Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammatory Bowel Disease-related Colorectal Cancer in the Asia-Pacific Region: Past, Present, and Future

Patients with inflammatory bowel disease (IBD) are at an increased risk of developing colorectal cancer (CRC), and key contributing factors include chronic colonic inflammation and the extent and duration of disease. This increase in risk is more likely to result from chronic inflammation of the colonic mucosa than from any clearly defined genetic predisposition. However, globally, the true magnitude of this risk is debatable, since results from different studies are heterogeneous in terms of geographical and methodological variables. The prevalence of IBD-related CRC in the Asia-Pacific region ranges from 0.3% to 1.8% and a recent study found that the cumulative incidence of IBD-related CRC is comparable to that in Western countries. However, the CRC mortality rate in the Asia-Pacific region is on the rise compared with that in Western countries, and a few Asian countries show particularly rapid upward trends in CRC incidence. Although our understanding of the molecular and clinical basis for IBD-related CRC has improved substantially, our means of prevention, endoscopic surveillance, chemoprevention, and prophylactic surgery remain modest at best. Furthermore, published data on IBD-related CRC in the Asia-Pacific region is lacking, and this review addresses many aspects including epidemiology, natural history, etiopathogenesis, morphology, and biological behaviors of IBD-related CRC and sporadic CRC in the Asia-Pacific region. In this review, we will also discuss the risk factors for CRC in IBD patients, endoscopic technology screening, and surveillance programs and management strategies for IBD-related CRC.
Multi-Way Compressed Sensing for Sparse Low-Rank Tensors

For linear models, compressed sensing theory and methods enable recovery of sparse signals of interest from few measurements-in the order of the number of nonzero entries as opposed to the length of the signal of interest. Results of similar flavor have more recently emerged for bilinear models, but no results are available for multilinear models of tensor data. In this contribution, we consider compressed sensing for sparse and low-rank tensors. More specifically, we consider low-rank tensors synthesized as sums of outer products of sparse loading vectors, and a special class of linear dimensionality-reducing transformations that reduce each mode individually. We prove interesting “oracle” properties showing that it is possible to identify the uncompressed sparse loadings directly from the compressed tensor data. The proofs naturally suggest a two-step recovery process: fitting a low-rank model in compressed domain, followed by per-mode decompression. This two-step process is also appealing from a computational complexity and memory capacity point of view, especially for big tensor datasets.
Comment: " Forecasting Economic and Financial Variables with Global Vars "

This paper reports the near term forecasting power of a large Global Vector Autoregressive (GVAR) model originally developed by Pesaran, Schuermann and Weiner, PSW, (2004) and subsequently fine-tuned and re-estimated over 1979Q1-1 The GVAR model explicitly specifies interdependencies between different countries and sub-regions in terms of three transparent channels: i) domestic variables are related to corresponding trade-weighted foreign variables to match the international trade pattern of the country under consideration; ii) non-zero pair wise correlations in residuals between countries and equations are allowed to capture a certain amount of dependence in idiosyncratic shocks, and iii) common observed shocks (viz, oil prices) that can affect all countries simultaneously are permitted. The key feature of the GVAR model as compared to factor structural VAR models is the direct introduction of observed country-specific foreign variables in the individual country models to deal with pervasive dependencies in the world economy in a more flexible manner. The authors first estimate the individual county-specific vector error correcting models, then these individual models are combined in an internally consistent manner to generate forecasts for all variables of all countries simultaneously. The 1-quarter and 4-quarter ahead forecasts for the eight quarters 2004Q1-2005Q4 are analyzed for 134 variables from 26 regions made up of 33
Automatic generation of memory consistency tests for chip multiprocessing

Chip multiprocessing (CMP) changed the architectural landscape of PCs and servers and is now changing the way personal mobile devices are designed. CMP requires access to shared variables in private memories, leading to complex chains of interacting events that must offer a consistent view of shared memory. Checking if a memory system implements a specified memory consistency model (MCM) is a challenging verification problem. We propose a generator of multi-threading random-instruction sequences for MCM checking. It complies with an arbitrary MCM and can be used by most checkers. Its ability to provide full coverage was evaluated through 1200 test cases.
Enzyme Supplementation to Soybean Based Diet in Rainbow trout (Oncorhynchusmykiss) Effects on Growth Parameters and Nitrogen and Phosphorus Digestibility

