gebhart/patrepeval huggingface dataset:
Unsupervised Learning of Depth and Ego-Motion from Monocular Video Using 3D Geometric Constraints (2018)

We present a novel approach for unsupervised learning of depth and ego-motion from monocular video. Unsupervised learning removes the need for separate supervisory signals (depth or ego-motion ground truth, or multi-view video). Prior work in unsupervised depth learning uses pixel-wise or gradient-based losses, which only consider pixels in small local neighborhoods. Our main contribution is to explicitly consider the inferred 3D geometry of the whole scene, and enforce consistency of the estimated 3D point clouds and ego-motion across consecutive frames. This is a challenging task and is solved by a novel (approximate) backpropagation algorithm for aligning 3D structures. We combine this novel 3D-based loss with 2D losses based on photometric quality of frame reconstructions using estimated depth and ego-motion from adjacent frames. We also incorporate validity masks to avoid penalizing areas in which no useful information exists. We test our algorithm on the KITTI dataset and on a video dataset captured on an uncalibrated mobile phone camera. Our proposed approach consistently improves depth estimates on both datasets, and outperforms the state-of-the-art for both depth and ego-motion. Because we only require a simple video, learning depth and ego-motion on large and varied datasets becomes possible. We demonstrate this by training on the low quality uncalibrated video dataset and evaluating on KITTI, ranking among top performing prior methods which are trained on KITTI itself.
Cloning, sequencing and expression of the genes encoding the sodium translocating N5‐methyltetrahydromethanopterin:coenzyme M methyltransferase of the methylotrophic archaeon Methanosarcina mazei Gö1 (1998)

The N5-methyltetrahydromethanopterin:coenzyme M methyltransferase of Methanosarcina mazei Gö1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. The eight open reading frames encoding the eight different subunits of the methyltransferase were identified and sequenced. All of these subunits are shown to be heterologously expressed in minicells of the Escherichia coli mutant DK6. Sequence comparisons with the methyltransferases of thermophilic and hypothermophilic methanogenic archaea are presented. The participation of the gene product of mtrD in sodium ion translocation as well as a consensus sequence of a corrinoid binding motif in MtrA are discussed.
Characterisation of Yersinia species isolated from a kennel and from cattle and pig farms (1993)

Between April 1984 and November 1986, 126 faeces samples were collected from puppies and bitches in a kennel and examined for Yersinia species; 45 (35.7 per cent) of them were positive. Thirty-eight isolates were Y enterocolitica, five were Y frederiksenii and two were Y intermedia. Twenty-one of the Y enterocolitica isolates belonged to serogroup 0:3 and 17 of these were L-sorbose negative; all these isolates were from puppies. One strain of Y frederiksenii and all the L-sorbose-negative Y enterocolitica serogroup 0:3 isolates were resistant to antimicrobial agents and showed four different patterns of resistance (ampicillin, cephalothin and tetracycline; ampicillin, cephalothin, streptomycin and tetracycline; ampicillin, chloramphenicol, cephalothin, streptomycin and sulfathiazole; and ampicillin, chloramphenicol, cephalothin, streptomycin, sulfathiazole and tetracycline. In January 1986, investigations were conducted on a cattle farm and a pig farm close to the kennel. Of 19 bovine faeces samples 11 (57.8 per cent) were positive for Yersinia species; eight yielded Y enterocolitica and four yielded Y frederiksenii. None of the Y enterocolitica isolates belonged to serogroup 0:3. Of 20 porcine faeces samples eight (40 per cent) were positive for Yersinia species; all eight yielded Y enterocolitica and four also yielded Y pseudotuberculosis. Two of the isolates of Y frederiksenii and two of the isolates of Y enterocolitica from the farms had the following resistance patterns: ampicillin, cephalothin and streptomycin; ampicillin, streptomycin and tetracycline; ampicillin, chloramphenicol, cephalothin, streptomycin, trimethoprim-sulphamethoxazole and tetracycline; and ampicillin, chloramphenicol, cephalothin, streptomycin, sulphatiazole, trimethoprim-sulphamethoxazole and tetracycline.(ABSTRACT TRUNCATED AT 250 WORDS)
p‐Coumaroyl‐CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway in Brachypodium distachyon (2013)

