bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA disruption assay is superior to conventional drug sensitivity assays in detecting cytotoxic drugs
Authors: Mapletoft Jonathan P. J. , St-Onge Renée J. , Guo Baoqing , Butler Phillipe , Masilamani Twinkle J. , D’costa Lavina , Pritzker Laura B. , Parissenti Amadeo M. 
Published: May 2020

AbstractConventional drug sensitivity assays used to screen prospective anti-cancer agents for cytotoxicity monitor biological processes associated with active growth and proliferation, used as proxies of cell viability. However, these assays are unable to distinguish between growth-arrested (but otherwise viable) cells and non-viable/dead cells. As a result, compounds selected based on the results of these assays may only be cytostatic, halting or slowing tumour progression temporarily, without tumour eradication. Because agents capable of killing tumour cells (cytotoxic drugs) are likely the most promising in the clinic, there is a need for drug sensitivity assays that reliably identify cytotoxic compounds that induce cell death. We recently developed a drug sensitivity assay, called the RNA disruption assay (RDA), which measures a phenomenon associated with tumour cell death. In this study, we sought to compare our assay’s performance to that of current commonly used drug sensitivity assays (i.e, the clonogenic, the cell counting kit-8 and the Trypan blue exclusion assays). We found that RNA disruption occurred almost exclusively when total cell numbers decreased (cytotoxic concentrations), with little to no signal detected until cells had lost viability. In contrast, conventional assays detected a decrease in their respective drug sensitivity parameters despite cells retaining their viability, as assessed using a recovery assay. We also found that the RDA can differentiate between drug-sensitive and -resistant cells, and that it can identify agents capable of circumventing drug resistance. Taken together, our study suggests that the RDA is a superior drug discovery tool, providing a unique assessment of cell death.
G3 and G9 Rotavirus genotypes in waste water circulation from two major metropolitan cities of Pakistan
Authors: Naqvi Syeda Sumera , Javed Sundus , Naseem Saadia , Sadiq Asma , Khan Netasha , Sattar Sadia , Shah Naseer Ali , Bostan Nazish 
Published: May 2020

AbstractRotavirus A (RVA) is a diarrheal pathogen affecting children under age five, particularly in developing and underdeveloped regions of the world due to malnutrition, poor healthcare and hygienic conditions. Water and food contamination are found to be major sources of diarrheal outbreaks. Pakistan is one of the countries with high RVA related diarrhea burden but with insufficient surveillance system. The aim of this study was to gauge the RVA contamination of major open sewerage collecting streams and household water supplies in two major metropolitan cities of Pakistan. Three concentration methods were compared using RNA purity and concentration as parameters, and detection efficiency of the selected method was estimated. Water samples were collected from 21 sites in Islamabad and Rawalpindi in two phases during the year 2014–2015. Meteorological conditions were recorded for each sampling day and site from Pakistan Meteorological Department (PMD). Nested PCR was used to detect the presence of RVA in samples targeting the VP7 gene. Logistic regression was applied to assess the association of weather conditions with RVA persistence in water bodies. Statistical analysis hinted at a temporal and seasonal pattern of RVA detection in water. Phylogenetic analysis of selected isolates showed a close association of environmental strains with clinical RVA isolates from hospitalized children with acute diarrhea during the same period. This is the first scientific report cataloging the circulating RVA strains in environmental samples from the region. The study highlights the hazards of releasing untreated sewerage containing potentially infectious viral particles into collecting streams, which could become a reservoir of multiple pathogens and a risk to exposed communities. Moreover, routine testing of these water bodies can present an effective surveillance system of circulating viral strains in the population.
3D Extension at Plate Boundaries Accommodated by Interacting Fault Systems
Authors: Collanega Luca , Corti Giacomo , Breda Anna , Massironi Matteo , Keir Derek 
Published: May 2020

