gebhart/patrepeval huggingface dataset:
A Photoelectronic Switching Device Using a Mixed Self-Assembled Monolayer (2005)

A cathodic-anodic biway photoelectronic device has been successfully constructed using a self-assembled monolayer (SAM). The SAM consists of two kinds of photofunctional thiol derivatives, a ruthenium complex-viologen linked compound (RuVS) and a phthalocyanine derivative (PcS), on a gold electrode. Structural characterization of the SAM has been carried out by absorption spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Photocurrent responses were measured in the presence of methyl viologen (MV2+) and oxygen as electron acceptors and triethanolamine (TEOA) as a sacrificial reagent. For the SAM of RuVS alone, intramolecular electron transfer (ET) was superior to intermolecular ET, resulting in anodic photocurrents even in the presence of MV2+ and oxygen at 0 V vs Ag/AgCl. On the contrary, only cathodic photocurrents were observed at 0 V for the SAM of PcS alone. Photocurrents from the mixed SAM of RuVS and PcS were roughly the sum of individual photocurrents from RuVS and PcS. In fact, photocurrents from the mixed SAM of RuVS and PcS were observed in the anodic direction below approximately 550 nm, and in the cathodic direction above approximately 550 nm at 0 V vs Ag/AgCl. In the case of the mixed SAM of RuS (ruthenium complex disulfide) and PcS, only cathodic photocurrents were observed at 0 V vs Ag/AgCl, due to the lack of an intramolecular ET pathway. The results indicate that in the mixed SAM of RuVS and PcS both dyes can individually function for opposite photocurrent generation. We have also applied the mixed SAM as a photoelectronic logic device by using two LEDs (470 and 640 nm). The system clearly operated as an XOR logic device.
Multiplexed, targeted gene editing in Nicotiana benthamiana for glyco‐engineering and monoclonal antibody production (2015)

Biopharmaceutical glycoproteins produced in plants carry N-glycans with plant-specific residues core α(1,3)-fucose and β(1,2)-xylose, which can significantly impact the activity, stability and immunogenicity of biopharmaceuticals. In this study, we have employed sequence-specific transcription activator-like effector nucleases (TALENs) to knock out two α(1,3)-fucosyltransferase (FucT) and the two β(1,2)-xylosyltransferase (XylT) genes within Nicotiana benthamiana to generate plants with improved capacity to produce glycoproteins devoid of plant-specific residues. Among plants regenerated from N. benthamiana protoplasts transformed with TALENs targeting either the FucT or XylT genes, 50% (80 of 160) and 73% (94 of 129) had mutations in at least one FucT or XylT allele, respectively. Among plants regenerated from protoplasts transformed with both TALEN pairs, 17% (18 of 105) had mutations in all four gene targets, and 3% (3 of 105) plants had mutations in all eight alleles comprising both gene families; these mutations were transmitted to the next generation. Endogenous proteins expressed in the complete knockout line had N-glycans that lacked β(1,2)-xylose and had a significant reduction in core α(1,3)-fucose levels (40% of wild type). A similar phenotype was observed in the N-glycans of a recombinant rituximab antibody transiently expressed in the homozygous mutant plants. More importantly, the most desirable glycoform, one lacking both core α(1,3)-fucose and β(1,2)-xylose residues, increased in the antibody from 2% when produced in the wild-type line to 55% in the mutant line. These results demonstrate the power of TALENs for multiplexed gene editing. Furthermore, the mutant N. benthamiana lines provide a valuable platform for producing highly potent biopharmaceutical products.
Targeting neurotensin receptors with agonists and antagonists for therapeutic purposes. (2002)

Neurotensin (NT) is a brain-gut tridecapeptide that fulfils a dual function, as a neurotransmitter/neuromodulator in the nervous system, and as a paracrine and circulating hormone in the periphery. Three NT receptors, NTS1, NTS2 and NTS3, have been cloned to date. NTS1 and NTS2 belong to the family of G protein-coupled receptors with seven transmembrane domains, whereas NTS3 is a single transmembrane domain protein that belongs to a recently identified family of sorting receptors. Most of the known peripheral and central effects of NT are mediated through NTS1. NTS2 might take part in the analgesic response elicited by central administration of NT; the biological roles of NTS3 are yet to be discovered. Most NT agonists and non-peptide antagonists developed to date have been studied for their NTS1-targeting abilities. Here, we will discuss the potential diagnostic and therapeutic uses of these compounds in cancer, schizophrenia, obesity and pain suppression.
The site-specific recombinase encoded by pinD in Shigella dysenteriae is due to the presence of a defective Mu prophage (1997)

