bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling double-strand breaks from direct and indirect action in a complete human genome single cell Geant4 model
Authors: Zhao Xiandong , Liu Ruirui , Zhao Tianyu , Reynoso Francisco J 
Published: September 2020

Abstract
The aim of this work is to develop and validate a computational model to investigate direct and indirect DNA damage by directly quantifying DNA strand breaks. A detailed geometrical target model was created in the Monte Carlo toolkit Geant4 to represent the nucleus of a single human cell with complete human genome. A calculation framework to simulate double-strand breaks (DSBs) was implemented using this single cell model in the Geant4-DNA extension. A detailed ellipsoidal single cell model was implemented using a compacted DNA structure representing the fibroblast cell in the G0/G1 phase of the cycle using a total of 6 Gbp within the nucleus to represent the complete human genome. This geometry was developed from the publicly available Geant4-DNA example (wholeNuclearDNA), and modified to record DNA damage for both the physical and chemical stages. A clustering algorithm was implemented in the analysis process in order to quantify direct, indirect, and mixed DSBs. The model was validated against published experimental and computational results for DSB Gy−1Gbp−1 and the relative biological effectiveness (RBE) values for 250 kVp and Co-60 photons, as well as 2–100 MeV mono-energetic protons. A general agreement was observed over the whole simulated proton energy range, Co-60 beam, and 250 kVp in terms of the yield of DSB Gy−1Gbp−1 and RBE. The DSB yield was 8.0 ± 0.3 DSB Gy−1Gbp−1 for Co-60, and 9.2 ± 0.2 DSB Gy−1Gbp−1 for 250 kVp, and between 11.1 ± 0.9 and 8.1 ± 0.5 DSB Gy−1Gbp−1 for 2–100 MeV protons. The results also show mixed DSBs composed of direct and indirect SSBs make up more than half of the total DSBs. The results presented indicate that the current model reliably predicts the DSB yield and RBE for proton and photon irradiations, and allows for the detailed computational investigation of direct and indirect effects in DNA damage.
Photo-irradiation induced green synthesis of highly stable silver nanoparticles using durian rind biomass: effects of light intensity, exposure time and pH on silver nanoparticles formation
Authors: Chutrakulwong Fueangfahkan , Thamaphat Kheamrutai , Limsuwan Pichet 
Published: September 2020

Abstract
The purpose of this work is to single-pot biosynthesize silver nanoparticles (AgNPs) using the extract from mesocarp and endocarp of durian rind under photo-irradiation. Without adding chemical substance, flavonoids, phenolic compounds and glucose dissolved in the extract served as the reducing agent; while proteins acted as the particle-stabilizing agent in the formation of AgNPs. The synthesis parameters i.e. light intensity, exposure duration, and pH value directly associated with the nucleation, growth, and aggregation of nanoparticles. The amount of synthesized AgNPs increased with increasing visible light intensity and exposure duration, while the size and stability of nanoparticles were decided by pH value adjustment. The size of synthesized AgNPs decreased when the pH value increased, on the contrary, the size increased when the pH value decreased. Under the optimized synthesis conditions (visible light intensity of 13,430 lx and pH value of 8.5), approximately 99% of silver ions was reduced to the spherical AgNPs with the mean diameter of 11.4 ± 3.2 nm within 5 min. The AgNPs remained uniformly dispersed in de-ionized water at no less than six months. The present environmental-friendly method is facile, rapid, and cost effective for the large scale preparation of AgNPs. The obtained AgNPs synthesized under optimum conditions could be applied for use in various fields such as antimicrobial activity, biosensors, and catalysis in the near future.
Enhanced interfacial reaction of precursor and low temperature substrate in HfO2 atomic layer deposition with highly Ar diluted O2 plasma
Authors: Kitajima Takeshi , Minowa Hidemichi , Nakano Toshiki 
Published: September 2020

