bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of tenuazonic acid production-inducing compounds and identification of NPD938 as a regulator of fungal secondary metabolism
Authors: Motoyama Takayuki , Ishii Tomoaki , Kamakura Takashi , Osada Hiroyuki
Published: August 2021

The control of secondary metabolism in fungi is essential for the regulation of various cellular functions. In this study, we searched the RIKEN Natural Products Depository (NPDepo) chemical library for inducers of tenuazonic acid (TeA) production in the rice blast fungus Pyricularia oryzae and identified NPD938. NPD938 transcriptionally induced TeA production. We explored the mode of action of NPD938 and observed that this compound enhanced TeA production via LAE1, a global regulator of fungal secondary metabolism. NPD938 could also induce production of terpendoles and pyridoxatins in Tolypocladium album RK99-F33. Terpendole production was induced transcriptionally. We identified the pyridoxatin biosynthetic gene cluster among transcriptionally induced secondary metabolite biosynthetic gene clusters. Therefore, NPD938 is useful for the control of fungal secondary metabolism.
mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences
Authors: Ho Quang-Thai , Le Nguyen Quoc Khanh , Ou Yu-Yen
Published: August 2021

In the past decade, convolutional neural networks (CNNs) have been used as powerful tools by scientists to solve visual data tasks. However, many efforts of convolutional neural networks in solving protein function prediction and extracting useful information from protein sequences have certain limitations. In this research, we propose a new method to improve the weaknesses of the previous method. mCNN-ETC is a deep learning model which can transform the protein evolutionary information into image-like data composed of 20 channels, which correspond to the 20 amino acids in the protein sequence. We constructed CNN layers with different scanning windows in parallel to enhance the useful pattern detection ability of the proposed model. Then we filtered specific patterns through the 1-max pooling layer before inputting them into the prediction layer. This research attempts to solve a basic problem in biology in terms of application: predicting electron transporters and classifying their corresponding complexes. The performance result reached an accuracy of 97.41%, which was nearly 6% higher than its predecessor. We have also published a web server on http://bio219.bioinfo.yzu.edu.tw, which can be used for research purposes free of charge.
Shared Genetic Etiology between Cortical Brain Morphology and Tobacco, Alcohol, and Cannabis Use
Authors: Rabinowitz Jill A , Campos Adrian I , Ong Jue-Sheng , García-Marín Luis M , Alcauter Sarael , Mitchell Brittany L , Grasby Katrina L , Cuéllar-Partida Gabriel , Gillespie Nathan A , Huhn Andrew S , Martin Nicholas G , Thompson Paul M , Medland Sarah E , Maher Brion S , Rentería Miguel E
Published: August 2021

Genome-wide association studies (GWAS) have identified genetic variants associated with brain morphology and substance use behaviors (SUB). However, the genetic overlap between brain structure and SUB has not been well characterized. We leveraged GWAS summary data of 71 brain imaging measures and alcohol, tobacco, and cannabis use to investigate their genetic overlap using linkage disequilibrium score regression. We used genomic structural equation modeling to model a “common SUB genetic factor” and investigated its genetic overlap with brain structure. Furthermore, we estimated SUB polygenic risk scores (PRS) and examined whether they predicted brain imaging traits using the Adolescent Behavior and Cognitive Development (ABCD) study. We identified 8 significant negative genetic correlations, including between (1) alcoholic drinks per week and average cortical thickness, and (2) intracranial volume with age of smoking initiation. We observed 5 positive genetic correlations, including those between (1) insula surface area and lifetime cannabis use, and (2) the common SUB genetic factor and pericalcarine surface area. SUB PRS were associated with brain structure variation in ABCD. Our findings highlight a shared genetic etiology between cortical brain morphology and SUB and suggest that genetic variants associated with SUB may be causally related to brain structure differences.
Remdesivir and Mortality in Patients With Coronavirus Disease 2019
Authors: Diaz George A , Christensen Alyssa B , Pusch Tobias , Goulet Delaney , Chang Shu-Ching , Grunkemeier Gary L , McKelvey Paul A , Robicsek Ari , French Tom , Parsons Guilford T , Doherty Glenn , Laurenson Charles , Roper Ryan , Hadlock Jennifer , Cover Cameron J , Footer Brent , Robinson Philip , Micikas Mary , Marfori Jennifer E , Cronenweth Charlotte , Mukkamala Yogavedya , Mackiewicz Jamie , Rai Ekra , Matson Martha Dickinson , Davila Jodie , Rueda Justin , Tipton Reda , Algren Heather , Ward Brittney C , Malkoski Stephen , Gluckman Tyler , Tallman Gregory B , Arguinchona Henry , Hammond Terese C , Standaert Steven , Christensen Joshua , Echaiz Jose F , Choi Robert , McClung Daniel , Pacifico Albert , Fee Martin , Sarafian Farjad , Berrington William R , Goldman Jason D
Published: August 2021

Background

The impact of remdesivir (RDV) on mortality rates in coronavirus disease 2019 (COVID-19) is controversial, and the mortality effect in subgroups of baseline disease severity has been incompletely explored. The purpose of this study was to assess the association of RDV with mortality rates in patients with COVID-19.

