gebhart/patrepeval huggingface dataset:
Co/Cu Nanowire Systems for GMR Sensing Applications (2011)

Since the discovery of giant magnetoresistance (GMR) in 1988 by Albert Fert and Peter Grunberg many companies have sought to develop practical applications for this intriguing effect of magnetic multilayer stacks. The applications of magnetic multilayer stacks are diverse, but in general they can serve as: magnetic field sensors (Simonds, 1995; Grunberg et al., 1986; Saurenbach et al., 1988; Baibich et al., 1988), non-volatile memories (Manalis et al., 1995; Chou et al., 1994), or variable resistors when small magnetic fields have to be measured. The first GMR sensor commercially available was introduced in 1995 by NVE Corporation. Since then, users can rely on a large variety of devices exploiting GMR: analogue and digital sensors, switches, gradient transducers for contactless positioning systems, e.g. gear tooth and encoder applications. Today, it is generally acknowledged that GMR sensors outperform the competing technologies such as AMR and Hall virtually in every application, and often at a significantly lower cost. The conventional GMR stacks are produced by vacuum deposition technology; more specifically, by this technique, a large variety of thin film materials are serially deposited, within a single vacuum chamber, one on top of another, to form multilayer stacks of tailored magnetic properties. The need to accurately control the nanometric thickness of each film, their extremely low roughness, and their purity do majorly contribute to the final cost of this type of systems. For this reason, the use of these devices, especially in low-margin markets such as the automotive, is still prohibitive for a number of potential field applications. In this context, alternative processes are envisaged to lower the final cost of GMR sensors. To this end, the pulsed electrodeposition into nanoporous templates (hereinafter template pulsed electrodepostion, TPED) is presented here as a competitive alternative to mass produce GMR sensors in the form of arrays of multilayer nanowires. As being a promising candidate for a low-cost production of sensors tailored for the aforementioned field uses (Pullini et al., 2007a), Co/Cu multilayer nanowire arrays fabricated by TPED (Fert & Piraux, 1999; Piraux et al., 1994) are discussed in this chapter. Specifically, the present chapter aims at presenting the criteria to model, design, develop Co/Cu-multilayer nanowire arrays, and discuss their potential exploitation perspectives to be used as magnetic field sensors. In a first part of this chapter a quasi-analytical analysis (QAD) of cylindrical Co/Cu/Co trilayer systems is detailed, and the equations drew to calculate the critical fields, the linearity,
E-Cadherin-Mediated Cell–Cell Contact Is Critical for Induced Pluripotent Stem Cell Generation (2010)

The low efficiency of reprogramming and genomic integration of virus vectors obscure the potential application of induced pluripotent stem (iPS) cells; therefore, identification of chemicals and cooperative factors that may improve the generation of iPS cells will be of great value. Moreover, the cellular mechanisms that limit the reprogramming efficiency need to be investigated. Through screening a chemical library, we found that two chemicals reported to upregulate E-cadherin considerably increase the reprogramming efficiency. Further study of the process indicated that E-cadherin is upregulated during reprogramming and the established iPS cells possess E-cadherin-mediated cell-cell contact, morphologically indistinguishable from embryonic stem (ES) cells. Our experiments also demonstrate that overexpression of E-cadherin significantly enhances reprogramming efficiency, whereas knockdown of endogenous E-cadherin reduces the efficiency. Consistently, abrogation of cell-cell contact by the inhibitory peptide or the neutralizing antibody against the extracellular domain of E-cadherin compromises iPS cell generation. Further mechanistic study reveals that adhesive binding activity of E-cadherin is required. Our results highlight the critical role of E-cadherin-mediated cell-cell contact in reprogramming and suggest new routes for more efficient iPS cell generation.
Gene therapy for solid tumors (1995)

