Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of dehydration and electrolyte disturbances in cases of perennial ryegrass toxicosis in Australian sheep.

CASE REPORT Perennial ryegrass toxicosis (PRGT) is a common disease entity in Australia, presenting as an association of clinical signs including alterations in normal behavioural, ataxia ('staggers'), ill thrift and gastrointestinal dysfunction ('scours'). Clinical signs can range in severity from mild (gait abnormalities and failure to thrive) to severe (seizures, lateral recumbency and death). Presentation across the flock is usually highly variable. PRGT is caused by toxins produced by the endophytic fungus Neotyphodium lolii, a symbiont of perennial ryegrass that is present in pastures across the temperate regions of Australia and Tasmania. A particular feature of PRGT in Australia is the occasional occurrence of large-scale sheep losses, suggesting other factors are influencing mortality rates compared with other PRGT risk zones such as North America and New Zealand. During 2011, producers in the state of Victoria experienced a mild outbreak of PRGT that affected large numbers of animals but with limited mortalities. Clinical samples taken from affected sheep showed a high incidence of dehydration and electrolyte abnormalities. CONCLUSION We speculate that changes in hydration status may be a contributory aetiological factor in those years in which high numbers of deaths are associated with PRGT outbreaks in Australia.
Supporting Dynamic Service Composition at Runtime based on End-user Requirements

Network-based software application services are receiving a lot of attention in recent years, as observed in developments as Internet of Services, Software as a Service and Cloud Computing. A service-oriented computing ecosystem is being created where the end-user is having an increasingly more active role in the service creation process. However, supporting end-users in the creation process, at runtime, is a difficult undertaking. Users have different requirements and preferences towards application services, use services in different situations and expect highly abstract mechanisms in the creation process. Furthermore, there are different types of end-users: some can deliver more detailed requirements or can be provided with more advanced request interface, while others can not. To tackle these issues and provide end-users with personalised service delivery, we claim that runtime automated service composition mechanisms are required. In this paper we present the DynamiCoS framework, which aims at supporting the different phases required to provide end-users with automatic service discovery, selection and composition process. In this paper we also present the developed prototype and its evaluation.
Efficient oblivious transfer protocols

1 Introduction Oblivious Transfer (OT) protocols allow one party, the sender,to transmit part of its inputs to another party, the chooser, in amanner that protects both of them: the sender is assured that thechooser does not receive more information than it is entitled,while the chooser is assured that the sender does not learn whichpart of the inputs it received. OT is used as a key component inmany applications of cryptography. Its computational requirementsare quite demanding and they are likely to be the bottleneck inmany applications that invoke it. 1.1 Contributions. This paper presents several significant improvements tooblivious transfer (OT) protocols of strings, and in particular:(i) Improving the efficiency of applications which many invocationsof oblivious transfer. (ii) Providing the first two-round OTprotocol whose security analysis does not invoke the random oraclemodel.
Audio-visual gender recognition in uncontrolled environment using variability modeling techniques

The problem of gender recognition using visual and acoustic cues has recently received significant attention. This paper explores the use of Total Variability (i-vectors) and Inter-Session Variability (ISV) modeling techniques for both unimodal and bimodal gender recognition, and compares them to several state-of-the-art algorithms. The experimental evaluation is conducted on the FERET and LFW databases for face-based gender recognition, on the NIST-SRE database for audio-based gender recognition, and on the MOBIO database for audio-visual gender recognition. Results on LFW show that the i-vectors technique outperforms state-of-the-art algorithms, which are based on Support Vector Machines (SVM) applied either on raw pixels, on Local Binary Patterns (LBP) or on Gabor filters, with an accuracy rate of about 95%. Results on NIST-SRE show that the i-vectors system is also superior to state-of-the-art GMM-based gender recognition systems, with a relative gain of about 11%. Finally, results on MOBIO show that i-vectors and ISV also take advantage of combining visual and acoustic cues using logistic regression. The resulting bimodal systems achieve accuracy rates of about 98%.
Prevention of bleeding in hemophilia patients with high-titer inhibitors

Inhibitor development is the most serious adverse event linked to the treatment of hemophilia, as it renders standard hemostatic therapy ineffective. Consequently, inhibitor patients are at increased risk for difficult-to-control bleeding and complications, particularly arthropathy and physical disability. Three randomized clinical trials in patients with inhibitors have demonstrated that compared with on-demand bypassing therapy, prophylaxis with a bypassing agent reduces joint and other types of bleeding and improves health-related quality of life. In hemophilia patients without inhibitors, the initiation of prophylaxis with factor (F) VIII or IX prior to the onset of recurrent hemarthroses can prevent the development of joint disease. Whether this is also true for bypassing agent prophylaxis remains to be determined.
A Direct Approach to Optimal Feeder Routing for Radial Distribution System

