gebhart/patrepeval huggingface dataset:
Synthesis of recombinant human relaxin H2 in bacteria and its effects on differentiation of carcinoembryonic stem cells (2017)

Experiments described in this thesis were designed to develop a reliable method for the synthesis of the recombinant human hormone relaxin H2. Several methods were tested to produce highly pure, biologically active protein quickly, inexpensively and consistently from batch to batch. Relaxin H2 synthesized in bacteria was assessed by SDS-PAGE gel electrophoresis, Western Dot Blotting, Liquid Chromatography/Ultra High Definition Mass Spectrometry, and in vivo blood pressure response experiments using rats. The recombinant relaxin H2 described in this study was compared with commercially available relaxin H2 and was determined to be of equal quality, purity, and biological activity. In addition, to determine whether or not relaxin H2 induced differentiation of murine carcinoembryonic stem cells P19CL6 into cardiomyocytes was compared with a standard methodology using DMSO-induced differentiation. Relaxin H2 induced differentiation but the onset was delayed by four days compared with DMSO treatment. The endpoint of differentiation was determined as the start of spontaneous contractions within clusters of cells in culture. The results revealed that both commercially obtained and bacterially produced relaxin H2 equally caused a four-day delay in the initiation of contractions by cardiac myocytes compared with DMSO-treated controls. Moreover, cDNA microarray analysis of P19CL6 cells in three separate cultures, induced with DMSO (1%, as a control), and experimental treatments with serelaxin (16.7 nM), and bacterially-derived RLN H2 (16.7nM), respectively. There were no differences observed between cell treatments with the serelaxin- and bacterially-derived RLN H2 in the activation/deactivation patterns of 125 affected genes during the progression of the differentiation process.
Differential Expression of S6K2 Dictates Tissue-Specific Requirement for S6K1 in Mediating Aberrant mTORC1 Signaling and Tumorigenesis (2011)

The S6K1 and S6K2 kinases are considered important mTOR signaling effectors, yet their contribution to tumorigenesis remains unclear. Aberrant mTOR activation is a frequent event in cancer that commonly results from heterozygous loss of PTEN. Here, we show for the first time a differential protein expression between S6K1 and S6K2 in both mouse and human tissues. Additionally, the inactivation of S6k1 in the context of Pten heterozygosity (Pten(+/-)) suggests a differential requirement for this protein across multiple tissues. This tissue specificity appears to be governed by the relative protein expression of S6k2. Accordingly, we find that deletion of S6k1 markedly impairs Pten(+/-) mediated adrenal tumorigenesis, specifically due to low expression of S6k2. Concomitant observation of low S6K2 levels in the human adrenal gland supports the development of S6K1 inhibitors for treatment of PTEN loss-driven pheochromocytoma.
An Investigation of Quantile Function Estimators Relative to Quantile Confidence Interval Coverage (2014)

In this article, we investigate the limitations of traditional quantile function estimators and introduce a new class of quantile function estimators, namely, the semi-parametric tail-extrapolated quantile estimators, which has excellent performance for estimating the extreme tails with finite sample sizes. The smoothed bootstrap and direct density estimation via the characteristic function methods are developed for the estimation of confidence intervals. Through a comprehensive simulation study to compare the confidence interval estimations of various quantile estimators, we discuss the preferred quantile estimator in conjunction with the confidence interval estimation method to use under different circumstances. Data examples are given to illustrate the superiority of the semi-parametric tail-extrapolated quantile estimators. The new class of quantile estimators is obtained by slight modification of traditional quantile estimators, and therefore, should be specifically appealing to researchers in estimating the extreme tails.
Enhancing the Acetylene Yield from Methane by Decoupling Oxidation and Pyrolysis Reactions: A Comparison with the Partial Oxidation Process (2016)

The partial oxidation (POX) of methane is one of the most important processes to produce acetylene and syngas. The reaction pathway analysis using a detailed chemical mechanism (modified GRI 3.0) showed that the exothermal oxidation and endothermic pyrolysis reactions were highly coupled in the original POX process, which limited the yield of acetylene. A new process that physically separated the heat supply and pyrolysis reactions was proposed to increase the acetylene yield. The maximum yield of acetylene was enhanced from 33% to 52% in the theoretical calculations assuming inert and instantaneous mixing. A jet-in-cross-flow (JICF) reactor was designed to realize this new process. The computational fluid dynamics (CFD) method coupled with the modified GRI 3.0 was applied to simulate the complex interaction between turbulent mixing and reactions. The results showed that a high acetylene yield of 41% could be obtained in the JICF reactor. The optimization of the reactor indicated that the optimum number of jets was 8, and the optimal mixing ratio was 0.566 for maximum acetylene yield. The maximum acetylene yield significantly decreased in a larger reactor, and mixing enhancement was the main way to further improve the acetylene yield.
Robust RGB-D Face Recognition Using Attribute-Aware Loss (2019)