Grass lignins contain substantial amounts of p-coumarate (pCA) that acylate the side-chains of the phenylpropanoid polymer backbone. An acyltransferase, named p-coumaroyl-CoA:monolignol transferase (OsPMT), that could acylate monolignols with pCA in vitro was recently identified from rice. In planta, such monolignol-pCA conjugates become incorporated into lignin via oxidative radical coupling, thereby generating the observed pCA appendages; however p-coumarates also acylate arabinoxylans in grasses. To test the authenticity of PMT as a lignin biosynthetic pathway enzyme, we examined Brachypodium distachyon plants with altered BdPMT gene function. Using newly developed cell wall analytical methods, we determined that the transferase was involved specifically in monolignol acylation. A sodium azide-generated Bdpmt-1 missense mutant had no (<0.5%) residual pCA on lignin, and BdPMT RNAi plants had levels as low as 10% of wild-type, whereas the amounts of pCA acylating arabinosyl units on arabinoxylans in these PMT mutant plants remained unchanged. pCA acylation of lignin from BdPMT-overexpressing plants was found to be more than three-fold higher than that of wild-type, but again the level on arabinosyl units remained unchanged. Taken together, these data are consistent with a defined role for grass PMT genes in encoding BAHD (BEAT, AHCT, HCBT, and DAT) acyltransferases that specifically acylate monolignols with pCA and produce monolignol p-coumarate conjugates that are used for lignification in planta.
The complex genetics of multiple sclerosis: pitfalls and prospects (2008)

The genetics of complex disease is entering a new and exciting era. The exponentially growing knowledge and technological capabilities emerging from the human genome project have finally reached the point where relevant genes can be readily and affordably identified. As a result, the last 12 months has seen a virtual explosion in new knowledge with reports of unequivocal association to relevant genes appearing almost weekly. The impact of these new discoveries in Neuroscience is incalculable at this stage but potentially revolutionary. In this review, an attempt is made to illuminate some of the mysteries surrounding complex genetics. Although focused almost exclusively on multiple sclerosis all the points made are essentially generic and apply equally well, with relatively minor addendums, to any other complex trait, neurological or otherwise.
Fumaric acid enhances DNA synthesis of rat hepatocytes by counteracting the toxicities of mitomycin C and aflatoxin B1. (1986)

The effect of fumaric acid was examined on DNA synthesis in hepatocytes or hepatoma cells from rats treated with toxic agents. Male Donryu rats were injected with mitomycin C or aflatoxin B1, singly or in combination with fumaric acid. After a specified period, hepatocytes were isolated from the liver by the collagenase perfusion method and placed in culture, and their activities for DNA synthesis were measured. The iv injection of rats with mitomycin C (0.5 mg/kg) reduced the semiconservative DNA synthesis of the hepatocytes, but simultaneous dosing of fumaric acid (40 mg/kg) enhanced the recovery of the DNA synthesis. The DNA synthesis of hepatoma cells, a 3'-methyl-4-(dimethylamino)azobenzene-induced transplantable cell line growing in the abdominal ascites of rats, was also reduced by the iv injection of mitomycin C but, in contrast to that of the hepatocytes, was little influenced by the simultaneous dosing of fumaric acid. The ip injection of fumaric acid also reduced the toxicity of aflatoxin B1 (0.25 mg/kg, ip), preventing the reduction of DNA synthesis as well as the occurrence of nuclear degenerative changes in the aflatoxin B1-exposed hepatocytes.
Stimulation of the respiratory burst in peripheral blood monocytes by lipoteichoic acid. The involvement of calcium ions and phospholipase A2. (1990)

