gebhart/patrepeval huggingface dataset:
Competitive Adsorption Effects in the Electrodeposition of Iron‐Nickel Alloys (1993)

Two‐step reaction mechanisms involving adsorbed monovalent intermediate ions for the electrodeposition of iron and nickel as single metals can be combined to form a predictive model for the codeposition of iron‐nickel alloys. Inhibition of the more noble nickel in the presence of iron is caused by preferential surface coverage of the adsorbed iron intermediate resulting from a difference between the two elements in Tafel constant for the electrosorption step. The role of hydrolyzed cations and surface pH is investigated and methods for evaluating the influence of pH are explored. The analysis shows that changes in surface pH with potential are not necessary for iron‐rich (anomalous) deposits, but that variations in pH from one electrolyte to another may influence deposit composition. The tendency toward iron‐rich deposits with increasing overpotential exists in all systems, however, and can be prevented only by decreasing the iron concentration of the bath. An extension of the analysis to account for transport limitations in baths with low iron concentration is developed and calculations with the model are presented to illustrate the effects of current density and electrolyte convection under conditions similar to those investigated experimentally in the literature.
5′-Substituted Thalidomide Analogs as Modulators of TNF-α (1998)

The synthesis of 5'-substituted thalidomide analogs is described. The amino acids 2 necessary to synthesize the target compounds were prepared by Michael reaction. Condensation of 2 with phthalic anhydrides followed by reaction with urea yielded 4 as diastereomeric mixtures. Furthermore glutethimide (5) was brominated by an improved method and the resulting compound 6 was reacted in several steps with sodium azide, hydrogen, and phthalic anhydride to give 8. In a similar manner, 6 was reacted with sodium azide and various phthalic anhydrides to give 9, 10, and 11. All final compounds were tested in vitro for their inhibitory activity on the release of TNF-alpha, using stimulated peripheral mononuclear blood cells (PBMCs). Compounds with an additional aromatic substituent in position 5' of the thalidomide molecule were more active than thalidomide. Compound 11 was able to reduce increased levels of IL-2 in vitro.
Current and future options for the management of phantom-limb pain (2012)

Phantom-limb pain (PLP) belongs among difficult-to-treat chronic pain syndromes. Treatment options for PLP are to a large degree implicated by the level of understanding the mechanisms and nature of PLP. Research and clinical findings acknowledge the neuropathic nature of PLP and also suggest that both peripheral as well as central mechanisms, including neuroplastic changes in central nervous system, can contribute to PLP. Neuroimaging studies in PLP have indicated a relation between PLP and the neuroplastic changes. Further, it has been shown that the pathological neuroplastic changes could be reverted, and there is a parallel between an improvement (reversal) of the neuroplastic changes in PLP and pain relief. These findings facilitated explorations of novel neuromodulatory treatment strategies, adding to the variety of treatment approaches in PLP. Overall, available treatment options in PLP include pharmacological treatment, supportive non-pharmacological non-invasive strategies (eg, neuromodulation using transcranial magnetic stimulation, visual feedback therapy, or motor imagery; peripheral transcutaneous electrical nerve stimulation, physical therapy, reflexology, or various psychotherapeutic approaches), and invasive treatment strategies (eg, surgical destructive procedures, nerve blocks, or invasive neuromodulation using deep brain stimulation, motor cortex stimulation, or spinal cord stimulation). Venues of further development in PLP management include a technological and methodological improvement of existing treatment methods, an implementation of new techniques and products, and a development of new treatment approaches.
Structure/function analysis of the integrin beta 1 subunit by epitope mapping (1993)

