gebhart/patrepeval huggingface dataset:
Phase I/II trial for the treatment of cutaneous and subcutaneous tumors using electrochemotherapy (1996)

ECT was an effective local treatment in the majority of nodules treated. The results thus far are very encouraging and the study is being continued.
Selective Proximal Renal Denervation Guided by Autonomic Responses Evoked via High-Frequency Stimulation in a Preclinical Canine Model (2015)

Renal afferent nerves can be mapped safely, and HFS-guided targeted proximal RDN can achieve apparent BP reduction and sympathetic inhibition.
Disruptive effect of diethylstilbestrol on microtubules. (1984)

Diethylstilbestrol, a unique carcinogen lacking measurable mutagenic potency in Salmonella, was shown to be an inhibitor of microtubule assembly in vitro using microtubule proteins isolated from porcine brains. The effective concentration of diethylstilbestrol was 10-200 microM, as determined by viscometry, turbidity measurement, and electron microscopic analysis.
Photofabricated Gelatin-Based Nerve Conduits: Nerve Tissue Regeneration Potentials (2004)

There is a strong demand for development of nerve guide conduit with prompt nerve regeneration potential for injury-induced nerve defect. Prior to study on nerve tissue engineering using Schwann cells or nerve stem cells, the effectiveness of photofabricated scaffolds based on photocurable gelatin was examined. This study describes the evaluation of in vivo nerve tissue regeneration potentials of three custom-designed and -fabricated prostheses (inner diameter, 1.2 mm; outer diameter, 2.4 mm; wall thickness, 0.60 mm; and length, 15 mm) made of photocured gelatin: a plain photocured gelatin tube (model I), a photocured gelatin tube packed with bioactive substances (laminin, fibronectin, and nerve growth factor) coimmobilized in a photocured gelatin rod (model II), and a photocured gelatin tube packed with bioactive substances coimmobilized in multifilament fibers (model III). These prostheses were implanted between the proximal and distal stumps 10 mm of the dissected right sciatic nerve of 70 adult male Lewis rats for up to 1 year. The highest regenerative potentials were found using the model III prosthesis, followed by the model II prosthesis. Markedly retarded neural regeneration was observed using the model I prosthesis. These were evaluated from the viewpoints of functional recovery, electrophysiological responses, and tissue morphological regeneration. The significance of the synergistic cooperative functions of multifilaments, which serve as a platform that provides contact guidance to direct longitudinal cell movement and tissue ingrowth and as a cell adhesive matrix with high surface area, and immobilized bioactive substances, which enhance nerve regeneration via biological stimulation, is discussed.
Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II fromDrosophila melanogaster (1999)

A bacterially expressed single chain antibody (scFv215) directed against the largest subunit of drosophila RNA polymerase II was analysed. Structure and function of the antigen binding site in scFv215 were probed by chain shuffling and by site-specific mutagenesis. The entire variable region of either the heavy or light chain was replaced by an unrelated heavy or light chain. Both replacements resulted in a total loss of binding activity suggesting that the antigen binding site is contributed by both chains. The functional contributions of each complementarity determining region (CDR) were investigated by site specific mutagenesis of each CDR separately. Mutations in two of the CDRs, CDR1 of light chain and CDR2 of heavy chain, reduced the binding activity significantly. Each of the amino acids in these two CDRs was replaced individually by alanine (alanine walking). Seven amino acid substitutions in the two CDRs were found to reduce the binding activity by more than 50%. The data support a computer model of scFv215 which fits an epitope model based on a mutational analysis of the epitope suggesting an alpha-helical structure for the main contact area.
Secure and selective dissemination of XML documents (2002)

