Miracle-dz/UniFAR-FTUs huggingface dataset:
Countering knowledge markets in agri-systems

Agriculture and rural society faces many challenges for viability, security and sustainability. Part of the challenge comes from society demanding a broader contribution from agriculture towards economic, environmental and social purposes. Emerging issues for land managers include food security, traceability and quality specifications. Accompanying these challenges has been increased privatization of agricultural knowledge service industries. This paper uses a case study of the Australian Dairy sector to critique privatization strategies that aim to improve the management of knowledge as a whole of sector response to adaptation and change. The field research involved three phases: a literature review; an interview program with sector stakeholders; and a workshop to co-construct a national strategy for knowledge management. This dairy case contributes to a broader debate on issues of public and private knowledge resource management. These contributions are critically dependent on the structural arrangements and on the processes used to align networks of practices.
Mobile Computing with Python James “ Wez ” Weatherall

This paper describes MoPy, a port of the Python 1.5. 2 interpreter to the Psion 5/Epoc32 platform and Koala, a CORBA-style Object Request and Event Broker implemented natively in Python. While primarily a direct POSIX-based port of the standard Python interpreter, MoPy also adds thread, socket and serial support for the Psion platform. The Koala ORB is designed particularly with MoPy in mind and aims to support interoperation of devices over the low-power Prototype Embedded Network. The low-power requirements of PEN impose severe bandwidth and latency penalties to which conventional RPC technologies are not typically well suited.
Association Study between Polycystic Ovarian Syndrome and the Susceptibility Genes Polymorphisms in Hui Chinese Women

Introduction Polycystic ovary syndrome (PCOS) is one of the most common endocrine-metabolic disorders. Evidence of familial aggregation analysis and different clinical traits among different regions and ethnicities indicated that the pathogenesis of PCOS is associated with multiple genetic and environmental factors. Our previous research had identified three susceptibility loci (rs2479106, DENND1A; rs13405728, LHCGR; rs13429458, THADA) for PCOS in Han Chinese women. The overall aim of this study was to investigate the relationship between three susceptibility gene polymorphisms and PCOS in Hui ethnic women. Methods 151 patients with PCOS (case group) and 99 healthy women (control group) were recruited from the Reproductive Medicine Center of the General Hospital of Ningxia Medical University. Clinical data and serum hormone characteristics of case and control groups were collected and analyzed. The three susceptibility single-nucleotide polymorphisms have been replicated in both case and control groups. Gene polymorphisms were detected by direct sequencing after polymerase chain reaction. Results The Body Mass Index, LH, LH/FSH ratio and total testosterone were significantly elevated in PCOS patients compared to control group (P<0.05). The frequencies of genotype and allele in rs13405728 were significantly different between the PCOS and the control groups (P<0.05). Of the SNP rs13405728, the PCOS cases with TT genotype stayed at a higher level of total testosterone, TG and LDL than those with the CC and CT genotypes. In contrary, there was no statistical difference between the two groups for SNP rs13429458 and rs2479106 (P>0.05). Conclusion The present study suggested that the SNP rs13405728 in the LHCGR gene was associated with PCOS in Hui ethnic women, and its TT genotype characterized with higher level of TT, TG and LDL.
A Cross‐industry Analysis of Large Firm Transactional Public Web Sites

This study examines how the Fortune 500 use transactional public Web sites (TPWS). It applies innovation diffusion theory to identify variables and construct a model to explain differences in adoption rates of TPWS across industries. The study finds high rates of TPWS adoption in the airline, computer and office equipment, commercial banking, and retailing industries. The study also explains why the rates of TPWS adoption vary across different industries. Characteristics of both the innovation and the industry’s environment affect TPWS adoption. A high level of TPWS adoption is associated with industries where: products, services, and sales processes “fit” electronic transactions, the level of price competition is extreme, competitors are aggressively adopting the same technology, and firms are experienced with related technologies and have already developed the necessary information technology infrastructure. The study is significant because it identifies the specific innovation and environmental characteristics that drive varying rates of TPWS adoption among large firms across different industries.
Testing the role of circadian genes in conferring risk for psychiatric disorders

