gebhart/patrepeval huggingface dataset:
A monoclonal antibody against meningococcus group B polysaccharides distinguishes embryonic from adult N-CAM. (1986)

The neural cell adhesion molecules (N-CAM) occur chiefly in two molecular forms that are selectively expressed at various stages of development. Highly sialylated forms prevalent in embryonic and neonatal brain are gradually replaced by less sialylated forms as development proceeds. Here we describe a monoclonal antibody raised against the capsular polysaccharides of meningococcus group B (Men B) which specifically distinguishes embryonic N-CAM from adult N-CAM. This antibody recognizes alpha 2-8-linked N-acetylneuraminic acid units (NeuAc alpha 2-8). Immunoblot together with immunoprecipitation experiments with cell lines or tissue extracts showed that N-CAM are the major glycoproteins bearing such polysialosyl units. Moreover we could not detect any sialoglycolipid reactive with this antibody in mouse brain or in the neural cell lines examined. By indirect immunofluorescence staining this anti-Men B antibody decorated cells such as AtT20 (D16/16), which expressed the embryonic forms of N-CAM, but not cells that expressed the adult forms. In primary cultures this antibody allowed us to follow the embryonic-to-adult conversion in individual cells. In addition, the existence of cross-reactive polysialosyl structures on Men B and N-CAM in embryonic brain cells for caution in efforts to develop immunotherapy against neonatal meningitis.
Lossless Data Embedding—New Paradigm in Digital Watermarking (2002)

One common drawback of virtually all current data embedding methods is the fact that the original image is inevitably distorted due to data embedding itself. This distortion typically cannot be removed completely due to quantization, bit-replacement, or truncation at the grayscales 0 and 255. Although the distortion is often quite small and perceptual models are used to minimize its visibility, the distortion may not be acceptable for medical imagery (for legal reasons) or for military images inspected under nonstandard viewing conditions (after enhancement or extreme zoom). In this paper, we introduce a new paradigm for data embedding in images (lossless data embedding) that has the property that the distortion due to embedding can be completely removed from the watermarked image after the embedded data has been extracted. We present lossless embedding methods for the uncompressed formats (BMP, TIFF) and for the JPEG format. We also show how the concept of lossless data embedding can be used as a powerful tool to achieve a variety of nontrivial tasks, including lossless authentication using fragile watermarks, steganalysis of LSB embedding, and distortion-free robust watermarking.
Randomized Double-Blind Clinical Trial of Subcutaneously Injected Deoxycholate Versus a Phosphatidylcholine-Deoxycholate Combination for the Reduction of Submental Fat (2009)

Under the conditions employed, injections of deoxycholate or phosphatidylcholine/deoxycholate into the submental fat produced minimal aesthetic improvement overall. No apparent differences in efficacy or adverse events were observed with the inclusion of phosphatidylcholine. Enhanced neck profiles in several subjects demonstrate a proof of concept that warrants further study utilizing a validated, submental profile grading scale and methods to optimize dose and technique.
Red Blood Cell Microparticles: Clinical Relevance (2012)

Microparticles are small phospholipid vesicles of less than 1 µm released into the blood flow by various types of cells such as endothelial, platelet, white or red blood cells. They are involved in many biological and physiological processes including hemostasis. In addition, an elevated number of microparticles in the blood is observed in various pathological situations. In the context of transfusion, erythrocyte-derived microparticles are found in red blood cell concentrates. Their role is not elucidated, and they are considered as a type of storage lesion. The purpose of this review is to present recent data showing that erythrocyte-derived microparticles most likely play a role in transfusion medicine and could cause transfusion complications.
Selective up-regulation of claudin-1 and claudin-2 in colorectal cancer. (2007)

Claudin-1 and claudin-2 were found to be overexpressed in CRC tissues. They may be useful as tumor markers and targets for the treatment of colorectal cancer.
Amount of DNA in plasma and cancer risk: A prospective study (2004)

