gebhart/patrepeval huggingface dataset:
Response of X-Ray-Sensitive CHO Mutant Cells (xrs-6c) to Radiation: II. Relationship between Cell Survival and the Induction of Chromosomal Damage with Low Doses of α Particles (1991)

The induction of cytotoxicity, chromosomal aberrations, and sister chromatid exchanges (SCEs) was measured in CHO K-1c cells and in isogenic X-ray-sensitive mutant xrs-6c cells that had been irradiated with X rays and alpha particles in isoleucine-deficient alpha-minimal essential medium in G1 phase of the cell cycle. There was a noticeable shoulder region on the survival curve for CHO K-1c cells irradiated with very low doses of alpha particles, whereas this feature was absent for xrs-6c cells with alpha-particle doses as low as 0.5 cGy. Higher frequencies of chromatid-type aberrations were induced in G1-phase xrs-6c cells than in G1-phase CHO K-1c cells by both gamma- and alpha-particle irradiation. Induction of nonlethal chromosomal aberrations was observed following exposure to 2-6 cGy of alpha particles, doses yielding 97-100% cell survival. Irradiation with 0.5 cGy of alpha particles induced SCE; nearly 60% of irradiated cells contained significantly increased levels of SCE. However, only 3% of the nuclei of cells exposed to 0.5 cGy of alpha-particle radiation were actually traversed by an alpha particle. The observation that a large fraction of cells apparently survive exposure to very low doses of alpha-particle radiation with persistent genetic damage manifested by both chromosomal aberrations and SCEs may have important implications for the carcinogenic hazards of high-LET radiation.
Scanning Capacitance Microscopy Measurements and Modeling: Progress Towards Dopant Profiling of Silicon (1995)

A scanning capacitance microscope (SCM) has been implemented by interfacing a commercial contact‐mode atomic force microscope with a high‐sensitivity capacitance sensor. The SCM has promise as a next‐generation dopant‐profiling technique because the measurement is inherently two dimensional, has a potential spatial resolution limited by tip diameter of at least 20 nm, and requires no current carrying metal–semiconductor contact. Differential capacitance images have been made with the SCM of a variety of bulk‐doped samples and in the vicinity of pn junctions and homojunctions. Also, a computer code has been written that can numerically solve Poisson’s equation for a model SCM geometry by using the method of collocation of Gaussian points. Measured data and model output for similar structures are presented. How data and model output can be combined to achieve an experimental determination of dopant profile is discussed.
Isolation and partial characterization of major protein antigens in the culture fluid of Mycobacterium tuberculosis (1991)

Five actively secreted proteins (MPT32, MPT45, MPT51, MPT53, and MPT63) and the MPT46 protein were purified to homogeneity from Mycobacterium tuberculosis culture fluid and compared with proteins previously purified by ourselves and other investigators. Antisera were obtained by immunization of rabbits with all of the newly isolated proteins identified to be immunogenic. Two-dimensional electrophoresis of culture fluids obtained each week for 2 to 10 weeks of culturing of M. tuberculosis revealed characteristic changes, permitting identification of two distinct groups of proteins being actively secreted from the mycobacterial cells or appearing later in the culture fluids as a result of the release of soluble proteins from the cytosol after lysis of bacteria. The N-terminal amino acid sequences of five MPTs were shown to be identical to those of proteins previously isolated by other investigators and given different designations, and five new sequences are given. These sequences and the use of the antisera may serve to identify these proteins with mycobacterial constituents isolated by other investigators. The previously identified but not isolated MPT45 protein was shown to correspond to the C component of the antigen 85 complex. The 27-kDa MPT51 protein was demonstrated to cross-react with the three components of the antigen 85 complex, and the N-terminal amino acid sequences of MPT51 and MPT59 showed 60% homology. This finding and the extensive cross-reactivity between the components of the antigen 85 complex may indicate that there is a family of closely related secreted proteins in mycobacteria.
Thiourea‐catalyzed Oxidative Coupling Reaction of N‐Phenyl Tetrahydroisoquinoline with β‐Keto Acids (2017)

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Semi-Supervised Deep Learning for Monocular Depth Map Prediction (2017)

