gebhart/patrepeval huggingface dataset:
Cross-presentation of human melanoma peptide antigen MART-1 to CTLs from in vitro reconstituted gp96/MART-1 complexes. (2004)

Heat shock proteins (HSPs) have two unique roles as constituents of tumor vaccines: (i) to shuttle associated tumor antigens into professional antigen-presenting cells (APCs) and (ii) to activate professional APCs. Here we investigated the shuttle function of the HSP gp96 (glycoprotein 96) for a human melanoma peptide antigen MART-1 that was noncovalently bound to gp96 in vitro. This in vitro complexing reaction was optimized using the radioiodinated MART-1 peptide and human gp96. Up to 20% of gp96 molecules could bind the peptide, assuming a 1:1 molar ratio. The binding was temperature-dependent and thus reversible. At -20 degrees C, 95% of the peptide remained complexed after 24 h, but 25% and 60% of the peptide dissociated at 37 degrees C within 6 and 24 h, respectively. This observation suggests that under the physiological conditions in APCs, spontaneous peptide dissociation from gp96 complexes may facilitate the delivery of peptide antigen into antigen presentation pathways. The gp96/MART-1 complexes stimulated an HLA A2-restricted MART-1-specific CTL clone dependent on the amount of complexed peptide and the presence of HLA-A2-positive APCs. The reaction was peptide-specific and could be blocked by an excess of untreated native gp96. These results show for the first time that peptide antigens from in vitro reconstituted gp96/peptide antigen complexes can be cross-presented by human APCs. These findings extend the scientific basis for further evaluating the use of either endogenous or in vitro reconstituted gp96/tumor-antigen complexes as tumor vaccines.
Three-dimensional analysis of the developing pituitary gland in the mouse (1998)

Prenatal development of the mouse pituitary gland was analyzed in three-dimensions by using confocal laser-scanning microscopy. In any wholemount preparation of the fetal pituitary gland from day 10 to day 18, immunofluorescence of laminin was observed in the deeper regions of the organ and demarcated the boundary of the epithelial tissue from the surrounding mesenchyme. Three-dimensional capillary networks in the fetal pituitary gland at day 13, day 15, and day 18 were visualized clearly by perfusing the blood vessels with an fluorescein isothiocyanate-labelled gelatin solution. During days 12-14, cellular plates protruded from the anterior wall of the pituitary anlage and extended toward the base of the infundibulum. At the same time, the mesenchyme situated among the cellular plates separated from the surrounding mesenchyme except at the anteroventral portion of the anlage. In a posterior wall of the anlage, intercellular depositions of laminin were found among the epithelial cells, some of which reached the laminin sheet in the basement membrane of the anlage. From days 15-18, the pituitary gland enlarged, and the mesenchyme spread radially from the median anteroventral portion to the lateral, posterior, and dorsal regions and finally expanded throughout the entire organ. At the periphery, the mesenchyme in the pituitary gland connected with that surrounding the capsule. Laminin was still found in the intercellular spaces between the epithelial cells, and most of the intercellular depositions of laminin were combined with the laminin sheet in the epithelial basement membrane. An abundance of vessels entered the organ from its anteroventral portion, spread, and connected with one another throughout the gland, similar to the distribution of mesenchyme. Intercellular laminin would induce the polarization of the contacting epithelial cells, resulting in rearrangement of the epithelial cells. The mesenchyme might spread in the pituitary gland, providing the intercellular laminin a foothold, in order to cleave the epithelial cell mass into lobules. The development of capillary nets in the adenohypophysis corresponded well with that of the mesenchyme. Because laminin localizes mainly in the basement membrane in the fetal organs, immunostaining of laminin clearly indicates the boundary between epithelial tissue and the mesenchyme. Three-dimensional observation of laminin in wholemount preparation is very useful for studying morphogenesis.
Phase Diagram of Superfluid<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">H</mml:mi><mml:mi mathvariant="normal">e</mml:mi></mml:mrow><mml:mprescripts/><mml:none/><mml:mn>3</mml:mn></mml:mmultiscripts></mml:math>in 99.3% Porosity Aerogel (2004)

