gebhart/patrepeval huggingface dataset:
Decade-Long Safety and Function of Retroviral-Modified Chimeric Antigen Receptor T Cells (2012)

The success of adoptive T cell gene transfer for treatment of cancer and HIV is predicated on generating a response that is both durable and safe. We report long-term results from three clinical trials to evaluate gammaretroviral vector-engineered T cells for HIV. The vector encoded a chimeric antigen receptor (CAR) composed of CD4 linked to the CD3ζ signaling chain (CD4ζ). CAR T cells were detected in 98% of samples tested for at least 11 years after infusion at frequencies that exceeded average T cell levels after most vaccine approaches. The CD4ζ transgene retained expression and function. There was no evidence of vector-induced immortalization of cells; integration site distributions showed no evidence of persistent clonal expansion or enrichment for integration sites near genes implicated in growth control or transformation. The CD4ζ T cells had stable levels of engraftment, with decay half-lives that exceeded 16 years, in marked contrast to previous trials testing engineered T cells. These findings indicate that host immunosuppression before T cell transfer is not required to achieve long-term persistence of gene-modified T cells. Further, our results emphasize the safety of T cells modified by retroviral gene transfer in clinical application, as measured in >500 patient-years of follow-up. Thus, previous safety issues with integrating viral vectors are hematopoietic stem cell or transgene intrinsic, and not a general feature of retroviral vectors. Engineered T cells are a promising form of synthetic biology for long-term delivery of protein-based therapeutics. These results provide a framework to guide the therapy of a wide spectrum of human diseases.
Extraction and Isolation of Lignin for Utilization as a Standard to Determine Lignin Concentration Using the Acetyl Bromide Spectrophotometric Method (2001)

Lignin extracted with acidic dioxane was investigated as a possible standard for quantitatively determining lignin content in plant samples using the spectrophotometric method employing acetyl bromide. Acidic dioxane lignins were analyzed for carbohydrate, total protein, nitrobenzene oxidation products, and UV spectral characteristics. Total carbohydrate content of isolated lignins ranged from 2.21 to 5.70%, while protein ranged from 0.95 to 6.06% depending upon the plant source of the original cell wall sample. Nitrobenzene analysis indicated differences in the amount of guaiacyl and syringyl units making up the lignins, but this did not alter the UV spectrum of lignin solubilized in acetyl bromide. Regression equations developed for the acetyl bromide method using the isolated lignins for all the plant samples were similar to each other. Lignin values obtained by the acetyl bromide method were similar to the lignin values obtained as acid insoluble residues following a Klason lignin procedure.
Secondary structure of lipidated Ras bound to a lipid bilayer (2008)

Ras proteins are small guanine nucleotide binding proteins that regulate many cellular processes, including growth control. They undergo distinct post-translational lipid modifications that are required for appropriate targeting to membranes. This, in turn, is critical for Ras biological function. However, most in vitro studies have been conducted on nonlipidated truncated forms of Ras proteins. Here, for the first time, attenuated total reflectance-FTIR studies of lipid-modified membrane-bound N-Ras are performed, and compared with nonlipidated truncated Ras in solution. For these studies, lipidated N-Ras was prepared by linking a farnesylated and hexadecylated N-Ras lipopeptide to a truncated N-Ras protein (residues 1-181). It was then bound to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer tethered on an attenuated total reflectance crystal. The structurally sensitive amide I absorbance band in the IR was detected and analysed to determine the secondary structure of the protein. The NMR three-dimensional structure of truncated Ras was used to calibrate the contributions of the different secondary structural elements to the amide I absorbance band of truncated Ras. Using this novel approach, the correct decomposition was selected from several possible solutions. The same parameter set was then used for the membrane-bound lipidated Ras, and provided a reliable decomposition for the membrane-bound form in comparison with truncated Ras. This comparison indicates that the secondary structure of membrane-bound Ras is similar to that determined for the nonlipidated truncated Ras protein for the highly conserved G-domain. This result validates the multitude of investigations of truncated Ras without anchor in vitro. The novel attenuated total reflectance approach opens the way for detailed studies of the interaction network of the membrane-bound Ras protein.
8300V Blocking Voltage AlGaN/GaN Power HFET with Thick Poly-AlN Passivation (2007)