Levels of plasma DNA concentrations in cancer patients have been shown to be higher than the plasma DNA concentrations found in healthy subjects. The value of plasma DNA levels for development of neoplastic or pulmonary disease was evaluated in a large prospective study. Plasma samples (n = 1,184) were analyzed from 776 controls, 359 cases of cancer (lung, bladder, oral cavity, pharynx, larynx, leukemia) and 49 deaths from chronic obstructive pulmonary disease (COPD), including never smokers and ex-smokers, from 9 countries across Europe. The amount of plasma DNA was variable across the European Prospective Investigation into Cancer and Nutrition (EPIC) centers. High DNA concentrations in some centers might be due to the type of population recruited and/or the treatment of the samples. An elevated and statistically significant odds ratio (OR) was found for COPD deaths (OR = 2.53; 95% CI = 1.06-6.02), while nonsignificant increased ORs were present for oral cancers, cancers of the pharynx and larynx and leukemia. When the analyses were stratified by time since recruitment (below or above 36 months), the increased ORs were limited to the more recent period of recruitment, i.e., a time elapsed between blood drawing and disease onset lower than 36 months. This was particularly true for COPD deaths (OR = 12.7; 95% CI = 1.57-103) and leukemia (OR = 2.37; 95% CI = 1.20-4.67).
<title>Knowledge-based segmentation of intrathoracic airways from multidimensional high-resolution CT images</title> (1994)

A critically important component in the development of new methods for treatment of pulmonary diseases is the development of sensitive techniques for assessing alterations in regional lung structure and function. We describe an automated method for segmentation of airway trees from 3-D sets of CT images. The method is based on a combination of conventional 3-D seeded region growing that is used to identify large airways, knowledge- based 2-D segmentation of individual CT slices to identify probable locations of smaller diameter airways, and merging of airway regions across the 3-D set of slices resulting in a tree-like airway structure. The preliminary validation of the method was done in eighty 3 mm thick CT sections from two 40 slice data sets of a canine thorax scanned with lungs held at 1.5 kPa and 2.5 kPa. The method's performance was compared with that of the conventional 3-D region growing method. The knowledge-based approach to identification of potential airways in individual image slices substantially outperforms the conventional method and promises to be applicable to in vivo pulmonary CT images.
Eradication of Established B-cell Lymphoma by CD19-specific Murine T Cells is Dependent on Host Lymphopenic Environment and Can be Mediated by CD4+ and CD8+ T Cells (2009)

B-cell malignancies seem to be particularly amenable to immunotherapy and as such make particularly attractive targets for adoptive T-cell therapy. Murine T cells gene-modified to express a chimeric immune receptor specific for CD19+ (aCD19z) efficiently kill CD19 B-cell lymphoma cells in vitro. aCD19z T cells also secrete high levels of interleukin-2 during culture with target cells in a CD86 independent manner. aCD19z T cells proved effective at eradicating established B-cell lymphoma in a syngeneic model system when combined with a lymphodepleting preconditioning regimen. In mice deficient of T, B, and natural killer cells (severe combined immunodeficient/Beige), aCD19z T cells efficiently eradicated long-term (13 d) established tumors with 100% of treated animals remaining tumor free for greater than 77 days. Although gene-modified CD4+ and CD8+ were both active in this setting, poor engraftment by CD8+ T cells coupled with the rigorous expansion of CD4+ cells in the Balb/c background suggests that CD4+ T cells may be playing a predominant role in lymphoma rejection in this model. Taken together, the therapeutic effectiveness of aCD19z T cells in this model supports a recently opened phase 1 trial of this receptor in non-Hodgkin lymphoma.
Targeting of Proteins Derived from Self‐Processing Polyproteins Containing Multiple Signal Sequences (2004)

