Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening for p53 and K-ras mutations in whole-gut lavage in chronic inflammatory bowel disease

Objectives Molecular screening for frequently mutated genes may increase the likelihood of identifying cancer risk groups, such as patients with longstanding inflammatory bowel disease. This study investigated the prevalence and time course of p53 and K-ras mutations in colonic lavage fluid of patients with inflammatory bowel disease. Methods Colonic lavage fluid from 190 patients with ulcerative colitis (73), Crohn's disease (58) or controls (49 non-tumour, 10 colorectal cancer) was studied by oligomer-specific hybridization for K-ras mutations and single-strand conformation polymorphism (SSCP) for p53 mutations. Follow-up investigations were carried out after 1–3 years. Results Mutations were most frequent in carcinomas (5/10, 50%) and rare in non-tumour controls (1/49, 2.0%). They were found in Crohn's colitis in 15.4%, in extensive ulcerative colitis in 18.6%, in left-sided ulcerative colitis in 13.3%, and in distal ulcerative colitis in 6.7% (P > 0.05). There was a positive association with disease duration (⩾11 years, P < 0.05). Follow-up investigations detected the same mutation in four patients and revealed new mutations in three patients. Conclusions In our large series of patients with inflammatory bowel disease, K-ras and p53 mutations could be detected with reasonable frequency and confirmed at follow-up in at least some patients. Our data encourage the use of molecular screening for the detection of malignant precursor lesions in at-risk patients.
Spontaneous pre-stimulus fluctuations in the activity of right fronto-parietal areas influence inhibitory control performance

Inhibitory control refers to the ability to suppress planned or ongoing cognitive or motor processes. Electrophysiological indices of inhibitory control failure have been found to manifest even before the presentation of the stimuli triggering the inhibition, suggesting that pre-stimulus brain-states modulate inhibition performance. However, previous electrophysiological investigations on the state-dependency of inhibitory control were based on averaged event-related potentials (ERPs), a method eliminating the variability in the ongoing brain activity not time-locked to the event of interest. These studies thus left unresolved whether spontaneous variations in the brain-state immediately preceding unpredictable inhibition-triggering stimuli also influence inhibitory control performance. To address this question, we applied single-trial EEG topographic analyses on the time interval immediately preceding NoGo stimuli in conditions where the responses to NoGo trials were correctly inhibited [correct rejection (CR)] vs. committed [false alarms (FAs)] during an auditory spatial Go/NoGo task. We found a specific configuration of the EEG voltage field manifesting more frequently before correctly inhibited responses to NoGo stimuli than before FAs. There was no evidence for an EEG topography occurring more frequently before FAs than before CR. The visualization of distributed electrical source estimations of the EEG topography preceding successful response inhibition suggested that it resulted from the activity of a right fronto-parietal brain network. Our results suggest that the fluctuations in the ongoing brain activity immediately preceding stimulus presentation contribute to the behavioral outcomes during an inhibitory control task. Our results further suggest that the state-dependency of sensory-cognitive processing might not only concern perceptual processes, but also high-order, top-down inhibitory control mechanisms.
Abnormal Mitochondrial Structure in Human Unfertilized Oocytes and Arrested Embryos

Abstract: To clarify the relationship between mitochondria and embryo development, we collected human unfertilized oocytes, early embryos, and arrested embryos. Unfertilized oocytes and poor‐quality embryos were collected, and the ultrastructure of mitochondria was determined by transmission electron micrography. Four criteria for determining the mitochondrial state were mitochondrial morphology, cristae shape, location, and number of mitochondria. In mature oocytes, mitochondria were rounded with arched cristae and a dense matrix and were distributed evenly in the ooplasm. In pronuclear zygotes, the size and shape of mitochondria were similar to those in mature oocytes; however, mitochondria appeared to migrate and concentrate around pronuclei. In this study, 67% of examined unfertilized oocytes had fewer mitochondria in the cytoplasm. A decreased number of mitochondria located near the nucleus was also demonstrated in 60% of arrested embryos. Fewer differentiated cristae were determined in all three arrested blastocyst stages of embryos. The relative expressions of oxidative phosphorylation genes in oocytes and embryos were also determined. These data imply that inadequate redistribution of mitochondria, unsuccessful mitochondrial differentiation, or decreased mitochondrial transcription may result in poor oocyte fertilization and compromised embryo development.
Semi-Automated Ultrasound Interpretation System Using Anatomical Knowledge Representation

