gebhart/patrepeval huggingface dataset:
Using CASE tools to improve the security of applications systems (2003)

The authors overview CASE (computer-aided software engineering) tools and reviews security extensions to the system development life cycle. They then focus on requirements analysis to illustrate how security can be included in a CASE environment by adding tools or extending existing ones. These tools can help identify, store, analyze, report, track, and validate requirements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Content-Based Scheduling of Virtual Machines (VMs) in the Cloud (2013)

Organizations of all sizes are shifting their IT infrastructures to the cloud because of its cost efficiency and convenience. Because of the on-demand nature of the Infrastructure as a Service (IaaS) clouds, hundreds of thousands of virtual machines (VMs) may be deployed and terminated in a single large cloud data center each day. In this paper, we propose a content-based scheduling algorithm for the placement of VMs in data centers. We take advantage of the fact that it is possible to find identical disk blocks in different VM disk images with similar operating systems by scheduling VMs with high content similarity on the same hosts. That allows us to reduce the amount of data transferred when deploying a VM on a destination host. In this paper, we first present our study of content similarity between different VMs, based on a large set of VMs with different operating systems that represent the majority of popular operating systems in use today. Our analysis shows that content similarity between VMs with the same operating system and close version numbers (e.g., Ubuntu 12.04 vs. Ubuntu 11.10) can be as high as 60%. We also show that there is close to zero content similarity between VMs with different operating systems. Second, based on the above results, we designed a content-based scheduling algorithm that lowers the network traffic associated with transfer of VM disk images inside data centers. Our experimental results show that the amount of data transfer associated with deployment of VMs and transfer of virtual disk images can be lowered by more than 70%, resulting in significant savings in data center network utilization and congestion.
Aripiprazole in Juvenile Bipolar Disorder Comorbid with Attention-Deficit/Hyperactivity Disorder:An Open Clinical Trial (2007)

Aripiprazole was effective in improving mania and ADHD symptoms, but neither JBD nor ADHD symptom remission was observed in most of the cases. Randomized placebo-controlled trials for JBD and ADHD are needed.
The Use of Magnetic Resonance Imaging to Noninvasively Detect Genetic Signatures in Oligodendroglioma (2008)

This new method of MR image interpretation may have the potential to augment the diagnostic assessment of patients with suspected low-grade glioma.
Endothelium-Dependent Response of the Rabbit Aorta to Femtomolar Concentrations of Angiotensin II (1991)

Thirty-five percent of endothelium-intact rabbit aortic rings tested contracted biphasically to angiotensin II (AII). The threshold concentration in these rings varied, ranging from 10(-16) to 10(-12) M. The remaining 65% contracted monophasically with a range of threshold concentrations of 10(-11)-10(-8) M. All endothelium-denuded rings tested contracted monophasically with a threshold concentration of 10(-10)-10(-8) M. The contractions of both types of rings were inhibited by 1-sar-8-ala-angiotensin II, but not phentolamine or indomethacin, indicating that the contractions were not mediated by secondary agonists such as noradrenaline or arachidonic acid metabolites. Bioassay studies revealed that 10(-16) M AII released an endothelial factor that modulated the action of AII, converting the monophasic response of an endothelium-denuded ring to a biphasic response to AII (10(-16)-10(-7) M). The results demonstrate for the first time the endothelium-dependent response of an artery to femtomolar concentrations of AII and support the existence of arterial angiotensin receptors capable of being saturated by circulating levels of the hormone.
B-aggressive Lymphoma Family Proteins Have Unique Domains That Modulate Transcription and Exhibit Poly(ADP-ribose) Polymerase Activity (2005)

BAL1 (B-aggressive lymphoma 1) was originally identified as a risk-related gene in diffuse large B-cell lymphoma. BAL1 encodes a nuclear protein with N-terminal macro domains and a putative C-terminal poly(ADP-ribose) polymerase (PARP) active site. Macro domains are sequences homologous to the non-histone region of histone macroH2A. Several lines of evidence suggest that these domains may modulate transcription, including a high concentration of histone macroH2A in the inactive X chromosome, direct interference with transcription factor binding in a positioned nucleosome, and structural similarity to DNA binding domains. Poly(ADP-ribosyl)ation is a critical post-translational modification that regulates chromatin configuration and transcription. In this report we describe two additional BAL family members, BAL2 and BAL3, with N-terminal macro domains and putative C-terminal PARP active sites and assess the function of these specific regions in BAL family members. Herein, we demonstrate that BAL macro domains repress transcription when tethered to a promoter. In addition, we show that BAL2 and BAL3, but not BAL1, exhibit PARP activity. In agreement with these data, BAL1 lacks several critical donor and acceptor residues that are conserved in the BAL2 and -3 PARP active sites. Of interest, BAL family members with inactive or functional PARP domains differed in their ability to repress transcription. BAL family members are the only described proteins with both PARP and macro domains, underscoring the potential functional significance of this unique combination.
Genetic Analysis Identifies a Function for the queC ( ybaX ) Gene Product at an Initial Step in the Queuosine Biosynthetic Pathway in Escherichia coli (2005)

