gebhart/patrepeval huggingface dataset:
Generic radial distortion calibration of a novel single camera based panoramic stereoscopic system (2011)

This work presents a novel panoramic stereoscopic system consisting of a fisheye lens camera and a hyperbolic mirror with co-axis installation. From the overlapping field of view captured through the fisheye lens and the reflection of the mirror, position of an object point in 3D Euclidean space can be reconstructed once the system geometry is calibrated. To deal with the non-single viewpoint issue in the catadioptric image, a generic radial distortion model is used to describe the imaging process with a series of viewing cones. The parameters of the viewing cones are estimated using a homography based method with observations of an LCD panel at a few unknown positions. Following this, a closed form solution for 3D reconstruction is used with a non-linear optimization to obtain an optimal calibration. A prototype of the proposed design is constructed. Quantitative experiments are conducted to evaluate the calibration result in terms of 3D reconstruction precision. With the calibration result, we also present potential robotic applications of the proposed system such as 3D environment reconstruction in a 360 degree horizontal field of view.
Hyperammonemic Encephalopathy in An Adenocarcinoma Patient Managed with Carglumic Acid (2014)

Hyperammonemic encephalopathy (he) is a rare complication of malignancy and chemotherapy. Although the cause of he is unclear, a functional arginine deficiency secondary to increased catabolism has been suggested as a possible mechanism. Either that deficiency or an undetermined metabolite could lead to inhibition of N-acetylglutamate synthase (nags), a urea cycle enzyme, resulting in hyperammonemia. We present a case of chemotherapy-induced he in a patient with no underlying primary urea cycle disorder. The patient had a successful trial of carglumic acid (a synthetic analog of the product of nags), which suggests that, at least in some cases, he can be treated by overcoming proximal inhibition of the urea cycle. Further, our case is the first in the literature to exclude genetic defects and disorders of the proximal urea cycle, suggesting that hyperammonemia in these patients is probably secondary to chemotherapy.
Scene Parsing through ADE20K Dataset (2017)

Scene parsing, or recognizing and segmenting objects and stuff in an image, is one of the key problems in computer vision. Despite the communitys efforts in data collection, there are still few image datasets covering a wide range of scenes and object categories with dense and detailed annotations for scene parsing. In this paper, we introduce and analyze the ADE20K dataset, spanning diverse annotations of scenes, objects, parts of objects, and in some cases even parts of parts. A scene parsing benchmark is built upon the ADE20K with 150 object and stuff classes included. Several segmentation baseline models are evaluated on the benchmark. A novel network design called Cascade Segmentation Module is proposed to parse a scene into stuff, objects, and object parts in a cascade and improve over the baselines. We further show that the trained scene parsing networks can lead to applications such as image content removal and scene synthesis <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Inhibition of the Hepatitis C Virus NS3/4A Protease (2000)

The hepatitis C virus NS3 protein contains a serine protease domain with a chymotrypsin-like fold, which is a target for development of therapeutics. We report the crystal structures of this domain complexed with NS4A cofactor and with two potent, reversible covalent inhibitors spanning the P1-P4 residues. Both inhibitors bind in an extended backbone conformation, forming an anti-parallel beta-sheet with one enzyme beta-strand. The P1 residue contributes most to the binding energy, whereas P2-P4 side chains are partially solvent exposed. The structures do not show notable rearrangements of the active site upon inhibitor binding. These results are significant for the development of antivirals.
Vaccine potential of a herpes simplex virus type 1 mutant with an essential glycoprotein deleted (1994)

