gebhart/patrepeval huggingface dataset:
Saccharomyces boulardiiStimulates Intestinal Immunoglobulin A Immune Response toClostridium difficileToxin A in Mice (2001)

Saccharomyces boulardii is a nonpathogenic yeast that protects against antibiotic-associated diarrhea and recurrent Clostridium difficile colitis. The administration of C. difficile toxoid A by gavage to S. boulardii-fed BALB/c mice caused a 1.8-fold increase in total small intestinal immunoglobulin A levels (P = 0.003) and a 4.4-fold increase in specific intestinal anti-toxin A levels (P < 0.001). Enhancing host intestinal immune responses may be an important mechanism for S. boulardii-mediated protection against diarrheal illnesses.
Crystal Structures of Cisplatin Bound to a Human Copper Chaperone (2009)

Copper trafficking proteins, including the chaperone Atox1 and the P(1B)-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.
Comparison of different methods to produce single‐strand DNA for identification of canned tuna by single‐strand conformation polymorphism analysis (1998)

By using single-strand conformation polymorphism (SSCP) analysis of three amplicons of the cytochrome b gene obtained by the polymerase chain reaction (PCR) it was possible to differentiate between various species of tunas and bonitos processed as canned fish. Four different techniques were used to produce single-strand DNA (ssDNA): (i) Denaturation of double-strand DNA (dsDNA) by formamide and alkali, (ii) two-step asymmetrical PCR, (iii) one-step asymmetrical PCR, and (iv) exonuclease digestion of the phosphorylated strand of dsDNA. The technique rendering optimal results depended on the type of amplicon (i.e. the sequence).
Over-expression of interleukin 10 in mucosal T cells of patients with active ulcerative colitis (2003)

Ulcerative colitis (UC), a chronic inflammatory bowel disease, exhibits pronounced increase of T lymphocytes in the inflamed mucosa. To understand the role of intestinal T lymphocytes in the pathogenesis of UC their cytokine production in the mucosa was analysed. Intestinal T lymphocytes of UC, Crohn's disease and control patients were analysed for cytokine mRNA levels by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) directly after isolation without in vitro stimulation. Frequencies of cytokine positive cells were determined in UC and control colon by immunomorphometry. T lymphocytes in normal colon expressed interleukin (IL)-2, interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha and transforming growth factor (TGF)-beta1, but not IL-4, IL-5 or IL-10. In UC, a highly significant increase in IL-10 mRNA levels in T lymphocytes and an increased frequency of IL-10 positive cells was seen in colon. IL-10 mRNA levels were also elevated in T lymphocytes of the non-inflamed ileum and correlated with disease activity at both locations. CD4+ T lymphocytes were the major source of IL-10 mRNA. IL-2, IFN-gamma and TNF-alpha mRNA levels were decreased in colonic T lymphocytes, and virtually no IL-2, IFN-gamma, TNF-alpha or TGF-beta positive cells were detected in basal lymphoid aggregates. However, scattered IL-10 positive cells were found here. Lamina propria outside the aggregates contained IL-10-, IFN-gamma, TNF-alpha and TGF-beta but not IL-2 positive cells. T cells of UC patients did not express IL-4 or IL-5. Taken, together the data suggest a generalized activation of IL-10 producing CD4+ T cells along the intestine of UC patients. The local environment seems to determine the biological consequences of elevated IL-10.
Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development (1998)

The formation of complex bacterial communities known as biofilms begins with the interaction of planktonic cells with a surface in response to appropriate environmental signals. We report the isolation and characterization of mutants of Pseudomonas aeruginosa PA14 defective in the initiation of biofilm formation on an abiotic surface, polyvinylchloride (PVC) plastic. These mutants are designated surface attachment defective (sad ). Two classes of sad mutants were analysed: (i) mutants defective in flagellar-mediated motility and (ii) mutants defective in biogenesis of the polar-localized type IV pili. We followed the development of the biofilm formed by the wild type over 8 h using phase-contrast microscopy. The wild-type strain first formed a monolayer of cells on the abiotic surface, followed by the appearance of microcolonies that were dispersed throughout the monolayer of cells. Using time-lapse microscopy, we present evidence that microcolonies form by aggregation of cells present in the monolayer. As observed with the wild type, strains with mutations in genes required for the synthesis of type IV pili formed a monolayer of cells on the PVC plastic. However, in contrast to the wild-type strain, the type IV pili mutants did not develop microcolonies over the course of the experiments, suggesting that these structures play an important role in microcolony formation. Very few cells of a non-motile strain (carrying a mutation in flgK) attached to PVC even after 8 h of incubation, suggesting a role for flagella and/or motility in the initial cell-to-surface interactions. The phenotype of these mutants thus allows us to initiate the dissection of the developmental pathway leading to biofilm formation.
One-dimensional stringlike cooperative migration of lithium ions in an ultrafast ionic conductor (2012)