AbstractComplex patterns of normal faults with multiple orientations and/or highly curved shapes have been traditionally explained by successive tectonic phases of 2-dimensional deformation. Alternatively, multiple fault sets have been proposed to develop simultaneously and in orthorhombic symmetry during a single phase of 3-dimensional deformation. We use analogue models of normal faults to demonstrate that, without the influence of pre-existing structures, 3D extension is preferentially accommodated by the alternate, rather than simultaneous, development of faults with different trends. By means of stress-driven interactions, 3D deformation can be partitioned into coupled systems of normal faults, which display geometries commonly observed in tectonic settings affected by interacting plate boundaries. Under radial extension, deformation is accommodated by major curvilinear grabens coupled with minor perpendicular faults, resulting in the triple junctions of grabens observed in Afar. On the other hand, the alternate development of perpendicular faults accommodates synchronous bi-directional and mutually perpendicular extension, giving the same fault pattern observed in the Barents Sea rift-shear margin.
ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
Authors: Karimian Emadoddin , Motamedian Ehsan 
Published: May 2020

AbstractThe development of new methods capable of more realistic modeling of microbial communities necessitates that their results be quantitatively comparable with experimental findings. In this research, a new integrated agent and constraint based modeling framework abbreviated ACBM has been proposed that integrates agent-based and constraint-based modeling approaches. ACBM models the cell population in three-dimensional space to predict spatial and temporal dynamics and metabolic interactions. When used to simulate the batch growth of C. beijerinckii and two-species communities of F. prausnitzii and B. adolescent., ACBM improved on predictions made by two previous models. Furthermore, when transcriptomic data were integrated with a metabolic model of E. coli to consider intracellular constraints in the metabolism, ACBM accurately predicted growth rate, half-rate constant, and concentration of biomass, glucose, and acidic products over time. The results also show that the framework was able to predict the metabolism changes in the early stationary compared to the log phase. Finally, ACBM was implemented to estimate starved cells under heterogeneous feeding and it was concluded that a percentage of cells are always subject to starvation in a bioreactor with high volume.
Generic Emergence of Modularity in Spatial Networks
Authors: Gilarranz Luis J. 
Published: May 2020

AbstractLandscape’s spatial structure has vast implications for the dynamics and distribution of species populations and ecological communities. However, the characterization of the structure of spatial networks has not received nearly as much attention as networks of species interactions counterparts. Recent experiments show the dynamical implications of modularity to buffer perturbations, and theory shows that several other processes might be impacted if spatial networks were modular, from disease transmission to gene flow. Yet the question is, are spatial networks actually modular? Even though some case studies have found modular structures, we lack a general answer to that question. Here, I show that modularity is a naturally emergent property of spatial networks. This finding is further reinforced by analyzing real patchy habitats. Furthermore, I show that there is no need for any other biological process other than dispersal in order to generate a significantly modular spatial network. Modularity is explained by the spatial heterogeneity in the density of habitat fragments. The fact that spatial networks are intrinsically modular might have direct consequences for population and evolutionary dynamics. Modules define the spatial limits of populations and the role each habitat fragment plays in ecological dynamics; they become the relevant scale at which a multitude of processes occur.
Matrine regulates H2O2-induced oxidative stress through long non-coding RNA HOTAIR/miR-106b-5p axis via AKT and STAT3 pathways
Authors: Xu Guanxue , Zhang Wei , Wang Zhenglong , Chen Man , Shi Bei 
Published: May 2020

