gebhart/patrepeval huggingface dataset:
Conformation of the transmembrane domains in peripheral myelin protein 22. Part 1. Solution‐phase synthesis and circular dichroism study of protected 17‐residue partial peptides in the first putative transmembrane domain* (2003)

Charcot-Marie-Tooth disease (CMT) is the most commonly inherited peripheral neuropathy. DNA duplication and point mutation of the gene encoding peripheral myelin protein 22 (PMP22) have been found in CMT type 1A dominants. To investigate the influence of the point mutation of PMP22 on the secondary structure, protected partial peptides in the putative first transmembrane domain, wild type Boc-IVLH(Bom)VAVLVLLFVSTIV-OMe (1) and its Pro16 mutant Boc-IVLH(Bom)VAVPVLLFVSTIV-OMe (2) were synthesized. Circular dichorism (CD)-spectral analysis suggested that peptide 1 adopts a stable alpha-helical conformation in membrane-mimetic solvent,1-BuOH/1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) system. On the contrary, the mutant 2 favors beta-sheet conformation in the same solvent system. Interestingly, alpha-helix to beta-sheet transition of 2 was observed at higher contents of 1-BuOH than 70%.
Recurrent <i>Pseudomonas aeruginosa</i> Pneumonia in Ventilated Patients: Relapse or Reinfection? (1998)

A prospective observational study was performed to determine whether recurrent episodes of pneumonia caused by Pseudomonas aeruginosa in ventilated patients were due to a relapse of the previous clone or to reinfection with a new one. Diagnosis was based on quantitative cultures of secretions obtained by bronchoscopy. Comparison of strains was made by chromosomal fingerprinting based on pulsed field gel electrophoresis (PFGE). Thirty-three (89.1%) of 37 patients survived the initial week after pneumonia diagnosis; six survivors (18.1%) had multiple episodes caused by the same species. Presence of adult respiratory distress syndrome (83.3% versus 22.2%, p = 0.02) was the only factor significantly associated with clinical recurrences. The 16 isolates from five patients (nine recurrences) were analyzed by PFGE. All new isolates from recurrent episodes, excepting one, were considered as relapses. These data suggest that most recurrent episodes of P. aeruginosa pneumonia in ventilated patients occur due to persistence of strains present in a prior infection.
<i>In Vivo</i> Studies on the Effect of Co-Encapsulation of CpG DNA and Antigen in Acid-Degradable Microparticle Vaccines (2009)

Protein-based vaccines have been explored as a safer alternative to traditional weakened or killed whole organism based vaccination strategies and have been investigated for their ability to activate the immune system against certain cancers. For optimal stimulation of T lymphocytes, protein-based vaccines should deliver protein antigens to antigen presenting cells in the context of appropriate immunostimulatory signals, thus mimicking actual pathogens. In this report, we describe the synthesis, characterization, and biological evaluation of immunostimulatory acid-degradable microparticles, which are suitable delivery vehicles for use in protein-based vaccines and cancer immunotherapy. Using a 3' conjugation strategy, we optimized the attachment of immunostimulatory CpG DNA to our vaccine carriers and demonstrated that under acidic conditions similar to those found in endosomal compartments, these new particles were capable of simultaneously releasing a model protein antigen and a CpG DNA adjuvant. We found in an in vivo cytotoxicity assay that the co-encapsulation of ovalbumin, a model antigen, and immunostimulatory agent in the same particle led to superior cytotoxic T lymphocyte activity compared to particles coadministered with adjuvant in an unbound form. In addition, we investigated the ability of these acid-degradable particles to induce protective immunity in the MO5 murine melanoma model and found that they were effective until tumor escape, which appeared to result from a loss of antigen expression by the cancer cells due to in vivo selection pressure.
Guidance, navigation, and control of an unmanned hovercraft (2013)

