gebhart/patrepeval huggingface dataset:
Fast-camera calibration of stereo vision system using BP neural networks (2010)

In position measurements by far-range photogrammetry, the scale between object and image has to be calibrated. It means to get the parameters of the perspective projection matrix. Because the image sensor of fast-camera is CMOS, there are many uncertain distortion factors. It is hard to describe the scale between object and image for the traditional calibration based on the mathematical model. In this paper, a new method for calibrating stereo vision systems with neural networks is described. A linear method is used for 3D position estimation and its error is corrected by neural networks. Compared with DLT (Direct Linear Transformation) and direct mapping by neural networks, the accuracy is improved. We have used this method in the drop point measurement of an object in high speed successfully.
Are tumours angiogenesis‐dependent? (2003)

The final proof of principle that cancer patients can be effectively treated with angiogenesis inhibitors is eagerly awaited. Various preclinical in vivo experiments have proven that most tumours need new vessel formation in order to grow and to form metastases. First of all, tumours do not grow in avascular corneas until new blood vessels reach the implant. Secondly, the introduction of only one angiogenic gene can cause a switch from tumour dormancy to progressive tumour growth. Thirdly, tumour growth can be inhibited and sometimes tumour regression can be obtained just by attacking the vascular compartment with specific angiogenesis inhibitors. These three examples of preclinical experiments and many others have led to the conclusion that, in general, tumours are angiogenesis-dependent. Supported by disappointing clinical results, the angiogenesis dependency of tumours has been questioned, mainly because of the immaturity and the presumed lack of a functional blood supply (oxygen delivery and discarding of waste products) from a newly formed tumour vasculature. However, human tumours are highly heterogeneous in vascular architecture, differentiation, and functional blood supply. Vascular immaturity is a natural consequence of a genetically based unlimited expansion of tumour cells, compared to the well-regulated growth of different organs during embryonic development, for example. Unlimited tumour expansion and therefore the continuous stimulation of vessel outgrowth prevent endothelial cells from generating a mature vasculature, but instead continuously stimulate them to expand the vascular compartment of the growing tumour. In this review, the translation of angiogenesis inhibitors as a treatment for cancer from preclinical experiments to the clinic is evaluated. The preclinical evidence that tumours are angiogenesis-dependent is summarized and explanations are put forward for why the clinical results so far are not as exciting as was expected from preclinical studies. Reviewing the translation, one may conclude that human tumours are heterogeneous in their vascular architecture and function and that tumour-induced angiogenesis in humans is a more complex (multifactorially regulated) process compared with angiogenesis in preclinical cancer models.
Electron-phonon coupling and intervalley splitting determine the linewidth of single-electron transport through PbSe nanocrystals (2009)

The linewidth of the resonances in the single-electron tunneling spectra has been investigated for PbSe semiconductor nanocrystals (NCs) with scanning tunneling spectroscopy at low temperature. The linewidth of the resonances corresponding to tunneling through the first conduction and valence levels is found to increase with decreasing size of the NCs. Based on theoretical calculations, this broadening is mainly induced by the coupling between the tunneling electrons and the longitudinal optical phonon mode of the NC, and by the splitting of the degenerate electronic levels between the different L-valleys in the Brillouin zone. For the smallest sizes, it is shown that the intervalley splitting is the major source of broadening.
Mechanisms Underlying Ion Transport in Lamellar Block Copolymer Membranes (2012)

Recent experiments have reported intriguing trends for the molecular weight (MW) dependence of the conductivity of block copolymer lamellae that contrast with the behavior of homopolymer matrices. By using coarse-grained simulations of the sorption and transport of penetrant cations, we probe the possible mechanisms underlying such behavior. Our results indicate that the MW dependence of conductivity of homopolymeric and block copolymeric matrices arise from different mechanisms. On the one hand, the solvation energies of cations, and, in turn, the charge carrier concentrations, themselves, exhibit a MW dependence in block copolymer matrices. Such trends are shown to arise from variations in the thickness of the conducting phase relative to that of the interfacial zones. Moreover, distinct mechanisms are shown to be responsible for the diffusivities of ions in homopolymer and block copolymer matrices. In the former, diffusivity effects associated with the free ends of the polymers play an important role. In contrast, in block copolymer lamellae, the interfacial zone between the blocks presents a zone of hindered diffusivity for ions and manifests as a molecular weight dependence of the ionic diffusivity. Together, the preceding mechanisms are shown to provide a plausible explanation for the experimentally observed trends for the conductivity of block copolymer matrices.
Contra-Friedel–Crafts tert-butylation of substituted aromatic rings via directed metallation and sulfinylation (2006)