Methods

In this retrospective cohort study we compared persons receiving RDV with those receiving best supportive care (BSC). Patients hospitalized between 28 February and 28 May 2020 with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection were included with the development of COVID-19 pneumonia on chest radiography and hypoxia requiring supplemental oxygen or oxygen saturation ≤94% with room air. The primary outcome was overall survival, assessed with time-dependent Cox proportional hazards regression and multivariable adjustment, including calendar time, baseline patient characteristics, corticosteroid use, and random effects for hospital.

Results

A total of 1138 patients were enrolled, including 286 who received RDV and 852 treated with BSC, 400 of whom received hydroxychloroquine. Corticosteroids were used in 20.4% of the cohort (12.6% in RDV and 23% in BSC). Comparing persons receiving RDV with those receiving BSC, the hazard ratio (95% confidence interval) for death was 0.46 (.31–.69) in the univariate model (P < .001) and 0.60 (.40–.90) in the risk-adjusted model (P = .01). In the subgroup of persons with baseline use of low-flow oxygen, the hazard ratio (95% confidence interval) for death in RDV compared with BSC was 0.63 (.39–1.00; P = .049).

Conclusion

Treatment with RDV was associated with lower mortality rates than BSC. These findings remain the same in the subgroup with baseline use of low-flow oxygen.
Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis
Authors: Yuasa Hideaki , Kajitani Rei , Nakamura Yuta , Takahashi Kazuki , Okuno Miki , Kobayashi Fumiya , Shinoda Takahiro , Toyoda Atsushi , Suzuki Yutaka , Thongtham Nalinee , Forsman Zac , Bronstein Omri , Seveso Davide , Montalbetti Enrico , Taquet Coralie , Eyal Gal , Yasuda Nina , Itoh Takehiko
Published: August 2021

The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.
Long-term neurodevelopment in children born with esophageal atresia: a systematic review
Authors: van Hoorn Camille E , ten Kate Chantal A , Rietman Andre B , Toussaint-Duyster Leontien C C , Stolker Robert Jan , Wijnen Rene M H , de Graaff Jurgen C
Published: August 2021

Background

Although the survival rate of esophageal atresia (EA) has increased to over 90%, the risk of functional long-term neurodevelopmental deficits is uncertain. Studies on long-term outcomes of children with EA show conflicting results. Therefore, we provide an overview of the current knowledge on the long-term neurodevelopmental outcome of children with EA.

Methods

We performed a structured literature search in Embase, Medline Ovid, Web of Science, Cochrane CENTRAL, and Google scholar on November 8, 2020 with the keywords ‘esophageal atresia’, ‘long-term outcome’, ‘motor development’, ‘cognitive development’, and ‘neurodevelopment’.

Results

The initial search identified 945 studies, of which 15 were included. Five of these published outcomes of multiple tests or tested at multiple ages. Regarding infants, one of six studies found impaired neurodevelopment at 1 year of age. Regarding preschoolers, two of five studies found impaired neurodevelopment; the one study assessing cognitive development found normal cognitive outcome. Both studies on motor function reported impairment. Regarding school-agers, the one study on neurodevelopmental outcome reported impairment. Cognitive impairment was found in two out of four studies, and motor function was impaired in both studies studying motor function.

Conclusions

Long-term neurodevelopment of children born with EA has been assessed with various instruments, with contrasting results. Impairments were mostly found in motor function, but also in cognitive performance. Generally, the long-term outcome of these children is reason for concern. Structured, multidisciplinary long-term follow-up programs for children born with EA would allow to timely detect neurodevelopmental impairments and to intervene, if necessary.
Bumblebees Exposed to a Neonicotinoid Pesticide Make Suboptimal Foraging Decisions
Authors: Siviter Harry , Johnson Anthony K , Muth Felicity
Published: August 2021

Bumblebees are important pollinators of agricultural crops and wildflowers, but many species are in decline. Neonicotinoid insecticides are the most commonly used insecticide globally and can have negative sublethal effects on bumblebee colony growth and reproduction. Individual bumblebees can visit hundreds to thousands of flowers a day to forage for their colony. As such, they are a model species for studying optimal foraging, and small impairments to an individual’s foraging decisions may have compounding effects on the colony’s nutritional intake. We exposed bumblebees (Bombus impatiens) to an acute, field-realistic dose of the neonicotinoid insecticide imidacloprid, before allowing them to forage on an artificial floral array. We found that neonicotinoid-exposed bumblebees made suboptimal foraging decisions, as they were more likely to visit flowers located further apart than control bees. This indicates that for a given flower patch, individual bees exposed to a neonicotinoid will likely use more energy and forage less efficiency than unexposed bees, although further studies that directly measure energetic cost are required to confirm this. Given the robust and growing body of evidence demonstrating negative sublethal effects of neonicotinoids on bees, sublethal assessments on non-Apis bees should be made mandatory within the regulatory process.
Risk factors for type 1 and type 2 myocardial infarction
Authors: Wereski Ryan , Kimenai Dorien M , Bularga Anda , Taggart Caelan , Lowe David J , Mills Nicholas L , Chapman Andrew R
Published: August 2021

Aims

Whilst the risk factors for type 1 myocardial infarction due to atherosclerotic plaque rupture and thrombosis are established, our understanding of the factors that predispose to type 2 myocardial infarction during acute illness is still emerging. Our aim was to evaluate and compare the risk factors for type 1 and type 2 myocardial infarction.

