Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring the Properties of Transcription Factor Regulation

The regulatory targets of transcription factors are costly to directly detect using existing technologies. Many computational models have thus been developed to infer the genes targeted by TFs using gene expression profiles, position weight matrices modeling TF protein binding, histone modifications, and other secondary datasets. We develop a framework for scoring the potential targets of various TFs using models that take the profile of motif hits on the proximity of transcription start sites as input, and describe methods to validate this framework using expression datasets. These models are then extended to include cis-regulatory regions inferred from epigenetic data. Thesis Supervisor: Manolis Kellis Title: Professor of Computer Science
Subjective memory complaints. Relations to objective memory function, gender, personality, affective status and stress.

The overall aim of this thesis was to enhance the understanding of patients with subjective memory complaints. The thesis is based on three empirical studies examining middle-aged and young old (< 70 years) non-demented patients assessed at a memory clinic. In the first study the personality characteristics of the patients were compared with a Swedish normative sample. The patients scored higher on neuroticism and agreeableness and lower on extraversion. The female patients were in the majority and scored higher than the males on a scale assessing symptoms of anxiety and depression. Approximately half of the patients had objectively verified memory impairment (OMI) according to the neuropsychological assessment while the remaining patients were classified as having subjective memory impairment (SMI). No differences were revealed regarding personality characteristics or affective status between the OMI and SMI groups. In the second study about half of the patients reported significant stressors in their private life and a majority of the patients reported significant change at work related to strain. No gender differences were revealed regarding the presence or intensity of stressors. However, the female patients reported a higher level of affective stress response than the males. A large number, above all the women, were on sick leave. Furthermore, both a lower affective stress response and a better performance on a test of executive function were related to a higher basal morning cortisol level. The third study investigated potential changes regarding clinical characteristics and neuro¬psychological test results after one year. A reduction of depressive symptoms and an improved performance on a test of executive function were found in the OMI patients at the follow-up. None of the patients had converted to dementia. In conclusion, subjective memory complaints, even in younger populations should not be neglected. Our studies emphasise the complexity of subjective memory complaints. The results imply the need for a comprehensive assessment of cognitive functions, psychiatric and psychosocial variables as well as a gender perspective.
Rethinking Web Design Models: Requirements for Addressing the Content

The objective of hypermedia design models is to produce a well-organised web site. The organisation is undertaken at the level of a particular building-block – an abstract data unit which may match a frame, paragraph or region on a Web page. The increasing sophistication of these models allows the designer to deal with interaction and personalisation, but precludes one of the basic features of hypertext – the text itself. This paper argues that this oversight remains a fundamental problem because the component of content production for many web sites is not an abstract data unit but the concepts embedded in the paragraphs, sentences and words of the content regions. Consequently there is a gap between the organisation of material and the origination of material that is not well-addressed by current design methods. The paper considers the problem of concept modelling in the Semantic Web, its implementation in various hypertext environments and whether this approach can inform the current generation of hypermedia design models.
VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

A major challenge in interpreting the large volume of mutation data identified by next-generation sequencing (NGS) is to distinguish driver mutations from neutral passenger mutations to facilitate the identification of targetable genes and new drugs. Current approaches are primarily based on mutation frequencies of single-genes, which lack the power to detect infrequently mutated driver genes and ignore functional interconnection and regulation among cancer genes. We propose a novel mutation network method, VarWalker, to prioritize driver genes in large scale cancer mutation data. VarWalker fits generalized additive models for each sample based on sample-specific mutation profiles and builds on the joint frequency of both mutation genes and their close interactors. These interactors are selected and optimized using the Random Walk with Restart algorithm in a protein-protein interaction network. We applied the method in >300 tumor genomes in two large-scale NGS benchmark datasets: 183 lung adenocarcinoma samples and 121 melanoma samples. In each cancer, we derived a consensus mutation subnetwork containing significantly enriched consensus cancer genes and cancer-related functional pathways. These cancer-specific mutation networks were then validated using independent datasets for each cancer. Importantly, VarWalker prioritizes well-known, infrequently mutated genes, which are shown to interact with highly recurrently mutated genes yet have been ignored by conventional single-gene-based approaches. Utilizing VarWalker, we demonstrated that network-assisted approaches can be effectively adapted to facilitate the detection of cancer driver genes in NGS data.
Scheduling and network coding in wireless multicast networks: A case for unequal time shares

