gebhart/patrepeval huggingface dataset:
Effective lysis of lymphoma cells with a stabilised bispecific single‐chain Fv antibody against CD19 and FcγRIII (CD16) (2005)

A recombinant bispecific single-chain fragment variable antibody (bsscFv), directed against the B-cell antigen CD19 and the low affinity Fc-receptor FcgammaRIII (CD16), was designed for use in the treatment of patients with leukaemias and lymphomas. The Fc-portions of whole antibodies were deliberately eliminated in this construct to avoid undesired effector functions. A stabilised bsscFv, ds[CD19 x CD16], was generated, in which disulphide bonds bridging the respective variable light (VL) and variable heavy (VH) chains were introduced into both component single-chain (sc)Fvs. After production in 293T cells and chromatographic purification, ds[CD19 x CD16] specifically and simultaneously bound both antigens. The serum stability of ds[CD19 x CD16] was increased more than threefold when compared with the unstabilised counterpart, while other biological properties were not affected by these mutations. In antibody-dependent cellular cytotoxicity experiments, ds[CD19 x CD16] mediated specific lysis of both CD19-positive malignant human B-lymphoid cell lines and primary tumour cells from patients with B-cell chronic lymphocytic leukaemia or B-cell acute lymphoblastic leukaemia. Natural killer cells, mononuclear cells (MNCs) from healthy donors and, in some instances, MNCs isolated from patients after allogeneic stem cell transplantation, were used as effectors. Thus, ds[CD19 x CD16] holds promise for the treatment of CD19(+) B-lineage malignancies.
Parkin protects human dopaminergic neuroblastoma cells against dopamine-induced apoptosis (2004)

Parkinson's disease (PD) is characterized by the selective degeneration of dopaminergic (DA) neurons in substantia nigra pars compacta (SNpc). A combination of genetic and environmental factors contributes to such a specific loss. Among the five PD-linked genes identified so far, parkin, a protein-ubiquitin E3 ligase, appears to be the most prevalent genetic factor in PD. Although a variety of substrates have been identified for parkin, none of them is selectively expressed in nigral DA neurons. It remains unclear how accumulation of these substrates in the absence of functional parkin may cause the selective death of DA neurons in SNpc. Here, we show that overexpression of parkin protected human DA neuroblastoma cell line (SH-SY5Y) against apoptosis induced by DA or 6-OHDA, but not by H(2)O(2) or rotenone. Parkin significantly attenuated dopamine-induced activation of c-Jun N-terminal kinase (JNK) and caspase-3. It also decreased the level of reactive oxygen species (ROS) and protein carbonyls in the cell. Inhibiting DA uptake through dopamine transporter or treating the cell with antioxidants significantly reduced oxidative stress and dopamine toxicity. Furthermore, PD-linked mutations of parkin significantly abrogated the protective effect of wild-type parkin, as well as its ability to suppress ROS and protein carbonylation. These results suggest that parkin protects against dopamine toxicity by decreasing oxidative stress and ensuing activation of apoptotic programs such as the JNK/caspase pathway. This protective function of parkin, which is greatly attenuated by its PD-linked mutations, may be uniquely important for the survival of DA neurons, as they are constantly threatened by oxyradicals produced during dopamine oxidation.
VEGF Receptor Subtypes KDR and FLT1 Show Different Sensitivities to Heparin and Placenta Growth Factor (1994)

Vascular endothelial growth factor (VEGF) is an angiogenic growth factor which binds to two structurally related tyrosine kinase receptors denoted KDR and FLT1. To compare the interaction of VEGF with each receptor, cell lines which express individual receptor subtypes were identified using Northern blot hybridization. Bovine aortic endothelial (ABAE) cells and WM35 melanoma cells were found to express KDR, while FLT1 was primarily expressed on SK-MEL-37. Both receptor subtypes were detected on another melanoma cell line (WM9). Heparin augmented VEGF binding to KDR-expressing cells (ABAE and WM35), but inhibited VEGF binding to FLT1-expressing cells (SK-MEL-37 and WM9). The concentration of heparin required for half maximal stimulation of VEGF binding to KDR-expressing cells (500 ng/ml) was 25 times greater than that required for half maximal inhibition of binding to FLT1-expressing cells (20 ng/ml). In WM9 cells, the effect of heparin was bimodal; low concentration inhibited, while higher concentrations stimulated binding of 125I-VEGF. Placenta growth factor (PIGF-1) is a recently described growth factor structurally similar to VEGF. PIGF-1 had a negligible or no effect on 125I-VEGF binding to KDR-expressing cells (ABAE, WM35), but did complete for binding to FLT1-expressing cells (SK-MEL-37 and WM9). Addition of heparin had no effect on its ability to compete for binding with 125I-VEGF. The data indicate differential regulation of the two VEGF receptors by heparin and extended specificity of FLT1 receptor, but not KDR, for binding PIGF-1 growth factor.
Measurement of Cytogenetic Damage in Rodent Blood with a Single‐Laser Flow Cytometer (2003)

