gebhart/patrepeval huggingface dataset:
Immunohistochemical Double-Hit Score Is a Strong Predictor of Outcome in Patients With Diffuse Large B-Cell Lymphoma Treated With Rituximab Plus Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone (2012)

The immunohistochemical DHS defined a large subset of DLBCLs with double-hit biology and was strongly associated with poor outcome in patients treated with R-CHOP.
Recent concepts on vitamin D in children and adolescents (2009)

Vitamin D is an important fat-soluble vitamin that functions as a prohormone and affects bone mineralization and calcium homeostasis. Vitamin D deficiency causesboth musculoskeletal manifestations, including rickets, and extra-musculoskeletal symptoms. Because vitamin D is naturally present in only some foods, intake of daily foods cannot meet the dietary reference intake for vitamin D. Sunlight is the main source of vitamin D in humans therefore, the lack of sunlight can easily cause vitamin D deficiency in children and adolescents. Vitamin D deficiency can be diagnosed on the basis ofits typical clinical manifestation, laboratory tests, and radiologic findings. Detection of vitamin D deficiency in children or adolescents necessitates the simultaneous administration of vitamin D and calcium supplements. To prevent vitamin D deficiency, 200 IU of daily vitamin D intake is recommended in infants, and 400 IU of daily vitamin D intake is recommended in Korean children and adolescents.
Chronic inflammation upregulates chemokine receptors and induces neutrophil migration to monocyte chemoattractant protein-1 (1999)

Monocyte chemoattractant protein-1 (MCP-1) is a CC chemokine that stimulates monocyte recruitment when injected into tissues of healthy animals. However, the function of this chemokine in models with preexisting inflammation is not known. Therefore, MCP-1 was superfused over the mesentery of naive rats or rats with chronic adjuvant-induced vasculitis. MCP-1 elicited increased leukocyte transendothelial migration in adjuvant-immunized rats compared with naive animals. Surprisingly, histology revealed that neutrophils constituted the majority of leukocytes recruited in adjuvant-immunized animals. In vitro, MCP-1 was also able to induce chemotaxis of neutrophils isolated from adjuvant-immunized rats but not from naive rats. Flow cytometry revealed novel expression of the CC chemokine receptors CCR1 and CCR2 on neutrophils from adjuvant-immunized animals. In naive animals, an antibody against CD18 blocked leukocyte adhesion and emigration in response to MCP-1. In adjuvant-immunized animals, leukocyte adhesion was reduced by antibodies against the alpha4-integrin but not by antibodies against CD18. However, the CD18 antibody did block emigration. To our knowledge, this study is the first to show increased sensitivity to a CC chemokine in a model with preexisting inflammation, and altered leukocyte recruitment profiles in response to MCP-1. It also demonstrates that CD18 is required for chemokine-induced leukocyte transendothelial migration, independent of its known role in mediating firm adhesion. J. Clin. Invest. 103:1269-1276 (1999).
Limiting dilution analysis of cytotoxic T lymphocytes to human immunodeficiency virus gag antigens in infected persons: in vitro quantitation of effector cell populations with p17 and p24 specificities. (1991)

The presence of cytotoxic T lymphocytes (CTL) to the gag antigens of human immunodeficiency virus (HIV) has been described in infected populations. We found that the majority of this immune response as measured in bulk CTL assays of unstimulated peripheral blood mononuclear cells (PBMC) is directed against the p24 component of the p55 gag precursor protein. Using limiting dilution analysis of this effector cell population we confirm that the majority of activated gag-specific CTL circulating in the PBMC of infected hemophilic patients are directed at p24 determinants and are present at frequencies of 1/36,000 to 1/86,000 lymphocytes. By performing in vitro stimulation after limiting dilution, the precursor population of gag-specific CTL are characterized and quantitated. HIV gag-specific CTL precursors are identified at frequencies of 1/1700 to 1/17,000 lymphocytes and are made up of cells with both p17 and p24 specificities. No HIV gag-specific CTL precursor cells are identified in the PBMC of HIV-uninfected individuals. These studies demonstrate that CTL directed at both p17 and p24 determinants make up the cellular immune repertoire in HIV-infected individuals but that only the p24-specific CTL are routinely found in an activated state in the circulation.
Nutrition and breast cancer. (1993)