In the recently developed ultrafast Li-ion conductor, Li10GeP2S12, our ab initio and molecular dynamics simulations have revealed a unique Li ion transport mechanism. The Li ions are discovered to migrate in a highly correlated fashion, stemming from the large Coulombic interaction between the mobile ions. The stringlike cooperative ionic motion is found to entail a rather low energy barrier, contributing to the unusually high ionic conductivity of this solid-state electrolyte. Such a collective migration mechanism may also be operative in other Li-ion battery electrolytes with high concentrations of mobile Li ions.
Diverse and potent activities of HGF/SF in skin wound repair (2004)

Genetic studies in the mouse have highlighted essential roles for several growth factors in skin repair and have offered a rationale for their use in therapy. The present study shows that the plasminogen-related growth factor HGF/SF (hepatocyte growth factor/scatter factor) promotes wound repair in homozygous diabetic db/db mice by recruiting neutrophils, monocytes, and mast cells to the wound; by promoting the migration of endothelial cells to the injured area; and by enhancing keratinocyte migration and proliferation. As a result, granulation tissue formation, wound angiogenesis, and re-epithelialization are all increased. The results demonstrate that HGF/SF affects and sustains all key cellular processes responsible for wound repair and point to a unique potential of this molecule for the therapy of chronic skin wounds.
In vivo localization of anti‐osteogenic sarcoma 791T monoclonal antibody in osteogenic sarcoma xenografts (1982)

Abstract Monoclonal antibody 791T/36, (mouse IgG 2b ) to the human osteogenic sarcoma 791T was isolated from hybridoma supernatants or ascites fluid and labelled with radioiodine. Following injection into immuno‐deprived CBA mice with subcutaneous xenografts of human osteogenic sarcomas 791T, 788T and 20s, reactive antibody was detectable in the circulation and there was a preferential uptake into tumour tissue compared with muscle, bone or visceral organs. The tumour uptake of radioactivity correlated with the size of the xenograft, up to 20% of the total body counts being within the tumour. Autoradiography of tissue sections showed activity mainly within the subcapsular regions of the xenografts. There was no tumour localization of radio‐labelled normal IgG. Furthermore, with a colon carcinoma and a bladder carcinoma, both unreactive with the 791T/36 antibody, there was no localization of radiolabelled antibody in xenograft growths. With 791T/36 monoclonal antibody labelled with 131 I localization into 791T xenografts could be visualized by whole‐body gamma scintigraphy with computerized 99m Tc‐pertechnetate or 113m In‐indium chloride‐labelled blood pool subtraction. These studies demonstrate the potential of monoclonal antibody to a human tumour for in vivo localization both for diagnostic purposes and as a carrier for therapeutic agents.
The evidence for interleukin-6 as an autocrine growth factor in malignancy. (1992)

Interleukin-6, IL-6, is a pleiotropic cytokine which plays a central role in defense mechanisms, including the immune response, acute phase reaction and hematopoiesis. Abnormal expression of the IL-6 gene has been suggested to be involved in the pathogenesis of a variety of diseases, especially rheumatoid arthritis, Castleman's disease, mesangial proliferative glomerulonephritis, multiple myeloma and Kaposi's sarcoma. In the case of multiple myeloma and Kaposi's sarcoma, the existence of an IL-6-IL-6 receptor autocrine loop has been implicated in the oncogenesis process. On the other hand, IL-6 has a potent anti-tumor activity against certain types of tumors. This anti-tumor effect is mediated by in vivo induction of tumor specific cytotoxic T cells and in part by a growth inhibitory activity of IL-6.
Fluid Saturation in Porous Media by X-Ray Technique (1951)

