Miracle-dz/UniFAR-FTUs huggingface dataset:
Athsq1 Is an Atherosclerosis Modifier Locus With Dramatic Effects on Lesion Area and Prominent Accumulation of Versican

Objective—Susceptibility to atherosclerosis is genetically complex, and modifier genes that do not operate via traditional risk factors are largely unknown. A mouse genetics approach can simplify the genetic analysis and provide tools for mechanistic studies. Methods and Results—We previously identified atherosclerosis susceptibility QTL (Athsq1) on chromosome 4 acting independently of systemic risk factors. We now report confirmation of this locus in congenic strains carrying the MOLF-derived susceptibility allele in the C57BL/6J-Ldlr−/− genetic background. Homozygous congenic mice exhibited up to 4.5-fold greater lesion area compared to noncongenic littermates (P<0.0001). Analysis of extracellular matrix composition revealed prominent accumulation of versican, a presumed proatherogenic matrix component abundant in human lesions but almost absent in the widely-used C57BL/6 murine atherosclerosis model. The results of a bone marrow transplantation experiment suggested that both accelerated lesion development and versican accumulation are mediated, at least in part, by macrophages. Interestingly, comparative mapping revealed that the Athsq1 congenic interval contains the mouse region homologous to a widely-replicated CHD locus on human chromosome 9p21. Conclusion—These studies confirm the proatherogenic activity of a novel gene(s) in the MOLF-derived Athsq1 locus and provide in vivo evidence for a causative role of versican in lesion development.
Differential polyamine sensitivity in inwardly rectifying Kir2 potassium channels

Recent studies have shown that Kir2 channels display differential sensitivity to intracellular polyamines, and have raised a number of questions about several properties of inward rectification important to the understanding of their physiological roles. In this study, we have carried out a detailed characterization of steady‐state and kinetic properties of block of Kir2.1–3 channels by spermine. High‐resolution recordings from outside‐out patches showed that in all Kir2 channels current–voltage relationships display a ‘crossover’ effect upon change in extracellular K+. Experiments at different concentrations of spermine allowed for the characterization of two distinct shallow components of rectification, with the voltages for half‐block negative (V11/2) and positive (V21/2) to the voltage of half‐block for the major steep component of rectification (V01/2). While V11/2 and V21/2 voltages differ significantly between Kir2 channels, they were coupled to each other according to the equation V11/2−V21/2= constant, strongly suggesting that similar structures may underlie both components. In Kir2.3 channels, the V21/2 was ∼50 mV positive to V01/2, leading to a pattern of outward currents distinct from that of Kir2.1 and Kir2.2 channels. The effective valency of spermine block (Z0) was highest in Kir2.2 channels while the valencies in Kir2.1 and Kir2.3 channels were not significantly different. The voltage dependence of spermine unblock was similar in all Kir2 channels, but the rates of unblock were ∼7‐fold and ∼16‐fold slower in Kir2.3 channels than those in Kir2.1 and Kir2.2 when measured at high and physiological extracellular K+, respectively. In all Kir2 channels, the instantaneous phase of activation was present. The instantaneous phase was difficult to resolve at high extracellular K+ but it became evident and accounted for nearly 30–50% of the total current when recorded at physiological extracellular K+. In conclusion, the data are consistent with the universal mechanism of rectification in Kir2 channels, but also point to significant, and physiologically important, quantitative differences between Kir2 isoforms.
Fast top-k search in knowledge graphs

