bluuebunny/crossref_metadata_2025 huggingface dataset:
State-Level Structural Stigma and Smoking Among Sexual Minority Adults in the USA, 2012–2014
Authors: Titus Andrea R , Gamarel Kristi E , Thrasher James F , Meza Rafael , Fleischer Nancy L
Published: November 2020

Background

Exposure to structural stigma (i.e., societal norms and policies that constrain access to resources) may help explain poor health outcomes among sexual minority (SM) individuals in the USA.

Purpose

We examined the relationship between structural stigma and smoking prevalence among U.S. SM and heterosexual adults.

Methods

We adapted an index to capture multiple state-level structural stigma indicators, including attitudes toward same-sex marriage; the geographical density of same-sex couples; and state-level policies toward SMs. The outcome variable was current smoking, derived from the National Adult Tobacco Survey (2012–2014). Poisson regression models stratified by SM status were used to assess the relationship between structural stigma and the prevalence ratio (PR) of current smoking. We included a squared term for stigma to explore nonlinear relationships between stigma and smoking. Interaction terms were used to examine effect modification by sex.

Results

Adjusted models suggested a curvilinear PR relationship between stigma and smoking for both SM (linear PR = 1.03 [0.97–1.08]; quadratic PR = 0.98 [0.97–1.00]) and heterosexual (linear PR = 1.00 [0.99–1.02]; quadratic PR = 0.99 [0.988–0.995]) adults. The quadratic term was significant (p < .05) for both SM and heterosexual respondents, however, the change in probability of smoking associated with structural stigma was more pronounced among SM individuals. Specifically, the highest and lowest exposures to stigma were associated with the lowest probabilities of smoking. There was no apparent effect modification by sex.

Conclusions

Findings lend support to addressing SM structural stigma as a driver of smoking, particularly among SM adults.
A Preliminary Investigation of the Underlying Mechanism Associating Daily Sleep Continuity Disturbance and Prescription Opioid Use Among Individuals With Sickle Cell Disease
Authors: Mun Chung Jung , Finan Patrick H , Smith Michael T , Carroll C Patrick , Smyth Joshua M , Lanzkron Sophie M , Haythornthwaite Jennifer A , Campbell Claudia M
Published: November 2020

Background

There are emerging data indicating that sleep disturbance may be linked with an increase in opioid use. The majority of sickle cell disease (SCD) patients experience sleep disturbances, which can elevate pain severity and pain catastrophizing, both of which are important predictors of opioid consumption.

Purpose

We conducted a preliminary investigation on the association between previous night sleep disturbance and short-acting opioid use, as well as the potential mediating roles of pain severity and pain catastrophizing. Because sex is associated with sleep disturbance, pain-related experiences, and opioid use, we also explored the potential moderating role of sex.

Methods

Participants were 45 SCD patients who were prescribed opioids. For 3 months, sleep diaries were collected immediately upon participants’ awakening. Daily pain severity, pain catastrophizing, and prescription opioid use measures were collected before bedtime.

Results

Multilevel structural equation modeling revealed that wake time after sleep onset (WASO) during the previous night (Time 1) predicted greater short-acting opioid use during the next day (Time 2). Pain severity and pain catastrophizing measured during the next day (Time 2) also mediated the association between the two. Sex moderation analysis showed that the positive association between WASO and pain severity was largely driven by women.

Conclusion

These findings provide some preliminary evidence as to the mechanism linking sleep continuity disturbance and opioid requirement in SCD patients. Future studies should replicate and extend these findings with clearer temporal information and employing more refined measures of sleep continuity and prescription opioid use in a larger sample.
The effect of social environment on bird song: listener-specific expression of a sexual signal
Authors: Jablonszky Mónika , Zsebők Sándor , Laczi Miklós , Nagy Gergely , Vaskuti Éva , Garamszegi László Zsolt
Published: November 2020

Animal signals should consistently differ among individuals to convey distinguishable information about the signalers. However, behavioral display signals, such as bird song are also loaded with considerable within-individual variance with mostly unknown function. We hypothesized that the immediate social environment may play a role in mediating such variance component, and investigated in the collared flycatcher (Ficedula albicollis) if the identity and quality of listeners could affect song production in signalers. After presenting territorial males with either a female or male social stimulus, we found in the subsequent song recordings that the among-stimulus effects corresponded to non-zero variance components in several acoustic traits indicating that singing males are able to plastically adjust their songs according to stimulus identity. Male and female stimuli elicited different responses as the identity of the female stimuli affected song complexity only, while the identity of male stimuli altered also song length, maximum frequency, and song rate. The stimulus-specific effect on song in some cases decreased with time, being particularly detectable right after the removal of the stimulus and ceasing later, but this pattern varied across the sex of the stimulus and the song traits. We were able to identify factors that can explain the among-stimulus effects (e.g., size and quality of the stimuli) with roles that also varied among song traits. Our results confirm that the variable social environment can raise considerable variation in song performance, highlighting that within-individual plasticity of bird song can play important roles in sexual signaling.
Ready, Set, Go: Community Science Field Campaign Reveals Habitat Preferences of Nonnative Asian Earthworms in an Urban Landscape
Authors: Ziter Carly D , Herrick Bradley M , Johnston Marie R , Turner Monica G
Published: November 2020

