gebhart/patrepeval huggingface dataset:
Dynamic OCT measurement of corneal deformation by an air puff in normal and cross-linked corneas (2012)

A new technique is presented for the non-invasive imaging of the dynamic response of the cornea to an air puff inducing a deformation. A spectral OCT instrument combined with an air tonometer in a non-collinear configuration was used to image the corneal deformation over full corneal cross-sections, as well as to obtain high speed measurements of the temporal evolution of the corneal apex. The entire deformation process can be dynamically visualized. A quantitative analysis allows direct extraction of several deformation parameters, such as amplitude, diameter and volume of the maximum deformation, as well as duration and speed of the increasing deformation period and the recovery period. The potential of the technique is demonstrated on porcine corneas in vitro under constant IOP for several conditions (untreated, after riboflavin instillation and under cross-linking with ultraviolet light), as well as on human corneas in vivo. The new technique has proved very sensitive to detect differences in the deformation parameters across conditions. We have confirmed non-invasively that Riboflavin and UV-cross-linking induce changes in the corneal biomechanical properties. Those differences appear to be the result of changes in constituent properties of the cornea, and not a consequence of changes in corneal thickness, geometry or IOP. These measurements are a first step for the estimation of the biomechanical properties of corneal tissue, at an individual level and in vivo, to improve diagnosis and prognosis of diseases and treatments involving changes in the biomechanical properties of the cornea.
Biology and Molecular Epidemiology of Diphtheria Toxin and thetoxGene (2000)

Diphtheria toxin (DT) is an extracellular protein of Corynebacterium diphtheriae that inhibits protein synthesis and kills susceptible cells. The gene that encodes DT (tox) is present in some corynephages, and DT is only produced by C. diphtheriae isolates that harbor tox+ phages. The diphtheria toxin repressor (DtxR) is a global regulatory protein that uses Fe2+ as co-repressor. Holo-DtxR represses production of DT, corynebacterial siderophore, heme oxygenase, and several other proteins. Diagnostic tests for toxinogenicity of C. diphtheriae are based either on immunoassays or on bioassays for DT. Molecular analysis of tox and dtxR genes in recent clinical isolates of C. diphtheriae revealed several tox alleles that encode identical DT proteins and multiple dtxR alleles that encode five variants of DtxR protein. Therefore, recent clinical isolates of C. diphtheriae produce a single antigenic type of DT, and diphtheria toxoid continues to be an effective vaccine for immunization against diphtheria.
Derivation of a Xeno‐Free Human Embryonic Stem Cell Line (2006)

Elimination of all animal material during both the derivation and long-term culture of human embryonic stem cells (hESCs) is necessary prior to future application of hESCs in clinical cell therapy. The potential consequences of transplanting xeno-contaminated hESCs into patients, such as an increased risk of graft rejection [Stem Cells 2006; 24:221-229] and the potential transfer of nonhuman pathogens, make existing hESC lines unsuitable for clinical applications. To avoid xeno-contamination during derivation and culture of hESCs, we first developed a xeno-free medium supplemented with human serum, which supports long-term (>50 passages) culture of hESCs in an undifferentiated state. To enable derivation of new xeno-free hESCs, we also established xeno-free human foreskin fibroblast feeders and replaced immunosurgery, which involves the use of guinea pig complement, with a modified animal-product-free derivation procedure. Here, we report the establishment and characterization (>20 passages) of a xeno-free pluripotent diploid normal hESC line, SA611.
Cutting Edge: Selective Impairment of CD8+ T Cell Function in Mice Lacking the TNF Superfamily Member LIGHT (2002)

Interactions of LIGHT and its receptors, herpesvirus entry mediator on T cells and lymphotoxin beta receptor on stromal cells, are implicated in the regulation of lymphoid organogenesis, costimulation of T cells, and activation of dendritic cells. In this work we report that LIGHT-deficient mice had normal lymphoid organs with T cells and APCs that normally responded to Ag stimulation and normally stimulated T cells. Although the number of Vbeta8(+) T cells in naive LIGHT(+/+) and LIGHT(-/-) mice was identical, Vbeta8(+)CD8(+) T cell proliferation in response to staphylococcal enterotoxin B was significantly lower in LIGHT(-/-) mice. Consistently, induction and cytokine secretion of CD8(+) CTL to MHC class I-restricted peptide was also reduced in LIGHT(-/-) mice. However, the proliferative response of Vbeta8(+)CD4(+) T cells to staphylococcal enterotoxin B was comparable in LIGHT(-/-) and LIGHT(+/+) mice. Our results suggest that LIGHT is required for activation of normal CD8(+) T cells but not CD4(+) T cells.
Immunotherapy of Malignant Disease with Tumor Antigen–Specific Monoclonal Antibodies (2009)

