Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct Methylation Changes at the IGF2-H19 Locus in Congenital Growth Disorders and Cancer

Background Differentially methylated regions (DMRs) are associated with many imprinted genes. In mice methylation at a DMR upstream of the H19 gene known as the Imprint Control region (IC1) is acquired in the male germline and influences the methylation status of DMRs 100 kb away in the adjacent Insulin-like growth factor 2 (Igf2) gene through long-range interactions. In humans, germline-derived or post-zygotically acquired imprinting defects at IC1 are associated with aberrant activation or repression of IGF2, resulting in the congenital growth disorders Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, respectively. In Wilms tumour and colorectal cancer, biallelic expression of IGF2 has been observed in association with loss of methylation at a DMR in IGF2. This DMR, known as DMR0, has been shown to be methylated on the silent maternal IGF2 allele presumably with a role in repression. The effect of IGF2 DMR0 methylation changes in the aetiology of BWS or SRS is unknown. Methodology/Principal Findings We analysed the methylation status of the DMR0 in BWS, SRS and Wilms tumour patients by conventional bisulphite sequencing and pyrosequencing. We show here that, contrary to previous reports, the IGF2 DMR0 is actually methylated on the active paternal allele in peripheral blood and kidney. This is similar to the IC1 methylation status and is inconsistent with the proposed silencing function of the maternal IGF2 allele. Beckwith-Wiedemann and Silver-Russell patients with IC1 methylation defects have similar methylation defects at the IGF2 DMR0, consistent with IC1 regulating methylation at IGF2 in cis. In Wilms tumour, however, methylation profiles of IC1 and IGF2 DMR0 are indicative of methylation changes occurring on both parental alleles rather than in cis. Conclusions/Significance These results support a model in which DMR0 and IC1 have opposite susceptibilities to global hyper and hypomethylation during tumorigenesis independent of the parent of origin imprint. In contrast, during embryogenesis DMR0 is methylated or demethylated according to the germline methylation imprint at the IC1, indicating different mechanisms of imprinting loss in neoplastic and non-neoplastic cells.
A calculus for communicating systems with time and probabilities

A process algebra that extends R. Milner's (1983) calculus of communicating systems (CCS) with probabilities and time is presented. With this calculus it is possible to describe real-time and reliability aspects of distributed systems. A (strong) bisimulation equivalence is defined, and a corresponding complete axiomatization is given. Several examples are included. <<ETX>>
Nanosecond T-Jump Experiment in Poly(glutamic acid): A Circular Dichroism Study

Poly(glutamic acid) has been studied with a nanosecond T-jump experiment. A new experimental set-up based on the frequency-quadrupling of an 82 MHz Titanium-Sapphire laser allows rapid CD measurements to be performed. Combining time-resolved absorption and circular dichroism at 204 and 220 nm, we are able to measure precisely the unfolding relaxation time as well as the helical fraction evolution. We show that only CD at 220 nm is relevant to observe the unfolding of an alpha helix whereas no change is observed for CD at 204 nm. Conversely, both absorptions yield information on the dynamics of the process.
Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain

We studied the global relationship between gene expression and neuroanatomical connectivity in the adult rodent brain. We utilized a large data set of the rat brain “connectome” from the Brain Architecture Management System (942 brain regions and over 5000 connections) and used statistical approaches to relate the data to the gene expression signatures of 17,530 genes in 142 anatomical regions from the Allen Brain Atlas. Our analysis shows that adult gene expression signatures have a statistically significant relationship to connectivity. In particular, brain regions that have similar expression profiles tend to have similar connectivity profiles, and this effect is not entirely attributable to spatial correlations. In addition, brain regions which are connected have more similar expression patterns. Using a simple optimization approach, we identified a set of genes most correlated with neuroanatomical connectivity, and find that this set is enriched for genes involved in neuronal development and axon guidance. A number of the genes have been implicated in neurodevelopmental disorders such as autistic spectrum disorder. Our results have the potential to shed light on the role of gene expression patterns in influencing neuronal activity and connectivity, with potential applications to our understanding of brain disorders. Supplementary data are available at http://www.chibi. ubc.ca/ABAMS.
CLKN: Cascaded Lucas-Kanade Networks for Image Alignment

