gebhart/patrepeval huggingface dataset:
AF-QCN: Approximate Fairness with Quantized Congestion Notification for Multi-tenanted Data Centers (2010)

Data Center Networks represent the convergence of computing and networking, of data and storage networks, and of packet transport mechanisms in Layers 2 and 3. Congestion control algorithms are a key component of data transport in this type of network. Recently, a Layer 2 congestion management algorithm, called QCN (Quantized Congestion Notification), has been adopted for the IEEE 802.1 Data Center Bridging standard: IEEE 802.1Qau. The QCN algorithm has been designed to be stable, responsive, and simple to implement. However, it does not provide weighted fairness, where the weights can be set by the operator on a per-flow or per-class basis. Such a feature can be very useful in multi-tenanted Cloud Computing and Data Center environments. This paper addresses this issue. Specifically, we develop an algorithm, called AF-QCN (for Approximately Fair QCN), which ensures a faster convergence to fairness than QCN, maintains this fairness at fine-grained time scales, and provides programmable weighted fair bandwidth shares to flows/flow-classes. It combines the QCN algorithm developed by some of the authors of this paper, and the AFD algorithm previously developed by Pan et. al. AF-QCN requires no modifications to a QCN source (Reaction Point) and introduces a very light-weight addition to a QCNcapable switch (Congestion Point). The results obtained through simulations and an FPGA implementation on a 1Gbps platform show that AF-QCN retains the good congestion management performance of QCN while achieving rapid and programmable (approximate) weighted fairness.
Modular Multi-Level Circuits from Immobilized DNA-Based Logic Gates (2007)

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.
Detecting insider threats by monitoring system call activity (2004)

One approach to detecting insider misbehavior is to monitor system call activity and watch for danger signs or unusual behavior. We describe an experimental system designed to test this approach. We tested the system's ability to detect common insider misbehavior by examining file system and process-related system calls. Our results show that this approach can detect many such activities.
Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials (1998)

Tyrosine kinases, first described as oncogenes, have been shown to play a role in normal cellular processes. Aberrations in tyrosine kinase activity lead to disease states. For fifteen years it has been postulated that the inhibition of tyrosine kinases may have therapeutic utility and the design and testing of inhibitors have been major focuses of research and development in both academic institutions and pharmaceutical companies. While early research focused on developing chemical entities that mimic phosphotyrosine, later research has focused on developing competitive adenosine triphosphate (ATP) inhibitors with various levels of selectivity on kinase targets. This review focuses on a discussion of tyrosine kinases thought to be important in disease, including platelet-derived growth factor (PDGF), fibroblast growth factor (FGF), vascular endothelial cell growth factor (VEGF), epidermal growth factor (EGF) receptors, HER-2 and Src. In addition, the classes of inhibitors designed to affect these targets and that have overcome research and development challenges and entered clinical trials are discussed. These include isoxazole, quinazoline, substituted pyrimidines and indolinone compounds, all of which are in clinical trials or near clinical development by SUGEN, Zeneca, Novartis, Pfizer and Parke-Davis. A summary of the chemistry and activity of these agents is provided.
Development of Branching in Living Radical Copolymerization of Vinyl and Divinyl Monomers (2006)

The branching copolymerization of 2-hydroxypropyl methacrylate (HPMA) with either ethylene glycol dimethacrylate (EGDMA) or bisphenol A dimethacrylate (BPDMA) as the branching agent has been carried out using atom transfer radical polymerization (ATRP) in methanol at 20 °C. With EGDMA, soluble branched copolymers were obtained provided that less than one branching agent was incorporated per primary chain: higher levels of EGDMA led to gelation, as expected. Analysis of the changes in the molecular weight and polydispersity of the polymers shows that the formation of highly branched chains occurs only at high (>90%) conversions. Chain coupling is close to the ideal behavior predicted by the Flory−Stockmayer theory, suggesting that all double bonds are equally reactive and that there is no significant cyclization, in contrast to conventional free radical polymerization. This analysis is confirmed by comparison of the consumption of the EGDMA branching agent with predictions from both theory and simulation. With BPDMA as the branching agent, similar results are obtained although branching is slightly less efficient.
Serum interleukin-6 levels correlate to tumor progression and prognosis in metastatic breast carcinoma. (1999)

