gebhart/patrepeval huggingface dataset:
Profiling and imaging of tissues by imaging ion mobility‐mass spectrometry (2007)

Molecular profiling and imaging mass spectrometry (IMS) of tissues can often result in complex spectra that are difficult to interpret without additional information about specific signals. This report describes increasing data dimensionality in IMS by combining two-dimensional separations at each spatial location on the basis of imaging ion mobility-mass spectrometry (IM-MS). Analyte ions are separated on the basis of both ion-neutral collision cross section and m/z, which provides rapid separation of isobaric, but structurally distinct ions. The advantages of imaging using ion mobility prior to MS analysis are demonstrated for profiling of human glioma and selective lipid imaging from rat brain.
Isolation and Characterization of Probiotic Bacillus Subtilis SK09 from Dairy Effluent (2010)

Health promoting microorganisms such as probiotics are recently been used as food additive and therapeutic supplement especially as enhancer of prophylaxis and digestion. Here we report the isolation and characterization of a probiotic bacillus species, with the ability to ferment lactose, from dairy effluent. Biochemical test and 16S rRNA sequencing were done in order to establish the species and strain details. The species was found to be Bacillus subtilis SK09 with a unique ability to ferment lactose. The strain was also subjected to commonly available antibiotics for its antibiotic susceptibility for its probiotic credibility.
<title>Optical heads based on coupled-cavity laser diode</title> (1995)

Optical heads wherein a laser diode (LD) is optically coupled through a small aperture to a recording medium acting as an external mirror are described. A flying head and a fiber- coupled head are presented, and their high-sensitivity, wavelength-free detection characteristics are demonstrated. A micro-lens head is also investigated. Interference undulations of the coupled-cavity laser with various spatial frequencies due to variations in the external-cavity length are completely explained. Anti-reflection (AR) coatings on the LD facet with reflectivities of better than -40 dB greatly suppress these undulations. To achieve practical heads, fundamental fabrication techniques including AR coating and monolithic integration on laser wafers are briefly mentioned.
Aspects of fibromyalgia in the general population: sex, pain threshold, and fibromyalgia symptoms. (1995)

Symptoms of FM are correlated with pain threshold in the general population, but tender point counts correlate better than dolorimetry. These 2 measures of pain threshold assay different but overlapping factors. Pain threshold is lower in women; and women have more FM symptoms. Decreased pain threshold correlates with all of the symptoms of FM, even in those who do not meet criteria for the syndrome. This suggests that decreased pain threshold, as measured by the tender point counts, is an intrinsically important aspect of patient distress, regardless of the extent and kind of concomitant disease; and that much can be learned about patients by employing this examination.
Fiber optic sensors in concrete structures: a review (1996)

Fiber optic sensors (FOSs) are ideally suited for monitoring strain in concrete structures due to their small size, low cost, ability to be embedded internally, and multiplexing capabilities. Several types of fiber optic strain sensor have been developed, including those based on intensity, polarization, interferometry, and fiber Bragg gratings (FBGs). The FBGs have the advantage of being absolute, linear in response, interrupt immune, and most readily multiplexed. The ability of embedded and surface mounted FOSs to detect strain in reinforced concrete has been demonstrated in several laboratory tests. Comparisons between various FOSs and traditional foil strain gages show good agreement. Sensors have been surface mounted on existing bridges to evaluate observed cracking and to monitor vibration due to traffic loading. FOSs have also been embedded in several newly constructed civil structures, including bridges, buildings, and dams, yielding information about static and dynamic strain, temperature, wind or water pressure, and structural health. Practical and logistical challenges to routine implementation of FOSs in civil structures are being addressed with each additional application.
Identification and Characterization of Staphylococcal Enterotoxin Types G and I from Staphylococcus aureus (1998)