A few tumor antigen (TA)-specific monoclonal antibodies (mAb) have been approved by the Food and Drug Administration for the treatment of several major malignant diseases and are commercially available. Once in the clinic, mAbs have an average success rate of approximately 30% and are well tolerated. These results have changed the face of cancer therapy, bringing us closer to more specific and more effective biological therapy of cancer. The challenge facing tumor immunologists at present is represented by the identification of the mechanism(s) underlying the patients' differential clinical response to mAb-based immunotherapy. This information is expected to lead to the development of criteria to select patients to be treated with mAb-based immunotherapy. In the past, in vitro and in vivo evidence has shown that TA-specific mAbs can mediate their therapeutic effect by inducing tumor cell apoptosis, inhibiting the targeted antigen function, blocking tumor cell signaling, and/or mediating complement- or cell-dependent lysis of tumor cells. More recent evidence suggests that TA-specific mAb can induce TA-specific cytotoxic T-cell responses by enhancing TA uptake by dendritic cells and cross-priming of T cells. In this review, we briefly summarize the TA-specific mAbs that have received Food and Drug Administration approval. Next, we review the potential mechanisms underlying the therapeutic efficacy of TA-specific mAbs with emphasis on the induction of TA-specific cellular immune responses and their potential to contribute to the clinical efficacy of TA-specific mAb-based immunotherapy. Lastly, we discuss the potential negative effect of immune escape mechanisms on the clinical efficacy of TA-specific mAb-based immunotherapy.
Comparison between red, green and blue light reflection photoplethysmography for heart rate monitoring during motion (2013)

Reflection photoplethysmography (PPG) using 530 nm (green) wavelength light has the potential to be a superior method for monitoring heart rate (HR) during normal daily life due to its relative freedom from artifacts. However, little is known about the accuracy of pulse rate (PR) measured by 530 nm light PPG during motion. Therefore, we compared the HR measured by electrocadiography (ECG) as a reference with PR measured by 530, 645 (red), and 470 nm (blue) wavelength light PPG during baseline and while performing hand waving in 12 participants. In addition, we examined the change of signal-to-noise ratio (SNR) by motion for each of the three wavelengths used for the PPG. The results showed that the limit of agreement in Bland-Altman plots between the HR measured by ECG and PR measured by 530 nm light PPG (±0.61 bpm) was smaller than that achieved when using 645 and 470 nm light PPG (±3.20 bpm and ±2.23 bpm, respectively). The ΔSNR (the difference between baseline and task values) of 530 and 470nm light PPG was significantly smaller than ΔSNR for red light PPG. In conclusion, 530 nm light PPG could be a more suitable method than 645 and 470nm light PPG for monitoring HR in normal daily life.
The Use of Fluorescein Diacetate and Phenosafranine for Determining Viability of Cultured Plant Cells (1972)

Various stains were tested with suspension cell cultures of Nicotiana tabacum (tobacco), Oryza sativa (rice), Glycine max (soybean), Daucus carota (carrot) and Lycopersicon esculentum (tomato). A drop of the culture medium containing each dye was mixed with a drop of cells on a microscope slide and viewed after 5 min. The most suitable dyes tested were fluorescein diacetate for viable cells and phenosafranine for dead cells. These dyes stained specifically whether the cells were from cultures of different ages, of different species or if the cells had been treated in various, often toxic, ways. The viability of the cells was confirmed by observing cyclosis and plasmolysis, and whether the cells could grow further when cultured.
THE SPECIFIC AMINO ACID REQUIREMENTS OF A MAMMALIAN CELL (STRAIN L) IN TISSUE CULTURE (1955)

