Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant Expression of Long Noncoding RNAs in Cervical Intraepithelial Neoplasia

Objective Long noncoding RNAs (lncRNAs) are a unique class of messenger RNA–like transcripts of at least 200 nucleotides in length with no significant protein-coding capacity. Aberrant lncRNA expression is emerging as a major component of the cancer transcriptome. Here, we sought to determine if differential lncRNA expression is a feature of the human cervical intraepithelial neoplasia (CIN) transcriptome. Methods Sequence data were derived from 16 long serial analyses of gene expression (L-SAGE) libraries constructed from cervical specimens representing mild (CIN1), moderate (CIN2), and severe (CIN3) histopathologic grades of CIN. A novel lncRNA discovery pipeline was developed to query the expression of lncRNAs within the SAGE data sets. Results A total of 2,230,370 sequence tags were delineated from the 16 SAGE libraries, representing the expression of 367,482 unique tags at varying abundance. Using a novel stepwise filtering strategy, we analyzed the cervical SAGE libraries and identified the expression profiles of 1056 lncRNAs in the human cervix. We present the first lncRNA expression profile derived from nonneoplastic cervical tissue and establish that changes in lncRNA expression do occur in cervical intraepithelial lesions. Our analysis also shows statistically significant aberrant expression of lncRNAs in the 3 CIN grades, suggesting that these unique noncoding RNA transcripts may contribute to the development and progression of precursor lesions. Conclusions Through the analysis of L-SAGE libraries constructed from cervical specimens, we provide the first lncRNA expression profile of the cervix and demonstrate aberrant expression in early-stage neoplasia.
Association of IL-10-1082A/G Polymorphism with Ischemic Stroke: Evidence from a Case-Control Study to an Updated Meta-Analysis.

BACKGROUND AND AIMS Interleukin-10 (IL-10) plays a vital part in the pathophysiology of vascular inflammation. Several studies have investigated the potential association between the IL-10-1082A/G polymorphism and the risk of ischemic stroke where the inflammatory process is involved, but the conclusions have been inconsistent. METHODS Three hundred eighty-six ischemic stroke patients and 386 healthy controls were recruited in the study. Genotyping was conducted by using the polymerase chain reaction-ligation detection reaction method. A meta-analysis was then performed by pooling our data with previous published studies. RESULTS In our case-control study, a lack of association was revealed between IL-10-1082A/G and ischemic stroke (p > 0.05). When combined with previous studies, however, a significant relationship between IL-10-1082A/G and ischemic stroke risk was found (G vs. A: OR = 0.73, 95% CI = 0.60-0.88, p < 0.01; GG vs. AA: OR = 0.61, 95% CI = 0.49-0.76, p < 0.01; GG+AG vs. AA: OR = 0.70, 95% CI = 0.54-0.91, p < 0.01; GG vs. AG+AA: OR = 0.68, 95% CI = 0.52-0.89, p < 0.01), as well as in subgroup analyses. Sensitivity analysis and publication bias assessment supported the reliability of the results from the meta-analysis. CONCLUSIONS Evidence from a case-control study to an updated meta-analysis suggests that the IL-10-1082A/G polymorphism is associated with ischemic stroke susceptibility.
inSensed: Wearable Collection of Multimedia based on Interest

We present a wearable data collection system that allows users to collect their experiences into a continually growing and adapting multimedia diary. The system, called iSensed, uses the patterns in sensor readings from a camera, microphone, and accelerometers, to classify the user's activities and automatically collect multimedia clips when the user is in aninterest- ing' situation. `Interest' is estimated by a user-trained rule relating the sequence of user ac- tivities/situations to their concept ofinterest'. This allows the multimedia information to be structured in a manner similar to the user's episodic memory, e.g., unusual and potentially important events are recorded chronologically, allowing rapid browsing and automatic struc- turing of the multimedia diary. The system is based on commercially available mobile devices, either a PDA or a camera phones, together with two small wireless accelerometers worn on the wrist and belt.
Dipterans Associated with a Decomposing Animal Carcass in a Rainforest Fragment in Brazil: Notes on the Early Arrival and Colonization by Necrophagous Species