XML ( eXtensible Markup Language ) has emerged as a prevalent standard for document representation and exchange on the Web. It is often the case that XML documents contain information of different sensitivity degrees that must be selectively shared by (possibly large) user communities. There is thus the need for models and mechanisms enabling the specification and enforcement of access control policies for XML documents. Mechanisms are also required enabling a secure and selective dissemination of documents to users, according to the authorizations that these users have. In this article, we make several contributions to the problem of secure and selective dissemination of XML documents. First, we define a formal model of access control policies for XML documents. Policies that can be defined in our model take into account both user profiles, and document contents and structures. We also propose an approach, based on an extension of the Cryptolope™ approach [Gladney and Lotspiech 1997], which essentially allows one to send the same document to all users, and yet to enforce the stated access control policies. Our approach consists of encrypting different portions of the same document according to different encryption keys, and selectively distributing these keys to the various users according to the access control policies. We show that the number of encryption keys that have to be generated under our approach is minimal and we present an architecture to support document distribution.
Priming Th1 Immunity to Viral Core Particles Is Facilitated by Trace Amounts of RNA Bound to Its Arginine-Rich Domain (2002)

Particulate hepatitis B core Ag (C protein) (HBcAg) and soluble hepatitis B precore Ag (E protein) (HBeAg) of the hepatitis B virus share >70% of their amino acid sequence and most T and B cell-defined epitopes. When injected at low doses into mice, HBcAg particles prime Th1 immunity while HBeAg protein primes Th2 immunity. HBcAg contains 5-20 ng RNA/microg protein while nucleotide binding to HBeAg is not detectable. Deletion of the C-terminal arginine-rich domain of HBcAg generates HBcAg-144 or HBcAg-149 particles (in which >98% of RNA binding is lost) that prime Th2-biased immunity. HBcAg particles, but not truncated HBcAg-144 or -149 particles stimulate IL-12 p70 release by dendritic cells and IFN-gamma release by nonimmune spleen cells. The injection of HBeAg protein or HBcAg-149 particles into mice primes Th1 immunity only when high doses of RNA (i.e., 20-100 microg/mouse) are codelivered with the Ag. Particle-incorporated RNA has thus a 1000-fold higher potency as a Th1-inducing adjuvant than free RNA mixed to a protein Ag. Disrupting the particulate structure of HBcAg releases RNA and abolishes its Th1 immunity inducing potency. Using DNA vaccines delivered intradermally with the gene gun, inoculation of 1 microg HBcAg-encoding pCI/C plasmid DNA primes Th1 immunity while inoculation of 1 microg HBeAg-encoding pCI/E plasmid DNA or HBcAg-149-encoding pCI/C-149 plasmid DNA primes Th2 immunity. Expression data show eukaryotic RNA associated with HBcAg, but not HBeAg, expressed by the DNA vaccine. Hence, codelivery of an efficient, intrinsic adjuvant (i.e., nanogram amounts of prokaryotic or eukaryotic RNA bound to arginine-rich sequences) by HBcAg nucleocapsids facilitates priming of anti-viral Th1 immunity.
Cloning and characterization of dipeptidyl peptidase 10, a new member of an emerging subgroup of serine proteases (2003)

Two dipeptidyl peptidase IV (DPPIV, DPP4)-related proteins, DPP8 and DPP9, have been identified recently [Abbott, Yu, Woollatt, Sutherland, McCaughan, and Gorrell (2000) Eur. J. Biochem. 267, 6140-6150; Olsen and Wagtmann (2002) Gene 299, 185-193; Qi, Akinsanya, Riviere, and Junien (2002) Patent application WO0231134]. In the present study, we describe the cloning of DPP10, a novel 796-amino-acid protein, with significant sequence identity to DPP4 (32%) and DPP6 (51%) respectively. We propose that DPP10 is a new member of the S9B serine proteases subfamily. The DPP10 gene is located on the long arm of chromosome 2 (2q12.3-2q14.2), close to the DPP4 (2q24.3) and FAP (2q23) genes. The active-site serine residue is replaced by a glycine residue in DPP10, resulting in the loss of DPP activity. The serine residue is also replaced in DPP6, which lacks peptidase activity. DPP8 and DPP9 share an identical active site with DPP4 (Gly-Trp-Ser-Tyr-Gly). In contrast with the previous results suggesting that DPP9 is inactive, we show that DPP9 is a DPP, hydrolysing Ala-Pro-(7-amino-4-methyl-coumarin) with similar pH-specificity and protease-inhibitor-sensitivity to those of DPP4 and DPP8. Northern-blot analysis shows that whereas DPP8 and DPP9 are widely expressed, DPP10 is expressed mainly in the brain and pancreas. DPP6, which has the highest amino acid identity with DPP10, has been shown previously [Nadal, Ozaita, Amarillo, de Miera, Ma, Mo, Goldberg, Misumi, Ikehara, Neubert et al. (2003) Neuron 37, 449-461] to associate with A-type K(+) channel subunits, modulating their transport and function in somatodendritic compartments of neurons. It is possible that DPP10 is involved in similar functions in the brain. Elucidation of the physiological or pathophysiological role of DPP8, DPP9 and DPP10 and characterization of their structure-function relationships will add impetus to the development of inhibitor molecules for pharmacological or therapeutic use.
Antihemophilic Factor Inhibitors (1976)