We report on continuous-wave NMR measurements of the energy gaps of the A-like and B-like superfluid phases of 3He at 28.4 mT confined to a 99.3% porosity silica aerogel. The gaps are suppressed by the presence of the aerogel in a temperature-independent manner, but the suppression is considerably stronger than expected from the suppression of T(c). We then use our measurements to calculate the free energy ratio between the A-like and B-like phases. The equilibrium AB transition temperature, derived from where this ratio reaches unity, is consistent with previous measurements of the initial displacement of the pinned AB interface on warming. On this basis, we present for the first time the equilibrium phase diagram of the A-like and B-like phases of superfluid 3He in aerogel.
The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-(<scp>l</scp>)-Threofuranosyl-(3′-2′)-CGAATTCG (2008)

TNA (alpha-( l)-threofuranosyl-(3'-2') nucleic acid) is a nucleic acid in which the ribofuranose building block of the natural nucleic acid RNA is replaced by the tetrofuranose alpha-( l)-threose. This shortens the repetitive unit of the backbone by one bond as compared to the natural systems. Among the alternative nucleic acid structures studied so far in our laboratories in the etiological context, TNA is the only one that exhibits Watson-Crick pairing not only with itself but also with DNA and, even more strongly, with RNA. Using NMR spectroscopy, we have determined the structure of a duplex consisting entirely of TNA nucleotides. The TNA octamer (3'-2')-CGAATTCG forms a right-handed double helix with antiparallel strands paired according to the Watson-Crick mode. The dominant conformation of the sugar units has the 2'- and 3'-phosphodiester substituents in quasi-diaxial position and corresponds to a 4'-exo puckering. With 5.85 A, the average sequential P i -P i+1 distances of TNA are shorter than for A-type DNA (6.2 A). The helix parameters, in particular the slide and x-displacement, as well as the shallow and wide minor groove, place the TNA duplex in the structural vicinity of A-type DNA and RNA.
Multiobjective Optimization of Building Design Using Artificial Neural Network and Multiobjective Evolutionary Algorithms (2008)

Building design is a very complex task, involving many parameters and conflicting objectives. In order to maximise the comfort and minimize the environmental impact, multiobjective optimization should be used. While some tools such as Genetic Algorithms (GA) exist, they are very seldom used in the industry, due to the large computational time they require. This thesis focuses on a specific approach called GAINN (Genetic Algorithm Integrating Neural Network), which combines the rapidity of evaluation of Artificial Neural Networks (ANN) with the optimization power of GAs. The thesis concentrates on a better handling of multiple objectives, in order to efficiently exploit the methodology and increase its accessibility for the non-expert. First, a Multiobjective Evolutionary Algorithm (MOEA), NSGA-II, has been selected and programmed in MATLAB. Then, two new MOEAs were developed, specifically designed to take advantage of GAINN fast evaluations. These two MOEAs have proven to be more efficient than NSGA-II on benchmark test functions, for a comparison based on a maximum runtime. In a second part of this thesis, developed MOEAs were used inside GAINN methodology to optimize the energy consumption and the thermal comfort in a residential building. This optimization was successful, and enabled significant improvements in terms of energy consumption and thermal comfort. It also enabled to illustrate very clearly the relation between these two objectives. This optimization however highlighted two limitations regarding the ANN, the number of training cases and the accuracy in the vicinity of optimal solutions. Finally, the developed algorithms were applied on a past optimization study, in order to highlight the improvements added to GAINN methodology by the use of MOEA.
Mechanism-Based Inactivation of VanX, a <scp>d</scp>-Alanyl-<scp>d</scp>-alanine Dipeptidase Necessary for Vancomycin Resistance (2000)

