Miracle-dz/UniFAR-FTUs huggingface dataset:
3 Gbps, 5000 ppm spread spectrum SerDes PHY with frequency tracking phase interpolator for serial ATA

We have developed a 5000 ppm spread spectrum Serializer/Deserializer (SerDes) physical layer (PHY) chip compliant with Serial AT Attachment (ATA). The chip was fabricated with a 0.15 /spl mu/m 1.5 V CMOS process and includes a self-running spread spectrum carrier generator to provide both transmit and receive block, a self-running phase interpolator to recover the +/-5000 ppm spread spectrum receive (RX) clock and data.
A Novel Anti-Histone H1 Monoclonal Antibody, SSV Monoclonal Antibody, Improves Lung Injury and Survival in a Mouse Model of Lipopolysaccharide-Induced Sepsis-Like Syndrome

Background. Histones play important roles in both host defenses and inflammation related to microbial infection. A peptide mimotope (SSV) was identified from a novel histone H1 monoclonal antibody (16G9 mAb) that was shown to inhibit the mixed lymphocyte reaction. In the present study, an anti-SSV producing hybridoma was established. We investigated the effects of SSV mAb in a mouse acute inflammation model induced by intraperitoneal injection of lipopolysaccharide (LPS). Methods. SSV mAb was generated and characterized. Mice were treated with SSV mAb or a control IgG antibody prior to LPS injection. Evaluation of survival rate and lung tissue on histological score was performed. The levels of inflammatory cytokines and histones H1, H3, and H4 in plasma and lung tissue were measured by ELISA. Results. Competitive ELISA revealed that SSV mAb binds to histone H1. SSV mAb improved lung injury and prolonged the survival of LPS-injected mice. Increased levels of histones H1, H3, and H4 and inflammatory cytokines (TNF-α, IL-1β, and IL-6) in plasma and lung tissue after LPS injection were ameliorated by SSV mAb. Conclusion. SSV mAb is shown to have anti-inflammatory activity and organ-protective effects, highlighting the importance of controlling histone H1 as well as H3 and H4 levels during inflammation.
Secure Storage of Fingerprint Biometrics Using Slepian-Wolf Codes

We describe a method to encode fingerprint biometrics securely for use, e.g., in encryption or access control. The system is secure because the stored data suffices to validate a probe fingerprint but not to recreate the original fingerprint biometric. Therefore, a breach in database security does not lead to the loss of biometric data. We present a model for a secure biometric system for which we can make strong encryption-like security guarantees. We derive a fundamental trade off between system security and the robustness of authentication. The trade off is quantified for simple statistical models. We outline an implementation and report the effectiveness of our method as tested on a data base consisting of 579 datasets, each containing roughly 15 measurements of a single finger.
Polycystin Expression in the Kidney and Other Tissues: Complexity, Consensus and Controversy

PKD1, the major gene mutated in autosomal dominant polycystic kidney disease, was identified in 1994, and fully sequenced in 1995. The protein which it encodes, polycystin-1, is the first member of a new family of proteins, whose functions presently remain unclear. This review seeks to highlight the difficulties researchers studying polycystin-1 have faced and to summarize the current areas of consensus and controversy between different groups, particularly with regard to the expression pattern, subcellular location and biochemical characterization of polycystin-1. Where relevant, more recent data regarding polycystin-2, the protein encoded by PKD2, will also be discussed.
Frame-wise HMM adaptation using state-dependent reverberation estimates

A novel frame-wise model adaptation approach for reverberation-robust distant-talking speech recognition is proposed. It adjusts the means of static cepstral features to capture the statistics of reverberant feature vector sequences obtained from distant-talking speech recordings. The means of the HMMs are adapted during decoding using a state-dependent estimate of the late reverberation determined by joint use of a feature-domain reverberation model and optimum partial state sequences. Since the parameters of the HMMs and the reverberation model can be estimated completely independently, the approach is very flexible with respect to changing acoustic environments. Due to the frame-wise model adaptation, some of the HMM limitations are relieved, and recognition results surpassing that of matched reverberant training are obtained at the cost of a moderately increased decoding complexity.
Treponema denticola Outer Membrane Inhibits Calcium Flux in Gingival Fibroblasts

