gebhart/patrepeval huggingface dataset:
A quantitative analysis to unveil specific binding proteins for bioactive compounds (2012)

The mechanisms of the action of bioactive compounds discovered via 'black box' assays using phenotypic indicators generally remain unknown, with the major challenges being the identification of target proteins. In this study, we aimed to develop an efficient methodology to unveil target proteins that are rarely characterised. Proof-of-concept experiments were performed using N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), a well-known calmodulin (CaM) antagonist, as a bait compound. The results showed that in our methodology CaM was identified as a W-7-specific binding protein in the cytosolic fraction of a rat brain extract, whereas other proteins acquired in the same experiment were recognised as non-specific binding proteins. The binding affinity of CaM to W-7 is not very high (dissociation constant: 1.6 × 10(-5) M), showing that the recognition specificity is applicable to compounds with very low binding affinities.
Dynamic changes of NuMA during the cell cycle and possible appearance of a truncated form of NuMA during apoptosis (1996)

We have demonstrated that dynamic redistribution of nuclear-mitotic apparatus (NuMA) protein in the cell cycle is correlated temporally and spatially with its biochemical modifications. In interphase, NuMA behaves solely as a 220 kDa nuclear matrix-associated protein. After initiation of DNA condensation during mitosis, NuMA is phosphorylated by Cdc2 kinase into a 240 kDa form which is transported quickly to the centrosomal region. Once cells have passed the metaphase-anaphase transition, the 240 kDa form of NuMA either becomes a 180 kDa truncated form which is fated to be degraded completely before mitotic exit, or returns to the 220 kDa form that relocates to the daughter nuclei and remains throughout interphase. Apparently, a proteolytic enzyme is activated during the late stages of mitosis. After induction of a 180 kDa form of NuMA in interphase HeLa cells by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, nuclear apoptotic phenomena including chromatin condensation, DNA fragmentation, and micronucleation were observed. However, the same treatment did not induce apoptosis in mitotic phase-arrested HeLa cells. The 180 kDa form of NuMA was demonstrated to be a truncated product, at least lacking the tail domain. When HL60 cells were stimulated by diverse apoptosis inducers such as camptothecin, staurosporine, cycloheximide, and A23187, the extent of NuMA cleavage to produce a 180 kDa product was comparable with the degree of oligonucleosomal laddering. NuMA cleavage is likely to be a consequence of the onset of apoptosis. The intact 220 kDa NuMA functions in interphase cells to retain the nuclear structural integrity. Additionally, NuMA appears to act as a nuclear structural target for a death protease during apoptosis.
Gradient waveform design for tensor-valued encoding in diffusion MRI (2020)

Diffusion encoding along multiple spatial directions per signal acquisition can be described in terms of a b-tensor. The benefit of tensor-valued diffusion encoding is that it unlocks the 'shape of the b-tensor' as a new encoding dimension. By modulating the b-tensor shape, we can control the sensitivity to microscopic diffusion anisotropy which can be used as a contrast mechanism; a feature that is inaccessible by conventional diffusion encoding. Since imaging methods based on tensor-valued diffusion encoding are finding an increasing number of applications we are prompted to highlight the challenge of designing the optimal gradient waveforms for any given application. In this review, we first establish the basic design objectives in creating field gradient waveforms for tensor-valued diffusion MRI. We also survey additional design considerations related to limitations imposed by hardware and physiology, potential confounding effects that cannot be captured by the b-tensor, and artifacts related to the diffusion encoding waveform. Throughout, we discuss the expected compromises and tradeoffs with an aim to establish a more complete understanding of gradient waveform design and its impact on accurate measurements and interpretations of data.
Extending the test template framework for specification-based testing of interactive systems (1999)

