gebhart/patrepeval huggingface dataset:
Production of Papillomavirus‐Based Gene Transfer Vectors (2007)

Papillomaviruses are a diverse group of pathogens that infect the skin and mucosal tissues of humans and various animal species. The viral genome is a circular, double-stranded DNA molecule approximately 8-kb in length. The non-enveloped papillomavirus capsid is composed of a virally encoded major coat protein, L1, and a minor coat protein, L2. L1 and L2 co-assemble when expressed in mammalian cells, and can promiscuously encapsidate essentially any <8-kb plasmid present in the cell nucleus. In the last several years, there has been rapid development of techniques for intracellular production of papillomavirus-based gene transfer vectors (also known as pseudoviruses). This unit outlines the production and propagative amplification of papillomaviral vectors. The system represents a highly tractable method for converting pre-existing mammalian expression plasmids into infectious virus stocks. The resulting vectors have utility for in vitro, as well as in vivo gene delivery applications.
Tenascin-C Binds Heparin by Its Fibronectin Type III Domain Five (1995)

Two sites on tenascin mediate interactions with glycosaminoglycan chains of proteoglycans. One is situated on the fibrinogen-like domain, whereas the other lies within the fibronectin type III homology region (Aukhil, I., Joshi, P., Yan, Y.Z., and Erickson, H.P. (1993) J. Biol. Chem. 268, 2542-2553.). We now characterize the latter binding site more closely by means of recombinant protein fragments derived from the type III homology region of tenascin. Using a heparin-Sepharose column, we localize the second heparin binding site to the fifth fibronectin type III domain. This is confirmed in solid phase assays by incubation of fusion proteins with biotin-labeled heparin. In addition, we demonstrate the binding of heparan sulfate and dermatan sulfate to domain five. Molecular modelling of this domain reveals a conserved heparin-binding motif that we propose as the putative binding site. The fact, that different glycosaminoglycans may bind to this domain, implies that different classes of proteoglycans may in vivo compete for the same site.
One-Pot Two-Step Synthesis of Quinoxalinones and Diazepinones via a Tandem Oxidative Amidation-Deprotection-Cyclization Sequence (2013)

This report discloses novel concise syntheses of quinoxalinones and diazepinones via a tandem oxidative amidation–deprotection–cyclization sequence. A selenium dioxide mediated oxidative amidation of arylglyoxals with secondary amines was carried out under microwave irradiation to give the corresponding α-keto amides, followed by an acid-promoted deprotection and cyclization to afford the desired products in moderate to good yields.
What Bugs Live in the Cloud? A Study of 3000+ Issues in Cloud Systems (2014)

We conduct a comprehensive study of development and deployment issues of six popular and important cloud systems (Hadoop MapReduce, HDFS, HBase, Cassandra, ZooKeeper and Flume). From the bug repositories, we review in total 21,399 submitted issues within a three-year period (2011-2014). Among these issues, we perform a deep analysis of 3655 "vital" issues (i.e., real issues affecting deployments) with a set of detailed classifications. We name the product of our one-year study Cloud Bug Study database (CbsDB) [9], with which we derive numerous interesting insights unique to cloud systems. To the best of our knowledge, our work is the largest bug study for cloud systems to date.
Phase I/II clinical trial of the humanized anti-EGF-r monoclonal antibody h-R3 labelled with 99mTc in patients with tumour of epithelial origin (2005)

The results of this study suggest that Tc-h-R3 could be used in patients in a safe and effective way, for the diagnosis of epithelial-derived tumours at the two evaluated dose levels.
An FPGA family optimized for high densities and reduced routing delay (2002)

The Act-2 family of CMOS field-programmable gate arrays (FPGAs) uses an electrically programmable antifuse and novel architectural and circuit features to obtain higher logic densities while increasing speed and routability. Improvements include: two new logic modules, novel I/O and clock driver circuitry, and more flexible and faster routing paths. New addressing circuitry shortens programming time and speeds complete testing for shorts, opens, and stuck-at faults. Fully automatic placement and complete routing are retrained. Special software tools used for architectural exploration and layout generation are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biological Pathways Involved in Tumor Angiogenesis and Bevacizumab Based Anti-Angiogenic Therapy with Special References to Ovarian Cancer (2017)

