gebhart/patrepeval huggingface dataset:
Sec61p Contributes to Signal Sequence Orientation According to the Positive-Inside Rule (2003)

Protein targeting to the endoplasmic reticulum is mediated by signal or signal-anchor sequences. They also play an important role in protein topogenesis, because their orientation in the translocon determines whether their N- or C-terminal sequence is translocated. Signal orientation is primarily determined by charged residues flanking the hydrophobic core, whereby the more positive end is predominantly positioned to the cytoplasmic side of the membrane, a phenomenon known as the "positive-inside rule." We tested the role of conserved charged residues of Sec61p, the major component of the translocon in Saccharomyces cerevisiae, in orienting signals according to their flanking charges by site-directed mutagenesis by using diagnostic model proteins. Mutation of R67, R74, or E382 in Sec61p reduced C-terminal translocation of a signal-anchor protein with a positive N-terminal flanking sequence and increased it for signal-anchor proteins with positive C-terminal sequences. These mutations produced a stronger effect on substrates with greater charge difference across the hydrophobic core of the signal. For some of the substrates, a charge mutation in Sec61p had a similar effect as one in the substrate polypeptides. Although these three residues do not account for the entire charge effect in signal orientation, the results show that Sec61p contributes to the positive-inside rule.
Matching algorithms to problems: an experimental test of the particle swarm and some genetic algorithms on the multimodal problem generator (2002)

A multimodal problem generator was used to test three versions of a genetic algorithm and the binary particle swarm algorithm in a factorial time-series experiment. Specific strengths and weaknesses of the various algorithms were identified.
Production of lymphocyte-activating factor (Interleukin 1) by macrophages activated with colony-stimulating factors. (1980)

Murine peritoneal exudate macrophages incubated with medium conditioned by L929 cells were stimulated to produce lymphocyte-activating factor (LAF, Interleukin 1). This stimulatory activity was partially neutralized by antiserum prepared against partially purified L cell colony-stimulating factor (CSF) and comigrated upon gel filtration with the myeloproliferative activity. LAF-inducing activity of three different L cell CSF preparations, including one purified to homogeneity, was dependent upon the concentration of CSF. A minimum of 1,000 to 3,000 units of CSF activity was required to stimulate macrophagfes to produce LAF. Concanavalin A (Con A) stimulated splenic supernatants also contained CSF and LAF-inducing activities that co-eluted upon gel filtration. LAF-inducing activities co-eluting with the two Con A CSF peaks (apparent m.w. of 25,000 and 35,000) were effective at minimum dilutions containing 1,000 to 3,000 units of CSF activity correlating in potency with L cell-derived CSF. Based on these data, it is proposed that CSF, whether of L cell or lymphoid origin, not only has myeloproliferative activities but also is capable of stimulating macrophages to produce LAF.
Prevention and treatment of urinary tract infection with probiotics: Review and research perspective (2008)

The spiralling costs of antibiotic therapy, the appearance of multiresistant bacteria and more importantly for patients and clinicians, unsatisfactory therapeutic options in recurrent urinary tract infection (RUTI) calls for alternative and advanced medical solutions. So far no sufficient means to successfully prevent painful and disabling RUTI has been found. Even though long-term oral antibiotic treatment has been used with some success as a therapeutic option, this is no longer secure due to the development of bacterial resistance. One promising alternative is the use of live microorganisms (probiotics) to prevent and treat recurrent complicated and uncomplicated urinary tract infection (UTI).The human normal bacterial flora is increasingly recognised as an important defence to infection. Since the advent of antibiotic treatment five decades ago, a linear relation between antibiotic use and reduction in pathogenic bacteria has become established as medical conventional wisdom. But with the use of antibiotics the beneficial bacterial flora hosted by the human body is destroyed and pathogenic bacteria are selectively enabled to overgrow internal and external surfaces. The benign bacterial flora is crucial for body function and oervgrowth with pathogenic microorganisms leads to illness. Thus the concept of supporting the human body's normal flora with live microorganisms conferring a beneficial health effect is an important medical strategy.
Isolation of Estrogen-Responsive Genes with a CpG Island Library (1998)

