Miracle-dz/UniFAR-FTUs huggingface dataset:
AHypothesis Test for Equality of Bayesian NetworkModels

Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately fit models can be directly compared, but it is difficult to assign statistical significance to any observed differences. There would therefore be an advantage to the development of a rigorous hypothesis test for homogeneity of network structure. In this paper, a generalized likelihood ratio test based on Bayesian network models is developed, with significance level estimated using permutation replications. In order to be computationally feasible, a number of algorithms are introduced. First, a method for approximating multivariate distributions due to Chow and Liu (1968) is adapted, permitting the polynomial-time calculation of a maximum likelihood Bayesian network with maximum indegree of one. Second, sequential testing principles are applied to the permutation test, allowing significant reduction of computation time while preserving reported error rates used in multiple testing. The method is applied to gene-set analysis, using two sets of experimental data, and some advantage to a pathway modelling approach to this problem is reported.
A Markov Random Field Approach for Dense Photometric Stereo

We present a surprisingly simple system that allows for robust normal reconstruction by photometric stereo using a uniform and dense set of photometric images captured at fixed viewpoint, in the presense of spurious noises caused by highlight, shadows and non-Lambertian reflections. Our system consists of a mirror sphere, a spotlight and a DV camera only. Using this, a dense set of unbiased but noisy photometric data that roughly distributed uniformly on the light direction sphere is produced. To simultaneously recover normal orientations and preserve discontinuities, we model the dense photometric stereo problem into two coupled Markov random fields (MRFs): a smooth field for normal orientations, and a spatial line process for normal orientation discontinuities. A very fast tensorial belief propagation method is used to approximate the maximum a posteriori (MAP) solution of the Markov network. We present very encouraging results on a wide range of difficult objects to show the efficacy of our approach.
Tonic vergence and vergence adaptation.

In the absence of an adequate visual stimulus, the eyes are typically converged by approximately 0.25 to 0.75 meter angles (MA). This vergence response (VR) was believed to reflect the level of tonic innervation to the extraocular muscles, and accordingly has been termed tonic vergence (TV). However, this estimation fails to consider the magnitude of the anatomical position of rest. The true typical value of TV is approximately 23 degrees. This paper will consider various aspects of this parameter, including both clinical and laboratory methods of measurement, and the relationship between TV and the distance heterophoria. In addition, the role of vergence (or prism) adaptation, i.e., the apparent change in TV after periods of sustained fixation, is discussed. This shift appears to result from the relatively prolonged decay of the slow fusional vergence response (VR), with no evidence for a change in the level of tonic innervation. On occasion, the decay of slow fusional vergence may take hours or even days to reach completion. This extended rate of decay will have a significant impact upon the clinical measurement of a number of binocular parameters, most notably the assessment of heterophoria under truly dissociated conditions (i.e., in the absence of any fusional VR). Furthermore, both the magnitude and rate of decay of vergence adaptation appear to vary with age, as well as the presence of oculomotor imbalance. It is concluded that the output of the slow fusional vergence mechanism, as reflected by the degree of vergence adaptation, makes a major contribution to the aggregate, sustained VR in most visually normal patients.
Annealing of nanoindentation-induced high pressure crystalline phases created in crystalline and amorphous silicon

Thermally induced phase transformation of Si-III/Si-XII zones formed by nanoindentation has been studied during low temperature (200<T<300 °C) thermal annealing by Raman microspectroscopy and transmission electron microscopy. Two sizes of spherical indenter tips have been used to create substantially different volumes of phase transformed zones in both crystalline (c-Si) and amorphous silicon (a-Si) to study the zone size and starting matrix effects. The overall transformation is from Si-III/XII to poly- or nanocrystalline Si-I through intermediate phases of Si-XIII and Si-IV. Attempts have been made to determine the exact transformation pathways. Two scenarios are possible: either Si-XII first transforms to Si-III before transforming to Si-I through the intermediate phases or that Si-XII goes through the intermediate phases while Si-III transforms directly to Si-I. Finally, the phase transformations are slower in the larger indents and the starting matrix (crystalline or amorphous) has a substantial effe.
Co-integration analysis between performance of business incubator and incubation fund

