gebhart/patrepeval huggingface dataset:
Adhesion Inhibition of F1C‐Fimbriated Escherichia coli and Pseudomonas aeruginosa PAK and PAO by Multivalent Carbohydrate Ligands (2003)

Abstract In order to evaluate their inhibition of bacterial adhesion, the carbohydrate sequences GalNAcβ1→4Gal and GalNAcβ1→4Galβ1→4Glc were synthesized. The disaccharide was conjugated to dendrons based on the 3,5‐di‐(2‐aminoethoxy)‐benzoic acid branching unit to yield di‐ and tetravalent versions of these compounds. A divalent compound was also prepared that had significantly longer spacer arms. Relevant monovalent compounds were prepared for comparison. Their anti‐adhesion properties against F1C‐fimbriated uropathogenic Escherichia coli were evaluated in an ELISA‐type assay by using a recombinant strain and also by using Pseudomonas aeruginosa strains PAO and PAK. Adhesion inhibition was observed in all cases, and multivalency effects of up to one order of magnitude were observed. The combination of spacer and multivalency effects led to a 38‐fold increase in the potency of a divalent inhibitor with long spacer arms towards the PAO strain when compared with the free carbohydrate.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies (2014)

Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
Low-Overhead Interactive Debugging via Dynamic Instrumentation with DISE (2005)

Breakpoints, watchpoints, and conditional variants of both are essential debugging primitives, but their natural implementations often degrade performance significantly. Slowdown arises because the debugger - the tool implementing the breakpoint/watchpoint interface - is implemented in a process separate from the debugged application. Since the debugger evaluates the watchpoint expressions and conditional predicates to determine whether to invoke the user, a debugging session typically requires many expensive application-debugger context switches, resulting in slowdowns of 40,000 times or more in current commercial and open-source debuggers! In this paper, we present an effective and efficient implementation of (conditional) breakpoints and watchpoints that uses DISE to dynamically embed debugger logic into the running application. DISE (dynamic instruction stream editing) is a previously proposed, programmable hardware facility for dynamically customizing applications by transforming the instruction stream as it is decoded. DISE embedding preserves the logical separation of application and debugger nstructions are added dynamically and transparently, existing application code and data are not statically modified - and has little startup cost. Cycle-level simulation on the SPEC 2000 integer benchmarks shows that the DISE approach eliminates all unnecessary context switching, typically limits debugging overhead to 25% or less for a wide range of watch-points, and outperforms alternative implementations.
cDNA cloning of the 43‐kDa latex allergen Hev b 7 with sequence similarity to patatins and its expression in the yeast Pichia pastoris (1998)

IgE-mediated hypersensitivity to latex proteins present in health care products, particularly in latex gloves, has become an important public health problem in recent years. We purified natural Hev b 7, a 43-kDa patatin-like allergen from the latex of Hevea brasiliensis and determined several internal peptide sequences. A heterologous hybridization probe of a patatin gene of potato, to which these peptides could be aligned best, was used to screen a latex cDNA library. The cDNA encoded an acidic protein of 388 amino acids with a molecular mass of 42.9 kDa. The deduced amino acid sequence had 39-42% identity to patatins from Solanum tuberosum. The purified recombinant Hev b 7 expressed in the yeast Pichia pastoris displayed, similarly to patatins from S. tuberosum, esterase activity. Both natural and recombinant Hev b 7 were recognized by IgE from sera of latex-sensitized allergic individuals. In contrast to patatins from S. tuberosum and Nicotiana tabacum, natural Hev b 7 lacked an N-terminal leader peptide for targeting to the endoplasmatic reticulum and was not glycosylated. These results establish the 43-kDa patatin-like protein as a latex allergen and raise the possibility of different cellular localization and function compared to S. tuberosum patatins.
Site-Specific Labeling of DNA and RNA Using an Efficiently Replicated and Transcribed Class of Unnatural Base Pairs (2011)

