gebhart/patrepeval huggingface dataset:
Unsupervised Learning of Geometry with Edge-aware Depth-Normal Consistency (2017)

Learning to reconstruct depths in a single image by watching unlabeled videos via deep convolutional network (DCN) is attracting significant attention in recent years. In this paper, we introduce a surface normal representation for unsupervised depth estimation framework. Our estimated depths are constrained to be compatible with predicted normals, yielding more robust geometry results. Specifically, we formulate an edge-aware depth-normal consistency term, and solve it by constructing a depth-to-normal layer and a normal-to-depth layer inside of the DCN. The depth-to-normal layer takes estimated depths as input, and computes normal directions using cross production based on neighboring pixels. Then given the estimated normals, the normal-to-depth layer outputs a regularized depth map through local planar smoothness. Both layers are computed with awareness of edges inside the image to help address the issue of depth/normal discontinuity and preserve sharp edges. Finally, to train the network, we apply the photometric error and gradient smoothness for both depth and normal predictions. We conducted experiments on both outdoor (KITTI) and indoor (NYUv2) datasets, and show that our algorithm vastly outperforms state of the art, which demonstrates the benefits from our approach.
Chemokine Receptors as Targets for Cancer Therapy (2009)

Chemokines and their receptors play critical roles in leukocyte trafficking during inflammatory processes. Although the role of chemokine receptors (CKRs) in cancer biology is a relatively new field of study, a growing body of data suggest that a number of CKRs, including CXCR4, CCR4, CCR7, and CCR10, may play diverse of roles in cancer growth, cancer metastasis, cancer angiogenesis, or the composition of the cancer microenvironment. Preclinical models of cancer indicate that cancer antagonists, most notably those for CXCR4, can block cancer growth either directly or by altering the cancer stroma. Highthroughput screening methods to identify effective CKR antagonists have been developed, but specificity, potency, and drug-delivery of validated candidate compounds remain issues that result in the clinical failure of many initially promising candidates. The recent approval of a CCR5 receptor antagonist in HIV suggests that safe, effective small molecular antagonists for other CKRs may not be far away. There is still a clear need to extend our understanding of the signalling pathways by which CKRs facilitate cancer processes. Because of the role of CKRs in cancer cell survival, the combination of CKR antagonists with traditional chemotoxic agents or with immunotherapy is an alluring strategy since this increases the specificity of treatment to the cancer and potentially limits additional systemic side effects.
Coenzyme M methylase activity of the 480-kilodalton corrinoid protein from Methanosarcina barkeri (1996)

Activity staining of extracts of Methanosarcina barkeri electrophoresed in polyacrylamide gels revealed an additional methylcobalamin:coenzyme M (methylcobalamin:CoM) methyltransferase present in cells grown on acetate but not in those grown on trimethylamine. This methyltransferase is the 480-kDa corrinoid protein previously identified by its methylation following inhibition of methyl-CoM reductase in otherwise methanogenic cell extracts. The methylcobalamin:CoM methyltransferase activity of the purified 480-kDa protein increased from 0.4 to 3.8 micromol/min/mg after incubation with sodium dodecyl sulfate (SDS). Following SDS-polyacrylamide gel electrophoresis analysis of unheated protein samples, a polypeptide with an apparent molecular mass of 48 kDa which possessed methylcobalamin:CoM methyltransferase activity was detected. This polypeptide migrated with an apparent mass of 41 kDa when the 480-kDa protein was heated before electrophoresis, indicating that the alpha subunit is responsible for the activity. The N-terminal sequence of this subunit was 47% similar to the N termini of the A and M isozymes of methylcobalamin:CoM methyltransferase (methyltransferase II). The endogenous methylated corrinoid bound to the beta subunit of the 480-kDa protein could be demethylated by CoM, but not by homocysteine or dithiothreitol, resulting in a Co(I) corrinoid. The Co(I) corrinoid could be remethylated by methyl iodide, and the protein catalyzed a methyl iodide:CoM transmethylation reaction at a rate of 2.3 micromol/min/mg. Methyl-CoM was stoichiometrically produced from CoM, as demonstrated by high-pressure liquid chromatography with indirect photometric detection. Two thiols, 2-mercaptoethanol and mercapto-2-propanol, were poorer substrates than CoM, while several others tested (including 3-mercaptopropanesulfonate) did not serve as methyl acceptors. These data indicate that the 480-kDa corrinoid protein is composed of a novel isozyme of methyltransferase II which remains firmly bound to a corrinoid cofactor binding subunit during isolation.
Protein phosphatase 4 interacts with the Survival of Motor Neurons complex and enhances the temporal localisation of snRNPs (2003)