In this paper, we investigate the problem of network coding and media scheduling in wireless multihop networks. Unique characteristics of the wireless media, such as omnidirectional transmissions and destructive interference, as well as having one transceiver per wireless node, imply new code design constraints for wireless networks. Here, we formulate a linear program to solve the joint scheduling and network coding problem. Using our formulation, we demonstrate that for a large percentage of randomly generated wireless networks, the optimal scheduling time shares are unequal. All the existing network code design algorithms are based on equal scheduling time shares or the considered joint optimization problems do not have sufficient information for scheduling flows during unequal time shares. Therefore, we provide these statistics to emphasize the importance of enabling the code design algorithms to include unequal time shares. Our simulations further show that the network throughput can be significantly improved if the network code is properly designed to incorporate unequal time shares.
Differential expression of metabotropic glutamate and GABA receptors at neocortical glutamatergic and GABAergic axon terminals

Metabotropic glutamate (Glu) receptors (mGluRs) and GABAB receptors are highly expressed at presynaptic sites. To verify the possibility that the two classes of metabotropic receptors contribute to axon terminals heterogeneity, we studied the localization of mGluR1α, mGluR5, mGluR2/3, mGluR7, and GABAB1 in VGLUT1-, VGLUT2-, and VGAT- positive terminals in the cerebral cortex of adult rats. VGLUT1-positive puncta expressed mGluR1α (∼5%), mGluR5 (∼6%), mGluR2/3 (∼22%), mGluR7 (∼17%), and GABAB1 (∼40%); VGLUT2-positive terminals expressed mGluR1α (∼10%), mGluR5 (∼11%), mGluR2/3 (∼20%), mGluR7 (∼28%), and GABAB1 (∼25%); whereas VGAT-positive puncta expressed mGluR1α (∼27%), mGluR5 (∼24%), mGluR2/3 (∼38%), mGluR7 (∼31%), and GABAB1 (∼19%). Control experiments ruled out the possibility that postsynaptic mGluRs and GABAB1 might have significantly biased our results. We also performed functional assays in synaptosomal preparations, and showed that all agonists modify Glu and GABA levels, which return to baseline upon exposure to antagonists. Overall, these findings indicate that mGluR1α, mGluR5, mGluR2/3, mGluR7, and GABAB1 expression differ significantly between glutamatergic and GABAergic axon terminals, and that the robust expression of heteroreceptors may contribute to the homeostatic regulation of the balance between excitation and inhibition.
El modelo probabilístico: características y modelos derivados

Presentamos en este trabajo una revision del estado del arte de la familia de los modelos probabilisticos de recuperacion de informacion. Partiendo de los principios basicos que sustentan estos modelos, estudiaremos diferentes modelos concretos: el modelo de independencia binaria �el mas basico�, el ya clasico BM25 y, finalmente, los modelos DFR �uno de los ultimos desarrollos�.
High-Dose, Extended-Interval Colistin Administration in Critically Ill Patients: Is This the Right Dosing Strategy? A Preliminary Study

In critically ill patients with otherwise untreatable nosocomial infection due to gram-negative bacteria susceptible only to colistin, a high-dose, extended-interval colistin dosing regimen is, according to the pharmacokinetic/pharmacodynamic behavior of the drug, associated with low renal toxicity and high efficacy.
Toward integrative genomics study of genetic resistance to Salmonella and Campylobacter intestinal colonization in fowl