Serum concentrations of tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1 beta, IL-2 and IL-6 were determined by enzyme-linked immunosorbent assay or chemiluminescent enzyme immunoassay in 46 Japanese patients with metastatic breast cancer. No IL-2 activity was detectable, only two patients had a detectable TNF-alpha level, and 4 had detectable IL-1 beta concentrations. No correlations were found between TNF-alpha and IL-1 beta levels and clinicopathological parameters. Twenty-two patients (48%) showed higher serum IL-6 levels than the cut-off value of 4 pg/ml. Significantly higher IL-6 levels were detected in patients with more than one metastatic site and with dominant metastatic visceral disease than in those with one metastatic site (median, 6.9 vs 1.1 pg/ml, P < 0.0001) or with dominant metastatic bone or soft tissue disease (median, 7.1 vs 2.4, P < 0.05). The patients with liver metastasis and pleural effusion showed significantly higher serum IL-6 levels than those without liver metastases (median, 17.2 vs 2 pg/ml, P = 0.0006) or pleural effusion (median, 12.1 vs 2.1 pg/ml, P = 0.02). A strong correlation was observed between IL-6 levels and C-reactive protein levels (r = 0.47, P = 0.0006). Patients unresponsive to chemo-endocrine therapy showed significantly higher serum IL-6 levels than those who responded to chemo-endocrine therapy (P = 0.0007). Moreover, the patients with high IL-6 levels showed significantly poorer survival than patients with low IL-6 levels. Multivariate analysis revealed that IL-6, as well as disease-free interval, is an independent prognostic factor of metastatic breast cancer. These results suggest that IL-6 levels are elevated and may be an aggressive parameter in patients with metastatic breast cancer. Higher IL-6 serum levels are found to predict a poorer response to chemo-endocrine therapy, and to represent a poorer prognostic predictor in metastatic breast cancer.
Enzyme-Catalyzed O2 Removal System for Electrochemical Analysis under Ambient Air: Application in an Amperometric Nitrate Biosensor (2012)

Electroanalytical procedures are often subjected to oxygen interferences. However, achieving anaerobic conditions in field analytical chemistry is difficult. In this work, novel enzymatic systems were designed to maintain oxygen-free solutions in open, small volume electrochemical cells and implemented under field conditions. The oxygen removal system consists of an oxidase enzyme, an oxidase-specific substrate, and catalase for dismutation of hydrogen peroxide generated in the enzyme catalyzed oxygen removal reaction. Using cyclic voltammetry, three oxidase enzyme/substrate combinations with catalase were analyzed: glucose oxidase with glucose, galactose oxidase with galactose, and pyranose 2-oxidase with glucose. Each system completely removed oxygen for 1 h or more in unstirred open vessels. Reagents, catalysts, reaction intermediates, and products involved in the oxygen reduction reaction were not detected electrochemically. To evaluate the oxygen removal systems in a field sensing device, a model nitrate biosensor based on recombinant eukaryotic nitrate reductase was implemented in commercial screen-printed electrochemical cells with 200 μL volumes. The products of the aldohexose oxidation catalyzed by glucose oxidase and galactose oxidase deactivate nitrate reductase and must be quenched for biosensor applications. For general application, the optimum catalyst is pyranose 2-oxidase since the oxidation product does not interfere with the biorecognition element.
The production of antibody fragments and antibody fusion proteins by yeasts and filamentous fungi (2003)

In this review we will focus on the current status and views concerning the production of antibody fragments and antibody fusion proteins by yeasts and filamentous fungi. We will focus on single-chain antibody fragment production (scFv and VHH) by these lower eukaryotes and the possible applications of these proteins. Also the coupling of fragments to relevant enzymes or other components will be discussed. As an example of the fusion protein strategy, the 'magic bullet' approach for industrial applications, will be highlighted.
Biomodulation of the toxic and nutritional effects of small bowel bacterial overgrowth in end-stage kidney disease using freeze-dried Lactobacillus acidophilus. (1996)

Small bowel bacterial overgrowth (SBBO), well known to occur in end-stage kidney failure, is responsible for producing uremic toxins and contributing to the patient's decreased nutritional well-being. In this study, 8 hemodialysis patients were treated with a course of oral Lactobacillus acidophilus (LBA) in an attempt to alter this SBBO. LBA treatment was effective in lowering 2 compounds generated in vivo. Serum dimethylamine (DMA) levels dropped from 224 +/- 47 to 154 +/- 47 micrograms/dl at the end of LBA treatment (p < 0.001). Nitrosodimethylamine, a carcinogen, levels also decreased significantly from 178 +/- 67 (untreated) to 83 +/- 49 ng/kg (after LBA treatment). Patients nutritional status, assessed as serum albumin, body weight, caloric intake, midarm muscle area (MAMA) and appetite improved modestly, but not significantly. LBA changed small bowel pathobiology by modifying metabolic actions of SBBO, reducing in vivo generation of toxins and carcinogens and promoting nutrition with no adverse side effects.
Specific Lipopolysaccharide Found in Cystic Fibrosis Airway Pseudomonas aeruginosa (1999)