The aim of the this study was to examine the effects of the diets based on Soybean Meal (40%) supplemented with exogenous enzymes on growth performance, feed utilization, apparent digestibility and reduce environment pollution waste output of nitrogen and phosphorus in rainbow trout (Oncorhynchus mykiss) culture. Trout groups (initial weight 87.00±1,5) method of random plots with 3 replications of 50 fish/pond with the ratio of 1050 fish in the concrete ponds. Diets consisted of 25% fish meal (FM) and 40% dehulled hexane extracted soybean meal (SBM) in control group (C0) and diet supplemented with protease enzyme (PRT; 2g/kg-1), diet supplemented with enzyme cocktail (MIX; cellulose, xylanase, endo-s-1,3:1,4-glucanase; 2g/kg-1) and diet supplemented with pyhtase enzyme (PHY; 2g/kg-1). About of growth performance were found while condition factor (1,21-1,23) were statistically similar (p>0.05), however specific growth rate, SGR, (1,118-1,340) and feed conversion ratio, FCR, (1,26-1,30) were obtained significantly different among groups (p<0,05). PRT and PHY groups significantly improved SGR and FCR better than control group. In this study, showed the highest nitrogen apperent digestibility coefficient, ADC (85,49±1,98) in PRT group while, the poorest value obtained (72,82±0.01) C0 group respectively (p<0,05). Also the best (58.57±0.49) and lowest (42.85±1.98) ADC was obtained PHT and C0 groups for phosphorus respectively (p<0,05). Keywords: rainbow trout, enzyme, growth performance, nitrogen, phosphorus, digestibility
Test generation across multiple layers

Complex software systems frequently come in many layers, each realized in a different programming language. This is a challenge for test generation, as the semantics of each layer have to be determined and integrated. An automatic test generator for Java, for instance, is typically unable to deal with the internals of lower level code (such as C-code), which results in lower coverage and fewer test cases of interest. In this paper, we sketch a novel approach to help search-based test generators for Java to achieve better coverage of underlying native code layers. The key idea is to apply test generation to the native layer first, and then to use the inputs to the native test cases as targets for search-based testing of the higher Java layers. We demonstrate our approach on a case study combining KLEE and EVOSUITE.
Using immunoglobulin Y as an alternative antibody for the detection of hepatitis A virus in frozen liver sections

An increasing amount of research has been conducted on immunoglobulin Y (IgY) because the use of IgY offers several advantages with respect to diagnostic testing, including its easy accessibility, low cost and translatability to large-scale production, in addition to the fact that it can be ethically produced. In a previous work, immunoglobulin was produced and purified from egg yolks (IgY) reactive to hepatitis A virus (HAV) antigens. In the present work, this anti-HAV-specific IgY was used in an indirect immunofluorescence assay to detect viral antigens in liver biopsies that were obtained from experimentally infected cynomolgus monkeys. Fields that were positive for HAV antigen were detected in liver sections using confocal microscopy. In conclusion, egg yolks from immunised hens may be a reliable source for antibody production, which can be employed for immunological studies.
Mechanisms involved in the desflurane-induced post-conditioning of isolated human right atria from patients with type 2 diabetes.