Salmonella enterica serotypes Enteritidis and Typhimurium and Campylobacter jejuni are responsible for most cases of food poisoning in Europe. These bacteria do not cause severe disease symptoms in chicken, but they are easily propagated by symptomless chicken carriers which cannot be easily isolated. This animal tolerance is detrimental to food safety. In this particular case, increasing animal's resistance is not sufficient, since some animals considered as resistant are able to carry bacteria during several weeks without displaying disease symptoms. We review studies aimed at evaluating the resistance of chicken to Salmonella and Campylobacter intestinal colonization, either a few days or several weeks after infection. While studies of the genetic control of Campylobacter colonization are only beginning, mostly due to technical difficulties in infection protocols, genetic studies of Salmonella colonization have been conducted for now more than 20 years. They have initially reported an estimation of the genetic parameters associated with resistance to Salmonella colonization and are now aimed at identifying the genomic regions controlling variation of this trait in experimental lines and commercial populations. With the advent of high-throughput genomics, we are closer than ever to identify the true genes controlling resistance to Enterobacteria colonization in chicken. The comparison of genes involved in early resistance to intestinal colonization with genes controlling resistance to bacteria persistence several weeks after infection (i.e., carrier-state) should soon highlight the differences between the molecular mechanisms underlying those two distinct phenotypes. It will also be highly interesting to compare the genes or genomic regions controlling Campylobacter and Salmonella, in order to evaluate the feasibility of a selection conducted on both bacteria simultaneously.
Characterisation of angiogenetic growth factor production in adipose tissue-derived mesenchymal cells

Abstract Optimal vascularisation of the graft site is significant for improving the outcome of fat grafting. Adipose tissue, specifically the stromal vascular fraction (SVF), is known to regulate its own vascular network. In order to assess the production of angiogenetic growth factors, this study investigated the content of insulin growth factor (IGF), vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), leptin, and metallothioneine-9 (MMP-9) in the SVF after incubation in differentiation or proliferation media. The SVF was isolated from human subcutaneous adipose tissue. Cells were either cultured in proliferation medium (PM) or in differentiation medium (DM). The samples were analysed for the respective factors using ELISA after 3 and 6 days. The GF levels showed a distinctive characteristic over time depending on the culture medium. IGF, PDGF, and MMP-9 levels decreased with PM and increased with DM. VEGF levels were increased in both media. Leptin showed a decrease in both media. The differentiation medium was associated with high inter-individual distribution in growth factor production except for PDGF and Leptin. In conclusion, incubation with differentiation medium produces a more reliable increase of selected growth factors than incubation with proliferation medium. Enrichment of fat grafts with growth factor-activated autologous SVF samples could help to enable better ingrowth of the transplanted tissue and a more stable outcome. The scattering of the results could explain the inter-individual differences regarding the outcome.
Low-dose almitrine bismesylate in the treatment of hypoxemia due to chronic obstructive pulmonary disease.

