gebhart/patrepeval huggingface dataset:
Bollgard® and Bollgard II® Efficacy in Near Isogenic Lines of 'DP50' Upland Cotton in Arizona (2001)

The Cry1Ac gene (Bollgard®) is available in cotton either alone ('B') or in combination (Bollgard II®) with a second gene, Cry2Ab ('X'). We evaluated these two different transgenes, separately and together, in near isogenic lines of the upland cotton variety ‘DP50’. DP50B was previously transformed with the Cry2Ab gene to give rise to the experimental line 985BX which was then back-crossed to DP50 to produce near isogenic single gene variants, 985B and 985X. The lepidopteran target was pink bollworm (PBW), Pectinophora gossypiella (Saunders), which was evaluated in two field studies through a series of samples from artificially and naturally-infested bolls. In one study (NTO), three cotton lines (DP50, DP50B, 985BX) were evaluated under three spray regimes. In the second study (Isoline), five near isogenic lines (DP50, DP50B, 985B, 985X, 985BX) were evaluated under two spray regimes: fully sprayed and lepidopteran unsprayed. In lines containing only one transgene, Cry1Ac or Cry2Ab, bolls had consistently fewer PBWs than the non-Bt variety. Very few PBWs developed into large (3rd instar) larvae in these Bt varieties. The majority (NTO: 83%; Isoline: 94%) of PBWs recovered were dead first instar larvae. Less than 5% of the DP50B bolls in the NTO study were infested with feral large (≥3rd instar) larvae, and large larvae were present in less than 2% of naturally-infested bolls of single-gene lines in the Isoline study. PBW age and mortality distributions confirmed that the single transgenes were effective in stopping PBW development and killing young instars. Cry2Ab displayed a broader spectrum of efficacy as it was significantly more effective against citrus peelminer (Marmara spp.), an incidental lepidopteran present in high densities in the tests. The two-gene (Cry1Ac + Cry2Ab) line showed better (at least 10-fold) efficacy than the single-gene lines against PBW large larvae infestation. The PBW age distributions found in this variety consisted almost entirely (98%) of dead first instar larvae. Less than 0.6% of the bolls of the two-gene variety in the NTO study were infested with large (≥3rd instar) larvae, and there was no infestation by large larvae in any of the naturally-infested bolls in the Isoline study. Yields and other agronomic parameters of the two-gene and single-gene varieties were superior or similar to the null parent. Second pick yields of all Bt varieties were significantly higher than the recurrent parent non-Bt line, suggesting a high degree of efficacy against typically high PBW densities during the late season. Cotton lines with transgenes (Cry1Ac & Cry2Ab) separately and combined demonstrated a high degree of efficacy and agronomic performance for usage in Arizona against PBW. The ramifications of isogenic comparisons of PBW incidence on efficacy and resistance monitoring are discussed.
The dynamic HomeFinder (1992)

We designed, implemented, and evaluated a new concept for visualizing and searching databases utilizing direct manipulation called dynamic queries. Dynamic queries allow users to formulate queries by adjusting graphical widgets, such as sliders, and see the results immediately. By providing a graphical visualization of the database and search results, users can find trends and exceptions easily. User testing was done with eighteen undergraduate students who performed significantly faster using a dynamic queries interface compared to both a natural language system and paper printouts. The interfaces were used to explore a real-estate database and find homes meeting specific search criteria.
Chronic active hepatitis in transgenic mice expressing interferon-gamma in the liver. (1994)

Interferon-gamma may play an important role in the immune response and in inflammatory diseases, including chronic active hepatitis. To understand the role of interferon-gamma in the regulation of inflammation and to establish a mouse model of chronic active hepatitis, we produced transgenic mice in which the mouse interferon-gamma gene was regulated by a liver-specific promoter, the serum amyloid P component gene promoter. Four transgenic mouse lines were generated, and two of these lines expressed mRNA of interferon-gamma in the liver. Levels of serum transaminases increased gradually as a function of age and were significantly higher than those of interferon-gamma-negative littermates after 4 weeks after birth. One transgenic mouse line showed a histology of chronic active hepatitis similar to that found in human patients, although cirrhotic changes such as fibrosis were scarce. Thus, the liver-specific production of interferon-gamma is sufficient to induce chronic inflammatory disease and this mouse is a transgenic model of chronic active hepatitis.
Dual Inhibition of PI3Kα and mTOR as an Alternative Treatment for Kaposi's Sarcoma (2008)

