gebhart/patrepeval huggingface dataset:
Fiber sensors for molecular detection (2010)

The demand on sensors for detecting chemical and biological agents is greater than ever before, including medical, environmental, food safety, military, and security applications. At present, most detection or sensing techniques tend to be either non-molecular specific, bulky, expensive, relatively inaccurate, or unable to provide real time data. Clearly, alternative sensing technologies are urgently needed. Recently, we have been working to develop a compact fiber optic surface enhanced Raman scattering (SERS) sensor system that integrates various novel ideas to achieve compactness, high sensitivity and consistency, molecular specificity, and automatic preliminary identification capabilities. The unique sensor architecture is expected to bring SERS sensors to practical applications due to a combination of 1) novel SERS substrates that provide the high sensitivity and consistency, molecular specificity, and applicability to a wide range of compounds; 2) a unique hollow core optical fiber probe with double SERS substrate structure that provides the compactness, reliability, low cost, and ease of sampling; and 3) an innovative matched spectral filter set that provides automatic preliminary molecule identification. In this paper, we will review the principle of operation and some of the important milestones of fiber SERS sensor development with emphasis on our recent work to integrate photonic crystal fiber SERS probes with a portable Raman spectrometer and to demonstrate a matched spectral filter for molecule identification.
Bid Is Required in NPe6‐PDT‐induced Apoptosis (2007)

Photodynamic therapy (PDT) employing photosensiter N-aspartyl chlorin e6 (NPe6) can induce lysosome disruption and initiate the intrinsic apoptotic pathway. Yet the precise signal transduction pathway remains poorly understood. In this study, we have investigated the molecular mechanism in NPe6-PDT-induced apoptosis in human lung adenocarcinoma cells (ASTC-a-1). A recombinant fluorescence resonance energy transfer (FRET) Bid probe was utilized to determine the kinetics of Bid cleavage. The results show that cleavage of the Bid-FRET probe occurred 150 +/- 5 min after NPe6-PDT treatment, and this process lasted for 45 +/- 5 min. The Bid cleavage coincided with a translocation of tBid from cytoplasm to mitochondria. Remarkably, a significant protection against cell death was observed by using small interfering RNA for Bid. Therefore, our study clearly showed the dynamics of Bid activation and redistribution during NPe6-PDT-induced apoptosis by using real-time analysis in living cells, and the inhibition of cell death by silencing Bid with interference strongly suggested that activation of Bid is required for inducing apoptosis in this experimental model.
Evidence for conservation of dietary lipid in the rat during lactation and the immediate period after removal of the litter. Decreased oxidation of oral [1-14C]triolein (1986)

Production of 14CO2 from an oral load of [1-14C]triolein was greatly decreased (70%) in lactating rats or immediately after (24-48 h) removal of the litter, compared with virgin rats. This decreased oxidation of dietary lipid was accompanied by accumulation of 14C-labelled lipid in lactating mammary gland or adipose tissue (after litter removal). No difference in 14CO2 production between lactating and virgin rats was observed when [1-14C]octanoate was administered. It is concluded that a major factor in this conservation of dietary triacylglycerol is the relative activity of lipoprotein lipase in the tissues.
Literature Review on Feature Selection Methods for High-Dimensional Data (2016)

Feature selection plays a significant role in improving the performance of the machine learning algorithms in terms of reducing the time to build the learning model and increasing the accuracy in the learning process. Therefore, the researchers pay more attention on the feature selection to enhance the performance of the machine learning algorithms. Identifying the suitable feature selection method is very essential for a given machine learning task with highdimensional data. Hence, it is required to conduct the study on the various feature selection methods for the research community especially dedicated to develop the suitable feature selection method for enhancing the performance of the machine learning tasks on high-dimensional data. In order to fulfill this objective, this paper devotes the complete literature review on the various feature selection methods for highdimensional data.
Biochemical characterization of membrane cofactor protein of the complement system. (1988)

