gebhart/patrepeval huggingface dataset:
LC-MS based serum metabonomic analysis for renal cell carcinoma diagnosis, staging, and biomarker discovery (2010)

A LC-MS based method, which utilizes both reversed-performance (RP) chromatography and hydrophilic interaction chromatography (HILIC) separations, has been carried out in conjunction with multivariate data analysis to discriminate the global serum profiles of renal cell carcinoma (RCC) patients and healthy controls. The HILIC was found necessary for a comprehensive serum metabonomic profiling as well as RP separation. The feasibility of using serum metabonomics for the diagnosis and staging of RCC has been evaluated. One-hundred percent sensitivity in detection has been achieved, and a satisfactory clustering between the early stage and advanced-stage patients is observed. The results suggest that the combination of LC-MS analysis with multivariate statistical analysis can be used for RCC diagnosis and has potential in the staging of RCC. The MS/MS experiments have been carried out to identify the biomarker patterns that made great contribution to the discrimination. As a result, 30 potential biomarkers for RCC are identified. It is possible that the current biomarker patterns are not unique to RCC but just the result of any malignancy disease. To further elucidate the pathophysiology of RCC, related metabolic pathways have been studied. RCC is found to be closely related to disturbed phospholipid catabolism, sphingolipid metabolism, phenylalanine metabolism, tryptophan metabolism, fatty acid beta-oxidation, cholesterol metabolism, and arachidonic acid metabolism.
Growth of Chromium Carbide in a Hot Wall DLICVD Reactor (2011)

Chromium carbide coatings were grown at 748 K in a hot wall CVD reactor fed by sublimation of bis(benzene)chromium, BBC (MOCVD) and by direct liquid injection using a BBC/toluene solution (DLICVD). The two types of coatings exhibit an amorphous structure and the same C content (22 at.%). DLICVD permits delivering higher mass flow rate of precursors and consequently the growth rate is 3 times higher and the thickness uniformity is better than using MOCVD. Chromium metal deposition has also been investigated by DLICVD in this hot wall reactor using BBC/toluene/additive as precursor. The purpose of the additive is to block carbide formation. Two additives have been studied: (i) hexachlorobenzene (C6Cl6) and (ii) thiophenol (C6H5SH). The ratio additive/BBC required for Cr metal deposition is a few percent. In this process, C6Cl6 is not decomposed and only traces of Cl (0.4 at.%) are found in the coatings. For a ratio C6Cl6/BBC > 27% the growth of any coating is blocked. The gas phase containing C6H5SH is more reactive since the onset of deposition occurs approximately 50 K before the temperature of the chlorinated compound. Furthermore, a sulfur contamination of 3 at.% has been analyzed in the coatings revealing a partial decomposition of the additive. The results are detailed and discussed in relation with previous works.
Fabrication of micropatterned ZnO/SiO2 core/shell nanorod arrays on a nanocrystalline diamond film and their application to DNA hybridization detection (2008)

Micropatterned ZnO/SiO2 core/shell nanorod arrays are successfully fabricated on nanocrystalline diamond (NCD) film surfaces, and their performance as a fluorescence signal enhancing platform for DNA hybridization detection is also investigated. The fabrication process, from oriented ZnO nanorod deposition, amine silanation, and attachment of a biofunctional cross-linking molecule to the covalent immobilization of probe oligonucleotides, is defined. X-Ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) are used to characterize ZnO/SiO2 core/shell nanorods. The sequence complementary and stability of the DNA-modified surface are demonstrated in hybridization experiments. The use of ZnO/SiO2 nanorod arrays not only greatly enhances the fluorescence signal collected but also decreases the nonspecific adsorption effect of ZnO nanomaterials after carrying out the hybridization reaction.
The Effective Nuclear Charges and the Softness of the Atomic Cores (1990)

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Spatiotemporal Parameters and Step Activity of a Specialized Stepping Pattern Used by a Transtibial Amputee During a Denali Mountaineering Expedition (2012)

