bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive Manufacturing: Subtractive and Additive
Authors: Liang Steven Y. , Feng Yixuan , Ning Jinqiang
Published: June 2020

Manufacturing is the key to today’s industrial competitiveness, and it is broadly classified into two categories, subtractive and additive. In current study, the ability to predictively model manufacturing performance attributes in both categories is introduced. In subtractive manufacturing, modeling of laser-assisted and ultrasonic vibration-assisted milling are presented. In laser-assisted milling, the laser preheating temperature field is predicted, and the dynamic recrystallization as well as grain growth triggered under high temperature is considered, which enhances the accuracy of force and residual stress prediction. In ultrasonic vibration-assisted milling, the intermittent effect is considered through tool-workpiece separation criteria. And the force reduction in ultrasonic vibration-assisted milling is accurately predicted. In additive manufacturing, laser-assisted metal additive manufacturing is introduced. And the predictive modeling of temperature field in powder bed metal additive manufacturing is presented. The model considers heat transfer boundary including heat loss from convection and radiation at the part boundary. Through the comparison between measured and calculated molten pool dimensions, the model is proven to have high computational efficiency and high prediction accuracy.
Tree decompositions of real-world networks from simulated annealing
Authors: Klemm Konstantin
Published: June 2020

Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network. Tree and branch decompositions considered here directly represent network structure as trees for recursive computation of network properties. Unlike coarse-graining approximations in terms of community structure or metapopulations, tree decompositions of sufficiently small width allow for exact results on equilibrium processes. Here we use simulated annealing to find tree decompositions of narrow width for a set of medium-size empirical networks. Rather than optimizing tree decompositions directly, we employ a search space constituted by so-called elimination orders being permutations on the network’s node set. For each in a database of empirical networks with up to 1000 edges, we find a tree decomposition of low width.
Frailty among middle-aged and older Canadians: population norms for the frailty index using the Canadian Longitudinal Study on Aging
Authors: Pérez-Zepeda Mario Ulises , Godin Judith , Armstrong Joshua J , Andrew Melissa K , Mitnitski Arnold , Kirkland Susan , Rockwood Kenneth , Theou Olga
Published: June 2020

Background

frailty is a public health priority now that the global population is ageing at a rapid rate. A scientifically sound tool to measure frailty and generate population-based reference values is a starting point.

Objective

in this report, our objectives were to operationalize frailty as deficit accumulation using a standard frailty index (FI), describe levels of frailty in Canadians ≥45 years old and provide national normative data.

Design

this is a secondary analysis of the Canadian Longitudinal Study on Aging (CLSA) baseline data.

Setting/participants

about 51,338 individuals (weighted to represent 13,232,651 Canadians), aged 45–85 years, from the tracking and comprehensive cohorts of CLSA.

Methods

after screening all available variables in the pooled dataset, 52 items were selected to construct an FI. Descriptive statistics for the FI and normative data derived from quantile regressions were developed.

Results

the average age of the participants was 60.3 years (95% confidence interval [CI]: 60.2–60.5), and 51.5% were female (95% CI: 50.8–52.2). The mean FI score was 0.07 (95% CI: 0.07–0.08) with a standard deviation of 0.06. Frailty was higher among females and with increasing age, and scores >0.2 were present in 4.2% of the sample. National normative data were identified for each year of age for males and females.

Conclusions

the standardized frailty tool and the population-based normative frailty values can help inform discussions about frailty, setting a new bar in the field. Such information can be used by clinicians, researchers, stakeholders and the general public to understand frailty, especially its relationship with age and sex.
Epidemiology of COVID-19 in older persons, Wuhan, China
Authors: Guo Yan , Liu Xinghua , Deng Mengyao , Liu Pulin , Li Fang , Xie Nianhua , Pang Yanhui , Zhang Xiaoxia , Luo Wen , Peng Ying , Yan Yaqiong , Li Gang , Yang Mei
Published: June 2020

Background

the epidemiological characteristics of older patients with COVID-19 was far from clear.

Objective

to explore the epidemiology of older patients with COVID-19 in Wuhan, China.

Design

a retrospective cross-sectional study.

Setting

a population-based study.

Subjects

the resident older patients (>65 years) diagnosed with COVID-19.

Methods

city-wide case series reported to Wuhan Center for Disease Control and Prevention from 12 December 2019 to 17 March 2020 were included. The epidemic curves were constructed by dates of disease onset.

Results

14,238 confirmed COVID-19 cases were older persons. The number of male cases were slightly less than female cases (1:1.01). The attack rate of COVID-19 in the older persons was 11.49‰ in Wuhan. There was a rapid increase of disease at the early stage of the epidemic and then a gradual and steady decrease was performed. 3,723 (26.15%) and 734 (5.16%) patients were diagnosed as severe and critical cases, respectively. The attributable crude fatality ratio of COVID-19 in the older population was 222.57/100,000, and the crude fatality ratio of COVID was 19.37%. The proportion of severe and critical cases, and fatality ratio were both higher in downtown area and increased with age.

