gebhart/patrepeval huggingface dataset:
Low Temperature, Selective Atomic Layer Deposition of Cobalt Metal Films Using Bis(1,4-di-tert-butyl-1,3-diazadienyl)cobalt and Alkylamine Precursors (2017)

The atomic layer deposition (ALD) of cobalt metal films is described using the precursor bis(1,4-di-tert-butyl-1,3-diazadienyl)cobalt and tert-butylamine or diethylamine. Platinum, copper, ruthenium, Si(100) with native oxide, thermal SiO2, hydrogen-terminated silicon, and carbon-doped oxide substrates were used with growth temperatures between 160 and 220 °C. Plots of growth rate versus pulse lengths showed saturative, self-limited behavior at ≥3.0 s for bis(1,4-di-tert-butyl-1,3-diazadienyl)cobalt and ≥0.1 s for tert-butylamine. An ALD window was observed between 170 and 200 °C, with a growth rate of 0.98 Å/cycle on platinum substrates. A plot of thickness versus the number of cycles at 200 °C on platinum substrates was linear between 25 and 1000 cycles, with a growth rate of 0.98 Å/cycle. A 98 nm thick film grown at 200 °C showed crystalline cobalt metal by X-ray diffraction. Atomic force microscopy of 10 and 98 nm thick cobalt metal films grown on platinum substrates at 200 °C showed rms roughness values that were ≤3.1% of the film thicknesses. X-ray photoelectron spectroscopy analyses were performed on 49 and 98 nm thick films grown on platinum substrates at 170 and 200 °C, respectively. Both samples showed oxidized cobalt on the film surface but revealed cobalt metal upon argon ion sputtering. The films showed >98% pure cobalt, with ≤0.9% each of oxygen, carbon, and nitrogen. On copper substrates, a plot of thickness versus the number of cycles was linear between 25 and 500 cycles, with a growth rate of 0.98 Å/cycle. In contrast, analogous growth studies on ruthenium substrates showed no films after 25 and 50 cycles, a small amount of growth at 100 cycles, and a growth rate of 0.98 Å/cycle at 200 and 500 cycles. No film growth was observed at 200 °C on Si(100) with native oxide, 100 nm thermal SiO2, hydrogen-terminated silicon, and carbon-doped oxide substrates after 500 cycles. Similarly, no growth was observed on these insulating substrates after 200 cycles at temperatures between 160 and 220 °C. Accordingly, this process affords inherently selective cobalt metal growth on metal substrates between 160 and 220 °C. Lower purity nitrogen carrier and purge gas (<99.9%) afforded a much lower growth rate, likely because of the formation of surface cobalt oxides and attendant reduced cobalt metal nucleation. A mechanism for cobalt metal growth is proposed in which 1 and tert-butylamine form an adduct, which then decomposes thermally to cobalt metal, 1,4-di-tert-butyl-1,3-diazadiene, and tert-butylamine.
Assay of Pulmonary Microvascular Endothelial Angiotensin-Converting Enzyme in Vivo: Comparison of Three Probes (1994)

We monitored the activity of pulmonary microvascular endothelial-bound angiotensin-converting enzyme (ACE) in vivo by means of multiple indicator-dilution-type techniques, utilizing three different probes: the hydrolysis of two substrates, [3H]-benzoyl-Phe-Ala-Pro (BPAP) and [14C]benzoyl-Ala-Gly-Pro (BAGP), and the binding of the inhibitor [3H]RAC-X-65 (RAC), all measured during a single transpulmonary passage in anesthetized rabbits, placed on total heart bypass, so that both systemic and pulmonary circulations were fully supported by means of a two-channel extracorporeal pump. Experiments were performed at pulmonary blood flows (Qb) of 250, 400, 560, and 800 ml/min in control or indomethacin-pretreated rabbits. ACE activity was also compared to that of pulmonary microvascular endothelial-bound 5'-nucleotidase, by measuring the dephosphorylation of its natural substrate 5'-[14C]AMP. We calculated substrate utilization, mean lung transit time (t), and volume of distribution (i.e., central blood volume) of all substrates, as well as inhibitor binding. We also calculated Amax/Km and Bmax products of enzyme mass and kinetic constants for substrates and inhibitor, respectively. As Qb increased, Amax/Km values for all three substrates and Bmax increased linearly, indicating microvascular recruitment. In experiments in which either BPAP and 5'-AMP metabolism or BAGP metabolism and RAC binding were studied concomitantly, a linear relationship was observed between Qb-induced changes in Amax/Km values of BPAP vs 5'-AMP as well as in Amax/Km of BAGP vs Bmax of RAC. Similarly, increasing Qb increased central blood volume and decreased t. Indomethacin had no effect on most of the hemodynamic or enzyme parameters measured. We conclude that in vivo assays of ACE proceed as predicted by Michaelis-Menten kinetics and offer insights into pulmonary endothelial pathophysiology.
Blood group MN precursors as human breast carcinoma‐associated antigens and “naturally” occurring human cytotoxins against them (1976)

