gebhart/patrepeval huggingface dataset:
On two-user degraded GBC with finite input constellations (2015)

Two-user Single-Input Single-Output degraded Gaussian broadcast channel (GBC) with finite input constellations is addressed in this paper. Multiple downlink multiple access schemes including orthogonal multiple access (OMA) schemes and non-orthogonal multiple access (NOMA) schemes are compared from several aspects. For OMA schemes, power control is not considered and constant power for each symbol is assumed. For NOMA schemes, two typical schemes are considered which are traditional linear superposition coding (SC) and recently proposed bit division multiplexing (BDM). BDM is essentially an instantiation of non-linear SC. Capacity region analysis and simulation results are performed to give an insight into the downlink multiple access schemes. The results show that BDM can increase the system throughput compared with OMA schemes and has lower implementation complexity as well as better practical performance compared with traditional linear SC. Given typical transmission rate requirements of two users, the gaps to the union theoretical SNR thresholds for two users by BDM are both less than 2.5dB with independent demapping employed at receiver, which are far better than those achieved by OMA schemes and traditional linear SC.
Activation of NLRC4 by Flagellated Bacteria Triggers Caspase-1–Dependent and –Independent Responses To Restrict Legionella pneumophila Replication in Macrophages and In Vivo (2011)

Although NLRC4/IPAF activation by flagellin has been extensively investigated, the downstream signaling pathways and the mechanisms responsible for infection clearance remain unclear. In this study, we used mice deficient for the inflammasome components in addition to wild-type (WT) Legionella pneumophila or bacteria deficient for flagellin (flaA) or motility (fliI) to assess the pathways responsible for NLRC4-dependent growth restriction in vivo and ex vivo. By comparing infections with WT L. pneumophila, fliI, and flaA, we found that flagellin and motility are important for the colonization of the protozoan host Acanthamoeba castellanii. However, in macrophages and mammalian lungs, flagellin expression abrogated bacterial replication. The flagellin-mediated growth restriction was dependent on NLRC4, and although it was recently demonstrated that NLRC4 is able to recognize bacteria independent of flagellin, we found that the NLRC4-dependent restriction of L. pneumophila multiplication was fully dependent on flagellin. By examining infected caspase-1(-/-) mice and macrophages with flaA, fliI, and WT L. pneumophila, we could detect greater replication of flaA, which suggests that caspase-1 only partially accounted for flagellin-dependent growth restriction. Conversely, WT L. pneumophila multiplied better in macrophages and mice deficient for NLRC4 compared with that in macrophages and mice deficient for caspase-1, supporting the existence of a novel caspase-1-independent response downstream of NLRC4. This response operated early after macrophage infection and accounted for the restriction of bacterial replication within bacteria-containing vacuoles. Collectively, our data indicate that flagellin is required for NLRC4-dependent responses to L. pneumophila and that NLRC4 triggers caspase-1-dependent and -independent responses for bacterial growth restriction in macrophages and in vivo.
RNA Interference Therapy in Lung Transplant Patients Infected with Respiratory Syncytial Virus (2010)

ALN-RSV01 was safe and may have beneficial effects on long-term allograft function in LTX patients infected with RSV. Clinical trial registered with www.clinicaltrials.gov (NCT 00658086).
Genetic Engineering With Plant Viruses (1992)

Plant Viruses as Agents to Modify the Plant Phenotype for Good or Evil (R.S.S. Fraser). The Stability and Utility of Plant Virus Replicons (Marianne J. Huisman, Lous Van Vloten-Doting, and Ben J.C. Cornelissen). Plant Virus Genomes as Sources of Novel Functions for Genetic Manipulations (David E. Sleat and T. Michael A. Wilson). Use of In Vitro Transcription to Study Gene Expression and Replication of Spherical, Positive Sense RNA Plant Viruses (Jozef J. Bujarski and W. Allen Miller). Molecular Pathology of Tobacco Mosaic Virus Revealed by Biologically Active cDNAs (Tetsuo Meshi, Yuichiro Watanabe, and Yoshimi Okada). Geminiviruses as Gene Vectors (P.M. Mullineaux, J.W. Davies, and C.J. Woolston). Genetic Engineering with Double-Stranded DNA Viruses (Simon N. Covey and Roger Hull). Expression of Plant Viral Genes in Transgenic Plants (Linda Hanley-Bowdoin and Cynthia Hemenway). Genetic Engineering with Viroids (Rosemarie W. Hammond and Robert A. Owens). The Impact of Genetic Engineering on Classical Plant Virology-Postscript and Perspectives (Stephen H. Howell and Milton Zaitlin).
Paralleled comparison of vectors for the generation of CAR-T cells (2016)