Abstract
Matrine is a main active constituent of Chinese herb Sophora flavescens Ait (Kushen), which has shown various pharmacological effects, and has been reported to exhibit protective effects in heart failure. In the present study, the underlying mechanism of matrine was explored in H2O2-induced H9c2 cell line. It was confirmed that matrine could alleviate H2O2-induced injury in H9c2 cells. And the down-regulation of long non-coding RNA HOTAIR induced by H2O2 could be reversed by treating with matrine. Moreover, overexpression of HOTAIR promoted cell viability and superoxide dismutase (SOD) level, but inhibited cell apoptosis and lactate dehydrogenase (LDH) level. We found that miR-106b-5p was a target of HOTAIR and negatively regulated by HOTAIR. Moreover, up-regulation of miR-106b-5p restored the effects of HOTAIR overexpression on cell viability, apoptosis, and the levels of LDH and SOD. In addition, matrine protected H9c2 cells from H2O2-induced injury through HOTAIR/miR-106b-5p axis. Furthermore, we discovered that matrine exerted protective effects on H2O2-induced H9c2 cells through activating STAT3 and AKT pathway. In brief, matrine modulated H2O2-induced myocardial oxidative stress repair through HOTAIR/miR-106b-5p axis via AKT and STAT3 signaling pathway. Our study may provide a therapeutic target for the therapy of oxidative stress heart diseases.
Récepteurs purinergiques et fibrose hépatique
Authors: Chouiter Amelle , Dali Abdel-Rafik , Dellis Olivier 
Published: May 2020

Pour la cinquième année, dans le cadre du module d’enseignement « Physiopathologie de la signalisation » proposé par l’université Paris-sud, les étudiants du Master « Biologie Santé » de l’université Paris-Saclay se sont confrontés à l’écriture scientifique. Ils ont sélectionné une quinzaine d’articles scientifiques récents dans le domaine de la signalisation cellulaire présentant des résultats originaux, via des approches expérimentales variées, sur des thèmes allant des relations hôte-pathogène aux innovations thérapeutiques, en passant par la signalisation hépatique et le métabolisme. Après un travail préparatoire réalisé avec l’équipe pédagogique, les étudiants, organisés en binômes, ont ensuite rédigé, guidés par des chercheurs, une Nouvelle soulignant les résultats majeurs et l’originalité de l’article étudié. Ils ont beaucoup apprécié cette initiation à l’écriture d’articles scientifiques et, comme vous pourrez le lire, se sont investis dans ce travail avec enthousiasme ! Trois de ces Nouvelles sont publiées dans ce numéro, les autres le seront dans des prochains numéros.
An uncommon morphological variation of coracobrachialis muscle
Authors: Chitra P S , Anandhi V 
Published: May 2020

AbstractThe Coracobrachialis muscle in the arm is more important morphologically than functionally. In many animals, the Coracobrachialis has three parts. During the process of evolution the third part has disappeared and only the first two parts are found in man, enclosing the musculocutaneous nerve between them. Morphologic variations of Coracobrachialis have been known for a long time and include accessory slips that attach to the lesser tubercle, medial supracondylar ridge and medial intermuscular septum. The existence of abnormal insertion of the corabrachialis muscle should be kept in mind in a patient presenting with high median nerve palsy together with symptoms of brachial artery compression and before carrying out post-mastectomy reconstruction using coracobrachialis as a transposition flap.
Civinini bar: incidence in North Indians and its clinical relevance
Authors: Verma Rakesh Kumar , Rani Archana , Rani Anita , Chopra Jyoti , Pankaj Arvind Kumar , Kumar Navneet , Diwan Rakesh Kumar 
Published: May 2020

Abstract
Background and aim: Ossified pterygospinous ligament is a major cause of the entrapment of the lingual nerve or a branch of the mandibular nerve and may cause mandibular neuralgia. It can also constitute an obstacle for the mandibular nerve block which is a preferred method for pain relief especially for the fractures of mandible or cancer patients. Systematic study of these bars in North Indian population is lacking. Therefore this study was carried out to see the incidence of ossified pterygospinous bars in North Indian population. Materials and methods : The present study was an attempt to find out the occurrence of ossified pterygospinous ligament (Civinini's bar) in 116 dried skulls of unknown sex were taken and the presence of ossified pterygospinous bar was noted. Results : It was observed that the ossified pterygospinous bars which is present between pterygospinous process of lateral pterygoid plate and spine of sphenoid also called as Civinini's bar can be divided into five types (Types I, II, III, IV, V). This bar encloses a foramen called as Civinini's foramen. A total incidence of 18.10% of various types of pterygospinous bars was observed, out of which 1.72% were Type I, 8.62%Type II, 3.45%Type III, 0% Type IV and 4.31 % were of Type V variety. Conclusion : Total prevalence of Civinini bar is 18.10% in North Indian population.The clinicians working on this area should be aware of this variation as its prevalence is quite high.
Pd-Catalyzed Domino Reactions Involving Alkenes To Access Substituted Indole Derivatives
Authors: Beccalli Egle M. , Christodoulou Michael S. , Foschi Francesca , Giofrè Sabrina 
Published: May 2020

