gebhart/patrepeval huggingface dataset:
Mesenchymal Stem Cells Expressing Insulin-like Growth Factor-I (MSCIGF) Promote Fracture Healing and Restore New Bone Formation in Irs1 Knockout Mice: Analyses of MSCIGF Autocrine and Paracrine Regenerative Effects (2011)

Failures of fracture repair (nonunions) occur in 10% of all fractures. The use of mesenchymal stem cells (MSC) in tissue regeneration appears to be rationale, safe, and feasible. The contributions of MSC to the reparative process can occur through autocrine and paracrine effects. The primary objective of this study is to find a novel mean, by transplanting primary cultures of bone marrow-derived MSCs expressing insulin-like growth factor-I (MSC(IGF)), to promote these seed-and-soil actions of MSC to fully implement their regenerative abilities in fracture repair and nonunions. MSC(IGF) or traceable MSC(IGF)-Lac-Z were transplanted into wild-type or insulin-receptor-substrate knockout (Irs1(-/-)) mice with a stabilized tibia fracture. Healing was assessed using biomechanical testing, microcomputed tomography (μCT), and histological analyses. We found that systemically transplanted MSC(IGF) through autocrine and paracrine actions improved the fracture mechanical strength and increased new bone content while accelerating mineralization. We determined that IGF-I adapted the response of transplanted MSC(IGF) to promote their differentiation into osteoblasts. In vitro and in vivo studies showed that IGF-I-induced osteoglastogenesis in MSCs was dependent of an intact IRS1-PI3K signaling. Furthermore, using Irs1(-/-) mice as a nonunion fracture model through altered IGF signaling, we demonstrated that the autocrine effect of IGF-I on MSC restored the fracture new bone formation and promoted the occurrence of a well-organized callus that bridged the gap. A callus that was basically absent in Irs1(-/-) left untransplanted or transplanted with MSCs. We provided evidence of effects and mechanisms for transplanted MSC(IGF) in fracture repair and potentially to treat nonunions.
Measuring Cognitive Distraction in the Automobile (2013)

Three experiments were undertaken to measure and understand cognitive distraction while driving. The experiments involved participants performing different mental tasks including: listening to the radio or a book on tape; conversing with a passenger; using a hand-held or hands-free cell phone; using a speech-to-text based email system; or using an auditory version of the Operation Span (OSPAN) task. In the first (control) experiment, participants performed tasks while seated at a computer monitor to establish the cognitive workload of each task. The second experiment involved a driving simulator with a lead vehicle. Brake reaction time and following distance were measured during the performance of the tasks. In the third experiment, participants drove an instrumented vehicle in a residential area while performing the tasks. High definition cameras were used to record eye movement data at critical locations, such as, pedestrian crosswalks, two- and four-way stops, and stoplights. Data was used to create a rating system for cognitive distraction with listening to the radio at 1.21 and using a speech-to-text system at 3.06. The data suggests that the introduction of voice-based systems may increase driver distraction.
Shift in the ratio of three‐repeat tau and four‐repeat tau mRNAs in individual cholinergic basal forebrain neurons in mild cognitive impairment and Alzheimer's disease (2006)

Molecular mechanisms underlying tauopathy remain undetermined. In the current study, single cell gene expression profiling was coupled with custom-designed cDNA array analysis to evaluate tau expression and other cytoskeletal elements within individual neuronal populations in patients with no cognitive impairment (NCI), mild cognitive impairment (MCI), and Alzheimer's disease (AD). Results revealed a shift in the ratio of three-repeat tau (3Rtau) to four-repeat tau (4Rtau) mRNAs within individual human cholinergic basal forebrain (CBF) neurons within nucleus basalis (NB) and CA1 hippocampal neurons during the progression of AD, but not during normal aging. A shift in 3Rtau to 4Rtau may precipitate a cascade of events in the selective vulnerability of neurons, ultimately leading to frank neurofibrillary tangle (NFT) formation in tauopathies including AD.
Trans-abdominal Active Magnetic Linkage for robotic surgery: Concept definition and model assessment (2012)

The novel concept of Trans-abdominal Active Magnetic Linkage for laparoendoscopic single site surgery has the potential to enable the deployment of a bimanual robotic platform trough a single laparoscopic incision. The main advantage of this approach consists in shifting the actuators outside the body of the patient, while transmitting a controlled robotic motion by magnetic field across the abdomen without the need for dedicated incisions. An actuation mechanism based on this approach can be comprised of multiple anchoring and actuation units, mixed depending upon the specific needs. A static model providing anchoring and actuation forces and torques available at the internal side of the magnetic link was developed to provide a tool to navigate among the many possibilities of such an open ended design approach. The model was assessed through bench top experiments, showing a maximum relative error of 4% on force predictions. An example of a single degree of freedom manipulator actuated with the proposed concept and compatible with a 12-mm access port is able to provide an anchoring force of 3.82 N and an actuation force of 2.95 N.
Human immunoglobulin allotypes: previously unrecognized determinants and alleles defined with monoclonal antibodies. (1983)

