gebhart/patrepeval huggingface dataset:
A phase II trial of AZD2171 (cediranib), an oral pan-VEGF receptor tyrosine kinase inhibitor, in patients with recurrent glioblastoma (2007)

2001 Background: AZD2171 (cediranib) is a potent, oral pan-VEGF receptor tyrosine kinase inhibitor with a half-life of 20 hours compatible with once-daily dosing. A primary target of AZD2171, VEGFR2, is expressed on glioblastoma endothelium. We have demonstrated normalization of tumor vessels in recurrent glioblastoma patients treated with daily doses of AZD2171. Normalization has rapid onset, is reversible and is associated with alleviation of brain edema [Cancer Cell 2007; 11: 83]. Methods: In this phase II study of 30 recurrent glioblastoma subjects the primary endpoint was the proportion of patients alive and progression-free at 6 months (APF6). Secondary endpoints include radiographic response proportion; progression-free survival; overall survival and toxicity. At this time we are presenting radiographic response data and toxicity on the first 16 consecutive patients and APF6, PFS and OS on all 30 patients. Complete information will be available on all 30 patients at the time of presentation. Results: Twenty-eight patients have experienced disease progression and two patients remain in follow-up without progression. The primary and secondary endpoints are tabulated below: Only one of the first 16 patients was removed from the study due to toxicity (fatigue). Dose limiting toxicities of hypertension, fatigue and diarrhea were observed in 9/16 patients. There were no intracerebral hemorrhages. AZD2171 alleviated brain edema, a major cause of morbidity in glioblastoma patients, and had a steroid-sparing effect in the first 16 patients enrolled. Blood biomarkers were serially assessed and elevated levels of bFGF, SDF1a and viable circulating endothelial cells correlated with disease progression. Conclusions: AZD2171 has activity in patients with recurrent glioblastoma. Combination studies of AZD2171 with radiation and chemotherapy are planned. [Table: see text] [Table: see text]
Mach-Zehnder-type evanescent wave biosensor in ion-exchanged glass using periodically segmented waveguide (1999)

Integratred optical Mach-Zehnder interferometric bio-sensors have been implemented in planar glass, by using ion-exchange waveguides. To simplify the fabrication of the sensors, periodically segmented waveguide has been used as the sensing arm, thus avoiding the need to open a sensing window over this arm. To evaluate the device performance, we performed two types of measurements. First, we measured the glucose concentration in a solution. The resulting sensitivity was less than 1 g/l, corresponding to less than 10<SUP>-4</SUP> in the cover index, for a sensor with a 1 cm long sensing arm, having a segmentation duty-cycle of (eta) equals 0.5. Second, we measured the thickness sensitivity, with respect to the adsorption of avidin molecules onto the glass substrate. The resulting thickness resolution was about 1 Angstrom. Considering that the avidin concentration in the buffer solution was 2.5 (mu) g/mL, that the full thickness of the avidin layer was 2.5 nm, and that the layer buildup time was 7 min., the corresponding sensitivity for the avidin sensor is about 0.25 nM/hr.
Preventing SQL Injection through Automatic Query Sanitization with ASSIST (2010)

Web applications are becoming an essential part of our everyday lives. Many of our activities are dependent on the functionality and security of these applications. As the scale of these applications grows, injection vulnerabilities such as SQL injection are major security challenges for developers today. This paper presents the technique of automatic query sanitization to automatically remove SQL injection vulnerabilities in code. In our technique, a combination of static analysis and program transformation are used to automatically instrument web applications with sanitization code. We have implemented this technique in a tool named ASSIST (Automatic and Static SQL Injection Sanitization Tool) for protecting Java-based web applications. Our experimental evaluation showed that our technique is effective against SQL injection vulnerabilities and has a low overhead.
Solid-phase peptide synthesis: an overview focused on the preparation of biologically relevant peptides (2014)

Tailor-made design preparation of complex peptide sequence including posttranslational modifications, fluorescent labels, unnatural amino acids are of exceptional value for biological studies of several important diseases. The possibility to obtain these molecules in sufficient amounts in relative short time is thanks to the solid-phase approach.
Synthesis of Novel Azole Antifungals by a Modified Sharpless Asymmetric Dihydroxylation (1994)