Methods and results

We conducted a secondary analysis of a multi-centre randomized trial population of 48 282 consecutive patients attending hospital with suspected acute coronary syndrome. The diagnosis of myocardial infarction during the index presentation and all subsequent reattendances was adjudicated according to the Universal Definition of Myocardial Infarction. Cox regression was used to identify predictors of future type 1 and type 2 myocardial infarction during a 1-year follow-up period. Within 1 year, 1331 patients had a subsequent myocardial infarction, with 924 and 407 adjudicated as type 1 and type 2 myocardial infarction, respectively. Risk factors for type 1 and type 2 myocardial infarction were similar, with age, hyperlipidaemia, diabetes, abnormal renal function, and known coronary disease predictors for both (P < 0.05 for all). Whilst women accounted for a greater proportion of patients with type 2 as compared to type 1 myocardial infarction, after adjustment for other risk factors, sex was not a predictor of type 2 myocardial events [adjusted hazard ratio (aHR) 0.82, 95% confidence interval (CI) 0.66–1.01]. The strongest predictor of type 2 myocardial infarction was a prior history of type 2 events (aHR 6.18, 95% CI 4.70–8.12).

Conclusions

Risk factors for coronary disease that are associated with type 1 myocardial infarction are also important predictors of type 2 events during acute illness. Treatment of these risk factors may reduce future risk of both type 1 and type 2 myocardial infarction.
Quality of life and family function are poorest when both patients with heart failure and their caregivers are depressed
Authors: Liljeroos Maria A , Miller Jennifer L , Lennie Terry A , Chung Misook L
Published: August 2021

Aims

Patients with heart failure (HF) and their family caregivers commonly experience depressive symptoms associated with low quality of life (QOL) at the individual level. However, there is a lack of knowledge about how QOL and family function are associated with depressive symptoms at the dyad level. The aim of this article is to compare QOL and family function among dyads stratified by depressive symptoms.

Methods and results

Outpatients with HF and their primary caregivers completed the Beck Depression Inventory-II for depressive symptoms, the Short Form 36 for physical and mental QOL, and the McMaster Family Assessment Device for a family function. Analysis of variance was used to compare QOL and family function among the four dyad groups. A total of 91 dyads were categorized into four groups: neither member having depressive symptoms (43.9%), only the caregiver having depressive symptoms (13.2%), only the patient having depressive symptoms (23.1%), and both members having depressive symptoms (20.9%). Dyads without depressive symptoms had the highest levels of physical and mental QOL among the groups. The dyads with both members having depressive symptoms had the lowest levels of physical and mental QOL (P < 0.001) and the lowest levels of general family functioning, problem-solving ability, and communication ability (P < 0.001). Intermediate levels of QOL were seen in dyads with only one member having depressive symptoms, and a similar pattern of intermediate scores was found in all three subscales of family function.

Conclusion

Dyads with both members having depressive symptoms may be at greatest risk of having poor QOL and low family functioning.
Olfactory Stimulation Successfully Improves Swallowing Function of Aged Rats Through Activating Central Neuronal Networks and Downstream DHPR–RyR-mediated Neuromuscular Activities
Authors: Chen Yea-Tzy , Chen Li-You , Renn Ting-Yi , Cheng Meng-Shan , Wang Chi-Te , Klimenkov Igor V , Sudakov Nikolay P , Liao Wen-Chieh , Chen Yea-Jyh , Chang Hung-Ming
Published: August 2021

Presbyphagia is age-related changes in swallowing function, which imposes a high risk of aspiration in older adults. Considering olfactory stimulation (OS) can influence behavioral activities by modulating neuronal excitability, the present study aims to determine whether OS could improve the swallowing function of aged rats through activating the central neuronal networks and downstream muscular activities participated in the control of swallowing. Aged male Wistar rats received OS by inhaling a mixture of plant-based volatile molecules twice a day for 12 days were subjected to functional magnetic resonance imaging (fMRI) and c-fos, choline acetyltransferase (ChAT) immunostaining to detect the neuronal activities of the orbitofrontal cortex (OFC) and medullary nuclei engaged in swallowing control, respectively. The functional effects of OS on downstream pharyngeal muscle activity were examined by evaluating the dihydropyridine receptor–ryanodine receptor (DHPR–RyR)-mediated intramuscular Ca2+ expression, and analyzing the amplitude/frequency of muscle contraction, respectively. In untreated rats, only moderate signal of fMRI and mild c-fos/ChAT expression was detected in the OFC and medullary nuclei, respectively. However, following OS, intense signals of fMRI and immunostaining were clearly expressed in the orbitofronto-medullary networks. Functional data corresponded well with above findings in which OS significantly enhanced DHPR–RyR-mediated intramuscular Ca2+ expression, effectively facilitated a larger amplitude of pharyngeal muscle contraction, and exhibited better performance in consuming larger amounts of daily dietary. As OS successfully activates the neuromuscular activities participated in the control of swallowing, applying OS may serve as an effective, easy, and safe strategy to greatly improve the swallow function of aging populations.
A fast sweeping method for calculating qP-wave traveltimes in 3-D vertical transversely isotropic media using a quadratic equation
Authors: Lu Yongming , Zhang Wei
Published: August 2021