Conclusions

the older persons are sensitive to COVID-19. The proportion of severe and critical cases and fatality ratio are higher than that in children and younger adults. Strengthen the protection and control strategies for the older adults are of priorities. More detailed epidemiological and clinical information should be measured in further studies.
Social context and noise affect within and between male song adjustments in a common passerine
Authors: Grabarczyk Erin E , Vonhof Maarten J , Gill Sharon A
Published: June 2020

Across populations, animals that inhabit areas with high anthropogenic noise produce vocalizations that differ from those inhabiting less noisy environments. Such patterns may be due to individuals rapidly adjusting their songs in response to changing noise, but individual variation is seldom explored. Therefore, we tested the hypothesis that male house wrens (Troglodytes aedon) immediately adjust their songs according to changing noise and that social context further modifies responses. We recorded songs, quantified noise, and defined social context within pairs as female fertile status and between males as number of conspecific neighbors. We used a reaction-norm approach to compare song trait intercepts (between-male effects) and slopes (within-male effects) as a function of noise. Individuals immediately adjusted song duration in response to changing noise. How they achieved adjustments varied: some sang shorter and others longer songs with greater noise, and individuals varied in the extent to which they adjusted song duration. Variation in song duration could be affected by competition as between-male noise levels interacted with number of neighbors to affect syllable duration. Neither within- nor between-male noise effects were detected for frequency traits. Rather, males with fertile mates sang lower-frequency songs and increased peak frequency with more neighbors. Among males, social context but not noise affected song frequency, whereas temporal structure varied between and within individuals depending on noise and social factors. Not all males adjusted signals the same way in response to noise, and selection could favor different levels of variation according to noise.
Detecting and correcting misclassified sequences in the large-scale public databases
Authors: Bagheri Hamid , Severin Andrew J , Rajan Hridesh
Published: June 2020

Motivation

As the cost of sequencing decreases, the amount of data being deposited into public repositories is increasing rapidly. Public databases rely on the user to provide metadata for each submission that is prone to user error. Unfortunately, most public databases, such as non-redundant (NR), rely on user input and do not have methods for identifying errors in the provided metadata, leading to the potential for error propagation. Previous research on a small subset of the NR database analyzed misclassification based on sequence similarity. To the best of our knowledge, the amount of misclassification in the entire database has not been quantified. We propose a heuristic method to detect potentially misclassified taxonomic assignments in the NR database. We applied a curation technique and quality control to find the most probable taxonomic assignment. Our method incorporates provenance and frequency of each annotation from manually and computationally created databases and clustering information at 95% similarity.

Results

We found more than two million potentially taxonomically misclassified proteins in the NR database. Using simulated data, we show a high precision of 97% and a recall of 87% for detecting taxonomically misclassified proteins. The proposed approach and findings could also be applied to other databases.

Availability and implementation

Source code, dataset, documentation, Jupyter notebooks and Docker container are available at https://github.com/boalang/nr.

Supplementary information

Supplementary data are available at Bioinformatics online.
More Mind Games: How ‘The Action’ and ‘The Odds’ have Changed in Prison
Authors: Liebling Alison , Williams Ryan , Lieber Elinor
Published: June 2020

Surviving prison has always involved ‘action’ and game playing. Higher stakes—‘life-trashing sentences’, the fear and risk of radicalization, increased incidences of homicide and labyrinth routes out—have compounded the experience of struggle: to be heard, for dignity, against exposure to violent injustice, and for release; the wrestling of ‘the self’ against a bleak and unyielding bureaucracy. In this article, we revisit McDermott and King’s Mind Games: Where the Action is in Prison showing how long-term prisoners are exposed to unregulated, unfathomable forms of power and action, and how long-term imprisonment feels increasingly like being ‘abandoned by humanity.’
Lost in sound: auditory perceptual abilities in neurodegenerative diseases
Authors: Särkämö Teppo , Sihvonen Aleksi J
Published: June 2020

This scientific commentary refers to ‘Impairments of auditory scene analysis in posterior cortical atrophy’, by Hardy et al. (doi:10.1093/brain/awaa221).
Is China Playing by the Rules? — Assessing China’s Reservations to International Human Rights Treaties
Authors: Wu Jingjing
Published: June 2020

In this paper, I examine two substantive reservations China has made to international human rights treaties, namely China’s reservation to Article 8.1(a) of the International Covenant on Economic, Social and Cultural Rights (ICESCR) and Article 6 of the Convention on the Rights of the Child (CRC), as well as the arguments China adopted to support them in the constructive dialogue between China and the two treaty committees. By positioning China’s reservations and its supporting arguments against the current criteria on making reservations to international human rights treaties, I argue that these two reservations are permissible and the arguments that support them are in general justifiable, all things considered. In conclusion, I reflect on China’s relationship with international human rights treaty bodies through the lens of reservations.
The Disproportionate Impact of COVID-19 on Racial and Ethnic Minorities in the United States
Authors: Tai Don Bambino Geno , Shah Aditya , Doubeni Chyke A , Sia Irene G , Wieland Mark L
Published: June 2020