Given a graph query Q posed on a knowledge graph G, top-k graph querying is to find k matches in G with the highest ranking score according to a ranking function. Fast top-k search in knowledge graphs is challenging as both graph traversal and similarity search are expensive. Conventional top-k graph search is typically based on threshold algorithm (TA), which can no long fit the demand in the new setting. This work proposes STAR, a top-k knowledge graph search framework. It has two components: (a) a fast top-k algorithm for star queries, and (b) an assembling algorithm for general graph queries. The assembling algorithm uses star query as a building block and iteratively sweeps the star match lists with a dynamically adjusted bound. For top-k star graph query where an edge can be matched to a path with bounded length d, we develop a message passing algorithm, achieving time complexity O(d2|E| + md) and space complexity linear to d|V| (assuming the size of Q and k is bounded by a constant), where m is the maximum node degree in G. STAR can further be leveraged to answer general graph queries by decomposing a query to multiple star queries and joining their results later. Learning-based techniques to optimize query decomposition are also developed. We experimentally verify that STAR is 5-10 times faster than the state-of-the-art TA-style graph search algorithm, and 10-100 times faster than a belief propagation approach.
Accumulate-Repeat-Accumulate Codes

In this paper, we propose an innovative channel coding scheme called accumulate-repeat-accumulate (ARA) codes. This class of codes can be viewed as serial turbo-like codes or as a subclass of low-density parity check (LDPC) codes, and they have a projected graph or protograph representation; this allows for high-speed iterative decoding implementation using belief propagation. An ARA code can be viewed as precoded repeat accumulate (RA) code with puncturing or as precoded irregular repeat accumulate (IRA) code, where simply an accumulator is chosen as the precoder. The amount of performance improvement due to the precoder will be called precoding gain. Using density evolution on their associated protographs, we find some rate-1/2 ARA codes, with a maximum variable node degree of 5 for which a minimum bit SNR as low as 0.08 dB from channel capacity threshold is achieved as the block size goes to infinity. Such a low threshold cannot be achieved by RA, IRA, or unstructured irregular LDPC codes with the same constraint on the maximum variable node degree. Furthermore, by puncturing the inner accumulator, we can construct families of higher rate ARA codes with thresholds that stay close to their respective channel capacity thresholds uniformly. Iterative decoding simulation results are provided and compared with turbo codes. In addition to iterative decoding analysis, we analyzed the performance of ARA codes with maximum-likelihood (ML) decoding. By obtaining the weight distribution of these codes and through existing tightest bounds we have shown that the ML SNR threshold of ARA codes also approaches very closely to that of random codes. These codes have better interleaving gain than turbo codes
Fragment Size Distribution of Blasted Rock Mass

Rock mass is a heterogeneous material, and the heterogeneity of rock causes sizes distribution of fragmented rocks in blasting. Prediction of blasted rock mass fragmentation has a significant role in the overall economics of opencast mines. Blasting as primary fragmentation can significantly decrease the cost of loading, transport, crushing and milling operations. Blast fragmentation chiefly depends on the specific blast design (geometry of blast holes drilling, the quantity and class of explosive, the blasting form, the timing and partition, etc.) and on the properties of the rock mass (including the uniaxial compressive strength, the rock mass elastic Young modulus, the rock discontinuity characteristics and the rock density). Prediction and processing of blasting results researchers can accomplish by a variety of existing software’s and models, one of them is the Kuz-Ram model, which is possibly the most widely used approach to estimating fragmentation from blasting. This paper shows the estimation of fragmentation using the "SB" program, which was created by the authors. Mentioned program includes the Kuz-Ram model. Models of fragmentation are confirmed and calibrated by comparing the estimated fragmentation with actual post-blast fragmentation from image processing techniques. In this study, the Kuz-Ram fragmentation model has been used for an open-pit limestone quarry in Dalmatia, southern Croatia. The resulting calibrated value of the rock factor enables the quality prognosis of fragmentation in further blasting works, with changed drilling geometry and blast design parameters. It also facilitates simulation in the program to optimize blasting works and get the desired fragmentations of the blasted rock mass.
Long Noncoding RNAs: Past, Present, and Future

Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology’s longstanding concern with the evolution and function of genomes.
Evaluation of the effectiveness of the Ministry of Food cooking programme on self-reported food consumption and confidence with cooking