Disturbed sleep and disrupted circadian rhythms are a common feature of psychiatric disorders, and many groups have postulated an association between genetic variants in circadian clock genes and psychiatric disorders. Using summary data from the association analyses of the Psychiatric Genomics Consortia (PGC) for schizophrenia, bipolar disorder and major depressive disorder, we evaluated the evidence that common SNPs in genes encoding components of the molecular clock influence risk to psychiatric disorders. Initially, gene‐based and SNP P‐values were analyzed for 21 core circadian genes. Subsequently, an expanded list of genes linked to control of circadian rhythms was analyzed. After correcting for multiple comparisons, none of the circadian genes were significantly associated with any of the three disorders. Several genes previously implicated in the etiology of psychiatric disorders harbored no SNPs significant at the nominal level of P < 0.05, and none of the the variants identified in candidate studies of clock genes that were included in the PGC datasets were significant after correction for multiple testing. There was no evidence of an enrichment of associations in genes linked to control of circadian rhythms in human cells. Our results suggest that genes encoding components of the molecular clock are not good candidates for harboring common variants that increase risk to bipolar disorder, schizophrenia, or major depressive disorder. © 2014 Wiley Periodicals, Inc.
On non-singular inhomogeneous cosmological models

In this talk we would like to review recent results on non-singular cosmological models. It has been recently shown that among stiff perfect fluid inhomogeneous spacetimes the absence of singularities is more common than it was expected in the literature. We would like to generalize these results and apply them to other matter sources.
On the existence of accessible paths in various models of fitness landscapes

We present rigorous mathematical analyses of a number of well-known mathematical models for genetic mutations. In these models, the genome is represented by a vertex of the n-dimensional binary hypercube, for some n, a mutation involves the flipping of a single bit, and each vertex is assigned a real number, called its fitness, according to some rules. Our main concernis with the issue of existence of (selectively) accessible paths; that is, monotonic paths in the hypercube along which fitness is always increasing. Our main results resolve open questions about three such models, which in the biophysics literature are known as house of cards (HoC), constrained house of cards (CHoC) and rough Mount Fuji (RMF). We prove that the probability of there being at least one accessible path from the all-zeroes node v^0 to the all-ones node v^1 tends respectively to 0, 1 and 1, as n tends to infinity. A crucial idea is the introduction of a generalization of the CHoC model, in which the fitness of v^0 is set to some α = α_n ∈ [0, 1]. We prove that there is a very sharp threshold at α_n = (ln n)/n for the existence of accessible paths from v^0 to v^1 . As a corollary we prove significant concentration, for α below the threshold, of the number of accessible paths about the expected value (the precise statement is technical; see Corollary 1.4). In the case of RMF, we prove that the probability of accessible paths from v^0 to v^1 existing tends to 1 provided the drift parameter θ = θ_n satisfies n(θ_n) → ∞, and for any fitness distribution which is continuous on its support and whose support is connected.
Building a Believable Agent for a 3D Boxing Simulation Game

This paper describes an approach used to build a practical AI solution for a 3D boxing simulation game. The features of the designed AI agent are based on our deliberate concentration on believability, i.e. human-likeness of agent’s behavior. We show how learning by observation and case-based reasoning techniques can be used to create an AI decision-making system for an industrial-level computer game. The chosen AI design principles support high usability and maintainability, which is important for game developers. We prove experimentally that our AI system provides both believable and effective behavior.
Genetic alterations and signaling pathways in the evolution of gliomas

