cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease
Creators: name: Douglas, Madeline G.
name: Kocher, Jacob F.
name: Cockrell, Adam S.
name: Baric, Ralph S.
name: Scobey, Trevor
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: We recently established a mouse model (288–330+/+) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 106 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 103 and 105 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10–1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease.
Study 3 (Prolific Experimental)
Creators: name: Lab, MaRSS
name: Fisher, Alexandra
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social Psychology
subject: Quantitative Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: Experimental Invariance

description: Additional exclusion criteria for our experiment on social class and relationship meaning.
Maxwell perturbations on asymptotically anti-de Sitter spacetimes: Generic boundary conditions and a new branch of quasinormal modes
Creators: name: Wang, Mengjie
name: Herdeiro, Carlos
name: Sampaio, Marco O. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Perturbations of asymptotically Anti-de-Sitter (AdS) spacetimes are often considered by imposing field vanishing boundary conditions (BCs) at the AdS boundary. Such BCs, of Dirichlet-type, imply a vanishing energy flux at the boundary, but the converse is, generically, not true. Regarding AdS as a gravitational box, we consider vanishing energy flux (VEF) BCs as a more fundamental physical requirement and we show that these BCs can lead to a new branch of modes. As a concrete example, we consider Maxwell perturbations on Kerr-AdS black holes in the Teukolsky formalism, but our formulation applies also for other spin fields. Imposing VEF BCs, we find a set of two Robin BCs, even for Schwarzschild-AdS black holes. The Robin BCs on the Teukolsky variables can be used to study quasinormal modes, superradiant instabilities and vector clouds. As a first application, we consider here the quasinormal modes of Schwarzschild-AdS black holes. We find that one of the Robin BCs yields the quasinormal spectrum reported in the literature, while the other one unveils a new branch for the quasinormal spectrum.
description: v2. Slight revision of the paper's title and other minor changes
Jumping species—a mechanism for coronavirus persistence and survival
Creators: name: Baric, Ralph S.
name: Menachery, Vineet D.
name: Graham, Rachel L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Zoonotic transmission of novel viruses represents a signiﬁcant threat to global public health and is fueled by globalization, the loss of natural habitats, and exposure to new hosts. For coronaviruses (CoVs), broad diversity exists within bat populations and uniquely positions them to seed future emergence events. In this review, we explore the host and viral dynamics that shape these CoV populations for survival, ampliﬁcation, and possible emergence in novel hosts.
Batch processing BioImage Analysis with Fiji
Creators: name: Haase, Robert
Publisher: name: Max Planck Institute of Molecular Cell Biology and Genetics (MPI CBG)
Year: 2019
Subjects: ImageJ2
Imglib2 development using IntellIJ

description: Introduction to Batch processing with Fiji. It was given at the NEUBIAS Satellite meeting: BioImage Analysts best practices Seminar in Luxembourg 2019.
Moral Choice When Harming is Unavoidable
Creators: name: Berman, Jonathan
name: Kupor, Daniella
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: Past research suggests that actors often seek to minimize harm at the cost of maximizing social welfare. However, this prior research has confounded a desire to minimize the negative impact caused by one’s actions (harm aversion) with a desire to avoid causing any harm whatsoever (harm avoidance). Across six studies (N = 2,152), we demonstrate that these two motives are distinct. When decision-makers can completely avoid committing a harmful act, they strongly prefer to do so. However, harming cannot always be avoided. Often, decision-makers must choose between committing less harm for less benefit and committing more harm for more benefit. In these cases, harm aversion diminishes substantially, and decision-makers become increasingly willing to commit greater harm to obtain greater benefits. Thus, value trade-offs that decision-makers refuse to accept when it is possible to completely avoid committing harm can suddenly become desirable when some harm must be committed.
Growth characteristics of fish species Gerres filamentosus (Cuvier, 1829) in coastal zone, Quang Binh province
Creators: name: Vo, Van Thiep
name: Tran, Thi Yen
name: Nguyen, Thi Huong Binh
name: Huynh, Ngoc Tam
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: The research was conducted from October 2013 to March 2014 by using the method applied in the current ichthyology study by GV Nikolski, Pravdin IF, OF Xakun, NA Buskaia and Mai Dinh Yen. Fish samples were collected in the coastal area of Quang Binh province. The study results showed that Gerres filamentosus (Cuvier, 1829) had the length romf 52mm to 230mm, corresponding to the weight from 4g to 185g. The age structure of the fish was simple that consisted of four age groups (0+ - 3+), the annual growth rate was relatively fast, the growth equation following Von Bertalanffy was as: Lt = 234.4 x [1- e-0.35 (t + 0.996)], Wt = 373.4 x [1-e-0.0244 (t + 0.2388)] 3.0676. Nghiên cứu được thực hiện từ tháng 10 năm 2013 đến tháng 3 năm 2014 bằng những phương pháp đang được áp dụng trong các nghiên cứu ngư loại hiện nay của G.V. Nikolski, I. F. Pravdin, O. F. Xakun, N. A. Buskaia và Mai Đình Yên, mẫu cá được thu tại vùng ven biển của tỉnh Quảng Bình. Kết quả nghiên cứu đã cho thấy cá Móm gai dài có chiều dài dao động từ 52mm – 230mm, tương ứng với khối lượng từ 4g – 185g. Cấu trúc tuổi cá Móm gai dài đơn giản, gồm 4 nhóm tuổi (0+ - 3+), tốc độ tăng trưởng hàng năm tương đối nhanh, phương trình sinh trưởng theo Von Bertalanffy có dạng Lt = 234,4 x [1-e-0,35(t + 0,996)], Wt = 373,4 x [1-e-0,0244(t + 0,2388)]3,0676.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model
Creators: name: Cressler, Clayton E.
