gebhart/patrepeval huggingface dataset:
Palladium‐Mediated Arylation of Lysine in Unprotected Peptides (2017)

A mild method for the arylation of lysine in an unprotected peptide is presented. In the presence of a preformed biarylphosphine-supported palladium(II)-aryl complex and a weak base, lysine amino groups underwent C-N bond formation at room temperature. The process generally exhibited high selectivity for lysine over other amino acids containing nucleophilic side chains and was applicable to the conjugation of a variety of organic compounds, including complex drug molecules, with an array of peptides. Finally, this method was also successfully applied to the formation of cyclic peptides by macrocyclization.
Combined Enzyme and Substrate Design: Grafting of a Cooperative Two‐Histidine Catalytic Motif into a Protein Targeted at the Scissile Bond in a Designed Ester Substrate (2007)

A histidine-based, two-residue reactive site for the catalysis of hydrolysis of designed sulfonamide-containing para-nitrophenyl esters has been engineered into a scaffold protein. A matching substrate was designed to exploit the natural active site of human carbonic anhydrase II (HCAII) for well-defined binding. In this we took advantage of the high affinity between the active site zinc atom and sulfonamides. The ester substrate was designed to position the scissile bond in close proximity to the His64 residue in the scaffold protein. Three potential sites for grafting the catalytic His-His pair were identified, and the corresponding N62H/H64, F131H/V135H and L198H/P202H mutants were constructed. The most efficient variant, F131H/V135H, has a maximum k(cat)/K(M) value of approximately 14 000 M(-1) s(-1), with a k(cat) value that is increased by a factor of 3 relative to that of the wild-type HCAII, and by a factor of over 13 relative to the H64A mutant. The results show that an esterase can be designed in a stepwise way by a combination of substrate design and grafting of a designed catalytic motif into a well-defined substrate binding site.
High-Capacity Fiber Field Trial Using Terabit/s All-Optical OFDM Superchannels With DP-QPSK and DP-8QAM/DP-QPSK Modulation (2012)

We report the results of two separate field trials aimed to achieve high fiber capacity over long-haul distances. In the first trial, 22 all-optical orthogonal frequency-division multiplexing superchannels with hybrid dual-polarization 8 quadrature amplitude modulation and dual-polarization quadrature phase-shift-keying (DP-QPSK) modulation were generated using a novel flexible format superchannel transmitter design. The signal carrying net 21.7 Tb/s data was transmitted over 1503 km of dispersion uncompensated field-installed standard single-mode fiber with the aid of hybrid Raman and erbium-doped fiber amplifier (EDFA) amplification and digital coherent detection. In the second trial, we extended the transmission distance to over 2531 km of field fiber using only EDFA for loss compensation. The increase in reach was achieved by reducing the net total data rate to 16.2 Tb/s and modulating the optical superchannel subcarriers with DP-QPSK only. To the best of our knowledge, we achieved the highest capacity field trial record to date at 21.7 Tb/s in the first trial, while the achieved capacity-distance product of 40.9 Pb/s ·km in the second trial is also the highest reported to date.
Optical chemical sensor using a multi-channel directional coupler with slot waveguides (2010)

We describe an optical chemical sensor using a multi-channel directional coupler with slot waveguides.
Areca nut-induced buccal mucosa fibroblast contraction and its signaling: a potential role in oral submucous fibrosis--a precancer condition (2013)