Membrane cofactor protein (MCP; formerly termed glycoprotein 45-70 to indicate its Mr) of complement is a widely distributed iC3/C3b binding protein with co-factor activity. On human mononuclear cells and cell lines and platelets, MCP is a doublet. The two forms differ in Mr by approximately 5 k and the upper species is predominant in most individuals. To further characterize these two forms, limited proteolytic digestions were performed. Of the four peptides produced, three have identical Mr indicating that the molecules are similar proteins. Both forms also have acidic isoelectric points and shift to a less acidic isoelectric point after treatment with neuraminidase. Glycosidase digestions indicate that both species contain N- and O-linked oligosaccharides but that the quantity of sialic acid is greater on the larger one. Pulse-chase experiments demonstrate approximately equal quantities of two precursor forms with Mr of 41 and 43 k. These two precursors possess N-linked high-mannose type of oligosaccharides and chase into the mature molecules which have complex sugars. The smaller precursor chases at a slower rate, possibly accounting for the reduced quantity of the smaller form of the mature form of MCP. These experiments indicate that the two forms of MCP are structurally similar and are derived from two distinct precursors. They also suggest that variations in the rate of processing of two intracellular precursors may account for the different quantities of the mature forms of this membrane protein.
Identification of Candidate Biomarkers of Therapeutic Response to Docetaxel by Proteomic Profiling (2009)

Docetaxel chemotherapy improves symptoms and survival in men with metastatic hormone-refractory prostate cancer (HRPC). However, approximately 50% of patients do not respond to Docetaxel and are exposed to significant toxicity without direct benefit. This study aimed to identify novel therapeutic targets and predictive biomarkers of Docetaxel resistance in HRPC. We used iTRAQ-mass spectrometry analysis to identify proteins associated with the development of Docetaxel resistance using Docetaxel-sensitive PC3 cells and Docetaxel-resistant PC3-Rx cells developed by Docetaxel dose escalation. Functional validation experiments were performed using recombinant protein treatment and siRNA knockdown experiments. Serum/plasma levels of the targets in patient samples were measured by ELISA. The IC(50) for Docetaxel in the PC3-Rx cells was 13-fold greater than the parent PC-3 cell line (P = 0.004). Protein profiling identified MIC-1 and AGR2 as respectively up-regulated and down-regulated in Docetaxel-resistant cells. PC-3 cells treated with recombinant MIC-1 also became resistant to Docetaxel (P = 0.03). Conversely, treating PC3-Rx cells with MIC-1 siRNA restored sensitivity to Docetaxel (P = 0.02). Knockdown of AGR2 expression in PC3 cells resulted in Docetaxel resistance (P = 0.007). Furthermore, increased serum/plasma levels of MIC-1 after cycle one of chemotherapy were associated with progression of the cancer (P = 0.006) and shorter survival after treatment (P = 0.002). These results suggest that both AGR2 and MIC-1 play a role in Docetaxel resistance in HRPC. In addition, an increase in serum/plasma MIC-1 level after cycle one of Docetaxel may be an indication to abandon further treatment. Further investigation of MIC-1 as a biomarker and therapeutic target for Docetaxel resistance in HRPC is warranted.
The influence of quantum-well composition on the performance of quantum dot lasers using InAs-InGaAs dots-in-a-well (DWELL) structures (2000)

The optical performance of quantum dot lasers with different dots-in-a-well (DWELL) structures is studied as a function of the well number and the indium composition in the InGaAs quantum well (QW) surrounding the dots. While keeping the InAs quantum dot density nearly constant, the internal quantum efficiency /spl eta//sub i/, modal gain, and characteristic temperature of 1-DWELL and 3-DWELL lasers with QW indium compositions from 10 to 20% are analyzed. Comparisons between the DWELL lasers and a conventional In/sub 0.15/Ga/sub 0.85/As strained QW laser are also made. A threshold current density as low as 16 A/cm/sup 2/ is achieved in a 1-DWELL laser, whereas the QW device has a threshold 7.5 times larger. It is found that /spl eta//sub i/ and the modal gain of the DWELL structure are significantly influenced by the quantum-well depth and the number of DWELL layers. The characteristic temperature T/sub 0/ and the maximum modal gain of the ground-state of the DWELL structure are found to improve with increasing indium in the QW It is inferred from the results that the QW around the dots is necessary to improve the DWELL laser's /spl eta//sub i/ for the dot densities studied.
Lessons from Tarceva in pancreatic cancer: where are we now, and how should future trials be designed in pancreatic cancer? (2008)

The biology of the epidermal growth factor receptor, mitogen-activated protein kinase, PI3K/mTOR network suggests that a combination of drugs targeting simultaneously different partners should improve survival.
Characterisation and differentiation of lactobacilli by lectin typing (2001)