Asian pheretimoid earthworms of the genera Amynthas and Metaphire (jumping worms) are leading a new wave of coinvasion into Northeastern and Midwestern states, with potential consequences for native organisms and ecosystem processes. However, little is known about their distribution, abundance, and habitat preferences in urban landscapes—areas that will likely influence their range expansion via human-driven spread. We led a participatory field campaign to assess jumping worm distribution and abundance in Madison, Wisconsin, in the United States. By compressing 250 person-hours of sampling effort into a single day, we quantified the presence and abundance of three jumping worm species across different land-cover types (forest, grassland, open space, and residential lawns and gardens), finding that urban green spaces differed in invasibility. We show that community science can be powerful for researching invasive species while engaging the public in conservation. This approach was particularly effective in the present study, where broad spatial sampling was required within a short temporal window.
Modulation of Nogo receptor 1 expression orchestrates myelin-associated infiltration of glioblastoma
Authors: Hong Jun-Hee , Kang Sangjo , Sa Jason K , Park Gunwoo , Oh Young Taek , Kim Tae Hoon , Yin Jinlong , Kim Sung Soo , D’Angelo Fulvio , Koo Harim , You Yeonhee , Park Saewhan , Kwon Hyung Joon , Kim Chan Il , Ryu Haseo , Lin Weiwei , Park Eun Jung , Kim Youn-Jae , Park Myung-Jin , Kim Hyunggee , Kim Mi-Suk , Chung Seok , Park Chul-Kee , Park Sung-Hye , Kang Yun Hee , Kim Jong Heon , Saya Hideyuki , Nakano Ichiro , Gwak Ho-Shin , Yoo Heon , Lee Jeongwu , Hur Eun-Mi , Shi Bingyang , Nam Do-Hyun , Iavarone Antonio , Lee Seung-Hoon , Park Jong Bae
Published: November 2020

As the clinical failure of glioblastoma treatment is attributed by multiple components, including myelin-associated infiltration, assessment of the molecular mechanisms underlying such process and identification of the infiltrating cells have been the primary objectives in glioblastoma research. Here, we adopted radiogenomic analysis to screen for functionally relevant genes that orchestrate the process of glioma cell infiltration through myelin and promote glioblastoma aggressiveness. The receptor of the Nogo ligand (NgR1) was selected as the top candidate through Differentially Expressed Genes (DEG) and Gene Ontology (GO) enrichment analysis. Gain and loss of function studies on NgR1 elucidated its underlying molecular importance in suppressing myelin-associated infiltration in vitro and in vivo. The migratory ability of glioblastoma cells on myelin is reversibly modulated by NgR1 during differentiation and dedifferentiation process through deubiquitinating activity of USP1, which inhibits the degradation of ID1 to downregulate NgR1 expression. Furthermore, pimozide, a well-known antipsychotic drug, upregulates NgR1 by post-translational targeting of USP1, which sensitizes glioma stem cells to myelin inhibition and suppresses myelin-associated infiltration in vivo. In primary human glioblastoma, downregulation of NgR1 expression is associated with highly infiltrative characteristics and poor survival. Together, our findings reveal that loss of NgR1 drives myelin-associated infiltration of glioblastoma and suggest that novel therapeutic strategies aimed at reactivating expression of NgR1 will improve the clinical outcome of glioblastoma patients.
Triglyceride-Rich Lipoprotein Remnants and Cardiovascular Disease
Authors: Duran Edward K , Pradhan Aruna D
Published: November 2020

Background

Triglycerides, cholesterol, and their metabolism are linked due to shared packaging and transport within circulating lipoprotein particles. While a case for a causal role of cholesterol-carrying low-density lipoproteins (LDLs) in atherosclerosis is well made, the body of scientific evidence for a causal role of triglyceride-rich lipoproteins (TRLs) is rapidly growing, with multiple lines of evidence (old and new) providing robust support.

Content

This review will discuss current perspectives and accumulated evidence that an overabundance of remnant lipoproteins stemming from intravascular remodeling of nascent TRLs—chylomicrons and very low-density lipoproteins (VLDL)—results in a proatherogenic milieu that augments cardiovascular risk. Basic mechanisms of TRL metabolism and clearance will be summarized, assay methods reviewed, and pivotal clinical studies highlighted.