Blood group MN active substances were found in benign and malignant human mammary glands. However, the precursor T (Thomsen-Friedenreich) antigen, as determined with human sera, occurred in all cancerous breast tissues tested but not in the benign mammary glands. Anti-T antibody, which is present in all human sera, was severely depressed in 21.16% of 189 breast carcinoma patients, compared with 3.62% of 470 persons of similar age without cancer. Of 720 persons tested approximately 85% of those with severely depressed anti-T had carcinoma; their IgG, IgM and IgA concentrations were of normal range. A >25%–90% increase in anti-T titer score was found in 65.6% of 32 patients bled 1–14 months after mastectomy for carcinoma as compared with 3.1% of 32 patients with breast biopsy who had no carcinoma. All differences in anti-T titer score changes reported are statistically highly significant. Injection of T antigen from human erythrocytes increased anti-T titer scores.
Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes (2017)

T cell specificity emerges from a myriad of processes, ranging from the biological pathways that control T cell signaling to the structural and physical mechanisms that influence how TCRs bind peptides and MHC proteins. Of these processes, the binding specificity of the TCR is a key component. However, TCR specificity is enigmatic: TCRs are at once specific but also cross-reactive. Although long appreciated, this duality continues to puzzle immunologists and has implications for the development of TCR-based therapeutics. In this review, we discuss TCR specificity, emphasizing results that have emerged from structural and physical studies of TCR binding. We show how the TCR specificity/cross-reactivity duality can be rationalized from structural and biophysical principles. There is excellent agreement between predictions from these principles and classic predictions about the scope of TCR cross-reactivity. We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology.
Scalable Coding of Plenoptic Images by Using a Sparse Set and Disparities (2015)

One of the light field capturing techniques is the focused plenoptic capturing. By placing a microlens array in front of the photosensor, the focused plenoptic cameras capture both spatial and angular information of a scene in each microlens image and across microlens images. The capturing results in a significant amount of redundant information, and the captured image is usually of a large resolution. A coding scheme that removes the redundancy before coding can be of advantage for efficient compression, transmission, and rendering. In this paper, we propose a lossy coding scheme to efficiently represent plenoptic images. The format contains a sparse image set and its associated disparities. The reconstruction is performed by disparity-based interpolation and inpainting, and the reconstructed image is later employed as a prediction reference for the coding of the full plenoptic image. As an outcome of the representation, the proposed scheme inherits a scalable structure with three layers. The results show that plenoptic images are compressed efficiently with over 60 percent bit rate reduction compared with High Efficiency Video Coding intra coding, and with over 20 percent compared with an High Efficiency Video Coding block copying mode.
Oligomerization-Dependent Regulation of Motility and Morphogenesis by the Collagen Xviii Nc1/Endostatin Domain (2001)