Abstract
The internal energy of metastable oxygen atoms in highly Ar diluted oxygen plasma was utilized in the initial stage of the atomic layer deposition of HfO2 on SiO2/Si(100) at low temperature of 150 °C. The highly Ar dilute oxygen plasma enhanced the oxidation of the incomplete chemisorption state of the precursor at low temperature, successfully formed Hf silicate interface, and decreased the impurity nitrogen atoms in the HfO2 film compared to the pure oxygen plasma ALD. Residual nitrogen atoms in the film were found to cause excessive precursor adsorption. The results of plasma emission spectroscopy and ion saturation current measurements show that the highly Ar-diluted O2 plasma can increase the O radical formation rate for ion fluxes at pressures above 100 Pa. The relatively high metastable oxygen atom irradiation is thought to be responsible for the removal of HfN bonds and enable ALD on low temperature substrates. Atomic force microscopy showed that the root mean square roughness in the high Ar dilution sample was 0.093 nm, indicating high flatness.
Spectroscopic investigation of a neon-operated DBD at atmospheric and intermediate pressure
Authors: Bansemer Robert , Scholten Laura Vilardell , Winter Jörn , Weltmann Klaus-Dieter 
Published: September 2020

Abstract
A sinusoidally-excited Venturi-DBD operating in neon has been investigated. The Ne(1s5) metastable density has been quantified spatially resolved using laser atomic absorption spectroscopy for different pressure levels. Density values of up to 7 · 1016 m−3 could be determined at atmospheric pressure and up to 3 · 1016 m−3 at 100 mbar. For all investigated parameters, the Ne(1s5) density was found to be distinctly higher in the proximity of the cathode than in the anode region. Complementary investigations of the discharge development using phase-resolved optical emission spectroscopy complete the characterization of the device. The discharge was found to show typical properties of a glow-like discharge regarding current waveform and luminosity distribution. In addition, the influence of nitrogen and oxygen impurities and admixtures in the process gas has been determined. A substantial impact was found on both the Ne(1s5) concentration and the current waveform.
Emergence of long-range correlations in random networks
Authors: Mizutaka Shogo , Hasegawa Takehisa 
Published: September 2020

Abstract
We perform an analysis of the long-range degree correlation of the giant component (GC) in an uncorrelated random network by employing generating functions. By introducing a characteristic length, we find that a pair of nodes in the GC is negatively degree-correlated within the characteristic length and uncorrelated otherwise. At the critical point, where the GC becomes fractal, the characteristic length diverges and the negative long-range degree correlation emerges. We further propose a correlation function for degrees of two nodes separated by the shortest path length l, which behaves as an exponentially decreasing function of distance in the off-critical region. The correlation function obeys a power-law with an exponential cutoff near the critical point. The Erdős-Rényi random graph is employed to confirm this critical behavior.
Histoplasmosis Caused by Histoplasma capsulatum var. duboisii: A Comprehensive Review of Cases From 1993 to 2019
Authors: Develoux M , Amona F M , Hennequin C 
Published: September 2020

Abstract

Background
Histoplasmosis caused by Histoplasma capsulatum var. duboisii (Hcd) is a rare, but probably underestimated, endemic infection described in intertropical Africa. Therefore, the epidemiology of the infection remains unclear, and there is no consensus on therapeutic management.

Methods
Using a comprehensive search on different Internet databases, we collected case reports of Hcd infection published from 1993 to 2019. Epidemiological and clinical charts and therapeutic strategies were analyzed.

Results
We found 94 well-documented cases of Hcd infection, and 30.1% of the patients were under 18 years old. Symptoms occurred in some patients several decades after leaving the endemic area. Cutaneous/subcutaneous lesions, bone infections, and lymphadenopathies, both isolated and combined, were the most frequent presentations. The human immunodeficiency virus (HIV) coinfection rate was at 20.8%, with fever, lymphadenopathies, and an absence of bone infection being the differentiating elements from patients living without HIV. The rate of disseminated forms (60.6% in our review) significantly increased as compared to studies published before 1993, but without correlation with HIV infection. The global mortality rate was at 23.4% by the end of follow-up. The outcome was not correlated with the antifungal drug prescribed, nor with HIV serologic status, but was correlated with the initiation of an antifungal therapy.

Conclusions
Hcd histoplasmosis is a severe fungal infection for which the precise mode of acquisition remains to be determined. There is a need for affordable and more specific diagnostic tools. Itraconazole and amphotericin B are the best therapeutic alternatives and should be available in all low-income countries of the endemic area.
Illness Severity and Outcomes Among Enteric Fever Cases From Bangladesh, Nepal, and Pakistan: Data From the Surveillance for Enteric Fever in Asia Project, 2016–2019
Authors: Longley Ashley T , Hemlock Caitlin , Date Kashmira , Luby Stephen P , Andrews Jason R , Saha Samir K , Bogoch Isaac I , Yousafzai Mohammad T , Garrett Denise O , Qamar Farah N 
Published: September 2020

Abstract

Background
Enteric fever can lead to prolonged hospital stays, clinical complications, and death. The Surveillance for Enteric Fever in Asia Project (SEAP), a prospective surveillance study, characterized the burden of enteric fever, including illness severity, in selected settings in Bangladesh, Nepal, and Pakistan. We assessed disease severity, including hospitalization, clinical complications, and death among SEAP participants.