(1) : University of California, Berkeley EECS Computer Science Division 535 Soda Hall Berkeley CA 94720 U.S.A. (510) 642-9716 E-mail : msdownes@yahoo.com (2) : University of California, Berkeley EECS Computer Science Division 387 Soda Hall # 1776 Berkeley CA 94720-1776 U.S.A. (510) 642-9838 E-mail : barsky@cs.berkeley. edu Abstract: Interpreting ultrasound data presents a significant challenge to medical personnel, which limits the cl ini al applications of the technology. We have addressed this issue by developing a prototype computer-based system des igned to aid non-expert medical practitioners in using ultra sound devices in a variety of different diagnostic situat ions. Essentially, the system treats the collection of im ages generated during an ultrasound examination as an or dered sequence of views of the anatomical environment and picks out key views in which the contents of the scan image c hanges. It stores descriptions of expected key views and match es incoming images to this key view sequence during an orientation phase of an examination. The prototype can guide a novice user through an examination of a patient’s abdomen and automatically identify anatomical structures wi thin the region. Overall, the design represents a novel app ro ch to processing and augmenting ultrasound data and to re pres nting spatial knowledge.
Detection and molecular characterization of equine infectious anemia virus in Mongolian horses

The genetic characterization and actual prevalence of EIAV in Mongolian horse in the disease endemic region is currently unknown. Here, 11 of 776 horse serum samples from four Mongolian provinces tested positive on agar gel immunodiffusion test. Genomic DNA extracted from all seropositive samples was subjected to nested PCR assay. Among these, three samples tested positive with nested PCR assay and were identified by sequencing analysis based on long termination repeat and tat gene of the virus. Two of the three sequences were identical, with 94.0% identity with the third. These two independent Mongolian EIAV sequences were retained functional motifs, with no dramatic changes but some variability in the U5 region; they were clustered with genotypes from European countries but not with those from China, U.S.A. , or Japan.
Strong Secrecy on the Binary Erasure Wiretap Channel Using Large-Girth LDPC Codes

For an arbitrary degree distribution pair (DDP), we construct a sequence of low-density parity-check (LDPC) code ensembles with girth growing logarithmically in block-length using Ramanujan graphs. When the DDP has minimum left degree at least three, we show using density evolution analysis that the expected bit-error probability of these ensembles, when passed through a binary erasure channel with erasure probability ϵ, decays as <i>O</i>(exp(-(<i>c</i><sub>1</sub>)<i>n(c</i><sub>2</sub>))) with the block-length <i>n</i> for positive constants <i>c</i><sub>1</sub> and <i>c</i><sub>2</sub>, as long as ϵ is less than the erasure threshold ϵ<sub>th</sub> of the DDP. This guarantees that the coset coding scheme using the dual sequence provides strong secrecy over the binary erasure wiretap channel for erasure probabilities greater than 1-ϵ<sub>th</sub>.
Formalizing interactive staged feature model configuration

Feature modeling an attractive technique for capturing commonality as well as variability within an application domain for generative programming and software product line engineering. Feature models symbolize an overarching representation of the possible application configuration space, and can hence be customized based on specific domain requirements and stakeholder goals. Most interactive or semi‐automated feature model customization processes neglect the need to have a holistic approach towards the integration and satisfaction of the stakeholder's soft and hard constraints, and the application‐domain integrity constraints. In this paper, we will show how the structure and constraints of a feature model can be modeled uniformly through Propositional Logic extended with concrete domains, called Pscr(𝒩). Furthermore, we formalize the representation of soft constraints in fuzzy 𝒫(𝒩) and explain how semi‐automated feature model customization is performed in this setting. The model configuration derivation process that we propose respects the soundness and completeness properties. Copyright © 2011 John Wiley & Sons, Ltd.
Flux: Groupon's automated, scalable, extensible machine learning platform

As machine learning becomes the driving force of the daily operation of companies within the information technology sector, infrastructure that enables automated, scalable machine learning is a core component of the systems of many large companies. Various systems and products are being built, offered, and open sourced. As an e-commerce company, numerous aspects of Groupon's business is driven by machine learning. To solve the scalability issue and provide a seamless collaboration between data scientists and engineers, we built Flux, a system that expedites the deployment, execution, and monitoring of machine learning models. Flux focuses on enabling data scientists to build model prototypes with languages and tools they are most proficient in, and integrating the models into the enterprise production system. It manages the life cycle of deployed models, and executes them in distributed batch mode, or exposes them as micro-services for real-time use cases. Its design focuses on automation and easy management, scalability, and extensibility. Flux is the central system for supervised machine learning tasks at Groupon and has been supporting multiple teams across the company.
Clearance of lysosomal glycogen accumulation by Transcription factor EB (TFEB) in muscle cells from lysosomal alpha-glucosidase deficient mice

