gebhart/patrepeval huggingface dataset:
Quantification and distribution of equine oocyte cortical granules during meiotic maturation and after activation (2002)

Abstract In vitro fertilization (IVF) is being routinely used in humans and several domestic species, however, limited success has been achieved in the horse. Although immature equine oocytes are capable of completing meiosis in vitro, subsequent fertilization, and embryonic development of those oocytes are questionable. The lack of development of these oocytes could be attributed to an impaired cytoplasmic maturation. In the horse, the study of oocyte cytoplasmic maturation and post‐fertilization development has been hindered by the lack of progress in IVF. In mammalian oocytes, migration of cortical granules (CG) has been used as an important criterion to evaluate cytoplasmic maturation. The aim of this study was to describe and quantify the CG distribution of equine oocytes during in vitro meiotic maturation and to assess activation of oocytes with calcium ionophore based upon fluorescein isothiocyanate (FITC)‐labeled Lens culinaris agglutinin (LCA) and laser confocal microscopy. The results of this study indicate that CG are distributed throughout the cytoplasm of oocytes at the germinal vesicle (GV) stage (immature). As maturation proceeds, a progressive centripetal migration of CG to the oocyte cortex occurs with the formation of a monolayer adjacent to the plasma membrane starting by the end of a 30 hr incubation period and increasing significantly after 36 hr. After activation, significant reduction in the number of CG was observed ( P < 0.001) suggesting that oocytes cultured under the present conditions possess the ability to release CG in response to the ele‐vation of intracellular free calcium. Mol. Reprod. Dev. 63: 451–458, 2002. © 2002 Wiley‐Liss, Inc.
Live attenuated HIV vaccines: pitfalls and prospects (2004)

Neither safety nor efficacy of the current live attenuated primate immunodeficiency virus vaccines has withstood the test of time. However, such viruses are invaluable tools to address two key questions: (1). what are the correlates of protection, and (2). what are the molecular determinants of viral immunopathogenesis?
Salt interpretation for depth imaging ‐ where geology is working in the geophysical world (2009)

Accurate salt interpretation incolves an integration of geology and geophysics. In the practice of salt interpretation and model building in depth imaging, we see two problems that could happen: exclusive geophysical interpretation without geological input and insufficient geological interpretation without understanding how the geophysical data are processed and without evaluating the limit and uncertainty of some geological data. Here we present two before‐after examples to show why these problems can happen, how the final imaging products can be improved through integrating geological and geophysical data in salt interpretation/modeling for depth migration, and why the cross‐training of geological, geophysical and interpretation skill sets are key factors in improving depth imaging products.
Limits of the output power in Er <sup>3+</sup> :ZBLANsinglemode fibrelasers (1995)

The saturation of the 2.71 µm laser output has been measured in erbium-doped ZBLAN singlemode fibres with Er3+ concentrations of 1000, 5000 and 10000 ppm mol. Limits of the single-mode-laser output are discussed.
Frameshift mutations of autophagy‐related genes <i>ATG2B, ATG5, ATG9B</i> and <i>ATG12</i> in gastric and colorectal cancers with microsatellite instability (2008)

Mounting evidence indicates that alterations of autophagy processes are directly involved in the development of many human diseases, including cancers. Autophagy-related gene (ATG) products are main players in the autophagy process. In humans there are 16 known ATG genes, of which four (ATG2B, ATG5, ATG9B and ATG12) have mononucleotide repeats with seven or more nucleotides. Frameshift mutations of genes with mononucleotide repeats are features of cancers with microsatellite instability (MSI). It is not known whether ATG genes with mononucleotide repeats are altered by frameshift mutations in gastric and colorectal carcinomas with MSI. For this, we analysed the mononecleotide repeats in ATG2B, ATG5, ATG9B and ATG12 in 32 gastric carcinomas with high MSI (MSI-H), 13 gastric carcinomas with low MSI (MSI-L), 43 colorectal carcinomas with MSI-H and 15 colorectal carcinomas with MSI-L by a single-strand conformation polymorphism (SSCP) analysis. We found ATG2B, ATG5, ATG9B and ATG12 mutations in 10, 2, 13 and 0 cancers, respectively. The mutations were detected in MSI-H cancers but not in MSI-L cancers. Gastric and colorectal cancers with MSI-H harboured one or more ATG mutations in 28.1% and 27.9%, respectively. Our data indicate that frameshift mutations in ATG genes with mononucleotide repeats are common in gastric and colorectal carcinomas with MSI-H, and suggest that these mutations may contribute to cancer development by deregulating the autophagy process.
<b>COSTIMULATION REGULATES THE KINETICS OF interleukin‐2 RESPONSE TO BACTERIAL SUPERANTIGENS</b> (1996)