A range of current information links nutrition and dietary factors to the risk of developing breast cancer, as well as to survival and outcomes after a diagnosis of breast cancer. Epidemiologic and other data suggest that high-fat and low-fiber diets are associated with an increased risk of breast cancer. Several pilot intervention studies have been performed to decrease dietary fat intake in women with breast cancer. Other studies suggest that weight gain after breast cancer is common and may be detrimental to survival. Taken together, all of these data suggest that further studies should be undertaken to better understand the relationship between nutritional factors and the development of breast cancer.
Interface-dependent magnetotransport properties for thin Pt films on ferrimagnetic Y3Fe5O12 (2014)

We have studied magnetoresistance and Hall effects for 1.8-nm-thick Pt films grown on a ferrimagnetic insulator Y3Fe5O12 in a wide temperature (0.46–300 K) and magnetic-field (−15 to 15 T) region. In the low-temperature regime where quantum corrections to conductivity are observed, weak antilocalization behavior observed in Pt films is critically suppressed when the film is attached to Y3Fe5O12. Hall resistance in the Pt film is also affected by Y3Fe5O12, and it exhibits logarithmic temperature dependence in a broad temperature range. The magnetotransport properties in the high-field range are significantly influenced by the interface between Pt and Y3Fe5O12.
Impact of the increasing use of immunosuppressants in Crohn’s disease on the need for intestinal surgery (2005)

Although immunosuppressants have been used more frequently over the last 25 years, there was no significant decrease of the need for surgery, or of intestinal complications of Crohn's disease.
Phycobilisomes: Structure and Dynamics (1982)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Isolation of murine fetal hemopoietic progenitor cells and selective fractionation of various erythroid precursors (1981)

Hemopoietic progenitor cells (colony- and cluster-forming cells in semisolid agar) were purified from light density CBA murine fetal liver cells using fluorescein-conjugated pokeweed mitogen (PWM) and a rhodamine-conjugated antineutrophil serum sandwich (alpha N) and three-parameter fluorescence-activated cell sorting. All clonable progenitor cells were highly enriched (36-50-fold) in PWM-positive (greater than channel 15), alpha N-negative (less than channel 30) fractions with relatively high intensity (greater than 100) low angle light scatter. No separation was achieved between different types of progenitor cells (granulocyte-macrophage and erythroid colony-forming cells). The enriched fraction was a pure population of large, basophilic, undifferentiated blast cells, and in agar cultures stimulated with colony-stimulating factors, up to 90% of the enriched cells were hemopoietic progenitor cells capable of varying levels of clonal proliferation. Further fractionation based on increasing fluorescence with PWM separated into discrete populations, nonproliferative morphologically recognizable erythroid cells, late erythroid progenitor cells (day 2 CFU-E), and cells forming pure or mixed erythroid burst colonies. In addition, the majority of pluripotential hemopoietic stem cells (CFU-SS) were clearly separated from progenitor cells forming colonies in vitro. The present techniques provide suitable numbers of enriched progenitor cells for a variety of biological and biochemical studies.
Binge-Eating Disorder in Adults (2016)

Agency for Healthcare Research and Quality.
Development of actuated and sensor integrated forceps for minimally invasive robotic surger (2005)

In minimally invasive surgery (MIS) the patient's skin forms a spatial barrier between the operation area and the surgeon. This prevents direct access to the operation site which causes a lack of dexterity and limits the sensation of tissue manipulation forces, therefore complicating MIS procedures significantly. A telepresence approach can overcome these limitations: Additional degrees of freedom (DoF) inside the patient provide full manipulability and force torque sensors at the distal end of the instrument allow precise measurement of interaction forces. Using a suitable man-machine interface and free cartesian motion kinaesthetic feedback can be achieved, thus providing a virtual open surgery environment to the surgeon. This article focuses on the development and first results of actuated and sensor integrated instruments as part of the DLR minimally invasive robotic surgery (MIRS) setup. The instruments as a front-end part of the MIRS setup form one base of a telepresence working environment and are crucial for semi-autonomous functions, e.g. motion compensation.
Abietane Diterpenoids from the Barks of Cryptomeria japonica (2006)