STUDY OBJECTIVE Assessment of acute and chronic effects of low-dose almitrine bismesylate (AB) in stable chronic obstructive pulmonary disease (COPD). STUDY DESIGN Oral administration of AB, 25 mg three times a day, for 6 months in all patients. Pulmonary function, blood gases, and peripheral nerve conduction velocity were measured at baseline and after long-term administration of AB. In addition, oral pharmacokinetics and effects on pulmonary circulation at rest were studied in half of the patients. Intravenous pharmacokinetics were measured after a single intravenous dose of 60 mg of AB 3 months before the start of oral AB treatment in the other seven patients. SETTING Outpatient clinic of a community hospital in a coal mining district in southwest Germany. PATIENTS Fourteen patients with clinically stable COPD and hypoxemia. RESULTS Acute effects of AB were as follows: a significant increase in arterial oxygen tension (PaO2) from 61 +/- 7 mm Hg to 74 +/- 8 mm Hg (p < 0.001), a decrease in arterial carbon dioxide tension (PaCO2) from 41 +/- 8 mm Hg to 38 +/- 7 mm Hg (p < 0.01), a rise of pH from 7.45 +/- 0.04 to 7.48 +/- 0.04 (p < 0.01), and a transient increase in mean pulmonary artery pressure from 26 +/- 7 to 29 +/- 6 mm Hg (not significant). After long-term treatment, once tissues were saturated with almitrine, improvement in gas exchange persisted with a PaO2 of 70 +/- 10 mm Hg (p < 0.001) and a PaCO2 of 39 +/- 6 mm Hg (not significant) without elevation of pH (7.45 +/- 0.04) or of pulmonary artery pressure (26 +/- 8 mm Hg). The terminal half-life of AB was 56 +/- 45 days after a single intravenous administration, and 55 +/- 16 days after long-term oral dosing. None of the patients developed clinically manifest peripheral neuropathy. Impaired asymptomatic peripheral motor nerve function was prevalent in 4 (29 percent) of the patients and remained unchanged during long-term AB administration. However, asymptomatic impairment of motor nerve conduction velocity developed in two patients with inadequate high AB plasma levels despite low-dose therapy. Both patients were known to have additional conditions predisposing for neuropathy. CONCLUSIONS Low-dose AB therapy, 75 mg daily, resulted in sustained elevation of arterial oxygen tension in hypoxemic patients with COPD. Although pulmonary artery pressure increased transiently after the first dose, it remained unchanged with long-term treatment despite persistent improvement of pulmonary gas exchange. (ABSTRACT TRUNCATED AT 250 WORDS)
A real-time approach for novelty detection and trajectories analysis for anomaly recognition in video surveillance systems

In this paper, we present a novel approach for automatic object detection and also using on-line trajectory clustering for RT anomaly detection in video streams. The proposed approach is based on two main steps. In the first step, a recently introduced approach called Recursive Density Estimation (RDE) is used for novelty detection. This method is using a Cauchy type of kernel which works on a frame-by-frame basis and does not require a pre-defined threshold to identify objects. In the second step, multifeature object trajectory is clustered on-line to identify anomalies in video streams. To identify an anomaly, first the trajectories are transformed into a set of features in a space to which eClustering approach identifies the modes and the corresponding clusters. At the end, by using cluster fusion the final common pattern is estimated and any sparse trajectories are considered as anomalous.
Behavioral modeling of switched-capacitor sigma-delta modulators

This paper presents a complete set of blocks implemented in the popular MATLAB SIMULINK environment, which allows designers to perform time-domain behavioral simulations of switched-capacitor (SC) sigma-delta (/spl Sigma//spl Delta/) modulators. The proposed set of blocks takes into account most of the SC /spl Sigma//spl Delta/ modulator nonidealities, such as sampling jitter, kT/C noise, and operational amplifier parameters (white noise, finite DC gain, finite bandwidth, slew rate and saturation voltages). For each block, a description of the considered effect as well as all of the implementative details are provided. The proposed simulation environment is validated by comparing the simulated behavior with the experimental results obtained from two actual circuits, namely a second-order low-pass and a sixth-order bandpass SC /spl Sigma//spl Delta/ modulator.
Different Movement of Hyolaryngeal Structures by Various Application of Electrical Stimulation in Normal Individuals

Objective To identify the differences in the movement of the hyoid bone and the vocal cord with and without electrical stimulation in normal subjects. Methods Two-dimensional motion analysis using a videofluoroscopic swallowing study with and without electrical stimulation was performed. Surface electrical stimulation was applied during swallowing using electrodes placed at three different locations on each subject. All subjects were analyzed three times using the following electrode placements: with one pair of electrodes on the suprahyoid muscles and a second pair on the infrahyoid muscles (SI); with placement of the electrode pairs on only the infrahyoid muscles (IO); and with the electrode pairs placed vertically on the suprahyoid and infrahyoid muscles (SIV). Results The main outcomes of this study demonstrated an initial downward displacement as well as different movements of the hyoid bone with the three electrode placements used for electrical stimulation. The initial positions of the hyoid bone with the SI and IO placements resulted in an inferior and anterior displaced position. During swallowing, the hyoid bone moved in a more superior and less anterior direction, resulting in almost the same peak position compared with no electrical stimulation. Conclusion These results demonstrate that electrical stimulation caused an initial depression of the hyoid bone, which had nearly the same peak position during swallowing. Electrical stimulation during swallowing was not dependent on the position of the electrode on the neck, such as on the infrahyoid or on both the suprahyoid and infrahyoid muscles.
The Prevalence of Attention Deficit Hyperactivity Symptoms in Schoolchildren in a Highly Consanguineous Community