The aim of this study was to investigate the mechanisms by which B7-related costimulatory molecules (CD80, CD86) increase T-cell responsiveness to extracellular ligands. As a model study, the in vitro response of purified splenic CD4+ T cells to a bacterial superantigen, SEB, was characterized. Previous analysis of this experimental model led us to conclude that expression of B7-related molecules is strictly required in order to activate CD4+ T cells in the presence of bacterial superantigens. In the present report, we demonstrate that antigen-presenting cell-derived costimulatory signals regulate the kinetics of interleukin-2 (IL-2) production by SEB-activated splenic CD4+ T cells. Indeed, experiments performed with purified subpopulations of antigen-presenting cells and using B7-transfected cell lines indicated that increased levels of CD80 and/or CD86 cell surface expression is associated with a faster kinetics of IL-2 production in response to SEB. Accordingly, blocking of CD80 or CD86-derived signals by specific monoclonal antibodies led to a slower kinetics of IL-2 production in response to SEB. Thus these data demonstrate that similar strength of signal through the T-cell receptor can lead to immune responses displaying distinct kinetics depending on the level of costimulatory ligands on APC.
A New Catheter Operating System for Medical Applications (2007)

This paper deals with a new catheter operating system for medical applications. We developed a highly precise remote control system by using a master-slave system. In order to insure the safety of the whole system, we design a simply micro force sensor. Also we expatiate on the design concept of the system and control of the system. We also carried out the operating simulation experiments "in vitro". The experimental results indicated the proposed catheter operating system works properly, it can be controlled by tele-operation, and it can effectively improve the operability in to aneurysm with force feedback for intravascular neurosurgery.
Inhibition of 6-Methylsalicylic Acid Synthesis by the Antibiotic Cerulenin (1975)

Cerulenin, a specific inhibitor of beta-ketoacyl-(acyl carrier protein) synthetase [EC 2.3.1.41] and 3-hydroxy-3-methylglutaryl-CoA synthetase [EC 4.1.3.5], was studied to determine whether it inhibits 6-methylsalicylic acid synthesis, in which so-called "polyketide" formation, a condensation step similar to that in fatty acid synthesis, is involved. In fact, 100 mug/ml (4.5 X 10(-4) M) of cerulenin inhibited 60% of 6-methylsalicylic acid synthetase activity and 68% of fatty acid synthetase activity of Penicillium urticae.
Potential synergies of drop‐in biofuel production with further co‐processing at oil refineries (2019)