T-lymphocytes genetically engineered with the chimeric antigen receptor (CAR-T) have shown great therapeutic potential in cancer treatment. A variety of preclinical researches and clinical trials of CAR-T therapy have been carried out to lay the foundation for future clinical application. In these researches, several gene-transfer methods were used to deliver CARs or other genes into T-lymphocytes, equipping CAR-modified T cells with a property of recognizing and attacking antigen-expressing tumor cells in a major histocompatibility complex-independent manner. Here, we summarize the gene-transfer vectors commonly used in the generation of CAR-T cell, including retrovirus vectors, lentivirus vectors, the transposon/transposase system, the plasmid-based system, and the messenger RNA electroporation system. The following aspects were compared in parallel: efficiency of gene transfer, the integration methods in the modified T cells, foreground of scale-up production, and application and development in clinical trials. These aspects should be taken into account to generate the optimal CAR-gene vector that may be suitable for future clinical application.
Fecal Microbiota Transplantation in Inflammatory Bowel Disease (2014)

The purpose of this article is to perform a systematic review of the literature on the use of fecal microbiota transplantation (FMT) in inflammatory bowel disease (IBD).There is an increasing interest of both physicians and patients in assessing the possible role of the FMT in the treatment of IBD.Electronic and manual bibliographic searches were performed to identify original reports in which subjects with IBD were treated with FMT. Because of the scarcity of studies with adequate sample size, case series and case reports were also considered. A critical appraisal of the clinical research evidence on the effectiveness, safety, and other parameters related to FMT was made. Data extraction was independently performed by 2 reviewers.We found a total of 31 publications on the use of FMT in IBD. The majority were case reports or case series, whereas 8 publications reported data from open-label trials including a very less number of patients. A total of 133 patients with IBD were managed with FMT. Of these, 57 subjects (43%) had a Clostridium difficile infection. A resolution or reduction of symptoms was reported in 80 of 113 (71%) patients with evaluable IBD. Moreover, FMT does not seem to provide the same safety profile showed for non-IBD individuals with C difficile infection.The available evidence is limited and weak. FMT has the potential to be somehow of help in managing patients with IBD, but considerable further efforts are necessary to make this procedure a valid option for these subjects.
A rapid method for recombination and site-specific mutagenesis by placing homologous ends on DNA using polymerase chain reaction. (1991)

We have developed a novel polymerase chain reaction (PCR) method that permits the rapid generation of site-specific mutants and recombinant DNA constructs with a minimum number of steps and primers. DNA segments are modified by using amplifying primers that add homologous ends to the polymerase chain reaction product(s). These homologous ends undergo recombination in vivo following transformation of recA-E. coli strains used routinely in cloning. In vivo circularization of PCR products containing plasmid sequences with a selective marker permits the rapid cloning of the desired mutant or recombinant. In the mutagenesis protocol, 7 of the 12 clones contained the product of interest, and 6 of these clones had no detected error (50% of the clones without detected errors). In each of several recombination protocols, at least 50% of the clones tested contained the insert of interest without detected errors.
Adaptive user interfaces for automotive environments (2002)