This paper proposes a data-driven approach for image alignment. Our main contribution is a novel network architecture that combines the strengths of convolutional neural networks (CNNs) and the Lucas-Kanade algorithm. The main component of this architecture is a Lucas-Kanade layer that performs the inverse compositional algorithm on convolutional feature maps. To train our network, we develop a cascaded feature learning method that incorporates the coarse-to-fine strategy into the training process. This method learns a pyramid representation of convolutional features in a cascaded manner and yields a cascaded network that performs coarse-to-fine alignment on the feature pyramids. We apply our model to the task of homography estimation, and perform training and evaluation on a large labeled dataset generated from the MS-COCO dataset. Experimental results show that the proposed approach significantly outperforms the other methods.
Scalable Bayesian Optimization Using Deep Neural Networks

Bayesian optimization is an effective methodology for the global optimization of functions with expensive evaluations. It relies on querying a distribution over functions defined by a relatively cheap surrogate model. An accurate model for this distribution over functions is critical to the effectiveness of the approach, and is typically fit using Gaussian processes (GPs). However, since GPs scale cubically with the number of observations, it has been challenging to handle objectives whose optimization requires many evaluations, and as such, massively parallelizing the optimization. In this work, we explore the use of neural networks as an alternative to GPs to model distributions over functions. We show that performing adaptive basis function regression with a neural network as the parametric form performs competitively with state-of-the-art GP-based approaches, but scales linearly with the number of data rather than cubically. This allows us to achieve a previously intractable degree of parallelism, which we apply to large scale hyperparameter optimization, rapidly finding competitive models on benchmark object recognition tasks using convolutional networks, and image caption generation using neural language models.
Superior Effects of Antiretroviral Treatment among Men Who have Sex with Men Compared to Other HIV At-Risk Populations in a Large Cohort Study in Hunan, China

This study assesses association between CD4 level at initiation of antiretroviral treatment (ART) on subsequent treatment outcomes and mortality among people infected with HIV via various routes in Hunan province, China. Over a period of 10 years, a total of 7333 HIV-positive patients, including 553 (7.5%) MSM, 5484 (74.8%) heterosexuals, 1164 (15.9%) injection drug users (IDU) and 132 (1.8%) former plasma donors (FPD), were recruited. MSM substantially demonstrated higher initial CD4 cell level (242, IQR 167–298) than other populations (Heterosexuals: 144 IQR 40–242, IDU: 134 IQR 38–224, FPD: 86 IQR 36–181). During subsequent long-term follow up, the median CD4 level in all participants increased significantly from 151 cells/mm3 (IQR 43–246) to 265 cells/mm3 (IQR 162–380), whereas CD4 level in MSM remained at a high level between 242 and 361 cells/mm3. Consistently, both cumulative immunological and virological failure rates (10.4% and 26.4% in 48 months, respectively) were the lowest in MSM compared with other population groups. Survival analysis indicated that initial CD4 counts ≤200 cells/mm3 (AHR = 3.14; CI, 2.43–4.06) significantly contributed to HIV-related mortality during treatment. Timely diagnosis and treatment of HIV patients are vital for improving CD4 level and health outcomes.
Marine current turbine generator system with induction machine growing neural gas (GNG) MPPT based on sensorless sea speed estimation

This paper presents a MPPT technique for high performance marine current generator with induction machine based on the Growing Neural Gas (GNG) network. The marine turbine characteristic curve has been firstly predicted by a BEM hydrodynamic formulation. The BEM analysis has been compared with experimental results obtained at the QinetiQ cavitation tunnel (Haslar Marine Technology Park). For the experimental application, a back-to-back power converter configuration with two voltage source converters has been considered, one on the machine side and the other on the grid side. Each converter has been controlled with a high performance vector control technique, respectively Field Oriented Control (FOC) and Voltage Oriented Control (VOC). A test setup has been built for the experimental assessment of the methodology. Experimental results show the correct behaviour of the proposed MPPT technique which permits to instantaneously estimate the sea speed and correspondingly to compute the optimal machine reference speed for tracking the maximum available power.
Low-Weight Polynomial Form Integers for Efficient Modular Multiplication