Queuosine (Q), one of the most complex modifications occurring at the wobble position of tRNAs with GUN anticodons, is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. Despite these important implications, its biosynthetic pathway has remained unresolved. Earlier, we observed that a naturally occurring strain of Escherichia coli B105 lacked Q modification in the tRNAs. In the present study, we developed a genetic screen to map the defect in E. coli B105 to a single gene, queC (renamed from ybaX), predicted to code for a 231-amino-acid-long protein with a pI of 5.6. As analyzed by mobility of tRNA(Tyr) on acid urea gels and two-dimensional thin-layer chromatography of the modified nucleosides, expression of QueC from a plasmid-borne copy confers a Q+ phenotype to E. coli B105. Further, analyses of tRNA(Tyr) from E. coli JE10651 (queA mutant), its derivative generated by deletion of chromosomal queC (queA deltaqueC), and E. coli JE7325, deficient in converting preQ0 to preQ1, have provided the first genetic evidence for the involvement of QueC at a step leading to production of preQ0, the first known intermediate in the generally accepted pathway that utilizes GTP as the starting molecule. In addition, we discuss the possibilities of collaboration of QueC with other cellular proteins in the production of preQ0.
Laser Direct Synthesis and Patterning of Silver Nano/Microstructures on a Polymer Substrate (2014)

This study presents a novel approach for the rapid fabrication of conductive nano/microscale metal structures on flexible polymer substrate (polyimide). Silver film is simultaneously synthesized and patterned on the polyimide substrate using an advanced continuous wave (CW) laser direct writing technology and a transparent, particle-free reactive silver ion ink. The location and shape of the resulting silver patterns are written by a laser beam from a digitally controlled micromirror array device. The silver patterns fabricated by this laser direct synthesis and patterning (LDSP) process exhibit the remarkably low electrical resistivity of 2.1 μΩ cm, which is compatible to the electrical resistivity of bulk silver. This novel LDSP process requires no vacuum chamber or photomasks, and the steps needed for preparation of the modified reactive silver ink are simple and straightforward. There is none of the complexity and instability associated with the synthesis of the nanoparticles that are encountered for the conventional laser direct writing technology which involves nanoparticle sintering process. This LDSP technology is an advanced method of nano/microscale selective metal patterning on flexible substrates that is fast and environmentally benign and shows potential as a feasible process for the roll-to-roll manufacturing of large area flexible electronic devices.
A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins (1997)

Computer analysis of a conserved domain, BRCT, first described at the carboxyl terminus of the breast cancer protein BRCA1, a p53 binding protein (53BP1), and the yeast cell cycle checkpoint protein RAD9 revealed a large superfamily of domains that occur predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain consists of approximately 95 amino acid residues and occurs as a tandem repeat at the carboxyl terminus of numerous proteins, but has been observed also as a tandem repeat at the amino terminus or as a single copy. The BRCT superfamily presently includes approximately 40 nonorthologous proteins, namely, BRCA1, 53BP1, and RAD9; a protein family that consists of the fission yeast replication checkpoint protein Rad4, the oncoprotein ECT2, the DNA repair protein XRCC1, and yeast DNA polymerase subunit DPB11; DNA binding enzymes such as terminal deoxynucleotidyltransferases, deoxycytidyl transferase involved in DNA repair, and DNA-ligases III and IV; yeast multifunctional transcription factor RAP1; and several uncharacterized gene products. Another previously described domain that is shared by bacterial NAD-dependent DNA-ligases, the large subunits of eukaryotic replication factor C, and poly(ADP-ribose) polymerases appears to be a distinct version of the BRCT domain. The retinoblastoma protein (a universal tumor suppressor) and related proteins may contain a distant relative of the BRCT domain. Despite the functional diversity of all these proteins, participation in DNA damage-responsive checkpoints appears to be a unifying theme. Thus, the BRCT domain is likely to perform critical, yet uncharacterized, functions in the cell cycle control of organisms from bacteria to humans. The carboxyterminal BRCT domain of BRCA1 corresponds precisely to the recently identified minimal transcription activation domain of this protein, indicating one such function.
Structure-activity relationships of dimeric Catharanthus alkaloids. 1. Deacetyl vinblastine amide (vindesine) sulfate (1978)