The 18aa 2A self-cleaving oligopeptide from foot-and-mouth disease virus can be used for co-expression of multiple, discrete proteins from a single ORF. 2A mediates a co-translational cleavage at its own C-terminus and is proposed to manipulate the ribosome into skipping the synthesis of a specific peptide bond (producing a discontinuity in the peptide backbone), rather than being involved in proteolysis. To explore the utility of the system to target discrete processing products, self-processing polyproteins comprising fluorescent proteins flanking 2A were constructed, permutating both the type of signal sequence and the location within the polyprotein. A polyprotein comprising a protein bearing an N-terminal signal sequence, 2A, then a protein lacking any signal sequence, was constructed. Interestingly, both proteins were translocated into the endoplasmic reticulum. Despite the discontinuity in the peptide backbone, the mammalian ribosome:translocon complex did not disassemble--the second protein (lacking any signal) 'slipstreamed' through the translocon formed by the first (signal-bearing) protein. These polyprotein systems provide a novel method of targeting proteins to different subcellular sites by transfection with a plasmid encoding a single ORF. The inclusion of a fluorescent reporter enables visualisation of expression levels, whilst inclusion of a selectable marker enables stable cell-lines to be established rapidly.
Alzheimer's neurofibrillary pathology and the spectrum of cognitive function: Findings from the Nun Study (2002)

The development of interventions designed to delay the onset of dementia highlights the need to determine the neuropathologic characteristics of individuals whose cognitive function ranges from intact to demented, including those with mild cognitive impairments. We used the Braak method of staging Alzheimer's disease pathology in 130 women ages 76-102 years who were participants in the Nun Study, a longitudinal study of aging and Alzheimer's disease. All participants had complete autopsy data and were free from neuropathologic conditions other than Alzheimer's disease lesions that could affect cognitive function. Findings showed a strong relationship between Braak stage and cognitive state. The presence of memory impairment was associated with more severe Alzheimer's disease pathology and higher incidence of conversion to dementia in the groups classified as having mild or global cognitive impairments. In addition to Braak stage, atrophy of the neocortex was significantly related to the presence of dementia. Our data indicate that Alzheimer's neurofibrillary pathology is one of the neuropathologic substrates of mild cognitive impairments. Additional studies are needed to help explain the variability in neuropathologic findings seen in individuals whose cognitive performance falls between intact function and dementia.
New prognostic histological parameter of invasive ductal carcinoma of the breast: Clinicopathological significance of fibrotic focus (2000)

Immunohistochemistry, DNA ploidy analysis and molecular genetics have made it possible to predict the outcome of breast cancer more precisely than routine histological examination alone. However, in routine practice, it is difficult to incorporate these methodologies in all cases. If certain histological parameters can accurately predict the outcome of patients with breast cancer, they would be more practical for routine use. We showed that the presence of fibrotic focus (FF) in invasive ductal carcinoma (IDC) is closely associated with c-erbB-2 or p53 protein expression, high proliferative activity, and high angiogenesis of the tumors. Furthermore, multivariate analyses with well-known prognostic parameters for IDC demonstrated that the presence of FF is the most useful independent parameter to predict IDC patient outcome. In addition, our data suggested that the interaction between tumor cells and stromal fibroblasts may play an important role in the formation of FF in IDC based on growth factor and growth factor receptor protein expression in the tumor cells and fibroblasts forming FF. Based on the results of our clinicopathological studies, we propose a new prognostic classification scheme for the prediction of IDC patient outcome, which consists of FF, nuclear atypia, and fat invasion. This classification has superior predicting power to existing prognostic classifications.
Trapping of intermediates during the refolding of recombinant human epidermal growth factor (hEGF) by cyanylation, and subsequent structural elucidation by mass spectrometry (1998)

Human epidermal growth factor (hEGF) contains 53 amino acids and three disulfide bonds. The unfolded, reduced hEGF is allowed to refold under mildly alkaline conditions. The folding is quenched at different time points by adjusting the pH to 3.0 with an acetic acid solution of 1-cyano-4-dimethylamino-pyridinium (CDAP) which traps folding intermediates via cyanylation of free sulfhydryl groups. The mixture of cyanylated intermediates is separated by reversed-phase HPLC; the fractions collected are identified by mass spectrometry. The disulfide structures of the intermediates are then determined by specific chemical cleavage and mass-mapping by MALDI-MS, a novel approach developed in our laboratory. The procedure of quenching and trapping of disulfide intermediates in acidic solution minimizes sulfhydryl-disulfide exchange, and therefore provides a good measure of folding kinetics and preservation of intermediate species. Our cyanylation methodology for disulfide mapping is simpler, faster, and more sensitive than the more conventional approach. Among 18 folding intermediates isolated and identified at different time points, disulfide structures of seven well-populated intermediates, including two non-native isomers with scrambled disulfide structures, one 2-disulfide intermediate, and four 1-disulfide intermediates, have been characterized; most of them possess non-native disulfide structures.
SYNCHRONIZATION OPERATIONS FOR DISCONNECTED IMAP4 CLIENTS (1994)