In 1999, Solinas introduced families of moduli called the generalized Mersenne numbers (GMNs), which are expressed in low-weight polynomial form, p=f(t), where t is limited to a power of 2. GMNs are very useful in elliptic curve cryptosystems over prime fields since modular reduction by a GMN requires only integer additions and subtractions. However, since there are not many GMNs and each GMN requires a dedicated implementation, GMNs are hardly useful for other cryptosystems. Here, we modify GMN by removing restriction on the choice of t and restricting the coefficients of f(t) to 0 and plusmn1. We call such families of moduli low-weight polynomial form integers (LWPFIs). We show an efficient modular multiplication method using LWPFI moduli. LWPFIs allow general implementation and there exist many LWPFI moduli. One may consider LWPFIs as a trade-off between general integers and GMNs
Investigation of Low Frequency Drift in fMRI Signal

Low frequency drift (0.0-0.015 Hz) has often been reported in time series fMRI data. This drift has often been attributed to physiological noise or subject motion, but no studies have been done to test this assumption. Time series T*2-weighted volumes were acquired on two clinical 1.5 T MRI systems using spiral and EPI readout gradients from cadavers, a normal volunteer, and nonhomogeneous and homogeneous phantoms. The data were tested for significant differences (P = 0.001) from Gaussian noise in the frequency range 0.0-0.015 Hz. The percentage of voxels that were significant in data from the cadaver, normal volunteer, nonhomogeneous and homogeneous phantoms were 13.7-49.0%, 22.1-61.9%, 46.4-68.0%, and 1.10%, respectively. Low frequency drift was more pronounced in regions with high spatial intensity gradients. Significant drifting was present in data acquired from cadavers and nonhomogeneous phantoms and all pulse sequences tested, implying that scanner instabilities and not motion or physiological noise may be the major cause of the drift.
Cortical Connections to Area TE in Monkey: Hybrid Modular and Distributed Organization

To investigate the fine anatomical organization of cortical inputs to visual association area TE, 2–3 small injections of retrograde tracers were made in macaque monkeys. Injections were made as a terminal procedure, after optical imaging and electrophysiological recording, and targeted to patches physiologically identified as object-selective. Retrogradely labeled neurons occurred in several unimodal visual areas, the superior temporal sulcus, intraparietal sulcus (IPS), and prefrontal cortex (PFC), consistent with previous studies. Despite the small injection size (<0.5 mm wide), the projection foci in visual areas, but not in IPS or PFC, were spatially widespread (4–6 mm in extent), and predominantly consisted of neurons labeled by only one of the injections. This can be seen as a quasi-modular organization. In addition, within each projection focus, there were scattered neurons projecting to one of the other injections, together with some double-labeled (DL) neurons, in a more distributed pattern. Finally, projection foci included smaller “hotspots,” consisting of intermixed neurons, single-labeled by the different injections, and DL neurons. DL neurons are likely the result of axons having extended, spatially separated terminal arbors, as demonstrated by anterograde experiments. These results suggest a complex, hybrid connectivity architecture, with both modular and distributed components.
Campylobacter diarrhoea and an association of recent disease with asymptomatic shedding in Egyptian children

SUMMARY A hospital-based case-control diarrhoea survey was conducted in Cairo. Egypt to determine the age-specific frequency of campylobacter infection among diarrhoeic and non-diarrhoeic children aged new born to 5 years. Campylobacter was the most common bacterial enteropathogen isolated from diarrhoeic stools. The overall prevalence of campylobacter isolations was 25·9% from stools of 143 diarrhoeic children compared to 15·2% of 132 non-diarrhoeic control children (P = 0·028) during the 4-month period of study. Children less than 1 year of age were at greatest risk of campylobacter infection with 32·6% of diarrhoeic patients culture positive, compared to 14·3% of controls. Asymptomatic shedding in controls was positively associated with a recent diarrhoeal episode (P = 0·019) and may be an important source of new infections.
Exploring the Validity of Corpus-derive d Measures of Semantic Similarity