From the bark of Cryptomeria japonica were isolated sugikurojins I (1) and J (2), and an abietane derivative (3) was obtained for the first time as a natural product. These structures were elucidated primarily through extensive NMR experiments. Sugikurojin I (1) has a unique skeleton incorporating an abietane diterpene and a 1,10-secocadinane sesquiterpene. Sugikurojin J (2) is a peroxyester of hydroxyabietane diterpene and isopimarane acid diterpene. Compound 3 was p-quinone acid, which occurred by cleavage between C-7 and C-8 of sugiol; it was deduced to [4'-isopropyl-1(S),3,3-trimethyl-3',6'-dioxo-bicyclohexyl-1',4'-dien-2(R)-yl]-acetic acid. Also obtained in this investigation were three known diterpenes (4-6).
Isothermal micro calorimetry – a new method for MIC determinations: results for 12 antibiotics and reference strains of E. coli and S. aureus (2009)

IMC can be a powerful tool for determining the effects of antibiotics on microorganisms in vitro. It easily provides accurate MICs - plus a potential means for analyzing and comparing the modes of action of antibiotics at subinhibitory concentrations. Also IMC is completely passive, so after evaluation, ampoule contents (media, bacteria, etc.) can be analyzed by any other method desired.
Apo2L/TRAIL and immune regulation (2006)

Apo2L/TRAIL is a member of the TNF family, with its receptors DR4 and DR5 containing a death domain. Multiple tumors are sensitive to Apo2L/TRAIL-induced apoptosis, while normal cells are not, so it constitutes a promising new antitumoral therapy. In this review we deal rather with the physiological role of Apo2L/TRAIL, which, in one hand, is clearly related with immune antitumoral surveillance. However, a role of Apo2L/TRAIL as a fine-tuning regulator of the immune system, especially in the regulation of CD8+ T cell activation and memory, has been also demonstrated. In fact, Apo2L/TRAIL can be considered as an additional mechanism needed to prevent the development of autoimmune disease. Indeed, recent developments indicate that Apo2L/TRAIL can be also useful as a treatment against certain chronic autoimmune diseases.
Randomized, multicenter, dose-ranging trial of retigabine for partial-onset seizures (2007)

Adjunctive therapy with retigabine is well tolerated and reduces the frequency of partial-onset seizures in a dose-dependent manner.
Broadband fiber optic amplifiers (2002)

Broadband fiber optic amplifiers are key elements of DWDM systems and enablers for optical networks. New amplifier technologies for extending gain-bandwidth and equalizing the power deviation among WDM signals are discussed toward the next generation of ultra.-high-capacity DWDM systems.
TGF-beta mediates natural suppressor activity of IL-2-activated lymphocytes. (1994)

In addition to generating cells with non-MHC-restricted cytotoxic activity that is characteristic of lymphokine-activated killer (LAK) cells, in vitro cultures of lymphocytes with relatively high concentrations of IL-2 generate cells that simultaneously exhibit two distinct types of suppressor activities: veto, the ability of cells to specifically suppress generation of allo-CTL against their own histocompatibility Ags; and natural suppression, the ability of these same cells to nonspecifically suppress the generation of allo-CTL against both their own and unrelated cell surface Ags. In contrast to veto, which is known to require cell-cell contact between veto-active cells and precursors of CTL, natural suppression is known to be mediated by soluble factors. To identify and characterize suppressor factors that might mediate the natural suppressor activity of IL-2-activated lymphocytes, murine spleen cells were cultured with 1000 U/ml IL-2, and, after varying periods of incubation, their LAK cytolytic activity and natural suppressor activity was determined and cell supernatants were collected and tested for their effects on mixed lymphocyte culture-induced generation of allo-CTL. Like the IL-2-activated lymphocytes themselves, supernatants of these cells nonspecifically inhibited mixed lymphocyte culture-induced generation of allo-CTL. Rabbit anti-TGF-beta specifically neutralized the suppressive effects of both LAK cell supernatants and the IL-2-activated lymphocytes themselves. These findings indicate that TGF-beta is the primary mediator of the natural suppressor activity of IL-2-activated lymphocytes.
Complementation ofBrucella abortusRB51 with a FunctionalwboAGene Results in O-Antigen Synthesis and Enhanced Vaccine Efficacy but No Change in Rough Phenotype and Attenuation (2000)

