gebhart/patrepeval huggingface dataset:
Contribution of Growth and Cell Cycle Checkpoints to Radiation Survival in Drosophila (2006)

Cell cycle checkpoints contribute to survival after exposure to ionizing radiation (IR) by arresting the cell cycle and permitting repair. As such, yeast and mammalian cells lacking checkpoints are more sensitive to killing by IR. We reported previously that Drosophila larvae mutant for grp (encoding a homolog of Chk1) survive IR as well as wild type despite being deficient in cell cycle checkpoints. This discrepancy could be due to differences either among species or between unicellular and multicellular systems. Here, we provide evidence that Grapes is needed for survival of Drosophila S2 cells after exposure to similar doses of IR, suggesting that multicellular organisms may utilize checkpoint-independent mechanisms to survive irradiation. The dispensability of checkpoints in multicellular organisms could be due to replacement of damaged cells by regeneration through increased nutritional uptake and compensatory proliferation. In support of this idea, we find that inhibition of nutritional uptake (by starvation or onset of pupariation) or inhibition of growth factor signaling and downstream targets (by mutations in cdk4, chico, or dmyc) reduced the radiation survival of larvae. Further, some of these treatments are more detrimental for grp mutants, suggesting that the need for compensatory proliferation is greater for checkpoint mutants. The difference in survival of grp and wild-type larvae allowed us to screen for small molecules that act as genotype-specific radiation sensitizers in a multicellular context. A pilot screen of a small molecule library from the National Cancer Institute yielded known and approved radio-sensitizing anticancer drugs. Since radiation is a common treatment option for human cancers, we propose that Drosophila may be used as an in vivo screening tool for genotype-specific drugs that enhance the effect of radiation therapy.
Collagen VI related muscle disorders (2005)

Mutations in the genes encoding collagen VI (COL6A1, COL6A2, and COL6A3) cause Bethlem myopathy (BM) and Ullrich congenital muscular dystrophy (UCMD), two conditions which were previously believed to be completely separate entities. BM is a relatively mild dominantly inherited disorder characterised by proximal weakness and distal joint contractures. UCMD was originally described as an autosomal recessive condition causing severe muscle weakness with proximal joint contractures and distal hyperlaxity. Here we review the clinical phenotypes of BM and UCMD and their diagnosis and management, and provide an overview of the current knowledge of the pathogenesis of collagen VI related disorders.
Improvement of health-related quality of life in adult women with 21-hydroxylase deficiency over a seven-year period (2012)

Health related quality of life (HRQoL) is impaired in adult patients with 21-hydroxylase deficiency (21-OHD). Up to now, only cross-sectional and no longitudinal studies are available. It is not known if HRQoL can be improved in adult 21-OHD patients. We performed a longitudinal, prospective, single centre, follow-up study over seven years including 15 adult female 21-OHD patients. Two standardized questionnaires (Short Form 12 (SF-12); Hospital Anxiety and Depression Scale (HADS)) were completed in 2003, 2006 and 2010. Adjustment for age and sex was performed by transformation of score values into age- and sex-adjusted Z-scores using data sets from respective normative groups. Data regarding glucocorticoid therapy, clinical and hormonal parameters were assessed. We found that two of eight scales of SF-12 showed a significant improvement and four of eight scales a positive trend to better scores. No significant changes were seen in scores for HADS or for steroid hormone levels. Daily hydrocortisone equivalent dose per body surface significantly decreased over the study period. No changes in BMI were observed over the study period. We conclude that improvement of HRQoL in adult female 21-OHD patients is possible. Several factors might be involved in this improvement including reduced daily hydrocortisone equivalent dose per body surface.
Porcine adenovirus-3 as a helper-dependent expression vector (1999)

Porcine adenovirus has been proposed as a potential vector for generating novel and effective vaccines for pigs. As a prerequisite for the generation of helper-dependent porcine adenovirus-3 (PAV-3) vectors, two E1-complementing porcine cell lines expressing E1 proteins of human adenovirus-5 (HAV-5) were made. These cell lines could be efficiently transfected with DNA and allowed the rescue and propagation of a PAV-3 recombinant, PAV201, containing a 0.597 kb E3 deletion and a 0.803 kb E1A deletion. Our data demonstrate that E1A proteins of HAV-5 have the capacity to transform foetal porcine retina cells and complement for the E1A proteins of PAV-3. The green fluorescent protein (GFP) gene placed under the control of a cytomegalovirus immediate early promoter was inserted into the E1A region of the PAV201 genome. Using these cell lines, a helper-dependent PAV-3 recombinant expressing GFP, PAV202, was constructed and characterized. The wild-type PAV-3 and the recombinant PAV202 expressing GFP were used to determine the ability of the virus to enter and replicate in cells of human and animal origin under cell culture conditions. Our results suggest that PAV-3 enters but does not replicate in dog, sheep, bovine and human cells.
Identification and Characterization of a Novel Family of Cyclic Nucleotide Phosphodiesterases (1998)

