Miracle-dz/UniFAR-FTUs huggingface dataset:
LSHTM Research Online

Background: Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century. Methodology/PrincipalFindings: Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters. Conclusions/Significance: The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICE Vch Hai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates. related to the strains circulating globally. Here, we have demonstrated that whole- genome sequencing is a valuable method to characterize V. cholerae isolates that circulated during the 2009 outbreak in the Northern Indian city of Chandigarh. Through comparative genomic analysis, we identified two clones that circulated during a single outbreak. Importantly, these clones contain significant differences in the structure of the cholera toxin gene and the Vibrio seventh pandemic island II. Our findings demonstrate the limitations of current molecular typing techniques and the importance of surveillance with whole-genome sequencing for iden-tifying V. cholerae clades with distinct genomic signatures.
Organic carbon at a remote site of the western Mediterranean Basin: composition, sources and chemistry during the ChArMEx SOP2 field experiment

32 33 Atmos. Chem. Phys. Discuss. , doi:10.5194/acp-2016-955, 2017 Manuscript under review for journal Atmos. Chem. Phys. Published: 23 January 2017 c © Author(s) 2017. CC-BY 3.0 License.
CLEP_A_308852 453..467

1Department of Medicine, The Ottawa Hospital Research Institute/The Ottawa Hospital, Ottawa, Ontario, Canada; 2Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada; 3ICES, Ottawa, Toronto, Ontario, Canada; 4Departments of Anesthesiology & Pain Medicine, University of Ottawa and Ottawa Hospital, Ottawa, Ontario, Canada; 5Department of Medicine at Schulich School of Medicine and Dentistry at Western University, London, Ontario, Canada; 6Cumming School of Medicine, Department of Medicine, University of Calgary, Calgary, Alberta, Canada; 7Department of Medicine, London Health Sciences Centre, London, Ontario, Canada; 8Faculty of Medicine, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; 9Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada Background: There is limited evidence on whether obstructive sleep apnea (OSA) can be accurately identified using health administrative data. Study Design and Methods: We derived and validated a case-ascertainment model to identify OSA using linked provincial health administrative and clinical data from all consecutive adults who underwent a diagnostic sleep study (index date) at two large academic centers (Ontario, Canada) from 2007 to 2017. The presence of moderate/severe OSA (an apnea– hypopnea index≥15) was defined using clinical data. Of 39 candidate health administrative variables considered, 32 were tested. We used classification and regression tree (CART) methods to identify the most parsimonious models via cost-complexity pruning. Identified variables were also used to create parsimonious logistic regression models. All individuals with an estimated probability of 0.5 or greater using the predictive models were classified as having OSA. Results: The case-ascertainment models were derived and validated internally through bootstrapping on 5099 individuals from one center (33% moderate/severe OSA) and validated externally on 13,486 adults from the other (45% moderate/severe OSA). On the external cohort, parsimonious models demonstrated c-statistics of 0.75–0.81, sensitivities of 59–60%, specificities of 87–88%, positive predictive values of 79%, negative predictive values of 73%, positive likelihood ratios (+LRs) of 4.5–5.0 and –LRs of 0.5. Logistic models performed better than CART models (mean integrated calibration indices of 0.02–0.03 and 0.06–0.12, respectively). The best model included: sex, age, and hypertension at the index date, as well as an outpatient specialty physician visit for OSA, a repeated sleep study, and a positive airway pressure treatment claim within 1 year since the index date. Interpretation: Among adults who underwent a sleep study, case-ascertainment models for identifying moderate/severe OSA using health administrative data had relatively low sensitivity but high specificity and good discriminative ability. These findings could help study trends and outcomes of OSA individuals using routinely collected health care data.
Extracting Environmental Research Trends using LDA

In this study, we compared topics of two distinct text data on environmental issues: environmental research reports and on-line environmental news using a Latent Dirichlet Allocation (LDA) analysis. For the environmental research reports, we used digitized research reports from the Korea Environment Institute, whereas for the newspaper, we crawled environment news articles on the Naver portal service. Once we extracted the topics, we compared the annual share of each topic in each text medium. From the LDA analysis, ten topics emerged from each medium. Six are common in both media, whereas four of the latest issues, namely, “gene variation,” “noise,” “health,” and “data,” only appeared in environmental news. In addition, among the six common topics, the share of “water pollution” and “waste” topics in environmental news appears to lead the share of the same two topics in the environmental research reports. These two results suggest that research topics tend to fall behind environmental issues in terms of latest interest. This study raises the possibility of using the LDA model to analyze research trends and find new research topics.
Reliability and Validity of the National Institutes of Health Stroke Scale for Neuroscience Nurses State-of-the-Science Nursing Review

