bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Exome Sequencing of Patients With Recurrent HSV-2 Lymphocytic Mollaret Meningitis
Authors: Hait Alon Schneider , Thomsen Michelle M , Larsen Simon M , Helleberg Marie , Mardahl Maibritt , Barfod Toke S , Christiansen Mette , Brandt Christian , Mogensen Trine H 
Published: September 2020

Abstract
Recurrent lymphocytic meningitis, also referred to as Mollaret meningitis, is a rare neurological disease characterized mainly by reactivation of herpes simplex virus 2 (HSV-2) from sensory ganglia. However, the underlying host immune determinants and viral factors rendering some individuals unable to maintain HSV-2 latency are largely unknown. We collected a cohort of 15 patients diagnosed with Mollaret meningitis. By whole-exome sequencing we identified rare host genetic variants predicted to be deleterious in molecules involved in (1) ubiquitin-proteasome pathways, (2) the autophagy machinery, and (3) cell proliferation/apoptosis. Moreover, infection of patient cells with HSV-2 or stimulation by virus-derived double-stranded DNA ligands revealed reduced antiviral interferon responses in most patients. These findings may contribute to a better understanding of disease pathogenesis and protective immunity to HSV in the central nervous system, and may ultimately be of importance for identification of targets for development of improved prophylaxis and treatment of this disease.
Occurrence of Accelerated Epigenetic Aging and Methylation Disruptions in Human Immunodeficiency Virus Infection Before Antiretroviral Therapy
Authors: Yang Chen Xi , Schon Emma , Obeidat Ma’en , Kobor Michael S , McEwen Lisa , MacIsaac Julie , Lin David , Novak Richard M , Hudson Fleur , Klinker Hartwig , Dharan Nila , Horvath Steve , Bourbeau Jean , Tan Wan , Sin Don D , Man S F Paul , Kunisaki Ken , Leung Janice M 
Published: September 2020

Abstract

Background
Whether accelerated aging develops over the course of chronic human immunodeficiency virus (HIV) infection or can be observed before significant immunosuppression on is unknown. We studied DNA methylation in blood to estimate cellular aging in persons living with HIV (PLWH) before the initiation of antiretroviral therapy (ART).

Methods
A total of 378 ART-naive PLWH who had CD4 T-cell counts &gt;500/µL and were enrolled in the Strategic Timing of Antiretroviral Therapy trial (Pulmonary Substudy) were compared with 34 HIV-negative controls. DNA methylation was performed using the Illumina MethylationEPIC BeadChip. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in PLWH compared with controls were identified using a robust linear model. Methylation age was calculated using a previously described epigenetic clock.

Results
There were a total of 56 639 DMPs and 6103 DMRs at a false discovery rate of &lt;0.1. The top 5 DMPs corresponded to genes NLRC5, VRK2, B2M, and GPR6 and were highly enriched for cancer-related pathways. PLWH had significantly higher methylation age than HIV-negative controls (P = .001), with black race, low CD4 and high CD8 T-cell counts, and duration of HIV being risk factors for age acceleration.

Conclusions
PLWH before the initiation of ART and with preserved immune status show evidence of advanced methylation aging.
Use of antibiotics to treat humans and animals in Uganda: a cross-sectional survey of households and farmers in rural, urban and peri-urban settings
Authors: Nayiga Susan , Kayendeke Miriam , Nabirye Christine , Willis Laurie Denyer , Chandler Clare I R , Staedke Sarah G 
Published: September 2020

Abstract

Background
Use of antibiotics to treat humans and animals is increasing worldwide, but evidence from low- and middle-income countries (LMICs) is limited. We conducted cross-sectional surveys in households and farms in Uganda to assess patterns of antibiotic use among humans and animals.

Methods
Between May and December 2018, a convenience sample of 100 households in Nagongera (rural), 174 households in Namuwongo (urban) and 115 poultry and piggery farms in Wakiso (peri-urban) were selected and enrolled. Using the ‘drug bag’ method, participants identified antibiotics they used frequently and the sources of these medicines. Prevalence outcomes were compared between different sites using prevalence ratios (PRs) and chi-squared tests.