Gliomas are the most common primary brain tumors. They account for more than 70% of all neoplasms of the central nervous system and vary considerably in morphology, location, genetic alterations, and response to therapy. Most frequent and malignant are glioblastomas. The vast majority (>90%) develops rapidly after a short clinical history and without evidence of a less malignant precursor lesion (primary or de novo glioblastoma). Secondary glioblastomas develop more slowly through progression from low‐grade or anaplastic astrocytoma. These glioblastoma subtypes constitute distinct disease entities that affect patients of different age, develop through distinct genetic pathways, show different RNA and protein expression profiles, and may differ in their response to radio‐ and chemotherapy. Recently, isocitrate dehydrogenase 1 (IDH1) mutations have been identified as a very early and frequent genetic alteration in the pathway to secondary glioblastomas as well as that in oligodendroglial tumors, providing the first evidence that low‐grade astrocytomas and oligodendrogliomas may share common cells of origin. In contrast, primary glioblastomas very rarely contain IDH1 mutations, suggesting that primary and secondary glioblastomas may originate from different progenitor cells, despite the fact that they are histologically largely indistinguishable. In this review, we summarize the current status of genetic alterations and signaling pathways operative in the evolution of astrocytic and oligodendroglial tumors. (Cancer Sci 2009; 100 2235–2241)
Improving cooperation in Virtual Learning Environments using multi-agent systems and AIML

The large number of messages posted on the forum, a key element in Distance Education Courses based on Virtual Learning Environment, which does not receive adequate feedback from the tutor in sufficient time is a typical problem faced by students in these environments. The tutors, in turn, feel a lack of tools to monitor activities carried out by the student. This article proposes an approach for solving these problems based on the concept of perception, using the multiagent system paradigm. The system is composed by intelligent agents, which act in a Moodle discussion forum using an AIML knowledge base. Agents solve questions about matters discussed at the forum, and they use perception to recommend the implementation of activities that the student has not done. The results from simulations based on real courses already completed show that there is a decrease in the workload of tutors. Students are reminded the deadline for the tasks automatically. It was necessary to create hundreds of AIML rules to get answers to good level. The partial results indicate that the approach of combining AIML and MAS is promising to improve the feedback from tutors and motivate students to conclude their work on time.
Selectome: a database of positive selection

Genome wide scans have shown that positive selection is relatively frequent at the molecular level. It is of special interest to identify which protein sites and which phylogenetic branches are affected. We present Selectome, a database which provides the results of a rigorous branch-site specific likelihood test for positive selection. The Web interface presents test results mapped both onto phylogenetic trees and onto protein alignments. It allows rapid access to results by keyword, gene name, or taxonomy based queries. Selectome is freely available at http://bioinfo.unil. ch/selectome/.
Combining the Opinions of Several Early Vision Modules using a Multi-Layer Perceptron.

This paper deals with the solution of a binary classification problem by acting on the combined evidence of several early vision modules. Each module provides an opinion on the identity of an individual image element based on a specific area of expertise, such as texture, motion, depth etc. The problems involved in reaching a consensus of opinion are discussed, and the effectiveness of using a trained Multi-Layer Perceptron as a tool for data fusion is examined. Some preliminary results are reported. The original version of the document has been extended with new Appendices to cover recent developments in the field of pattern recognition and machine learning. We hope to show with this additional material that this approach to solving the data fusion problem is just as valid now as when we first suggested it, and does not have the failings of more recent and quite widespread approaches. Research Initiative in Pattern Recognition, DRA Electronics Division, St. Andrews Road, Malvern, Worcs. AI Vision Research Unit, University of Sheffield, Sheffield, Yorks. Computing and Maths Dept., Oxford Polytechnic, Oxford.
Difference Detection and Visualization in UML Class Diagrams

: Analyzing typical diagram life cycles results in the observation that they usually undergo several modiﬁcations during the development process. The better the tracking of such changes the more information can be obtained from them. As class diagrams are among the most widely used and most important UML diagram types, this paper investigates the concept of class diagram difﬁng and applies it to several application areas such as software design, implementation documentation, roundtrip modeling, and model driven development. I present the design of a change-detection implementation, which automatically detects differences between class diagrams and visualizes them by the use of color.
Biparametric versus multiparametric MRI in the diagnosis of prostate cancer