BACKGROUND Desflurane triggers post-conditioning in the diabetic human myocardium. We determined whether protein kinase C (PKC), mitochondrial adenosine triphosphate-sensitive potassium (mitoK(ATP)) channels, Akt, and glycogen synthase kinase-3β (GSK-3β) were involved in the in vitro desflurane-induced post-conditioning of human myocardium from patients with type 2 diabetes. METHODS The isometric force of contraction (FoC) of human right atrial trabeculae obtained from patients with type 2 diabetes was recorded during 30 min of hypoxia followed by 60 min of reoxygenation. Desflurane (6%) was administered during the first 5 min of reoxygenation either alone or in the presence of calphostin C (PKC inhibitor) or 5-hydroxydecanoate (5-HD) (mitoK(ATP) channel antagonist). Phorbol 12-myristate 13-acetate (PKC activator) and diazoxide (a mitoK(ATP) channel opener) were superfused during early reoxygenation. The FoC at the end of the 60 min reoxygenation period was compared among treatment groups (FoC(60); mean and sd). The phosphorylation of Akt and GSK-3β was studied using western blotting. RESULTS Desflurane enhanced the recovery of force [FoC(60): 79 (3)% of baseline] after 60 min of reoxygenation when compared with the control group (P>0.0001). Calphostin C and 5-HD abolished the beneficial effect of desflurane-induced post-conditioning (both P<0.0001). Phorbol 12-myristate 13-acetate and diazoxide enhanced the FoC(60) when compared with the control group (both P<0.0001). Desflurane increased the level of phosphorylation of Akt and GSK-3β (P<0.0001). CONCLUSIONS Desflurane-induced post-conditioning in human myocardium from patients with type 2 diabetes was mediated by the activation of PKC, the opening of the mitoK(ATP) channels, and the phosphorylation of Akt and GSK-3β.
High-speed direct digital frequency synthesizers in 0.25-μm CMOS

Two high-speed direct digital frequency synthesizers (DDFS) have been fabricated in CMOS 0.25 /spl mu/m technology. Both DDFS provides two quadrature phase 12 bit outputs with a spectral purity of 80 dBc. The first circuit reaches a maximum operating frequency of 600 MHz. The second circuit operates up to 480 MHz clock speed while dissipating only 72 /spl mu/W/MHz. The proposed circuits employ an innovative high-speed architecture for sine and cosine functions approximation, based on a hardware-effective linear interpolation approach name as "dual-slope".
Robust Monocular Epipolar Flow Estimation

We consider the problem of computing optical flow in monocular video taken from a moving vehicle. In this setting, the vast majority of image flow is due to the vehicle's ego-motion. We propose to take advantage of this fact and estimate flow along the epipolar lines of the egomotion. Towards this goal, we derive a slanted-plane MRF model which explicitly reasons about the ordering of planes and their physical validity at junctions. Furthermore, we present a bottom-up grouping algorithm which produces over-segmentations that respect flow boundaries. We demonstrate the effectiveness of our approach in the challenging KITTI flow benchmark [11] achieving half the error of the best competing general flow algorithm and one third of the error of the best epipolar flow algorithm.
Role of early vascular damage in the pathogenesis of gastric haemorrhagic mucosal lesions induced by indomethacin in rats

Early vascular injury is a key element in the pathogenesis of gastric haemorrhagic mucosal lesions which develop rapidly after intragastric (i.g.) administration of ethanol, HCl or NaOH. The sequence of vascular events leading to gastric lesions has not, however, been investigated in detail with ulcerogenic non‐steroidal anti‐inflammatory drugs such as indomethacin (IND). Accordingly, experiments were performed in rats using the vascular tracer Monastral blue to assess whether vascular lesions precede and are subsequently associated with mucosal lesions induced by oral (p.o.) or subcutaneous (s.c.) administration of IND. Fasted female Sprague–Dawley rats (150–180 g) were given IND either at 100 mg/kg, p.o. or 200 mg/kg s.c. and killed 15, 30, 120 or 240 minutes later. Monastral blue, 3% saline 1 ml/kg, was injected intravenously under ether anaesthesia 3 minutes before autopsy and the formalin fixed, glycerol cleared stomachs were examined microscopically for deposition of the dye particles on damaged blood vessels. The percentage area of Monastral blue labelled vessels (measured by stereomicroscopic planimetry) at 15 minutes after oral IND was 10.1 ± 1.5% (mean ± s.e.m.) of glandular stomach and increased progressively to 64.5 ± 3.0% at 240 minutes. Gastric haemorrhagic lesions (also measured by stereomicroscopic planimetry) were first evident at 30 minutes (0.2 ± 0.03%; mean ± s.e.m.), and developed progressively to 2.0±0.3% total area of glandular mucosa at 240 minutes. Subcutaneous injection of IND resulted in a delayed time of onset for the appearance and the extent of mucosal lesions (first appearing at 120 minutes, 0.1 ± 0.03% area) compared with that from oral administration of the drug, but as with oral IND the vascular damage (first appearance at 15 minutes, 7.5 ± 3.6%) clearly preceded the occurrence of gastric lesions. The observations of microvascular dye labelling were paralleled by observations of the electronmicroscopic appearance of endothelial cell disruption in the region adjacent to superficial mucous cells and accumulation of red blood cells in the interstitium at 20–60 minutes. We conclude that vascular injury precedes haemorrhagic mucosal damage in the pathogenesis of IND‐induced acute gastric mucosal lesions.
PUBCRAWL: Protecting Users and Businesses from CRAWLers