In Brief Specialized mountaineering stepping patterns have not been studied in persons with transtibial amputation (TTA). The purpose of this report was to describe spatiotemporal differences between the specialized French technique and traditional stepping in an individual with TTA and report his step activity during a climbing expedition in Denali, AK, USA. A 51-year-old old man with TTA recorded step count and activities during a summit attempt on Mt. McKinley (Denali). After the climb, the subject traversed a GAITRite walkway simulating French and traditional stepping to compare spatiotemporal differences between stepping patterns. The climber completed 8 days on the trail, with a total step count of 62,421 and average daily count of 10,404. Approximately 27% of the steps were taken using the French technique. Five total events were logged: one dermatologic, three musculoskeletal events, and the culminating event was cardiovascular in nature, where the climber reported overheating and exertion requiring climb cessation and evacuation. For velocity, the French technique was slower than traditional stepping. Stride, step, and double support times were greater in the French technique compared with traditional stepping. Spatially, stride and step lengths were greater in the traditional compared with the French technique. The base of support width was wider in the French than in the traditional stepping. Musculoskeletal rather than dermatologic issues predominated in the event log. Fatigue ultimately concluded the climb, warranting further investigation into balancing component durability and mass in terms of prosthetic foot selection. As altitude increased, the French technique was selected as the preferred stepping strategy. The French technique is ultimately a slower stepping technique favoring stability over mobility. We hypothesized that dermatological and prosthetic component issues would predominate in the case climber’s event log. In fact, musculoskeletal issues predominated. However, a fatigue issue ultimately concluded the climb which warrants further investigation into balancing component durability and mass in terms of prosthetic foot selection. In terms of stepping techniques, as the altitude became progressively higher, the French technique was selected by the climber. The French technique is ultimately a slower stepping technique with qualities suggestive of heightened stepping stability as opposed to mobility.
Purification, crystallization and preliminary crystallographic analysis of the<i>Hermes</i>transposase (2005)

DNA transposition is the movement of a defined segment of DNA from one location to another. Although the enzymes that catalyze transposition in bacterial systems have been well characterized, much less is known about the families of transposase enzymes that function in higher organisms. Active transposons have been identified in many insect species, providing tools for gene identification and offering the possibility of altering the genotypes of natural insect populations. One of these active transposons is Hermes, a 2749-base-pair element from Musca domestica that encodes its own transposase. An N-terminally deleted version of the Hermes transposase (residues 79-612) has been overexpressed and purified, and crystals that diffract to 2.1 A resolution have been obtained at 277 K by the hanging-drop method.
New low loss inverted microstrip line using gap waveguide technology for slot antenna applications (2011)

Recently, a new transmission line concept, called gap-waveguide, has been introduced. This technology generates a quasi-TEM mode in the gap between parallel metal plates and prohibits all other modes to propagate by making use of artificial magnetic conductors (AMCs) in the forms of e.g. lid of nails or mushrooms-type EBG surfaces. It has been shown how such geometry can replace standard microstrip lines and waveguides since it needs neither dielectric nor metal joints, being then an advantageous alternative that can be used for several applications at high frequency. This paper shows how the gap waveguide can also be realized in printed technology creating a new type of inverted microstrip line, called microstrip gap waveguide, which has low loss and large bandwidths can be achieved.
NIWA-REKA, HAPOPO, ME PAOA (2011)

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Analysis of the linkage of MYRIP and MYO7A to melanosomes by RAB27A in retinal pigment epithelial cells (2007)

The apical region of the retinal pigment epithelium (RPE) typically contains melanosomes. Their apical distribution is dependent on RAB27A and the unconventional myosin, MYO7A. Evidence from studies using in vitro binding assays, melanocyte transfection, and immunolocalization have indicated that the exophilin, MYRIP, links RAB27A on melanosomes to MYO7A, analogous to the manner that melanophilin links RAB27A on melanocyte melanosomes to MYO5A. To test the functionality of this hypothesis in RPE cells, we have examined the relationship among MYRIP, RAB27A and MYO7A with studies of RPE cells in primary culture (including live-cell imaging), analyses of mutant mouse retinas, and RPE cell fractionation experiments. Our results indicate that the retinal distribution of MYRIP is limited to the RPE, mainly the apical region. In RPE cells, RAB27A, MYRIP, and MYO7A were all associated with melanosomes, undergoing both slow and rapid movements. Analyses of mutant mice provide genetic evidence that MYRIP is linked to melanosomes via RAB27A, but show that recruitment of MYRIP to apical RPE is independent of melanosomes and RAB27A. RAB27A and MYRIP also associated with motile small vesicles of unknown origin. The present results provide evidence from live RPE cells that the RAB27A-MYRIP-MYO7A complex functions in melanosome motility. They also demonstrate that RAB27A provides an essential link to the melanosome.
Real-time PCR genotyping using displacing probes (2004)

