gebhart/patrepeval huggingface dataset:
IL-15 drives the specific migration of CD94+ and TCR-γδ+ intraepithelial lymphocytes in organ cultures of treated celiac patients (2001)

The results we describe in this report indicate that IL-15 might have a key role in modulating and driving intraepithelial infiltration and ultimately in the pathogenesis of CD.
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome (2010)

We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.
MHCII Is Required for -Synuclein-Induced Activation of Microglia, CD4 T Cell Proliferation, and Dopaminergic Neurodegeneration (2013)

Accumulation of α-synuclein (α-syn) in the brain is a core feature of Parkinson disease (PD) and leads to microglial activation, production of inflammatory cytokines and chemokines, T-cell infiltration, and neurodegeneration. Here, we have used both an <i>in vivo</i> mouse model induced by viral overexpression of α-syn as well as <i>in vitro</i> systems to study the role of the MHCII complex in α-syn-induced neuroinflammation and neurodegeneration. We find that <i>in vivo</i>, expression of full-length human α-syn causes striking induction of MHCII expression by microglia, while knock-out of MHCII prevents α-syn-induced microglial activation, antigen presentation, IgG deposition, and the degeneration of dopaminergic neurons. <i>In vitro</i>, treatment of microglia with aggregated α-syn leads to activation of antigen processing and presentation of antigen sufficient to drive CD4 T-cell proliferation and to trigger cytokine release. These results indicate a central role for microglial MHCII in the activation of both the innate and adaptive immune responses to α-syn in PD and suggest that the MHCII signaling complex may be a target of neuroprotective therapies for the disease.
Oxide‐ and Zeolite‐Supported “Molecular” Metal Clusters: Synthesis, Structure, Bonding, and Catalytic Properties (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
WT1-specific serum antibodies in patients with leukemia. (2001)

WT1 is an oncogenic protein expressed by the Wilms' tumor gene and overexpressed in the majority of acute myelogenous leukemias (AMLs) and chronic myelogenous leukemias (CMLs). The current study analyzed the sera of patients with AML and CML for the presence of antibodies to full-length and truncated WT1 proteins. Sixteen of 63 patients (25%) with AML had serum antibodies reactive with WT1/full-length protein. Serum antibodies from all 16 were also reactive with WT1/NH2-terminal protein. By marked contrast, only 2 had reactivity to WT1/COOH-terminal protein. Thus, the level of immunological tolerance to the COOH terminus may be higher than to the NH2 terminus. The WT1/COOH-terminal protein contains four zinc finger domains with homology to other self-proteins. By implication, these homologies may be related to the increased immunological tolerance. Results in patients with CML were similar with antibodies reactive to WT1/full-length protein detectable in serum of 15 of 81 patients (19%). Antibodies reactive with WT1/NH2-terminal protein were present in the serum of all 15, whereas antibodies reactive with WT1/COOH-terminal protein were present in only 3. By contrast to results in leukemia patients, antibodies reactive with WT1/full-length protein were detected in only 2 of 96 normal individuals. The greater incidence of antibody in leukemia patients provides strong evidence that immunization to the WT1 protein occurred as a result of patients bearing malignancy that expresses WT1. These data provide further stimulus to test therapeutic vaccines directed against WT1 with increased expectation that the vaccines will be able to elicit and/or boost an immune response to WT1.
Rapid prenatal diagnosis of common chromosome aneuploidies by QF‐PCR, results of 9 years of clinical experience (2009)

Our study supports the possibility of reducing the load of prenatal cytogenetic tests if the pregnancies are carefully monitored by non-invasive screening. In case of abnormal QF-PCR results, medical action can be taken within few hours from sampling. In cases of negative QF-PCR results, cytogenetic analyses might only be performed for fetuses with ultrasound abnormalities. In countries where large-scale cytogenetic tests are not available, QF-PCR may be used as the only prenatal diagnostic procedure.
Cyclophilin Interactions with Incoming Human Immunodeficiency Virus Type 1 Capsids with Opposing Effects on Infectivity in Human Cells (2004)

