat or asymptotically hyperbolic initial data sets carrying a non-compact boundary. Under suitable dominant energy conditions (DECs) imposed both on the interior and along the boundary, we prove the corresponding positive mass inequalities under the assumption that the underlying manifold is spin. In the asymptotically flat case, we also prove a rigidity statement when the energy-momentum vector is light-like. Our treatment aims to underline both the common features and the differences between the asymptotically Euclidean and hyperbolic settings, especially regarding the boundary DECs.
Stage III disease of ovarian, tubal and peritoneal cancers can be accurately diagnosed with pre-operative CT. Japan Clinical Oncology Group Study JCOG0602
Authors: Onda Takashi , Tanaka Yumiko Oishi , Kitai Satomi , Manabe Tomoko , Ishikawa Mitsuya , Hasumi Yoko , Miyamoto Kenichi , Ogawa Gakuto , Satoh Toyomi , Saito Toshiaki , Kasamatsu Takahiro , Nakanishi Toru ,   Japan Clinical Oncology Group
Published: August 2020

Purpose

Computed tomography of the abdomen and pelvis is a useful imaging modality for identifying origin and extent of ovarian cancer before primary debulking surgery. However, the International Federation of Gynecology and Obstetrics staging for ovarian cancer is determined based on surgico-pathological findings. The purpose of this study is to determine whether computed tomography staging can be the surrogate for surgico-pathological International Federation of Gynecology and Obstetrics staging in advanced ovarian cancer undergoing neoadjuvant chemotherapy.

Methods

Computed tomography staging was compared with surgico-pathological International Federation of Gynecology and Obstetrics staging in primary debulking surgery arm patients in a randomized controlled trial comparing primary debulking surgery and neoadjuvant chemotherapy (JCOG0602). The cancer of primary debulking surgery arm was identically diagnosed regarding the origin and extent with the cancer of neoadjuvant chemotherapy arm before accrual, using imaging studies (computed tomography and/or magnetic resonance imaging), cytological examination (ascites, pleural effusion or tumor contents fluid) and tumor marker (CA125 > 200 U/mL and CEA < 20 ng/mL). Institutional computed tomography staging was also compared with computed tomography staging by central review.

Results

Among 149 primary debulking surgery arm patients, 147 patients who underwent primary debulking surgery immediately were analyzed. Positive predictive values and sensitivity of computed tomography staging for surgical stage III disease (extra-pelvic peritoneal disease and/or retroperitoneal lymph node metastasis) were 99%. Meanwhile, positive predictive values for the presence of small (≤2 cm) extra-pelvic peritoneal disease were low; <20% in omentum. Accuracy of institutional computed tomography staging was comparable with computed tomography staging by central review.

Conclusions

Preoperative computed tomography staging in each institution can be the surrogate for surgico-pathological diagnosis in stage III disease of ovarian cancer patients undergoing neoadjuvant chemotherapy without diagnostic surgery, but reliability of diagnosis of stage IIIB disease is inadequate.

Clinical trial registration: UMIN000000523(UMIN-CTR).
Cancer Care Evaluation Scale (CCES): measuring the quality of the structure and process of cancer care from the perspective of patients with cancer
Authors: Masukawa Kento , Sato Kazuki , Shimizu Megumi , Morita Tatsuya , Miyashita Mitsunori
Published: August 2020

Objective

To evaluate the quality of the structure and process of cancer care from the perspective of patients with cancer, we developed a Cancer Care Evaluation Scale.

Methods

Two anonymous online surveys of patients with cancer in Japan were conducted using a convenience sample of 400 adult cancer outpatients.

Results

In total, 162 patients participated in the online surveys. Factor analysis revealed that the Cancer Care Evaluation Scale had the following 12 domains: (i) relationship with physician, (ii) relationship with nurse, (iii) physical care by physician, (iv) physical care by nurse, (v) psycho-existential care, (vi) help with decision-making for patients, (vii) coordination and consistency, (viii) environment, (ix) cost, (x) availability, (xi) care for the side effects of cancer treatment by a physician, and (xii) care for the side effects of cancer treatment by a nurse. The Cancer Care Evaluation Scale was correlated with overall care satisfaction (r = 0.75), but not with the quality of life (r = 0.40). In regard to rest–retest reliability, most items showed an intraclass correlation coefficient of 0.7 or higher.