The highly polymorphic system of serologically defined genetic markers on human IgG heavy chains (Gm allotypes) is second only to the HLA complex in terms of the large number of determinants, alleles, and haplotypes that can be used for analyses of disease associations and other genetic studies. However, present typing methods are based on the use of anti-Gm antisera that are derived mainly from fortuitously immunized human donors, often requiring processing before use, and must be used in a hemagglutination-inhibition assay that cannot be used in typing for isoallotypic determinants (currently termed "non-markers"). In studies presented here, we describe an allotyping system that utilizes monoclonal antibodies in a "sandwich" modification of the solid-phase radioimmunoassay, which is capable of reliable quantitative typing of allotypic, isoallotypic, and isotypic immunoglobulin determinants. We show that these highly reproducible, easily disseminated, and essentially inexhaustible reagents can be used for rapid, sensitive, and quantitative Gm typing. Using this system we define two previously unrecognized Gm determinants, one of which, found to date only in Caucasians, is different from all known Gm markers and thus defines previously unrecognized alleles and haplotypes. The other determinant co-segregates with the conventional G3m(b1) marker but is distinct from that marker on serological grounds. The successful preparation of mouse monoclonal antibodies that detect human Gm allotypic differences and the development of an assay system capable of typing isoallotypic as well as allotypic determinants opens the way to further dissection and application of this rich genetic system.
Hypothalamic Y2 receptors: Central coordination of energy homeostasis and bone mass regulation (2002)

Neuropeptide Y (NPY) in the central nervous system is a major regulator of food consumption and energy homeostasis. It also regulates blood pressure, induces anxiolysis, enhances memory retention and affects circadian rhythms, as well as modulates hormone release. Five Y receptors are known that mediate the action of NPY and its two other family members, peptide YY and pancreatic polypeptide. Increased NPY signaling due to elevated NPY expression in the hypothalamus leads to the development of obesity and its related phenotypes, type 2 diabetes and cardiovascular disease. Dysregulation in NPY signaling also causes alterations in bone formation. The large number of Y receptors has made it difficult to delineate their individual contributions to these physiological processes. However, recent studies analyzing Y-receptor knockout models have started to unravel some of the individual functions of these Y receptors. Particularly, the use of conditional knockout models has made it possible to pinpoint a specific functional contribution to an individual Y receptor in a particular location. From these studies, the predominantly presynaptically expressed Y2 receptor in the arcuate nucleus of the hypothalamus has emerged as a prime candidate for mediating satiety as well as a candidate for regulating bone formation. (c) 2002 Prous Science. All rights reserved.
Digital Multiplexed Gene Expression Analysis Using the NanoString nCounter System (2011)

This unit presents the protocol for the NanoString nCounter Gene Expression Assay, a robust and highly reproducible method for detecting the expression of up to 800 genes in a single reaction with high sensitivity and linearity across a broad range of expression levels. The methodology serves to bridge the gap between genome-wide (microarrays) and targeted (real-time quantitative PCR) expression profiling. The nCounter assay is based on direct digital detection of mRNA molecules of interest using target-specific, color-coded probe pairs. It does not require the conversion of mRNA to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. Each target gene of interest is detected using a pair of reporter and capture probes carrying 35- to 50-base target-specific sequences. In addition, each reporter probe carries a unique color code at the 5' end that enables the molecular barcoding of the genes of interest, while the capture probes all carry a biotin label at the 3' end that provides a molecular handle for attachment of target genes to facilitate downstream digital detection. After solution-phase hybridization between target mRNA and reporter-capture probe pairs, excess probes are removed and the probe/target complexes are aligned and immobilized in the nCounter cartridge, which is then placed in a digital analyzer for image acquisition and data processing. Hundreds of thousands of color codes designating mRNA targets of interest are directly imaged on the surface of the cartridge. The expression level of a gene is measured by counting the number of times the color-coded barcode for that gene is detected, and the barcode counts are then tabulated.
Selective Induction of Tissue Inhibitor of Metalloproteinase-1 in Bleomycin-Induced Pulmonary Fibrosis (2001)