Advances in molecular biology have proven that there is a genetic basis to the process of carcinogenesis that allows for the consideration of entirely new approaches to the treatment of cancer. The development of an ability to selectively destroy cancer cells through the manipulation of DNA may provide the opportunity to dramatically improve the quality of care and treatment of cancer patients by decreasing systemic toxicities and enhancing efficacy. These new therapies may occur through the restoration of genetic health, such as the insertion of normal tumor suppressor genes or via down-regulation of oncogene or growth factor receptor expression. Other possibilities include the targeting of genetic alterations in tumor cells that will enhance tumor immunogenicity or induce a specific sensitivity to a prodrug. In this chapter, we have reviewed the current status of gene therapy for solid tumors in the United States and evolving new approaches for this emerging clinical discipline.
Methane Storage in Metal–Organic Frameworks: Current Records, Surprise Findings, and Challenges (2013)

We have examined the methane uptake properties of six of the most promising metal organic framework (MOF) materials: PCN-14, UTSA-20, HKUST-1, Ni-MOF-74 (Ni-CPO-27), NU-111, and NU-125. We discovered that HKUST-1, a material that is commercially available in gram scale, exhibits a room-temperature volumetric methane uptake that exceeds any value reported to date. The total uptake is about 230 cc(STP)/cc at 35 bar and 270 cc(STP)/cc at 65 bar, which meets the new volumetric target recently set by the Department of Energy (DOE) if the packing efficiency loss is ignored. We emphasize that MOFs with high surface areas and pore volumes perform better overall. NU-111, for example, reaches ~75% of both the gravimetric and the volumetric targets. We find that values for gravimetric uptake, pore volume, and inverse density of the MOFs we studied scale essentially linearly with surface area. From this linear dependence, we estimate that a MOF with surface area 7500 m(2)/g and pore volume 3.2 cc/g could reach the current DOE gravimetric target of 0.5 g/g while simultaneously exhibiting around ~200 cc/cc volumetric uptake. We note that while values for volumetric uptake are based on ideal single crystal densities, in reality the packing densities of MOFs are much lower. Finally, we show that compacting HKUST-1 into wafer shapes partially collapses the framework, decreasing both volumetric and gravimetric uptake significantly. Hence, one of the important challenges going forward is to find ways to pack MOFs efficiently without serious damage or to synthesize MOFs that can withstand substantial mechanical pressure.
The evolving definition of advanced prostate cancer. (2004)

Each year more patients present with prostate cancer at increasingly younger ages and with earlier stage disease, resulting in the potential for longer survival time, longer-term hormonal therapy, and a heightened risk of developing biochemical recurrence after treatment. It seems clear that clinicians need to broaden the definition of "advanced" prostate cancer to include recent knowledge that will influence the form and timing of treatment as well as the monitoring of disease progression. A more contemporary definition should include patients with lower-grade disease and with an increased risk of progression and/or death from prostate cancer along with those with widely disseminated metastatic disease. Treatment alternatives for these patients should be evaluated based on a risk stratification equation toward a goal of the greatest efficacy and the least patient harm over time given that increasing numbers of these patients are entering treatment long before they develop widespread osteoblastic metastases.
Inducible gene knockout of transcription factor recombination signal binding protein‐J reveals its essential role in T versus B lineage decision (2002)

The transcription factor recombination signal binding protein-J (RBP-J) functions immediately downstream of the cell surface receptor Notch and mediates transcriptional activation by the intracellular domain of all four kinds of Notch receptors. To investigate the function of RBP-J, we introduced loxP sites on both sides of the RBP-J exons encoding its DNA binding domain. Mice bearing the loxP-flanked RBP-J alleles, RBP-J(f/f), were mated with Mx-Cre transgenic mice and deletional mutation of the RBP-J gene in adult mice was induced by injection of the IFN-alpha inducer poly(I)-poly(C). Here we show that inactivation of RBP-J in bone marrow resulted in a block of T cell development at the earliest stage and increase of B cell development in the thymus. Lymphoid progenitors deficient in RBP-J differentiate into B but not T cells when cultured in 2'-deoxyguanosine-treated fetal thymic lobes by hanging-drop fetal thymus organ culture. Competitive repopulation assay also revealed cell autonomous deficiency of T cell development from bone marrow of RBP-J knockout mouse. Myeloid and B lineage differentiation appears normal in the bone marrow of RBP-J-inactivated mice. These results suggest that RBP-J, probably by mediating Notch signaling, controls T versus B cell fate decision in lymphoid progenitors.
Quantification of plasma DNA as a screening tool for lung cancer. (2004)