Conclusion

The validity and reliability of the Cancer Care Evaluation Scale were confirmed, suggesting that this tool is useful for evaluating the quality of cancer care from the perspective of patients with cancer.
COVID-19 emergency measures and the impending authoritarian pandemic
Authors: Thomson Stephen , Ip Eric C
Published: August 2020

COVID-19 has brought the world grinding to a halt. As of early August 2020, the greatest public health emergency of the century thus far has registered almost 20 million infected people and claimed over 730,000 lives across all inhabited continents, bringing public health systems to their knees, and causing shutdowns of borders and lockdowns of cities, regions, and even nations unprecedented in the modern era. Yet, as this Article demonstrates—with diverse examples drawn from across the world—there are unmistakable regressions into authoritarianism in governmental efforts to contain the virus. Despite the unprecedented nature of this challenge, there is no sound justification for systemic erosion of rights-protective democratic ideals and institutions beyond that which is strictly demanded by the exigencies of the pandemic. A Wuhan-inspired all-or-nothing approach to viral containment sets a dangerous precedent for future pandemics and disasters, with the global copycat response indicating an impending ‘pandemic’ of a different sort, that of authoritarianization. With a gratuitous toll being inflicted on democracy, civil liberties, fundamental freedoms, healthcare ethics, and human dignity, this has the potential to unleash humanitarian crises no less devastating than COVID-19 in the long run.
Oncologists’ Reluctance to Use the Terms Hope and Cure: A Bibliometric Analysis of Articles From Two High-Impact Oncology Journals
Authors: Corn Benjamin W , Feldman David , Schapira Lidia , Steensma David P , Loprinzi Charles L , Bian Jiang
Published: August 2020

The words cure and hope are important terms in oncology, reflecting a balance of aspirations and realism for physicians and patients. Yet, some have suggested that oncologists are reluctant to use these terms. We tested this hypothesis by performing a bibliometric analysis of the frequency of use of these words in JAMA Oncology (JAMA Oncol) and the Journal of Clinical Oncology (JCO). The text of all articles in 3 categories—primary research, editorials, and narrative essays—appearing in JCO from 2000 to 2018 and in JAMA Oncol from 2015 to 2019 was analyzed. These analyses compared, across these categories, the proportion of articles containing the words cure and hope, as well as the proportion of total sentences containing these words. There were statistically significant differences in frequency of the use of the terms cure and hope as a function of the type of article published in the JCO and JAMA Oncol (2-sided P values ranging from .005 to <.001). Results were similar for both journals, with minor exceptions. Both hope and cure were used in a greater number of articles and sentences in the narrative and editorial categories than in primary research. Moreover, hope was used more often in narrative essays than in editorials. The relative reluctance to use these terms in more scientifically oriented original reports, despite concomitant improvements in oncologic outcomes, may reflect a bias worthy of future exploration.
Central venous catheter placement leading to an emergent paramedian sternotomy: a case report
Authors: Cooley-Rieders Keaton , Donayre Carlos E , Nelson Ariana M
Published: August 2020

Perioperative cardiac tamponade during central venous catheter placement is rare. We present a case of tamponade from pulmonary artery injury during dialysis catheter placement resulting in complicated sternotomy and hospital course. A 52-year-old female experienced intraoperative hypotension, rapidly identified as tamponade, that was treated with an emergent paramedian sternotomy. Patient experienced postdischarge dehiscence and osteomyelitis requiring multiple reoperations. This case is the first report of a deviated paramedian sternotomy performed mainly through ribs. The complications experienced outline the importance of effective multidisciplinary knowledge of best practices to stabilize tamponade pathology, mitigating morbidity and mortality.
Core-collapse supernovae in binaries as the origin of galactic hyper-runaway stars
Authors: Evans F A , Renzo M , Rossi E M
Published: August 2020