Malaria is endemic in Malaysia. Leishmaniasis is a protozoan infection rarely reported in Malaysia. Here, a 24-year-old Nepalese man who presented with prolonged fever and hepatosplenomegaly is reported. Blood film examination confirmed a Plasmodium vivax malaria infection. Despite being adequately treated for malaria, his fever persisted. Bone marrow examination showed presence of Leishman-Donovan complex. He was successfully treated with prolonged course of amphotericin B. The case highlights the importance of awareness among the treating physicians of this disease occurring in a foreign national from an endemic region when he presents with fever and hepatosplenomegaly. Coinfection with malaria can occur although it is rare. It can cause significant delay of the diagnosis of leishmaniasis.
Active Flow Control for High Lift Airfoils: Separation Versus Circulation Control (2007)

*† ‡ § Wind tunnel investigations were conducted with the goal of gaining a better understanding of the mechanisms governing Active Flow Control (AFC) for flows dominated by large separated regions and its effects on separation control versus circulation control. Inviscid solutions were calculated to gain insight into the pressure distribution around the leading edge and flap shoulder as well as set goals for the AFC application. This series of tests utilized the ADVINT 5%-scale airfoil model. Steady blowing AFC was used extensively in conjunction with a surface tangent, downstream facing slot located immediately upstream of the flap on the trailing edge of the main element. AFC amplitude sweeps were performed for several flap deflections and free stream velocities over a wide range of angles of attack. The data were compared to the inviscid solutions to show that significantly enhanced lift can be obtained without controlling flow separation, and lift can be enhanced beyond inviscid levels through control of separation in addition to circulation enhancement for an extremely high energy input. The tests also reveal two other important mechanisms for control of aerodynamic forces on lifting bodies: the direct momentum vectoring of the AFC and “super inviscid” performance along surfaces with the aid of high-speed attached jets. Optimizing the performance with AFC requires understanding these two mechanisms in addition to separation and circulation control, and the dependence of all four on the various control parameters. Understanding previous results, including those referred to as “super circulation” or Coanda type upper-surface blowing, requires the type of insight revealed by the present experiments. The results are also very helpful in deciding on the choice of AFC methodology between steady and unsteady suction or blowing and zero mass flux (ZMF).
Spontaneous release of interferon gamma by intestinal lamina propria lymphocytes in Crohn's disease. Kinetics of in vitro response to interferon gamma inducers. (1991)

The spontaneous induced release of interferon gamma (IFN gamma) by cultured intestinal lamina propria lymphocytes was investigated in patients with Crohn's disease. In contrast to normal lymphocytes, intestinal lymphocytes from these patients spontaneously released IFN gamma and seemed to contain IFN gamma in their cytoplasm. Autologous peripheral lymphocytes did not release IFN gamma. When stimulated with interferon inducers lamina propria lymphocytes from Crohn's disease tissue showed an increase in IFN gamma release 24 hours after induction with no appreciable further increase over the next two days of culture, while in control cells, either peripheral or intestinal, IFN gamma release progressively increased, peaking 72 hours after induction. These findings indicate that in Crohn's disease the intestinal lymphocytes are stimulated in vivo to produce IFN gamma and that the spontaneous IFN gamma production is compartmentalised to the gut lymphocytes. These data support the concept that locally released IFN gamma has a crucial role in cell interactions in the lamina propria and contribute to the locally occurring immune phenomena in Crohn's disease, including the increased epithelial expression of major histocompatibility complex class II antigens.
Transformations of Cyclic Olefins Mediated by Tungsten Nitrosyl Complexes (2008)