Rapamycin (or sirolimus), the prototypical inhibitor of the mammalian target of rapamycin (mTOR) and an immunosuppressant used for the prevention of renal transplant rejection, has recently emerged as an effective treatment for Kaposi's sarcoma (KS), an enigmatic vascular tumor and a model for pathologic angiogenesis. Indeed, recent work supports a role for mTOR as a central player in the transformation of endothelial cells by the KS-associated herpesvirus-encoded G protein-coupled receptor (vGPCR), the viral oncogene believed to be responsible for causing KS. However, emerging evidence that rapamycin may transiently promote the activation of Akt may limit its use as an anti-KS therapy. Here, we show that activation of Akt in endothelial cells expressing vGPCR is augmented by treatment with rapamycin, resulting in the up-regulation of several Akt proliferative and survival pathways. However, use of a novel dual phosphatidylinositol 3-kinase alpha (PI3Kalpha)/mTOR inhibitor, PI-103, effectively and independently blocked activation of both PI3K and mTOR in vGPCR-expressing endothelial cells. This resulted in more effective inhibition of endothelial cell proliferation and survival in vitro and tumor growth in vivo. Our results suggest that PI-103 may be an effective therapeutic option for the treatment of patients with KS. Moreover, as KS may serve as a model for pathologic angiogenesis, our results further provide the basis for the early assessment of PI-103 as an antiangiogenic chemotherapeutic.
Absorptive-mediated endocytosis of cationized albumin and a beta-endorphin-cationized albumin chimeric peptide by isolated brain capillaries. Model system of blood-brain barrier transport. (1987)

Cationized albumin (pI greater than 8), unlike native albumin (pI approximately 4), enters cerebrospinal fluid (CSF) rapidly from blood. This suggests that a specific uptake mechanism for cationized albumin may exist at the brain capillary wall, i.e. the blood-brain barrier. Isolated bovine brain capillaries rapidly bound cationized [3H]albumin and approximately 70% of the bound radioactivity was resistant to mild acid wash, which is assumed to represent internalized peptide. Binding was saturable and a Scatchard plot gave a maximal binding capacity (Ro) = 5.5 +/- 0.7 micrograms/mgp (79 +/- 10 pmol/mgp), and a half-saturation constant (KD) = 55 +/- 8 micrograms/ml (0.8 +/- 0.1 microM). The binding of cationized [3H]albumin (pI = 8.5-9) was inhibited by protamine, protamine sulfate, and polylysine (molecular weight = 70,000) with a Ki of approximately 3 micrograms/ml for all three proteins. The use of cationized albumin in directed delivery of peptides through the blood-brain barrier was examined by coupling [3H]beta-endorphin to unlabeled cationized albumin (pI = 8.5-9) using the bifunctional reagent, N-succinimidyl 3-(2-pyridyldithio)proprionate. The [3H]beta-endorphin-cationized albumin chimeric peptide was rapidly bound and endocytosed by isolated bovine brain capillaries, and this was inhibited by unlabeled cationized albumin but not by unconjugated beta-endorphin or native bovine albumin. Cationized albumin provides a new tool for studying absorptive-mediated endocytosis at the brain capillary and may also provide a vehicle for directed drug delivery through the blood-brain barrier.
Reversal of abnormal collagen production in Crohn’s disease intestinal biopsies treated with regenerating agents (2003)

This finding offers a rationale for using RGTAs in the treatment of intestinal fibrosis in CD, thus opening up a potential new therapeutic field for this family of drugs.
Dysregulated intrathymic development in the IL-2-deficient mouse leads to colitis-inducing thymocytes (1997)

