gebhart/patrepeval huggingface dataset:
Cystic Fibrosis Gene Therapy in the UK and Elsewhere (2015)

The cystic fibrosis transmembrane conductance regulator (CFTR) gene was identified in 1989. This opened the door for the development of cystic fibrosis (CF) gene therapy, which has been actively pursued for the last 20 years. Although 26 clinical trials involving approximately 450 patients have been carried out, the vast majority of these trials were short and included small numbers of patients; they were not designed to assess clinical benefit, but to establish safety and proof-of-concept for gene transfer using molecular end points such as the detection of recombinant mRNA or correction of the ion transport defect. The only currently published trial designed and powered to assess clinical efficacy (defined as improvement in lung function) administered AAV2-CFTR to the lungs of patients with CF. The U.K. Cystic Fibrosis Gene Therapy Consortium completed, in the autumn of 2014, the first nonviral gene therapy trial designed to answer whether repeated nonviral gene transfer (12 doses over 12 months) can lead to clinical benefit. The demonstration that the molecular defect in CFTR can be corrected with small-molecule drugs, and the success of gene therapy in other monogenic diseases, is boosting interest in CF gene therapy. Developments are discussed here.
Abnormalities in proximal small bowel motility in patients with cirrhosis (1993)

Because altered intestinal motility could be involved in the pathogenesis of small intestine bacterial overgrowth observed in some patients with cirrhosis, we investigated fasting proximal small bowel motility in 16 cirrhotic patients and 8 healthy controls. In addition, the effects of oral tetracycline administration on duodenal motility were investigated in seven cirrhotic patients with evidence of bacterial overgrowth. The mean duration and characteristics of the migrating motor complex were analyzed. Cyclic activity was observed in all healthy controls. It was absent in two cirrhotic patients showing a prolonged phase 2-like pattern. The duration of cycles was significantly longer in the remaining 14 patients with cirrhosis (166 +/- 19 min) compared with controls (81 +/- 14 min; p < 0.02). This difference was caused by a prolonged phase 2 (138 +/- 19 min in patients with cirrhosis vs. 52 +/- 11 min in controls; p < 0.02). Marked changes in the contraction pattern during phase 2 were noted in cirrhotic patients. They were characterized by multiple clusters (frequency, 12 +/- 1/hr; duration, 38 +/- 3 sec) of contractions (frequency, 11 +/- 1 cpm) separated by quiescent periods (duration, 2.4 +/- 0.2 min). This motility profile filled up 58% +/- 8% of the total duration of phase 2, and it was observed in patients with and without bacterial overgrowth. Treatment with tetracycline was followed by only mild modifications, such as a reduction of the fraction of phase 2 occupied by multiple-clustered contractions. In conclusion, an altered proximal small bowel motility has been observed in patients with cirrhosis. These disturbances appear not to be dependent on the presence of bacterial overgrowth.
A study of coupling interactions in finite arbitrarily-shaped grooves in electromagnetic scattering problem (2010)

A study of coupling between finite number of general-shaped grooves in electromagnetic plane-wave scattering problem is presented. The formulation for a single groove [1] is extended to two grooves. The importance of inclusion of coupling interaction between two grooves in scattering analysis is presented and its dependence on the grooves separation distance and the angle of incident of the electromagnetic field is demonstrated quantitatively. For larger angle of incident and smaller separation distance between grooves indicate larger discrepancy between between simulation results with and without inclusion of the coupling effects. Although the results presented here considers two grooves, the formulation can be extended to arbitrary number of grooves.
Salmonella typhimurium invasion induces apoptosis in infected macrophages. (1996)