Lipoteichoic acid (LTA) from Streptococcus faecalis stimulates the respiratory burst in peripheral blood monocytes (mon), as measured by cytochrome C reduction. The effect of LTA was time and dose dependent. LTA stimulated the respiratory burst in a biphasic manner within a range of 1 to 1000 ng/ml.10(6) mon, with maximal activity at 50 ng/ml. At this concentration LTA increased the activity from 0.97 +/- 0.2 to 4.88 +/- 0.2 nmol.10(6) mon/20 min. The role of calcium ions in the effect of LTA in stimulating respiratory burst was studied by changing the availability of calcium ions in the medium, and by measuring the effect of LTA on 45Ca2+ uptake and on intracellular Ca2+ levels. Removal of extracellular calcium ions in the presence of the calcium chelator EGTA, abolished the LTA-stimulated respiratory burst. LTA (50 ng/ml) was found to increase 45Ca2+ uptake into monocytes within seconds (from 2200 +/- 242 in the untreated cells to 4642 +/- 365 cpm/min in the LTA-treated mon). At this concentration, LTA stimulated an immediate rise in the intracellular free Ca2+ concentration to 155 +/- 15 nM as compared with 120 +/- 14 nM in the unstimulated monocytes. LTA caused a specific release of arachidonic acid indicating the involvement of phospholipase A2 in the transduction signal stimulating the respiratory burst by LTA.
Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale (2004)

DNA may seem an unlikely molecule from which to build nanostructures, but this is not correct. The specificity of interaction that enables DNA to function so successfully as genetic material also enables its use as a smart molecule for construction on the nanoscale. The key to using DNA for this purpose is the design of stable branched molecules, which expand its ability to interact specifically with other nucleic acid molecules. The same interactions used by genetic engineers can be used to make cohesive interactions with other DNA molecules that lead to a variety of new species. Branched DNA molecules are easy to design, and the can assume a variety of structural motifs. These can be used for purposes both of specific construction, such as polyhedra, and for the assembly of topological targets. A variety of two-dimensional periodic arrays with specific patterns have been made. DNA nanomechanical devices have been built with a series of different triggers, small molecules, nucleic acid molecules and proteins. Recently, progress has been made in self-replication of DNA nano-constructs, and in the scaffolding of other species into DNA arrangements.
NMR investigations of the N‐linked oligosaccharides at individual glycosylation sites of human lutropin (1991)

Human lutropin or luteinizing hormone (hLH) is a heterodimeric glycoprotein, composed of two subunits. hLH alpha (N-glycosylated at Asn52 and Asn78) and hLH beta (N-glycosylated at Asn30). The sugar chains were liberated by hydrazinolysis from intact hLH beta and from glycopeptides obtained after tryptic digestion of hLH alpha, subsequently reduced and fractionated as alditols by anion-exchange and ion-suppression amine-adsorption HPLC and identified mainly by one-dimensional (1D) and two-dimensional (2D) 1H-NMR spectroscopy. The results indicate predominantly diantennary. N-acetyllactosamine-type structures at all three glycosylation sites. The oligosaccharides attached to Asn52 (hLH alpha) and Asn30 (hLH beta) show a remarkably similar pattern, with mainly chain-terminating 4-sulphated 2-deoxy-2-N-acetylamino-D-galactose (GalNAc) and a sulphated/sialylated structure as the major single component. However, virtually all N-glycans on the beta subunit bear a fucose residue alpha 1-6-linked to the proximal GlcNAc, whereas those at Asn52 (and Asn78) of the alpha subunit are predominantly non-fucosylated. The oligosaccharides at Asn78 (hLH alpha) are sialylated rather than sulphated and contain the unique sequence NeuAc alpha 2-6 GalNAc beta 1-4GlcNAc beta 1-2 Man alpha 1-3 as part of the majority of mono- and disialylated compounds. The major single constituent at Asn78 has the following structure: [formula, see text]
Non-Aqueous Emulsions as Vehicles for Capsule Fillings (1984)