Prothrombin complex concentrates have been evaluated in the treatment of acute bleeding episodes occurring in 11 hemophilic and two nonhemophilic patients with factor VIII inhibitors. In several of the hemophilic patients, a continued fall in inhibitor levels has been observed coincident with continued use of the concentrate Proplex, and one of these patients is now responsive to factor VIII therapy. The therapeutic effectiveness of prothrombin complex products appears to be related to the presence of small amounts of activated factors or to the continued formation of factor Xa in vivo as a result of the increased levels of prothrombin and factors VII and X. Until high-potency activated products are available, prothrombin concentrates offer an effective means of treating patients with factor VIII inhibitor. (<i>JAMA</i>236:2061-2064, 1976)
Cryopreservation of Human Embryonic Stem Cells with a New Bulk Vitrification Method1 (2010)

To increase the manipulation efficiency and storage capability of vitrified human embryonic stem cells, a new bulk vitrification method was established using transformed cryovials. This method vitrified a large number of cell clumps, as opposed to those cryopreserved by a slow-freezing method with conventional cryovials at one time (round). After warming, vitrified human embryonic stem cells exhibited a much higher survival rate than the slow-freezing cells. The vitrified stem cells continued to express markers of pluripotency and formed teratomas in mice with severe combined immunodeficiency, confirming the pluripotency of vitrified-warmed human embryonic stem cell clumps. The new bulk vitrification method is superior to and more practical than the open pulled straw vitrification method and the slow-freezing method for the cryopreservation of human embryonic stem cells.
Multitone system in an unlimited bandwidth multipath Rician fading environment (1993)

The author analyzes the performances of a coherent multitone communication system over a specular multipath fading radio channel with unlimited bandwidth. It is shown that each carrier suffers from a multipath interference term and a cross-carrier term as well. The average bit error probability is derived for a channel with 2 paths having Rician distributed gains, and uniformly distributed delay and phase angle. The performance of the multitone system is compared with the one obtained by means of a one-tone QPSK system for the same bit rate and a same bandwidth.
A spherand containing an enforced cavity that selectively binds lithium and sodium ions (1979)

A new type of ligand system is reported which, by means of a rigid support structure, focuses the twenty-four electrons of six attached oxygens on an enforced cavity; the system complexes Li+ and Na+, but rejects other alkali or alkaline earth ions, solvents, and parts of its own support structure.
Highly efficient and flexible total synthesis of coelenterazine (1997)

M. Keenan, K. Jones and F. Hibbert, Chem. Commun., 1997, 323 DOI: 10.1039/A607460J
In Vitro Propagation and Storage of Brugmansia versicolor Lagerheim (2004)

Brugmansia versicolor Lagerheim of the family Solanaceae was propagated through shoot tip culture and shoots were cold-stored in vitro at 5, 10 or 15°C under light or dark condition. All the shoots died after cold storage for 6 months at 5°C irrespective of light condition. When shoots were stored for 12 months at 15°C under light illumination, the best 100% survival rate was obtained. The plants regenerated from shoots stored for 6 or 12 months retained the ability to accumulate scopolamine as much as the control plants which were raised from shoots maintained under normal culture condition without cold-storage. These findings show that slow growth storage of in vitro B. versicolor shoots at 15°C can be used as a germplasm conservation system for short-or medium-term duration without deterioration of the ability to accumulate the secondary metabolites.
Human Complement Factor I Does Not Require Cofactors for Cleavage of Synthetic Substrates (2004)