Collagen XVIII (c18) is a triple helical endothelial/epithelial basement membrane protein whose noncollagenous (NC)1 region trimerizes a COOH-terminal endostatin (ES) domain conserved in vertebrates, Caenorhabditis elegans and Drosophila. Here, the c18 NC1 domain functioned as a motility-inducing factor regulating the extracellular matrix (ECM)-dependent morphogenesis of endothelial and other cell types. This motogenic activity required ES domain oligomerization, was dependent on rac, cdc42, and mitogen-activated protein kinase, and exhibited functional distinction from the archetypal motogenic scatter factors hepatocyte growth factor and macrophage stimulatory protein. The motility-inducing and mitogen-activated protein kinase-stimulating activities of c18 NC1 were blocked by its physiologic cleavage product ES monomer, consistent with a proteolysis-dependent negative feedback mechanism. These data indicate that the collagen XVIII NC1 region encodes a motogen strictly requiring ES domain oligomerization and suggest a previously unsuspected mechanism for ECM regulation of motility and morphogenesis.
Molecular Genetic Alterations of Chromosome 17 and p53 Nuclear Overexpression in Human Bladder Cancer (1993)

We set out to define the alterations of chromosome 17 in human bladder tumors and to correlate p53 nuclear over-expression with 17p deletions in those neoplasms. We studied 60 bladder tumors by restriction fragment-length polymorphism analysis directed at five different loci on chromosome 17. The same tumors were studied with a panel of mouse monoclonal antibodies (PAb1801, PAb240, and PAb1620) to mutant and wild-type p53 proteins using immunohistochemistry. Deletion of 17p correlated with grade (p = 0.039), stage (p = 0.004), and the presence of vascular invasion (p = 0.056). None of the pathologic parameters correlated with 17q deletions. p53 nuclear overexpression correlated with grade (p = 0.027), stage (p = 0.008), vascular invasion (p = 0.021), and the presence of nodal metastases (p = 0.007). In superficial (Ta) lesions, 17p was not deleted, whereas 55% of T1 and T2-T4 tumors showed a loss of heterozygosity. Mutations of p53 as detected by immunohistochemistry were seen in superficial as well as invasive tumors, whereas loss of heterozygosity was seen only in invasive tumors. A strong correlation was found between the presence of mutation and the loss of heterozygosity of the remaining allele (p = 0.0003). Additional follow-up and further studies are required to better define the role of p53 nuclear overexpression and 17p deletions as markers of tumor progression in human bladder cancer.
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion (2017)

CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies (2006)

Clefts on protein surfaces are avoided by antigen-combining sites of conventional antibodies, in contrast to heavy-chain antibodies (HCAbs) of camelids that seem to be attracted by enzymes' substrate pockets. The explanation for this pronounced preference of HCAbs was investigated. Eight single domain antigen-binding fragments of HCAbs (VHH) with nanomolar affinities for lysozyme were isolated from three immunized dromedaries. Six of eight VHHs compete with small lysozyme inhibitors. This ratio of active site binders is also found within the VHH pool derived from polyclonal HCAbs purified from the serum of the immunized dromedary. The crystal structures of six VHHs in complex with lysozyme and their interaction surfaces were compared to those of conventional antibodies with the same antigen. The interface sizes of VHH and conventional antibodies to lysozyme are very similar as well as the number and chemical nature of the contacts. The main difference comes from the compact prolate shape of VHH that presents a large convex paratope, predominantly formed by the H3 loop and interacting, although with different structures, into the concave lysozyme substrate-binding pocket. Therefore, a single domain antigen-combining site has a clear structural advantage over a conventional dimeric format for targeting clefts on antigenic surfaces.
Large scale analysis of positional effects of single-base mismatches on microarray gene expression data (2010)

The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.
Growth of the Pig (1993)

Growth regulation with particular reference to the pig, P.J. Reeds et al physiology and principles of muscle growth, J. Novakofki and R.H. McCusker endocrine regulation of porcine adipose tissue development - cellular and metabolic aspects, G.J. Hausman and D.B. Hausman mapping genes for growth and development, L.B. Schook and P.A. Clamp the physical environment and swine growth, S.E. Curtis the social environment and swine growth, H.W. Gonyou why sick animals don't grow - an immunological explanation, K.W. Kelley et al nutrition and growth - the concept and application of an ideal protein for swine growth, D.H. Baker et al evaluating pork carcasses for composition and quality, R.G. Kauffman and R.D. Warner strategies for improving swine grwoth, M.B. Wheeler and B.R. White use of exogenous agents to regulate growth composition, D.H. Beermann factors affecting the eating quality of pork, M. Ellis and F.K. McKeith.
Novel peptidomimetic inhibitors of signal transducer and activator of transcription 3 dimerization and biological activity (2004)