Remnant lipoproteins are rendered highly atherogenic by their high cholesterol content, altered apolipoprotein composition, and physicochemical properties. The aggregate findings from multiple lines of evidence suggest that TRL remnants play a central role in residual cardiovascular risk.
OGDA: a comprehensive organelle genome database for algae
Authors: Liu Tao , Cui Yutong , Jia Xuli , Zhang Jing , Li Ruoran , Yu Yahui , Jia Shangang , Qu Jiangyong , Wang Xumin
Published: November 2020

Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.
Quantitative levels of serumN-glycans in type 1 diabetes and their association with kidney disease
Authors: Colombo Marco , Asadi Shehni Akram , Thoma Ioanna , McGurnaghan Stuart J , Blackbourn Luke A K , Wilkinson Hayden , Collier Andrew , Patrick Alan W , Petrie John R , McKeigue Paul M , Saldova Radka , Colhoun Helen M ,   the Scottish Diabetes Research Network (SDRN) Type 1 Bioresource Investigators
Published: November 2020

We investigated associations of quantitative levels of N-glycans with hemoglobin A1c (HbA1c), renal function and renal function decline in type 1 diabetes. We measured 46 total N-glycan peaks (GPs) on 1565 serum samples from the Scottish Diabetes Research Network Type 1 Bioresource Study (SDRNT1BIO) and a pool of healthy donors. Quantitation of absolute abundance of each GP used 2AB-labeled mannose-3 as a standard. We studied cross-sectional associations of GPs and derived measures with HbA1c, albumin/creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR), and prospective associations with incident albuminuria and final eGFR.

All GPs were 1.4 to 3.2 times more abundant in SDRTN1BIO than in the healthy samples. Absolute levels of all GPs were slightly higher with higher HbA1c, with strongest associations for triantennary trigalactosylated disialylated, triantennary trigalactosylated trisialylated structures with core or outer arm fucose, and tetraantennary tetragalactosylated trisialylated glycans. Most GPs showed increased abundance with worsening ACR. Lower eGFR was associated with higher absolute GP levels, most significantly with biantennary digalactosylated disialylated glycans with and without bisect, triantennary trigalactosylated trisialylated glycans with and without outer arm fucose, and core fucosylated biantennary monogalactosylated monosialylated glycans. Although several GPs were inversely associated prospectively with final eGFR, cross-validated multivariable models did not improve prediction beyond clinical covariates.

Elevated HbA1c is associated with an altered N-glycan profile in type 1 diabetes. Although we could not establish GPs to be prognostic of future renal function decline independently of HbA1c, further studies to evaluate their impact in the pathogenesis of diabetic kidney disease are warranted.
Genealogy from a distance: the media of correspondence and the Mormon church, 1910–45*
Authors: Hjorthén Adam
Published: November 2020

This article adopts a media historical approach to studying the modern history of genealogy, suggesting an alternative to both the dominant methodologies and periodization of the field. Empirically, it focuses on the ways in which correspondence was adopted as a tool for long-distance research by the Church of Jesus Christ of Latter-day Saints in 1910–45, examining in particular its research networks in Sweden. The article demonstrates that letter-writing was a research method dependent on record accessibility and interpersonal reliability. It also had the benefit of becoming its own resource, sustaining its relevance into the twenty-first century.
A metabarcoding comparison of taxonomic richness and composition between the water column and the benthic boundary layer
Authors: Parry H E , Atkinson A , Somerfield P J , Lindeque P K
Published: November 2020

Zooplankton monitoring in shelf seas predominantly uses nets that miss the benthic boundary layer (BBL) just above the seabed. However, this boundary between pelagic and benthic assemblages can be faunistically rich, having its own distinct hyperbenthic fauna and acting as a low-light refuge for overwintering or dielly migrating zooplankton. To compare species richness and composition between pelagic and BBL habitats, we sampled a long-term monitoring site in the Western English Channel seasonally. Metabarcoding methods applied to vertical net samples (top 50 m in a ∼54-m water column) and those from a hyperbenthic sledge generated >100 000 sequences clustered into 294 operational taxonomic units. Of these, 215 were found in the BBL and 170 in the water column. Some key taxa (e.g. mysids) were native to the BBL; by contrast, other delicate taxa (e.g. ctenophores) seemed to avoid the BBL. The major contrasts in plankton composition related to the seasonal cycle rather than to pelagic-BBL differences, suggesting that the basic dynamics of the site are captured by our ongoing long-term weekly resolution monitoring. Overall, metabarcoding approaches, applied to both water column and BBL, provide an independent view of plankton dynamics, and augment existing traditional methods.
Recognition of ecosystem-based management principles in key documents of the seabed mining regime: implications and further recommendations
Authors: Guilhon Maila , Montserrat Francesc , Turra Alexander
Published: November 2020

New human uses on the marine environment, such as deep-sea mining (DSM), have necessitated the adoption of more holistic approaches such as ecosystem-based management (EBM) to secure sustainable development. The United Nations Convention on the Law of the Sea (UNCLOS) and the rules, regulations, and procedures adopted by the International Seabed Authority (ISA) represent the main regulatory framework to govern DSM activities. This study aimed to examine whether UNCLOS and ISA documents include references to EBM principles, and if these references vary in documents through time. Following a literature review, 26 EBM principles were collated into 8 general categories, and their adherence to 5 key documents related to the DSM regime was analysed. Results demonstrated a trend in recognizing EBM principles in documents over time, especially in the Draft Regulations for Exploitation. However, the mere recognition of EBM principles in the regulatory framework does not guarantee that the approach will be clearly understood and appropriately incorporated by contractors throughout the process. For such, further clarification on the meaning of the Ecosystem Approach in the DSM context and building the capacity of the ISA Legal and Technical Commission are among the recommendations presented by this study.
The global burden of chronic hepatitis B virus infection: comparison of country-level prevalence estimates from four research groups
Authors: Schmit Nora , Nayagam Shevanthi , Thursz Mark R , Hallett Timothy B
Published: November 2020

Background

Progress towards viral hepatitis elimination goals relies on accurate estimates of chronic hepatitis B virus (HBV)-infection prevalence. We compared existing sources of country-level estimates from 2013 to 2017 to investigate the extent and underlying drivers of differences between them.