The in vivo rodent micronucleus test is widely utilized to screen chemicals for genotoxic activity. Double-strand chromosome breaks or dysfunction of the mitotic spindle apparatus can lead to micronuclei formation in dividing cells. Erythrocytes have become the target population of choice, as precursor cells are continuously dividing and micronuclei are readily observable after extrusion of nuclei. The traditional method has been to stain peripheral blood or bone marrow smears and microscopically determine the frequency of micronucleated erythrocytes. Because these events are rare, the process is tedious and time consuming. This unit describes a procedure for fixing and staining rodent peripheral blood for flow cytometric enumeration. The combination of reagents provides for differential labeling and enumeration of four subpopulations: mature erythrocytes, micronucleus-containing mature erythrocytes, young erythrocytes (reticulocytes), and micronucleus-containing young erythrocytes. Malaria-infected rodent erythrocytes, which closely mimic micronucleus-containing erythrocytes, serve as a biological standard to facilitate rational and consistent equipment calibration.
Introspective Black Box Failure Prediction for Autonomous Driving (2020)

Failures in autonomous driving caused by complex traffic situations or model inaccuracies remain inevitable in the near future. While much research is focused on how to prevent such failures, comparatively little research has been done on predicting them. An early failure prediction would allow for more time to take actions to resolve challenging situations. In this work, we propose an introspective approach to predict future disengagements of the car by learning from previous disengagement sequences. Our method is designed to detect failures as early as possible by using sensor data from up to ten seconds before each disengagement. The car itself is treated as a black box, with only its state data and the number of detected objects being required. Since no model-specific knowledge is needed, our method is applicable to any self-driving system. Currently, no public data of real-life disengagements is available. To test our approach, we therefore use autonomous driving data provided by BMW that was collected with BMW research vehicles over multiple months. We show that an LSTM classifier trained with sequences of state data can predict failures up to seven seconds in advance with an accuracy of more than 80%. This is two seconds earlier than comparable approaches from the literature.
Proteinase-activated Receptors, Targets for Kallikrein Signaling (2006)

Serine proteinases like thrombin can signal to cells by the cleavage/activation of proteinase-activated receptors (PARs). Although thrombin is a recognized physiological activator of PAR(1) and PAR(4), the endogenous enzymes responsible for activating PAR(2) in settings other than the gastrointestinal system, where trypsin can activate PAR(2), are unknown. We tested the hypothesis that the human tissue kallikrein (hK) family of proteinases regulates PAR signaling by using the following: 1) a high pressure liquid chromatography (HPLC)-mass spectral analysis of the cleavage products yielded upon incubation of hK5, -6, and -14 with synthetic PAR N-terminal peptide sequences representing the cleavage/activation motifs of PAR(1), PAR(2), and PAR(4); 2) PAR-dependent calcium signaling responses in cells expressing PAR(1), PAR(2), and PAR(4) and in human platelets; 3) a vascular ring vasorelaxation assay; and 4) a PAR(4)-dependent rat and human platelet aggregation assay. We found that hK5, -6, and -14 all yielded PAR peptide cleavage sequences consistent with either receptor activation or inactivation/disarming. Furthermore, hK14 was able to activate PAR(1), PAR(2), and PAR(4) and to disarm/inhibit PAR(1). Although hK5 and -6 were also able to activate PAR(2), they failed to cause PAR(4)-dependent aggregation of rat and human platelets, although hK14 did. Furthermore, the relative potencies and maximum effects of hK14 and -6 to activate PAR(2)-mediated calcium signaling differed. Our data indicate that in physiological settings, hKs may represent important endogenous regulators of the PARs and that different hKs can have differential actions on PAR(1), PAR(2), and PAR(4).
Secure Time Synchronization for Wireless Sensor Networks Based on Bilinear Pairing Functions (2010)