We investigate the use of adaptive user interfaces for in-car information access. These interfaces attempt to efficiently provide content the driver needs and wants, and gather feedback on these preferences through the driver's interaction with the system. In this way, the performance of the system improves as it unobtrusively builds a more accurate model of the user. The three systems presented here are: the Adaptive Route Advisor for navigation; the Adaptive News Reader for news stories; and the Adaptive Place Advisor for restaurant selection. All of these systems provide useful information to a driver, and we argue that they do not negatively impact safety because they are replacing other less effective, information sources. We intend to test this hypothesis in future studies.
Liposome and Lipid Bilayer Arrays Towards Biosensing Applications (2010)

Sensitive and selective biosensors for high-throughput screening are having an increasing impact in modern medical care. The establishment of robust protein biosensing platforms however remains challenging, especially when membrane proteins are involved. Although this type of proteins is of enormous relevance since they are considered in >60% of the pharmaceutical drug targets, their fragile nature (i.e., the requirement to preserve their natural lipid environment to avoid denaturation and loss of function) puts strong additional prerequisites onto a successful biochip. In this review, the leading approaches to create lipid membrane-based arrays towards the creation of membrane protein biosensing platforms are described. Liposomes assembled in micro- and nanoarrays and the successful set-ups containing functional membrane proteins, as well as the use of liposomes in networks, are discussed in the first part. Then, the complementary approaches to create cell-mimicking supported membrane patches on a substrate in an array format will be addressed. Finally, the progress in assembling free-standing (functional) lipid bilayers over nanopore arrays for ion channel sensing will be reported. This review illustrates the rapid pace by which advances are being made towards the creation of a heterogeneous biochip for the high-throughput screening of membrane proteins for diagnostics, drug screening, or drug discovery purposes.
Solid phase synthesis of polynucleotides. VIII. Synthesis of mixed oligodeoxyribonucleotides by the phosphotriester solid phase method1 (1983)

A solid phase method for the simultaneous synthesis of mixed oligonucleotides using a phosphotriester approach has been developed. For this synthesis, a mixture of mono or dimeric coupling units is used, and a slight difference in the reactivity of those units is found. However, this difference does not hamper the simultaneous, mixed oligonucleotide synthesis, and the sequence analysis of a product demonstrates the existence of all desired sequences in the final mixture.
Infections in breast implants: a review with a focus on developing countries (2014)

The risk of surgical site infection is always present in surgery; the use of prosthetic materials is linked to an increased possibility of infection. Breast augmentation and breast reconstruction with implants are gaining popularity in developing countries. Implant infection is the main complication related to breast aesthetic and reconstructive surgery. In the present paper, we reviewed the current microbiological knowledge about implant infections, with particular attention to risk factors, diagnosis, clinical management, and antibiotic prophylaxis, focusing on reports from developing countries. After breast aesthetic surgery, up to 2.9% of patients develop a surgical site infection, with an incidence of 1.7% for acute infections and 0.8% for late infections. The rate of surgical site infection after post-mastectomy breast reconstruction is usually higher, ranging from 1% to 53%. The clinical features are not constant, and bacterial culture with antibiogram is the gold standard for diagnosis and for identification of antibiotic resistance. While waiting for culture results, empiric therapy with vancomycin and extended-spectrum penicillins or cephalosporins is recommended. Some patients require removal of the infected prosthesis. The main methods to bring down the risk of infection are strict asepsis protocol, preoperative antibiotic prophylaxis, and irrigation of the surgical pocket and implant with an antibiotic solution.
Anti-inflammatory effects of Melatonin: A mechanistic review (2018)

N-acetyl-5-methoxy-tryptamine (melatonin) is a natural substance produced both by plants, as a secondary metabolite, and animals, by the pineal gland and other tissues. In humans, melatonin participates in numerous functions including the regulation of mood, sleep, reproduction, promotion of immunomodulation, antioxidant defense and as an anti-inflammatory agent. The anti-inflammatory activity of melatonin could yield beneficial effects on intake, particularly against the chronic inflammation which underlies many chronic diseases. This review aims to provide an assessment of the literature data on the anti-inflammatory activity of melatonin, with a particular focus on the mechanisms responsible for this behavior. We can conclude that many <i>in vitro</i> studies and <i>in vivo</i> studies in experimental animal model systems show that melatonin exerts anti-inflammatory activity in a number of chronic diseases which affect different organs in different circumstances. Clinical trials, however, often fail to reach positive results and are thus far inconclusive. Thus, in the future, long-term well-designed investigations on melatonin-rich foods or melatonin food supplements could provide valuable information towards public health recommendations on melatonin, taking into account both the nature of the compound and the optimal dose, for protection from long-term inflammation linked to chronic diseases.
Gold Deposition by Galvanic Displacement on Semiconductor Surfaces:  Effect of Substrate on Adhesion (2001)