Site-specific labeling of enzymatically synthesized DNA or RNA has many potential uses in basic and applied research, ranging from facilitating biophysical studies to the in vitro evolution of functional nucleic acids and the construction of various nanomaterials and biosensors. As part of our efforts to expand the genetic alphabet, we have developed a class of unnatural base pairs, exemplified by d5SICS-dMMO2 and d5SICS-dNaM, which are efficiently replicated and transcribed, and which may be ideal for the site-specific labeling of DNA and RNA. Here, we report the synthesis and analysis of the ribo- and deoxyribo-variants, (d)5SICS and (d)MMO2, modified with free or protected propargylamine linkers that allow for the site-specific modification of DNA or RNA during or after enzymatic synthesis. We also synthesized and evaluated the α-phosphorothioate variant of d5SICSTP, which provides a route to backbone thiolation and an additional strategy for the postamplification site-specific labeling of DNA. The deoxynucleotides were characterized via steady-state kinetics and PCR, while the ribonucleosides were characterized by the transcription of both a short, model RNA as well as full length tRNA. The data reveal that while there are interesting nucleotide and polymerase-specific sensitivities to linker attachment, both (d)MMO2 and (d)5SICS may be used to produce DNA or RNA site-specifically modified with multiple, different functional groups with sufficient efficiency and fidelity for practical applications.
Metformin-Induced Reduction of CD39 and CD73 Blocks Myeloid-Derived Suppressor Cell Activity in Patients with Ovarian Cancer (2018)

Metformin is a broadly prescribed drug for type 2 diabetes that exerts antitumor activity, yet the mechanisms underlying this activity remain unclear. We show here that metformin treatment blocks the suppressive function of myeloid-derived suppressor cells (MDSC) in patients with ovarian cancer by downregulating the expression and ectoenzymatic activity of CD39 and CD73 on monocytic and polymononuclear MDSC subsets. Metformin triggered activation of AMP-activated protein kinase α and subsequently suppressed hypoxia-inducible factor α, which was critical for induction of CD39/CD73 expression in MDSC. Furthermore, metformin treatment correlated with longer overall survival in diabetic patients with ovarian cancer, which was accompanied by a metformin-induced reduction in the frequency of circulating CD39<sup>+</sup>CD73<sup>+</sup> MDSC and a concomitant increase in the antitumor activities of circulating CD8<sup>+</sup> T cells. Our results highlight a direct effect of metformin on MDSC and suggest that metformin may yield clinical benefit through improvement of antitumor T-cell immunity by dampening CD39/CD73-dependent MDSC immunosuppression in ovarian cancer patients.<b>Significance:</b> The antitumor activity of an antidiabetes drug is attributable to reduced immunosuppressive activity of myeloid-derived tumor suppressor cells. <i>Cancer Res; 78(7); 1779-91. ©2018 AACR</i>.
Stroma of human benign prostatic hyperplasia: preferential tissue for androgen metabolism and oestrogen binding (1981)

Abstract. Because of the well known stromal-epithelial interaction of various urogenital organs, it was of interest to compare quantitatively steroid metabolism and binding in epithelium (E) and stroma (S) of the human benign prostatic hyperplasia (BPH). Testosterone 5α-reductase activity was determined by thin-layer chromatography and androgen as well as oestrogen binding sites by a charcoal adsorption technique after a steroid incubation period of 18 h at 0°C, using methyltrienolone (R1881) and oestradiol-17β as tritiated ligands and unlabelled R1881 and diethylstilboestrol as the respective competitors. The main results were as follows: (1) using biochemical markers (acid phosphatase, hydroxyproline), an on average 17% contamination of E by S and 6% of S by E was found, (2) the molar optimum of NADPH for the enzyme reaction was nearly identical in E and S, ranging between 1 and 0.1 m m , (3) the apparent Michaelis constant (K m ) of 5α-reductase was in both fractions identical, the mean being 0.15 (μ m , (4) the maximal rate of 5α-reductase activity (pmol 5α-reduced metabolites · mg protein −1 · 1 h −1 ) was 161 ± 28 ( sem ; n = 20), 66 ± 4.6 and 148 ± 6.6 in S, E and whole tissue fraction of BPH, respectively. In two normal prostates the means were: 88, 53 and 73, respectively, (5) the androgen binding sites were evenly distributed between the cytosol of E and S, while measurable oestrogen binding sites were found in 42% of the analyzed S but only in 5% of analyzed E. In conclusion: the 2.4 times higher 5·-reductase activity in S compared to E of the BPH is responsible for the about 2 to 2.5 times higher activity in the whole tissue fraction of BPH if compared with the normal prostate. Furthermore, due to our preliminary binding studies, oestrogens might play an important role in the S fraction of BPH.
Cationic polyamines inhibit anthrax lethal factor protease (2006)