Several approaches to the production of vaccines to human herpesviruses have been proposed. Subunit vaccines, subunits delivered by live vectors, and rationally attenuated vaccines have all been shown to be efficacious in animal models but suffer from uncertainties as to the roles of individual genes involved in pathogenesis and the most relevant components of the immune response required for protection in humans and the target antigens involved. With these problems in mind, we examined the vaccine potential of a fully disabled herpes simplex virus type 1 mutant that is capable of only a single round of replication, since a virus of this type should induce the full spectrum of immune responses but has no pathogenic potential. A virus has been described which lacks essential glycoprotein H (gH) and can be propagated in a cell line which supplies gH in trans (A. Forrester, H. Farrell, G. Wilkinson, J. Kaye, N. Davis-Poynter, and T. Minson, J. Virol. 66:341-348, 1992). Infection of normal cells with this mutant is indistinguishable from a wild-type infection, except that the resulting progeny are gH negative and noninfectious: the virus is self-limiting. Infection of mice by the ear pinna route was similarly self-limiting in that input infectivity decreased rapidly at the inoculation site and no infectivity was detected in sensory ganglia. Animals given a wide range of doses of the gH-negative mutant produced both humoral and T-cell responses to herpes simplex virus type 1 and proved solidly resistant to challenge with a high dose of wild-type virus. The gH-negative mutant is presumably capable of establishing a latent infection, but since no infectious virus was detected in numerous attempts to reactivate the mutant, the risk of a pathogenic outcome is minimal.
Design of Si/SiGe heterojunction complementary metal-oxide-semiconductor transistors (2002)

A design is presented and computer-simulated for high-mobility Si/SiGe heterojunction CMOS transistors. Comparing 0.2 /spl mu/m Si/SiGe FETs to bulk Si FETs, an increase is predicted in current drive of 125% and 23% in the p-FET and n-FET, respectively. For given propagation delay (55 ns), simulated loaded ring oscillators at 1.5 V exhibit 4.6 times reduction in power-delay-product compared to bulk Si CMOS oscillators of the same design rules operating at 2.5 V.
Medleydb: A Multitrack Dataset For Annotation-Intensive Mir Research. (2014)

[TODO] Add abstract here.
Decoding Visual Information From a Population of Retinal Ganglion Cells (1997)

Decoding visual information from a population of retinal ganglion cells. J. Neurophysiol. 78: 2336-2350, 1997. This work investigates how a time-dependent visual stimulus is encoded by the collective activity of many retinal ganglion cells. Multiple ganglion cell spike trains were recorded simultaneously from the isolated retina of the tiger salamander using a multielectrode array. The stimulus consisted of photopic, spatially uniform, temporally broadband flicker. From the recorded spike trains, an estimate was obtained of the stimulus intensity as a function of time. This was compared with the actual stimulus to assess the quality and quantity of visual information conveyed by the ganglion cell population. Two algorithms were used to decode the spike trains: an optimized linear filter in which each action potential made an additive contribution to the stimulus estimate and an artificial neural network trained by back-propagation to match spike trains with stimuli. The two methods performed indistinguishably, suggesting that most of the information about this stimulus can be extracted by linear operations on the spike trains. Individual ganglion cells conveyed information at a rate of 3.2 +/- 1.7 bits/s (mean +/- SD), with an average information content per spike of 1.6 bits. The maximal possible rate of information transmission compatible with the measured spiking statistics was 13.9 +/- 6.3 bits/s. On average, ganglion cells used 22% of this capacity to encode visual information. When a decoder received two spike trains of the same response type, the reconstruction improved only marginally over that obtained from a single cell. However, a decoder using an ON and an OFF cell extracted as much information as the sum of that obtained from each cell alone.Thus cells of opposite response type encode different and nonoverlapping features of the stimulus. As more spike trains were provided to the decoder, the total information rate rapidly saturated, with 79% of the maximal value obtained from a local cluster of just four neurons of different functional types. The decoding filter applied to a given neuron's spikes within such a multiunit decoder differed substantially from the filter applied to that same neuron in a single-unit decoder. This shows that the optimal interpretation of a ganglion cell's action potential depends strongly on the simultaneous activity of other nearby cells. The quality of the stimulus reconstruction varied greatly with frequency: flicker components below 1 Hz and above 10 Hz were reconstructed poorly, and the performance was optimal near 2.5 Hz. Further analysis suggests that temporal encoding by ganglion cell spike trains is limited by slow phototransduction in the cone photoreceptors and a corrupting noise source proximal to the cones.
Human cyclin A and the retinoblastoma protein interact with similar but distinguishable sequences in the adenovirus E1A gene product. (1991)

