Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced apoptosis of ovarian cancer cells via nanocarrier-mediated codelivery of siRNA and doxorubicin

A folate conjugated ternary copolymer, FA–PEG–PEI–PCL, of poly(ethylene glycol) (PEG), poly(ethylene imine) (PEI), and poly(ɛ-caprolactone) (PCL) was synthesized. The copolymer self-assembled into cationic micelles capable of co-delivering siRNA and the anticancer drug doxorubicin (DOX). This dual functional nanocarrier demonstrated low cytotoxicity and high performance in drug/siRNA delivery. Upon the codelivery of siRNA, targeting the Bcl-2 gene, and DOX, using the folate-targeted nanocarrier, DOX-induced apoptosis in the skov-3 cells overexpressing folate receptor was significantly enhanced through a mechanism of downregulating the antiapoptotic protein Bcl-2, while simultaneously upregulating the proapoptotic protein Bax. This work suggested that the combination of Bcl-2 siRNA and DOX therapies is feasible, based on our dual functional nanocarrier, which set up a good basis for a future in vivo test.
Essential Cloud Storage Systems Security Methodologies

The demand to have secure environments for systems’ information on cloud systems is arising since this should be more secure and far away from our systems damage disasters and data corruption. The dream became real with the cloud computing. Cloud computing is being more famous and used especially in the enterprises where the cost matters. These enterprises can reduce IT costs by using cloud computing services. Most of the enterprises that don’t use cloud computing have a fear of the platform security and the information security. The users always seek for verifying the confidentiality and integrity of their data and computations before using cloud computing. Many researches have been established in these two fields for the infrastructure, platform security, data confidentiality and integrity. This paper, presents two examples for platform security and a comparison between three techniques for how can users secure the data and computations, at cloud environment, to keep the confidentiality and integrity. The ultimate goal of providing such a comparison is to encourage enterprises and users to use the cloud storage systems on secure infrastructures and platforms that maintain their customers/own data privacy.
An Introduction to Metabolic Networks and Their Structural Analysis

There has been a renewed interest for metabolism in the computational biology community, leading to an avalanche of papers coming from methodological network analysis as well as experimental and theoretical biology. This paper is meant to serve as an initial guide for both the biologists interested in formal approaches and the mathematicians or computer scientists wishing to inject more realism into their models. The paper is focused on the structural aspects of metabolism only. The literature is vast enough already, and the thread through it difficult to follow even for the more experienced worker in the field. We explain methods for acquiring data and reconstructing metabolic networks, and review the various models that have been used for their structural analysis. Several concepts such as modularity are introduced, as are the controversies that have beset the field these past few years, for instance, on whether metabolic networks are small-world or scale-free, and on which model better explains the evolution of metabolism. Clarifying the work that has been done also helps in identifying open questions and in proposing relevant future directions in the field, which we do along the paper and in the conclusion.
Prediction of Formation Pressure Gradients of NC98 Field-Sirte Basin-Libya

The prediction of formation pore pressure and fracture pressure gradients is a significant step towards the drilling plan. In this study, the formation pressures of twelve wells from NC98 field-Sirte Basin (Waha Oil Company) were calculated by employing empirical methods, Eaton’s equations, that depend on the real drilling and well-logging data. Regarding the results, the normal pore pressure in the NC98 field in Sirte basin is 0.437 Psi/ft, and it is extending from the top of the wells in the investigated area to 7,000 ft. A subnormal to normal pore pressure zone is noticed in the interval of 7,000 ft. to 9,000 ft. Then, slightly subnormal to somewhat abnormal (overpressure) region is seen from 9,000 ft. to 11,200 ft. Beyond to that depth and down to the top of the reservoir, the overpressure zone was clearly observed. Based on the results, the casing setting depth and the equivalent mud weight were simply determined for the area of study.
Operator dependence of 3-D ultrasound-based computational fluid dynamics for the carotid bifurcation