Results
Nearly all respondents in Nagongera and Namuwongo reported using antibiotics to treat household members, most within the past month (74.7% Nagongera versus 68.8% Namuwongo, P = 0.33). Use of metronidazole was significantly more common in Namuwongo than in Nagongera (73.6% versus 40.0%, PR 0.54, 95% CI: 0.42–0.70, P &lt; 0.001), while the opposite was true for amoxicillin (33.3% versus 58.0%, PR 1.74, 95% CI: 1.33–2.28, P &lt; 0.001).Veterinary use of antibiotics within the past month was much higher in Wakiso than in Nagongera (71.3% versus 15.0%, P &lt; 0.001). At both sites, oxytetracycline hydrochloride was the most frequently used veterinary antibiotic, but it was used more commonly in Wakiso than in Nagongera (76.5% versus 31.0%, PR 0.41, 95% CI: 0.30–0.55, P &lt; 0.001).

Conclusions
Antibiotics are used differently across Uganda. Further research is needed to understand why antibiotics are relied upon in different ways in different contexts. Efforts to optimize antibiotic use should be tailored to specific settings.
Factors influencing choices of empirical antibiotic treatment for bacterial infections in a scenario-based survey in Vietnam
Authors: Vu Thi Lan Huong , Vu Quoc Dat , Hoang Bao Long , Nguyen Thi Cam Tu , Ta Thi Dieu Ngan , Nadjm Behzad , van Doorn H Rogier 
Published: September 2020

Abstract

Background
Antimicrobial stewardship (AMS) programmes have been implemented around the world to guide rational use of antibiotics but implementation is challenging, particularly in low- and middle-income countries, including Vietnam. Understanding factors influencing doctors’ prescribing choices for empirical treatment can help design AMS interventions in these settings.

Objectives
To understand doctors’ choices of antibiotics for empirical treatment of common bacterial infections and the factors influencing decision-making.

Methods
We conducted a cross-sectional survey among medical professionals applying for a postgraduate programme at Hanoi Medical University, Vietnam. We used a published survey developed for internal medicine doctors in Canada. The survey was self-administered and included four clinical scenarios: (i) severe undifferentiated sepsis; (ii) mild undifferentiated sepsis; (iii) severe genitourinary infection; and (iv) mild genitourinary infection.

Results
A total of 1011/1280 (79%), 683/1188 (57.5%), 718/1157 (62.1%) and 542/1062 (51.0%) of the participants selected combination therapy for empirical treatment in scenarios 1, 2, 3 and 4, respectively. Undifferentiated sepsis (OR 1.82, 95% CI 1.46–2.27 and 2.18, 1.51–3.16 compared with genitourinary) and severe infection (1.33, 1.24–1.43 and 1.38, 1.21–1.58 compared with mild) increased the likelihood of choosing a combination therapy and a carbapenem regimen, respectively. Participants with higher acceptable minimum threshold for treatment coverage and young age were also more likely to prescribe carbapenems.

Conclusions
Decision-making in antibiotic prescribing among doctors in Vietnam is influenced by both disease-related characteristics and individual factors, including acceptable minimum treatment coverage. These findings are useful for tailoring AMS implementation in Vietnam and other, similar settings.
A Bayesian framework for estimating the risk ratio of hospitalization for people with comorbidity infected by SARS-CoV-2 virus
Authors: Gao Xiang , Dong Qunfeng 
Published: September 2020

Abstract

Objective
Estimating the hospitalization risk for people with comorbidities infected by the SARS-CoV-2 virus is important for developing public health policies and guidance. Traditional biostatistical methods for risk estimations require: (i) the number of infected people who were not hospitalized, which may be severely undercounted since many infected people were not tested; (ii) comorbidity information for people not hospitalized, which may not always be readily available. We aim to overcome these limitations by developing a Bayesian approach to estimate the risk ratio of hospitalization for COVID-19 patients with comorbidities.

Materials and Methods
We derived a Bayesian approach to estimate the posterior distribution of the risk ratio using the observed frequency of comorbidities in COVID-19 patients in hospitals and the prevalence of comorbidities in the general population. We applied our approach to 2 large-scale datasets in the United States: 2491 patients in the COVID-NET, and 5700 patients in New York hospitals.