Staphylococcal enterotoxins are exotoxins produced by Staphylococcus aureus that possess emetic and superantigenic properties. Prior to this research there were six characterized enterotoxins, staphylococcal enterotoxin types A to E and H (referred to as SEA to SEE and SEH). Two new staphylococcal enterotoxin genes have been identified and designated seg and sei (staphylococcal enterotoxin types G and I, respectively). seg and sei consist of 777 and 729 nucleotides, respectively, encoding precursor proteins of 258 (SEG) and 242 (SEI) deduced amino acids. SEG and SEI have typical bacterial signal sequences that are cleaved to form toxins with 233 (SEG) and 218 (SEI, predicted) amino acids, corresponding to mature proteins of 27,043 Da (SEG) and 24,928 Da (SEI). Biological activities for SEG and SEI were determined with recombinant S. aureus strains. SEG and SEI elicited emetic responses in rhesus monkeys upon nasogastric administration and stimulated murine T-cell proliferation with the concomitant production of interleukin 2 (IL-2) and gamma interferon (IFN-gamma), as measured by cytokine enzyme-linked immunoassays. SEG and SEI are related to other enterotoxins of S. aureus and to streptococcal pyrogenic exotoxin A (SpeA) and streptococcal superantigen (SSA) of Streptococcus pyogenes. Phylogenetic analysis and comparisons of amino acid and nucleotide sequence identities were performed on related staphylococcal and streptococcal protein toxins to group SEG and SEI among the characterized toxins. SEG is most similar to SpeA, SEB, SEC, and SSA (38 to 42% amino acid identity), while SEI is most similar to SEA, SEE, and SED (26 to 28% amino acid identity). Polyclonal antiserum was generated against purified histidine-tagged SEG and SEI (HisSEG and HisSEI). Immunoblot analysis of the enterotoxins, toxic-shock syndrome toxin 1, and SpeA with antiserum prepared against HisSEG and HisSEI revealed that SEG shares some epitopes with SEC1 while SEI does not.
Transient JMJD2B-Mediated Reduction of H3K9me3 Levels Improves Reprogramming of Embryonic Stem Cells into Cloned Embryos (2012)

Correct reprogramming of epigenetic marks in the donor nuclei is crucial for successful cloning by nuclear transfer. Specific epigenetic modifications, such as repressive histone lysine methylation marks, are known to be very stable and difficult to reprogram. The discovery of histone lysine demethylases has opened up opportunities to study the effects of removing repressive histone lysine methylation marks in donor cells prior to nuclear transfer. In this study, we generated mouse embryonic stem (ES) cells for the inducible expression of JMJD2B (also known as KDM4B), a demethylase that primarily removes the histone-3 lysine-9 trimethylation (H3K9me3) mark. Induction of jmjd2b in the ES cells decreased total levels of H3K9me3 by 63%. When these cells were used for nuclear transfer, H3K9me3 levels were normalized within minutes following fusion with an enucleated oocyte. This transient reduction of H3K9me3 levels improved in vitro development into cloned embryos by 30%.
Variable Stability of a Selectable Provirus after Retroviral Vector Gene Transfer into Human Cells (1986)

Human lymphoblasts deficient in the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) were infected with an amphotropic helper-free retroviral vector expressing human HPRT cDNA. The stability and expression of the HPRT provirus in five cell lines with different proviral integration sites were examined by determining HPRT mutation and reversion frequencies and by blot hybridization studies. Mutation to the HPRT-negative phenotype occurred at frequencies of approximately 4 X 10(-5) to 3 X 10(-6) per generation. Most mutations in each of the five cell lines were associated with partial or complete deletions or rearrangements of the provirus. Several mutants retained a grossly intact HPRT provirus, and in one such mutant HPRT shutdown resulted from a revertible epigenetic mechanism that was not associated with global changes in proviral methylation. Therefore, mutation and shutdown of the HPRT provirus in human lymphoblasts result from mechanisms similar to those reported for several other avian and mammalian replication-competent retroviruses.
Multiple-Activity Human Body Tracking in Unconstrained Environments (2010)