Thin gold films are grown on Si and Ge substrates by galvanic displacement from fluoride-containing solutions. The physical and chemical properties of the metal−semiconductor interface are characterized by a variety of techniques, including photoelectron spectroscopy, atomic force microscopy, and electron microscopy. Displaced gold films exhibit strong adhesion to germanium substrates but not to silicon. This behavior is explained by the presence of a chemical bond at the Au−Ge interface, which is not observed in the Au−Si system. The implications of these findings for semiconductor metallization by galvanic displacement methods are discussed.
Encipherment and Conditional Access (1994)

This article discusses modeling conditional access in any television environment (terrestrial broadcasting, cable, and satellite). After conditional access has been defined, two models are presented that correspond to two different systems, widespread in Europe: • Distribution of control words. This model is illustrated by a proprietary system of Canal-Plus, used by about 3.5 million subscribers in France. This proprietary system is known as Discret 1. • Distribution of authorizations. This model is illustrated by an open system used by about 1 million receivers throughout Europe: Kinnevik (500,000); FilmNet (250,000); France Telecom (60,000); Canal-Plus (60,000); Polycom; Maxat; KabelKanal, and others. Known as Eurocrypt, this open system is standardized by CEN/CENELEC (Eurocrypt, EN 50 094:1992). — The emergence of digital signals technically facilitates the design of open systems, and the use of strong cryptography becomes justified. The encipherment techniques appear at three different levels: for managing entitlements (updating authorization keys and distributing access rights); for checking entitlements; and for scrambling program components. This modelization emphasizes the impact of standardization and the reserve for further evolution. The knowledge gained from existing systems allows the determination of the axes for additional developments, specifically in relation to digital television.
In situ Synthesis of Oligonucleotide Arrays on Surfaces Coated with Crosslinked Polymer Multilayers (2011)

We report an approach to the in situ synthesis of oligonucleotide arrays on surfaces coated with crosslinked polymer multilayers. Our approach makes use of methods for the 'reactive' layer-by-layer assembly of thin, amine-reactive multilayers using branched polyethyleneimine (PEI) and the azlactone-functionalized polymer poly(2-vinyl-4,4'-dimethylazlactone) (PVDMA). Post-fabrication treatment of film-coated glass substrates with d-glucamine or 4-amino-1-butanol yielded hydroxyl-functionalized films suitable for the Maskless Array Synthesis (MAS) of oligonucleotide arrays. Glucamine-functionalized films yielded arrays of oligonucleotides with fluorescence intensities and signal-to-noise ratios (after hybridization with fluorescently labeled complementary strands) comparable to those of arrays fabricated on conventional silanized glass substrates. These arrays could be exposed to multiple hybridization-dehybridization cycles with only moderate loss of hybridization density. The versatility of the layer-by-layer approach also permitted synthesis directly on thin sheets of film-coated poly(ethylene terephthalate) (PET) to yield flexible oligonucleotide arrays that could be readily manipulated (e.g., bent) and cut into smaller arrays. To our knowledge, this work presents the first use of polymer multilayers as a substrate for the multi-step synthesis of complex molecules. Our results demonstrate that these films are robust and able to withstand the ~450 individual chemical processing steps associated with MAS (as well as manipulations required to hybridize, image, and dehybridize the arrays) without large-scale cracking, peeling, or delamination of the thin films. The combination of layer-by-layer assembly and MAS provides a means of fabricating functional oligonucleotide arrays on a range of different materials and substrates. This approach may also prove useful for the fabrication of supports for the solid-phase synthesis and screening of other macromolecular or small-molecule agents.
Antiangiogenic Therapies: Going beyond Their Limits (2013)