Background Since multiparametric magnetic resonance imaging (mp-MRI) of the prostate exceeds 30 min, minimizing the evaluation time of significant (Gleason scores > 6) prostate cancer (PCa) would be beneficial. A reduced protocol might be sufficient for the diagnosis. Purpose To study whether a short unenhanced biparametric MRI (bp-MRI) matches mp-MRI in detecting significant PCa. Material and Methods A total of 204 men (median age, 65 years; mean ± SD, 64.1; range 45–75 years; median serum PSA level, 14 ng/mL; range, 2.2–120 ng/mL; median prostate volume, 60 mL; range, 23–263 mL) fulfilled the criteria for being enrolled. They underwent mp-MRI and prostate biopsy from January through June 2014. Of the included patients, 9.3% underwent prostatectomy, 90.7% had TRUS-bx, and 10.8 had MRI-targeted TRUS-bx. Two radiologists separately assessed the mp-MRI examination (T2-weighted [T2W] imaging, diffusion-weighted imaging [DWI], apparent diffusion coefficient map [ADC-map] and dynamic contrast-enhanced imaging [DCE]). Two months later, the bp-MRI version (T2W imaging, DWI, and ADC-map) was evaluated. Results Reader 1: Assessing mp-MRI: 0 false negatives, sensitivity of 1, and specificity 0.04. Assessing bp-MRI: four false negatives, sensitivity of 0.94, and specificity 0.15. Reader 2: Assessing mp-MRI: five false negatives, sensitivity of 0.93, and specificity 0.16. Assessing bp-MRI: three false negatives, sensitivity of 0.96, and specificity 0.15. Intra-reader agreement Cohen’s Kappa (κ) was 0.87 for reader 1 (95% confidence interval [CI], 0.83–0.92) and 0.84 for reader 2 (95% CI 0.78–0.89). Conclusion Bp-MRI is as good as mp-MRI at detecting PCa. A large prospective study seems to be strongly warranted.
Towards simultaneous localization and transformation with a single moving camera

In the research field of robot navigation and control, how to determine the transformation on line among sensors and robots is a challenging problem. A simultaneous localization and transformation (SLAT) approach is proposed to tackle with the problem with a single camera. The purpose is to determine the transformations among fixed cameras. An extended Kalman filter (EKF) is recursively applied to determine simultaneous localization of a single camera and the speed-up robust feature (SURF) points on unknown feature boards in the fields of view of the fixed cameras. Then, the transformations among fixed cameras can be readily determined by virtue of the detected SURF feature points. The proposed approach can be applied to calibrate the transformations among vision sensors for the purpose of real-time navigation and control.
MIRU-VNTR Genotyping of Mycobacterium tuberculosis Strains Using QIAxcel Technology: A Multicentre Evaluation Study

Background Molecular genotyping of M.tuberculosis is an important laboratory tool in the context of emerging drug resistant TB. The standard 24-loci MIRU-VNTR typing includes PCR amplification followed by the detection and sizing of PCR fragments using capillary electrophoresis on automated sequencers or using agarose gels. The QIAxcel Advanced system might offer a cost-effective medium-throughput alternative. Methods Performance characteristics of the QIAxcel Advanced platform for the standard 24 VNTR loci panel was evaluated at two centres on a total of 140 DNA specimens using automated capillary electrophoresis as a reference method. Additionally 4 hypervariable MIRU-VNTR loci were evaluated on 53 crude DNA extracts. The sizing accuracy, interlaboratory reproducibility and overall instrument’s performance were assessed during the study. Results An overall concordance with the reference method was high reaching 98.5% and 97.6% for diluted genomic and crude DNA extracts respectively. 91.4% of all discrepancies were observed in fragments longer than 700bp. The concordance for hypervariable loci was lower except for locus 4120 (96.2%). The interlaboratory reproducibility agreement rates were 98.9% and 91.3% for standard and hypervariable loci, respectively. Overall performance of the QIAxcel platform for M.tuberculosis genotyping using a panel of standard loci is comparable to that of established methods for PCR fragments up to 700bp. Inaccuracies in sizing of longer fragments could be resolved through using in-house size markers or introduction of offset values. To conclude, the QiaXcel system could be considered an effective alternative to existing methods in smaller reference and regional laboratories offering good performance and shorter turnaround times.
Genetic Algorithm Based Approach for Optimization of Conducting Angles in Cascaded Multilevel Inverter