Supervised deep learning often suffers from the lack of sufficient training data. Specifically in the context of monocular depth map prediction, it is barely possible to determine dense ground truth depth images in realistic dynamic outdoor environments. When using LiDAR sensors, for instance, noise is present in the distance measurements, the calibration between sensors cannot be perfect, and the measurements are typically much sparser than the camera images. In this paper, we propose a novel approach to depth map prediction from monocular images that learns in a semi-supervised way. While we use sparse ground-truth depth for supervised learning, we also enforce our deep network to produce photoconsistent dense depth maps in a stereo setup using a direct image alignment loss. In experiments we demonstrate superior performance in depth map prediction from single images compared to the state-of-the-art methods.
Stepwise improvements in catalytic effectiveness: independence and interdependence in combinations of point mutations of a sluggish triosephosphate isomerase (1991)

Second-site suppressor changes that improve the catalytic potency of a sluggish mutant of the enzyme triosephosphate isomerase have been examined both individually and in combination. Each of the second-site mutations increases the specific catalytic activity of a triosephosphate isomerase in which the catalytic base, glutamate-165, has been changed to aspartate. These second-site suppressors are G10S, S96P, S96T, E97D, V167D, and G233R. Not one of these changes enhances the value of kcat/Km for the wild-type enzyme, which is consistent with the knowledge that the reaction catalyzed by the wild-type enzyme is already diffusion-controlled. Indeed, two of the changes, S96P and V167D, are catalytically deleterious to the wild-type isomerase. When pairs of second-site suppressors are combined with the primary lesion E165D, six pairs show additive independence while the effects of eight other pairs are less than additive. The sites fall into two clusters: pairs within a cluster always interfere with one another and do not produce additive improvements in catalytic activity, whereas combinations of changes from different clusters tend to be additive in their effects. No combination of second-site suppressor mutations behaves synergistically, though there seems to be no a priori reason to exclude this possibility. Since the catalytic potency of each of the six second-site suppressor mutants can be further improved by the introduction of (at least) one of the other five changes, it is evident that none of the double mutants lies at a local catalytic maximum. In these cases, therefore, the opportunity exists for at least two "steps" of monotonic catalytic improvement along each of six different "paths" in protein space.
A New 24-nor-Oleanane Triterpenoid from Salvia carduacea (2002)

A new triterpenoid (1) has been isolated from the acetone extract of the leaves of Salvia carduacea, together with other compounds described previously. The structure of 1 [2alpha,3alpha-dihydroxy-24-nor-4(23),12-oleanadien-28-oic acid] was elucidated by spectroscopic methods, particularly by extensive 1D and 2D NMR studies.
A new VLSI memory cell using capacitance coupling (CC cell) (1984)

A new VLSI memory cell is proposed, which offers a small cell area, about 6F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (F is the feature size), readout signal gain, and high alpha-particle immunity. Since it employs capacitance coupling in a write operation, it requires only one bit line and is called a capacitance coupling (CC) cell. A CC cell consists of three transistors and a capacitor, which are integrated in a small area by sharing their nodes with one another. The charge is stored in a high-concentration p-type diffused layer (p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer) in a shallow n-type diffused layer (n-layer). The p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer potential controls the readout current which flows through the n-layer. To obtain both the p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -Iayer isolation and the large readout signal, trench isolation was employed. Experimental test devices having 0.7-µm deep n-layer, 0.2-µm deep p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer, and 1.5-µm deep trench isolation region were fabricated. They showed complete CC cell operation and "0"/"1" readout current ratio of more than 10.
Optimization of Immobilized Bacterial Disaccharides for Surface Plasmon Resonance Imaging Measurements of Antibody Binding (2008)