Methods

The four commonly cited sources of global-prevalence estimates, i.e. the Institute for Health Metrics and Evaluation, Schweitzer et al., the World Health Organization (WHO) and the CDA Foundation, were compared by calculating pairwise differences between sets of estimates and assessing their within-country variation. Differences in underlying empirical data and modelling methods were investigated as contributors to differences in sub-Saharan African estimates.

Results

The four sets of estimates across all ages were comparable overall and agreed on the global distribution of HBV burden. The WHO and the CDA produced the most similar estimates, differing by a median of 0.8 percentage points. Larger discrepancies were seen in estimates of prevalence in children under 5 years of age and in sub-Saharan African countries, where the median pairwise differences were 2.7 percentage and 2.4 percentage points for all-age prevalence and in children, respectively. Recency and representativeness of included data, and different modelling assumptions of the age distribution of HBV burden, seemed to contribute to these differences.

Conclusion

Current prevalence estimates, particularly those from the WHO and the CDA based on more recent empirical data, provide a useful resource to assess the population-level burden of chronic HBV-infection. However, further seroprevalence data in young children are needed particularly in sub-Saharan Africa. This is a priority, as monitoring progress towards elimination depends on improved knowledge of prevalence in this age group.
The Effect of IL-6 Inhibitors on Mortality Among Hospitalized COVID-19 Patients: A Multicenter Study
Authors: Sinha Pranay , Jafarzadeh S Reza , Assoumou Sabrina A , Bielick Catherine G , Carpenter Bethanne , Garg Shivani , Harleen Sahni , Neogi Tuhina , Nishio Midori Jane , Sagar Manish , Sharp Veronika , Kissin Eugene Y
Published: November 2020

Background

The effectiveness of interleukin-6 inhibitors (IL-6i) in ameliorating coronavirus disease 2019 (COVID-19) remains uncertain.

Methods

We analyzed data for patients aged ≥18 years admitted with a positive severe acute respiratory syndrome coronavirus 2 polymerase chain reaction test at 4 safety-net hospital systems with diverse populations and high rates of medical comorbidities in 3 US regions. We used inverse probability of treatment weighting via machine learning for confounding adjustment by demographics, comorbidities, and disease severity markers. We estimated the average treatment effect, the odds of IL-6i effect on in-hospital mortality from COVID-19, using a logistic marginal structural model.

Results

Of 516 patients, 104 (20.1%) received IL-6i. Estimate of the average treatment effect adjusted for confounders suggested a 37% reduction in odds of in-hospital mortality in those who received IL-6i compared with those who did not, although the confidence interval included the null value of 1 (odds ratio = 0.63; 95% confidence interval, .29–1.38). A sensitivity analysis suggested that potential unmeasured confounding would require a minimum odds ratio of 2.55 to nullify our estimated IL-6i effect size.

Conclusions

Despite low precision, our findings suggested a relatively large effect size of IL-6i in reducing the odds of COVID-19–related in-hospital mortality.
The role of antimicrobial stewardship in preventing KPC-producing Klebsiella pneumoniae
Authors: Carrara Elena , Conti Michela , Meschiari Marianna , Mussini Cristina
Published: November 2020

Antimicrobial stewardship programmes are widely considered to be a core component of the response to the antimicrobial resistance threat. However, a positive impact of these interventions in terms of microbiological outcomes remains difficult to demonstrate, especially when focusing on specific resistant phenotypes. The first part of this review aims to explore the complex relationship between antibiotic exposure and resistance development in KPC-producing Klebsiella pneumoniae. In the second part we aim to summarize published examples of antimicrobial stewardship interventions intended to impact on the epidemiology of KPC-producing K. pneumoniae. For this purpose, a literature search was performed and seven studies were included in the review. Both restrictive and non-restrictive interventions were associated with an overall reduction in antibiotic consumption, and a decrease in carbapenem resistance rates was observed in five studies. The overall quality of the evidence was low, mainly due to the poor reporting of microbiological outcomes, lack of a control group and suboptimal study design. Although the link between antibiotic use and resistance development is supported by strong evidence, demonstrating the impact of antimicrobial stewardship interventions on microbiological outcomes remains difficult. Studies with adequate design and appropriate outcome measures are needed to further promote antimicrobial stewardship and elucidate which interventions are more successful for controlling the spread of KPC-producing K. pneumoniae.
Application of Bayesian networks to generate synthetic health data
Authors: Kaur Dhamanpreet , Sobiesk Matthew , Patil Shubham , Liu Jin , Bhagat Puran , Gupta Amar , Markuzon Natasha
Published: November 2020

Objective

This study seeks to develop a fully automated method of generating synthetic data from a real dataset that could be employed by medical organizations to distribute health data to researchers, reducing the need for access to real data. We hypothesize the application of Bayesian networks will improve upon the predominant existing method, medBGAN, in handling the complexity and dimensionality of healthcare data.