Results
Our results consistently indicated that cardiovascular diseases carried the highest hospitalization risk for COVID-19 patients, followed by diabetes, chronic respiratory disease, hypertension, and obesity, respectively.

Discussion
Our approach only needs (i) the number of hospitalized COVID-19 patients and their comorbidity information, which can be reliably obtained using hospital records, and (ii) the prevalence of the comorbidity of interest in the general population, which is regularly documented by public health agencies for common medical conditions.

Conclusion
We developed a novel Bayesian approach to estimate the hospitalization risk for people with comorbidities infected with the SARS-CoV-2 virus.
Size optimization methods to approximate equivalent mechanical behaviour in thermoplastics
Authors: Althammer Florian , Ruf Florian , Middendorf Peter 
Published: September 2020

Abstract
This paper investigates the possibility of producing an equivalent structural behaviour of two components each consisting of a different material. This is achieved through the implementation of structural optimizations. It is assumed that the initial structure is produced by conventional injection moulding and the structure to be optimized is 3D printed. For comparison, two material pairings currently used in both processes are considered. As a structural optimization method, thickness optimizations are performed in order to change the resulting cross-section of the prototype. At the beginning, the mechanical problem is formulated analytically and methods for structural optimization are evaluated. With finite element analysis, two methods are presented, which introduce the generation of a variable thickness distribution in rib structures. The first method represents a state-of-the art optimization. Ribs are directly optimized by approximating cross-section forces and moments of the prototype rib and the initial rib. The second method represents a new approach to the optimization of thin-walled structures. Local stress distributions and resulting triaxiality states, which are approximated in an intermediate step, are analysed. A newly developed finite element structure is presented, with which it is possible to generate discrete triaxiality fields and determine the necessary local thickening. This method can be used in order to produce functional prototypes in early design stage. The substituted plastic parts are usually produced by injection moulding, which initially requires a high expenditure of time and money for tool construction. Additive manufacturing represents a solution here to accelerate the development process. However, these 3D-printed prototypes are, regarding the material properties and resulting mechanical behaviour, different to the injection-moulded ones.
TEM observation of compacted DNA of Synechococcus elongatus PCC 7942 using DRAQ5 labeling with DAB photooxidation and osmium black
Authors: Ghosh Ilika , Atsuzawa Kimie , Arai Aoi , Ohmukai Ryuzo , Kaneko Yasuko 
Published: September 2020

Abstract
To visualize the fine structure of compacted DNA of Synechococcus elongatus PCC 7942, which appears at a specific time in the regular light/dark cycle prior to cell division, ChromEM with some modifications was applied. After staining DNA with DRAQ5, the cells were fixed and irradiated by red laser in the presence of 3,3ʹ-diaminobenzidine and subsequently fixed with OsO4. A system with He–Ne laser (633 nm) was set up for efficient irradiation of the bacterial cells in aqueous solution. The compacted DNA was visualized by transmission electron microscopy, in ultrathin sections as electron dense staining by osmium black.
A case of colonic intussusception and obstruction secondary to giant colonic lipoma
Authors: Law Yi Ying , Patel Rhea , Cusick Marianne , Van Eps Jeffrey L 
Published: September 2020

Abstract
Lipomas are benign soft tissue tumors found throughout the body including the gastrointestinal (GI) tract. Colonic lipomas are typically asymptomatic, incidentally identified during endoscopy or at the time of autopsy. However, giant lipomas larger than 4 cm usually manifest symptoms such as abdominal pain, obstruction, melena or intussusception. The transverse colon is the least common location for colonic lipoma. We report on a 54-year-old man with acute large bowel obstruction secondary to a long segment colo-colonic intussusception from a giant lipoma originating in the transverse colon. The diagnosis was suggested by advanced imaging and confirmed on endoscopy. He was treated successfully by laparoscopic extended right hemicolectomy with ileocolonic anastomosis. This case highlights the complexity of presentation and surgical management of large bowel obstruction and colonic intussusception, as well as the rare entity of giant colonic lipoma.
The Semantics and Syntax of Stem IV in Soqotri1
Authors: Bulakh M. 
Published: September 2020