Based on the data of business incubator's performance and incubation fund, the dynamic interactions are studied between performance of business incubator and incubation fund through co-integration test. The results indicates that long time dynamic co-integration relationship exists between graduated tenants and incubation fund and in the short term the change of incubation fund has a strong impact on the number of graduated tenants. The paper also finds that there is no long-term co-integration relationship between the total income of tenants and incubation fund.1
Frequency Modulated Continuous Wave System for Optical Fiber Intensity Sensors With Optical Amplification

We report on the use of erbium doped fiber (EDF) amplification to enhance a frequency modulated continuous wave (FMCW) technique for referencing optical intensity sensors located between two Bragg grating structures. The experiment combines the concept of FMCW with the spectrally selective mirror properties of Bragg gratings to interrogate with referencing properties intensity based sensors. The interrogation system without amplification yields a sensor resolution of around 0.078 dB. When the EDF amplifier is introduced into the experimental set up, the sensor sensitivity does not change, but the signal-to-noise ratio is improved, resulting into an enhanced resolution of 0.025 dB. We also obtain a remote sensing operation at a location of 50 km, showing the feasibility of this configuration to be used as a remote sensing application.
Chronic Wound Characterization using Bayesian Classifier under Telemedicine Framework

Chronic wound CW treatment by large is a burden for the government and society due to its high cost and time consuming treatment. It becomes more serious for the old age patient with the lack of moving flexibility. Proper wound recovery management is needed to resolve this problem. Careful and accurate documentation is required for identifying the patient's improvement and or deterioration timely for early diagnostic purposes. This paper discusses the comprehensive wound diagnostic method using three important modules, viz. Wounds Data Acquisition WDA module, Tele-Wound Technology Network TWTN module and Wound Screening and Diagnostic WSD module. Here the wound image characterization and diagnosis tool has been proposed under telemedicine to classify the percentage wise wound tissue based on the color variation over regular intervals for providing a prognostic treatment with better degree of accuracy. The Bayesian classifier based wound characterization BWC technique is proposed that able to identify wounded tissue and correctly predict the wound status with a good degree of accuracy. Results show that BWC technique provides very good accuracy, i.e. 87.40%, whereas the individual tissue wise accuracy for granulation tissue is 89.44%, slough tissue is 81.87% and for necrotic tissue is 90.91%.
A Novel Tool to Measure Extracellular Glutamate in the Zebrafish Nervous System In Vivo

Abstract Glutamate is the major excitatory neurotransmitter in the brain. Its release and eventual recycling are key to rapid sustained neural activity. We have paired the gfap promoter region with the glutamate reporter molecule, iGluSnFR, to drive expression in glial cells throughout the nervous system. Tg(gfap:iGluSnFR) is expressed on the glial membrane of Müller glia cells in the retina, which rapidly respond to stimulation and the release of extracellular glutamate. As glial cells are associated with most, if not all, synapses, Tg(gfap:iGluSnFR) is a novel and exciting tool to measure neuronal activity and extracellular glutamate dynamics in many regions of the nervous system.
L-myc polymorphism in head and neck nonmelanoma skin and lower lip cancers.

OBJECTIVE To evaluate the presence of L-myc gene variations as a genetic predisposition to head and neck nonmelanoma skin cancer (HNNMSC) and lower lip cancer (LLC). DESIGN A case-control study. SETTING An academic institute laboratory. PARTICIPANTS Twenty-four patients with HNNMSC and 27 with LLC were compared with 51 age- and sex-matched control subjects. MAIN OUTCOME MEASURES Polymerase chain reaction restriction fragment length polymorphism and agarose gel electrophoresis were used to determine the L-myc oncogene genotypes. RESULTS The presence of the LS genotype was found to be significantly increased in the study group, whereas the LL genotype was not detected. The S allele was also more frequent in the study group. The SS genotype was found to correlate with aggressive tumor behavior in patients with HNNMSC and a family history of cancer. Patients with LLC displayed significantly less of the SS genotype. CONCLUSIONS The L-myc gene polymorphism may help detect and prevent HNNMSC and LLC in susceptible individuals. It may also contribute to estimation of tumor behavior in patients with HNNMSC.
Autoinducer-2 Production in Campylobacter jejuni Contributes to Chicken Colonization