Monoclonal antibodies (mAbs) have been produced against the chicken beta 1 subunit that affect integrin functions, including ligand binding, alpha subunit association, and regulation of ligand specificity. Epitope mapping of these antibodies was used to identify regions of the subunit involved in these functions. To accomplish this, we produced mouse/chicken chimeric beta 1 subunits and expressed them in mouse 3T3 cells. These chimeric subunits were fully functional with respect to heterodimer formation, cell surface expression, and cell adhesion. They differed in their ability to react with a panel anti-chicken beta 1 mAbs. Epitopes were identified by a loss of antibody binding upon substitution of regions of the chicken beta 1 subunit by homologous regions of the mouse beta 1 subunit. The identification of the epitope was confirmed by a reciprocal exchange of chicken and mouse beta 1 domains that resulted in the gain of the ability of the mouse subunit to interact with a particular anti-chicken beta 1 mAb. Using this approach, we found that the epitopes for one set of antibodies that block ligand binding mapped toward the amino terminal region of the beta 1 subunit. This region is homologous to a portion of the ligand-binding domain of the beta 3 subunit. In addition, a second set of antibodies that either block ligand binding, alter ligand specificity, or induce alpha/beta subunit dissociation mapped to the cysteine rich repeats near the transmembrane domain of the molecule. These data are consistent with a model in which a portion of beta 1 ligand binding domain rests within the amino terminal 200 amino acids and a regulatory domain, that affects ligand binding through secondary changes in the structure of the molecule resides in a region of the subunit, possibly including the cysteine-rich repeats, nearer the transmembrane domain. The data also suggest the possibility that the alpha subunit may exert an influence on ligand specificity by interacting with this regulatory domain of the beta 1 subunit.
SOF: a semi‐supervised ontology‐learning‐based focused crawler (2012)

SUMMARY The rapid increase in the volume of data available on the Internet makes it increasingly impractical for a crawler to index the whole Web. Instead, many intelligent crawlers, known as ontology‐based semantic focused crawlers, have been designed by making use of Semantic Web technologies for topic‐centered Web information crawling. Ontologies, however, have constraints of validity and time, which may influence the performance of the crawlers. Ontology‐learning‐based focused crawlers are therefore designed to automatically evolve ontologies by integrating ontology learning technologies. Nevertheless, surveys indicate that the existing ontology‐learning‐based focused crawlers do not have the capability to automatically enrich the content of ontologies, which makes these crawlers unreliable in the open and heterogeneous Web environment. Hence, in this paper, we propose a framework for a novel semi‐supervised ontology‐learning‐based focused (SOF) crawler, the SOF crawler, which embodies a series of schemas for ontology generation and Web information formatting, a semi‐supervised ontology learning framework, and a hybrid Web page classification approach aggregated by a group of support vector machine models. A series of tests are implemented to evaluate the technical feasibility of this proposed framework. The conclusion and the future work are summarized in the final section. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Ectodysplasin is released by proteolytic shedding and binds to the EDAR protein (2001)

Anhidrotic ectodermal dysplasia (EDA) is an X-linked disorder characterized by abnormal development of ectoderm and its appendices. The EDA gene encodes different isoforms of ectodysplasin, a transmembrane protein. The two longest isoforms, ectodysplasin-A1 and -A2, which differ by an insertion of two amino acids, are trimeric type II membrane proteins with an extracellular portion containing a short collagenous domain and a TNF ligand motif in the C-terminal region. We show that ectodysplasin is released from cells to the culture medium. Deletion constructs were used to localize the cleavage site and show that the putative recognition sequence of a furin-like enzyme is needed for the cleavage. Some EDA patients have missense mutations affecting this recognition sequence, suggesting that cleavage has biological significance in vivo. EDAR, a recently cloned member of the TNFR family and the product of the downless gene, is able to co-precipitate ectodysplasin, confirming that they form a ligand-receptor pair. In situ hybridization and immunostaining studies show that ectodysplasin and EDAR are expressed in adjacent or partially overlapping layers in the developing human skin. We conclude that as a soluble ligand, ectodysplasin is able to interact with EDAR and mediate signals needed for the development of ectodermal appendages.
Dextran‐spermine conjugate: an efficient vector for gene delivery (2003)

