Miracle-dz/UniFAR-FTUs huggingface dataset:
Yield of diagnostic tests for celiac disease in individuals with symptoms suggestive of irritable bowel syndrome: systematic review and meta-analysis.

BACKGROUND Individuals with irritable bowel syndrome (IBS) report abdominal pain, bloating, and diarrhea, symptoms similar to those in celiac disease. Studies suggest that the prevalence of celiac disease is increased in individuals with IBS; however, evidence is conflicting, and current guidelines do not always recommend screening for celiac disease in these individuals. METHODS We conducted a systematic review and meta-analysis to estimate prevalence of celiac disease in unselected adults who met diagnostic criteria for IBS. MEDLINE (1950 to May 31, 2008) and EMBASE (1980 to May 31, 2008) were searched. Case series and case-control studies that used serologic tests for celiac disease were eligible for inclusion. Prevalence of positive serologic indications of celiac disease and biopsy-proved celiac disease were extracted and pooled for all studies and were compared between cases and controls using an odds ratio and 95% confidence interval. RESULTS Fourteen studies were identified comprising 4204 individuals, of whom 2278 (54%) met diagnostic criteria for IBS. Pooled prevalence of positive IgA-class antigliadin antibodies, either positive endomysial antibodies or tissue transglutaminase, and biopsy-proved celiac disease were 4.0% (95% confidence interval, 1.7-7.2), 1.63% (0.7-3.0), and 4.1% (1.9-7.0), respectively. Pooled odds ratios (95% confidence intervals) for positive IgA-class antigliadin antibodies, either positive endomysial antibodies or tissue transglutaminase, and biopsy-proved celiac disease in cases meeting diagnostic criteria for IBS compared with controls without IBS were 3.40 (1.62-7.13), 2.94 (1.36-6.35), and 4.34 (1.78-10.6). CONCLUSION Prevalence of biopsy-proved celiac disease in cases meeting diagnostic criteria for IBS was more than 4-fold that in controls without IBS.
Systematic comparison of RNA-Seq normalization methods using measurement error models

MOTIVATION Further advancement of RNA-Seq technology and its application call for the development of effective normalization methods for RNA-Seq data. Currently, different normalization methods are compared and validated by their correlations with a certain gold standard. Gene expression measurements generated by a different technology or platform such as Real-time reverse transcription polymerase chain reaction (qRT-PCR) or Microarray are usually used as the gold standard. Although the current approach is intuitive and easy to implement, it becomes statistically inadequate when the gold standard is also subject to measurement error (ME). Furthermore, the current approach is not informative, because the correlation of a normalization method with a certain gold standard does not provide much information about the exact quality of the normalized RNA-Seq measurements. RESULTS We propose to use the system of ME models based on qRT-PCR, Microarray and RNA-Seq gene expression data to compare and validate RNA-Seq normalization methods. This approach does not assume the existence of a gold standard. The performance of a normalization method can be characterized by a group of parameters of the system, which are referred to as the performance parameters, and these performance parameters can be consistently estimated. Different normalization methods can thus be compared by comparing their corresponding estimated performance parameters. We applied the proposed approach to compare five existing RNA-Seq normalization methods using the gene expression data of two RNA samples from the microArray Quality Control and Sequencing Quality Control projects and gained much insight about the pros and cons of these methods.
Dynamic Mechanical Properties of the Tissue-engineered Matrix Associated with Individual Chondrocytes