Cyclophilin A (CypA) is a peptidyl-prolyl isomerase that binds to the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1) and by doing so facilitates HIV-1 replication. Although CypA is incorporated into HIV-1 virions by virtue of CypA-Gag interactions that occur during virion assembly, in this study we show that the CypA-CA interaction that occurs following the entry of the viral capsid into target cells is the major determinant of CypA's effects on HIV-1 replication. Specifically, by using normal and CypA-deficient Jurkat cells, we demonstrate that the presence of CypA in the target and not the virus-producing cell enhances HIV-1 infectivity. Moreover, disruption of the CypA-CA interaction with cyclosporine A (CsA) inhibits HIV-1 infectivity only if the target cell expresses CypA. The effect of CsA on HIV-1 infection of human cells varies according to which particular cell line is used as a target, and CA mutations that confer CsA resistance and dependence exert their effects only if target cells, and not if virus-producing cells, are treated with CsA. The differential effects of CsA on HIV-1 infection in different human cells appear not to be caused by polymorphisms in the recently described retrovirus restriction factor TRIM5alpha. We speculate that CypA and/or CypA-related proteins affect the fate of incoming HIV-1 capsid either directly or by modulating interactions with unidentified host cell factors.
Overexpression of nucleolin in chronic lymphocytic leukemia cells induces stabilization of bcl2 mRNA (2006)

B-cell chronic lymphocytic leukemia (CLL) is characterized by the accumulation of clonal B cells that are resistant to apoptosis as a result of bcl2 oncogene overexpression. Studies were done to determine the mechanism for the up-regulation of bcl-2 protein observed in CD19+ CLL cells compared with CD19+ B cells from healthy volunteers. The 11-fold higher level of bcl-2 protein in CLL cells was positively correlated with a 26-fold elevation in the cytosolic level of nucleolin, a bcl2 mRNA-stabilizing protein. Measurements of the bcl2 heterogeneous nuclear/bcl2 mRNA (hnRNA)/mRNA ratios and the rates of bcl2 mRNA decay in cell extracts indicated that the 3-fold higher steady-state level of bcl2 mRNA in CLL cells was the result of increased bcl2 mRNA stability. Nucleolin was present throughout the nucleus and cytoplasm of CLL cells, whereas in normal B cells nucleolin was only detected in the nucleus. The addition of recombinant human nucleolin to extracts of normal B cells markedly slowed the rate of bcl2 mRNA decay. SiRNA knockdown of nucleolin in MCF-7 cells resulted in decreased levels of bcl2mRNA and protein but no change in beta-actin. These results indicate that bcl-2 overexpression in CLL cells is related to stabilization of bcl2 mRNA by nucleolin.
Learning to Segment Object Candidates (2015)

Recent object detection systems rely on two critical steps: (1) a set of object proposals is predicted as efficiently as possible, and (2) this set of candidate proposals is then passed to an object classifier. Such approaches have been shown they can be fast, while achieving the state of the art in detection performance. In this paper, we propose a new way to generate object proposals, introducing an approach based on a discriminative convolutional network. Our model is trained jointly with two objectives: given an image patch, the first part of the system outputs a class-agnostic segmentation mask, while the second part of the system outputs the likelihood of the patch being centered on a full object. At test time, the model is efficiently applied on the whole test image and generates a set of segmentation masks, each of them being assigned with a corresponding object likelihood score. We show that our model yields significant improvements over state-of-the-art object proposal algorithms. In particular, compared to previous approaches, our model obtains substantially higher object recall using fewer proposals. We also show that our model is able to generalize to unseen categories it has not seen during training. Unlike all previous approaches for generating object masks, we do not rely on edges, superpixels, or any other form of low-level segmentation.
Optimal design and placement of pilot symbols for channel estimation (2002)