Directed metallation and sulfinylation yields sulfoxides which undergo ipso nucleophilic aromatic substitution with tertiary and secondary alkyllithiums, giving aromatic rings bearing alkyl groups generally incompatible with directed metallation methods and with regioselectivity complementary with classical Friedel-Crafts substitution.
Diabetes With Mitochondrial Gene tRNALYS Mutation (1994)

This observation is the first report of association of diabetes with the mitochondrial tRNA(LYS) mutation. Insulin secretory capacity was significantly lower in the mutant members than in the nonmutated members. These findings suggest that the pancreatic beta-cell secretory defect of insulin might be one of the phenotypes of the mitochondrial tRNA(LYS) mutation.
Direct binding to and tyrosine phosphorylation of the alpha subunit of the type I interferon receptor by p135tyk2 tyrosine kinase. (1994)

Binding of type I interferons (IFNs) to their receptors induces rapid tyrosine phosphorylation of multiple proteins, including the alpha and beta subunits of the receptor, the polypeptides that form the transcriptional activator ISGF3 alpha (Stat113, Stat84, and Stat91), and the p135tyk2 and Jak-1 tyrosine kinases. In this report, we demonstrate that the alpha subunit of the type I IFN receptor (IFN-R) corresponds to the product of a previously cloned receptor subunit cDNA and, further, that the p135tyk2 tyrosine kinase directly binds and tyrosine phosphorylates this receptor subunit. Glutathione S-transferase (GST) fusion proteins encoding the different regions of the cytoplasmic domain of the alpha subunit can bind the p135tyk2 contained in human cell lysates. The association between the alpha subunit and Tyk2 was demonstrated by immunoblotting with anti-Tyk2 and antiphosphotyrosine antibodies and by using an in vitro kinase assay. Analogous experiments were then performed with recombinant baculoviruses encoding constitutively active Jak family tyrosine kinases. In this case, p135tyk2, but not Jak-1 or Jak-2 protein, binds to the GST-IFN-R proteins, suggesting that the interaction between these two proteins is both direct and specific. We also demonstrate that Tyk2, from extracts of either IFN alpha-treated human cells or insect cells infected with the recombinant baculoviruses, can catalyze in vitro phosphorylation of GST-IFN-R protein in a specific manner. Deletion mutants of the GST-IFN-R protein were used to localize both the binding and tyrosine phosphorylation site(s) to a 46-amino-acid juxtamembrane region of the alpha subunit, which shows sequence homology to functionally similar regions of other cytokine receptor proteins. These data support the hypothesis that the Tyk2 protein functions as part of a receptor complex to initiate intracellular signaling in response to type I IFNs.
A Collapsin Response Mediator Protein 2 Isoform Controls Myosin II-Mediated Cell Migration and Matrix Assembly by Trapping ROCK II (2012)

Collapsin response mediator protein 2 (CRMP-2) is known as a regulator of neuronal polarity and differentiation through microtubule assembly and trafficking. Here, we show that CRMP-2 is ubiquitously expressed and a splice variant (CRMP-2L), which is expressed mainly in epithelial cells among nonneuronal cells, regulates myosin II-mediated cellular functions, including cell migration. While the CRMP-2 short form (CRMP-2S) is recognized as a substrate of the Rho-GTP downstream kinase ROCK in neuronal cells, a CRMP-2 complex containing 2L not only bound the catalytic domain of ROCK II through two binding domains but also trapped and inhibited the kinase. CRMP-2L protein levels profoundly affected haptotactic migration and the actin-myosin cytoskeleton of carcinoma cells as well as nontransformed epithelial cell migration in a ROCK activity-dependent manner. Moreover, the ectopic expression of CRMP-2L but not -2S inhibited fibronectin matrix assembly in fibroblasts. Underlying these responses, CRMP-2L regulated the kinase activity of ROCK II but not ROCK I, independent of GTP-RhoA levels. This study provides a new insight into CRMP-2 as a controller of myosin II-mediated cellular functions through the inhibition of ROCK II in nonneuronal cells.
Golgi endo-alpha-D-mannosidase from rat liver, a novel N-linked carbohydrate unit processing enzyme. (1987)