Gene-targeted mice lacking the IL-2 gene (IL-2 -/- mice) develop various forms of autoimmunity as well as severe colitis, either spontaneously in a conventional environment or after immunization with 2,4,6-trinitrophenol (TNP)-conjugated keyhole limpet hemocyanin (KLH) in a specific pathogen-free environment. We show here that the induction of colitis with TNP-KLH induces a change in the thymocyte population characterized by decreased numbers of double positive (DP; CD4+CD8+) thymocytes (IL-2 +/+, 45.2 x 10(6) vs IL-2 -/-, 23.6 x 10(6)) and increased numbers of single positive (SP; CD4+CD8- or CD4-CD8+) thymocytes (IL-2 +/+, 5.3 x 10(6) vs IL-2 -/-, 20.9 x 10(6)). The latter also bear activation markers. In addition, thymocytes from TNP-KLH-immunized IL-2 -/- mice produce more IFN-gamma and less IL-4 than similarly immunized IL-2 +/+ mice. These defects in thymocyte maturation and lymphokine production are IL-12 driven, since they are prevented when immunized IL-2 -/- mice are coadministered with anti-lL-12. Furthermore, we demonstrate that IL-2 -/- mice exhibit decreased cortical apoptosis as determined by thymocyte numbers and detection of apoptotic cells in situ. Finally, we show that colitis-inducing thymocytes are generated in the immunized IL-2 -/- thymus, since IL-2 +/+ mice develop colitis following injection of small numbers of single positive thymocytes from immunized IL-2 -/- mice but not from IL-2 +/+ mice. Taken together, these data indicate that, in the absence of IL-2, thymocyte maturation is abnormally directed by IL-12 toward the generation of mature, activated Th1-type thymocytes that are capable of mediating colitis.
Fermentative Production of Poly(β-L-malic acid), a Polyelectrolytic Biopolyester, byAureobasidiumsp (1993)

Many strains of a black yeast, identified as Aureobasidium sp., were isolated by a selective medium, which contained mannitol as a main carbon source, and found to produce an extracellular biopolyester from glucose. The biopolyester was recovered as its calcium salt (61 g) from culture filtrate (1 liter). The acid hydrolysis and the transmethylation of the polyester proved L-malic acid to be its monomeric repeating unit. The saponification of the polyester, however, gave fumaric and maleic acids in about 20% yield, in addition to the malic acid. 1H NMR analysis proved the main-chain ester linkage of the polyester to be β-type. The apparent molecular mass was estimated to be distributed between about 6 and 11 kDa in a buffer (pH 6.8) with a high ionic strength (0.2 M).
Sort vs. hash revisited (1994)

Efficient algorithms for processing large volumes of data are very important both for relational and new object-oriented database systems. Many query-processing operations can be implemented using sort- or hash-based algorithms, e.g. intersections, joins, and duplicate elimination. In the early relational database systems, only sort-based algorithms were employed. In the last decade, hash-based algorithms have gained acceptance and popularity, and are often considered generally superior to sort-based algorithms such as merge-join. In this article, we compare the concepts behind sort- and hash-based query-processing algorithms and conclude that (1) many dualities exist between the two types of algorithms, (2) their costs differ mostly by percentages rather than by factors, (3) several special cases exist that favor one or the other choice, and (4) there is a strong reason why both hash- and sort-based algorithms should be available in a query-processing system. Our conclusions are supported by experiments performed using the Volcano query execution engine.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High Breakdown Voltage Achieved on AlGaN/GaN HEMTs With Integrated Slant Field Plates (2006)

A self-aligned "slant-field-plate" technology is presented as an improvement over the discrete multiple field plates for high breakdown voltage AlGaN/GaN HEMTs. Devices were tested in Fluorinert to eliminate the breakdown of air, which was identified to limit the breakdown voltage in AlGaN/GaN HEMTs. A single integrated field plate, which is self-aligned with the gate, is shown to support more than a kilovolt breakdown voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">br</sub> up to 1900 V was measured with Fluorinert). Devices made with this technology show a good large signal-frequency behavior. Various issues regarding breakdown measurements and interpretation of measurement results are presented
Cylinder by Cylinder Engine Pressure and Pressure Torque Waveform Determination Utilizing Speed Fluctuations (1989)