Lactobacillus isolates from healthy Estonian and Swedish children were characterised by a lectin typing technique; 56 isolates from six species (L. acidophilus, L. paracasei, L. plantarum, L. fermentum, L. brevis and L. buchneri) were tested. The typing system was based on an agglutination assay with a panel of six commercially available lectins, which were chosen on the basis of their carbohydrate specificities. The isolates were also subjected to proteolytic degradation before lectin typing to decrease auto-agglutination of whole cells in the assay. The 56 isolates were divided into 15 different lectin types by their lectin agglutination patterns. Proteolytic treatment reduced auto-agglutination for the majority of species, apart from L. acidophilus, which remained predominantly auto-agglutinating (eight of nine strains). The system produced stable and reproducible results under standardised culture conditions. Lactobacilli are important bacteria for use as probiotics and this system may supplement current molecular typing techniques and may help in identification of strains that could be useful in this role.
Autocatalytic Equation Describing the Change in Molecular Weight during Hydrolytic Degradation of Aliphatic Polyesters (2010)

The autocatalytic equation derived in this study describes and even predicts the evolution of the number average molecular weight of aliphatic polyesters upon hydrolytic degradation. The main reaction in the degradation of aliphatic polyesters is autocatalytic hydrolysis of ester bonds, which causes the molecular weight to decrease. During hydrolysis of the ester bonds in the main chain of the polyester, the chains are cleaved and the end group concentrations will rise. The fundamentals of this equation are based on that principle. To validate the derived equation, the hydrolytic degradation of poly(4-methylcaprolactone), poly(epsilon-caprolactone), poly(d,l-lactide), and two different poly(d,l-lactide-co-glycolide) copolymers was monitored after immersion in a PBS buffer (pH = 7.4) at 37 degrees C. The number average molecular weight, mass loss, and crystallinity were determined after different time intervals. The experimental results confirm that hydrolytic degradation of aliphatic polyesters is a bulk erosion process. When comparing the M(n), calculated with the new autocatalytic equation, with the experimental results, it was found that the new model can predict the decrease of the M(n) upon hydrolytic degradation for semicrystalline and amorphous polymers, as well as for copolymers, without the need for complicated mathematics and excessive input parameters. This is a major improvement with respect to earlier proposed models in literature.
Olfactory Mucosa Autografts in Human Spinal Cord Injury: A Pilot Clinical Study (2006)

This study shows that olfactory mucosa autograft transplantation into the human injured spinal cord is feasible, relatively safe, and potentially beneficial. The procedure involves risks generally associated with any surgical procedure. Long-term patient monitoring is necessary to rule out any delayed side effects and assess any further improvements.
Isolation of lux reporter gene fusions in Pseudomonas fluorescens DF57 inducible by nitrogen or phosphorus starvation (1995)

We have used transposon Tn.5 mutagenesis to insert a promoter-less 1uxAB gene-cassette into multiple locations in the chromosome of a Pseudomonas fluorescens strain, thereby bringing the iux reporter genes under the control of resident promoters.To identify reporter bacteria responsive to nutritional stresses we isolated and characterized a collection of 23 gene fusions consistently displaying bioluminescence under nitrogen starvation and 12 phosphorus starvation inducible fusions.Bioluminescence of one group of mutants was induced after 4 to 6 h of starvation and was continuously expressed at a high level, whereas a second group was induced earlier and the bioluminescence subsequently declined.Finally, a third group was induced later after 24 h of starvation.Four strains were selected for further study, namely, two Tn5-Zux containing strains which were induced by nitrogen starvation and two strains induced by phosphorus starvation.Another two strains, carrying constitutively expressed lux fusions, were included as controls.An analysis of biochemical characters, as well as LPS and protein composition, did not reveal any discernible differences between the mutants and the wild-type strain.Survival experiments with the selected Tn5-Zux containing strains showed that they all performed comparably to the wild-type under carbon and nitrogen starvation, whereas some of the strains were less resistant to phosphorus starvation.Expression of bioluminescence by the mutants during carbon, nitrogen and phosphorus starvation was detectable even after 18 days and was not affected by high osmolarity or low temperature.
Vascular Endothelial Growth Factor Induces Expression of the Antiapoptotic Proteins Bcl-2 and A1 in Vascular Endothelial Cells (1998)