ABSTRACT Treponema denticola is a cultivable oral spirochete which perturbs the cytoskeleton in cultured cells of oral origin, but intracellular signalling pathways by which it affects actin assembly are largely unknown. As the outer membrane (OM) of Treponema denticola disrupts actin-dependent processes that normally require precise control of intracellular calcium, we studied the effects of an OM extract on internal calcium release, ligand-gated and calcium release-activated calcium channels, and related mechanosensitive cation fluxes in human gingival fibroblasts (HGF). Single-cell ratio fluorimetry demonstrated that in resting cells loaded with Fura-2, baseline intracellular Ca2+ concentration ([Ca2+]i) was not affected by treatment with OM extract, but normal spontaneous [Ca2+]ioscillations were dramatically increased in frequency for 20 to 30 min followed by complete blockade. OM extract inhibited ATP-induced and thapsigargin-induced release of calcium from intracellular stores by 40 and 30%, respectively. Addition of Ca2+ to the extracellular pool following depletion of intracellular Ca2+ by thapsigargin and extracellular Ca2+ by EGTA yielded 59% less replenishment of [Ca2+]i in OM extract-treated than in control HGF. In cells loaded with collagen-coated ferric oxide beads to stimulate integrin-dependent calcium release, baseline [Ca2+]i was nearly doubled but was not significantly different in control and OM extract-treated cells. Magnetically generated tensile forces on the beads induced >300% increases of [Ca2+]i above baseline. Cells preincubated with OM extract exhibited dose-dependent and time-dependent reductions in stretch-induced [Ca2+]i transients, which were due to neither loss of beads from the cells nor cell death. The T. denticola OM inhibitory activity was eliminated by heating the OM extract to 60°C and by boiling but not by phenylmethylsulfonyl fluoride treatment. Thus nonlipopolysaccharide, nonchymotrypsin, heat-sensitive protein(s) in T. denticola OM can evidently inhibit both release of calcium from internal stores and uptake of calcium through the plasma membrane, possibly by interference with calcium release-activated channels.
The Effects of Pre-slaughter Stress and Season on the Activity of Plasma Creatine Kinase and Mutton Quality from Different Sheep Breeds Slaughtered at a Smallholder Abattoir

The objective of the current study was to determine the effect of pre-slaughter stress, season and breed on the activity of plasma creatine kinase (CK) and the quality of mutton. One hundred and seventy-three (173) castrated sheep from Dormer (DM), South African Mutton Merino (SAMM), Dorper (DP) and Blackhead Persian (BP) sheep breeds were used in the study. The animals were grouped according to age-groups as follows: Group 1 (6 to 8 months), Group 2 (9 to 12 months) and Group 3 (13 to 16 months). Blood samples were collected during exsanguinations using disposable vacutainer tubes for CK analysis. Representative samples of the Muscularis longissimuss thoracis et. lumborum (LTL) were collected from 84 castrated sheep, of different breeds (28 per breed) 24 h after slaughter. The following physico-chemical characteristics of mutton were determined; meat pH (pH24), color (L*, a* and b*), thawing and cooking losses and Warner Braztler Shear Force (WBSF). The activity of plasma CK was significantly higher (p<0.001) in summer (1,026.3±105.06) and lower in winter (723.3±77.75). There were higher values for L* (33.7±0.94), b* (11.5±0.48) and WBSF (29.5±1.46) in summer season than in winter season; L* (29.4±0.64), b* (10.2±0.33) and WBSF (21.2±0.99). The activity of plasma CK was influenced by the type of breed with Dormer having the highest (p>0.001) levels (1,358.6±191.08) of CK. South African Mutton Merino had higher values for pH24 (5.9±0.06), L* (34.2±0.97), b* (12.2±0.50) and WBSF (26.8±1.51) and Blackhead Persian had higher values (35.5±2.17) for cooking loss (CL%) than the other breeds. Computed Principal Component Analyses (PCA) on the activity of plasma CK and physico-chemical characteristics of mutton revealed no correlations between these variables. However, positive correlations were observed between pH24, L*, a*, b*, CL% and WBSF. Relationships between pre-slaughter stress, CK activity and physico-chemical characteristics of mutton were also observed. It was therefore concluded that although mutton quality and creatine kinase were not related, pre-slaughter stress, season and breed affected the activity of creatine kinase and mutton quality.
The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors

Next Generation Sequencing studies generate a large quantity of genetic data in a relatively cost and time efficient manner and provide an unprecedented opportunity to identify candidate causative variants that lead to disease phenotypes. A challenge to these studies is the generation of sequencing artifacts by current technologies. To identify and characterize the properties that distinguish false positive variants from true variants, we sequenced a child and both parents (one trio) using DNA isolated from three sources (blood, buccal cells, and saliva). The trio strategy allowed us to identify variants in the proband that could not have been inherited from the parents (Mendelian errors) and would most likely indicate sequencing artifacts. Quality control measurements were examined and three measurements were found to identify the greatest number of Mendelian errors. These included read depth, genotype quality score, and alternate allele ratio. Filtering the variants on these measurements removed ~95% of the Mendelian errors while retaining 80% of the called variants. These filters were applied independently. After filtering, the concordance between identical samples isolated from different sources was 99.99% as compared to 87% before filtering. This high concordance suggests that different sources of DNA can be used in trio studies without affecting the ability to identify causative polymorphisms. To facilitate analysis of next generation sequencing data, we developed the Cincinnati Analytical Suite for Sequencing Informatics (CASSI) to store sequencing files, metadata (eg. relatedness information), file versioning, data filtering, variant annotation, and identify candidate causative polymorphisms that follow either de novo, rare recessive homozygous or compound heterozygous inheritance models. We conclude the data cleaning process improves the signal to noise ratio in terms of variants and facilitates the identification of candidate disease causative polymorphisms.
Patient education and self-management in the rheumatic diseases: a self-efficacy approach.

As stated in the standards for arthritis patient education recently developed by a task force of the National Arthritis Advisory Board in the United States (1,2), patient education can improve the lives of patients with rheumatic diseases. Patients need a formal body of knowledge and skills in order to manage the disease on a day-to-day basis. These standards give the following definition of patient education:
Adult Bone Marrow Stromal Cells Differentiate into Neural Cells in Vitro


Bone marrow stromal cells (BMSC) normally give rise to bone, cartilage, and mesenchymal cells. Recently, bone marrow cells have been shown to have the capacity to differentiate into myocytes, hepatocytes, and glial cells. We now demonstrate that human and mouse BMSC can be induced to differentiate into neural cells under experimental cell culture conditions. BMSC cultured in the presence of EGF or BDNF expressed the protein and mRNA for nestin, a marker of neural precursors. These cultures also expressed glial fibrillary acidic protein (GFAP) and neuron-specific nuclear protein (NeuN). When labeled human or mouse BMSC were cultured with rat fetal mesencephalic or striatal cells, a small proportion of BMSC-derived cells differentiated into neuron-like cells expressing NeuN and glial cells expressing GFAP.
Personalization of web-search using short-term browsing context

Search and browsing activity is known to be a valuable source of information about user's search intent. It is extensively utilized by most of modern search engines to improve ranking by constructing certain ranking features as well as by personalizing search. Personalization aims at two major goals: extraction of stable preferences of a user and specification and disambiguation of the current query. The common way to approach these problems is to extract information from user's search and browsing long-term history and to utilize short-term history to determine the context of a given query. Personalization of the web search for the first queries in new search sessions of new users is more difficult due to the lack of both long- and short-term data. In this paper we study the problem of short-term personalization. To be more precise, we restrict our attention to the set of initial queries of search sessions. These, with the lack of contextual information, are known to be the most challenging for short-term personalization and are not covered by previous studies on the subject. To approach this problem in the absence of the search context, we employ short-term browsing context. We apply a widespread framework for personalization of search results based on the re-ranking approach and evaluate our methods on the large scale data. The proposed methods are shown to significantly improve non-personalized ranking of one of the major commercial search engines. To the best of our knowledge this is the first study addressing the problem of short-term personalization based on recent browsing history. We find that performance of this re-ranking approach can be reasonably predicted given a query. When we restrict the use of our method to the queries with largest expected gain, the resulting benefit of personalization increases significantly
Meat quality characteristics of the springbok (Antidorcas marsupialis)