The success of cell-based tissue engineering approaches in restoring biological function will be facilitated by a comprehensive fundamental knowledge of the temporal evolution of the structure and properties of the newly synthesized matrix. Here, we quantify the dynamic oscillatory mechanical behavior of the engineered matrix associated with individual chondrocytes cultured in vitro for up to 28 days in alginate scaffolds. The magnitude of the complex modulus (|E*|) and phase shift (d) were measured in culture medium using Atomic Force Microscopy (AFM)-based nanoindentation in response to an imposed oscillatory deformation (amplitude $ 5 nm) as a function of frequency (f = 1–316 Hz), probe tip geometry (2.5 mm radius sphere and 50 nm radius square pyramid), and in the absence and presence of growth factors (GF, insulin growth factor-1, IGF-1, and osteogenic protein-1, OP-1). |E*| for all conditions increased nonlinearly with frequency dependence approximately f 1/2 and ranged between $ 1 and 25 kPa. This result, along with theoretical calculations of the characteristic poroelastic relaxation frequency, f p , ($ 50–90 Hz) suggested that this time-dependent behavior was governed primarily by fluid flow-dependent poroelasticity, rather than flow-independent viscoelastic processes associated with the solid matrix. |E*(f)| increased, (f) decreased, and the hydraulic permeability, k, decreased with time in culture and with growth factor treatment. This trend of a more elastic-like response was thought to be associated with increased macromolecular biosynthesis, density, and a more mature matrix structure/organization. Cell-based tissue engineering holds great potential for therapies involving regeneration and/or replacement of damaged cartilage. Such approaches typically involve seeding cells (e.g., chondrocytes, stem cells) within macromolecular scaffolds or in scaffold-free environments and subjecting them to stimulatory biochemical and/or mechanical factors in vitro or in vivo to promote synthesis and growth of neo-tissue. The ultimate goal and challenge is to produce a material with structural, biochemical and biomechanical properties similar enough to healthy cartilage so that upon maturation in vivo it can restore physiological function. To achieve this objective, it is important to understand the temporal evolution of the properties of the newly synthesized matrix. At early stages, matrix is formed around individual cells within the scaffold and these cell–matrix composites are often isolated from each other. As culture time increases, growth of neighboring cell-associated matrices leads to the formation of a more continuous neo-tissue which undergoes further evolution in structure and properties in vitro or in vivo. Throughout this process, the cell-associated matrix is …
Connected-digit speaker-dependent speech recognition using a neural network with time-delayed connections

An analog neural network that can be taught to recognize stimulus sequences is used to recognize the digits in connected speech. The circuit computes in the analog domain, using linear circuits for signal filtering and nonlinear circuits for simple decisions, feature extraction, and noise suppression. An analog perceptron learning rule is used to organize the subset of connections used in the circuit that are specific to the chosen vocabulary. Computer simulations of the learning algorithm and circuit demonstrate recognition scores >99 % for a single-speaker connected-digit data base. There is no clock. The circuit is data driven, and there is no necessity for endpoint detection or segmentation of the speech signal during recognition. Training in the presence of noise provides noise immunity up to the trained level. For the speech problem studied, the circuit connections need only be accurate to about 3-b digitization depth for optimum performance. The algorithm used maps efficiently onto analog neutral network hardware. >
Letters of Recommendation: Rating, Writing, and Reading by Clerkship Directors of Internal Medicine

Background: Letters of Recommendations (LORs) are used for applications to medical school and graduate medical education, but how they are used by current internal medicine educators is unknown. Description: In 2006, the Clerkship Directors of Internal Medicine conducted its annual, voluntary survey, and one section pertained to LORs. Survey items were categorized into questions regarding rating, writing, and reading LORs with answers on 3- to 5-point scales. Evaluation: The response rate for the 110 institution members was 75%. When rating LORs, the most important factor was depth of understanding of the trainee (98% essential or important), followed by a numerical comparison to other students (94%), grade distribution (92%), and summary statement (91%). Although most (78%) agreed that reading LORs in general were important for trainee selection, few agreed that this was because of the ability to discern marginal performance (31%) or predict future performance (25%). Conclusions: LORs remain an important part of the application process for medical school and internal medicine residency. Letter writers should convey a great depth of understanding of the applicant, provide a numerical comparison with other students (including a denominator), and give a specific summary statement.
Improved estimation of hyperbolic frequency modulated chirp signals

