gebhart/patrepeval huggingface dataset:
Optimizing DOP‐PCR for universal amplification of small DNA samples in comparative genomic hybridization (1997)

The standard comparative genomic hybridization (CGH) protocol relies on availability of macroscopic tumor samples, which do not contain too much interfering normal cells. Recently, CGH after universal amplification of genomic DNA with degenerate oligonucleotide primed PCR (DOP-PCR) has been used to detect genetic aberrations in microdissected tumor specimens. However, owing to the technical difficulties, CGH results of only few microdissected samples have so far been published. We have developed an improved protocol for DOP-PCR, which includes direct incorporation of fluorochrome-conjugated nucleotides into the PCR product. Among the four polymerase enzymes tested, ThermoSequenase gave the best yield, with PCR products ranging from 100–4,000 bp. A two-step PCR-procedure was used, consisting of a preamplification with low stringency conditions followed by amplification in more stringent conditions. The method was first validated by hybridizing DOP-PCR-amplified normal DNA against nick-translated reference DNA, which showed uniform and even hybridization result for all chromosomes. Comparison of DOP-PCR CGH to conventional CGH in MCF-7 breast cancer cell line further indicated that genetic aberrations can be reliably detected after DOP-PCR amplification. The sensitivity of the DOP-PCR-CGH was tested by serial dilution of MCF-7 DNA. Fifty picograms of sample DNA (corresponding roughly to two MCF-7 cells) was sufficient for high quality CGH. Experiments with cells microdissected from intraductal breast cancer demonstrated that carcinoma cells from 1 to 2 ducts were sufficient for a successful DOP-PCR CGH analysis. We conclude that the improved DOP-PCR-CGH protocol provides a powerful tool to study genetic aberrations in different histological subpopulations of malignant as well as precancerous lesions. DOP-PCR also improves the success rate of conventional paraffin-block CGH, because a poor quality or a too low yield of extracted DNA can be compensated by universal DNA amplification by DOP-PCR. Genes Chromosom. Cancer 18:94–101, 1997. © 1997 Wiley-Liss, Inc.
Influence of PMMA-Chain-End Tethered Polyhedral Oligomeric Silsesquioxanes on the Miscibility and Specific Interaction with Phenolic Blends (2005)

Two different molecular weights of poly(methyl methacrylate) (PMMA) and PMMA containing polyhedral oligomeric silsesquioxane (PMMA−POSS) homopolymers have been prepared via the atom transfer radical polymerization (ATRP) technique. The miscibility and specific interaction behaviors of PMMA−POSS and PMMA with phenolic resin were investigated by differential scanning calorimetry and Fourier transform infrared spectroscopy (FTIR). FTIR results reveal that at least three competing equilibriums are present in the phenolic/PMMA−POSS blend: self-association of phenolic (hydroxyl−hydroxyl), hydroxyl−siloxane interassociation between phenolic and POSS, and hydroxyl−carbonyl interassociation between phenolic and PMMA. Among these blends, single and higher Tgs of these phenolic/PMMA−POSS blends were observed than the corresponding phenolic/PMMA blends at same composition, revealing that a stronger interassociation interaction of hydroxyl−siloxane than the hydroxyl−carbonyl interaction. Furthermore, we also found the screening effect in phenolic/LPMMA−POSS blends that tends to significantly decrease the hydrogen bond formation of the hydroxyl−carbonyl interassociation.
Microstructure and Li‐Ion Conductivity of Hot‐Pressed Cubic Li 7 La 3 Zr 2 O 12 (2015)

The effect of hot‐pressing temperature on the microstructure and Li‐ion transport of Al‐doped, cubic Li 7 La 3 Zr 2 O 12 ( LLZO ) was investigated. At fixed pressure (62 MPa), the relative density was 86%, 97%, and 99% when hot‐pressing at 900°C, 1000°C, and 1100°C, respectively. Electrochemical impedance spectroscopy showed that the percent grain‐boundary resistance decreased with increasing hot‐pressing temperature. Hot pressing at 1100°C resulted in a total conductivity of 0.37 mS/cm at room temperature where the grain boundaries contributed to 8% of the total resistance; one of the lowest grain‐boundary resistances reported. We believe hot pressing is an appealing technique to minimize grain‐boundary resistance and enable correlations between LLZO composition and bulk ionic conductivity.
Biological Applications and Transmission Electron Microscopy Investigations of Mesoporous Silica Nanoparticles (2006)