Simple and reliable genotyping technology is a key to success for high-throughput genetic screening in the post-genome era. Here we have developed a new real-time PCR genotyping approach that uses displacement hybridization-based probes: displacing probes. The specificity of displacing probes could be simply assessed through denaturation analysis before genotyping was implemented, and the probes designed with maximal specificity also showed the greatest detection sensitivity. The ease in design, the simple single-dye labeling chemistry and the capability to adopt degenerated negative strands for point mutation genotyping make the displacing probes both cost effective and easy to use. The feasibility of this method was first tested by detecting the C282Y mutation in the human hemochromatosis gene. The robustness of this approach was then validated by simultaneous genotyping of five different types of mutation in the human beta-globin gene. Sixty-two human genomic DNA samples with nine known genotypes were accurately detected, 32 random clinical samples were successfully screened and 114 double-blind DNA samples were all correctly genotyped. The combined merits of reliability, flexibility and simplicity should make this method suitable for routine clinical testing and large-scale genetic screening.
STEAP2 is down-regulated in breast cancer tissue and suppresses PI3K/AKT signaling and breast cancer cell invasion in vitro and in vivo (2019)

The six-transmembrane epithelial antigen of prostate 2 (STEAP2) protein was identified in advanced prostate cancer, and is highly over-expressed in various types of cancer. This study aimed to investigate the prognostic value and the function of STEAP2 in breast cancer. STEAP2 mRNA and protein expressions in breast normal and cancer tissues, breast cancer cell lines (MCF-7, BT-549, BT-474, MDA-MB-361, HCC1937, and MDA-MB-468) and normal mammary epithelial cell lines (HBL-100 and MCF-10A) were evaluated by immunohistochemistry, real time RT-qPCR and western blotting. The expression of STEAP2 in breast cancer tissues and its value of evaluating the prognosis of breast cancer patients was validated in the Public Databases (Oncomine and Kaplan-Meier plotter database). Lentiviral vectors with STEAP2 cDNA and shRNA were constructed and used to infect breast cancer cell lines and normal mammary epithelial cell line to investigate the effects of STEAP2 up- and down- regulation on the biological behavior of breast cells. The low expression of STEAP2 was detected in breast cancer tissues, which was associated with malignant phenotype and poor prognosis of breast cancer. The public databases analyses were consistent with our findings. STEAP2 up-regulation hindered cellular proliferation, invasion and metastasis abilities by inhibiting EMT process and suppressing PI3K/AKT/mTOR signaling pathway. On the other hand, STEAP2 down-regulation could promote cell proliferation and invasion by inducing EMT and activating the PI3K/AKT/mTOR signaling pathway. Collectively, STEAP2 acted as an anti-oncogene in breast cancer development, which suggested a new research objective for the future studies.
Regulation of macropinocytosis in v-Src-transformed fibroblasts: cyclic AMP selectively promotes regurgitation of macropinosomes (1998)