International audience
Mutational analysis of domain I of Pseudomonas exotoxin. Mutations in domain I of Pseudomonas exotoxin which reduce cell binding and animal toxicity. (1988)

Pseudomonas exotoxin (PE) is a single polypeptide chain that contains 613 amino acids and is arranged into three structural domains. Domain I is responsible for cell recognition, II for translocation of PE across membranes and III for ADP ribosylation of elongation factor 2. Treatment of PE with reagents that react with lysine residues has been shown to lead to a reduction in cytotoxic activity apparently due to a modification of domain I (Pirker, R., FitzGerald, D. J. P., Hamilton, T. C., Ozols, R. F., Willingham, M. C., and Pastan, S. (1985) Cancer Res. 45, 751-757). To determine which lysine residues are important in cell recognition, all 12 lysines in domain I were converted to glutamates by site-directed mutagenesis. Also, two deletion mutants encompassing almost all of domain I (amino acids 4-252) or most of domain I (amino acids 4-224) were studied. The mutant proteins were produced in Escherichia coli, purified, and tested for their cytotoxic activity against Swiss 3T3 cells and in mice. The data indicate that conversion of lysine 57 to glutamate reduces cytotoxic activity towards 3T3 cells 50-100-fold and in mice about 5-fold. Deletion of amino acids 4-224 causes a similar reduction in toxicity towards cells and mice. Deletion of most of the rest of domain I (amino acids 4-252) causes a further reduction in toxicity toward cells and mice indicating this second region between amino acids 225 and 252 of domain I is also important in the toxicity of PE. Competition assays indicated that the ability of PEGlu57 to bind to 3T3 cells was greatly diminished, accounting for its diminished cytotoxic activity.
Use of retroviral-mediated gene transfer to deliver and test function of chimeric antigen receptors in human T-cells (2014)

Chimeric antigen receptors (CARs) are genetically delivered fusion molecules that elicit T-cell activation upon binding of a native cell surface molecule. These molecules can be used to generate a large number of memory and effector T-cells that are capable of recognizing and attacking tumor cells. Most commonly, stable CAR expression is achieved in T-cells using retroviral vectors. In the method described here, retroviral vectors are packaged in a two-step procedure. First, H29D human retroviral packaging cells (a derivative of 293 cells) are transfected with the vector of interest, which is packaged transiently in vesicular stomatitis virus (VSV) G pseudotyped particles. These particles are used to deliver the vector to PG13 cells, which achieve stable packaging of gibbon ape leukaemia virus (GALV)-pseudotyped particles that are suitable for infection of human T-cells. The key advantage of the method reported here is that it robustly generates polyclonal PG13 cells that are 100% positive for the vector of interest. This means that efficient gene transfer may be repeatedly achieved without the need to clone individual PG13 cells for experimental pre-clinical testing. To achieve T-cell transduction, cells must first be activated using a non-specific mitogen. Phytohemagglutinin (PHA) provides an economic and robust stimulus to achieve this. After 48-72 h, activated T-cells and virus-conditioned medium are mixed in RetroNectin-coated plasticware, which enhances transduction efficiency. Transduced cells are analyzed for gene transfer efficiency by flow cytometry 48 h following transduction and may then be tested in several assays to evaluate CAR function, including target-dependent cytotoxicity, cytokine production and proliferation.
Mutation of Ki-ras and N-ras oncogenes in myelodysplastic syndromes (1988)

