gebhart/patrepeval huggingface dataset:
Camera calibration with precise extraction of feature points using projective transformation (2003)

In this paper, we propose a method for precise camera calibration which conducts feature point extraction and camera parameter estimation iteratively. Many of conventional researches on camera calibration have focused on how to calculate camera parameters using data obtained from input images, that is, location of feature points. However, these input images suffer from distortions caused by perspective and lens imperfections. In our proposed method, at the beginning of the procedure, projective transformation matrices between image planes and a calibration target and lens distortion parameters are approximately estimated. These parameters are used in order to reduce the influence of distortions in input images. After the removal of distortions, feature points in processed images are localized precisely and used to update/calculate the projective transformation matrices, the lens distortion parameters and intrinsic camera parameters. These procedures are iterated until they converge and this iteration results in precise estimation of the parameters. The effectiveness of the proposed method has been recognized through experiments using synthesized data and real images.
A new efficient gene disruption cassette for repeated use in budding yeast (1996)

The dominant kanr marker gene plays an important role in gene disruption experiments in budding yeast, as this marker can be used in a variety of yeast strains lacking the conventional yeast markers. We have developed a loxP-kanMX-loxP gene disruption cassette, which combines the advantages of the heterologous kanr marker with those from the Cre-lox P recombination system. This disruption cassette integrates with high efficiency via homologous integration at the correct genomic locus (routinely 70%). Upon expression of the Cre recombinase the kanMX module is excised by an efficient recombination between the loxP sites, leaving behind a single loxP site at the chromosomal locus. This system allows repeated use of the kanr marker gene and will be of great advantage for the functional analysis of gene families.
Simultaneous Determination of the Size and Surface Charge of Individual Nanoparticles Using a Carbon Nanotube-Based Coulter Counter (2003)

A resistive-pulse Coulter counter based on a membrane containing a single multiwall carbon nanotube (MWNT) channel was used to simultaneously determine the size and surface charge of carboxy-terminated polystyrene nanoparticles. The membrane was prepared from an epoxy section containing a MWNT channel mounted on a poly(dimethylsiloxane) (PDMS) support structure. The PDMS support reduced the background noise level by a factor of > 20 compared to the Si/Si3N4 support structure used in our previous study. The lower noise level makes it possible to accurately measure the height and width of resistive-pulse signals resulting from transport of individual particles through the MWNT channel. Particle sizes, calculated from current pulse heights, were comparable to those determined by transmission electron microscope (TEM). The width of the current pulses is a measure of the nanoparticle transport time, and it permits calculation of the electrokinetic surface charge. Different types of polystyrene nanoparticles having nearly the same size, but different electrokinetic surface charge, could be resolved on the basis of the difference in their transport time.
Long‐Term Survival of Dopamine Neurons Derived from Parthenogenetic Primate Embryonic Stem Cells (Cyno‐1) After Transplantation (2005)

Dopamine (DA) neurons can be derived from human and primate embryonic stem (ES) cells in vitro. An ES cell-based replacement therapy for patients with Parkinson's disease requires that in vitro-generated neurons maintain their phenotype in vivo. Other critical issues relate to their proliferative capacity and risk of tumor formation, and the capability of migration and integration in the adult mammalian brain. Neural induction was achieved by coculture of primate parthenogenetic ES cells (Cyno-1) with stromal cells, followed by sequential exposure to midbrain patterning and differentiation factors to favor DA phenotypic specification. Differentiated ES cells were treated with mitomycin C and transplanted into adult immunosuppressed rodents and into a primate (allograft) with out immunosuppression. A small percentage of DA neurons survived in both rodent and primate hosts for the entire term of the study (4 and 7 months, respectively). Other neuronal and glial populations derived from Cyno-1 ES cells showed, in vivo, phenotypic characteristics and growth and migration patterns similar to fetal primate transplants, and a majority of cells (>80%) expressed the forebrain transcription factor brain factor 1. No teratoma formation was observed. In this study, we demonstrate long-term survival of DA neurons obtained in vitro from primate ES cells. Optimization of differentiation, cell selection, and cell transfer is required for functional studies of ES-derived DA neurons for future therapeutic applications.
4 Gbps high-density AC coupled interconnection (2003)

AC coupled interconnects enable multi-gigabit-persecond communication data rates between integrated circuits with very high pin counts and low power consumption. AC coupling can be realized with either series capacitive or inductive coupling elements. Capacitive AC coupling offers better performance when low power I/O buffers are required and when there is sufficient area to dedicate to coupling capacitors in the top-level metal of each IC. At a slight expense of circuit complexity, inductive AC coupling can be used to bring I/O pad pitches down to 75 /spl mu/m and maintain a controlled impedance connection. A novel physical structure, buried solder bumps, are used as a solution for providing DC power and ground connections across the same surface as the AC connections. When used in conjunction with NRZ-tolerant receivers, and current-mode signaling, highly effective interconnect structures can be built. As well as presenting both physical and circuit aspects of this work, experimental results are shown.
Interleukin 2 gene transfer prevents NKG2D suppression and enhances antitumor efficacy in combination with cisplatin for head and neck squamous cell cancer. (2002)