Stable transformation of Rat-1 fibroblasts by the v-Src oncoprotein results into the constitutive formation of macropinosomes. In the present report, we found that macropinosomes do not fuse with transferrin-containing endosomes and investigated the effects of cyclic AMP as a regulator of macropinocytosis in this cell system. The permeant analogs dibutyryl cyclic AMP and 8-bromo-cyclic AMP, as well as the pharmacological activator of adenylate cyclase forskolin, similarly decreased by about 35% the net endocytic accumulation of the fluid-phase tracer horseradish peroxidase at intervals >5 minutes in v-Src-transformed cells but not in the non-transformed parental Rat-1 cell line. However, and in contrast to the phospholipase C inhibitor 2-nitro-4-carboxyphenyl-N, N-diphenylcarbamate or the phosphatidylinositol 3-kinase inhibitor wortmannin, dibutyryl cyclic AMP neither returned the peroxidase accumulation rate of v-Src-transformed cells to that of parental Rat-1/control cells, nor prevented macropinosome formation, as shown by confocal microscopy. Detailed analysis of the kinetics of tracer entry and efflux in transformed cells revealed that dibutyryl cyclic AMP inhibited peroxidase accumulation only after intervals >5 minutes, due to accelerated peroxidase regurgitation, but did not alter the rate of transferrin recycling. Taken together, these data indicate that, in v-Src-transformed fibroblasts, macropinocytosis and micropinocytosis serve different pathways and that cyclic AMP affects neither micropinocytosis nor the formation of macropinosomes, but selectively promotes regurgitation therefrom.
A Novel Query Obfuscation Scheme with User Controlled Privacy and Personalization (2017)

Web Search Engines are tools that help users find information. These search engines use the information provided by users, in terms of their search history to build their "user profiles". Rich user profiles enable the search engines to provide better personalized search results. However, this puts the user's privacy at risk. Apart from the risk of exposing one's identity, there is the added disadvantage of being subjected to unsolicited advertising and potential disclosure of sensitive information. Rich user profiles contain a lot of personally identifiable information, which can attract unwarranted malicious interests. It is important that sensitive data collection be curbed or at least obfuscated at the source. To that effect this work is a novel approach towards providing a balance between privacy preservation and personalization by keeping the user in control of his privacy Vs personalization decisions. This work supports complex queries and obfuscates them by adding a set of fake queries that are semantically related to the original query where both the semantic distance and the number of fake queries are user controlled parameters.
Selective Elimination of Human Pluripotent Stem Cells by a Marine Natural Product Derivative (2014)

One of the current obstacles to stem cell therapy is the tumorigenic potential of residual undifferentiated stem cells. The present study reports rediscovery of a synthetic derivative of okadaic acid, a marine polyether toxin, as a reagent that selectively induces the death of human pluripotent stem cells. Cell-based screening of 333 cytotoxic compounds identified methyl 27-deoxy-27-oxookadaate (molecule 1) as a substrate of two ATP-binding cassette (ABC) transporters, ABCB1 (MDR1) and ABCG2 (BCRP), whose expression is repressed in human embryonic stem cells and induced pluripotent stem cells. The results demonstrate that selective elimination of human pluripotent stem cells can be achieved by designing cytotoxic small molecules with appropriate ABC-transporter selectivity.
Experimental Components Analysis of Brief Theory-Based HIV/AIDS Risk-Reduction Counseling for Sexually Transmitted Infection Patients. (2005)

An experimental components analysis of brief HIV risk-reduction counseling based on the information-motivation-behavioral skills (IMB) model was conducted with 432 men and 193 women receiving sexually transmitted infection (STI) clinic services. Following baseline assessments, participants were randomly assigned to 1 of 4 90-min risk-reduction counseling sessions that deconstructed the IMB model within a full factorial design. Participants were followed for 9 months, with STI diagnoses monitored over 12 months. Men who received the full IMB session evidenced relatively greater use of risk-reduction behavioral skills and relatively lower rates of unprotected intercourse over 6-months follow-up and had fewer new STIs. For women, however, the motivational counseling demonstrated the most positive outcomes. Results suggest that brief single-exposure HIV prevention counseling can reduce HIV transmission risks.
Biotechnology: Proteins to PCR : a course in strategies and lab techniques (1995)

This is a manual which aims to give students a chance to explore the process and techniques of characterizing and purifying a protein, and of subsequent cloning of the associated gene. Each chapter emphasizes the process of discovery, and the strategies and rationale for each experiment. To minimize cost and avoid extensive laboratory preparation, the experiments in this manual use readily available materials and organisms, the bacterium Escherichia coli and the yeast Saccharomyces carlsbergensis. Laboratory topics include: microbiological methods (handling, storage, media); organism growth and protein production; enzyme and protein essays (specific activity); batch purification of proteins; gel filtration and ion exchange chromatographies; genomic and plasmid DNA isolation; and DNA sequencing and computer analysis.
RAPID REPORT: An<i>in vivo</i>tethered toxin approach for the cell-autonomous inactivation of voltage-gated sodium channel currents in nociceptors (2010)