Betel quid (BQ) chewing is an oral habit that increases the risk of oral cancer and oral submucous fibrosis (OSF), a precancerous condition showing epithelial atrophy and tissue fibrosis. Persistent fibroblast contraction may induce the fibrotic contracture of tissue. In this study, we found that areca nut extract (ANE) (200-1200 µg/ml) stimulated buccal mucosa fibroblast (OMF)-populated collagen gel contraction. Arecoline but not arecaidine-two areca alkaloids, slightly induced the OMF contraction. Exogenous addition of carboxylesterase (2U/ml) prevented the arecoline- but not ANE-induced OMF contraction. OMF expressed inositol triphosphate (IP3) receptors. ANE-induced OMF (800 µg/ml) contraction was inhibited by U73122 [phospholipase C (PLC) inhibitor] and 2-aminoethoxydiphenyl borate (IP3 receptor antagonist), respectively. Ethylene glycol tetraacetic acid and verapamil, two calcium mobilization modulators, also suppressed the ANE-induced OMF contraction. ANE induced calcium/calmodulin kinase II and myosin light chain (MLC) phosphorylation in OMF. Moreover, W7 (a Ca(2+)/calmodulin inhibitor), HA1077 (Rho kinase inhibitor), ML-7 (MLC kinase inhibitor) and cytochalasin B (actin filament polymerization inhibitor) inhibited the ANE-induced OMF contraction. Although ANE elevated reactive oxygen species (ROS) level in OMF, catalase, superoxide dismutase and N-acetyl-L-cysteine showed no obvious effect on ANE-elicited OMF contraction. These results indicate that BQ chewing may affect the wound healing and fibrotic processes in OSF via inducing OMF contraction by ANE and areca alkaloids. AN components-induced OMF contraction was related to PLC/IP3/Ca(2+)/calmodulin and Rho signaling pathway as well as actin filament polymerization, but not solely due to ROS production.
Noise-Driven Adaptation: and Mathematical Analysis (2002)

Fairhall et al. (2001) recently reported on variance adaptation processes in cells of the fly visual system, and qualitatively similar effects have been observed in various vertebrate preparations. To better understand the contributions of somatic mechanisms to this kind of adaptation, we recorded intracellularly from neurons of rat sensorimotor cortex while stimulating with a noise current whose standard deviation was varied parametrically. We observed systematic variance-dependent adaptation (where adaptation is defined as a scaling of a nonlinear transfer function), similar in many respects to the effects observed The fact that similar phenomena could be observed in such different preparations led us to investigate a simple model of stochastic stimulus-driven neural activity. The simplest such model, the leaky integrate-and-fire (LIF) cell driven by noise current, permits us to analytically compute many quantities relevant to our observations on adaptation; we show that the LIF model displays adaptive behavior which is quite similar to the effects observed and .
Fusion flame in uncompressed fuel by nonlinear force driven Petawatt- picosecond laser pulses (2011)

Plasma block acceleration by 10 20 cm/s 2 was measured first by Sauerbrey as predicted from nonlinear (ponderomotive) force interaction by picoseconds laser pulses of higher than TW power if an extremely high contrast ratio prevented relativistic self-focusing [1]. This permitted the a fusion-flame ignition of solid density deuterium tritium according to Chu and Bobin [2] and finally the possibility to use hydrogen-boron11 (HB11)fuel with laser pulses in the multipetawatt range [3] based on hydrodynamic computations. Fusion energy is then produced by less radioactivity emission than from burning coal. In order to study the enormous electric fields of the highly inhomogeneous flame, the genuine two-fluid hydrodynamics is applied and reported that a shock process is generated propagating in the uncompressed fuel after the initiation by the ps laser pulse. This is related to the shock ignition of fusion [4], however in contrast to the usual thermal pressure dominated shocks, now driven by non-thermal direct conversion of the laser energy into plasma motion by the nonlinear force.
Beneficial Antioxidative and Antiperoxidative Effect of Cinnamaldehyde Protect Streptozotocin-Induced Pancreatic β-Cells Damage in Wistar Rats (2014)

The present study was aimed to evaluate the antioxidant defense system of cinnamaldehyde in normal, diabetic rats and its possible protection of pancreatic β-cells against its gradual loss under diabetic conditions. In vitro free radical scavenging effect of cinnamaldehyde was determined using DPPH (1,1-diphenyl-2-dipicrylhydrazyl), superoxide radical, and nitric oxide radical. Streptozotocin (STZ) diabetic rats were orally administered with cinnamaldehyde at concentrations of 5, 10 and 20 mg/kg body weight for 45 days. At the end of the experiment, the levels of plasma lipid peroxides and antioxidants such as vitamin C, vitamin E, ceruloplasmin, catalase, superoxide dismutase, reduced glutathione and glutathione peroxidase were determined. A significant increase in the levels of plasma glucose, vitamin E, ceruloplasmin, and lipid peroxides and significant decrease in the levels of plasma insulin and reduced glutathione were observed in the diabetic rats. Also the activities of pancreatic antioxidant enzymes were altered in the STZ-induced diabetic rats. The altered enzyme activities were reverted to near-normal levels after treatment with cinnamaldehyde and glibenclamide. Histopathological studies also revealed a protective effect of cinnamaldehyde on pancreatic β-cells. Cinnamaldehyde enhances the antioxidant defense against reactive oxygen species produced under hyperglycemic conditions and thus protects pancreatic β-cells against their loss and exhibits antidiabetic properties.
Lysine Propionylation To Boost Sequence Coverage and Enable a “Silent SILAC” Strategy for Relative Protein Quantification (2018)

