Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of infection in irritable bowel syndrome

A clinically distinct subset of Irritable Bowel syndrome (IBS) could be induced or exaggerated by bowel infection that is called post-infective IBS (PI-IBS) which is characterized by diarrhea predominant symptoms with less psychiatric illness. The purpose of this work was to study whether some bowel infections contribute to the pathogenesis of IBS and whether the treatment of such infections reduces IBS symptoms. 100 patients with symptoms suggestive of IBS according to Rome II Criteria were chosen from Internal Medicine outpatient clinic-Al Hussein university hospital. They were 64 females and 36 males, aged 18-52 years old with mean age 38,2  3,6 years. They were submitted to: full clinical examination and frequent stool examinations (direct smear and culture) before, soon after and six months after administration of drug therapies for common stool-positive associated bowel infections (diloxanide for E. histolytica, metronidazole for Giardia lamblia, Ketoconazole for Candida, ciprofloxacin for Salmonella and neomycin for Pseudomonas). Results obtained showed that 24% of patients had diarrhea predominant symptoms, 13 patients (54%) out of them had history suggestive of acute gastroenteritis. 80 patients had initial positive stool examination and continued the post treatment six months follow up study. Out of them, 13 patients had stool positive for Salmonella typhi mixed with E. histolytica; ten of them (76.9%) showed a statistically significant persistent clinical and laboratory improvement after ciprofloxacin therapy (P < 0.01). So Salmonella typhi may be implicated in IBS pathogenesis. Six patients showed isolated Giardia lamblia infection; four of them (66.7%) showed a statistically significant persistent clinical and laboratory improvement after metronidazole thereby (P < 0.05). Giardia lamblia parasite may be considered in triggering or exaggerating IBS symptoms. 24 patients had isolated E. histolytica infection; only one of them (4.2%) showed sustained clinical and Laboratory improvement after diloxanide therapy -statistically insignificant result- (P > 0.05). This finding makes the correlation between E. histolytica infection and IBS is unlikely. 20 patients had isolated Candida overgrowth on stool examination; eight of them (40%) showed a statistically significant clinical and laboratory improvement after Ketoconazole therapy (P < 0.05). Therefore Candida overgrowth may induce or exaggerate IBS symptoms. Finally, no growth was noticed for shigella sp. or E. coli, this may exclude the role of such organisms in IBS pathogenesis.
Multi-modal deep learning for predicting progression of Alzheimer's disease using bi-linear shake fusion

Alzheimer’s Disease (AD) which causes declination of cognitive function is one of the most severe social issues in the world. It has already been known that AD cannot be cured and treatment can only delay its progression. Therefore, it is very important to detect AD in early stage and prevent it to be worse. Furthermore, sooner the progression is detected, better the prognosis will be. In this research, we developed a novel multi-modal deep learning method to predict conversion from Mild Cognitive Impairment (MCI), which is the stage between cognitively normal older people and AD. In our method, the multi-modal input data are defined as structural Magnetic Resonance Imaging (MRI) images and clinical data including several cognitive scores, APOE genotype, gender and age obtained from Alzheimer’s Disease Neuroimaging Initiative cohort (ADNI). Our criteria of selecting these input data are that they are mostly obtained by non-invasive examination. The proposed method integrates features obtained from MRI images and clinical data effectively by using bi-linear fusion. Bi-linear fusion computes the products of all elements between image and clinical features, where the correlation between them are included. That led to a big improvement of prediction accuracy in the experiment. The prediction model using bi-linear fusion achieved to predict conversion in one year with 0.86 accuracy, comparing with 0.76 accuracy using linear fusion. The proposed method is useful for screening examination for AD or deciding a stratification approach within clinical trials since it achieved a high accuracy while the input data is relatively easy to be obtained.
Motor imagery based on adaptive parameterless empirical wavelet transform and selective integrated classification