We examined the role of vascular endothelial growth factor (VEGF) in preventing apoptosis in primary human umbilical vein endothelial (HUVE) cells. VEGF was capable of preventing serum starvation-induced apoptosis at concentrations between 10 and 100 ng/ml. The addition of VEGF to serum-starved HUVE cells led to a 5. 2-fold induction of Bcl-2 after 36 h and to a transient, 2.4-fold induction of A1 after a 7-h incubation, as quantitated by real time reverse transcriptase-polymerase chain reaction analysis. Western blot analysis demonstrated a 2-3-fold induction of Bcl-2 protein after 18-36 h of exposure to VEGF and a transient induction of A1 after 7 h of VEGF stimulation. Moreover, overexpression of Bcl-2 by means of transient biolistic transfection experiments of HUVE cells was sufficient to prevent endothelial cells from apoptotic cell death in the absence of VEGF. These findings indicate that Bcl-2 plays an important role in mediating the survival activity of VEGF on endothelial cells.
Association of Adiponectin Mutation With Type 2 Diabetes (2002)

Adiponectin, also referred to as AdipoQ or ACRP30, is a plasma protein produced and secreted exclusively from adipose tissue. The protein contains a collagen-like domain and a C1q-like globular domain. A protease-generated globular segment enhances fatty acid oxidation in muscles, thereby modulating lipid and glucose metabolism. Plasma adiponectin levels are inversely correlated with the severity of insulin resistance. A recent genome-wide scan study mapped a susceptibility locus for type 2 diabetes and the metabolic syndrome to chromosome 3q27, where the adiponectin gene is located. Here, we screened Japanese patients with type 2 diabetes and age- and BMI-matched nondiabetic control subjects for mutations in adiponectin gene. We identified four missense mutations (R112C, I164T, R221S, and H241P) in the globular domain. Among these mutations, the frequency of I164T mutation was significantly higher in type 2 diabetic patients than in age- and BMI- matched control subjects (P < 0.01). Furthermore, plasma adiponectin concentrations of subjects carrying I164T mutation were lower than those of subjects without the mutation. All the subjects carrying I164T mutation showed some feature of metabolic syndrome, including hypertension, hyperlipidemia, diabetes, and atherosclerosis. Our findings suggest that I164T mutation is associated with low plasma adiponectin concentration and type 2 diabetes.
In Vivo Therapy of Hepatocellular Carcinoma with a Tumor-Specific Adenoviral Vector Expressing Interleukin-2 (1997)

A recombinant adenovirus (AdVAFP1-IL2) containing the murine alpha-fetoprotein (AFP) promoter was constructed to direct hepatocellular carcinoma (HCC)-specific expression of the human interleukin-2 (IL-2) gene. In vitro testing of AdVAFP1-IL2 showed HCC-specific IL-2 gene expression three to four orders of magnitude higher in AFP-producing HCC lines compared to non-AFP producing non-HCC lines. The in vivo efficacy and tumor specificity of AdVAFP1-IL2 was evaluated compared to AdVCMV-IL2 (in which the IL-2 gene is driven by the strong constitutive cytomegalovirus promoter) in the treatment of established human HCC (Hep 3B/Hep G2) xenografts growing in CB-17/SCID mice. Intratumoral injection of AdV resulted in growth retardation and regression in a majority of established hepatomas, but with a much wider therapeutic index and less systemic toxicity using the AFP vector. This study illustrates the superiority of using transcriptionally targeted recombinant AdV vectors in cytokine-based gene therapy.
C-C chemokines, pivotal in protection against HIV type 1 infection (1998)

Exposure to HIV type 1 (HIV-1) does not usually lead to infection. Although this could be because of insufficient virus titer, there is now abundant evidence that some individuals resist infection even when directly exposed to a high titer of HIV. This protection recently has been correlated with homozygous mutations of an HIV-1 coreceptor, namely CCR5, the receptor for the beta-chemokines. Moreover, earlier results already had shown that the same chemokines markedly suppress the nonsyncitial inducing variants of HIV-1, the chief virus type transmitted from person to person. CCR5 mutation, as a unique mechanism of protection, is, however, suspect because HIV-1 variants can use other chemokine receptors as their coreceptor. Moreover, recent results have established that infection can indeed sometimes occur with such mutations. Here, we report on transient natural resistance over time of most of 128 hemophiliacs who were inoculated repeatedly with HIV-1-contaminated Factor VIII concentrate from plasma during 1980-1985 before the development of the HIV blood test. Furthermore, and remarkably, 14 subjects remain uninfected to this date, and in these subjects we found homozygous CCR5 mutations in none but in most of them overproduction of beta chemokines. In vitro experiments confirmed the potent anti-HIV suppressive effect of these chemokines.
Targeting CD123 in acute myeloid leukemia using a T-cell–directed dual-affinity retargeting platform (2015)