This article deals with parameter estimation of product signals consisting of hyperbolic FM and chirp factors. A computationally simple algorithm that decouples estimation of the chirp parameters from those of the hyperbolic FM part is presented. It relies on a simple data transformation that removes the hyperbolic FM component, leaving one with the simpler problem of estimating chirp parameters. For the latter, the high-order ambiguity function (HAF) is adopted. Schemes for estimating the hyperbolic FM parameter are also proposed. The method improves on existing approaches and is shown to provide performance close to the Cramer-Rao bound.
Impacts of Retransmission Limit on Stability and Throughput Regions of S-ALOHA Systems

Limiting the number of retransmissions in practical random access systems such as S-ALOHA and IEEE 802.11 systems has been used, since it was often considered as a way of preventing the system from being congested, by dropping packets in retransmission or letting users know network congestion after the maximum of retransmissions. Therefore, it can be expected that the smaller the maximum of retransmissions is allowed, the smaller the backlog size gets with a higher packet dropping probability. This paper explores how such a retransmission limit alters the shape of the stability and throughput regions of S-ALOHA systems. To do this, we first consider an S-ALOHA system, where two users with infinite queue length have different packet arrival rate and retransmission probability, which is called <italic> asymmetric</italic> user. Then, we obtain those results of the systems with <inline-formula><tex-math notation="LaTeX"> $N$</tex-math></inline-formula> <italic>symmetric</italic> users.
Photo classification by integrating image content and camera metadata

Despite years of research, semantic classification of unconstrained photos is still an open problem. Existing systems have only used features derived from the image content. However, Exif metadata recorded by the camera provides cues independent of the scene content that can be exploited to improve classification accuracy. Using the problem of indoor-outdoor classification as an example, analysis of metadata statistics for each class revealed that exposure time, flash use, and subject distance are salient cues. We use a Bayesian network to integrate heterogeneous (content-based and metadata) cues in a robust fashion. Based on extensive experimental results, we make two observations: (1) adding metadata to content-based cues gives highest accuracies; and (2) metadata cues alone can outperform content-based cues alone for certain applications, leading to a system with high performance, yet requiring very little computational overhead. The benefit of incorporating metadata cues can be expected to generalize to other scene classification problems.
Effect of Data Transformation on Residue

Recently, Aguilar-Ruiz [2005] considers a data matrix containing both scaling and shifting factors and shows that the mean squared residue [Cheng and Church, 2000], called RESIDUE(II) in this paper, is useful to discover shifting patterns, but not appropriate to find scaling patterns. This finding draws our attention on the weakness of RESIDUE(II) measure and the need of new approaches to discover both scaling and shifting patterns in the considered matrix. To resolve the weakness of RESIDUE(II) in finding scaling patterns, we propose a simple remedy that still uses the same residue measure. The main idea is to remove hidden scaling factors in the considered data matrix by taking a specific data transformation. We investigate various data transformations including no transformation, double centering, mean centering, standard deviation normalization, and Z-score transformation. Further, we apply these data transformations to row/column dimension of data matrix models with different global/local scaling and global/local shifting factors. First, we characterize the properties of the data transformations on different data matrix models, including six Euclidean co-clustering schemes in Bregman co-clustering algorithms [Banerjee et al., 2007] and other existing data models in the literature. In particular, we formally analyze the effect of each data transformation on the two residues [Cho et al., 2004], here called RESIDUE(I) and RESIDUE(II), respectively. Then, we apply all the data transformations to publicly available human cancer gene expression datasets and empirically validate the analysis results by using the minimum sum squared residue co-clustering (MSSRCC) algorithms [Cho et al., 2004]. In conclusion, through column standard deviation normalization or column Z-score transformation, we are able to overcome the shortcoming of RESIDUE(II) in finding scaling patterns and discover both scaling and shifting patterns.
Individual and Complementary Effects of Human Papillomavirus Oncogenes on Epithelial Cell Proliferation and Differentiation