name: Butler, Marguerite A.
name: King, Aaron A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study.
description: 38 pages, in press at Systematic Biology
Tracking Theory, TrackMate and Mastodon
Creators: name: Haase, Robert
name: Jug, Florian
name: Pietzsch, Tobias
Publisher: name: Max Planck Institute of Molecular Cell Biology and Genetics (MPI CBG)
Year: 2019

description: Introduction to Tracking with Trackmate and Mastodon. This lecture was given at the NEUBIAS Training School TS10 in Luxembourg 2019.
Education for environment: A useful concept
Creators: name: Giap, Binh Nga
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: By analyzing the relationship between sustainable development and education, the author developed the guidelines proposal for the practical work in environmental education and its application to guide instruction and research in Vietnam. Trên cơ sở phân tích mối quan hệ tác động qua lại giữa giáo dục và sự phát triển bền vững cũng như tiếp cận những định nghĩa của một số tác giả khác về giáo dục môi trường. Tác giả đưa ra định hướng thực hành trong giáo dục môi trường. Định hướng này ứng dụng trong giảng dạy và nghiên cứu giáo dục môi trường tại Việt Nam.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
Renewables Projection with Storage in the Brazilian Electricity Matrix using OSeMOSYS
Creators: name: Dias, Bruno Henriques
name: Borba, Bruno S. M.
name: Bitencourt, Leonardo A.
name: Barbosa, Pedro Henrique P.
name: Maycoln José Tonelli
Publisher: name: Zenodo
Year: 2023
Subjects: Long Term Planning
Brazilian Power System
Energy Transition
Decarbonisation

description: This poster presents the study on the increase of Solar and Wind energy generation in the Brazilian Power System, as a way to achieve the NetZero by 2050. This study was conducted using the OSeMOSYS as a deliverable of the Energy Modelling Platform for Latin America and The Caribbean Course - EMP-LAC 2023.
Multi-view fusion
Creators: name: Haase, Robert
name: Vellutini, Bruno C.
Publisher: name: Max Planck Institute of Molecular Cell Biology and Genetics (MPI CBG)
Year: 2019

description: Introduction to Multiview fusion of Light sheet data with Fiji. This lecture was given at the NEUBIAS Training School TS10 in Luxembourg 2019 and at the EMBO practical course on light sheet microscopy in Dresden 2018.
Renewables Projection with Storage in the Brazilian Electricity Matrix using OSeMOSYS
Creators: name: Dias, Bruno H.
name: Borba, Bruno S. M.
name: Bitencourt, Leonardo A.
name: Barbosa, Pedro Henrique P.
name: Maycoln José Tonelli
Publisher: name: Zenodo
Year: 2023

description: Study on the increase of Solar and Wind energy generation in the Brazilian Power System, as a way to achieve the NetZero by 2050. This study was conducted using the OSeMOSYS as a deliverable of the Energy Modelling Platform for Latin America and The Caribbean Course - EMP-LAC 2023.
Chiral Dynamics and S-wave contributions in Semileptonic $D_s/B_s$ decays into $π^+π^-$
Creators: name: Shi, Yu-Ji
name: Wang, Wei
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: In this work, we study the semileptonic decay modes $B_s^0\to π^+π^-\ell^+\ell^-$ and $D_s^+\to π^+π^-\ell^+ ν$ in the kinematics region where the $π^+π^-$ system has a invariant mass in the range $0.5$-$1.3$ GeV. These processes are valuable towards the determination of S-wave $π^+π^-$ light-cone distribution amplitudes whose normalizations are scalar form factors. We compare the results for scalar form factors predicted in unitarized chiral perturbation theory and extracted from the data on the $B_s\to J/ψπ^+π^-$. Then the $B_s\to π^+π^-$ and $D_s\to π^+π^-$ form factors are calculated in light-cone sum rules, based on which predictions for differential decay widths are made. The results are in good agreement with the experimental data on the $B_s$ and $D_s$ decays into $π^+π^-$. More accurate measurements at BEPC, LHC and KEKB in future will be helpful to examine our formalism and constrain the input parameters more precisely.
description: 15 pages,9 figures
An effective DNA vaccine platform for Middle East respiratory syndrome coronavirus
Creators: name: Baric, Ralph S.
