gebhart/patrepeval huggingface dataset:
Attention-Driven Loss for Anomaly Detection in Video Surveillance (2019)

Recent video anomaly detection methods focus on reconstructing or predicting frames. Under this umbrella, the long-standing inter-class data-imbalance problem resorts to the imbalance between foreground and stationary background objects in video anomaly detection and this has been less investigated by existing solutions. Naively optimizing the reconstructing loss yields a biased optimization towards background reconstruction rather than the objects of interest in the foreground. To solve this, we proposed a simple yet effective solution, termed attention-driven loss to alleviate the foreground-background imbalance problem in anomaly detection. Specifically, we compute a single mask map that summarizes the frame evolution of moving foreground regions and suppresses the background in the training video clips. After that, we construct an attention map through the combination of the mask map and background to give different weights to the foreground and background region respectively. The proposed attention-driven loss is independent of backbone networks and can be easily augmented in most existing anomaly detection models. Augmented with attention-driven loss, the model is able to achieve AUC 86.0% on Avenue, 83.9% on Ped1, 96% on Ped2 datasets. Extensive experimental results and ablation studies further validate the effectiveness of our model.
A Survey of BitTorrent Performance (2010)

Since its inception, BitTorrent has proved to be the most popular approach for sharing large files using the peer-to-peer paradigm. BitTorrent introduced several innovative mechanisms such as tit-for-tat (TFT) and rarest first to enable efficient distribution of files among the participating peers. Several studies examining the performance of BitTorrent and its mechanisms have been published in the literature. In this paper, we present a survey of performance studies of BitTorrent from 2003 to 2008. We categorize these studies based on the techniques used, the mechanisms studied and the resulting observations about BitTorrent performance. Many of the performance studies also suggested modifications to BitTorrent's mechanisms to further improve its performance. We also present a survey of the suggested improvements and categorize them into different groups.
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity (2019)

Supplementary data are available at Bioinformatics online.
Analytic Network Process approach for automatic teller machines deployment problem (2015)

Deciding facility location is a hard and sophisticated problem for decision makers as there are many criteria some of which are conflicting and subjective. Determining the location of an automatic teller machine (ATM) for deployment is also a challenging decision for banks which has not been addressed adequately in the literature up to now. Where to locate the automatic teller machines is a strategic and long-term decision therefore making the right decision is important for the banks. In this paper, both qualitative and quantitative criteria that should be considered are defined for ATM deployment problem. The criteria are categorized into main clusters in accordance with their similar characteristics and the interdependencies between them are explained. Analytic Network Process (ANP) methodology is preferred to evaluate the importance levels of these criteria. This study intends to build up a generic framework that can be used afterwards to determine the best locations for off-site ATMs of a bank which cover all customer demand and keep costs at a minimum level in ATM deployment problem. The study also covers the banks which have ATMs or do not have any ATMs and searching for the best locations in order to deploy new ATMs.
Phosphorylation Regulates the Ubiquitin-independent Degradation of Yeast Pah1 Phosphatidate Phosphatase by the 20S Proteasome (2015)

Saccharomyces cerevisiae Pah1 phosphatidate phosphatase, which catalyzes the conversion of phosphatidate to diacylglycerol for triacylglycerol synthesis and simultaneously controls phosphatidate levels for phospholipid synthesis, is subject to the proteasome-mediated degradation in the stationary phase of growth. In this study, we examined the mechanism for its degradation using purified Pah1 and isolated proteasomes. Pah1 expressed in S. cerevisiae or Escherichia coli was not degraded by the 26S proteasome, but by its catalytic 20S core particle, indicating that its degradation is ubiquitin-independent. The degradation of Pah1 by the 20S proteasome was dependent on time and proteasome concentration at the pH optimum of 7.0. The 20S proteasomal degradation was conserved for human lipin 1 phosphatidate phosphatase. The degradation analysis using Pah1 truncations and its fusion with GFP indicated that proteolysis initiates at the N- and C-terminal unfolded regions. The folded region of Pah1, in particular the haloacid dehalogenase-like domain containing the DIDGT catalytic sequence, was resistant to the proteasomal degradation. The structural change of Pah1, as reflected by electrophoretic mobility shift, occurs through its phosphorylation by Pho85-Pho80, and the phosphorylation sites are located within its N- and C-terminal unfolded regions. Phosphorylation of Pah1 by Pho85-Pho80 inhibited its degradation, extending its half-life by ∼2-fold. The dephosphorylation of endogenously phosphorylated Pah1 by the Nem1-Spo7 protein phosphatase, which is highly specific for the sites phosphorylated by Pho85-Pho80, stimulated the 20S proteasomal degradation and reduced its half-life by 2.6-fold. These results indicate that the proteolysis of Pah1 by the 20S proteasome is controlled by its phosphorylation state.
Pain Suppression by Peripheral Nerve Stimulation (1977)