There have been many attempts to devise chemically defined media which will permit the propagation of mammalian cells in tissue culture, without supplementation by serum, plasma, or tissue extractives.To date, these attempts have not been successful.Although some of these media, notably those recently developed by Morgan, Morton, and Parker (1) and by Healy, Fisher, and Parker (Z), permit the survival of some cell lines for long periods, in our hands none has allowed continuing multiplication on serial subculture.Growth can be obtained on the addition to such media of a small amount of serum, but the medium is then no longer chemically defmed and no longer permits the delimitation of the essential growth requirements of the cell.Recognizing this di&ulty, Fischer (3) had used the expedient of supplementing a defined medium with dialyzed chicken plasma, serum, and embryo extract, in the hope that the essential small molecular weight components of the defined medium could then be identified.On the omission of either cystine, arginine, tryptophan, glutamine, or histidine and proline, there was in fact a decrease in the amount of radial growth from a chick embryo myoblast explant.However, growth was not prevented, and no single component could be rigorously characterized as essential to survival and growth.In the light of the dat,a to be reported here, it is possible (a) that the culture materials used by Fischer were not adequately dialyzed, (b) that the large amount,s of plasma and serum employed (more than 50 per cent by volume) contained compounds which could substitute in part for the amino acids, or (c) that the diameter of radial growth around the explant was not a true measure of cell proliferation.In any event, in the simpler system used here, in which cells were grown on a glass surface, the addition of small amounts of dialyzed horse serum to an otherwise defined medium permitted long term propagation of the adult mouse fibroblast (L strain).In such a limiting medium, the omission of a single essential growth factor now resulted in the early death of the culture, and it proved 839
Management and control functions in ATM switching systems (1994)

As research has progressed, it has become clear that the main difficulties in ATM pertain to its operational details rather than the concept. And it seems likely that these control issues will be much more complicated and costly for ATM switches when compared with current telephone circuit switches. The asynchronous transfer mode (ATM) is the target switching technique for the future public broadband integrated services digital network (B-ISDN). The purpose of this article is to examine the management and control functions in ATM switching systems implied by current industry standards and agreements on OAM and traffic control. Until now, ATM research in the areas of switch design and traffic control have progressed essentially independently. First, we briefly review the B-ISDN Protocol Reference Model and its representation of the different information flows in ATM. Network management and traffic control principles in ATM, and in particular OAM, are overviewed. With this information as background, we attempt to infer their implications on the functional blocks of an ATM switching system. An example switch architecture model with distributed management and control functions is outlined, and some design issues are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Helical Crystallization of Proteins on Carbon Nanotubes: A First Step towards the Development of New Biosensors (1999)

Two distinct proteins, streptavidin and HupR, bind and form regular helical arrays on the surface of multiwalled carbon nanotubes under appropriate conditions (see picture). The decoration of the outer surface of these nanostructures with biological macromolecules was investigated by electron microscopy.
Systemic Gene Transfer of a Hexosaminidase Variant Using an scAAV9.47 Vector Corrects G M2 Gangliosidosis in Sandhoff Mice (2016)

GM2 gangliosidosis is a group of neurodegenerative diseases caused by β-hexosaminidase A (HexA) enzyme deficiency. There is currently no cure. HexA is composed of two similar, nonidentical subunits, α and β, which must interact with the GM2 activator protein (GM2AP), a substrate-specific cofactor, to hydrolyze GM2 ganglioside. Mutations in either subunit or the activator can result in the accumulation of GM2 ganglioside within neurons throughout the central nervous system. The resulting neuronal cell death induces the primary symptoms of the disease: motor impairment, seizures, and sensory impairments. This study assesses the long-term effects of gene transfer in a Sandhoff (β-subunit knockout) mouse model. The study utilized a modified human β-hexosaminidase α-subunit (μ-subunit) that contains critical sequences from the β-subunit that enables formation of a stable homodimer (HexM) and interaction with GM2AP to hydrolyze GM2 ganglioside. We investigated a self-complementary adeno-associated viral (scAAV) vector expressing HexM, through intravenous injections of the neonatal mice. We monitored one cohort for 8 weeks and another cohort long-term for survival benefit, behavioral, biochemical, and molecular analyses. Untreated Sandhoff disease (SD) control mice reached a humane endpoint at approximately 15 weeks, whereas treated mice had a median survival age of 40 weeks, an approximate 2.5-fold survival advantage. On behavioral tests, the treated mice outperformed their knockout age-matched controls and perform similarly to the heterozygous controls. Through the enzymatic and GM2 ganglioside analyses, we observed a significant decrease in the GM2 ganglioside level, even though the enzyme levels were not significantly increased. Molecular analyses revealed a global distribution of the vector between brain and spinal cord regions. In conclusion, the neonatal delivery of a novel viral vector expressing the human HexM enzyme is effective in ameliorating the SD mouse phenotype for long-term. Our data could have implications not only for treatment of SD but also for Tay-Sachs disease (α-subunit deficiency) and similar brain disorders.
Multimodal MR Synthesis via Modality-Invariant Latent Representation (2017)