Abstract Objective To evaluate the effectiveness of the Ministry of Food (MoF) cooking programme on self-reported food consumption and confidence with cooking. Design A quantitative and qualitative evaluation of the MoF 8-week cooking course, using a pre-test/post-test study. Pre, post and 6-month follow-up quantitative outcomes were measured using self-administered questionnaires to record number of portions of fruit and vegetables (F&V) consumed per day, number of snacks consumed per day and participants’ cooking confidence levels (highest score of 5). Qualitative evaluations were undertaken using structured telephone interviews. Setting MoF centre in Leeds Kirkgate Market, UK. Subjects Adults (n 795, 43 % male) on MoF courses from 2010 to 2014, 462 of whom completed questionnaires at all three time points. Results Six months after the course, self-reported F&V intake increased significantly by 1·5 (95 % CI 1·3, 1·6, P<0·001) portions per day to 4·1 (95 % CI 4·0, 4·3). The number of snacks reported decreased significantly over the same period by −0·9 (CI−1·0, −0·8, P<0·001) snacks per day. Cooking confidence increased over the same period by 1·7 (95 % CI 1·6, 1·9, P<0·001) to 4·4 (CI 4·4, 4·5). Age and disability, but not deprivation or ethnicity, were associated with changes in self-reported F&V intake and cooking confidence scores at 6 months; and gender with the latter outcome. Qualitative results supported quantitative findings and revealed specific beneficial gains in cooking skills/preparation, nutritional awareness, food purchasing and other social benefits. Conclusions MoF community-based cooking interventions can have significant positive effects on dietary behaviour, food choice and cooking confidence.
The Determinants of Banks’ Capital Ratio in Developing Countries: Empirical Evidence from Tunisia

In this paper, we try to study the determinants of the banks' capital ratio in an emerging country. To do so, we model the relationships between some variables of the banks and this ratio. Our aim is to explain its high level. We try also to answer to a new question. Is it affected by the same factors in the emerging countries as in the industrialized ones? The sample is composed of 18 banks. The data are half yearly. The period sample is from 2002 to 2008. We find that the interest margin and the risk affect strongly the capital ratio. They explain the excess of the capital held by the Tunisian banks. So, this excess is not explained only by regulatory pressures. The deposit variability and the intermediation rate have the same sign. But, the equity cost and the deposits ratio both have a negative impact. The determinants are the same for all the countries.
A Histological, Histochemical and Ultrastructural Study on the Fundic Region of the Stomach of Nile Catfish (Clarias gariepinus)

The present work was carried out on 20 specimens of both sexes of Nile catfish in order to observe the morphological and histological as well as the fine structure of fundic gland region of the stomach. The present study demonstrated the presence of folded mucosa in the fundic region of the stomach and its surface epithelium was lined by simple columnar mucosecretory cells. The lamina propria contained simple tubular branched glands. The fundic glands were made up of oxyntico-peptic cells. The glandular cells were positive to PAS and negative to Alcian blue and showed strong positive activity for acid phosphatase. The electron microscopic examination revealed that the oxyntico-peptic cells contained a dense tubulovesicular system that may participate in hydrochloric acid production, in addition to the extensive presence of mitochondria and rough endoplasmic reticulum. The Golgi complex is involved in the formation of secretory or zymogen granules. Oval to roundshaped enteroendocrine cells were scattered among the glandular and superficial columnar cells, which stained positive to Grimelius stain. The glands were surrounded by collagenous fibers and smooth muscle fibers
Associations between stroke lesion location and verbal fluency tests in a sub-acute stroke population