Web crawlers are automated tools that browse the web to retrieve and analyze information. Although crawlers are useful tools that help users to find content on the web, they may also be malicious. Unfortunately, unauthorized (malicious) crawlers are increasingly becoming a threat for service providers because they typically collect information that attackers can abuse for spamming, phishing, or targeted attacks. In particular, social networking sites are frequent targets of malicious crawling, and there were recent cases of scraped data sold on the black market and used for blackmailing. In this paper, we introduce PUBCRAWL, a novel approach for the detection and containment of crawlers. Our detection is based on the observation that crawler traffic significantly differs from user traffic, even when many users are hidden behind a single proxy. Moreover, we present the first technique for crawler campaign attribution that discovers synchronized traffic coming from multiple hosts. Finally, we introduce a containment strategy that leverages our detection results to efficiently block crawlers while minimizing the impact on legitimate users. Our experimental results in a large, well-known social networking site (receiving tens of millions of requests per day) demonstrate that PUBCRAWL can distinguish between crawlers and users with high accuracy. We have completed our technology transfer, and the social networking site is currently running PUB-CRAWL in production.
Ontology-Based Data Access with a Horn Fragment of Metric Temporal Logic

We advocate datalogMTL, a datalog extension of a Horn fragment of the metric temporal logic MTL, as a language for ontology-based access to temporal log data. We show that datalogMTL is EXPSPACE-complete even with punctual intervals, in which case MTL is known to be undecidable. Nonrecursive datalogMTL turns out to be PSPACE-complete for combined complexity and in AC0 for data complexity. We demonstrate by two real-world use cases that nonrecursive datalogMTL programs can express complex temporal concepts from typical user queries and thereby facilitate access to log data. Our experiments with Siemens turbine data and MesoWest weather data show that datalogMTL ontology-mediated queries are efficient and scale on large datasets of up to 11GB.
Hybrid integration of GaAs-based VCSEL array with amorphous silicon sensor

We describe an optoelectronic module incorporating a vertical-cavity surface-emitting laser (VCSEL) array with a semitransparent light monitor. The power monitor is a p-i-n amorphous silicon photodetector fabricated on glass. Sets of micromachined springs for electrical contacting are also fabricated in the same process on the same glass substrate. Hybrid packages are formed by pressing the compliant springs against individual contact pads of the GaAs VCSEL array in a flip-chip assembly process. The light sensor is aligned directly on top of the laser elements. Most of the laser light is transmitted through the sensor, yet a large dynamic range is maintained because of the sensors exceedingly low dark current.
Fast iodide-SAD phasing for high-throughput membrane protein structure determination

A potentially universal method for the de novo solution of the crystal structures of membrane proteins is described. We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide–single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins—the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein–coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.
Resting-State Connectivity of the Left Frontal Cortex to the Default Mode and Dorsal Attention Network Supports Reserve in Mild Cognitive Impairment