Understanding information flow in sensory pathways requires cell-selective approaches to manipulate the activity of defined neurones. Primary afferent nociceptors, which detect painful stimuli, are enriched in specific voltage-gated sodium channel (VGSC) subtypes. Toxins derived from venomous animals can be used to dissect the contributions of particular ion currents to cell physiology. Here we have used a transgenic approach to target a membrane-tethered isoform of the conotoxin MrVIa (t-MrVIa) only to nociceptive neurones in mice. T-MrVIa transgenic mice show a 44 +/- 7% reduction of tetrodotoxin-resistant (TTX-R) VGSC current densities. This inhibition is permanent, reversible and does not result in functional upregulation of TTX-sensitive (TTX-S) VGSCs, voltage-gated calcium channels (VGCCs) or transient receptor potential (TRP) channels present in nociceptive neurones. As a consequence of the reduction of TTX-R VGSC currents, t-MrVIa transgenic mice display decreased inflammatory mechanical hypersensitivity, cold pain insensitivity and reduced firing of cutaneous C-fibres sensitive to noxious cold temperatures. These data validate the use of genetically encoded t-toxins as a powerful tool to manipulate VGSCs in specific cell types within the mammalian nervous system. This novel genetic methodology can be used for circuit mapping and has the key advantage that it enables the dissection of the contribution of specific ionic currents to neuronal function and to behaviour.
Design and Application of an α‐Helix‐Mimetic Scaffold Based on an Oligoamide‐Foldamer Strategy: Antagonism of the Bak BH3/Bcl‐xL Complex (2003)

Die Verhinderung des programmierten Zelltods durch das antiapoptotische Protein Bcl-xL, das an die BH3-Domäne des proapoptotischen Proteins Bak bindet, spielt bei mehreren Arten von Krebs eine Rolle. Ein kompetitiver Assay und Bindungsstudien haben ergeben, dass das Polyamidgerüst 1, das auf der Grundlage eines gezielten Strukturdesigns synthetisiert wurde, die Bindung von Bcl-xl an die BH3-Domäne beeinflussen kann.
Reversal of signal-mediated cellular retention by subunit assembly of human acetylcholinesterase. (1994)

The interrelationship between signal-mediated endoplasmic reticulum retention and control of subunit assembly in secreted complex proteins was examined in recombinant 293 cells expressing human acetylcholinesterase (HuAChE). This was achieved by analyzing the mutual effects of co-residing retention and dimerization signals on enzyme secretion by transfected cells. The function of putative signals within the COOH-terminal tetrapeptide CSDL of HuAChE was examined by site-directed mutagenesis. The CSDL tetrapeptide carries the free cysteine (Cys-580) involved in subunit assembly, yet it fails to function as a KDEL-type retention signal. This was demonstrated by mutations that increase similarity to the canonical retention signal (substitution of CSDL by KSDL) or those that deviate from it (substitution to CSAL). Cells expressing both types of mutants exhibited cell-associated HuAChE levels identical to that of wild type enzyme. Appendage of an engineered KDEL retention signal to a dimerization-impaired HuA-ChE subunit (the C580A mutant) resulted in intracellular retention of large amounts of fully active enzyme not prone to proteolytic degradation. On the other hand, attachment of KDEL to a native, dimerization-competent HuAChE polypeptide did not lead to intracellular retention and allowed efficient secretion of enzyme to the cell growth medium. Yet, appendage of KDEL to the native HuAChE led to some retardation in the transport of enzyme molecules through the Golgi apparatus, as manifested by increase in cellular population of endo H-resistant dimers, when compared with wild type enzyme. Taken together, these results indicate (alpha) that sub-unit dimerization mediated by the COOH-terminal cysteine of HuAChE can reverse the signal-mediated retention by masking recognition of KDEL by its cognate receptor and (b) that the native sequences of the acetylcholinesterase subunit polypeptide do not appear to function as a coupled retention/dimerization signal in the control of secretion of assembled enzyme molecules.