Existing convolutional neural network (CNN) based face recognition algorithms typically learn a discriminative feature mapping, using a loss function that enforces separation of features from different classes and/or aggregation of features within the same class. However, they may suffer from bias in the training data such as uneven sampling density, because they optimize the adjacency relationship of the learned features without considering the proximity of the underlying faces. Moreover, since they only use facial images for training, the learned feature mapping may not correctly indicate the relationship of other attributes such as gender and ethnicity, which can be important for some face recognition applications. In this paper, we propose a new CNN-based face recognition approach that incorporates such attributes into the training process. Using an attribute-aware loss function that regularizes the feature mapping using attribute proximity, our approach learns more discriminative features that are correlated with the attributes. We train our face recognition model on a large-scale RGB-D data set with over 100K identities captured under real application conditions. By comparing our approach with other methods on a variety of experiments, we demonstrate that depth channel and attribute-aware loss greatly improve the accuracy and robustness of face recognition.
How datapath allocation affects controller delay (1994)

We present an allocation approach which considers the controller's effect on system delay to minimize the system cycle time. Most allocation algorithms and conditional resource sharing methods emphasize minimum number of resources or area. Previous works have not modeled the resulting controller's structure and its contribution to the system delay in a controller/datapath system. The allocation method generates a controller with minimum delay on the system's critical path. Therefore the resulting system cycle time will be shorter than other allocation approaches. >
High‐yield expression of a viral peptide vaccine in transgenic plants (2001)

A high-yield production of a peptide vaccine in transgenic plants is described here. A 21-mer peptide, which confers protection to dogs against challenge with virulent canine parvovirus, has been expressed in transgenic plants as an amino-terminal translational fusion with the GUS gene. Transformants were selected on the basis of their GUS activities, showing expression levels of the recombinant protein up to 3% of the total leaf soluble protein, a production yield comparable to that obtained with the same epitope expressed by chimeric plant viruses. The immunogenicity of the plant-derived peptide was demonstrated in mice immunized either intraperitoneally or orally with transgenic plant extracts, providing the suitability of the GUS fusions approach for low-cost production of peptide vaccines.
Notes on the care, restoration and repair of microsurgical instruments (2006)

Abstract The high cost of microsurgical instruments is multiplied by failure to care for them appropriately. This paper describes effective practical measures for the care of microsurgical instruments; and shows detailed procedures for restoring and repairing the instruments most often damaged: jewelers′ forceps and scissors.
Palladium complex in a room temperature ionic liquid: a convenient recyclable reagent for catalytic oxidation (2014)

Palladium (Pd)-catalyzed carbonylation of alcohols proceeds in ionic liquid (IL) media (1-ethyl-3-methylimidazolium hexafluorophosphate). Carbonylation of primary/secondary alcohols to aldehydes/ketones was greatly accelerated by the use of a Pd-based catalyst in the presence of NaOCl as an oxidant. The catalyst was more easier to recycle in the IL [Emim]PF6 with an equal-proportioned CH2Cl2 than in the single CH2Cl2 or IL.
Genetic characterization of a pentatricopeptide repeat protein gene, <i>orf687</i>, that restores fertility in the cytoplasmic male‐sterile Kosena radish (2003)

Cytoplasmic male sterility (CMS) in plants is a maternally inherited inability to produce functional pollen, and is often associated with mitochondrial DNA abnormalities. Specific nuclear loci that suppress CMS, termed as restorers of fertility (Rf), have been identified. Previously, we identified an Rf for the CMS Kosena radish and used genetic analysis to identify the locus and create a contig covering the critical interval. To identify the Rf gene, we introduced each of the lambda and cosmid clones into the CMS Brassica napus and scored for fertility restoration. Fertility restoration was observed when one of the lambda clones was introduced into the CMS B. napus. Furthermore, introduction of a 4.7-kb BamHI/HpaI fragment of the lambda clone is enough to restore male fertility. A cDNA strand isolated from a positive fragment contained a predicted protein (ORF687) of 687 amino acids comprising 16 repeats of the 35-amino acid pentatricopeptide repeat (PPR) motif. Kosena CMS radish plants were found to express an allele of this gene possessing four substituted amino acids in the second and third repeats of the PPR suggesting that the domains formed by these repeats in ORF687 are essential for fertility restoration. Protein levels of the Kosena CMS-associated mitochondrial protein ORF125 were considerably reduced in plants in which fertility was restored, although mRNA expression was normal. Regarding the possible role for PPR-containing proteins in the regulation of the mitochondrial gene, we propose that ORF687 functions either directly or indirectly to lower the levels of ORF125, resulting in the restoration of fertility in CMS plants.
Major and Lethal Complications of Liposuction: A Review of 72 Cases in Germany between 1998 and 2002 (2008)