Invasive Salmonella typhimurium induces dramatic cytoskeletal changes on the membrane surface of mammalian epithelial cells and RAW264.7 macrophages as part of its entry mechanism. Noninvasive S. typhimurium strains are unable to induce this membrane ruffling. Invasive S. typhimurium strains invade RAW264.7 macrophages in 2 h with 7- to 10-fold higher levels than noninvasive strains. Invasive S. typhimurium and Salmonella typhi, independent of their ability to replicate intracellularly, are cytotoxic to RAW264.7 macrophages and, to a greater degree, to murine bone marrow-derived macrophages. Here, we show that the macrophage cytotoxicity mediated by invasive Salmonella is apoptosis, as shown by nuclear morphology, cytoplasmic vacuolization, and host cell DNA fragmentation. S. typhimurium that enter cells causing ruffles but are mutant for subsequent intracellular replication also initiate host cell apoptosis. Mutant S. typhimurium that are incapable of inducing host cell membrane ruffling fail to induce apoptosis. The activation state of the macrophage plays a significant role in the response of macrophages to Salmonella invasion, perhaps indicating that the signal or receptor for initiating programmed cell death is upregulated in activated macrophages. The ability of Salmonella to promote apoptosis may be important for the initiation of infection, bacterial survival, and escape of the host immune response.
4,4′-Isopropylidine-Bis[2-Isopropyl]Phenol, a New Inhibitor for Cell Wall Formation of Bacillus subtilis (1976)

4,4'-Isopropylidine-bis[2-isopropyl]phenol was found to possess antimicrobial activity against gram-positive bacteria and some fungi, whereas it had no effect on gram-negative organisms. The drug has a potent inhibitory action on the synthesis of cell wall mucopeptides of Bacillus subtilis by inhibiting the enzyme d-glutamate ligase, which is responsible for the incorporation of d-glutamic acid into uridine 5'-diphosphate-muramyl-l-alanine. The drug had a weak lytic effect on protoplasts and inhibited protein synthesis, whereas no significant effect on the synthesis of deoxyribonucleic acid and ribonucleic acid was found.
Angiogenesis as a Therapeutic Target in Malignant Gliomas (2009)

Currently, adult glioblastoma (GBM) patients have poor outcomes with conventional cytotoxic treatments. Because GBMs are highly angiogenic tumors, inhibitors that target tumor vasculature are considered promising therapeutic agents in these patients. Encouraging efficacy and tolerability in preliminary clinical trials suggest that targeting angiogenesis may be an effective therapeutic strategy in GBM patients. However, the survival benefits observed to date in uncontrolled trials of antiangiogenic agents have been modest, and several obstacles have limited their effectiveness. This article reviews the rationale for antiangiogenic agents in GBM, their potential mechanisms of action, and their clinical development in GBM patients. Although challenges remain with this approach, ongoing studies may improve upon the promising initial benefits already observed in GBM patients.
Merchandising (1991)

The term 'merchandising' has as many definitions as there are types of retailers, but for the purpose of this book, it will be taken to mean the creation of a selling environment. This may be achieved through: (i) the choice of 'the mix' of merchandise to be offered to the customer; (ii) the choice of the amount of space to allocate to different items of merchandise; (iii) the choice of position, or display of particular products; and, (iv) the use of another sensory means such as music, touch or smell.
Passive mode locking of a semiconductor diode laser (1984)

By using a GaAs/GaAIAs multiple-quantum-well sample as a saturable absorber in an external resonator, we have passively mode locked a GaAs laser to obtain pulses as short as 1.6 psec, the shortest pulses ever observed to our knowledge from a mode-locked diode laser in a regulator pulse train.
Aortocoronary Saphenous Vein Graft Disease (1998)

Aortocoronary saphenous vein graft disease, with its increasing clinical sequelae, presents an important and unresolved dilemma in cardiological practice. During the 1st month after bypass surgery, vein graft attrition results from thrombotic occlusion, while later the dominant process is atherosclerotic obstruction occurring on a foundation of neointimal hyperplasia. Although the risk factors predisposing to vein graft atherosclerosis are broadly similar to those recognized for native coronary disease, the pathogenic effects of these risk factors are amplified by inherent deficiencies of the vein as a conduit when transposed into the coronary arterial circulation. A multifaceted strategy aimed at prevention of vein graft disease is emerging, elements of which include: continued improvements in surgical technique; more effective antiplatelet drugs; increasingly intensive risk factor modification, in particular early and aggressive lipid-lowering drug therapy; and a number of evolving therapies, such as gene transfer and nitric oxide donor administration, which target vein graft disease at an early and fundamental level. At present, a key measure is to circumvent the problem of vein graft disease by preferential selection of arterial conduits, in particular the internal mammary arteries, for coronary bypass surgery whenever possible.
An Adaptive Digital Method of Imbalances Cancellation in LINC Transmitters (2005)