The creation of new blood vessels from existing ones, which is a mechanism called "angiogenesis", is essential in cancer to supply cancerous growth. Moreover, the development and the progression of the tumor and its metastases are the result of an efficient vascular response. Cancer cells release and activate different angiogenic growth factors and their receptors in the tumor microenvironment to promote the angiogenic process. The most important pro-angiogenic factor is the "Vascular Endothelial Growth Factor" (VEGF) because of its mitogen activity on vascular endothelium. Bevacizumab is a monoclonal antibody that obstructs the binding of circulating vascular endothelial growth factor to its receptors and has been approved for the treatment of primary and recurrent ovarian cancer but also for many other solid tumors.
Pilot assisted channel estimation for OFDM in mobile cellular systems (2002)

The use of pilot symbols for channel estimation introduces overhead and it is thus desirable to keep the number of pilot symbols to a minimum. The number of needed pilot symbols for a desired bit error rate and Doppler frequency is highly dependent on the pilot pattern used in orthogonal frequency division multiplexed, OFDM, systems. Five different pilot patterns are analysed by means of resulting bit error rate, which is derived from channel statistics. Rearrangement of the pilot pattern enables a reduction in the number of needed pilot symbols up to a factor 10, still retaining the same performance. The analysis is general and can be used for performance analysis and design of pilot patterns for any OFDM system.
Scanning (2012)

Surprise is an odd emotion. People like to be surprised — an unexpected visit from a friend, a gift from our spouse, a beautiful spring day. Sometimes people even pay to be surprised — at the fair or the cinema. But surprise is not a good thing at work. Being surprised means that either something that was expected to happen didn’t or something that was not supposed to happen did. It’s just not right even when the surprise is a good thing. At work, one is supposed to know what is going on and what is about to happen all the time — to know and be prepared for everything that occurs. One is not supposed to be surprised at work.
Properties of a Trehalose Phosphate Synthetase from Mycobacterium smegmatis (1971)

Abstract An enzyme system was isolated and partially purified from Mycobacterium smegmatis which catalyzes the synthesis of trehalose-phosphate from glucose 6-phosphate and a number of different glucose sugar nucleotides. Adenosine diphosphate-d-glucose (ADP-Glc), cytidine diphosphate-d-glucose (CDP-Glc), guanosine diphosphate-d-glucose (GDP-Glc), deoxythymidine diphosphate-d-glucose (TDP-Glc), and uridine diphosphate-d-glucose (UDP-Glc) are all able to serve as glucosyl donors in this reaction. However, when the pyrimidine sugar nucleotides (CDP-Glc, TDP-Glc, UDP-Glc) were used as substrates, there was an almost absolute requirement for a high molecular weight polyanion for activity. On the other hand, when the purine sugar nucleotides (ADP-Glc, GDP-Glc) were used as substrates, fairly good enzymatic activity was observed in the absence of polyanion and this activity only increased 2 to 4-fold in the presence of optimum concentrations of polyanion. Various properties of the enzyme system were examined with UDP-Glc and GDP-Glc as substrates. The enzymatic activity with both of these sugar nucleotides appears to reside in the same protein since (a) heat inactivation studies at several different temperatures in the presence or absence of polyanion result in the simultaneous disappearance of both activities, (b) both activities remain together throughout a variety of purification procedures, and (c) the two activities have the same pH optimum and Mg++ concentration and are affected in the same way by other cations. The Km for GDP-Glc was about 1 x 10-3 m in the presence or absence of polyanion, whereas that for UDP-Glc in the presence of optimum concentrations of polyanion was about 4 x 10-5 m. When the concentration of polyanion is lowered (suboptimal), the Km for UDP-Glc is increased. The partially purified enzyme has an almost absolute requirement for a high molecular weight polyanion when pyrimidine glucose nucleotides are used as substrates. Various RNAs, particularly that isolated from M. smegmatis, chondroitin sulfate, and heparin are the best activators of the enzyme whereas various mononucleoside phosphates, salts, and various proteins do not activate the enzyme. Activation of the enzyme by the polyanion is inhibited by high salt concentration as well as by high concentrations of mononucleoside phosphates. The polyanion does not appear to cause activation by protecting the enzyme or substrates from degradation, nor by binding or removal of products or inhibitors. Since the [G-3H]polynucleotide activator isolated from M. smegmatis binds to the enzyme fraction, it may cause a conformational change in the protein, leading to a more active form of the enzyme, and one which is now able to utilize glucose nucleotides with pyrimidine bases.
A new method for label-free imaging of biomolecular interactions (2004)

