gebhart/patrepeval huggingface dataset:
Analysis of surfactin synthetase subunits in srfA mutants of Bacillus subtilis OKB105 (1994)

The srfA operon of Bacillus subtilis functions in the biosynthesis of the lipopeptide antibiotic surfactin. On the basis of nucleotide sequence and genetic analysis, it is believed to encode three enzymes (E1A, E1B, and E2) that catalyze the incorporation of the surfactin substrate amino acids. Insertion, deletion, and amino acid substitution mutations of srfA were analyzed for subunit composition and activity as determined by assays of both amino acid-dependent ATP-PPi exchange and aminoacyl thioester formation. Insertion mutations in srfAA (encoding E1A, the subunit that incorporates Glu, Leu, and D-Leu) eliminated production and activity of all three enzymes. Deletions within srfAA and extending from srfAA to srfAB (encoding E1B, which incorporates Val, Asp, and D-Leu) abolished the activity and production of all three enzymes. Insertions between srfAA and srfAB and within srfAB eliminate the production and activity of E1B and E2. An insertion mutation in srfAC (encoding E2, which incorporates Leu) abolished the activity of E2 only. Mutations of the active serine in the putative 4'-phosphopantetheine-binding motif of the second and third domains of E1A eliminated thioester formation and severely reduced the ATP-PPi exchange activity of the two domains. However, the same mutation in the first domain of E1B had little effect on Val-dependent ATP-PPi exchange activity but abolished thioester formation. These results indicate that the coding assignments of the srfA genes are srfAA (E1A), srfAB (E1B), and srfAC (E2).
Experimental Study on Higher Order Reflection by Monodomain Cholesteric Liquid Crystals (1983)

Abstract Reflection spectra have been measured in the spectral region of the second and the third order selective reflections for monodomain cholesterics of various cell thicknesses at various angles of incidence. Thicker cells give rise to higher reflectance at larger angles of incidence. The second order reflection region consists of three bands which show characteristic polarization correlation: The central band is a total reflection band, where incident light of any polarization is reflected. The reflected light is a polarized when it polarized light is incident and vice versa. Contrary to the central band, two side bands are selectively reflected; σ(π) polarized light is reflected in the longer (shorter) wavelength band retaining its polarization. The third order reflection bands observed for the first time have been found to give the same polarization characteristics as that of the second order reflection bands.
Packet-oriented communication protocols for Smart Grid Services over low-speed PLC (2009)

Advanced metering infrastructures require reliable communication links. This paper proposes a protocol stack for smart metering based on the parameters of a robust low-speed PLC physical layer. The protocol stack under consideration implements IPv6 on top of a contention-free media access control sub-layer, thereby allowing for maximum flexibility. Simulation results show that this protocol stack allows data transfers at acceptable latencies, despite low data rates at the physical layer.
A comparative study on the physicochemical and biological stability of IgG1 and monoclonal antibodies during spray drying process (2014)

The IgG1 and trastuzumab demonstrated similar behavior in spray drying process. The combination of excipients containing trahalose, hydroxypropyl beta cyclodextrin and beta cyclodextrin with proper ratio improved the physical and chemical stability of both IgG1 and monoclonal antibody.
Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes (2006)

Sulfur is a functionally important element of living matter. Incorporation into biomolecules occurs by two basic strategies. Sulfide is added to an activated acceptor in the biosynthesis of cysteine, from which methionine, coenzyme A and a number of biologically important thiols can be constructed. By contrast, the biosyntheses of iron sulfur clusters, cofactors such as thiamin, molybdopterin, biotin and lipoic acid, and the thio modification of tRNA require an activated sulfur species termed persulfidic sulfur (R-S-SH) instead of sulfide. Persulfidic sulfur is produced enzymatically with the IscS protein, the SufS protein and rhodanese being the most prominent biocatalysts. This review gives an overview of sulfur incorporation into biomolecules in prokaryotes with a special emphasis on the properties and the enzymatic generation of persulfidic sulfur as well as its use in biosynthetic pathways.
Boosting Nearest Neighbor Classi.ers for Multiclass Recognition (2006)