Traveltime computations are an important aspect of seismic data processing applications such as traveltime tomography, migration and seismic source localization. Seismic anisotropy is a widespread feature of the Earth. Solutions to the eikonal equation that account for such anisotropy are needed for high-resolution seismic imaging and inversion. The fast sweeping method (FSM) has been widely used in computing the first-arrival traveltimes for anisotropic media because it does not need to expand the wave front from the point of the smallest traveltime. To apply FSM on strong anisotropic media, one has to solve the slowness equation derived from the Christoffel equation. All the previous developed FSM methods transform the quartic coupled slowness surface equation of quasi-P (qP) and quasi-SV (qSV) waves to the quartic equation in terms of the unknown traveltime, then numerically solve this quartic equation to compute the first-arrival traveltimes of the qP waves. However, the computational cost is significantly increased due the numerically solving the quartic equation, especially for the 3-D problems. In this study, we find a way to transform the quartic slowness equation into a quadratic one if a specific triangular-pyramid stencil around a target point is used. As the quadratic equation has the analytical solution and does not need a numerical solver, the computational efficiency of the scheme is greatly improved. We apply this methodology to develop an efficient 3-D FSM to compute the first-arrival traveltimes for qP waves in 3-D vertical transversely isotropic (VTI) media. We use both layered VTI model and complex VTI model to demonstrate the efficiency of the proposed method to obtain accurate traveltimes in 3-D VTI media involving strong anisotropy.
Welcoming the Unwelcome: Refugee Flows, Refugee Rights, and Political Violence
Authors: Savun Burcu
Published: August 2021

This article examines refugee-related violence by exploring the effect of extensive refugee rights on the risk of civil conflict and violent attacks against refugees by local population. The provision of fundamental rights, such as the freedom of movement, can reduce refugee groups’ grievances, the risk of radicalization, and the ability of militant organizations to recruit refugees, thereby decreasing the risk of civil conflict. Regarding the behavior of local population toward refugees, two opposing effects of refugee rights may be at play. Extensive refugee policies may trigger civilian backlash by aggravating the perception of threat posed by refugees and increase the risk of civilian attacks against refugees. On the other hand, allowing refugees to integrate into society may provide economic benefits for locals and facilitate socialization between groups, reducing the motivation of citizens to target refugees. Using an original global dataset on refugee rights, I find that liberal refugee policies are associated with a reduction in the risk of civil conflict as well as anti-refugee violence in host states. This suggests that host governments and international organizations should give greater priority to guaranteeing refugee rights and promoting income-generating activities among uprooted populations to minimize potential security risks associated with refugees.
Crohn’s and Colitis Canada’s 2021 Impact of COVID-19 and Inflammatory Bowel Disease in Canada: Mental Health and Quality of Life
Authors: Graff Lesley A , Fowler Sharyle , Jones Jennifer L , Benchimol Eric I , Bitton Alain , Huang James Guoxian , Kuenzig M Ellen , Kaplan Gilaad G , Lee Kate , Mukhtar Mariam S , Tandon Parul , Targownik Laura E , Windsor Joseph W , Bernstein Charles N
Published: August 2021

There has been a dramatic rise in mental health difficulties during the coronavirus disease 2019 (COVID-19) pandemic. While young adults have the lowest risk of hospitalization and mortality due to COVID-19, they have been identified as being at highest risk of detrimental mental health outcomes during the pandemic, along with women, those with lower socioeconomic status and those with pre-existing mental health conditions. Somewhat of a crisis in mental health has emerged across the general population through the evolution of the pandemic. A national Canadian survey identified a quadrupling of those experiencing pervasive elevated anxiety symptoms early in the pandemic compared to pre-pandemic levels, and a doubling of those with pervasive elevated depressive symptoms. Independent of the pandemic, persons with inflammatory bowel disease (IBD) can face multiple challenges related to their disease, which can result in a significant psychosocial burden and psychologic distress. Anxiety and depression have been found to be more prevalent in persons with IBD. Many potential factors contribute to the increased psychologic distress and negative impacts on mental health of the COVID-19 pandemic on persons with IBD. These include the fears of contracting COVID-19 or infecting other people. Many believe that IBD or its treatments predispose them to an increased risk of COVID-19 or a worse outcome if acquired. Concerns about access to health care add to mental distress. People with IBD generally report lower quality of life (QOL) compared to community controls. Psychologic interventions, in addition to adequate disease control, have been shown to improve health-related QOL. Uncertainty is another factor associated with reduced health-related QOL. Most studies suggest that persons with IBD have suffered QOL impairment during the pandemic in comparison to the pre-pandemic period. Uncertainties brought on by the pandemic are important contributors for some of the reduction in QOL.
Temperature induces activity reduction in a Neotropical ungulate
Authors: Peterson Michaela , Jorge Maria Luisa S P , Jain Avarna , Keuroghlian Alexine , Oshima Júlia Emi F , Richard-Hansen Cécile , Berzins Rachel , Ribeiro Milton Cezar , Eaton Don
Published: August 2021

