gebhart/patrepeval huggingface dataset:
Targeting of Active Sialyltransferase to the Plant Golgi Apparatus (1998)

Glycosyltransferases in the Golgi apparatus synthesize cell wall polysaccharides and elaborate the complex glycans of glycoproteins. To investigate the targeting of this type of enzyme to plant Golgi compartments, we generated transgenic Arabidopsis plants expressing alpha-2,6-sialyltransferase, a glycosyltransferase of the mammalian trans-Golgi cisternae and the trans-Golgi network. Biochemical analysis as well as immunolight and immunoelectron microscopy of these plants indicate that the protein is targeted specifically to the Golgi apparatus. Moreover, the protein is predominantly localized to the cisternae and membranes of the trans side of the organelle. When supplied with the appropriate substrates, the enzyme has significant alpha-2,6-sialyltransferase activity. These results indicate a conservation of glycosyltransferase targeting mechanisms between plant and mammalian cells and also demonstrate that glycosyltransferases can be subcompartmentalized to specific cisternae of the plant Golgi apparatus.
Argatroban Anticoagulant Therapy in Patients With Heparin-Induced Thrombocytopenia (2001)

Argatroban anticoagulation, compared with historical control subjects, improves clinical outcomes in patients who have heparin-induced thrombocytopenia, without increasing bleeding risk.
Comparison of fixatives for maximal retention of radiolabeled glycoconjugates for autoradiography, including use of sodium sulfate to release unincorporated [35S]-sulfate. (1989)

Previous studies have used [35S]-sulfate as a specific marker to autoradiographically localize sulfated glycosaminoglycans, proteoglycans, and glycoproteins. Embryonic chicks were labeled with [35S]-sulfate, followed by previously reported routine fixation and processing techniques. Subsequent processing revealed loss of radiolabeled macromolecules and retention of unincorporated label in the tissue, using these procedures. Biochemical analysis after various fixation and processing procedures demonstrated that an additional agent, such as cetylpyridinium chloride, was necessary in the fixative to retain the highly aqueous soluble sulfated macromolecular components. Molecular sieve chromatography was used to monitor digestate solutions for the identity of glycosaminoglycans and proteoglycans as indicated by selective enzymatic removal. Retained unincorporated [35S]-sulfate could be completely removed by rinsing the tissue in dehydration solutions containing exogenous sodium sulfate. This new procedure ensures the quantitative retention of sulfate labeled macromolecules in fixed tissue with the complete removal of unincorporated radiotracer, both of which are necessary for meaningful autoradiography.
A Phase II, Randomized, Safety and Immunogenicity Study of a Re-Derived, Live-Attenuated Dengue Virus Vaccine in Healthy Adults (2012)

Two formulations of a new live tetravalent dengue virus (DENV) vaccine produced using re-derived master seeds from a precursor vaccine and that same precursor vaccine as a control were compared in a placebo-controlled, randomized, observer-blind, phase II trial of 86 healthy adults. Two vaccine doses were administered 6 months apart; a third dose was offered to a subset. Symptoms and signs of dengue-like illness reported after vaccination were mild to moderate, transient, and occurred with similar frequency among recipients of the new DENV vaccine and placebo, except for rash. Neither dengue nor vaccine-related serious adverse events were reported. The first DENV vaccine dose was moderately immunogenic; the second dose increased the potency and breadth of the neutralizing antibody response. Tetravalent response rates to the new formulations were 60% and 66.7% in unprimed subjects. A third dose did not increase tetravalent antibody rates. The new DENV vaccine candidates merit additional evaluation.
T-cell Responses to Oncogenic Merkel Cell Polyomavirus Proteins Distinguish Patients with Merkel Cell Carcinoma from Healthy Donors (2014)

These T-cell epitopes represent ideal targets for antigen-specific immune therapy of MCC, and enable tracking and characterization of MCPyV-specific immune responses.
Immunogenicity of Outer Membrane Proteins in a Lipopolysaccharide-Deficient Mutant ofNeisseria meningitidis: Influence of Adjuvants on the Immune Response (1999)