In order to isolate novel estrogen-responsive genes, we utilized a CpG island library in which the regulatory regions of genes are enriched. CpG islands were screened for the ability to bind to a recombinant estrogen receptor protein with a genomic binding site (GBS) cloning method. Six CpG islands were selected, and they contained perfect, imperfect, and/or multiple half-palindromic estrogen-responsive elements (EREs). Northern blot analysis of various human cells showed that all these genomic fragments hybridized to specific mRNAs, suggesting that the genes associated with these EREs might be transcribed in human cells. Then cDNAs associated with two of them, EB1 and EB9, were isolated from libraries of human placenta and MCF-7 cells derived from a human breast cancer, respectively. Both transcripts were increased by estrogen in MCF-7 cells. The increase is inhibited by actinomycin D but not by cycloheximide, indicating that no protein synthesis is required for the up-regulation. The cDNA associated with EB1 encodes a 114-amino-acid protein similar to the cytochrome c oxidase subunit VIIa, named COX7RP (cytochrome c oxidase subunit VII-related protein). The cDNA associated with EB9 is homologous only to an express sequence tag and was named EBAG9 (estrogen receptor-binding fragment-associated gene 9). The palindromic ERE of EB1 is located in an intron of COX7RP, and that of EB9 is in the 5' upstream region of the cDNA. Both EREs had significant estrogen-dependent enhancer activities in a chloramphenicol acetyltransferase assay, when they were inserted into the 5' upstream region of the chicken beta-globin promoter. We therefore propose that the CpG-GBS method described here for isolation of the DNA binding site from the CpG island library would be useful for identification of novel target genes of certain transcription factors.
FlowVisor: A Network Virtualization Layer (2009)

Network virtualization has long been a goal of of the network research community. With it, multiple isolated logical networks each with potentially different addressing and forwarding mechanisms can share the same physical infrastructure. Typically this is achieved by taking advantage of the flexibility of software (e.g. [20, 23]) or by duplicating components in (often specialized) hardware[19]. In this paper we present a new approach to switch virtualization in which the same hardware forwarding plane can be shared among multiple logical networks, each with distinct forward-ing logic. We use this switch-level virtualization to build a research platform which allows multiple network experiments to run side-by-side with production traffic while still providing isolation and hardware forwarding speeds. We also show that this approach is compatible with commodity switching chipsets and does not require the use of programmable hardware such as FPGAs or network processors. We build and deploy this virtualization platform on our own production network and demon-strate its use in practice by running five experiments simultaneously within a campus network. Further, we quantify the overhead of our approach and evaluate the completeness of the isola-tion between virtual slices.
Macrophage stimulation with Murabutide, an HIV-suppressive muramyl peptide derivative, selectively activates extracellular signal-regulated kinases 1 and 2, C / EBPβ and STAT1: role of CD14 and Toll-like receptors 2 and 4 (2001)

The smallest unit of bacterial peptidoglycans known to be endowed with biological activities is muramyl dipeptide (MDP). A clinically acceptable synthetic derivative of MDP, namely murabutide (MB), has been found to present interesting pharmacological properties and to suppress HIV-1 replication in monocyte-derived macrophages (MDM). We have addressed the signaling events activated in MDM following stimulation with either MB or the potent immunostimulant LPS. We also examined whether signaling by muramyl peptides involves the use of cell surface receptors, including CD14 and Toll-like receptor 2 (TLR2) or TLR4 that are known to be signal-transducing receptors for other bacterial cell wall components. We demonstrate that, unlike LPS, the safe immunomodulator MB selectively activates extracellular signal-regulated kinases (Erk) 1/2, in the absence of detectable Jun N-terminal kinase (JNK) or p38 mitogen-activated kinase activation. Furthermore, STAT1 activation but weak or no activation of STAT3 or STAT5 respectively, could be detected in MB-stimulated MDM. Using MonoMac6 cells, we observed high C/EBPbeta and AP-1 but weaker and transient NF-kappaB activation by MB.Moreover, the truncated form of C/EBPbeta, known to repress HIV-1 transcription, was detected in extracts from MB-treated THP-1 cells. Surprisingly, neither MB nor MDP were able to transduce signals via CD14 and TLR2 or 4. These findings present major differences in the early cell activation process between LPS and muramyl peptides, and strongly argue for the implication of co-receptors other than TLR2 and TLR4 in mediating the signaling events induced by defined subunits of bacterial peptidoglycans.
Rule based synonyms for entity extraction from noisy text (2008)