The adenovirus early region 1A (E1A) proteins associate with several cellular proteins in adenovirus infected or transformed cells. Recently, two of the cellular proteins that bind to E1A encoded proteins have been identified. p105 has been shown to be the product of the retinoblastoma tumor suppressing gene. p60 has been shown to be a human cyclin A. Previously studies have shown that E1A protein sequences encoded by conserved domains 1 and 2 are required for interactions with the retinoblastoma protein (pRB). We have demonstrated here that amino acids 30 to 60 and 121 to 127 within the E1A proteins are required for interaction with p60/cyclin A. These are the same sites within conserved domains 1 and 2 that are required for E1A protein association with pRB. However, the association of p60/cyclin A does not appear to require pRB. We also demonstrate that another cellular protein, 130K, interacts with E1A at essentially the same sites. It is interesting that mutations in these regions destroy the ability of E1A to function as an oncogene, thereby raising the possibility that interaction with several different cellular proteins may be needed for transformation by E1A.
‘Image and treat’: an individualized approach to urological tumors (2010)

Tumor-specific targets and biomarkers are being studied for PET/CT and radioimmunotherapy. This may lead to development of new therapeutic strategies. However, considerable investment in new research will be required for personalized medicine to be routinely used in uro-oncology.
Single-qubit-gate error below10−4in a trapped ion (2011)

With a ${}^{9}{\mathrm{Be}}^{+}$ trapped-ion hyperfine-state qubit, we demonstrate an error probability per randomized single-qubit gate of $2.0(2)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}$, below the threshold estimate of ${10}^{\ensuremath{-}4}$ commonly considered sufficient for fault-tolerant quantum computing. The ${}^{9}{\mathrm{Be}}^{+}$ ion is trapped above a microfabricated surface-electrode ion trap and is manipulated with microwaves applied to a trap electrode. The achievement of low single-qubit-gate errors is an essential step toward the construction of a scalable quantum computer.
Autocrine Sonic hedgehog signaling promotes gastric cancer proliferation through induction of phospholipase Cγ1 and the ERK1/2 pathway (2016)

Increased SHH expression is associated with shorter survival in gastric cancer patients, and SHH could represent a useful biomarker or therapeutic target for this disease.
Characterization of nerve growth factor receptor in neural crest tumors using monoclonal antibodies. (1984)

The nerve growth factor (NGF) receptor was characterized by using a new series of anti-receptor monoclonal antibodies (MAbs). These MAbs (i) showed significantly greater reactivity with a melanoma cell line expressing higher levels of NGF receptor, (ii) inhibited the binding of 125I-labeled NGF to its receptor, and (iii) immunoprecipitated both metabolically labeled and 125I-labeled NGF affinity-labeled receptor. These experiments defined the receptor as a 75-kDa cell-surface protein. The NGF receptor was visualized by immunoperoxidase staining in tissue sections of human nevi, melanomas, neurofibromas, a pheochromocytoma, and peripheral nerves. Uniform staining of the cytoplasm suggests that, in addition to cell-surface NGF receptors, there is a population of intracellular receptors.
Rapid [gamma]-Aminobutyric Acid Synthesis and the Inhibition of the Growth and Development of Oblique-Banded Leaf-Roller Larvae (1996)

The hypothesis that rapid [gamma]-aminobutyrate (GABA) accumulation is a plant defense against phytophagous insects was investigated. Increasing GABA levels in a synthetic diet from 1.6 to 2.6 [mu]mol g-1 fresh weight reduced the growth rates, developmental rates, and survival rates of cultured Choristoneura rosaceana cv Harris larvae. Simulation of the mechanical damage resulting from phytophagous activity increased soybean (Glycine max L.) leaf GABA 10- to 25-fold within 1 to 4 min. Pulverizing leaf tissue resulted in a value of 2.15 ([plus or minus]0.11 SE) [mu]mol GABA g-1 fresh weight.
Myristoylation-dependent replication and assembly of human immunodeficiency virus 1. (1990)

