gebhart/patrepeval huggingface dataset:
Antigenic Determinants of Staphylococcus aureus Type 5 and Type 8 Capsular Polysaccharide Vaccines (1998)

Bacterial capsular polysaccharides (CP) are carbohydrate polymers comprised of repeating saccharide units. Several of these CP have side chains attached to their backbone structures. The side chains may include O-acetyl, phosphate, sialic acid, and other moieties. Those moieties represent the immunodominant epitopes and the most functional ones. The clinically significant Staphylococcus aureus type 5 CP (CP 5) and type 8 CP (CP 8) are comprised of a trisaccharide repeat unit with one O-acetyl group attached to each repeat unit. The immunogenicity of these CP and the functionality of antibodies to the backbone and the O-acetyl moieties were investigated. Immunization with the native CP conjugates (CP with 75% O-acetylation) elicited a high proportion of antibodies directed against the O-acetyl moiety. Nonetheless, all of the vaccinees produced antibodies to the backbone moieties as well. Conjugate vaccines made of de-O-acetylated CP elicited backbone antibodies only. Antibodies to both backbone and O-acetyl groups were found to be opsonic against S. aureus strains which varied in their O-acetyl content. Absorption studies with O-acetylated and de-O-acetylated CP showed that (i) native CP conjugates generated antibodies to both backbone and O-acetyl groups and (ii) O-acetylated isolates were opsonized by both populations of antibodies while the non-O-acetylated strains were predominantly opsonized by the backbone antibodies. These results suggest that S. aureus CP conjugate vaccines elicit multiple populations of antibodies with diverse specificities. Moreover, the antibodies of different specificities (backbone or O-acetyl) are all functional and efficient against the variations in bacterial CP that may occur among clinically significant S. aureus pathogenic isolates.
A hidden surface algorithm for computer generated halftone pictures (1969)

The application of computer graphics to problem solving has increased over the past few years. The representation of data in the form of line drawings, graphics, charts, diagrams and line plots has been explored extensively. This paper addresses itself to some new techniques used to solve problems associated with extending the power of computer graphics to include black and white, and color shading. In particular it presents a new method for converting data describing three-dimensional objects into data that can be used to generate two-dimensional halftone images. It deals with some problems that arise in black and white, and color shading.
A two-channel adaptive filtering approach for recognition of the QRS morphology (2002)

An approach for QRS morphology classification is proposed. The cross-correlation structure between two electrocardiogram (ECG) channels is used to characterize different QRS morphologies. The classifier consists of a bank of adaptive filters, one for each QRS morphology; each filter has the QRS samples sequence of an ECG channel as reference input, and attempts to predict the QRS samples sequence of the other channel. A cumulative error and a prefixed threshold are used to decide the class assignment or a new class generation. The classifier was tested on the MIT-BIH database, showing satisfying sensitivity and positive predictive accuracy values. The method can be used to add useful information and to improve the performance of a template matching classifier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase I/II Trial of Weekly Intravenous 130-nm Albumin-Bound Paclitaxel As Initial Chemotherapy in Patients With Stage IV Non–Small-Cell Lung Cancer (2008)

NAB-paclitaxel 125 mg/m(2) administered on days 1, 8, and 15 of a 28-day cycle was well tolerated and demonstrated encouraging single-agent activity. No corticosteroid premedication was administered and no hypersensitivity reactions were seen. Additional studies of single-agent NAB-paclitaxel as well as platinum-based combinations are warranted.
Why decision support fails and how to fix it (1995)