Identification of named entities such as person, organization and product names from text is an important task in information extraction. In many domains, the same entity could be referred to in multiple ways due to variations introduced by different user groups, variations of spellings across regions or cultures, usage of abbreviations, typographical errors and other reasons associated with conventional usage. Identifying a piece of text as a mention of an entity in such noisy data is difficult, even if we have a dictionary of possible entities. Previous approaches treat the synonym problem as part entity disambiguation and use learning-based methods that use the context of the words to identify synonyms. In this paper, we show that existing domain knowledge, encoded as rules, can be used effectively to address the synonym problem to a considerable extent. This makes the disambiguation task simpler, without the need for much training data. We look at a subset of application scenarios in named entity extraction, categorize the possible variations in entity names, and define rules for each category. Using these rules, we generate synonyms for the canonical list and match these synonyms to the actual occurrence in the data sets. In particular, we describe the rule categories that we developed for several named entities and report the results of applying our technique of extracting named entities by generating synonyms for two different domains.
IL-12p70–producing patient DC vaccine elicits Tc1-polarized immunity (2013)

These findings underscore the essential role of IL-12p70 in the development of therapeutic type 1 antigen-specific CD8+ T cell immunity in humans with cancer.
Characterization of individual polynucleotide molecules using a membrane channel (1996)

We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.
HP's International Cryptography Framework: compromise or threat? (1997)

Hewlett-Packard (HP) has developed the International Cryptography Framework (ICF), the strongest encryption system approved for export by the US government to date. The hardware-software system provides various levels of encryption strength, depending on government regulations in the USA and importing countries. In some cases, ICF will allow US manufacturers to export stronger encryption products than regulations have permitted in the past. The US computer industry has said this is necessary for it to compete more effectively in the international marketplace. However, some say ICF may prove to be a Trojan horse in the war over electronic communications privacy. They contend that millions of people will buy ICF-enabled equipment that has weak encryption and that would permit the US government to decrypt data transmissions easily.
ChemInform Abstract: Stereoselective Total Synthesis of Testosterone and Androsterone via A/B‐Ring Construction of the Steroidal Ring System by Intramolecular Diels‐Alder Reaction. (1986)

Abstract As illustrated in the scheme, a total synthesis of testosterone (XIII) is possible starting from the reaction between the indanone (I) and the dioxolane (II).
Prostate cancer: correlation between local and systemic disease. (1999)

We can deduce that periodical carrying-out of the TRUS (twice a year) constitute a reliable index not only of local procedure of the pt. but also predicting the systemic course of the disease, making the routine carrying out of the other check-up unnecessary, that could be reserved for cases with precise clinical indication.
Critical Role of cAMP Response Element Binding Protein Expression in Hypoxia-elicited Induction of Epithelial Tumor Necrosis Factor-α (1999)

Tissue hypoxia is intimately associated with a number of chronic inflammatory conditions of the intestine. In this study, we investigated the impact of hypoxia on the expression of a panel of inflammatory mediators by intestinal epithelia. Initial experiments revealed that epithelial (T84 cell) exposure to ambient hypoxia evoked a time-dependent induction of the proinflammatory markers tumor necrosis factor-alpha (TNF-alpha), interleukin-8 (IL-8), and major histocompatibility complex (MHC) class II (37 +/- 6.1-, 7 +/- 0.8-, and 9 +/- 0.9-fold increase over normoxia, respectively, each p < 0.01). Since the gene regulatory elements for each of these molecules contains an NF-kappaB binding domain, we investigated the influence of hypoxia on NF-kappaB activation. Cellular hypoxia induced a time-dependent increase in nuclear p65, suggesting a dominant role for NF-kappaB in hypoxia-elicited induction of proinflammatory gene products. Further work, however, revealed that hypoxia does not influence epithelial intercellular adhesion molecule 1 (ICAM-1) or MHC class I, the promoters of which also contain NF-kappaB binding domains, suggesting differential responses to hypoxia. Importantly, the genes for TNF-alpha, IL-8, and MHC class II, but not ICAM-1 or MHC class I, contain cyclic AMP response element (CRE) consensus motifs. Thus, we examined the role of cAMP in the hypoxia-elicited phenotype. Hypoxia diminished CRE binding protein (CREB) expression. In parallel, T84 cell cAMP was diminished by hypoxia (83 +/- 13.2% decrease, p < 0.001), and pharmacologic inhibition of protein kinase A induced TNF-alpha and protein release (9 +/- 3.9-fold increase). Addback of cAMP resulted in reversal of hypoxia-elicited TNF-alpha release (86 +/- 3.2% inhibition with 3 mM 8-bromo-cAMP). Furthermore, overexpression of CREB but not mutated CREB by retroviral-mediated gene transfer reversed hypoxia-elicited induction of TNF-alpha defining a causal relationship between hypoxia-elicited CREB reduction and TNF-alpha induction. Such data indicate a prominent role for CREB in the hypoxia-elicited epithelial phenotype and implicate intracellular cAMP as an important second messenger in differential induction of proinflammatory mediators.
Cloning and Functional Characterization of the Ornithokinin Receptor (1997)