The critical role of signal transducer and activator of transcription 3 (Stat3) in the growth and survival of human tumor cells identifies it as a promising target for cancer drug discovery. We previously identified a Stat3 SH2 domain-binding phosphopeptide, PY*LKTK, and its tripeptide derivatives, PY*L and AY*L (where Y* represents phosphotyrosine), which inhibit Stat3 biochemical activity and biological function. Here, we report novel peptidomimetic compounds based on PY*L (or AY*L) with substitution of the Y-1 residue by benzyl, pyridyl, or pyrazinyl derivatives that are selective and greater than 5-fold more potent in disrupting Stat3 activity in vitro than lead tripeptides. The biological activities of these derivatives mirror that originally observed for peptides. In this context, the representative peptidomimetic ISS 610 with 4-cyanobenzoate substitution inhibits constitutive Stat3 activity in Src-transformed mouse fibroblasts and human breast and lung carcinoma cells. This effect is not evident with the non-phosphorylated counterpart, ISS 610NP, consistent with interaction of peptidomimetics with the SH2 domain of Stat3. Moreover, ISS 610 induces cell growth inhibition and apoptosis of Src-transformed fibroblasts that contain persistently active Stat3. We present the first report of a peptidomimetic approach to design of small-molecule inhibitors of Stat3 that are also among the first examples of disruptors of transcription factor dimerization with the potential for novel cancer therapy.
Sparse distance learning for object recognition combining RGB and depth information (2011)

In this work we address joint object category and instance recognition in the context of RGB-D (depth) cameras. Motivated by local distance learning, where a novel view of an object is compared to individual views of previously seen objects, we define a view-to-object distance where a novel view is compared simultaneously to all views of a previous object. This novel distance is based on a weighted combination of feature differences between views. We show, through jointly learning per-view weights, that this measure leads to superior classification performance on object category and instance recognition. More importantly, the proposed distance allows us to find a sparse solution via Group-Lasso regularization, where a small subset of representative views of an object is identified and used, with the rest discarded. This significantly reduces computational cost without compromising recognition accuracy. We evaluate the proposed technique, Instance Distance Learning (IDL), on the RGB-D Object Dataset, which consists of 300 object instances in 51 everyday categories and about 250,000 views of objects with both RGB color and depth. We empirically compare IDL to several alternative state-of-the-art approaches and also validate the use of visual and shape cues and their combination.
Studies on Uricosuric Diuretics. II. Substituted 7,8-Dihydrofuro(2,3-g)-1,2-benzisoxazole-7-carboxylic acids and 7,8-Dihydrofuro(2,3-g)benzoxazole-7-carboxylic acids. (1991)

A series of substituted 7,8-dihydrofuro[2,3-g]-1,2-benzisoxazole-7-carboxylic acids 9 and 7,8-dihydrofuro[2,3-g]benzoxazole-7-carboxylic acids 12 were synthesized and evaluated for uricosuric and diuretic activities in rats. Many of the benzisoxazole derivatives 9 showed uricosuric and only weak diuretic activities, whereas the benzoxazoles 12 exhibited potent diuretic activities with little affecting urate excretion. Among these compounds, 5-chloro-7,8-dihydro-3-phenylfuro[2,3-g]-1,2-benzisoxazole-7-carbo xylic acid (9b, AA-193) was found to be a potent uricosuric agent without diuretic activity and was selected for further development.
In vitro measurement of myocardial impedivity anisotropy with a miniature rectangular tube (2003)

