Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of SNR estimation error on turbo code with high-order modulation

The sensitivity of turbo-code performance to SNR estimation error is investigated in high-order modulated systems. The estimated SNR is applied in bit-metric calculation for a turbo decoder. We analyze the roles that the SNR value has played in binary transmission and multi-level transmission and identify the difference which finally leads to the different sensitivity behavior of the turbo decoder in different modulation schemes. Extensive simulation results are presented to demonstrate the performance sensitivity over AWGN and fading channels. We show that turbo code is more sensitive to SNR estimation accuracy in high-order modulation than in BPSK. Both under-estimation and overestimation lead to significant performance degradation. The BER performance versus SNR estimation offset exhibits an obvious "V"-like shape. Moreover, the turbo-code parameters such as interleaver size and constraint length are also important factors that affect the performance sensitivity to SNR mismatch. Codes with large interleaver size or long constraint length tend to be more sensitive to the estimation error.
Identification of essential amino acids in the Streptococcus mutans glucosyltransferases

A comparison of the amino acid sequences of the glucosyltransferases (GTFs) of mutans streptococci with those from the alpha-amylase family of enzymes revealed a number of conserved amino acid positions which have been implicated as essential in catalysis. Utilizing a site-directed mutagenesis approach with the GTF-I enzyme of Streptococcus mutans GS-5, we identified three of these conserved amino acid positions, Asp413, Trp491, and His561, as being important in enzymatic activity. Mutagenesis of Asp413 to Thr resulted in a GTF which expressed only about 12% of the wild-type activity. In contrast, mutagenesis of Asp411 did not inhibit enzyme activity. In addition, the D413T mutant was less stable than was the parental enzyme when expressed in Escherichia coli. Moreover, conversion of Trp491 or His561 to either Gly or Ala resulted in enzymes devoid of GTF activity, indicating the essential nature of these two amino acids for activity. Furthermore, mutagenesis of the four Tyr residues present at positions 169 to 172 which are part of a subdomain with homology to the direct repeating sequences present in the glucan-binding domain of the GTFs had little overall effect on enzymatic activity, although the glucan products appeared to be less adhesive. These results are discussed relative to the mechanisms of catalysis proposed for the GTFs and related enzymes.
Effects of Chronic Hypoxia on the Circulating and Pancreatic Renin-Angiotensin System

Introduction The circulating renin–angiotensin system (RAS) plays a crucial role in the regulation of blood pressure, electrolytes, and fluid homeostasis. In contrast to the circulating RAS, the presence of an intrinsic RAS has been demonstrated in different tissues/organs, which may affect both local and global functions of a biologic system. Our previous studies provided solid evidence of the existence of a local RAS in rat pancreas. Our further investigation showed that such a pancreatic RAS could be activated by experimental models of chronic hypoxia and chemically induced pancreatitis. These previous findings formed the basis for the current study. Methodology Adult Sprague–Dawley rats were exposed to isobaric hypoxia (10% O2), and the effects on the circulating and pancreatic RAS were documented. Results The current study shows that exposure of rats to isobaric hypoxia caused a time-dependent increase in plasma renin activity. The activation of circulating RAS by hypoxia was associated with a parallel upregulation of local RAS components, including the mRNA expression of angiotensinogen and angiotensin II receptor types I and II in the pancreas. Conclusion The upregulation of local pancreatic RAS, along with its counterpart circulating RAS, may be responsible for both physiologic and pathophysiologic aspects of a biologic system under chronic hypoxic stress.
Coregulator Interactions with the Thyroid Hormone Receptor

The thyroid hormone receptor (TR) directly regulates the transcription of thyroid hormone-responsive genes in response to changing levels of thyroid hormone. Mechanistically TR utilizes a complex set of binding interactions, with hormone, response elements, and coregulatory proteins, to provide specific local control of patterns of transcriptional response that are partially responsible for inducing the tissue-selective responses to the circulating hormone. One of the apparently dominant phenomena in the regulation of thyroid hormone responses is the protein interactions between TR and its coregulators. This review summarizes the current state of knowledge with respect to the identity of these coregulators, their interaction with TR, and the consequences of those interactions.
Molecular basis for the action of the collagen-specific chaperone Hsp47/SERPINH1 and its structure-specific client recognition

