gebhart/patrepeval huggingface dataset:
MUC1 is activated in a B-cell lymphoma by the t(1;14)(q21;q32) translocation and is rearranged and amplified in B-cell lymphoma subsets (2000)

The band 1q21 is among the most common sites affected by chromosomal translocations in lymphoid, myeloid, epithelial, and sarcomatous lesions. In non-Hodgkin's lymphoma (NHL), translocations and duplications affecting this chromosomal site are frequently, but not exclusively, seen in association with primary abnormalities such as the t(14;18)(q32;q21) and t(8;14)(q24;q32) translocations, suggesting a role for 1q21 rearrangements in tumor progression. We report here the characterization and cloning of breakpoints in a case of extranodal ascitic B-cell lymphoma with a t(1;14)(q21;q32) translocation. The breakpoints on the der(1) and der(14) chromosomes were mapped by fluorescence in situ hybridization and Southern blot analysis and cloned using an IGHG (Cgamma) probe. The translocation linked the IGHG4 switch (Sgamma4) sequences of the productively rearranged allele to chromosome 1 sequences downstream of MUC1, leaving the MUC1 transcriptional unit intact. MUC1 was markedly overexpressed in the tumor at the mRNA and protein levels relative to lymphoma cell lines lacking a 1q21 rearrangement. Presumably, MUC1 transcription is aberrantly regulated by the IGHA (Calpha) 3' enhancer element retained on the same chromosome. Screening of a panel of B-cell lymphomas by Southern blot analysis identified a subset with a 3' MUC1 breakpoint and another with low-level amplification of MUC1. MUC-1 mucin has previously been shown to be frequently overexpressed in human epithelial cancers and to be associated with tumor progression and poor clinical outcome. Thus, MUC1 activation by chromosomal translocation, rearrangement, and amplification, identified here for the first time in NHL, is consistent with its suggested role in tumorigenesis. (Blood. 2000;95:2666-2671)
Pseudopotential Analog for Zero-Range Photoassociation and Feshbach Resonance (2006)

A zero-range approach to atom-molecule coupling is developed in analogy to the Fermi-Huang pseudopotential approach to collisions. It is shown by explicit comparison to an exactly solvable finite-range model that replacing the molecular bound-state wave function with a regularized delta function can reproduce the exact scattering amplitude in the long-wavelength limit. Using this approach, we find an analytical solution to the two-channel Feshbach resonance problem for two atoms in a spherical harmonic trap, highlighting the strong dependence of the effective scattering length and bare-molecule population on the atom-molecule coupling strength.
Efficient block motion estimation using integral projections (1996)

Several efficient techniques have previously been proposed to reduce the computational burden of block matching for motion estimation in video coding. The goal is efficient motion estimation with minimal error in the motion-compensated predicted image. We present a block motion estimation scheme which is based on matching of integral projections of motion blocks with those of the search area in the previous frame. Like many other techniques, ours operates in a sequence of decreasing search radii, but it performs an exhaustive search at each level of the hierarchy. The projection method is much less computationally costly than block matching and has a prediction accuracy of competitive quality with both full block matching and other efficient techniques. Our algorithm also takes advantage of the similarity of motion vectors in adjacent blocks in typical imagery by subsampling the motion vector field. It has the added advantage of allowing parallel computation of vertical and horizontal displacements.
Optimizing Broadband SBS Slow Light in an Optical Fiber (2006)

We describe how to optimize slow-light via stimulated Brillouin scattering in a room temperature optical fiber that is pumped with a spectrally broadened laser. Our recent experimental results on broadband SBS slow-light will be discussed.
A Real-Time Health Monitoring System for Remote Cardiac Patients Using Smartphone and Wearable Sensors (2015)

