Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Various Extracellular Matrix Proteins on the Growth of HL-1 Cardiomyocytes

We present the physical and biochemical effects of extracellular matrixes (ECMs) on HL-1 cardiomyocytes. ECMs play major roles in cell growth, adhesion and the maintenance of native cell functions. We investigated the effects of 6 different cell culture systems: 5 different ECM-treated surfaces (fibronectin, laminin, collagen I, gelatin and a gelatin/fibronectin mixture) and 1 nontreated surface. Surface morphology was scanned and analyzed using atomic force microscopy in order to investigate the physical effects of ECMs. The attachment, growth, viability, proliferation and phenotype of the cells were analyzed using phase-contrast microscopy and immunocytochemistry to elucidate the biochemical effects of ECMs. Our study provides basic information for understanding cell-ECM interactions and should be utilized in future cardiac cell research and tissue engineering.
Improving Satellite-Driven PM2.5 Models with VIIRS Nighttime Light Data in the Beijing-Tianjin-Hebei Region, China

Previous studies have estimated ground-level concentrations of particulate matter 2.5 (PM2.5) using satellite-derived aerosol optical depth (AOD) in conjunction with meteorological and land use variables. However, the impacts of urbanization on air pollution for predicting PM2.5 are seldom considered. Nighttime light (NTL) data, acquired with the Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership (S-NPP) satellite, could be useful for predictions because they have been shown to be good indicators of the urbanization and human activity that can affect PM2.5 concentrations. This study investigated the potential of incorporating VIIRS NTL data in statistical models for PM2.5 concentration predictions. We developed a mixed-effects model to derive daily estimations of surface PM2.5 levels in the Beijing–Tianjin–Hebei region using 3 km resolution satellite AOD and VIIRS NTL data. The results showed the addition of NTL information could improve the performance of the PM2.5 prediction model. The NTL data revealed additional details for predication results in areas with low PM2.5 concentrations and greater apparent seasonal variation due to the seasonal variability of human activity. Comparison showed prediction accuracy was improved more substantially for the model using NTL directly than for the model using the vegetation-adjusted NTL urban index that included NTL. Our findings indicate that VIIRS NTL data have potential for predicting PM2.5 and that they could constitute a useful supplemental data source for estimating ground-level PM2.5 distributions.
Regulation of Endothelial Cell Proliferation and Vascular Assembly through Distinct mTORC2 Signaling Pathways

ABSTRACT Mammalian target of rapamycin (mTOR) is a serine/threonine kinase that regulates a diverse array of cellular processes, including cell growth, survival, metabolism, and cytoskeleton dynamics. mTOR functions in two distinct complexes, mTORC1 and mTORC2, whose activities and substrate specificities are regulated by complex specific cofactors, including Raptor and Rictor, respectively. Little is known regarding the relative contribution of mTORC1 versus mTORC2 in vascular endothelial cells. Using mouse models of Raptor or Rictor gene targeting, we discovered that Rictor ablation inhibited vascular endothelial growth factor (VEGF)-induced endothelial cell proliferation and assembly in vitro and angiogenesis in vivo, whereas the loss of Raptor had only a modest effect on endothelial cells (ECs). Mechanistically, the loss of Rictor reduced the phosphorylation of AKT, protein kinase Cα (PKCα), and NDRG1 without affecting the mTORC1 pathway. In contrast, the loss of Raptor increased the phosphorylation of AKT despite inhibiting the phosphorylation of S6K1, a direct target of mTORC1. Reconstitution of Rictor-null cells with myristoylated AKT (Myr-AKT) rescued vascular assembly in Rictor-deficient endothelial cells, whereas PKCα rescued proliferation defects. Furthermore, tumor neovascularization in vivo was significantly decreased upon EC-specific Rictor deletion in mice. These data indicate that mTORC2 is a critical signaling node required for VEGF-mediated angiogenesis through the regulation of AKT and PKCα in vascular endothelial cells.
A 92m W 76.8GOPS vector matching processor with parallel Huffman decoder and query re-ordering buffer for real-time object recognition