We report the cloning, expression, and characterization of a new family of cyclic nucleotide phosphodiesterase (PDE) that has unique kinetic and inhibitor specificities. A clone corresponding to the C terminus of this PDE was initially identified by a bioinformatic approach and used to isolate a cDNA that is likely full-length. This novel PDE, designated as MMPDE9A1, shows highest mRNA expression in kidney with lower levels in liver, lung, and brain. The mRNA size by Northern blot analysis is approximately 2.0 kilobases, and the cDNA encoding PDE9A1 is 1929 base pairs in length. The largest open reading frame predicts a protein of 534 amino acids with a molecular mass of 62,000 Da. When expressed in COS-7 cells, PDE9A1 activity was not inhibited well by either the nonselective inhibitor 3-isobutyl-1-methyl-xanthine or the new selective PDE5 inhibitor, sildenafil, but it is inhibited by the PDE1/5 inhibitor (+)-cis-5,6a, 7,8,9 hyl] phenylmethyl]-5-methyl-cylopent[4,5]imidao[2, 1-b]purin-49(3H)one (SCH51866) with an IC50 of 1.55 microM. This new phosphodiesterase is highly specific for cGMP. Its Km of approximately 0.07 microM for cGMP is the lowest yet reported for a PDE, being at least 40-170 times lower than that of PDE5 and PDE6, respectively.
Preparing stents with masking and etching technology (2003)

Nowadays the progress of medical techniques is inconceivable without the application and development of microelectronics technology. Since the beginning of the 70's more and more electronic innovations - e.g. micro motors, micro robots, sensor and microcircuit implants fabricated by thin and thick film technology, the use of lasers in surgery etc. - have helped the work of medical doctors worldwide. With the application of this technology, in the past years, many lives have been saved or in many cases, the most drastic interventions (amputation) could be avoided. For example, the stenosis (narrowing of the arteries) formerly could only be medicated by vascular surgery. Since the appearance of stents, this intervention has been simplified significantly.
Reduction of type V collagen using a dominant-negative strategy alters the regulation of fibrillogenesis and results in the loss of corneal-specific fibril morphology. (1996)

A number of factors have been implicated in the regulation of tissue-specific collagen fibril diameter. Previous data suggest that assembly of heterotypic fibrils composed of two different fibrillar collagens represents a general mechanism regulating fibril diameter. Specifically, we hypothesize that type V collagen is required for the assembly of the small diameter fibrils observed in the cornea. To test this, we used a dominant-negative retroviral strategy to decrease the levels of type V collagen secreted by chicken corneal fibroblasts. The chicken alpha 1(V) collagen gene was cloned, and retroviral vectors that expressed a polycistronic mRNA encoding a truncated alpha 1(V) minigene and the reporter gene LacZ were constructed. The efficiency of viral infection was 30-40%, as determined by assaying beta-galactosidase activity. To assess the expression from the recombinant provirus, Northern analysis was performed and indicated that infected fibroblasts expressed high steady-state levels of retroviral mRNA. Infected cells synthesized the truncated alpha 1(V) protein, and this was detectable only intracellularly, in a distribution that colocalized with lysosomes. To assess endogenous alpha 1(V) protein levels, infected cell cultures were assayed, and these consistently demonstrated reductions relative to control virus-infected or uninfected cultures. Analyses of corneal fibril morphology demonstrated that the reduction in type V collagen resulted in the assembly of large-diameter fibrils with a broad size distribution, characteristics similar to fibrils produced in connective tissues with low type V concentrations. Immunoelectron microscopy demonstrated the amino-terminal domain of type V collagen was associated with the small-diameter fibrils, but not the large fibrils. These data indicate that type V collagen levels regulate corneal fibril diameter and that the reduction of type V collagen is sufficient to alter fibril assembly so that abnormally large-diameter fibrils are deposited into the matrix.
B Cell Receptor-Mediated Calcium Signaling Is Impaired in B Lymphocytes of Type Ia Patients with Common Variable Immunodeficiency (2010)

