gebhart/patrepeval huggingface dataset:
An energy-efficient, dynamic voltage scaling neural stimulator for a proprioceptive prosthesis (2012)

This paper presents an energy-efficient neural stimulator capable of providing charge-balanced asymmetric pulses. Power consumption is reduced by implementing a fully-integrated DC-DC converter that uses a reconfigurable switched capacitor topology to provide 4 output voltages for Dynamic Voltage Scaling (DVS). DC conversion efficiencies of between 63% and 76% are achieved using integrated capacitances of under 1nF and the DVS approach offers power savings of up to 53.5% compared to the front end of a typical current controlled neural stimulator. A novel charge balancing method is used which has a low level of accuracy on a single pulse and a much higher accuracy over a series of pulses. The method used is robust to process and component variation and does not require any initial or ongoing calibration. Monte-Carlo simulations indicate that the charge imbalance can be less than 0.014% (at ±3σ) of charge delivered for a series of pulses. The circuit has been designed in a commercially-available 0.18µm HV CMOS technology and is estimated to require a die area of approximately 0.9mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for a 16 channel implementation.
Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008 (2008)

Outbreaks of Clostridium difficile infections (CDI) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America and Europe. This emerging strain is referred to as PCR ribotype 027 (Type 027). Since 2005, individual countries have developed surveillance studies about the spread of type 027.C. difficile Type 027 has been reported in 16 European countries. It has been responsible for outbreaks in Belgium, Germany, Finland, France, Ireland, Luxembourg, The Netherlands, Switzerland and the United Kingdom (England, Wales, Northern Ireland and Scotland). It has also been detected in Austria, Denmark, Sweden, Norway, Hungary, Poland and Spain. Three countries experienced imported patients with CDI due to Type 027 who acquired the infection abroad.The antimicrobial resistance pattern is changing, and outbreaks due to clindamycin-resistant ermB positive Type 027 strains have occurred in three European countries. Ongoing epidemiological surveillance of cases of CDI, with periodic characterisation of the strains involved, is required to detect clustering of cases in time and space and to monitor the emergence of new, highly virulent clones.
Ultraviolet Radiation and the Development of Non-Melanoma and Melanoma Skin Cancer: Clinical and Experimental Evidence (1991)

Clinical and experimental evidence explaining and supporting the role of UV radiation as a causal factor for the induction and promotion of nonmelanoma and malignant melanoma skin cancer are presented. While there is excellent animal experimental data and human epidemiologic evidence supporting the causal relationship of UVR (UVB, as well as UVA radiation) for basal and squamous cell carcinomas, the data establishing a direct causal relationship between melanoma and exposure to sunlight appear to be complex. They do, however, suggest a definite promotional role of sunlight in the causation of melanoma. Using a hairless pigmented mouse strain (Skh-hr2), experiments were initiated to examine the role of UVR in the induction of melanoma. A single application of DMBA as an initiator and subsequent thrice-weekly exposures to either UVB (290-320 nm) or UVA (320-400 nm) or the combined exposures of UVA and UVB resulted in the formation of blue nevus-like lesions. Repeated UVR exposures for over 30 weeks resulted in the development of melanoma (38%), as well as lymphoma and squamous cell carcinoma only in those mice that were pretreated with DMBA and had developed nevi. Mice receiving UVB, UVA, or the combination treatments of UVB plus UVA without DMBA pretreatment developed papillomas and squamous cell carcinoma but no melanoma. These studies indicate that some initiation event is essential to transform melanocytes to blue nevus-like lesions before UVR (UVB + UVA) can act as a promoter and accelerate the development of malignant melanoma, as as well as lymphoma.
Inverses of Linear Sequential Circuits (1968)

Abstract—This paper states the necessary and sufficient conditions for the existence of a feedforward inverse for a feedforward linear sequential circuit and gives an implicit procedure for constructing such inverses. It then goes on to give the necessary and sufficient conditions for the existence of general inverses with finite delay and gives procedures for constructing a class of such inverses. The discussion considers both the transfer function matrix description and the structural matrix description of the linear sequential circuit, together with the complementary nature of the results obtained from these two viewpoints. Finally, a large part of the work is motivated by results and techniques which have been applied in the study of continuous-time linear dynamical systems and thus serves to point out the advantages which may accrue through simultaneous study of both continuous-time systems and linear sequential circuits.
Structural Control of Mesoporous Silica Nanoparticles in a Binary Surfactant System (2005)

The grain size and regularity of the hexagonal array of mesoporous silica nanoparticles were investigated in a binary surfactant system composed of cetyltrimethylammonium chloride and triblock copolymer EO106PO60EO106. Structural control was achieved by varying the parameters for the prior hydrolysis of silicon alkoxide under an acidic condition and the subsequent assembly of silicates and surfactants under a basic condition. The formation of the mesoscale architectures was based on the balance between the ordered assembly of anionic silicates and the cationic surfactant through electrostatic interaction and the inhibition of grain growth with a nonionic amphiphilic agent through hydrogen bonds.
Detection of depth and orientation discontinuities in range images using mathematical morphology (2002)