Background: In stroke hospitalizations, verbal fluency tests are used to evaluate executive abilities in order to assess the integrity of functioning and language. Prior studies show that clustering and switching during verbal fluency tasks are related to functioning of specific brain regions, such that they are thought to be more sensitive in detecting impairments in frontal regions compared to other brain regions. Objective: Investigate the hypothesis that the stroke lesion location predicts both quantitative and qualitative (clustering and switching) aspects of fluency. Patients with frontal lesions will perform poorly on switching and phonemic tasks, while the patients with temporal lesions will perform poorly on clustering semantic tasks. Method: Stroke inpatients (N=99) completed verbal fluency measures and structural brain scans within 72 hours of admission. Healthy controls (N=39) were recruited and administered verbal fluency measures. Fluency performance was evaluated by valid qualitative and quantitative analysis. Results: Lesion location did not predict qualitative aspects of fluency and provided no support that frontal region lesions result in impairments in executive function. Hemispheric lesion location was not significant. Stroke patients preformed more poorly on fluency measures compared to controls. Conclusion: Verbal fluency performance is affected by vascular brain damage resulting from stroke, but lesion location does not differentially affect qualitative or quantitative aspects of verbal fluency performance. Correspondence to: GM Babulal, Department of Neurology, Washington University School of Medicine, Campus Box 8111 4488 Forest Park, St. Louis, MO 63110, USA; Tel: (952) 334-8536; E-mail: babulalg@neuro.wustl. edu
The Quality of Systematic Reviews in Hand Surgery: An Analysis Using AMSTAR

Background: Systematic reviews constitute the top of the “level-of-evidence pyramid. ” Despite their strengths, they have been found to be of varying quality, thus raising concerns about their validity and role in influencing clinical practice. In the present study, a quality analysis of systematic reviews with a focus on hand surgery was performed. Methods: A PubMed search was performed to identify all systematic reviews published up to and including December of 2011 in eight surgical journals. Two authors independently reviewed the literature and extracted data from included reviews. Discrepancies were resolved by consensus. Quality assessment was performed using AMSTAR. Results: The initial search retrieved 687 articles. After screening titles and abstracts, 635 articles were excluded. Full-text review of the remaining 52 articles resulted in further exclusion of 10 articles, leaving 42 systematic reviews for final analysis. A significant increase in the number of published systematic reviews over time was noted (p = 0.04), with the majority of systematic reviews being published in The Journal of Hand Surgery (n = 19) and Plastic and Reconstructive Surgery (n = 12). Although a significant improvement in the quality of systematic reviews was noted over time (p = 0.01), a median AMSTAR score of 7 indicated the bulk of reviews to be of fair to good quality. Conclusions: The trend to publish more systematic reviews in hand surgery is paralleled by an increase in the quality of systematic reviews. Nonetheless, increased efforts are indicated to further improve the quality of systematic reviews in hand surgery.
Ideal fermion delocalization in five dimensional gauge theories

We discuss ideal delocalization of fermions in a bulk $SU(2)\ifmmode\times\else\texttimes\fi{}SU(2)\ifmmode\times\else\texttimes\fi{}U(1)$ Higgsless model with a flat or warped extra dimension. So as to make an extra dimensional interpretation possible, both the weak and hypercharge properties of the fermions are delocalized, with the $U(1{)}_{Y}$ current of left-handed fermions being correlated with the $SU(2{)}_{W}$ current. We find that (to subleading order) ideal fermion delocalization yields vanishing precision electroweak corrections in this continuum model, as found in corresponding theory-space models based on deconstruction. In addition to explicit calculations, we present an intuitive argument for our results based on Georgi's spring analogy. We also discuss the conditions under which the essential features of an $SU(2)\ifmmode\times\else\texttimes\fi{}SU(2)\ifmmode\times\else\texttimes\fi{}U(1)$ bulk gauge theory can be captured by a simpler $SU(2)\ifmmode\times\else\texttimes\fi{}SU(2)$ model.
Reliability of lead (Pb) free SAC solder interconnects with different PWB surface finishes under mechanical loading