New vehicles were developed based on non-aqueous emulsions. They may be classified as progress or supplimentation to the actual respectively conventional filling masses for soft gelatin capsules, but also for liquid or semi-solid hard gelatin capsule filling techniques.IN-VITRO dissolution rate studies exhibit a clear superiority of PEG filling masses about oil-wax bases, which show extremely slow release rates.These experiencies may therefore open an interesting way of attaining better bioavailabilities in certain cases with soft gelatin capsules as well as with hard gelatin capsules.But in the following corresponding IN-VIVO tests, which are carried out as urine recoveries, the whole loss of superiority of the PEG compounds is impressingly shown. On the contrary the PEG bases exhibit IN-VIVO the lowest recoveries, while the non-aqueous emulsions at least those with the Riboflavin indicate a tendency towards a more favorable gastrointestinal absorption.
Generation of Specific Human CD8+ T Cell Responses to the Myeloproliferative Disorder Associated V617F Mutated JAK2 Kinase by Use of Analog Peptide Vaccine Candidates. (2005)

Abstract The recent identification of the JAK2 V617F mutation in myeloproliferative diseases including polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis has the potential to serve as a new therapeutic target for these disorders. We hypothesized that the mutated JAK2 kinase sequence could generate new immunogenic peptide-epitopes that could be recognized by the human immune system. Therefore, such sequences could be potential vaccine candidates. The myeloproliferative diseases, especially PV and ET, are ideal diseases for a vaccine approach as they are indolent disorders and also not suitable for use of possibly toxic chemotherapies. Using computer based predictive algorithms, potentially immunogenic nonamer peptides spanning the V617F region of JAK2 were identified. Since JAK2 is a normally expressed self-protein, the goal is to break immune tolerance to the mutated JAK2 sequence without allowing significant recognition of the native sequence. Therefore, synthetic analogs of the V617F mutated peptides with stronger predictive binding to MHC were designed by introducing single amino-acid substitutions into the HLA-A0201 and A0301 binding positions. Corresponding non-mutated native sequences showed little predicted binding. The binding of the mutated and synthetic analog peptides was confirmed in vitro using an MHC class I stabilization assay on TAP deficient cells. Native sequences bound poorly as expected. JAK2 peptides derived from V617F sequences as well as their analogs were used to elicit MHC-restricted, peptide-specific CTL responses in an in vitro model using T-cells from either HLA-A0201 or A0301 healthy donors after stimulation with autologous monocyte-derived dendritic cells. The analog peptides were shown to be immunogenic in vitro, and activated CD8+ T cells that recognized the synthetic analog peptide pulsed targets as determined by an IFN-gamma ELISPOT assay. In addition, and most importantly, these T cells cross-reacted with cellular targets that were pulsed with the mutated V617F peptide associated with the myeloproliferative diseases, but not with the native JAK2 peptide. These analog peptides thus satisfied our initial goals for a vaccine candidate. Further studies with these peptides and others eliciting CD4+ responses will determine their potential for successful use as vaccine candidates
Carbon Nanotube Transistor Arrays for Multistage Complementary Logic and Ring Oscillators (2002)

This work demonstrates multistage complementary NOR, OR, NAND, and AND logic gates and ring oscillators (frequency ∼220 Hz) with arrays of p- and n-type nanotube field effect transistors (FETs). The demonstration is made possible by progress in three aspects of nanotube synthesis and integration. First, patterned growth leads to large numbers of nanotube FETs in an array, as up to 70% of individual nanotubes are semiconductors. Second, metal electrodes are successfully embedded underneath nanotubes and used as local gates. Third, complementary logic gates are made possible by converting p-type FETs in an array into n-type FETs by a local electrical manipulation and doping approach.
Derivation of Induced Pluripotent Stem Cells from Human Peripheral Blood T Lymphocytes (2010)

Induced pluripotent stem cells (iPSCs) hold enormous potential for the development of personalized in vitro disease models, genomic health analyses, and autologous cell therapy. Here we describe the generation of T lymphocyte-derived iPSCs from small, clinically advantageous volumes of non-mobilized peripheral blood. These T-cell derived iPSCs ("TiPS") retain a normal karyotype and genetic identity to the donor. They share common characteristics with human embryonic stem cells (hESCs) with respect to morphology, pluripotency-associated marker expression and capacity to generate neurons, cardiomyocytes, and hematopoietic progenitor cells. Additionally, they retain their characteristic T-cell receptor (TCR) gene rearrangements, a property which could be exploited for iPSC clone tracking and T-cell development studies. Reprogramming T-cells procured in a minimally invasive manner can be used to characterize and expand donor specific iPSCs, and control their differentiation into specific lineages.
Leak-Tight Piezoelectric Microvalve for High-Pressure Gas Micropropulsion (2004)