The immunogenicity of outer membrane complexes (OMCs) or heat-inactivated bacteria of a lipopolysaccharide (LPS)-deficient mutant derived from meningococcal strain H44/76 was studied. The immune response in BALB/c mice to the major outer membrane proteins was poor compared to the immune response elicited by wild-type immunogens. However, addition of external H44/76 LPS to mutant OMCs entirely restored the immune response. By using an LPS-deficient mutant, it may be possible to substitute a less toxic compound as adjuvant in meningococcal outer membrane vaccines. Therefore, a broad panel of adjuvants were tested for their potential to enhance the immunogenicity of LPS-deficient OMCs. AlPO(4), Rhodobacter sphaeroides LPS, monophosphoryl lipid A and alkali-hydrolyzed meningococcal LPS showed significantly lower adjuvant activity than did H44/76 LPS. Adjuvant activity similar to H44/76 LPS was found for Escherichia coli LPS, meningococcal icsB and rfaC LPS, QuilA, subfractions of QuilA, and MF59. Good adjuvant activity was also found with meningococcal htrB1 LPS, containing penta-acylated lipid A. Antisera elicited with the less active adjuvants showed relatively high immunoglobulin G1 (IgG1) titers, whereas strong adjuvants also induced high IgG2a and IgG2b responses in addition to IgG1. Antisera with the IgG2a and IgG2b isotypes showed high bactericidal activity, indicating that adjuvants promoting the IgG2a and IgG2b response contribute most to the protective mechanism. Thus, this study demonstrates that the immunogenicity of meningococcal LPS-deficient OMCs can be restored by using less toxic adjuvants, which opens up new avenues for development of vaccines against meningococcal disease.
A Rapid and Simple Method Using the Detergent Triton X114 for Preparation of Outer Membrane Proteins from Bacteria Containing Mycolic Acids. (2001)

A rapid and simple method using the detergent Triton X114 to prepare outer membrane proteins from whole cells of bacteria containing mycolic acids, α-alkyl, β-hydroxyl fatty acids is described. SDS-PAGE analysis and subsequent N-terminal amino acid sequencing revealed that the proteins prepared from whole cells by this method were almost identical to outer membrane proteins prepared by the conventional cell-disruption and differential-centrifugation method. Therefore, this method is useful to prepare outer membrane proteins from whole cells of Mycolata, bacteria containing mycolic acids.
A mouse model of a human congenital disorder of glycosylation caused by loss of PMM2 (2016)

The most common congenital disorder of glycosylation (CDG), phosphomannomutase 2 (PMM2)-CDG, is caused by mutations in PMM2 that limit availability of mannose precursors required for protein N-glycosylation. The disorder has no therapy and there are no models to test new treatments. We generated compound heterozygous mice with the R137H and F115L mutations in Pmm2 that correspond to the most prevalent alleles found in patients with PMM2-CDG. Many Pmm2<sup>R137H/F115L</sup> mice died prenatally, while survivors had significantly stunted growth. These animals and cells derived from them showed protein glycosylation deficiencies similar to those found in patients with PMM2-CDG. Growth-related glycoproteins insulin-like growth factor (IGF) 1, IGF binding protein-3 and acid-labile subunit, along with antithrombin III, were all deficient in Pmm2<sup>R137H/F115L</sup> mice, but their levels in heterozygous mice were comparable to wild-type (WT) littermates. These imbalances, resulting from defective glycosylation, are likely the cause of the stunted growth seen both in our model and in PMM2-CDG patients. Both Pmm2<sup>R137H/F115L</sup> mouse and PMM2-CDG patient-derived fibroblasts displayed reductions in PMM activity, guanosine diphosphate mannose, lipid-linked oligosaccharide precursor and total cellular protein glycosylation, along with hypoglycosylation of a new endogenous biomarker, glycoprotein 130 (gp130). Over-expression of WT-PMM2 in patient-derived fibroblasts rescued all these defects, showing that restoration of mutant PMM2 activity is a viable therapeutic strategy. This functional mouse model of PMM2-CDG, in vitro assays and identification of the novel gp130 biomarker all shed light on the human disease, and moreover, provide the essential tools to test potential therapeutics for this untreatable disease.
Substorm Recovery Phase (1989)