This paper introduces a simulation and evaluation of guidance, navigation, and control algorithms applied to an autonomous hovercraft. A line-of-sight guidance law is adopted in conjunction with a neural network based adaptive dynamic inversion control scheme for the underactuated hovercraft following a prescribed path. The simulation result demonstrates that the guidance and control scheme can be effective in waypoint following of the underactuated hovercraft, especially, when external disturbances exist. It is also shown that the error signals are bounded using Lyapunov's direct method.
Endocytosis of endogenously synthesized HIV-1 envelope protein. Mechanism and role in processing for association with class II MHC (1995)

CD4+ T cell clones specific for the HIV-1 envelope (env) protein are able to recognize not only uninfected APC that have taken up and processed exogenous env protein, but also virally infected cells expressing the env protein. We have evaluated the hypothesis that endocytosis of endogenously synthesized env protein from the plasma membrane of infected cells permits entry of the protein into the MHC class II-restricted Ag processing pathway. We show here that the env protein of HIV-1 is internalized at a surprisingly high rate through a mechanism that is dependent upon a tyrosine-containing motif located in the cytoplasmic domain of the gp41 subunit. Mutation of a critical cytoplasmic tyrosine residue or truncation of the C-terminal portion of the cytoplasmic domain resulted in forms of the env protein that did not undergo rapid internalization. However, by a variety of assays, these poorly internalized forms of the env protein were processed for class II-restricted Ag presentation as efficiently as wild-type env protein, indicating that internalization by this pathway is not essential for class II-restricted presentation. In addition, a secreted form of the env protein was presented efficiently by class II MHC under conditions that prevented re-uptake by endocytosis. Taken together, these results suggest that although rapid endocytosis from the cell surface is likely to be a major mechanism by which endogenously synthesized env protein is processed for association with class II MHC, an internal pathway may also be used.
Novel Domain-Specific Actions of Amyloid Precursor Protein on Developing Synapses (1998)

The effect of the secretory form of amyloid precursor protein (sAPP) on synaptic transmission was examined by using developing neuromuscular synapses in Xenopus cell cultures. The frequency of spontaneous postsynaptic currents (SSCs) was reduced by the addition of sAPP, whereas the amplitude of impulse-evoked postsynaptic currents (ESCs) was increased by sAPP. These opposing effects on spontaneous versus evoked release were separated by using the specific domain of APP. The C-terminal fragment of sAPP (CAPP) only reduced SSC frequency and did not affect ESCs. By contrast, the N-terminal fragment of sAPP (NAPP) did not affect SSC frequency but did increase ESC amplitude. The reduction of SSC frequency by sAPP appears to be mediated by activation of potassium channels through a cGMP-dependent pathway, whereas the increase of ESC amplitude is mediated by a different pathway involving activation of protein kinase(s). These results suggest the potential role of sAPP as a modulator of synaptic activity by two specific domains.
Route Planning for Unmanned Air Vehicles with Multiple Missions Using an Evolutionary Algorithm (2007)

In this paper, the route-planning problem for unmanned air vehicles with multiple missions is studied with the proposal of a novel evolutionary route planner. In the new planner, the individual candidates are evaluated with respect to the workspace. Therefore the computation of the configuration space is avoided. With digital terrain elevation data, our approach can find a near-optimal route that can increase the surviving probability efficiently. By using a problem-specific representation of candidate solutions and genetic operators, our algorithm can take into account different kinds of mission constraints and generate the solutions in real-time.
Phosphorylation in the carboxyl-terminal domain of the capsid protein of hepatitis B virus: evaluation with a monoclonal antibody (1991)

The capsid protein of hepatitis B virus (p21c) is made of 183 amino acids coded for by the C gene. By using p21c isolated from Dane particles (hepatitis B virus) as an immunogen, a monoclonal antibody (no. 2212) which recognized an epitope dependent on the phosphorylation of p21c was raised. The binding of no. 2212 antibody to authentic p21c was completely inhibited by a synthetic undecapeptide with a sequence of RRRSQSPRRRR, representing amino acids 165 to 175 of p21c, only when the peptide was phosphorylated. Either or both of Ser-168 and Ser-170 were phosphorylated in p21c in vivo, therefore, and contributed to the manifestation of the epitope. No. 2212 antibody bound to p21c from core particles derived from Dane particles or hepatocellular carcinoma tissues (PLC/342) propagated in nude mice but did not bind to p21c from core particles expressed in Escherichia coli or yeast cells, indicating different states of phosphorylation in them. Nonphosphorylated p21c showed a higher affinity for the viral DNA than did phosphorylated p21c. Since the serum from an asymptomatic carrier, with a high titer for antibody to hepatitis B core antigen, specifically bound to phosphorylated undecapeptide (amino acids 165 to 175), the epitope would stimulate humoral antibody responses in the human host.
Clozapine therapy for Parkinson’s disease and other movement disorders (1994)