&lt;div class="htmlview paragraph"&gt;Using an elastic model of the engine -drivetrain system, measured speed fluctuation data is passed back through the model to determine the fluctuation waveform of both the total engine torque being developed and the engine pressure torque. The torque fluctuation waveforms are available on a cylinder by cylinder basis. Utilizing the engine pressure torque fluctuation waveform, the mean level of engine torque being developed is obtained, thus providing the full engine pressure torque waveform. Finally, the engine pressure torque waveform is used to obtain the cylinder pressure waveform which gave rise to it. Knowledge of these torques and of the cylinder pressure provides the basis for both open loop and adaptive engine control strategies.&lt;/div&gt;
Suppression of toxin production in Clostridium difficile VPI 10463 by amino acids (1999)

The impact of various growth conditions on the expression of toxins and other proteins by Clostridium difficile VPI 10463 was studied. During non-starved conditions, the rate of toxin synthesis paralleled that of total protein during both exponential growth and stationary phase, and in both defined and complex media. Biotin limitation reduced growth rate and bulk protein synthesis, whereas toxin expression continued, leading to a 50- to 200-fold increase in intracellular toxin levels. Concomitantly, several 22 kDa proteins were up-regulated as revealed by two-dimensional PAGE analysis. The toxin yield was 30-fold higher in peptone yeast extract (PY) than in PY containing glucose (PYG). By contrast, glucose limitation reduced toxin yields by 20- to 100-fold in defined media. By elevating the buffering capacity and bicarbonate concentration, toxin yields were increased by 10-fold in PY and PYG. The high toxin production by C. difficile during growth in PY was lowered 100-fold by adding a blend of nine amino acids and several 60-100 kDa proteins were concomitantly down-regulated. It was concluded that toxin expression in C. difficile VPI 10463 was not affected by growth rate, growth phase, catabolite repression or the stringent response. Instead the co-expression of toxins and a few specific additional proteins appeared to be influenced by metabolic pathways involving CO2 assimilation, carboxylation reactions and metabolism of certain amino acids.
Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination (2013)

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.
Antigen Receptor–Induced Activation and Cytoskeletal Rearrangement Are Impaired in Wiskott-Aldrich Syndrome Protein–Deficient Lymphocytes (1999)

The Wiskott-Aldrich syndrome protein (WASp) has been implicated in modulation of lymphocyte activation and cytoskeletal reorganization. To address the mechanisms whereby WASp subserves such functions, we have examined WASp roles in lymphocyte development and activation using mice carrying a WAS null allele (WAS(-)(/)(-)). Enumeration of hemopoietic cells in these animals revealed total numbers of thymocytes, peripheral B and T lymphocytes, and platelets to be significantly diminished relative to wild-type mice. In the thymus, this abnormality was associated with impaired progression from the CD44(-)CD25(+) to the CD44(-)CD25(-) stage of differentiation. WASp-deficient thymocytes and T cells also exhibited impaired proliferation and interleukin (IL)-2 production in response to T cell antigen receptor (TCR) stimulation, but proliferated normally in response to phorbol ester/ionomycin. This defect in TCR signaling was associated with a reduction in TCR-evoked upregulation of the early activation marker CD69 and in TCR-triggered apoptosis. While induction of TCR-zeta, ZAP70, and total protein tyrosine phosphorylation as well as mitogen-activated protein kinase (MAPK) and stress-activated protein/c-Jun NH(2)-terminal kinase (SAPK/JNK) activation appeared normal in TCR-stimulated WAS(-)(/)(-) cells, TCR-evoked increases in intracellular calcium concentration were decreased in WASp-deficient relative to wild-type cells. WAS(-)(/)(-) lymphocytes also manifested a marked reduction in actin polymerization and both antigen receptor capping and endocytosis after TCR stimulation, whereas WAS(-)(/)(-) neutrophils exhibited reduced phagocytic activity. Together, these results provide evidence of roles for WASp in driving lymphocyte development, as well as in the translation of antigen receptor stimulation to proliferative or apoptotic responses, cytokine production, and cytoskeletal rearrangement. The data also reveal a role for WASp in modulating endocytosis and phagocytosis and, accordingly, suggest that the immune deficit conferred by WASp deficiency reflects the disruption of a broad range of cellular behaviors.
Generic Routing Encapsulation over IPv4 networks (1994)