The association between vascular wall shear stress (WSS) and the local development of atherosclerotic plaque makes estimation of in vivo WSS of considerable interest. Three-dimensional ultrasound (3DUS) combined with computational fluid dynamics (CFD) provides a potentially valuable tool for acquiring subject-specific WSS, but the interoperator and intraoperator variability associated with WSS calculations using this method is not known. Here, the accuracy, reproducibility and operator dependence of 3DUS-based computational fluid dynamics were examined through a phantom and in vivo studies. A carotid phantom was scanned and reconstructed by two operators. In the in vivo study, four operators scanned a healthy subject a total of 11 times, and their scan data were processed by three individuals. The study showed that with some basic training, operators could acquire accurate carotid geometry for flow reconstructions. The variability of measured cross-sectional area and predicted shear stress was 8.17% and 0.193 N/m/sup 2/ respectively for the in vivo study. It was shown that the variability of the examined parameters was more dependent on the scan operators than the image processing operator. The range of variability of geometrical and flow parameters reported here can be used as a reference for future in vivo studies using the 3DUS-based CFD approach.
A Novel Low Power, High Speed 14 Transistor CMOS Full Adder Cell with 50% Improvement in Threshold Loss Problem

Full adders are important components in applications such as digital signal processors (DSP) architectures and microprocessors. In addition to its main task, which is adding two numbers, it participates in many other useful operations such as subtraction, multiplication, division,, address calculation,. etc. In most of these systems the adder lies in the critical path that determines the overall speed of the system. So enhancing the performance of the 1-bit full adder cell (the building block of the adder) is a significant goal.Demands for the low power VLSI have been pushing the development of aggressive design methodologies to reduce the power consumption drastically. To meet the growing demand, we propose a new low power adder cell by sacrificing the MOS Transistor count that reduces the serious threshold loss problem, considerably increases the speed and decreases the power when compared to the static energy recovery full (SERF) adder. So a new improved 14T CMOS l-bit full adder cell is presented in this paper. Results show 50% improvement in threshold loss problem, 45% improvement in speed and considerable power consumption over the SERF adder and other different types of adders with comparable performance.
Representing the Connectivity of Upland Areas to Floodplains and Streams in SWAT+

In recent years, watershed modelers have put increasing emphasis on capturing the interaction of landscape hydrologic processes instead of focusing on streamflow at the watershed outlet alone. Understanding the hydrologic connectivity between landscape elements is important to explain the hydrologic response of a watershed to rainfall events. The Soil and Water Assessment Tool+ (SWAT+) is a new version of SWAT with improved runoff routing capabilities. Subbasins may be divided into landscape units (LSUs), e.g., upland areas and floodplains, and flow can be routed between these LSUs. We ran three scenarios representing different extents of connectivity between uplands, floodplains, and streams. In the first and second scenarios, the ratio of channelized flow from the upland to the stream and sheet flow from the upland to the floodplain was 70/30 and 30/70, respectively, for all upland/floodplain pairs. In the third scenario, the ratio was calculated for each upland/floodplain pair based on the upland/floodplain area ratio. Results indicate differences in streamflow were small, but the relative importance of flow components and upland areas and floodplains as sources of surface runoff changed. Also, the soil moisture in the floodplains was impacted. The third scenario was found to provide more realistic results than the other two. A realistic representation of connectivity in watershed models has important implications for the identification of pollution sources and sinks.
Prognostic Implication of 15-Hydroxyprostaglandin Dehydrogenase Down-Regulation in Patients with Colorectal Cancer

Purpose Prostaglandin (PG) E2 is known to be closely related to cancer progression and is inactivated by 15-hydroxyprostaglandin dehydrogenase (PGDH). 15-PGDH is shown to have tumor suppressor activity and to be down-regulated in various cancers, including colorectal cancer (CRC). Therefore, we evaluated the expression of 15-PGDH and its prognostic effect in patients with CRC. Methods 15-PGDH expression was examined by using immunohistochemistry in 77 patients with CRC. Its prognostic significance was statistically evaluated. Results Negative 15-PGDH expression was noted in 55.8% of the 77 cases of CRC. 15-PGDH expression showed no correlation with any of the various clinicopathologic parameters. The status of lymph node metastasis, tumor-node-metastasis stages, and pre-operative carcinoembryonic antigen levels showed significant prognostic effect. However, univariate analysis revealed down-regulation of 15-PGDH not to be a predictor of poor survival. The 5-year overall survival rate was 71.7% in the group with positive expression of 15-PGDH and 67.1% in the group with negative expression of 15-PGDH, but this difference was not statistically significant (P = 0.751). Conclusion 15-PGDH was down-regulated in 55.8% of the colorectal cancer patients. However, down-regulation of 15-PGDH showed no prognostic value in patients with CRC. Further larger scale or prospective studies are needed to clarify the prognostic effect of 15-PGDH down-regulation in patients with colorectal cancer.
P1D-4 Fast Rotating Single Element Ultrasound Transducer for Image-Guided Thermal