This paper describes the results of our development of a leak-tight piezoelectric microvalve, operating at extremely high upstream pressures for microspacecraft applications. The device is a normally closed microvalve assembled and fabricated primarily from micromachined silicon wafers. The microvalve consists of a custom-designed piezoelectric stack actuator bonded onto silicon valve components (such as the seat, boss, and tether) with the entire assembly contained within a stainless steel housing. The valve seat configurations include narrow-edge seating rings and tensile-stressed silicon tethers that enable the desired, normally closed, leak-tight operation. Leak testing of the microvalve was conducted using a helium leak detector and showed leak rates of 5/spl times/10/sup -3/ sccm at 800 psi (5.516 MPa). Dynamic microvalve operation (switching rates of up to 1 kHz) was successfully demonstrated for inlet pressures in the range of 0/spl sim/1000 psi. The measured static flow rate for the microvalve under an applied potential of 10 V was 52 sccm at an inlet pressure of 300 psi. The measured power consumption, in the fully open state, was 3 mW at an applied potential of 30 V. The measured dynamic power consumption was 180 mW for 100 Hz continuous operation at 100psi.
Algae–bacteria interactions: Evolution, ecology and emerging applications (2015)

Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions - from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae-roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal-bacterial interactions to various environmental and bio-technological applications.
Regulation of in situ complement activation via the lectin pathway in patients with IgA nephropathy. (2001)

The lectin pathway, which is initiated by mannose-binding lectin (MBL) and MBL-associated serine protease (MASP), is one of the possible routes to activate the complement cascade in immunoglobulin A (IgA) nephropathy. The purpose of this study was to elucidate the regulatory mechanism of the pathway. Levels of complement activation products and regulatory proteins were measured in sera from 27 patients with IgA nephropathy, and generation of fluid-phase complement activation products in the presence of pooled normal human serum was quantified to evaluate activation in vitro. Although there were no significant differences in the serum levels and in vitro activation between the MBL-MASP positive (n = 14) and negative (n = 13) groups, there were positive correlations between complement activation products (Bb fragment and C4d fragment) and regulatory proteins (factor H, C4-binding protein, and C1 inhibitor) in the MBL-MASP-positive group. Furthermore, immunohistochemical studies demonstrated glomerular deposition of the regulatory protein (C4-binding protein, alpha2-macroglobulin, and factor H) in all patients in the MBL-MASP-positive group. These findings suggest that the regulatory proteins control in situ complement activation via the lectin pathway immediately, and continuous activation due to inadequate control will lead to the advanced glomerular injury.
Cyclosporin A modulates the course of woodchuck hepatitis virus infection and induces chronicity (1991)

Immunosuppression is known to influence the state of chronic hepatitis B virus infection, and is thought to increase the risk of developing chronic infection in newly exposed individuals. Cyclosporin A (CsA), an immunosuppressive agent that inhibits Th cell function, was administered to woodchucks chronically infected with woodchuck hepatitis virus (WHV), and resulted in a decreased severity of chronic hepatitis and an increased viremia during the treatment. Adult woodchucks inoculated with WHV and given CsA for 14 wk had increased viremias, decreased acute phase liver injury, and developed chronic infections at a higher rate compared with immunocompetent woodchucks given virus alone (chronicity in seven of seven WHV + CsA + vs zero of nine WHV + CsA-; p less than 0.001). These results in a relevant animal model of hepatitis B virus infection indicate: 1) that liver injury in acute hepadnavirus infections is immune-mediated and not a direct cytopathic effect of virus replication; 2) that Th cells function in the inflammatory response and in the immunologic control of hepadnavirus infection; and 3) that suppression of Th cell function in acute hepadnavirus infection decreases liver injury but alters the outcome of infection in favor of chronicity. These results also suggest continued challenges in the application of CsA in liver transplantation for hepatitis B virus-induced diseases.