Online telemedicine systems are useful due to the possibility of timely and efficient healthcare services. These systems are based on advanced wireless and wearable sensor technologies. The rapid growth in technology has remarkably enhanced the scope of remote health monitoring systems. In this paper, a real-time heart monitoring system is developed considering the cost, ease of application, accuracy, and data security. The system is conceptualized to provide an interface between the doctor and the patients for two-way communication. The main purpose of this study is to facilitate the remote cardiac patients in getting latest healthcare services which might not be possible otherwise due to low doctor-to-patient ratio. The developed monitoring system is then evaluated for 40 individuals (aged between 18 and 66 years) using wearable sensors while holding an Android device (i.e., smartphone under supervision of the experts). The performance analysis shows that the proposed system is reliable and helpful due to high speed. The analyses showed that the proposed system is convenient and reliable and ensures data security at low cost. In addition, the developed system is equipped to generate warning messages to the doctor and patient under critical circumstances.
Comparison of three techniques for the ex vivo elimination of T cells from human bone marrow. (1985)

The high incidence of graft-vs-host disease (GVHD) in allogeneic bone marrow transplantation (BMT) is a significant cause of morbidity and mortality, despite pharmacological prophylactic regimes. Laboratory technologies have been developed to eliminate the immunocompetent T-lymphocyte, the proposed effector cell in the GVHD reaction. In this study, three techniques for the ex vivo purging of T cells from human bone marrow (BM) were compared. BM treatment groups consisted of T-cell depletion by the monoclonal antibodies OKT3 and OKT11A plus complement (MoAb + C), soybean agglutination followed by sheep erythrocyte rosette depletion, or triple rosetting with neuraminidase-treated sheep erythrocytes. Mean final cell yields were 37.2 +/- 4.0%, 2.8 +/- 0.8%, and 2.5 +/- 1.3%, respectively, while final yields of BM progenitor cells, assayed in the double-layer soft-agar CFU-c assay, were 28.5 +/- 6.5%, 3.9 +/- 2.1%, and 10.5 +/- 3.8%, respectively. The three techniques were comparably efficient in elimination of mitogenic responses to irradiated allogeneic lymphoblastoid cells and cytotoxic lymphocyte responses of the BM. Immunofluorescence after T-cell depletion showed greater than 97.5% of all OKT3-positive cells to be eliminated by each technique. Despite the fact that all three techniques were effective in T-cell depletion, treatment with anti-T-cell MoAbs + C proved less labor-intensive and resulted in higher cell yields.
Differential Killing of Salmonella enterica Serovar Typhi by Antibodies Targeting Vi and Lipopolysaccharide O:9 Antigen (2016)

Salmonella enterica serovar Typhi expresses a capsule of Vi polysaccharide, while most Salmonella serovars, including S. Enteritidis and S. Typhimurium, do not. Both S. Typhi and S. Enteritidis express the lipopolysaccharide O:9 antigen, yet there is little evidence of cross-protection from anti-O:9 antibodies. Vaccines based on Vi polysaccharide have efficacy against typhoid fever, indicating that antibodies against Vi confer protection. Here we investigate the role of Vi capsule and antibodies against Vi and O:9 in antibody-dependent complement- and phagocyte-mediated killing of Salmonella. Using isogenic Vi-expressing and non-Vi-expressing derivatives of S. Typhi and S. Typhimurium, we show that S. Typhi is inherently more sensitive to serum and blood than S. Typhimurium. Vi expression confers increased resistance to both complement- and phagocyte-mediated modalities of antibody-dependent killing in human blood. The Vi capsule is associated with reduced C3 and C5b-9 deposition, and decreased overall antibody binding to S. Typhi. However, purified human anti-Vi antibodies in the presence of complement are able to kill Vi-expressing Salmonella, while killing by anti-O:9 antibodies is inversely related to Vi expression. Human serum depleted of antibodies to antigens other than Vi retains the ability to kill Vi-expressing bacteria. Our findings support a protective role for Vi capsule in preventing complement and phagocyte killing of Salmonella that can be overcome by specific anti-Vi antibodies, but only to a limited extent by anti-O:9 antibodies.
Bcl::Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System (2011)

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.
Parameter Based Methods for Compound Selection from Chemical Databases (1996)