Tin/silver/copper (SAC) solder alloys have been introduced as primary alternatives to the eutectic tin-lead solder. SAC alloys are relatively new alloy systems in packaging applications and existing studies are limited and confined mainly to the materials, assembly process, and finite element modeling. It is essential to conduct research focusing on the material aspects of the SAC alloy coupled with its effect on reliability using both experimental methods and finite element simulations. The focus of this paper is experimental study of lead-free solder package test boards under cyclic bend load and drop impact loading. Amkor CTBGA 288 components were assembled on eight layer test boards (JESD22-B111) with Sn/Ag/Cu (95.5Sn3.8Ag0.7Cu) solder using three different PWB pad surface finishes to study the effect of the surface finish on the interconnect reliability. The pad finishes were immersion Au, immersion Ag and the organic solder preservative (OSP). The test specimens were subjected to cyclic bend fatigue and board level drop tests. Strain gage measurements were taken at numerous locations across populated and unpopulated PWBs and the data were used to create contour plots to identify variations in stress due to location and localized stiffness due to components. Results are presented with failure mode and analysis of those packages with different pad finishes and loading conditions. Finite element models were also created for the bend test boards to investigate the stress distribution and stress concentration
Multilocus Genetic Risk Scores for Venous Thromboembolism Risk Assessment

Background Genetics plays an important role in venous thromboembolism (VTE). Factor V Leiden (FVL or rs6025) and prothrombin gene G20210A (PT or rs1799963) are the genetic variants currently tested for VTE risk assessment. We hypothesized that primary VTE risk assessment can be improved by using genetic risk scores with more genetic markers than just FVL‐rs6025 and prothrombin gene PT‐rs1799963. To this end, we have designed a new genetic risk score called Thrombo inCode (TiC). Methods and Results TiC was evaluated in terms of discrimination (Δ of the area under the receiver operating characteristic curve) and reclassification (integrated discrimination improvement and net reclassification improvement). This evaluation was performed using 2 age‐ and sex‐matched case–control populations: SANTPAU (248 cases, 249 controls) and the Marseille Thrombosis Association study (MARTHA; 477 cases, 477 controls). TiC was compared with other literature‐based genetic risk scores. TiC including F5 rs6025/rs118203906/rs118203905, F2 rs1799963, F12 rs1801020, F13 rs5985, SERPINC1 rs121909548, and SERPINA10 rs2232698 plus the A1 blood group (rs8176719, rs7853989, rs8176743, rs8176750) improved the area under the curve compared with a model based only on F5‐rs6025 and F2‐rs1799963 in SANTPAU (0.677 versus 0.575, P<0.001) and MARTHA (0.605 versus 0.576, P=0.008). TiC showed good integrated discrimination improvement of 5.49 (P<0.001) for SANTPAU and 0.96 (P=0.045) for MARTHA. Among the genetic risk scores evaluated, the proportion of VTE risk variance explained by TiC was the highest. Conclusions We conclude that TiC greatly improves prediction of VTE risk compared with other genetic risk scores. TiC should improve prevention, diagnosis, and treatment of VTE.
Suppression of CUGBP1 inhibits growth of hepatocellular carcinoma cells.

PURPOSE The multifunctional RNA-binding protein, CUGBP1, regulates splicing, stability and translation of mRNAs. Previous studies have shown that CUGBP1 is expressed at high levels in the liver, although its role in hepatocellular carcinoma is unknown. Our aim was to determine if CUGBP1 could regulate hepatocellular carcinoma growth. METHODS Expression levels of CUGBP1 were analyzed in 70 hepatic carcinoma and 20 normal hepatic tissue samples by immunohistochemistry (IHC). Using lentivirus-mediated short hairpin RNA (shRNA), CUGBP1 expression in human hepatocellular carcinoma HepG2 cells was knocked-down. The effect of CUGBP1 on hepatic cancer cell growth was investigated. RESULTS CUGBP1 was expressed in 85.7% hepatocellular carcinoma specimens compared with 50% in normal liver specimens. CUGBP1 silencing remarkably decreased the proliferation of HepG2 cells, as determined by MTT assay. Flow cytometry analysis showed that knock-down of CUGBP1 led to G0/G1 phase cell cycle arrest, accompanied by sub-G1 accumulation. Moreover, depletion of CUGBP1 resulted in downregulation of cyclin B1 and upregulation of cyclin D1. CONCLUSION These results suggest that CUGBP1 is essential for the growth of hepatocellular carcinoma cells. Knockdown of CUGBP1 might be a potential therapeutic approach for human hepatocellular carcinoma.