We propose a multi-input multi-output fully convolutional neural network model for MRI synthesis. The model is robust to missing data, as it benefits from, but does not require, additional input modalities. The model is trained end-to-end, and learns to embed all input modalities into a shared modality-invariant latent space. These latent representations are then combined into a single fused representation, which is transformed into the target output modality with a learnt decoder. We avoid the need for curriculum learning by exploiting the fact that the various input modalities are highly correlated. We also show that by incorporating information from segmentation masks the model can both decrease its error and generate data with synthetic lesions. We evaluate our model on the ISLES and BRATS data sets and demonstrate statistically significant improvements over state-of-the-art methods for single input tasks. This improvement increases further when multiple input modalities are used, demonstrating the benefits of learning a common latent space, again resulting in a statistically significant improvement over the current best method. Finally, we demonstrate our approach on non skull-stripped brain images, producing a statistically significant improvement over the previous best method. Code is made publicly available at https://github.com/agis85/multimodal_brain_synthesis.
Selective killing of human monocytes and cytokine release provoked by sphingomyelinase (beta-toxin) of Staphylococcus aureus (1996)

The best-known activity of Staphylococcus aureus sphingomyelinase C, alias beta-toxin, is as a hemolysin that provokes hot-cold lysis of erythrocytes which contain substantial amounts of sphingomyelin in the plasma membrane. Sheep erythrocytes are most susceptible, and we found that one hemolytic unit, representing the toxin concentration that elicits 50% hemolysis of 2.5 X 10(8) erythrocytes per ml, corresponds to 0.05 enzyme units or to approximately 0.25 microg of sphingomyelinase per ml. The cytotoxic action of beta-toxin on nucleated cells has not been described in any detail before, and the present investigation was undertaken to fill this information gap. We now identify beta-toxin as a remarkably potent monocytocidal agent. At a concentration of 0.001 U/ml, corresponding to approximately 5 ng/ml, beta-toxin killed over 50% of human monocytes (10(6) cells per ml) within 60 min. By contrast, 1 to 5 microg of beta-toxin per ml had no cytocidal effects on human granulocytes, fibroblasts, lymphocytes, or erythrocytes. A selective monocytocidal action was also observed with sphingomyelinase C from Bacillus cereus and a Streptomyces sp., whereas phospholipase A2 and phospholipase D at 100 U/ml were without effect. Monocytes succumbing to the action of beta-toxin processed and released interleukin-1beta, soluble interleukin-6 receptor, and soluble CD14 into the supernatant. Thus, monocyte killing by beta-toxin is associated with cytokine-related events that are important for the initiation and progression of infectious disease. These findings uncover a potentially important role for sphingomyelinase as a determinant of microbial pathogenicity.
The Relationship between the Number of Metastatic Lymph Nodes and Prognosis of Patients with Colorectal Cancer. (1992)

1977年から1989年までに当科で治癒切除を受けた大腸癌取扱い規約のstage III, IVの大腸癌症例のうち, 深達度ss, sまたはa1, a2の100例を対象として, 転移リンパ節個数と予後の関係について検討した. 転移個数を1個, 2個, 3個, および4個以上に分けて5年生存率を比較すると, それぞれ56%, 63%, 34%, 35%であった. 転移個数を2個以下と3個以上の2群に分けて5年生存率を比較すると, それぞれ59%, 35%であり, 両群間に有意差が認められた. 一方, TNM分類に準じた3個以下と4個以上の比較では, それぞれ54%, 35%であり, 統計学的有意差ではなかった. さらに, 大腸癌取扱い規約に基づくn1転移陽性例のみの比較でも, 転移個数3個以上では2個以下に比して治療成績不良であった. 以上より, 転移リンパ節個数2個以下と3個以上の2群に群別することは, 予後を推測するうえで有用であると考えられる.
An Improved Sub-Packetization Bound for Minimum Storage Regenerating Codes (2014)