Complement factor I (fI) plays a major role in the regulation of the complement system. It circulates in an active form and has very restricted specificity, cleaving only C3b or C4b in the presence of a cofactor such as factor H (fH), complement receptor type 1, membrane cofactor protein, or C4-binding protein. Using peptide-7-amino-4-methylcoumarin derivatives, we investigated the substrate specificity of fI. There is no previous report of synthetic substrate cleavage by fI, but five substrates were found in this study. A survey of 15 substrates and a range of inhibitors showed that fI has specificity similar to that of thrombin, but with much lower catalytic activity than that of thrombin. fI amidolytic activity has a pH optimum of 8.25, typical of serine proteases and is insensitive to ionic strength. This is in contrast to its proteolytic activity within the fI-C3b-fH reaction, in which the pH optimum for C3b cleavage is <5.5 and the reaction rate is highly dependent on ionic strength. The rate of cleavage of tripeptide 7-amino-4-methylcoumarins by fI is unaffected by the presence of fH or C3(NH(3)). The amidolytic activity is inhibited by the synthetic thrombin inhibitor Z-D-Phe-Pro-methoxypropylboroglycinepinanediol ester, consistent with previous reports, and by benzenesulfonyl fluorides such as Pefabloc SC. Suramin inhibits fI directly at concentration of 1 mM. Within a range of metal ions tested, only Cr(2+) and Fe(3+) were found to inhibit both the proteolytic and amidolytic activity of fI.
Cytokine Control of Adult Neural Stem Cells (2009)

The neuropoietic cytokine family includes interleukin-6 (IL-6), leukemia inhibitory factor (LIF), and ciliary neurotrophic factor (CNTF), among others. These cytokines have been shown to alter neural stem cell (NSC) self-renewal and progenitor cell division and differentiation, which could be mediated by the Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway. Using neurospheres from the adult mouse subventricular zone (SVZ), we found that acute or chronic exposure to LIF or CNTF differentially affects sphere development and sphere growth. Both cytokines also favor the amplification of NSCs. Contrasting results were obtained with IL-6 or leptin, although both cytokines also activate the JAK/STAT pathway. Stimulating NSC self-renewal in vivo could be of therapeutic interest for treating neurodegeneration. When applied to the adult mouse brain, chronic LIF stimulates NSC self-renewal but prevents the emergence of more differentiated progeny. On the other hand, acute LIF treatment stimulates SVZ regeneration, most likely through an increase in NSCs. These results reveal that cytokine effects could vary as a function of exposure duration and suggest that, in the search for strategies to promote brain repair, in vivo acute LIF treatment could promote cell replacement.
Is standardization more important than methodology for assay of total protein in cerebrospinal fluid? (1986)

Four manual micromethods for protein determination, two turbidimetric (trichloroacetic and sulfosalicylic acid-sodium sulfate) and two colorimetric (Lowry and Coomassie Brilliant Blue--sodium dodecyl sulfate, CBB-SDS) were used to compare the standard curves for total protein (0.30 to 3 g/L) produced with three reference materials: bovine serum albumin, human serum albumin, and diluted human serum. We measured the apparent protein content of a sample of pooled human cerebrospinal fluid by all four methods and with use of all three standards. The only reference material that gave similar results with all four methods was diluted human serum; the CBB-SDS was the only method that gave identical results with all three reference materials. We then measured the protein concentration of 28 individual cerebrospinal fluid samples by the four methods, with diluted human serum as standard. Results by all methods correlated well, but only the sulfosalicylic acid and the CBB-SDS methods gave equivalent results. We conclude that the choice of standard is more important than the method used. However, the CBB-SDS method may be the preferred method because it produced identical standard curves with all three protein standards.
Apomictic and Sexual Ovules ofBoecheraDisplay Heterochronic Global Gene Expression Patterns (2010)