Protein phosphatase 4 (PPP4) is a ubiquitous essential protein serine/threonine phosphatase found in higher eukaryotes. Coordinate variation of the levels of the catalytic subunit (PPP4c) and the regulatory subunit (R2) suggests that PPP4c and R2 form a heterodimeric core to which other regulatory subunits bind. Two proteins that specifically co-purify with Flag-epitope-tagged R2 expressed in HEK-293 cells were identified as Gemin3 and Gemin4. These two proteins have been identified previously as components of the Survival of Motor Neurons (SMN) protein complex, which is functionally defective in the hereditary disorder spinal muscular atrophy. Immuno-sedimentation of the epitope-tagged SMN protein complex from HeLa cells expressing CFP-SMN showed that the SMN protein interacts, as previously reported, with Gemin2 (SIP1), Gemin3 and Gemin4 and in addition associates with PPP4c. The SMN complex has been implicated in the assembly and maturation of small nuclear ribonucleoproteins (snRNPs). Expression of GFP-R2-PPP4c in HeLa cells enhances the temporal localisation of newly formed snRNPs, which is consistent with an association of R2-PPP4c with the SMN protein complex.
Expression Patterns and Mutant Phenotype ofteosinte branched1Correlate With Growth Suppression in Maize and Teosinte (2002)

The evolution of domesticated maize from its wild ancestor teosinte is a dramatic example of the effect of human selection on agricultural crops. Maize has one dominant axis of growth, whereas teosinte is highly branched. The axillary branches in maize are short and feminized whereas the axillary branches of teosinte are long and end in a male inflorescence under normal growth conditions. Previous QTL and molecular analysis suggested that the teosinte branched1 (tb1) gene of maize contributed to the architectural difference between maize and teosinte. tb1 mutants of maize resemble teosinte in their overall architecture. We analyzed the tb1 mutant phenotype in more detail and showed that the highly branched phenotype was due to the presence of secondary and tertiary axillary branching, as well as to an increase in the length of each node, rather than to an increase in the number of nodes. Double-mutant analysis with anther ear1 and tassel seed2 revealed that the sex of the axillary inflorescence was not correlated with its length. RNA in situ hybridization showed that tb1 was expressed in maize axillary meristems and in stamens of ear primordia, consistent with a function of suppressing growth of these tissues. Expression in teosinte inflorescence development suggests a role in pedicellate spikelet suppression. Our results provide support for a role for tb1 in growth suppression and reveal the specific tissues where suppression may occur.
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big- , NMT and PTS1 (2003)

Many posttranslational modifications (N-myristoylation or glycosylphosphatidylinositol (GPI) lipid anchoring) and localization signals (the peroxisomal targeting signal PTS1) are encoded in short, partly compositionally biased regions at the N- or C-terminus of the protein sequence. These sequence signals are not well defined in terms of amino acid type preferences but they have significant interpositional correlations. Although the number of verified protein examples is small, the quantification of several physical conditions necessary for productive protein binding with the enzyme complexes executing the respective transformations can lead to predictors that recognize the signals from the amino acid sequence of queries alone. Taxon-specific prediction functions are required due to the divergent evolution of the active complexes. The big-Pi tool for the prediction of the C-terminal signal for GPI lipid anchor attachment is available for metazoan, protozoan and plant sequences. The myristoyl transferase (NMT) predictor recognizes glycine N-myristoylation sites (at the N-terminus and for fragments after processing) of higher eukaryotes (including their viruses) and fungi. The PTS1 signal predictor finds proteins with a C-terminus appropriate for peroxisomal import (for metazoa and fungi). Guidelines for application of the three WWW-based predictors (http://mendel.imp.univie.ac.at/) and for the interpretation of their output are described.
NS3-4A of hepatitis C virus is a chymotrypsin-like protease (1995)