Collagen is the most abundant protein in animals and is a major component of the extracellular matrix in tissues such as skin and bone. A distinctive structural feature of all collagen types is a unique triple-helical structure formed by tandem repeats of the consensus sequence Xaa-Yaa-Gly, in which Xaa and Yaa frequently are proline and hydroxyproline, respectively. Hsp47/SERPINH1 is a procollagen-specific molecular chaperone that, unlike other chaperones, specifically recognizes the folded conformation of its client. Reduced functional levels of Hsp47 were reported in severe recessive forms of osteogenesis imperfecta, and homozygous knockout is lethal in mice. Here we present crystal structures of Hsp47 in its free form and in complex with homotrimeric synthetic collagen model peptides, each comprising one Hsp47-binding site represented by an arginine at the Yaa-position of a Xaa-Yaa-Gly triplet. Two of these three binding sites in the triple helix are occupied by Hsp47 molecules, which bind in a head-to-head fashion, thus making extensive contacts with the leading and trailing strands of the collagen triple helix. The important arginine residue within the Xaa-Arg-Gly triplet is recognized by a conserved aspartic acid. The structures explain the stabilization of the triple helix as well as the inhibition of collagen-bundle formation by Hsp47. In addition, we propose a pH-dependent substrate release mechanism based on a cluster of histidine residues.
Killing the Golden Goose? The Decline of Science in Corporate R&D

Scientific knowledge is believed to be the wellspring of innovation. Historically, firms have also invested in research to fuel innovation and growth. In this paper, we document a shift away from scientific research by large corporations between 1980 and 2007. We find that publications by company scientists have declined over time in a range of industries. We also find that the value attributable to scientific research has dropped, whereas the value attributable to technical knowledge (as measured by patents) has remained stable. These effects appear to be associated with globalization and narrower firm scope, rather than changes in publication practices or a decline in the usefulness of science as an input into innovation. Large firms appear to value the golden eggs of science (as reflected in patents) but not the golden goose itself (the scientific capabilities). These findings have important implications for both public policy and management.
Exploiting SNOMED CT Concepts & Relationships for Clinical Information Retrieval: Australian e-Health Research Centre and Queensland University of Technology at the TREC 2012 Medical Track

The Australian e-Health Research Centre and Queensland University of Technology recently participated in the TREC 2012 Medical Records Track. This paper reports on our methods, results and experience using an approach that exploits the concept and inter-concept relationships defined in the SNOMED CT medical ontology. Our concept-based approach is intended to overcome specific challenges in searching medical records, namely vocabulary mismatch and granularity mismatch. Queries and documents are transformed from their term-based originals into medical concepts as defined by the SNOMED CT ontology, this is done to tackle vocabulary mismatch. In addition, we make use of the SNOMED CT parent-child `is-a' relationships between concepts to weight documents that contained concept subsumed by the query concepts; this is done to tackle the problem of granularity mismatch. Finally, we experiment with other SNOMED CT relationships besides the is-a relationship to weight concepts related to query concepts. Results show our concept-based approach performed significantly above the median in all four performance metrics. Further improvements are achieved by the incorporation of weighting subsumed concepts, overall leading to improvement above the median of 28% infAP, 10% infNDCG, 12% R-prec and 7% Prec@10. The incorporation of other relations besides is-a demonstrated mixed results, more research is required to determined which SNOMED CT relationships are best employed when weighting related concepts.
Data mining crystallization databases: Knowledge‐based approaches to optimize protein crystal screens