Abstract Somatic mutation of the N-ras oncogene occurs frequently in de novo acute myeloid leukemia (AML). By virtue of their relation to AML, myelodysplastic syndromes (MDS) provide an in vivo model of human leukemogenesis. By using a strategy for analysis of gene mutation based on in vitro amplification of target sequences by the polymerase chain reaction (PCR) and selective oligonucleotide hybridization we analyzed the mutational status of codons 12, 13, and 61 of Ha-ras, K-ras, and N- ras in peripheral blood (PB) and/or bone marrow (BM) in 34 cases of primary MDS. Mutations at codon 12 of Ki-ras or N-ras were detected in three cases (9%): one of six cases of refractory anemia with excess blasts (RAEB) and two of nine cases of chronic myelomonocytic leukemia (CMML). The nucleotide substitution differed in each. In all cases the mutant allele was detectable in PB cells. A sustained hematologic remission was achieved after low-dose cytarabine therapy in the case of RAEB. Neither case of CMML exhibited signs of disease progression during follow-up at 7 and 12 months. In contrast, four of 31 patients without the ras mutation underwent transformation to AML within 12 months of genetic analysis. We conclude that ras mutations in MDS are heterogeneous and may develop at an early stage during the evolution of MDS. Their detection in PB cells illustrates the potential utility of ras mutation as a clonal marker in myeloid malignancy.
History on Fire (2010)

A desirable outcome of the History Wars would be new work uncontaminated by the shoddy and politicised history writing of the last half-century. The need is urgent. The fourth edition of Richard Broome's Aboriginal Australians has recently been issued by Allen and Unwin. In print since 1982, this is one of the most important Left books ever published in Australia. It has sold 50,000 copies and has moulded and influenced generations of teachers and their students. For the new edition, and in the shadow of the History Wars, Professor Broome has completely rewritten the text. There is the now obligatory denigration of Keith Windschuttle, and some parts of Broome's narrative have changed to deal with criticism of his work. It may have a nice cover but it is one of the great intellectual disasters of our times for, amongst other serious problems, Broome uses and endorses a poorly researched and plagiarised book on Aboriginal massacres, the same poor book he used five years ago in his acclaimed and prize-winning Aboriginal Victorians.
Real-Time Adaptive Foreground/Background Segmentation (2005)

The automatic analysis of digital video scenes often requires the segmentation of moving objects from a static background. Historically, algorithms developed for this purpose have been restricted to small frame sizes, low frame rates, or offline processing. The simplest approach involves subtracting the current frame from the known background. However, as the background is rarely known beforehand, the key is how to learn and model it. This paper proposes a new algorithm that represents each pixel in the frame by a group of clusters. The clusters are sorted in order of the likelihood that they model the background and are adapted to deal with background and lighting variations. Incoming pixels are matched against the corresponding cluster group and are classified according to whether the matching cluster is considered part of the background. The algorithm has been qualitatively and quantitatively evaluated against three other well-known techniques. It demonstrated equal or better segmentation and proved capable of processing PAL video at full frame rate using only 35%–40% of a GHz Pentium 4 computer.
Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition (2013)

Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of MYCN. Genome-wide expression analysis showed downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knockdown phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in 3 in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma.
Mechanisms of Enhanced β-Adrenergic Reserve From Cardiac Resynchronization Therapy (2009)

CRT improves rest and beta-adrenergic-stimulated myocyte function and calcium handling, upregulating beta(1) receptors and adenylate cyclase activity and suppressing G(i)-coupled signaling associated with novel RGS upregulation. The result is greater rest and sympathetic reserve despite reduced myocardial neurostimulation as components underlying its net benefit.
Carbon doping of GaN with CBr4 in radio-frequency plasma-assisted molecular beam epitaxy (2004)

Carbon tetrabromide (CBr4) was studied as an intentional dopant during rf plasma molecular beam epitaxy of GaN. Secondary ion mass spectroscopy was used to quantify incorporation behavior. Carbon was found to readily incorporate under Ga-rich and N-rich growth conditions with no detectable bromine incorporation. The carbon incorporation [C] was found to be linearly related to the incident CBr4 flux. Reflection high-energy electron diffraction, atomic force microscopy and x-ray diffraction were used to characterize the structural quality of the film’s postgrowth. No deterioration of structural quality was observed for [C] from mid 1017 to ∼1019 cm−3. The growth rate was also unaffected by carbon doping with CBr4. The electrical and optical behavior of carbon doping was studied by co-doping carbon with silicon. Carbon was found to compensate the silicon although an exact compensation factor was difficult to extract from the data. Photoluminescence was performed to examine the optical performance of the films. Carbon doping was seen to monotonically decrease the band edge emission. Properties of carbon-doped GaN are interpreted to be consistent with recent theoretical work describing incorporation of carbon as function of Fermi level conditions during growth.
Shared access packet transmission systems for compressed digital video (1989)