Palladium-catalyzed domino reactions are advanced tools in achieving various nitrogen-containing heterocycles in an efficient and economical manner due to the reduced number of steps in the process. This review highlights recent advances in domino processes aimed at the synthesis of indole derivatives and polycyclic systems containing the indole nucleus in intra/intra- or intra/intermolecular reactions. In particular, we consider domino processes that involve a double bond in a step of the sequence, which allow the issue of regioselectivity in the cyclization to be faced and overcome. The different sections in this review focus on the synthesis of the indole nucleus and functionalization of the scaffold starting from different substrates that have been identified as activated starting materials, which involve a halogenated moiety or unactivated unsaturated systems. In the former case, the reaction is under Pd(0) catalysis, and in the second case a Pd(II) catalytic species is required and then an oxidant is necessary to reconvert the Pd(0) into the active Pd(II) species. On the other hand, the second method has the advantage that it uses easy available and inexpensive substrates.1	Introduction2	Indole Scaffold Synthesis2.1	Activated Substrates2.2	Unactivated Substrates3	Functionalization of Indole Scaffold3.1	Activated Substrates3.2	Unactivated Substrates4	Conclusions
Data Migration: A Thorny Issue in Electronic Health Record Transitions—Case Studies and Review of the Literature
Authors: Schreiber Richard , Garber Lawrence 
Published: May 2020

Abstract
Objective To review the existing literature regarding data migration during electronic health record (EHR)-to-EHR transitions and add two case studies on this topic.
Methods Very few publications exist that detail the processes and potential pitfalls of data migration during EHR transitions. One of the authors participated in a panel discussion at the American Medical Informatics Association symposium in 2015; at the time, only five empiric or experiential research articles on any aspect of EHR transitions were available. Of those, only two mentioned their experiences with data migration or conversions. A detailed PubMed and CINAHL (Cumulative Index to Nursing and Allied Health Literature) search in March 2019 yielded only one more article giving details about data migration.
Results The two new case studies contrast starkly: one relied on manual abstraction and data entry, whereas the other leveraged several electronic tools. The literature reflects this diversity of approach: no two sites have reported the same approaches. The authors identify nine domains of potential consequences of the currently available techniques and offer mitigating strategies.
Discussion Very little empiric information exists in the peer-reviewed literature regarding data migrations during EHR-to-EHR transitions; yet the case studies reflect that much remains suitable for a prospective study.
Conclusion This report adds two new case studies to the six already reported in the literature. There is a wide disparity in techniques of data migration, each with its own set of pros and cons, which sites must consider during an EHR-to-EHR transition. Such transitions would benefit from prospective research on evaluation and knowledge discovery.
Progressive Vestibular Schwannoma following Subtotal or Near-Total Resection: Dose-Escalated versus Standard-Dose Salvage Stereotactic Radiosurgery
Authors: Sherry Alexander D. , Khattab Mohamed H. , Manzoor Nauman , Totten Douglas J. , Luo Guozhen , Chambless Lola B. , Rivas Alejandro , Haynes David S. , Cmelak Anthony J. , Attia Albert 
Published: May 2020