Methods
We analyzed clinical and laboratory data from blood culture–confirmed enteric fever cases enrolled in SEAP hospitals and associated network laboratories from September 2016 to September 2019. We used hospitalization and duration of hospital stay as proxies for severity. We conducted a follow-up interview 6 weeks after enrollment to ascertain final outcomes.

Results
Of the 8705 blood culture-confirmed enteric fever cases enrolled, we identified 6 deaths (case-fatality ratio, .07%; 95% CI, .01–.13%), 2 from Nepal, 4 from Pakistan, and none from Bangladesh. Overall, 1.7% (90/5205) of patients recruited from SEAP hospitals experienced a clinical complication (Bangladesh, 0.6% [18/3032]; Nepal, 2.3% [12/531]; Pakistan, 3.7% [60/1642]). The most identified complications were hepatitis (n = 36), septic shock (n = 22), and pulmonary complications/pneumonia (n = 13). Across countries, 32% (2804/8669) of patients with hospitalization data available were hospitalized (Bangladesh, 27% [1295/4868]; Nepal, 29% [455/1595]; Pakistan, 48% [1054/2206]), with a median hospital stay of 5 days (IQR, 3–7).

Conclusions
While defined clinical complications and deaths were uncommon at the SEAP sites, the high proportion of hospitalizations and prolonged hospital stays highlight illness severity and the need for enteric fever control measures, including the use of typhoid conjugate vaccines.
Severe Acute Respiratory Syndrome Coronavirus 2 RNA in Plasma Is Associated With Intensive Care Unit Admission and Mortality in Patients Hospitalized With Coronavirus Disease 2019
Authors: Prebensen Christian , Myhre Peder L , Jonassen Christine , Rangberg Anbjørg , Blomfeldt Anita , Svensson My , Omland Torbjørn , Berdal Jan-Erik 
Published: September 2020

Abstract
The clinical significance of severe acute respiratory syndrome coronavirus 2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58 of 123 (47%) patients hospitalized with coronavirus disease 2019. RNA was detected more frequently, and levels were higher, in patients who were admitted to the intensive care unit and/or died.
China’s Role in Global Economic Governance Revisited: Evidence from a Comparative Analysis of Chinese and Japanese BITs
Authors: Blanchard Jean-Marc F , Zeng Ka 
Published: September 2020

Abstract
A large proportion of debates about China’s impacts on global economic governance lack systematic empirical analysis. We engage the debate about if China is a revolutionary, revisionist, or status quo state through a deep dive into China’s behaviors with respect to Bilateral Investment Treaties (BITs). This research strategy is à propos because BITs represent the de facto regime governing foreign direct investment (FDI) globally, and China is the world’s second largest signatory of BITs. Drawing upon a database that we created using material on BITs available from the United Nations Conference on Trade and Development, we systematically examine the substantive and procedural provisions of China’s BITs from 2000 onward. Using a qualitative methodology discussed in-depth in our article, we also put China’s BIT practices in comparative perspective by comparing them against the BIT practices of Japan, a leading developed economy with BIT practices reflecting those of other established economies. Our multivariate analysis demonstrates China is not a revolutionary or dramatically revisionist player with respect to BITs. It champions positions that are neither hyper-conservative (state friendly) nor hyper-liberal (FDI friendly). To be more precise, China’s policies, especially with respect to substantive provisions, tend to be conservative, with, to some extent, some liberal aspects. Our analysis, then, indicates that commentators, businesspeople, and policymakers should be cautious about proffering claims that China is dramatically reshaping global economic governance. Aside from this important contribution to the debate, our work also expands knowledge about China’s BITs specifically and BITs generally, which does not reflect adequate attention to BITs from East Asian countries.
Ckj consolidation among Q1 Urology and Nephrology journals
Authors: Ortiz Alberto 
Published: September 2020