Cystic fibrosis (CF) patients develop chronic airway infections with Pseudomonas aeruginosa (PA). Pseudomonas aeruginosa synthesized lipopolysaccharide (LPS) with a variety of penta- and hexa-acylated lipid A structures under different environmental conditions. CF patient PA synthesized LPS with specific lipid A structures indicating unique recognition of the CF airway environment. CF-specific lipid A forms containing palmitate and aminoarabinose were associated with resistance to cationic antimicrobial peptides and increased inflammatory responses, indicating that they are likely to be involved in airway disease.
<title>Controlling The Groove Depth Of Holographic Gratings</title> (1983)

The diffraction efficiency of a grating depends critically on the groove profile, which in the case of holographic gratings is usually more or less sinusiodal. In order to obtain high efficiency it is thus of great importance to have accurate control of the groove depth during the fabrication process. Usually the groove depth is determined by adjusting the exposure, and then developing the substrate for a fixed time. In this work, a technique is studied where also the development time may be varied in order to obtain the desired groove depth. After interrupting the development, the groove depth of the photo-resist grating, without metallic coating, is determined by measuring the diffraction efficiency in tranmission and comparing it with theoretical efficiencies. Good accuracy is achieved since, in the groove depth range where the efficiency of the final reflection grating has a maximum, the transmission efficiency of the photoresist grating increases rapidly with increasing groove depth. A great advantage is achieved by using a HeNe laser for the efficiency measurements. Since the resist is insensitive to red light, the measurements do not affect the sinusoidal solubility distribution, and the development can be continued to increase the groove depth, if desired.
Neuroprotective Actions of FK506 in Experimental Stroke:In VivoEvidence against an Antiexcitotoxic Mechanism (1997)

The cellular mechanisms underlying the neuroprotective action of the immunosuppressant FK506 in experimental stroke remain uncertain, although in vitro studies have implicated an antiexcitotoxic action involving nitric oxide and calcineurin. The present in vivo study demonstrates that intraperitoneal pretreatment with 1 and 10 mg/kg FK506, doses that reduced the volume of ischemic cortical damage by 56-58%, did not decrease excitotoxic damage induced by quinolinate, NMDA, and AMPA. Similarly, intravenous FK506 did not reduce the volume of striatal quinolinate lesions at a dose (1 mg/kg) that decreased ischemic cortical damage by 63%. The temporal window for FK506 neuroprotection was defined in studies demonstrating efficacy using intravenous administration at 120 min, but not 180 min, after middle cerebral artery occlusion. The noncompetitive NMDA receptor antagonist MK801 reduced both ischemic and excitotoxic damage. Histopathological data concerning striatal quinolinate lesions were replicated in neurochemical experiments. MK801, but not FK506, attenuated the loss of glutamate decarboxylase and choline acetyltransferase activity induced by intrastriatal injection of quinolinate. The contrasting efficacy of FK506 in ischemic and excitotoxic lesion models cannot be explained by drug pharmacokinetics, because brain FK506 content rose rapidly using both treatment protocols and was sustained at a neuroprotective level for 3 d. Although these data indicate that an antiexcitotoxic mechanism is unlikely to mediate the neuroprotective action of FK506 in focal cerebral ischemia, the finding that intravenous cyclosporin A (20 mg/kg) reduced ischemic cortical damage is consistent with the proposed role of calcineurin.
Evolution of phototaxis (2009)

Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present.
A New Model for Prediction of Drug Distribution in Tumor and Normal Tissues: Pharmacokinetics of Temozolomide in Glioma Patients (2008)

Difficulties in direct measurement of drug concentrations in human tissues have hampered the understanding of drug accumulation in tumors and normal tissues. We propose a new system analysis modeling approach to characterize drug distribution in tissues based on human positron emission tomography (PET) data. The PET system analysis method was applied to temozolomide, an important alkylating agent used in the treatment of brain tumors, as part of standard temozolomide treatment regimens in patients. The system analysis technique, embodied in the convolution integral, generated an impulse response function that, when convolved with temozolomide plasma concentration input functions, yielded predicted normal brain and brain tumor temozolomide concentration profiles for different temozolomide dosing regimens (75-200 mg/m(2)/d). Predicted peak concentrations of temozolomide ranged from 2.9 to 6.7 microg/mL in human glioma tumors and from 1.8 to 3.7 microg/mL in normal brain, with the total drug exposure, as indicated by the tissue/plasma area under the curve ratio, being about 1.3 in tumor compared with 0.9 in normal brain. The higher temozolomide exposures in brain tumor relative to normal brain were attributed to breakdown of the blood-brain barrier and possibly secondary to increased intratumoral angiogenesis. Overall, the method is considered a robust tool to analyze and predict tissue drug concentrations to help select the most rational dosing schedules.
Random Sampling: A New Strategy for Marine Acquisition (2010)