Lexical co-occurrence counts from large corpora have been used to construct highdimensional vector-space models of language. In this type of model words are represented as vectors (or points) in a hyperspace, and distances between word vectors are generally considered to reflect semantic similarity. Two issues must be addressed if a vector-space model is to be used as a 'semantic' measuring device: reliability and validity. Do context vectors reliably measure what they are supposed to be measuring? Does ‘semantic distance’ correlate with other variables that predict variation? A simple, principled method for determining and improving the reliability of co-occurrence vectors is presented and tested in two corpus experiments. The validity question is addressed using psychological data from a semantic similarity rating task as the criterion measure.
Heat Shock Protein 72 Expressing Stress in Sepsis: Unbridgeable Gap between Animal and Human Studies—A Hypothetical “Comparative” Study

Heat shock protein 72 (Hsp72) exhibits a protective role during times of increased risk of pathogenic challenge and/or tissue damage. The aim of the study was to ascertain Hsp72 protective effect differences between animal and human studies in sepsis using a hypothetical “comparative study” model. Forty-one in vivo (56.1%), in vitro (17.1%), or combined (26.8%) animal and 14 in vivo (2) or in vitro (12) human Hsp72 studies (P < 0.0001) were enrolled in the analysis. Of the 14 human studies, 50% showed a protective Hsp72 effect compared to 95.8% protection shown in septic animal studies (P < 0.0001). Only human studies reported Hsp72-associated mortality (21.4%) or infection (7.1%) or reported results (14.3%) to be nonprotective (P < 0.001). In animal models, any Hsp72 induction method tried increased intracellular Hsp72 (100%), compared to 57.1% of human studies (P < 0.02), reduced proinflammatory cytokines (28/29), and enhanced survival (18/18). Animal studies show a clear Hsp72 protective effect in sepsis. Human studies are inconclusive, showing either protection or a possible relation to mortality and infections. This might be due to the fact that using evermore purified target cell populations in animal models, a lot of clinical information regarding the net response that occurs in sepsis is missing.
A deep learning methodology to proliferate golden signoff timing

Signoff timing analysis remains a critical element in the IC design flow. Multiple signoff corners, libraries, design methodologies, and implementation flows make timing closure very complex at advanced technology nodes. Design teams often wish to ensure that one tool's timing reports are neither optimistic nor pessimistic with respect to another tool's reports. The resulting “correlation” problem is highly complex because tools contain millions of lines of black-box and legacy code, licenses prevent any reverse-engineering of algorithms, and the nature of the problem is seemingly “unbounded” across possible designs, timing paths, and electrical parameters. In this work, we apply a “big-data” approach to the timer correlation problem. We develop a machine learning-based tool, Golden Timer eXtension (GTX), to correct divergence in flip-flop setup time, cell arc delay, wire delay, stage delay, and path slack at timing endpoints between timers. We propose a methodology to apply GTX to two arbitrary timers, and we evaluate scalability of GTX across multiple designs and foundry technologies / libraries, both with and without signal integrity analysis. Our experimental results show reduction in divergence between timing tools from 139.3ps to 21.1ps (i.e., 6.6×) in endpoint slack, and from 117ps to 23.8ps (4.9× reduction) in stage delay. We further demonstrate the incremental application of our methods so that models can be adapted to any outlier discrepancies when new designs are taped out in the same technology / library. Last, we demonstrate that GTX can also correlate timing reports between signoff and design implementation tools.
Premorbid nutrition and short term outcome of stroke: a multicentre study from India