Covalent linkage of myristic acid to the N-terminal glycine residue of Pr55gag, the precursor of the major structural proteins of human immunodeficiency virus 1 (HIV-1), facilitates an essential step in virus assembly and propagation. Substitution of the myristoyl-acceptor glycine with alanine, in a functional clone of HIV-1, eliminates virus replication. Complementation of this defect, in trans, restores infectious particle production. The nonmyristoylated (myr-) gag precursor accumulates in infected cells and is not processed into the mature capsid components of the intact virion. However, myr- Pr55gag can be processed by purified HIV protease in vitro, demonstrating that the myristoyl moiety is not required for cleavage by the protease. Myristoylation of Pr55gag is not necessary for localization but is required for stable membrane association and assembly of HIV-1.
The behavior of cells during the evaluation of gap junctional intercellular communication by metabolic cooperation assay. (1996)

The behavior of cells during the assessment of gap junctional intercellular communication (GJIC) by metabolic cooperation assay was studied, either under standard conditions, or with the simultaneous addition of an inhibitor of GJIC-ethylene glycol, and eventually plus dibutyryl cyclic adenosine monophosphate. Generally, the behavior of cells in the course of the assay did not depend significantly on the combination of drugs used. Cell locomotion during the assay was minimal, and consequently the results depended, almost solely on the probability of mutual contact between donor and recipient cells during the seeding. The first significant decrease in recovery of recipient cells, that is a detectable GJIC, was observed 30 min after the assay had started. Final results of the assay depended on the first 12 h of the experiment, in which the maximum decrease in the recovery of recipient cells, that is the maximum GJIC, was reached. The longer duration of the assay did not affect the results significantly.
Use of Sulfated Linked Cyclitols as Heparan Sulfate Mimetics to Probe the Heparin/Heparan Sulfate Binding Specificity of Proteins (2005)

Heparin and heparan sulfate (HS) are structurally diverse glycosaminoglycans (GAG) that are known to interact, via unique structural motifs, with a wide range of functionally distinct proteins and modulate their biological activity. To define the GAG motifs that interact with proteins, we assessed the ability of 15 totally synthetic HS mimetics to interact with 10 functionally diverse proteins that bind heparin/HS. The HS mimetics consisted of cyclitol-based pseudo-sugars coupled by linkers of variable chain length, flexibility, orientation, and hydrophobicity, with variations in sulfation also being introduced into some molecules. Three of the proteins tested, namely hepatocyte growth factor, eotaxin, and elastase, failed to interact with any of the sulfated linked cyclitols. In contrast, each of the remaining seven proteins tested exhibited a unique reactivity pattern with the panel of HS mimetics, with tetrameric cyclitols linked by different length alkyl chains being particularly informative. Thus, compounds with short alkyl spacers (2-3 carbon atoms) effectively blocked the interaction of fibroblast growth factor-1 (FGF-1) and lipoprotein lipase with heparin/HS, whereas longer chain spacers (7-10 carbon atoms) were required for optimal inhibition of FGF-2 and vascular endothelial growth factor binding. This effect was most pronounced with the chemokine, interleukin-8, where alkyl-linked tetrameric cyclitols were essentially inactive unless a spacer of >7 carbon atoms was used. The heparin-inhibitable enzymes heparanase and cathepsin G also displayed characteristic inhibition patterns, cathepsin G interacting promiscuously with most of the sulfated cyclitols but heparanase activity being inhibited most effectively by HS mimetics that structurally resemble a sulfated pentasaccharide. These data indicate that a simple panel of HS mimetics can be used to probe the HS binding specificity of proteins, with the position of anionic groups in the HS mimetics being critical.
Die Position 5 im Oxotremorin‐Gerüst: Eine zentrale Stelle für die Steuerung der Aktivität am muscarinischen Rezeptor (1987)