Quantification in proteomics largely relies on the incorporation of stable isotopes, with protocols that either introduce the label through metabolic incorporation or chemical tagging. Most methods rely on the use of trypsin and/or LysC to generate labeled peptides. Although alternative proteases can enhance proteome coverage, generic quantitative methods that port over to such enzymes are lacking. Here we describe a quantification strategy amenable to most proteases, which involves propionylation of metabolically labeled lysine, using a "silent stable isotope labeling by amino acids in cell culture (SILAC)" strategy that reveals isotopic labels on second-stage mass spectrometry (MS2) fragmentation in a tandem mass tag (TMT)-like manner. We selectively propionylated lysine residues prior to digestion to generate pure ArgC-like digestion for trypsin and novel ArgN-like digestions for LysargiNase, by restricting digestion at lysine. The modification offers highly complementary sequence coverage, and even enhanced protein identification rates in certain situations (GluC digestion). Propionylated lysine residues were present in the majority of identified peptides generated from digests of cell lysates and led to the consistent release of an intense cyclic imine reporter ion at mass-to-charge ratio ( m/ z) 140 using higher-energy collisional dissociation. We grew A549 cells in media containing either l-1-<sup>13</sup>C-lysine or l-6-<sup>13</sup>C-lysine, to generate proteins that share the same accurate mass when paired. Peptides were indistinguishable on the first-stage mass spectrometry (MS1) level and, upon fragmentation, released reporter ions at m/ z 140 and m/ z 141, without otherwise affecting sequence ion mass. The quantification approach is independent of the number of peptide lysines and offers a new strategy for quantitative proteomics.
ChemInform Abstract: Resolution of 7,7‐Dimethylbicyclo(3.2.0)hept‐2‐en‐6‐one Using Mortierella ramanniana and 3α,20β‐Hydroxysteroid Dehydrogenase, Photochemistry of 3‐Hydroxy‐7,7‐dimethylbicyclo(3.2.0)heptan‐6‐ones, and the Synthesis of (+)‐Eldanolide. (1987)

Abstract The racemic ketones (I) are transformed to the alcohols (±)‐(II) and (±)‐(IV) which, on photolysis, give rise to formation of the lactone (III).
The Ingrowth of New Bone Tissue and Initial Mechanical Properties of a Degrading Polymeric Composite Scaffold (1995)

Trabecular bone deficiency causes a dilemma at surgery in a variety of clinical situations, including trauma, tumor resection, and reconstruction. A synthetic material to replace trabecular bone would be biocompatible, provide temporary mechanical strength to the reconstructed region, and serve as a scaffold upon which new bone could grow (i.e., osteoconduction). In addition, it should serve as a carrier for osteoinductive biomolecules, degrade into nontoxic materials that the body can excrete via normal metabolic pathways, and allow the new bone to remodel along lines of local stress. A particulate filled composite based on an unsaturated linear polyester was designed as a candidate material for this application. The components are mixed with a monomer that cross links the double bonds of the unsaturated polyester. Degradation occurs via hydrolytic degradation of the backbone polymer's ester linkages. This strategy of prepolymer synthesis via condensation polymerization in the laboratory followed by cross linking the unsaturated prepolymer via radical polymerization at surgery offers design flexibility. The radical polymerization allows curing during surgery to facilitate reconstruction of various shaped defects. The laboratory synthesis of the prepolymer allows alterations of its composition and physical properties to effect desired properties in the resulting composite. This study investigates the effect of several composite material formulations on the in vitro mechanical properties and the associated in vivo histologic characteristics of the resulting material. The prepolymer molecular weight, presence of a leachable salt, and amount of cross linking monomer had strong effects on the resulting strength and modulus of the composite. These strengths were on the order of 5 MPa, a magnitude appropriate for consideration of the material as a temporary trabecular bone substitute. The in vivo studies in a rat proximal tibia model demonstrated progressive growth of new bone against the receding surface of the degrading material, and ingrowth of new bone trabeculae into the interior of the degrading specimen. The specimen was also well integrated with the surrounding bone, with no internal fibrosis. There was an absence of a foreign body inflammatory response to the presence of this material over a 5-week time span. This material may thus be an attractive candidate for temporary replacement of trabecular bone, facilitating both osteoconduction and osteoinduction.
Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom (2017)

Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared with Britons and 800 000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 and 5% (P<2.2 × 10<sup>-16</sup>). When stratified by their functional annotations, loss-of-function variants showed the highest proportional enrichment in Finns (P=0.0291). In the non-coding part of the genome, variants in conserved regions (P=0.002) and promoters (P=0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using population isolates.
[Bacterial pathogens of periprosthetic infections and diagnostic possibilities]. (2006)

Standard cultivation methods remain a highly successful and useful tool for identifying the PPI causative agents.
High Channel Low Loss Optical Splitter using Silica-based PLC on Quartz Substrate (2008)

We have designed and fabricated the 2x32 optical splitter and the 1x64 optical splitter with the low insertion loss <16.5dB and <19.3dB, respectively for 1.31μm-band and 1.49μm-1.55ゼm-band by using silica-based PLC on a quartz substrate.
Policy Reuse for Communication Load Balancing in Unseen Traffic Scenarios (2023)

With the continuous growth in communication network complexity and traffic volume, communication load balancing solutions are receiving increasing attention. Specifically, reinforcement learning (RL)-based methods have shown impressive performance compared with traditional rule-based methods. However, standard RL methods generally require an enormous amount of data to train, and generalize poorly to scenarios that are not encountered during training. We propose a policy reuse framework in which a policy selector chooses the most suitable pre-trained RL policy to execute based on the current traffic condition. Our method hinges on a policy bank composed of policies trained on a diverse set of traffic scenarios. When deploying to an unknown traffic scenario, we select a policy from the policy bank based on the similarity between the previous-day traffic of the current scenario and the traffic observed during training. Experiments demonstrate that this framework can outperform classical and adaptive rule-based methods by a large margin.
Etude du comportement de l'hélium et des défauts lacunaires dans le tungstène (2010)

Comm. Orale
Novel Vaccination Strategies against Tuberculosis (2014)

The tuberculosis (TB) pandemic continues to rampage despite widespread use of the BCG (Bacillus Calmette-Guérin) vaccine. Novel vaccination strategies are urgently needed to arrest global transmission and prevent the uncontrolled development of multidrug-resistant forms of Mycobacterium tuberculosis. Over the last two decades, considerable progress has been made in the field of vaccine development with numerous innovative preclinical candidates and more than a dozen vaccines in clinical trials. These vaccines are developed either as boosters of the current BCG vaccine or as novel prime vaccines to replace BCG. Given the enormous prevalence of latent TB infection, vaccines that are protective on top of an already established infection remain a high priority and a significant scientific challenge. Here we discuss the current state of TB vaccine research and development, our understanding of the underlying immunology, and the requirements for an efficient TB vaccine.
External Cavity Laser Biosensor (2013)

We demonstrated a single-mode and biomolecule-induced tunable external cavity laser biosensor. This system achieves large dynamic range, high-Q resonance, and self-referencing through dual-mode lasing for high sensitivity label-free detection.
Hot-wall batch-type CVD tool for high-k (Ba,Sr)TiO/sub 3/ capacitors (2002)