Time synchronization is crucial for wireless sensor networks (WSNs) and secure time synchronization is a key requirement for many sophisticated applications running on these networks. Most of the existing secure time synchronization protocols incur high communication and storage costs, and are subject to a few known security attacks. In this paper, we propose a novel secure time synchronization protocol for both homogeneous and heterogeneous WSN models; the protocol uses pairing-based cryptography to secure the time synchronization and to reduce the communication and storage requirements of each node. Security analysis of the protocol shows that it is highly robust against different attacks, namely selective forwarding attack, wormhole attack, masquerade attack, message manipulation attack, replay attack and delay attack.
PREVENTION OF BONE MARROW AND CARDIAC GRAFT REJECTION IN AN H-2 HAPLOTYPE DISPARATE MOUSE COMBINATION BY AN ANTI-LFA-1 ANTIBODY (1995)

The aim of the present study was to compare the preventive effect of a nondepleting monoclonal antibody specific for the LFA-1 alpha chain (CD11a) on the rejection of bone marrow, vascularized cardiac, and nonvascularized skin grafts in the same haplotype-disparate mouse strain combination. A 7-day treatment with a total dose of 0.5 mg of anti-LFA-1 antibody (H-129) had no effect on the rejection of BDF1(H-2b/d) skin grafts by CDF1 (H-2k/d)-treated mice. In contrast, the same treatment regimen significantly prolonged the survival of BDF1 cardiac allografts in CDF1 mice: 7 out of 10 mice had a functional graft after 70 days, whereas all control mice had rejected their graft by 11 days. Nevertheless, cardiac allografts were ultimately rejected. In contrast, infusion of anti-LFA-1 antibody was able to promote definitive engraftment of T-depleted BDF1 marrow in 9 gray-irradiated CDF1 recipients: in surviving mice, engraftment increased from 10% in controls to 78% in antibody-treated recipients. In mice that tolerated their cardiac graft for more than 70 days, there was a slight delay in the rejection of donor skin graft but no in vitro evidence of tolerance. In contrast, mice with successful marrow engraftment did not reject donor skin graft and failed to mount proliferative and cytotoxic responses against donor alloantigens, whatever the percentage of engrafted donor leukocytes. These results indicate that a nondepleting anti-LFA-1 antibody can efficiently protect against rejection of MHC-incompatible heart and bone marrow. The protective effect of anti-LFA-1 antibody was associated with the induction of T cell tolerance toward donor antigens after bone marrow transplantation.
Studies of the cellulolytic system of Trichoderma reesei QM 9414 (1988)

Limited action of papain on the native forms of two cellobiohydrolases (CBH) from Trichoderma reesei (CBH I, 65 kDa, and CBH II, 58 kDa) leads to the isolation of the respective core fragments (56 kDa and 45 kDa) which are fully active on small, soluble substrates, but have a strongly reduced activity (respectively 10% and 50% of the initial value) on microcrystalline cellulose (Avicel). By partial sequencing at the C terminus of the CBH I core and at the N terminus of the CBH II core the papain cleavage sites have been assigned in the primary structures (at about residue 431 and 82 respectively). This limited action of papain on the native enzymes indicates the presence of hinge regions linking the core to these terminal glycopeptides. The latter conserved sequences appear either at the C or N terminus of several cellulolytic enzymes from Trichoderma reesei [Teeri et al. (1987) Gene 51, 43-52]. The specific activities of the intact enzymes and their cores on two forms of insoluble cellulose (crystalline, amorphous) differentiate the CBH I and CBH II in terms of adsorption and catalytic properties. Distinct functions can be attributed to the terminal peptides: for intact CBH II the N-terminal region contributes in the binding onto both cellulose types; the homologous C-terminal peptide in CBH I, however, only affects the interaction with microcrystalline cellulose. It could be inferred that CBH I and its core bind preferentially to crystalline regions. This seems to be corroborated by the results of CBH I/CBH II synergism experiments.
Preparation of water‐swollen hydrogel membranes for gas separation (2001)