The coronavirus disease 2019 (COVID-19) pandemic has disproportionately affected racial and ethnic minority groups, with high rates of death in African American, Native American, and LatinX communities. Although the mechanisms of these disparities are being investigated, they can be conceived as arising from biomedical factors as well as social determinants of health. Minority groups are disproportionately affected by chronic medical conditions and lower access to healthcare that may portend worse COVID-19 outcomes. Furthermore, minority communities are more likely to experience living and working conditions that predispose them to worse outcomes. Underpinning these disparities are long-standing structural and societal factors that the COVID-19 pandemic has exposed. Clinicians can partner with patients and communities to reduce the short-term impact of COVID-19 disparities while advocating for structural change.
Superiority of a Novel Mp1p Antigen Detection Enzyme Immunoassay Compared to Standard BACTEC Blood Culture in the Diagnosis of Talaromycosis
Authors: Thu Nguyen T M , Chan Jasper F W , Ly Vo Trieu , Ngo Hoa T , Hien Ha T A , Lan Nguyen P H , Chau Nguyen V V , Cai Jian-Piao , Woo Patrick C Y , Day Jeremy N , van Doorn Rogier , Thwaites Guy , Perfect John , Yuen Kwok , Le Thuy
Published: June 2020

Background

Talaromycosis is an invasive mycosis endemic in Southeast Asia and causes substantial morbidity and mortality in individuals with advanced human immunodeficiency virus (HIV) disease. Current diagnosis relies on isolating Talaromyces marneffei in cultures, which takes up to 14 days and is detectable only during late-stage infection, leading to high mortality.

Methods

In this retrospective case-control study, we assessed the accuracy of a novel Mp1p antigen-detecting enzyme immunoassay (EIA) in stored plasma samples of 372 patients who had culture-proven talaromycosis from blood or sterile body fluids (reference standard) and 517 individuals without talaromycosis (338 healthy volunteers; 179 with other infections). All participants were recruited between 2011 and 2017 in Vietnam.

Results

Of cases and controls, 66.1% and 75.4%, respectively, were male; the median age was 33 and 37, respectively. All cases were HIV infected; median CD4 count was 10 cells/μL. At an optical density cutoff of 0.5, the specificity was 98.1% (95% CI, 96.3%–99.0%); the sensitivity was superior to blood culture (86.3% [95% CI, 82.3%–89.5%] vs 72.8% [95% CI, 68.0%–77.2%]) (P < .001, McNemar test). The time to diagnosis was 6 hours vs 6.6 ± 3.0 days for blood culture. Paired plasma and urine testing in the same patients (n = 269) significantly increased sensitivity compared to testing plasma alone or testing urine alone (P < .001 and P = .02, respectively, McNemar test).

Conclusions

The Mp1p EIA is highly specific and is superior in sensitivity and time to diagnosis compared to blood culture for the diagnosis of talaromycosis. Paired plasma and urine testing further increases sensitivity, introducing a new tool for rapid diagnosis, enabling early treatment and potentially reducing mortality.
Clinical Presentation and Outcomes of Pregnant Women With Coronavirus Disease 2019: A Systematic Review and Meta-analysis
Authors: Matar Reem , Alrahmani Layan , Monzer Nasser , Debiane Labib G , Berbari Elie , Fares Jawad , Fitzpatrick Fidelma , Murad Mohammad H
Published: June 2020

Background

Descriptions of coronavirus disease 2019 (COVID-19) have focused on the nonpregnant adult population. This study aims to describe the clinical characteristics and perinatal outcomes of COVID-19 in pregnancy.

Methods

We searched databases from December 2019 to 30 April 2020. Eligible studies reported clinical characteristics, radiological findings, and/or laboratory testing of pregnant women during infection. Data were pooled across studies using a random-effects model.

Results

Twenty-four studies (136 women) were included. The most common symptoms were fever (62.9%) and cough (36.8%). Laboratory findings included elevated C-reactive protein (57%) and lymphocytopenia (50%). Ground-glass opacity was the most common radiological finding (81.7%). Preterm birth rate was 37.7% and cesarean delivery rate was 76%. There was 1 maternal death. There were 2 fetal COVID-19 cases.