A new method for producing label-free high-resolution images of biomolecular binding to the surface of a biosensor is demonstrated. The biosensor incorporates a guided mode resonance filter that, when illuminated with white light, is designed to reflect only a narrow band of wavelengths where the reflected wavelength is tuned by the adsorption of biological material onto the sensor surface. In this work, an instrument is used to acquire spatial maps of the resonant reflected wavelength in order to produce images of bound biomolecule patterns as applied by a microarray spotter. The biosensor imaging capability is expected to yield applications in pharmaceutical compound screening, genomics, proteomics, and molecular diagnostics, where there is a need to screen large numbers of biochemical interactions against samples using low volumes of reagents.
Quantitative flow cytometry for the differential diagnosis of leukemic B-cell chronic lymphoproliferative disorders (2000)

We have investigated whether the quantitative flow cytometry is an useful tool to better characterize B-cell chronic lymphoproliferative disorders (CLDs). Peripheral blood samples from 104 patients with leukemic B-cell disorders and 20 healthy donors were analyzed. Directly phycoerythrin-conjugated CD19, CD20, CD22, CD23, CD79b, and CD5 monoclonal antibodies (MoAbs) and QuantiBRITE pre-calibrated beads were used to calculate the number of antigen molecules per cell, expressed as antibody binding capacity (ABC). As compared to normal controls, in chronic lymphocytic leukemias (CLL) all MoAbs tested, with the exception of CD23 and CD5, showed lower ABC levels. In prolymphocytic leukemias (PL), CD5 and CD23 antigens were constantly absent while lower CD19 and CD22 ABC levels were observed. Hairy cell leukemias (HCL) displayed very high levels of CD20 and CD22. Of interest, splenic lymphomas with villous lymphocytes (SLVL) could be discriminated from HCL for higher CD79b and lower CD19 ABC values. Finally, higher CD20 levels were detected in follicular lymphomas (FL), whereas higher CD79b and CD5 levels characterized mantle cell lymphomas (MCL). Seven out of 61 CLL cases were defined as morphologically atypical. When compared with typical forms, lower levels of CD19 and CD23 and higher CD20 and CD22 ABC values were detected. However, we failed to demonstrate quantitative differences between atypical CLL and MCL. Our results suggest that quantitative flow cytometry may be a useful additional tool to better identify some types of B-cell CLDs.
Oxygen-Controlled Three-Dimensional Cultures to Analyze Tumor Angiogenesis (2010)

Tumor angiogenesis is controlled by the integrated action of physicochemical and biological cues; however, the individual contributions of these cues are not well understood. We have designed alginate-based microscale tumor models to define the distinct importance of oxygen concentration, culture dimensionality, and cell-extracellular matrix interactions on the angiogenic capability of oral squamous cell carcinoma, and have verified the relevance of our findings with U87 glioblastoma cells. Our results revealed qualitative differences in the microenvironmental regulation of vascular endothelial growth factor (VEGF) and interleukin-8 (IL-8) secretion in three-dimensional (3D) culture. Specifically, IL-8 secretion was highest under ambient conditions, whereas VEGF secretion was highest in hypoxic cultures. Additionally, 3D integrin engagement by RGD-modified alginate matrices increased IL-8 secretion independently of oxygen, whereas VEGF secretion was only moderately affected by cell-extracellular matrix interactions. Using two-dimensional migration assays and a new 3D tumor angiogenesis model, we demonstrated that the resulting angiogenic signaling promotes tumor angiogenesis by increasing endothelial cell migration and invasion. Collectively, tissue-engineered tumor models improve our understanding of tumor angiogenesis, which may ultimately advance anticancer therapies.
Induction and maintenance of clinical remission by interferon‐β in patients with steroid‐refractory active ulcerative colitis—an open long‐term pilot trial (2002)