The linear amplification using nonlinear components (LINC) technique is a well-known power amplifier linearization method to reduce adjacent channel interference in a nonconstant envelope modulation system. Its major drawback is the inherent sensitivity to gain and phase imbalances between the two amplifier branches. In this paper, a novel full-digital base band method is described which corrects any gain and phase imbalances in LINC transmitters mainly due to the unmatching of the two amplifier paths. Amplifiers are characterized by a level-dependent complex gain using a memoryless model. The method uses adaptive signal processing techniques to obtain the optimal complex coefficient to adjust gain and phase imbalances. Its main advantage is the ability to track the input signal variations and adapt to the changes of amplifier nonlinear characteristics. Other effects are included in the analysis such as quadrature modulator and demodulator imbalances and loop delay. A computer simulation has been carried out to verify the method functionality.
Cyclic amplification and selection of targets for multicomponent complexes: myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. (1992)

Myogenin is one of four muscle-specific basic helix-loop-helix regulatory factors involved in controlling myogenesis. We here describe various protein complexes that increase the affinity of myogenin for DNA. We mixed an oligonucleotide containing a degenerate center large enough to accommodate multiple binding sites with crude myotube nuclear extracts and used cyclic amplification and selection of targets with an antimyogenin monoclonal antibody to isolate protein-DNA complexes. Since each cycle of selection results in the enrichment for the sequences with the highest affinity, we isolated multicomponent sites in which myogenin binding was increased by its interaction with other DNA binding proteins. Myogenin interacts with members of the nuclear factor 1 family, the muscle-specific factor myocyte-specific enhancer-binding factor 2, and another factor, COMP1 (cooperates with myogenic proteins 1), that binds to the sequence TGATTGAC. Myogenin also exhibits cooperative binding with other proteins that recognize CANNTG motifs, and various constraints on spacing and orientation were observed. The application of this approach to other transcription factors should not only help identify the different functions of myogenin versus other members of the muscle basic helix-loop-helix regulatory family but also help define the general combinatorial mechanisms involved in eukaryotic gene regulation.
Heparan sulfate enhances growth of transformed human cells. (1984)

Previous studies showed that cell surface heparan sulfate (HS) is involved in density-dependent growth regulation of normal human cells. In this study the effects of HS on proliferation of transformed cells were studied in vitro. Exogenously added HS prepared from normal tissues (rat kidney and bovine kidney) enhanced growth of transformed human and animal cells (gamma ray- or virus-transformed WI-38, and HeLa cells and chemically induced mouse hepatoma cells), but inhibited that of normal human and animal cells (WI-38, 3T3, and rabbit liver cells). HS was less effective on growth of both normal and transformed human cells at higher cell density. Although the exogenous HS did not bind to cells tightly, HS was found to affect cell growth not by modulation of growth-related substances in the medium, but through contact with the cell surface. HS preparation from tumour cells (mouse hepatoma cells) exerted similar effects on cell growth. Heparin, structurally similar to HS, inhibited growth of both normal and transformed human cells. These findings suggest that: 1. HS plays a particular function in contact regulation of cell proliferation. 2. Transformation-related changes in the structure of HS molecules do not much affect the function of HS. 3. The cellular transformation, however, is accompanied by alteration in the growth-regulating system sensitive to extracellular HS.
Inhibitory Effects of Glibenclamide on Cystic Fibrosis Transmembrane Regulator, Swelling-Activated, and Ca 2+ -Activated Cl − Channels in Mammalian Cardiac Myocytes (1997)