Much of the research has been focused on developing the optimization techniques, varying from classical to nontraditional soft computing techniques, to solve the distribution system planning problem. Most of the methods preserve the distinctions and niceties, but dependent on complex search algorithm with a lot of convergence related issues that require more time to reach a firm conclusion at planning stage. This paper proposes a simple direct solution that significantly reduces the inherent difficulties of finding the solution and ensures optimum solution at the same time. Moreover, the concept of principle of optimality is effectively used to make the proposed technique more computationally efficient and useful. The effectiveness of the developed planning technique has been verified with different test cases.
Can Computer-Based Learning Environments (CBLEs) Be Used as Self-Regulatory Tools to Enhance Learning?

In this commentary, we utilize a social cognitive view of self-regulation to analyze the computer-based learning environments (CBLEs) that are described in the various articles in this volume. Although these CBLEs are creative ways of engaging students' metacognitive processes, their impact on students' motivational beliefs and self-reactions has been given relatively little attention to date. Self-regulation research on these sources of motivation in traditional learning environments has shown that they can play a vital role in explaining students' self-initiative and perseverance in the face of setbacks. When analyzing the forms of self-regulatory instruction that were employed, 2 of the CBLEs followed the first 2 sequential levels of a graduated "social-to-self" pattern advocated by social cognitive researchers. However, the other CBLEs often made nonsequential use of such social cognitive instructional processes as modeling, tutoring, providing feedback, and self-research.
A Natural Language Dialogue System for Impression-based Music Retrieval

Abstract —Impression-based music retrieval is the best way toﬁnd pieces of music that suit the preferences, senses, or mentalstates of users. A natural language interface (NLI) is more usefuland effective than a graphical user interface for impression-basedmusic retrieval since an NLI interprets users’ spontaneous inputsentences to represent musical impressions and generates queryvectors for music retrieval. Existing impression-based musicretrieval systems, however, have no dialogue capabilities formodifying the most recently used query vector. We evaluateda natural language dialogue system we developed that deals notonly with 164 impression words but also with 14 comparativeexpressions, such as “a little more” and “more and more,” and,if necessary, modiﬁes the most recently used query vector througha dialogue. We also evaluated performance using 35 participantsto determine the effectiveness of our dialogue system. Index Terms —Music retrieval, impression-based, naturallangauge dialogue.
High‐throughput capillary electrophoresis for the identification and differentiation of seven species of Eimeria from chickens

A capillary electrophoretic approach has been evaluated for the identification of seven currently recognised species of Eimeria infecting chickens. The second internal transcribed spacer of ribosomal DNA is PCR‐amplified from any of the seven species using a single set of oligonucleotide primers (one of which is fluorescently labelled). The amplicons are heat‐denatured and subjected to capillary electrophoresis in a MegaBACE™ 1000 (Amersham). The chromatograms captured are stored electronically and then analysed using MegaBACE Fragment Profiler software. Using control DNA samples representing monospecific lines of Eimeria, specific peaks in the chromatograms were defined for the unequivocal identification of each of the seven species and their differentiation. Electrophoretic reading and analysis are carried out automatically, thus making it a time‐ and cost‐effective method. This procedure should find applicability as a tool for the quality control of Eimeria vaccines, the monitoring of coccidiosis outbreaks and the high‐throughput analysis of oocyst samples for epidemiological surveys.
GENETIC TRANSFORMATION AND HYBRIDIZATION

We have assessed the use of a homeobox gene knotted1 (kn1) from maize as a selectable marker gene for plant transformation. The kn1 gene under the control of cauliflower mosaic virus 35S promoter (35S::kn1) was introduced into Nicotiana tabacum cv. Xanthi via Agrobacterium-mediated transformation. Under nonselective conditions (without antibiotic selection) on a hormonefree medium (MS), a large number of transgenic calli and shoots were obtained from explants that were infected with Agrobacterium tumefaciens LBA4404 harboring the 35S::kn1 gene. On the other hand, no calli or shoots were produced from explants that were infected with an Agrobacterium strain harboring pBI121 (nptII selection) or from uninfected controls cultured under identical conditions. Relative to kanamycin selection conferred by nptII, the use of kn1 resulted in a 3-fold increase in transformation efficiency. The transgenic status of shoots obtained was confirmed by both histochemical detection of GUS activity and molecular analysis. The results presented here suggest that kn1 gene could be used as an effective alternative selection marker with a potential to enhance plant transformation efficiency in many plant species. With kn1 gene as a selection marker gene, no antibiotic-resistance Communicated by P. Lakshmanan K. Luo · X. Zheng · Y. Xiao · Y. Pei ( ) Biotechnology Research Center, Southwest University, Chongqing, 400716 P.R. China e-mail: peiyan@swau.edu. cn Y. Chen Department of Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 P.R. China D. Zhao Key Laboratory of Agricultural Biotechnology, Guizhou University, Guizhou, 550025 P.R. China K. Luo · X. Zheng · Y. Chen · R. McAvoy · Y. Li ( ) Department of Plant Science, University of Connecticut, Storrs, CT 06269, USA e-mail: yi.li@uconn.edu or herbicide-resistance genes are needed so that potential risks associated with the use of these traditional selection marker genes can be eliminated.
Learning-based prediction of embedded memory timing failures during initial floorplan design

