gebhart/patrepeval huggingface dataset:
Stereo from uncalibrated cameras (2003)

The problem of computing placement of points in 3-D space, given two uncalibrated perspective views, is considered. The main theorem shows that the placement of the points is determined only up to an arbitrary projective transformation of 3-space. Given additional ground control points, however, the location of the points and the camera parameters may be determined. The method is linear and noniterative, whereas previously known methods for solving the camera calibration and placement problem to take proper account of both ground-control points and image correspondences are unsatisfactory in requiring either iterative methods or model restrictions. As a result of the main theorem, it is possible to determine projective invariants of 3-D geometric configurations from two perspective views.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biological and clinical importance of the p53 tumor suppressor gene (1996)

The p53 tumor suppressor gene controls cellular growth after DNA damage through mechanisms involving growth arrest and apoptosis. Mutations that inactivate p53 occur commonly in virtually all human malignancies and can be detected by sequencing of the p53 gene, immunohistochemical staining of tumor tissue with anti-p53 antibodies, single-strand conformation polymorphisms, or other biological assays. Identification of p53 mutation in the germ line is diagnostic of the cancer-prone Li-Fraumeni syndrome. Alterations of the p53 gene result in defective cellular responses after DNA damage and predispose cells to dysregulated growth, tumor formation and progression, and potential resistance (of tumor cells) to certain chemotherapeutic agents or ionizing radiation. A variety of tumors involving mutant p53 have a worse prognosis than tumors of the same type containing no p53 mutations. New diagnostic and therapeutic strategies are evolving as the p53 pathways of cell-cycle arrest and apoptosis become elucidated.
Significant Increases in Pulping Efficiency in C4H-F5H-Transformed Poplars:  Improved Chemical Savings and Reduced Environmental Toxins (2003)

The gene encoding ferulate 5-hydroxylase (F5H) was overexpressed in poplar (Populus tremula × Populus alba) using the cinnamate-4-hydroxylase (C4H) promoter to drive expression specifically in cells involved in the lignin biosynthetic pathway and was shown to significantly alter the mole percentage of syringyl subunits in the lignin, as determined by thioacidolysis. Analysis of poplar transformed with a C4H-F5H construct demonstrated significant increases in chemical (kraft) pulping efficiency from greenhouse-grown trees. Compared to wild-type wood, decreases of 23 kappa units and increases of >20 ISO brightness units were observed in trees exhibiting high syringyl monomer concentrations. These changes were associated with no significant modification in total lignin content and no observed phenotypic differences. C4H-F5H-transformed trees could increase pulp throughputs at mills by >60% while concurrently decreasing chemicals employed during processing (chemical pulping and bleaching) and, consequently, the amount of deleterious byproducts released into the environment. Keywords: Ferulate 5-hydroxylase (F5H); lignin biosynthesis; poplar; lignin degradation; syringyl lignin; lignin monomers; pulping; thioacidolysis; DFRC
Charge-Induced Reversible Strain in a Metal (2003)

Dimension changes on the order of 0.1% or above in response to an applied voltage have been reported for many types of materials, including ceramics, polymers, and carbon nanostructures, but not, so far, for metals. We show that reversible strain amplitudes comparable to those of commercial piezoceramics can be induced in metals by introducing a continuous network of nanometer-sized pores with a high surface area and by controlling the surface electronic charge density through an applied potential relative to an electrolyte impregnating the pores.
Wafer Bonding and Layer Splitting for Microsystems (1999)

In advanced microsystems various types of devices (metal-oxide semiconductor field-effect transistors, bipolar transistors, sensors, actuators, microelectromechanical systems, lasers) may be on the same chip, some of which are 3D structures in nature. Therefore, not only materials combinations (integrated materials) are required for optimal device performance of each type but also process technologies for 3D device fabrication are essential. Wafer bonding and layer transfer are two of the fundamental technologies for the fabrication of advanced microsystems. In this review, the generic nature of both wafer bonding and hydrogen-implantation-induced layer splitting are discussed. The basic processes underlying wafer bonding and the layer splitting process are presented. Examples of bonding and layer splitting of bare or processed semiconductor and oxide wafers are described.
Macroscopic Resonant Tunneling in the Presence of Low Frequency Noise (2008)