Due to rapid change of fiber orientation, it is difficult to measure myocardial impedivity separately in a longitudinal or transverse fiber direction without mutual influence in the two directions. Previously published values of the longitudinal and the transverse myocardial impedivity were derived indirectly from measurements that mixed the impedivity in all directions. Those values are questionable because the derivations were based on a simplified uniform myocardial fiber model. In this paper, a miniature rectangular tube was devised to facilitate direct measurement of myocardial impedivity in a uniform fiber direction. The average transverse-to-longitudinal ratio of the measured in vitro swine myocardial impedivity was about 1.66 from 1 Hz to 1 kHz and dropped to 1.25 at 1 MHz. The result is important for accurate modeling of the electrical property of myocardium in biomedical research of radio-frequency cardiac catheter ablation.
Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-Organization (2011)

Via Dissipative Particle Dynamics (DPD) approach, we study the spontaneous insertion of amphiphilic nanotubes into a lipid vesicle, which is immersed in a hydrophilic solvent. Individual lipids are composed of a hydrophilic head group and two hydrophobic tails. Each nanotube encompasses an ABA architecture, with a hydrophobic shaft (B) and two hydrophilic ends (A). To facilitate the selective transport of species through the nanotubes, we introduce hydrophilic tethers at one end of the tube. We show that nanotubes initially located in the host solvent spontaneously penetrate the vesicles membrane and assume a transmembrane position, with the hydrophilic tethers extending from the surface of the vesicle. Adding nanotubes one at a time after the previous nanotube has been inserted, we characterize the interactions among the nanotubes that have self-assembled into the vesicles membrane and focus on their clustering within the membrane. We also show that the nanotube insertion and clustering within the vesicle strongly affects the vesicle shape in cases of a sufficiently large number of tubes. Ultimately, these nanotube-lipid systems can be used for creating hybrid controlled release vesicles.
Combinatorial Approach to the Catalytic Hydrosilylation of Styrene Derivatives: Catalyst Systems Composed of Organoiron(0) or (II) Precursors and Isocyanides (2015)

(COT)2Fe and the open ferrocenes (MPDE)2Fe (MPDE = η5-3-methylpentadienyl) and (DMPDE)2Fe (DMPDE = η5-2,4-dimethylpentadienyl) were found to function as catalyst precursors for the hydrosilylation of alkenes in the presence of auxiliary ligands. Screening trials determined that the optimal catalyst system was composed of (COT)2Fe and adamantyl isocyanide, allowing the selective hydrosilylation of styrene derivatives with trisubstituted hydrosiloxanes and a polydimethylsiloxane bearing Me2SiH moieties as the end groups. Under the appropriate conditions, the dehydrogenative silylation side reaction was completely suppressed, and the reaction TON exceeded 5000.
Rearrangements of IgH, TCRD and TCRG genes as clonality marker of childhood acute lymphoblastic leukemia. (2005)

We propose a panel of 13 types of rearrangements (primer pairs) sufficient for tumor cell clonality detection in 96% of patients with ALL. Applications of PCR-based analysis of rearranged IgH, TCRD and TCRG genes for discrimination of mono- and oligoclonality and identification of the origin of relapse were demonstrated.
Antimicrobial effect of polyphenols from apple skins on human bacterial pathogens (2006)

Apples possess many beneficial properties for the human health related with their high content in phenolic compounds. The antimicrobial effect of these compounds from the skin of two apple varieties, Royal Gala and Granny Smith, against human pathogens was examined. The phenolic compounds were extracted with the following solvents: A, acetone: water: acetic acid; B, ethyl acetate: methanol: water and C, ethanol: water. Total phenolic, flavonoid and non-flavonoid contents were analyzed in the extracts. The antimicrobial effect was determined using the agar diffusion method. The highest inhibitory effect of both apple varieties corresponded to extract A, which contained a high phenolic content. The Granny Smith extracts with higher phenolic content presented a superior antimicrobial effect against the selected microorganisms: Escherichia coli, Escherichia coli ATCC 25922, Escherichia coli ATCC 35218, Staphylococcus aureus ATCC 25923, Staphylococcus aureus ATCC 29213, Pseudomonas aeruginosa ATCC 27853, Enterococcus faecalis ATCC 29212 and Listeria monocytogenes. The most sensitive microorganisms
Effects of Antidepressant Treatment on Neuroactive Steroids in Major Depression (1998)

These results provide the first clinical evidence of a possible role of neuroactive steroids in successful antidepressant therapy.