Abstract Cationic Polysaccharides based on oligoamine‐dextran conjugates were synthesized and tested as vectors for gene transfection. Dextran with 40 kDa in average molecular weight was oxidized under mild conditions by potassium periodate to obtain the respective polyaldehydes in relatively high yields (∼90%). The oxidized dextran was reacted by reductive animation with various oligoamines of 2 to 4 amino groups to obtain the corresponding imine‐conjugates. These water‐soluble polymers were then reduced by excess of sodium borohydride to obtain the corresponding amine‐conjuagtes in 30‐40% overall yield. The electrostatic interactions of the representative polycations with plasmid DNA were evaluated as a function of charge ratio (+/−, polymer/DNA) and ionic strength of the medium applying the ethidium‐bromide quenching assay. Although most synthetic polycations formed stable complexes with Plasmid DNAs, only the dextran‐spermine conjugate of a defined amino content and molecular weight was able to transfect cells with high efficiency.
A 25-Amino Acid Sequence of the Arabidopsis TGD2 Protein Is Sufficient for Specific Binding of Phosphatidic Acid (2009)

Genetic analysis suggests that the TGD2 protein of Arabidopsis is required for the biosynthesis of endoplasmic reticulum derived thylakoid lipids. TGD2 is proposed to be the substrate-binding protein of a presumed lipid transporter consisting of the TGD1 (permease) and TGD3 (ATPase) proteins. The TGD1, -2, and -3 proteins are localized in the inner chloroplast envelope membrane. TGD2 appears to be anchored with an N-terminal membrane-spanning domain into the inner envelope membrane, whereas the C-terminal domain faces the intermembrane space. It was previously shown that the C-terminal domain of TGD2 binds phosphatidic acid (PtdOH). To investigate the PtdOH binding site of TGD2 in detail, the C-terminal domain of the TGD2 sequence lacking the transit peptide and transmembrane sequences was fused to the C terminus of the Discosoma sp. red fluorescent protein (DR). This greatly improved the solubility of the resulting DR-TGD2C fusion protein following production in Escherichia coli. The DR-TGD2C protein bound PtdOH with high specificity, as demonstrated by membrane lipid-protein overlay and liposome association assays. Internal deletion and truncation mutagenesis identified a previously undescribed minimal 25-amino acid fragment in the C-terminal domain of TGD2 that is sufficient for PtdOH binding. Binding characteristics of this 25-mer were distinctly different from those of TGD2C, suggesting that additional sequences of TGD2 providing the proper context for this 25-mer are needed for wild type-like PtdOH binding.
Oncogenic BRAF Is Required for Tumor Growth and Maintenance in Melanoma Models (2006)

The usual paradigm for developing kinase inhibitors in oncology is to use a high-affinity proof-of-concept inhibitor with acceptable metabolic properties for key target validation experiments. This approach requires substantial medicinal chemistry and can be confounded by drug toxicity and off-target activities of the test molecule. As a better alternative, we have developed inducible short-hairpin RNA xenograft models to examine the in vivo efficacy of inhibiting oncogenic BRAF. Our results show that tumor regression resulting from BRAF suppression is inducible, reversible, and tightly regulated in these models. Analysis of regressing tumors showed the primary mechanism of action for BRAF to be increased tumor cell proliferation and survival. In a metastatic melanoma model, conditional BRAF suppression slowed systemic tumor growth as determined by in vivo bioluminescence imaging. Taken together, gain-of-function BRAF signaling is strongly associated with in vivo tumorigenicity, confirming BRAF as an important target for small-molecule and RNA interference-based therapeutics.
Cloning and characterization of the genes for two distinct cephalosporin acylases from a Pseudomonas strain (1987)

Pseudomonas sp. strain SE83 converts cephalosporin C and 7 beta-(4-carboxybutanamido)cephalosporanic acid (GL-7ACA) to 7-aminocephalosporanic acid (7ACA). A DNA library of this strain was constructed in Escherichia coli and screened for the ability to deacylate GL-7ACA to 7ACA. Apparently, two distinct genes, designated acyI and acyII, were cloned on 4.8- and 6.0-kilobase-pair BglII fragments, respectively. The enzymes encoded by the two genes showed different substrate specificities, and the acyII-encoded enzyme was found to yield 7ACA from cephalosporin C by direct deacylation. Expression of the two genes in E. coli was strongly dependent on a promoter of the vector. The coding regions for acyI and acyII were localized on the 2.5- and 2.8-kilobase-pair fragments, respectively, by subcloning experiments, and high expression of both genes was obtained by placing them under the control of the lacUV5 promoter. The acyII-encoded enzyme was purified and shown to be composed of two nonidentical subunits with molecular weights of 26,000 and 57,000. Maxicell analysis revealed three acyII-specific polypeptides, two of which corresponded to the above subunits. The third polypeptide with a molecular weight of 83,000 was suggested to be the precursor of both subunits.
Experimental Reproduction of Bovine Fetal Neospora Infection and Death with a Bovine Neospora Isolate (1994)