Abstract Water‐swollen hydrogel (WSH) membranes for gas separation were prepared by the dip‐coating of asymmetric porous polyetherimide (PEI) membrane supports with poly(vinyl alcohol) (PVA)–glutaraldehyde (GA), followed by the crosslinking of the active layer by a solution method. Crosslinked PVA/GA film of different blend compositions (PVA/GA = 1/0.04, 0.06, 0.08, 0.10, 0.12 mol %) were characterized by differential scanning calorimetry (DSC) and their water‐swelling ratio. The swelling behavior of PVA/GA films of different blend compositions was dependent on the crosslinking density and chemical functional groups created by the reaction between PVA and GA, such as the acetal group, ether linkage, and unreacted pendent aldehydes in PVA. The permeation performances of the membranes swollen by the water vapor contained in a feed gas were investigated. The behavior of gas permeation through a WSH membrane was parallel to the swelling behavior of the PVA/GA film in water. The permeation rate of carbon dioxide through the WSH membranes was 10 5 (cm 3 cm −2 s −1 cmHg) and a CO 2 /N 2 separation factor was about 80 at room temperature. The effect of the additive (potassium bicarbonate, KHCO 3 ) and catalyst (sodium arsenite, NaASO 2 ) on the permeation of gases through these WSH membranes was also studied. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 80: 1785–1791, 2001
Genetic element from human surfactant protein SP-C gene confers bronchiolar-alveolar cell specificity in transgenic mice (1991)

Transgenic mice bearing chimeric genes consisting of 5'-sequences derived from the human surfactant protein C (SP-C) gene and the bacterial chloramphenicol acetyltransferase (CAT) gene were generated. Analysis of CAT activity was utilized to demonstrate tissue-specific and developmental expression of chimeric genes containing 3.7 kb of sequences from the human SP-C gene. Lung-specific expression of the 3.7 SP-C-CAT transgene was observed in eight distinct transgenic mouse lines. Expression of the 3.7 SP-C-CAT transgene was first detected in fetal lung on day 11 of gestation and increased dramatically with advancing gestational age, reaching adult levels of activity before birth. In situ hybridization demonstrated that expression of 3.7 SP-C-CAT mRNA was confined to the distal respiratory epithelium. Antisense CAT hybridization was detected in bronchiolar and type II epithelial cells in the adult lung of the 3.7 SP-C-CAT transgenic mice. In situ hybridization of four distinct 3.7 SP-C-CAT transgenic mouse lines demonstrated bronchiolar-alveolar expression of the chimeric CAT gene, although the relative intensity of expression at each site varied within the lines studied. Glucocorticoids increased murine SP-C mRNA in fetal lung organ culture. Likewise, expression of 3.7 SP-C-CAT transgene increased during fetal lung organ or explant culture and was further enhanced by glucocorticoid in vitro. The 5'-regions of human SP-C conferred developmental, lung epithelial, and glucocorticoid-enhanced expression of bacterial CAT in transgenic mice. The increased expression of SP-C accompanying prenatal lung development and exposure to glucocorticoid is mediated, at least in part, at the transcriptional level, being influenced by cis-active elements contained within the 5'-flanking region of the human SP-C gene.
Determination of Double-Bond Positions in Highly Unsaturated Fatty Acids by GC-MS (1991)

A method for determining double-bond positions in highly unsaturated fatty acids by GC-MS was developed and is conducted as follows : A highly unsaturated fatty acid methyl ester is partially reduced with hydrazine or deuterated hydrazine. After acidification, the resulting mixture containing several kinds of unsaturated esters along with one saturated ester is recovered by hexane extraction and then separated by argentation TLC according to the number of double bonds. The isolated methyl monoenoate fraction corresponding to standard methyl cis-monoenoates is subjected to I2-catalyzed reaction with dimethyl disulfide. The resulting dimethyl disulfide adducts of methyl monoenoates areanalyzed by GC-MS. The cleavage between the methylthio-substituted carbons yielded sets of key fragment ions showing the original double-bond positions in the monoenoate carbon chain. The GC-MS data on the structures of methyl monoenoates derived from the starting highly unsaturated ester confirmed the original double-bond positions in the molecule of the starting ester. Separately using hydrazine and deuterated hydrazine as reducing reagents for the simultaneous analysis of the same sample provided further useful data for identifying the sample structure owing to the resulting shift of key fragment ions with deuterium atoms.This method was applied to the analysis of polyenoic fatty acids in eel total lipid. The most highly unsaturated fatty acid in the lipids was found to be cis-4, cis-7, cis-10, cis-13, cis-16, cis-19-docosahexaenoic acid based on mass spectral data.
<title>Carbon fiber polymer-matrix structural composite as a semiconductor</title> (1998)