Plasma DNA quantification has a strong power to discriminate lung cancer from the healthy and from the healthy and benign lung disease, less power to discriminate lung cancer from benign lung disease. Plasma DNA quantification may be useful as a screening tool for lung cancer.
Architecture of the SWI/SNF-Nucleosome Complex (2008)

The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning approximately 50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.
Synthesis of a Regioregular Zwitterionic Conjugated Oligoelectrolyte, Usable as an Optical Probe for Detection of Amyloid Fibril Formation at Acidic pH (2005)

Changes of the optical properties of conjugated polyelectrolytes have been utilized to monitor noncovalent interactions between biomolecules and the conjugated polyelectrolytes in sensor applications. A regioregular, zwitterionic conjugated oligoelectrolyte was synthesized in order to create a probe with a defined set of optical properties and hereby facilitate interpretation of biomolecule-oligoelectrolyte interactions. The synthesized oligoelectrolyte was used at acidic pH as a novel optical probe to detect amyloid fibril formation of bovine insulin and chicken lysozyme. Interaction of the probe with formed amyloid fibrils results in changes of the geometry and the electronic structure of the oligoelectrolyte chains, which were monitored with absorption and emission spectroscopy.
Four peptide hormones decrease the number of human breast adenocarcinoma cells (2005)

Four peptide hormones significantly decrease the number of human breast adenocarcinoma cells within 24 h and inhibit the proliferation of these cells for at least 96 h. Their mechanism of doing so involves inhibition of DNA synthesis and a decrease in cells in the S phase of the cell cycle mediated in part by cyclic GMP.
Thin film deposition and microelectronic and optoelectronic device fabrication and characterization in monocrystalline alpha and beta silicon carbide (1991)

The deposition of silicon carbide thin films and the associated technologies of impurity incorporation, etching, surface chemistry, and electrical contacts for fabrication of solid-state devices capable of operation at temperatures to 925 K are addressed. The results of several research programs in the United States, Japan and the Soviet Union, and the remaining challenges related to the development of silicon carbide for microelectronics are presented and discussed. It is concluded that the combination of alpha -SiC on alpha -SiC appears especially viable for device fabrication. In addition, considerable progress in the understanding of the surface science, ohmic and Schottky contacts, and dry etching have recently been made. The combination of these advances has allowed continual improvement in Schottky diode p-n junction, MESFET, MOSFET, HBT, and LED devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Brain-Derived Neurotrophic Factor in Brain Disorders: Focus on Neuroinflammation (2018)

Brain-derived neurotrophic factor (BDNF) is one of the most studied neurotrophins in the healthy and diseased brain. As a result, there is a large body of evidence that associates BDNF with neuronal maintenance, neuronal survival, plasticity, and neurotransmitter regulation. Patients with psychiatric and neurodegenerative disorders often have reduced BDNF concentrations in their blood and brain. A current hypothesis suggests that these abnormal BDNF levels might be due to the chronic inflammatory state of the brain in certain disorders, as neuroinflammation is known to affect several BDNF-related signaling pathways. Activation of glia cells can induce an increase in the levels of pro- and antiinflammatory cytokines and reactive oxygen species, which can lead to the modulation of neuronal function and neurotoxicity observed in several brain pathologies. Understanding how neuroinflammation is involved in disorders of the brain, especially in the disease onset and progression, can be crucial for the development of new strategies of treatment. Despite the increasing evidence for the involvement of BDNF and neuroinflammation in brain disorders, there is scarce evidence that addresses the interaction between the neurotrophin and neuroinflammation in psychiatric and neurodegenerative diseases. This review focuses on the effect of acute and chronic inflammation on BDNF levels in the most common psychiatric and neurodegenerative disorders and aims to shed some light on the possible biological mechanisms that may influence this effect. In addition, this review will address the effect of behavior and pharmacological interventions on BDNF levels in these disorders.
Custom-designed glycopolymer syntheses by terpolymerizations (1992)