Abstract Drop‐in biofuels have been defined as functionally equivalent to petroleum‐based transportation fuels and are fully compatible with the existing petroleum infrastructure. They will be essential in sectors such as aviation if we are to achieve emission reduction and climate mitigation goals. Currently, ‘conventional’ drop‐in biofuels, which are primarily based on upgrading of lipids / oleochemicals, are the only significant source of commercial volumes of drop‐in biofuels. However, the necessary increased, future volumes will likely come from ‘advanced’ drop‐in biofuels based on biomass feedstocks such as forest and agriculture residues. Biocrudes / bio‐oils produced from lignocellulosic feedstocks using thermochemical technologies such as gasification, pyrolysis, and hydrothermal liquefaction need to be further upgraded to drop‐in biofuels. However, advanced drop‐in biofuels have been slow to reach commercial maturity due to significant technical challenges, high capital costs, and the challenge of generally lower oil prices. It is likely that the co‐processing of drop‐in biofuels with conventional petroleum refining could considerably reduce capital costs. Initially, co‐processing is likely to be established through the upgrading of conventional / oleochemical feedstocks (lipids). Lipids are readily available in large volumes (global production in 2017 was ~185 million metric tonnes) and can be more easily integrated into oil‐refinery processes. In contrast, lignocellulose‐derived biocrudes / bio‐oils are not yet available in significant volumes and are more complex to co‐process in a refinery. The likely strategies for co‐processing of oleochemicals (lipids) and bio‐oil and biocrude feedstocks based on different insertion points within the refinery infrastructure are discussed. © 2019 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Chemical Industry and John Wiley & Sons, Ltd.
Preparing for and handling the results of regulatory inspections of biomedical facilities. (1995)

Although there have been numerous presentations on how to conduct and survive a government inspection, it appears that these sessions do not always adequately include suggestions from those who have been the subjects of regulatory inspections. This paper will include comments from the experience of one of the regulated. Remarks apply to experience with U.S. regulatory authorities, principally the U.S. Food and Drug Administration (FDA) and the U.S. Environmental Protection Agency (EPA). This paper attempts to give guidance on how to prepare for an inspection and what to do at the debriefing and after the inspector(s) leave your facility.
StereoScan: Dense 3d reconstruction in real-time (2011)

Accurate 3d perception from video sequences is a core subject in computer vision and robotics, since it forms the basis of subsequent scene analysis. In practice however, online requirements often severely limit the utilizable camera resolution and hence also reconstruction accuracy. Furthermore, real-time systems often rely on heavy parallelism which can prevent applications in mobile devices or driver assistance systems, especially in cases where FPGAs cannot be employed. This paper proposes a novel approach to build 3d maps from high-resolution stereo sequences in real-time. Inspired by recent progress in stereo matching, we propose a sparse feature matcher in conjunction with an efficient and robust visual odometry algorithm. Our reconstruction pipeline combines both techniques with efficient stereo matching and a multi-view linking scheme for generating consistent 3d point clouds. In our experiments we show that the proposed odometry method achieves state-of-the-art accuracy. Including feature matching, the visual odometry part of our algorithm runs at 25 frames per second, while - at the same time - we obtain new depth maps at 3-4 fps, sufficient for online 3d reconstructions.
Affine Parameter Estimation from the Trace Transform (2006)

In this paper, we assume that we are given the images of two segmented objects, one of which may be an affinely distorted version of the other, and wish to recover the values of the parameters of the affine transformation between the two images. The images may also differ by the overall level of illumination. The multiplicative constant of such difference may also be recovered. We present a generic theoretical framework to solve this problem. In terms of this framework, other proposed methods may be interpreted. We show how, in this framework, one can recover the affine parameters in a way that is robust to various effects, such as occlusion and illumination variation. The proposed method is generic enough to be applicable also to matching two images that do not depict the same scene or object.
Functional Analysis of RNA Structures Present at the 3′ Extremity of the Murine Norovirus Genome: the Variable Polypyrimidine Tract Plays a Role in Viral Virulence (2010)

Interactions of host cell factors with RNA sequences and structures in the genomes of positive-strand RNA viruses play various roles in the life cycles of these viruses. Our understanding of the functional RNA elements present in norovirus genomes to date has been limited largely to in vitro analysis. However, we recently used reverse genetics to identify evolutionarily conserved RNA structures and sequences required for norovirus replication. We have now undertaken a more detailed analysis of RNA structures present at the 3' extremity of the murine norovirus (MNV) genome. Biochemical data indicate the presence of three stable stem-loops, including two in the untranslated region, and a single-stranded polypyrimidine tract [p(Y)] of variable length between MNV isolates, within the terminal stem-loop structure. The well-characterized host cell pyrimidine binding proteins PTB and PCBP bound the 3'-untranslated region via an interaction with this variable sequence. Viruses lacking the p(Y) tract were viable both in cell culture and upon mouse infection, demonstrating that this interaction was not essential for virus replication. However, competition analysis with wild-type MNV in cell culture indicated that the loss of the p(Y) tract was associated with a fitness cost. Furthermore, a p(Y)-deleted mutant showed a reduction in virulence in the STAT1(-/-) mouse model, highlighting the role of RNA structures in norovirus pathogenesis. This work highlights how, like with other positive-strand RNA viruses, RNA structures present at the termini of the norovirus genome play important roles in virus replication and virulence.
Mity model: <i>Tetranychus urticae</i>, a candidate for chelicerate model organism (2007)

Chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks) are the second largest group of arthropods and are of immense importance for fundamental and applied science. They occupy a basal phylogenetic position within the phylum Arthropoda, and are of crucial significance for understanding the evolution of various arthropod lineages. Chelicerates are vectors of human diseases, such as ticks, and major agricultural pests, such as spider mites, thus this group is also of importance for both medicine and agriculture. The developmental genetics of chelicerates is poorly understood and a challenge for the future progress for many aspects of chelicerate biology is the development of a model organism for this group. Toward this end, we are developing a chelicerate genetic model: the two-spotted spider mite Tetranychus urticae. T. urticae has the smallest genome of any arthropod determined so far (75 Mbp, 60% of the size of the Drosophila genome), undergoes rapid development and is easy to maintain in the laboratory. These features make T. urticae a promising reference organism for the economically important, poorly studied and species-rich chelicerate lineage.
Site-specific nanopatterning of functional metallic and molecular arbitrary features in nanofluidic channels (2015)

We established a versatile method for site-specific nanopatterning of functional metallic and molecular arbitrary features in glass nanofluidic channels, with well-controlled feature sizes ranging from tens to hundreds of nanometers and precisely controlled placements in the range of several tens of nanometers. With the method, we achieved the fabrication of quasi-0D, quasi-1D, 2D, and 3D gold nanopatterns in nanofluidic channels, as well as a high-density fluorescent molecular nanoarray in arrayed femtoliter nanofluidic channels. The method opens the way for precise functionalization of nanofluidic channels, which has been greatly challenging in the field of nanofluidics.
The effects of heme oxygenase-1 transfection on hypoxia-reoxygenation injury in vitro of liver cells (2009)

Objective To investigate the effects of transfection of heme oxygenase-1 adenovirus vector (Ad-HO-1) in vitro on hypoxia-reoxygenation injury of human liver ceils. Methods Human liver cell line L-02 cells were cultured for 24, 48 and 72 h (24-h, 48-h and 72-h groups), after adding cryopreserved Ad-HO-1. And L-02 cells were co-cultured with the adenovirus vector vehicle as controls. The HO-1 mRNA expression level of liver cells in each group was detected by reverse transcription PCR. HO-1 expression was detected by indirect immunofluorescence labeling. An inverted fluorescence microscope was applied to observe enhanced green fluorescent protein (EGFP) expression in liver cells 24 and 72 h after transfection. The liver cells in blank control group (culture for 48 h) and 48-h group were cultured for 4 h under hypoxia, followed by culture for 8 h under oxygen condition. The survival rate of cells in two groups was tested by MTT assay. Results HO-1 rnRNA expression in 24-h, 48-h and 72-h groups was significantly higher than in control group, and with the prolongation of the transfection time, HO-1 mRNA expression level was gradually increased. In blank control, 24-h, 48-h, and 72-h groups, HO-1 expression rate was 2.0%, 29%, 85.6%, and 84.6%, respectively. After hypoxia-reoxygenation culture, survival rate in blank control and 48-h groupswas (37.7±3.5)% and (89.4±5.2)% respectively (P<0.01).Conclusion Ad-HO-1 in vitro can be effectively transfected into human liver cells. The hypoxia-reoxygenation injury to liver cells with transfection was milder than that to control cells.