Nearest neighbor classifiers are a popular method for multiclass recognition in a wide range of computer vision and pattern recognition domains. At the same time, the accuracy of nearest neighbor classi?ers is sensitive to the choice of distance measure. This paper introduces an algorithm that uses boosting to learn a distance measure for multiclass k-nearest neighbor classification. Given a family of distance measures as input, AdaBoost is used to learn a weighted distance measure, that is a linear combination of the input measures. The proposed method can be seen both as a novel way to learn a distance measure from data, and as a novel way to apply boosting to multiclass recognition problems that does not require output codes. In our approach, multiclass recognition of objects is reduced to a single binary recognition task, defined on triples of objects. Preliminary experiments with eight UCI datasets yield no clear winner among our method, boosting using output codes, and k-nn classification using an unoptimized distance measure. Our algorithm did achieve lower error rates in some of the datasets, which indicates that it is a method worth considering for nearest neighbor recognition in various pattern recognition domains.
Competition and cooperation in the formation of information technology interoperability standards: A process model of Web services core standards (2010)

Standards formation is a key dimension in the competitive strategy of ICT firms, as a successful strategy would result in the emergence of favorable IT interoperability standards. This paper examines the standardization efforts of core Web services standards and the results indicate that resource dependencies and strategies adopted by dominant firms to extend their platforms influence the standards formation process. Communities of practice and standard-setting bodies are leveraged by dominant firms in the formation and adoption of standards. We propose a process model of standard setting consisting of five intertwined states: resource pooling, linkages, signaling and implementation, institutionalization, and extension.
Demonstration of Epstein-Barr virus in carcinomas of various sites. (2002)

EBV is an etiological agent in infectious mononucleosis, is implicated in some malignant lymphomas and lymphoepithelioma-like carcinomas, and has been sporadically reported in carcinomas of the breast, lung, and other sites. We studied immunohistochemically benign and malignant tumors of the breast, lung, colon, and prostate and found EBV in some carcinomas of those sites. Also, EBV reactions were noted in hyperplasias and dysplasias, e.g., breast carcinomas in situ and prostatic intraepithelial neoplasia. Benign tumor counterparts were negative. PCR analysis of selected cases confirmed the presence of EBV. Our results suggest that EBV is not restricted to lymphoepithelioma-like carcinomas but may play an oncogenic role in frequent epithelial cancers and possibly also in hyperplasias and certain dysplasias preceding carcinomas.
The Prognostic Role of Androgen Receptor in Patients with Early-Stage Breast Cancer: A Meta-analysis of Clinical and Gene Expression Data (2016)

<b>Purpose:</b> Androgen receptor (AR) expression has been observed in about 70% of patients with breast cancer, but its prognostic role remains uncertain.<b>Experimental Design:</b> To assess the prognostic role of AR expression in early-stage breast cancer, we performed a meta-analysis of studies that evaluated the impact of AR at the protein and gene expression level on disease-free survival (DFS) and/or overall survival (OS). Eligible studies were identified by systematic review of electronic databases using the MeSH-terms "breast neoplasm" and "androgen receptor" and were selected after a qualitative assessment based on the REMARK criteria. A pooled gene expression analysis of 35 publicly available microarray data sets was also performed from patients with early-stage breast cancer with available gene expression and clinical outcome data.<b>Results:</b> Twenty-two of 33 eligible studies for the clinical meta-analysis, including 10,004 patients, were considered as evaluable for the current study after the qualitative assessment. AR positivity defined by IHC was associated with improved DFS in all patients with breast cancer [multivariate (M) analysis, HR 0.46; 95% confidence interval (CI) 0.37-0.58, <i>P</i> < 0.001] and better OS [M-HR 0.53; 95% CI, 0.38-0.73, <i>P</i> < 0.001]. Thirty-five datasets including 7,220 patients were eligible for the pooled gene expression analysis. High <i>AR</i> mRNA levels were found to confer positive prognosis overall in terms of DFS (HR 0.82; 95% CI 0.72-0.92;<i>P</i> = 0.0007) and OS (HR 0.84; 95% CI, 0.75-0.94; <i>P</i> = 0.02) only in univariate analysis.<b>Conclusions:</b> Our analysis, conducted among more than 17,000 women with early-stage breast cancer included in clinical and gene expression analysis, demonstrates that AR positivity is associated with favorable clinical outcome. <i>Clin Cancer Res; 23(11); 2702-12. ©2016 AACR</i>.
Cell surface expression of glycosylated, nonglycosylated, and truncated forms of a cytoplasmic protein pyruvate kinase. (1988)