Abstract Two algorithms for the selection of subsets of compounds from chemical databases are presented and discussed. The first is designed to select representative subsets whilst the second is intended to select compounds which cover the available property space. Both make use of calculated physicochemical parameters in contrast to more common methods based on molecular fingerprints. This is an approach to molecular similarity which has proved successful in the past. The methods are illustrated with examples and discussed.
L (+) lactic acid fermentation and its product polymerization (2004)

Lactic acid has been first introduced to us as early as 1780 as a sour component of milk. Ever since we have found its applications in food, pharmaceutical, cosmetic industries etc. Now there are emerging uses as a potential feedstock for the biodegradable polymer industry. The microorganisms being used for lactic acid fermentation, the raw materials reported, the various novel fermentation processes and its processing methods have been reviewed. The properties and applications of lactic acid, its derivatives and polymer have been discussed. The various routes to polymerization and the companies presently involved in lactic acid production have been covered.
Fibrin sealant: current and potential clinical applications. (1996)

There are few well-controlled studies of the clinical efficacy of fibrin sealant, defined by lives saved or reduced need for blood transfusions. Evaluation of fibrin sealant in trauma situations, e.g. liver laceration, has been difficult to perform. Only recently has fibrin sealant been actively promoted by US manufacturers as a commercially valuable alternative to the relatively inexpensive crude bovine thrombin and cryoprecipitate that are in current use. Regulatory agencies and manufacturers are aware that patients in the USA are receiving a suboptimal form of fibrin glue since cryoprecipitate is not virally inactivated and has a variable fibrinogen concentration. In addition, bovine thrombin is not regulated with respect to factor V content or any other impurities. During the past year regulatory agencies, together with manufacturers and clinicians, have begun to define clinically valid endpoints for efficacy of a commercially prepared fibrin sealant. These may include improvement in hemostasis compared with a placebo or agents considered to be 'standard of care'. Thus, the regulatory agencies may be willing to consider studies in animals that demonstrate efficacy as well as surrogate endpoints, such as reduced factor concentrate requirements in patients with severe hemophilia requiring dental extraction. As fibrin sealant becomes available in a liquid and potentially in a bandage form, it may also become an essential matrix for recombinant factors that can affect endothelial function.
Daily stress as a trigger of migraine attacks: Results of thirteen single-subject studies. (1990)

A 6-month longitudinal study examined whether migraine attacks were preceded by or occurred on stressful days. Every evening 13 patients filled out a questionnaire assessing daily stress. Analyses on single-subject level tested whether attacks occurred more often than expected by chance 3, 2, or 1 day after or on day when stress scores were in the upper third of the subject's distribution. Increased stress was generally not found for Days 2 and 3 before an attack, but often for Day 1 and on the migraine day itself. The latter findings were also significant on a group level.
7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection (2008)

Templated nucleic acid detection is an emerging bioanalytical method that makes use of the target DNA or RNA strand to initiate a fluorogenic reaction. The Staudinger reduction holds particular promise for templated sensing of nucleic acids because the involved functional groups are highly chemoselective. Here, the azidomethoxy group, which can be removed under Staudinger conditions, is used to cage 7-hydroxycoumarin fluorophores. Reduction by phosphines and subsequent loss of the azidomethoxy substituent induce a significant bathochromic shift of the major absorbance band in the near UV region. When excited at the appropriate wavelength, this change in the absorbance spectrum translates into a substantial fluorescence turn-on signal. The described profluorophores are readily conjugated to amino-modified DNAs and are rapidly uncaged by a triphenylphosphine-DNA probe under the control of a DNA template. In addition, turnover of the probes on the target strand occurs and yields substantial signal amplification.
p53 Attenuates Lipopolysaccharide-Induced NF-κB Activation and Acute Lung Injury (2009)