We report ultra high voltage AlGaN/GaN heterojunction transistors (HFETs) on sapphire with thick poly-AlN passivation. Extremely high blocking voltage of 8300 V is achieved while maintaining relative low specific on-state resistance (Ron*A) of 186 mOmegaldrcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Via-holes through sapphire at the drain electrodes enable very efficient layout of the lateral HFET array as well as better heat dissipation.
Protective Effect of Flavonoids against Aging- and Lipopolysaccharide-Induced Cognitive Impairment in Mice (2003)

Flavonoids, naturally occurring polyphenolic compounds, are known to inhibit both lipopolysaccharide (LPS) stimulated tumor necrosis factor alpha and interleukin 6 release which modulate the proinflammatory molecules that have been reported in many progressive neurodegenerative disorders, including Alzheimer's disease (AD), viral and bacterial meningitis, AIDS dementia complex, and stroke. The present experiments were performed to study the possible effects of exogenously administered flavonoids (apigenin-7-glucoside and quercetin) on the cognitive performance in aged and LPS-treated mice (an animal model for AD) using passive avoidance and elevated plus-maze tasks. Aged and LPS-treated mice showed poor retention of memory in step-through passive avoidance and in plus-maze tasks. Chronic administration of the flavonoids apigenin-7-glucoside (5-20 mg/kg i.p.) and quercetin (25-100 mg/kg i.p.) dose dependently reversed the age-induced and LPS-induced retention deficits in both test paradigms. However, flavonoids after chronic administration in young mice did not show any improvement of memory retention in both paradigms. Apigenin-7-glucoside showed more efficacy as compared with quercetin in both models that may be probably due to its greater efficacy to inhibit cyclooxygenase-2 and inducible nitric oxide synthase. Chronic treatment with flavonoids did not alter the locomotor activity in both young and aged mice; however, aged mice showed improvement of performance on Rota-Rod test. The results showed that chronic treatment with flavonoids reverses cognitive deficits in aged and LPS-intoxicated mice which suggests that modulation of cyclooxygenase-2 and inducible nitric synthase by flavonoids may be important in the prevention of memory deficits, one of the symptoms related to AD.
Development of ASICs for CdTe pixel and line sensors (2005)

We are developing low noise analog ASICs for hard X-ray and gamma-ray astronomy. They are based on a sub-micron CMOS process. Our design includes a finely-adjustable high-resistance circuit, which, for example, enables us to realize a pole-zero-cancellation in the analog chain. A two-dimensional ASIC with a fast read-out scheme and a one-dimensional ASIC with an improved analog design are developed and verified. With the latter ASIC connected with a CdTe detector, we have obtained a radioactive source spectrum with an energy resolution of 4.6 keV (FWHM) at 59.5 keV.
Axillary management in breast cancer: What's new for 2012? (2012)

Sentinel lymph node (SLN) biopsy has become standard care for management of the axilla in invasive breast cancer, replacing axillary lymph node dissection (ALND) in most subjects, with a progressively diminishing role of ALND. Advances in preoperative imaging have also changed the algorithm for axillary management, and ultrasound-guided needle biopsy has been shown to triage >50% of subjects with node metastases to ALND. However, the past two years have witnessed remarkable and practice-changing advances in our knowledge and approach to management of the axilla, with availability of high-level evidence that demands reappraisal of practice and challenges the role of routine ALND for SLN-positive patients. In particular, for the group of patients defined by eligibility criteria in the Z0011 trial, it appears that ALND has little or no effect on local recurrence and survival, or on the choice of local or systemic therapies. We review the available evidence on staging and management of the axilla in breast cancer, and outline our interpretation of its implications for clinical practice.
Expression of metabotropic glutamate receptor subtype mRNA (mGluR1–8) in human cerebellum (1999)