Abstract This paper describes the application of x-ray theory to design procedures inconnection with fluid saturation determinations during fluid flow experimentswith porous media. A reliable and rapid method for calibrating the x-rayapparatus is described. Extension of the method to fluid saturationdeterminations in three-fluid systems is described. Introduction In research on oil production problems a method is required which will givequickly the quantity of each component of a fluid flow system present at anycross-section of a porous medium. The sample of porous medium under investigation is usually referred to as acore. The ratio of the volume of one component to the total fluid volume isdefined as the saturation of the porous medium by that component. This ratio isgenerally given as per cent saturation. Some means of measuring saturation which have received considerationinclude: electrical conductivity of the fluids; emissions from radioactivetracers dissolved in the fluids; the radioactivity of silver caused byreflection of neutrons from hydrogen atoms in the fluids, the attenuation of amicrowave beam, the diminution and phase shift of ultrasonic wave trains, andthe reduction in intensity of x-ray beams in passing through the fluids. X-rays have already been used with some success. Since every material has adifferent power to absorb x-rays, the reduction in intensity of an x-ray beamas it passes through a core depends on the fluids present. The strength of theemergent beam can be found by converting its energy into a measurable form suchas heat or ionic current, or by its effect on a photographic plate orfluorescent screen.. The beam strengths could be interpreted as quantities ofknown fluids in the core if, previously, these beam strengths had beenidentified with a known combination of the same fluids. With some fluidcombinations it might be desirable to dissolve powerful x-ray absorbingmaterials in one or more of the fluids, to increase the differences in the beamstrengths for various fluid saturations. Boyer, Morgan and Muskat have described a method of measuring two componentfluid saturation. One component was air or water; the other, mineral seal oilin which was dissolved 25 per cent by weight of iodobenzene to increase itsabsorbing power. The x-ray source was a tungsten target tube operated at 43 kvpotential. The beam emerging from the core was measured as ionic currentflowing across an air-filled ionization chamber by means of an amplifyingcircuit and galvanometer. Another portion of the beam from the x-ray tube waspassed through a metal plate and measured in another ionization chamber. Thisportion, called the monitor beam, was used as an indication of the performanceof the x-ray tube. The galvanometer readings were calibrated against air-oilcore saturations, gravimetrically determined. The method was apparentlyestablished by experimental means. T.P. 3169
CELL TRANSPLANTATION OF GENETICALLY ALTERED CELLS ON BIODEGRADABLE POLYMER SCAFFOLDS IN SYNGENEIC RATS (1993)

Many severe metabolic deficiencies in children are caused by a single gene defect with a resultant single gene product deficiency. These diseases may be amenable to permanent cure using new techniques of gene transfer and cell transplantation. In many in vivo models of retroviral mediated gene therapy, a significant limiting factor is the ability to transplant a sufficient number of modified cells. To potentially circumvent this problem, we have developed a biodegradable polymer implant system capable of supporting large numbers of genetically modified cells. In this study, we inserted a reporter gene into syngeneic cultured normal fibroblasts and then transplanted these genetically modified cells into animals using synthetic biodegradable polymer fibers as temporary cell delivery scaffolds. To begin to develop a system capable of delivering desirable proteins secreted by genetically modified cells, Fischer 344 adult rat fibroblasts were transduced in tissue culture with a retrovirus containing the reporter gene Lac Z. These genetically modified cells (1.1 x 10(7) cells/graft) were then attached to the biodegradable polymer fibers and the polymer-cell graft was transplanted subdermally into syngeneic recipients (n = 9). There was persistence of the modified cells with expression of the reporter gene for at least 30 days. The estimated number of genetically modified cells per implanted graft decreased from a pretransplant value of 1.1 +/- 0.6 x 10(7) to 3.2 +/- 0.7 x 10(6) by 15 days after transplantation (P < 0.01). Thereafter, the cell number did not vary significantly to the conclusion of the study at day 30 (3.6 +/- 1.0 x 10(6) cells/graft). Evidence of ingrowth and incorporation of other stromal elements was present in the graft by 1 week post-transplantation, as judged by counterstained hematoxylin and eosin micrograph sections. Migration of modified cells to areas outside of the polymer-cell graft was not detected. Over the course of the study, there was little degradation of the polymer implant, although by day 30, evidence of early dissolution was evident. The number of polymer fibers per high power field increased slightly from 62.5 +/- 5.8 on day 1 to 77.3 +/- 26.6 on day 30 (P > 0.2). These data suggest that the use of biodegradable polymer fibers may permit the transplantation of genetically modified cells in sufficient numbers to deliver a therapeutically useful product. Polymer matrices allow for the attachment and site-specific transplantation of genetically modified cells.
The Antiinflammatory IgG (2008)

