bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract
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

AbstractRecent 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

Abstract
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

Abstract

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

Abstract

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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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 (&lt;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

AbstractThe 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

Abstract
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

Abstract

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 &lt;90 mL/min/1.73 m2 was found in 14 patients (77%), whereas a GFR &lt;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 &gt;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.
全谷物食品开发技术解决方案
Authors: Bin Tan , Nana Wu , Xiaotong Zhai 
Published: June 2020

Abstract
鉴于全谷物的健康益处，全球范围内一直在致力于增加其消费量，许多国家都在制定关于全谷物推荐摄入量的膳食指南。在中国，全谷 物的摄入不足，部分原因是由于全谷物食品开发的技术障碍。本文重 点介绍了在全产业链中潜在的全谷物食品开发解决方案，以及新食品 技术在全谷物食品开发中的应用，使全谷物具有优良口感、安全性、同 时尽可能保留其中的生物活性物质。
Too Few, Too Little: Parliaments’ Response to Sexism and Sexual Harassment
Authors: Verge Tània 
Published: June 2020

Abstract
Despite the increasingly reported incidence of sexual harassment among female elected representatives and staff members around the world, many more cases may not surface due to the power asymmetries, partisan logics and male organisational culture underpinning parliaments. No workplace is immune to sexual harassment, but when such misconducts occur in parliaments women’s right to fully and equally participate in political life is severely infringed. While international organisations have issued numerous resolutions calling parliaments to take action, this article shows that most legislative chambers in Europe and the Americas lag behind the adoption of adequate preventative measures, complaint mechanisms and reparation measures.