The expression of metabotropic glutamate receptor (mGluR) mRNAs in the human cerebellar neocortex was investigated using in situ hybridization. mGluR1, 3 and 4 mRNAs were most abundant and widely distributed, whereas mGluR2, 5 and 7 mRNA expression was circumscript. mRNAs coding for mGluR1, 3, 4 and 7 were expressed in Purkinje cells. mGluR1 and 4 mRNAs detectable in granule cells and mGluR1, 2, 3, 4 and 7 mRNAs in Golgi cells. mGluR5 mRNA was detectable in putative Bergmann glia as well as mGluR3 mRNA, which was widely expressed in glial cells. mGluR8 mRNA expression was very low in a subset of stellate/basket cells of the molecular layer whereas mGluR6 mRNA was not detectable in the cerebellar cortex.
DNA hybridization assay using ATTOPHOS, a fluorescent substrate for alkaline phosphatase. (1992)

A fluorometric procedure for the detection of DNA-DNA hybrids is described. The procedure involved the detection of probe-bound alkaline phosphatase with the fluorescent substrate ATTOPHOS. This substrate is converted to ATTOFLUOR by alkaline phosphatase and fluoresces strongly at 550 nm when excited with a wavelength of 440 nm. DNA hybridization assays were performed both with dilutions of purified target plasmid DNA (pSE9 or PBR322) and whole bacterial cells. Streptavidin-alkaline phosphatase conjugates were added to react with bound probe. Fluorometric assays, as well as colorimetric assays, using 5-bromo-4-chloro-3-indolylphosphate + nitroblue tetrazolium for alkaline phosphatase activity were performed. The fluorescence of the substrate was measured at time intervals, and the slope of the regression line calculated. A slope four times greater than that of background was considered positive. One hundred femtograms or 2.2 x 10(4) molecules of homologous DNA were detected with the fluorescent assay as compared with 10,000 femtograms or 2.2 x 10(6) molecules of homologous DNA with the colorimetric assay. Similar results were obtained with whole cells. Approximately 1 x 10(3) homologous cells were detected fluorometrically and 1 x 10(5) cells were detected colorimetrically. Based on these results, we conclude that, in our hands, the DNA hybridization assay described here using ATTOPHOS as the substrate for alkaline phosphatase is a very sensitive assay for the detection of DNA-DNA hybrids.
Biomimetic Macroporous Hydrogels: Protein Ligand Distribution and Cell Response to the Ligand Architecture in the Scaffold (2009)

Macroporous hydrogels (MHs), cryogels, are a new type of biomaterials for tissue engineering that can be produced from any natural or synthetic polymer that forms a gel. Synthetic MHs are rendered bioactive by surface or bulk modifications with extracellular matrix components. In this study, cell response to the architecture of protein ligands, bovine type-I collagen (CG) and human fibrinogen (Fg), immobilised using different methods on poly(2-hydroxyethyl methacrylate) (pHEMA) macroporous hydrogels (MHs) was analysed. Bulk modification was performed by cross-linking cryo-co-polymerisation of HEMA and poly(ethylene glycol)diacrylate (PEGA) in the presence of proteins (CG/pHEMA and Fg/pHEMA MHs). The polymer surface was modified by covalent immobilisation of the proteins to the active epoxy (ep) groups present on pHEMA after hydrogel fabrication (CG-epHEMA and Fg-epHEMA MHs). The concentration of proteins in protein/pHEMA and protein-epHEMA MHs was 80-85 and 130-140 mug/ml hydrogel, respectively. It was demonstrated by immunostaining and confocal laser scanning microscopy that bulk modification resulted in spreading of CG in the polymer matrix and spot-like distribution of Fg. On the contrary, surface modification resulted in spot-like distribution of CG and uniform spreading of Fg, which evenly coated the surface. Proliferation rate of fibroblasts was higher on MHs with even distribution of the ligands, i.e., on Fg-epHEMA and CG/pHEMA. After 30 days of growth, fibroblasts formed several monolayers and deposited extracellular matrix filling the pores of these MHs. The best result in terms of cell proliferation was obtained on Fg-epHEMA. The ligands displayed on surface of these scaffolds were in native conformation, while in bulk-modified CG/pHEMA MHs most of the proteins were buried inside the polymer matrix and were less accessible for interactions with specific antibodies and cells. The method used for MH modification with bioligands strongly affects spatial distribution, density and conformation of the ligand on the scaffold surface, which, in turn, influence cell-surface interactions. The optimal type of modification varies depending on intrinsic properties of proteins and MHs.
Induction of IgG antibodies against GD3 ganglioside in rabbits by an anti-idiotypic monoclonal antibody. (1991)