Conclusions

The clinical picture in pregnant women with COVID-19 did not differ from the nonpregnant population; however, the rate of preterm birth and cesarean delivery are considerably higher than international averages.
Thomas Carlyle and Stoicism
Authors: Jordan Alexander
Published: June 2020

Recent studies have pointed to the importance of Thomas Carlyle’s engagement with classical thought, especially Epicureanism and Cynicism. However, in these recent studies, Carlyle’s debts to Stoicism have received only passing attention. Previous scholars hardly considered the question at all, and those who did argued that Carlyle could never have accepted the passive withdrawal and indifference of the Stoics. By way of corrective, the current article offers a comprehensive account of Carlyle’s engagement with Stoicism, showing that he subscribed to an active interpretation of the latter that emphasized will, duty, and heroic action. Indeed, contemporaries were well aware of Carlyle’s debts to Stoicism, pointing out that his thought stood in stark contradiction to Christian doctrines of original sin. Thus, while Carlyle’s Stoicism was compatible with his hereditary Calvinism insofar as divine providence and duty were concerned, there was a significant contradiction regarding the question of sin. In this sense, Carlyle’s Stoicism made an important contribution to the ‘meliorist’ revolt against orthodox Christianity.
Complex relationships between physiological stress and endoparasite infections in natural populations
Authors: Romeo Claudia , Wauters Lucas A , Santicchia Francesca , Dantzer Ben , Palme Rupert , Martinoli Adriano , Ferrari Nicola
Published: June 2020

Short-term elevation of glucocorticoids (GCs) is one of the major physiological mechanisms by which vertebrates cope with challenging environmental or social factors (stressors). However, when exposure to stressors occurs repeatedly or over a prolonged period of time, animals may experience chronic elevation of GCs, which reduces the immune response efficiency and can lead to higher intensity of parasitic infection. Here, we used invasive gray squirrels Sciurus carolinensis introduced in Northern Italy and their 2 most prevalent gastrointestinal parasites, the nematode Strongyloides robustus and coccidia of the genus Eimeria, as a model to investigate relationships among macroparasite infection and concentrations of fecal glucocorticoid metabolites (FGMs), an integrated measure of circulating GCs. Our results revealed an association of FGMs with infection by St. robustus, but not with coccidia. Individuals with higher FGMs appear to be responsible for the greatest St. robustus egg shedding within gray squirrel populations, thus possibly acting as superspreaders. However, FGMs were negatively associated with adult St. robustus, suggesting that the abundance of adults of this nematode species does not induce elevation in FGMs, but is only affected by it through immune-mediated effects on its fecundity. Finally, the relationship between St. robustus (both eggs and adult parasites) and FGMs was not linear, suggesting that only high levels of physiological stress influence parasite infection. Our findings highlight that the direction and magnitude of the stress–infection relationship may depend not only on the specific host–parasite system, but also on the different life stages of the same parasite.
Limited time window for retinal gene therapy in a preclinical model of ciliopathy
Authors: Datta Poppy , Ruffcorn Avri , Seo Seongjin
Published: June 2020

Retinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to ‘optimally’ treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet–Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.
Renal pathology in a mouse model of severe Spinal Muscular Atrophy is associated with downregulation of Glial Cell-Line Derived Neurotrophic Factor (GDNF)
Authors: Allardyce Hazel , Kuhn Daniela , Hernandez-Gerez Elena , Hensel Niko , Huang Yu-Ting , Faller Kiterie , Gillingwater Thomas H , Quondamatteo Fabio , Claus Peter , Parson Simon H
Published: June 2020

Spinal muscular atrophy (SMA) occurs as a result of cell-ubiquitous depletion of the essential survival motor neuron (SMN) protein. Characteristic disease pathology is driven by a particular vulnerability of the ventral motor neurons of the spinal cord to decreased SMN. Perhaps not surprisingly, many other organ systems are also impacted by SMN depletion. The normal kidney expresses very high levels of SMN protein, equivalent to those found in the nervous system and liver, and levels are dramatically lowered by ~90–95% in mouse models of SMA. Taken together, these data suggest that renal pathology may be present in SMA. We have addressed this using an established mouse model of severe SMA. Nephron number, as assessed by gold standard stereological techniques, was significantly reduced. In addition, morphological assessment showed decreased renal vasculature, particularly of the glomerular capillary knot, dysregulation of nephrin and collagen IV, and ultrastructural changes in the trilaminar filtration layers of the nephron. To explore the molecular drivers underpinning this process, we correlated these findings with quantitative PCR measurements and protein analyses of glial cell-line-derived neurotrophic factor, a crucial factor in ureteric bud branching and subsequent nephron development. Glial cell-line-derived neurotrophic factor levels were significantly reduced at early stages of disease in SMA mice. Collectively, these findings reveal significant renal pathology in a mouse model of severe SMA, further reinforcing the need to develop and administer systemic therapies for this neuromuscular disease.
Learning in foreign and domestic value chains: the role of opportunities and capabilities
Authors: Belderbos René , Grimpe Christoph
Published: June 2020