Abstract This study aimed to provide the first checklist of forensically-important dipteran species in a rainforest environment in Northeastern Brazil, a region exposed to high rates of homicides. Using a decomposing pig, Sus scrofa L. (Artiodactyla: Suidae), carcass as a model, adult flies were collected immediately after death and in the early stages of carcass decomposition. To confirm actual colonization of the carcass, insects that completed their larval development on the resource were also collected and reared until adult stage. A diverse assemblage of dipterans composed of at least 28 species from seven families with necrophagous habits was observed within minutes after death. Besides Calliphoridae and Sarcophagidae, species from forensically-important families such as Phoridae, Anthomyiidae, and Fanniidae were also registered. Eleven species were shown to complete their development on the carcass. The majority of individuals emerged from larvae collected at the dry stage of decomposition. Hemilucilia segmentaria Fabricius (Diptera: Calliphoridae), H. semidiaphana (Rondani), and Ophyra chalcogaster (Wiedemann) (Muscidae) were the dominant species among the colonizers, which supports their importance as forensic evidence in Brazil.
UvA-DARE ( Digital Academic Repository ) Inverse modelling of in situ soil water dynamics : investigating the effect of different prior distributions of the soil hydraulic parameters

In situ observations of soil water state variables under natural boundary conditions are often used to estimate the soil hydraulic properties. However, many contributions to the soil hydrological literature have demonstrated that the information content of such data is insufficient to accurately and precisely estimate all the soil hydraulic parameters. In this case study, we explored to which degree prior information about the soil hydraulic parameters can help improve parameter identifiability in inverse modelling of in situ soil water dynamics under natural boundary conditions. We used percentages of sand, silt, and clay as input variables to the ROSETTA pedotransfer function that predicts the parameters in the van Genuchten-Mualem (VGM) model of the soil hydraulic functions. To derive additional information about the correlation structure of the predicted parameters, which is not readily provided by ROSETTA, we employed a Monte Carlo approach. We formulated three prior distributions that incorporate to different extents the prior information about the VGM parameters derived with ROSETTA. The inverse problem was posed in a formal Bayesian framework and solved using Markov chain Monte Carlo (MCMC) simulation with the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm. Synthetic and real-world soil water content data were used to illustrate the approach. The results of this study demonstrated that prior information about the soil hydraulic Correspondence to: B. Scharnagl (benedikt.scharnagl@tu-bs.de) parameters significantly improved parameter identifiability and that this approach was effective and robust, even in case of biased prior information. To be effective and robust, however, it was essential to use a prior distribution that incorporates information about parameter correlation.
Distinct Patterns of Wnt3a and Wnt5a Signaling Pathway in the Lung from Rats with Endotoxic Shock

Septic shock is a syndrome with severe hypotension and multiple organ dysfunction caused by an imbalance between pro-inflammatory and anti-inflammatory response. The most common risk factor of acute lung injury is severe sepsis. Patients with sepsis-related acute respiratory distress syndrome have higher mortality. Recent studies reveal regulatory roles of Wnt3a and Wnt5a signaling in inflammatory processes. Wnt3a signaling has been implicated in anti-inflammatory effects, whereas Wnt5a signaling has been postulated to have pro-inflammatory properties. However, the balance between Wnt3a and Wnt5a signaling pathway in the lung of rats with endotoxic shock has not been determined. Thus, we investigated the major components of Wnt3a and Wnt5a signaling pathway in the lung of endotoxemic rats. Male Wistar rats were intravenously infused with saline or lipopolysaccharide (LPS, 10 mg/kg). The changes of hemodynamics, biochemical variables, and arterial blood gas were examined during the experimental period. At 6 h after saline or LPS, animals were sacrificed, and lungs were obtained for analyzing superoxide production, water accumulation, histologic assessment, and protein expressions of Wnt3a and Wnt5a signaling pathway. Animals that received LPS showed circulatory failure, multiple organ dysfunction, metabolic acidosis, hyperventilation, lung edema, and high mortality. The lung from rats with endotoxic shock exhibited significant decreases in the levels of Wnt3a, Fzd1, Dsh1, phosphorylated GSK-3β at Ser9, and β-catenin. In contrast, the expressions of Wnt5a, Fzd5, and CaMKII were up-regulated in the lung of endotoxemic rats. These findings indicate the major components of Wnt3a and Wnt5a signaling in the lung are disturbed under endotoxic insult.
An Interesting Case of Tolosa-Hunt Syndrome in a Young Male