Several stars detected moving at velocities near to or exceeding the Galactic escape speed likely originated in the Milky Way disc. We quantitatively explore the ‘binary supernova scenario’ hypothesis, wherein these ‘hyper-runaway’ stars are ejected at large peculiar velocities when their close, massive binary companions undergo a core-collapse supernova and the binary is disrupted. We perform an extensive suite of binary population synthesis simulations evolving massive systems to determine the assumptions and parameters that most impact the ejection rate of fast stars. In a simulation tailored to eject fast stars, we find the most likely hyper-runaway star progenitor binary is composed of a massive (${\sim}30\, \mathrm{ M}_{\odot }$) primary and an ${\sim}3\!-\!4\, \mathrm{ M}_{\odot }$ companion on an orbital period that shrinks to ≲1 d prior to the core collapse following a common-envelope phase. The black hole remnant formed from the primary must receive a natal kick ≳1000 km s−1 to disrupt the binary and eject the companion at a large velocity. We compare the fast stars produced in these simulations to a contemporary census of early-type Milky Way hyper-runaway star candidates. We find that these rare objects may be produced in sufficient number only when poorly constrained binary evolution parameters related to the strength of post-core-collapse remnant natal kicks and common-envelope efficiency are adjusted to values currently unsupported – but not excluded – by the literature. We discuss observational implications that may constrain the existence of these putative progenitor systems.
Central velocity dispersion catalogue of LAMOST-DR7 galaxies
Authors: Napolitano Nicola R , D’Ago Giuseppe , Tortora Crescenzo , Zhao Gang , Luo A-Li , Tang Baitian , Zhang Wei , Zhang Yong , Li Rui
Published: August 2020

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) is a major facility to carry out spectroscopic surveys for cosmology and galaxy evolution studies. The seventh data release of the LAMOST ExtraGAlactic Survey (LEGAS) is currently available and including redshifts of 193 361 galaxies. These sources are spread over $\sim 11\, 500$ deg2 of the sky, largely overlapping with other imaging (SDSS and HSC) and spectroscopic (BOSS) surveys. The estimated depth of the galaxy sample, r ∼ 17.8, the high signal-to-noise ratio, and the spectral resolution R = 1800, make the LAMOST spectra suitable for galaxy velocity dispersion (VD) measurements, which are invaluable to study the structure and formation of galaxies and to determine their central dark matter content. We present the first estimates of central VD of $\sim 86\, 000$ galaxies in LAMOST footprint. We have used a wrap-up procedure to perform the spectral fitting using ppxf, and derive VD measurements. Statistical errors are also assessed by comparing LAMOST VD estimates with the ones of SDSS and BOSS over a common sample of $\sim 51\, 000$ galaxies. The two data sets show a good agreement, within the statistical errors, in particular when VD values are corrected to 1 effective radius aperture. We also present a preliminary mass–σ relation and find consistency with previous analyses based on local galaxy samples. These first results suggest that LAMOST spectra are suitable for galaxy VD measurements to complement the available catalogues of galaxy internal kinematics in the Northern hemisphere. We plan to expand this analysis to next LAMOST data releases.
The SAMI galaxy survey: a range in S0 properties indicating multiple formation pathways
Authors: Deeley Simon , Drinkwater Michael J , Sweet Sarah M , Diaz Jonathan , Bekki Kenji , Couch Warrick J , Forbes Duncan A , Bland-Hawthorn Joss , Bryant Julia J , Croom Scott , Cortese Luca , Lawrence Jon S , Lorente Nuria , Medling Anne M , Owers Matt , Richards Samuel N , van de Sande Jesse
Published: August 2020