The recovery phase of the magnetospheric substorm is studied numerically by means of a two-dimensional time-dependent nonlinear resistive MHD code. The initial configuration was chosen from the earlier numerical model in which the magnetospheric substorm was driven by the solar wind plasmas. In order to study the recovery phase, the entering solar wind energy flux was reduced when the magnetospheric substorm was in its expansive phase. The system was found to respond instantly to this change and the result showed many characteristic features related to the recovery phase including the tailward motion of thex-point of the reconnected magnetic field lines and the restoration of a tail-like configuration of the magnetic field. Thex-point moved at almost the same speed of the plasma flow in the upstream region, which was considerably smaller than the speed of the plasma jetting or the speed of the plasmoid. As the recovery phase progressed, the plasma jetting across thex-point was reduced very much in the Earthside region. Although the plasma flow was generally in the Earthward direction in the Earthside region of thex-point, the tailward flow was also found near thex-point. The current density was reduced near thex-point and the neutral sheet was broadened in the recovered region. The plasma sheet also became thick in this region. During the recovery of the substorm, the energy conversion rate, both in the form of plasma acceleration and the Joule heating, was reduced. These results on the recovery phase together with the earlier simulation result on the expansive phase indicate that driven reconnection can be a viable mechanism for the magnetospheric substorm including the recovery phase.
Identification and characterization of citrulline‐modified brain proteins by combining HCD and CID fragmentation (2013)

Citrullination is a protein PTM of arginine residues catalyzed by peptidylarginine deiminase. Protein citrullination has been detected in the CNS and associated with a number of neurological diseases. However, identifying citrullinated proteins from complex mixtures and pinpointing citrullinated residues have been limited. Using RP LC and high-resolution MS, this study determined in vitro citrullination sites of glial fibrillary acid protein (GFAP), neurogranin (NRGN/RC3), and myelin basic protein (MBP) and in vivo sites in brain protein extract. Human GFAP has five endogenous citrullination sites, R30, R36, R270, R406, and R416, and MBP has 14 in vivo citrullination sites. Human NRGN/RC3 was found citrullinated at residue R68. The sequence of citrullinated peptides and citrullination sites were confirmed from peptides identified in trypsin, Lys-C, and Glu-C digests. The relative ratio of citrullination was estimated by simultaneous identification of citrullinated and unmodified peptides from Alzheimer's and control brain samples. The site occupancy of citrullination at the residue R68 of NRGN ranged from 1.6 to 9.5%. Compared to CID, higher-energy collisional dissociation (HCD) mainly produced protein backbone fragmentation for citrullinated peptides. CID-triggered HCD fragmentation is an optimal approach for the identification of citrullinated peptides in complex protein digests.
GASOLINE PRODUCTION FROM PALM OIL VIA CATALYTIC CRACKING USING MCM-41: DETERMINATION OF OPTIMUM CONDITION (2015)

The catalytic cracking of palm oil involves parallel cracking reactions which produce organic liquid product (OLP), non-condensable gas and coke. OLP consists of gasoline, kerosene and diesel; all can be used as alternative fuels. The objective of this study was to determine the effect of operating conditions: oil to catalyst (O/C) ratios and Weight Hourly Space Velocities (WHSVs)) to the feed conversion, OLP yield and gasoline yield. The optimum conditions of OLP production was also obtained in this study. The experiment was conducted in a fixed bed microreactor at a temperature of 450°C. The WHSVs were varied at a range of 15 to 25 h-1.While the O/C ratios were varied at the range of 30 to 50. The results show that the highest yield of OLP was 60.73 wt % at O/C ratio of 32.50 and WHSV of 19.38 h-1.
Different regulation of thymidine kinase during the cell cycle of normal versus DNA tumor virus-transformed cells. (1994)

We compared the cell cycle regulation of thymidine kinase (TK) after centrifugal elutriation in normal human and mouse cells (primary cells, diploid fibroblasts) with its expression in cells transformed with different DNA tumor viruses. Normal cells showed a rise of TK enzyme activity near the G1/S boundary, which peaked in S phase, and in G2 returned approximately to the level of G1. Conversely, in cells derived from viral transformation, TK activity remained high throughout S and G2 phases, although it was induced to a comparable extent at the onset of DNA replication. In addition, transformed cells exhibited much more enzyme activity during all phases of the cell cycle. The observed differences in expression were due neither to different rates of protein turnover nor to differences in enzyme stability. Enzyme activity was always totally paralleled by the protein level. In all normal cells, the pattern of TK mRNA variation during the cell cycle was similar to that of enzyme activity. In all transformed lines, however, mRNA levels were higher and did not fluctuate throughout the cell cycle. Recently we showed (Ogris et al., 1993) that the E2F binding site present in the TK promoter is a target for trans activation of the TK gene by polyoma virus large T antigen. Using cells expressing this antigen under the control of a hormone-inducible promoter, we were able to switch TK cell cycle expression from the normal to the transformed status. Obviously, DNA tumor viruses suppress transcriptional down-regulation of the endogenous DNA precursor pathway enzyme TK during the eukaryotic cell cycle, maybe to improve conditions for their own replication.
T cell immunity after a viral infection versus T cell tolerance induced by soluble viral peptides (1993)