A post-translationally modified portion of IgG seems to be the critical agent that mediates the antiinflammatory effect of this molecule.
Potent High-Affinity Antibodies for Treatment and Prophylaxis of Respiratory Syncytial Virus Derived from B Cells of Infected Patients (2009)

Native human Abs represent attractive drug candidates; however, the low frequency of B cells expressing high-quality Abs has posed a barrier to discovery. Using a novel single-cell phenotyping technology, we have overcome this barrier to discover human Abs targeting the conserved but poorly immunogenic central motif of respiratory syncytial virus (RSV) G protein. For the entire cohort of 24 subjects with recent RSV infection, B cells producing Abs meeting these stringent specificity criteria were rare, <10 per million. Several of the newly cloned Abs bind to the RSV G protein central conserved motif with very high affinity (K(d) 1-24 pM). Two of the Abs were characterized in detail and compared with palivizumab, a humanized mAb against the RSV F protein. Relative to palivizumab, the anti-G Abs showed improved viral neutralization potency in vitro and enhanced reduction of infectious virus in a prophylaxis mouse model. Furthermore, in a mouse model for postinfection treatment, both anti-G Abs were significantly more effective than palivizumab at reducing viral load. The combination of activity in mouse models for both prophylaxis and treatment makes these high-affinity human-derived Abs promising candidates for human clinical testing.
Predicting Sequences of User Actions (1998)

AAAI/ICML 1998 Workshop on Predicting the Future: AI Approaches to Time-Series Analysis 1 People display regularities in almost everything they do. This paper proposes characteristics of an idealized algorithm that, when applied to sequences of user actions, would allow a user interface to adapt over time to an individual’s pattern of use. We describe a simple predictive method with these characteristics and show its predictive accuracy on a large dataset of UNIX commands to be at least as good as others that have been considered, while using fewer computational and memory resources.
IBM Multichip Multilayer Ceramic Modules for LSI Chips-Design for Performance and Density (1980)

The design objectives and features of two modules are outlined which, with their LSI chips, give significant advantages of performance, power reduction, logic gate density, and reliability in their IBM 4300 processor applications. In these applications an average module gate density of 196 gates/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is achieved. This is 30 times the density achieved in IBM's monolithic systems technology (MST). Even larger density improvements are realized at the card level.
Detecting Kernel-Level Rootkits Through Binary Analysis (2005)

A rootkit is a collection of tools used by intruders to keep the legitimate users and administrators of a compromised machine unaware of their presence. Originally, root-kits mainly included modified versions of system auditing programs (e.g., ps or netstat on a Unix system). However, for operating systems that support loadable kernel modules (e.g., Linux and Solaris), a new type of rootkit has recently emerged. These rootkits are implemented as kernel modules, and they do not require modification of user-space binaries to conceal malicious activity. Instead, these rootkits operate within the kernel, modifying critical data structures such as the system call table or the list of currently-loaded kernel modules. This paper presents a technique that exploits binary analysis to ascertain, at load time, if a module's behavior resembles the behavior of a rootkit. Through this method, it is possible to provide additional protection against this type of malicious modification of the kernel. Our technique relies on an abstract model of module behavior that is not affected by small changes in the binary image of the module. Therefore, the technique is resistant to attempts to conceal the malicious nature of a kernel module.
Resonator Theory for Hollow Waveguide Lasers (1974)