The interactions between proteins and immobilized carbohydrates are crucial to biological events such as cell signaling and immune response. The modification of surfaces with carbohydrates to create sensing platforms provides a pathway to study these interactions in a laboratory setting. In this work, a family of structurally related Salmonella disaccharide epitopes is immobilized on thin gold films in an array format to probe antibody binding with surface plasmon resonance (SPR) imaging. The disaccharides are modified with an alkyl thiol linker for facile immobilization to gold. Small differences in the stereochemistry of the immobilized, modified disaccharides are shown to greatly influence the binding of a monoclonal antibody. Specifically, binding is only observed to an immobilized abequose dideoxyhexose relative to a tyvelose or a paratose analogue. However, both the amount and relative strength of bound antibody depends on the distribution of disaccharide moieties in a mixed monolayer of the epitope and a nonbinding diluent molecule. We thoroughly characterize the mixed monolayers with a variety of techniques to understand the optimal density and distribution of the disaccharide for antibody capture. This work reinforces the importance of controlling the density of ligands at the interface for optimized surface based bioassays.
Parameters to Aid in Optimizing Progenitor Collection in Children (2005)

Journal of Pediatric Hematology/Oncology: September 2005 - Volume 27 - Issue 9 - p 465 doi: 10.1097/01.mph.0000188516.23608.d1
Role of NADPH oxidase and ANG II in diabetes-induced retinal leukostasis (2007)

We studied whether angiotensin II (ANG II) via superoxide may contribute to retinal leukostasis and thus to the pathogenesis of retinopathies. We studied: 1) whether intravitreal ANG II induces retinal leukostasis that is altered by antioxidants or by apocynin, a NAD(P)H oxidase inhibitor and 2) whether retinal leukostasis induced by diabetes in rats is also altered by these treatments. Rats were injected intravitreally with ANG II (20 microg in 2 microl), and divided into the following three groups: 1) untreated; 2) treated with tempol doses ( approximately 3 mM/day) and N-acetylcysteine (NAC; approximately 1 g.kg(-1).day(-1)); and 3) treated with apocynin ( approximately 2 mM/day), both in the drinking water. Rats with streptozotocin-induced diabetes were similarly treated. Leukostasis was evaluated 48 h after ANG II or 2 wk after diabetes induction. ANG II increased retinal leukostasis from 0.3 +/- 0.5 to 3.7 +/- 0.4 leukocytes/ mm(2) (P < 0.01), and these changes were markedly decreased by treatment with tempol + NAC or apocynin, and also by a blocking antibody against vascular endothelial growth factor given intravitreally (P < 0.01). In addition, incubation of dihydroethidium-loaded retina sections with ANG II caused marked increase in superoxide formation. Compared with normal controls, retinal leukostasis in diabetic rats markedly increased from 0.2 +/- 0.3 to 3.8 +/- 0.1 leukocytes/mm(2) (P < 0.01). Diabetic retinal leukostasis was also decreased by treatment with tempol-NAC and normalized by apocynin. Thus increases in intravitreal ANG II can induce retinal leukostasis, which appears to be mediated via increasing superoxide generation by NAD(P)H oxidase, and by VEGF. The activity of NAD(P)H oxidase is required for leukostasis to occur in the diabetic retina.
The cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologous to a site-specific recombinase (1990)

The nucleotide sequence of the sporulation gene spoIVC cisA in Bacillus subtilis was determined and found to encode a protein of 500 amino acid residues with a calculated molecular weight of 57,481, which is in good agreement with the size of the gene product estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid sequence of the N-terminal region of this protein is homologous to the site-specific DNA recombinases. Hybridization of a 3.6-kilobase EcoRI fragment carrying the spoIVC cisA gene with the EcoRI-restricted chromosomal DNA prepared from cells of various stages showed that DNA rearrangement occurs only in the mother cell in the region adjacent to spoIVC cisA 3 h after the initiation of sporulation. This result coincides with that of Stragier et al. (P. Stragier, B. Kunkel, L. Kroos, and R. Losick, Science 243:507-512, 1989). The timing of the DNA rearrangement coincides very well with the timing of spoIVC cisA gene expression. The DNA rearrangement was not observed in spoIVC cisA mutants. These results strongly suggest that the spoIVC cisA gene encodes a site-specific DNA recombinase having a very important role in sporulation.
Bisphosphonate risedronate reduces metastatic human breast cancer burden in bone in nude mice. (1995)