Several lines of evidence have demonstrated B cell intrinsic activation defects in patients with common variable immunodeficiency (CVID). The rapid increase of intracellular free calcium concentrations after engagement of the BCR represents one crucial element in this activation process. The analysis of 53 patients with CVID for BCR-induced calcium flux identified a subgroup of patients with significantly reduced Ca2+ signals in primary B cells. This subgroup strongly corresponded to the class Ia of the Freiburg classification. Comparison at the level of defined B cell subpopulations revealed reduced Ca2+ signals in all mature B cell populations of patients with CVID class Ia when compared with healthy individuals and other groups of patients with CVID but not in circulating transitional B cells. BCR-induced Ca2+ responses were the lowest in CD21low B cells in patients as well as healthy donors, indicating an additional cell-specific mechanism inhibiting the Ca2+ flux. Although proximal BCR signaling events are unperturbed in patients' B cells, including normal phospholipase Cgamma2 phosphorylation and Ca2+ release from intracellular stores, Ca2+ influx from the extracellular space is significantly impaired. CD22, a negative regulator of calcium signals in B cells, is highly expressed on CD21low B cells from patients with CVID Ia and might be involved in the attenuated Ca2+ response of this B cell subpopulation. These data from patients with CVID suggest that a defect leading to impaired BCR-induced calcium signaling is associated with the expansion of CD21low B cells, hypogammaglobulinemia, autoimmune dysregulation, and lymphadenopathy.
HIV-1 neutralizing antibodies induced by native-like envelope trimers (2015)

A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs.
LiDAR-Video Driving Dataset: Learning Driving Policies Effectively (2018)

Learning autonomous-driving policies is one of the most challenging but promising tasks for computer vision. Most researchers believe that future research and applications should combine cameras, video recorders and laser scanners to obtain comprehensive semantic understanding of real traffic. However, current approaches only learn from large-scale videos, due to the lack of benchmarks that consist of precise laser-scanner data. In this paper, we are the first to propose a LiDAR-Video dataset, which provides large-scale high-quality point clouds scanned by a Velodyne laser, videos recorded by a dashboard camera and standard drivers' behaviors. Extensive experiments demonstrate that extra depth information help networks to determine driving policies indeed.
Modifying the sequence of an immunoglobulin V-gene alters the resulting pattern of hypermutation (1996)

Affinity maturation of antibodies requires localized hypermutation and antigen selection. Hypermutation is particularly active in certain regions (notably the CDRs of light and heavy chains) due to the local accumulation of hot spots. We have now analyzed the role of individual nucleotides in the origin of hot spots and show that mutability is largely defined by the nucleotide sequence. We compared the mutability profile of wild-type and modified kappa transgenes that contain silent mutations in the CDR1 segment. We found a new hot spot created at the third base of Ser-31 when its wild-type AGT codon was substituted by AGC. Two major hot spots associated with this AGC vanished when Ser-31 was encoded by the synonymous TCA. In addition to these, which were the most prominent changes, there were compensatory alterations in mutability of residues not directly related to the introduced silent mutations, so that the average hypermutation remained constant. Thus, mutations arising early in the immune response, even silent ones, could affect the mutability of critical residues and alter the pattern of affinity maturation. When analyzing hybridomas, we detected such alterations, but they seemed to better correlate with changes in average rather than local mutation rates. Overall, this paper shows how evolution could have optimized the mutability of individual residues to minimize deleterious mutations. Thus, the optimal strategy for affinity maturation may involve the incorporation of multiple point mutations before antigen selection of the relevant cells.
Familial dysmyelination in a Long Evans rat mutant. (1995)

Tremors were observed in 15 Long Evans rats beginning at 10 to 12 days of age. These were followed by progressively worsening ataxia, hind limb paresis, episodes of immobility, and seizures by 5 to 14 weeks. Gross lesions were not observed at necropsy in rats euthanized and perfused at 4 to 16 weeks of age. Neurohistologic examination revealed dysmyelination in the central nervous system. Astrogliosis in the white matter with marked increase of expression of the glial fibrillary acid protein marker was accompanied by diffuse microgliosis. Scattered glial cells, interpreted to be oligodendrocytes, contained minute periodic acid-Schiff-positive cytoplasmic granules. Large mineralized periodic acid-Schiff-positive and laminated structures were observed in the cerebellar white matter, midbrain, and thalamus of rats over 6 weeks old. Neuronal degeneration and loss was evident in the cortex, hippocampus, and midbrain. Large axonal spheroids were found in the ventral and lateral funiculi of the spinal cord. An ultrastructural study of four affected rats revealed an almost complete absence of myelinated axons and normal sheaths, and degeneration and necrosis of oligodendrocytes. The Long Evans shaker rat represents a novel myelin mutant with a remarkable survival period and appears to have an autosomal recessive mode of inheritance.
Phlebography (1972)