Key words: 
Heine oxygenase;  Adenoviridae;  Cell hypoxia;  Reperfusion injury;  Hepatocytes
Automatic parking identification and vehicle guidance with road awareness (2016)

Advanced driver assistance systems (ADAS) are becoming more common in safety and convenience applications. The computer vision based ADAS described in this paper, is an add-on system, suitable to variety of cars. It detects vacant legal parking spots, and safely guides the vehicle into the selected parking. Detection can be performed in both indoor parking lots and along roadsides. The system is composed of three standard computer-connected webcams, which are attached to the vehicle. Upon slowing down, the system starts searching automatically for a right hand-side vacant parking spot, while being aware to parking color signs. Once detected, the parking orientation is determined, and the driver is notified. Once a parking is selected by the driver, the relative position between the vehicle and the parking spot is monitored. Vocal and visual parking guidance instructions are presented to the driver. In addition, if during parking, an object is moving on the road towards the car, a safety alert is given. The system is universal in the sense that, as an add-on system, it can be installed on any private 4-wheeled vehicle, and is suited to urban driving environment.
Incidence of Tissue Coring With the 25-Gauge Quincke and Whitacre Spinal Needles (1996)

The 25-gauge Quincke and 25-gauge Whitacre spinal needles currently used in anesthesia can produce tissue coring.
Temperature, humidity, and dimension dependence of the bending motion of ionomer-based polymer actuators (2016)

This paper focuses on the effects of temperature, humidity, and dimensions on the displacement of ionomer-based polymer actuators. The amount of displacement and velocities of the actuation strongly increased with increasing humidity and temperature. We attributed this behavior to a change in the Young's modulus (the stiffness) and ion conductivity based on water uptake. To evaluate the dependence of the velocity of the displacement on humidity and temperature, we examined three velocities (i.e. the initial, bending, and backtracking velocities). The observed increase in the bending velocity at higher relative humidity (RH) levels arises from an increase in the water uptake, which enhances ion conductivity and decreases the film stiffness. The ratio of the bending velocity to the backtracking velocity at higher RH decreased because of a drastic increase of the backtracking velocity at higher RH. This result would be explained by an increase in the ion conductivity accompanying a decrease in the stiffness. Furthermore, we compared the difference in the amount of displacement of the actuator using actuators of two widths (2 and 10 mm) at 30, 60, and 90% RH and at 25 °C. The difference in the width of the actuator did not completely affect the displacement. These results are reasonably explained by considering the amount of mobile ions per unit volume of the films of the actuators. Copyright © 2016 John Wiley & Sons, Ltd.
Nutrition and catering: 3. Nutrient losses in cook-freeze and cook-chill catering. (1984)

Information on nutrient losses in cook-chill and cook-freeze catering systems is reviewed, which is limited and conflicting. In general it suggests that cook-freeze systems result in better vitamin C retention than conventional systems with significant warmholding periods. Losses of vitamin C, and possibly other labile nutrients appear to be significant in cook-chill systems.
Successive catalytic reactions specific to Pd-based rotaxane complexes as a result of wheel translation along the axle (2010)

Rotaxane-structure-specific Pd-catalyzed rearrangement of propargyl or allyl urethane groups to oxazolidinone moieties proceeded efficiently. The conversion took place successively by the translation of the wheel along the axle, thus providing a novel macrocyclic catalytic system.
Rheology of Mucin (2000)

Mucins are secreted from epithelial cells of the gastrointestinal (GI), genitourinary, and respiratory tracts to form mucous gels protecting mucosal surfaces from damaging effects and agents (1 1,2). Mucous gels are not pure mucin but contain other components secreted into the gel, e.g., IgA and protein, lipid, and nucleic acid from shed epithelial cells, and particularly, in the lower GI tract from bacteria. When measuring the rheological properties of mucous/mucin gels, it is essential to consider the effect of these nonmucin components. Mucin alone is the gel-forming component of mucus; other components can inhibit gel formation and strength. Thus, cellular debris has been shown to reduce markedly gel strength and even inhibit gel formation (3,4).