. In this paper we introduce a framework for specificationbased testing of interactive systems. Interactive systems can be analysed and developed in terms of functionality, presentation and behaviour. Testing information for interactive systems can be derived from formal specifications of these aspects. The paper uses the Multi-modal Airline Travel Information System (MATIS) specification of Duke and Harrison which provides a partial specification for each aspect. We derive testing information from the specifications of functionality and behaviour, and we extend the Test Template Framework to encompass behavioural testing information. 1 Introduction An interactive system is one in which &quot;each user entry causes a response from or action by the system&quot; [IEEE, 1990]. Interaction is a significant component of contemporary software systems and graphical user interfaces are now almost universal. Interactive systems can be viewed as conceptually and architecturally composed of func...
Obstructive nephropathy in the rat: possible roles for the renin-angiotensin system, prostaglandins, and thromboxanes in postobstructive renal function. (1980)

Relief of unilateral ureteral obstruction (UUO) of 24 h duration in rats is followed by severe renal vasoconstriction in the postobstructive kidney (POK). The present study examined possible roles of renal prostaglandins (PG) and thromboxanes (TX), as well as the renin-angiotensin system, in this vasoconstriction. Administration of the cyclooxygenase inhibitor indomethacin, which blocks both PG and TX production, failed to improve POK hemodynamics in UUO rats. To explore the possible role of the TX compounds, which include the potent vasoconstrictor thromboxane A2 (TXA2), UUO rats were infused with imidazole, an agent that blocks synthesis of TX, but not of PG. Imidiazole led to two- to threefold increases in the clearance of both inulin and rho-aminohippuric acid by the POK. This effect of imidazole was abolished by indomethacin, suggesting that the amelioration of POK vasoconstriction by imidazole was a result of inhibition of vasoconstrictor TX synthesis (e.g. TXA2), with PG vasodilators (e.g. PGE2 or PG12) still active. Urea, infused in a solution whose osmolality and volume were identical to the imidazole infusion, failed to improve hemodynamics in the POK, making it unlikely that nonspecific effects of volume expansion or osmotic diuresis mediated the beneficial effect of imidazole. Further studies examined the possible role of the renin-angiotensin systems in the vasoconstriction of the POK. UUO rats infused with the angiotensin II antagonist, Saralasin, exhibited no significant improvement in POK function, a finding that might be at least partly attributable to agonist/vasoconstrictor properties of Saralasin. In other experiments, treatment of UUO rats with the angiotensin-converting enzyme blocker SQ 14225 (Captopril), in order to inhibit angiotensin II formation, led to at least twofold increases in the clearance of both inulin and rho-aminohippuric acid in the POK. It is unlikely that Captopril exerted this beneficial effect by potentiating the vasodilator kinins, because the effect was not diminished by administration of either carboxypeptidase B (which destroys the kinins) or Trasylol (which blocks kinin synthesis). Thus, these results suggest that both angiotensin II, as well as metabolites of the PG-TX system, may be important determinants of postobstructive renal hemodynamics in the rat.
More Robust Hashing: Cuckoo Hashing with a Stash (2009)

Cuckoo hashing holds great potential as a high-performance hashing scheme for real applications. Up to this point, the greatest drawback of cuckoo hashing appears to be that there is a polynomially small but practically significant probability that a failure will occur during the insertion of an item, requiring an expensive rehashing of all items in the table. In this paper, we show that this failure probability can be dramatically reduced by the addition of a very small constant-sized stash. We demonstrate both analytically and through simulations that stashes of size equivalent to only three or four items yield tremendous improvements, enhancing cuckoo hashing's practical viability in both hardware and software. Our analysis naturally extends previous analyses of multiple cuckoo hashing variants, and the approach may prove useful in further related schemes.
Permeability, Pore Pressure, and Leakoff-Type Distributions in Rocky Mountain Basins (2005)