Carbohydrate derivatives having lectin binding properties and bearing N-acryloyl functionality have been copolymerized under three-component terpolymerization conditions with acrylamide and N-acryloylated effector molecules to provide water-soluble glycopolymers with custom designed physico-chemical properties.
Inducible Expression of GDNF in Transplanted iPSC-Derived Neural Progenitor Cells (2018)

Trophic factor delivery to the brain using stem cell-derived neural progenitors is a powerful way to bypass the blood-brain barrier. Protection of diseased neurons using this technology is a promising therapy for neurodegenerative diseases. Glial cell line-derived neurotrophic factor (GDNF) has provided benefits to Parkinsonian patients and is being used in a clinical trial for amyotrophic lateral sclerosis. However, chronic trophic factor delivery prohibits dose adjustment or cessation if side effects develop. To address this, we engineered a doxycycline-regulated vector, allowing inducible and reversible expression of a therapeutic molecule. Human induced pluripotent stem cell (iPSC)-derived neural progenitors were stably transfected with the vector and transplanted into the adult mouse brain. Doxycycline can penetrate the graft, with addition and withdrawal providing inducible and reversible GDNF expression in vivo, over multiple cycles. Our findings provide proof of concept for combining gene and stem cell therapy for effective modulation of ectopic protein expression in transplanted cells.
MicroRNA profiling of clear cell renal cell carcinoma by whole‐genome small RNA deep sequencing of paired frozen and formalin‐fixed, paraffin‐embedded tissue specimens (2010)

Renal cell carcinoma (RCC) is one of the leading causes of cancer mortality. Characterization of microRNA (miRNA) expression of RCC will help disclose new pathogenic pathways in tumourigenesis and progression and may lead to the development of molecular biomarkers and target-specific therapies for diagnosis, prognostication and treatment. With limitations in test specificity and the ability to detect novel miRNA and other small non-coding RNAs (smRNAs), microarray and RT-PCR techniques are being replaced by the evolving deep-sequencing technologies, at least in the discovery phase. Until now, cancer miRNA profiling of human benign and tumour specimen sets, using smRNA deep-sequencing (smRNA-seq), has not been reported. Specifically, due to concern over possible poor RNA quality/integrity, formalin-fixed paraffin-embedded (FFPE) samples have not been used for such studies. Here, we performed whole-genome smRNA-seq analysis using a benign and RCC specimen set and have successfully profiled the miRNA expression. Studies performed on paired frozen and FFPE specimens showed very similar results. Moreover, a comparison study of microarray, deep-sequencing and RT-PCR methodologies also showed a high correlation among the three technologies. To our knowledge, this is the first study to demonstrate that FFPE specimens can be used reliably for miRNA deep-sequencing analysis, making future large-scale clinical cohort/trial-based studies possible.
Delivery of a Secretable Adenosine Deaminase Through Microcapsules–A Novel Approach to Somatic Gene Therapy (1994)