Reserve refers to the phenomenon of relatively preserved cognition in disproportion to the extent of neuropathology, e.g., in Alzheimer’s disease. A putative functional neural substrate underlying reserve is global functional connectivity of the left lateral frontal cortex (LFC, Brodmann Area 6/44). Resting-state fMRI-assessed global LFC-connectivity is associated with protective factors (education) and better maintenance of memory in mild cognitive impairment (MCI). Since the LFC is a hub of the fronto-parietal control network that regulates the activity of other networks, the question arises whether LFC-connectivity to specific networks rather than the whole-brain may underlie reserve. We assessed resting-state fMRI in 24 MCI and 16 healthy controls (HC) and in an independent validation sample (23 MCI/32 HC). Seed-based LFC-connectivity to seven major resting-state networks (i.e., fronto-parietal, limbic, dorsal-attention, somatomotor, default-mode, ventral-attention, visual) was computed, reserve was quantified as residualized memory performance after accounting for age and hippocampal atrophy. In both samples of MCI, LFC-activity was anti-correlated with the default-mode network (DMN), but positively correlated with the dorsal-attention network (DAN). Greater education predicted stronger LFC-DMN-connectivity (anti-correlation) and LFC-DAN-connectivity. Stronger LFC-DMN and LFC-DAN-connectivity each predicted higher reserve, consistently in both MCI samples. No associations were detected for LFC-connectivity to other networks. These novel results extend our previous findings on global functional connectivity of the LFC, showing that LFC-connectivity specifically to the DAN and DMN, two core memory networks, enhances reserve in the memory domain in MCI.
Analysis and Comparative Study on Phonetic Matching Techniques

for names in large databases containing spelling variations has always been a problem. The first solution to the problem was proposed by Robert Russell in 1912 as he proposed SoundEx algorithm. SoundEx algorithm matches the names based on the sound of the words. The technique which is based on the pronunciation of the word is known as phonetic matching. SoundEx algorithm is one of the phonetic matching algorithms. We have discussed the other phonetic matching algorithm like edit distance algorithm, K-String and Q gram algorithm, Guth algorithm, Daitch Mokotoff algorithm and Metaphone coding algorithm. Our main focus is on the SoundEx algorithm and this paper also describes the issues with SoundEx algorithm.
Lack of replication of interaction between EBNA1 IgG and smoking in risk for multiple sclerosis

Background: Epstein-Barr virus infection, smoking, HLA-A*02, and DRB1*15 have all been proposed as risk factors for multiple sclerosis (MS). In 2010, Simon et al. described an interaction on the multiplicative scale between EBNA1 immunoglobulin G (IgG) and smoking regarding risk of MS, a finding that we attempted to replicate. Methods: This Swedish case-control study consisted of patients with newly diagnosed MS and matched controls. Using logistic regression, we analyzed association to MS risk and interactions between EBNA1 IgG and smoking, HLA-DRB1*15, and A*02, respectively, on the multiplicative scale. In addition, we analyzed interactions on the additive scale using attributable proportion due to interaction (AP). Results: We did not observe any interaction on the multiplicative scale between EBNA1 IgG and any of the 3 risk factors, smoking, DRB1*15, or absence of A*02, although in a conditional analysis the interaction with absence of A*02 becomes significant. However, we observed interactions on the additive scale between EBNA1 IgG and DRB1*15 (AP = 0.34, 95% confidence interval 0.11–0.57, p = 5 × 10−3) and between EBNA1 IgG and absence of A*02 (AP = 0.36, 0.13–0.59, p = 2 × 10−3) but not between smoking and DRB1*15 and EBNA1 IgG. The interaction between EBNA1 IgG and DRB1*15 was not significant in the conditional analysis. Conclusion: We did not observe any interaction between EBNA1 IgG and smoking, regardless of scale used, and thus did not replicate the observations from Simon et al.
Exploiting associations between word clusters and document classes for cross‐domain text categorization †

Cross‐domain text categorization targets on adapting the knowledge learnt from a labeled source domain to an unlabeled target domain, where the documents from the source and target domains are drawn from different distributions. However, in spite of the different distributions in raw‐word features, the associations between word clusters (conceptual features) and document classes may remain stable across different domains. In this paper, we exploit these unchanged associations as the bridge of knowledge transformation from the source domain to the target domain by the non‐negative matrix tri‐factorization. Specifically, we formulate a joint optimization framework of the two matrix tri‐factorizations for the source‐ and target‐domain data, respectively, in which the associations between word clusters and document classes are shared between them. Then, we give an iterative algorithm for this optimization and theoretically show its convergence. The comprehensive experiments show the effectiveness of this method. In particular, we show that the proposed method can deal with some difficult scenarios where baseline methods usually do not perform well. © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 100–114, 2011