ABSTRACT Inactivation of luxS, encoding an AI-2 biosynthesis enzyme, in Campylobacter jejuni strain 81-176 significantly reduced colonization of the chick lower gastrointestinal tract, chemotaxis toward organic acids, and in vitro adherence to LMH chicken hepatoma cells. Thus, AI-2 production in C. jejuni contributes to host colonization and interactions with epithelial cells.
DNA and protein analyses of tick-derived isolates of Borrelia burgdorferi from California

Nine isolates of Borrelia burgdorferi from ixodid ticks collected in northern California were characterized. Restriction endonuclease analysis, pulsed-field gel electrophoresis, and Western blot (immunoblot) analysis were used in this study. Four isolates were very similar to each other. The others shared some similarities but were classified as having unique genotypes. A strain from an Ixodes neotomae tick displayed the greatest genetic and antigenic diversity when compared to the isolates collected from Ixodes pacificus ticks. A computerized library based on DNA banding patterns of the isolates by restriction enzyme analysis is also reported. This library was created by using a scanning laser densitometer.
A Petri Net Based Approach for Modelling and Analyzing Interorganizational Workflows with Dynamic Structure

Interorganizational workflows represent a special type of workflows that involve more than one organization. In this paper, an interorganizational workflow will be modelled using a special class of nested Petri nets, dynamic interorganizational workflow nets (DIWF-nets). DIWF-nets can model interorganizational workflows in which some of the local workflows can be removed, during the execution of the workflow, due to exceptional situations. Our approach permits a clear distinction between the component workflows and the communication structure. The paper defines a notion of behavioural correctness (soundness) and proves this property is decidable for DIWF-nets.
Stereo Vision using Heterogeneous Sensors for Complex Scene Monitoring

The intelligent monitoring of complex scenes usually requires the adoption of different sensors depending on the type of application (i.e. radar, sonar, chemical, etc.). From the past few years, monitoring is mainly represented by visual-surveillance. In this field, the research has proposed great innovation improving the surveillance from the standard CCTV to modern systems now able to infer behaviors in limited contexts. Though, when environments allow the creation of complex scenes (i.e. crowds, clutter, etc.) robust solutions are still far to be available. In particular, one of the major problems is represented by the occlusions that often limit the performance of the algorithms. As matter of fact, the majority of the proposed visual surveillance solutions processes the data flow generated by a single camera. These methods fail to correctly localize an occluded object in the real environment. Stereo vision can be introduced to solve such a limit but the number of needed sensors would double. Thus, to obtain the benefits of the stereo vision discharging some of its drawbacks, a novel framework in stereo vision is proposed by adopting the sensors available in common visual-surveillance networks. In particular, we will focus on the analysis of a stereo vision system which is build from a pairs of heterogeneous sensors, i.e., static and PTZ cameras with a task to locate objects accurately.
Mesenchymal stromal cells multipotency and plasticity: induction toward the hepatic lineage.