Materials and Methods

We employed Bayesian networks to learn probabilistic graphical structures and simulated synthetic patient records from the learned structure. We used the University of California Irvine (UCI) heart disease and diabetes datasets as well as the MIMIC-III diagnoses database. We evaluated our method through statistical tests, machine learning tasks, preservation of rare events, disclosure risk, and the ability of a machine learning classifier to discriminate between the real and synthetic data.

Results

Our Bayesian network model outperformed or equaled medBGAN in all key metrics. Notable improvement was achieved in capturing rare variables and preserving association rules.

Discussion

Bayesian networks generated data sufficiently similar to the original data with minimal risk of disclosure, while offering additional transparency, computational efficiency, and capacity to handle more data types in comparison to existing methods. We hope this method will allow healthcare organizations to efficiently disseminate synthetic health data to researchers, enabling them to generate hypotheses and develop analytical tools.

Conclusion

We conclude the application of Bayesian networks is a promising option for generating realistic synthetic health data that preserves the features of the original data without compromising data privacy.
Effects of birth weight and dietary fat on intake, body composition, and plasma thyroxine in neonatal lambs
Authors: Ramos-Nieves Jose M , Giesy Sarah L , McGuckin Molly M , Boisclair Yves R
Published: November 2020

Intrauterine growth restriction (IUGR) is often observed in one of the fetuses carried by well-fed prolific ewes. This condition is the result of an insufficient placental size to cover the nutritional needs of the fetus during the near exponential growth phase of the last trimester. After birth, these IUGR offspring have an elevated appetite and lower maintenance energy requirements, suggesting dysregulation of homeostatic systems governing energy metabolism. It is also unknown whether the consequent increase in fatness occurs similarly in both visceral and carcass fractions. To address these questions, lambs differing in birth size (BS, IUGR vs. Normal, 2.6 ± 0.05 vs. 4.2 ± 0.07 kg, P < 0.001) were offered unlimited amounts of a low fat [LF; 22% of dry matter (DM)] or a high fat (HF; 38% of DM) milk replacer and slaughtered on day 14 of postnatal age (n = 7 to 8 for each BS × Diet); a second group of IUGR lambs (n = 3 for each diet) was slaughtered when they reached 8.5 kg, corresponding to the weight of Normal lambs on day 14. When normalized to body weight (BW), the DM and energy intake of IUGR lambs were higher than those of Normal lambs over the first 14 d of life (BS, P < 0.01), but contrary to expectations, the HF diet did not exacerbate these effects of the IUGR condition. Intrauterine growth restricted lambs had increased viscera fat with both diets (BS and Diet, P < 0.05) but increased carcass fat only with the LF diet (BS × Diet, P = 0.08); the fatness promoting effect of the IUGR condition was increased in both body fractions when lamb groups were compared at the fixed BW of 8.5 kg. A subset of metabolic hormones was analyzed, including the metabolic rate-setting hormone thyroxine (T4) and its possible positive regulator leptin. Plasma T4 was lower in IUGR than in Normal lambs at birth (P < 0.05) but then disappeared by day 7 of postnatal life (BS × Day, P < 0.01). On the other hand, the HF diet had no effect on plasma T4 over the first 3 d but caused an increase, irrespective of BS by day 11 (Diet × Day, P < 0.001). Plasma leptin increased with dietary fat and time (P < 0.06) but bore no relation to the effects of BS or Diet on plasma T4. These data show that IUGR and Normal lambs are similarly unable to adjust caloric intake in early life and that the fatness promoting effects of the IUGR condition are more pronounced in the viscera than in the carcass. These data also reveal dynamic regulation of plasma T4 by BS and Diet in neonatal lambs.
Primary capicua transcriptional repressor-rearranged sarcoma of the lung
Authors: Mizukami Yasushi , Takahashi Yuki , Sugita Shintaro , Wakabayashi Kento , Suzuki Hiroaki , Hasegawa Tadashi , Noguchi Hiroko , Adachi Hirofumi
Published: November 2020

A 60-year-old man had a malignant left lower lung tumour with no metastases and underwent video-assisted thoracoscopic left lower lobectomy and lymphadenectomy. Pathological examination led to a diagnosis of capicua transcriptional repressor (CIC)-rearranged sarcoma. He has had 3.5 years of recurrence-free survival. CIC-rearranged sarcoma is a Ewing-like sarcoma that shows pathological findings similar to Ewing sarcoma. Most of CIC-rearranged sarcoma is CIC-double homeobox 4 protein (DUX4) fusion. Pulmonary CIC-rearranged sarcoma is extremely rare and has an unfavourable prognosis. However, complete resection can produce prognosis of long-term survival, and thus, surgery is an important option.
Civil Dissent and Repression: An Agency-Centric Perspective
Authors: Koren Ore , Mukherjee Bumba
Published: November 2020