The possibility of quantifying the superimposed signal of glutamate and glutamine (Glx) and its components by ¹H magnetic resonance spectroscopy (MRS) in the spinal cord is an exciting challenge with important clinical applications in neurological conditions. The spinal cord is a particularly difficult region of interest due to its small volume, magnetic field inhomogeneities and physiological motion. In this study, we investigated for the first time the feasibility of obtaining quantitative measurements of Glx in healthy cervical spinal cord by ¹H MRS at 3 T. The aim of this study was to compare two commercially available MRS sequences by spectral simulations and in vivo. A short echo time (TE) point resolved spectroscopy (PRESS) with TE = 30 ms and a stimulated echo acquisition mode (STEAM) with TE = 11 ms and mixing time (TM) = 17 ms were compared for reliability of Glx fit. Data allowed us to determine sample size estimates for future clinical studies for the first time. Results showed that PRESS provided a reliable fit for Glx in all cases (Cramér Rao lower bounds < 20%) whereas no reliable Glx fits were achieved using STEAM. Neither protocol provided reliable Glu quantification. The power calculations showed that a minimum sample size of 17 subjects per group was needed to detect Glx changes of > 20% using the PRESS sequence. This study proposed a clinically feasible MRS method for Glx detection in the human cervical cord in vivo including sample sizes needed for conclusive clinical studies.
The HlyU Protein Is a Positive Regulator of rtxA1 , a Gene Responsible for Cytotoxicity and Virulence in the Human Pathogen Vibrio vulnificus (2007)

Vibrio vulnificus is an opportunistic human pathogen that preferentially infects compromised iron-overloaded patients, causing a fatal primary septicemia with very rapid progress, resulting in a high mortality rate. In this study we determined that the HlyU protein, a virulence factor in V. vulnificus CMCP6, up-regulates the expression of VV20479, a homologue of the Vibrio cholerae RTX (repeats in toxin) toxin gene that we named rtxA1. This gene is part of an operon together with two other open reading frames, VV20481 and VV20480, that encode two predicted proteins, a peptide chain release factor 1 and a hemolysin acyltransferase, respectively. A mutation in rtxA1 not only contributes to the loss of cytotoxic activity but also results in a decrease in virulence, whereas a deletion of VV20481 and VV20480 causes a slight decrease in virulence but with no effect in cytotoxicity. Activation of the expression of the rtxA1 operon by HlyU occurs at the transcription initiation level by binding of the HlyU protein to a region upstream of this operon.
Enzymatic deacylation of the lipid A moiety of Salmonella typhimurium lipopolysaccharides by human neutrophils. (1983)

Lipid A, the toxic moiety of Gram-negative bacterial lipopolysaccharides (endotoxins), is a glucosamine disaccharide to which fatty acid and phosphate residues are covalently attached. Recent studies of Salmonella lipid A indicate that 3-hydroxytetradecanoic acid (3-OH-14:0) residues are directly linked to the glucosamine backbone and the nonhydroxylated fatty acids (principally dodecanoic and tetradecanoic acids) are esterified to the hydroxyl groups of some of the 3-OH-14:0 molecules. We report here that the granule fraction of human neutrophils contains one or more enzymes that partially deacylate Salmonella typhimurium lipid A by removing the nonhydroxylated fatty acids, leaving almost all of the 3-OH-14:0 residues linked to glucosamine. The available evidence suggests that similar reactions also occur in living neutrophils that ingest lipopolysaccharides by antibody-dependent phagocytosis.
The integrated stress response prevents demyelination by protecting oligodendrocytes against immune-mediated damage (2007)

In response to ER stress, the pancreatic endoplasmic reticulum kinase (PERK) coordinates an adaptive program known as the integrated stress response (ISR) by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2alpha). IFN-gamma, which activates the ER stress response in oligodendrocytes, is believed to play a critical role in the immune-mediated CNS disorder multiple sclerosis (MS) and its mouse model, experimental autoimmune encephalomyelitis (EAE). Here we report that CNS delivery of IFN-gamma before EAE onset ameliorated the disease course and prevented demyelination, axonal damage, and oligodendrocyte loss. The beneficial effects of IFN-gamma were accompanied by PERK activation in oligodendrocytes and were abrogated in PERK-deficient animals. Our results indicate that IFN-gamma activation of PERK in mature oligodendrocytes attenuates EAE severity and suggest that therapeutic approaches to activate the ISR could prove beneficial in MS.
Genetic alterations in pancreatic carcinoma. (2003)