We suggest that the benefits of learning in international value chains for firms’ innovation performance are heterogeneous and depend on the specific source of learning (customers, suppliers, or competitors), whether these sources are based in countries that are technologically advanced or less advanced (learning opportunities), on technology leadership (learning capabilities) on the part of the focal firm, and on the simultaneous learning that occurs from domestic firms. Using direct survey evidence on learning and innovation by German firms, we confirm that technology leaders benefit from advanced foreign customer and supplier learning, that technology laggards benefit from less advanced foreign customer learning and advanced foreign competitor learning, and that both leaders and laggards benefit from domestic customer learning. The findings suggest a tradeoff between the opportunities to learn from foreign or domestic customers.
Misallocation of scientific credit: the role of hierarchy and preferences. An extension of Lissoniet al.(2013)
Authors: Lissoni Francesco , Montobbio Fabio , Zirulia Lorenzo
Published: June 2020

We extend the results in Lissoni et al. (2013, J. Econ. Behav. Organ., 95, 49–69) on scientific credit misallocation, as measured by misalignment between authorship and inventorship recognition in patent-publication pairs. Extending the analysis to European data, we confirm that, other things being equal, the probability of exclusion of a scientific author from a publication-related patent declines with seniority and increases for women. In addition, we find that the senior scientists’ power to exclude other authors plays a more important role in explaining the patterns of exclusion than differences in authors’ attribution preferences. The unfavorable treatment of young and/or female scientists emerges in particular when patents are owned by companies or individuals, thus providing a warning flag on those institutional arrangements that favor company or individual ownership of academic patents.
Reference-adjusted and standardized all-cause and crude probabilities as an alternative to net survival in population-based cancer studies
Authors: Lambert Paul C , Andersson Therese M-L , Rutherford Mark J , Myklebust Tor Åge , Møller Bjørn
Published: June 2020

Background

In population-based cancer survival studies, the most common measure to compare population groups is age-standardized marginal relative survival, which under assumptions can be interpreted as marginal net survival; the probability of surviving if it was not possible to die of causes other than the cancer under study (if the age distribution was that of a common reference population). The hypothetical nature of this definition has led to confusion and incorrect interpretation. For any measure to be fair in terms of comparing cancer survival, then differences between population groups should depend only on differences in excess mortality rates due to the cancer and not differences in other-cause mortality rates or differences in the age distribution.

Methods

We propose using crude probabilities of death and all-cause survival which incorporate reference expected mortality rates. This makes it possible to obtain marginal crude probabilities and all-cause probability of death that only differ between population groups due to excess mortality rate differences. Choices have to be made regarding what reference mortality rates to use and what age distribution to standardize to.

Results

We illustrate the method and some potential choices using data from England for men diagnosed with melanoma. Various marginal measures are presented and compared.

Conclusions

The new measures help enhance understanding of cancer survival and are a complement to the more commonly used measures.
Ethical Implementation of Immunity Passports During the COVID-19 Pandemic
Authors: Voo Teck Chuan , Clapham Hannah , Tam Clarence C
Published: June 2020

A number of countries are planning the use of “immunity passports” as a way to ease restrictive measures and allow infected and recovered people to return to work during the COVID-19 pandemic. This paper brings together key scientific uncertainties regarding the use of serological tests to assure immune status and a public health ethics perspective to inform key considerations in the ethical implementation of immunity passport policies. Ill-conceived policies have the potential to cause severe unintended harms that could result in greater inequity, the stigmatization of certain sectors of society, and heightened risks and unequal treatment of individuals due to erroneous test results. Immunity passports could, however, be used to achieve collective benefits and benefits for specific populations besides facilitating economic recovery. We conclude that sector-based policies that prioritize access to testing based on societal need are likely to be fairer and logistically more feasible, while minimizing stigma and reducing incentives for fraud. Clear guidelines need to be set out for which sectors of society should be prioritized for testing, and rigorous mechanisms should be in place to validate test results and identify cases of reinfection.
Ethnic and Gender Hierarchies in the Crucible of War
Authors: Webster Kaitlyn , Torres Priscilla , Chen Chong , Beardsley Kyle
Published: June 2020

Recent scholarship shows war can catalyze reforms related to gender power imbalances, but what about reforms related to ethnic inequalities? While war can disrupt the political, social and economic institutions at the root of ethnic hierarchy—just as it can shake up the institutions at the root of gender hierarchy—war is also prone to have either a reinforcing effect or a pendulum effect. Our project uses data from the Varieties of Democracy project to examine specific manifestations of changes in gender and ethnic civil-liberty equality (1900–2015). Interstate war, but not intrastate war, tends to be followed by gains in ethnic civil-liberty equality, and intrastate war tends to be followed by long-term gains in gender civil-liberty equality. Wars with government losses are prone to lead to improvements in civil-liberty equality along both dimensions. In considering overlapping gender and ethnic hierarchies, we find that when wars open up space for gains in gender equality, they also facilitate gains in equality for excluded ethnic groups.
The Micro-Foundations of the Resource Curse: Mineral Ownership and Local Economic Well-Being in Sub-Saharan Africa
Authors: Wegenast Tim , Khanna Arpita Asha , Schneider Gerald
Published: June 2020