Tolosa-Hunt syndrome is a rare disease with a limited number of cases reported in the literature. It typically presents with orbital pain associated with palsy of the third, fourth, or sixth cranial nerve. We present an interesting case of Tolosa-Hunt syndrome in a young male who responded well to high-dose steroids and in a few days had significant improvement in his retro-orbital pain and ocular movements.
Seedling Root Growth as a Function of Soil Density and Water Content

Compaction caused by some intensive forest management practices can reduce tree growth, but growth reduction is the result of complex interactions between soil properties and tree physiological processes, which may differ by species. We used a 7 by 7 factorial greenhouse experiment to create a matrix of bulk density (ρ b ) and volumetric water content (θ v ) to better understand soil compaction effects on seedling growth of: (i) ponderosa pine (Pinus ponderosa var. ponderosa Dougl. ex Laws) grown on Dome and Cohasset soils; (ii) shortleaf pine (Pinus echinata Mill.) on a Clarksville soil; and (iii) loblolly pine (Pinus taeda L.) on an Argent soil. Models of root length density (RLD) were developed using multiple regression. The general model of RLD = b 0 + b 1 θ v + b 2 ρ b + b 3 θ 2 v described rooting response for the Clarksville-shortleaf and Argent-loblolly soil-species combinations (p = 0.005). However, the ponderosa pine RLD response on Cohasset soil was linear and there was an interaction between θ v and ρ b in the Dome soil. Shoot mass of seedlings growing within the least limiting water range (LLWR) was greater than those growing outside the range for all soil-species combinations except the Argent-loblolly pine (p = 0.05). The loblolly pines had greater shoot mass at 0, above the upper LLWR limits (aeration limiting). Least limiting water range has potential as a soil quality indicator, but seedling response was not always associated with LLWR. Root length density (RLD) response surface models in conjunction with seasonal site water data have potential for determining compaction-induced soil limitations for tree growth, but need to be field tested and calibrated for both soil and species.
Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

In Escherichia coli, tetracycline prevents translation. When subject to tetracycline, E. coli express TetA to pump it out by a mechanism that is sensitive, while fairly independent of cellular metabolism. We constructed a target gene, PtetA-mRFP1-96BS, with a 96 MS2-GFP binding site array in a single-copy BAC vector, whose expression is controlled by the tetA promoter. We measured the in vivo kinetics of production of individual RNA molecules of the target gene as a function of inducer concentration and temperature. From the distributions of intervals between transcription events, we find that RNA production by PtetA is a sub-Poissonian process. Next, we infer the number and duration of the prominent sequential steps in transcription initiation by maximum likelihood estimation. Under full induction and at optimal temperature, we observe three major steps. We find that the kinetics of RNA production under the control of PtetA, including number and duration of the steps, varies with induction strength and temperature. The results are supported by a set of logical pairwise Kolmogorov-Smirnov tests. We conclude that the expression of TetA is controlled by a sequential mechanism that is robust, whereas sensitive to external signals.
Effects of a decision support system on the diagnostic accuracy of users: a preliminary report.