The research presented and discussed within involves the development of novel biological applications of mesoporous silica nanoparticles (MSN) and an investigation of mesoporous material by transmission electron microscopy (TEM). Mesoporous silica nanoparticles organically functionalized shown to undergo endocytosis in cancer cells and drug release from the pores was controlled intracellularly and intercellularly. Transmission electron microscopy investigations demonstrated the variety of morphologies produced in this field of mesoporous silica nanomaterial synthesis. A series of room-temperature ionic liquid (RTIL) containing mesoporous silica nanoparticle (MSN) materials with various particle morphologies, including spheres, ellipsoids, rods, and tubes, were synthesized. By changing the RTIL template, the pore morphology was tuned from the MCM-41 type of hexagonal mesopores to rotational moire type of helical channels, and to wormhole-like porous structures. These materials were used as controlled release delivery nanodevices to deliver antibacterial ionic liquids against Escherichia coli K12. The involvement of a specific organosiloxane function group, covalently attached to the exterior of fluorescein doped mesoporous silica nanoparticles (FITC-MSN), on the degree and kinetics of endocytosis in cancer and plant cells was investigated. The kinetics of endocystosis of TEG coated FITC-MSN is significantly quicker than FITC-MSN as determined by flow cytometry experiments. The fluorescence confocal microscopy investigation showed the endocytosis of TEG coated-FITC MSN triethylene glycol grafted fluorescein doped MSN (TEG coated-FITC MSN) into both KeLa cells and Tobacco root protoplasts. Once the synthesis of a controlled-release delivery system based on MCM-41-type mesoporous silica nanorods capped by disulfide bonds with superparamagnetic iron oxide nanoparticles was completed. The material was characterized by general methods and the dosage and kinetics of the antioxidant dependent release was measured. Finally, the biological interaction of the material was determined along with TEM measurements. An electron investigation proved that the pore openings of the MSN were indeed blocked by the Fe3O4 nanoparticles. The biological interaction investigation demonstrated Fe3O4-capped MSN endocytosis into HeLa cells. Not only does the material enter the cells through endocytosis, but it seems that fluorescein was released from the pores most probably caused by disulfide bond reducing molecules, antioxidants. In addition to endocytosis and release, the Fe3O4-capped MSN propelled the cells across a cuvette upon induction of a magnet force. Finally, an important aspect of materials characterization is transmission electron microscopy. A TEM investigation demonstrated that incorporating different functional groups during the synthesis (co-condensation) changed the particle and pore morphologies.
Nucleotide sequence of theBacillus subtilisxylose isomerase gene: extensive homology between theBacillusandEscherichia colienzyme (1985)

The xylose isomerase gene from Bacillus subtilis was cloned from a genomic BamH1 library by complementation of an isomerase defective Escherichia coli strain as previously described. The ATG initiation codon is preceded by a Shine-Dalgarno sequence and two hexamers being characteristic for the promoter region of Bacillus genes. The structural gene consists of 1320 base pairs, thus coding for a polypeptide chain of 440 amino acids with a molecular weight of 49 680. The polypeptide primary structure shows over 50% homology to that of the E. coli xylose isomerase.
A Novel Tumor Antigen Derived from Enhanced Degradation of Bax Protein in Human Cancers (2011)

Cancer cells frequently exhibit defects in apoptosis, which contribute to increased survival and chemotherapeutic resistance. For example, genetic mutations or abnormal proteasomal degradation can reduce expression of Bax which limits apoptosis. In cancers where abnormal proteasomal degradation of Bax occurs, we hypothesized that Bax peptides that bind to human leukocyte antigen (HLA) class I molecules would be generated for presentation to CD8(+) T cells. To test this hypothesis, we generated T cells against pooled Bax peptides, using the blood of healthy human donors. Although T-cell responses were of low frequency (0.15%), a CD8(+) T-cell clone (KSIVB17) was isolated that optimally recognized Bax(136-144) peptide (IMGWTLDFL) presented by HLA-A*0201. KSIVB17 was able to recognize and kill a variety of HLA-matched cancer cells including primary tumor cells from chronic lymphocytic leukemia (CLL). No reactivity was seen against HLA-matched, nontransformed cells such as PHA blasts and skin fibroblasts. Furthermore, KSIVB17 reactivity corresponded with the proteasomal degradation patterns of Bax protein observed in cancer cells. Taken together, our findings suggest a new concept for tumor antigens based on regulatory proteins that are ubiquitously expressed in normal cells, but that have abnormally enhanced degradation in cancer cells. Bax degradation products offer candidate immune antigens in cancers such as CLL in which increased Bax degradation correlates with poor clinical prognosis.
Circadian Variations in the Occurrence of Cardiac Arrests (1998)