We develop a theory of macroscopic resonant tunneling of flux in a double-well potential in the presence of realistic flux noise with a significant low-frequency component. The rate of incoherent flux tunneling between the wells exhibits resonant peaks, the shape and position of which reflect qualitative features of the noise, and can thus serve as a diagnostic tool for studying the low-frequency flux noise in SQUID qubits. We show, in particular, that the noise-induced renormalization of the first resonant peak provides direct information on the temperature of the noise source and the strength of its quantum component.
Activation of the Ras signaling pathway by the CD40 receptor (1996)

The CD40 receptor is an important molecule regulating B lymphocyte proliferation, maturation, Ab class switching, and cell survival. In the present study, we identified signal transduction events triggered by cross-linking the CD40 receptor. Stimulation of Daudi B cells with anti-CD40 resulted in activation of p21ras, an important switch point in the regulation of cell growth and differentiation. Ras activation correlated with a stimulation of Rac1 and MEK-1 as well as tyrosine phosphorylation of phosphatidylinositol 3-kinase. Inhibition of endogenous Ras by transfection of transdominant inhibitory Ras prevented tyrosine phosphorylation or stimulation of phosphatidylinositol 3-kinase, Rac1, or MEK-1 upon CD40 receptor triggering, proving an activation of the Ras pathway by CD40. Ras activation was partially inhibited by either herbimycin A or calphostin pretreatment and completely inhibited by preincubation with a combination of both inhibitors, indicating a synergistic role for protein tyrosine kinases and diglycerides in Ras activation after CD40 stimulation. In support of a role for diglycerides, we detected a 30 +/- 5% decrease of cellular phosphatidylcholine content, correlating with a threefold increase of diacylglycerol synthesis induced by CD40. Supporting a role for protein tyrosine kinase, we measured a five- to eightfold stimulation of p56lyn and p58blk kinase activity. These results suggest the activation of the Ras pathway via an additive function of src kinases and phospholipases that may be important in the mediation of biologic effects after CD40 receptor engagement.
Advanced flow lithography and barcoded particles (2012)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.
Chemical Design of Direct-Gap Light-Emitting Silicon (2002)

Quantum confinement effect has been the dominant approach guiding the search for light-emitting silicon. By first-principles total energy calculations of Si delta-doped with oxygen layers, however, we show that this generally accepted mechanism is ineffective. Instead, a different mechanism is proposed based on defect engineering where the oxygen atoms chemically shift the valence band edge of Si away from the zone center, resulting in the desired optical functionality. Our calculation suggests new design principles for light-emitting silicon as well as providing the microscopic origin for the observed strong luminescence and band gap increase in the SiO(001) multi-delta-layers.
Allelic imbalance on chromosome I in human breast cancer. I. Minisatellite and rflp analysis (1995)

In order to characterise the role of chromosome 1 more fully in breast cancer, polymorphic markers mapping along the length of the whole chromosome were used to assess a panel of 71 tumour-lymphocyte pairs for allelic imbalance. Complex patterns of alterations were established that are consistent with cytogenetic data in the literature. Deletion mapping of individuals with loss of heterozygosity identified five independent smallest common regions of deletion, two of which are novel. There are also three discrete regions showing a gain in copy number of one homologue. The two arms of the chromosome may be subject to different events; the short arm primarily undergoes interstitial deletions, whereas the long arm is subject to whole arm events (as both gains and losses) as well as regional deletions.
Molecular cloning of putative odorant-binding and odorant-metabolizing proteins (1991)

Olfactory reception occurs via the interaction of odorants with the chemosensory cilia of the olfactory receptor cells located in the nasal epithelium. The cDNA clones from mRNA specific to olfactory mucosa were studied. One of these clones, OBPII, encodes a secretory protein with significant homology to odorant-binding protein (OBP), a protein with broad odorant-binding ability, and is expressed in the lateral nasal gland, which is the site of expression of OBP. The OBPII sequence also shows significant homology to the VEG protein, which is thought to be involved in taste transduction. OBPII is a new member of the lipophilic molecule carrier protein family. The second cDNA clone encodes a novel homologue of glutathione peroxidase, an enzyme involved in cellular biotransformation pathways. Its expression appears to be localized to the Bowman's glands, the site of several previously identified olfactory-specific biotransformation enzymes.
Room-temperature reactive bonding by using nano scale multilayer systems (2011)