name: Cockrell, Adam S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Middle East respiratory syndrome coronavirus (MERS-CoV) is an ongoing emerging infectious disease across the Arabian Peninsula, with the majority of cases occurring in Saudi Arabia. Through September 23, 2016 the World Health Organization reported about 1,806 total cases, including 643 deaths from 27 countries (http://www.who.int/emergencies/mers-cov/en/). The disease is comprised of a lower respiratory infection wherein individuals exhibit pneumonia-like symptoms that often lead to multi-organ failure and death (1). In addition to close contact with infected camels, transmission from human-to-human most commonly occurs in the hospital setting through close contact between patients and hospital workers (1). MERS-CoV has also been isolated from objects within patient rooms including bed sheets, bed rails, and IV fluid hangers (2), which may all be potential sources of transmission. Several cases of MERS-CoV have been associated with travelers returning home from the Middle East and developing symptoms, including two cases of health care workers returning to the United States (3). The potential for global spread was recently illustrated by a South Korean national returning home from visiting the Arabian Peninsula in May, 2015, and initiating an outbreak that infected 186 people resulting in 20% mortality and a nationwide economic crisis (4). Nonetheless, MERS-CoV is not thought to be sustained in the human population through human-to-human transmission, but may instead be continuously re-introduced into the human population from a zoonotic source, most likely dromedary camels because of high seropositive rates in herds throughout the Middle East (5,6). As camels are integral to the Saudi Arabian culture and economy, nationwide culling of camel herds is not feasible. Consequently, camel vaccination is being considered (7); however, therapeutic strategies have primarily focused on interfering with MERS-CoV infection in humans (3,5).
Physiological properties of new species of Acidithiobacillus isolated from abandoned Tin mine in Ha Thuong, Thai Nguyen province
Creators: name: Nguyen, Tuyet Anh
name: Nguyen, Thi Thuy Tuyen
name: Duong, Thi Thuy
name: Le, Thi Phuong Quynh
name: Hoang, Cuong Tu
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: Acidophilic bacteria are able to tolerate acidic environment and also contribute to the lowering of environmental pH value, implying potential applications in metal-leaching technology extracting metals from tailings and electronic wastes. In this study, we conducted a sampling campaign in abandoned Tin mine in Ha Thuong, Thai Nguyen province, to isolate acidophilic bacteria and to study physiological characteristics of the isolated bacteria. As a result, two acidophilic bacteria were successfully isolated and identification by 16S rDNA gene sequences showed that the two bacteria are similar to Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans (98% and 94% of similarity, respectively). Both strains are tolerant of pH in the range of 3 and have the ability to grow optimally at temperatures of 30°C. Vi khuẩn ưa axit có ý nghĩa ứng dụng trong công nghệ tách rút kim loại từ quặng đuôi và ngay cả từ rác thải linh kiện điện tử. Trong nghiên cứu này, chúng tôi đã tiến hành thu mẫu ở mỏ thiếc bỏ hoang ở Hà Thượng, Thái Nguyên nhằm phân lập được nhóm vi khuẩn ưa axit và qua đó nghiên cứu một số đặc điểm sinh lý của vi khuẩn này. Kết quả chúng tôi đã phân lập được hai chủng vi khuẩn ưa axit. Định dạng bằng nhận diện trình tự gen 16S rADN cho thấy hai vi khuẩn này có độ tương đồng là 98% với vi khuẩn Acidithiobacillus ferrooxidans và 94% Acidithiobacillus thiooxidans. Cả hai chủng vi khuẩn đều có tính chịu pH trong khoảng 3 và có khả năng sinh trưởng tối ưu ở nhiệt độ 30°C.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
Renewables Projection with Storage in the Brazilian Electricity Matrix using OSeMOSYS
Creators: name: Dias, Bruno H.
name: Borba, Bruno S. M.
name: Bitencourt, Leonardo A.
name: Barbosa, Pedro Henrique P.
name: Maycoln José Tonelli
Publisher: name: Zenodo
Year: 2023
Subjects: Long Term Planning
Brazilian Power System
Energy Transition
Decarbonisation

description: Study on the increase of Solar and Wind energy generation in the Brazilian Power System, as a way to achieve the NetZero by 2050. This study was conducted using the OSeMOSYS as a deliverable of the Energy Modelling Platform for Latin America and The Caribbean Course - EMP-LAC 2023.