Based upon the studies reported herein, we chose linear polyamines related to spermine as potential lead optimization candidates and additional testing in cell-based models where cell penetration could be studied. During our screening process, we reproducibly demonstrated that the potencies of certain compounds, including neomycin but not neamine or spermine, were different depending upon the presence or absence of nucleic acids. Differential sensitivity to the presence/absence of nucleic acids may be an additional point to consider when comparing various classes of active compounds for lead optimization.
Protective Immunization against Inhalational Anthrax: A Comparison of Minimally Invasive Delivery Platforms (2004)

A new anthrax vaccine under clinical investigation is based on recombinant Bacillus anthracis protective antigen (rPA). Here, we investigated microneedle-based cutaneous and nasal mucosal delivery of rPA in mice and rabbits. In mice, intradermal (id) delivery achieved up to 90% seroconversion after a single dose, compared with 20% after intramuscular (im) injection. Intranasal (inl) delivery of a liquid formulation required 3 doses to achieve responses that were comparable with those achieved via the id or im routes. In rabbits, id delivery provided complete protection against aerosol challenge with anthrax spores; in addition, novel powder formulations administered inl provided complete protection, whereas a liquid formulation provided only partial protection. These results demonstrate, for the first time, that cutaneous or nasal mucosal administration of rPA provides complete protection against inhalational anthrax in rabbits. The novel vaccine/device combinations described here have the potential to improve the efficacy of rPA and other biodefense vaccines.
Tau Truncation is a Productive Posttranslational Modification of Neurofibrillary Degeneration in Alzheimers Disease (2010)

Deposits of the misfolded neuronal protein tau are major hallmarks of neurodegeneration in Alzheimer's disease (AD) and other tauopathies. The etiology of the transformation process of the intrinsically disordered soluble protein tau into the insoluble misordered aggregate has attracted much attention. Tau undergoes multiple modifications in AD, most notably hyperphosphorylation and truncation. Hyperphosphorylation is widely regarded as the hottest candidate for the inducer of the neurofibrillary pathology. However, the true nature of the impetus that initiates the whole process in the human brains remains unknown. In AD, several site-specific tau cleavages were identified and became connected to the progression of the disease. In addition, western blot analyses of tau species in AD brains reveal multitudes of various truncated forms. In this review we summarize evidence showing that tau truncation alone is sufficient to induce the complete cascade of neurofibrillary pathology, including hyperphosphorylation and accumulation of misfolded insoluble forms of tau. Therefore, proteolytical abnormalities in the stressed neurons and production of aberrant tau cleavage products deserve closer attention and should be considered as early therapeutic targets for Alzheimer's disease.
Multiprotein HIV Type 1 Clade B DNA and MVA Vaccines: Construction, Expression, and Immunogenicity in Rodents of the MVA Component (2004)