VanX is a zinc-dependent D-Ala-D-Ala amino dipeptidase required for high-level resistance to vancomycin. The enzyme is also able to process dipeptides with bulky C-terminal amino acids [Wu, Z., Wright, G. D., and Walsh, C. T. (1995) Biochemistry 34, 2455-2463]. We took advantage of this observation to design and synthesize the dipeptide-like D-Ala-D-Gly(SPhip-CHF(2))-OH (7) as a potential mechanism-based inhibitor. VanX-mediated peptide cleavage generates a highly reactive 4-thioquinone fluoromethide which is able to covalently react with enzyme nucleophilic residues, resulting in irreversible inhibition. Inhibition of VanX by 7 was time-dependent (K(irr) = 30+/-1 microM; k(inact) = 7.3+/- 0.3 min(-1)) and active site-directed, as deduced from substrate protection experiments. Nucleophilic compounds such as sodium azide, potassium cyanide, and glutathione did not protect the enzyme from inhibition, indicating that the generated nucleophile inactivates VanX before leaving the active site. The failure to reactivate the dead enzyme by gel filtration or pH modification confirmed the covalent nature of the reaction that leads to inactivation. Inactivation was associated with the elimination of fluoride ion as deduced from (19)F NMR spectroscopy analysis and with the production of fluorinated thiophenol dimer 12. These data are consistent with suicide inactivation of VanX by dipeptide 7. The small size of the VanX active site and the presence of a number of nucleophilic side chains at the opening of the active site gorge [Bussiere, D. E., et al. (1998) Mol. Cell 2, 75-84] associated with the high observed partition ratio of 7500+/-500 suggest that the inhibitor is likely to react at the entrance of the active site cavity.
Yield Optimization through Statistical Analysis of Recipe Changes (2007)

Semiconductor industry increasingly faces the challenge of rapid yield learning in the context of shrinking device sizes. Turning the "art" of the yield learning into measurable, analyzable and fully predictable process is the holy grail of the industry. Today's foundry collects terabytes of data in hopes of finding discerning patterns that could be used for yield optimization. In the paper we turn our attention to one of the most obvious sources of process control and yield optimization - tool recipes. Statistically analyzing the relationship between changes in recipe parameters and the final yield of the devices, we study emerging patterns, derive functional dependencies between process parameters and product yield, and use this acquired knowledge for overall process optimization.
Factoring Algorithms for Computing K-Terminal Network Reliability (1986)

Let GK denote a graph G whose edges can fail and with a set K ⊆ V specified. Edge failures are independent and have known probabilities. The K-terminal reliability of GK, R(GK), is the probability that all vertices in K are connected by working edges. A factoring algorithm for computing network reliability recursively applies the formula R(GK) = piR(GK * ei) + qiR(GK - ei) where GK * ei is GK, with edge ei contracted, GK - ei is GK with ei deleted and pi = 1 - qi is the reliability of edge ei. Various reliability-preserving reductions can be performed after each factoring operation in order to reduce computation. A unified framework is provided for complexity analysis and for determining optimal factoring strategies. Recent results are reviewed and extended within this framework.
Effects of proinsulin C-peptide on nitric oxide, microvascular blood flow and erythrocyte Na+,K+-ATPase activity in diabetes mellitus type I (2000)

This study was conducted to evaluate the influence of proinsulin C-peptide on erythrocyte Na(+),K(+)-ATPase and endothelial nitric oxide synthase activities in patients with type I diabetes. In a randomized double-blind study design, ten patients with type I diabetes received intravenous infusions of either human C-peptide or physiological saline on two different occasions. C-peptide was infused at a rate of 3 pmol.min(-1).kg(-1) for 60 min, and thereafter at 10 pmol.min(-1).kg(-1) for 60 min. At baseline and after 60 and 120 min, laser Doppler flow (LDF) was measured following acetylcholine iontophoresis or mild thermal stimulation (44 degrees C), and venous blood samples were collected to determine plasma cGMP levels and erythrocyte membrane Na(+),K(+)-ATPase activity. The LDF response to acetylcholine increased during C-peptide infusion and decreased during saline infusion [18.6+/-19.2 and -13.2+/-9.4 arbitrary units respectively; mean+/-S.E.M.; P<0.05). No significant change in LDF was observed after thermal stimulation. The baseline plasma concentration of cGMP was 5.5+/-0.6 nmol.l(-1); this rose to 6.8+/-0.9 nmol.l(-1) during C-peptide infusion (P<0.05). Erythrocyte Na(+),K(+)-ATPase activity increased from 140+/-29 nmol of P(i).h(-1).mg(-1) in the basal state to 287+/-5 nmol of P(i). h(-1).mg(-1) during C-peptide infusion (P<0.01). There was a significant linear relationship between plasma C-peptide levels and erythrocyte Na(+),K(+)-ATPase activity during the C-peptide infusion (r=0.46, P<0.01). No significant changes in plasma cGMP levels or Na(+),K(+)-ATPase activity were observed during saline infusion. This study demonstrates an effect of human proinsulin C-peptide on microvascular function, which might be mediated by an increase in NO production and an activation of the erythrocyte Na(+),K(+)-ATPase. These mechanisms are compatible with the previous observed microvascular effects of C-peptide in patients with type I diabetes.
Late treatment with polyene antibiotics can prolong the survival time of scrapie-infected animals (1997)