The DNA inversion systems are made up of an invertible DNA segment and a site-specific recombinase gene. Five systems are known in prokaryotes: the Salmonella typhimurium H segment and hin gene (H-hin), phage Mu G-gin, phage P1 C-cin, Escherichia coli e14 P-pin, and Shigella sonnei B-pinB systems. In this report a site-specific recombinase (pinD) gene of Shigella dysenteriae was cloned and sequenced. pinD mediated inversion of five known segments at the same extent in E. coli. Although one inv sequence was identified, no invertible region was detected in a cloned fragment. The predicted amino acid sequences of PinD and three ORFs showed high homology to those of Gin and its flanking gene products. An ORF homologous to Mom of Mu conserved a functional activity to modify intracellular plasmid DNA. Southern analysis showed that the cloned fragment contains two homologous regions corresponding to the left and right ends of the Mu genome. Together these results indicated that the pinD gene in S. dysenteriae is derived from a Mu-like prophage.
AnnoSearch: Image Auto-Annotation by Search (2006)

Although it has been studied for several years by computer vision and machine learning communities, image annotation is still far from practical. In this paper, we present AnnoSearch, a novel way to annotate images using search and data mining technologies. Leveraging the Web-scale images, we solve this problem in two-steps: 1) searching for semantically and visually similar images on the Web, 2) and mining annotations from them. Firstly, at least one accurate keyword is required to enable text-based search for a set of semantically similar images. Then content-based search is performed on this set to retrieve visually similar images. At last, annotations are mined from the descriptions (titles, URLs and surrounding texts) of these images. It worth highlighting that to ensure the efficiency, high dimensional visual features are mapped to hash codes which significantly speed up the content-based search process. Our proposed approach enables annotating with unlimited vocabulary, which is impossible for all existing approaches. Experimental results on real web images show the effectiveness and efficiency of the proposed algorithm.
Continuous wave operation of 640–660 nmselectively oxidised AlGaInP vertical-cavity lasers (1995)

The performance of AlGaInP visible vertical-cavity laser diodes fabricated using selective oxidation is reported. At room temperature, the lasers exhibit continuous wave operation from 678 to 642 nm, with 642 nm being the shortest wavelength attained to date. In addition, these lasers possess the lowest threshold currents (660 µA) and voltages (150 mV above photon energy) reported for visible vertical-cavity lasers.
Integration of Prealbumin into Child-Pugh Classification Improves Prognosis Predicting Accuracy in HCC Patients Considering Curative Surgery (2018)

<b><i>Background and Aims:</i></b> The poor outcomes of hepatocellular carcinoma (HCC) patients may be due to not only malignant tumors but also limited liver function. Therefore, as stated in major guidelines, only patients with relatively normal liver function (Child-Pugh A) would be referred for curative hepatectomy. Even so, the postsurgery survival rate of patients is still extremely poor. Direct curative resection may benefit most patients. This study aimed to improve the prognosis predicting accuracy of the Child-Pugh scoring system. <b><i>Methods:</i></b> This study included two cohorts: cohort A being composed of 613 HCC patients, with a 23-month median postsurgery follow-up time; and cohort B being composed of 554 tumor-free chronic liver disease patients. Kaplan-Meier test and Cox model were used for survival analysis. Independent-samples <i>t</i> test or one-way ANOVA was used to test the differences between different groups. <b><i>Results:</i></b> Serum prealbumin levels were found inversely correlated with worsening of fibrotic scores (<i>r</i> = -0.482, <i>p</i> < 0.001). Lower levels of presurgery prealbumin was an independent factor of poor postsurgery prognosis in Child-Pugh A patients, with a hazard ratio of 0.731 (<i>p</i> = 0.001). By integrating prealbumin together with total bilirubin level, serum albumin concentration and prothrombin time, a modified liver disease prognosis scoring system was developed to define traditional Child-Pugh A HCC patients as Modified Child-Pugh MCP-1, MCP-2 and MCP-3, with median postsurgery overall survival times of 44.00, 28.00 and 11.00 months respectively. <b><i>Conclusions:</i></b> Preoperative serum prealbumin is a valuable prognosis predicting biomarker for Child-Pugh A HCC patients who may be under consideration for curative resection. With serum prealbumin included as one of the parameters, the MCP scoring system might improve the postsurgery survival predicting accuracy for HCC patients.
Co‐ordinate regulation of distinct host cell signalling pathways by multifunctional enteropathogenic Escherichia coli effector molecules (2002)