This is a study of the long range effects of pain suppression obtained by electrical stimulation of peripheral nerves. These cases were followed during 12--46 months and evaluated personally and by questionnaires. Selection for surgery was done exclusively on the basis of the results of a preoperative peripheral nerve stimulation test. Of 37 cases observations, 18 were considered significantly relieved; that is, more than 50% of the intensity and/or duration of pain was consistently admitted. The results obtained in the acute preoperative trial could be reproduced indefinitely in some cases for as long as 46 months. Correlation of the results with the disease producing the pain revealed as benefitting for painful syndromes associated with peripheral nerve disorders, amputation, soft tissue injuries (nerves?), and some recurrent lumbar disc surgeries. Sciatic, ulnar and occipital nerve implantations were particularly rewarding. The best and worse results were analyzed. The complications appear to be largely preventable and of no serious consequences. Our analysis suggests that most failures take place within 2 years from implantation. Experience seems to be accumulating showing that a number of patients may receive sustained relief beyond this period.
Sequential Estimation of Demand and Roughness in Water Distribution System (2011)

Pipe roughness and water consumption at a demand node are the most uncertain input variables in a simulation model because they are not typically directly measurable. Instead, information provided from field measurements are used to estimate them indirect way. Parameter estimation is the process of adjusting model parameters so that the simulation model represents the real system adequately by fitting the model output to the field data. To provide more accurate estimates and account for all associated uncertainties, the two variables, i.e., demand and roughness, must be estimated simultaneously. This study proposes a two-step sequential method for dual estimation of demand and roughness coefficient based on a weighted least squares (WLS) scheme using field measurements of pipe flow rates and nodal pressure heads under multiple demand loading conditions. The algorithm is applied to a simple hypothetical system using synthetically generated field data. The proposed two-step sequential model provides accurate estimates with little effort in terms of simulation time.
Absorption and desorption of hydrogen, deuterium, and tritium for Zr–V–Fe getter (1984)

Nonevaporable getters have wide applicability for developing the tritium handling techniques for thermonuclear fusion devices. From this viewpoint, mechanisms of the absorption and desorption of hydrogen isotopes and the isotope effects were investigated for a Zr–V–Fe alloy (St-707) by means of the mass analyzed thermal desorption spectroscopy. It was observed that the absorption rate was proportional to the first power of the pressure, indicating that the rate limiting step is the dissociative adsorption of hydrogen isotopes on the surface. The activation energy was very small, in the order of magnitude of a few tens of calories per mole in a temperature range from −196 to 200 °C. The desorption rate was proportional to the square of the amount of absorption, indicating that the rate limiting step is the associative desorption reaction of hydrogen atoms or ions diffused to the surface from the bulk. The rate constants for hydrogen and deuterium were determined as kd(H2)=(5.3+2.6−1.7)exp[−(28.0±0.7)×103/RT] and kd(D2)=(5.0+2.7−1.7)exp[−(28.6±0.8)×103/RT] in [1/Pa 1 s], respectively, where R is in [cal/mol deg]. With regard to tritium, the rate constant was evaluated as kd(T2)=(5.0+20−4.0)exp[−(29.3±3)×103/RT], however, the frequency factor will have to be corrected by knowing the relative sensitivity factor of the mass spectrometer for tritium (T2).
Scalable and Physical Radar Sensor Simulation for Interacting Digital Twins (2020)