The fate of in vivo activated CD8+ cytotoxic T cells was studied in transgenic mice expressing a T cell receptor (TCR) specific for the lymphocytic choriomeningitis virus (LCMV) glycoprotein peptide 33-41 presented by major histocompatibility complex (MHC) class I molecules. LCMV infection of TCR transgenic mice induced LCMV-specific effector and memory T cells whereas injection of soluble LCMV glycoprotein peptide 33-41 resulted in tolerance by peripheral deletion and anergy of LCMV-specific T cells after an initial expansion phase. Similarly, LCMV peptide 33-41-specific tolerance could be achieved in normal C57BL/6 mice and was not abrogated by an LCMV infection. These results obtained with a classically MHC-restricted peptide antigen parallel previous findings with retroviral or bacterial superantigens and indicate a possibility to modulate specifically mature peripheral cytotoxic T lymphocytes in vivo.
HSDPA/HSUPA for UMTS (2006)

Preface. Acknowledgements. Abbreviations. 1. Introduction (Harri Holma and Antti Toskala). 1.1 WCDMA technology and deployment status. 1.2 HSPA standardization and deployment schedule. 1.3 Radio capability evolution with HSPA. 2. HSPA standardization and background (Antti Toskala and Karri Ranta-Aho) 2.1 3GPP. 2.2 References. 3. HSPA architecture and protocols (Antti Toskala and Juho Pirskanen). 3.1 Radio resource management architecture. 3.2 References. 4. HSDPA principles (Juho Pirskanen and Antti Toskala). 4.1 HSDPA vs Release 99 DCH. 4.2 Key technologies with HSDPA. 4.3 High-speed dedicated physical control channel. 4.4 BTS measurements for HSDPA operation. 4.5 Terminal capabilities. 4.6 HSDPA MAC layer operation. 4.7 References. 5. HSUPA principles (Karri Ranta-Aho and Antti Toskala). 5.1 HSUPA vs Release 99 DCH. 5.2 Key technologies with HSUPA. 5.3 E-DCH transport channel and physical channels. 5.4 Physical layer procedures. 5.5 MAC layer. 5.6 Iub parameters. 5.7 Mobility. 5.8 UE capabilities and data rates. 5.9 References and list of related 3GPP specifications. 6. Radio resource management (Harri Holma, Troels Kolding, Klaus Pedersen, and Jeroen Wigard). 6.1 HSDPA radio resource management. 6.2 HSUPA radio resource management. 6.3 References. 7. HSDPA bit rates, capacity and coverage (Frank Frederiksen, Harri Holma, Troels Kolding, and Klaus Pedersen). 7.1 General performance factors. 7.2 Single-user performance. 7.3 Multiuser system performance. 7.4 Iub transmission efficiency. 7.5 Capacity and cost of data delivery. 7.6 Round trip time. 7.7 HSDPA measurements. 7.8 HSDPA performance evolution. 7.9 Conclusions. 7.10 Bibliography. 8. HSUPA bit rates, capacity and coverage (Jussi Jaatinen, Harri Holma, Claudio Rosa, and Jeroen Wigard). 8.1 General performance factors. 8.2 Single-user performance. 8.3 Cell capacity. 8.4 HSUPA performance enhancements. 8.5 Conclusions. 8.6 Bibliography. 9. Application and end-to-end performance (Chris Johnson, Sandro Grech, Harri Holma, and Martin Kristensson) 9.1 Packet application introduction. 9.2 Always-on connectivity. 9.3 Application performance over HSPA. 9.4 Application performance vs network load. 9.5 References. 10. Voice-over-IP (Harri Holma, Esa Malkama ki, and Klaus Pedersen). 10.1 VoIP motivation. 10.2 IP header compression. 10.3 VoIP over HSPA. 10.4 References. 11. RF requirements of an HSPA terminal (Harri Holma, Jussi Numminen, Markus Pettersson, and Antti Toskala). 11.1 Transmitter requirements. 11.2 Receiver requirements. 11.3 Frequency bands and multiband terminals. 11.4 References. Index.
Perspectives on cognitive neuroscience (1992)