30 INTRODUCTION 31 MATERIALS AND METHODS 32 RESULTS AND DISCUSSION 34 CONCLUSION 44 REFERENCES 45 CHAPTER 4: THE PHYSICAL ATTRIBUTES OF SPRINGBOK 47 (ANTIDORCAS MARSUPIALIS) MEAT AS INFLUENCED BY AGE, GENDER AND PRODUCTION REGION ABSTRACT 47 INTRODUCTION 48 MATERIALS AND METHODS 49 RESULTS AND DISCUSSION 53 CONCLUSION 60 REFERENCES 6147 INTRODUCTION 48 MATERIALS AND METHODS 49 RESULTS AND DISCUSSION 53 CONCLUSION 60 REFERENCES 61
A study on using Python vs Weka on dialysis data analysis

Health data has been drastically increasing in capacity and variety. Due to large and complex collection of datasets, it is difficult to process data using traditional data processing techniques. Machine Learning techniques, such as KNN and Naïve Bayes, have been used. Python and Weka are tools that are widely used in the field of data analytics. Therefore, this paper gives the comprehensive comparison between both tools together with some machine learning algorithms on data analytic of Dialysis Dataset. The results show that using Python provides the better performance in term of correct/incorrect instances, precision, and recall.
Mantle-crust Interaction in Granite Petrogenesis in Post-collisional Settings: Insights from the Danubian Variscan Plutons of the Romanian Southern Carpathians

viii Chapter One: Post-collisional Late Variscan Magmatism in the Danubian Domain (South Carpathians, Romania) Documented by Zircon U/Pb LA-ICP-MS . 1 Note to Reader . 1 Abstract .
Novel chemistry of invasive plants: exotic species have more unique metabolomic profiles than native congeners

It is often assumed that exotic plants can become invasive when they possess novel secondary chemistry compared with native plants in the introduced range. Using untargeted metabolomic fingerprinting, we compared a broad range of metabolites of six successful exotic plant species and their native congeners of the family Asteraceae. Our results showed that plant chemistry is highly species-specific and diverse among both exotic and native species. Nonetheless, the exotic species had on average a higher total number of metabolites and more species-unique metabolites compared with their native congeners. Herbivory led to an overall increase in metabolites in all plant species. Generalist herbivore performance was lower on most of the exotic species compared with the native species. We conclude that high chemical diversity and large phytochemical uniqueness of the exotic species could be indicative of biological invasion potential.
Neodymium isotopic constraints for the origin of Mesoproterozoic felsic magmatism, Gawler Craton, South Australia

Mesoproterozoic felsic magmatism of the Gawler Range Volcanics and Hiltaba Suite granites occurred at 1585–1595 Ma across much of the Gawler Craton, South Australia. Nd isotopic analysis of this felsic magmatism, combined with petrological and geochemical arguments, suggest derivation by partial melting of both Paleoproterozoic and Archean crust. The majority of samples analyzed have Nd isotopic and geochemical characteristics compatible with the involvement of Paleoproterozoic crust stabilized during the 1.85–1.71 Ga Kimban orogeny as sources for the Mesoproterozoic magmatism; others require derivation from sources dominated by Archean rocks. This cycle of Paleoproterozoic crustal stabilization followed by involvement of this crust Mesoproterozoic felsic magmatism is one previously documented from many parts of Mesoproterozoic Laurentia. On the basis of models proposing East Australia–Antarctica to be the conjugate landmass at the rifted margin of western North America, it appears that the voluminous mag.
Time-dependent Photoionization in a Dusty Medium. II. Evolution of Dust Distributions and Optical Opacities