Cancer of the exocrine pancreas represents the fifth leading cause of cancer death in the Western population with an average survival after diagnosis of 3 to 6 months and a five-year survival rate under 5%. Our understanding of the molecular carcinogenesis has improved in the last few years due to the development of novel molecular biological techniques. Pancreatic cancer is a multi-stage process resulting from the accumulation of genetic changes in the somatic DNA of normal cells. In this article we describe major genetic alterations of pancreatic cancer, mutations in the proto-oncogene K-RAS and the tumor suppressors INK4A, TP53 and DPC4/SMAD4. The accumulation of these genetic changes leads to a profound disturbance in cell cycle regulation and continuous growth. The knowledge of the underlying molecular mechanisms will offer new therapeutic and diagnostic options and hopefully improve the outcome of this aggressive disease.
Room-Temperature Wafer Bonding of Silicon and Lithium Niobate by Means of Argon-Beam Surface Activation (2002)

Abstract We have developed a method to bond silicon and piezoelectric ceramics wafers at room temperature. In the method, the wafers are bonded in vacuum after sputter etching by argon beam. It is not necessary to apply high pressure to force two specimens together in the bonding process. A 3-inch single crystal lithium niobate wafers was successfully bonded to a 4-inch silicon wafer. The bonding was so strong that fracture from the bulk material was observed after tensile tests. It is supposed that the argon-beam etching removes contaminant layers on the surface and surface atoms become in an active state, which is important for the strong bond formation at room temperature. This bonding method provides very low damage integration between silicon and piezoelectric materials such as lithium niobate. Keywords: Wafer BondingRoom-temperature BondingArgon BeamSurface ActivationLithium NiobateSilicon
A fast and conformal heating scheme for producing large thermal lesions using a 2D ultrasound phased array (2007)

The treatment conformability and the total treatment time of large tumors are both important issues in ultrasound thermal therapy. Previous heating strategies all show their restrictions in achieving these two issues to satisfactory levels simultaneously. This work theoretically presents a new heating strategy which is capable of both increasing the treatment conformability and shortening the treatment time, when using a 2D ultrasound phased array transducer. To perform this, a set of the multiple-foci patterns (considered the basic heating units) were temporally switched to steer the beam at different focal planes with the lesion length being well-controlled. Then, to conformally cover an irregular target volume, the 2D phased array was laterally shifted by a positioning system to deposit a suitable heating unit to cover a subvolume part. Results demonstrated that the totally treatment time can be largely reduced. The heating rate can be increased up to 0.96 cm3/min compared to the previously reported 0.26 cm3/min. Also, the proposed scheme showed that the tumor regions can be completely treated with the normal tissue damage at satisfactory level. The feasibility of the proposed strategy for irregular tumor treatment was also demonstrated. This study offers useful information in large tumor treatment in ultrasound thermal therapy.
[Incidence of juvenile-onset diabetes in Denmark. A prospective registration in the counties of Fyn, Ribe, Sønderjylland and Vejle]. (1997)

To provide contemporary figures of the incidence of childhood onset diabetes mellitus in Denmark, a prospective routine registration system has been established. The present study covered the population of children aged 0-14 years in four Danish counties, observed during the calendar years 1989 through 1993 concerning new cases of the disease. A total of 201 cases (113 boys and 88 girls) were registered, corresponding with a sex- and age-adjusted incidence rate of 17.4 per 100,000 person-years. Based on a validation analysis the study material is considered virtually complete. Overall, the incidence among boys was slightly higher than among girls, but not statistically significantly so. The incidence rate increased with age for both boys and girls. The results confirm that the incidence of childhood onset diabetes in Denmark is relatively high. Compared with previous Danish studies there has been an increase of about 20-25% in the incidence during the last 20 years. Our study stresses the importance of a continuous registration of new cases of childhood diabetes in Denmark, thereby providing clues for further aetiological studies as well as providing reference values for the planning of the diabetes health care. Our results indicate that at least two independent ascertainment sources must be employed to ensure complete registration in studies that rely upon voluntary registration as the primary reporting source.
Genes required for the engulfment of cell corpses during programmed cell death in Caenorhabditis elegans. (1991)