Automation, artificial intelligence and sensor-enabled applications are part of everyday life comprising technical systems that utilize environment-perceiving sensors. Here, rough environments often require robust sensor technologies such as radar, coupled with application-specific software evaluating the measured data. The rising complexity of underlying sensor systems (hard- and software) and complex physical interactions with dynamic environments require development-related validations that use virtual methods primarily focusing on close-to-reality sensor simulation. To allow for a wide range of applications, we propose the use of reusable building blocks that generically model and mimic the physical structure from the real world. This includes the whole path between sensor and 3D environment with respect to sensor-intrinsic characteristics as well as environmental influences such as rain. At the same time, computational scalability of each building block allows physical simulations generating reliable sensor data even in real-time applications. As a result, Digital Twins of relevant components, systems and environments are no longer acting on their own but interacting within Virtual Testbeds allowing for virtual validation of radar-based applications with respect to the operational environment.
3-Phosphoinositide-Dependent Protein Kinase-1/Akt Signaling Represents a Major Cyclooxygenase-2-Independent Target for Celecoxib in Prostate Cancer Cells (2004)

Regarding the involvement of cyclooxygenase-2 (COX-2)-independent pathways in celecoxib-mediated antineoplastic effects, the following two issues remain outstanding: identity of the non-COX-2 targets and relative contributions of COX-2-dependent versus -independent mechanisms. We use a close celecoxib analog deficient in COX-2-inhibitory activity, DMC (4-[5-(2,5-dimethylphenyl)-3(trifluoromethyl)-1H-pyrazol-1-yl]benzene-sulfonamide), to examine the premise that Akt signaling represents a major non-COX-2 target. Celecoxib and DMC block Akt activation in PC-3 cells through the inhibition of phosphoinositide-dependent kinase-1 (PDK-1) with IC(50) of 48 and 38 micro M, respectively. The consequent effect on Akt activation is more pronounced (IC(50) values of 28 and 20 micro M, respectively), which might be attributed to the concomitant dephosphorylation by protein phosphatase 2A. In serum-supplemented medium, celecoxib and DMC cause G(1) arrest, and at higher concentrations, they induce apoptosis with relative potency comparable with that in blocking Akt activation. Moreover, the effect of daily oral celecoxib and DMC at 100 and 200 mg/kg on established PC-3 xenograft tumors is assessed. Celecoxib at both doses and DMC at 100 mg/kg had marginal impacts. However, a correlation exists between the in vitro potency of DMC and its ability at 200 mg/kg to inhibit xenograft tumor growth through the inhibition of Akt activation. Analysis of the tumor samples indicates that a differential reduction in the phospho-Akt/Akt ratio was noted in celecoxib- and DMC-treated groups vis-à-vis the control group. Together, these data underscore the role of 3-phosphoinositide-dependent protein kinase-1/Akt signaling in celecoxib-mediated in vitro antiproliferative effects in prostate cancer cells.
High-Pressure Organic Chemistry. 19. High-Pressure-Promoted, Silica Gel-Catalyzed Reaction of Epoxides with Nitrogen Heterocycles<sup>1</sup><sup>,</sup> (1996)

The reaction of epoxides with nitrogen heterocycles such as indoles, pyrroles, imidazoles, and pyrazoles was studied under both high-pressure and silica gel-catalyzed conditions. Whereas it has been reported that the treatment of indole with styrene oxide at 10 kbar and 42 °C for 24 h gave 2-(3-indolyl)-2-phenylethanol in 56% yield, the same compound was obtained in 88% yield when the reaction was conducted on silica gel at rt for 1 week. Similarly, efficient reaction of epoxides with pyrroles, imidazoles, and pyrazoles was achieved. In terms of stereochemical features, the epoxide ring opening reaction of (R)-(+)-styrene oxide with indole was found to proceed stereoselectively in an SN2 fashion at the benzyl carbon, in either case.
Gm3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. (1988)