An epoxy-matrix composite with continuous crossply carbon fibers was found to be a semiconductor in the through- thickness direction, with a tunable energy gap of 10<SUP>-2</SUP>-10<SUP>-1</SUP> eV. The higher the pressure during composite fabrication by lamination, the higher the interlaminar stress and the greater the energy gap, which is the activation energy for electron jumping from one lamina to the adjacent one in the composite. The semiconducting behavior involves the contact electrical resistivity between adjacent laminae in the composite decreasing reversibly with increasing temperature. The concept of optoelectronic and electronic devices made from carbon fiber polymer-matrix composites is provided. Devices include solar cells, light emitting diodes, lasers, infrared detectors and transistors.Thus, a new dimension is added to smart structures and a new field of electronics is born.
Recombinant immunotoxins for the treatment of Hodgkin's disease (Review). (2000)

In recent years, substantial experience has been accumulated with tumor-specific immunotherapeutics which seem to be effective against minimal residual disease. The coupling of toxins to monoclonal antibodies has indicated promising results in early clinical trials. Recombinant DNA technology makes it possible to genetically fuse coding regions of V genes or cytokines to modified toxin domains. These recombinant immunotoxins can easily be manipulated to increase the cytotoxic potency or affinity. Binding single-chain variable fragments (scFv) expressed as chimeric fusion proteins on the surface of filamentous bacteriophages were selected on Hodgkin-derived cell lines. This technique was also used to create a new humanized anti-CD30 scFv which exhibits similar binding to the CD30 antigen when compared to its murine predecessor. ScFvs were then inserted into a new bacterial expression vector and thus fused to a deletion mutant of Pseudomonas exotoxin. Anti-CD25(scFv)-ETA' and anti-CD30(scFv)-ETA' were isolated from E. coli periplasm and purified by metal chelate affinity and size exclusion chromatography. All immunotoxins produced showed specific cytotoxicity against Hodgkin lymphoma cell lines as documented by competitive assays. In addition, these constructs were highly efficient in the treatment of disseminated human Hodgkin's disease in SCID mice. These in vivo data indicate a possible clinical impact for patients with relapsed CD25- and/or CD30-positive lymphoma.
Dense Human Body Correspondences Using Convolutional Networks (2015)

We propose a deep learning approach for finding dense correspondences between 3D scans of people. Our method requires only partial geometric information in the form of two depth maps or partial reconstructed surfaces, works for humans in arbitrary poses and wearing any clothing, does not require the two people to be scanned from similar viewpoints, and runs in real time. We use a deep convolutional neural network to train a feature descriptor on depth map pixels, but crucially, rather than training the network to solve the shape correspondence problem directly, we train it to solve a body region classification problem, modified to increase the smoothness of the learned descriptors near region boundaries. This approach ensures that nearby points on the human body are nearby in feature space, and vice versa, rendering the feature descriptor suitable for computing dense correspondences between the scans. We validate our method on real and synthetic data for both clothed and unclothed humans, and show that our correspondences are more robust than is possible with state-of-the-art unsupervised methods, and more accurate than those found using methods that require full watertight 3D geometry.
THE INHERITANCE OF ERUCIC ACID CONTENT IN RAPESEED (BRASSICA NAPUS) (1964)

Genetic analysis of F 2 , F 3 , and backcross populations supported the hypothesis that erucic acid content in seed oil of plants of Brassica napus L. is governed by two genes displaying no dominance and acting in an additive manner. Environment appeared to influence erucic acid content, especially in genotypes capable of producing a large amount of this acid. Methods for the breeding of plants of Brassica campestris L. with zero erucic acid are outlined and it is suggested that similar methods could be used to breed for or against other fatty acids.