A hot-wall batch type BST-CVD tool with fast thermal processing (FTP) furnace and individual vaporizing liquid source supply system (ILSS) was developed for uniform deposition of BST. We also employed an in-situ multi-step (IMS) process that is sequential repetition of thin amorphous BST deposition and its crystallization in the same reactor to reconcile conformal BST deposition and good electrical performances. BST deposited by our hot-wall CVD shows slight substrate dependence (metal coated or not), therefore hotwall CVD is superior to a single slice tool for reduction of test wafer running. IMS deposited BST shows almost 100% step coverage, lower carbon impurity concentration than single step deposited BST and sufficient electrical characteristics (leakage current <10/sup -7/ A/cm/sup 2/, Teq<0.5 nm) for both SRO and Ru electrodes.
Miniaturized cross-lines rectangular ring-shaped flexible multiband antenna (2019)

A compact, flexible antenna for wireless applications, i.e., WLAN/WiMAX/Wi-Fi, UMTS2100, C-Band, and DSRC is presented. The quad-band antenna is designed and analyzed in terms of efficiency, gain, ...
CF Patients’ Airway Epithelium and Sex Contribute to Biosynthesis Defects of Pro-Resolving Lipids (2022)

Specialized pro-resolving lipid mediators (SPMs) as lipoxins (LX), resolvins (Rv), protectins (PD) and maresins (MaR) promote the resolution of inflammation. We and others previously reported reduced levels of LXA4 in bronchoalveolar lavages from cystic fibrosis (CF) patients. Here, we investigated the role of CF airway epithelium in SPMs biosynthesis, and we evaluated its sex specificity. Human nasal epithelial cells (hNEC) were obtained from women and men with or without CF. Lipids were quantified by mass spectrometry in the culture medium of hNEC grown at air-liquid interface and the expression level and localization of the main enzymes of SPMs biosynthesis were assessed. The 5-HETE, LXA4, LXB4, RvD2, RvD5, PD1 and RvE3 levels were significantly lower in samples derived from CF patients compared with non-CF subjects. Within CF samples, the 12-HETE, 15-HETE, RvD3, RvD4, 17-HODHE and PD1 were significantly lower in samples derived from females. While the mean expression levels of 15-LO, 5-LO and 12-LO do not significantly differ either between CF and non-CF or between female and male samples, the SPMs content correlates with the level of expression of several enzymes involved in SPMs metabolism. In addition, the 5-LO localization significantly differed from cytoplasmic in non-CF to nucleic (or nuclear envelope) in CF hNEC. Our studies provided evidence for lower abilities of airway epithelial cells derived from CF patients and more markedly, females to produce SPMs. These data are consistent with a contribution of CF airway epithelium in the abnormal resolution of inflammation and with worse pulmonary outcomes in women.
Appendix C: List of Files Used in Hands‐On Experiments and Exercises (2006)

This appendix lists all the experiment and exercise fi les used in this book. The book is written in such a way that the main text of each chapter is supplemented with examples, quizzes, exercises, hands-on experiments, and exercise problems. These fi les are located in the directories: c:\adsp\chap{x}\exp{x}_{no.}_<option> for Blackfi n and LabVIEW experiments c:\adsp\chap{x}\exercise{x}_{no.} for Blackfi n and LabVIEW exercises c:\adsp\chap{x}\MATLAB_ex{x} for MATLAB examples and exercises
Highly Efficient InGaN-based LED with Embedded Cubic Airvoids (2014)

Highly efficient InGaN-based LEDs with embedded sidewall passivation cubic airvoids made by nanoimprint lithography were demonstrated. The LEDs with embedded airvoids exhibit a 45% enhancement of light output at 20 mA compared with conventional LEDs.
Effects of chloramphenicol on the development of immune responses to canine distemper virus in Beagle pups (1982)

The effect of oral chloramphenicol (CHPC) on the development of immune responses to canine distemper virus (CDV) in Beagle pups was studied. Dogs were treated with CHPC for 14 days at a dose of 50 mg/kg, three times a day. Hematologic changes in CHPC-treated dogs included: polychromasia, anisocytosis, and target cell formation of red blood cells concurrent with vacuolation of lymphocytes and basophilic granule formation in neutrophils. Dogs given this therapy showed normal in vivo and in vitro immune responses after CDV vaccination and survived a virulent CDV challenge, whereas untreated, unvaccinated dogs became ill or died after challenge exposure. The results of this study indicate that CHPC therapy does not interfere with either the prechallenge immune response to attenuated viral antigen or the efficient immune mechanisms invoked during virulent virus challenge.