The transcriptional factor p53 has primarily been characterized for its central role in the regulation of oncogenesis. A reciprocal relationship between the activities of p53 and NF-kappaB has been demonstrated in cancer cells, but there is little information concerning interactions between p53 and NF-kappaB in inflammatory processes. In this study, we found that neutrophils and macrophages lacking p53, i.e., p53(-/-), have elevated responses to LPS stimulation compared with p53(+/+) cells, producing greater amounts of proinflammatory cytokines, including TNF-alpha, IL-6, and MIP-2, and demonstrating enhanced NF-kappaB DNA-binding activity. p53(-/-) mice are more susceptible than are p53(+/+) mice to LPS-induced acute lung injury (ALI). The enhanced response of p53(-/-) cells to LPS does not involve alterations in intracellular signaling events associated with TLR4 engagement, such as activation of MAPKs, phosphorylation of IkappaB-alpha or the p65 subunit of NF-kappaB, or IkappaB-alpha degradation. Culture of LPS-stimulated neutrophils and macrophages with nutlin-3a, a specific inducer of p53 stabilization, attenuated NF-kappaB DNA-binding activity and production of proinflammatory cytokines. Treatment of mice with nutlin-3a reduced the severity of LPS-induced ALI. These data demonstrate that p53 regulates NF-kappaB activity in inflammatory cells and suggest that modulation of p53 may have potential therapeutic benefits in acute inflammatory conditions, such as ALI.
Oil biosynthesis in microsomal membrane preparations from Mortierella alpina (2000)

Microsomal membrane preparations from Mortierella alpina catalysed the conversion of sn-glycerol 3-phosphate and [(14)C]oleoyl-CoA to radioactive phosphatidic acid, diacylglycerol and triacylglycerol. Experiments with lysophosphatidic acid and [(14)C]oleoyl-CoA gave a similar pattern of radioactivity in the complex lipids. The specific activity of lysophosphatidate acyltransferase was almost eight times greater than sn-glycerol-3-phosphate acyltransferase, indicating that the first acylation step was limiting in oil assembly in the microsomal membranes. Little conversion of radioactive oleate into phosphatidylcholine occurred, suggesting that triacylglycerol assembly and its relationship to phosphatidylcholine metabolism differed to that found in oilseeds.
Surface “Priming” for Layer-by-Layer Deposition:  Polyelectrolyte Multilayer Formation on Allylamine Plasma-Modified Poly(tetrafluoroethylene) (1997)

Allylamine plasma polymerization is reported as a method to surface-modify PTFE and to prepare substrates that promote layer-by-layer assembly of polyelectrolytes. Two conditions for the plasma polymerization that differ in radiofrequency power were studied. Both conditions (10 and 50 W) produce substrates that support layer-by-layer assembly, and well-defined multilayer structures are apparent in samples with greater than ∼10 layers. The substrates prepared at lower power yield more reproducible initial layer data; infrared spectra indicate a higher surface density of amine groups in the samples prepared at 10 W that likely leads to a higher surface charge density upon exposure to acidic aqueous solution. Poly(allylamine hydrochloride) and poly(sodium styrenesulfonate) were used to construct multilayer assemblies. XPS and contact angle data indicate stratified layers. XPS analysis also indicates that the stoichiometry of the assembly process is two ammonium ions per sulfonate group and that the average individual layer thickness is ∼6.1 Å.
Clinical Uses of Intravenous Immunoglobulins (1990)

Intravenous immunoglobulin is safe and effective in treating several human diseases. Additional randomized trials are needed.
HEMATOLOGIC CORRELATES AND THE ROLE OF ERYTHROCYTE CR1 (C3b RECEPTOR) IN THE DEVELOPMENT OF AIDS (1986)