Because global climate change results in increasingly extreme temperatures and more frequent droughts, behavioral thermoregulation is one avenue by which species may adjust. Changes in activity patterns in response to temperature have been observed in a number of mammal species, but rarely have been investigated in humid tropical habitats. Here we examine the relationship between activity patterns and microclimate temperatures for white-lipped peccaries (Tayassu pecari, Tayassuidae, Cetartiodactyla) in four distinct biomes—the Cerrado, the Pantanal, the Atlantic Forest, and the Amazon. From 2013 to 2017, we monitored 30 white-lipped peccaries fitted with GPS collars that included accelerometers and temperature sensors. White-lipped peccaries were primarily diurnal, with peaks of activity in the morning and late afternoon, except in the Amazon where activity was high throughout the day. Total time active did not vary seasonally. White-lipped peccaries were significantly less likely to be active as temperatures increased, with the probability of being active decreasing by >49% in all biomes between 30 and 40°C. Our findings indicate that white-lipped peccaries are likely to be adversely impacted by rising temperatures, through being forced to reduce foraging time during their prime active periods.
Changes in native small mammal populations with removal of invasive ant
Authors: Morehart Morgan A , Gitzen Robert A , Terhune Theron M , Lepczyk Christopher A , Sisson D Clay
Published: August 2021

Efforts to remove invasive species may benefit native species, but the effects can be complex and unpredictable. Thus, studies of invasive-species removal provide important information for guiding management and providing insight about variation in post-removal impacts within the community. Using southern pine-grassland ecosystems as a model system, we hypothesized that removal of the long-established red-imported fire ant (Solenopsis invicta, hereafter RIFA) would positively influence altricial Peromyscus species, due to increased survival of young in the nest and thus increased recruitment to the population, but would not impact semi-precocial hispid cotton rats (Sigmodon hispidus), which are mobile more quickly after birth and thus at less risk of depredation by RIFA. We compared small mammal populations on sites treated with a granular insecticide (Extinguish Plus) to remove RIFA in southwestern Georgia, United States, from April 2018 to December 2019. As expected, we detected no difference in cotton rat recruitment. However, contrary to our prediction, the same was true for cotton mice (Peromyscus gossypinus) and oldfield mice (Peromyscus polionotus). We found RIFA removal increased survival both of cotton rats and cotton mice, increasing average population rate of change (λ) on treated sites during the study period. In contrast, we observed lower survival of oldfield mice, with similar λ estimates on treated and untreated sites, but low sample sizes were problematic for this species. Our results show that removal of invasive species can have positive impacts for native species, but both the magnitude of RIFA effects on small mammals and mechanisms by which impacts occur are complex.
Integrative Taxonomy ofDermacentor variabilis(Ixodida: Ixodidae) with Description of a New Species,Dermacentor similisn. sp.
Authors: Lado Paula , Glon Mael G , Klompen Hans
Published: August 2021

Dermacentor variabilis is the most widely distributed three-host tick in North America, and transmits a variety of pathogens. Within the United States, this species has a discontinuous distribution, widespread east of the Rocky Mountains and with a few populations west of the Rockies. Phylogenetic evidence based on individual markers or relatively small data sets has suggested that populations at both sides of this geographic barrier may correspond to two different species. In this study, we further explore this hypothesis using an integrative taxonomy framework. Both molecular (mitochondrial and nuclear markers) and morphological analyses of specimens collected from central-eastern and western states were performed to explore species delimitation in this taxon. Results from these analyses were consistent, and provide strong evidence that D. variabilis actually corresponds to two species. Herein, the western populations are described as a new species, Dermacentor similis n. sp. The usefulness of integrative taxonomy in the context of species delimitation is also discussed.
Competition, Ownership, and the Impact of Government Outsourcing on Employees
Authors: Petersen Ole Helby , Andersen Lotte Bøgh , Bhatti Yosef , Houlberg Kurt
Published: August 2021