Tissue inhibitors of metalloproteinases (TIMPs) are multifunctional proteins that have the capacity to modify cellular activities and to modulate matrix turnover. We demonstrate that TIMP-1 messenger RNA (mRNA) and protein expression are selectively and markedly increased in a murine model of bleomycin-induced pulmonary fibrosis. Northern analysis showed that lung steady-state TIMP-1 mRNA levels increased 14-fold after bleomycin administration compared with control mice. Expression of the genes for TIMP-2, TIMP-3, and interstitial collagenase (matrix metalloproteinase-13) was unaltered in the injured lung. In situ hybridization demonstrated that TIMP-1 gene induction was spatially restricted to areas of lung injury. Metalloproteinase inhibitory activity of relative molecular mass of ~ 21 to 28 kD, corresponding to the molecular weights for TIMP-1 and TIMP-2, was identified in lung extracts of bleomycin-injured mice by reverse zymography. Western analysis demonstrated that TIMP-1 protein levels in bronchoalveolar lavage fluid (BALF) of bleomycin-treated mice increased 220- and 151-fold at Days 4 and 28, respectively, compared with control mice. TIMP-2 immunoreactive protein in the BALF increased 20- and 103-fold relative to controls at Days 4 and 28, respectively. These results demonstrate that TIMP-1 gene expression is selectively increased, and that the expression of TIMP-1 and TIMP-2 is differentially regulated in bleomycin-induced pulmonary fibrosis. The profound and durable increase in TIMP-1 and TIMP-2 proteins suggests an important regulatory role for these antiproteases in the inflammatory and fibrotic responses to bleomycin-induced lung injury.
Constructing lexical transducers (1994)

Article Free AccessConstructing lexical transducers Share on Author: Lauri Karttunen Rank Xerox Research Centre, Grenoble Rank Xerox Research Centre, GrenobleView Profile Authors Info & Claims COLING '94: Proceedings of the 15th conference on Computational linguistics - Volume 1August 1994 Pages 406–411https://doi.org/10.3115/991886.991957Published:05 August 1994 19citation206DownloadsMetricsTotal Citations19Total Downloads206Last 12 Months3Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Synthesis and Characterization of Positive‐Charge Functionalized Mesoporous Silica Nanoparticles for Oral Drug Delivery of an Anti‐Inflammatory Drug (2008)

Abstract We synthesized mesoporous silica nanoparticles (MSN) with different densities of surface positive charges. The positive surface charge was generated by incorporating trimethylammonium (TA) functional groups into the framework of MSN (MSN–TA) via direct co‐condensation of a TA‐silane and tetraethoxysilane (TEOS) in the presence of a base as a catalyst. These MSN–TA samples have well‐defined hexagonal structures with an average particle diameter of 100 nm, pore size of 2.7 nm, and surface area of about 1000 m 2 g −1 . Anionic drug molecules, Orange II (a fluorescent tracing molecule), and sulfasalazine (an anti‐inflammatory prodrug used for bowel disease), were effectively loaded into these MSN–TA samples and remained inside of the MSN–TA under acidic environment (pH 2–5). The amounts of loading of both Orange II and sulfasalazine were increased with increasing positive charge densities resulting from the increasing number of TA groups. When these drug‐loaded MSN–TA nanoparticles were placed in physiological buffer solution (pH 7.4), a partial negative surface charge on the MSN–TA was generated due to the deprotonation of silanol groups, and the strong electrostatic repulsion triggered a sustained release of the loaded molecules. MSN–TA as a nanovehicle for pH‐dependent loading and controllable release of anionic drug molecules can be used as an oral delivery drug systems targeting at intestine. These drugs can be remained trapped in the nanovehicle when passing through the stomach's acidic environment and be released in intestine where the environmental pH is close to neutral.
Controlled partial embedding of carbon nanotubes within flexible transparent layers (2007)

Applications of carbon nanotubes (CNTs) like field emission displays, super-capacitors, and cell growth scaffolds can benefit from controllable embedding of the CNTs in a material such that the CNTs are anchored and protrude a desired length. We demonstrate a simple method for anchoring densely packed, vertically aligned arrays of CNTs into silicone layers using spin-coating, CNT insertion, curing, and growth substrate removal. CNT arrays of 51 and 120 µm in height are anchored into silicone layers of thickness 26 and 36 µm, respectively. Scanning electron microscopy (SEM) and optical microscopy are used to characterize the sample morphology, a 5.5 m s(-1) impinging water jet is used to apply shear stress, and a tensile test shows that the silicone layer detaches from the substrate before the CNTs are ripped from the layer. The CNTs are thus well anchored in the silicone layers. The spin-coating process gives control over layer thickness, and the method should have general applicability to various nanostructures and anchoring materials.
Dual role of HIV Tat in regulation of apoptosis in T cells (1997)