Brucella abortus RB51 is a stable rough, attenuated mutant vaccine strain derived from the virulent strain 2308. Recently, we demonstrated that the wboA gene in RB51 is disrupted by an IS711 element (R. Vemulapalli, J. R. McQuiston, G. G. Schurig, N. Srirauganathan, S. M. Halling, and S. M. Boyle, Clin. Diagn. Lab. Immunol. 6:760-764, 1999). Disruption of the wboA gene in smooth, virulent B. abortus, Brucella melitensis, and Brucella suis results in rough, attenuated mutants which fail to produce the O polysaccharide (O antigen). In this study, we explored whether the wboA gene disruption is responsible for the rough phenotype of RB51. We complemented RB51 with a functional wboA gene, and the resulting strain was designated RB51WboA. Colony and Western blot analyses indicated that RB51WboA expressed the O antigen; immunoelectron microscopy revealed that the O antigen was present in the cytoplasm. Crystal violet staining, acryflavin agglutination, and polymyxin B sensitivity studies indicated that RB51WboA had rough phenotypic characteristics similar to those of RB51. Bacterial clearance studies of BALB/c mice indicated no increase in the survival ability of RB51WboA in vivo compared to that of RB51. Vaccination of mice with live RB51WboA induced antibodies to the O antigen which were predominantly of the immunoglobulin G2a (IgG2a) and IgG3 isotypes. After in vitro stimulation of splenocytes with killed bacterial cells, quantitation of gamma interferon in the culture supernatants indicated that RB51WboA immunization induced higher levels of gamma interferon than immunization with RB51. Mice vaccinated with RB51WboA were better protected against a challenge infection with the virulent strain 2308 than those vaccinated with RB51. These studies indicate that in addition to the disruption of the wboA gene there is at least one other mutation in RB51 responsible for its rough phenotype. These studies also suggest that the expressed O antigen in RB51WboA is responsible either directly or indirectly for the observed enhancement in the T-cell response.
Effect of CpG Oligodeoxynucleotides on the Immunogenicity of Pfs25, aPlasmodium falciparumTransmission-Blocking Vaccine Antigen (2003)

Antibodies directed against Pfs25, a protein present on the surface of zygotes and ookinetes of Plasmodium falciparum, completely block pathogen transmission. We evaluated the immunomodulatory effect of CpG oligodeoxynucleotides (ODN) on the immunogenicity of recombinant Pfs25 (rPfs25) formulated in alum (Al). Immunization of mice with rPfs25 plus CpG ODN improved both the antibody titer (a 30-fold-higher antibody response than that with rPfs25-Al alone) and avidity. Coadministration of CpG ODN dramatically enhanced the titer of immunoglobulin G2A (IgG2a) compared to the titer of the IgG1-dominant response caused by rPfs25-Al alone, and the sera from the CpG ODN-coadministered group completely blocked the transmission of P. falciparum parasites to mosquitoes, as determined by membrane feeding assays. However, transmission-blocking experiments revealed that blocking efficacy was dependent on high-titer antibody levels, independent of isotypes. These results suggest that CpG ODN can be used as an adjuvant to enhance the immunogenicity of rPfs25 as a malaria transmission-blocking vaccine.
Delivery of Bioactive Peptides and Proteins Across Oral (Buccal) Mucosa (2001)

The identification of an increasing array of highly potent, endogenous peptide and protein factors termed cytokines, that can be efficiently synthesized using recombinant DNA technology, offers exciting new approaches for drug therapy. However, the physico-chemical and biological properties of these agents impose limitations in formulation and development of optimum drug delivery systems as well as on the routes of delivery. Oral mucosa, including the lining of the cheek (buccal mucosa), floor of mouth and underside of tongue (sublingual mucosa) and gingival mucosa, has received much attention in the last decade because it offers excellent accessibility, is not easily traumatized and avoids degradation of proteins and peptides that occurs as a result of oral administration, gastrointestinal absorption and first-pass hepatic metabolism. Peptide absorption occurs across oral mucosa by passive diffusion and it is unlikely that there is a carrier-mediated transport mechanism. The principal pathway is probably via the intercellular route where the major permeability barrier is represented by organized array of neutral lipids in the superficial layers of the epithelium. The relative role of aqueous as opposed to the lipid pathway in drug transport is still under investigation; penetration is not necessarily enhanced by simply increasing lipophilicity, for other effects, such as charge and molecular size, also play an important role in absorption of peptide and protein drugs. Depending on the pharmacodynamics of the peptides, various oral mucosal delivery systems can be designed. Delivery of peptide/protein drugs by conventional means such as solutions has some limitations. The possibility of excluding a major part of drug from absorption by involuntary swallowing and the continuous dilution due to salivary flow limits a controlled release. However these limitations can be overcome by adhesive dosage forms such as gels, films, tablets, and patches. They can localize the formulation and improve the contact with the mucosal surface to improve absorption of peptides and proteins. Addition of absorption promoters/permeabilizers in bioadhesive dosage forms will be essential for a successful peptide/protein delivery system.
Support for software interrupts in log-based rollback-recovery (1998)