The problem of designing and placing pilot symbols for the estimation of frequency-selective random channels is considered. The channel is assumed to be a block-fading model with finite impulse response (FIR). For both single-input single-output (SISO) and multiple-input multiple-output (MIMO) channels, under the assumption of independent and identical distributed channel taps, the Cramer-Rao bound (CRB) on the mean square error (MSE) of semi-blind channel estimators is derived and minimized with respect to pilot symbols and their placement. It is shown that the optimal strategy is to place pilot symbols satisfying certain orthogonality condition in such a way that data and pilot symbols with higher power are in the middle of the packet. The results also indicate that the optimal pilot placements are independent of channel probability distribution. For constant modulus symbols, we show that the quasi-periodic placement and its generalization in the multiuser case turn out to be optimal. We further consider estimating channels with correlated taps and show that the previous placement strategy is also optimal among orthogonal pilot sequences.
NK Cells Eliminate Cryptococcus neoformans by Potentiating the Fungicidal Activity of Macrophages Rather than by Directly Killing Them upon Stimulation with IL‐12 and IL‐18 (2000)

In the present study, we examined whether natural killer (NK) cells have direct fungicidal activity against Cryptococcus neoformans. Splenic NK cells were obtained from SCID mice and stimulated with a combination of interleukin (IL)-12 and IL-18 in flat culture plates or round tubes. They were then or at the same time cultured with the yeast cells and the number of viable yeast cells was examined. We could not detect direct fungicidal activity by NK cells under any culture condition, although they produced a large amount of IFN-gamma and exerted marked cytotoxic activity against YAC-1 cells. On the other hand, NK cells significantly potentiated the nitric oxide-mediated cryptococcocidal activity of thioglycolate-elicited peritoneal macrophages obtained from SCID mice upon stimulation with IL-12 and IL-18. The culture supernatants of NK cells stimulated with IL-12 and IL-18 provided similar results when used in place of NK cells. The induction of macrophage anticryptococcal activity by NK cells and NK cell culture supernatants were both mediated by IFN-gamma because the specific mAb almost completely abrogated such effect. Considered collectively, our results suggested that NK cells may play a regulatory role in potentiating macrophage-mediated fungicidal mechanisms in host resistance to infection with C. neoformans rather than exerting a direct killing activity against the fungal pathogen.
Antiviral and Antiproliferative Activities of Interferon-α 1 : The Role of Cysteine Residues (1986)

Site-specific in vitro mutagenesis was used to direct serine for cysteine substitutions within the sequence of human interferon-alpha 1 (IFN-alpha 1). Antiviral specific activities and antiproliferative activities of IFN-alpha 1 analogs, expressed in M13 as fusion proteins, were assessed following purification by monoclonal antibody affinity chromatography. Based on analysis of IFN-alpha 2, IFN-alpha 1 contains two disulfide bridges between cysteine residues 29 and 139 and cysteine residues 1 and 99. IFN-alpha 1 also contains a fifth cysteine residue at position 86. The series of serine for cysteine substitutions performed indicated that IFN-alpha 1 molecules unable to form the residue 29 to residue 139 disulfide bridge have substantially reduced antiviral and antiproliferative activities, IFN-alpha 1 molecules unable to form the residue 1 to residue 99 disulfide bridge have only marginally altered antiviral and antiproliferative activities, the low antiviral activity of IFN-alpha 1 compared with other human IFN-alpha subtypes is not due to the formation of nonnative disulfide bridges involving the fifth cysteine residue at position 86, which the other subtypes lack, and (iv) the reduced biological activities of certain analogs may be due to the formation of nonnative disulfide bridges.
Endoscopic Treatment of Vesicoureteral Reflux with a Self-Detachable Balloon System (1992)