An enzyme has been found in Triton-treated rat liver Golgi membranes which trims Glc1Man9GlcNAc to Man8GlcNAc with the release of Glc alpha 1-3Man. By removing a glucosylmannose disaccharide and yielding only one Man8GlcNAc isomer, this endo-alpha-D-mannosidase provides a processing route alternative to the sequential actions of alpha-glucosidase II and alpha-mannosidase I. The endomannosidase was fully active in the presence of 1-deoxynojirimycin and EDTA which inhibited exoglycosidase release of glucose and mannose, respectively, and these agents were, therefore, included in the standard assay. The specific activity of the endomannosidase was found to be 69-fold greater in Golgi than in rough endoplasmic reticulum (RER) membranes, and Golgi-RER mixing experiments excluded the possibility that the low activity in the RER was the result of some inhibitor present in this fraction. The neutral pH optimum (approximately 7.0) of the enzyme was consistent with a role in N-linked oligosaccharide processing. The existence of an endo-alpha-D-mannosidase pathway for glucose removal could provide an explanation for the incomplete block in oligosaccharide processing which is observed in cells with inhibited or deficient alpha-glucosidase.
Comparison of Efficiency of Infection of Human Gene Therapy Target Cells via Four Different Retroviral Receptors (1996)

The relative efficiency of transduction of gene therapy target cells was measured for retroviruses bearing the envelopes of amphotropic murine leukemia virus (MLV-A), xenotropic murine leukemia virus (MLV-X), gibbon ape leukemia virus (GALV), feline leukemia virus subgroup B (FeLV-B), and the feline endogenous virus RD114. These viruses use various cell-surface receptors. Activated peripheral blood lymphocytes (PBL) and primary melanoma cultures were infected relatively poorly by MLV-X pseudotypes. RD114 pseudotypes infected PBL relatively well, whereas bone marrow progenitor cells were efficiently infected by all viruses. Helper-free virus bearing the envelopes of MLV-A, RD114, or GALV was similarly tested. All infected melanoma or bone marrow progenitor cells efficiently, whereas MLV-A was relatively inefficient for infection of PBL. The general utility of RD114 pseudotyped virus for gene delivery coupled with its resistance to inactivation by human serum makes this envelope the most suitable choice for in vivo gene therapy.
Vascular endothelial growth factor is induced in response to transforming growth factor-beta in fibroblastic and epithelial cells. (1994)

Transforming growth factor beta (TGF-beta) is a multifunctional polypeptide that regulates the proliferation and differentiation of various cells and has an angiogenic effect in vivo, although it inhibits the growth of cultured endothelial cells. We report here that TGF-beta treatment of quiescent cultures of mouse embryo-derived AKR-2B cells, which are growth-stimulated by TGF-beta, and human lung adenocarcinoma A549 cells, which are growth-inhibited by TGF-beta, results in the induction of vascular endothelial growth factor (VEGF) mRNA and protein. Maximal VEGF mRNA levels occurred 4-8 h after stimulation with a decline to background levels in 24 h. In contrast, the related placenta growth factor mRNA was not induced by TGF-beta in these cells. No VEGF receptor mRNA was seen in AKR-2B cells. Also, TGF-beta treatment of endothelial cells, which express the FLT1 and KDR/FLK-1 receptors for VEGF, did not cause VEGF induction. Because VEGF is known to be a strong angiogenic factor for endothelial cells, the results suggest that the angiogenic effect of TGF-beta on endothelial cells in blood vessels may be mediated at least partly by a paracrine induction of VEGF in other surrounding cell types.
On-line single droplet deposition for MALDI mass spectrometry (2004)