Although this open pilot study included only a small number of patients, the high response rate suggests that interferon-beta may be a safe and effective treatment for steroid-refractory active ulcerative colitis.
Productivity Impact of IT Investment in Singapore (1994)

While much empirical research has been done on the âproductivity paradoxâ problem in the United States (for a recent survey, see Brynjolfsson 1993), there has been little comparable research among newly industrializing economies (NIES). The recent work of Kraemer and Dedrick (1993) shows some correlation of XT investment-GDP ratio with GDP growth rate for a cross section of eleven Asia-Pacific economies, but since no attempt is made to control for other influencing factors (e.g., non-IT related investment), such correlations may be spurious. Whether NI&amp; face the productivity paradox therefore remains an open question.
The Roles of Claudin Superfamily Proteins in Paracellular Transport (2001)

The claudin superfamily consists of at least 18 homologous proteins in humans. These proteins are important structural and functional components of tight junctions in paracellular transport. Complexed with two other integral transmembrane proteins, occludin and junctional adhesion molecule, claudins are located in both epithelial and endothelial cells in all tight junction-bearing tissues. Claudins interact directly with tight junction-specific, membrane-associated guanylate kinase homologues, ZO-1, ZO-2, and ZO-3, and indirectly with AF-6 and the myosin-binding molecule cingulin. These protein-protein interactions promote scaffolding of the tight junction transmembrane proteins and provide a link to the actin cytoskeleton for transducing regulatory signals to and from tight junctions. The distinct permeability properties observed in different epithelia and endothelia seemingly result from the restricted tissue expression, variability of the homopolymer and heteropolymer assembly, regulated transcription and translation, and the subcellular localization of claudin family proteins. Defects in claudins are causatively associated with a variety of human diseases, demonstrating that claudins play important roles in human physiology. In conditions where the cell adhesion function contributed by tight junctions is essential, such as in altered paracellular transport, in proliferative diseases, and during morphogenesis, the claudin superfamily of homologous proteins provides the molecular basis for the uniqueness of tight junctions and emerges as a new target for intervention.
Ruthenium: A superior compensator of InP (1998)

The 4d-transition metal ruthenium presents a new dopant to fabricate thermally stable semi-insulating InP layers for both electron and hole injection. The layers are grown by low-pressure metalorganic chemical vapor deposition using tertiarybutylphosphine and trimethylindium as source materials for InP growth. Using bis(η5-2,4-dimethyl-pentadienyl)ruthenium(II) as precursor Ru doping concentrations of the order of 4×1018 cm−3 are achieved, determined by means of secondary ion mass spectroscopy. The Ru diffusion coefficient in InP is determined to DRu(800 °C)⩽1×10−15 cm2/s which is four orders of magnitude smaller than for Fe. Resistivities obtained under electron and hole injection are above 6×107 Ω cm and 5×108 Ω cm, respectively. In deep level transient spectroscopy measurements under electron emission and hole emission, one deep level each with concentrations around 1016 cm−3, is observed.
Automatic PCB inspection systems (1995)

There are more than 50 process steps required to fabricate a printed circuit board (PCB). To ensure quality, human operators simply inspect the work visually against prescribed standards. The decisions made by this labor intensive, and therefore costly, procedure often also involve subjective judgements. Automatic inspection systems remove the subjective aspects and provide fast, quantitative dimensional assessments. Machine vision may answer the manufacturing industry's need to improve product quality and increase productivity. The major limitation of existing inspection systems is that all the algorithms need a special hardware platform to achieve the desired real-time speeds. This makes the systems extremely expensive. Any improvements in speeding up the computation process algorithmically could reduce the cost of these systems drastically. However, they remain a better option than increasingly error prone, and slow manual human inspection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanism of Vascular Relaxation Induced by the Nitric Oxide (NO)/Nucleophile Complexes, a New Class of NO-Based Vasodilators (1993)