A vector matching processor with memory bandwidth optimizations is proposed to achieve real-time matching of 128 dimensional SIFT features extracted from VGA video. The main bottleneck of feature-vector matching is the off-chip database access. We employ the locality sensitive hashing (LSH) algorithm which reduces the number of database comparisons required to match each query. In addition, database compression using Huffman coding increases the effective external bandwidth. Dedicated parallel Huffman decoder hardware ensures fast decompression of the database. A flexible query re-ordering buffer exploits overlapping accesses between queries by enabling out-of-order query processing to minimize redundant off-chip access. As a result, the 76.8 GOPS feature matching processor implemented in a 0.13um CMOS process achieves 43200 queries/second on a 100 object database while consuming peak power of 92mW.
Disulfide Bond Formation Contributes to Herpes Simplex Virus Capsid Stability and Retention of Pentons

ABSTRACT Disulfide bonds reportedly stabilize the capsids of several viruses, including papillomavirus, polyomavirus, and simian virus 40, and have been detected in herpes simplex virus (HSV) capsids. In this study, we show that in mature HSV-1 virions, capsid proteins VP5, VP23, VP19C, UL17, and UL25 participate in covalent cross-links, and that these are susceptible to dithiothreitol (DTT). In addition, several tegument proteins were found in high-molecular-weight complexes, including VP22, UL36, and UL37. Cross-linked capsid complexes can be detected in virions isolated in the presence and absence of N-ethylmaleimide (NEM), a chemical that reacts irreversibly with free cysteines to block disulfide formation. Intracellular capsids isolated in the absence of NEM contain disulfide cross-linked species; however, intracellular capsids isolated from cells pretreated with NEM did not. Thus, the free cysteines in intracellular capsids appear to be positioned such that disulfide bond formation can occur readily if they are exposed to an oxidizing environment. These results indicate that disulfide cross-links are normally present in extracellular virions but not in intracellular capsids. Interestingly, intracellular capsids isolated in the presence of NEM are unstable; B and C capsids are converted to a novel form that resembles A capsids, indicating that scaffold and DNA are lost. Furthermore, these capsids also have lost pentons and peripentonal triplexes as visualized by cryoelectron microscopy. These data indicate that capsid stability, and especially the retention of pentons, is regulated by the formation of disulfide bonds in the capsid.
Simultaneous localisation and map building using split covariance intersection

This paper develops a simultaneous localisation and map building (SLAM) algorithm which utilises the split covariance intersection (SCI) update rule. This algorithm decomposes estimates into a correlated component (whose precise structure is unknown) and a lower bound on an independent component. For a map of n beacons, the storage is O(n) and the computational costs are constant irrespective of map size. In a simple simulation example we show that the SCI algorithm, through exploiting a lower bound on independent information, performs substantially better than the traditional covariance intersection SLAM algorithm.
orchard: Paternity program for autotetraploid species

Advances in molecular marker technology have provided new opportunities to study the population genetics of polyploid taxa. Paternity analysis using microsatellite markers can be used in detection of gene flow between individuals and populations, in mating system analysis, to identify factors that influence fecundity and fertility, to identify behaviour of parent–offspring relationships and in the analysis of the reproductive success of different ecological groups. As there is no specific program for carrying out paternity analysis in tetraploid species, specialized software was designed for the assignment of paternity for autotetraploid species. orchard is a novel implementation of exclusion and likelihood statistics for carrying out paternity analysis of autotetraploids. First, the program performs an exclusion method, and then, a likelihood statistic is used with nonexcluded candidate fathers. Optional features include estimation of allele dosage of known mother trees and the estimation of pollen flow distances. orchard was tested using a data set of microsatellite data of Dipteryx odorata, a tetraploid Amazonian tree species.
Network Time Protocol (version 2) specification and implementation

This document describes the Network Time Protocol (NTP), specifies its formal structure and summarizes information useful for its implementation. NTP provides the mechanisms to synchronize time and coordinate time distribution in a large, diverse internet operating at rates from mundane to lightwave. It uses a returnable-time design in which a distributed subnet of time servers operating in a self-organizing, hierarchical-master-slave configuration synchronizes local clocks within the subnet and to national time standards via wire or radio. The servers can also redistribute reference time via local routing algorithms and time daemons. This is an Internet Standard Recommended Protocol with assigned number RFC-1119.
Media Exposure to Bioterrorism: Stress and the Anthrax Attacks