Government outsourcing to third-party vendors is widespread and intended to strengthen the organizational incentive to deliver public services more efficiently. However, it is unclear how outsourcing influences the public workforce, and little is known about the effect on employees who change from working for the government to working for the vendor receiving the outsourcing contract. In this article, we theoretically argue that the introduction of competition and private ownership in public service delivery may have negative consequences for employees’ remuneration, employment, and health outcomes. We assess these arguments using unique individual-level register data of 1,478 Danish relatively low-skilled employees who changed job from public to private employment due to government outsourcing. Using a difference-in-difference (DiD) approach, we estimate the effect on employees’ remuneration, employment and income transfers, and use of health services compared to an exact matched control group of public employees who did not experience outsourcing. Our findings suggest that outsourcing significantly decreased employee remuneration and employment and increased public income transfers, while the effect on health services use was marginal and transitory. Potential mechanisms explaining these findings include the vendor’s incentive to reduce the workforce and increase productivity, the stress of changing jobs, and poorer person–environment fit. The results suggest that outsourcing has high costs for employees, some of which are passed on to the government itself through increased expenditure for public income transfers. We propose pathways for further theoretical and empirical research on employee consequences of government outsourcing.
Supradiaphragmatic accessory liver tissue mimicking pleural tumour: excision by transdiaphragmatic uniportal video-assisted thoracoscopic surgery (U-VATS)
Authors: Fang Chen Chuan , Neerudu Manjuvani , Hernandez Luis A
Published: August 2021

We describe a case of an extremely rare intrathoracic supradiaphragmatic accessory liver tissue that was excised via transdiaphragmatic uniportal video-assisted thoracoscopic surgery. The intrathoracic mass that was radiologically detected was found to be mimicking a pleural tumour because of its supradiaphragmatic location as well as the presence of a clear cleavage plane separating the mass and the liver completely. This, to our knowledge, is the first described case that was resected via transdiaphragmatic uniportal approach in the literature.
HbA1c Below the Reportable Range
Authors: Pant Vivek
Published: August 2021

This case report concerns a 71 year old female patient who had a very low glycosylated hemoglobin (HbA1c) despite having a high level of fasting blood glucose. The patient had a decreased erythrocyte count, elevated red blood cell indices, and a reticulocyte count with no evidence of hemoglobinopathy. She reported receiving hydroxychloroquine treatment for systemic lupus erythematosus. Subsequent laboratory investigations revealed hemolysis with formation of cold agglutinin. Because cold agglutinins can interfere with HbA1c assays, the specimens were reanalyzed after warming. The complete blood count results improved, but the HbA1c result did not change. In patients in whom medications and/or medical conditions may interfere with HbA1c levels, alternative measures of glycemic control, such as fructosamine, could be beneficial.
Galaxy cluster cores as seen with VLT/MUSE: New strong-lensing analyses of RX J2129.4 + 0009, MS 0451.6 − 0305, and MACS J2129.4 − 0741
Authors: Jauzac Mathilde , Klein Baptiste , Kneib Jean-Paul , Richard Johan , Rexroth Markus , Schäfer Christoph , Verdier Aurélien
Published: August 2021

We present strong-lensing analyses of three galaxy clusters, RX J2129.4 + 0009 (z = 0.235), MS 0451.6 − 0305 (z = 0.55), and MACS J2129.4 − 0741 (z = 0.589), using the powerful combination of Hubble Space Telescope (HST) multiband observations, and Multi-Unit Spectroscopic Explorer (MUSE) spectroscopy. In RX J2129, we newly spectroscopically confirm 15 cluster members. Our resulting mass model uses 8 multiple image systems as we include a galaxy–galaxy lensing system north-east of the cluster, and is composed of 71 haloes including one dark matter cluster-scale halo and two galaxy-scale haloes optimized individually. For MS 0451, we report the spectroscopic identification of two new systems of multiple images in the northern region and 112 cluster members. Our mass model uses 16 multiple image systems and 146 haloes, including 2 large-scale haloes and 7 galaxy-scale haloes independently optimized. For MACS J2129, we report the spectroscopic identification of one new multiple image system at z = 4.41, and newly measure spectroscopic redshifts for four cluster members. Our mass model uses 14 multiple image systems, and is composed of 151 haloes, including 2 large-scale haloes and 4 galaxy-scale haloes independently optimized. Our best models have rms of 0.29, 0.6, 0.74 arcsec in the image plane for RX J2129, MS 0451, and MACS J2129, respectively. This analysis presents a detailed comparison with the existing literature showing excellent agreements, and discuss specific studies of lensed galaxies, e.g. a group of submillimetre galaxies at z = 2.9 in MS 0451, and a bright z = 2.1472 red singly imaged galaxy in MACS J2129.
2D surface brightness modelling of large 2MASS galaxies – I: photometry and structural parameters
Authors: Ríos-López Emmanuel , Añorve Christopher , Ibarra-Medel Héctor J , López-Cruz Omar , Alvira-Enríquez Joaquín , Iacobuta Gabriela , Valerdi Mabel
Published: August 2021