In a sample of 4,920 Native Americans of the Pima and Papago tribes, there is a very strong negative association between the Gm haplotype Gm3;5,13,14 and type 2--or non-insulin-dependent--diabetes mellitus (prevalence ratio = 0.27, 95% confidence interval 0.18-0.40). One might conclude from this observation that the absence of this haplotype--or the presence of a closely linked gene--is a causal risk factor for the disease. It is shown that Gm3;5,13,14 is a marker for Caucasian admixture, and it is most likely the presence of Caucasian alleles and the concomitant decrease of Indian alleles that lowers the risk for diabetes, rather than the direct action of the haplotype or of a closely linked locus. This study demonstrates both the potential confounding effect of admixture on the interpretation of disease association studies and the importance of considering genetic admixture (or excluding individuals with genetic admixture) in studies of genetic markers of disease. The relationship between this admixture marker and the prevalence of diabetes also suggests a strong genetic component in the susceptibility to type 2 diabetes in Pima and Papago Indians.
Adenovirus-mediated gene transfer of endostatin <i>in vivo</i> results in high level of transgene expression and inhibition of tumor growth and metastases (2000)

Inhibition of angiogenesis has been shown to be an effective strategy in cancer therapy in mice. However, its widespread application has been hampered by difficulties in the large-scale production of the antiangiogenic proteins. This limitation may be resolved by in vivo delivery and expression of the antiangiogenic genes. We have constructed a recombinant adenovirus that expresses murine endostatin that is biologically active both in vitro, as determined in endothelial cell proliferation assays, and in vivo, by suppression of angiogenesis induced by vascular endothelial growth factor 165. Persistent high serum levels of endostatin (605-1740 ng/ml; mean, 936 ng/ml) were achieved after systemic administration of the vector to nude mice, which resulted in significant reduction of the growth rates and the volumes of JC breast carcinoma and Lewis lung carcinoma (P < 0.001 and P < 0.05, respectively). In addition, the endostatin vector treatment completely prevented the formation of pulmonary micrometastases in Lewis lung carcinoma (P = 0.0001). Immunohistochemical staining of the tumors demonstrated a decreased number of blood vessels in the treatment group versus the controls. In conclusion, the present study clearly demonstrates the potential of vector-mediated antiangiogenic gene therapy as a component in cancer therapy.
Insight into the Balancing Effect of Active Cu Species for Hydrogenation of Carbon–Oxygen Bonds (2015)

Hydrogenation of carbon–oxygen (C–O) bonds plays a significant role in organic synthesis. Cu-based catalysts have been extensively investigated because of their high selectivity in C–O hydrogenation. However, no consensus has been reached on the precise roles of Cu0 and Cu+ species for C–O hydrogenation reactions. Here we resolve this long-term dispute with a series of highly comparable Cu/SiO2 catalysts. All catalysts represent the full-range distribution of the Cu species and have similar general morphologies, which are detected and mutually corroborated by multiple characterizations. The results demonstrate that, when the accessible metallic Cu surface area is below a certain value, the catalytic activity of hydrogenation linearly increases with increasing Cu0 surface area, whereas it is primarily affected by the Cu+ surface area. Furthermore, the balancing effect of these two active Cu sites on enhancing the catalytic performance is demonstrated: the Cu+ sites adsorb the methoxy and acyl species, while the Cu0 facilitates the H2 decomposition. This insight into the precise roles of active species can lead to new possibilities in the rational design of catalysts for hydrogenation of C–O bonds.
Release of soluble pilin antigen coupled with gene conversion in Neisseria gonorrhoeae. (1987)

Gene conversion appears to be the frequent mechanism in Neisseria gonorrhoeae that leads to an altered expression of pilin, the subunit component of the pili. In this process segments of variable sequence information, the minicassettes, are transferred from silent storage loci into an expression locus. As a putative consequence of the rearrangement in the pilE gene, gonococci can enter a different phase of pilin production. Although the removal of a 7-amino acid leader peptide results in the production of typical P+ pilin used to form pili, the loss of an additional 39 amino acids yields S-pilin, a soluble form of pilin that is efficiently secreted into the extracellular environment. Both pilin types can coexist in an apparently homogeneous culture. Ps cells usually are piliated, although less extensively with regard to the length and the number of the pili when compared with P+ cells. Ps cells form T3/T4-type colonies also typical of nonpiliated cells (P-). The observations further suggest that the classical nonsecretory P- phenotype is not generated as a rule by precise gene conversion but rather by genetic changes that cause the production of an over-length pilin (L-pilin).
A Highly Productive Implementation of an Out-of-Order Processor Generator (2017)