Previous studies on human papillomavirus (HPV) type 16 protein functions have established the oncogenic nature of three viral proteins: E5, E6 and E7. Here we have studied the functions of these proteins by functional deletion of the individual E5, E6 or E7, or both E6 and E7 oncogenes in the context of the whole viral genome. These mutants, or the intact wild-type genome, were expressed from the natural viral promoters along with differentiation of epithelial HaCaT cells in three-dimensional collagen raft cultures. High episomal viral copy numbers were obtained using a transfection-based loxp-HPV16-eGFP-N1 vector system. All epithelial equivalents carrying the different HPV type 16 genomes showed pronounced hyperplastic and dysplastic morphology. Particularly the E7 oncogene, with contribution of E6, was shown to enhance cell proliferation. Specifically, the crucial role of E7 in HPV-associated hyperproliferation was clearly manifested. Based on morphological characteristics, immunohistochemical staining for differentiation and proliferation markers, and low expression of E1^E4, we propose that our raft culture models produce cervical intraepithelial neoplasia (CIN)1 and CIN2-like tissue. Our experimental setting provides an alternative tool to study concerted functions of HPV proteins in the development of epithelial dysplasia.
Attitudes to and use of complementary medicine among physicians in the United Kingdom.

OBJECTIVES To evaluate the use of attitudes to complementary and alternative medicine (CAM) among UK physicians. DESIGN Postal questionnaire. SUBJECTS All Members and Fellows of the Royal College of Physicians. RESULTS Twelve thousand, one hundred and sixty eight Members and Fellows were surveyed and a response rate of 23% (n = 2,875) was obtained. Responses from the small numbers of general practitioners (n = 127) were not included in the analyses, resulting in a sample size of 2,748: 79% of respondents were in NHS practice, 32% of respondents practised CAM themselves, and 41% referred patients to CAM; of those who referred patients, 78% referred between 0-3 patients per month. CAM is used by physicians more frequently in private as compared to NHS practice. Acupuncture, aromatherapy and manipulative medicine (osteopathy and chiropractic) are the most commonly referred to and the most commonly practised therapies. Eighty seven percent of those using CAM themselves, or as part of their clinical team's commitment, had not had any CAM training. Attitudes to CAM were generally positive, particularly among those in palliative care, rehabilitation, nuclear medicine, and genito-urinary medicine. CONCLUSIONS Our conclusions must be tempered by the limited response rate, but assuming all non-responders were disinterested in CAM, then at least one in ten UK specialist physicians are actively involved in CAM treatments, although only 13% of our sample had received any CAM training.
[Comparative ultrastructural study of the process of hemoglobin degradation by P. berghei (Vincke and Lips, 1948) as a function of the state of maturity of the host cell].

By serial sectioning and 3D reconstruction we have been able to demonstrate that the type of system for hemoglobin digestion in two strains of Plasmodium berghei, N and RC, is dependent on the maturity of the host cell. In parasites growing in erythrocytes, both systems for the endocytosis of hemoglobin-micropinocytosis and the cytostomal system (i.e. a cytostome budding a cytostomal tube that releases food vacuoles)-are fully functional and produce a great quantity of residual pigment. Parasites growing in reticulocytes have a disrupted cytostomal system; no tube is formed and only food vacuoles are visible in their cytoplasm. Residual pigment is smaller in size and in quantity. The reduced quantity of pigment in reticulocytes is explained by our observation of the exocytosis of pigment. We propose a hypothesis that relates the process of degradation of hemoglobin to the maturity of the host cell and a possible mechanism of protection against chloroquine, a drug known for its affinity for malarial pigment.
Cid, Centre for User Oriented It Design C I D -2 4 3 I S S N 1 4 0 3 -0 7 2 1 the Lom Rdf Binding -principles and Implementation the Lom Rdf Binding -principles and Implementation

This paper will discuss some of the advantages and complexities in using the Resource Description Framework, RDF, to express learning object metadata following the IEEE LOM standard. We will describe some details of the current draft for a complete RDF binding for LOM and discuss some of the constructs used in that binding. We will then present a so-called SHAME Query Model of this binding that can be used to specify and visualize application profile constraints when using this binding. A metadata editor for RDF-based LOM metadata, which was built with the help of this Query model, will be briefly introduced.
Enhanced compositional safety analysis for distributed embedded systems using LTS equivalence