Amphotericin B (AmB) is one of the few drugs able to prolong survival times in experimental scrapie and delays the accumulation of PrPres, a specific marker of this disease in the brain in vivo. Previous reports showed that the AmB effect is observed only if the drug is administered around the time of infection. In the present study, intracerebrally infected mice were treated with AmB or one of its derivatives, MS-8209, between 80 and 140 days postinoculation. We observed an increased incubation time and a delay in PrPres accumulation and glial fibrillary acidic protein gene expression. Treatment starting at 80 days postinoculation was as efficient as long-term treatment starting the day of inoculation. Our results indicate that polyene antibiotics may interfere, throughout the course of the experimental disease, with the propagation of the scrapie agent.
Application of surface modifying macromolecules in polyethersulfone membranes: Influence on PES surface chemistry and physical properties (1999)

Novel surface modifying macromolecules (SMMs) were developed for incorporation into polyethersulfone (PES) membranes, intended for pervaporation applications. These materials were synthesized with a diisocyanate, polypropylene oxide (PPO), and a fluoro-alcohol, and characterized for elemental analysis, molecular weight, and glass transition temperatures. PES/SMM blends with eight types of SMMs were characterized for surface and physical properties and compared with PES. Water droplet contact angle measurements and X-ray photoelectron spectroscopy data showed that the SMMs migrated to the surface and rendered the PES material more hydrophobic. While advancing contact angle data were equivalent to those of pure Teflon™, the highest average values of receding angles of these systems were less than those of commercial Teflon™. The opaqueness of PES/SMMs films and data from differential scanning calorimetry experiments showed that the SMMs were either immiscible or only partially miscible with PES. It was also observed, for a fixed PES concentration of 25 wt %, that increases in the molecular weight of the SMMs and the weight fraction of PPO in the SMMs led to phase separation in the ternary PES/SMMs/dimethylacetamide (i.e., membrane casting solution) system. On the other hand, in the binary PES/SMMs system (i.e., cast membrane film), an increasing weight fraction of fluorine in the SMMs contributed to an increase in the phase separation. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 73: 1363–1378, 1999
Optimal Parametric Design for Water-Alternating-Gas (WAG) Process in a CO2-Miscible Flooding Reservoir (2010)

Summary A pragmatic method has been developed to efficiently design the production-injection parameters to optimize the water-alternating-gas (WAG) performance in a field-scale CO2-miscible flooding project. The net present value (NPV) is selected as the objective function, while the controlling variables are chosen to be the injection rates, ratios of gas slug size to water slug size (WAG ratio) and cycle time (i.e., the injection time for each gas or water slug) for the injectors and bottomhole pressures (BHPs) for the producers. A hybrid technique, which integrates the orthogonal array (OA) and Tabu technique into the genetic algorithm (GA), is then developed and employed to determine the optimum WAG production-injection parameters. Sensitivity analysis of the WAG parameters on oil recovery is conducted and a field case is finally presented to demonstrate the successful application of the newly developed technique.
Sinus Headache, Migraine, and the Otolaryngologist (2005)

"Sinus headache" is a common complaint in the otolaryngology office. Recent literature has shown that the majority of patients with this complaint satisfy the diagnostic criteria for migraine. This review article presents an overview of the sinus headache literature, with emphasis on the incidence, identification, and treatment of migraine headache for the otolaryngologist.
Extraction of scandium from red mud by modified activated carbon and kinetics study (2008)

激活的碳(交流) 被 tri 丁基磷酸盐(TBP ) 为有选择地从红泥提取钪修改并且由赌注(Brunauer-Emmett-Teller ) 表面区域描绘了。修改交流有优先的吸附到钪。到钪的吸附能力和选择上的吸附物剂量，吸附温度，和时间的影响被检验。最佳吸附物剂量(6.25 g/L ) ，吸附温度(308 K ) ，和吸附时间(40 min ) 被弄明白。一个 pseudo-second-order 动力学模特儿为描述钪的吸附过程被雇用。
New Method to Single-Crystal Micrometer-Sized Ultra-Thin Silver Nanosheets: Synthesis and Characterization (2008)