It has been proposed that S0 galaxies are either fading spirals or the result of galaxy mergers. The relative contribution of each pathway and the environments in which they occur remain unknown. Here, we investigate stellar and gas kinematics of 219 S0s in the SAMI Survey to look for signs of multiple formation pathways occurring across the full range of environments. We identify a large range of rotational support in their stellar kinematics, which correspond to ranges in their physical structure. We find that pressure-supported S0s with v/σ below 0.5 tend to be more compact and feature misaligned stellar and gas components, suggesting an external origin for their gas. We postulate that these S0s are consistent with being formed through a merger process. Meanwhile, comparisons of ellipticity, stellar mass, and Sérsic index distributions with spiral galaxies show that the rotationally supported S0s with v/σ above 0.5 are more consistent with a faded spiral origin. In addition, a simulated merger pathway involving a compact elliptical and gas-rich satellite results in an S0 that lies within the pressure-supported group. We conclude that two S0 formation pathways are active, with mergers dominating in isolated galaxies and small groups, and the faded spiral pathway being most prominent in large groups ($10^{13}\lt \rm {M_{halo}}\lt 10^{14}$).
Resolving small-scale cold circumgalactic gas in TNG50
Authors: Nelson Dylan , Sharma Prateek , Pillepich Annalisa , Springel Volker , Pakmor Rüdiger , Weinberger Rainer , Vogelsberger Mark , Marinacci Federico , Hernquist Lars
Published: August 2020

We use the high-resolution TNG50 cosmological magnetohydrodynamical simulation to explore the properties and origin of cold circumgalactic medium (CGM) gas around massive galaxies (M⋆ > 1011 M⊙ ) at intermediate redshift ($z \sim 0.5$). We discover a significant abundance of small-scale, cold gas structure in the CGM of ‘red and dead’ elliptical systems, as traced by neutral H i and Mg ii. Halos can host tens of thousands of discrete absorbing cloudlets, with sizes of order a kpc or smaller. With a Lagrangian tracer analysis, we show that cold clouds form due to strong $\delta \rho / \bar{\rho } \gg 1$ gas density perturbations that stimulate thermal instability. These local overdensities trigger rapid cooling from the hot virialized background medium at ∼107 K to radiatively inefficient ∼104 K clouds, which act as cosmologically long-lived, ‘stimulated cooling’ seeds in a regime where the global halo does not satisfy the classic tcool/tff < 10 criterion. Furthermore, these small clouds are dominated by magnetic rather than thermal pressure, with plasma β ≪ 1, suggesting that magnetic fields may play an important role. The number and total mass of cold clouds both increase with resolution, and the mgas ≃ 8 × 104 M⊙ cell mass of TNG50 enables the ∼ few hundred pc, small-scale CGM structure we observe to form. Finally, we make a preliminary comparison against observations from the COS-LRG, LRG-RDR, COS-Halos, and SDSS LRG surveys. We broadly find that our recent, high-resolution cosmological simulations produce sufficiently high covering fractions of extended, cold gas as observed to surround massive galaxies.
A systematic ageing method I: H ii regions D118 and D119 in NGC 300
Authors: Stevance H F , Eldridge J J , McLeod A , Stanway E R , Chrimes A A
Published: August 2020

Accurately determining the age of H ii regions and the stars they host is as important as it is challenging. Historically, the most popular method has been isochrone fitting to Hertzsprung–Russell diagrams or colour–magnitude diagrams. Here, we introduce a different method for age determination using BPASS (Binary Population and Spectral Synthesis) and hoki . We infer the most likely ages of the regions D118 and D119 NGC 300 to be log(age/yr) = $6.86^{+0.05}_{-0.06}$ and we also deduce stellar mass and number counts by comparison with the BPASS models. We compare how our binary and single-star models perform and find that the latter are unable to predict 20 per cent (±10 per cent) of our sample. We also discuss how results obtained from isochrone fitting would differ. We conclude that ages could be underestimated by ∼0.2 dex and that the limitations of the isochrone method is not solely due to the lack of binary stars. We propose that the method presented here is more reliable and more widely applicable since it can be used on smaller samples. Alongside this study, we release new hoki features to allow easy implementation of this method.
Non-radially pulsating stars as microlensing sources
Authors: Sajadian Sedighe , Ignace Richard
Published: August 2020