Objective: The objective of the present study was to find the prevalence of attention deficit hyperactivity (ADH) symptoms in a sample of primary schoolchildren in Qatar and investigate the behaviour of the children with and without ADH symptoms in a highly consanguineous community. Subjects and Methods: A total of 2,500 primary school students, aged 6–12 years, were randomly selected from the government primary schools, and 1,869 students (947 boys and 922 girls) gave consent to participate in this study. An Arabic questionnaire was used to collect the sociodemographic variables and a standardized Arabic version of the Conners’ Teacher Rating Scale for ADH symptoms. Results: Of the 947 boys, 158 (16.7%; 95% confidence interval, CI, 14.4–19.2) and of the 922 girls, 50 (5.4%; 95% CI 4.1–7.1) scored above the cut-off (≧15) for ADH symptoms, thus giving an overall prevalence of 11.1% (95% CI 9.7–12.6). The children who had higher scores for ADH symptoms were in the age group of 6–9 years. Children who had higher scores for ADH symptoms had a poorer school performance than those with lower scores (p = 0.002). Two hundred (96.2%) children with ADH were disobedient, 126 (60.6%) noisy and hyperactive, 76 (36.5%) very cranky, 78 (37.5%) troublesome and 79 (37.9%) nervous. The logistic regression identified socio-economic condition, number of children, school performance and poor relationship between parents as the main contributors to ADH. Although the univariate analysis showed a significant relationship (p = 0.010) between ADH symptoms and consanguineous parents, logistic regression did not support this association (p = 0.075). This suggests that consanguinity has no impact on ADH children. Conclusion: The study revealed that ADH is a common problem among schoolchildren. The children with higher scores for ADH symptoms had a poorer school performance than those with lower scores. A significant difference exists between the behaviour of children with and without ADH.
Salivary Biomarkers: Toward Future Clinical and Diagnostic Utilities

SUMMARY The pursuit of timely, cost-effective, accurate, and noninvasive diagnostic methodologies is an endeavor of urgency among clinicians and scientists alike. Detecting pathologies at their earliest stages can significantly affect patient discomfort, prognosis, therapeutic intervention, survival rates, and recurrence. Diagnosis and monitoring often require painful invasive procedures such as biopsies and repeated blood draws, adding undue stress to an already unpleasant experience. The discovery of saliva-based microbial, immunologic, and molecular biomarkers offers unique opportunities to bypass these measures by utilizing oral fluids to evaluate the condition of both healthy and diseased individuals. Here we discuss saliva and its significance as a source of indicators for local, systemic, and infectious disorders. We highlight contemporary innovations and explore recent discoveries that deem saliva a mediator of the body's physiological condition. Additionally, we examine the current state of salivary diagnostics and its associated technologies, future aspirations, and potential as the preferred route of disease detection, monitoring, and prognosis.
Computational and information-theoretic soundness and completeness of formal encryption

We consider expansions of the Abadi-Rogaway logic of indistinguishability of formal cryptographic expressions. We expand the logic in order to cover cases when partial information of the encrypted plaintext is revealed. We consider not only computational, but also purely probabilistic, information-theoretic interpretations. We present a general, systematic treatment of the expansions of the logic for symmetric encryption. We establish general soundness and completeness theorems for the interpretations. We also present applications to specific settings not covered in earlier works: a purely probabilistic one based on one-time pad, and computational settings of the so-called type-2 (which-key revealing) and type-3 (which-key and length revealing) encryption schemes based on computational complexity.