A numerical technique has been developed for analyzing the transverse modes of waveguide lasers with external mirrors. Propagation outside the guide is computed with the Fresnel-Kirchhoff diffraction integral and within the guide by decomposing the fields into the characteristic modes of the guide structure. The transverse modes of the entire waveguide-mirror system fall into a number of distinct classes: TE(0m), TM(0m), EH(1m), EH(2m), etc. For each class of modes, the, corresponding guide modes form a complete and orthogonal set and may be used as basis vectors to describe those modes. This reduces the mode analysis of the waveguide resonator to the diagonalization of a small (5 x 5 or 10 x 10) complex matrix. Guide losses, coupling losses, and mode shapes will be discussed for a number of interesting cases, with the Fresnel number of the waveguide ranging from 0.1 to 1.0 and with various values of mirror curvature and position. It will be shown that some vales of resonator parameters are particularly advantageous for achieving single mode operation.
New Therapeutic Directions for Advanced Pancreatic Cancer: Targeting the Epidermal Growth Factor and Vascular Endothelial Growth Factor Pathways (2008)

In advanced pancreatic cancer, single-agent gemcitabine became the standard therapy approximately 10 years ago. Subsequently, combinations of gemcitabine with fluorouracil, cisplatin, irinotecan, oxaliplatin, or pemetrexed produced no clear survival benefit. Among the newer approaches, targeting human epidermal growth factor receptor (HER-1/EGFR) shows promise. The U.S. Food and Drug Administration recently approved erlotinib (a HER-1/EGFR tyrosine kinase inhibitor) combined with gemcitabine for the first-line treatment of advanced pancreatic cancer. This combination showed a statistically significant survival benefit over gemcitabine alone in locally advanced or metastatic disease (the median overall survival time was 6.24 months versus 5.91 months; hazard ratio, 0.82; p = .038); however, the clinical significance of this survival difference has been questioned. Additionally, a large phase III trial where the addition of cetuximab (an anti-HER-1/EGFR monoclonal antibody [mAb]) to gemcitabine failed to result in a longer overall survival time than with gemcitabine alone has been reported. Targeting vascular endothelial growth factor (VEGF) with bevacizumab (a recombinant, humanized IgG1 mAb that binds to VEGF) in combination with gemcitabine was investigated in a phase II trial, with promising outcomes that were unfortunately not supported by a subsequent phase III study. While the future treatment of pancreatic cancer may be influenced by the potential of certain biomarkers to predict better response to molecular-targeted therapies, allowing individualization of patient therapy, there are currently no clear candidates, and this remains an interesting area for further investigation.
Myofibroblasts Induce Ectopic Activity in Cardiac Tissue (2007)

Focal ectopic activity in cardiac tissue is a key factor in the initiation and perpetuation of tachyarrhythmias. Because myofibroblasts as present in fibrotic remodeled myocardia and infarct scars depolarize cardiomyocytes by heterocellular electrotonic interactions via gap junctions in vitro, we investigated using strands of cultured ventricular cardiomyocytes coated with myofibroblasts, whether this interaction might give rise to depolarization-induced abnormal automaticity. Whereas uncoated cardiomyocyte strands were invariably quiescent, myofibroblasts induced synchronized spontaneous activity in a density dependent manner. Activations appeared at spatial myofibroblast densities >15.7% and involved more than 80% of the preparations at myofibroblast densities of 50%. Spontaneous activity was based on depolarization-induced automaticity as evidenced by: (1) suppression of activity by the sarcolemmal K(ATP) channel opener P-1075; (2) induction of activity in current-clamped single cardiomyocytes undergoing depolarization to potentials similar to those induced by myofibroblasts in cardiomyocyte strands; and (3) induction of spontaneous activity in cardiomyocyte strands coated with connexin 43 transfected Hela cells but not with communication deficient HeLa wild-type cells. Apart from unveiling the mechanism underlying the hallmark of monolayer cultures of cardiomyocytes, ie, spontaneous electromechanical activity, these findings open the perspective that myofibroblasts present in structurally remodeled myocardia following pressure overload and infarction might contribute to arrhythmogenesis by induction of ectopic activity.