Distributed storage systems employ codes to provide resilience to failure of multiple storage disks. In particular, an (n, k) maximum distance separable (MDS) code stores k symbols in n disks such that the overall system is tolerant to a failure of up to n - k disks. However, access to at least k disks is still required to repair a single erasure. To reduce repair bandwidth, array codes are used where the stored symbols or packets are vectors of length ℓ. The MDS array codes have the potential to repair a single erasure using a fraction 1/(n - k) of data stored in the remaining disks. We introduce new methods of analysis, which capitalize on the translation of the storage system problem into a geometric problem on a set of operators and subspaces. In particular, we ask the following question: for a given (n, k), what is the minimum vector-length or subpacketization factor ℓ required to achieve this optimal fraction? For exact recovery of systematic disks in an MDS code of low redundancy, i.e., k/n > 1/2, the best known explicit codes have a subpacketization factor ℓ, which is exponential in k. It has been conjectured that for a fixed number of parity nodes, it is in fact necessary for ℓ to be exponential in k. In this paper, we provide a new log-squared converse bound on k for a given ℓ, and prove that k ≤ 2 log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> I(log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">δ</sub> ℓ + 1), for an arbitrary number of parity nodes r = n - k, where δ = r/(r - 1).
Comparison of Gene Therapy with Interleukin-2 Gene Modified Fibroblasts and Tumor Cells in the Murine CT-26 Model of Colorectal Carcinoma (1995)

We compared the efficacy of gene therapy mediated by interleukin-2 (IL-2) gene-modified tumor cells to gene therapy mediated by IL-2 transduced fibroblasts in the CT-26 model of murine colorectal carcinoma. We transduced CT-26 tumor cells and BALB/c 3T3 fibroblasts with three different retroviral vectors using three different promoters for the human IL-2 gene: DC/TKIL-2 (thymidine kinase promoter), LXSN-iIL2 (long terminal repeat promoter), and LNCX-iIL2 (cytomegalovirus promoter). These transductions resulted in CT-26 and 3T3 subclones that secreted different amounts of IL-2. Immunization of animals with either CT-26/IL-2 cells or with fibroblast/IL-2 cells mixed with CT-26 induced similar levels of immunity that protected 62-82% of animals against a subsequent tumor challenge with parental CT-26. However, mice developed tumors at the site of inoculation in 46% of the animals immunized with CT-26/IL-2 cells. In a separate experiment, CT-26/IL-2 cells were exposed to 6,000 cGy of gamma irradiation to prevent tumor growth at the site of inoculation. Although the CT-26/IL-2 cells continued to secrete IL-2 after irradiation, they were no longer effective at inducing antitumor immunity. In contrast, both irradiated and nonirradiated fibroblast/IL-2 cells, mixed with irradiated CT-26, were equally effective at inducing antitumor immunity. These data suggest that in the CT-26 model, fibroblast-mediated IL-2 gene therapy has advantages for the induction of antitumor immunity and abrogation of tumorigenic potential at the site of inoculation compared with tumor cell-mediated IL-2 gene therapy.
Generation and analysis of large synthetic social contact networks (2009)

We describe ¿first principles¿ based methods for developing synthetic urban and national scale social contact networks. Unlike simple random graph techniques, these methods use real world data sources and combine them with behavioral and social theories to synthesize networks. We develop a synthetic population for the United States modeling every individual in the population including household structure, demographics and a 24-hour activity sequence. The process involves collecting and manipulating public and proprietary data sets integrated into a common architecture for data exchange and then using these data sets to generate new relations. A social contact network is derived from the synthetic population based on physical co-location of interacting persons. We use graph measures to compare and contrast the structural characteristics of the social networks that span different urban regions. We then simulate diffusion processes on these networks and analyze similarities and differences in the structure of the networks.
A humanized anti-IL-6 antibody (ALD518) in non-small cell lung cancer (2011)

IL-6-mediated inflammation may contribute to NSCLC-related morbidity and mortality. In preclinical and Phase I and II trials ALD518 targeting IL-6 appears well tolerated and ameliorates NSCLC-related anemia and cachexia. Other clinical outcomes need further study, and may include effects on overall survival, hypercoagulability associated with lung cancer and decreased resistance to EGF-pathway inhibitors.