Recombinant modified vaccinia virus Ankara (MVA) expressing SIV or SHIV Gag-Pol and Env, alone or in conjunction with a related DNA vaccine, effectively controls immunodeficiency virus infections in nonhuman primates. Here we describe the construction, characterization, and immunogenicity of MVA/HIV 48, a candidate HIV-1 clade B Gag-Pol-Env vaccine. A novel transfer vector was designed to allow the incorporation of HIV genes regulated by vaccinia virus promoters together with a reporter gene into a single site in the MVA genome and to automatically delete the reporter after the initial isolation of the recombinant MVA. MVA/HIV 48 contains chimeric HIV-1 HXB-2/BH10 gag-pol sequences, a deletion of integrase, inactivating point mutations in reverse transcriptase, and HIV-1 ADA env sequences with a truncation of most of the cytoplasmic domain to enhance expression on the plasma membrane. Cells infected with MVA/HIV 48 expressed HIV proteins, which were processed to the expected size. The Env was inserted into the plasma membrane and was functional in a CCR5 coreceptor-dependent cell fusion assay. Moreover, virus-like particles were released into the medium and budding particles containing Env were visualized by immunoelectron microscopy. Rodents that were immunized with MVA/HIV 48 produced antibodies, which neutralized a heterologous HIV-MN strain, and Gag-specific CD8 T cells. In the accompanying paper, we show that MVA/HIV 48 provided efficient boosting of an HIV DNA vaccine.
HIV protease genotype and viral sensitivity to HIV protease inhibitors following saquinavir therapy (1998)

Recruitment of Val-48/Met-90 mutations was not found to be synonymous with cross-resistance. Indeed, the majority of isolates with these mutations retained sensitivity to at least one protease inhibitor (Val-48, 86%; Met-90, 77%). The recruitment of accessory mutations may occur only after the selection of key resistance mutations. Furthermore, Met-90 was found to be a poor marker of cross-resistance in SQV-treated patients.
Overview of Current Therapeutics and Novel Candidates Against Influenza, Respiratory Syncytial Virus, and Middle East Respiratory Syndrome Coronavirus Infections (2019)

Emergence and re-emergence of respiratory virus infections represent a significant threat to global public health, as they occur seasonally and less frequently (such as in the case of influenza virus) as pandemic infections. Some of these viruses have been in the human population for centuries and others had recently emerged as a public health problem. Influenza viruses have been affecting the human population for a long time now; however, their ability to rapidly evolve through antigenic drift and antigenic shift causes the emergence of new strains. A recent example of these events is the avian-origin H7N9 influenza virus outbreak currently undergoing in China. Human H7N9 influenza viruses are resistant to amantadines and some strains are also resistant to neuraminidase inhibitors greatly limiting the options for treatment. Respiratory syncytial virus (RSV) may cause a lower respiratory tract infection characterized by bronchiolitis and pneumonia mainly in children and the elderly. Infection with RSV can cause severe disease and even death, imposing a severe burden for pediatric and geriatric health systems worldwide. Treatment for RSV is mainly supportive since the only approved therapy, a monoclonal antibody, is recommended for prophylactic use in high-risk patients. The Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging respiratory virus. The virus was first recognized in 2012 and it is associated with a lower respiratory tract disease that is more severe in patients with comorbidities. No licensed vaccines or antivirals have been yet approved for the treatment of MERS-CoV in humans. It is clear that the discovery and development of novel antivirals that can be used alone or in combination with existing therapies to treat these important respiratory viral infections are critical. In this review, we will describe some of the novel therapeutics currently under development for the treatment of these infections.
Understanding the Protonation Behavior of Linear Polyethylenimine in Solutions through Monte Carlo Simulations (2009)

The success of polyethyleneimine (PEI) as a nonviral-based gene delivery vector has been attributed to its proton buffering capacity. Despite the great interest in PEI for its use in nonviral-based gene delivery, the protonation behavior of PEI in solution is not well understood. Earlier experimental studies have reported inconsistent values of the protonation state of PEI. In this work, we report our investigation of the protonation behavior of a realistic linear PEI (lPEI) with computational approaches. Reported experimental pK(a) values of several diamine compounds are first examined. A screened Coulombic interaction with a distance dependence dielectric is shown to reproduce the shifted pK(a) values of the model diamine compounds. Then atomistic molecular dynamic simulations of lPEI chain with 20 repeating units are performed and the results are used to provide parameters for a coarse-grained polyamine model. The screened Coulombic interaction is then incorporated in the coarse-grained lPEI chain and computational titrations are performed. The obtained computational titration curves of lPEI in solutions were found to be in best agreement with experimental results by Smits et al., but the computational titration curves have too strong of a dependence on salt concentration compared to the experimental results by Smits et al. Disregarding the discrepancy in the salt dependence, our computational titrations reveal that approximately 55% of the lPEI amine groups are protonated under physiological conditions in solution with a nearly alternating arrangement of protonated and nonprotonated amines. Titrations of lPEI in the presence of a polyanion are also performed to determine how the charge state of lPEI could be affected by complexation with DNA in gene therapy preparations. While the presence of the polyanion increases the degree of protonation of the PEI, many of PEI amines remain unprotonated under physiological conditions, providing evidence that PEI complexed with DNA could still have proton buffering capacity. Potential sources of error that have resulted in the inconsistency of previously reported protonation states of PEI were also discussed.
Tumor-infiltrating macrophages and dendritic cells in human colorectal cancer: relation to local regulatory T cells, systemic T-cell response against tumor-associated antigens and survival (2007)