There is controversy about the use of polytetrafluoroethylene (Teflon) paste in children for the endoscopic treatment of vesicoureteral reflux due to evidence of particle migration. However, there are definite advantages in treating patients endoscopically. It is evident that the ideal substance should be able to be delivered endoscopically, conserve its volume, and be nonmigratory and nonantigenic. Towards this goal we developed a catheter with an inflatable, detachable and self-sealing silicone balloon that would fit through a 19 gauge cystoscopic needle. Hydroxy-ethyl-methyl acrylate, a hydrophilic polymer that solidifies within 60 minutes after the addition of ferrous sulfate, was chosen as the filling material for the balloon. Conceptually, the sealed balloon would prevent the migration of hydroxy-ethyl-methyl acrylate and the solidified polymer would prevent volume loss. To test this system reflux was created in 6 Hanford mini-pigs by unroofing the ureters bilaterally. In 2 pigs a previously described method of open surgery was used and in the other 4 reflux was created endoscopically using the resectoscope and laparoscopic scissors. The presence of bilateral reflux was confirmed 4 weeks later with a cystogram and the balloon was implanted unilaterally through a cystoscope. The opposite ureter served as an internal control in all animals. A repeat cystogram was performed 2 to 4 weeks after implantation, demonstrating resolution of reflux in the treated side and persistence of reflux in the opposite untreated ureter. Serial cystograms, ultrasound and excretory urography showed no reflux on the implanted side nor any evidence of obstruction. Tissue sections from various organs showed no evidence of particle migration, granuloma formation or inflammatory reaction. Short-term results show that the balloon implants are able to correct reflux without evidence of obstruction.
Identifying Brennan's Prose (2007)

The 1963 volume of the prose of Christopher Brennan sought to collect, with some exceptions, the prose works that could be ascribed to him with undeniable certainty. This left, uncollected, a number of pieces whose aetiology remained, as the editors implied, suspect. Is it not time to apply modern, computer-aided methods to determine whether the authorship of such suspected pieces is that of Brennan himself? Should we not concern ourselves with applying such methods to these works, in the course of enlightening ourselves?
Integrated bronchoscopic video tracking and 3D CT registration for virtual bronchoscopy (2003)

Lung cancer assessment involves an initial evaluation of 3D CT image data followed by interventional bronchoscopy. The physician, with only a mental image inferred from the 3D CT data, must guide the bronchoscope through the bronchial tree to sites of interest. Unfortunately, this procedure depends heavily on the physician's ability to mentally reconstruct the 3D position of the bronchoscope within the airways. In order to assist physicians in performing biopsies of interest, we have developed a method that integrates live bronchoscopic video tracking and 3D CT registration. The proposed method is integrated into a system we have been devising for virtual-bronchoscopic analysis and guidance for lung-cancer assessment. Previously, the system relied on a method that only used registration of the live bronchoscopic video to corresponding virtual endoluminal views derived from the 3D CT data. This procedure only performs the registration at manually selected sites; it does not draw upon the motion information inherent in the bronchoscopic video. Further, the registration procedure is slow. The proposed method has the following advantages: (1) it tracks the 3D motion of the bronchoscope using the bronchoscopic video; (2) it uses the tracked 3D trajectory of the bronchoscope to assist in locating sites in the 3D CT "virtual world" to perform the registration. In addition, the method incorporates techniques to: (1) detect and exclude corrupted video frames (to help make the video tracking more robust); (2) accelerate the computation of the many 3D virtual endoluminal renderings (thus, speeding up the registration process). We have tested the integrated tracking-registration method on a human airway-tree phantom and on real human data.
Activin receptor-like kinases: a novel subclass of cell-surface receptors with predicted serine/threonine kinase activity. (1993)

Human cDNA clones encoding four novel putative transmembrane protein serine/threonine kinases, denoted activin receptor-like kinase (ALK) -1, -2, -3 and -4, were obtained using a polymerase chain reaction (PCR)-based strategy. The PCR primers were designed based upon the sequence similarity between the activin receptor type II and Daf-1. The cDNA clones for ALK-1, -2 and -3 encode complete proteins of 503, 509 and 532 amino acids respectively. The ALK-4 cDNA is incomplete and the predicted protein of 383 amino acids has a truncated extracellular domain. The ALKs share similar domain structures, comprising predicted signal sequences at the N-terminals, followed by hydrophilic cysteine-rich ligand-binding domains, single hydrophobic transmembrane regions and C-terminal intracellular portions that consist almost entirely of putative serine/threonine kinase domains. The ALKs have approximately 40% sequence identity to activin receptors type II and IIB, transforming growth factor-beta (TGF-beta) type II receptor and Daf-1 in the kinase domains. However, the sequence identities are higher (60-79%) between ALK-1, -2, -3 and -4, suggesting that they form a subfamily among the putative receptor serine/threonine kinases. The extracellular domains of ALKs show only little sequence identity to other putative receptor serine/threonine kinases, but the cysteine residues are conserved. Their structural properties suggest that ALK-1 to -4 are receptors that may bind ligands that are members of the TGF-beta superfamily. The expression of mRNA in human tissues varied for the different ALKs; ALK-2 and ALK-4 showed ubiquitous tissue expression patterns, whereas the distribution of ALK-1 and ALK-3 varied strongly between different tissues with more restricted expression patterns. These results suggest that each ALK may have different in vivo functions.
Disruption of YPS1 and PEP4 genes reduces proteolytic degradation of secreted HSA/PTH in Pichia pastoris GS115 (2013)