We study the microlensing of non-radially pulsating (NRP) stars. Pulsations are formulated for stellar radius and temperature using spherical harmonic functions with different values of l, m. The characteristics of the microlensing light curves from NRP stars are investigated in relation to different pulsation modes. For the microlensing of NRP stars, the light curve is not a simple multiplication of the magnification curve and the intrinsic luminosity curve of the source star, unless the effect of finite source size can be ignored. Three main conclusions can be drawn from the simulated light curves. First, for modes with m ≠ 0 and when the viewing inclination is more nearly pole-on, the stellar luminosity towards the observer changes little with pulsation phase. In this case, high-magnification microlensing events are chromatic and can reveal the variability of these source stars. Secondly, some combinations of pulsation modes produce nearly degenerate luminosity curves (e.g. (l, m) = (3, 0), (5, 0)). The resulting microlensing light curves are also degenerate, unless the lens crosses the projected source. Finally, for modes involving m = 1, the stellar brightness centre does not coincide with the coordinate centre, and the projected source brightness centre moves in the sky with pulsation phase. As a result of this time-dependent displacement in the brightness centroid, the time of the magnification peak coincides with the closest approach of the lens to the brightness centre as opposed to the source coordinate centre. Binary microlensing of NRP stars and in caustic-crossing features are chromatic.
The impact of starbursts on element abundance ratios
Authors: Johnson James W , Weinberg David H
Published: August 2020

We investigate the impact of bursts in star formation on the predictions of one-zone chemical evolution models, adopting oxygen (O), iron (Fe), and strontium (Sr), as representative α, iron-peak, and s-process elements, respectively. To this end, we develop and make use of the Versatile Integrator for Chemical Evolution (VICE), a python package designed to handle flexible user-specified evolutionary parameters. Starbursts driven by a temporary boost of gas accretion rate create loops in [O/Fe]–[Fe/H] evolutionary tracks and a peak in the stellar [O/Fe] distribution at intermediate values. Bursts driven by a temporary boost of star formation efficiency have similar effects, and they also produce a population of α-deficient stars during the depressed star formation phase following the burst. This α-deficient population is more prominent if the outflow rate is tied to a time-averaged star formation rate (SFR) instead of the instantaneous SFR. Theoretical models of Sr production predict a strong metallicity dependence of supernova and asymptotic giant branch star yields, though comparison to data suggests an additional, nearly metallicity-independent source. Evolution of [Sr/Fe] and [Sr/O] during a starburst is complex because of this metallicity dependence and the multiple time-scales at play. Moderate amplitude (10–20 per cent) sinusoidal oscillations in SFR produce loops in [O/Fe]–[Fe/H] tracks and multiple peaks in [O/Fe] distributions, a potential source of intrinsic scatter in observed sequences. We investigate the impact of a factor ∼2 enhancement of Galactic star formation ∼2 Gyr ago, as suggested by some recent observations. VICE is publicly available at .
Solving Kepler’s equation with CORDIC double iterations
Authors: Zechmeister M
Published: August 2020