Enteropathogenic Escherichia coli (EPEC) is a major cause of paediatric diarrhoea and a model for the family of attaching and effacing (A/E) pathogens. A/E pathogens encode a type III secretion system to transfer effector proteins into host cells. The EPEC Tir effector protein acts as a receptor for the bacterial surface protein intimin and is involved in the formation of Cdc42-independent, actin-rich pedestal structures beneath the adhered bacteria. In this paper, we demonstrate that EPEC binding to HeLa cells also induces Tir-independent, cytoskeletal rearrangement evidenced by the early, transient formation of filopodia-like structures at sites of infection. Filopodia formation is dependent on expression of the EPEC Map effector molecule - a protein that targets mitochondria and induces their dysfunction. We show that Map-induced filopodia formation is independent of mitochondrial targeting and is abolished by cellular expression of the Cdc42 inhibitory WASP-CRIB domain, demonstrating that Map has at least two distinct functions in host cells. The transient nature of the filopodia is related to an ability of EPEC to downregulate Map-induced cell signalling that, like pedestal formation, was dependent on both Tir and intimin proteins. The ability of Tir to downregulate filopodia was impaired by disrupting a putative GTPase-activating protein (GAP) motif, suggesting that Tir may possess such a function, with its interaction with intimin triggering this activity. Furthermore, we also found that Map-induced cell signalling inhibits pedestal formation, revealing that the cellular effects of Tir and Map must be co-ordinately regulated during infection. Possible implications of the multifunctional nature of EPEC effector molecules in pathogenesis are discussed.
The formation of P particle increased immunogenicity of norovirus P protein (2012)

As a commentary on a recently published paper in Immunology, this article summaries the principle of norovirus P particle as a promising vaccine against noroviruses. It emphasizes the importance of P particle formation in the immune enhancement of the vaccine and methods for production/verification of high quality P particles which may be easily neglected by researchers.
Talazoparib Is a Potent Radiosensitizer in Small Cell Lung Cancer Cell Lines and Xenografts (2018)

Abstract Purpose: Small cell lung cancer (SCLC) is an aggressive malignancy with a critical need for novel therapies. Our goal was to determine whether PARP inhibition could sensitize SCLC cells to ionizing radiation (IR) and if so, to determine the contribution of PARP trapping to radiosensitization. Experimental Design: Short-term viability assays and clonogenic survival assays (CSA) were used to assess radiosensitization in 6 SCLC cell lines. Doses of veliparib and talazoparib with equivalent enzymatic inhibitory activity but differing PARP trapping activity were identified and compared in CSAs. Talazoparib, IR, and their combination were tested in three patient-derived xenograft (PDX) models. Results: Talazoparib radiosensitized 5 of 6 SCLC cell lines in short-term viability assays and confirmed in 3 of 3 cell lines by CSAs. Concentrations of 200 nmol/L talazoparib and 1,600 nmol/L veliparib similarly inhibited PAR polymerization; however, talazoparib exhibited greater PARP trapping activity that was associated with superior radiosensitization. This observation further correlated with an increased number of double-stranded DNA breaks induced by talazoparib as compared with veliparib. Finally, a dose of 0.2 mg/kg talazoparib in vivo caused tumor growth inhibition in combination with IR but not as a single agent in 3 SCLC PDX models. Conclusions: PARP inhibition effectively sensitizes SCLC cell lines and PDXs to IR, and PARP trapping activity enhances this effect. PARP inhibitors, especially those with high PARP trapping activity, may provide a powerful tool to improve the efficacy of radiotherapy in SCLC. Clin Cancer Res; 24(20); 5143–52. ©2018 AACR.
The Velo-Cardio-Facial Syndrome: A Clinical and Genetic Analysis (1981)