Abstract
The present study considers the function of the pattern of the so-called stem IV, primarily associated with causatives, in Soqotri (Modern South Arabian). It focuses on the correlation between the semantics of the source verb and that of the derived verb, examines the semantic classes which are compatible with the causative morpheme, and establishes several factors which influence the employment of stem IV. A special subsection deals with syntax of stem IV verbs.
Evidentiality and Mirativity in Traditional Negev Arabic: Morphological, Lexical and Discourse-Syntactic Strategies
Authors: Henkin Roni 
Published: September 2020

Abstract
Evidentiality as a typological category pertains to the source of information from the speaker's point of view without specifying it. This information may be conveyed as non-witnessed, inferred or surprising (mirative), among other possibilities. Evidentiality strategies and mirativity strategies are usually secondary extensions of other primary functions, such as resultativity. These strategies may be grammatical, syntactic or discursive, and I also include here lexical items with no other function. In Traditional Negev Arabic, as spoken by elderly Bedouin in Southern Israel, grammatical evidentiality was noted in 1992. Since then, however, evidentiality in Arabic has only been recognized in some peripheral dialects in contact with evidential languages. This study analyses the interaction and pragmatic-rhetorical effects of three strategies for evidentiality and mirativity in oral narrative texts in Traditional Negev Arabic: a grammatical strategy via the evidential participle; a lexical strategy via evidential particles; and a discourse-syntactic strategy via presentatives, combining visual evidence with mirativity and often inference. These strategies tend to cluster together in narrative peaks, creating saturated environments of high dramatic tension. Their complex interaction is highly effective in focalizing and achieving pragmatic and rhetorical ends in this under-studied and rapidly disappearing oral narrative tradition.
Novel cytokinin oxidase/dehydrogenase inhibitors for enhancing grain yield in crop plants and potential applications in the biotechnology industry
Authors: Gupta Manoj Kumar , Gouda Gayatri , Donde Ravindra , Vadde Ramakrishna , Behera Lambodar 
Published: September 2020

This article comments on:Nisler J, Kopečný D, Pěkná Z, Končitíková R, Koprna R, Murvanidze N, Werbrouck SPO, Havlíček L, De Diego N, Wimmer Z, Briozzo P, Moréra S, Zalabák D, Spíchal L, Strnad M. 2021. Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture. Journal of Experimental Botany 72, 355–370.
Search for intrinsic NALs in BAL/mini-BAL quasar spectra
Authors: Itoh Daisuke , Misawa Toru , Horiuchi Takashi , Aoki Kentaro 
Published: September 2020

ABSTRACT
Some fraction of narrow absorption lines (NALs) are physically associated to the quasar/host-galaxy materials (i.e. intrinsic NALs) like those of broad absorption lines (BALs) and mini-BALs. The relation between these three types of absorption lines has not been understood yet, however one interpretation is that these absorption features correspond to different inclination angles. In this study, we search for intrinsic NALs in 11 BAL/mini-BAL quasar spectra retrieved from VLT/UVES public archive, in order to test a possible relation of intrinsic NALs and BALs/mini-BALs in the geometry models. We use partial coverage analysis to separate intrinsic NALs from ones which are associated to cosmologically intervening materials like foreground galaxies and intergalactic medium (i.e. intervening NALs). We identify one reliable and two possible intrinsic NAL systems out of 36 NAL systems in 9 BAL/mini-BAL quasar spectra after removing two quasars without clear BAL features. In spite of a small sample size, we placed a lower limit on the fraction of BAL/mini-BAL quasars that have at least one intrinsic C iv NAL ($\sim 33^{+33}_{-18}{{\ \rm per\ cent}}$). This can be interpreted that intrinsic NAL absorbers exist everywhere regardless of inclination angle. We found that one of the intrinsic NAL systems detected in SDSS J121549.80−003432.1 is located at a large radial distance of R &gt; 130 kpc, using a method of photoionization model with ground/excited-state lines. Considering the wide range of intrinsic NAL absorber distribution in inclination angles and radial distances, it suggests that origins and geometry of them are more complicated than we expected.
Radial derivatives as a test of pre-big bang events on the Planck data
Authors: Fernández-Cobos R , Marcos-Caballero A , Martínez-González E 
Published: September 2020