The polyprotein encoded by a single open reading frame of hepatitis C virus (HCV) is processed by host- and virus-encoded proteases. The viral protease NS3 is responsible for the cleavage of at least four sites (NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B junctions) in the nonstructural protein region. To characterize the protease function of NS3 and NS4 on various target sites, efficient cis- and trans-cleavage assay systems were developed by using in vitro transcription and translation. Deletion of the C-terminal two-thirds from NS3 in an NS3-NS4A-4B polypeptide (NS3 delta C-4A-4B) hampered cleavage of the NS3/4A junction but not that of the NS4A/4B junction. As a consequence, expression of NS3 delta C-4A-4B containing an internal deletion of NS3 results in an NS3 delta C-4A fusion protein. NS3 delta C-4A shows very efficient and specific trans-cleavage activity at NS4A/4B, NS4B/5A, and NS5A/5B junctions. In addition, the biochemical properties of HCV NS3 delta C-4A were further elucidated by adding known protease inhibitors in trans-cleavage reactions. The HCV protease NS3-4A is inhibited by chymotrypsin-specific inhibitors N-tosyl-L-phenylalanine chloromethyl ketone (TPCK), chymostatin, and Pefabloc SC but not by trypsin-like protease inhibitors antipain, leupeptin, and N-alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK) or by the protease inhibitors E-64, bestatin, pepstatin, and phosphoramidon. This finding strongly suggests that HCV protease NS3-4A is a chymotrypsin-like serine protease.
24-Hydroxylation of 1,25-dihydroxyergocalciferol. An unambiguous deactivation process. (1986)

1,24,25-Trihydroxyergocalciferol was isolated from bovine kidney homogenates incubated with 1,25-dihydroxyergocalciferol and from chick kidney homogenates incubated with 24,25-dihydroxyergocalciferol. The identity was established by ultraviolet absorbance, sensitivity to periodate, nuclear magnetic resonance, and mass spectrometry. The new metabolite had an affinity equal to 1,24,25-trihydroxycholecalciferol for the bovine-thymus and chick-intestinal 1,25-dihydroxyvitamin D receptor and had an affinity twice that of 1,24,25-trihydroxycholecalciferol for the rat-intestinal receptor. It was 3- and 6-fold less competitive than either 1,25-dihydroxycholecalciferol or 1,24,25-trihydroxycholecalciferol, respectively, for the rat plasma vitamin D transport protein. 1,24,25-Trihydroxyergocalciferol was at least 10-fold less active than 1,25-dihydroxycholecalciferol, 1,25-dihydroxyergocalciferol, and 1,24,25-trihydroxycholecalciferol at stimulating intestinal-calcium transport and was also relatively ineffective at stimulating bone-calcium resorption in rats. Moreover, in rats, [3H]1,24,25-trihydroxyergocalciferol was cleared from plasma approximately 40% faster than [3H]1,24,25-trihydroxycholecalciferol. These data suggest that C-24 hydroxylation of 1,25-dihydroxyergocalciferol represents a significant in vivo deactivation step, whereas equivalent deactivation of 1,25-dihydroxycholecalciferol seems to involve metabolic steps subsequent to C-24 hydroxylation (C-24 ketonization). C-24 ketonization of 1,25-trihydroxyergocalciferol would not be anticipated due to the presence of the 24(S)-methyl group. These results reveal further dissimilarities between ergocalciferol and cholecalciferol metabolism in mammals and suggest a mechanism for the lesser tendency of ergocalciferol to cause hypercalcemia relative to cholecalciferol.
CD19-targeted CAR T-cell therapeutics for hematologic malignancies: interpreting clinical outcomes to date (2016)