In previous work, we developed the idea to solve Kepler’s equation with a CORDIC-like algorithm, which does not require any division, but still requires multiplications in each iteration. Here we overcome this major shortcoming and solve Kepler’s equation using only bitshifts, additions and one initial multiplication. We prescale the initial vector with the eccentricity and the scale correction factor. The rotation direction is decided without correction for the changing scale. We find that double CORDIC iterations are self-correcting and compensate for possible wrong rotations in subsequent iterations. The algorithm needs 75 per cent more iterations and delivers the eccentric anomaly and its sine and cosine terms times the eccentricity. The algorithm can also be adopted for the hyperbolic case. The new shift-and-add algorithm brings Kepler’s equation close to hardware and allows it to be solved with cheap and simple hardware components.
Insight-HXMT observations of Swift J0243.6+6124: the evolution of RMS pulse fractions at super-Eddington luminosity
Authors: Wang P J , Kong L D , Zhang S , Chen Y P , Zhang S N , Qu J L , Ji L , Tao L , Ge M Y , Lu F J , Chen L , Song L M , Li T P , Xu Y P , Cao X L , Chen Y , Liu C Z , Bu Q C , Cai C , Chang Z , Chen G , Chen T X , Chen Y B , Cui W , Cui W W , Deng J K , Dong Y W , Du Y Y , Fu M X , Gao G H , Gao H , Gao M , Gu Y D , Guan J , Guo C C , Han D W , Huang Y , Huo J , Jia S M , Jiang L H , Jiang W C , Jin J , Jin Y J , Li B , Li C K , Li G , Li M S , Li W , Li X , Li X B , Li X F , Li Y G , Li Z W , Liang X H , Liao J Y , Liu B S , Liu G Q , Liu H W , Liu X J , Liu Y N , Lu B , Lu X F , Luo Q , Luo T , Ma X , Meng B , Nang Y , Nie J Y , Ou G , Sai N , Shang R C , Song X Y , Sun L , Tan Y , Tuo Y L , Wang C , Wang G F , Wang J , Wang L J , Wang W S , Wang Y S , Wen X Y , Wu B Y , Wu B B , Wu M , Xiao G C , Xiao S , Xiong S L , Yang J W , Yang S , Yang Yan Ji , Yang Yi Jung , Yi Q B , Yin Q Q , You Y , Zhang A M , Zhang C M , Zhang F , Zhang H M , Zhang J , Zhang T , Zhang W C , Zhang W , Zhang W Z , Zhang Y , Zhang Y F , Zhang Y J , Zhang Y , Zhang Zhao , Zhang Zhi , Zhang Z L , Zhao H S , Zhao X F , Zheng S J , Zheng Y G , Zhou D K , Zhou J F , Zhu Y X , Zhu Y , Zhuang R L
Published: August 2020

Based on Insight-HXMT data, we report on the pulse fraction evolution during the 2017–2018 outburst of the newly discovered first Galactic ultraluminous X-ray (ULX) source Swift J0243.6+6124. The pulse fractions of 19 observation pairs selected in the rising and fading phases with similar luminosity are investigated. The results show a general trend of the pulse fraction increasing with luminosity and energy at supercritical luminosity. However, the relative strength of the pulsation between each pair evolves strongly with luminosity. The pulse fraction in the rising phase is larger at luminosity below 7.71 × 1038 erg s−1, but smaller at above. A transition luminosity is found to be energy independent. Such a phenomenon is first confirmed by Insight-HXMT observations and we speculate that it may have relation with the radiation-pressure-dominated accretion disc.
Machine learning applied to multifrequency data in astrophysics: blazar classification
Authors: Arsioli B , Dedin P
Published: August 2020

The study of machine learning (ML) techniques for the autonomous classification of astrophysical sources is of great interest, and we explore its applications in the context of a multifrequency data-frame. We test the use of supervised ML to classify blazars according to its synchrotron peak frequency, either lower or higher than 1015 Hz. We select a sample with 4178 blazars labelled as 1279 high synchrotron peak (HSP: $\rm \nu$-peak > 1015 Hz) and 2899 low synchrotron peak (LSP: $\rm \nu$-peak < 1015 Hz). A set of multifrequency features were defined to represent each source that includes spectral slopes ($\alpha _{\nu _1, \nu _2}$) between the radio, infra-red, optical, and X-ray bands, also considering IR colours. We describe the optimization of five ML classification algorithms that classify blazars into LSP or HSP: Random forests (RFs), support vector machine (SVM), K-nearest neighbours (KNN), Gaussian Naive Bayes (GNB), and the Ludwig auto-ML framework. In our particular case, the SVM algorithm had the best performance, reaching 93 per cent of balanced accuracy. A joint-feature permutation test revealed that the spectral slopes alpha-radio-infrared (IR) and alpha-radio-optical are the most relevant for the ML modelling, followed by the IR colours. This work shows that ML algorithms can distinguish multifrequency spectral characteristics and handle the classification of blazars into LSPs and HSPs. It is a hint for the potential use of ML for the autonomous determination of broadband spectral parameters (as the synchrotron ν-peak), or even to search for new blazars in all-sky data bases.