This paper focuses on room-temperature reactive bonding by using nano scale multilayer systems. The exothermic reaction within the Ti/a-Si multilayer is used as an internal heat source for bonding. Herein, we used lithographical, wet etching and electro-plating procedures to generate very thin integrated reactive multilayer systems. The reaction in the very thin films generated enough heat to self-propagate and to melt tin films. High-speed camera imaging was used to characterize the reaction kinetics and the propagation of the reaction front onto substrates. Furthermore, we demonstrated a strong dependence on substrate material for adhesion after the reaction front has passed.
Leucine Aminopeptidase RNAs, Proteins, and Activities Increase in Response to Water Deficit, Salinity, and the Wound Signals Systemin, Methyl Jasmonate, and Abscisic Acid1 (1999)

LapA RNAs, proteins, and activities increased in response to systemin, methyl jasmonate, abscisic acid (ABA), ethylene, water deficit, and salinity in tomato (Lycopersicon esculentum). Salicylic acid inhibited wound-induced increases of LapA RNAs. Experiments using the ABA-deficient flacca mutant indicated that ABA was essential for wound and systemin induction of LapA, and ABA and systemin acted synergistically to induce LapA gene expression. In contrast, pin2 (proteinase inhibitor 2) was not dependent on exogenous ABA. Whereas both LapA and le4 (L. esculentum dehydrin) were up-regulated by increases in ABA, salinity, and water deficit, only LapA was regulated by octadecanoid pathway signals. Comparison of LapA expression with that of the PR-1 (pathogenesis-related 1) and GluB (basic beta-1,3-glucanase) genes indicated that these PR protein genes were modulated by a systemin-independent jasmonic acid-signaling pathway. These studies showed that at least four signaling pathways were utilized during tomato wound and defense responses. Analysis of the expression of a LapA1:GUS gene in transgenic plants indicated that the LapA1 promoter was active during floral and fruit development and was used during vegetative growth only in response to wounding, Pseudomonas syringae pv tomato infection, or wound signals. This comprehensive understanding of the regulation of LapA genes indicated that this regulatory program is distinct from the wound-induced pin2, ABA-responsive le4, and PR protein genes.
Cortex mapping reveals regionally specific patterns of genetic and disease-specific gray-matter deficits in twins discordant for schizophrenia (2002)

The symptoms of schizophrenia imply disruption to brain systems supporting higher-order cognitive activity, but whether these systems are impacted differentially against a background of diffuse cortical gray-matter deficit remains ambiguous. Some unaffected first-degree relatives of schizophrenics also manifest cortical gray-matter deficits, but it is unclear whether these changes are isomorphic with those in patients, and the answer is critical to understanding the neurobiological conditions necessary for disease expression given a predisposing genotype. Here we report three-dimensional cortical surface maps (probabilistic atlases matching subjects' anatomy point by point throughout cortex) in monozygotic (MZ) and dizygotic (DZ) twins discordant for chronic schizophrenia along with demographically matched control twins. A map encoding the average differences between schizophrenia patients and their unaffected MZ co-twins revealed deficits primarily in dorsolateral prefrontal cortex, superior temporal gyrus, and superior parietal lobule. A map encoding variation associated with genetic proximity to a patient (MZ co-twins > DZ co-twins > control twins) isolated deficits primarily in polar and dorsolateral prefrontal cortex. In each case, the statistical significance was confirmed through analysis of 10,000 Monte Carlo permutations, and the remaining cortex was shown to be significantly less affected by contrast analysis. The disease-related deficits in gray matter were correlated with measures of symptom severity and cognitive dysfunction but not with duration of illness or antipsychotic drug treatment. Genetic and disease-specific influences thus affect gray matter in partially nonoverlapping areas of predominantly heteromodal association cortex, changes that may act synergistically in producing overt behavioral features of the disorder.
Increased Resistance of Peptides to Serum Proteases by Modification of their Amino Groups (2003)