Recent research on the role of clozapine in the treatment of Parkinson's disease and other movement disorders is discussed. Most clinical trials have shown resolution of or improvement in psychotic symptoms accompanying Parkinson's disease without worsening of parkinsonian symptoms. Adverse effects appear to be mild at dosages of < 100 mg/day; sedation is the most frequent problem. Most of these studies have serious limitations, however; until better studies have been completed, the decision to use clozapine for Parkinson's disease-related psychosis should be made on a case-by-case basis, with thorough evaluation of risks, benefits, and other therapeutic options. Some patients with Parkinson's disease have shown improvement in tremor and other abnormal movements when given clozapine. Clozapine cannot be recommended for treating tardive dyskinesia on the basis of the research done so far; some trials show dramatic resolution of symptoms, others no benefit. Anticholinergics or dopamine-reuptake inhibitors should be considered before clozapine is given to patients with tardive dyskinesia because of clozapine's potential for serious adverse effects. A few patients with Huntington's disease have responded to clozapine, but again no conclusions can be drawn. Clozapine appears to offer no real advantage over haloperidol for treating choreiform movements in Huntington's disease. The frequency of tics in Tourette's syndrome does not seem to be reduced by clozapine. Clozapine has shown some efficacy as a treatment for psychosis and abnormal movements in Parkinson's disease. Results have been less promising for other movement disorders. Further study in larger populations is needed before any definitive conclusions about clozapine's place in movement disorder therapy can be made.
Interactions of immunoliposomes with target cells. (1983)

We have covalently attached a monoclonal antibody (11-4.1) against the murine major histocompatibility antigen, H-2Kk, on the surface of liposomes. The interaction of these antibody-coated liposomes (immunoliposomes) with target cells, RDM-4 lymphoma (H-2Kk), was investigated. About 90% of the immunoliposomes taken up by target cells at 4 degrees C could be removed by a mild protease treatment of the cells, whereas only 30% of the uptake at 37 degrees C was labile to the same treatment. Furthermore, the uptake of immunoliposomes at 37 degrees C was inhibitable by cytochalasin B or by a combination of 2-deoxyglucose and NaN3. These results suggest that immunoliposome binding to the target cell surface is the primary uptake event at 4 degrees C and that the surface-bound liposomes are rapidly internalized by the cells at 37 degrees C, probably via an endocytic pathway. Studies with fluorescence microscopy of target cells treated with immunoliposomes containing carboxyfluorescein also supported this conclusion. If endocytosis is the mechanism by which immunoliposomes gain entry into target cells, the efficacy of a cytotoxic drug encapsulated would depend on the resistance of the drug to lysosomal inactivation and its ability to escape from the lysosomal system. Consistent with this notion, we observed that methotrexate encapsulated in liposomes bearing 11-4.1 antibody specifically inhibited deoxy[6-3H]uridine incorporation into DNA in target RDM-4 cells but not in P3-X63-Ag8 myeloma cells (H-2Kd) at the same doses. The observed cytotoxic effect of encapsulated methotrexate could be reversed by the treatment of cells with a lysosomotropic amine, chloroquine, which has been shown to increase the intralysosomal pH of mammalian cells. On the other hand, cytosine-beta-D-arabinofuranoside encapsulated in immunoliposomes showed no target-specific killing, probably because the drug is readily inactivated in the lysosomal system. These results are discussed in terms of the drug carrier potential of immunoliposomes.
Process and film characterization of low pressure tetraethylorthosilicate–borophosphosilicate glass (1986)