We have studied a sample of 101 bright 2MASS galaxies from the Large Galaxy Atlas (LGA), whose morphologies span from early to late types. We have generated estimates for structural parameters through a two-dimensional surface brightness photometric decomposition in the three 2MASS bands (J, H, and Ks). This work represents a detailed multicomponent photometric study of nearby galaxies. We report total magnitudes, effective radii, and concentration indices, among other parameters, in the three 2MASS bands. We found that the integrated total magnitudes of early-type galaxies (ETGs) measured on 2MASS LGA mosaics are ∼0.35 mag dimmer, when compared with images generated from IRSA image tile service; nevertheless, when comparing late-type galaxies (LTGs) we did not find any difference. Therefore, for ETGs we present the results derived on IRSA image tiles, while for LTGs we used data from the LGA mosaics. Additionally, by combining these structural parameters with scaling relations and kinematic data, we separated classical bulges from pseudo-bulges. We found that ${\sim} 40{{\ \rm per\ cent}}$ of the objects in our sample are classified as pseudo-bulges, which are found preferentially in LTGs. Also, our findings confirm trends reported earlier in the distributions for some physical parameters, such as Sérsic index and B/T and q ratios. In general, our results are in agreement with previous one-dimensional studies. In a companion paper, we revise some of the scaling relations among global galaxy properties, as well as their interrelation with Supermassive Black Holes.
Strong lensing signatures of self-interacting dark matter in low-mass haloes
Authors: Gilman Daniel , Bovy Jo , Treu Tommaso , Nierenberg Anna , Birrer Simon , Benson Andrew , Sameie Omid
Published: August 2021

Core formation and runaway core collapse in models with self-interacting dark matter (SIDM) significantly alter the central density profiles of collapsed haloes. Using a forward modelling inference framework with simulated data-sets, we demonstrate that flux ratios in quadruple image strong gravitational lenses can detect the unique structural properties of SIDM haloes, and statistically constrain the amplitude and velocity dependence of the interaction cross-section in haloes with masses between 106 and 1010 M⊙. Measurements on these scales probe self-interactions at velocities below $30 \ \rm {km} \ \rm {s^{-1}}$, a relatively unexplored regime of parameter space, complimenting constraints at higher velocities from galaxies and clusters. We cast constraints on the amplitude and velocity dependence of the interaction cross-section in terms of σ20, the cross-section amplitude at $20 \ \rm {km} \ \rm {s^{-1}}$. With 50 lenses, a sample size available in the near future, and flux ratios measured from spatially compact mid-IR emission around the background quasar, we forecast $\sigma _{20} \lt 11\rm {\small {--}}23 \ \rm {cm^2} \rm {g^{-1}}$ at $95 {{\ \rm per\ cent}}$ CI, depending on the amplitude of the subhalo mass function, and assuming cold dark matter (CDM). Alternatively, if $\sigma _{20} = 19.2 \ \rm {cm^2}\rm {g^{-1}}$ we can rule out CDM with a likelihood ratio of 20:1, assuming an amplitude of the subhalo mass function that results from doubly efficient tidal disruption in the Milky Way relative to massive elliptical galaxies. These results demonstrate that strong lensing of compact, unresolved sources can constrain SIDM structure on sub-galactic scales across cosmological distances, and the evolution of SIDM density profiles over several Gyr of cosmic time.
The IMF and multiplicity of stars from gravity, turbulence, magnetic fields, radiation, and outflow feedback
Authors: Mathew Sajay Sunny , Federrath Christoph
Published: August 2021

We perform a series of three-dimensional, magnetohydrodynamical simulations of star cluster formation including gravity, turbulence, magnetic fields, stellar radiative heating, and outflow feedback. We observe that the inclusion of protostellar outflows (1) reduces the star formation rate by a factor of ∼2, (2) increases fragmentation, and (3) shifts the initial mass function (IMF) to lower masses by a factor of 2.0 ± 0.2, without significantly affecting the overall shape of the IMF. The form of the sink particle (protostellar objects) mass distribution obtained from our simulations matches the observational IMFs reasonably well. We also show that turbulence-based theoretical models of the IMF agree well with our simulation IMF in the high-mass and low-mass regime, but do not predict any brown dwarfs, whereas our simulations produce a considerable number of sub-stellar objects, which are produced by dynamical interactions (ejections). We find that these dynamical interactions also play a key role for the binary separation distribution and stellar kinematics in general. Our numerical model of star cluster formation also reproduces the observed mass dependence of multiplicity. Our multiplicity fraction estimates generally concur with the observational estimates for different spectral types. We further calculate the specific angular momentum of all the sink particles and find that the average value of $1.5 \times 10^{19}\, \mathrm{cm^2\, s^{-1}}$ is consistent with observational data. The specific angular momentum of our sink particles lies in the range typical of protostellar envelopes and binaries. We conclude that the IMF is controlled by a combination of gravity, turbulence, magnetic fields, radiation, and outflow feedback.
Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul
Authors: Brucato Nicolas , André Mathilde , Tsang Roxanne , Saag Lauri , Kariwiga Jason , Sesuki Kylie , Beni Teppsy , Pomat William , Muke John , Meyer Vincent , Boland Anne , Deleuze Jean-François , Sudoyo Herawati , Mondal Mayukh , Pagani Luca , Gallego Romero Irene , Metspalu Mait , Cox Murray P , Leavesley Matthew , Ricaut François-Xavier
Published: August 2021

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains
Authors: Alvarez-Carreño Claudia , Penev Petar I , Petrov Anton S , Williams Loren Dean
Published: August 2021