A recently proposed therapeutic approach for lysosomal storage disorders (LSDs) relies upon the ability of transcription factor EB (TFEB) to stimulate autophagy and induce lysosomal exocytosis leading to cellular clearance. This approach is particularly attractive in Glycogen Storage Disease type II (a severe metabolic myopathy and a paradigm for LSDs, also called Pompe disease) as the currently available therapy, replacement of the missing enzyme acid alpha-glucosidase, fails to reverse skeletal muscle pathology. Pompe disease is characterized by both lysosomal abnormality and dysfunctional autophagy. Here we show that TFEB is a viable therapeutic target in Pompe disease: overexpression of TFEB in a newly established conditionally immortalized skeletal muscle cell model reduced glycogen load and lysosomal size; and in the muscle fibers of GFP-LC3 Pompe disease mouse model significantly increased the motility of lysosomes in the fibers, and stimulated the fusion between lysosomes and autophagosomes under stress. Hence, modulation of TFEB activity holds promise for the development of a better therapy. In addition, the newly developed mouse and cell models have many potential applications such as large-scale drug screening for Pompe disease.
The toxicity of staphylococcal enterotoxin B in mice is mediated by T cells

Staphylococcal enterotoxin B (SEB) has been shown in the past to be a potent T cell stimulant in mouse or man. The toxin acts as a superantigen that is, it binds to class II MHC proteins and, as such a complex, stimulates T cells bearing particular V beta s as part of their receptors. The toxin also has several pathological effects, causing, in mice, rapid weight loss, thymus atrophy, immunosuppression, and, at high doses, death. The data in this paper show that at least one of these effects, weight loss, is T cell mediated. Staphylococcal enterotoxin-mediated weight loss is MHC dependent, and is almost absent in animals expressing MHC class II molecules, which, complexed with SEB, are poor T cell stimulants. Also, mice that lack T cell function, genetically or because of cyclosporin A treatment, lose no or less weight than controls in response to SEB. Finally, animals bred such that they express few T cells bearing V beta s with which SEB can interact lose much less weight in response to the toxin than littermate controls that have higher numbers of reactive T cells. It is therefore suggested that the pathological effects of the staphylococcal, T cell- stimulating toxins in mouse and man may be partially or wholly the consequence of massive T cell stimulation.
Text-Independent Speech Recognition

Introduction Speaker identification is an area with many different applications. The most practical uses can be found in areas such as security, surveillance, and automatic transcription in a multispeaker environment. The goal of this project is to understand the development and implementation of a text-independent speaker recognition system. We will analyze the system by interpreting feature matching and extraction characteristics. After the textindependent speaker recognition system is understood, we will attempt to model it using Ptolemy. We hope to be able to model a system that will simulate a text-independent speaker system. As part of the literature review, we looked at various journals, IEEE proceedings, and other resources describing the applications of speaker recognition systems.
Children With Cancer, Fever, and Treatment-Induced Neutropenia: Risk Factors Associated With Illness Requiring the Administration of Critical Care Therapies

Objectives: To identify clinical and laboratory characteristics of pediatric patients with cancer, fever, and treatment-induced neutropenia, available at initial presentation, that are independently associated with the development of illnesses requiring administration of critical care therapies. Methods: We retrospectively collected historical, clinical, and laboratory data on initial presentation for all pediatric (younger than18 years) cancer patients admitted for fever and treatment-induced neutropenia at our institution over a 5-year period. The outcome variable was the need for administration of a critical care therapy within 24 hours of admission. A multivariable analysis was performed and internally validated using bootstrap analysis. Results: We identified 303 events in 143 patients, of which 36 (11.9%) received a critical care therapy. Higher temperature at presentation and capillary filling time (CFT) of >3 seconds retained significance in the multivariable analysis and were validated by the bootstrap analysis. The positive and negative predictive values of the presence of either temperature of ≥39.5°C or CFT of >3 seconds were 35% and 91%, respectively. Conclusions: Pediatric patients with cancer, fever, and treatment-induced neutropenia who present with higher fever or prolonged CFT are at increased risk of developing life-threatening illnesses requiring administration of critical care therapies, independent of hematologic factors, type of cancer, or other physiologic signs of sepsis.
Parity and institutional delivery in rural Tanzania: a multilevel analysis and policy implications.

OBJECTIVES We assess the extent to which the use of healthcare facilities for childbirth varies by parity, conditional on socio-economic, psychological and health characteristics. We also assess differences in the determinants of institutionalized delivery for first-time mothers and multiparous, and explore village-level variations in observed relationships. METHODS Survey data from a three-stage cross-sectional cluster sample of 1205 women from a rural district of Tanzania were analysed using random-intercept multilevel models. RESULTS Use of health facilities for delivery was low (39%), with odds of institutionalized delivery three times higher among nulliparous women (0 children prior to current delivery) compared with women with one to four children; and 30% lower among women with five or more children compared with those with one to four children. In parity group analyses, women with at least some education and women with more than three antenatal care visits had higher odds of institutionalized delivery among nulliparous. Belief in the importance of institutionalized delivery increased the odds of delivering in a facility among multiparous women; so did health insurance for women with five or more children. We found a significant variation in institutionalized delivery among multiparous women based on their village of residence (one to four and five or more children), but these variations were not observed among nulliparous women. CONCLUSION Parity is a pivotal determinant of the use of health facilities for delivery, and its significance varies by village of residence; hence, interventions targeting women according to parity may increase the use of facilities for delivery in rural Tanzania. Future research should focus on the village-level characteristics that influence institutionalized delivery in multiparous.
A realistic analytical model of IEEE 802.11p for Wireless Access in Vehicular Networks