Tumor growth requires induction of an angiogenic program, and targeting of this program with antiangiogenic drugs shows an impact on tumor progression. However, although they are effective at reducing angiogenesis, these therapies have not produced widespread or enduring clinical benefit, which openly exposes their limitations. Here, we describe the current limitations of these therapies, including the known mechanisms and current controversies. Further, we present some of the recent approaches to predict these limitations and strategies to overcome them. With the development of meaningful predictive biomarkers and effective treatments that impede these limitations, longer and more robust efficacies will be achieved for a wider population of patients.
Shroom3-mediated recruitment of Rho kinases to the apical cell junctions regulates epithelial and neuroepithelial planar remodeling (2008)

Remodeling of epithelial sheets plays important roles in animal morphogenesis. Shroom3 is known to regulate the apical constriction of epithelial cells. Here, we show that Shroom3 binds ROCKs and recruits them to the epithelial apical junctions. We identified the Shroom3-binding site (RII-C1) on ROCKs, and found that RII-C1 could antagonize the Shroom3-ROCK interaction, interfering with the action of Shroom3 on cell morphology. In the invaginating neural plate/tube, Shroom3 colocalized with ROCKs at the apical junctions; Shroom3 depletion or RII-C1 expression in the tube removed these apically localized ROCKs, and concomitantly blocked neural tube closure. Closing neural plate exhibited peculiar cell assemblies, including rosette formation, as well as a planar-polarized distribution of phosphorylated myosin regulatory light chain, but these were abolished by ROCK inhibition or RII-C1 expression. These results demonstrate that the Shroom3-ROCK interaction is crucial for the regulation of epithelial and neuroepithelial cell arrangement and remodeling.
No patient left behind: The promise of immune priming with epigenetic agents (2017)

Checkpoint inhibitors, monoclonal antibodies that inhibit PD-1 or CTLA-4, have revolutionized the treatment of multiple cancers. Despite the enthusiasm for the clinical successes of checkpoint inhibitors, and immunotherapy, in general, only a minority of patients with specific tumor types actually benefit from treatment. Emerging evidence implicates epigenetic alterations as a mechanism of clinical resistance to immunotherapy. This review presents evidence for that association, summarizes the epi-based mechanisms by which tumors evade immunogenic cell death, discusses epigenetic modulation as a component of an integrated strategy to boost anticancer T cell effector function in relation to a tumor immunosuppression cycle and, finally, makes the case that the success of this no-patient-left-behind strategy critically depends on the toxicity profile of the epigenetic agent(s).
Characterisation of Dog Allergens by Means of Immunoblotting (1993)

Sera from 75 patients with clinical type I allergy against dogs were investigated by means of immunoblotting using extracts prepared from dog hair/dander (CAN XI D) and saliva. In addition, selected sera were tested on extracts made of hair, skin, salivary glands (parotis and submandibularis), serum and liver. A 69-kD IgE-binding protein was identified in all extracts tested with an incidence of approximately 40% and shown to be dog albumin by means of inhibition experiments. In 96% of patients' sera IgE antibodies reactive with a 19-kD and/or a 23-kD protein of the hair/dander extract (CAN XI D) were observed. IgE binding to a 23-kD band was also detected in the hair and saliva extracts, but not in skin, salivary gland, serum and liver extracts. A 19-kD IgE-binding protein was strongly expressed in skin and to a lesser degree in saliva, but not in hair, serum and liver. Preincubation of patients sera with the hair extract and subsequent probing with the hair/dander extract (CAN XI D) inhibited IgE binding to the 23 kD protein whereas preincubation with the skin extract abolished IgE binding to the 19-kD protein. Using the hair/dander extract as inhibitor, IgE binding to the 19- and 23-kD proteins of saliva was abrogated. Thus it is concluded that the 23-kD protein is preferentially expressed in hair and saliva whereas the 19-kD protein is found in saliva and skin. Furthermore these two proteins are likely to represent immunologically independent major allergens.