PART I: LEVEL OF ANALYSIS: Introduction Patricia S. Churchland and Terrence J. Senjnowski: Perspectives on cognitive neuroscience Richard F. Thompson and Mark A. Gluck: Basic substrates of basic associative learning and memory Tim Tully: Drosophila's role in identifying the building blocks of associative learning and memory Nicholas J. Mackintosh: Simple conditioning Craig H. Bailey: Morphological basis of short- and long-term memory in Aplysia Bruce L. McNaughton and Paul Smolensky: Connectionist and neural modelling: converging in the hippocampus Gary Lynch, John Larson, Ursula Stabubli and Jose Ambros-Ingerson: An experimental psychologist's view of cognitive science Commentary on Part I PART II: DISSOCIATIONS AND MODELS: Introduction Lawrence Weiskrantz: Dissociations and associations in neuropsychology Daniel L. Schachter and Lynn Nadel: Varieties of spatial memory: a problem for cognitive neuroscience David S. Olton, Cynthia Wible and Alicja L. Markowska: A comparative analysis of the role of the hippocampal system in memory Marcia K. Johnson and William Hirst: Processing subsystems of memory Raymond P. Kesner: The emergence of multidimentional approaches to the structural organization of memory Morris Moscovitch and Carlo Umilta: Consciousness and nonconscious processes in memory and attention Commentary on Part II PART II: MODULATION AND COGNITION: Introduction James L. McGaugh: Neuromodulation and the storage of information: involvement of the Amygdaloid complex George F. Koob: Arousal, stress and inverted U-shaped curves: implications for cognitive function Michael W. Eysenck: Anxiety and cognitive functioning: a multi-faceted approach Howard Leventhal: Emotion: prospectus for conceptual and empirical development Commentary on Part III PART IV: CLINICAL PERSPECTIVES: Introduction Muriel D. Lezek: Identifying neuropsychological deficits William Milberg and Marilyn Albert: The speed of constituent mental operations and its relationship to neuronal representation Brenda Rapp and Alfonso Caramazza: Cognitive neuropsychology: from impaired performance to normal cognitive structure Shepard Siegel: Feed-forward processes in drug tolerance and dependence Ruben C. Gur and Raquel E. Gur: The impact of neuroimaging on human neuropsychology Alan M. Palmer and David M. Bowen: Neurochemical approaches to cognitive disorders Anthony C. Santucci, Vahram Haroutunian, Linda M. Bierer and Kenneth L. Davis: Approaches to the treatment of Alzheimer's disease Commentary on Part IV Concluding remarks.
The Neuropathology of Chronic Traumatic Encephalopathy (2015)

Repetitive brain trauma is associated with a progressive neurological deterioration, now termed as chronic traumatic encephalopathy (CTE). Most instances of CTE occur in association with the play of sports, but CTE has also been reported in association with blast injuries and other neurotrauma. Symptoms of CTE include behavioral and mood changes, memory loss, cognitive impairment and dementia. Like many other neurodegenerative diseases, CTE is diagnosed with certainty only by neuropathological examination of brain tissue. CTE is a tauopathy characterized by the deposition of hyperphosphorylated tau (p-tau) protein as neurofibrillary tangles, astrocytic tangles and neurites in striking clusters around small blood vessels of the cortex, typically at the sulcal depths. Severely affected cases show p-tau pathology throughout the brain. Abnormalities in phosphorylated 43 kDa TAR DNA-binding protein are found in most cases of CTE; beta-amyloid is identified in 43%, associated with age. Given the importance of sports participation and physical exercise to physical and psychological health as well as disease resilience, it is critical to identify the genetic risk factors for CTE as well as to understand how other variables, such as stress, age at exposure, gender, substance abuse and other exposures, contribute to the development of CTE.
Ultrasonic enhancement of bead-based bioaffinity assays (2006)

Ultrasonic radiation forces can be used for non-intrusive manipulation and concentration of suspended micrometer-sized particles. For bioanalytical purposes, standing-wave ultrasound has long been used for rapid immuno-agglutination of functionalized latex beads. More recently, detection methods based on laser-scanning fluorometry and single-step homogeneous bead-based assays show promise for fast, easy and sensitive biochemical analysis. If such methods are combined with ultrasonic enhancement, detection limits in the femtomolar region are feasible. In this paper, we review the development of standing-wave ultrasonic manipulation for bioanalysis, with special emphasis on miniaturization and ultrasensitive bead-based immunoassays.