Cardiac arrests do not occur randomly during the day, but rather follow certain periodic patterns. These patterns are probably associated with patterns of daily activities. The hypothesis that cardiac arrests are triggered by a person's activity rather than by some underlying characteristics of his or her disease is supported by the lack of association between the times of the first and second arrests in the patients with recurrent arrests.
SuperGlue: Learning Feature Matching With Graph Neural Networks (2020)

This paper introduces SuperGlue, a neural network that matches two sets of local features by jointly finding correspondences and rejecting non-matchable points. Assignments are estimated by solving a differentiable optimal transport problem, whose costs are predicted by a graph neural network. We introduce a flexible context aggregation mechanism based on attention, enabling SuperGlue to reason about the underlying 3D scene and feature assignments jointly. Compared to traditional, hand-designed heuristics, our technique learns priors over geometric transformations and regularities of the 3D world through end-to-end training from image pairs. SuperGlue outperforms other learned approaches and achieves state-of-the-art results on the task of pose estimation in challenging real-world indoor and outdoor environments. The proposed method performs matching in real-time on a modern GPU and can be readily integrated into modern SfM or SLAM systems. The code and trained weights are publicly available at github.com/magicleap/SuperGluePretrainedNetwork.
von Willebrand factor binds specifically to sulfated glycolipids. (1986)

The human plasma glycoprotein Factor VIII/von Willebrand factor (vWF) binds specifically and with high affinity to sulfatides (galactosylceramide-I3-sulfate). vWF does not bind to gangliosides, neutral glycolipids, phospholipids, or cholesterol 3-sulfate. Although the largest oligomers of vWF bind preferentially to sulfatides, vWF monomers and dimers also bind but with reduced affinity. vWF binding is inhibited at high ionic strength or low pH, by some sulfated polysaccharides and by antibodies to vWF. Binding of vWF to sulfatides is probably responsible for its agglutination of aldehyde-fixed erythrocytes and may play a role in vWF-induced platelet adhesion or platelet aggregation.
Human papillomaviruses: are we ready to type? (1989)

The issue of determining which human papillomavirus (HPV) is present in a clinical specimen (typing specimens for HPVs) is receiving attention because HPVs cause condyloma acuminata and are associated with the continuum of disease which ranges from dysplasia to invasive genital cancer. Morphological inspection of precancerous lesions is not sufficient to determine which lesions will progress and which will not. A number of research tools based primarily on deoxyribonucleic acid hybridization have been developed. These permit identification and typing of HPV in genital tract scrapings or biopsies. Some HPV types (e.g., HPV-16 and HPV-18) have been identified in high-grade dysplasias and carcinomas more commonly than other types (e.g., HPV-6) and have been designated "high risk" types for cervical cancer. Thus, the question arises whether HPV typing would improve patient management by providing increased sensitivity for detection of patients at risk or by providing a prognostic indicator. In this review, the available typing methods are reviewed from the standpoint of their sensitivity, specificity, and ease of application to large-scale screening programs. Data implicating HPVs in the genesis of genital tract cancers are reviewed, as is the association of specific HPV types with specific outcomes. We conclude that there is currently no simple, inexpensive assay for HPV types, although such assays may be developed in the future. Analysis of the typing data indicates that, while HPV types can be designated high risk and low risk, these designations are not absolute and thus the low-risk group should not be ignored. In addition, interpretation of the data is complicated by finding high-risk types in individuals with no indication of disease. Insufficient data exist to indicate whether knowledge of the presence of a given HPV type is a better prognostic indicator than cytological or histological results. Thus, more research is needed before it can be determined whether typing information will augment the method currently in use for deciding treatment regimen and whether it warrants widespread use.
Cyclotides Suppress Human T-Lymphocyte Proliferation by an Interleukin 2-Dependent Mechanism (2013)