A single droplet generator was coupled with a rotating ball inlet matrix-assisted laser desorption/ionization (MALDI) time of flight (TOF) mass spectrometer. Single droplets with 100 picoliter volume were ejected by a piezoelectric-actuated droplet generator and deposited onto a matrix-coated rotating stainless steel ball at atmospheric pressure. The single droplet deposit was transported to the vacuum side of the instrument where ionization was accomplished using a UV pulsed laser. Using this on-line interface, it was possible to obtain protonated molecule signal from as little as 10 fmol analyte.
Combination of Integrin-Binding Peptide and Growth Factor Promotes Cell Adhesion on Electron-Beam-Fabricated Patterns (2011)

Understanding and controlling cell adhesion on engineered scaffolds is important in biomaterials and tissue engineering. In this report we used an electron-beam (e-beam) lithography technique to fabricate patterns of a cell adhesive integrin ligand combined with a growth factor. Specifically, micron-sized poly(ethylene glycol) (PEG) hydrogels with aminooxy- and styrene sulfonate-functional groups were fabricated. Cell adhesion moieties were introduced using a ketone-functionalized arginine-glycine-aspartic acid (RGD) peptide to modify the O-hydroxylamines by oxime bond formation. Basic fibroblast growth factor (bFGF) was immobilized by electrostatic interaction with the sulfonate groups. Human umbilical vein endothelial cells (HUVECs) formed focal adhesion complexes on RGD- and RGD and bFGF-immobilized patterns as shown by immunostaining of vinculin and actin. In the presence of both bFGF and RGD, cell areas were larger. The data demonstrate confinement of cellular focal adhesions to chemically and physically well-controlled microenvironments created by a combination of e-beam lithography and "click" chemistry techniques. The results also suggest positive implications for addition of growth factors into adhesive patterns for cell-material interactions.
Ballistic transport in a semiconductor with collisions (1981)

At low temperature in a high mobility semiconductor such as GaAs the transit time of electrons across a short device may become comparable or even less than the time between collisions. Under such conditions electrons may move almost ballistically accelerating in the electric field. Such a situation is analyzed in the frame of a simple model assuming a single energy independent relaxation time. This model allows solving a problem in an analytical form. The model predicts that at high injection level (voltages larger than a punchthrough voltage) the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-V</tex> characteristics change from the case described by the Child-Langmuir law for a short device and/or a large time between collisions to the case described by the Mott-Gurney law in the collision-dominated case. At low injection level the space oscillations of the electric field with the wavelength <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\lambda = 2\pi\v/\omega_{p}</tex> may appear (ω <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</inf> is the plasma frequency and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">v</tex> is the electron velocity) and the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-V</tex> characteristic may become multivalued (S-type) due to the influence of the positive donor charge leading to the space overshoot of electrons.
Of the three tegument proteins that package mRNA in herpes simplex virions, one (VP22) transports the mRNA to uninfected cells for expression prior to viral infection (2002)

An earlier report has shown that herpes simplex virus 1 virions package RNA. Experiments designed to reveal the identity of the virion proteins capable of binding the RNA and to show whether the mRNA carried in the newly infected cells was expressed showed the following: (i) (32)P-labeled riboprobe generated by in vitro transcription of the U(S)8.5 ORF bound three proteins identified as the products of U(S)11, U(L)47, and U(L)49 (VP22) genes. (ii) Viral RNA was bound to U(L)47 or U(S)11 proteins immune precipitated from cells transduced with baculoviruses expressing U(L)47 or U(S)11 and then superinfected with HSV-1 under conditions that blocked DNA synthesis and assembly of virions. (iii) Virions were purified from cells transduced with a baculovirus encoding a U(S)8.5 protein fused to green fluorescent protein and superinfected with an HSV-1 mutant lacking the U(S)8-12 genes. HEp-2 cells infected with these virions expressed the chimeric protein in approximately 1% of infected cells. (iv) In mixed cultures, untreated Vero cells acquired the mRNA encoding the green fluorescent-U(S)8.5 chimeric protein from HEp-2 cells doubly transduced with the genes encoding VP22 and the chimeric protein. The transfer was RNase sensitive and VP22 dependent, indicating that the RNA encoded by the chimeric gene was transferred to Vero cells as mRNA. We conclude that (i) three virion proteins are capable of binding RNA; (ii) the packaged RNA can be expressed in newly infected cells; and (iii) the U(L)47 protein was earlier reported to shuttle from nucleus to the cytoplasm and may transport RNA. VP22 thus appears to be a member of a new class of viral proteins whose major function is to bind and transport infected cell mRNA to uninfected cells to create the environment for effective initiation of infection.
Clustering short time series gene expression data (2005)