Human breast cancer frequently metastasizes to the skeleton to cause osteolysis and subsequent pain, pathological fracture, and hypercalcemia. Because bone continuously releases growth factors stored in bone matrix by bone resorption during physiological remodeling and, thus, possibly provides a favorable microenvironment for metastatic breast cancer cells to proliferate, inhibitors of bone resorption used either prophylactically or in patients with established disease, therefore, would seem likely to be useful adjuvant therapy in patients with breast cancer. However, the parameters for monitoring progressive osteolytic bone disease in humans are imprecise. We examined the effects of the third generation bisphosphonate, risedronate, which is a specific inhibitor of osteoclastic bone resorption, in a bone metastasis model in nude mice in which intracardiac injection of the human breast cancer cell line MDA-231 leads to osteolytic bone metastases. Risedronate (4 micrograms/animal/day) was given s.c. to animals (a) after radiologically small but defined osteolytic metastases were observed; (b) simultaneously with MDA-231 cell inoculation through the entire experimental period; or (c) by short-term prophylactic administration before inoculation of MDA-231 cells. In all experiments, risedronate either slowed progression or inhibited the development of bone metastases assessed radiographically. Furthermore, mice treated continuously with risedronate showed significantly longer survival than did control mice. Histomorphometrical analysis revealed that osteoclast numbers were diminished at metastatic tumor sites. Unexpectedly, there was also a marked decrease in tumor burden in bone in risedronate-treated animals. In contrast, the growth of metastatic breast cancer in soft tissues surrounding bones was not affected by risedronate. Moreover, risedronate had no effects on the local growth of s.c. implanted MDA-231 breast cancers in nude mice or on MDA-231 cell proliferation in culture. These data demonstrate that risedronate decreases metastatic MDA-231 breast cancer burden selectively in bone, as well as suppresses progression of established osteolytic lesions and prevents the development of new osteolytic lesions; thus, the data suggest that inhibition of osteoclastic bone resorption may be a useful adjunctive therapy for the treatment of cancers that have colonized in bone.
The Impact of Alanyl‐Glutamine on Clinical Safety, Nitrogen Balance, Intestinal Permeability, and Clinical Outcome in Postoperative Patients: A Randomized, Double‐Blind, Controlled Study of 120 Patients (1999)

Ala-Gln-supplemented PN was clinically safe, had better nitrogen balance, and maintained intestinal permeability in postoperative patients. The clinical outcome of the patients in study group was better; it was significantly different from the control group.
Secreted products of a nonmucoid Pseudomonas aeruginosa strain induce two modes of macrophage killing: external-ATP-dependent, P2Z-receptor-mediated necrosis and ATP-independent, caspase-mediated apoptosis (2000)

A nonmucoid clinical isolate of Pseudomonas aeruginosa, strain 808, elaborated ATP-dependent and ATP-independent types of cytotoxic factors in the growth medium. These cytotoxic factors, active against macrophages, were secreted during the exponential phase of growth in a complex medium. Commensurate with the appearance of the cytotoxic activities in the cell-free growth medium, several ATP-utilizing enzymic activities, such as adenylate kinase, nucleoside diphosphate kinase and 5'-nucleotidase (ATPase and/or phosphatase), were detected in the medium. These ATP-utilizing enzymes are believed to convert external ATP, presumably effluxed from macrophages, to various adenine nucleotides, which then activate purinergic receptors such as P2Z, leading to enhanced macrophage cell death. Pretreatment of macrophages with periodate-oxidized ATP (oATP), which is an irreversible inhibitor of P2Z receptor activation, prevented subsequent ATP-induced macrophage cell death. A second type of cytotoxic factor(s) operated in an ATP-independent manner such that it triggered activation of apoptotic processes in macrophages, leading to proteolytic conversion of procaspase-3 to active caspase-3. This cytotoxic factor(s) did not appear to act on procaspase-3 present in macrophage cytosolic extracts. Intact macrophages, when exposed to the cytotoxic factor(s) for 6-16 h, underwent apoptosis and demonstrated the presence of active caspase-3 in their cytosolic extracts. Interestingly, two redox proteins, azurin and cytochrome c(551), were detected in the cytotoxic preparation. When cell-line-derived or peritoneal macrophages or mast cells were incubated overnight with Q-Sepharose column flow-through fraction or with a mixture of azurin and cytochrome c(551), they underwent extensive cell death due to induction of apoptosis.
Extracellular Acidic pH Inhibits Oligodendrocyte Precursor Viability, Migration, and Differentiation (2013)