Studies were conducted to determine the pathogenic potential of the recently isolated bovine Neospora protozoa (BPA-1) for the bovine fetus. Cows chosen for study had Neospora titers < 160 using an indirect immunofluorescent antibody (IFA) test. Four experimental groups were studied. In group 1, 2 fetuses were inoculated in utero at 118 days gestation with culture-derived Neospora tachyzoites. A pregnant control cow was housed in the same pen, observed daily and screened serologically for evidence of exposure to Neospora. In group 2, 2 cows were infected with Neospora tachyzoites at 138 or 161 days gestation, and 1 control cow was given uninfected cell culture suspension simultaneously at 154 days gestation. Groups 3 (85 days gestation) and 4 (120 days gestation) each consisted of 2 cows infected with Neospora tachyzoites and 1 control cow given uninfected material at the same stage of gestation. Dead fetuses were surgically removed from the infected cows in group 1 on postinfection day (PID) 17. The histopathology was compatible with protozoal fetal infection, and protozoa were identified by immunohistochemistry. Viable fetuses were removed surgically from cows in group 2 on PID 28-30. The histopathology was compatible with protozoal fetal infection, protozoa were identified by immunoperoxidase techniques, and Neospora tachyzoites were reisolated in vitro from tissues of the 2 infected fetuses. In groups 3 and 4, the control fetus and 1 infected fetus were removed surgically between PID 26 and PID 33. The remaining infected cows were observed until fetal death or abortion occurred.(ABSTRACT TRUNCATED AT 250 WORDS)
Calyciphylline G, a Novel Alkaloid with an Unprecedented Fused‐Hexacyclic Skeleton from Daphniphyllum calycinum (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The Initial Detection and Partial Characterization of Circulating Tumor Cells in Neuroendocrine Prostate Cancer (2015)

CTCs from patients with NEPC have unique morphologic characteristics, which were also identified in a subset of CRPC patients with aggressive clinical features potentially undergoing NEPC transition.
Corner stitching for simple rectilinear shapes [VLSI layouts] (1997)

This paper extends the corner-stitching data structure proposed by Ousterhout (1984) for manipulating rectangular objects in very large scale integration (VLSI) layouts to L-shaped objects. This provides additional flexibility in the design of very large scale integration (VLSI) circuits. Our technique is fundamentally different from Ousterhout's and other extensions to the corner stitching data structure in that it modifies the underlying topology of the data structure. This gives rise to differences in the implementation of operations on the data structure. Our data structure is guaranteed to require less memory than the original data structure. Experiments show that our data structure required about 15%-17% less memory than the original data structure on VLSI layouts but was slower by a factor of two to eight. Extensions of corner stitching to T- and Z-shaped tiles are also described.
Efficacy of body ties under dynamic switching conditions in partially depleted SOI CMOS technology (2002)

Historically, body ties have been designed using removal of DC floating-body (FB) effects (e.g., kink, breakdown voltage) as the main criteria. It has been implicitly assumed that the transient FB effects would be minimized too with such a tie. However, such body ties while "suppressing" DC effects, may not necessarily be effective in AC/transient conditions, since the body (dis)charging time constants may be much larger than desired. For example, in a digital SOI CMOS circuit, with the gate switching at a few tens of ps, the efficacy of the body tie may be little or none at all, depending on the response time /spl tau//sub B/(=R/sub B/C/sub B/) of the body. Hence, in order to design effective body ties in transients, dynamic (dis)charging effects due to R/sub B/ and C/sub B/ in the body must be included.
Early detection of electrical defects in deep trench capacitors using voltage contrast inspection (2013)