An improved synthesis of the azole antifungal building block (Figure), exemplified by a formal synthesis of Sch 45450, is described. Asymmetric induction was achieved by a modified Sharpless dihydroxylation (AD) reaction which generated products with excellent enantiomeric excess.
Positive‐working aqueous base developable photosensitive polybenzoxazole precursor/organoclay nanocomposites (2005)

Abstract Positive‐working aqueous base developable photosensitive polybenzoxazole (PBO) precursor/organoclay nanocomposites have been prepared through the addition of an organoclay to a PBO precursor. The organoclay was formed by a cation exchange reaction between a Na + ‐montmorillonite clay and an ammonium salt of dodecylamine. The PBO precursor used in this study was a polyhydroxyamide that was prepared from a low‐temperature polymerization of 2′2′‐bis(3‐amino‐4‐hydroxyphenyl) hexafluoropropane and 4,4′‐oxydibenzoyl chloride with an inherent viscosity of 0.3 dL/g. The photosensitive resin/clay formulations were prepared from the precursor with 2,3,4‐tris(1‐oxo‐2‐diazonaphthoquinone‐5‐sulfonyloxy)‐benzophenone photosensitive compound and 3–5 wt % organoclay. The PBO precursor/clay was subsequently thermally cured to PBO/clay at 350°C. Both X‐ray diffraction and transmission electron microscope analyses showed that the organoclay was dispersed in the PBO matrix in a nanometer scale. The thermal expansion coefficient of PBO/clay film, which contained 5 wt % organoclay, was decreased 33% compared to the pure PBO film. The PBO/clay nanocomposite films also displayed higher thermal stability, glass transition temperature, and water resistance than the pure PBO film. The photosensitive PBO precursor/clay nanocomposite showed a line/space pattern with a resolution of 5 μm and its sensitivity and contrast were not affected by the organoclay. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 2350–2356, 2005
The Circular Bacteriocins Gassericin A and Circularin A (2004)

Gassericin A, a bacteriocin produced by Lactobacillus gasseri LA39, shows antibacterial activity against a number of Gram-positive food-borne pathogenic bacteria. Circularin A produced by Clostridium beijerinckii ATCC25752 is active against C. tyrobutyricum, a known cheese-spoilage bacterium. Both bacteriocins were purified to homogeneity from culture supernatants by reverse-phase chromatography and the subsequently determined amino acid sequences were used to clone the bacteriocin structural genes. Mature gassericin A and circularin A are class V circular bacteriocins comprised of 58 and 69 amino acid residues, respectively. Both bacteriocins are resistant to several peptidases and proteases, as are other cyclic bacteriocins. Heterologous expression of gassericin A in Escherichia coli was used to produce a non-cyclic mature peptide, which was shown to have a specific activity 173-fold lower than the circular molecule. The minimal region for production and secretion of active circularin A is comprised of five genes, as was deduced by heterologous gene expression in Enterococcus faecalis. Gassericin A and circularin A have limited mutual similarity in their primary sequences. Unlike most bacteriocins, including gassericin A, circularin A has a three-amino-acid-leader sequence.
A Survey of Near-Data Processing Architectures for Neural Networks (2022)

Data-intensive workloads and applications, such as machine learning (ML), are fundamentally limited by traditional computing systems based on the von-Neumann architecture. As data movement operations and energy consumption become key bottlenecks in the design of computing systems, the interest in unconventional approaches such as Near-Data Processing (NDP), machine learning, and especially neural network (NN)-based accelerators has grown significantly. Emerging memory technologies, such as ReRAM and 3D-stacked, are promising for efficiently architecting NDP-based accelerators for NN due to their capabilities to work as both high-density/low-energy storage and in/near-memory computation/search engine. In this paper, we present a survey of techniques for designing NDP architectures for NN. By classifying the techniques based on the memory technology employed, we underscore their similarities and differences. Finally, we discuss open challenges and future perspectives that need to be explored in order to improve and extend the adoption of NDP architectures for future computing platforms. This paper will be valuable for computer architects, chip designers, and researchers in the area of machine learning.
Adversarial Attacks on Neural Networks for Graph Data (2018)