This memo addresses the case of using IP as the delivery protocol or
the payload protocol and the special case of IP as both the delivery
and payload. This memo also describes using IP addresses and
autonomous system numbers as part of a GRE source route. This memo
provides information for the Internet community. This memo does not
specify an Internet standard of any kind.
Crosstalk between Human IgG Isotypes and Murine Effector Cells (2012)

Development of human therapeutic Abs has led to reduced immunogenicity and optimal interactions with the human immune system in patients. Humanization had as a consequence that efficacy studies performed in mouse models, which represent a crucial step in preclinical development, are more difficult to interpret because of gaps in our knowledge of the activation of murine effector cells by human IgG (hIgG) remain. We therefore developed full sets of human and mouse isotype variants of human Abs targeting epidermal growth factor receptor and CD20 to explore the crosstalk with mouse FcγRs (mFcγRs) and murine effector cells. Analysis of mFcγR binding demonstrated that hIgG1 and hIgG3 bound to all four mFcγRs, with hIgG3 having the highest affinity. hIgG1 nevertheless was more potent than hIgG3 in inducing Ab-dependent cellular cytotoxicity (ADCC) and Ab-dependent cellular phagocytosis with mouse NK cells, mouse polymorphonuclear leukocytes, and mouse macrophages. hIgG4 bound to all mFcγRs except mFcγRIV and showed comparable interactions with murine effector cells to hIgG3. hIgG4 is thus active in the murine immune system, in contrast with its inert phenotype in the human system. hIgG2 bound to mFcγRIIb and mFcγRIII, and induced potent ADCC with mouse NK cells and mouse polymorphonuclear leukocytes. hIgG2 induced weak ADCC and, remarkably, was unable to induce Ab-dependent cellular phagocytosis with mouse macrophages. Finally, the isotypes were studied in s.c. and i.v. tumor xenograft models, which confirmed hIgG1 to be the most potent human isotype in mouse models. These data enhance our understanding of the crosstalk between hIgGs and murine effector cells, permitting a better interpretation of human Ab efficacy studies in mouse models.
Interaction of DNA with clusters of amino acids in proteins (2004)

Protein-DNA interactions facilitate the fundamental functions of living cells and are universal in all living organisms. Several investigations have been carried out, essentially identifying pairs of interactions between the amino acid residues in proteins and the bases in DNA. In the present study, we have detected the recognition motifs that may constitute a cluster of spatially interacting residues in proteins, which interact with the bases of DNA. Graph spectral algorithm has been used to detect side chain clusters comprising Arg, Lys, Asn, Gln and aromatic residues from proteins interacting with DNA. We find that the interaction of proteins with DNA is through clusters in about half of the proteins in the dataset and through individual residues in the rest. Furthermore, inspection of the clusters has revealed additional interactions in a few cases, which have not been reported earlier. The geometry of the interaction between the DNA base and the protein residue is quantified by the distance d and the angle theta. These parameters have been identified for the cation-pi/H-bond stair motif that was reported earlier. Among the Arg, Lys, Asn and Gln residues, the range of (d, theta) values of the interacting Arg clearly falls into the cation-pi and the hydrogen bond interactions of the 'cation-pi/H-bond' stair motif. Analysis of the cluster composition reveals that the Arg residue is predominant than the Lys, Asn and Gln residues. The clusters are classified into Type I and Type II based on the presence or absence of aromatic residues (Phe, Tyr) in them. Residue conservation in these clusters has been examined. Apart from the conserved residues identified previously, a few more residues mainly Phe, Tyr and Arg have also been identified as conserved and interactive with the DNA. Interestingly, a few residues that are parts of interacting clusters and do not interact directly with the DNA have also been conserved. This emphasizes the importance of recognizing the protein side chain cluster motifs interacting with the DNA, which could serve as signatures of protein-DNA recognition in the families of DNA binding proteins.