We reported a new method, which uses Cu+ as the efficient and clean reducing agent, to synthesize micrometer-sized ultra-thin silver (Ag) nanosheets in organic solvent containing oleylamine (OAm). The as-synthesized Ag nanosheets are single-crystal, with regular triangular, truncated triangular, hexagonal, and dodecahedral (truncated hexagonal) shapes, with 3−8 μm edge length and 25 ± 15 nm thickness, which are in contrast to the previous reported micrometer-sized metal nanosheets with thickness above 40 nm. Analysis is performed by X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, selected area electron diffraction, X-ray photoelectron spectroscopy, UV−vis-NIR absorption and transmittance spectroscopy, and optical microscopy, indicating that single-crystal Ag nanosheets are of high quality with a large in-plane size, ultra-thin thickness, and top and bottom enclosed by {111} facets. The present study provides a simple and extendable method to synthesis of micrometer-scale ultra-thin metal nanosheets holding promises for novel physical properties and functional nanodevices.
Redefining the number needed to excise (2013)

The number needed to excise (NNE) is a metric used to convey the efficiency of dermatological practice by serving as a gauge for the diagnostic accuracy of melanoma. Rather than an NNE for melanoma alone, we assert that the NNE should measure all skin cancer types and we present data on NNE from two clinical sites demonstrating the utility and trends in NNE over time.
DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2 (2009)

A subtelomeric region, 4q35.2, is implicated in facioscapulohumeral muscular dystrophy (FSHD), a dominant disease thought to involve local pathogenic changes in chromatin. FSHD patients have too few copies of a tandem 3.3-kb repeat (D4Z4) at 4q35.2. No phenotype is associated with having few copies of an almost identical repeat at 10q26.3. Standard expression analyses have not given definitive answers as to the genes involved. To investigate the pathogenic effects of short D4Z4 arrays on gene expression in the very gene-poor 4q35.2 and to find chromatin landmarks there for transcription control, unannotated genes and chromatin structure, we mapped DNaseI-hypersensitive (DH) sites in FSHD and control myoblasts. Using custom tiling arrays (DNase-chip), we found unexpectedly many DH sites in the two large gene deserts in this 4-Mb region. One site was seen preferentially in FSHD myoblasts. Several others were mapped >0.7 Mb from genes known to be active in the muscle lineage and were also observed in cultured fibroblasts, but not in lymphoid, myeloid or hepatic cells. Their selective occurrence in cells derived from mesoderm suggests functionality. Our findings indicate that the gene desert regions of 4q35.2 may have functional significance, possibly also to FSHD, despite their paucity of known genes.
Estimation of Cerebral Blood Flow From Dynamic Susceptibility Contrast MRI Using A Tissue Model (2005)

Cerebral perfusion measurements are of great clinical and research interest. Positron emission tomography (PET) is considered the gold standard for cerebral perfusion measurement, but is not widely available and entails exposure of the subject to radioactivity. Dynamic susceptibility contrast (DSC) MRI methods are becoming more widely available on the newest generation of MRI scanners. The standard analysis methods of this data have significant disadvantages that include the use of a single, difficult to measure, arterial input function for the entire brain and the need to perform a numerical deconvolution on the logarithm of noisy data. These methods are not yet fully validated and remain qualitative in nature. Using a modification of the standard tracer kinetic principles we implemented a tissue perfusion model that has several advantages over standard methods. The model parameters were estimated using Bayes probability theory in a group of patients with varying degrees of hemodynamic impairment and were found to provide additional physiologic information that was not available using standard techniques.
Fuzzy Logic Inference System for Identification and Prevention of Coronavirus (COVID-19) (2020)

Now a days Novel Coronavirus named COVID-19 becomes major health concern causing severe health issue in human beings and it becomes a pandemic. It’s a kind of zoonotic that means it can transmit animals to humans. It may spread via polluted hands or metals. No specific treatment is available so far for COVID-19, so initial identification and preventions for COVID-19 will be crucial to control or to break down the chain of COVID-19. For this purpose, we have proposed a fuzzy inference system to diagnose the COVID-19 disease by taking six input factor like as; Ethanol, Atmospheric Temperature (AT), Body Temperature (BT), Breath Shortness (BS), Cough and Cold and the output factor has divided into three linguistic categories which denotes the severity level of the infected patients.