Study on culture conditions of several strains of toluene-degrading bacteria isolated from common ornamental houseplants
Creators: name: Phan, Due Thanh
name: Nguyen, Thi Cuc
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: This article studies the impact of some environmental conditions and the nutrition of culturing medium on the growth of bacteria and theirs capacity of toluene removal. The 5 bacterial strains isolated from leaf samples of three different common houseplants in Vietnam are Gram-negative, rod-shaped bacteria. The cells are single or arranged in chains. The cell size is relatively small and ranged from 0.7 to 2.5mm. These bacteria prefer the incubating temperature from 28°C to 32°C and a neutral pH 6.5 to 7.5. They are able to assimilate different nitrogen and carbon sources. In the liquid SH1 medium containing 200ppm toluene five selected strains have shown the ability to degrade toluene at a rate of 12.8 to 75.2% in comparison with the control at 30°C at a speed of 200rpm for over 120 hours. These 5 studied strains are potentially useful in bioremediation strategies to remove airborne toluene. 5 chủng vi khuẩn có khả năng phân giải toluene được phân lập từ lá một số cây cảnh phổ biến ở Việt Nam là vi khuẩn G (-), dạng trực khuẩn và kích thước tế bào từ 0,7 – 2,5m. Một số điều kiện môi trường nuôi cấy thích hợp cho 5 chủng vi khuẩn nghiên cứ gồm nhiệt độ 28°C-32°C, pH 6,5-7,5, có khả năng đồng hoá nhiều nguồn nitơ và ba nguồn carbon khác nhau. Trong điều kiện môi trường dịch SH1 chứa 200ppm toluene, 5 chủng vi khuẩn này cho thấy khả năng phân giải toluene từ 12,8 – 75,2%. Đây là các chủng vi khuẩn có tiềm năng ứng dụng để loại bỏ toluene từ không khí ô nhiễm.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
Reply to “Statins may decrease the Fatality Rate of MERS Infection”
Creators: name: Totura, Allison L.
name: Baric, Ralph S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Since the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) on the Arabian Peninsula in 2012, there has been a steady stream of MERS cases geographically focused in the Middle East, indicating that either zoonotic transmission from camel to human or person-to-person transmission likely takes place on a frequent basis (1). As reaffirmed by the recent MERS outbreak in South Korea, highly pathogenic coronaviruses are capable of causing epidemics affecting hundreds of individuals as a result of sustained person-to-person transmission in nosocomial settings that can be linked to a single traveler who became an index patient (2). Currently, the best public health strategy to circumvent sustained coronavirus transmission in an outbreak situation is to quarantine individuals who have a history of contact with confirmed cases of MERS. In the most recent outbreak in South Korea, this led to the isolation and monitoring of more than 16,000 individuals, a feat that may not be economically or logistically feasible in future outbreaks (2). Due to the diversity and presence of prepandemic zoonotic coronaviruses in bat populations, we may expect the continual reemergence of highly pathogenic coronaviruses related to MERS-CoV, SARS-CoV (severe acute respiratory syndrome coronavirus), or other CoV strains to be a future risk to global public health (3, 4). There is clearly a need for coronavirus-specific medical countermeasure strategies against these respiratory pathogens, as studies indicate that general antiviral medications like interferon and ribavirin are ineffective in MERS or SARS patients (5, 6).
Families of minimally non-Golod complexes and their polyhedral products
Creators: name: Limonchenko, Ivan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 13F55, 55U10

description: We consider families of simple polytopes $P$ and simplicial complexes $K$ well-known in polytope theory and convex geometry, and show that their moment-angle complexes have some remarkable homotopy properties which depend on combinatorics of the underlying complexes and algebraic properties of their Stanley--Reisner rings. We introduce infinite series of Golod and minimally non-Golod simplicial complexes $K$ with moment-angle complexes $\mathcal Z_K$ having free integral cohomology but not homotopy equivalent to a wedge of spheres or a connected sum of products of spheres respectively. We then prove a criterion for a simplicial multiwedge and composition of complexes to be Golod and minimally non-Golod and present a class of minimally non-Golod polytopal spheres.
description: 13 pages, Construction 3.9 and Theorem 3.10 added
Push button reproduction attempt of a research claim from Teney, C. (2016) in European Sociological Review
Creators: name: Talbert, Eli
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences

description: Poor national economic performances significantly increase the negative and decrease the positive EU-framing dimensions. The effect is stronger on the materialist dimensions of EU [European Union] framing (H1); that poor national economic performances significantly decrease the positive EU-framing dimensions is the portion selected. This reflects the following statement from the paper's abstract: "The results show, first, that poor economic performances increase negative and decrease positive dimensions of EU framing." The author runs a multilevel regression analysis to take the structure of the repeated cross-sectional sampling design into account. The author built scales ranging from 0 to 1 for each of four framing dimensions that are then used as dependent variables in the analysis. These four scales measure the relative frequency with which the respondent associates each frame to the EU. The author uses a stepwise procedure to build the multilevel models (see Table 3). The first model of Table 3 is selected, and the analysis selected is for ‘Cosmopolitan.’ The independent variable selected is for unemployment rate (see ‘Model 1 – Cosmopolitan’ column of Table 3 for details). The effects of unemployment rates and GDP growth are significant on all EU-framing dimensions (with the exception of an insignificant effect of unemployment rate on the libertarian dimension) and go in the expected direction: an increase in unemployment rates and a decrease in GDP growth implies a higher level of negative EU framing (i.e. the communitarian and libertarian dimensions) and a lower level of positive EU framing (i.e. the cosmopolitan and utilitarian dimensions) (from ‘Model 1 – Cosmopolitan’ column in Table 3, ‘Unempl. rate’ independent variable: estimate = -0.00340; t statistic = -4.03; P < 0.001). The focal test in the original paper is: The effects of unemployment rates and GDP growth are significant on all EU-framing dimensions (with the exception of an insignificant effect of unemployment rate on the libertarian dimension) and go in the expected direction: an increase in unemployment rates and a decrease in GDP growth implies a higher level of negative EU framing (i.e. the communitarian and libertarian dimensions) and a lower level of positive EU framing (i.e. the cosmopolitan and utilitarian dimensions) (from ‘Model 1 – Cosmopolitan’ column in Table 3, ‘Unempl. rate’ independent variable: estimate = -0.00340; t statistic = -4.03; P < 0.001).