It has been shown that a very deep and selective interstitial thermal therapy can be performed using a rotating flat miniature ultrasound transducer. This heating modality would be significantly improved by implementing imaging and monitoring. The space limitations in interstitial applications require combining imaging and therapy on the same transducer. In conventional endoscopic ultrasound imaging, a miniprobe can be positioned inside the lumen of an organ and fast rotation of a single element transducer enables real time peripheral imaging of the lumen. Based on this idea, we proposed an original therapeutic strategy. Imaging can be interrupted for a short period of time corresponding to an angle Deltaalpha in order to apply high intensity ultrasound for thermal ablation. First, theoretical simulations were conducted. A 1D thermal model of the transducer demonstrated that this operating mode is not critical for the transducer. Simulations using the BioHeat Transfer Equation showed that Deltaalpha=pi/4 induced efficient therapy. An applicator was built in order to test this treatment strategy. The active element consisted in a 2.5 times 7.5 mm2 dual mode single element transducer operating at a frequency of 11 MHz. The applicator was driven in rotation at 7-turns per second pace. Experiments were performed in vitro on porcine liver. Ultrasound images were reconstructed and the size of the -6 dB point spread function at focal distance was 0.55 mm times 0.25 mm. The electronics for performing the therapeutic strategy considered above was set up. Up to 8 millimeters-deep thermal lesions were obtained with Deltaalpha=pi/4 and peak intensity of 110 W/cm 2. This work demonstrated that thermal lesions can be performed with a fast-rotating dual mode transducer. This approach enabled real-time image-guided therapy
Uncertainty analysis of the water balance technique for measuring seepage from animal waste lagoons.

Water balance measurements can be used to estimate seepage rates from animal waste lagoons and earthen storages. This method requires detailed measurements of depth changes and cumulative evaporation during 5- to 10-d periods. Quantifying the uncertainty surrounding the measurements is crucial if data from seepage tests are used to determine if lagoons are meeting engineering specifications and operating within regulatory guidelines. Uncertainty analyses, using a 95% confidence interval, were applied to field data collected during studies of animal waste lagoons in Kansas and Oklahoma. Changes in depth were measured with float-based recorders and evaporation was estimated from meteorological observations. Results showed that rate changes in depth could be measured to within +/-0.28 mm d(-1) or better when wind speeds at the start and end of the test were less than 4 m s(-1). Uncertainty in evaporation was the most significant factor affecting the seepage estimate, and surface temperature and relative humidity were the main sources of imprecision in the evaporation calculations. Evaporation could be estimated to within 10 to 20%, with the largest uncertainty occurring during windy conditions. Uncertainty in the calculated seepage rate increased as evaporation increased. When evaporation rates are low (e.g., <4 mm d(-1)), seepage can be estimated to within +/-0.5 mm d(-1) with 95% confidence. A precision of +/-0.25 mm d(-1) is possible when research-grade instruments are deployed under favorable weather conditions. A measurement duration of 5 d is adequate for most water balance tests. In many cases, precision of the water balance technique will be sufficient in determining if a working lagoon is within regulatory guidelines.
IQ in Early Adulthood, Socioeconomic Position, and Unintentional Injury Mortality by Middle Age: A Cohort Study of More Than 1 Million Swedish Men

The authors evaluated the little-examined association between intelligence (IQ) and injury mortality and, for the first known time, explored the extent to which IQ might explain established socioeconomic inequalities in injury mortality. A nationwide cohort of 1,116,442 Swedish men who underwent IQ testing at about 18 years of age was followed for mortality experience for an average of 22.6 years. In age-adjusted analyses in which IQ scores were classified into 4 groups, relative to the highest scoring category, the hazard ratio in the lowest was elevated for all injury types: poisonings (hazard ratio (HR) = 5.82, 95% confidence interval (CI): 4.25, 7.97), fire (HR = 4.39, 95% CI: 2.51, 7.77), falls (HR = 3.17, 95% CI: 2.19, 4.59), drowning (HR = 3.16, 95% CI: 1.85, 5.39), and road injury (HR = 2.17, 95% CI: 1.91, 2.47). Dose-response effects across the full IQ range were evident (P-trend < 0.001). Control for potential covariates, including socioeconomic position, had little impact on these gradients. When socioeconomic disadvantage—indexed by parental and subject's own occupational social class—was the exposure of interest, IQ explained a sizable portion (19%–86%) of the relation with injury mortality. These findings suggest that IQ may have an important role both in the etiology of injuries and in explaining socioeconomic inequalities in injury mortality.
Radiation-hardened MRAM-based LUT for non-volatile FPGA soft error mitigation with multi-node upset tolerance