The present in situ study adds new data to the discussion on the interaction between the innate and adoptive immune system. Our data strongly support the hypothesis that tumor-infiltrating DC are a key factor at the interface between innate and adaptive immune response in malignant disease. Tumor infiltrating S100-positive DC show an inverse relationship with the systemic antigen-specific T-cell response, a positive correlation with regulatory T cells, and a positive association with survival in CRC. These data put tumor-infiltrating DC at the center of the relevant immune response in CRC.
Binding and Cleavage Specificities of Human Argonaute2 (2009)

The endonuclease Argonaute2 (Ago2) mediates the degradation of the target mRNA within the RNA-induced silencing complex. We determined the binding and cleavage properties of recombinant human Ago2. Human Ago2 was unable to cleave preformed RNA duplexes and exhibited weaker binding affinity for RNA duplexes compared with the single strand RNA. The enzyme exhibited greater RNase H activity in the presence of Mn2+ compared with Mg2+. Human Ago2 exhibited weaker binding affinities and reduced cleavage activities for antisense RNAs with either a 5'-terminal hydroxyl or abasic nucleotide. Binding kinetics suggest that the 5'-terminal heterocycle base nucleates the interaction between the enzyme and the antisense RNA, and the 5'-phosphate stabilizes the interaction. Mn2+ ameliorated the effects of the 5'-terminal hydroxyl or abasic nucleotide on Ago2 cleavage activity and binding affinity. Nucleotide substitutions at the 3' terminus of the antisense RNA had no effect on human Ago2 cleavage activity, whereas 2'-methoxyethyl substitutions at position 2 reduced binding and cleavage activity and 12-14 reduced the cleavage activity. RNase protection assays indicated that human Ago2 interacts with the first 14 nucleotides at the 5'-pole of the antisense RNA. Human Ago2 preloaded with the antisense RNA exhibited greater binding affinities for longer sense RNAs suggesting that the enzyme interacts with regions in the sense RNA outside the site for antisense hybridization. Finally, transiently expressed human Ago2 immunoprecipitated from HeLa cells contained the double strand RNA-binding protein human immunodeficiency virus, type 1, trans-activating response RNA-binding protein, and deletion mutants of Ago2 showed that trans-activating response RNA-binding protein interacts with the PIWI domain of the enzyme.
Growth of strained Si and strained Ge heterostructures on relaxed Si1−xGex by ultrahigh vacuum chemical vapor deposition (2004)

Numerous applications require the growth of planar strained-layer heterostructures on relaxed Si1−xGex. After briefly reviewing these applications as well as the challenges in growing such heterostructures, we provide experimental examples illustrating the influence of lattice mismatch, growth temperature, and film composition on the morphology of thin strained layers in the Ge–Si alloy system. Procedures for growing strained Si and strained Ge single and double heterostructures via ultrahigh vacuum chemical vapor deposition are described in detail. We demonstrate planar growth of strained Ge layers with lattice mismatches as high as 2%, planar Si layers on any Si1−xGex lattice constant, and double heterostructures that are comprised of a strained Ge layer capped with strained Si. Notably, the techniques described here have already been applied to the fabrication of extremely high mobility p- and n-channel metal–oxide–semiconductor field-effect transistors and germanium-on-insulator substrates.