The quantitative evidence on whether extractive industries generate economic wealth at the local level is far from conclusive. In line with recent studies highlighting the moderating role of institutions and governance structures in the resource–development nexus, we argue that the effect of mining on local economic well-being is largely driven by different control rights regimes. We claim that domestic mineral production stimulates local income more than internationally controlled extraction, since national mining companies promote more backward economic linkages and have higher incentives to engage in local capacity building. To test our micro-level arguments, we combine information on districts’ economic well-being as well as individual's assessments of their personal economic situation with our own dataset on the control rights of copper, gold, and diamond mines. Relying on these data, we perform district- and individual-level analyses of sub-Saharan Africa covering the period from 1997 to 2015. Our instrumental variable estimations and fixed effects models show that the presence of domestic mining companies is associated with increased local wealth. Multinational firms, by contrast, are linked to increased regional unemployment. They largely fail to promote subnational economic well-being.
Generating sequential electronic health records using dual adversarial autoencoder
Authors: Lee Dongha , Yu Hwanjo , Jiang Xiaoqian , Rogith Deevakar , Gudala Meghana , Tejani Mubeen , Zhang Qiuchen , Xiong Li
Published: June 2020

Objective

Recent studies on electronic health records (EHRs) started to learn deep generative models and synthesize a huge amount of realistic records, in order to address significant privacy issues surrounding the EHR. However, most of them only focus on structured records about patients’ independent visits, rather than on chronological clinical records. In this article, we aim to learn and synthesize realistic sequences of EHRs based on the generative autoencoder.

Materials and Methods

We propose a dual adversarial autoencoder (DAAE), which learns set-valued sequences of medical entities, by combining a recurrent autoencoder with 2 generative adversarial networks (GANs). DAAE improves the mode coverage and quality of generated sequences by adversarially learning both the continuous latent distribution and the discrete data distribution. Using the MIMIC-III (Medical Information Mart for Intensive Care-III) and UT Physicians clinical databases, we evaluated the performances of DAAE in terms of predictive modeling, plausibility, and privacy preservation.

Results

Our generated sequences of EHRs showed the comparable performances to real data for a predictive modeling task, and achieved the best score in plausibility evaluation conducted by medical experts among all baseline models. In addition, differentially private optimization of our model enables to generate synthetic sequences without increasing the privacy leakage of patients’ data.

Conclusions

DAAE can effectively synthesize sequential EHRs by addressing its main challenges: the synthetic records should be realistic enough not to be distinguished from the real records, and they should cover all the training patients to reproduce the performance of specific downstream tasks.
Combatting human trafficking in the United States: how can medical informatics help?
Authors: Unertl Kim M , Walsh Colin G , Clayton Ellen Wright
Published: June 2020

Objective

Human trafficking is a global problem taking many forms, including sex and labor exploitation. Trafficking victims can be any age, although most trafficking begins when victims are adolescents. Many trafficking victims have contact with health-care providers across various health-care contexts, both for emergency and routine care.

Materials and Methods

We propose 4 specific areas where medical informatics can assist with combatting trafficking: screening, clinical decision support, community-facing tools, and analytics that are both descriptive and predictive. Efforts to implement health information technology interventions focused on trafficking must be carefully integrated into existing clinical work and connected to community resources to move beyond identification to provide assistance and to support trauma-informed care.

Results

We lay forth a research and implementation agenda to integrate human trafficking identification and intervention into routine clinical practice, supported by health information technology.

Conclusions

A sociotechnical systems approach is recommended to ensure interventions address the complex issues involved in assisting victims of human trafficking.
Prostatic cystadenoma presenting as a large multilocular pelvic male mass
Authors: Saadi Mohamed Hafedh , Saadi Ahmed , Charkoun Marouene , Saadi Cyrine , Ghorbel Zinet , Bouafif Marwa , Ksantini Mariem , Sayari Sofiene , Bouzouita Abderazek , Derouiche Amine , Ben Slama Riadh , Ayed Haroun , Ben Moussa Mounir , Rammeh Soumaya , Chebil Mohamed
Published: June 2020

Multilocular cystadenoma are benign lesions located most commonly between the rectum and the bladder. Their presence manifests as obstructive or/and irritative lower urinary tract symptoms or transit disorders. Computed tomography scan and magnetic resonance imaging may help to establish the diagnosis. Surgery is the established treatment standard, with a high risk of recurrence in case of incomplete excision of the lesions. Here we report a case of 59-year-old man presenting with an acute urinary retention due to a giant multilocular prostatic cystadenoma treated by complete excision. The diagnosis has never been suspected before surgery and has been confirmed histologically after complete excision.
Alleviation mechanisms of metal(loid) stress in plants by silicon: a review
Authors: Vaculík Marek , Lukačová Zuzana , Bokor Boris , Martinka Michal , Tripathi Durgesh Kumar , Lux Alexander
Published: June 2020