Exploration of the effects of "minor" structural differences on the antitumor activity and toxicity of dimeric Catharanthus alkaloids resulted in the preparation of deacetylvinblastine amide (vindesine, VDS) from either vinblastine (VLB) or deacetylvinblastine. Adequate amounts of vindesine for biological testing were prepared by preferential hydrazinolysis of the C23-ester in the vindoline moiety of VLB, followed by hydrogenolysis of the resulting deacetylvinblastine hydrazide. Vindesine in its activity spectrum against rodent tumor systems resembles vincristine (VCR) rather than its parent VLB, while its neurotoxic potential appears to be less than that of VCR. The experimental models developed to estimate this potential include in vitro measurements of axoplasmic transport effects in the cat sciatic nerve and the estimation of neuromuscular disturbances in chickens and monkeys by vindesine in comparison with VCR. A radioimmunoassay for VLB, VCR, and VDS, developed by means of deacetylvinblastine acid azide, has been used to study the pharmacokinetics of vindesine in man. The clinical investigation of vindesine is in progress. Deacetylvinblastine, in contrast to earlier reports, showed activity against several murine tumor systems.
New Insights and New Therapies in Vitiligo (2005)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Crystal Structure of the Shank PDZ-Ligand Complex Reveals a Class I PDZ Interaction and a Novel PDZ-PDZ Dimerization (2003)

The Shank/proline-rich synapse-associated protein family of multidomain proteins is known to play an important role in the organization of synaptic multiprotein complexes. For instance, the Shank PDZ domain binds to the C termini of guanylate kinase-associated proteins, which in turn interact with the guanylate kinase domain of postsynaptic density-95 scaffolding proteins. Here we describe the crystal structures of Shank1 PDZ in its peptide free form and in complex with the C-terminal hexapeptide (EAQTRL) of guanylate kinase-associated protein (GKAP1a) determined at 1.8- and 2.25-A resolutions, respectively. The structure shows the typical class I PDZ interaction of PDZ-peptide complex with the consensus sequence -X-(Thr/Ser)-X-Leu. In addition, Asp-634 within the Shank1 PDZ domain recognizes the positively charged Arg at -1 position and hydrogen bonds, and salt bridges between Arg-607 and the side chains of the ligand at -3 and -5 positions contribute further to the recognition of the peptide ligand. Remarkably, whether free or complexed, Shank1 PDZ domains form dimers with a conserved beta B/beta C loop and N-terminal beta A strands, suggesting a novel model of PDZ-PDZ homodimerization. This implies that antiparallel dimerization through the N-terminal beta A strands could be a common configuration among PDZ dimers. Within the dimeric structure, the two-peptide binding sites are arranged so that the N termini of the bound peptide ligands are in close proximity and oriented toward the 2-fold axis of the dimer. This configuration may provide a means of facilitating dimeric organization of PDZ-target assemblies.
The UK D-MAC/packet standard for DBS (1988)

The United Kingdom standard for direct broadcasting by satellite (DBS) is described. A multiplexed analog component (MAC) vision format was devised to overcome the inherent limitations of PAL. The resulting D-MAC/packet system offers improved pictures compared to PAL, together with rugged high-quality digital sound, secure encryption, the flexibility to provide widescreen pictures and, in the future, higher definition. The system is evolutionary in concept, and can be used in conjunction with existing television displays. The single-wire baseband format of D-MAC/packet takes up a bandwidth of approximately 8.5 MHz. It consists of time-compressed components of the luminance and color-difference vision signals, together with a 20.25 Mb/s digital data burst in duobinary form. Frequency modulation is applied for satellite transmission, while for distribution on cable networks, vestigial sideband amplitude modulation can be used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical pulse generation with a frequency shifted feedback laser (1988)

A pulsed ring dye laser is constructed in which the light is shifted in frequency before being fed back into the gain medium. The active medium is R6G dye pumped by a continuous wave argon-ion laser. An acousto-optic modulator is used to shift the frequency of the light inside the ‘‘cavity.’’ With this device, we have generated optical pulses with a 9.6 ps FWHM of the autocorrelation trace and measured periods as short as 0.9 ns.
Confocal microscopy through a fiber-optic imaging bundle (1993)

The concept for a new type of confocal microscope with a fiber-optic imaging bundle is presented, and experimental results are shown to demonstrate the principle. The primary advantage of the system is the flexbility of imaging samples that would otherwise be inaccessible to confocal microscopy.
Bovine anaplasmosis: elimination of the carrier state with injectable long-acting oxytetracycline. (1983)