SH3 and OB are the simplest, oldest, and most common protein domains within the translation system. SH3 and OB domains are β-barrels that are structurally similar but are topologically distinct. To transform an OB domain to a SH3 domain, β-strands must be permuted in a multistep and evolutionarily implausible mechanism. Here, we explored relationships between SH3 and OB domains of ribosomal proteins, initiation, and elongation factors using a combined sequence- and structure-based approach. We detect a common core of SH3 and OB domains, as a region of significant structure and sequence similarity. The common core contains four β-strands and a loop, but omits the fifth β-strand, which is variable and is absent from some OB and SH3 domain proteins. The structure of the common core immediately suggests a simple permutation mechanism for interconversion between SH3 and OB domains, which appear to share an ancestor. The OB domain was formed by duplication and adaptation of the SH3 domain core, or vice versa, in a simple and probable transformation. By employing the folding algorithm AlphaFold2, we demonstrated that an ancestral reconstruction of a permuted SH3 sequence folds into an OB structure, and an ancestral reconstruction of a permuted OB sequence folds into a SH3 structure. The tandem SH3 and OB domains in the universal ribosomal protein uL2 share a common ancestor, suggesting that the divergence of these two domains occurred before the last universal common ancestor.
Access flow volume (Qa) and survival in a haemodialysis population: an analysis of 5208 Qa measurements over a 9-year period
Authors: Yadav Reshabh , Gerrickens Michael W M , van Kuijk Sander M J , Vaes Roel H D , Snoeijs Maarten G J , Scheltinga Marc R M
Published: August 2021

Background

The aim of this study was to determine associations between characteristics of arteriovenous access (AVA) flow volume (Qa; mL/min) and 4-year freedom from cardiovascular mortality (CVM) in haemodialysis (HD) patients.

Methods

HD patients who received a primary AVA between January 2010 and December 2017 in one centre were analysed. Initial Qa was defined as the first Qa value obtained in a well-functioning AVA by a two-needle dilution technique. Actual Qa was defined as access flow at a random point in time. Changes in actual Qa were expressed per 3-month period. CVM was assessed according to the European Renal Association–European Dialysis and Transplant Association classification. The optimal cut-off point for initial Qa was identified by a receiver operating characteristics curve. A joint modelling statistical technique determined longitudinal associations between Qa characteristics and 4-year CVM.

Results

A total of 5208 Qa measurements (165 patients; 103 male, age 70 ± 12 years, autologous AVA n = 146, graft n = 19) were analysed. During follow-up (December 2010–January 2018, median 36 months), 79 patients (48%) died. An initial Qa <900 mL/min was associated with an increased 4-y CVM risk {hazard ratio [HR] 4.05 [95% confidence interval (CI) 1.94–8.43], P < 0.001}. After 4 years, freedom from CVM was 34% lower in patients with a Qa <900 mL/min (53 ± 7%) versus a Qa ≥900 mL/min (87 ± 4%; P < 0.001). An association between increases in actual Qa per 3-month period and mortality was found [HR 4.48/100 mL/min (95% CI 1.44–13.97), P = 0.010], indicating that patients demonstrating increasing Qa were more likely to die. In contrast, actual Qa per se was not related to survival.

Conclusions

Studying novel AVA Qa characteristics may contribute to understanding excess CVM in HD patients.
Importance of the intersection of age and sex to understand variation in incidence and survival for primary malignant gliomas
Authors: Wang Gi-Ming , Cioffi Gino , Patil Nirav , Waite Kristin A , Lanese Robert , Ostrom Quinn T , Kruchko Carol , Berens Michael E , Connor James R , Lathia Justin D , Rubin Joshua B , Barnholtz-Sloan Jill S
Published: August 2021

Background

Gliomas are the most common type of malignant brain and other CNS tumors, accounting for 80.8% of malignant primary brain and CNS tumors. They cause significant morbidity and mortality. This study investigates the intersection between age and sex to better understand variation of incidence and survival for glioma in the United States.

Methods

Incidence data from 2000 to 2017 were obtained from CBTRUS, which obtains data from the NPCR and SEER, and survival data from the CDC’s NPCR. Age-adjusted incidence rate ratios (IRR) per 100 000 were generated to compare male-to-female incidence by age group. Cox proportional hazard models were performed by age group, generating hazard ratios to assess male-to-female survival differences.

Results

Overall, glioma incidence was higher in males. Male-to-female incidence was lowest in ages 0-9 years (IRR: 1.04, 95% CI: 1.01-1.07, P = .003), increasing with age, peaking at 50-59 years (IRR: 1.56, 95% CI: 1.53-1.59, P < .001). Females had worse survival for ages 0-9 (HR: 0.93, 95% CI: 0.87-0.99), though male survival was worse for all other age groups, with the difference highest in those 20-29 years (HR: 1.36, 95% CI: 1.28-1.44). Incidence and survival differences by age and sex also varied by histological subtype of glioma.

Conclusions

To better understand the variation in glioma incidence and survival, investigating the intersection of age and sex is key. The current work shows that the combined impact of these variables is dependent on glioma subtype. These results contribute to the growing understanding of sex and age differences that impact cancer incidence and survival.