The National Institutes of Health Stroke Scale (NIHSS) is used widely among stroke neurologists and neuroscience nurses. It is most commonly used with acute ischemic stroke (AIS) but is also used to assess patients after hemorrhagic stroke or a suspected transient ischemic attack. The scale is used widely to assess patient status acutely, to assess treatment efficacy, and to predict outcome. This article provides a review of pertinent information about the reliability, validity, instruction, and competency on the scale for neuroscience nurses. The NIHSS was introduced as a 15-item scale, later reduced to 14 items developed by stroke neurologists from the University of Cincinnati, the University of Iowa and the National Institutes of Health-National Institute of Neurological Disorders and Stroke. This graded physical examination is a measure of impairment that assesses level of consciousness using 3 items, speech, language, cognition, inattention, visual field abnormalities, motor strength (4 items), sensory impairment, and ataxia. It was designed specifically for AIS clinical trials, and potential scores range from 0 to 42. A modified version that removed the initial level of consciousness item, as well as the ataxia, facial weakness, and dysarthria items resulted in an 11-item scale with potential scores ranging from 0 to 31. Training and certification in use of the NIHSS are recommended. Formal training can be found in ≥2 places (www. strokeassociation.com or www.ninds.gov). Since the success of the National Institute of Neurological Disorders and Stroke intravenous recombinant tissue plasminogen activator (rt-PA) trial, it has been acknowledged that performing and documenting a physical examination in the most efficient and useful manner is a key element of nursing care for the patient with AIS. The most efficient manner for assessing patients who are awake is to use the NIHSS. In AIS it is advisable for the neurologist and nurse to perform the initial assessment together. Nurses should perform a complete bedside NIHSS assessment on admission to the intensive care unit and then an abbreviated version can be performed for the more frequent assessments needed for the patient who is post treatment with intravenous rt-PA. A complete NIHSS should be done if there is evidence of neurological decline or if there is an increase in the abbreviated score.
The Administration of Online Programs in Statewide Systems: A Case Study of the University System of New Hampshire

As enrollments in postsecondary online programs have grown, many institutions have pursued a more centralized business model that consolidates their online programming under a single executive leader, a statewide system office, or a coalition of institutions that have merged operations and assets. In this study, the researchers used an exploratory case study design--using both surveys and interviews--to investigate how online programs are administered at four institutions in the University System of New Hampshire (USNH). Several findings emerged from the data. First, participants struggled finding a common vocabulary when talking about online programs and the potential benefits of system-level collaboration; second, administrators frequently prioritized their local program tasks over system-wide collaboration; and third, although there was not a strategic plan in place to help institutions collaborate, participants agreed that such a plan would be valuable.
In uence of OLA and FA ligands on the optical and electronic properties of Cu

The use of formamide (FA) as an alternative capping ligand to oleylamine (OLA) during the preparation of Cu2ZnSnS4 (CZTS) nanoparticle inks was investigated. Photoluminescence properties of the selenised CZTS absorber layers revealed quasi-donor acceptor pairs (QDAP) as the main transition for carrier recombination with similar electrostatic potential uctuations in both type of ligands. In OLA layers the transition shifts from QDAP to band-impurity as temperature rises. Solar cell devices fabricated from FA Cu2ZnSn(Se,S) 4 were shunted due to the high porosity of the lm while in contrast, the combination of FA+OLA absorber yielded reduced back conCorresponding author Contributed equally Email addresses:s.campbell@northumbria.ac. uk (S. Campbell), y.qu@northumbria.ac. uk (Y. Qu), leon.bowen@durham.ac. uk (L. Bowen), patrick.chapon@horiba.com (P. Chapon), vincent.barrioz@northumbria.ac. uk (V. Barrioz), neil.beattie@northumbria.ac. uk (N. S. Beattie), guillaume.zoppi@northumbria.ac. uk (G. Zoppi) Preprint submitted to Solar Energy February 22, 2018 tact barrier height, lower series resistance and higher ll factor and e ciency compared to OLA devices. This is a direct result of the removal of the ne grain carbon rich layer from the back contact interface usually present in lms prepared with OLA only.
Formal Refinement Checking in a System-level Design Methodology