Recent studies have provided evidence that sulfonylureas, in addition to blocking ATP-sensitive K+ (KATP) channels, also inhibit cystic fibrosis transmembrane regulator (CFTR) Cl- channels in epithelial and cardiac cells. The purpose of this study was to test whether the sulfonylurea glibenclamide might also inhibit other types of cardiac Cl- channels. Whole-cell patch-clamp techniques were used to compare the effects of glibenclamide on CFTR Cl- currents in guinea pig ventricular myocytes, swelling-activated Cl- currents in guinea pig atrial myocytes, and Ca(2+)-activated Cl- currents in canine ventricular myocytes. Glibenclamide markedly inhibited CFTR Cl- currents in a voltage-independent manner at 22 degrees C, with estimated IC50 values of 12.5 and 11.0 mumol/L at +50 and -100 mV, respectively. The outwardly rectifying swelling-activated Cl- current in atrial cells was less sensitive to glibenclamide, and the block exhibited voltage dependence. At 22 degrees C, the estimated IC50 values were 193 and 470 mumol/L at +50 and -100 mV, respectively, and block was enhanced at 35 degrees C. Macroscopic Cl- currents activated by a rise in intracellular Ca2+, induced by either Ca(2+)-induced Ca2+ release or by external application of the Ca2+ ionophore A23187, were also markedly inhibited at 22 degrees C by glibenclamide in a voltage-independent manner. The estimated IC50 values were 61.5 and 69.9 mumol/L at +50 and -100 mV, respectively. These results suggest that glibenclamide, an inhibitor of cardiac CFTR Cl- channels, also inhibits swelling-activated and Ca(2+)-activated Cl- channels at higher concentrations. The results also suggest that studies attributing the beneficial or deleterious effects of sulfonylurea compounds in the heart solely to blockade of KATP channels should use submicromolar concentrations of these agents to minimize possible secondary interactions with cardiac Cl- channels.
Facebook immune system (2011)

Popular Internet sites are under attack all the time from phishers, fraudsters, and spammers. They aim to steal user information and expose users to unwanted spam. The attackers have vast resources at their disposal. They are well-funded, with full-time skilled labor, control over compromised and infected accounts, and access to global botnets. Protecting our users is a challenging adversarial learning problem with extreme scale and load requirements. Over the past several years we have built and deployed a coherent, scalable, and extensible realtime system to protect our users and the social graph. This Immune System performs realtime checks and classifications on every read and write action. As of March 2011, this is 25B checks per day, reaching 650K per second at peak. The system also generates signals for use as feedback in classifiers and other components. We believe this system has contributed to making Facebook the safest place on the Internet for people and their information. This paper outlines the design of the Facebook Immune System, the challenges we have faced and overcome, and the challenges we continue to face.
Compact read-only memory with lensless phase-conjugate holograms (1996)

A new approach to holographic storage that uses lensless phase-conjugate holograms is proposed and demonstrated. Near-field holography is used for data recording, and a phase-conjugate reference beam is used for data retrieval. The data array can be directly transferred from the storage medium to the sensor without the need for imaging optics. It is shown that large space -bandwidth product holographic images (N x N x 10(6)) with pixel sizes of a few micrometers are feasible with a reasonable-sized recording material.
Ibrutinib enhances chimeric antigen receptor T-cell engraftment and efficacy in leukemia (2016)

Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy is highly promising but requires robust T-cell expansion and engraftment. A T-cell defect in chronic lymphocytic leukemia (CLL) due to disease and/or therapy impairs ex vivo expansion and response to CAR T cells. To evaluate the effect of ibrutinib treatment on the T-cell compartment in CLL as it relates to CAR T-cell generation, we examined the phenotype and function of T cells in a cohort of CLL patients during their course of treatment with ibrutinib. We found that ≥5 cycles of ibrutinib therapy improved the expansion of CD19-directed CAR T cells (CTL019), in association with decreased expression of the immunosuppressive molecule programmed cell death 1 on T cells and of CD200 on B-CLL cells. In support of these findings, we observed that 3 CLL patients who had been treated with ibrutinib for ≥1 year at the time of T-cell collection had improved ex vivo and in vivo CTL019 expansion, which correlated positively together and with clinical response. Lastly, we show that ibrutinib exposure does not impair CAR T-cell function in vitro but does improve CAR T-cell engraftment, tumor clearance, and survival in human xenograft models of resistant acute lymphocytic leukemia and CLL when administered concurrently. Our collective findings indicate that ibrutinib enhances CAR T-cell function and suggest that clinical trials with combination therapy are warranted. Our studies demonstrate that improved T-cell function may also contribute to the efficacy of ibrutinib in CLL. These trials were registered at www.clinicaltrials.gov as #NCT01747486, #NCT01105247, and #NCT01217749.
Status of Cytomegalovirus Prevention and Treatment in 2000 (2000)