The soluble cytoplasmic protein pyruvate kinase (PK) has been expressed at the cell surface in a membrane-anchored form (APK). The hybrid protein contains the NH2-terminal signal/anchor domain of a class II integral membrane protein (hemagglutinin/neuraminidase, of the paramyxovirus SV5) fused to the PK NH2 terminus. APK contains a cryptic site that is used for N-linked glycosylation but elimination of this site by site-specific mutagenesis does not prevent cell surface localization. Truncated forms of the APK molecule, with up to 80% of the PK region of APK removed, can also be expressed at the cell surface. These data suggest that neither the complete PK molecule nor its glycosylation are necessary for intracellular transport of PK to the cell surface, and it is possible that specific signals may not be needed in the ectodomain of this hybrid protein to specify cell surface localization.
Low-Field Drift Velocities and Reactions of Nitrogen Ions in Nitrogen (1967)

Drift velocities and reactions of nitrogen ions have been investigated at 300\ifmmode^\circ\else\textdegree\fi{}K at values of $\frac{E}{N}$ (the ratios of electric field to number density) between 1.5 and 20\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}16}$ V ${\mathrm{cm}}^{2}$, and at pressures between 0.5 and 1 Torr. Ions were produced in a glow discharge and were gated into a drift cell, withdrawn through a slit, and their mass and intensity were determined as a function of the drift time by a mass analyzer. Comparison of experimental results with theoretical calculations allowed the determination of true drift velocities and reaction rates for ions undergoing reaction during the drift time. The ions in nitrogen were found to occur in two groups, $\mathrm{N}_{2}^{}{}_{}{}^{+}$-$\mathrm{N}_{4}^{}{}_{}{}^{+}$ and ${\mathrm{N}}^{+}$-$\mathrm{N}_{3}^{}{}_{}{}^{+}$, such that interactions within the groups are much faster than any interactions between the groups. Rate constants for the reaction $\mathrm{N}_{2}^{}{}_{}{}^{+}$+${\mathrm{N}}_{2}$+${\mathrm{N}}_{2}$\ensuremath{\rightarrow}$\mathrm{N}_{4}^{}{}_{}{}^{+}$+${\mathrm{N}}_{2}$ were found to vary from 7\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}29}$ to 2\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}29}$ ${\mathrm{cm}}^{6}$/sec between $\frac{E}{N}$ of 5\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}16}$ and 18\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}16}$ V ${\mathrm{cm}}^{2}$, while for the reverse reaction the rates varied from 0.3\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}13}$ to 110\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}13}$ ${\mathrm{cm}}^{3}$/sec. The pressure dependences of the reaction rates were consistent with a three-body forward reaction and a two-body reverse reaction over our limited pressure range. For the ${\mathrm{N}}^{+}$-$\mathrm{N}_{3}^{}{}_{}{}^{+}$ system, the interaction of ${\mathrm{N}}^{+}$ with the neutral gas to produce $\mathrm{N}_{3}^{}{}_{}{}^{+}$ was observed at $\frac{E}{N}=5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}16}$ V ${\mathrm{cm}}^{2}$ with a rate constant of 3\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}29}$ ${\mathrm{cm}}^{6}$/sec. No reactions could be positively identified which produced ${\mathrm{N}}^{+}$ over the range of our experimental parameters.
Division of Labor Among the Yeast Sol Proteins Implicated in tRNA Nuclear Export and Carbohydrate Metabolism (2004)