Impact of corona virus (COVID-19) on Clinical trials and clinical research: A systematic review
Creators: name: Sathian, Brijesh
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences

description: There is no meta analysis published till date in this topic. Globally, as of the 18th of August 2020, there have been 21,756,357 confirmed cases of COVID-19, including 771,635 deaths, reported by the World Health Organization. The current Corona virus disease-19 (COVID-19) pandemic is affecting the clinical research in most parts of the world. The focus on the development of a vaccine for SARS-CoV-2 and the treatment of COVID-19 is disrupting many upcoming and ongoing clinical trials on other diseases around the globe. On March 18, 2020 the Food and Drug Administration (FDA) issued new an updated guide for the conduct of clinical trials during this critical situation. The potential challenges are due to social distancing and quarantine resulting in study participants and trial personnel not being available for in-person study visits and/or being followed-up. Due to the sudden onset and wide-spread impact of COVID-19, its influence on managing clinical trials and research needs urgent attention. Therefore, our systematic review of the literature aims to assess the impact of The COVID-19 pandemic on the conduction of clinical trials and research. Design Plan Study type Meta-Analysis - A systematic review of published studies. Blinding No blinding is involved in this study. Is there any additional blinding in this study? There is no medical intervention being addressed in the study. The search for the relevant articles for review will be included keywords "COVID-19” AND "clinical trial" in PubMed, MEDLINE, EMBASE and Google scholar electronic databases in the period from 08 December 2019 through 05th September 2020. The current situation results in delaying subject enrollment and operational gaps in most on-going clinical trials, which in turn has a negative impact on trial program’s and data integrity. Globally, most sites conducting clinical trials other than COVID-19 are experiencing a decrease in productivity and or a complete halt of operations in lieu of slowdown or pause due to this pandemic, thus affecting clinical research and development in general. Data extraction The titles of the studies resulted from the database searches will be screened initially and relevant papers will be selected. Then the abstracts and full texts will be reviewed according to the inclusion criteria for final selection. The titles, abstracts and full-text articles will be reviewed independently by three researchers (BS, MA, BR, vanTE, and IB). Extracted data will include authors, origin of studies, source population, study setting and period, inclusion/exclusion criteria, data sources and sample size.
Reply to "Comment on two-mode stability islands around AdS"
Creators: name: Buchel, Alex
name: Green, Stephen R.
name: Lehner, Luis
name: Liebling, Steven L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We respond to the criticisms of a recent comment by Bizoń and Rostworowski [arXiv:1410.2631].
description: 2 pages, 1 figure
Preliminary data on the aquatic invertebrate fauna of the Ma River, Thanh Hoa province
Creators: name: Ngo, Xuan Nam
name: Nguyen, Quoc Huy
name: Nguyen, Nguyen Hang
name: Pham, Thi Diep
name: Mai, Trong Hoang
name: Lai, Ngoc Ca
name: Dinh, Thi Hai Yen
name: Nguyen, Van Vinh
name: Le, Duc Giang
name: Nguyen, Quang Huy
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: A field survey for the invertebrate fauna conducted in the Ma River, Thanh Hoa province in 2013. The research applied multivariable analysis performed by the Primer v.6 software, such as CLUSTER, one-way ANOSIM, BEST and DIVERSE. The results showed a list of 138 aquatic invertebrate species. Of these, most were freshwater wide-distributing species coupled with others characterized for brackish and marine waters. The biodiversity status was quite high compared to several other rivers in the North of Vietnam. The list contained many economic-valued species and 2 of these were listed in the Red Data Book of Vietnam. The aquatic invertebrates showed a significant relation to the two different combinations of physiochemical factors for zooplanktons and zoobenthos, respectively. The values of the species number, abundance and Shannon-Weiner index for both of zooplanktons and zoobenthos showed a curved trend from the upper river segments to lower river segments. These figures for zooplanktons peaked in the middle river segments, whereas the numbers for zoobenthos achieved the highest numbers in the estuaries. The species composition of the estuaries differentiated significantly from that of other freshwater habitats. Năm 2013 đã tiến hành một đợt điều tra khu hệ động vật không xương sống sông Mã, tỉnh Thanh Hóa. Nghiên cứu sử các phân tích đa biến thông qua phần