Axon remyelination in the central nervous system requires oligodendrocytes that produce myelin. Failure of this repair process is characteristic of neurodegeneration in demyelinating diseases such as multiple sclerosis, and it remains unclear how the lesion microenvironment contributes to decreased remyelination potential of oligodendrocytes. Here, we show that acidic extracellular pH, which is characteristic of demyelinating lesions, decreases the migration, proliferation, and survival of oligodendrocyte precursor cells (OPCs), and reduces their differentiation into oligodendrocytes. Further, OPCs exhibit directional migration along pH gradients toward acidic pH. These in vitro findings support a possible in vivo scenario whereby pH gradients attract OPCs toward acidic lesions, but resulting reduction in OPC survival and motility in acid decreases progress toward demyelinated axons and is further compounded by decreased differentiation into myelin-producing oligodendrocytes. As these processes are integral to OPC response to nerve demyelination, our results suggest that lesion acidity could contribute to decreased remyelination.
Application of a new network concept for faster service deployment (2003)

A network concept in which the end office performs only the basic transport services for circuit connections as well as signal interworking is presented. Services are controlled from a centralized location and provided from one or more service modules which are connected to the network via standardized ISDN (intergrated-services digital network) interfaces. This allows services to be introduced by a centralized system instructing one or more service modules, thus eliminating further changes to the end office. It is shown how the proposed network can readily provide this basic transport service and signal interworking.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Advanced Tumor Stage Is an Independent Risk Factor of Postoperative Infectious Complications After Colorectal Surgery (2013)

Advanced tumors increase the risk of infectious complications after colorectal resection, with other risk factors including malnutrition, obesity, and resection by laparotomy. Optimization of modifiable risk factors through nutritional repletion and the choice of a minimally invasive operation should be considered.
Synthesis and Evaluation of Antiviral Activity of L-Acosamine and L-Ristosamine Nucleosides of Furanose Configuration. (1991)

Mercuric-catalyzed hydrolysis of acetylated L-rhamnal 1 gives an alpha,beta-unsaturated aldehyde 2. 1,4-Addition of DBU-phthalimide salt with concomitant acetyl shift resulted in L-ribo and L-arabino isomers of 5-O-acetyl-2,3,6-trideoxy-3-phthalimido-hexofuranose 3 and 4. After acetylation at the anomeric center, coupling with silylated thymine resulted in three new nucleosides, with L-acosamine and L-ristosamine of furanose configuration as the carbohydrate moiety. The target compounds have been evaluated for their antiviral activity against HIV and HSV-1.
Photosynthesis and Inorganic Carbon Usage by the Marine Cyanobacterium, Synechococcus sp (1982)

The marine cyanobacterium, Synechococcus sp. Nägeli (strain RRIMP N1) changes its affinity for external inorganic carbon used in photosynthesis, depending on the concentration of CO(2) provided during growth. The high affinity for CO(2) + HCO(3) (-) of air-grown cells (K((1/2)) < 80 nanomoles [pH 8.2]) would seem to be the result of the presence of an inducible mechanism which concentrates inorganic carbon (and thus CO(2)) within the cells. Silicone-oil centrifugation experiments indicate that the inorganic carbon concentration inside suitably induced cells may be in excess of 1,000-fold greater than that in the surrounding medium, and that this accumulation is dependent upon light energy. The quantum requirements for O(2) evolution appear to be some 2-fold greater for low CO(2)-grown cells, compared with high CO(2)-grown cells. This presumably is due to the diversion of greater amounts of light energy into inorganic carbon transport in these cells.A number of experimental approaches to the question of whether CO(2) or HCO(3) (-) is primarily utilized by the inorganic carbon transport system in these cells show that in fact both species are capable of acting as substrate. CO(2), however, is more readily taken up when provided at an equivalent concentration to HCO(3) (-). This discovery suggests that the mechanistic basis for the inorganic carbon concentrating system may not be a simple HCO(3) (-) pump as has been suggested. It is clear, however, that during steady-state photosynthesis in seawater equilibrated with air, HCO(3) (-) uptake into the cell is the primary source of internal inorganic carbon.