T-cell-directed killing of tumor cells using bispecific antibodies is a promising approach for the treatment of hematologic malignancies. Here we describe our preclinical work with a dual-affinity retargeting (DART) molecule generated from antibodies to CD3 and CD123, designed to redirect T cells against acute myeloid leukemia blasts. The CD3×CD123 DART (also referred to as MGD006/S80880) consists of 2 independent polypeptides, each composed of the VH of 1 antibody in tandem with the VL of the other antibody. The target antigen CD123 (interleukin 3RA) is highly and differentially expressed in acute myeloid leukemia (AML) blasts compared with normal hematopoietic stem and progenitor cells. In this study we demonstrate that the CD3×CD123 DART binds to both human CD3 and CD123 to mediate target-effector cell association, T-cell activation, proliferation, and receptor diversification. The CD3×CD123 DART also induces a dose-dependent killing of AML cell lines and primary AML blasts in vitro and in vivo. These results provide the basis for testing the CD3×CD123 DART in the treatment of patients with CD123(+) AML.
pH Regulates Vascular Endothelial Growth Factor Binding to Fibronectin (2004)

Hypoxia is one of the major signals that induces angiogenesis. Hypoxic conditions lead to reduced extracellular pH. Vascular endothelial growth factor (VEGF) binding to endothelial cells and the extracellular matrix (ECM) increases at acidic pH (7.0-5.5). These interactions are dependent on heparan sulfate proteoglycans, but do not depend on the presence of VEGF receptors. Here we report that VEGF(165) and VEGF(121) binding to fibronectin also increased at acidic pH, and that these interactions are further enhanced by the addition of heparin. These results reveal that the accepted non-heparin-binding isoform of VEGF (VEGF(121)) is converted into a heparin-binding growth factor under acidic conditions. Interestingly, we did not observe increased binding of VEGF to collagen type I at acidic pH in the presence or absence of heparin, indicating that this effect is not a general property of all heparin-binding ECM proteins. The high level of VEGF binding at acidic pH was also rapidly reversed as demonstrated by increased rates of VEGF dissociation from fibronectin and fibronectin-heparin matrices as the pH was raised. The VEGF released from fibronectin retained its ability to stimulate the activation of extracellular-regulated kinase 1/2 in endothelial cells. These results suggest that VEGF may be stored in the extracellular matrix via interactions with fibronectin and heparan sulfate in tissues that are in need of vascularization so that it can aid in directing the dynamic process of growth and migration of new blood vessels.
Molecular analysis by electron microscopy of the removal of psoralen-photoinduced DNA cross-links in normal and Fanconi's anemia fibroblasts. (1990)

The induction and fate of psoralen-photoinduced DNA interstrand cross-links in the genome of Fanconi's anemia (FA) fibroblasts of complementation groups A and B, and of normal human fibroblasts, were investigated by quantitative analysis of totally denatured DNA fragments visualized by electron microscopy. 8-Methoxypsoralen (5 x 10(-5) M) interstrand cross-links were induced as a function of the near ultraviolet light dose. With time of postexposure incubation, a fraction of interstrand cross-links disappeared in all cell lines. However, 24 h after treatment, this removal was significantly lower in the two FA group A cell lines examined (34-39%) than in the FA group B and normal cell lines (43-53 and 47-57%, respectively). These data indicate that FA cells are at least able to recognize and incise interstrand cross-links, as normal cells do, although group A cells seem somewhat hampered in this process. This is in accord with data obtained on the same cell lines using another biochemical assay (D. Papadopoulo, D. Averbeck, and E. Moustacchi. Mutat. Res., DNA Repair Rep., 184: 271-280, 1987). Since the fate of cross-links in FA constituted a controversial matter, it is important to stress that two different methodologies applied to genetically well defined cell lines led to the same conclusions.