Position 5 at the Oxotremorine Skeleton as the Stearing Position for Activity at the Muscarinic Receptors Substitution of the Ch 2 group at position 5 of oxotremorine ( 2 ) by electronegative atoms like O‐ or N‐atom, or by sterically bulkier groups like methyl, N ‐formyl, or N ‐acetyl Changes the pharmacological profile of oxotremorine drastically. The O‐ and N‐analogues were potent but unselective (M 1 /M 2 ) muscarinic agonists. The methyl analogue ((R)‐BOK‐1) is a muscarine antagonist which is 10 times more potent on the ganglion cervical superius (pA 2 = 9.3) than pirenzepine and is able to distinguish between the ileal and ganglion receptor by a factor of 100. The N ‐formyl derivative differentiates between the two receptors by a factor of 500 with a potency comparable to pirenzepine. The two M 1 ‐selective antagonists have higher affinity to the rat‐ganglion receptors compared to the affinity to rat‐cortex homogenate. The synthesis and the pharmacological activity of several new oxotremorine analogues are discussed.
Suppression of NLRX1 in chronic obstructive pulmonary disease (2015)

Cigarette smoke (CS) and viruses promote the inflammation and remodeling associated with chronic obstructive pulmonary disease (COPD). The MAVS/RIG-I-like helicase (MAVS/RLH) pathway and inflammasome-dependent innate immune pathways are important mediators of these responses. At baseline, the MAVS/RLH pathway is suppressed, and this inhibition must be reversed to engender tissue effects; however, the mechanisms that mediate activation and repression of the pathway have not been defined. In addition, the regulation and contribution of MAVS/RLH signaling in CS-induced inflammation and remodeling responses and in the development of human COPD remain unaddressed. Here, we demonstrate that expression of NLRX1, which inhibits the MAVS/RLH pathway and regulates other innate immune responses, was markedly decreased in 3 independent cohorts of COPD patients. NLRX1 suppression correlated directly with disease severity and inversely with pulmonary function, quality of life, and prognosis. In murine models, CS inhibited NLRX1, and CS-induced inflammation, alveolar destruction, protease induction, structural cell apoptosis, and inflammasome activation were augmented in NLRX1-deficient animals. Conversely, MAVS deficiency abrogated this CS-induced inflammation and remodeling. Restoration of NLRX1 in CS-exposed animals ameliorated alveolar destruction. These data support a model in which CS-dependent NLRX1 inhibition facilitates MAVS/RHL activation and subsequent inflammation, remodeling, protease, cell death, and inflammasome responses.
Effect RANKL Produced by Periodontal Ligament Cells on Orthodontic Tooth Movement (2016)

The bone remodeling process involved in orthodontic tooth movement consists of bone resorption on the compression side and bone formation on the tension side of the teeth. Osteoclasts play an important role in bone remodeling and are necessary for orthodontic tooth movement. Receptor activator of nuclear factor-κB ligand (RANKL) is essential for osteoclast formation and differentiation. Several cell types have been reported to be capable of producing RANKL. We are interested in whether there is a dominant cell type which RANKL production is critical in generating orthodontic tooth movement. In this study, we used a Cre recombinase mouse model to study the effect of RANKL deletion in periodontal ligament cells on orthodontic tooth movement. We found RANKL deletion in periodontal ligament cells significantly decreased the amount of orthodontic tooth movement and reduced the number of osteoclasts formed on the compression side after subjecting the teeth to orthodontic force. It suggests RANKL production from periodontal ligament cells contributes greatly to orthodontic tooth movement and serves as an important source of RANKL in osteoclastogenesis during orthodontic tooth movement.
Directional random oligonucleotide primed (DROP) global amplification of cDNA: its application to subtractive cDNA cloning (1996)

We describe a method of global PCR amplification of cDNA such that the strand sense is maintained. The products of this process are random primed fragments ranging in size from 100 to 500 bp which facilitates uniform PCR amplification of total cDNA. Directional incorporation of a T7 RNA polymerase initiator/promoter sequence allows efficient synthesis of total sense RNA from this material and the use of a biotinylated primer permits the separation of single-stranded cDNA. Isolation of these products from different cell types provides a renewable source of target single-stranded cDNA and driver RNA from limited cell numbers and we demonstrate their use for subtractive hybridisation cloning of differentially expressed cDNAs.
Activated tumor-infiltrating CD4+ regulatory T cells restrain antitumor immunity in patients with primary or metastatic liver cancer (2012)

Our results show that tumor-associated Tregs are critical for immune evasion in liver cancer, and we propose that GITRL constitutes a rational treatment for this disease.