OBJECTIVES To assess the effects of incomplete data upon the output of a computerized diagnostic decision support system (DSS), to assess the effects of using the system upon the diagnostic opinions of users, and to explore if these effects vary as a function of clinical experience. DESIGN Experimental pilot study. Four clusters of nine cases each were constructed and equated for case difficulty. Definitive findings were omitted from the case abstracts. Subjects were randomly assigned to one of four clusters and were trained on the DSS prior to use. SUBJECTS The study involved 16 physicians at three levels of clinical experience (six general internists, four residents in internal medicine, and six fourth-year medical students), from three academic medical centers. PROCEDURE Each subject worked up nine cases, first without and then with ILIAD consultation. They were asked to offer up to six potential diagnoses and to list up to three steps that should be the next items in the diagnostic workup. Effects of DSS consultation were measured by changes in the position of the correct diagnosis in the lists of differential diagnoses, pre- and post-consultation. RESULTS The DSS lists of diagnostic possibilities contained the correct diagnosis in 38% of cases, about midway between the levels of accuracy of residents and attending general internists. In over 70% of cases, the DSS output had no effect on the position of the correct diagnosis in the subjects' lists. The system's diagnostic accuracy was unaffected by the clinical experience of the users.
Loss of FilaminC (FLNc) Results in Severe Defects in Myogenesis and Myotube Structure

ABSTRACT FilaminC (FLNc) is the muscle-specific member of a family of actin binding proteins. Although it interacts with many proteins involved in muscular dystrophies, its unique role in muscle is poorly understood. To address this, two models were developed. First, FLNc expression was stably reduced in C2C12 myoblasts by RNA interference. While these cells start differentiation normally, they display defects in differentiation and fusion ability and ultimately form multinucleated “myoballs” rather than maintain elongated morphology. Second, a mouse model carrying a deletion of last 8 exons of Flnc was developed. FLNc-deficient mice die shortly after birth, due to respiratory failure, and have severely reduced birth weights, with fewer muscle fibers and primary myotubes, indicating defects in primary myogenesis. They exhibit variation in fiber size, fibers with centrally located nuclei, and some rounded fibers resembling the in vitro phenotype. The similarity of the phenotype of FLNc-deficient mice to the filamin-interacting TRIO null mice was further confirmed by comparing FLNc-deficient C2C12 cells to TRIO-deficient cells. These data provide the first evidence that FLNc has a crucial role in muscle development and maintenance of muscle structural integrity and suggest the presence of a TRIO-FLNc-dependent pathway in maintaining proper myotube structure.
Brain functional connectivity alterations in a rat model of excessive alcohol drinking: A resting-state network analysis

Alcohol use disorders (AUD) are a major public health concern. Understanding the brain network alterations is of the utmost importance to diagnose and develop treatment strategies. Employing resting-state functional magnetic resonance imaging, we have performed a longitudinal study in a rat model of chronic excessive alcohol consumption, to identify functional alterations in brain networks triggered by alcohol drinking. Two time points were considered: 1) before alcohol consumption (control condition) and 2) after 30 days of alcohol drinking (alcohol condition). We first identified nine resting-state networks with group independent component analysis. Afterwards, dual regression was applied to obtain subject-specific time courses and spatial maps. L2-regularized partial correlation analysis between pairs of networks showed that functional connectivity (FC) between the retrosplenial-visual and striatal networks decreases due to alcohol consumption, whereas FC between the prefrontal-cingulate and striatal networks increases. Analysis of subject-specific spatial maps revealed FC decreases within networks after alcohol drinking, including the striatal, motor-parietal, prefrontal-cingulate, retrosplenial-visual and left motor-parietal networks. Overall, our results unveil a generalized decrease in brain FC induced by alcohol drinking in genetically predisposed animals, even after a relatively short period of exposure (1 month). The only exception to this hypo-connectivity state is the functional association between the striatal and prefrontal-cingulate networks, which increases after drinking, supporting evidence in human alcoholics.
Continuation and Maintenance ECT: A Review of Recent Research

Continuation and maintenance electroconvulsive therapy (ECT) is used to reduce the risk for relapse and recurrence of illness in patients who fare poorly with continuation and maintenance medication regimens. Despite the potential value of these ECT schedules, both are relatively neglected in clinical practice. This article therefore reviews the last decade of research on the subject. Although the research comprises mostly single and multiple case reports and small open studies, continuation and maintenance ECT does emerge as a safe and effective treatment for relapse- and recurrence-prone patients who have responded to a course of ECT.
Under Consideration for Publication in J. Functional Programming Monadic Augment and Generalised Short Cut Fusion