SOL1, the founding member of the S. cerevisiae SOL family, was previously identified as a multi-copy suppressor of the los1 defect in tRNA-mediated nonsense suppression. Here we report that the four-member SOL family is not essential and that individual family members appear to have distinct functions. SOL1-SOL4 are homologous to genes encoding 6-phosphogluconolactonase (6Pgl) involved in the pentose phosphate pathway. Both Sol3p and Sol4p affect this activity. However, Sol4p does not act as a los1 multi-copy suppressor. In contrast, neither Sol1p nor Sol2p, both of which correct the los1 defect in nonsense suppression, possess detectable 6Pgl activity. Rather, Sol1p and Sol2p appear to function in tRNA nuclear export as sol1 and sol2 mutants possess elevated levels of nuclear tRNA. Members of the Sol protein family appear to have different subcellular distributions. Thus, Sol3p and Sol4p likely function in carbohydrate metabolism, while Sol1p and Sol2p appear to have roles in tRNA function and nuclear export, thereby defining an unusual protein family whose individual members are biochemically distinct and spatially dispersed.
Post-translational assembly and glycosylation of laminin subunits in parietal endoderm-like F9 cells (1985)

Non-reducing and reducing sodium dodecyl sulphate/polyacrylamide-gel electrophoresis of laminin synthesized in parietal endoderm-like F9 cells demonstrated that only AB1B2 complex goes through intracellular traffic for oligosaccharide side-chain processing and secretion. Glycosylation was not necessary for subunit assembly. Assembly was suggested to proceed through B1B2 to AB1B2. Among the pools of monomer subunits, the B2 pool was smallest.
Indium-111-labeled polyclonal human immunoglobulin: identifying focal infection in patients positive for human immunodeficiency virus. (1993)

Pooled human immunoglobulin labeled with indium-111 (111In-HIgG) was used to identify the presence and extent of infection in patients positive for human immunodeficiency virus (HIV), presenting with either symptoms and/or signs of acute chest infection or with pyrexia without localizing signs or symptoms. Fifty-five studies were performed in 51 patients with suspected chest infection or pyrexia without localizing signs. Of these, 111In-HIgG identified intrapulmonary accumulation in 17 patients with Pneumocystis carinii pneumonia, eight with bacterial pneumonia, five with cytomegalovirus pneumonia, three with pulmonary Mycobacterium avium intracellulare infection and one with a fungal pneumonia. There was no intrapulmonary accumulation of 111In-HIgG in five patients with bronchopulmonary Kaposi's sarcoma and in three patients with intrathoracic lymphoma. Quantification of lung/heart activity was significantly increased (p < 0.05) in patients with active chest infection compared with those with intrapulmonary tumor or no active lung pathology. Indium-111-HIgG scintigraphy also localized at 14 sites of extrapulmonary infection, including six patients with colitis. There were no false-negative studies but false-positive uptake was seen in four studies. These results confirm that 111In-HIgG correctly identifies the presence and extent of infection in patients positive for HIV antibody.
In situ investigation of the low pressure MOCVD growth of III-V compounds using reflectance anisotropy measurements (1991)

Recent in situ applications of reflectance anisotropy (RA) to the study of the growth of 111-V materials by low pressure MOCVD are reviewed. These results illustrate the extreme sensitivity of the RA technique. During heterojunction growth the first 1-2 seconds are dominated by the change of group V species. Over the time scale of several minutes the signal exhibits damped oscillations correlated to the growth rate. An optical model is proposed to account for this behaviour. A difference in the optical anisotropy between growing and non-growing AsH3 stabilized InAs surface is observed. Large reflectance anisotropies during the growth of lattice-mismatched semiconductors are also presented. It is shown that these anisotropies are related to 3-dimensional growth. The beginning of the lattice-mismatched growth is quantitatively described by an optical model based on effective medium theories. More generally RA technique appears a very promising new method for in situ monitoring of epitaxial processes.
Acute human <i>vs.</i> mouse graft <i>vs.</i> host disease in normal and immunodeficient mice (1992)