Abstract This study examined media exposure and adjustment to anthrax bioterrorism attacks and the terrorist attacks on 9/11 in a sample of 300 people who lived distant from the attacks. Measures of direct and indirect exposure to terrorism, perceived risk of anthrax exposure, psychological distress, and outlook were assessed at 2 to 3 months and at 8 months after the first reported anthrax attack. Initial anthrax media exposure was a powerful predictor of distress, whereas subsequent anthrax media exposure only predicted negative changes in outlook over time. Perceived risk of anthrax exposure predicted distress and outlook but did not appear to mediate the effects of media exposure. Determining the nature and consequences of media exposure to threatening and frightening events like terrorism will help predict and manage response to future bioterrorism.
Prediction of First Lactation 305-day Milk Yield Based on Monthly Test Day Records Using Artificial Neural Networks in Sahiwal Cattle

In the present study, first lactation 305-day lactation milk yield (FL305DMY) was predicted by artificial neural network (ANN) using monthly test day milk yields records of 588 Sahiwal cows. A total of five monthly test day milk yields (2, 3, 5, 7, 8 monthly test day record) were used in neural networks to train data using Bayesian regularization (BR) algorithm. Results showed that the accuracy of prediction of all the models increased with the addition of test day milk yields as input variables. The best neural network model was able to predict FL305DMY with 93.18% accuracy. Further, comparison was made between multiple linear regression (MLR) and ANN for accuracy of prediction and there was no significant different found between ANN and MLR for prediction of FL305DMY in Sahiwal cows.
Determination of the Specific Substrate Sequence Motifs of Protein Kinase C Isozymes*

Protein kinase C (PKC) family members play significant roles in a variety of intracellular signal transduction processes, but information about the substrate specificities of each PKC family member is quite limited. In this study, we have determined the optimal peptide substrate sequence for each of nine human PKC isozymes (α, βI, βII, γ, δ, ε, η, μ, and ζ) by using an oriented peptide library. All PKC isozymes preferentially phosphorylated peptides with hydrophobic amino acids at position +1 carboxyl-terminal of the phosphorylated Ser and basic residues at position −3. All isozymes, except PKCμ, selected peptides with basic amino acids at positions −6, −4, and −2. PKCα, -βI, -βII, -γ, and -η selected peptides with basic amino acid at positions +2, +3, and +4, but PKCδ, -ε, -ζ, and -μ preferred peptides with hydrophobic amino acid at these positions. At position −5, the selectivity was quite different among the various isozymes; PKCα, -γ, and -δ selected peptides with Arg at this position while other PKC isozymes selected hydrophobic amino acids such as Phe, Leu, or Val. Interestingly, PKCμ showed extreme selectivity for peptides with Leu at this position. The predicted optimal sequences from position −3 to +2 for PKCα, -βI, -βII, -γ, -δ, and -η were very similar to the endogenous pseudosubstrate sequences of these PKC isozymes, indicating that these core regions may be important to the binding of corresponding substrate peptides. Synthetic peptides based on the predicted optimal sequences for PKCα, -βI, -δ, -ζ, and -μ were prepared and used for the determination of Km and Vmax for these isozymes. As judged by Vmax/Km values, these peptides were in general better substrates of the corresponding isozymes than those of the other PKC isozymes, supporting the idea that individual PKC isozymes have distinct optimal substrates. The structural basis for the selectivity of PKC isozymes is discussed based on residues predicted to form the catalytic cleft.
HPV group‐ and type‐specific concordance in HPV infected sexual couples