Available at http://www.cs.cmu.edu/~jernst/st/
N-sided Surface Generation from Arbitrary Boundary Edges (2000)

This paper discusses a general theory and an implementation method for generating a surface patch with concave edges, holes, ridges and valleys in CAD/CAM applications. The surface generation method, which has been proposed to create an N-sided patch with holes, is first reviewed. Such surfaces are generally classified as transfinite surfaces, in which a surface is interpolated to span given curves. In the proposed method, each boundary edge defined in a two-dimensional domain has an appropriate blending function. The function is defined so that the derivatives are 0 on the edges, and the function values are 1 on one edge and 0 on the other edges, and each edge in the three-dimensional space is blended smoothly. A revised method is also introduced in this paper. The previously proposed method has some problems in that a surface may not be generated appropriately for concave edges, and the surface has to be manipulated manually if it has holes. This causes distortion and overlap in mapping from a 2D domain into 3D space. In the new method, the blending function is revised, and the boundary edges in the 2D domain are obtained from the edges in the 3D space beforehand. Thus, it is shown that an N-sided patch with concave edges, holes, ridges and valleys can be suitably generated.
Interplanetary H Lyα Observations from a Sounding Rocket (2001)

We describe a Self-Compensating All-Reflecting Interferometer used to measure diffuse interplanetary H Lyα emission (λ ~ 1216 Å) of interstellar origin at high spectral resolution (λ/Δλ ~ 100,000). The instrument is capable of resolving the separation between the Doppler-shifted, interplanetary neutral H emission from the Earth's geocoronal emission line. We present the optical layout and mechanical design that enable the instrument to maintain alignment through a sounding rocket flight. We find an H Lyα spectrum, including both geocoronal emission and interplanetary scattered features, which we have fitted using Gaussian line profiles. The interplanetary H line is fitted with a 7900 ± 2400 K line width. The geocoronal line width is fitted with a 1900 ± 500 K Gaussian. The Doppler shift between the geocoronal and interplanetary line is 0.145 Å, corresponding to an apparent interplanetary wind velocity of 16 ± 7 km s-1. We show how full line-profile measurements of interplanetary H emission can advance current studies of the heliospheric interface region and very local interstellar medium.
What Clinical and Symptom Features and Comorbid Disorders Characterize Outpatients with Anxious Major Depressive Disorder: A Replication and Extension (2006)

This study clearly replicates our previous STAR*D findings and supports the notion that anxious depression may be a valid diagnostic subtype of MDD, with distinct psychiatric comorbidities and clinical and sociodemographic features.
Proteomics Analysis of Human Amniotic Fluid (2007)

Amniotic fluid is a dynamic and complex mixture that reflects the physiological status of the developing fetus. In this study, the human amniotic fluid (AF) proteome of a 16-18-week normal pregnancy was profiled and analyzed to investigate the composition and functions of this fluid. Due to the complexity of AF, we utilized three different fractionation strategies to provide greater coverage. Two types of two-dimensional LC/MS/MS as well as an LC-SDS-PAGE-LC-MS/MS platform were used. A total of 16 AF samples between gestational ages of 16 and 18 weeks from women carrying chromosomally normal fetuses were analyzed by one of the three fractionation methods followed by a common reverse phase LC-MS/MS step. Mascot and The Global Proteome Machine engines were used to search the International Protein Index human database for peptide sequence identification. The list of proteins was generated by combining the results of both engines through the PeptideProphet of Scaffold software. All identified proteins were combined to generate the AF proteome comprising 1,026 unique gene matches or 842 non-redundant proteins. This list includes most of the currently used biomarkers for pregnancy-associated pathologic conditions such as preterm delivery, intra-amniotic infection, and chromosomal anomalies of the fetus. The subcellular localization, tissue expression, functions, and networks of the AF proteome were analyzed by various bioinformatic tools. These data will contribute to the better understanding of amniotic fluid function and to the discovery of novel biomarkers for prenatal diagnosis of fetal abnormalities.