Protein crystallization is a major bottleneck in protein X‐ray crystallography, the workhorse of most structural proteomics projects. Because the principles that govern protein crystallization are too poorly understood to allow them to be used in a strongly predictive sense, the most common crystallization strategy entails screening a wide variety of solution conditions to identify the small subset that will support crystal nucleation and growth. We tested the hypothesis that more efficient crystallization strategies could be formulated by extracting useful patterns and correlations from the large data sets of crystallization trials created in structural proteomics projects. A database of crystallization conditions was constructed for 755 different proteins purified and crystallized under uniform conditions. Forty‐five percent of the proteins formed crystals. Data mining identified the conditions that crystallize the most proteins, revealed that many conditions are highly correlated in their behavior, and showed that the crystallization success rate is markedly dependent on the organism from which proteins derive. Of the proteins that crystallized in a 48‐condition experiment, 60% could be crystallized in as few as 6 conditions and 94% in 24 conditions. Consideration of the full range of information coming from crystal screening trials allows one to design screens that are maximally productive while consuming minimal resources, and also suggests further useful conditions for extending existing screens. Proteins 2003;51:562–568. © 2003 Wiley‐Liss, Inc.
Assessing the HER2 Status in Mucinous Epithelial Ovarian Cancer on the Basis of the 2013 ASCO/CAP Guideline Update

Her2 gene amplification and protein overexpression are important factors in predicting clinical sensitivity to anti-HER2 monoclonal antibody therapy in breast, gastric, or gastro-esophageal junction cancer patients. The purpose of this study was to evaluate the HER2 status in the mucinous epithelial ovarian cancer (EOC). Adopting the 2013 American Society for Clinical Oncology and the College of American Pathologists guideline update for HER2 testing, 49 tissue microarray samples of mucinous EOC were analyzed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) tests. The prevalence of HER2 positivity in Asian mucinous EOC was 9 of 49 Asian women (18.37%). The overall concordance was 100% between IHC and FISH results. Her2 gene copies before chromosome-17 correction increased significantly in a stepwise order through the negative, equivocal, and positive IHC result categories (P<0.001), as did the Her2 gene copies after chromosome-17 correction (P<0.001). Of the Taiwanese cohort (n=21), HER2 heterogeneity was 4.76% (1/21) in all but 14.26% (1/7) in HER2-positive cancer. In conclusion, we demonstrated that the prevalence of HER2 positivity in both Asian and white women was comparable; complete HER2 concordance existed between IHC and FISH tests for the Her2 gene copies per tumor cell either before or after correction of chromosome-17, and this can be applied as a potentially valuable tool to analyze the HER2 status. Polysomy-17 was absent under the CEP17 cutoff ≥3. The existence of HER2 heterogeneity can be discerned in certain HER2-expressed primary mucinous EOC in Taiwanese women.
Optimum Combining in Dual-Hop AF Relaying for Maximum Spectral Efficiency in the Presence of Co-Channel Interference

The performance of optimum combining (OC) in amplify-and-forward (AF) relaying systems in the presence of co-channel interference (CCI) is analyzed using a tight approximation for the signal-to-interference-plus-noise ratio (SINR) at the destination. Two types of relaying protocols are studied, all-relay transmission with OC and best-relay transmission with OC. When CCI is present only at the destination, both relaying protocols achieve diversity gains up to M when interferer powers are scaled with the source and the relay powers, where M is the number of relays. Best-relay transmission with OC maximizes the spectral efficiency as each communication consumes only two time slots.
Comparison of the fatigue behaviour of two different forms of PMMA

This study investigates the fatigue behaviour of two forms of polymethylmethacrylate (PMMA): pure PMMA in the form of acrylic glass and PMMA-based bone cement. Acrylic glass demonstrated superior fatigue strength compared to hand-mixed porous bone cement but was significantly weaker than pore-free bone cement. The greater fatigue strength of bone cement in comparison to acrylic glass was attributed to its composite-like microstructure, containing pre-polymerized beads which are absent in the amorphous structure of acrylic glass. In tests conducted on notched specimens, the porous bone cement demonstrated superior fatigue strength to acrylic glass. The results could be predicted using the theory of critical distances, with errors no larger than 14%. This approach allowed us to show that, although porosity had a negative influence on the fatigue strength of the plain specimens in comparison to acrylic glass, the presence of porosity had no effect when the samples contained a notch or a hole. This finding is interesting when considering the effort put into removing porosity from bone cement during surgical operations, where it is used in situations where there are sharp stress concentrations in the form of protruding bone and the design features of artificial implants.
Separation and Properties of a Red Cell Sensitizing Substance from Streptococci