Monads are commonplace programming devices that are used to uniformly structure computations ; in particular, they are often used to mimic the effects of impure features such as state, error handling, and I/O. This paper further develops the monadic programming paradigm by investigating the extent to which monadic computations can be optimised by using generalisations of short cut fusion to eliminate monadic structures whose sole purpose is to " glue together " monadic program components. Ghani, Uustalu, and Vene have recently shown that every inductive type has an associated build combinator and an associated short cut fusion rule. They have also used the notion of a parameterised monad to describe those monads that give rise to inductive types, and have shown that the standard augment combinators and cata/augment fusion rules for algebraic data types can be generalised to fixed points of all parameterised monads. We revisit these augment combinators and generalised short cut fusion rules for such types but consider them from a functional programming perspective, rather than a categorical one. In addition to making the category-theoretic ideas of Ghani, Uustalu, and Vene more easily accessible to a wider audience of functional programmers, we demonstrate their practical applicability by developing nontrivial application programs and performing modest benchmarking on them. We also show how the cata/augment rules can serve as the basis for deriving additional generic fusion laws, thus opening the way for an algebra of fusion. Finally, we offer deep theoretical insights, arguing that the augment combina-tors are monadic in nature, and thus that the cata/build and cata/augment rules are arguably the best generally applicable fusion rules obtainable.
Adiposity and weight change in mid-life in relation to healthy survival after age 70 in women: prospective cohort study

Objective To examine the hypothesis that mid-life adiposity is associated with a reduced probability of maintaining an optimal health status among those who survive to older ages. Design Prospective cohort study. Setting The Nurses’ Health Study, United States. Participants 17 065 women who survived until at least the age of 70, provided information on occurrence of chronic disease, cognitive function, physical function, and mental health at older ages, and were free from major chronic diseases at mid-life (mean age was 50 at baseline in 1976). Main outcome measures Healthy survival to age 70 and over was defined as having no history of 11 major chronic diseases and having no substantial cognitive, physical, or mental limitations. Results Of the women who survived until at least age 70, 1686 (9.9%) met our criteria for healthy survival. Increased body mass index (BMI) at baseline was significantly associated with linearly reduced odds of healthy survival compared with usual survival, after adjustment for various lifestyle and dietary variables (P<0.001 for trend). Compared with lean women (BMI 18.5-22.9), obese women (BMI ≥30) had 79% lower odds of healthy survival (odds ratio 0.21, 95% confidence interval 0.15 to 0.29). In addition, the more weight gained from age 18 until mid-life, the less likely was healthy survival after the age of 70. The lowest odds of healthy survival were among women who were overweight (BMI ≥25) at age 18 and gained ≥10 kg weight (0.18, 0.09 to 0.36), relative to women who were lean (BMI 18.5-22.9) and maintained a stable weight. Conclusions These data provide evidence that adiposity in mid-life is strongly related to a reduced probability of healthy survival among women who live to older ages, and emphasise the importance of maintaining a healthy weight from early adulthood.
Microvascular Development in Porcine Right and Left Ventricular Walls

Patients with congenital heart disease who have a morphological right ventricle (RV) serving as a systemic ventricle have an increased incidence of RV dysfunction. A different structural response of microvessels to increased pressure load in the RV is a possible mechanism for this dysfunction. To examine the merit of this hypothesis, we explored the possibility that in the normal heart, the branching architecture of microvasculature in walls of the left ventricle (LV) and RV mature differently. The branching structure of intramyocardial arterioles and their downstream branches were investigated using three-dimensional (3D) micro-computed tomography (CT) images in different regions of the RV and LV walls of normal fetal, 1-mo, and 5-mo old pigs. The results point to a significant difference in the volume of myocardium perfused per vessel cross-sectional area (CSA) between the LV and RV walls at 5 mo. We speculate that this difference may be related to the reserve functional capacity of the LV, which requires a corresponding reserve in the expansion capacity of vasculature in the LV wall.