The concordance of human papillomavirus (HPV) groups and types was evaluated in 45 sexual couples with both partners HPV infected, by analyzing cervical samples from women and three genital sites (penile brushing, urethral brushing, and semen) from men. When grouping HPV types, no significant HPV group sharing was found between partners, either considering samples from any male site (concordance: 55.5%; P = 0.11) or from each site (concordance by penile brushing, 37.8%; urethral brushing, 24.5%; semen, 22.3%; P > 0.05). Examining individual HPV types, using samples from any male site, concordance was found in 29 (64.4%; P = 0.036) couples; significant concordance was evident for 16 HPV genotypes, the most frequent being HPV‐6, ‐66, ‐31, ‐51, and ‐53. Using samples from specific male sites, concordance was found by penile brushing in 24 (53.3%) couples, urethral brushing in 16 (35.5%), and semen in 7 (15.5%; P = 0.014). Among the 16 HPV types shared by examining samples from any male site, 9 (56.3%) were in common by penile brushing, 11 (68.7%) by urethral brushing, and 6 (37.5%; P = 0.48) by semen. Combined penile brushing and urethral brushing sampling identified all the 29 couples concordant by the three male sites; combined penile brushing and semen detected 26 (89.6%) concordant couples. The most adequate approach to the assessment of HPV concordance in sexual couples could be based on the analysis of individual HPV types and the sampling of men by penile brushing combined with urethral brushing. The high and significant degree of HPV type‐specific concordance confirms HPV transmission between sexual partners. J. Med. Virol. 79:1882–1888, 2007. © 2007 Wiley‐Liss, Inc.
Nutritional adequacy of diets containing growing up milks or unfortified cow's milk in Irish children (aged 12–24 months)

Background Growing up milks (GUM) are milk-based drinks with added vitamins and minerals intended for children aged 12–36 months. Few data are available on the consumption of GUM and their role in the diets of young children. Objective To determine the nutritional adequacy of two groups of 12–24-month-old Irish children by type of milk consumption (consumers or non-consumers of GUM). Design Using data from a cross-sectional study of Irish children, the National Pre-School Nutrition Survey (2010–2011), two groups of children were defined. The groups included children aged 12–24 months with an average daily total milk intake of at least 300 g and consuming GUM (≥100 g/day) together with cow's milk (n=29) or cow's milk only (n=56). Results While average total daily energy intakes were similar in both consumers and non-consumers of GUM, intakes of protein, saturated fat, and vitamin B12 were lower and intakes of carbohydrate, dietary fibre, iron, zinc, vitamins C and D were higher in consumers of GUM. These differences in nutrient intakes are largely attributable to the differences in composition between GUM and cow's milk. For both consumers and non-consumers of GUM, intakes of carbohydrate and fat were generally in line with recommendations while intakes of protein, dietary fibre and most micronutrients were adequate. For children consuming cow's milk only, high proportions had inadequate intakes of iron and vitamin D; however, these proportions were much lower in consumers of GUM. Conclusions Consumption of GUM reduced the risk of inadequacies of iron and vitamin D, two nutrients frequently lacking in the diets of young children consuming unfortified cow's milk only.
Measurement of the common source inductance of typical switching device packages

The common source inductance is one of the major causes of deterioration of the switching speed and susceptibility of the false triggering for semiconductor switching devices. Practical design of this inductance requires selection of an appropriate semiconductor package because this inductance is greatly dependent on the physical package structure. However, few studies have reported a list of the common source inductance of commercially available packages. In order to list and compare the common source inductance among typical semiconductor packages, this paper carried out measurement of this inductance of actual switching devices mounted on experimental PCBs. This paper employed a recently proposed straightforward measurement technique directly applicable to switching devices mounted on PCBs. As a result, a basic database of the common source inductance of typical packages was presented. The common source inductance was found to be determined mainly by the package type. However, in TO-247 and TO-220 packages, approximately one-third of the total common source inductance was found to possibly vary among the switching devices of the same package due to the dependence on the current rating. Investigation of the physical package structure implied that this dependence was caused by the stray inductance of the bonding wires connecting the semiconductor chip to the source terminal.
Hypermethylation of the GSTP1 promoter region in breast cancer is associated with prognostic clinicopathological parameters.