Moskowitz, Merwin (Purdue University, Lafayette, Ind.). Separation and properties of a red cell sensitizing substance from streptococci. J. Bacteriol. 91:2200–2204. 1966. —An antigen that binds onto red cells and causes them to be agglutinated by antiserum was separated from streptococci. Various procedures to extract the antigen from streptococci were investigated, and the greatest amount of antigen was obtained by extraction of cells with a phenol-water mixture. The reaction of the antigen with red cells was shown to be reversible by use of the Ashby mixed agglutination technique. The antigen also combines with a number of different tissues, and it was demonstrated that the antigen could be transferred from red cells to tissues and vice versa. An hypothesis is presented on the basis of these findings which suggests a possible role for this antigen in the etiology of rheumatic fever.
One-shot learning by inverting a compositional causal process

People can learn a new visual class from just one example, yet machine learning algorithms typically require hundreds or thousands of examples to tackle the same problems. Here we present a Hierarchical Bayesian model based on com-positionality and causality that can learn a wide range of natural (although simple) visual concepts, generalizing in human-like ways from just one image. We evaluated performance on a challenging one-shot classification task, where our model achieved a human-level error rate while substantially outperforming two deep learning models. We also tested the model on another conceptual task, generating new examples, by using a "visual Turing test" to show that our model produces human-like performance.
Orlicz capacities and applications to some existence questions for elliptic pdes having measure data

We study the sequence u n , which is solution of in Ω an open bounded set of R N and un = 0 on ∂Ω, when f n tends to a measure concentrated on a set of null Orlicz-capacity. We consider the relation between this capacity and the N -function Φ , and prove a non-existence result.
Do not crawl in the DUST: Different URLs with similar text

We consider the problem of DUST: Different URLs with Similar Text. Such duplicate URLs are prevalent in Web sites, as Web server software often uses aliases and redirections, and dynamically generates the same page from various different URL requests. We present a novel algorithm, DustBuster, for uncovering DUST; that is, for discovering rules that transform a given URL to others that are likely to have similar content. DustBuster mines DUST effectively from previous crawl logs or Web server logs, without/examining page contents. Verifying these rules via sampling requires fetching few actual Web pages. Search engines can benefit from information about DUST to increase the effectiveness of crawling, reduce indexing overhead, and improve the quality of popularity statistics such as PageRank.
Adrenergic receptor polymorphisms and platelet reactivity after treatment with dual antiplatelet therapy with aspirin and clopidogrel in acute coronary syndrome

Summary Platelet response to clopidogrel shows inter-individual variability that is partially explained by genetic polymorphisms. This variability affects clinical outcome when clopidogrel is administered in patients with acute coronary syndrome (ACS). Catecholamines, released during ACS, contribute to platelet aggregation through platelet α2A- (α2A-AR) and β2-adrenergic receptor (β2-AR) stimulation. It was the objective of this study to assess the potential influence of α2A-AR and β2-AR gene polymorphisms on platelet reactivity after dual antiplatelet therapy with aspirin and clopidogrel in ACS. We screened 641 ACS patients for 6.3/6.7 kb α2A-AR polymorphism, and for Arg16Gly and Gln27Glu β2-AR polymorphism. After 600 mg clopidogrel, we assessed ADP 10 μmol-induced platelet aggregation (ADP-Ag) and vasoactive stimulated phosphoprotein (VASP). All single nucleotide polymorphisms were in Hardy-Weinberg equilibrium. A slight though negligible association was found between 6.3 kb allele of α2A-AR with platelet reactivity ADPAg induced (beta: –2.91 [-5.68;-0.14], p=0.04). A borderline not significant reduction in PRI VASP was observed in 6.3 kb α2A-AR carriers (beta: –3.81 [-0.09;7.72], p=0.06). No significant effect on platelet parameters was observed for the other tested polymorphisms. Common α2A- and β2-adrenergic receptor polymorphisms do not show any major impact on residual platelet reactivity in non-ST-elevation ACS when a dual antiplatelet therapy with 250 mg aspirin and 600 mg clopidogrel is administered.
Genome-Wide Screening Reveals an EMT Molecular Network Mediated by Sonic Hedgehog-Gli1 Signaling in Pancreatic Cancer Cells