The pyrolytic decomposition of tetraethylorthosilicate (TEOS) has been used to deposit highly doped borophosphosilicate glass (BPSG) films. The experiments were carried out in a modified low pressure chemical vapor deposition furnace in the 620–680 °C range at a deposition pressure of 0.5 Torr. Trimethylborate and phosphine together with oxygen were found to be the best dopant source combination. The deposited layers adhere strongly to the quartzware and low particle counts of typically less than 0.2 per cm2 were measured. The thickness uniformity was below ±6%, the dopant uniformity was ±0.1 wt. % over a wafer. If compared to low pressure SiH4–BPSG films, the TEOS–BPSG shows superior step coverage and much higher chemical stability up to dopant levels of about 5 wt. % B, 5 wt. % P. The etch rate behavior in buffered HF corresponds to the trends reported for SiH4–BPSG. The electrical characterization of thin TEOS–BPSG and TEOS–SiO2 layers yielded an electrical breakdown strength in the 7–8 MV/cm range. The glass flow properties (wet and dry ambient) were investigated and found to be very good in the 800–850 °C region. By using a rapid optical anneal system, the required step tapering could be achieved at time/temperature combinations of 40 s/900 °C or 10 s/1000 °C. Detailed infrared studies showed strong interaction among the different oxide absorption bands of the TEOS–BPSG layers.
Studies on Some Infrared Stimulable Phosphors (1957)

Physical properties of the two phosphor systems SrS: Ce,Sm, and SrS: Eu,Sm, as well as the base material SrS, have been studied. The optical studies concern spectra of transmission, excitation, fluorescence, phosphorescence, stimulation, and stimulated emission. Relative storage efficiencies of the major exciting wavelengths have been measured. Time characteristics of the phosphorescence and the infrared exhaustion have been determined. The dc photoconductive response as a function of the wavelength of the incident light has been studied. A simplified band-theory model which correlates all of the experimental data in conjunction with the electronic structures of the activators is presented.
Utilizing Low‐Cost Eggshell Particles to Enhance the Mechanical Response of Mg–2.5Zn Magnesium Alloy Matrix (2017)

The search for lightweight high‐performance materials is growing exponentially primarily due to ever‐increasing stricter environmental regulations and stringent service conditions. To cater to these requirements, the use of low‐cost reinforcements has been explored in the Mg matrix to develop Economically Conscious Magnesium (ECo–Mg) composites. In this study, eggshell particles (3, 5, and 7 wt%) reinforced Mg–Zn composites are synthesized using blend‐press‐sinter powder metallurgy technique. The results reveal that the addition of eggshell particles enhances microhardness, thermal stability, damping, and yield strength with an inappreciable change in the density. In particular, Mg2.5Zn7ES composite do not ignite till ≈750 °C. The overall combination of properties exhibited by Mg–Zn–ES composites exceeds many of currently used commercial alloys in the transportation sector. An attempt is made, in this study, to interrelate microstructure and properties and to study the viability of compression and ignition properties with a comparison to commercially used Mg alloys.
Fast Distance Preserving Level Set Evolution for Medical Image Segmentation (2006)

Accurate and fast image segmentation algorithms are of paramount importance for a wide range of medical imaging applications. Level set algorithms based on narrow band implementation have been among the most widely used segmentation algorithms. However, the accuracy of standard level set algorithms is compromised by the fact that their evolution schemes deteriorate the signed distance level set functions required for accurate computation of normals and curvatures. The most common remedy is to use an ad-hoc reinitialization step to rebuild the signed distance function frequently. Meanwhile, complex upwind finite difference schemes are required for stable evolution. They together make the overall computation expensive. In this paper, we propose a novel fast narrow band distance preserving level set evolution algorithm that eliminates the need for both reinitialization and complex upwind finite difference schemes. This is achieved by incorporating into a variational level set formulation with a signed distance preserving term that regularizes the evolution. As a result, stable, accurate, fast evolution could be obtained using a simple finite difference scheme within a very narrow band, defined as the union of all 3times3 pixel blocks around the zero crossing pixels. Also, our method allows the use of larger time step to speed up the convergence while ensuring accurate result, as well as the use of more general and computational efficient initial level set functions rather than the signed distance functions required by standard level set methods. The proposed algorithm has been applied on both synthetic and real images of different modalities with promising results
Structured Approach to Advanced Candidate Selection and Treatment Design of Stimulation Treatments (2000)