Cisplatin has been the most promising single chemotherapeutic agent usedagainst head and neck squamous cell cancer to date. However, dose-related toxicity has been one of the major limiting factors in cisplatin-based therapies, because high doses are required for obtaining a significant antitumor effect. To face the challenge of this limiting factor, a novel interleukin 2 (IL-2)-based combination strategy has been developed. Here we show that the strategy of combination of cisplatin with nonviral IL-2 gene therapy resulted in significant antitumor effects while avoiding dose-limiting toxicity in a head and neck squamous cell cancer murine model. Cisplatin systemic therapy alone suppressed NKG2D expression in lymphocytes. The use of local regional IL-2 gene transfer prevented NKG2D suppression. The combination strategy demonstrated a clear synergistic interaction between cisplatin and IL-2, and NKG2D-based cytotoxicity manifested by increased tumor specific lysis from CTLs and natural killer cells. Moreover, the combination of cisplatin and IL-2 gene therapy greatly enhanced apoptosis and growth inhibition in the treated tumors. This novel combination strategy holds promise for the treatment of head and neck cancer, and the mechanism of NKG2D in activating natural killer and CTL receptors provides a foundation for additional investigation, and development of immune modulation and chemotherapy regimens.
Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation. (1992)

Programmed cell death (PCD) plays a key role in developmental biology and in maintenance of the steady state in continuously renewing tissues. Currently, its existence is inferred mainly from gel electrophoresis of a pooled DNA extract as PCD was shown to be associated with DNA fragmentation. Based on this observation, we describe here the development of a method for the in situ visualization of PCD at the single-cell level, while preserving tissue architecture. Conventional histological sections, pretreated with protease, were nick end labeled with biotinylated poly dU, introduced by terminal deoxy-transferase, and then stained using avidin-conjugated peroxidase. The reaction is specific, only nuclei located at positions where PCD is expected are stained. The initial screening includes: small and large intestine, epidermis, lymphoid tissues, ovary, and other organs. A detailed analysis revealed that the process is initiated at the nuclear periphery, it is relatively short (1-3 h from initiation to cell elimination) and that PCD appears in tissues in clusters. The extent of tissue-PCD revealed by this method is considerably greater than apoptosis detected by nuclear morphology, and thus opens the way for a variety of studies.
Evaluation of residual stress gradients in ductile cast iron using critical refracted longitudinal (Lcr) wave technique (1995)

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Development of the Mouse Inner Ear and Origin of Its Sensory Organs (1998)

The molecular mechanisms dictating the morphogenesis and differentiation of the mammalian inner ear are largely unknown. To better elucidate the normal development of this organ, two approaches were taken. First, the membranous labyrinths of mouse inner ears ranging from 10.25 to 17 d postcoitum (dpc) were filled with paint to reveal their gross development. Particular attention was focused on the developing utricle, saccule, and cochlea. Second, we used bone morphogenetic protein 4 (BMP4) and lunatic fringe (Fng) as molecular markers to identify the origin of the sensory structures. Our data showed that BMP4 was an early marker for the superior, lateral, and posterior cristae, whereas Fng served as an early marker for the macula utriculi, macula sacculi, and the sensory portion of the cochlea. The posterior crista was the first organ to appear at 11.5 dpc and was followed by the superior crista, the lateral crista, and the macula utriculi at 12 dpc. The macula sacculi and the cochlea were present at 12 dpc but became distinguishable from each other by 13 dpc. Based on the gene expression patterns, the anterior and lateral cristae may share a common origin. Similarly, three sensory organs, the macula utriculi, macula sacculi, and cochlea, seem to arise from a single region of the otocyst.
Purification of a protein from Bacillus thuringiensis toxic to larvae of lepidoptera (1968)

The protein toxin of the parasporal body or crystal of Bacillus thuringiensis (Mattés isolate) has been purified severalfold by a combination of Sephadex G-200 gel filtration and ammonium sulphate precipitation. It has been shown that the use of highly alkaline conditions for dissolution of the crystals does not lead to serious artifacts. The crystal toxin has been shown to be quantitatively related to the crystal antigen. It is possible that there is a second distinct toxin present in the crystal and this too can be detected by its antigenic reaction. Purified toxic protein has been hydrolysed in vitro by regurgitated Pieris brassicae gut enzymes, chymotrypsin, trypsin and subtilisin. In each case the digest contained a product that was still antigenic, had mol.wt. about 40000 and was toxic to P. brassicae larvae. Smaller toxic molecules (mol.wt. approx. 10000) that did not react as antigens were also produced by proteolysis. It is possible that these smaller molecules were hydrolytic products of the larger digestion product.
Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules (2006)

Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH(3) groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of four molecular conformations in a controlled manner. Statistical analyses and structural calculations reveal that all reversible switching mechanisms are initiated by a single tunneling-electron energy-transfer process, which induces bond rotation within the phytyl-chain.
Patch Clamp Techniques for Studying Ionic Channels in Excitable Membranes (1984)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Human STELLAR , NANOG , and GDF3 Genes Are Expressed in Pluripotent Cells and Map to Chromosome 12p13, a Hotspot for Teratocarcinoma (2004)

Genes required to maintain pluripotency in human embryonic stem (hES) cells are largely unknown, with the exception of OCT-4, a homolog of mouse Oct-4, which is critical for the establishment of the embryonic inner cell mass and the generation of totipotent mouse embryonic stem (mES) cell lines. In the current study, we identified two genes with expression similar to OCT-4, in that they are largely restricted to pluripotent hES cells, premeiotic germ lineage cells, and testicular germ cell tumor cells. Furthermore, we determined that upon hES cell differentiation, their expression is downregulated. The genes we identified in the current study include the human stella-related (STELLAR) gene, which encodes a highly divergent protein (with just 32.1% identity to mouse stella over the 159 amino acid sequence) that maps to human chromosome 12p13. Notably, human STELLAR is located distal to a previously uncharacterized homeobox gene, which is the human homolog of the recently identified murine gene, Nanog, and proximal to the GDF3 locus, whose transcription is restricted to germ cell tumor cells. Our characterization of STELLAR, NANOG, and GDF3 suggests that they may play a similar role in humans as in mice, in spite of their remarkable evolutionary divergence.
Diagnosis of breast cancer using elastic-scattering spectroscopy: preliminary clinical results (2000)

We report on the first stages of a clinical study designed to test elastic-scattering spectroscopy, mediated by fiberoptic probes, for three specific clinical applications in breast-tissue diagnosis: (1) a transdermal-needle (interstitial) measurement for instant diagnosis with minimal invasiveness similar to fine-needle aspiration but with sensitivity to a larger tissue volume, (2) a hand-held diagnostic probe for use in assessing tumor/resection margins during open surgery, and (3) use of the same probe for real-time assessment of the "sentinel" node during surgery to determine the presence or absence of tumor (metastatic). Preliminary results from in vivo measurements on 31 women are encouraging. Optical spectra were measured on 72 histology sites in breast tissue, and 54 histology sites in sentinel nodes. Two different artificial intelligence methods of spectral classification were studied. Artificial neural networks yielded sensitivities of 69% and 58%, and specificities of 85% and 93%, for breast tissue and sentinel nodes, respectively. Hierarchical cluster analysis yielded sensitivities of 67% and 91%, and specificities of 79% and 77%, for breast tissue and sentinel nodes, respectively. These values are expected to improve as the data sets continue to grow and more sophisticated data preprocessing is employed. The study will enroll up to 400 patients over the next two years.
MRI correlates of neurofibrillary tangle pathology at autopsy (2008)

Patterns of gray matter loss are associated with neurofibrillary tangle (NFT) pathology, specifically with NFT burden at Braak stages III and IV and with Braak stage itself at higher stages. This validates three-dimensional patterns of atrophy on MRI as an approximate in vivo surrogate indicator of the full brain topographic representation of the neurodegenerative aspect of Alzheimer disease pathology.
In vivo phosphorylation sites in fetal and adult rat tau. (1993)

Fetal tau and tau in paired helical filaments show similar immunoreactivities with several phosphorylation-dependent paired helical filament-polyclonals and monoclonals, suggesting that the two molecules share several distinct phosphorylated epitopes. To make clear the similarities and differences between the two, we have undertaken work to identify the in vivo phosphorylation sites in fetal rat tau. We have approached this problem by identifying phosphopeptides by means of mass spectrometry and sequencing of those phosphopeptides after modification with ethanethiol. Although remarkable heterogeneity was present, fetal tau was found to bear at most 10 phosphates at Ser-189, Ser-190, Ser-193, Ser-226, Ser-387, Ser-395, Thr-172, Thr-222, and, presumably, Ser-391 and Thr-208 (numbering is according to the longest form of rat tau; Kosik, K. S., Orecchio, L. D., Bakalis, S., and Neve, R. L. (1989) Neuron 2, 1389-1397). In contrast, adult rat tau was much less phosphorylated; only Thr-172, Ser-190, Ser-193, Thr-222, and Ser-395 were phosphorylated to a slight-to-moderate extent. All these sites except for Ser-189 and Ser-391 were followed by Pro residues. Thus, tau is an in vivo substrate for proline-directed protein kinase(s), and its phosphorylation state is developmentally regulated.
Ordered Multistep Synthesis in a Single Solution Directed by DNA Templates (2005)