mền Primer v.6, bao gồm: CLUSTER, one-way ANOSIM, BEST và DIVERSE. Kết quả phân tích thu được 138 loài với thành phần loài chủ yếu là những loài nước ngọt thường gặp và phân bố rộng, ngoài ra còn có các loài đặc trưng cho nước lợ và mặn. Trong số các loài thu được, nhiều loài có giá trị kinh tế và 2 loài có tên trong Sách Đỏ Việt Nam. Khu hệ động vật không xương sống sông Mã có quan hệ chặt với hai nhóm chỉ số thủy lý hóa học khác nhau, tương ứng cho động vật nổi và động vật đáy. Giá trị các chỉ số sinh học gồm số lượng loài, mật độ và Shannon-Weiner hồi quy theo đường cong phi tuyến từ thượng lưu tới hạ lưu; đạt giá trị cao nhất tại cửa sông đối với động vật đáy và vùng trung lưu với động vật nổi. Thành phần loài cửa sông khác biệt rõ rệt với thành phần loài các sinh cảnh nước ngọt khác.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
A Digital Health Landscape to Investigate Impediments to Reliable, Timely and Integrated Electronic Patient Data Sharing in Lower Middle and Low Income Countries: A Systematic Review
Creators: name: Alunyu, Andrew
name: Wamema, Joseph
name: Kiwanuka, Achilles
name: Moses, Bagyendera
name: Mercy, Amiyo
name: Andrew, Kambugu
name: Nabukenya, Josephine
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Health Information Technology
subject: Public Health
subject: Medicine and Health Sciences

description: This systematic review (SR) is part of the methods and data collection techniques in the large project that aims to explore the feasibility of existing international digital health standards to facilitate development of contextual standardized digital health to improve data use for action in Low Resource settings.
Nematode communities act as bio-indicator of status and processes of an agricultural soil ecosystem in Thanh An, Binh Phuoc province
Creators: name: Duong, Duc Hieu
name: Le, Thi Phuong Anh
name: Bui, Thi Thu Nga
name: Ngo, Xuan Quang
name: Nguyen, Dinh Tu
name: Nguyen, Huu Hung
name: Nguyen, Vu Thanh
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: Nematode communities in black pepper (Piper nigrum L.) agricultural soil in Thanh An, Binh Phuoc province, were investigated. Soil samples were collected in February 2012 at 9 selected sites belonging to 3 pepper groves. The structure of nematode communities and critical ecological indices were determined to estimate environmental status. 26 genera were found. Of those, plant parasitic nematodes such as Meloidogyne, Helicotylenchus, Hoplolaimus, Psilenchus, and Tylenchidae always appear with high frequency and density, whereas the carnivorous nematodes were rarely detected. The nematode density correlates to the concentration of the total organic matter which correlates closely to the (Ba + Fu) proportion showed by the regression equation y = 0.0223x + 1.6819 with R2 = 1. The ecological triangle model, but not the maturity index (MI), apparently showed the status and processes (decomposition and mineralization) which may be happening in the soils of areas studied. The first grove is rich in nutrient but stressed by chemicals. The second grove is stable, with no chemical stress, but has low nutrient contents. The third grove is affected by chemicals but to a lesser extent than the first one. Các quần xã tuyến trùng trong hệ sinh thái đất trồng tiêu ở khu vực xã Thanh An, tỉnh Bình Phước được nghiên cứu. Các mẫu đất được thu nhận trong tháng hai năm 2012 tại 9 điểm thuộc 3 vườn tiêu. Cấu trúc quần xã tuyến trùng và các chỉ số sinh thái đã được xác định để qua đó đánh giá trạng thái môi trường. Tổng cộng có 26 giống tuyến trùng được tìm thấy. Trong đó, các loài tuyến trùng ký sinh thực vật như Meloidogyne, Helicotylenchus, Hoplolaimus, Psilenchus, và tuyến trùng ăn nấm Tylenchidae luôn xuất hiện với tần suất và mật độ cao, trong khi tuyến trùng ăn thịt lại hiếm khi được phát hiện. Mật độ tuyến trùng tương quan với lượng chất hữu cơ tổng số mà nó tương quan chặt chẽ với với tỉ lệ nhóm (Ba + Fu) được thể hiện ở phương trình hồi quy là y = 0.0223x + 1.6819 với R2 = 1. Mô hình tam giác sinh thái, nhưng không phải chỉ số tăng trưởng MI, thể hiện rõ trạng thái và các quá trình (sự phân hủy và sự khoáng hóa) có lẽ đang diễn ra trong đất của khu vực được nghiên cứu. Vườn thứ nhất thì giàu dinh dưỡng nhưng bị áp lực bởi hóa chất. Vườn thứ hai khá ổn định, không chịu áp lực hóa chất, nhưng hàm lượng dinh dưỡng rất kém. Vườn thứ ba bị tác động bởi hóa chất nhưng ở mức độ thấp hơn vườn thứ nhất.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
Small molecule inhibitors of the SARS-CoV Nsp15 endoribonuclease
Creators: name: Frieman M
name: Bhardwaj K
name: Ortiz-Alcantara J
name: Baric R
name: Palaninathan S
name: Kao C