Abstract Because many oilfield workers see matrix treatments of wells as a low-tech operation, they often fail to pay attention to candidate selection and treatment design. This lack of attention may have led to the relatively low success rate of these treatments. A 1997 survey in a major oil company indicated that one out of every three to four jobs fails to produce more oil or gas after the treatment. This failure represents a loss to the company of over $10 million (U.S.), plus a missed extra production capacity of nearly 40,000 BOPD. The probable main cause for this poor performance is the lack of a structured approach to the following: selecting the right candidate wells and the appropriate treatmentdefining and implementing a structured treatment design procedure To improve the situation, a task force investigated the problem and mapped out a total process, which consists of the following steps: A candidate well is selected by comparing its actual performance against its theoretical potential. Then, the source of poor performance is identified, if applicable. Based on this information, the treatment type can be identified and designed, ultimately resulting in an operational stimulation program. The task force concluded that individual pieces of design software and some design rules existed for many elements, but they lacked an integrated overall approach. The team decided to create a software package by integrating "fuzzy" rules with appropriate mathematical models to guide field engineers through the individual design steps in a consistent, structured manner. This paper describes various elements of the integrated software package that was designed to meet these needs.
XML access control using static analysis (2003)

Access control policies for XML typically use regular path expressions such as XPath for specifying the objects for access control policies. However such access control policies are burdens to the engines for XML query languages. To relieve this burden, we introduce static analysis for XML access control. Given an access control policy, query expression, and an optional schema, static analysis determines if this query expression is guaranteed not to access elements or attributes that are permitted by the schema but hidden by the access control policy. Static analysis can be performed without evaluating any query expression against an actual database. Run-time checking is required only when static analysis is unable to determine whether to grant or deny access requests. A nice side-effect of static analysis is query optimization: access-denied expressions in queries can be evaluated to empty lists at compile time. We have built a prototype of static analysis for XQuery, and shown the effectiveness and scalability through experiments.
Microtubule-dependent transport of secretory vesicles visualized in real time with a GFP-tagged secretory protein (1997)

Biosynthetic transport from the trans-Golgi network (TGN) to the plasma membrane (PM) is mediated by secretory vesicles. We analyzed secretory vesicle transport in real time using a GFP-tagged secretory protein, hCgB-GFP, consisting of human chromogranin B (hCgB) and green fluorescent protein (GFP). The fusion protein was expressed transiently in Vero cells or in a stable clone after induction with butyrate. After arrest of the biosynthetic protein transport at 20 degrees C, fluorescent hCgB-GFP colocalized with TGN38, a marker of the TGN. Subsequent release of the secretion block at 37 degrees C led to the formation of green fluorescent vesicles. Confocal analysis revealed that these vesicles were devoid of TGN38 and of Texas Red-coupled transferrin and cathepsin D, markers of the endosomal/lysosomal pathway. As determined by fluorometry and metabolic labelling hCgB-GFP was secreted from the TGN to the PM with a t(1/2) of 20-30 minutes. Video-microscope analysis of green fluorescent vesicles showed brief periods of rapid directed movement with maximal velocities of 1 microm/second. Vesicle movement occurred in all directions, centrifugal, centripetal and circumferential, and 50% of the vesicles analyzed reversed their direction of movement at least once within an observation period of 45 seconds. In the presence of nocodazole the movement of fluorescent vesicles ceased. Concomitantly, secretion of hCgB-GFP was slowed but not completely blocked. We suggest that microtubules (MT) facilitate the delivery of secretory vesicles to the PM by a stochastic transport, thereby increasing the probability for a vesicle/target membrane encounter.