General-purpose serial-thread performance gains have become more difficult for industry to realize due to the slowing down of process improvements. In this new regime of poor process scaling, continued performance improvement relies on a number of small-scale micro- architectural enhancements. However, software simulator-based models, which computer architecture research has largely relied upon, may not be well-suited for evaluating ideas at the necessary fidelity.To facilitate architecture research during this fallow period of Moore’s Law, we propose using processor simulators built from synthesizable processor designs. This thesis describes the design of a synthesizable, industry-competitive processor built on recent advancements in open-source hardware: we leverage the new open-source RISC-V instruction set architecture, the new Chisel hardware construction language, and the Rocket-chip processor generator.Our processor generator is called BOOM, and it designed for use in education, research, and industry. Like most contemporary high-performance cores, BOOM is superscalar (able to execute multiple instructions per cycle) and out-of-order (able to execute instructions as their dependencies are resolved and not restricted to their program order).The BOOM generator was implemented using the Chisel hardware construction language, allowing for the rapid implementation of parameterized designs. The Chisel description generates synthesizable implementations of BOOM that can target both FPGAs and ASIC tool-flows. The BOOM effort culminated in a test chip that was fabricated in the TSMC 28 nm HPM process (high performance mobile) using the foundry-provided standard-cell library and memory compiler.This thesis highlights two aspects of the BOOM design: its industry-competitive branch prediction and its configurable execution datapath. The remainder of the thesis discusses the BOOM tape-out, which was performed by two graduate students and demonstrated the ability to quickly adapt the design to the physical design issues that arose.
Chemical modification of amino groups in cardiotoxin III from Taiwan cobra Naja naja atra) venom. (1993)

Cardiotoxin III (CTX III), a major cardiotoxin analogue isolated from the Taiwan cobra (Naja naja atra) venom was modified, either with trinitrobenzene sulfonate (TNBS) or 4-chloro-3,5-dinitrobenzoate (CDNB). Under the conditions of limited reagent availability, three mono-TNP derivatives modified at Lys-5, 12, or 44, and three mono-CDNP derivatives at Lys-12, 23, or 44 were isolated, respectively. The biological activities of CTX III were more or less affected after each of these reactive amino groups were modified. In particular, the hemolytic activity to human erythrocytes and cytotoxicity on NS-1 cells of CTX III decreased to 31% and 50%, respectively, when Lys-12 was trinitrophenylated. More pronounced alteration in these activities was observed as this amino group was carboxydinitrophenylated. A good correlation between the hemolytic activity and cytotoxicity was found. These results indicate that epsilon-amino group at Lys-12 is most closely related to the hemolytic and cytotoxic activities of CTX III. The antigenicity of modified derivatives still remained intact as measured by ELISA.
The Benefit of Subcutaneous Glucagon During Closed-Loop Glycemic Control in Rats With Type 1 Diabetes (2008)

Because of its prolonged action, subcutaneously administered insulin has a potential for overcorrection hypoglycemia during closed-loop glucose control. For this reason, we hypothesized that subcutaneous glucagon, whose action is faster, could lessen the risk for hypoglycemia during closed-loop control. We therefore compared insulin alone versus insulin plus glucagon in diabetic rats in a controlled closed-loop study. Both hormones were delivered by algorithms based on proportional error, derivative error, and the glucose history. Based on this algorithm, glucagon was delivered when glucose was declining and approaching a hypoglycemic level. The delivery of glucagon was largely reciprocal with the delivery of insulin. With the addition of glucagon, there was less hypoglycemia at the glucose nadir, less hyperglycemia later in the study, and lower absolute error values during these periods. We also found that for 7 days after glucagon reconstitution, commercially available glucagon retained its original ability to quickly raise glucose level. We conclude that when subcutaneous insulin delivery is accompanied by subcutaneous glucagon, glycemic control during closed-loop treatment is improved. Since its action is faster than that of insulin, glucagon may prove useful during closed-loop diabetes control.