Summary The permeability, pore pressure, and leakoff type interpreted from more than 1,200 diagnostic fracture-injection/falloff tests were collected in a database and statistically evaluated for four Rocky Mountain basins. The statistical analysis includes the range of observed permeability and pore pressure and the fracture leakoff type distribution. The analysis reveals that pressure-dependent leakoff, fracture-tip extension during shut-in, and fracture-height recession during shut-in are the most common leakoff types. Overall, pressure-dependent leakoff, which can be indicative of highly productive fractured reservoirs, is the most common leakoff type in all Rocky Mountain basins. The analysis also shows orders-of-magnitude variation in gas permeability within all basins, with observed gas permeability ranging from less than 0.001 to greater than 0.10 md.
Advanced Interconnect Design for High Data Rate Perpendicular Magnetic Recording (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> For present write channel current waveforms, a bandwidth efficiency of 1/2 bps/Hz is shown to be achievable which is 1/4 that of the read channel bandwidth efficiency. Further, with an improved write channel current waveform, the writer bandwidth requirement can be reduced by 1/2 to enable a bandwidth efficiency of 1 bps/Hz. </para>
Neuropeptide FF receptors in rat brain: A quantitative light-microscopic autoradiographic study using [125I][D.Tyr1, (NMe)Phe3]NPFF (1996)

The anatomical localization of neuropeptide FF receptors was examined by in vitro autoradiography techniques in rat brain sections by using [125I][D.Tyr1, (NMe)Phe3]NPFF. The specific binding of [125I][D.Tyr1, (NMe)Phe3]NPFF reached 90% of the total binding at 0.05 nM in rat spinal cord sections. Up to 40% of the specific binding of[125I][D.Tyr1, (NMe)Phe3]NPFF to rat spinal cord sections was still detectable following fixation with glutaraldehyde. Afterwards, the distribution of NPFF receptors was studied by light microscopy and their densities by microdensitometry with an image analysis system. In the light microscope, [125I][D.Tyr1, (NMe)Phe3]NPFF labelling appeared more or less uniformly distributed over nerve-cell bodies and surrounding neuropil. High concentrations of binding sites were detected in the presubiculum, parafascicular thalamic nucleus, gracile nucleus, spinal trigeminal tract nucleus, and a number of brainstem nuclei, with virtually no labelling in the cerebellum. In several areas a rostrocaudal gradient of sites concentration was observed. Neuropeptide FF receptors are well-placed to control incoming sensory and autonomic information processing. In contrast, the more recently developed areas of the forebrain possessed low density of sites. The distribution of [125I][D.Tyr1, (NMe)Phe3]NPFF binding sites should suggest anatomical substrates for the actions of neuropeptide FF.
Biological Control of Aflatoxin Contamination of Crops (2004)

Aflatoxin contamination of crops compromises the safety of food and feed supplies and causes significant economic losses each year. Of the many research approaches being studied to reduce and, ultimately, eliminate aflatoxin contamination, biological control is one of the more promising, particularly for the near‐term. Numerous organisms have been tested for biological control of aflatoxin contamination including bacteria, yeasts, and nontoxigenic strains of the causal organisms, Aspergillus flavus and A. parasiticus. Most of the field successes to date have been achieved by applying certain nontoxigenic strains of A. flavus and A. parasiticus to soil of susceptible crops, such as peanuts, cotton, and corn. The applied strains occupy the same niche as the naturally occurring toxigenic strains and competitively exclude them when crops are susceptible to infection. Various formulations have been used to apply the nontoxigenic strains to soil, but the most effective methods have been to combine the desired strain with a carrier/substrate, such as a small grain. This was done either by minimally growing the desired strain on sterilized grain or by coating the surface of the grain with conidia of the strain. After application to the field and uptake of moisture, the fungus completely colonizes the grain, and abundant sporulation provides inoculum levels sufficient to achieve a competitive advantage for the nontoxigenic strain. In several years of field studies, particularly with peanuts and cotton, significant reductions in aflatoxin contamination in the range of 70–90% have been achieved consistently. Two separate products have recently received EPA registration as biopesticides to control aflatoxin contamination in cotton (AF36) and peanuts (afla‐guard®).
A framework to enforce access control over data streams (2010)