Improving recognition rate of motor imagery (MI)-related electroencephalography (EEG) is of great importance for numerous brain computer interface (BCI) applications. However, the performance of a typical BCI system greatly relies on the effectiveness of the extracted features from raw EEG signals and the ability of the classifier to correctly identify different MI patterns. Therefore, in this paper, a new recognition method based on adaptive parameterless empirical wavelet transform (APEWT) and selective integrated classification model is proposed to enhance the classification accuracy of MI-related EEG signal. First, the APEWT is used to decompose EEG signals from different MI patterns into several intrinsic mode functions (IMFs), each of which contains different rhythm information over different frequency bands. Then several related modes are optimally selected based on the correlation coefficients calculated between each IMF component and the original signal to reconstruct EEG signals. Next, in order to further extract useful pattern information from both the time domain and frequency domain, the energy spectrum features of multiple time segments from the reconstructed signals and marginal spectrum features of different frequency bands corresponding to those selected modes are investigated, respectively. Finally, the extracted multiple features from time domain and frequency domain are input into the selective integrated classification model to build an MI recognition system. The selective integrated classification model consists of several extreme learning machines (ELMs) as the basic classifiers, different weights are assigned, respectively, to ELM basic classifiers based on their corresponding classification performances, and several basic ELM classifiers with good performances are selected to construct the final integrated model. The proposed method is evaluated on two public datasets, including BCI Competition Ⅱ dataset Ⅲ and BCI Competition IV dataset 2 b, and is compared with four different combination methods where different features in time domain or frequency domain in the feature extraction stage and different ELMs based classification models are considered. Experimental results demonstrate that the proposed method outperformed four combination methods and the existing methods recently reported in the literature using the same datasets in terms of classification accuracy and area under the ROC curve receiver operating characteristic metric. Specifically, our proposed method achieves the highest average classification accuracy (89.95%) in the compared methods, which indicates its better classification performance and generalization capability. In addition, the proposed method exhibits high computational efficiency, thus providing a new solution for online recognition of MI-related BCI and having the potential to be embedded in a practical system for controlling an external device.
Arginine is essential for the α-amylase inhibitory activity of the α-amylase/subtilisin inhibitor (BASI) from barley seeds

Treatment of barley alpha-amylase/subtilisin inhibitor (BASI) with reagents specific for arginine, histidine, methionine and tyrosine residues and amino and carboxyl groups indicates that an arginine residue(s) is essential for its action on the target enzyme barley alpha-amylase 2. Phenylglyoxal modified eight out of 12 arginine residues in BASI. Kinetic analysis shows that the inactivation of BASI follows a pseudo-first-order reaction and is due to reaction with one molecule of phenylglyoxal; the second-order rate constant is determined to be 2.95 M-1.min-1. At pH 8.0, BASI and barley alpha-amylase 2 form an inactive 1:1 complex. The Ki value of this association is 2.2 x 10(-10) M. The alpha-amylase protects four arginine residues and also the alpha-amylase inhibitory activity of BASI against phenylglyoxal. When BASI from the phenylglyoxal-modified target enzyme-inhibitor complex is isolated and subjected to a second treatment with phenylglyoxal, four additional arginine residues are modified, with concomitant loss of the inhibitory activity. These results are discussed in relation to a three-dimensional model of BASI based on the known structure of the corresponding inhibitor from wheat.
Regulation of Adipocyte Transcription by PPARgamma Ligands