BACKGROUND Human mesenchymal stromal cells (MSCs) can be isolated from a variety of adult and perinatal tissues and exert multipotency and self renewal properties which make them suitable for cell-based therapy. Their potential plasticity extended to non-mesodermal-derived tissues has been indicated, although it is still a debated issue. In this study we have isolated MSCs from both adult and fetal tissues. Their growth, immunophenotype and multi-lineage differentiation potentials have been analyzed, focusing, in particular, on the hepatic differentiation. METHODS Cells were isolated from bone marrow (BMSC), adipose tissue (ATSC) and second trimester amniotic fluid (AFSC), upon a written informed consent obtained from donor patients. Cells were expanded and growth kinetics was assessed by means of proliferation assay. Their immunophenotype was analyzed using cytometry and multi-lineage differentiation potential was evaluated by means of in vitro differentiation assays. Finally, the expression of tissue-specific markers was also assessed by mean of semi-quantitative PCR. RESULTS Bipolar spindle-shaped cells were successfully isolated from all these tissues. Interestingly, ATSCs and AFSCs showed a higher proliferation potential than BMSCs. Mesodermal differentiation capacity was verified in all MSC populations, even if AFSCs were not able to undergo adipogenesis in our culture conditions. Furthermore, we showed that MSC cultured in appropriate conditions were able to induce hepatic-associated genes, such as ALB and TDO2. CONCLUSION Taken together the data here reported suggest that MSCs from both adult and fetal tissues are capable of tissue-specific commitment along mesodermal and non-mesodermal lineages. In particular we have demonstrated that a specific hepatogenic commitment can be efficiently induced, proposing these cells as suitable tool for cell-based applications aimed at liver regeneration.
Finding "Abstract Fields" of Web Pages and Query Specific Retrieval - THUIR at TREC 2004 Web Track

In this year's TREC Web Track research, THUIR participated in the Mixed-query Task. This task involves a single query set comprising 3 kinds of queries (Homepage Finding, Named Page Finding and Topic distillation) which are mixed and unlabelled. Efforts have been made on two directions: to find a strong and robust unified approach which works well for all kinds of queries, and to build a query-specific retrieval strategy that classifies queries by types and perform specific approaches. The using of non-content information has been studied in both approaches. With topic distillation and navigational search tasks in the last year, we are able to build a training set with 150 topics and corresponding relevant qrels. This training set is used to evaluate effectiveness of different methods in mixed query search. Experiments in section 2, 3 and 4 are all based on this set.
EFFECT OF IONS ON THE METABOLISM OF EJACULATED AND EPIDIDYMAL RAM SPERMATOZOA.

Summary. The effects of potassium, magnesium, calcium and phosphate ions on the metabolism of ejaculated and epididymal ram spermatozoa have been studied. Respiration and fructolysis were measured and isotopically labelled fructose was used to assess the contribution of fructose oxidation to total oxygen uptake. Potassium and phosphate ions significantly increased both respiration and fructolysis; magnesium and calcium had much less influence and there were few significant interactions between the ions tested. The most significant effect of washing spermatozoa free of seminal plasma was the reduction in the oxidation of substrates other than fructose. Washing also tended to accentuate the effects of other treatments. There were differences between ejaculated and epididymal spermatozoa in the response of oxidative metabolism to potassium but, in general, the metabolic patterns of these cells were similar.
A cooperative transponder system for improved traffic safety, localizing road users in the 5 GHz band

Abstract. We present a multi-user cooperative mobile transponder system which enables cars to localize pedestrians, bicyclists and other road users in order to improve traffic safety. The system operates at a center frequency of 5.768 GHz, offering the ability to test precision localization technology at frequencies close to the newly designated automotive safety related bands around 5.9 GHz. By carrying out a roundtrip time of flight measurement, the sensor can determine the distance from the onboard localization unit of a car to a road user who is equipped with an active transponder, employing the idea of a secondary radar and pulse compression. The onboard unit sends out a pseudo noise coded interrogation pulse, which is answered by one or more transponders after a short waiting time. Each transponder uses a different waiting time in order to allow for time division multiple access. We present the system setup as well as range measurement results, achieving an accuracy up to centimeters for the distance measurement and a range in the order of hundred meters. We also discuss the effect of clock drift and offset on distance accuracy for different waiting times and show how the system can be improved to further increase precision in a multiuser environment.
Segmentation Methods of Echocardiography Images for Left Ventricle Boundary Detection