Adoptive transfer of T cells genetically modified to express chimeric antigen receptors (CARs) targeting CD19 has produced impressive results in treating patients with B-cell malignancies. Although these CAR-modified T cells target the same antigen, the designs of CARs vary as well as several key aspects of the clinical trials in which these CARs have been studied. It is unclear whether these differences have any impact on clinical outcome and treatment-related toxicities. Herein, we review clinical results reflecting the investigational use of CD19-targeted CAR T-cell therapeutics in patients with B-cell hematologic malignancies, in light of differences in CAR design and production, and outline the limitations inherent in comparing outcomes between studies.
Pulsed Photoacoustic Study of the Diffusion of Chromophores in Human Skin (1997)

The technique of pulsed photoacoustic spectroscopy was used to investigate the diffusion of chromophores in human skin. The kinetic of diffusion has been studied for five solutions at different concentrations in a mixture of chromophores, as used in commercial sunscreens. In addition to the classical macroscopic interpretation of the diffusion process, a new method is shown to give more detailed information on chromophore presence at different depths in skin. For the first time, results are expressed in the frequency domain by means of the Fourier transform applied to the photoacoustic signal. The spectra are discussed versus the depth in skin samples and the time of diffusion kinetics. This new method of data analysis is shown to be very useful for understanding the influence of the internal structure of a medium on the penetration rate of chromophores into skin.
American Society of Gene & Cell Therapy 17th Annual Meeting (2014)

Spinal cord injury or diseases such as amyotrophic lateral sclerosis can cause the loss of motor neurons and therefore result in muscular paralysis. Stem cells may improve functional recovery after injury by promoting endogenous regeneration, or directly replacing neurons. Effective directional migration of grafted neural cells to reconstruct functional connections is crucial in the process. Steady direct current electric fi elds (EFs) play an important role in the development of the central nervous system. A strong biological effect of EFs is the induction of directional cell migration. In this study, embryonic stem (ES) cells were differentiated using a two-step procedure. The first step was to enhance the neuralization process by adding Noggin and fi broblast growth factor in the cell culture medium. The second step was to induce motor neuron specifi cation by adding retinoic acid and smoothened agonist as cell culture culture supplement. The cells were then treated with brain-derived neurotrophic factor, ciliary neurotrophic factor, glial cell-derived neurotrophic factor and neurotrophin-3 for neurite elongation. The migration of neural precursors from embryoid bodies in EFs was studied. We found that the migration of neural precursors from the embryoid body was toward the cathode pole. We also investigated the EFs-directed migration of dissociated single motor neurons using time-lapse photography.Similarly, single motor neurons migrated to the cathode and the reversal of EFs poles reversed the migration direction of the cells. The directedness and displacement of cathodal migration became more signifi cant when the field strength was increased from 50mV/mm to 100mV/mm. EFs stimulation did not infl uence the cell migration velocity. Our work suggested that EFs may serve as a guidance cue to direct grafted cell migration in vivo.
III. An essay on the cohesion of fluids (1805)