ABSTRACT
Although the search for azimuthal patterns in cosmological surveys is useful to characterize some effects depending exclusively on an angular distance within the standard model, they are considered as a key distinguishing feature of some exotic scenarios, such as bubble collisions or conformal cyclic cosmology (CCC). In particular, the CCC is a non-stardard framework that predicts circular patterns on the cosmic microwave background intensity fluctuations. Motivated by some previous works that explore the presence of radial gradients, we apply a methodology based on the radial derivatives to the latest release of Planck data. The new approach allows exhaustive studies to be performed at all-sky directions at a healpix resolution of Nside = 1024. Specifically, two different analyses are performed focusing on weight functions in both small (up to a 5-deg radius) and large scales. We present a comparison between our results and those shown by An, Meissner & Nurowski (2017) and An et al. (2018). In addition, a possible polarization counterpart of these circular patterns is also analysed for the most promising case. Taking into account the limitations to characterize the significance of the results, including the possibility of suffering a look-elsewhere effect, no strong evidence of the kind of circular patterns expected from CCC is found in the Planck data for either the small or the large scales.
Illuminating dark matter halo density profiles without subhaloes
Authors: Fielder Catherine E , Mao Yao-Yuan , Zentner Andrew R , Newman Jeffrey A , Wu Hao-Yi , Wechsler Risa H 
Published: September 2020

ABSTRACT
Cold dark matter haloes consist of a relatively smooth dark matter component as well as a system of bound subhaloes. It is the prevailing practice to include all mass, including mass in subhaloes, in studies of halo density profiles in simulations. However, often in observational studies satellites are treated as having their own distinct dark matter density profiles in addition to the profile of the host. This difference can make comparisons between theoretical and observed results difficult. In this work, we investigate density profiles of the smooth components of host haloes by excluding mass contained within subhaloes. We find that the density profiles of the smooth halo component (without subhaloes) differ substantially from the conventional halo density profile, declining more rapidly at large radii. We also find that concentrations derived from smooth density profiles exhibit less scatter at fixed mass and a weaker mass dependence than standard concentrations. Both smooth and standard halo profiles can be described by a generalized Einasto profile, an Einasto profile with a modified central slope, with smaller residuals than either a Navarro–Frenk–White or Einasto profile. These results hold for both Milky Way-mass and cluster-mass haloes. This new characterization of smooth halo profiles can be useful for many analyses, such as lensing and dark matter annihilation, in which the smooth and clumpy components of a halo should be accounted for separately.
CancerImmunityQTL: a database to systematically evaluate the impact of genetic variants on immune infiltration in human cancer
Authors: Tian Jianbo , Cai Yimin , Li Yue , Lu Zequn , Huang Jinyu , Deng Yao , Yang Nan , Wang Xiaoyang , Ying Pingting , Zhang Shanshan , Zhu Ying , Zhang Huilan , Zhong Rong , Chang Jiang , Miao Xiaoping 
Published: September 2020

AbstractTumor-infiltrating immune cells as integral component of the tumor microenvironment are associated with tumor progress, prognosis and responses to immunotherapy. Genetic variants have been demonstrated to impact tumor-infiltrating, underscoring the heritable character of immune landscape. Therefore, identification of immunity quantitative trait loci (immunQTLs), which evaluate the effect of genetic variants on immune cells infiltration, might present a critical step toward fully understanding the contribution of genetic variants in tumor development. Although emerging studies have demonstrated the determinants of germline variants on immune infiltration, no database has yet been developed to systematically analyze immunQTLs across multiple cancer types. Using genotype data from TCGA database and immune cell fractions estimated by CIBERSORT, we developed a computational pipeline to identify immunQTLs in 33 cancer types. A total of 913 immunQTLs across different cancer types were identified. Among them, 5 immunQTLs are associated with patient overall survival. Furthermore, by integrating immunQTLs with GWAS data, we identified 527 immunQTLs overlapping with known GWAS linkage disequilibrium regions. Finally, we constructed a user-friendly database, CancerImmunityQTL (http://www.cancerimmunityqtl-hust.com/) for users to browse, search and download data of interest. This database provides an informative resource to understand the germline determinants of immune infiltration in human cancer and benefit from personalized cancer immunotherapy.