Major risk factors for the development of severe complications are insufficient standards of hygiene, the infiltration of multiple liters of wetting solution, permissive postoperative discharge, and selection of unfit patients. The lack of surgical experience was a notorious contributing factor, particularly regarding the timely identification of developing complications. This is in fact the first study reporting deaths related to liposuction performed entirely under true tumescent anesthesia.
Robust Adaptive Estimation of Graph Signals Based on Welsch Loss (2022)

This paper considers the problem of adaptive estimation of graph signals under the impulsive noise environment. The existing least mean squares (LMS) approach suffers from severe performance degradation under an impulsive environment that widely occurs in various practical applications. We present a novel adaptive estimation over graphs based on Welsch loss (WL-G) to handle the problems related to impulsive interference. The proposed WL-G algorithm can efficiently reconstruct graph signals from the observations with impulsive noises by formulating the reconstruction problem as an optimization based on Welsch loss. An analysis on the performance of the WL-G is presented to develop effective sampling strategies for graph signals. A novel graph sampling approach is also proposed and used in conjunction with the WL-G to tackle the time-varying case. The performance advantages of the proposed WL-G over the existing LMS regarding graph signal reconstruction under impulsive noise environment are demonstrated.
Methamphetamine and the expanding complications of amphetamines. (1999)

During the past 10 years, the use of methamphetamine has increased rapidly in the West and throughout the United States. Because of this increase, our attention has focused on methamphetamine's toxicity. Methamphetamine and related compounds generate many of the same toxic effects as cocaine. Because of methamphetamine's widespread use, clinicians should be familiar with its medical effects and toxicity and with treatment options for acute and long-term effects of methamphetamine abuse.
Structure-function correlation and biostability of antibody CDR-derived peptides as tumour imaging agents. (1998)

Based on the CDR3 V(H) sequence of a monoclonal antibody (ASM2) raised against epithelial cancer cells, the synthetic peptide YCAREPPTRTFAYWG (EPPT1) has been found to have an appreciable affinity (Kd = 20 microM) for the deglycosylated mucin-derived peptide antigen YVTSAPDTRPAPGST (PDTRP). The technetium-radiolabelled form of this peptide has been found to be a good tumour-imaging candidate for diagnosis of breast carcinoma. Several EPPT1 peptide analogues were synthesised. A differential biostability was obtained blocking the end groups of EPPT1. The susceptibility to proteolytic degradation was significantly decreased for the C-amidated form of EPPT1 than the N-acetylated form. Using resonant mirror biosensor technique, the EPPT1 analogues were classified as active and non-active peptides according to their PDTRP-binding properties. The binding of EPPT1 to PDTRP in free solution was also determined unambiguously by CD spectroscopy. CD spectra of both active and non-active peptides showed the presence of irregular conformations in H2) and SDS above cmc. In TFE, significant degree of ordered conformations of alpha-helix or beta-turn type were induced but did not correlate well with their binding properties. In SDS below cmc a conformational difference was observed between the active and non-active peptides. The active peptides exhibited CD spectra of aggregation of beta-strand type whilst the non-active showed CD spectra similar to those in H2O and SDS above cmc, critical micelle concentration. A good correlation between the extended conformation of beta-strand type and the binding affinity of the active peptides suggests this conformation as the binding feature of the EPPT tumour-imaging peptides. These information are vital for the design of novel EPPT analogues. Any modification to improve binding affinity must retain the ability of the peptides to adopt the extended conformation of beta-strand type.
Formation of in-volume nanogratings with sub-100-nm periods in glass by femtosecond laser irradiation (2015)

We present direct experimental observation of the morphological evolution during the formation of nanogratings with sub-100-nm periods with the increasing number of pulses. Theoretical simulation shows that the constructive interference of the scattering light from original nanoplanes will create an intensity maximum located between the two adjacent nanoplanes, resulting in shortening the nanograting period by half. The proposed mechanism explains the formation of nanogratings with periods beyond those predicted by the nanoplasmonic model.
Human Rhinovirus Type 54 Infection via Heparan Sulfate Is Less Efficient and Strictly Dependent on Low Endosomal pH (2007)

K-type major-group human rhinoviruses (HRVs) (including HRV54) share a prominent lysine residue in the HI surface loop of VP1 with all minor-group HRVs. Despite the presence of this residue, they cannot use members of the low-density lipoprotein receptor family for productive infection. Reexamining all K-type viruses for receptor usage, we noticed that HRV54 is able to replicate in RD cells that lack the major-group receptor intercellular adhesion molecule 1 (ICAM-1). By using receptor blocking assays, inhibition of sulfation, enzymatic digestion, and proteoglycan-deficient cell lines, we show here that wild-type HRV54, without any adaptation, uses heparan sulfate (HS) proteoglycan as an alternate receptor. However, infection via HS is less efficient than infection via ICAM-1. Moreover, HRV54 has an acid lability profile similar to that of the minor-group virus HRV2. In ICAM-1-deficient cells its replication is completely blocked by the H(+)-ATPase inhibitor bafilomycin A1, whereas in ICAM-1-expressing cells it replicates in the presence of the drug. Thus, use of a "noncatalytic" receptor requires the virus to be highly unstable at low pH.
Highly Bright Yellow-Green-Emitting CuInS<sub>2</sub> Colloidal Quantum Dots with Core/Shell/Shell Architecture for White Light-Emitting Diodes (2015)