The problem of designing shared access packet-transport-based transmission systems for compressed video signals is studied. The feasibility of using conventional link-level and transport-level protocol services to transmit compressed video is examined by focusing on two practically important scenarios for compressed video transmission: (1) multipoint-to-multipoint video transmission using a 200 Mb/s implicit token passing (ITP) fiber-optic local area network (LAN); and (2) point-to-multipoint broadcast video distribution using a 90 Mb/s packet time-division multiplexing (packet-TDM) direct-broadcast satellite channel. To evaluate the performance of such shared-access broadband packet video systems accurate simulation models were developed that were driven by realistic 'broadcast quality' compressed video sources for the ITP-LAN and packet-TDM systems. The models were used to determine design tradeoffs between channel throughput, video quality (measured by clipping probability), and the transport-level and media-access-level protocol features and parameters implemented in the packet video network interface unit.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift (2024)

Training Deep Neural Networks is complicated by the fact that the distribution of each layer's inputs changes during training, as the parameters of the previous layers change. This slows down the training by requiring lower learning rates and careful parameter initialization, and makes it notoriously hard to train models with saturating nonlinearities. We refer to this phenomenon as internal covariate shift, and address the problem by normalizing layer inputs. Our method draws its strength from making normalization a part of the model architecture and performing the normalization for each training mini-batch. Batch Normalization allows us to use much higher learning rates and be less careful about initialization. It also acts as a regularizer, in some cases eliminating the need for Dropout. Applied to a state-of-the-art image classification model, Batch Normalization achieves the same accuracy with 14 times fewer training steps, and beats the original model by a significant margin. Using an ensemble of batch-normalized networks, we improve upon the best published result on ImageNet classification: reaching 4.9% top-5 validation error (and 4.8% test error), exceeding the accuracy of human raters.
A novel transferrin receptor-targeted hybrid peptide disintegrates cancer cell membrane to induce rapid killing of cancer cells (2011)

TfR-lytic peptide might provide a potent and selective anticancer therapy for patients.
A rearrangeable multichannel free-space optical switch based on multistage network configuration (1991)

A rearrangeable 128*128-channel optical switch based on a multistage network configuration is demonstrated. The properties of optical components required for achieving up to 1000*1000-channel switches are discussed, taking into account the diffraction limit and liquid crystal light modulator (LCLM) crosstalk. An examination of the insertion loss and crosstalk properties of the switch reveals an average loss and crosstalk of 7.9 and -21.2 dB, respectively, and worst-case loss and crosstalk of 11.0 and -12.8 dB, respectively. Such low-loss and low-crosstalk properties indicate that the proposed switch structure is suitable for a large-scale rearrangeable switch.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A New Model for the Effect of Molecular Imposters on the Shape of Faceted Molecular Crystals (2009)

In a solution crystallization process, dissolved molecules that are structurally related to the solute (here termed “imposters”) can exert effects on the shape of the solute crystal. We propose a new model for the effect of imposters based on a mechanistic description of the way a molecular imposter affects a growing crystal surface. Crystals growing at relatively small supersaturations are known to grow by a flow of steps across crystal faces manifested as spirals originating from screw dislocations. We argue that, when the imposter is present on the surface at low concentrations, it has no net effect on these spirals except in the region where the first turn of a spiral occurs. The model is applied to α-glycine growing from water in the presence of l-alanine, and our shape prediction compares favorably with available experimental data.