Although access control is currently a key component of any computational system, it is only recently that mechanisms to guard against unauthorized access to streaming data have started to be investigated. To cope with this lack, in this article, we propose a general framework to protect streaming data, which is, as much as possible, independent from the target stream engine. Differently from RDBMSs, up to now a standard query language for data streams has not yet emerged and this makes the development of a general solution to access control enforcement more difficult. The framework we propose in this article is based on an expressive role-based access control model proposed by us. It exploits a query rewriting mechanism, which rewrites user queries in such a way that they do not return tuples/attributes that should not be accessed according to the specified access control policies. Furthermore, the framework contains a deployment module able to translate the rewritten query in such a way that it can be executed by different stream engines, therefore, overcoming the lack of standardization. In the article, besides presenting all the components of our framework, we prove the correctness and completeness of the query rewriting algorithm, and we present some experiments that show the feasibility of the developed techniques.
Purging Practices for Pipe Welding (1976)

TIG welding process is being predominantly used in the fabrication of carbon, alloy and stainless steel pipings of various diameters in critical sections. TIG welding with consumable inserts and insert gas backing is preferred for depositing the ischolar_main bead. Argon gas is preferred in such applications as in Nuclear Steam heat exchangers due to its following properties : 1. Smoother and quieter arc action. 2. Lower arc voltage at given current value and arc length. 3. Greater cleaning action in welding. 4. Lower flow rates for good shielding. 5. Easier arc starting.
Antigenicity of bovine papillomavirus type 1 (BPV-1) L1 virus-like particles compared with that of intact BPV-1 virions (1996)

Virus-like-particles (VLPs) of various papillomavirus (PV) types have been produced by expressing recombinant L1 proteins in eukaryotic cells. Although VLPs have the same ultrastructural appearance as native virions and their immunogenicity appears to be similar, their antigenicity has not been carefully evaluated. For this reason, the antigenicity of intact bovine PV type 1 (BPV-1) virions was compared with that of BPV-1 recombinant L1 VLPs by ELISA using a well-characterized panel of polyclonal and monoclonal antibodies generated against intact and denatured BPV-1 particles. The structural integrity of the authentic virions and recombinant VLPs was verified by electron microscopy. The specificity of antibodies raised against intact BPV-1 virions and their reactivity with VLPs revealed that the immunodominant, type-specific, conformational epitopes of intact virions were reproduced on VLPs. However, many monoclonal antibodies that define cross-reactive, non-conformational (linear) epitopes cryptic to the authentic BPV-1 virion tested positively when reacted with intact VLPs. One monoclonal antibody, which recognizes a BPV-1 and deer PV surface conformational epitope, did not react with VLPs. Therefore, although VLPs can be used to immunize animals against infection, the external exposure of broadly cross-reactive epitopes of intact L1 VLPs suggests that the use of L1 VLPs in antigenicity studies such as serological screening should be done with caution.
[Combined treatment with beta-receptor blocker pindolol and diureticum trichlormethiazidum in patients with essential hypertony in stadium II WHO (author's transl))]. (1977)

A double blind study was performed concerning effects and endurance of a combined therapy with beta-receptor blocker Pindolol (LB 46 Visken Sandoz/2 X 2 tabletes per 5 mg daily and Trichlormethiazidum Eurinol Spofa 3-dicholor-methyl-6-chlor-7-sulfamoyl 3,4-dihydro-1,2, 4-benzothiadiazin-1, 1-dyoxydum) 1 X1 tablet per 4 mg daily in 74 patients with essential hypertony in stadium II WHO. Reduction of the systolic as well as the diastolic blood pressure was already highly significant after the first two weeks of treatment (p less than 0.05). Heart frequency dropped from the average of 86,6 +/-8,6 per minute to 74 +/-16.8 per minute. All patients endured the medication very well.
The <i>Agrobacterium</i> Ti Plasmids (2014)