A triolefin and a tripeptide were prepared in a single solution (see scheme) by ordered multistep synthesis. Temperature-sensitive variations in DNA secondary structure were used to orchestrate a series of effective molarity changes among four reactants of comparable intrinsic reactivity, resulting predominantly in one ordered product out of many possibilities. This approach mimics the selective control of effective molarity at precise moments during biosynthesis.
The Pharmacotherapy of Chronic Pain: A Review (2006)

The past two decades have contributed a large body of preclinical work that has assisted in our understanding of the underlying pathophysiological mechanisms that cause chronic pain. In this context, it has been recognized that effective treatment of pain is a priority and that treatment often involves the use of one or a combination of agents with analgesic action. The current review presents an evidence-based approach to the pharmacotherapy of chronic pain. Medline searches were done for all agents used as conventional treatment in chronic pain. Published papers up to June 2005 were included. The search strategy included randomized, controlled trials, and where available, systematic reviews and meta-analyses. Further references were found in reference sections of papers located using the above search strategy. Agents for which there were no controlled trials supporting efficacy in treatment of chronic pain were not included in the present review, except in cases where preclinical science was compelling, or where initial human work has been positive and where it was thought the reader would be interested in the scientific evidence to date.
Double‐stranded RNA induces iNOS gene expression in Schwann cells, sensory neuronal death, and peripheral nerve demyelination (2007)

Inflammation in the peripheral nervous system (PNS) is one of the characteristics of virus-induced peripheral neuropathy. In this inflammatory response, Schwann cells are actively involved. Previously, toll-like receptor 3 (TLR3) was reported as a receptor for double-stranded RNA (dsRNA) that induces antiviral and inflammatory responses in cells of the innate immune system. In this study, we investigated the expression and putative role of TLR3 in Schwann cells. TLR3 was constitutively expressed in Schwann cells. Stimulation with polyinosinic-polycytidylic acid, a synthetic dsRNA analogue, induced the expression of inducible nitric oxide synthase (iNOS) gene in Schwann cells. Studies on the intracellular signal transduction pathways using iSC, an immortalized Schwann cell line, revealed that dsRNA induces the activation of NF-kappaB, p38, and c-Jun N-terminal kinase (JNK). The activation of NF-kappaB, p38, JNK, and dsRNA-dependent protein kinase is required for dsRNA-mediated iNOS gene expression. However, the activation of PI3 kinase and GSK-3beta inhibited iNOS gene induction, a process mediated by their inhibitory effects on NF-kappaB and p38 activation. dsRNA-induced NO production caused neuronal cell death in cultured dorsal root ganglion. Finally, the introduction of dsRNA into the rat sciatic nerve induced iNOS gene expression and peripheral nerve demyelination in vivo. Taken together, these data suggest that viral RNA may induce inflammatory Schwann cell activation via TLR3 and peripheral nerve damage in the PNS.
Vitamin C depletion and pressure sores in elderly patients with femoral neck fracture. (1992)

Low concentrations of leucocyte vitamin C appear to be associated with subsequent development of pressure sores in elderly patients with femoral neck fractures.
Apomorphine nodules in Parkinson’s disease: best practice considerations (2008)

Apomorphine hydrochloride infusion therapy is used by approximately 1000 people with advanced Parkinson's disease in the UK (Britannia Pharmaceuticals Ltd, 2008). Subcutaneous nodules that develop as a result of these infusions can cause discomfort and may impact on the effectiveness of the drug therapy. Community nursing teams have a key role in supporting patients on apomorphine; they may be responsible for administering the drug, or supporting and empowering the patient or their carer to administer the infusion. A recent randomized controlled pilot study by a research group at the University of Hertfordshire investigated the use of therapeutic ultrasound for the treatment of apomorphine nodules. A number of observations about apomorphine nodules and the technique used to site infusions were made which may help to promote safe and effective management of apomorphine therapy. This article is a collaboration between one of the researchers and a Parkinson's disease nurse specialist from the University College of London Hospitals NHS Foundation Trust. It draws on best practice observations from both research and clinical experience and puts them in context of published research. It summarizes best practice considerations for administering infusions, identifies the current treatment and management options that participants from the trial reported using on their nodules, emphasizes the need for standardized documentation and suggests a rating system that may be useful to document nodule severity.