A technique for the detection of depth and orientation discontinuities in range images is described. This method uses basic morphological operators to extract these discontinuities from a dense range map. The authors describe how to extract depth discontinuities using the morphological edge operator of J.S.J. Lee et al. (1987) and how to use a top-hat operator to localize the exact positions of these discontinuities. The detection of orientation discontinuities is then discussed in detail. The calculation of a good estimate of the surface normals using anisotropic filtering inhibited at depth discontinuities is demonstrated. Once these estimates of the normals are calculated, operations similar to those used in depth discontinuity detection are used to locate orientation discontinuities at abrupt variations of the surface normals. Experimental results demonstrate computation of the positions of these discontinuities at pixel precision as well as very efficient use of morphological operators to localize abrupt variations in a noisy image signal in less than 1 s using a Datacube image processor.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prokaryotic Gene Expression (1999)

Abstract Prokaryotic gene expression is not only of theoretical interest but also of highly practical significance. It has impl]ications for other biological problems, such as developmental biology and cancer, brings insights into genetic engineering and expression systems, and has consequences for important aspects of applied research. For example, the molecular basis of bacterial pathogenicity has implications for new antibiotics and in crop development. Prokaryotic Gene Expression is a major review of the subject, providing up-to-date coverage as well as numerous insights by the prestigious authors. Topics covered include operons; protein recognition of sequence specific DNA- and RNA-binding sites; promoters; sigma factors, and variant tRNA polymerases; repressors and activators; post-transcriptional control and attenuation; ribonuclease activity, mRNA stability, and translational repression; prokaryotic DNA topology, topoisomerases, and gene expression; regulatory networks, regulatory cascades and signal transduction; phosphotransfer reactions; switch systems, transcriptional and translational modulation, methylatiaon, and recombination mechanisms; pathogenicity, toxin regulation and virulence determinants; sporulation and genetic regulation of antibiotic production; origins of regulatory molecules, selective pressures and evolution of prokaryotic regulatory mechanisms systems. Over 1100 references to the primary literature are cited. Prokaryotic Gene Expression is a comprehensive and authoritative review of current knowledge and research in the area. It is essential reading for postgraduates and researchers in the field. Advanced undergraduates in biochemistry, molecular biology, and microbiology will also find this book useful.
Dissecting Wnt/β-catenin signaling during gastrulation using RNA interference in mouse embryos (2005)

Differential gene regulation integrated in time and space drives developmental programs during embryogenesis. To understand how the program of gastrulation is regulated by Wnt/beta-catenin signaling, we have used genome-wide expression profiling of conditional beta-catenin mutant embryos. Known Wnt/beta-catenin target genes, known components of other signaling pathways, as well as a number of uncharacterized genes were downregulated in these mutants. To further narrow down the set of differentially expressed genes, we used whole-mount in situ screening to associate gene expression with putative domains of Wnt activity. Several potential novel target genes were identified by this means and two, Grsf1 and Fragilis2, were functionally analyzed by RNA interference (RNAi) in completely embryonic stem (ES) cell-derived embryos. We show that the gene encoding the RNA-binding factor Grsf1 is important for axial elongation, mid/hindbrain development and axial mesoderm specification, and that Fragilis2, encoding a transmembrane protein, regulates epithelialization of the somites and paraxial mesoderm formation. Intriguingly, the knock-down phenotypes recapitulate several aspects of Wnt pathway mutants, suggesting that these genes are components of the downstream Wnt response. This functional genomic approach allows the rapid identification of functionally important components of embryonic development from large datasets of putative targets.
Positive Selection of FLP-Mediated Unequal Sister Chromatid Exchange Products in Mammalian Cells (1997)

Site-specific recombination provides a powerful tool for studying gene function at predetermined chromosomal sites. Here we describe the use of a blasticidin resistance system to select for recombination in mammalian cells using the yeast enzyme FLP. The vector is designed so that site-specific recombination reconstructs the antibiotic resistance marker within the sequences flanked by the FLP target sites. This approach allows the detection of DNA excised by FLP-mediated recombination and facilitates the recovery of recombination products that would not be detected by available screening strategies. We used this system to show that the molecules excised by intrachromosomal recombination between tandem FLP recombinase target sites do not reintegrate into the host genome at detectable frequencies. We further applied the direct selection approach to recover a rare FLP-mediated recombination event displaying the characteristics of an unequal sister chromatid exchange between FLP target sites. Implications of this approach for the generation of duplications to assess their effect on gene dosage and chromosome stability are discussed.
Electro-optically tunable wavelength selective polarisation convertor in Zn:LiTaO 3 (1992)