Deep learning models for graphs have achieved strong performance for the task of node classification. Despite their proliferation, currently there is no study of their robustness to adversarial attacks. Yet, in domains where they are likely to be used, e.g. the web, adversaries are common. Can deep learning models for graphs be easily fooled? In this work, we introduce the first study of adversarial attacks on attributed graphs, specifically focusing on models exploiting ideas of graph convolutions. In addition to attacks at test time, we tackle the more challenging class of poisoning/causative attacks, which focus on the training phase of a machine learning model.We generate adversarial perturbations targeting the node's features and the graph structure, thus, taking the dependencies between instances in account. Moreover, we ensure that the perturbations remain unnoticeable by preserving important data characteristics. To cope with the underlying discrete domain we propose an efficient algorithm Nettack exploiting incremental computations. Our experimental study shows that accuracy of node classification significantly drops even when performing only few perturbations. Even more, our attacks are transferable: the learned attacks generalize to other state-of-the-art node classification models and unsupervised approaches, and likewise are successful even when only limited knowledge about the graph is given.
Active planar inverted-F antennas for wireless applications (2003)

We present an electrically small antenna for use with high efficiency power amplifiers for wireless applications. A planar inverted-F antenna design is described that can be optimized as a class-F termination for use as a load at the output of a field effect transistor (FET) for optimum output power and efficiency. An active planar inverted-F antenna is shown to have greater than 50% power-added efficiency at several frequencies between 1 GHz and 2 GHz by scaling the radiating element. These antennas are also shown to provide a copolarized field component in the azimuth plane and a cross-polarized field component in the elevation plane.
Bedtime insulin added to daytime sulfonylureas improves glycemic control in uncontrolled type II diabetes (1993)

A late-night dose of NPH insulin was added to a regimen of daytime sulfonylureas in a group of obese patients with type II diabetes whose hyperglycemia was not controlled with maximal doses of oral hypoglycemic agents. This treatment proved to be beneficial and is a useful alternative to conventional insulin therapy in this group of patients.
비할로겐형 phosphate계 난연제의 합성 및 특성결정 (2014)

난연제 가운데 가장 많이 사용되는 할로겐 함유 난연제는 사용상 환경적인 제한을 받고 있어서 비할로겐타입인인계에 기초한 난연제가 각광을 받고 있다. 난연제는 수지에 가해지는 경우에 흔히 열분해와 기계적 특성저하를 일으킨다. 물성의 열화를 최소화하고 충분한 난연성을 얻기 위한 시도로 새로운 난연제에 대한 연구를 수행하였다. 본 연구에있어서는 diaryl alkyl phosphate esters, aromatic phosphate esters 및 phosphonium nitron 난연제 등 세가지형태의 비할로겐 인계에 기초한 난연제를 합성하여 GC, IR 및 TGA 등으로 합성 및 열적 특성을 확인하였다.
Cell analysis system based on compact disk technology (2002)

We built a cell analysis system based on immunomagnetic cell selection and alignment and analysis of fluorescent signals employing CD-technology that is as good or better than current commercial analyzers. The cell analysis can be performed in whole blood or any other type of cell suspension without extensive sample preparation.
The Application of Management Information System in Internet of Things based on RFID Technology (2013)

Radio Frequency Identification (RFID) is a non-contact automatic identification technology; it is the use of radio frequency signal through space coupling non-contact transmission of information, and through the message reaches the target identification technology. The basic principle of RFID is the use of radio frequency signal and its spatial coupling, transmission characteristics, for still or moving in the identifying items of automatic recognition. RFID has the advantages of high precision, strong ability to adapt to the environment, strong interference resistance, and quick operation. This article elaborated the RFID technology based on management information system in Internet of things and discusses the RFID technology in the management system in the application of convenience, describes the system's entire work flow and management data analysis design. The paper presents the application of management information system in Internet of things based on RFID technology. Copyright © 2013 IFSA.
Grating-based spectral X-ray dark-field imaging for correlation with structural size measures (2020)