Rising complexity, increasing performance requirements, and shortening time-to-market demands necessitate newer design paradigms for embedded system design. Such newer design methodologies require raising the level of abstraction for design entry, reuse of intellectual property blocks as virtual components, refinement based design, and formal verification to prove correctness of refinement steps. The problem of combining various components from different designers and companies, designed at different levels of abstraction, and embodying heterogeneous models of computation is a difficult challenge for the designer community today. Moreover, one of the gating factors for widespread adoption of the system-level design paradigm is the lack of formal models, method and tools to support refinement. In the absence of provably correct and adequate behavioral synthesis techniques, the refinement of a system-level description towards its implementation is primarily a manual process. Furthermore, proving that the implementation preserves the properties of the higher system-level design-abstraction is an outstanding problem. In this paper, we address these issues and define a formal refinement-checking methodology for system-level design. Our methodology is based on a polychronous model of computation of the multi-clocked synchronous formalism SIGNAL. This formalism is implemented in the POLYCHRONY workbench. We demonstrate the effectiveness of our approach by the experimental case study of a SPECC modeling example. First, we define a technique to systematically model SPECC programs in the signal formalism. Second, we define a methodology to compare system-level models of SPECC programs and to validate behavioral equivalence relations between these models at different levels of abstraction. Although we use SPECC modeling examples to illustrate our technique, our methodology is generic and language-independent and the model that supports it conceptually minimal by offering a scalable notion and a flexible degree of abstraction.
Genetic background and development stage of maize in � uence disease severity and yield loss due to maize lethal necrosis ( MLN ) and Maize chlorotic mottle virus ( MCMV )

SURESH L.M. (  l.m.suresh@cgiar.org ) CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo https://orcid.org/0000-0001-6438-6502 Yoseph Beyene CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo MacDonald B. Jumbo ICRISAT: International Crops Research Institute for the Semi-Arid Tropics Dan Makumbi CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo Wilson Mwaura CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo Faith Njeru CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo Juan Burgueño CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo Boddupalli M. Prasanna CIMMYT: Centro Internacional de Mejoramiento de Maiz y Trigo
Edinburgh Research Explorer Non-DNA binding, dominant-negative, human PPARgamma mutations cause lipodystrophic insulin resistance

PPAR g is essential for adipogenesis and metabolic homeostasis. We describe mutations in the DNA and ligand binding domains of human PPAR g in lipodystrophic, severe insulin resistance. These receptor mutants lack DNA binding and transcriptional activity but can translocate to the nucleus, interact with PPAR g coactivators and inhibit coexpressed wild-type receptor. Expression of PPAR g target genes is markedly attenuated in mutation-containing versus receptor haploinsufﬁcent primary cells, indicating that such dominant-negative inhibition operates in vivo. Our observations suggest that these mutants restrict wild-type PPAR g action via a non-DNA binding, transcriptional interference mechanism, which may involve sequestration of functionally limiting
for – time for advancing from network signature to mechanistic equations

: The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains
Title: Experimental Investigation of the Kelvin-Helmholtz Instabilities of Cylindrical Gas Columns in Viscous Fluids Abbreviated title: Hydrodynamic Instability in Viscous Fluid

This paper derives analytical solutions for the critical Kelvin-Helmholtz (KH) instability conditions at the interface between a cylindrical gas column and a pool of viscous immiscible fluid confined in a chamber of finite size. The analysis focuses on conditions of negligible heat and mass transfer. The derivations are based on the established approaches reported in the literature with different boundary conditions. The most unstable instability conditions have also been calculated numerically. Experiments designed to measure the actual air column break-up conditions in water have been carried out to validate the analytical models. Comparisons show that the most unstable conditions predicted by the Viscous Corrections of the Viscous Potential Flow KH model are the best match to the experimentally measured break-up conditions. Parametric investigation of the instability theories shows that the vapour column size has a noticeable effect on the critical conditions, but has a negligible effect
Fast Maximum Likelihood for Blind Identification of Multiple FIR Channels