The piecewise deterministic execution model is a fundamental assumption in many log-based rollback-recovery protocols. Process execution in this model consists of intervals, each starting with the receipt of a message at an application-defined execution point. Execution within each interval is deterministic and messages are the only source of nondeterminism that affects the computation. This simple model excludes the nondeterminism that results when asynchronous signals or interrupts occur at arbitrary execution points. As a result, a wide range of applications cannot use log-based rollback-recovery in practice. We present a solution that removes this restriction and allows applications to replay interrupts at the same execution points during recovery. The solution relies on using a software counter to compute the number of instructions between the asynchronous signals during normal operation. Should a failure occur, the instruction counts are used to force the replay of these signals at the same execution points. The execution of the application thus can be replayed to recreate the prefailure state while accommodating nondeterminism due to asynchronous signals. We then use the deterministic replay of interrupts to solve another problem, namely tracking nondeterminism due to interleaved shared memory access in multithreaded applications on a single processor. We use the instruction counter solution to implement a user-level thread package in which thread scheduling decisions can be replayed if a failure occurs. By repeating the scheduling decisions during an execution replay, threads access the shared memory in the same order and the execution to be reconstructed. This technique allows multithreaded applications to use log-based rollback-recovery with low overhead, which was not previously possible. We carried out two prototype implementations that have shown the overhead is no more than a 6 percent slowdown in application execution on the DEC Alpha, and from 6 percent to 18 percent on the Inter Pentium. Thus, restrictions of the piecewise deterministic execution model can be lifted at a reasonable cost.
Interaction of integrins alpha v beta 3 and glycoprotein IIb-IIIa with fibrinogen. Differential peptide recognition accounts for distinct binding sites. (1990)

Glycoprotein (GP) IIb-IIIa is the major fibrinogen receptor on platelets and participates in platelet aggregation at the site of a wound. Integrin alpha v beta 3, which contains an identical beta-subunit, is expressed on endothelial cells and also serves as a fibrinogen receptor. Here, we demonstrate by several criteria that purified GPIIb-IIIa and integrin alpha v beta 3 bind to distinct sites on fibrinogen. First, a plasmin-generated fragment of fibrinogen lacking the RGD sequence at residues 572-574 retained the ability to bind GPIIb-IIIa, but failed to bind integrin alpha v beta 3. Second, a monoclonal antibody which exclusively recognizes the RGD sequence at fibrinogen A alpha chain residues 572-574 abolished interaction between integrin alpha v beta 3 and fibrinogen, but had only a minimal effect on fibrinogen binding to GPIIb-IIIa. Finally, we show that the difference in recognition of sites on fibrinogen by these two integrins is probably a consequence of their remarkably different ligand binding properties. Peptides corresponding to fibrinogen gamma chain residues 400-411 effectively blocked RGD sequence and fibrinogen binding by GPIIb-IIIa, but had no effect on the ability of integrin alpha v beta 3 to bind these ligands. We also show that integrin alpha v beta 3 has a higher affinity than GPIIb-IIIa for a synthetic hexapeptide containing the RGD sequence. In fact, this RGD-containing peptide was 150-fold more effective at blocking fibrinogen binding to integrin alpha v beta 3 than to GPIIb-IIIa. Collectively, our results demonstrate that integrins alpha v beta 3 and GPIIb-IIIa display qualitative and quantitative differences in their ligand binding properties, as is evident by their ability to interact with synthetic peptides. The ultimate result of these differences is the recognition of distinct sites on fibrinogen by the two integrins. These observations may have relevance in the processes of hemostasis and wound healing.