Due to acoustic interferences and artifacts which are inherent in echocardiography images, automatic segmentation of anatomical structures in cardiac ultrasound images is a real challenge. This paper surveys state-of-the-art researches on echocardiography data segmentation methods, concentrating on methods techniques developed for clinical data. We present a classification of methodologies for echocardiography image segmentation. By choosing ten recent papers which have proposed innovative ideas that they proved certain clinical advantages or potential especial role to the echocardiography segmentation task. The contribution of the paper would be serving as a tutorial of the field for both clinicians and technologists, providing large number of segmentation techniques in a comprehensive and systematic manner and critically review recent approaches in terms of their performance and degree of clinical evaluation with respect to the final goal of cardiac functional analysis.
Targeted metabolomics on the shikimate and aromatic amino acid biosynthetic pathways

Wheeler, Robin E. M.S., Purdue University, May 2016. Targeted Metabolomics on the Shikimate and Aromatic Amino Acid Biosynthesis Pathways. Major Professor: John A. Morgan. The shikimate and aromatic amino acid biosynthesis pathways are some of the most studied biosynthetic pathways in nature due to their fundamental importance. Interest in this field stems from synthesis of the essential amino acids, tryptophan, tyrosine and phenylalanine. The pathways also are important as generating the precursors of thousands of secondary metabolites and lignin. Inhibiting the pathway has led to discovery of herbicides, pesticides as well as tuberculosis drugs. However there is currently a lack of a comprehensive targeted method for detecting and quantifying the majority of the intermediates in these pathways. Often multiple extraction and detection methods are used in a single paper to gather the desired data, which are a strain on time and resources. Here we developed two more comprehensive methods. The methods consisted of a single extraction coupled with an acidic and a neutral acetate buffer Using TBA as an ion paring agent. The chromatography was in the reverse phase mode on a C8 column. In the neutral extracts we used OPA as a derivitization reagent, while in the acidic method the extracts were run directly after concentration. The compounds are further separated and quantified in a MS/MS with a triple-quad detector. We are able to separate and detect 15 compounds in standards and validated the method on plant extracts from Arabidopsis
Strongly coupled phases ofN = 1 S-duality

We analyze S-duality of orientifolds of the Calabi-Yau cone over the rst del Pezzo surface (dP1). The S-duals of known phases, described by quiver gauge theories, contain intrinsically strongly-coupled sectors. These sectors are realized by a higher multiplicity intersection of NS5 branes and D5 branes atop an O5 plane, and can be thought of as stuck at the innite coupling point between two Seiberg-dual gauge theories. We argue that such sectors appear generically in orientifolds of non-orbifold singularities, where in many examples every orientifold phase contains such a sector. Understanding such sectors is therefore key to understanding orientifolds of Calabi-Yau singularities. We construct the strongly-coupled sectors for dP1 orientifolds using deconnement, and show that they have interesting, non- trivial properties. Using this construction, we verify the predictions of S-duality for dP1.
Data verification in information-centric networking with efficient revocable certificateless signature

Information-centric networking (ICN), a strong candidate for future internet architecture, consists of two kinds of packets, interest and data packets, both of which carry the name of data content to be requested (or delivered). The data packet is associated with a public key signature so that the data receiver can verify the data packet's correctness, integrity and provenance. Certificate-based signature (based on Public Key Infrastructure-PKI) and ID-based signature have been proposed to meet this purpose. In this paper, we propose to apply certificateless signature to fulfill this aim, because it not only mitigates the demand of PKI (for certificate-based signature), but also eliminates the key escrow problem (for identity-based signature), while still being able to leverage the ICN's naming feature. Moreover, it is essentially important to allow efficient user revocation for any signature scheme to better meet applications' demand. Motivated by these, we propose an efficient revocable certificateless signature scheme, greatly reducing the revocation complexity from linear (with respect to the works in the literature) to logarithmic complexity. The proposed scheme is based on the two key techniques, cover set and secret sharing technique, and is provably secure in the random oracle model. In addition, we present the case study of applying the proposed revocable certificateless signature in the ICN and evaluate the scheme's performance to show its feasibility.