In this paper, a genetic algorithm (GA) optimization technique is applied to cascaded multilevel inverter to remove pre specified order of harmonics and to reduce THD. Genetic Algorithm is developed as the preferred solution algorithm of specific harmonic elimination (PWM-SHE) switching pattern. This paper describes an efficient genetic algorithm that reduces significantly the computational burden resulting in fast convergence. An 11-level and 9-level inverter is chosen as a case study, and optimum switching angles are determined to eliminate low order harmonics and to reduce THD. Comparison has been done between the 9-level and 11-level with respect to the consideration of THD. Simulation results validate purpose method.
Optimal simultaneous superpositioning of multiple structures with missing data

Motivation: Superpositioning is an essential technique in structural biology that facilitates the comparison and analysis of conformational differences among topologically similar structures. Performing a superposition requires a one-to-one correspondence, or alignment, of the point sets in the different structures. However, in practice, some points are usually ‘missing’ from several structures, for example, when the alignment contains gaps. Current superposition methods deal with missing data simply by superpositioning a subset of points that are shared among all the structures. This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether. Results: Here, we present a general solution for determining an optimal superposition when some of the data are missing. We use the expectation–maximization algorithm, a classic statistical technique for dealing with incomplete data, to find both maximum-likelihood solutions and the optimal least-squares solution as a special case. Availability and implementation: The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d. org. Contact: dtheobald@brandeis.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Perceptual Depth Preserving Saliency based Image Compression

The paper tackles the task of preserving depth cue in single images for human perception of depth despite compression artifact. The process is mainly divided into 2 steps; saliency map computation and image compression on the basis of salient regions. The idea is that the regions which are less blurred should be more salient rather than blurred regions. For saliency computation the proposed method first obtains the blur information for the image using frequency information. Then we generate saliency map by region combining on the basis of this blur index. These saliency values are used to vary the quality parameter over the blocks in the image for JPEG compression. Experimental results show that the proposed scheme yields good results over normal JPEG compresssion in terms of PSNR values.
Vagal Blocking Improves Glycemic Control and Elevated Blood Pressure in Obese Subjects with Type 2 Diabetes Mellitus

Background. An active device that downregulates abdominal vagal signalling has resulted in significant weight loss in feasibility studies. Objective. To prospectively evaluate the effect of intermittent vagal blocking (VBLOC) on weight loss, glycemic control, and blood pressure (BP) in obese subjects with DM2. Methods. Twenty-eight subjects were implanted with a VBLOC device (Maestro Rechargeable System) at 5 centers in an open-label study. Effects on weight loss, HbA1c, fasting blood glucose, and BP were evaluated at 1 week to 12 months. Results. 26 subjects (17 females/9 males, 51 ± 2 years, BMI 37 ± 1 kg/m2, mean ± SEM) completed 12 months followup. One serious adverse event (pain at implant site) was easily resolved. At 1 week and 12 months, mean excess weight loss percentages (% EWL) were 9 ± 1% and 25 ± 4% (P < 0.0001), and HbA1c declined by 0.3 ± 0.1% and 1.0 ± 0.2% (P = 0.02, baseline 7.8 ± 0.2%). In DM2 subjects with elevated BP (n = 15), mean arterial pressure reduced by 7 ± 3 mmHg and 8 ± 3 mmHg (P = 0.04, baseline 100 ± 2 mmHg) at 1 week and 12 months. All subjects MAP decreased by 3 ± 2 mmHg (baseline 95 ± 2 mmHg) at 12 months. Conclusions. VBLOC was safe in obese DM2 subjects and associated with meaningful weight loss, early and sustained improvements in HbA1c, and reductions in BP in hypertensive DM2 subjects. This trial is registered with ClinicalTrials.gov NCT00555958.