Abstract Cytomegalovirus (CMV) infection continues to be a problem in selected populations following hematopoietic stem cell transplantation (SCT). Although there have been no new antiviral agents for management of this infection in recent years, the methods for using the existing agents have improved with newer assays for detection of virus. In addition, our understanding of immunity to CMV has undergone considerable expansion. This paper will address these new aspects relating to CMV infection in the setting of SCT. In Section I Dr. Zaia reviews the pathogenesis of CMV and the current epidemiology of CMV disease following marrow or blood allo-SCT with emphasis on late-onset disease. The current lab tests available for preemptive management are summarized including the role for conventional shell vial cultures, and a comparison of the CMV antigenemia assay with the new nucleic acid-based assays, including the hybrid capture assay, the NASBA assay, and “real-time” PCR assays. Use of antiviral agents with these tests in the preemptive management of CMV infection is discussed. Ultimately, what is necessary is restoration of adequate CMV immunity, and that requires understanding the basics of the CMV-specific immune response. In Section II, Dr. Sissons traces the evolution of the CTL response from primary infection into memory and reviews recent advances in the understanding of cytotoxic T cell based immunity to CMV, based on the use of T cell clonotypic analysis and markers of T cell memory and activation, with conventional CTL functional assays. In Section III Dr. Riddell presents approaches to correction of the problem of CMV pathogenesis, namely direct restoration of the CMV-specific cellular immune deficiency. Attempts at passive therapies will be reviewed with the focus on current problems and approaches to these problems. In Section IV, Dr. Diamond presents work on the identification of multiple HLA-allele specific cytotoxic T cell epitopes specific for CMV-pp65 and - pp150. Specific epitopes are recognized by CMV-seropositive individuals including healthy donors, SCT recipients, and AIDS patients, indicating their potential usefulness as vaccines. One of these epitopes is recognized by most individuals who express the HLA A*0201 Class I allele. Pre-clinical evaluation in HLA2.1 transgenic mice of vaccine structures utilizing this epitope, and alternative delivery systems are described. Possible methods for vaccination of donor and/or recipient of a SCT as well as their limitations, utilizing synthetic or viral vaccines, are discusseed.
9,10‐Dihydro‐2,5‐dimethoxyphenanthrene‐1,7‐diol, from Eulophia ochreata, inhibits inflammatory signalling mediated by Toll‐like receptors (2010)

RSCL-0520 blocked signals generated by TLR4 activation, as shown by down-regulation of NF-kappaB-regulated inflammatory cytokines. The inhibitory effect involved both MyD88-dependent and -independent signalling cascades. Our data elucidated the molecular mechanisms involved, and support the search for plant-derived TLR antagonists, as potential anti inflammatory agents.
The Zinc Finger Protein A20 Inhibits TNF-induced NF-κB–dependent Gene Expression by Interfering with an RIP- or TRAF2-mediated Transactivation Signal and Directly Binds to a Novel NF-κB–inhibiting Protein ABIN (1999)

The zinc finger protein A20 is a tumor necrosis factor (TNF)- and interleukin 1 (IL-1)-inducible protein that negatively regulates nuclear factor-kappa B (NF-kappaB)-dependent gene expression. However, the molecular mechanism by which A20 exerts this effect is still unclear. We show that A20 does not inhibit TNF- induced nuclear translocation and DNA binding of NF-kappaB, although it completely prevents the TNF- induced activation of an NF-kappaB-dependent reporter gene, as well as TNF-induced IL-6 and granulocyte macrophage-colony stimulating factor gene expression. Moreover, NF-kappaB activation induced by overexpression of the TNF receptor-associated proteins TNF receptor-associated death domain protein (TRADD), receptor interacting protein (RIP), and TNF recep- tor-associated factor 2 (TRAF2) was also inhibited by expression of A20, whereas NF-kappaB activation induced by overexpression of NF-kappaB-inducing kinase (NIK) or the human T cell leukemia virus type 1 (HTLV-1) Tax was unaffected. These results demonstrate that A20 inhibits NF-kappaB-dependent gene expression by interfering with a novel TNF-induced and RIP- or TRAF2-mediated pathway that is different from the NIK-IkappaB kinase pathway and that is specifically involved in the transactivation of NF-kappaB. Via yeast two-hybrid screening, we found that A20 binds to a novel protein, ABIN, which mimics the NF-kappaB inhibiting effects of A20 upon overexpression, suggesting that the effect of A20 is mediated by its interaction with this NF-kappaB inhibiting protein, ABIN.