Agrobacterium tumefaciens is a plant pathogen with the capacity to deliver a segment of oncogenic DNA carried on a large plasmid called the tumor-inducing or Ti plasmid to susceptible plant cells. A. tumefaciens belongs to the class Alphaproteobacteria, whose members include other plant pathogens (Agrobacterium rhizogenes), plant and insect symbionts (Rhizobium spp. and Wolbachia spp., respectively), human pathogens (Brucella spp., Bartonella spp., Rickettsia spp.), and nonpathogens (Caulobacter crescentus, Rhodobacter sphaeroides). Many species of Alphaproteobacteria carry large plasmids ranging in size from ∼100 kb to nearly 2 Mb. These large replicons typically code for functions essential for cell physiology, pathogenesis, or symbiosis. Most of these elements rely on a conserved gene cassette termed repABC for replication and partitioning, and maintenance at only one or a few copies per cell. The subject of this review is the ∼200-kb Ti plasmids carried by infectious strains of A. tumefaciens. We will summarize the features of this plasmid as a representative of the repABC family of megaplasmids. We will also describe novel features of this plasmid that enable A. tumefaciens cells to incite tumor formation in plants, sense and respond to an array of plant host and bacterial signal molecules, and maintain and disseminate the plasmid among populations of agrobacteria. At the end of this review, we will describe how this natural genetic engineer has been adapted to spawn an entire industry of plant biotechnology and review its potential for use in future therapeutic applications of plant and nonplant species.
Synthesis of porcine brain natriuretic peptide-32 using silver tetrafluoroborate as a new deprotecting reagent of the S-trimethylacetamidomethyl group. (1990)

Silver tetrafluoroborate (AgBF4) in trifluoroacetic acid (TFA) has been found to cleave the S-trimethylacetamidomethyl (Tacm) group or the S-acetamidomethyl (Acm) group without affecting other functional groups in the peptide chain. Newly isolated porcine brain natriuretic peptide-32 (pBNP-32) was synthesized using AgBF4 and Cys(Tacm) derivatives. The synthetic pBNP-32 had the highest chick rectum relaxant activity among the ANP-BNP families.
Hypoxia drives transient site-specific copy gain and drug-resistant gene expression (2015)

Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer.
Satellite Doppler-Data Processing Using a Microcomputer (1978)

This paper describes a microcomputer which was developed to compute ground radio beacon-position locations using satellite measurements of Doppler frequency shift. Both the computational algorithms and the microcomputer hardware incorporating these algorithms are discussed. Results are presented wherein this microcomputer in conjunction with the Nimbus-6 random-access measurement system (RAMS) provides real-time calculation of beacon latitude and longitude.
Texture Profile Analysis and Functional Properties of Gelatin from the Skin of Three Species of Fresh Water Fish (2014)

The texture profile analysis and functional properties of gelatin from fresh water fish (carps) and porcine skin were measured. Texture profile analysis revealed that the porcine gelatin showed significantly higher values for hardness, springiness, cohesiveness, gumminess, and chewiness than carp skin gelatin (p < 0.05). The bloom strength of gelatin from a porcine source was higher (466.40 g) than carp skin. The solubility profile of gelatin from carps and porcine as function of sodium chloride concentration indicated a maximum solubility at 0.3 M. The relationship between emulsion capacity values and concentration of proteins were found to be inversed in all of the gelatin samples.
The Isolation and Characterization of Dihydropteridine Reductase from Sheep Liver (1972)

Abstract Dihydropteridine reductase has been obtained from sheep liver in essentially homogeneous form. The enzyme exists as a dimer of molecular weight 41,000 to 42,800. The subunit molecular weight has been determined to be 21,300. In the presence of the quinonoid tautomer of either dihydrobiopterin or dihydro-6, 7-dimethylpterin, DPNH is a better substrate than TPNH. Evidence indicates that the activity of this enzyme is far greater than that of the known pterindependent hydroxylases in all tissues examined.