Wavelength dependent TE↔TM convesion with 98% efficiency has been obtained using a periodic, strain inducing SiO2 film on an LiTaO3 waveguide. Electro-optic tuning of the peak wavelength from 616 to 680 nm was demonstrated.
Serial Affinity Chromatography as a Selection Tool in Glycoproteomics (2013)

Glycan-targeting affinity chromatography systems are becoming increasingly important as tools in the purification, enrichment, and identification of glycoproteins. The great advantage of this strategy is that immobilized lectin and antibody selectors allow specific glycan structures to be matched with a particular protein. It is also possible to show that a glycan seen at one site in a glycoprotein may not be present at another glycosylation site in the same glycoprotein. A problem with single-column affinity chromatography is how to obtain information on glycan diversity within the oligosaccharide portions of captured glycoproteins. Although all the glycoprotein species bearing a particular glycan feature will be captured by an affinity column, there is no way of knowing whether the ligand being targeted appears alone or coresides with a series of other glycan features in the same oligosaccharide conjugate. The work being described here examines the utility of serial affinity columns in determining whether individual glycan structures appear alone or together with other glycans in specific proteins. Four different types of affinity columns were examined in two series; the LEL → HPA → anti-Le(x)Ab → anti-sLe(x)Ab series and the anti-sLe(x)Ab → anti-Le(x)Ab → HPA → LEL series. Patterns in protein capture from these two series were very different. Thus, serial affinity chromatography (SAC) can be a valuable tool in recognizing diversity in protein glycosylation, especially when the order of columns in the SAC series is varied. Two clear types of diversity were recognized. One is the independent occurrence of different affinity-targetable glycan features in the same glycoprotein. The other is that multiple targetable glycan features were coresident in the same glycoprotein. The great advantage of this method is that it couples easily with current methods used in glycoproteomics.
Chromosome III of Saccharomyces cerevisiae: An ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes (1990)

Using lambda phage vector EMBL4, we isolated 344 clones containing segments of chromosome III of Saccharomyces cerevisiae, analysed their physical structure with eight restriction enzymes and sorted the data in contiguous groups with computer programmes. Furthermore, we performed Southern hybridizations between the sorted contiguous clone groups and interrelated them into larger groups. In this way, we constructed an ordered clone bank that covers almost the whole of chromosome III with a single gap of several kilobases in length. The consensus physical map thus obtained totals 334.6 kb, which is in good agreement with the size of this chromosome estimated by pulsed-field gel electrophoresis. Southern hybridization analysis with the DNA probes containing telomere-specific sequences showed that the bank contained a telomere at a position corresponding to the right arm terminus of chromosome III. Also, five Ty elements were found to be present. To estimate the number of genes on this chromosome and to analyse their levels of expression, we performed a series of Northern hybridization experiments using total poly(A)+ RNA from vegetatively growing cells and appropriate restriction enzyme fragments from the bank. Thus, we identified a total of 156 transcripts on chromosome III, indicating, on an average, one gene in every 2 kb on this chromosome. The transcripts were visually categorized into five groups according to their apparent levels of expression. It was found that the genes located near both termini are expressed only at low levels and that highly expressed genes are rather scattered over the chromosome.
Monoclonal antibodies against the CD44 [In(Lu)-related p80], and Pgp-1 antigens in man recognize the Hermes class of lymphocyte homing receptors. (1989)

An 85- to 95 kDa class of lymphocyte surface molecules, defined in man by antibodies of the Hermes series, is involved in lymphocyte binding to high endothelial venules and is likely of central importance in the process of lymphocyte homing. In this report, we have examined the relationship between these Hermes-defined "homing-receptors" and two other 80 to 95 kDa lymphocyte surface molecules that have been extensively studied--CD44 [In(Lu)-related p80] defined by mAb A1G3 and A3D8, and Pgp-1 defined by antibody IM7. Our findings indicate that, in man, similar or identical glycoprotein(s) are recognized by these independently and diversely obtained antibodies. All antibodies showed identical immunohistologic patterns of reactivity on a variety of lymphoid and nonlymphoid human tissues, and demonstrated similar bands on Western blots of both crude tonsil lymphocyte lysates and highly purified Hermes-1 Ag preparations. Similarly, purified CD44/p80 Ag from RBC and human serum bound Hermes-1. Preclearing of tonsil lysates with the Hermes-1 antibody removed antigenic activity for all antibodies. Cross-blocking experiments demonstrated that A3D8, IM7 (anti-Pgp-1), and Hermes-2 antibodies recognize overlapping epitopes. Finally, expression of the epitopes defined by the Hermes-1, Hermes-3, H2-7, and H3-61 antibodies on RBC was shown to be regulated by the In(Lu) gene. These findings unify several different lines of investigation, and suggest the possibility that the CD44/Pgp-1/Hermes class of molecules may serve as cell-cell or cell-substrate adhesion/recognition elements for both hematolymphoid and non-hematolymphoid cell types.
Low Resistivity FIB Depositions Within High Aspect Ratio Holes (1996)