We have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera. We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (n = 577) that were found in a single developmental stage and differentially expressed between the sexual and apomictic ovules, and (3) sex-specific (n = 237) and apomixis-specific (n = 1106) tags that were found in all four developmental stages but in only one reproductive mode. Most heterochronic and stage-specific tags were significantly downregulated during early apomictic ovule development, and 110 were associated with reproduction. By contrast, most late stage-specific tags were upregulated in the apomictic ovules, likely the result of increased gene copy number in apomictic (hexaploid) versus sexual (triploid) endosperm or of parthenogenesis. Finally, we show that apomixis-specific gene expression is characterized by a significant overrepresentation of transcription factor activity. We hypothesize that apomeiosis is associated with global downregulation at the megaspore mother cell stage. As the diploid apomict analyzed here is an ancient hybrid, these data are consistent with the postulated link between hybridization and asexuality and provide a hypothesis for multiple evolutionary origins of apomixis in the genus Boechera.
Learning to Detect and Classify Malicious Executables in the Wild (2006)

We describe the use of machine learning and data mining to detect and classify malicious executables as they appear in the wild. We gathered 1,971 benign and 1,651 malicious executables and encoded each as a training example using n-grams of byte codes as features. Such processing resulted in more than 255 million distinct n-grams. After selecting the most relevant n-grams for prediction, we evaluated a variety of inductive methods, including naive Bayes, decision trees, support vector machines, and boosting. Ultimately, boosted decision trees outperformed other methods with an area under the ROC curve of 0.996. Results suggest that our methodology will scale to larger collections of executables. We also evaluated how well the methods classified executables based on the function of their payload, such as opening a backdoor and mass-mailing. Areas under the ROC curve for detecting payload function were in the neighborhood of 0.9, which were smaller than those for the detection task. However, we attribute this drop in performance to fewer training examples and to the challenge of obtaining properly labeled examples, rather than to a failing of the methodology or to some inherent difficulty of the classification task. Finally, we applied detectors to 291 malicious executables discovered after we gathered our original collection, and boosted decision trees achieved a true-positive rate of 0.98 for a desired false-positive rate of 0.05. This result is particularly important, for it suggests that our methodology could be used as the basis for an operational system for detecting previously undiscovered malicious executables.
Monoclonal antibodies to respiratory syncytial virus proteins: identification of the fusion protein (1983)

Six monoclonal antibodies directed against respiratory syncytial virus proteins were produced. Each was characterized by immunoprecipitation and indirect immunofluorescence. One was directed against the nucleocapsid protein. NP 44, two were directed against a 37,000-dalton protein, two were directed against the major envelope glycoprotein, GP 90, and one was directed against the 70,000-dalton envelope protein, VP 70. Indirect immunofluorescence stain patterns of infected HEp-2 cells defined GP 90 and VP 70 as viral proteins expressed on the cell surface, whereas NP 44 and the 37,000-dalton protein were detected as intracytoplasmic inclusions. One of the anti-GP 90 antibodies neutralized virus only in the presence of complement but did not inhibit cell-cell fusion. The anti-VP 70 antibody neutralized virus without complement and inhibited cell-cell fusion of previously infected HEp-2 cells, thus identifying VP 70 as the fusion protein.
<title>Characterization of application-specific probes for SPMs</title> (1997)

This paper addresses the problem of determining the absolute force constant of Atomic Force Microscope cantilevers. In the method presented, the cantilever under test is deflected against a reference cantilever of known spring constant. The relative deflection of the two cantilevers is related to their spring constants. The novelty of our approach is in the use of a micromachined reference cantilever of a precisely controlled force constant. Preliminary results show that our method is capable of measuring the force constant of cantilevers in the range of 0.1 to 10 N/m with an accuracy of better than 20%. The error is dominated by the non-linear effects in the force versus distance curves used for the measurement.