Anti-idiotypic MAb were raised in syngeneic mice against a mouse MAb recognizing GD3 ganglioside (MAb R24). Two anti-idiotypic MAb, designated BEC2 and BEC3, recognized distinct determinants on MAb R24 that mapped near or within the GD3-binding site. New Zealand white rabbits, which express GD3 on normal tissues, were immunized with either BEC2, BEC3, or control MAb FLOPC-21. All rabbits developed high and equivalent titers of antibodies against mouse immunoglobulins. Immunization with BEC2 and BEC3 induced rabbit antibodies expressing R24 idiotype as demonstrated by their ability to inhibit BEC2 binding to R24. Antibodies (IgG and IgM) reacting with GD3 developed in five of eight rabbits immunized with BEC2 but not in rabbits immunized with BEC3 or with control MAb. Serum antibodies against GD3 did not cross-react with other gangliosides. These results show that MAb BEC2 can mimic GD3 ganglioside and can induce antibodies against GD3 ganglioside despite expression of GD3 on normal rabbit tissue.
Cyclophosphamide given after active specific immunization augments antitumor immunity by modulation of Th1 commitment of CD4+ T cells (1998)

These results suggest that the protective immunity induced by ASI was augmented through the modification of the Th1 and Th2 balance by CPA injection after ASI.
Monte Carlo sampling methods using Markov chains and their applications (1970)

A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and difficulties of assessing the error in Monte Carlo estimates. Examples of the methods, including the generation of random orthogonal matrices and potential applications of the methods to numerical problems arising in statistics, are discussed.
Unsynchronized two-terminal fault location estimation (1996)

A technique for power system fault location estimation which uses data from both ends of a transmission line and which does not require the data to be synchronized is described. The technique fully utilizes the advantages of digital technology and numerical relaying which are available today and can easily be applied for offline analysis. This technique allows for accurate estimation of the fault location irrespective of the fault type, fault resistance, load currents, and source impedances. Use of two-terminal data allows the algorithm to eliminate previous assumptions in fault location estimation, thus increasing the accuracy of the estimate. The described scheme does not require real-time communications, only offline post-fault analysis. The paper also presents fault analysis techniques utilizing the additional communicated information.
Exceptional Behavior over the Whole Adsorption−Storage−Delivery Cycle for NO in Porous Metal Organic Frameworks (2008)

Two porous metal organic frameworks (MOFs), [M2(C8H2O6)(H2O)2] x 8 H2O (M = Co, Ni), perform exceptionally well for the adsorption, storage, and water-triggered delivery of the biologically important gas nitric oxide. Adsorption and powder X-ray diffraction studies indicate that each coordinatively unsaturated metal atom in the structure coordinates to one NO molecule. All of the stored gas is available for delivery even after the material has been stored for several months. The combination of extremely high adsorption capacity (approximately 7 mmol of NO/g of MOF) and good storage stability is ideal for the preparation of NO storage solids. However, most important is that the entire reservoir of stored gas is recoverable on contact with a simple trigger (moisture). The activity of the NO storage materials is proved in myography experiments showing that the NO-releasing MOFs cause relaxation of porcine arterial tissue.
Enhanced Learning Deficits in Female Rats Following Lifetime Pb Exposure Combined with Prenatal Stress (2010)