It has already been asserted, by Mr. Monge and others, that the phenomena of capillary tubes are referable to the cohesive attraction of the superficial particles only of the fluids em­ployed, and that the surfaces must consequently be formed into curves of the nature of lintearias, which are supposed to be the results of a uniform tension of a surface, resisting the pressure of a fluid, either uniform, or varying according to a given law. Segner, who appears to have been the first that maintained a similar opinion, has shown in what manner the principle may be deduced from the doctrine of attraction, but his demonstration is complicated, and not perfectly satisfactory; and in applying the law to the forms of drops, he has neglected to consider the very material effects of the double curvature, which is evidently the cause of the want of a perfect coinci­dence of some of his experiments with his theory. Since the time of Segner, little has been done in investigating accurately and in detail the various consequences of the principle. It will perhaps be most agreeable to the experimental phi­losopher, although less consistent with the strict course of logical argument, to proceed in the first place to the comparison of this theory with the phenomena, and to inquire afterwards for its foundation in the ultimate properties of matter. But it is necessary to premise one observation, which appears to be new, and which is equally consistent with theory and with experiment; that is, that for each combination of a solid and a fluid, there is an appropriate angle of contact between the surfaces of the fluid, exposed to the air, and to the solid. This angle, for glass and water, and in all cases where a solid is perfectly wetted by a fluid, is evanescent: for glass and mer­cury, it is about 140°, in common temperatures, and when the mercury is moderately clean.
Synthesis and in Vitro Testing of J591 Antibody−Dendrimer Conjugates for Targeted Prostate Cancer Therapy (2004)

Targeted therapeutics using antibodies are an attractive option over conventional cancer chemotherapeutics due to their potential to deliver a therapeutic specifically to cancer tissue without damaging normal tissue. However, there are known problems with immunoconjugates such as decreased immunoreactivity and poor solubility. Using dendrimers as carriers for these agents has the potential to resolve these issues. We synthesized J591 anti-PSMA (prostate specific membrane antigen) antibody dendrimer conjugates containing fluorophores on the dendrimer. The in vitro studies of these conjugates show that they specifically bind to cells expressing PSMA. Confocal microscopy experiments document the binding and internalization of these conjugates. This research encourages the further study of antibody-dendrimer-drug conjugates for use in targeted therapeutics.
Polymer brushes here, there, and everywhere: Recent advances in their practical applications and emerging opportunities in multiple research fields (2012)

Abstract Bottom‐up surface processing with well‐defined polymeric structures becomes increasingly important in many current technologies. Polymer brushes, that is, assemblies of macromolecules tethered at one end to a substrate, provide an exemplary system of materials capable of achieving such a goal. While the focus in the past decades has been mostly on their synthetic aspects and the in‐depth study of their interesting properties, from several years now the core area of research has already started to shift towards specific practical applications. Ample functional versatility and relative ease of preparation are special strengths of polymer brushes, lending them a strong interdisciplinary character. To this end, this work is entirely dedicated to bringing together the latest research on applications of polymer brushes in multiple research fields. The aim of this review are twofold: first, to give a critical discussion of the current status of development of application‐oriented research on polymer brushes, and second, to inform the reader as to what can be done with polymer brushes in multiple research fields. It is therefore hoped that the juxtaposition of perspectives from different disciplines in one place will stimulate and contribute to the ongoing process of cross‐fertilization that is driving this fascinating and emerging area of polymer science. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Preparation and Characterization of Hyaluronate-Hydroxyethyl Acrylate Blend Hydrogel for Controlled Release Device. (2000)

Hyaluronate-hydroxyethyl acrylate blend hydrogels were investigated as matrices for controlled release devices. Glycidyl methacrylate (GMA) derivatized HA (GMA-HA) was synthesized by coupling of GMA to HA in the presence of a suitable catalyst. These hydrogels were prepared by a free radical copolymerization of GMA-HA and hydroxyethyl acrylate. The water content of these hydrogels at equilibrium swelling in water (Ww) was 0.978+/-0.0073 (n=18); however, these hydrogel was mechanically tough and could be used as disk shape. The hydrogels swelling were found to depend on ionic strength and pH. The dried hydrogels quickly regained their original condition in water, and they swelled to more than 90% of its initial water contents after 30 min. This swelling-deswelling behavior was reproducible. The release of chlorpromazine HCl as a model cationic drug from the gels was suppressed significantly in water. The release increased with increasing the ionic strength and decreasing pH of bulk solutions.