Thirty-nine patients with the velo-cardio-facial syndrome are described in order to further delineate this probably common recurrent pattern congenital malformation syndrome. Frequent features include cleft palate, cardiac anomalies, typical facies, and learning disabilities. Less frequent findings include microcephaly, mental retardation, small stature, slender hands and digits, minor auricular anomalies and inguinal hernia. Ths Robin malformation sequence was found in four patients. The congenital heart anomalies most frequently involved a ventricular septal defect, with or without a right-sided aortic arch. There were four instances of familial transmission in the sample population. These included two cases of maternal transmission of the syndrome to daughters, one case of maternal transmission to a son, and one case of maternal transmission to both a son and daughter. There was no particular difference in expression between male and female patients so that even though X-linked dominant transmission is possible, the velo-cardio-facial syndrome is likely to be an autosomal dominant recurrent pattern syndrome.
Reverse Transcriptase-Coupled Quantitative Real Time PCR Analysis of Cell-Free Transcription on the Chromatin-Assembled p21 Promoter (2011)

We first report a proof-of-concept demonstration that incorporating RT-qPCR in cell-free transcription assays can be a simpler and faster alternative method to the conventional radioisotope-mediated transcription assays. This method will be useful for developing high throughput in vitro transcription assays and provide quantitative data for RNA transcripts generated in a defined cell-free transcription reaction.
Association of Serum Level of Growth Differentiation Factor 15 with Liver Cirrhosis and Hepatocellular Carcinoma (2015)

Hepatocellular carcinoma (HCC) and liver cirrhosis are associated with high mortality worldwide. Currently, alpha-fetoprotein (AFP) is used as a standard serum marker for the detection of HCC, but its sensitivity and specificity are unsatisfactory, and optimal diagnostic markers for cirrhosis are lacking. We previously reported that growth differentiation factor 15 (GDF15) was significantly induced in HCV-infected hepatocytes. This study aimed to investigate GDF15 expression and its correlation with hepatitis virus-related liver diseases. A total of 412 patients with various liver diseases were studied. Healthy and Mycobacterium tuberculosis-infected subjects were included as controls. Serum and tissue GDF15 levels were measured. Serum GDF15 levels were significantly increased in patients with HCC (6.66±0.67 ng/mL, p<0.0001) and cirrhosis (6.51±1.47 ng/mL, p<0.0001) compared with healthy controls (0.31±0.01 ng/mL), though the GDF15 levels in HBV and HCV carriers were moderately elevated (1.34±0.19 ng/mL and 2.13±0.53 ng/mL, respectively). Compared with HBV or HCV carriers, GDF15 had a sensitivity of 63.1% and a specificity of 86.6% at the optimal cut-off point of 2.463 ng/mL in patients with liver cirrhosis or HCC. In HCC patients, the area under the receiver operating curve was 0.84 for GDF15 and 0.76 for AFP, but 0.91 for the combined GDF15 and AFP. Serum GDF15 levels did not significantly differ between the high-AFP and low-AFP groups. GDF15 protein expression in HCC was significantly higher than that in the corresponding adjacent paracarcinomatous tissue and normal liver. Using a combination of GDF15 and AFP will improve the sensitivity and specificity of HCC diagnosis. Further research and the clinical implementation of serum GDF15 measurement as a biomarker for HCC and cirrhosis are recommended.
Topology optimization of nonlinear structures for energy absorption (2008)

This paper presents a method for topology optimization of both geometrically and materially nonlinear structures for energy absorption. The optimization problem is formulated by using the element as design variables. The element sensitivity number is derived from using the adjoint method to address two principle design parameters, namely absorbed energy per unity volume and absorbed energy ratio. Filter techniques are used to smooth sensitivities in space and to eliminate unnecessary structural details below a certain length-scale. The bi-directional evolutionary optimization (BESO) technique is used to search for the optimal design in the whole design domain by gradually removing and adding material. Several examples are presented to verify the proposed method.
6:1 aspect ratio silicon pillar based thermal neutron detector filled with B10 (2008)