This report describes investigations that have elucidated the nature, extent, and mechanism of the cyclic-olefin oligomerization effected by a series of tungsten precatalysts, with particular focus on Cp*W(NO)(CH2CMe3)2 (1) and Cp*W(NO)(CH2SiMe3)(η2-CPhCH2) (2). Upon thermolysis, these precatalysts oligomerize simple cyclic olefins, from cyclopentene to cyclooctene, into ring-retaining oligomers as high as dodecamers (depending on the substrate) with remaining sites of unsaturation. Precatalyst initiation involves the coupling of one equivalent of the substrate with the reactive 16e intermediate thermally generated by the precatalyst (i.e., an alkylidene by 1 or an η2-alkyne complex by 2), followed by rearrangement of the coupled ligand in the metal’s coordination sphere either to an olefin or to a diene (with concomitant loss of two hydrogen atoms). The rearranged ligand is displaced from the metal center as two equivalents of substrate coordinate to form a putative bis-olefin complex, Cp*W(NO)(cyclic olefin)2, that represents the convergent entry point to the catalytic cycle for the precatalysts. The coordinated olefins undergo metal-mediated coupling to form a metallacyclopentane complex. The metallacycle then undergoes β-hydrogen activation and reductive elimination to generate an η2-cyclic-olefin dimer. Further incorporation of substrate leads to formation of trimers and higher oligomers. Alternatively, expulsion of any coordinated oligomer from the tungsten center regenerates the reactive bis-olefin complex. Finally, decomposition of the tungsten catalyst species is consistent with a bimetallic pathway. All new organometallic complexes have been characterized by conventional spectroscopic and analytical methods, and the solid-state molecular structures of several compounds have been established by X-ray crystallographic analyses.
Membranes from both Th1 and Th2 T cell clones stimulate B cell proliferation and prepare B cells for lymphokine-induced differentiation to secrete Ig (1991)

Abstract Plasma membranes from the mitogen-activated mouse Th2 cell clone D10.G4.1 have recently been shown to provide the cell contact-dependent signals necessary for the induction of small B cell proliferation. Together with the Th2-derived lymphokines IL-4 and IL-5, these membranes stimulate production of Ig isotypes identical to those produced when B cells were stimulated by intact Th2 cells. In contrast, Th1 clones are poor inducers of Ig production in vitro. This could be solely due to differences in the lymphokines released by Th1 and Th2 cells or to differences in the cell-cell contact signals delivered by activated Th1 and Th2 cells. We report that membranes from three different activated Th1 clones induced strong Ag-independent proliferation of small dense B cells. The level of B cell proliferation was enhanced approximately fourfold by the addition of lymphokine-containing supernatant from Con A-activated Th2 cells and was unaffected by any of the lymphokine-containing supernatants from Con A-activated Th1 clones. As with D10.G4.1 membranes, Th1 membranes alone induced B cell proliferation but not secretion of Ig. However, addition of supernatant from Con A-activated D10.G41 cells, but not any supernatants from Con A-activated Th1 cells, induced Ig secretion of all isotypes. These effects were shown to not simply result from increased B cell numbers after stimulation with Th2 lymphokines. Thus, Th1 cell clones seem to poorly induce antibody responses entirely because of their lymphokine repertoire and not because of differences or deficiencies in the ability of these cells to deliver cell contact-dependent signals to B cells.
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer (2008)

Paired-end sequencing is emerging as a key technique for assessing genome rearrangements and structural variation on a genome-wide scale. This technique is particularly useful for detecting copy-neutral rearrangements, such as inversions and translocations, which are common in cancer and can produce novel fusion genes. We address the question of how much sequencing is required to detect rearrangement breakpoints and to localize them precisely using both theoretical models and simulation. We derive a formula for the probability that a fusion gene exists in a cancer genome given a collection of paired-end sequences from this genome. We use this formula to compute fusion gene probabilities in several breast cancer samples, and we find that we are able to accurately predict fusion genes in these samples with a relatively small number of fragments of large size. We further demonstrate how the ability to detect fusion genes depends on the distribution of gene lengths, and we evaluate how different parameters of a sequencing strategy impact breakpoint detection, breakpoint localization, and fusion gene detection, even in the presence of errors that suggest false rearrangements. These results will be useful in calibrating future cancer sequencing efforts, particularly large-scale studies of many cancer genomes that are enabled by next-generation sequencing technologies.