Rosiglitazone (rosi) is a powerful insulin sensitizer, but serious toxicities have curtailed its widespread clinical use. Rosi functions as a high-affinity ligand for PPARgamma, the adipocyte-predominant nuclear receptor (NR). The classic model of NR action, involving binding of ligand to the NR on DNA, explains positive regulation of gene expression, but both ligand-dependent transcriptional repression and indirect regulation are not well understood. We have addressed these issues by studying the direct effects of rosiglitazone on gene transcription, using global run-on sequencing (GRO-seq). Rosi-induced changes in gene body transcription were pronounced after 10 minutes and correlated with steady-state mRNA levels as well as with transcription at nearby enhancers (eRNAs). Up-regulated eRNAs occurred almost exclusively at PPARg binding sites, to which rosi treatment recruited coactivators including MED1, p300, and CBP, without changes in binding of the corepressor NCoR. By contrast, down-regulated eRNAs fell in sites devoid of PPARg but enriched for a variety of other TFs in the C/EBP and AP-1 families. These enhancers lost coactivator binding upon rosi treatment, suggesting that rosi treatment causes redistribution of coactivators to PPARg sites and away from enhancers containing other TFs, leading to transcriptional repression at these eRNAs and their target genes. We also investigated the function of MRL-24, a compound that has been shown to lack PPARg transactivation activity and regulate a distinct subset of PPARg target genes while functioning as an equally effective insulin sensitizer as rosi. Though our goal was to identify whether MRL-24 regulates the same functional enhancers marked by eRNAs as rosi, we instead found that MRL-24 does not control a distinct subset of target genes, but rather acts as a partial agonist for PPARg. Together, these studies further our understanding of transcriptional regulation by modulation of PPARg activity, including insights into determining functional enhancers and mechanisms of transcriptional repression by activation of a NR. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Pharmacology First Advisor Mitchell A. Lazar Subject Categories Genetics | Molecular Biology This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1456 REGULATION OF ADIPOCYTE TRANSCRIPTION BY PPAR LIGANDS
Consistency of different tropospheric models and mapping functions for precise GNSS processing

The TOmographic Model of the IONospheric electron content (TOMION) software implements a simultaneous precise geodetic and ionospheric modeling, which can be used to test new approaches for real-time precise GNSS modeling (positioning, ionospheric and tropospheric delays, clock errors, among others). In this work, the software is used to estimate the Zenith Tropospheric Delay (ZTD) emulating real time and its performance is evaluated through a comparative analysis with a built-in GIPSY estimation and IGS final troposphere product, exemplified in a two-day experiment performed in East Australia. In addition, the troposphere mapping function was upgraded from Niell to Vienna approach. On a first scenario, only forward processing was activated and the coordinates of the Wide Area GNSS network (relative) were loosely constrained, without fixing the carrier phase ambiguities, for both reference and rover receivers and the ionospheric modeling was turned off. On a second one, precise point positioning (PPP) was implemented, every 900 seconds, introducing IGS transmitted orbits and clocks. Comparisons between TOMION and GIPSY estimates and IGS final product have been performed and the agreement between the the first two ones was of ±5mm, while both were over 2cm biased with respect to IGS products, despite using IGS satellite clocks and orbits for TOMION computations. Moreover, the standard deviation of the TOMIONs estimates computed in PPP mode was between 3 and 13mm, when compared to both external references. Additionally, Vienna mapping function showed in general a fairly better agreement than Niell although further improvement could be achieved for such estimations with coefficients for the Vienna mapping function calculated from raytracing as well as integrating meteorological comparative parameters.
The pathology of the thymus in myasthenia gravis

Myasthenia gravis (MG) is an autoantibody mediated autoimmune disease characterized by skeletal muscle fatigability and weakness through different types of immune attacks against various proteins of the postsynaptic membrane or in the neuromuscular cleft of the neuromuscular junction. In a subset of patients with autoantibodies against the muscle type acetylcholine receptors (AChRs) there is strong evidence that the thymus is involved in the pathogenesis of MG, while its role is questionable or unknown in MG due to autoantibodies against muscle specific kinase (MuSK), lipoprotein receptor like protein 4 and agrin. Here we describe the thymic alterations that have repeatedly been encountered in MG, i.e., thymic follicular hyperplasia (TFH) (thymitis), ‘thymic atrophy’, thymoma and thymolipoma. The potential link of non-thymic tumors [e.g., follicular dendritic cell (FDC) sarcoma] with MG will be discussed.
Investigation Of Dopamine Dynamics In Bdnf+/- Mice Using In Vivo Microdialysis And Electrochemical Analysis Of Purine And Monoamine Molecules Using A Boron-Doped Diamond Electrode