Long-acting oxytetracycline was administered intramuscularly (20 mg/kg) at 3-day intervals to each of 16 naturally infected Anaplasma marginale carrier beef cows; 8 of the 16 cows were given 3 injections and the other 8 cows were given 4 injections. Four cows seropositive for A marginale served as untreated controls. Rapid card agglutination and complement fixation tests were performed 5 times during the 130-day posttreatment period. All treated cows became negative to both serologic procedures, whereas control cows remained seropositive. Three splenectomized calves that received pooled blood from the treated cows, 120 days following treatment, remained free of anaplasmosis for 60 days following inoculation. One splenectomized calf that received blood from the control cows developed anaplasmosis. It was concluded that long-acting oxytetracycline can be used to eliminate the naturally acquired carrier state of anaplasmosis in cattle.
Normal and radiculopathic cutaneous pain tolerance levels evaluated by heat-beam dolorimetry (1990)

The heat-beam dolorimeter has previously been used to obtain cutaneous pain tolerance measures in normal volunteers and patients with chronic pain. In the present study, normal reference data were collected at two stimulus intensities for 24 volunteers, and the stimulus-effect relationship (decreasing tolerance latency with increasing stimulus intensity) was found significant (p less than 0.001) for all body sites tested. No overall sex differences were found; males behaved slightly more stoically than females, with differences significant only at the T3 site over the breasts. At the second evaluation at the higher stimulus intensity, females exhibited lower pain tolerance (greater pain sensitivity) at the right breast than males (p less than 0.05). No significant lateral asymmetry was found in cutaneous pain tolerance except at the dorsum of the hand: the right hand evinced elevated pain tolerance compared with the left hand in both right- and left-handed subjects. Eight radiculopathic pain patients with clinically involved left L5 nerve roots were evaluated and their responses were compared with the volunteer normal reference data. The radiculopathic group evinced elevated tolerance levels in both the radiculopathic dermatome and noninvolved sites compared with normal individuals (p less than 0.05).
B-5354a, b and c, New Sphingosine Kinase Inhibitors, Produced by a Marine Bacterium. Taxonomy, Fermentation, Isolation, Physico-chemical Properties and Structure Determination. (2000)

In the course of our screening for inhibitors of sphingosine kinase, we found a series of active compounds in a culture broth of a novel marine bacterium, SANK 71896. The structures of the compounds, named B-5354a, b and c, were elucidated by a combination of spectroscopic analyses to be new esters of 4-amino-3-hydroxybenzoic acid with long-chain unsaturated alcohols. B-5354a, b and c inhibit sphingosine kinase activity with IC50 values of 21, 58 and 38 microm, respectively.
Photonic band gaps and defects in two dimensions: Studies of the transmission coefficient (1993)

Using the transfer-matrix technique for the propagation of electromagnetic waves in dielectric structures, we calculate the transmission coefficient versus the frequency of the incident wave for different polarizations in two-dimensional periodic and/or random arrangements of dielectric cylinders. This technique has been applied to cases where the plane-wave method fails or becomes too time consuming, such as when the dielectric constant is frequency dependent or has a nonzero imaginary part, and when defects are present in an otherwise periodic system. For all the cases studied, the results compared well with experiment.
Purification and characterization of glucose oxidase from ligninolytic cultures of Phanerochaete chrysosporium (1986)

Glucose oxidase, an important source of hydrogen peroxide in lignin-degrading cultures of Phanerochaete chrysosporium, was purified to electrophoretic homogeneity by a combination of ion-exchange and molecular sieve chromatography. The enzyme is a flavoprotein with an apparent native molecular weight of 180,000 and a denatured molecular weight of 80,000. This enzyme does not appear to be a glycoprotein. It gives optimal activity with D-glucose, which is stoichiometrically oxidized to D-gluconate. The enzyme has a relatively broad pH optimum of 4 to 5. It is inhibited by Ag+ (10 mM) and o-phthalate (100 mM), but not by Cu2+, NaF, or KCN (each 10 mM).
Rotaxanes as ligands: from molecules to materials (2006)

This tutorial review documents the discovery and application of the supramolecular template (1,2-bis(pyridinium)ethane) subset (24-crown-8) for preparing interlocked molecules. Focus is on the supramolecular chemistry of the pseudorotaxanes formed with various pyridinium axles and crown ether wheels and how this particular class of mechanically linked molecule has been (i) used to construct rudimentary molecular machines such as molecular shuttles and flip switches, (ii) used as ligands for coordination chemistry and (iii) used to create metal-organic framework (MORF) materials.
Engagement: Hard Lessons Learnt (2010)

Communication and transparency, or the lack thereof, can have a significant impact on the fortunes of a mining project.
MaltParser: A Data-Driven Parser-Generator for Dependency Parsing (2006)

We introduce MaltParser, a data-driven parser generator for dependency parsing. Given a treebank in dependency format, MaltParser can be used to induce a parser for the language of the treebank. MaltParser supports several parsing algorithms and learning algorithms, and allows user-defined feature models, consisting of arbitrary combinations of lexical features, part-of-speech features and dependency features. MaltParser is freely available for research and educational purposes and has been evaluated empirically on Swedish, English, Czech, Danish and Bulgarian. 1.