Do governments make a strategic choice in deciding what type of security agent to use for repression? Research acknowledges the role of auxiliary groups such as militias in repression, yet surprisingly little attention is given to the state's formal domestic security agents, such as the police. We show that formal security organizations and auxiliary groups enhance the government's ability to repress by acting as strategic complements. As the better-regulated force, formal agents are often employed against violent riots, when regimes worry more about the ability to control the agents and their behavior more than about being visibly linked to the violence. In contrast, auxiliaries are often used to repress nonviolent campaigns, when the government seeks to benefit from agency loss in order not to be associated with the violence, which can be costly in these contexts. We empirically verify these linkages on country-month data for Africa using panel vector-autoregression (pVAR), which accounts for endogeneity, not only between the dependent and independent variables, but also the dependent variables. We complement these statistical results with case-based evidence and descriptive original data from non-African countries.
Risk trade-off analysis of returning home and radiation exposure after a nuclear disaster using a happy life expectancy indicator
Authors: Murakami Michio , Takebayashi Yoshitake , Ono Kyoko , Tsubokura Masaharu
Published: November 2020

It is crucial to evaluate ethical issues regarding evacuation orders, especially after a nuclear disaster. After the Fukushima accident in 2011, the Japanese government ordered the affected people to evacuate. The evacuation orders have now been lifted in many areas. A risk trade-off analysis between benefits and risk associated with returning home would help in evaluating the justification for the lifting of the evacuation order in the aftermath of a nuclear disaster. Here, we performed a risk trade-off analysis among people returning home after the lifting of an evacuation order between an increase in emotional happiness (positive effect) and loss of life expectancy due to additional radiation exposure (negative effect), using a happy life expectancy (HpLE) indicator. Emotional happiness was estimated using questionnaires distributed among the affected people who lived in municipalities where evacuation orders were lifted. Loss of life expectancy was estimated under a scenario that returnees received 20 mSv in the year of return and subsequent radiation exposure. Increase in emotional happiness due to returning home was ~1–2 orders of magnitude higher among women aged 20, 40 and 65 years than the loss of life expectancy due to additional radiation exposure. This finding has implications for the justification for the lifting of evacuation orders.
Epidemiology of imported infectious diseases, China, 2014–18
Authors: Wu Yang , Liu Meng-Yang , Wang Jin-Long , Zhang Hai-Yang , Sun Yu , Yuan Yang , Zhou Shi-Xia , Wang Yi-Xing , Wang Zhi-Bo , Zhu Ying-Xuan , Han Yong , Liu Meng-Meng , Li Wei-Ming , Wang Li-Ping , Guo Xiu-Hua , Fang Li-Qun , Liu Wei
Published: November 2020

Background

The frequent movement of population between countries brings an increasing number of travel-related infections. This study aims to define the spectrum and dynamics of imported infections observed from international travel in the Chinese mainland.

Methods

Sick travellers were screened by inbound sentinel surveillance and post-travel clinic visits from 2014 to 18. The infections were classified as respiratory, gastrointestinal, vector-borne, blood/sexually transmitted and mucocutaneous. The analysed variables included the place of origin of the travellers (Chinese or foreign) and the time when travel-related infection was present (at the time of return, during travel and post-travel visits to the clinic).

Results

In total, 58 677 cases were identified amongst 1 409 265 253 travellers, with an incidence of 41.64/million, comprising during-travel incidence of 27.44/million and a post-travel incidence of 14.20/million. Respiratory infections constituted the highest proportion of illnesses during travel (81.19%, 31 393 of 38 667), which mainly came from Asian countries and tourists; with influenza virus and rhinovirus infections being mainly diagnosed. Vector-borne diseases constituted the highest proportion of post-travel illnesses (98.14%, 19 638 of 20 010), which were mainly diagnosed from African countries and labourers; with malaria and dengue fever being mainly diagnosed. The differential infection spectrum varied in terms of the traveller’s demography, travel destination and travel purpose. As such, a higher proportion of foreign travellers had blood/sexually transmitted diseases (89.85%, 2832 of 3152), while Chinese citizens had a higher prevalence of vector-borne diseases (85.98%, 19 247 of 22 387) and gastrointestinal diseases (79.36%, 1115 of 1405). The highest incidence rate was observed amongst travellers arriving from Africa, while the lowest was observed amongst travellers arriving from Europe.

Conclusions

The findings might help in preparing recommendations for travellers and also aid in primary care or other clinics that prepare travellers before trips abroad. The findings will also help to identify locations and the associated types of infections that might require attention.
Machine Learning Prediction of SARS-CoV-2 Polymerase Chain Reaction Results with Routine Blood Tests
Authors: Tschoellitsch Thomas , Dünser Martin , Böck Carl , Schwarzbauer Karin , Meier Jens
Published: November 2020

Objective

The diagnosis of COVID-19 is based on the detection of SARS-CoV-2 in respiratory secretions, blood, or stool. Currently, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to test for SARS-CoV-2.