Embedded memories are critical to success or failure of complex system-on-chip (SoC) products. They can be significant yield detractors as a consequence of occupying substantial die area, creating placement and routing blockages, and having stringent Vccmin and power integrity requirements. Achieving timing-correctness for embedded memories in advanced nodes is costly (e.g., closing the design at multiple (logic-memory) cross-corners). Further, multiphysics (e.g., crosstalk, IR, etc.) signoff analyses make early understanding and prediction of timing (-correctness) even more difficult. With long tool and design closure subflow runtimes, design teams need improved prediction of embedded memory timing failures, as early as possible in the implementation flow. In this work, we propose a learning-based methodology to perform early prediction of timing failure risk given only the netlist, timing constraints, and floorplan context (wherein the memories have been placed). Our contributions include (i) identification of relevant netlist and floorplan parameters, (ii) the avoidance of long P&R tool runtimes (up to a week or even more) with early prediction, and (iii) a new implementation of Boosting with Support Vector Machine regression with focus on negative-slack outcomes through weighting in the model construction. We validate accuracy of our prediction models across a range of “multiphysics” analysis regimes, and with multiple designs and floorplans in 28FDSOI foundry technology. Our work can be used to identify which memories are “at risk”, guide floorplan changes to reduce predicted “risk”, and help refine underlying SoC implementation methodologies. Experimental results in 28nm FDSOI technology show that we can predict P&R slack with multiphysics analysis to within 253ps (average error less than 10ps) using only post-synthesis netlist, constraints and floorplan information. Our predictions are 40% more accurate than the predictions (worst-case error of 358ps and average error of 42ps) of a nonlinear Support Vector Machine model that uses only post-synthesis netlist information.
Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways

ABSTRACT Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways are chemical mediators of microbial interactions in diverse environments. However, little is known about their distribution, evolution, and functional roles in bacterial symbionts associated with animals. A prominent example is colibactin, a largely unknown family of secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS biosynthetic pathway that inflicts DNA damage upon eukaryotic cells and contributes to colorectal cancer and tumor formation in the mammalian gut. Thus far, homologs of this pathway have only been found in closely related Enterobacteriaceae, while a divergent variant of this gene cluster was recently discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of honey bees and identified a homologous colibactin biosynthetic pathway related to those found in Enterobacteriaceae. We show that the colibactin genomic island (GI) has conserved gene synteny and biosynthetic module architecture across F. perrara, Enterobacteriaceae, and the Pseudovibrio strain. Comparative metabolomics analyses of F. perrara and E. coli further reveal that these two bacteria produce related colibactin pathway-dependent metabolites. Finally, we demonstrate that F. perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a colibactin pathway-dependent manner. Together, these results support that divergent variants of the colibactin biosynthetic pathway are widely distributed among bacterial symbionts, producing related secondary metabolites and likely endowing its producer with functional capabilities important for diverse symbiotic associations.
An Improved Soil Moisture Retrieval Algorithm for ERS and METOP Scatterometer Observations

The scatterometers onboard the European Remote Sensing satellites (ERS-1 & ERS-2) and the METeorological OPerational satellite (METOP) have been shown to be useful for surface soil moisture retrieval using the so-called TU-Wien change detection method. This paper presents an improved soil moisture retrieval algorithm based on the existing TU-Wien method but with new parameterization as well as a series of modifications. The new algorithm, WAter Retrieval Package 5 (WARP5), copes with some limitations identified in the earlier method WARP4 and provides the possibility of migrating soil moisture retrieval from ERS-SCAT to METOP-ASCAT data. The WARP5 algorithm results in a more robust and spatially uniform soil moisture product, thanks to its new processing elements, including a method for the correction of azimuthal anisotropy of backscatter, a comprehensive noise model, and new techniques for calculation of the model parameters. Cross-comparisons of WARP4 and WARP5 data sets with the Oklahoma Mesonet in situ observations and also with European Centre of Medium Range Weather Forecast (ECMWF) ReAnalysis (ERA-Interim) global modeled data show that the new algorithm has a better performance and effectively corrects retrieval errors in certain areas.
Role of Zinc Finger Domains of the Transcription Factor Neuron-restrictive Silencer Factor/Repressor Element-1 Silencing Transcription Factor in DNA Binding and Nuclear Localization*