X-ray dark-field (XDF) imaging accesses information on the small-angle scattering properties of the sample. With grating interferometry, the measured scattering signal is related to the sample's autocorrelation function, which was previously demonstrated for simple samples, such as mono-dispersed microspheres for which the autocorrelation function is mathematically given. However, in potential clinical applications of XDF imaging, complex microstructures, such as lung parenchyma are under investigation. Their bahaviour in XDF imaging is not yet known and no mathematical description of the autocorrelation function is derived so far. In this work we demonstrate the previously established correlation of the XDF data of complex sample structures with their autocorrelation function to be impractical. Furthermore, we propose an applicable correlation between XDF and the sample's structural parameter on the basis of mean chord length, a medically-approved measure for alveolar structure, known to be affected by structural lung diseases. Our findings reveal a correlation between energy-dependent XDF imaging and the sample's mean chord length. By that, a connection between a medical measure for alveoli and XDF is achieved, which is particularly important regarding potential future XDF lung imaging applications for the assessment of alveoli size in diagnostic lung imaging.
Natural language processing for web document representation (2010)

The World Wide Web has brought us to an era where information is abundantly available and\neasily accessible from all over the world. With important decision-makings becoming more\ndependent on these huge resources, there is a growing need for techniques which is able to\nproduce more comprehensible representations of text documents for users by using Natural\nLanguage Processing (NLP) techniques\nNLP concerns the issues of portraying information in natural (human) language. It can provide\nhuman language-like representations of documents to be further processed for data mining\npurposes.\nThis project aims to study various NLP-based representation methods for web text documents,\nwith the focus on semantic analysis based models, namely the sentence-level semantic analysis\nmodel and the concept-based analysis model. Moreover, an important part of the project is spent\non the design and development of an integrated Semantic Analysis Tool (SAT) based on the\naforementioned models.
Formation and Spectroscopic Manifestation of Silver Clusters on Silver Bromide Surfaces (1998)

AgBr microcrystals that have been treated with reducing agents to form small silver clusters on their surface have been examined with low-temperature optical and optically detected magnetic resonance methods. These investigations have indicated that these treatments produce two closely related Ag clusters that are spectroscopically active. One of the centers manifests itself by low-temperature emission bands at 550 and 640 nm and an absorption band at 442 nm. The other center, which absorbs at 430 nm, acts as a surface hole trap that completely changes the nature of the AgBr donor acceptor recombination. These centers are only observable on crystals with {111} faces. Spectroscopic and theoretical considerations suggest that these spectroscopically prominent centers are silver dimers in two different surface configurations.
Introduction of impermeable actin-staining molecules to mammalian cells by optoporation (2014)

The selective insertion of foreign materials, such as fluorescent markers or plasmids, into living cells has been a challenging problem in cell biology due to the cell membrane's selective permeability. However, it is often necessary that researchers insert such materials into cells for various dynamical and/or drug delivery studies. This problem becomes even more challenging if the study is to be limited to specific cells within a larger population, since other transfection methods, such as viral transfection and lipofection, are not realizable with a high degree of spatial selectivity. Here, we have used a focused femtosecond laser beam to create a small transient hole in the cellular membrane (optoporation) in order to inject nanomolar concentrations of rhodamine phalloidin (an impermeable dye molecule for staining filamentous actin) into targeted living mammalian cells (both HEK and primary cortical neurons). Following optoporation, the dye bound to the intracellular actin network and rise in fluorescence intensity was observed. Theoretical dynamics of the dye's diffusion is discussed, and numerical simulations of diffusion time constants are found to match well with experimental values.
Solid-Phase Synthesis of Symmetrical 5‘,5‘-Dinucleoside Mono-, Di-, Tri-, and Tetraphosphodiesters (2007)

Four classes of phosphitylating reagents were subjected to reactions with aminomethyl polystyrene resin-bound p-acetoxybenzyl alcohol to yield the corresponding polymer-bound mono-, di-, tri-, and tetraphosphitylating reagents. The solid-phase reagents were reacted with unprotected nucleosides (e.g., thymidine, adenosine, 3'-azido-3'-deoxythymidine, cytidine, or inosine) in the presence of 5-(ethylthio)-1H-tetrazole. Polymer-bound nucleosides underwent oxidation with tert-butyl hydroperoxide, deprotection of cyanoethoxy groups with DBU, and the acidic cleavage, respectively, to afford 5',5'-dinucleoside mono-, di-, tri-, and tetraphosphodiesters in 59-78% yield.
Linkage of Genetic Markers on Human Chromosomes 20 and 12 to NIDDM in Caucasian Sib Pairs With a History of Diabetic Nephropathy (1997)