Circulating immune complexes (CICs) are common in patients with the acquired immunodeficiency syndrome (AIDS) as in anemia. In our previous reports, we observed that the deposition of CICs on erythrocytes via C3b receptors (CR1) resulted in a defective CIC clearing system of erythrocytes and in high membrane osmotic fragility of such erythrocytes. We investigated the functional activity of erythrocyte CR1 in 89 patients with AIDS, 41 with AIDS related complex (ARC), 102 healthy homosexual volunteers, and 37 heterosexual males, in relation to the presence of CICs, antibody to lymphadenopathy associated virus/human T lymphotropic virus-III (LAV/HTLV-III), anemia, and the direct and indirect Coombs' tests. CICs were frequently found in all groups except heterosexual males. Absence of CR1 activity was observed in 85% of patients with AIDS, and in 59% with ARC. Impaired CR1 activity also occurred in the homosexual volunteer group. Positive direct Coombs' test and the presence of CICs correlated inversely with CR1 activity while a lowered hematocrit and the presence of antibody to LAV/HTLV-III correlated directly. Neither the sera nor the eluates from erythrocytes with a positive IgG Coombs' test contained IgG antibody against erythrocytes. This suggests decremental loss of CR1 activity progressing from asymptomatic LAV/HTLV-III antibody positive homosexual volunteers to the prodromal spectrum of ARC and finally progressing to a total disappearance in overt AIDS. Of 8 homosexuals volunteers demonstrating the composite of impaired CR1 activity, positive antibody to LAV/HTLV-III, and polyvalent positive direct Coombs' test (with gamma, mu, and C3b), all developed ARC or overt AIDS within 2 years of these observations.
EXPRESSION OF PRIMARY CILIA IN MAMMALIAN CELLS (1996)

Mammalian cells in vivo frequently express primary cilia. Although some fully differentiated cell types rarely, if ever, express them, most do, indicating that they are regular cell organelles. Their expression can also be explored in vitro, where conditions--physical and chemical, intrinsic and extrinsic--permit experimental approaches which give far greater control than in vivo. This 'state of the art' paper covers briefly the general biology of primary cilia, highlights the current situation with regard to our understanding of their relevance and importance in cell biology from various facets of our recent research, much of it in collaboration with other laboratories world-wide, and outline future work aimed at answering some basic and applied questions about them, within a context of an increasing awareness that signalling between cells is of the utmost importance in understanding proliferation control and its value in cancer research, the major remit of this unit.
Regulation of scavenger receptor, class B, type I, a high density lipoprotein receptor, in liver and steroidogenic tissues of the rat. (1996)

The scavenger receptor, class B, type I (SR-BI) binds HDL and mediates the selective transfer of cholesteryl esters from HDL to cultured cells. The tissue distribution of SR-BI in mice suggests that this receptor may deliver HDL-cholesterol to the liver and to nonplacental steroidogenic tissues. To examine the role of SR-BI in vivo, we determined its tissue and cell type-specific expression pattern and regulation in rats. High levels of immunodetectable SR-BI were present in the adrenal gland, ovary, and liver. In pregnant animals, the mammary gland also expressed high levels of the protein. SR-BI was localized by immunofluorescence to the surfaces of steroidogenic cells in the zona fasciculata and zona reticularis of the adrenal gland and to the corpus luteal cells of the ovary. High-dose estrogen treatment dramatically reduced SR-BI in the liver and increased SR-BI in the adrenal gland and corpus luteal cells of the ovary. These estrogen-induced increases in SR-BI in the adrenal gland and ovary were accompanied by enhanced in vivo uptake of fluorescent lipid from HDL. The administration of human chorionic gonadotropin induced a dramatic increase in SR-BI in the steroidogenic Leydig cells of the testes. These findings suggest that SR-BI mediates physiologically relevant uptake of cholesterol from HDL to nonplacental steroidogenic tissues in vivo.
Activation of the bgl operon by adaptive mutation (1998)

In growing Escherichia coli K12 cells, the cryptic bgl operon is activated 98% of the time by insertions of IS1 or IS5 into the control region, designated bglR. The activated bgl operon permits utilization of the beta-glucoside sugar arbutin as a sole carbon and energy source. The bgl operon is also activated by late-occurring mutations during prolonged selection on arbutin. The late-occurring mutations that occurred during prolonged carbon starvation in the presence of arbutin were "adaptive mutations" because they were specific to the presence of arbutin, and they did not occur during prolonged starvation in the absence of arbutin. The spectrum of late-arising mutations differed from that of early-arising, growth-dependent mutations in that 20% of the late-arising mutants resulted from mutations at the hns locus. This provides the first direct evidence for adaptive mutagenesis mediated by the insertion of IS elements. Because no special genetic background is required to select Bgl+ mutants, this affords the opportunity to study IS-element-mediated adaptive mutagenesis in a variety of genetic backgrounds, including the backgrounds of natural isolates of E. coli.