Improvement of learning cycle time and mean time to detect issues is integral to keeping up with the increasing pace needed in semiconductor technology development. Use of electron beam voltage contrast inspection as an early assessment of electrical defectivity of embedded dynamic random access memory in IBM's deep trench capacitor technology allows for detection of all major initial processing electrical defects months before conventional techniques. Product-like and specially designed on chip diagnostic structures are inspected as soon as active layer patterning and isolation is complete. This enables much earlier identification of electrical defectivity. Examples discussed include electrically open single connections, electrical short circuits to neighboring cells in an array, and cells that have short circuits to the silicon substrate. Physical failure analysis and correlation to other in-line measurement and electrical test signals were performed to verify the voltage contrast inspection results. Robust and reliable results enable regular use of this technique to assess electrical health of critical structures earlyin the process sequence on and to facilitate increased yield improvement learning cycles beyond what is otherwise possible.
Hyperimmune antisera against synthetic peptides representing the glycoprotein of human immunodeficiency virus type 2 can mediate neutralization and antibody-dependent cytotoxic activity. (1991)

Twenty-five 13- to 35-amino-acid-long peptides representing regions of human immunodeficiency virus type 2 (HIV-2), strain SBL6669, envelope proteins were evaluated for their immunogenic activity in guinea pigs. The peptides were selected to provide homologous representation of sites in the HIV-1 envelope proteins that were previously documented to have a particular immunogenic importance. A number of the HIV-2 peptides were found to be capable of inducing strain SBL6669 neutralizing and antibody-dependent cellular cytotoxicity (ADCC) antibodies. Two overlapping peptides covering amino acids 311-337 representing the central and C-terminal part of the variable third (V3) region, terminology according to Modrow et al. [Modrow, S., Hahn, B., Shaw, G. M., Gallo, R. C., Wong-Staal, F. & Wolf, H. (1987) J. Virol. 61, 570-578], showed the most pronounced capacity to induce neutralizing antibodies. One of the peptides (amino acids 318-337) also induced antibodies mediating ADCC. Two additional regions in the large glycoprotein, gp125, containing linear sites reacting with neutralizing antibodies were identified (amino acids, 119-137 and 472-509). The transmembrane protein, gp36, of HIV-2 harbored two regions of importance for induction of neutralizing antibodies (amino acids 595-614 and 714-729). ADCC activity was induced by two additional gp125-specific peptides (amino acids 291-311 and 446-461). Thus, except for the single V3-specific site there was no correlation between linear immunogenic sites stimulating neutralizing antibody and ADCC activity. These findings pave the way for development of synthetic vaccines against HIV-2 and possibly also simian immunodeficiency virus infections. The capacity of such a product to induce protective immunity can be evaluated in macaque monkeys.
Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus (2006)

Streptomyces kanamyceticus 12-6 is a derivative of the wild-type strain developed for industrial kanamycin (Km) production. Southern analysis and DNA sequencing revealed amplification of a large genomic segment including the entire Km biosynthetic gene cluster in the chromosome of strain 12-6. At 145 kb, the amplifiable unit of DNA (AUD) is the largest AUD reported in Streptomyces. Striking repetitive DNA sequences belonging to the clustered regularly interspaced short palindromic repeats family were found in the AUD and may play a role in its amplification. Strain 12-6 contains a mixture of different chromosomes with varying numbers of AUDs, sometimes exceeding 36 copies and producing an amplified region >5.7 Mb. The level of Km production depended on the copy number of the Km biosynthetic gene cluster, suggesting that DNA amplification occurred during strain improvement as a consequence of selection for increased Km resistance. Amplification of DNA segments including entire antibiotic biosynthetic gene clusters might be a common mechanism leading to increased antibiotic production in industrial strains.
Surface texturing for silicon solar cells using reactive ion etching technique (2003)

Surface texturing is an effective and more lasting technique in reducing reflections and improving light trapping compared to antireflection coatings. A surface texturing technique using reactive ion etching (RIE) method suitable for crystalline and multi crystalline solar cells, which resulted in surfaces with negligible reflection in the visible band is described. Different texturing structures (pillars, holes and black silicon) have been studied and compared in the wavelength range from 250nm-2500nm. It is found that the reflectance of the textured column structures were less than 0.4% at wavelengths from 500 nm to 1000 nm and showed a minimum of 0.29% at 1000 nm while the reflectivity from black silicon is around 1% and hole structures is around 6.8% in the same wavelength range.