Recent reports of persistent engraftment of human lymphocytes and myeloid cells in hereditary immunodeficient severe combined immunodeficient mice (SCID) and beige athymic nude X-linked immunodeficiency (Bg/Nu/XID) mice have raised the question of why attempts to graft human cells into artificially immunosuppressed normal mice have failed so far. In the present study we provide evidence that this difference is due to the absence of natural antibodies in the mutant mice. We demonstrate that human PBL can be grafted in normal mice immunosuppressed by heavy doses of total body irradiation, provided the transplant is performed when the recipients lack natural antibodies in their serum, e.g. as in newborn normal mice, in mice treated with anti-mouse IgM antibody from birth, and in 3-week-old B cell-deficient CBA/N mice. In all cases, large numbers of human PBL were required. Under these conditions an acute and fatal graft vs. host disease (GVHD) developed in the recipients, regardless of whether these were artificially immunosuppressed or hereditary immunodeficient. The clinical manifestations and the histopathology of this xenogeneic acute GVHD are quite different from those of allogeneic GVHD. The former is primarily confined to the hematolymphoid tissues and locations close to accumulations of proliferating lymphoblasts, such as the peritoneal cavity in case of i.p. transplantation. The discordant xenogeneic GVHD is induced by human T lymphocytes and can be abrogated by treatment with anti-human T cell serum.
Design, Synthesis, and Antileukemic Activity of Stereochemically Defined Constrained Analogues of FTY720 (Gilenya) (2013)

FTY720 functions as an immunosuppressant due to its effect on sphingosine-1-phosphate receptors. At doses well above those needed for immunosuppression, FTY720 also has anti-neoplastic actions. Our published work suggests that at least some of FTY720's anti-cancer activity is independent of its effects on S1P receptors and due instead to its ability to induce nutrient transporter down-regulation. Compounds that trigger nutrient transporter loss but lack FTY720's S1P receptor-related, dose-limiting toxicity have the potential to be effective and selective anti-tumor agents. In this study, a series of enantiomerically pure and stereochemically diverse O-substituted benzyl ethers of pyrrolidines was generated and tested for the ability to kill human leukemia cells. The stereochemistry of the hydroxymethyl was found to be a key determinant of compound activity. Moreover, phosphorylation of this group was not required for anti-leukemic activity.
A Slip-Line Field for Ploughing During Orthogonal Cutting (1998)

Under normal machining conditions, the cutting forces are primarily due to the bulk shearing of the workpiece material in a narrow zone called the shear zone. However, under finishing conditions, when the uncut chip thickness is of the order of the cutting edge radius, a ploughing component of the forces becomes significant as compared to the shear forces. Predicting forces under these conditions requires an estimate of ploughing. A slip-line field is developed to model the ploughing components of the cutting force. The field is based on other slip-line fields developed for a rigid wedge sliding on a half-space and for negative rake angle orthogonal cutting. It incorporates the observed phenomena of a small stable build-up of material adhered to the edge and a raised prow of material formed ahead of the edge. The model shows how ploughing forces are related to cutter edge radius—a larger edge causing larger ploughing forces. A series of experiments were run on 6061-T6 aluminum using tools with different edge radii—including some exaggerated in size—and different levels of uncut chip thickness. Resulting force measurements match well to predictions using the proposed slip-line field. The results show great promise for understanding and quantifying the effects of edge radius and worn tool on cutting forces.
IN VIVO STUDY OF HEAD IMPACTS IN FOOTBALL (2007)

Differences in the frequency and magnitude of head acceleration after impact exist between a Division I college team and a high school team. Compared with linemen, skill position players typically sustain the highest-level impacts. Additional data collection and analysis are required to correlate concussion diagnosis with acceleration magnitude and impact location.