Seismic data acquired in marine acquisition is typically undersampled for both receivers and sources, and regularly distributed along parallel lines. The theory of compressive sampling considers that if data is undersampled, the seismic wavefield is better reconstructed if the measurements are randomly distributed. In this paper we investigate how random sampling can be implemented in different types of marine acquisition geometries. 3D finite‐difference modeling data were generated to simulate acquisition geometries with regular and random sampling.
Methods for Detection of Aflatoxins in Agricultural Food Crops (2014)

Aflatoxins are toxic carcinogenic secondary metabolites produced predominantly by two fungal species: Aspergillus flavus and Aspergillus parasiticus . These fungal species are contaminants of foodstuff as well as feeds and are responsible for aflatoxin contamination of these agro products. The toxicity and potency of aflatoxins make them the primary health hazard as well as responsible for losses associated with contaminations of processed foods and feeds. Determination of aflatoxins concentration in food stuff and feeds is thus very important. However, due to their low concentration in foods and feedstuff, analytical methods for detection and quantification of aflatoxins have to be specific, sensitive, and simple to carry out. Several methods including thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), mass spectroscopy, enzyme-linked immune-sorbent assay (ELISA), and electrochemical immunosensor, among others, have been described for detecting and quantifying aflatoxins in foods. Each of these methods has advantages and limitations in aflatoxins analysis. This review critically examines each of the methods used for detection of aflatoxins in foodstuff, highlighting the advantages and limitations of each method. Finally, a way forward for overcoming such obstacles is suggested.
Specialized Video and Physiological Data Coding System for Remote Monitoring (2006)

Patient monitoring via video and physiological data recording can now be performed outside hospitals. This procedure, usually performed in a prolonged manner, generates a considerable amount of data, which calls for efficient ways for archiving and transmission. In this work, we present a specialized system to code the video and the physiological data recorded from a patient, aiming at a reduced bandwidth requirement compared to the conventional methods. We've developed an object-based approach to coding the monitoring video. By applying two change detection methods, we decompose a video frame into three video object planes (VOPs) representing the background, the stationary foreground and the moving foreground. These VOPs are coded at different frame rates, leading to a reduced overall bit rate. For coding the physiological data (using electroencephalogram, i.e. EEG, as an example), we present an effective solution by using a combination of the lifting scheme and the SPIHT algorithm. This approach is featured with a wavelet-quantization algorithm that enables a scalable transmission. The feasibility of this proposed system is demonstrated by our experimental results
Intercellular Adhesion Molecule-1–Deficient Mice Are Resistant Against Renal Injury After Induction of Diabetes (2003)

Diabetic nephropathy is a leading cause of end-stage renal failure. Several mechanisms, including activation of protein kinase C, advanced glycation end products, and overexpression of transforming growth factor (TGF)-beta, are believed to be involved in the pathogenesis of diabetic nephropathy. However, the significance of inflammatory processes in the pathogenesis of diabetic microvascular complications is poorly understood. Accumulation of macrophages and overexpression of leukocyte adhesion molecules and chemokines are prominent in diabetic human kidney tissues. We previously demonstrated that intercellular adhesion molecule (ICAM)-1 mediates macrophage infiltration into the diabetic kidney. In the present study, to investigate the role of ICAM-1 in diabetic nephropathy, we induced diabetes in ICAM-1-deficient (ICAM-1(-/-)) mice and ICAM-1(+/+) mice with streptozotocin and examined the renal pathology over a period of 6 months. The infiltration of macrophages was markedly suppressed in diabetic ICAM-1(-/-) mice compared with that of ICAM-1(+/+) mice. Urinary albumin excretion, glomerular hypertrophy, and mesangial matrix expansion were significantly lower in diabetic ICAM-1(-/-) mice than in diabetic ICAM-1(+/+) mice. Moreover, expressions of TGF-beta and type IV collagen in glomeruli were also suppressed in diabetic ICAM-1(-/-) mice. These results suggest that ICAM-1 is critically involved in the pathogenesis of diabetic nephropathy.
State of the art. Antiviral treatment of HIV infection. (1996)

Antiretroviral drugs have been the mainstay of treatment for HIV infection. New categories of antiretrovirals and recommendations for treatment have emerged as a result of basic science research, new understandings of the infectious process, and data from clinical studies. This article summarizes the currently available drugs for nurses who act as educators and advocates in helping HIV-infected persons explore their treatment options.