Background Little is known about the impact of premorbid undernutrition on stroke outcome in developing countries. Aim To study the impact of premorbid undernutrition status, measured by the Subjective Global Assessment (SGA) tool, on short term stroke outcome. Methods First ever stroke patients admitted to six major hospitals in North and South India participated in this study from 1 March 2008 to 30 September 2009. The SGA tool was administered within 48 h of stroke onset, and 6 months premorbid nutritional status was rated as well nourished (A rating) and undernourished (B and C ratings) using this tool. Stroke outcome was assessed after 30 days using the modified Rankin scale (mRs), and a mRs score >3 was defined as a poor outcome. Statistical analyses were performed using SPSS Statistics V.17. 0. Results Of 477 patients enrolled, 448 patients were included in the analyses. Mean age was 58.1±13.7 years (range 16–96) and 281 (62.7%) patients were men. At admission, premorbid undernutrition was found in 121 (27.2%) patients. Older age (OR 4.99, CI 1.26 to 19.64, p=0.021), hypertension (OR 1.99, CI 1.04 to 3.79, p=0.037) and patients from Andhra Pradesh State (OR 1.87, CI 1.05 to 3.32, p=0.032) were predictors of undernutrition in multiple logistic regression analysis. Premorbid undernutrition (OR 1.99, CI 1.20 to 3.31, p=0.007) and length of hospital stay (OR 3.41, CI 1.91 to 6.06, p<0.0001) were the independent predictors of poor outcome in the multiple logistic regression model. Conclusions High rates of premorbid undernutrition in stroke patients were found. Age, hypertension and patients from Andhra Pradesh State were predictors of premorbid undernutrition. Premorbid undernutrition was associated with poor stroke outcome. The results provide opportunities for primary prevention and improving stroke outcome.
Integrating World Englishes into a university conversation class in South Korea

Almost three decades have passed since Kachru (1985) proposed his three-circle model of World Englishes. Although this model is often challenged, few would deny its significance in opening the dialogue and raising awareness of issues related to World Englishes. The context of the project described in this paper is South Korea, one of what Kachru's model refers to as an ‘expanding circle country’. Reflecting on the idea of South Korea as an ‘expanding circle country’, this article briefly examines how Korea has expanded and continues to expand as a nation, juxtaposing it alongside the university speaking class I was teaching, as I look toward expanding both my own and my students' minds through exploring World Englishes within a university speaking course.
Blood vessel invasion and axillary lymph node involvement as prognostic indicators for human breast cancer

Blood vessel invasion and axillary lymph node involvement were examined in 175 breast cancer patients. The incidence of blood vessel invasion was 35%. The presence of blood vessel invasion was highly associated with early disease recurrence. The association of poor prognosis with blood vessel invasion was independent of clinical stage, menopausal status, node status, tumor size, or postsurgical treatment. Those patients with blood vessel invasion and two or more positive nodes were at extremely high risk for early recurrence (70% recurrence by two years compared with 15% recurrence in the remainder of the patients). Thus, blood vessel invasion is a useful indicator of early recurrence in patients with primary breast cancer and, in combination with node status, is a prognostic indicator with high discriminatory power.
A Blocker of N- and T-type Voltage-Gated Calcium Channels Attenuates Ethanol-Induced Intoxication, Place Preference, Self-Administration, and Reinstatement

There is a clear need for new therapeutics to treat alcoholism. Here, we test our hypothesis that selective inhibitors of neuronal calcium channels will reduce ethanol consumption and intoxication, based on our previous studies using knock-out mice and cell culture systems. We demonstrate that pretreatment with the novel mixed N-type and T-type calcium channel antagonist 1-(6,6-bis(4-fluorophenyl)hexyl)-4-(3,4,5-trimethoxybenzyl)piperazine (NP078585) reduced ethanol intoxication. NP078585 also attenuated the reinforcing and rewarding properties of ethanol, measured by operant self-administration and the expression of an ethanol conditioned place preference, and abolished stress-induced reinstatement of ethanol seeking. NP078585 did not affect alcohol responses in mice lacking N-type calcium channels. These results suggest that selective calcium channel inhibitors may be useful in reducing acute ethanol intoxication and alcohol consumption by human alcoholics.