INVESTIGATION OF DOPAMINE DYNAMICS IN BDNF+/MICE USING IN VIVO MICRODIALYSIS AND ELECTROCHEMICAL ANALYSIS OF PURINE AND MONOAMINE MOLECULES USING A BORON-DOPED DIAMOND ELECTRODE by JOHNNA ANN BIRBECK August 2013 Advisor: Tiffany A. Mathews Major: Chemistry (Analytical) Degree: Doctor of Philosophy The goal of the first study was to determine if a reduction in brain-derived neurotrophic factor (BDNF) levels in female mice lead to a dysregulation in their dopaminergic system. Through a series of in vivo microdialysis and slice voltammetry experiments, we have discerned that female BDNF mice are hyperdopaminergic similar to their male BDNF counterparts. The in vivo microdialysis method zero-net flux highlighted that female BDNF mice had increased extracellular dopamine (DA) levels, while stimulated regional release by high potassium potentiated DA release from vesicular mediated depolarization. Using the complementary technique of fast scan cyclic voltammetry, electrical stimulation evoked greater release in the female BDNF mice, while uptake was not different from female wildtype mice. When the psychostimulant methamphetamine was administered, female BDNF mice had potentiated DA release compared to their wildtype counterparts. Taken together, the DA
SSR-based DNA fingerprints reveal the genetic diversity of Sicilian olive (Olea europaea L.) germplasm

Summary Twelve published simple sequence repeat (SSR; microsatellite) markers, belonging to the ssrOeUA-DCA, GAPU and UDO series, were tested in a panel of 46 accessions of olive germplasm belonging to 30 unique cultivars collected in seven Provinces of Sicily. Four well-known reference olive cultivars were also added. The analysis was carried out on an automatic capillary sequencer using fluorescent dyes, and fragment sizes were determined using internal standards. The results allowed us to rank the SSRs assayed according to their information content and reproducibility. Up to 115 alleles were identified (119, if those unique to sport mutations were included), the frequency of which allowed genetic relationships among accessions to be investigated. The probability that two unrelated genotypes displayed the same SSR pattern at all loci examined was calculated to be as low as 1.18 10–11. Sixteen accessions were identified as synonyms. Of these, eight matched perfectly with another accession at all SSR loci examined. The others showed one or two allelic differences from the reference accession. These were interpreted as mutations. Otherwise, all accessions were clearly separated from each other. Two likely parentages were also identified (‘Giarfara’ = ‘Nocellara del Belice’ ‘Cacaridduni’; and ‘Pizzo di Corvo’ = ‘Nocellara Etnea’ ‘Tonda Iblea’). The genetic diversity of the pool represented by the unique accessions was very high, reflecting the richness of the olive germplasm accumulated in Sicily. A database of the accessions is available to the scientific community (http://www.unipa.it/germolive/ssr.html) to facilitate comparisons of data.
Socrates Sim: A Dialog Simulation Framework to Support Task Completion Dialog Research

In this thesis, we propose an end-to-end dialog simulation framework, called Socrates Sim, to support task-completion dialog research. The goal of the framework is to provide a set of tools that will simulate generate between a user simulator and a dialog agent in order to evaluate the performance of the dialog agent and generate annotated data. Specifically, the Socrates Sim framework allows the researcher to define the custom dialog domains, build user simulators, and run multiple simulations with a provided dialog agent. To demonstrate the flexibility of the framework to generalize to new domains, implement end-to-end simulations in the following domains: restaurant recommendations and movie bookings. The framework is implemented in Python 3.6 and made available on GitHub (https://github.com/dhairyadalal/socrates).
Computer-Generated Holograms for 3D Imaging

Holography is usually considered as the ultimate way to visually reproduce a three-dimensional scene. Computer-generated holography constitutes an important branch of holography, which enables visualization of artificially generated scenes as well as real three-dimensional scenes recorded under white-light illumination. In this article, we present a comprehensive survey of methods for synthesis of computer-generated holograms, classifying them into two broad categories: wavefront-based methods and ray-based methods. We examine their modern implementations in terms of the quality of reconstruction and computational efficiency. As it is an integral part of computer-generated holography, we devote a special section to speckle suppression, which is also discussed under two categories following the classification of underlying computer-generated hologram methods.
A Survey on Computational Metaphor Processing