Compounds formed by reacting nitric oxide (NO) with various nucleophiles have been shown to dilate aortic segments with a potency that correlates strongly with the amount of NO they release spontaneously in aqueous buffers. We performed experiments aimed at confirming their mechanism of action and using the data to design improvements in their pharmacologic properties. That the vasorelaxant action these agents induce is endothelium-independent was demonstrated by exposure of denuded versus intact aortic segments to the diethylamine/NO complex (DEA/NO); denudation had no significant effect on potency. Similarly, NG-monomethyl-L-arginine, an NO synthase inhibitor, did not affect the action of DEA/NO. However, both the vasorelaxant potency of DEA/NO and the amount of cyclic guanosine monophosphate it induced were significantly diminished by the guanylate cyclase inhibitor, methylene blue. The results support the view that the NO/nucleophile adducts induce vasodilation by spontaneously releasing NO, which then activates guanylate cyclase. This mechanistic conclusion suggests that not only potency but also duration of action, a clinically relevant parameter not studied in the previous investigation, might also be controllable by structural modification. We tested this hypothesis by comparing DEA/NO and the spermine/NO adduct (SPER/NO), whose half-lives (t1/2) are 2.1 and 39 min, respectively, for persistence of their dilatory effects. The response to DEA/NO rapidly peaked (maximum at 5 min) and receded during the 60-min observation period; SPER/NO required 15 min to reach peak relaxation but maintained this level throughout the experiment.(ABSTRACT TRUNCATED AT 250 WORDS)
Solution Structure of the DNA-Binding Domain of a Human Papillomavirus E2 Protein:  Evidence for Flexible DNA-Binding Regions (1996)

The three-dimensional structure of the DNA-binding domain of the E2 protein from human papillomavirus-31 was determined by using multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. A total of 1429 NMR-derived distance and dihedral angle restraints were obtained for each of the 83-residue subunits of this symmetric dimer. The average root mean square deviations of 20 structures calculated using a distance geometry-simulated annealing protocol are 0.59 and 0.90 angstroms for the backbone and all heavy atoms, respectively, for residues 2-83. The structure of the human virus protein free in solution consists of an eight-stranded beta-barrel and two pairs of alpha-helices. Although the overall fold of the protein is similar to the crystal structure of the bovine papillomavirus-1 E2 protein when complexed to DNA, several small but interesting differences were observed between these two structures at the subunit interface. In addition, a beta-hairpin that contacts DNA in the crystal structure of the protein-DNA complex is disordered in the NMR structures, and steady-state 1H-15N heteronuclear NOE measurements indicate that this region is highly mobile in the absence of DNA. The recognition helix also appears to be flexible, as evidenced by fast amide exchange rates. This phenomenon has also been observed for a number of other DNA-binding proteins and may constitute a common theme in protein/DNA recognition.
Supporting per-processor local-allocation buffers using lightweight user-level preemption notification (2005)

One challenge for runtime systems like the Java™ platform that depend on garbage collection is the ability to scale performance with the number of allocating threads. As the number of such threads grows, allocation of memory in the heap becomes a point of contention. To relieve this contention, many collectors allow threads to preallocate blocks of memory from the shared heap. These per-thread local-allocation buffers (LABs) allow threads to allocate most objects without any need for further synchronization. As the number of threads exceeds the number of processors, however, the cost of committing memory to local-allocation buffers becomes a challenge and sophisticated LAB-sizing policies must be employed.To reduce this complexity, we implement support for local-allocation buffers associated with processors instead of threads using multiprocess restartable critical sections (MP-RCSs). MP-RCSs allow threads to manipulate processor-local data safely. To support processor-specific transactions in dynamically generated code, we have developed a novel mechanism for implementing these critical sections that is efficient, allows preemption-notification at known points in a given critical section, and does not require explicit registration of the critical sections. Finally, we analyze the performance of per-processor LABs and show that, for highly threaded applications, this approach performs better than per-thread LABs, and allows for simpler LAB-sizing policies.