Methods

In this retrospective cohort analysis, we evaluated whether machine learning could exclude SARS-CoV-2 infection using routinely available laboratory values. A Random Forests algorithm with 28 unique features was trained to predict the RT-PCR results.

Results

Out of 12,848 patients undergoing SARS-CoV-2 testing, routine blood tests were simultaneously performed in 1357 patients. The machine learning model could predict SARS-CoV-2 test results with an accuracy of 86% and an area under the receiver operating characteristic curve of 0.74.

Conclusion

Machine learning methods can reliably predict a negative SARS-CoV-2 RT-PCR test result using standard blood tests.
Accelerating computation of the density-field filtering scale σ(R) and non-linear mass by an order of magnitude
Authors: Krolewski Alex , Slepian Zachary
Published: November 2020

The non-linear mass is a characteristic scale in halo formation that has many applications across cosmology. Naively, computing it requires repeated numerical integration to calculate the variance of the power spectrum on different scales and determine which scales exceed the threshold for non-linear collapse. We accelerate calculation of both the non-linear mass and the rms amplitude of the power spectrum σ(R) by working in configuration space and approximating the correlation function as a polynomial at r ≤ 5 h−1 Mpc. This enables an analytic rather than numerical solution for the non-linear mass, accurate across a variety of cosmologies to 0.1–$1{{\ \rm per\ cent}}$ in mass (depending on redshift) and 20–60× faster than the standard numerical method. We also present a further acceleration of the non-linear mass (400–1000× faster than the standard method) in which we determine the polynomial coefficients using a Taylor expansion in the cosmological parameters rather than re-fitting a polynomial to the correlation function. Our method is also 500× faster than the standard method for σ(R) for a typical case of NR = 100 desired R values, with timing essentially independent of NR. Our approach can be used for quick calculation of the halo mass function, halo mass–bias relation, and cosmological calculations involving the non-linear mass.
The Human Phenotype Ontology in 2021
Authors: Köhler Sebastian , Gargano Michael , Matentzoglu Nicolas , Carmody Leigh C , Lewis-Smith David , Vasilevsky Nicole A , Danis Daniel , Balagura Ganna , Baynam Gareth , Brower Amy M , Callahan Tiffany J , Chute Christopher G , Est Johanna L , Galer Peter D , Ganesan Shiva , Griese Matthias , Haimel Matthias , Pazmandi Julia , Hanauer Marc , Harris Nomi L , Hartnett Michael J , Hastreiter Maximilian , Hauck Fabian , He Yongqun , Jeske Tim , Kearney Hugh , Kindle Gerhard , Klein Christoph , Knoflach Katrin , Krause Roland , Lagorce David , McMurry Julie A , Miller Jillian A , Munoz-Torres Monica C , Peters Rebecca L , Rapp Christina K , Rath Ana M , Rind Shahmir A , Rosenberg Avi Z , Segal Michael M , Seidel Markus G , Smedley Damian , Talmy Tomer , Thomas Yarlalu , Wiafe Samuel A , Xian Julie , Yüksel Zafer , Helbig Ingo , Mungall Christopher J , Haendel Melissa A , Robinson Peter N
Published: November 2020

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.
Demographic change and regional labour markets
Authors: Böhm Michael J , Gregory Terry , Qendrai Pamela , Siegel Christian
Published: November 2020

Like many other countries, Germany has experienced rapid population and workforce ageing, yet with substantial variation across regions. In this paper we first use this spatial variation between 1975 and 2014 to estimate quasi-causal supply effects of ageing on regional labour market outcomes, drawing on the identification strategy of Böhm and Siegel (2020). We find in our panel of German labour market regions that workforce mean age has considerable negative effects on the wage returns to age. We also obtain suggestive evidence that relative employment rates of older workers decline when mean age rises. A decomposition of the heterogeneous regional trends using our estimates shows that ageing of rural regions is mainly driven by supply (reflecting local population dynamics) whereas urban ageing is driven by demand (reflecting responses to economic conditions). We discuss the differential implications of these drivers for regional policy.
Role of placental inflammatory mediators and growth factors in patients with rheumatic diseases with a focus on systemic sclerosis
Authors: Motta Francesca , Codullo Veronica , Ramoni Véronique , Cesari Stefania , Ferrario Giuseppina , Fiandrino Giacomo , Beneventi Fausta , Rampello Stefania , Johnsson Hanna , Montecucco Carlomaurizio , Graham Gerard J
Published: November 2020

Objectives

Pregnancy in SSc is burdened with an increased risk of obstetric complications. Little is known about the underlying placental alterations. This study aimed to better understand pathological changes and the role of inflammation in SSc placentas. Leucocyte infiltration, inflammatory mediators and atypical chemokine receptor 2 (ACKR2) expression in SSc placentas were compared with those in other rheumatic diseases (ORD) and healthy controls (HC).