Current helium-3 tube based thermal neutron detectors have shortcomings in achieving simultaneously high efficiency and low voltage while maintaining adequate fieldability performance. By using a three-dimensional silicon p-i-n diode pillar array filled with boron-10 these constraints can be overcome. The fabricated pillar structured detector reported here is composed of 2μm diameter silicon pillars with a 4μm pitch and height of 12μm. A thermal neutron detection efficiency of 7.3+∕−0.6% and a neutron-to-gamma discrimination of 105 at 2V reverse bias were measured for this detector. When scaled to larger aspect ratio, a high efficiency device is possible.
Production of Deoxygenated Biomass Fast Pyrolysis Oils via Product Gas Recycling (2013)

A bench scale fluidized bed system was modified to recycle and utilize the gaseous products of biomass fast pyrolysis as fluidization gas and to create a reactive gas atmosphere to replace, in part or in full, the added nitrogen gas. The effect of the presence of the reducing atmosphere on the pyrolysis oils produced was studied for three different biomass feedstocks, white oak, switchgrass, and pennycress presscake, and compared with those produced under an inert N2 atmosphere as the control. The reductive atmosphere, consisting primarily of CO, CO2, H2, and light hydrocarbons, had a significant deoxygenation effect on the pyrolysis oil produced from oak and switchgrass. The effect was significantly smaller for the pyrolysis of pennycress presscake, which inherently produces a lower oxygen product. When oak and switchgrass were used as feedstocks, pyrolysis oils with molar C/O ratios of 9.1 and 8.5 were achieved, respectively, which is increased from about 2.1 for the control experiments for each feedstock. The pyrolysis oils produced under the reducing atmosphere were richer in aromatic hydrocarbons and nonmethoxylated phenolics and had lesser concentrations of levoglucosan and acids than were the pyrolysis oils in the control experiments. These pyrolysis oils had lower total acid numbers (TAN) and higher energy content than those produced in the control experiments. These results compare favorably to zeolite catalyzed fast pyrolysis but without the added catalyst cost and concern for catalyst deactivation or need for regeneration.
STUDIES ON CYSTINE IN WOOL (1960)

Some experiments were carried out to find out the relationship between sulfhydryl group and supercontraction of wool in phenol solution. The results obtained are summarized as follows:1) Supercontraction of wool by phenol depends rather on the total contents of sulphydryl groups of wool than the amounts of cross-linkages between keratin molecules, thus Burley's conclusions in regards to supercontraction are accepted to be adequate.2) The fact that the degree of supercontraction increases in alkaline phenol solution could be explained not only by the action of ionic states of phenol, but also by increase of sulfhydryl-groups, generated by the hydrolysis of disulphide bonds.3) Those wools which are less damaged, having small alkali solubility, have not always better-shrink-resisting properties, and vice versa. The best way to improve both properties of reduced wool are to use in one process the oxidation of sulphydryl groups and formalization.4) The mechanism of setting of wool fabrics on the case of crabbing have been hitherto explained by the formation of cross-linkages between-SOH and -NH2 groups, but in our conclusions from the experiment, parts played by sulfhydryl groups are mainly responsible for crabbing, just as in the case of setting by thioglycollic acid and of supercontraction by phenol.After all, the appearent difference between setting processes and supercontraction occurs by whether wool samples were tensed or not during these processes.
Opposing effects of 12‐o‐tetradecanoylphorbol 13‐acetate on human myeloid and lymphoid cell proliferation (1983)

The effect of 12-O-tetradecanoylphorbol 13-acetate (TPA) on human hematopoietic cells has been investigated. It was found that 1-10 ng/ml of TPA totally abrogated erythroid and granulocytic colony growth and, simultaneously in the presence of PHA, stimulated T-lymphocyte colony formation. TPA concentrations insufficient to inhibit myeloid colony growth also failed to stimulate lymphocyte colony formation. Optimal culture conditions for the growth of these colonies required the presence of TPA, PHA, and leukocyte-conditioned medium in the cultures. Cells within the colonies were 80-90% E-rosette positive and by monoclonal antibody characterization contained 45-66% OKT3-positive cells. Colony-forming cells were found in both E-rosette-positive and-negative fractions. Although by cell surface marker characterization the cells within the colonies had properties of T-cells, the exact relationship of cells forming colonies under these conditions to those detected in other T-cell colony assays remain to be determined.
Executive Summary: Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2011)

The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.