After programmed cell death, a cell corpse is engulfed and quickly degraded by a neighboring cell. For degradation to occur, engulfing cells must recognize, phagocytose and digest the corpses of dying cells. Previously, three genes were known to be involved in eliminating cell corpses in the nematode Caenorhabditis elegans: ced-1, ced-2 and nuc-1. We have identified five new genes that play a role in this process: ced-5, ced-6, ced-7, ced-8 and ced-10. Electron microscopic studies reveal that mutations in each of these genes prevent engulfment, indicating that these genes are needed either for the recognition of corpses by other cells or for the initiation of phagocytosis. Based upon our study of double mutants, these genes can be divided into two sets. Animals with mutations in only one of these sets of genes have relatively few unengulfed cell corpses. By contrast, animals with mutations in both sets of genes have many unengulfed corpses. These observations suggest that these two sets of genes are involved in distinct and partially redundant processes that act in the engulfment of cell corpses.
Human cytotoxic T-cell lines with restricted specificity for squamous cell carcinoma of the head and neck. (1993)

Human cytotoxic T-lymphocyte (CTL) lines with specificity restricted for autologous squamous cell carcinoma of the head and neck (SCCHN) were established from peripheral blood lymphocytes obtained at the time of surgery and again at two different times after surgery from a patient with cancer of the tongue. The CTL lines were cultured in the presence of interleukin (IL) 2, IL4, and autologous tumor (AuTu) cell monolayers. All three lines were CD3+CD8+CD11b-HLA-DR+ T-cell receptor alpha/beta+. They were tested in 4-h51Cr release assays against SCCHN cell lines (n = 5) and a variety of nonsquamous human tumor (n = 5) and normal (n = 5) cell targets and was found to lyse only AuTu (PCI-50) and three allogenic SCCHN cell lines. Lysis of AuTu and the three allogenic SCCHN targets by the established CTL lines appeared to be major histocompatibility complex class I restricted, since it was blocked by monoclonal antibodies to class I histocompatibility complex antigens. The CTL lines proliferated in vitro in response to autologous PCI-50 or an allogenic SCCHN cell line (PCI-1). The lines have been maintained in culture in the presence of AuTu monolayers and retained cytotoxicity against AuTu for over 20 weeks. The AuTu (PCI-50) cell line was tested for in vitro sensitivity to cytotoxic or cytostatic effects of various effector cells, including the CTL lines. PCI-50 targets were resistant to lysis by resting human mononuclear cells but sensitive to IL2-activated natural killer cells in 4-h 51Cr release assays. In comparison with IL2-activated natural killer cells, the CTL line mediated lower levels of lysis against AuTu. Growth of PCI-50 cells in culture was significantly inhibited by a combination of gamma-interferon and IL2 or by high concentrations of tumor necrosis factor alpha. While supernants of IL2-activated natural killer cells were growth inhibitory, those of the CTL line were not. On the other hand, lysis of AuTu targets by the CTL line was increased by preincubation of the tumor cells with tumor necrosis factor alpha or gamma-interferon. These cytokines augmented expression of HLA-class I, HLA-class II, and intercellular adhesion molecule I, but not squamous cell carcinoma-associated antigens, E7 and A9, on PCI-50 cells. The CTL lines described are the first with restricted specificity for autologous SCCHN ever reported and their availability will facilitate studies of the AuTu T-cell response in head and neck cancer.
Novel genomic determinants of apoptotic defects in acute lymphoblastic leukemia (2006)