Real-time systems such as aeronautic systems, medical systems, and nuclear power plant systems are generally operated in a standalone mode. In the home network and ubiquitous computing systems, integrated services related with several embedded systems are focused, which is called distributed embedded systems. Safety issues of distributed embedded systems are very important since they are closely related to our living. In this research, distributed embedded systems and its safety properties are described by Labeled Transition Systems (LTS). For efficiently checking safety issues, we enhance the existing compositional safety analysis technique [10] using LTS equivalence concept.
Apoptosis and the Nervous System

Abstract: Apoptosis is now recognized as a normal feature in the development of the nervous system and may also play a role in neurodegenerative diseases and aging. This phenomenon has been investigated intensively during the last 6‐7 years, and the progress made in this field is reviewed here. Besides a few in vivo studies, a variety of neuronal preparations from various parts of the brain, the majority of which were primary cultures, and some cell lines have been investigated. Several apoptosis‐inducing agents have been identified, and these include lack of neurotrophic support, neurotransmitters, neurotoxicants, modulators of protein phosphorylation and calcium homeostasis, DNA‐damaging agents, oxidative stress, nitric oxide, and ceramides. The precise signaling cascade is not well established, and there are lacunae in many suggested pathways. However, it appears certain that the Bcl family of proteins is involved in the apoptotic pathway, and these proteins in turn affect the processing of interleukin‐1β converting enzyme (ICE)/caspases. The available evidence suggests that there may be several apoptotic pathways that may depend on the cell type and the inducing agent, and most of the pathways may converge at the ICE/caspases step.
Seasonal changes of whole root system conductance by a drought-tolerant grape root system

The role of root systems in drought tolerance is a subject of very limited information compared with above-ground responses. Adjustments to the ability of roots to supply water relative to shoot transpiration demand is proposed as a major means for woody perennial plants to tolerate drought, and is often expressed as changes in the ratios of leaf to root area (AL:AR). Seasonal root proliferation in a directed manner could increase the water supply function of roots independent of total root area (AR) and represents a mechanism whereby water supply to demand could be increased. To address this issue, seasonal root proliferation, stomatal conductance (gs) and whole root system hydraulic conductance (kr) were investigated for a drought-tolerant grape root system (Vitis berlandieri×V. rupestris cv. 1103P) and a non-drought-tolerant root system (Vitis riparia×V. rupestris cv. 101-14Mgt), upon which had been grafted the same drought-sensitive clone of Vitis vinifera cv. Merlot. Leaf water potentials (ψL) for Merlot grafted onto the 1103P root system (–0.91±0.02 MPa) were +0.15 MPa higher than Merlot on 101-14Mgt (–1.06±0.03 MPa) during spring, but dropped by approximately –0.4 MPa from spring to autumn, and were significantly lower by –0.15 MPa (–1.43±0.02 MPa) than for Merlot on 101-14Mgt (at –1.28±0.02 MPa). Surprisingly, gs of Merlot on the drought-tolerant root system (1103P) was less down-regulated and canopies maintained evaporative fluxes ranging from 35–20 mmol vine−1 s−1 during the diurnal peak from spring to autumn, respectively, three times greater than those measured for Merlot on the drought-sensitive rootstock 101-14Mgt. The drought-tolerant root system grew more roots at depth during the warm summer dry period, and the whole root system conductance (kr) increased from 0.004 to 0.009 kg MPa−1 s−1 during that same time period. The changes in kr could not be explained by xylem anatomy or conductivity changes of individual root segments. Thus, the manner in which drought tolerance was conveyed to the drought-sensitive clone appeared to arise from deep root proliferation during the hottest and driest part of the season, rather than through changes in xylem structure, xylem density or stomatal regulation. This information can be useful to growers on a site-specific basis in selecting rootstocks for grape clonal material (scions) grafted to them.