The ability of synthetic protein fragments to survive the degradative action of aminopeptidases and serum proteolytic enzymes can be remarkably enhanced by slight modifications at their N-terminal alpha-amino group. This can be achieved by addition of beta-alanine or amino acids of the D-configuration, amino acids which are seldom found in a living organism. These modifications do scarcely modify the chemical and physical properties of the peptides, and should be preferred, especially for in vivo tests, to drastic alterations of peptides as produced by dinitrophenylation or dansylation of the amino groups.
Treatment of Severe Diabetes Mellitus by Insulin Infusion (1974)

A new and simple form of insulin therapy for diabetic hyperglycaemia and ketoacidosis has been developed using a continuous intravenous infusion of insulin at a rate of 2.4 U/hr to maintain serum insulin concentration at physiological levels. This rate raises the mean serum insulin to 83 muU/ml and has a therapeutic effect which is not augmented by higher infusion rates. The response to such low doses of insulin indicates a need for a reappraisal of currently held theories about insulin resistance in diabetic ketoacidosis. In 11 diabetic patients with a mean plasma glucose of 514 mg/100 ml this therapy produced continuous falls in plasma glucose at a mean rate of 75 mg/100 ml/hr, and 10 out of 11 patients recovered within eight hours. This form of therapy is simple to institute, not complicated by hypoglycaemia, and avoids the confusion and empiricism of previously described forms of therapy.
A Deep Learning Mammography-based Model for Improved Breast Cancer Risk Prediction (2019)

Background Mammographic density improves the accuracy of breast cancer risk models. However, the use of breast density is limited by subjective assessment, variation across radiologists, and restricted data. A mammography-based deep learning (DL) model may provide more accurate risk prediction. Purpose To develop a mammography-based DL breast cancer risk model that is more accurate than established clinical breast cancer risk models. Materials and Methods This retrospective study included 88 994 consecutive screening mammograms in 39 571 women between January 1, 2009, and December 31, 2012. For each patient, all examinations were assigned to either training, validation, or test sets, resulting in 71 689, 8554, and 8751 examinations, respectively. Cancer outcomes were obtained through linkage to a regional tumor registry. By using risk factor information from patient questionnaires and electronic medical records review, three models were developed to assess breast cancer risk within 5 years: a risk-factor-based logistic regression model (RF-LR) that used traditional risk factors, a DL model (image-only DL) that used mammograms alone, and a hybrid DL model that used both traditional risk factors and mammograms. Comparisons were made to an established breast cancer risk model that included breast density (Tyrer-Cuzick model, version 8 [TC]). Model performance was compared by using areas under the receiver operating characteristic curve (AUCs) with DeLong test (<i>P</i> < .05). Results The test set included 3937 women, aged 56.20 years ± 10.04. Hybrid DL and image-only DL showed AUCs of 0.70 (95% confidence interval [CI]: 0.66, 0.75) and 0.68 (95% CI: 0.64, 0.73), respectively. RF-LR and TC showed AUCs of 0.67 (95% CI: 0.62, 0.72) and 0.62 (95% CI: 0.57, 0.66), respectively. Hybrid DL showed a significantly higher AUC (0.70) than TC (0.62; <i>P</i> < .001) and RF-LR (0.67; <i>P</i> = .01). Conclusion Deep learning models that use full-field mammograms yield substantially improved risk discrimination compared with the Tyrer-Cuzick (version 8) model. © RSNA, 2019 <i>Online supplemental material is available for this article.</i> See also the editorial by Sitek and Wolfe in this issue.
Hyperbranched Polyether Polyols: A Modular Approach to Complex Polymer Architectures (2000)

A versatile modular system for complex branched polymer architectures has been developed through exploitation of the multibranching polymerization chemistry of glycidol. This report summarizes recent advances in the preparation of these novel polymers and describes the modular concept used to tailor their topology to give functional materials, such as the dye-loaded molecular nanocapsule depicted in the Figure.
PDGF-AA and PDGF-BB biosynthesis: proprotein processing in the Golgi complex and lysosomal degradation of PDGF-BB retained intracellularly. (1992)