Apoptosis has been suggested to be one of the major mechanisms of depletion of CD4+ T cells in HIV-1-infected individuals. Remarkably, HIV-1-infected cells appear protected from apoptosis, whereas bystander cells show increased apoptosis in lymph nodes of infected individuals. In this work, we present evidence that the trans-activating protein of HIV-1, Tat, has a dual role in regulation of apoptosis in T cells. While addition of exogenous Tat protein induced apoptosis in uninfected T cells, T cell clones stably expressing the Tat protein were protected from activation-induced apoptosis. The addition of exogenous Tat potentiated anti-CD3 mAb, anti-Fas IgM mAb, and TNF-alpha-induced apoptosis of T cells. Pretreatment of Tat with anti-Tat Ab abrogated Tat-induced apoptosis, but did not affect anti-Fas IgM Ab-induced apoptosis. Endogenously expressed Tat was analyzed in Jurkat T cell clones transfected with either full-length tat gene (101 amino acids), or in control cells containing an empty vector. The Tat101-transfected clones were resistant to anti-CD3-induced apoptosis, when compared with cells transfected with vector alone. Furthermore, cross-linking of CD4 molecules on T cells with gp160 and anti-gp160 Ab showed markedly decreased apoptosis in Tat101 cells compared with that induced in cells transfected with vector alone. Taken together, our results indicate that HIV-1 Tat can regulate apoptosis that may contribute to the immunopathogenesis of AIDS.
Proliferative enteropathy: a global enteric disease of pigs caused byLawsonia intracellularis (2005)

Proliferative enteropathy (PE; ileitis) is a common intestinal disease affecting susceptible pigs raised under various management systems around the world. Major developments in the understanding of PE and its causative agent, Lawsonia intracellularis, have occurred that have led to advances in the detection of this disease and methods to control and prevent it. Diagnostic tools that have improved overall detection and early onset of PE in pigs include various serological and molecular-based assays. Histological tests such as immunohistochemistry continue to be the gold standard in confirming Lawsonia-specific lesions in pigs post mortem. Despite extreme difficulties in isolating L. intracellularis, innovations in the cultivation and the development of pure culture challenge models, have opened doors to better characterization of the pathogenesis of PE through in vivo and in vitro L. intracellularis-host interactions. Advancements in molecular research such as the genetic sequencing of the entire Lawsonia genome have provided ways to identify various immunogens, metabolic pathways and methods for understanding the epidemiology of this organism. The determinations of immunological responsiveness in pigs to virulent and attenuated isolates of L. intracellularis and identification of various immunogens have led to progress in vaccine development.
Establishment of rat embryonic stem cell lines that can participate in germline chimerae at high efficiency (2009)

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New Coding Tools for Illumination and Focus Mismatch Compensation in Multiview Video Coding (2007)

We propose new tools for multiview video coding (MVC) that aim to compensate for mismatches between video frames corresponding to different views. Such mismatches could be caused by different shooting positions of the cameras and/or heterogeneous camera settings. In particular, we consider illumination and focus mismatches across views, i.e., such that different portions of a video frame can undergo different illumination and blurriness/sharpness changes with respect to the corresponding areas in frames from the other views. Models for illumination and focus mismatches are proposed and new coding tools are developed from the models. We propose a block-based illumination compensation (IC) technique and a depth-dependent adaptive reference filtering (ARF) approach for cross-view prediction in multiview video coding. In IC, disparity field and illumination changes are jointly computed as part of the disparity estimation search. IC can be adaptively applied by taking into account the rate-distortion characteristics of each block. For ARF, the disparity fields are used to estimate scene depth, such that video frames are first divided into regions with different scene-depth levels. A 2-D filter is then selected for each scene-depth level. These filters are chosen to minimize residual energy, with the goal of compensating for focus mismatches. The resulting filters are applied to the reference frames to generate better matches for cross-view prediction. Furthermore, we propose a coding system that combines IC and ARF. Adjustments are made so as to maximize the gains achieved by using both coding tools, while reducing the complexity of the final integrated system. We analyze the complexity of all proposed methods and present simulation results of IC, ARF and combined system for different multiview sequences based on the H.264/AVC reference codec. When applying the proposed tool to cross-view coding we observe gains of up 1.3 dB as compared to directly using an H.264/AVC codec to perform predictive coding across views.
Discriminative Color Descriptors (2013)

Color description is a challenging task because of large variations in RGB values which occur due to scene accidental events, such as shadows, shading, specularities, illuminant color changes, and changes in viewing geometry. Traditionally, this challenge has been addressed by capturing the variations in physics-based models, and deriving invariants for the undesired variations. The drawback of this approach is that sets of distinguishable colors in the original color space are mapped to the same value in the photometric invariant space. This results in a drop of discriminative power of the color description. In this paper we take an information theoretic approach to color description. We cluster color values together based on their discriminative power in a classification problem. The clustering has the explicit objective to minimize the drop of mutual information of the final representation. We show that such a color description automatically learns a certain degree of photometric invariance. We also show that a universal color representation, which is based on other data sets than the one at hand, can obtain competing performance. Experiments show that the proposed descriptor outperforms existing photometric invariants. Furthermore, we show that combined with shape description these color descriptors obtain excellent results on four challenging datasets, namely, PASCAL VOC 2007, Flowers-102, Stanford dogs-120 and Birds-200.