Silicon (Si), although not considered as an essential element for plants in general, can ameliorate the phytotoxicity induced by excess metal(loid)s whether non-essential (e.g. Cd, Pb, Cr, Al, As, and Sb) or essential (e.g. Cu, Ni, and Zn). The Si-enhanced resistance allowing plants to cope with this type of abiotic stress has been developed at multiple levels in plants. Restriction of root uptake and immobilization of metal(loid)s in the rhizosphere by Si is probably one of the first defence mechanism. Further, retention of elements in the root apoplasm might enhance the resistance and vigour of plants. At the cellular level, the formation of insoluble complexes between Si and metal(loid)s and their storage within cell walls help plants to decrease available element concentration and restrict symplasmic uptake. Moreover, Si influences the oxidative status of plants by modifying the activity of various antioxidants, improves membrane stability, and acts on gene expression, although its exact role in these processes is still not well understood. This review focuses on all currently known plant-based mechanisms related to Si supply and involved in amelioration of stress caused by excess metal(loid)s.
High-energy processes in starburst-driven winds
Authors: Müller Ana L , Romero Gustavo E , Roth Markus
Published: June 2020

Starburst galaxies generate large-scale winds powered by the activity in the star-forming regions located in the galactic discs. Fragmentation of the disc produced by the outbreak of the wind results in the formation of clouds. Bowshocks caused by the supersonic outflow appear around such clouds. In this paper, we discuss the acceleration of relativistic particles and the production of non-thermal radiation in such scenario. Cosmic rays accelerated at the bowshocks do not reach the highest energies, although the high-energy luminosity generated is significant. We show that up to ∼10 per cent of the gamma-ray emission in starbursts might come from these sources outside the galactic discs. Discrete X-ray sources with a power-law component are also expected.
The influence of angular momentum and environment on the H i gas of late-type galaxies
Authors: Murugeshan Chandrashekar , Kilborn Virginia , Jarrett Thomas , Wong O Ivy , Obreschkow Danail , Glazebrook Karl , Cluver Michelle E , Fluke Christopher J
Published: June 2020

We use high-resolution H i data from the Westerbork H i Survey of Spiral and Irregular Galaxies (WHISP) to study the H i and angular momentum properties of a sample of 114 late-type galaxies. We explore the specific baryonic angular momentum–baryonic mass (jb–Mb) relation, and find that an unbroken power law of the form $j_\mathrm{ b} \propto M_\mathrm{ b}^{0.55 \pm 0.02}$ fits the data well, with an intrinsic scatter of ∼0.13 ± 0.01 dex. We revisit the relation between the atomic gas fraction, fatm, and the integrated atomic stability parameter q (the fatm–q relation), originally introduced by Obreschkow et al., and probe this parameter space by populating it with galaxies from different environments, in order to study the influence of the environment on their jb, fatm, and q values. We find evidence that galaxies with close neighbours show a larger intrinsic scatter about the fatm–q relation compared to galaxies without close neighbours. We also find enhanced star formation rate among the deviating galaxies with close neighbours. In addition, we use the bulge-to-total (B/T) ratio as a morphology proxy, and find a general trend of decreasing B/T values with increasing disc stability and H i fraction in the fatm–q plane, indicating a fundamental link between mass, specific angular momentum, gas fraction, and morphology of galaxies.
A self-lensing supermassive binary black hole at radio frequencies: the story of Spikey continues
Authors: Kun Emma , Frey Sándor , Gabányi Krisztina É
Published: June 2020

The quasar J1918+4937 was recently suggested to harbour a milliparsec-separation binary supermassive black hole (SMBH), based upon modelling the narrow spike in its high-cadence Kepler optical light curve. Known binary SMBHs are extremely rare, and the tight constraints on the physical and geometric parameters of this object are unique. The high-resolution radio images of J1918+4937 obtained with very long baseline interferometry (VLBI) indicate a rich one-sided jet structure extending to 80 mas. Here we analyse simultaneously made sensitive 1.7- and 5-GHz archive VLBI images as well as snapshot 8.4/8.7-GHz VLBI images of J1918+4937, and show that the appearance of the wiggled jet is consistent with the binary scenario. We develop a jet structural model that handles eccentric orbits. By applying this model to the measured VLBI component positions, we constrain the inclination of the radio jet, as well as the spin angle of the jet emitter SMBH. We find the jet morphological model is consistent with the optical and radio data, and that the secondary SMBH is most likely the jetted one in the system. Furthermore, the decade-long 15-GHz radio flux density monitoring data available for J1918+4937 are compatible with a gradual overall decrease in the total flux density caused by a slow secular change of the jet inclination due to the spin–orbit precession. J1918+4937 could be an efficient high-energy neutrino source if the horizon of the secondary SMBH is rapidly rotating.
On the determination of lognormal flux distributions for astrophysical systems
Authors: Shah Zahir , Misra Ranjeev , Sinha Atreyee
Published: June 2020