Platelet-derived growth factor is a potent mitogen for cells of mesenchymal origin. It is made up of two polypeptide chains (A and B) combined in three disulfide-linked dimeric forms (AA, AB, and BB). Here, the biosynthesis and proteolytic processing of the two homodimeric forms of PDGF (AA and BB) were studied in CHO cells stably transfected with A-chain (short splice version) or B-chain cDNA. PDGF-AA was processed to a 30-kD molecule which was secreted from the cells. In contrast, PDGF-BB formed two structurally distinct end products; a minor secreted 30-kD form and a major cell-associated 24-kD form. Immunocytochemical studies at light- and electron-microscopical levels revealed presence of PDGF in the Golgi complex, in lysosomes, and to a smaller extent in the ER. From analysis of cells treated with brefeldin A, an inhibitor of ER to Golgi transport, it was concluded that dimerization occurs in the ER, whereas the proteolytic processing of PDGF-AA and PDGF-BB precursors normally occurs in a compartment distal to the ER. Exposure of the cultures to the lysosomal inhibitor chloroquine led to an increased cellular accumulation of PDGF-BB, as determined both by metabolic labeling experiments and immunocytochemical methods, indicating that the retained form of PDGF-BB is normally degraded in lysosomes. Structural analysis of the two end products of PDGF-BB revealed that the secreted 30-kD form is a dimer of peptides processed as the B-chain of PDGF purified from human platelets, and that the retained 24-kD form is made up of subunits additionally processed in the NH2-terminus. Also, the 24-kD form was shown to be composed of proteolytic fragments held together by disulfide bridges. Taken together these findings suggest that the newly synthesized PDGF A- and B-chains are dimerized in the ER and thereafter transferred to the Golgi complex for proteolytic processing. From there, PDGF-AA is carried in vesicles to the cell surface for release extracellularly by exocytosis. A smaller part of PDGF-BB (the 30-kD form) is handled in a similar way, whereas the major part (the 24-kD form) is generated by additional proteolysis in the Golgi complex, from which it is slowly carried over to lysosomes for degradation.
A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. (1991)

A minimal model for the mitotic oscillator is presented. The model, built on recent experimental advances, is based on the cascade of post-translational modification that modulates the activity of cdc2 kinase during the cell cycle. The model pertains to the situation encountered in early amphibian embryos, where the accumulation of cyclin suffices to trigger the onset of mitosis. In the first cycle of the bicyclic cascade model, cyclin promotes the activation of cdc2 kinase through reversible dephosphorylation, and in the second cycle, cdc2 kinase activates a cyclin protease by reversible phosphorylation. That cyclin activates cdc2 kinase while the kinase triggers the degradation of cyclin has suggested that oscillations may originate from such a negative feedback loop [Félix, M. A., Labbé, J. C., Dorée, M., Hunt, T. & Karsenti, E. (1990) Nature (London) 346, 379-382]. This conjecture is corroborated by the model, which indicates that sustained oscillations of the limit cycle type can arise in the cascade, provided that a threshold exists in the activation of cdc2 kinase by cyclin and in the activation of cyclin proteolysis by cdc2 kinase. The analysis shows how miototic oscillations may readily arise from time lags associated with these thresholds and from the delayed negative feedback provided by cdc2-induced cyclin degradation. A mechanism for the origin of the thresholds is proposed in terms of the phenomenon of zero-order ultrasensitivity previously described for biochemical systems regulated by covalent modification.
Isolation and characterization of a cDNA clone encoding the 19 kDa protein of signal recognition particle (SRP): expression and binding to 7SL RNA (1988)

Signal recognition particle (SRP) consists of a 7SL RNA molecule and 6 protein subunits. We have isolated and characterized cDNA clones from human liver which encode the 19kDa protein subunit (SRP19). This subunit binds to the RNA directly and mediates binding of a second polypeptide, the 54kDa subunit which is involved in signal sequence recognition. Amino acid sequences deduced from the human cDNA sequence were identical to amino acid sequences of tryptic peptides from canine pancreatic SRP19. In vitro transcription and translation of the human cDNA resulted in a protein product the same size as canine SRP19 which could be immunoprecipitated by an antiserum raised against canine SRP19. SRP19 synthesized in a cell-free system specifically bound to 7SL RNA. The sequence of SRP19 is discussed with respect to its binding to 7SL RNA.