In this paper, we have developed a radiation-hardened non-volatile lookup table (LUT) circuit utilizing spin Hall effect (SHE)-magnetic random access memory (MRAM) devices. The design is motivated by modeling the effect of radiation particles striking hybrid complementary metal oxide semiconductor/spin based circuits, and the resistive behavior of SHE-MRAM devices via established and precise physics equations. The models developed are leveraged in the SPICE circuit simulator to verify the functionality of the proposed design. The proposed hardening technique is based on using feedback transistors, as well as increasing the radiation capacity of the sensitive nodes. Simulation results show that our proposed LUT circuit can achieve multiple node upset (MNU) tolerance with more than 38% and 60% power-delay product improvement as well as 26% and 50% reduction in device count compared to the previous energy-efficient radiation-hardened LUT designs. Finally, we have performed a process variation analysis showing that the MNU immunity of our proposed circuit is realized at the cost of increased susceptibility to transistor and MRAM variations compared to an unprotected LUT design.
Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

ABSTRACT The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters.
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. When these indices were first introduced, they were based on fairly simple assumptions about which genes are most highly expressed: the CAI was originally based on the codon composition of a set of only 24 highly expressed genes, and the codon usage on assumptions about which functional classes of genes are highly expressed in fast-growing bacteria. Given the recent advent of genome-wide expression data, we should be able to improve on these assumptions. Here, we measure, in yeast, the degree to which consideration of the current genome-wide expression data sets improves the performance of both numerical indices. Indeed, we find that by changing the parameterization of each model its correlation with actual expression levels can be somewhat improved, although both indices are fairly insensitive to the exact way they are parameterized. This insensitivity indicates a consistent codon bias amongst highly expressed genes. We also attempt direct linear regression of codon composition against genome-wide expression levels (and protein abundance data). This has some similarity with the CAI formalism and yields an alternative model for the prediction of expression levels based on the coding sequences of genes. More information is available at http://bioinfo.mbb. yale.edu/expression/codons.
Reducing the performance impact of instruction cache misses by writing instructions into the reservation stations out-of-order

In conventional processors, each instruction cache fetch brings in a group of instructions. Upon encountering an instruction cache miss, the processor will wait until the instruction cache miss is serviced before continuing to fetch any new instructions. The paper presents a new technique, called out-of-order issue, which allows the processor to temporarily ignore the instructions associated with the instruction cache miss. The processor attempts to fetch the instructions that follow the group of instructions associated with the miss. These instructions are then decoded and written into the processor's reservation stations. Later, after the instruction cache miss has been serviced, the instructions associated with the miss are decoded and written into the reservation stations. (We use the term issue to indicate the act of writing instructions into the reservation stations. With this technique, instructions are not written into the reservation stations in program order. Hence, the term out-of-order issue.) We introduce the concept of out-of-order issue, describe its implementation, and present some initial data showing the performance gains possible with out-of-order issue.
Toward an integrative assessment of open government: Proposing conceptual lenses and practical components

ABSTRACT Open government, as a concept, should be understood through a holistic perspective. It is not enough to provide access to government information without redesigning processes and changing regulations. However, little work has been done to measure the components of open government and provide guidance for implementation. We argue that one way to start filling this gap is through the development of models that integrate concepts, theories, and practical perspectives. However, very few of the existing models attempt to explain the functions and characteristics of open government, which could then provide guidance for its development. This article is based on two main sources in order to propose an integrative open government assessment model: (1) a literature review of previous assessment models and theoretical perspectives to build a richer integrative model that goes beyond websites and (2) the results from a longitudinal research study performed from 2006 to 2012 using a multicomponent model to measure open government websites from a practitioners’ perspective. As a result, this article identifies knowledge gaps and proposes a new evaluation approach to open government based on two sets of components: one from practice and the other one from theory. This model contributes to existing knowledge and helps government organizations to better understand and implement open government initiatives.