Abstract
The Clinical Kidney Journal (ckj) impact factor from Clarivate’s Web of Science for 2019 was 3.388. This consolidates ckj among journals in the top 25% (first quartile, Q1) in the Urology and Nephrology field according to the journal impact factor. The manuscripts contributing the most to the impact factor focused on chronic kidney disease (CKD) epidemiology and evaluation, CKD complications and their management, cost-efficiency of renal replacement therapy, pathogenesis of CKD, familial kidney disease and the environment–genetics interface, onconephrology, technology, SGLT2 inhibitors and outcome prediction. We provide here an overview of the hottest and most impactful topics for 2017–19.
SGLT2 inhibitors for non-diabetic kidney disease: drugs to treat CKD that also improve glycaemia
Authors: Fernandez-Fernandez Beatriz , Sarafidis Pantelis , Kanbay Mehmet , Navarro-González Juan F , Soler María José , Górriz Jose Luis , Ortiz Alberto 
Published: September 2020

Abstract
Sodium–glucose co-transporter-2 (SGLT2) inhibitors decreased cardiovascular (CV) events and improved renal outcomes in CV safety studies in type 2 diabetes melitus (T2DM) patients at high CV risk. Canagliflozin also improved kidney outcomes in diabetic kidney disease in the Canagliflozin and Renal Events in Diabetes and Nephropathy Clinical Evaluationtrial. More recently, the Dapagliflozin and Prevention of Adverse Outcomes in Heart Failure (DAPA-HF) trial showed that dapagliflozin improved CV outcomes in patients with HF with or without diabetes. Protection from HF in non-diabetics was confirmed for empagliflozin in the EMPagliflozin outcomE tRial in Patients With chrOnic heaRt Failure With Reduced Ejection Fraction (EMPEROR-Reduced) trial. A meta-analysis of DAPA-HF and EMPEROR-Reduced confirmed reductions in all-cause and CV death and the combined risk of CV death or worsening HF, as well as in the composite renal endpoint {hazard ratio [HR] 0.62 [95% confidence interval (CI) 0.43–0.90]} without differences based on the presence of diabetes or baseline estimated glomerular filtration rate (eGFR). Moreover, the Study to Evaluate the Effect of Dapagliflozin on Renal Outcomes and Cardiovascular Mortality in Patients With Chronic Kidney Disease (DAPA-CKD) showed that dapagliflozin as an add-on over renin–angiotensin system blockade in patients with chronic kidney disease (CKD; with or without T2DM) reduced the HR for the primary endpoint (time to the first occurrence of ≥50% eGFR decline, end-stage kidney disease or renal or CV death) to 0.61 (95% CI 0.51–0.72) and for the secondary endpoints of worsening renal function or death from kidney failure [HR 0.56 (95% CI 0.45–0.68)], hospitalization for HF or CV death [HR 0.71 (95% CI 0.55–0.92)] and all-cause mortality [HR 0.69 (95% CI 0.53–0.88)]. These beneficial effects were consistent in patients with and without T2DM. In conclusion, SGLT2 inhibitors offer CV and kidney protection in both diabetic and non-diabetic CKD and, additionally, improve glycaemic control in T2DM, making them first-line therapy for CKD independent from diabetic status.
Radial incision and cutting for dilation before endoscopic submucosal dissection in patients with esophageal cancer on the distal side of severe benign esophageal strictures
Authors: Nakajo Keiichiro , Yoda Yusuke , Kadota Tomohiro , Murano Tatsuro , Shinmura Kensuke , Ikematsu Hiroaki , Akimoto Tetsuo , Yano Tomonori 
Published: September 2020

ABSTRACT
We investigated the efficacy and safety of radial incision and cutting as a novel dilation method for strictures just before endoscopic submucosal dissection in patients with metachronous esophageal cancer localized on the distal side of strictures and determined the optimal dilation method. Consecutive patients who underwent endoscopic submucosal dissection for superficial esophageal squamous cell carcinomas localized on the distal side of severe strictures were investigated retrospectively and assigned to a radial incision and cutting (19 patients; 23 lesions) or an endoscopic balloon dilation (20 patients; 20 lesions) group. We evaluated the passage success rates of cap-wearing endoscopes with diameters ≥8.9 mm, the procedural success, en bloc resection, complete resection, major adverse event rates, and total procedure times. Compared to the endoscopic balloon dilation group, the passage success rate of a conventional endoscope with a transparent cap (87% vs. 50%) and procedural success rate (96% vs. 63%) were significantly higher in the radial incision and cutting group. The mean procedure time of ‘dilation and ESD’ was significantly shorter in the radial incision and cutting group than in the endoscopic balloon dilation group. Neither group experienced any serious adverse events. Radial incision and cutting followed by endoscopic submucosal dissection was effective and safe in patients with superficial esophageal squamous cell carcinomas localized on the distal side of severe benign esophageal strictures. Endoscopic submucosal dissection using a cap-wearing endoscope was possible with radial incision and cutting, and the procedure time was shorter than that for endoscopic balloon dilation.
Trans Men’s Access to Knowledgeable Providers and Their Experiences in Health Care Settings: Differences by Demographics, Mental Health, and Degree of Being “Out” to Providers
Authors: Seelman Kristie L , Kattari Shanna K , Harvey Penny , Bakko Matthew 
Published: September 2020