Abstract The latest IC modification requirement is to decrease the resistivity of Focused Ion Beam (FIB) deposits, especially deposits within a FIB machined hole. The resistivity of platinum conductor deposited by FIB within a hole is much greater (5000-50000 μΩ-cm) than that deposited on a surface (~200 μΩ-cm) (1). Auger analysis of surface deposited platinum conductor gives the composition ratios as ~ 50% platinum, ~34% carbon, ~15% gallium and ~1 % Oxygen. The escape solid angle of the organic carrier is much less from a hole than from a surface; therefore, we find more of the non-conductive organic material is trapped inside the hole which increases the fill resistivity. With its planarization and multiple metal levels, advanced IC process technology forces contact to lower level metal to be through high aspect ratio holes. To make a low resistance contact through such a hole, deposited material must have a high ratio of platinum to carbon and Oxygen. An improved technique is needed to remove the organic carrier molecules and deposit material containing this higher platinum percentage. The way to achieve such deposition is to adjust gas arrival rate and beam current to produce a deposition rate that allows sufficient time for the organic carrier molecules to escape. Using this method, we can to obtain fill resistivity of about 1000-2500 μΩ-cm within high aspect ratio holes. This paper discusses in detail the technique to achieve such low resistivity in high aspect ratio holes. On the surface where space is not so limited, a greater deposition rate yields shorter times to resistance as well as better step coverage, but within a hole a lower resistivity material is needed to result in good conductance to lower level metal.
Circumvention of outer surface protein A immunity by host-adapted Borrelia burgdorferi (1995)

Outer surface protein A (OspA), which is abundantly expressed in cultured Borrelia burgdorferi, appears to be down-regulated or masked following low-dose infection, and OspA immunization did not prevent infection, dissemination, or disease development with host-adapted spirochetes. Seroconversion of mice to B. burgdorferi OspA depended on dose and viability of inoculated spirochetes. Mice inoculated with > 10(4) live spirochetes and > 10(7) heat-killed spirochetes seroconverted to OspA, but mice inoculated with fewer spirochetes did not seroconvert to OspA at 2 weeks after inoculation. Growth temperature of spirochetes was not a factor for infectious dose or seroconversion to OspA. Spirochetes grown at 30, 34, or 38 degrees C had the same median infectious dose. Growth temperature did not influence infectious dose when mice were inoculated intraperitoneally or intradermally and did not influence dose-related immunologic recognition of OspA. Mice hyperimmunized with recombinant OspA-glutathione S-transferase (GT) fusion protein or GT (controls) were challenged by syringe inoculation with 10(3) spirochetes or by transplantation of infected skin from syngenic mice infected for 2 or 8 weeks. OspA-GT-immunized mice resisted syringe challenge but developed disseminated infections following transplantation of infected skin. Identical results were obtained in mice passively immunized with hyperimmune serum to OspA-GT or GT and then challenged by syringe or infected skin transplant. The number of spirochetes in infected skin, determined by quantitative PCR directed toward both plasmid and genomic targets, was less than the syringe challenge dose.
The Effects of the Nude (nu/nu) Mutation on Bleomycin-induced Pulmonary Fibrosis (1983)

Previous reports have suggested that the immune system is involved in the lung fibrogenic response to certain agents or treatments. In the present study, we have evaluated the impact of the athymic (nude) mutation on the development of pulmonary fibrosis in mice induced by a single intratracheal instillation of bleomycin (0.75 units/animal). Histologic examination revealed that cellular infiltration, fibroblast proliferation, and connective tissue accumulation were diminished in the nude mice when compared with euthymic (het) control mice. In contrast to control animals treated with saline, total lung hydroxyproline in the nude mouse was not significantly increased at 14 and 30 days after bleomycin treatment. Net collagen synthesis, as assessed by measuring the rate of incorporation of tritiated proline in an organ culture system, was increased above control values in both nude and euthymic mice at 14 days after bleomycin treatment, although these values returned to normal at 30 days. However, lung collagen synthetic rates, normalized to dry lung weights, were significantly higher at 14 days in euthymic bleomycin-treated control mice than in the nude bleomycin-treated animals. The data indicate that the nude athymic mutation protects, at least partially, against bleomycin-induced pulmonary fibrosis, thus suggesting a role for the cellular immune system in regulating the fibrogenic response to this drug.