Aims The role of sonic hedgehog (SHH) in epithelial mesenchymal transition (EMT) of pancreatic cancer (PC) is known, however, its mechanism is unclear. Because SHH promotes tumor development predominantly through Gli1, we sought to understand its mechanism by identifying Gli1 targets in pancreatic cancer cells. Methods First, we investigated invasion, migration, and EMT in PC cells transfected with lentiviral Gli1 interference vectors or SHH over-expression vectors in vitro and in vivo. Next, we determined the target gene profiles of Gli1 in PC cells using cDNA microarray assays. Finally, the primary regulatory networks downstream of SHH-Gli1 signaling in PC cells were studied through functional analyses of these targets. Results Our results indicate there is decreased E-cadherin expression upon increased expression of SHH/Gli1. Migration of PC cells increased significantly in a dose-dependent manner within 24 hours of Gli1 expression (P<0.05). The ratio of liver metastasis and intrasplenic miniature metastasis increased markedly upon activation of SHH-Gli1 signals in nude mice. Using cDNA microarray, we identified 278 upregulated and 59 downregulated genes upon Gli1 expression in AsPC-1 cells. The data indicate that SHH-Gli1 signals promote EMT by mediating a complex signaling network including TGFβ, Ras, Wnt, growth factors, PI3K/AKT, integrins, transmembrane 4 superfamily (TM4SF), and S100A4. Conclusion Our results suggest that targeting the molecular connections established between SHH-Gli1 signaling and EMT could provide effective therapies for PC.
Influence of Glass Fiber wt% and Silanization on Mechanical Flexural Strength of Reinforced Acrylics

The aim is to evaluate the flexural strength of acrylic resin bars depending on the addiction of glass fibers with or without previous 3-methacryloxypropyl-trimethoxysilane (silane) application. Short fibers (3 mm) were treated and added to an acrylic resin powder, being further mixed with acrylic liquid to create bars (25 × 2 × 2 mm) of 11 experimental groups (N = 10), according to the interaction of experimental factors: weight % of glass fibers: (0.5; 1; 3; 4; 6 and 7) and silane application (with silane (S) or without silane (N)). Flexural strength and scanning microscopy evaluation were performed (SEM). Data (MPa) were submitted to ANOVA and Tukey (α = 5%). A significant difference between groups was observed (p = 0.001): S7%(128.85 ± 35.76)a, S6% (119.31 ± 11.97)ab, S4% (116.98 ± 25.23)ab, N4% (107.85 ± 24.88)abc, S1% (96.29 ± 20.65)bc, S0.5% (89.29 ± 7.33)cd, S3% (89.0 ± 11.27)cd, N3% (86.79 ± 17.63)cd, N1% (85.43 ± 16.44)cd, Control (73.29 ± 25.0)de, N0.5% (59.58 ± 19.46)e. For N groups, it was not possible to include more than 4%wt fibers. SEM showed better fiber-resin interaction for S groups, and fractures around fibers on N groups. Previous silane application enables the addiction of greater quantity of glass fibers and better interaction with the acrylic resin resulting in higher flexural strength. Without silane, fibers seem to act as initial crack points due to poor interaction.
Estimation of Resilient Modulus of Unbound Aggregates Using Performance-Related Base Course Properties

AbstractThis study aims at developing an accurate and efficient methodology to estimate the resilient modulus of unbound aggregates. First, a new resilient modulus model is proposed to incorporate the moisture dependence of the resilient modulus in addition to the stress dependence in existing models. Second, prediction models are developed to conveniently and accurately determine the coefficients in the proposed model. In order to characterize the moisture dependence of unbound aggregates, the degree of saturation and the matric suction parameter are added into the proposed model. The soil-water characteristic curve (SWCC) is used to determine the matric suction value at any given moisture content. The moisture dependence of the model is validated for selected materials with different moisture contents. In order to develop prediction models for the coefficients in the proposed model, laboratory experiments and multiple regression analysis are conducted on 20 different base course materials. The laborator.