Methods for complete lower extremity phlebography are based on experience with over 600 examinations. A tilting table with undercouch tube and television monitoring is used. Tourniquets at the ankle and lower thigh are placed initially, and 50 to 100 ml of iothalamate meglumine injection are administered through a 20-gauge needle placed in a dorsal vein of the foot. Usually the iliac veins and inferior vena cava are demonstrable with the assistance of a Valsalva maneuver, calf compression, and rapid injection into the foot; but, if unsuccessful, direct femoral vein or pertrochanteric injections are made. Special complications include phlebothrombosis (preventable by flushing the veins with saline) or local sepsis. Pulmonary embolism secondary to calf compression has not been seen. Interpretation depends heavily upon identification of thrombus as a cylindrical or round translucency in the opacified vein. A completely occluded vein may be totally blocked or bypassed by collaterals. Common causes for artifacts are underfilling, dilution, or streamlining.
The D-2 Digital Video Recorder (1990)

Introduction to D-2 composite digital conversion composite digital video coding and processing digital magnetic recording error correction D-2 tape transports and control systems the D-2 signal system digital audio in D-2.
Neutrophil platelet endothelial cell adhesion molecule-1 participates in neutrophil recruitment at inflammatory sites and is down-regulated after leukocyte extravasation (1997)

Platelet endothelial cell adhesion molecule-1 (PECAM-1), a member of the Ig superfamily, is found on endothelial cells and neutrophils, and has been shown to be involved in the migration of leukocytes across the endothelium. Although studies have supported a role for endothelial PECAM-1 in this process, the participation of neutrophil PECAM-1 in vivo has not been unambiguously demonstrated. Therefore, to examine the involvement of neutrophil PECAM-1 in leukocyte recruitment, we studied the effect of a blocking Ab against murine PECAM-1 on neutrophil recruitment in an established model of murine peritonitis and in a murine model for studying leukocyte-endothelial interactions involving the human vasculature. These studies not only confirmed that neutrophil PECAM-1 is important in the accumulation of neutrophils at inflammatory sites, but that extravasated neutrophils displayed decreased surface expression of PECAM-1. In vitro, the surface expression of murine neutrophil PECAM-1 was not decreased significantly by inflammatory mediators, but was reduced after transendothelial migration. These studies, consistent with previous in vitro observations, confirm that neutrophil PECAM-1, as well as endothelial PECAM-1, is involved in the recruitment of neutrophils into inflammatory sites in vivo, and suggest that the expression of neutrophil PECAM-1 is down-regulated after extravasation into inflamed tissues possibly as a result of engagement of its ligand.
Self-assembly of supramolecular nanostructures from phenylalanine derived bolaamphiphiles (2007)

The growth and self-assembly of phenylalanine derived bolaamphiphiles was investigated. The self-assembly process was studied at hydrophobic–hydrophilic interfaces and under aqueous conditions at different pH. The formation of various structures in microscale and nanoscale was examined using atomic force microscopy, transmission electron microscopy, dynamic light scattering, ultraviolet-visible spectroscopy and infrared spectroscopy. It was observed that the types of structures formed were dependent on both the growth conditions and the chain lengths of the hydrocarbons linking the head groups. At lower pH, tubular formations were observed in high yield for all bolaamphiphiles synthesized compared to higher pH. As the size of the hydrophobic chain length connecting the amino acid head groups increased, the nanotubes were formed in higher yield and were observed to be more elongated and well-defined. In some cases, nanofibers, spheres and rod-like structures were also obtained at aqueous/organic interfaces and in different pH. The investigation of the self-assembly process of such peptide bolaamphiphiles can give further insight into the dynamics of formation of various supramolecular structures. The materials formed were found to be highly stable and can be potentially used as scaffolds for biomaterials and fabrication of nanodevices.
GadY, a Small-RNA Regulator of Acid Response Genes inEscherichia coli (2004)

A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes encoding two transcriptional regulators of the acid response, gadX (yhiX) and gadW (yhiW). Given that IS183 is encoded in the gad gene cluster and because of its role in regulating acid response genes reported here, this RNA has been renamed GadY. We show that GadY exists in three forms, a long form consisting of 105 nucleotides and two processed forms, consisting of 90 and 59 nucleotides. The expression of this small RNA is highly induced during stationary phase in a manner that is dependent on the alternative sigma factor sigmaS. Overexpression of the three GadY RNA forms resulted in increased levels of the mRNA encoding the GadX transcriptional activator, which in turn caused increased levels of the GadA and GadB glutamate decarboxylases. A promoter mutation which abolished gadY expression resulted in a reduction in the amount of gadX mRNA during stationary phase. The gadY gene was shown to overlap the 3' end of the gadX gene, and this overlap region was found to be necessary for the GadY-dependent accumulation of gadX mRNA. We suggest that during stationary phase, GadY forms base pairs with the 3'-untranslated region of the gadX mRNA and confers increased stability, allowing for gadX mRNA accumulation and the increased expression of downstream acid resistance genes.
Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing (2015)

Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.