The interaction of a radiation field with a dusty medium is a relevant issue in several astrophysical contexts. We use the time-dependent photoionization code in a dusty medium developed by Perna & Lazzati to study the modifications in the dust distribution and the relative optical opacities when a strong X-ray/UV radiation flux propagates into a medium. We find that silicates are preferentially destroyed with respect to graphite, and the extinction curve becomes significantly flatter (hence implying less reddening), with the characteristic bump at 2175 Å being highly suppressed because of the destruction of the small graphite grains. This could explain the observational lack of such a feature in gamma-ray-burst afterglow and active galactic nuclei spectra. For a very intense and highly variable source irradiating a compact and dense region, time variability in the optical opacity resulting from dust destruction can be observed on a relatively short timescale. We show that, under these circumstances, monitoring the time variability of the opacity can yield powerful clues to the properties of dust in the environment of the source. In particular, it allows one to break the observational degeneracy as to whether a gray extinction is the result of a low dust-to-gas ratio or of a dust grain distribution that is skewed toward large grains.
Evaluation of Snoop-Energy Reduction Techniques for Chip-Multiprocessors

Chip multiprocessors (CMPs) have become an interesting micro-architectural style for high-end systems as well as low-power systems. While power-performance tradeoffs differ in these systems, a high power consumption can lead to devastating power densities in the former and a reduced operating time in the latter owing to limited battery capacity. In this paper, we focus on the energy wasted in the snoopy cache protocols that keep the L1 caches in CMPs consistent. Previous studies have focussed on the energy wasted by snoop accesses in the private caches in SMP systems and found that it can be a big fraction of the total energy. We apply two techniques serial snooping and Jetty that were developed for SMP servers and see if they can lead to energy savings in a CMP. We find that the techniques are not well suited for a CMP and analyze why. Serial snooping does not work well because all caches have to be searched even if none can supply the data, which happens to be the case most of the time. Jetty, does not perform well because the snoop energy saved by the filtering is offset by the energy lost in the filters.
Relationship between the calcium content in soil and the calcium content of flue-cured tobacco in Enshi tobacco-growing area

Distribution of the calcium content in soil and the calcium content of flue-cured tobacco in Enshi tobacco-growing area of Hubei Province and their relationships were analyzed. The results indicated that: (1) the average content in soil of total and exchangeable calcium was 2124.60 and 1091.44 mg/kg in Enshi tobacco-growing area. The calcium content showed the trends of high altitude > middle altitude >lower altitude among different altitudes, and the trends of 0 to 20 > 20 to 40 > 40 to 60 cm in different soil depths. (2) Significant differences of the calcium content of flue-cured tobacco were found among the different cultivars and grades, indicating the trends of Yunyan87 >Yunyan85 > K326, the trends of X2F > C3F > B2F, and the trends of high altitude > middle altitude > lower altitude. (3) The calcium content in soil and the calcium content of flue-cured tobacco were both increased with the altitude height going up. When the exchangeable calcium content in soil was grouped and increasing, the calcium content of flue-cured tobacco also increased. Linear regression equation was established between the calcium content of flue-cured tobacco and the exchangeable calcium content in soil with high significant correlation coefficient. Key words: Calcium content in soil, calcium content of flue-cured tobacco, altitude height, relationship analysis, Enshi tobacco-growing area.
Plasma DNA level in predicting therapeutic efficacy in advanced nonsmall cell lung cancer

Assessment of total plasma DNA can be a promising noninvasive tool for monitoring the effect of cytotoxic therapies in order to predict therapeutic efficacy at an early stage. Cell-free plasma DNA levels were quantified before the first, second and third cycle of chemotherapy in 42 patients with advanced nonsmall cell lung cancer and correlated with response to therapy, as assessed by computed tomography following the third chemotherapy cycle. A significantly lower plasma DNA level, measured before various treatment cycles, was found in patients with remission or stable disease than in those with progression. Higher levels and insufficient decrease in plasma DNA levels during the course of chemotherapy indicated poor outcome. For predicting insufficient therapy response, a sensitivity of 26.9% was achieved at 100% specificity using plasma DNA levels before the first therapy cycle. Prediction of disease progression was achieved with a sensitivity of 35.7% at 100% specificity using plasma DNA levels before the first therapy cycle. Monitoring of plasma DNA levels during the course of chemotherapy could identify patients who are likely to exhibit an insufficient therapeutic response and disease progression at an early stage. This may help in individualising treatment, and could lead to better management of advanced-stage lung cancer.