Human serum albumin (HSA) and human parathyroid hormone (1-34) [PTH (1-34)] fusion protein [HSA/PTH (1-34)] is a promising long-acting form of PTH (1-34) for osteoporosis treatment. Secretory expression of intact HSA/PTH (1-34) in Pichia pastoris GS115 was accompanied by two degradation fragments, with molecular weights around 66 kDa, in addition to the well-known ~45 kDa HSA-truncated fragment, resulting in a low yield of intact protein. In this study, two internal cleavage sites were identified in the PTH (1-34) portion of the fusion protein by Western Blot analysis. To minimize proteolytic cleavages, several protease genes including PEP4 (encoding proteinase A), PRB1 (proteinase B) and seven YPSs genes (yapsin family members) were knocked out respectively by disruption of the individual genes and the selective combinations. Reduced degradation was observed by single disruption of either PEP4 gene or YPS1 gene, and the lowest level of degradation was observed in a pep4△yps1△ double disruptant. After 72 h of induction, more than 80 % of the HSA/PTH (1-34) secreted by the pep4△yps1△ double disruptant remained intact, in comparison to only 30 % with the wild-type strain.
Expression of the full-length products of the human papillomavirus type 6b (HPV-6b) and HPV-11 L2 open reading frames by recombinant baculovirus, and antigenic comparisons with HPV-11 whole virus particles (1990)

The L2 open reading frames (ORFs) of human papillomavirus (HPV) types 6b and 11 were expressed as full-length non-fusion proteins in Spodoptera frugiperda (Sf-9) cells using recombinant baculovirus. Both proteins were detected on Western blots as immunoreactive bands which migrated with apparent Mrs of 76K and 78K, respectively, and contained both cross-reactive and type-specific epitopes, as determined by polyclonal antisera directed against defined subregions of the HPV-6b and HPV-11 L2 ORFs. In addition, the minor capsid protein of HPV-11 particles co-migrates with the HPV-11 L2 ORF product and is immunoreactive with HPV-11 L2-specific antisera. These observations indicate that the anomalous electrophoretic mobilities of papillomavirus L2 ORF proteins can be explained without invoking post-transcriptional processing events and that the minor capsid protein of HPV-11 is antigenically and biophysically related to the HPV-11 L2 ORF product.
Nanoscale Gap Fabrication by Carbon Nanotube-Extracted Lithography (CEL) (2003)

Carbon nanotube (CNT) -extracted lithography (CEL) was developed to create high-quality nanoscale gaps defined by the size of CNTs. An individual multiwalled CNT (MWCNT) was deposited across electrodes by the composite electric field guided assembly method (CEGA) developed previously. After blanket deposition of a metal layer, the MWCNT was removed to obtain a nanoscale gap. The CEL can provide a technique for the mass fabrication of well-defined and precisely positioned nanosized gaps in a reproducible manner.
Drivability improvement on deep-submicron MOSFETs by elevation of source/drain regions (1999)

Deep submicron MOSFETs with elevated source/drain (S/D) structures, where S/D extension regions were partially elevated besides deep S/D regions, were fabricated by use of Si selective epitaxial growth technique. As fairly compared with a well-developed conventional MOSFET, we clarify an advantage of the elevated S/D structures, i.e., improvement upon driving performance with keeping excellent short-channel characteristics, which is enhanced for decrease in gate sidewall spacer width. The experimental results are explained in terms of the reduction in S/D parasitic resistance by addition of the Si epitaxial layer where the impurity profile is suitable.