Cyclotides are a diverse and abundant group of ribosomally synthesized plant peptides containing a unique cyclic cystine-knotted topology that confers them with remarkable stability. Kalata B1, a representative member of this family of mini-proteins, has been found to inhibit the proliferation of human peripheral blood mononuclear cells. Analysis of T-cell proliferation upon treatment with chemically synthesized kalata B1 mutants revealed a region comprising inter-cysteine loops 1 and 2 of the cyclotide framework to be important for biological activity. Cytokine signaling analysis using an 'active' kalata B1 mutant [T20K], and the reference drug cyclosporin A (CsA) demonstrated that treatment of activated T-lymphocytes with these compounds decreased the expression of the interleukin-2 (IL-2) surface receptor as well as IL-2 cytokine secretion and IL-2 gene expression, whereas the 'inactive' kalata B1 mutant [V10K] did not cause any effects. The anti-proliferative activity of [T20K] kalata B1 was antagonized by addition of exogenous IL-2. Furthermore, treatment with [T20K] kalata B1 led to an initial reduction of the effector function, as indicated by the reduced IFN-γ and TNF-α production, but the levels of both cytokines stabilized over time and returned to their normal levels. On the other hand, the degranulation activity remained reduced. This indicated that cyclotides interfere with T-cell polyfunctionality and arrest the proliferation of immune-competent cells through inhibiting IL-2 biology at more than one site. The results open new avenues to utilize native and synthetically-optimized cyclotides for applications in immune-related disorders and as immunosuppressant peptides.
Mechanism of anion selectivity and stoichiometry of the Na + /I - symporter (NIS) (2011)

I(-) uptake in the thyroid, the first step in thyroid hormone biosynthesis, is mediated by the Na(+)/I(-) symporter (NIS) with an electrogenic 2Na(+):1I(-) stoichiometry. We have obtained mechanistic information on NIS by characterizing the congenital I(-) transport defect-causing NIS mutant G93R. This mutant is targeted to the plasma membrane but is inactive. Substitutions at position 93 show that the longer the side chain of the neutral residue at this position, the higher the K(m) for the anion substrates. Unlike WT NIS, which mediates symport of Na(+) and the environmental pollutant perchlorate electroneutrally, G93T/N/Q/E/D NIS, strikingly, do it electrogenically with a 21 stoichiometry. Furthermore, G93E/Q NIS discriminate between anion substrates, a discovery with potential clinical relevance. A 3D homology model of NIS based on the structure of the bacterial Na(+)/galactose transporter identifies G93 as a critical player in the mechanism of the transporter: the changes from an outwardly to an inwardly open conformation during the transport cycle use G93 as a pivot.
Supporting collaboration in large-scale multi-user workspaces (2013)

Scale-up feasibility of the graphitized sand filter (GS1) for Microcystin-LR (MC-LR) removal and its impact on other water pollutants (WPs) was assessed through a mass-balance study, using a laboratory-based drinking water treatment plant (DWTP) micromodel named: SAP-1©. The treatment system comprised: raw water tank, pre-oxidation tank (oxidant: potassium permanganate), followed by a coagulation/flocculation tank (alum supplemented), sedimentation tank, filtration module and finally disinfection tank (dosed with hypochlorite solution). Two filter modules (FMs) were studied: a) FM1: graphitized-sand media + sand media = ½ GS1 + ½ sand and b) FM2: ½ sand + ½ sand. The MC-LR removal study (initial concentration: 50 μg/L) was performed for two varieties of MC-LR source: a) commercial MC-LR, and b) algal-biomass released MC-LR. Along with MC-LR, other WPs were also evaluated including metal ions (Fe<sup>2+</sup> and Cu<sup>2+</sup>), total coliform, turbidity, ammonia-N and dissolved organic carbon. The removal efficiency of these WPs was determined for each treatment unit (as it passed). FM1 was able to reduce the inflow residual of MC-LR (coming from the preceding unit: sedimentation unit) from 12.1 μg/L and 25.4 μg/L (for commercial and algal-cell MC-LR source, respectively) to <0.61 μg/L and hence successfully complying the WHO guidelines (<1 μg/L). The protein phosphatase 1A (PP1A) toxicity assay confirmed a much safer and more toxic-free filtrate (by 40%-50%) for FM1 as compared to the filtrate obtained from FM2. The techno-economic evaluation showed that for an annual household filter application, 160 CAD needs to be spent on one GS1-based filter unit as compared to over 6000 CAD (equivalent price) for the conventional sand-based filter to provide MC-LR-free water. The present study demonstrates the feasibility of the utilization of these units in household filtration systems.
Making a local map of indoor environments by swiveling a camera and a sonar (2003)