UNLABELLED Breast cancer is one of the most common cancer affecting women and the recent research is focused on identifying new genetic and epigenetic prognostic and predictive factors. Glutathione S-transferase P1 (GSTP1) is abiotransformation enzyme expressed in normal breast epithelial cells which can be epigenetically inactivated in breast cancer. We have shown, that application of nested two-stage methylation-specific PCR (MSP) is asuitable method for analysis of epigenetically silenced GSTP1 in formalin-fixed paraffin-embedded (FFPE) tissues from breast cancer patients. Of 45 breast tumors, 11 (24, 4%) were found to have methylated GSTP 1promoter region. We were able to demonstrate the correlation between the hypermethylation of the GSTP1 promoter region and histological grade of the tumor (p KEYWORDS breast cancer, prognostic factors, hypermethylation, GSTP1, methylation-specific PCR.
A Software Tool for Retrieving Land Surface Temperature from

Remote sensing is a powerful and well-known tool in the collection, analysis, and modeling of environmental data, however, not much attention has been given to the use of thermal infrared (TIR) remote sensing. Land surface temperature (LST) is a key parameter for many environmental studies such as global environmental change, climate models, and human-environment interactions. In this study, a software tool which retrieves LST from Advanced Spaceborne Thermal Emission and reflection Radiometer (ASTER) imagery has been developed in Visual Basic . NET. The tool consists of five main modules: 1- Converting DN to Radiances, 2- Calculating surface reflectances, 3- Calculating NDVI, 4- Calculating emissivity and 5- Calculating surface temperature. In this tool, Jimenez Munoz and Sobrino’s Single Channel (SCJM&S) Algorithm for ASTER was employed. With this tool, user can be able to calculate LST using (1) atmospheric parameters such as atmospheric transmissivity, upwelling and downwelling atmospheric radiances, (2) atmospheric water-vapor content. Hopefully, this program will be a useful tool for scientists/persons who are interested in studying thermal environments.
An Efficient Approach to Short-Term Load Forecasting at the Distribution Level

Short-term load forecasting at the distribution level predicts the load of substations, feeders, transformers, and possibly customers from half an hour to one week ahead. Effective forecasting is important for the planning and operation of distribution systems. The problem, however, is difficult in view of complicated load features, the large number of distribution-level nodes, and possible switching operations. In this paper, a new forecasting approach within the hierarchical structure is presented to solve these difficulties. Load of the root node at any user-defined subtree is first forecast by a wavelet neural network with appropriate inputs. Child nodes categorized as “regular” and “irregular” based on load pattern similarities are then forecast separately. Load of a regular child node is simply forecast as the proportion from the parent node load forecast while the load of an irregular child node is forecast by an individual neural network model. Switching operation detection and follow-up adjustments are also performed to capture abnormal changes and improve the forecasting accuracy. This new approach captures load characteristics of nodes at different levels, takes advantage of pattern similarities between a parent node and its child nodes, detects abnormalities, and provides high quality forecasts as demonstrated by two practical datasets.
Rehabilitation of a periodontal patient with rapidly progressing marginal alveolar bone loss: 1-year follow-up.

BACKGROUND The present case report describes a 1-year follow-up of functional rehabilitation of a young periodontal patient with severely advanced, rapidly progressing marginal bone loss treated by using a new splinting material, i.e., glass fiber-reinforced composite (FRC). Apart from one single tooth, the young man had retained all his natural teeth. TREATMENT Periodontal treatment was based on cleaning and root planing enabled by partial-thickness-flap operations. This method was selected to avoid further damage to the remaining alveolar bone. After healing for 6 months, a cavity retained internal FRC splint was constructed and 1 missing lower molar was replaced by an inlay-retained FRC resin-bonded fixed partial denture (FPD). A 12 months follow-up period revealed a healthy periodontium and good functional and esthetic results. CONCLUSIONS The new material allows the use of periodontal treatment methods instead of prosthetic alternatives, which until now have been a more generally used approach in the treatment of severely advanced periodontal cases. Internal fiber-reinforced composite splinting being affordable for the patient, easy for the clinician to construct and giving good esthetic and functional results, suggests that the method may be a valuable aid in periodontal treatment.