In the last decade, the problem of computational metaphor processing has garnered immense attention from the domains of computational linguistics and cognition. A wide panorama of approaches, ranging from a hand-coded rule system to deep learning techniques, have been proposed to automate different aspects of metaphor processing. In this article, we systematically examine the major theoretical views on metaphor and present their classification. We discuss the existing literature to provide a concise yet representative picture of computational metaphor processing. We conclude the article with possible research directions.
STUDI TENTANG KERAGAMAN GENETIK MELALUIPOLIMORFISME PROTEIN DARAH DAN PUTIH TELUR PADA TIGAJENIS AYAM KEDU PERIODE “LAYER”

Genetic variation of five blood protein loci and three egg white protein loci in three kinds of kedu chicken (kedu chicken with black skin and black feather (HH), kedu chicken with black skin and white feather (HP), kedu chicken with white skin and white feather (PP) were investigated by using polyacrilamide gel electrophoresis. The result showed that five blood loci (pre-albumin, albumin, post-transferin, transferin and hemoglobin) and three egg white loci (lysozim, ovalbumin and conalbumin) were found to be polymorphic in three kind of kedu chicken. Kedu chicken (HP) was highest average heterozygosity than HH and PP was shown by blood and egg white protein polymorphism. There were no difference on blood and egg white protein as genetic variation (P>0,05). Average of heterozygosity of kedu chicken of high production and low production were not different (P>0,05). Genetic distance between three population of kedu chicken showed that kedu chicken HP was close to population of PP than those of HH. Keragaman genetik dari lima lokus protein darah dan tiga lokus protein putih telur pada tiga jenis ayam kedu ( ayam kedu kulit hitam bulu hitam (HH), ayam kedu kulit hitam bulu putih (HP) dan ayam kedu kulit putih bulu putih (PP)) dianalisis menggunakan elektroforesis gel poliakrilamid. Hasil penelitian menunjukkan bahwa lima lokus protein darah (pre-albumin, albumin, posttransferin, transferin dan hemoglobin) tiga lokus protein putih telur (lisozim, ovalbumin and conalbumin) memiliki karakter polimorfik yang sama namun mempunyai tingkat keragaman yang berbeda. Ayam kedu HP memiliki nilai rataan heterosigositas tertinggi dibandingkan dengan ayam kedu jenis HH dan PP dilihat dengan elektroforesis darah. Rataan Heterosigositas tiga jenis ayam kedu yang dilihat dengan elektroforesis putih telur menunjukkan bahwa HP memiliki nilai tertinggi. Polimorfisme darah tidak berbeda nyata (P>0,05) dengan telur dalam menentukan keragaman genetik. Heterosigositas Ayam kedu produksi telur tinggi tidak berbeda nyata (P>0,05) dengan ayam kedu produksi telur rendah. Hubungan kekerabatan antara tiga jenis ayam kedu menunjukkan bahwa HP terdekat dengan PP terjauh dengan HH.
Basic Study on Elderly Tele-nursing Model for Emote Nursing by Smart Device

: This study was carried out to examine the development of an “elderly tele-nursing model” for care provided in-home by family members and through remote nursing systems in a super-aging society. This model studied the travel time, cost, and means of transportation of care providers. The pre-survey results regarding elderly tele-nursing show that a son/daughter can visit a parent more than once a week. In the results, the time required for elderly tele-nursing was influenced by whether or not the visitor uses the shinkansen (bullet train of Japan). In the main survey, based on 40 questionnaires, clear differences were observed according to whether visits were “every two weeks” or “once per month”. Furthermore, this result was also indicated by t -tests.
A 31.5-to-40.5 GHz injection-locked CMOS frequency tripler with injection-current enhancement technique

This letter presents an injection-locked 36 GHz frequency tripler (ILFT) for 5G applications. With the high order transformer based LC tank, over the target operating frequency range its phase response is flat at around 0 degree, and the injection-current is enhanced with a 3 rd harmonic LC tail filter, thereby achieving a wide locking range. Fabricated in a 65nm CMOS process, the ILFT consumes about 7.2 mW from a 0.6 V supply, and its core area without the output buffer and input matching network is only 0.25×0.4 mm 2 . With 0 dBm input injection power, the proposed ILFT achieves a locking range from 31.5 to 40.5GHz (25%).