textabstractThe treatment of pediatric acute leukemia has greatly improved over the past 4 decades, \nresulting in long-term disease-free survival of approximately 80% for ALL1-3 and 60% for \nAML.4 Despite this progress, a considerable number of children ultimately relapse with a \ndisease that is highly refractory to further treatment. A high proportion of the contemporary \ntreatment failures can be contributed to cellular drug resistance. However, relatively little is \nknown about the causes of cellular drug resistance in childhood acute leukemia. \n\n In the last years it has become clear that most, if not all, chemotherapeutic agents \nultimately induce programmed cell death or apoptosis in their target cells.5 Defects in the \napoptosis route allow genetically instable cells to survive and are thought of as one of the \nmajor driving forces behind leukemogenesis.6,7 These observations led to the hypothesis \nthat aberrations in the apoptosis pathway contribute to cellular drug resistance in children \nwith acute leukemia. Therefore, a thorough knowledge of the aberrations in the apoptosis \nroute is critical for understanding the causes of treatment failure and for a rational \napproach to drug design and therapy.
Estrogen treatment of spinal cord injury attenuates calpain activation and apoptosis (2006)

Spinal cord injury (SCI) is a devastating neurologic injury, and currently, the only recommended pharmacotherapy is high-dose methylprednisolone, which has limited efficacy. Estrogen is a multi-active steroid with anti-oxidant and anti-apoptotic effects. Estrogen may modulate intracellular Ca2+ and prevent inflammation. For this study, male rats were divided into three groups. Sham-group animals received a laminectomy at T12. Injured rats received both laminectomy and 40 gram centimeter force SCI. Estrogen-group rats received 4 mg/kg 17beta-estradiol (estrogen) at 15 min and 24 hr post-injury, and vehicle-group rats received equal volumes of dimethyl sulfoxide. Animals were sacrificed at 48 hr post-injury, and 1-cm segments of the lesion, rostral penumbra, and caudal penumbra were excised. The degradation of 68 kD neurofilament protein (NFP) and estrogen receptors (ER) was examined by Western blot analysis. Protein levels of calpain and the activities of calpain and caspase-3 were also examined. Levels of cytochrome c were determined in both cytosolic and mitochondrial fractions. Cell death with DNA fragmentation was examined using the TUNEL assay. At the lesion, samples from both vehicle and estrogen treated animals showed increased levels of 68 kD NFP degradation, calpain content, calpain activity, cytochrome c release, and degradation of ERalpha and ERbeta, as compared to sham. In the caudal penumbra, estrogen treatment significantly attenuated 68 kD NFP degradation, calpain content, calpain activity, levels of cytosolic cytochrome c, and ERbeta degradation. At the lesion, vehicle-treated animals displayed more TUNEL+ cells, and estrogen treatment significantly attenuated this cell death marker. We conclude that estrogen may inhibit cell death in SCI through calpain inhibition.
Biomimetics: Small 9/2010 (2010)

The cover image shows a scanning electron microscopy image of bioinspired subwavelength structures (SWS) with parabolic shape, which are fabricated by simple process steps based on the combination of laser interference lithography, thermal reflow, and subsequent pattern transfer. The insets depict the reflected light from the flat surface (top) and parabola-shaped SWS (bottom), respectively. The fabricated SWS with parabolic shape show antireflection properties over a broader wavelength range compared to that of a flat surface and even conventional cone-shaped SWS, thus opening up new possibilities for various optoelectronic device applications to improve optical performance. For more information, please read the Communication “Bioinspired Parabola Subwavelength Structures for Improved Broadband Antireflection” by Y. T. Lee el al., beginning on page 984.
Role of Lung Pericytes and Resident Fibroblasts in the Pathogenesis of Pulmonary Fibrosis (2013)

We conclude that the lung contains an extensive population of Foxd1 progenitor-derived pericytes that are an important lung myofibroblast precursor population.
Slippery pre-suffused surfaces (2011)

We describe the slippery behaviour of textured solids filled with oil, on which other liquids are found to slip and be removed easily. We describe the criteria for achieving this slippery behaviour, and illustrate the concept by two examples, namely the lotus effect (removal of dust by mobile drops) and the coffee stain effect.