Pb (lead) exposure and stress are co-occurring risk factors (particularly in low socioeconomic communities) that also act on common biological substrates and produce common adverse outcomes, including cognitive impairments. This study sought to determine whether lifetime Pb exposure combined with prenatal stress would enhance the cognitive deficits independently associated with each of these risk factors and to explore associated mechanisms of any observed impairments. Learning was evaluated using a multiple schedule of repeated learning and performance in female rats subjected to lifetime Pb exposure (0 or 50 ppm Pb in drinking water beginning in dams 2 months prior to breeding; blood Pb levels ∼10 μg/dl), to prenatal restraint stress on gestational days 16 and 17, or to both. Blood Pb, corticosterone levels, brain monoamines, and hippocampal nerve growth factor levels were also measured. Sequence-specific learning deficits produced by Pb, particularly the number of responses to correctly learn response sequences, were further enhanced by stress, whereas performance measures were unimpaired. Statistical analyses indicated significant relationships among corticosterone levels, frontal cortex dopamine (DA), nucleus accumbens dopamine turnover, and total responses required to learn sequences. This study demonstrates that Pb and stress can act together to produce selective and highly condition-dependent deficits in learning in female rats that may be related to glucocorticoid-mediated interactions with mesocorticolimbic regions of brain. These findings also underscore the critical need to evaluate toxicants in the context of other risk factors pertinent to human diseases and disorders.
Parallelization of a wave propagation application using a data parallel compiler (2002)

The paper presents the parallelization process of a wave propagation application using the PANDORE environment. The PANDORE environment has been designed to facilitate the programming of data distributed applications for distributed memory computers or clusters of workstations. The compilation schemes are described and the distribution of the well known Jacobi kernel is detailed. Finally, the different steps of the parallelization of the wave propagation application are described and the results of this experiment are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Unpowered Wireless Corrosion Sensor for Steel Reinforced Concrete (2006)

Prototype sensors have been developed to detect the onset of corrosion in steel reinforced concrete using non-invasive techniques. These sensors are designed to be extremely simple and low cost. The sensors are embedded in the concrete and are powered and interrogated through the use of inductively coupled magnetic fields. New analysis and data processing techniques show that the sensor can provide useful information about the current extent of corrosion.
Osteoblasts isolated from mouse calvaria initiate matrix mineralization in culture. (1983)

A method is presented for isolating osteoblasts from newborn mouse calvaria without the use of digestive enzymes. The procedure is based on the ability of osteoblasts to migrate from bone onto small glass fragments (Jones, S.J., and A. Boyde, 1977, Cell Tissue Res., 184:179-193). The isolated cells were cultured for up to 14 d in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum and 50 micrograms/ml of ascorbic acid. 7-d cultures were incubated for 24 h with [3H]proline. High levels of collagen synthesis relative to total protein were found, as measured by collagenase digestion of medium and cell layer proteins. Analysis of pepsin-digested proteins from the same cultures by SDS PAGE showed that type I collagen was predominantly produced with small amounts of type III and V (alpha 1 chains) collagens. Osteoblasts grown in the presence of beta-glycerophosphate were able to initiate mineral deposition in culture. Electron microscopic analysis of the cultures revealed the presence of needle-shaped apatite-like crystals associated with collagen fibrils and vesicles in the extracellular space. Mouse skin fibroblasts cultured under identical conditions failed to initiate mineralization. Electron histochemical studies revealed the presence of alkaline phosphatase activity, associated with osteoblast membranes, matrix vesicles and on or near collagen fibrils. Thus these isolated osteoblasts retained in culture their unique property of initiating mineralization and therefore represent a model of value for studying the mineralization process in vitro.
XTRACT (2000)

XML is rapidly emerging as the new standard for data representation and exchange on the Web. An XML document can be accompanied by a Document Type Descriptor (DTD) which plays the role of a schema for an XML data collection. DTDs contain valuable information on the structure of documents and thus have a crucial role in the efficient storage of XML data, as well as the effective formulation and optimization of XML queries. In this paper, we propose XTRACT, a novel system for inferring a DTD schema for a database of XML documents. Since the DTD syntax incorporates the full expressive power of regular expressions , naive approaches typically fail to produce concise and intuitive DTDs. Instead, the XTRACT inference algorithms employ a sequence of sophisticated steps that involve: (1) finding patterns in the input sequences and replacing them with regular expressions to generate “general” candidate DTDs, (2) factoring candidate DTDs using adaptations of algorithms from the logic optimization literature, and (3) applying the Minimum Description Length (MDL) principle to find the best DTD among the candidates. The results of our experiments with real-life and synthetic DTDs demonstrate the effectiveness of XTRACT's approach in inferring concise and semantically meaningful DTD schemas for XML databases.