Many current gene therapy protocols require genetic modification of autologous cells. An alternate approach is to use universal recombinant cell lines engineered to secrete in vivo the desired gene products. Enclosing these cells within immunoprotective devices before implantation would prevent rejection of the nonautologous donor cells. To overcome the limitation that not all therapeutic gene products are secreted, we now propose to fuse a signal sequence to the amino terminus of a nonsecreted protein such as human adenosine deaminase (ADA), thus directing the product into a secretory pathway for release from the cells. A fusion gene constructed between the cDNA of the beta-lactamase signal sequence and human ADA expressed a product after in vitro transcription and translation that was immunologically similar to the human protein. Mouse fibroblasts transfected with the fusion gene demonstrated secreted ADA activity that resembled the human cytosolic enzyme in its heat stability, pH optimum, KM, electrophoretic mobility, and immunologic reactivity. Hence, the secreted enzyme expressed from the fusion gene is antigenically and enzymatically similar to the authentic human form. When transfected mouse fibroblasts or myoblasts were enclosed in permselective alginate-poly-L-lysine alginate microcapsules, ADA activity was secreted from the microcapsules and the cells remained viable for over 5 months. Hence, a secretable and functional human ADA has been constructed that can be delivered from recombinant cells within immunoprotective capsules. The success of this strategy provides the prototype for engineering nonsecreted gene products for therapy via this novel method of somatic gene therapy.
The Genomic, Biochemical, and Cellular Responses of the Retina in Inherited Photoreceptor Degenerations and Prospects for the Treatment of These Disorders (2010)

The association of more than 140 genes with human photoreceptor degenerations, together with studies of animal models of these monogenic diseases, has provided great insight into their pathogenesis. Here we review the responses of the retina to photoreceptor mutations, including mechanisms of photoreceptor death. We discuss the roles of oxidative metabolism, mitochondrial reactive oxygen species, metabolic stress, protein misfolding, and defects in ciliary proteins, as well as the responses of Müller glia, microglia, and the retinal vasculature. Finally, we report on potential pharmacologic and biologic therapies, the critical role of histopathology as a prerequisite to treatment, and the exciting promise of gene therapy in animal models and in phase 1 trials in humans.
Particle-filter-based Pose Estimation from Controlled Motion with Application to Visual Servoing (2014)

In this paper, we present a Bayesian algorithm based on particle filters to estimate the camera pose for vision-based control. The state model is represented as a relative camera pose between the current and initial camera frames. The particles in the prior motion model are drawn using the velocity control signal collected from the visual controller of the robot. The pose samples are evaluated using an epipolar geometry measurement model and a suitable weight is associated with each sample. The algorithm takes advantage of the a priori knowledge about motion, i.e., the velocity computed by the visual servo control, to estimate the magnitude of the translation in addition to its direction, hence producing a full camera motion estimate. Its application to position-based visual servoing is demonstrated. Experiments are carried out using a real robot setup. The results show the efficiency of the proposed filter over the motion measurements of the robot. In addition, the filter was able to recover the split performed by the robot joints.
A peptide nucleic acid (PNA) is more rapidly internalized in cultured neurons when coupled to a retro-inverso delivery peptide. The antisense activity depresses the target mRNA and protein in magnocellular oxytocin neurons (1998)

A peptide nucleic acid (PNA) antisense for the AUG translation initiation region of prepro-oxytocin mRNA was synthesized and coupled to a r etro-inverso peptide that is rapidly taken up by cells. This bioconjugate was internalized by cultured cerebral cortex neurons within minutes, according to the specific property of the vector peptide. The PNA alone also entered the cells, but more slowly. Cell viability was unaffected when the PNA concentrations were lower than 10 microM and incubation times less than for 24 h. Magnocellular neurons from the hypothalamic supraoptic nucleus, which produce oxytocin and vasopressin, were cultured in chemically defined medium. Both PNA and vector peptide-PNA depressed the amounts of the mRNA coding for prepro-oxytocin in these neurons. A scrambled PNA had no effect and the very cognate prepro-vasopressin mRNA was not affected. The antisense PNA also depressed the immunocytochemical signal for prepro-oxytocin in this culture in a dose- and time-dependent manner. These results show that PNAs driven by the retro-inverso vector peptide are powerful antisense reagents for use on cells in culture.