Determining whether the flux distribution of an astrophysical source is a Gaussian or a lognormal, provides key insight into the nature of its variability. For light curves of moderate length (<103), a useful first analysis is to test the Gaussianity of the flux and logarithm of the flux, by estimating the skewness and applying the Anderson–Darling (AD) method. We perform extensive simulations of light curves with different lengths, variability, Gaussian measurement errors, and power spectrum index β (i.e. P(f) ∝ f−β), to provide a prescription and guidelines for reliable use of these two tests. We present empirical fits for the expected standard deviation of skewness and tabulated AD test critical values for β = 0.5 and 1.0, which differ from the values given in the literature that are for white noise (β = 0). Moreover, we show that for white noise, for most practical situations, these tests are meaningless, since binning in time alters the flux distribution. For β ≳ 1.5, the skewness variance does not decrease with length and hence the tests are not reliable. Thus, such tests can be applied only to systems with β ≳ 0.5 and β ≲ 1.0. As an example of the prescription given in this work, we reconfirm that the Fermi data of the blazar, 3FGL J0730.2−1141, show that its γ-ray flux is consistent with a lognormal distribution and not with a Gaussian one.
Ctf18-RFC and DNA Pol ϵ form a stable leading strand polymerase/clamp loader complex required for normal and perturbed DNA replication
Authors: Stokes Katy , Winczura Alicja , Song Boyuan , De Piccoli Giacomo , Grabarczyk Daniel B
Published: June 2020

The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA loader that links all these processes together by an unknown mechanism. Here, we use integrative structural biology combined with yeast genetics and biochemistry to highlight the specific functions that Ctf18-RFC plays within the leading strand machinery via an interaction with the catalytic domain of DNA Pol ϵ. We show that a large and unusually flexible interface enables this interaction to occur constitutively throughout the cell cycle and regardless of whether forks are replicating or stalled. We reveal that, by being anchored to the leading strand polymerase, Ctf18-RFC can rapidly signal fork stalling to activate the S phase checkpoint. Moreover, we demonstrate that, independently of checkpoint signaling or chromosome cohesion, Ctf18-RFC functions in parallel to Chl1 and Mrc1 to protect replication forks and cell viability.
Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation
Authors: Schroeder Griffin M , Dutta Debapratim , Cavender Chapin E , Jenkins Jermaine L , Pritchett Elizabeth M , Baker Cameron D , Ashton John M , Mathews David H , Wedekind Joseph E
Published: June 2020

Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.
Long-term outcome of the survivors of infantile hypercalcaemia with CYP24A1 and SLC34A1 mutations
Authors: Janiec Agnieszka , Halat-Wolska Paulina , Obrycki Łukasz , Ciara Elżbieta , Wójcik Marek , Płudowski Paweł , Wierzbicka Aldona , Kowalska Ewa , Książyk Janusz B , Kułaga Zbigniew , Pronicka Ewa , Litwin Mieczysław
Published: June 2020

Background

Infantile hypercalcaemia (IH) is a vitamin D3 metabolism disorder. The molecular basis for IH is biallelic mutations in the CYP24A1 or SLC34A1 gene. These changes lead to catabolism disorders (CYP24A1 mutations) or excessive generation of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] (SLC34A1 mutations). The incidence rate of IH in children and the risk level for developing end-stage renal disease (ESRD) are still unknown. The aim of this study was to analyse the long-term outcome of adolescents and young adults who suffered from IH in infancy.

Design

Forty-two children (23 girls; average age 10.7 ± 6.3 years) and 26 adults (14 women; average age 24.2 ± 4.4 years) with a personal history of hypercalcaemia with elevated 1,25(OH)2D3 levels were included in the analysis. In all patients, a genetic analysis of possible IH mutations was conducted, as well as laboratory tests and renal ultrasonography.

Results

IH was confirmed in 20 studied patients (10 females). CYP24A1 mutations were found in 16 patients (8 females) and SLC34A1 in 4 patients (2 females). The long-term outcome was assessed in 18 patients with an average age of 23.8 years (age range 2–34). The average glomerular filtration rate (GFR) was 72 mL/min/1.73 m2 (range 15–105). Two patients with a CYP24A1 mutation developed ESRD and underwent renal transplantation. A GFR <90 mL/min/1.73 m2 was found in 14 patients (77%), whereas a GFR <60 mL/min/1.73 m2 was seen in 5 patients (28%), including 2 adults after renal transplantation. Three of 18 patients still had serum calcium levels >2.6 mmol/L. A renal ultrasound revealed nephrocalcinosis in 16 of 18 (88%) patients, however, mild hypercalciuria was detected in only one subject.

Conclusions

Subjects who suffered from IH have a greater risk of progressive chronic kidney disease and nephrocalcinosis. This indicates that all survivors of IH should be closely monitored, with early implementation of preventive measures, e.g. inhibition of active metabolites of vitamin D3 synthesis.