The transcription factor neuron-restrictive silencer factor/repressor element-1 (RE-1) silencing transcription factor (NRSF/REST) contains nine zinc finger domains and binds to the DNA element, neuron-restrictive silencer element/repressor element-1. REST4, a C-terminally truncated form of NRSF/REST, contains the five N-terminal zinc fingers and binds weakly to DNA yet is transported into the nucleus. To study the contribution of zinc fingers 6–8 to DNA binding, each was mutated. A mutation in zinc finger 6 or 8 had little effect; however, mutation of zinc finger 7 diminished DNA binding. Mutations in any two of these zinc fingers eliminated DNA binding. The contribution of zinc fingers 2–5 to nuclear targeting was studied. Deletion of zinc finger 5 prevented nuclear targeting. Mutations in zinc finger 2, 4, or 5 did not abolish nuclear targeting. However, a zinc finger 3 mutation together with a zinc finger 2 mutation localized to the nuclear envelope. A zinc finger 3 mutation alone or in combination with a zinc finger 4 or 5 mutation produced a punctate nuclear distribution. These results suggest the presence of signals for nuclear targeting, for nuclear entry, and for release from the translocation machinery within zinc fingers 2–5 of REST4.
Harmonization of laboratory results by data adjustment in multicenter clinical trials

Background/Aims In multicenter clinical trials, laboratory tests are performed in the laboratory of each center, mostly using different measuring methodologies. The purpose of this study was to evaluate coefficients of variation (CVs) of laboratory results produced by various measuring methods and to determine whether mathematical data adjustment could achieve harmonization between the methods. Methods We chose 10 clinical laboratories, including Green Cross Laboratories (GC Labs), the central laboratory, for the measurement of total cholesterol, high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), serum triglycerides, creatinine, and glucose. The serum panels made with patient samples referred to GC Labs were sent to the other laboratories. Twenty serum samples for each analyte were prepared, sent frozen, and analyzed by each participating laboratory. Results All methods used by participating laboratories for the six analytes had traceability by reference materials and methods. When the results from the nine laboratories were compared with those from GC Labs, the mean CVs for total cholesterol, HDL-C, LDL-C, and glucose analyzed using the same method were 1.7%, 3.7%, 4.3%, and 1.7%, respectively; and those for triglycerides and creatinine analyzed using two different methods were 4.5% and 4.48%, respectively. After adjusting data using Deming regression, the mean CV were 0.7%, 1.4%, 1.8%, 1.4%, 1.6%, and 0.8% for total cholesterol, HDL-C, LDL-C, triglyceride, creatinine, and glucose, respectively. Conclusions We found that more comparable results can be produced by laboratory data harmonization using commutable samples. Therefore, harmonization efforts should be undertaken in multicenter trials for accurate data analysis (CRIS number; KCT0001235).
Efficient Graph Matching

Application domains such as bioinformatics and web technology represent complex objects as graphs where nodes represent basic objects (i.e. atoms, web pages etc.) and edges model relations among them. In biochemical databases proteins are naturally represented as labeled graphs: the nodes are atoms and the edges are chemical links. In computer vision, graphs can be used to represent images at different levels of abstraction. In a low-level representation (Pailloncy, Deruyver, & Jolion, 1999), the nodes of a graph correspond to pixels and the edges to spatial relations between pixels. At higher levels of description (Hong & Huang, 2001), nodes are image regions and edges are spatial relations among them. In a Web graph (Deutsch, Fernandez, Florescu, Levy, & Suciu, 1999) nodes are web pages and edges are links between them. In all these domains, substructure queries that search for all exact or approximate occurrences of a given query graph in the graphs of the database can be useful. Research efforts in graph searching have taken three directions: the first is to study matching algorithms for particular graph structures (planar graphs, bounded valence graphs and association graphs); the second is to use elaborate tricks to reduce the number of generated matching maps (Cordella, Foggia, Sansone, & Vento, 2004); and the third is, since graph searching problem is NP-complete, to provide polynomial approximate algorithms. In the context of querying in a database of graphs many of the existing methods are designed for specific applications. For example, several querying methods for semi-structured databases have been proposed. In addition, commercial products and academic projects (Kelley 2002) for subgraph searching in biochemical databases are available. These two examples have a different underlying data model (a web-page database is a large graph whereas a biochemical database is a collection of graphs). In these two applications regular path expressions and indexing methods are used during query time to respectively locate substructures in the database and to avoid unnecessary traversals of the database. In general graph databases, there are some searching methods where the data graph and the query graph must have the same size. Other methods allow the query to be considerably smaller than the database graphs. A common idea in the above algorithms is to index the subgraph matches in the database and organize them in suitable data structures.