AbstractObjective Local failure of incompletely resected vestibular schwannoma (VS) following salvage stereotactic radiosurgery (SRS) using standard doses of 12 to 13 Gy is common. We hypothesized that dose-escalated SRS, corrected for biologically effective dose, would have superior local control of high-grade VS progressing after subtotal or near-total resection compared with standard-dose SRS.Design Retrospective cohort study.Setting Tertiary academic referral center.Participants Adult patients treated with linear accelerator-based SRS for progressive VS following subtotal or near-total resection.Main Outcome Measures Dose-escalated SRS was defined by a biologically effective dose exceeding a single-fraction 13-Gy regimen. Study outcomes were local control and neurologic sequelae of SRS. Binary logistic regression was used to evaluate predictors of study outcomes.Results A total of 18 patients with progressive disease following subtotal (71%) and near-total (39%) resection of Koos grade IV disease (94%) were enrolled. Of the 18 patients, 7 were treated with dose-escalated SRS and 11 with standard-dose SRS. Over a median follow-up of 32 months after SRS, local control was 100% in the dose-escalated cohort and 91% in the standard-dose cohort (p = 0.95). Neurologic sequelae occurred in 28% of patients, including 60% of dose-escalated cohort and 40% of the standard-dose cohort (p = 0.12), although permanent neurologic sequelae were low at 6%.Conclusions Dose-escalated SRS has similar local control of recurrent VS following progression after subtotal or near-total resection and does not appear to have higher neurologic sequalae. Larger studies are needed.
Network effects govern the evolution of maritime trade
Authors: Kosowska-Stamirowska Zuzanna 
Published: May 2020

Significance
Over 70% of the total value of international trade is carried by sea, accounting for 80% of all cargo volumes. Maritime trade flows impact both the economic development of the concerned regions and their ecosystems. Shipping routes are constantly evolving and likely to be affected by the consequences of climate change, while, at the same time, ships are a considerable source of pollution. This work performs a rigorous and comprehensive analysis of maritime trade flows on a global scale over a long period, taking into account aspects of evolution, reactions to shocks, and discovering predictive models. We use machine learning methods to uncover the single dominant dynamics that govern the evolution of the structure and the intensity of maritime trade.
Creativity in collaborative poetry translating
Authors: Lobejón Santos Sergio , Jones Francis 
Published: May 2020

Abstract
This study examines how creative solutions to translation problems are negotiated and selected in ‘poettrios’
(teams consisting of a source poet, a target-language poet and a bilingual language mediator working from pre-prepared, literal
translation drafts of poems), and compares creativity in this mode to that in solo poetry translating (Jones 2011). The interactions and outputs taken from real-time recordings, work-in-progress drafts and
participant interviews from several poettrios translating original poems from English into Dutch and from Dutch into English in
two workshops were coded and analysed quantitatively and qualitatively. The results show that creativity in poetry translating is
an eminently cognitive activity in which creative solutions typically emerge through the incremental contributions of the
complementary expertises of the individual poettrio members, with occasional radical leaps. In this incremental scaffolding
process, and similarly to solo translating, poettrios first consider non-creative options, then creative adjustments and, finally,
creative transformations. Radical solutions are generally only accepted when a departure from the source-text surface meaning
is deemed necessary to achieve the double aim of retaining the source poem’s message while producing an acceptable poem in the
target culture (Holmes 1988).
Measuring individual external doses of Tokyo Electric Power Company Holdings employees living in Fukushima prefecture
Authors: Uchiyama Keizo , Ishii Toshiaki , Koyabu Ken , Takizawa Koichi , Muto Shoichi 
Published: May 2020

Abstract
Since the accident at Fukushima Daiichi Nuclear Power Plant, individual external doses of residents have been investigated. To accurately analyse survey data, a variety of information, including the activity patterns of many residents, needs to be integrated. However, such large-scale surveys have not yet been conducted and actual individual external doses in Fukushima are unclear. In this study, the individual external doses of approximately 300 Tokyo Electric Power Company Holdings employees, who live and work in Fukushima Prefecture outside the Fukushima Daiichi Nuclear Power Plant, were measured. The employees carried GPS loggers and personal dosimeters capable of measuring dose in counts per minute. The employees’ individual external doses were compared along with their activity patterns. It was found that the annual additional individual external dose estimated based upon actual measurements was 1 mSv or less, and the influence on the individual external dose was also revealed.