The IEEE 802.11p is an emerging wireless protocol dedicated for Wireless Access in the Vehicular Environment (WAVE). It employs the Enhanced Distributed Channel Access (EDCA) mechanism to access the channel. Its objective is to provide differentiated services to vehicular networks which are delay-sensitive and requires high communication throughput. In this paper, we carry out comprehensive performance analysis of the IEEE 802.11p standard. We propose a Markov chain-based analytical model that depicts accurate representation of the IEEE 802.11p MAC sub-layer. We take into account the internal collision probability that occur among different Access Categories (ACs) in the same vehicle. We also consider an unsaturated traffic condition and include the probability of finding the medium busy when sensed during the backoff period. We study the performance of the system in terms of average throughput and average time delay.
Differences in Signaling Properties of the Cytoplasmic Domains of the Insulin Receptor and Insulin-like Growth Factor Receptor in 3T3-L1 Adipocytes*

Insulin and insulin-like growth factors (IGFs) elicit distinct but overlapping biological effects in vivo. To investigate whether differences in intrinsic signaling capacity of receptors contribute to biological specificity, we constructed chimeric receptors containing the extracellular portion of the neurotrophin receptor TrkC fused to the intracellular portion of the insulin or IGF-I receptors. Chimeras were stably expressed in 3T3-L1 adipocytes at levels comparable to endogenous insulin receptors and were efficiently activated by neurotrophin-3. The wild-type insulin receptor chimera mediated approximately 2-fold greater phosphorylation of insulin receptor substrate 1 (IRS-1), association of IRS-1 with phosphoinositide 3-kinase, stimulation of glucose uptake, and GLUT4 translocation, compared with the IGF-I receptor chimera. In contrast, the IGF-I receptor chimera mediated more effective Shc phosphorylation, association of Shc with Grb2, and activation of mitogen-activated protein kinase compared with the insulin receptor chimera. The two receptors elicited similar activation of protein kinase B, p70S6 kinase, and glycogen synthesis. We conclude that the insulin receptor mediates some aspects of metabolic signaling in adipocytes more effectively than the IGF-I receptor, as a consequence of more efficient phosphorylation of IRS-1 and greater recruitment/activation of phosphoinositide 3-kinase.
Performance evaluation of strategies for integration of elastic and stream traffic

This paper deals with the integration of `stream'' traffic and `elastic'' traffic in one single network, e.g. an ATM-based or an IP-based network. Here stream traffic refers to traffic with a certain bandwidth guarantee, whereas elastic traffic flows can adapt their rates to the link bandwidth left over by the stream flows. First, models are developed that describe different strategies for sharing link capacities between the stream and elastic flows. Then we give mathematical methods for obtaining performance measures, in particular call blocking probabilities and file transfer delays. Finally, these methods are used for assessing and comparing the efficiency gains achieved by the integration strategies.
Activity Schedules

teacher, has a new student with Asperger’s syndrome in her classroom. John has a very difficult time moving from one activity to the next. Often he will simply refuse to transition to the next activity by sitting down on the floor and not moving. Other times he will scream and physically lash out at his peers and the teacher. Kate noticed that the problem behaviors usually occur during a change in his anticipated daily routines. These outbursts are very disruptive to the rest of the class, and some of the other students have begun to avoid John during classroom activities. John’s parents report similar difficulties at home during transitions or changes in his schedule. Kate needs to find some research-based strategies to help John more readily accept changes in his schedule and daily activities. Refusing to transition from one activity to the next or between steps in a single activity can impact a student’s academic progress, socialization, and independence. Problem behaviors during transitions can impact the effectiveness of teacher instruction and disrupt other students’ activities. As a result, the child with the behavior problem may be excluded from peer social circles. Difficulty with transitions can significantly limit a student’s ability to independently complete activities across environments throughout the school day (e.g., Forest, Horner, Lewis-Palmer, & Todd, 2004; Scheuermann & Webber, 2002; Schreibman, Whalen, & Stahmer, 2000). Autism spectrum disorder (ASD) is characterized by a qualitative impairment in at least two of the three following areas: social interaction; communication; and restricted repetitive and stereotyped patterns of behavior, interests, and activities. In addition, individuals diagnosed with autism demonstrate delays or abnormal functioning with onset before age 3 in social interaction, language used for social communication, and/or symbolic or imaginative play (American Psychiatric Association, APA, 2000). Students diagnosed with ASD often struggle