Methods

A case–control study was conducted on eight pregnant SSc patients compared with 16 patients with ORD and 16 HC matched for gestational age. Clinical data were collected. Placentas were obtained for histopathological analysis and immunohistochemistry (CD3, CD20, CD11c, CD68, ACKR2). Samples from four SSc, eight ORD and eight HC were analysed by qPCR for ACKR2 expression and by multiplex assay for cytokines, chemokines and growth factors involved in angiogenesis and inflammation.

Results

The number of placental CD3, CD68 and CD11 cells was significantly higher in patients affected by rheumatic diseases (SSc+ORD) compared with HC. Hepatocyte growth factor was significantly increased in the group of rheumatic diseases patients (SSc+ORD) compared with HC, while chemokine (C-C motif) ligand 5 (CCL5) was significantly higher in SSc patients compared with ORD and HC. CCL5 levels directly correlated with the number of all local inflammatory cells and higher levels were associated with histological villitis.

Conclusions

Inflammatory alterations characterize placentas from rheumatic disease patients and could predispose to obstetric complications in these subjects.
Revisiting Schizophrenia from an Evolutionary Perspective: An Association Study of Recent Evolutionary Markers and Schizophrenia
Authors: Bhattacharyya Upasana , Deshpande Smita N , Bhatia Triptish , Thelma B K
Published: November 2020

The persistence of schizophrenia in human populations at a high prevalence and with a large heritability estimate despite reduced fertility and increased mortality rate is a Darwinian paradox. This may be likely if the genomic components that predispose to schizophrenia are also advantageous for the acquisition of important human traits, such as language and cognition. Accordingly, an emerging group of genomic markers of recent evolution in humans, namely human accelerated regions (HARs), since our divergence from chimpanzees, are gaining importance for neurodevelopmental disorders, such as schizophrenia. We hypothesize that variants within HARs may affect the expression of genes under their control, thus contributing to disease etiology. A total of 49 HAR single nucleotide polymorphisms (SNPs) were prioritized from the complete repertoire of HARs (n = 2737) based on their functional relevance and prevalence in the South Asian population. Test of association using 2 independent schizophrenia case-control cohorts of north Indian ethnicity (discovery: n = 930; replication: n = 1104) revealed 3 SNPs (rs3800926, rs3801844, and rs764453) from chromosome 7 and rs77047799 from chromosome 3 to be significantly associated (combined analysis: Bonferroni corrected P < .002–.000004). Of note, these SNPs were found to alter the expression of neurodevelopmental genes such as SLC25A13, MAD1L1, and ULK4; a few from the HOX gene family; and a few genes that are implicated in mitochondrial function. These SNPs may most likely alter binding sites of transcription factors, including TFCP2, MAFK, SREBF2, E2F1, and/or methylation signatures around these genes. These findings reiterate a neurodevelopmental basis of schizophrenia and also open up a promising avenue to investigate HAR-mediated mitochondrial dysfunction in schizophrenia etiology.
Public Service Reform in Post-Conflict Societies
Authors: Blum Jurgen Rene , Rogger Daniel
Published: November 2020

Building a capable public service is a key component of post-conflict state building. An effective public service is fundamental to the regulation of society, to managing public funds, and to service delivery. Yet in post-conflict environments, there is typically a tradeoff between the long-term objective of state building and securing the peace in the short term. To buy peace, political elites hand out public jobs and resources to constituents regardless of merit. Donors frequently rely on “parallel” project delivery structures rather than public servants to address citizens’ pressing service delivery needs. Both of these practices may achieve short-term objectives but undermine state building. In the face of these trade-offs, how can capable public services be built in post-conflict societies? This paper aims to summarize the evidence base regarding this question. It does so by reviewing the evidence from post-conflict settings, and by discussing the validity of findings on public service reform from non-conflict settings. Given the distinctive tradeoffs invoked by securing the peace, and limited prior research on post-conflict settings, this topic presents a wide-open research agenda.
Darwin’s closet: the queer sides of The descent of man (1871)
Authors: Brooks Ross
Published: November 2020

Charles Darwin’s published and unpublished writings contain a plethora of references to sex variations, including intersexualities (‘hermaphroditism’), transformations of sex and non-heteronormative sexual behaviours. Marking the 150th anniversary of his major sexological work The descent of man, this historical review examines a range of strategies that Darwin deployed in order to accommodate such variations within his evolutionism, while simultaneously attempting to mitigate the potential for condoning sexual phenomena that were feared and reviled in Victorian bourgeois society. Although he moved to cast sex-variant animals, human and non-human, as biological misfits and failures, Darwin’s commitment to the principle of primordial intersexuality (dual-sexed origins) nonetheless occasioned some of the queerest evolutionary narratives of the 19th century. Similarly, his construal of the ‘unnatural crimes’ of indigenous peoples was contained within a hierarchical narrative of the backwardness of ‘savages’ and civilizational supremacy but was readily subject to challenge and queer reinterpretations, not least with reference to the ‘extreme sensuality’ of the classical Greeks. Despite working to subdue the queer potentialities of his evolutionism, Darwin nonetheless laid the foundations for a new, modernist sexology to emerge, a situation that was exploited by a cohort of Darwinist sexologists, Sigmund Freud chief among them, who followed in his path.