The potential contribution of maturity-onset diabetes of the young (MODY) genes to NIDDM susceptibility in African-American and Caucasian NIDDM-affected sibling pairs with a history of adult-onset diabetic nephropathy has been evaluated. Evidence for linkage to NIDDM was found with polymorphic loci that map to the long arms of human chromosomes 20 and 12 in regions containing the MODY1 and MODY3 genes. Nonparametric analysis of chromosome 20 inheritance data collected with the MODY1-linked marker D20S197 provides evidence for linkage to NIDDM with a P value of 0.005 in Caucasian sib pairs using affected sibpair (ASP) analyses. Non-parametric analysis of chromosome 12 inheritance data collected with the MODY3-linked markers D12S349 and D12S86 provides evidence for linkage to NIDDM with P values of 0.04 and 0.006, respectively, in Caucasian sib pairs using similar analyses. No evidence for linkage of MODY1 and MODY3 markers to NIDDM in African-American sib pairs was observed. In addition, no evidence for linkage to MODY2 (glucokinase-associated MODY) was observed with either study population. Results of multipoint maximum logarithm of odds (LOD) score analysis were consistent with the ASP results. A maximum LOD score of 1.48 was calculated for linkage to MODY1-linked loci and 1.45 to MODY3-linked loci in Caucasian sib pairs. Tabulation of allele sharing in affected sib pairs with D20S197 and D12S349 suggests that affected sibling pairs may inherit susceptibility genes simultaneously from chromosome 20 and chromosome 12. The results suggest that genes contributing to NIDDM in the general Caucasian population are located in the regions containing the MODY1 and MODY3 genes.
Phase-sensitive fiber-optic parametric amplifiers and their applications (2010)

We review some fundamental and practical aspects of fiber-optic parametric amplifiers (FOPAs). In particular, their unique phase-sensitive amplification ability along with the corresponding ultralow noise figure will be discussed. Applications of both phase-insensitive and phase-sensitive FOPAs will also be covered.
On structure and suboptimality in placement (2005)

Regular structures are present in many types of circuits. If this structure can be identified and utilized, performance can be improved dramatically. In this paper, we present a novel placement approach that successfully identifies regularity, and obtains placements that are superior to other "general purpose" methods. This method has been integrated into our Feng Shui 2.6 bisection-based placement tool.On experiments with the PEKO benchmarks, our results are within 32% of optimal for both the large and small suites. The largest example, with 2.1 million cells, can be completed in sixteen hours. The majority of our run time is during detail placement--global placement takes under three hours. The success of our method shows that it can find structure, even when the structure was not expected or intended.As part of this work, we have made a number of observations related to the nature of suboptimality in placement. These observations have shown that some neglected research areas have great potential, while problems that receive considerable attention are essentially adequately solved.
The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amiohydrolase, EC 3.5.1.5) to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme (1999)

Cyanobacteria assigned to the genus Synechococcus are an important component of oligotrophic marine ecosystems, where their growth may be constrained by low availability of fixed nitrogen. Urea appears to be a major nitrogen resource in the sea, but little molecular information exists about its utilization by marine organisms, including Synechococcus. Oligonucleotide primers were used to amplify a conserved fragment of the urease (urea amidohydrolase, EC 3.5.1.5) coding region from cyanobacteria. A 5.7 kbp region of the genome of the unicellular marine cyanobacterium Synechococcus sp. strain WH7805 was then cloned, and genes encoding three urease structural subunits and four urease accessory proteins were sequenced and identified by homology. The WH7805 urease had a predicted subunit composition typical of bacterial ureases, but the organization of the WH7805 urease genes was unique. Biochemical characteristics of the WH7805 urease enzyme were consistent with the predictions of the sequence data. Physiological data and sequence analysis both suggested that the urease operon may be nitrogen-regulated by the ntcA system in WH7805. Inactivation of the large subunit of urease, ureC, prevented WH7805 and Synechococcus WH8102 from growing on urea, demonstrating that the urease genes cloned are essential to the ability of these cyanobacteria to utilize urea as a nitrogen source.