Abstruct-This paper develops a fast maximum likelihood method for estimating the impulse responses of multiple FIR channels driven by an arbitrary unknown input. The resulting method consists of two iterative steps, where each step minimizes a quadratic function. The two-step maximum likelihood (TSML) method is shown to be high-SNR efficient, i.e., attaining the CramCr-Rao lower bound (CRB) at high SNR. The TSML method exploits a novel orthogonal complement matrix of the generalized Sylvester matrix. Simulations show that the TSML method significantly outperforms the cross-relation (CR) method and the subspace (SS) method and attains the CRB over a wide range of SNR. This paper also studies a Fisher information (FI) matrix to reveal the identifiability of the M-channel system. A strong connection between the FI-based identifiability and the CR-based identifiability is established.
Multi-Model Identiﬁcation of HVAC System

: Heat, ventilation and air conditioning (HVAC) is a crucial system for maintaining acceptable air quality and keeping the building and its occupants healthy. There are some challenges in controlling and identifying this system as it commonly operates in different operation conditions. Furthermore, various types of un-controlled sources disturb the steady operations. In addition, an HVAC system is an inherently nonlinear system and varies with time. As a result, conventional methods are not successful in identifying and controlling this system. This paper proposes a new multi-model approach in which the clustering and regression steps are performed simultaneously to tackle this problem. Cost functions of clustering and regression steps are combined and optimized using an iterative algorithm. After identifying the local models, a gap metric based approach is used to develop a global model of the process. The proposed approach is tested on a simulated ventilation unit system and real-world dataset. The results show the performance of the proposed method of identifying the ventilation system.
ScholarWorks @ UTRGV ScholarWorks @ UTRGV Effects of Donor- and Supporter-Based Campaign Networks on Effects of Donor- and Supporter-Based Campaign Networks on Crowdfunding Campaign Success Crowdfunding Campaign Success

Driven by the increasing popularity of crowdfunding, academic researchers have examined the impacts of internal social capital accumulated on crowdfunding platforms and external social capital formed through online and offline friend networks on campaign success. However, no research has examined the impacts of social networks from a structural perspective. In the current research, we investigate the extent to which donor- and supporter-based campaign network centralities affect the amount of capital a fundraising campaign is able to generate. Using a panel data set collected from a donation-based crowdfunding platform, Fundly, we reveal that campaign network centralities based on strong ties (shared donors) and weak ties (shared supporters) are more important predictors of fundraising success than the number of donors a campaign has.
Response Characteristics Prediction of Surge Protective Device Based on NARX Neural Network

The nonlinear autoregressive network with exogenous inputs (NARX) is a recurrent dynamic neural architecture, which is commonly used for input–output modeling of nonlinear dynamical systems. Due to the lack of accurate mathematical model for the performance analysis on surge protective devices (SPDs), with the input of fast rising time electromagnetic pulse (FREMP), the NARX neural network is employed to predict the response characteristics of SPD in this paper. In order to verify the feasibility of this method, SPD test system is set up according to IEC 61000-4-24. The results show that the response curve estimated by the proposed model is in good agreement with experimental results, especially the waveform parameters such as response time, pulse peak, and residual voltage. The good forecasting performance of the network suggests that the NARX model used in this paper has good generalization ability. Moreover, with less measured data it can predict the response of the SPD under different voltage levels that were not yet measured.
The Sphagnum genome project: a new model for ecological and evolutionary genomics

The inception of the Sphagnum genome project marks the first plant-based sequencing project aimed specifically at carbon cycling genomics in a plant system relevant to ecological and evolutionary genomics. Sphagnum provides considerable intra- and inter - specific variation at the nucleotide level, and in physiology, morphology, net production, decomposition and carbon accumulation (peat formation). Together with their large number of species, their diversity in mating patterns, clear patterns of niche differentiation, Sphagnum provides an exceptionally valuable complement to Physcomitrella patens and Ceratodon purpureus as moss models for genomic research. Here we review the organismal biology of Sphagnum including phylogeny, life cycle, mating systems, ecology and niche differentiation. We include the current state of Sphagnum genomic resources, in vitro methods and germplasm. A use-case is provided to address questions concerning epigenetics and reproduction.