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The severe acute respiratory syndrome (SARS) virus encodes several unusual RNA processing enzymes, including Nsp15, an endoribonuclease that preferentially cleaves 3’ of uridylates through a ribonuclease A (RNase A)-like mechanism. Crystal structures of Nsp15 confirmed that the Nsp15 active site is structurally similar to that of RNase A. These similarities and our molecular docking analysis lead us to hypothesize that previously characterized RNase A inhibitors will also inhibit the SARS-CoV Nsp15. Benzopurpurin B, C-467929, C-473872, N-306711, N-65828, N-103019 and congo red were tested for effects on Nsp15 endoribonuclease activity. A fluorescence assay revealed that the IC50 values for inhibiting endoribonuclease activity were between 0.2 µM and 40 µM. These compounds were demonstrated to bind SARS-CoV Nsp15 by a differential scanning fluorimetry assay. Benzopurpurin B also inhibited the endoribonuclease activities of the Nsp15 orthologs from two other coronaviruses: mouse hepatitis virus (MHV) and infectious bronchitis virus (IBV). Benzopurpurin B, C-473872, and congo red reduced infectivity of MHV in L2 cells by 8- to 26- fold. The more effective drugs caused a decrease in MHV RNA accumulation. All three compounds reduced the infectivity of the SARS-CoV in Vero cells.
Post City : a study in colonization on the Texas plains
Creators: name: Eaves, Charles Dudley, 1896-
Publisher: name: The University of Texas at Austin
Year: 1943
Subjects: subject: Post City
subject: Post
subject: Post Colony
subject: Texas
subject: History
subject: C. W. Post
subject: Charles William Post
subject: Colonization
subject: Post (Tex.)--History
subject: Post, C. W. (Charles William), 1854-1914

description: C. W. Post has become a legend in West Texas. Even to this day he is often the topic of conversation wherever West Texas folk may gather. It is true they know very little about Post. Some are inclined to look upon him as a kind of will-o'-the-wisp who, years ago, flitted in and out of a utopian community, and who with the magic wand caused a great cotton factory suddenly to spring out of the ground, clouds to obey his will by giving forth rain, and a whole town and country to spring into life with amazing rapidity. To others, he is known only as the restless genius who produced Post Toasties, Grape Nuts, Postum, and who had some mysterious connection with West Texas. Many are interested in finding out more about his plans and achievements in this region. Since the monumental collection of official records of the Post Colony has recently been made available for investigation, it is now possible to trace the development of this interesting colonial adventure from early beginnings to maturity as well as underlying motives of its founder. The subject matter of this study falls logically, as well as chronologically, into two main divisions, the building and colonization of Post City, and the improvement and colonization of farms. The construction of farm and city homes went on simultaneously during the first year, 1907; and while the building of city homes and business houses gained momentum, farm improvement was at a virtual standstill until the great farm colonization movement began in 1914. By the time the settlement of farms approached completion in 1917, the Post Colony may be said to have reached maturity. It was thought advisable, however, to deviate from this dual organization in the first chapter which introduces the founder, himself, as well as in the chapters on employees, transportation, trees, colonization and community building. The last five topics relate to both main divisions. Chapters on building the town, business enterprises, waterworks and town government relate almost wholly to urban matters. Farm operations, rainmaking and livestock are essentially agrarian in nature
Comparison of Low-Mass and High-Mass Star Formation
Creators: name: Tan, Jonathan C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: I review theoretical models of star formation and how they apply across the stellar mass spectrum. Several distinct theories are under active study for massive star formation, especially Turbulent Core Accretion, Competitive Accretion and Protostellar Mergers, leading to distinct observational predictions. These include the types of initial conditions, the structure of infall envelopes, disks and outflows, and the relation of massive star formation to star cluster formation. Even for Core Accretion models, there are several major uncertainties related to the timescale of collapse, the relative importance of different processes for preventing fragmentation in massive cores, and the nature of disks and outflows. I end by discussing some recent observational results that are helping to improve our understanding of these processes.
description: 9 pages, to appear in proceedings of IAU Symp. 315, From interstellar clouds to star-forming galaxies: universal processes?, eds. P. Jablonka, P. Andre, F. F. S. van der Tak
Humanized mice develop coronavirus respiratory disease
Creators: name: Baric, Ralph S.