Abstract
Transgender adults face a health care system rife with stigma, including a lack of culturally responsive providers and high likelihood of discrimination and mistreatment. However, there is a gap in knowledge about trans men—those assigned a female sex at birth who identify as men or as transmasculine—including subgroups, such as trans men of color. Using data from the U.S. Transgender Survey, the largest transgender survey conducted in the United States, this study analyzes whether trans men’s access to knowledgeable providers and their experiences of mistreatment in health care were related to demographic and mental health characteristics and degree of being “out” to providers. Among 7,950 trans men, respondent race and ethnicity, education level, disability status, psychological distress, suicidality, and being less “out” were associated with assessing one’s health care provider as not knowledgeable about trans-related care. Mistreatment in health care was more common among Alaska Native/American Indian trans men; those who lived in or near poverty; those who were queer, pansexual, bisexual, or an orientation not listed; those with a disability; those experiencing distress or suicidality; and those who were more “out.” This article discusses how findings can inform culturally responsive health care interventions with trans men.
Dormant Plasmodium falciparum Parasites in Human Infections Following Artesunate Therapy
Authors: Peatey Christopher , Chen Nanhua , Gresty Karryn , Anderson Karen , Pickering Paul , Watts Rebecca , Gatton Michelle L , McCarthy James , Cheng Qin 
Published: September 2020

Abstract

Background
Artemisinin monotherapy of Plasmodium falciparum infection is frequently ineffective due to recrudescence. Artemisinin-induced dormancy, shown in vitro and in animal models, provides a plausible explanation. To date, direct evidence of artemisinin-induced dormancy in humans is lacking.

Methods
Blood samples were collected from Plasmodium falciparum 3D7- or K13-infected participants before and 48–72 hours after single-dose artesunate (AS) treatment. Parasite morphology, molecular signature of dormancy, capability and dynamics of seeding in vitro cultures, and genetic mutations in the K13 gene were investigated.

Results
Dormant parasites were observed in post-AS blood samples of 3D7- and K13-infected participants. The molecular signature of dormancy, an up-regulation of acetyl CoA carboxylase, was detected in 3D7 and K13 samples post-AS, but not in pre-AS samples. Posttreatment samples successfully seeded in vitro cultures, with a significant delay in time to reach 2% parasitemia compared to pretreatment samples.

Conclusions
This study provides strong evidence for the presence of artemisinin-induced dormant parasites in P. falciparum infections. These parasites are a likely reservoir for recrudescent infection following artemisinin monotherapy and artemisinin combination therapy (ACT). Combination regimens that target dormant parasites or remain at therapeutic levels for a sufficient time to kill recovering parasites will likely improve efficacy of ACTs.
No Evidence of Varicella-Zoster Virus Infection in Temporal Artery Biopsies of Anterior Ischemic Optic Neuropathy Patients With and Without Giant Cell Arteritis
Authors: Verdijk Robert M , Ouwendijk Werner J D , Kuijpers Robert W A M , Verjans Georges M G M 
Published: September 2020

Abstract

Background
To test the hypothesis that varicella-zoster virus (VZV) infection contributes to temporal arteritis pathogenesis, comprehensive in situ analysis was performed on temporal artery biopsies of 38 anterior ischemic optic neuropathy (AION) patients, including 14 (37%) with giant cell arteritis.

Methods
Biopsies were completely sectioned, and, on average, 146 serial sections per patient were stained for VZV glycoprotein E.

Results
Four of 38 AION patients showed VZV glycoprotein E staining, but VZV infection was not confirmed by staining for VZV IE63 protein and VZV-specific polymerase chain reaction on adjacent sections.

Conclusions
This study refutes the premise that VZV is casually related to AION with and without giant cell arteritis.