This paper proposes a method of making a local map of indoor environments by swiveling a camera and a sonar. By swiveling a camera, an omni-directional panoramic image of high azimuth angle solution can be obtained. Meanwhile, regions of constant depth (RCD) corresponding to boundary edges and walls can be obtained by swiveling a sonar. Since many vertical lines exist in indoor environments, a local map of indoor environments can be acquired based upon position of a vertical line in space. From a 2D image, we cannot know its depth in space. At the same time, we cannot also distinguish the RCDs of boundary vertical lines from those of walls and others. However, since a boundary vertical line in space not only appears in images but also has a corresponding RCD, a local map can be acquired by fusing the metrical information from a sonar and the texture information from a camera. This paper proposes the method of fusing and gives the experimental results in a real indoor environment.
Targeting Heat Shock Proteins in Prostate Cancer (2013)

Heat shock proteins (HSPs) and chaperones are highly conserved stress-induced factors. They regulate not only protein folding and stability but are also actively involved in protein transport and transcriptional regulation. HSPs have cytoprotective roles and are essential for cancer cell survival. Noteworthy, HSPs are often upregulated in cancer. Therefore, HSPs emerged as drug targets for cancer therapy. Especially for prostate cancer (PCa) therapy, a battery of different compounds has been identified that act with different modes to inhibit PCa growth. The androgen receptor (AR) is a major player in PCa progression and is a well-known interacting factor of HSPs. Since the AR function is very dependent on HSP activity, many emerging compounds address the AR-associated HSPs as novel drug targets. Here, we provide an insight into the different classes of HSPs, their association with the human AR, the role of HSPs in human PCa development and review also the targeting of HSPs in human PCa. Further, the function and the underlying molecular mechanisms of specific compounds that are currently under investigation for the use against PCa growth will be comprehensively summarized.
Spin-based reader-writer synchronization for multiprocessor real-time systems (2021)

Reader preference, writer preference, and task-fair reader-writer locks are shown to cause undue blocking in multiprocessor real-time systems. Phase-fair reader writer locks, a new class of reader-writer locks, are proposed as an alternative. Three local-spin phase-fair lock algorithms, one with constant remote-memory-reference complexity, are presented and demonstrated to be efficiently implementable on common hardware platforms. Both task and phase-fair locks are evaluated and contrasted to mutex locks in terms of hard and soft real-time schedulability—each under both global and partitioned scheduling—under consideration of runtime overheads on a multicore Sun “Niagara” UltraSPARC T1 processor. Formal bounds on worst-case blocking are derived for all considered lock types.
Cytotoxicity of a shiga toxin A subunit-CD4 fusion protein to human immunodeficiency virus-infected cells (1994)

Shiga toxin (STX) is a ribosome-inactivating cytotoxin produced by Shigella dysenteriae serotype 1. The enzymatic domain of the STX A polypeptide has been defined by introducing amino- and carboxy-terminal deletions in the polypeptide and assessing activity in a cell-free translation system. Three recombinant forms of StxA which possess enzymatic activity were genetically fused to a 165-amino-acid polypeptide derived from CD4, the cellular receptor for human immunodeficiency virus type 1 (HIV-1). This strategy eliminated the STX receptor-binding subunit and directed the hybrid toxins to cells expressing the HIV-1 surface glycoprotein gp120. A bacterial lysate containing these toxin chimeras killed the HIV-1-infected T-cell line 8E5 but was not cytotoxic toward the uninfected parental cell line A3.01. This cytotoxic activity was specifically inhibited by monoclonal antibodies which block the interaction between CD4 and gp120. These StxA-CD4 hybrids add to the repertoire of recombinant fusion proteins which possess the capacity to selectively kill HIV-1-infected T cells.
NOVEL MICROARCHITECTURAL DYNAMICS IN RHEGMATOGENOUS RETINAL DETACHMENTS IDENTIFIED WITH INTRAOPERATIVE OPTICAL COHERENCE TOMOGRAPHY (2013)

Microarchitectural changes occur during intraoperative repair of retinal detachments, including significant alterations in foveal configuration and persistent subretinal fluid. These features may help to prognosticate outcomes. These findings also suggest a possible novel mechanism for postrhegmatogenous retinal detachment MH formation.