name: Sims, Amy C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Coronavirus infections historically were associated with mild upper respiratory tract diseases in infants, children, and adults. Human coronavirus (HCoV)-OC43 and HCoV-229E were associated with 15–30% of common colds in winter and occasionally linked with lower respiratory tract disease in populations with chronic underlying diseases. HCoV research was complicated by the lack of a reverse genetic system or animal model. These viruses propagated poorly, and the number of reagents was limited. However, coronaviruses are capable of rapid host switching and evolution in changing ecologies (1), suggesting that their diversity and role in human disease were underappreciated. The 21st century heralded the arrival of the more pathogenic coronaviruses, like severe acute respiratory syndrome (SARS)-CoV. Then, HCoV-NL63 was identified as an important cause of severe lower respiratory tract infections in children and adults, including a tentative linkage with Kawasaki disease (2), and HCoV-HKU1 was identified in adults with pneumonia (3–5), renewing interest in the replication mechanisms and pathogenesis of HCoV-OC43 and HCoV-229E. In this issue of PNAS, Lassnig et al. (6) describe a transgenic mouse model to study HCoV-229E replication and pathogenesis, laying the groundwork for developing transgenic mouse models for other HCoVs.
Codon Bias Patterns of $E.coli$'s Interacting Proteins
Creators: name: Dilucca, Maddalena
name: Cimini, Giulio
name: Semmoloni, Andrea
name: Deiana, Antonio
name: Giansanti, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, $CompAI$, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for $E.coli$, comparing $CompAI$ with other widely used indices: $tAI$, $CAI$, and $Nc$. We show that $CompAI$ and $tAI$ capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, $CAI$ and $Nc$ appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of $tAI$ and $CompAI$ with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in $E.coli$. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by $CompAI$ and $tAI$). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, $CompAI$ turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation.
Effective control of neem (Azadirachta indica A. Juss) cake to plant parasitic nematodes and fungi in black pepper diseases in vitro
Creators: name: Duong, Duc Hieu
name: Ngo, Xuan Quang
name: Do, Dang Giap
name: Le, Thi Anh Hong
name: Nguyen, Vu Thanh
name: Nic, Smol
Publisher: name: Journal of Vietnamese Environment
Year: 2014

description: Neem cake is a product of the cold pressing from the neem kernels to obtain neem oil. Bio-active substances from neem cake extracted solutions were evaluated for their potential to control the root knot nematodes and other pests of plants. In this study different concentrations of the solution extracted from neem cake was tested against the second stage juveniles of the plant parasitic nematode Meloidogyne spp. and four phytopathogenic fungi: Rhizoctonia solani, Sclerotium rolfsii, Collectotrichum spp. and Phytopthora capsici. Toxicity of neem cake extractions is represented by the EC50 value for the second-stage juvenile (J2) of Meloidogyne spp. and the four phytopathogenic fungi via Probit analysis. A 5% dilution of the solvent extracting from neem cake already caused 100% larval mortality after 24 hours exposure. Undiluted neem cake extraction effectively inhibited the growth of the four phytopathogenic fungi. The EC50 value of neem cake on J2-larvae of Meloidogyne nematode and on the fungi Rhizoctonia solani, Sclerotium rolfsii, Collectotrichum spp. and Phytophthora capsici was 0.51, 0.74, 0.30, 0.51 and 4.33%, respectively. Bánh dầu neem là sản phẩm của quá trình ép nhân hạt neem để lấy dầu. Các hoạt chất sinh học từ dịch chiết bánh dầu neem đã được đánh giá có tiềm năng lớn trong phòng trừ tuyến trùng nốt sưng và các loài dịch hại khác của nhiều loại cây trồng. Trong nghiên cứu này các nồng độ dịch chiết khác nhau của bánh dầu neem đã được thử nghiệm khả năng diệt tuyến trùng (ấu trùng tuổi 2 thuộc giống Meloidogyne spp.) và ức chế 4 loài nấm bệnh như: Rhizoctonia solani, Sclerotium rolfsii, Collectotrichum spp. và Phytopthora capsici. Độc tính của dịch chiết bánh dầu neem được biểu diễn bởi giá trị EC50 đối với ấu trùng tuổi 2 của tuyến trùng Meloidogyne spp. và các loài nấm bệnh thông qua phân tích Probit. Dịch chiết bánh dầu neem ở nồng độ 5% đã làm chết 100% cá thể IJ2 của Meloidogyne spp sau 24 giờ phơi nhiễm. Dịch nguyên chất bánh dầu neem ức chế cả 4 loài nấm bệnh. Giá trị EC50 của bánh dầu neem lên ấu trùng tuổi 2 của Meloidogyne spp và các loài nấm bệnh Rhizoctonia solani, Sclerotium rolfsii, Collectotrichum spp. and Phytophthora capsici tương ứng là 0.51, 0.74, 0.30, 0.51 và 4.33%.
description: Journal of Vietnamese Environment, Vol 6 No 3 (2014)
A differential-geometric analysis of the Bergman representative map
Creators: name: Yoo, Sungmin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Complex Variables (math.CV)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 32C15 (Primary), 53B35, 53C55 (Secondary)

description: We show that the exponential map of the Bochner connection on the restricted holomorphic tangent bundle of a complex manifold admitting the positive-definite Bergman metric coincides with the inverse of Bergman's representative map. We also present a generalization of the Lu theorem, as an application.