In this study, we report bright yellow-green-emitting CuInS2 (CIS)-based quantum dots (QDs) and two-band white light-emitting diodes (LEDs) using them. To achieve high quantum efficiency (QE) of yellow-green-emitting CIS QDs, core/shell/shell strategy was introduced to high quality CIS cores (QE = 31.7%) synthesized by using metal-oleate precursors and 1-dodecanethiol. The CIS/ZnS/ZnS QDs showed a high QE of 80.0% and a peak wavelength of 559 nm under the excitation of 450 nm, which is well matched with dominant wavelength of blue LEDs. The formation of core/shell/shell structure was confirmed by X-ray diffraction, transmission electron microscopy, and inductively coupled plasma-optical emission spectroscopy analyses. Intense and broad yellow-green emission band of the CIS/ZnS/ZnS is beneficial for bright two-band white light. When the CIS/ZnS/ZnS was coated on the blue LEDs, the fabricated white LED showed bright natural white light (luminous efficacy (η(L)) = 80.3 lm·W(-1), color rendering index (R(a)) = 73, correlated color temperature (T(c)) = 6140 K). The QD-white LED package showed a high light conversion efficiency of 72.6%. In addition, the CIS/ZnS/ZnS-converted white LED showed relatively stable white light against the variation of forward bias currents of 20-150 mA [color coordinates (x, y) = (0.3320-0.3207, 0.2997-0.2867), R(a) = 70-72, T(c) = 5497-6375 K].
pMHC-class II nanovaccine to treat autoimmune diseases (2014)

Our lab has been developing a nanoparticle-based therapy consisting of the administration of peptide/major histocompatibility complex (pMHC) class I-coated iron oxide nanoparticles (NPs). This therapy has proven to be successful in both preventing and reverting T1D. The studies carried out in our lab have allowed us to elucidate the nature of the protection afforded by this therapy. The administration of the peptide/MHC class I-coated NPs induced the expansion of low-avidity antigen-specific CD8+ T-cells with regulatory properties. In addition, evidence suggests that the treatment-expanded cells are derived from antigen-experienced precursors generated during the autoimmune process. The same treatment into a knock-in mouse that lacks the cognate epitope neither resulted in expansion nor was able to induce diabetes reversal. Our findings with the MHC class I-coated nanoparticles urged us to ask whether the paradigm that applies for CD8+ T-cells could also apply for autorreactive CD4+ T-cells. That is, whether the autoimmune process leads autorreactive to the generation of CD4+ T-cells designed to become immune regulators in order to try to prevent further damage. Through their involvement as both effectors and regulators in most autoimmune and hypersensitivity disorders, CD4+ T-cells are, conceptually, as good (if not better) targets for immune modulation as CD8+ T-cells. To answer the above question, we followed the same approach used for the study of CD8+ T-cells. We hypothesized that pMHC class II-coated NPs would be equally effective in the expansion of CD4+ T-cells with regulatory properties. And, therefore, we expected the NP treatment to be able to blunt autoimmune progression. The studies presented in this thesis support this hypothesis. Systemic administration of disease-relevant pMHCII-coated NPs blunted the autoimmune attack in a model of type 1 diabetes and experimental autoimmune encephalomyelitis. In both cases, this was mediated by the expansion of IL-10- and TGF-β1 producing CD4+ T-cells, with a surface and transcriptional phenotype identical to the so-called type 1 regulatory (Tr1) T-cells. In addition, we confirmed that the suppression of autoimmunity was mediated by IL-10 and TGF-β1 produced by these cells and the induction of several regulatory networks downstream of the Tr1 activation, such as the expansion of IL-10-producing Bregs and the suppression of cytokine production by CD11b+ myeloid antigen-presenting cells. Further characterization of the origin of the NP-expanded Tr1 cells led us to conclude that NPs selectively target Tr1 precursors contained in the cognate memory pool, with basal regulatory capability. In summary, these studies conclude that chronic inflammation induces the generation of a memory pool of regulatory cell precursors in order to prevent further tissue damage. Furthermore, our pMHCII nanovaccine can induce the expansion/differentiation of these precursors in order to achieve a therapeutical balance between pathological and regulatory cells and blunt the autoimmune process.