Kinins are proinflammatory peptides that dilate vessels, increase vascular permeability, contract smooth muscles, and provoke pain. The known mammalian kinin receptors are classified as two subtypes, i.e. the B1 receptor triggered by [des-Arg9]bradykinin and inhibited by [des-Arg9,Leu8]bradykinin, and the B2 receptor stimulated by bradykinin and antagonized by HOE140. Here we report the cloning of a non-mammalian kinin receptor gene amplified from genomic chicken DNA. The protein predicted from the open reading frame shows 31 and 49% sequence identity to the human B1 and B2 receptors, respectively, suggesting that it represents a G protein-coupled receptor of the kinin receptor family. The recombinantly expressed chicken receptor had IC50 values of 4.7 nM for the authentic ligand, ornithokinin ([Thr6,Leu8]bradykinin), 3.8 nM for HOE140, and >/=10 microM for bradykinin, [des-Arg9]bradykinin, and [des-Arg9,Leu8]bradykinin. Ornithokinin and HOE140 at nanomolar concentrations stimulated intracellular inositol phosphate accumulation and induced a significant transient rise in intracelluar free Ca2+, whereas bradykinin was ineffective even at 100 nM. Hence the principal B2 receptor antagonist HOE140 is a potent agonist of the chicken kinin receptor. This unique pharmacological profile classifies the ornithokinin receptor as a novel subtype among kinin receptors and will facilitate further molecular studies on ligand binding and receptor activation.
Polyanhydride Networks from Thiol−Ene Polymerizations (2010)

Thiol−ene photopolymerization was used in the synthesis of elastomeric polyanhydrides. Side reactions involving the addition of thiol to the anhydride were observed but take place at a much slower rate than photoinitiated thiol−ene polymerization. The thermomechanical properties, including the glass transition temperature (Tg) as well as tensile and compressive modulus, of the cross-linked material were studied using dynamic mechanical analysis. Tg values ranged from −15 to approximately −50 °C and were dependent on the degree of cross-linking. The Young’s and compressive modulus measurements confirm that these types of networks are a soft rubber-like material at room and body temperature and become softer as the cross-linking density is reduced. The hydrophobicity/hydrophilicity of these networks was analyzed by water contact angle measurements. The polyanhydrides were moderately hydrophobic, with water contact angle averages ranging from 82° to 92°. This hydrophobicity, coupled with the high reactivity of the anhydride groups, results in the material eroding via the surface erosion mechanism.
Weight Loss With Naltrexone SR/Bupropion SR Combination Therapy as an Adjunct to Behavior Modification: The COR‐BMOD Trial (2010)

This 56-week, randomized, placebo-controlled trial examined the efficacy and safety of naltrexone plus bupropion as an adjunct to intensive behavior modification (BMOD). A total of 793 participants (BMI = 36.5 ± 4.2 kg/m²) was randomly assigned in a 1:3 ratio to: (i) placebo + BMOD (N = 202); or (ii) naltrexone sustained-release (SR, 32 mg/day), combined with bupropion SR (360 mg/day) plus BMOD (i.e., NB32 + BMOD; N = 591). Both groups were prescribed an energy-reduced diet and 28 group BMOD sessions. Co-primary end points were percentage change in weight and the proportion of participants who lost ≥5% weight at week 56. Efficacy analyses were performed on a modified intent-to-treat population (ITT; i.e., participants with ≥1 postbaseline weight while taking study drug (placebo + BMOD, N = 193; NB32 + BMOD, N = 482)). Missing data were replaced with the last observation obtained on study drug. At week 56, weight loss was 5.1 ± 0.6% with placebo + BMOD vs. 9.3 ± 0.4% with NB32 + BMOD (P < 0.001). A completers analysis revealed weight losses of 7.3 ± 0.9% (N = 106) vs. 11.5 ± 0.6% (N = 301), respectively (P < 0.001). A third analysis, which included all randomized participants, yielded losses of 4.9 ± 0.6 vs. 7.8 ± 0.4%, respectively (P < 0.001). Significantly more NB32 + BMOD- vs. placebo + BMOD-treated participants lost ≥5 and ≥10% of initial weight, and the former had significantly greater improvements in markers of cardiometabolic disease risk. NB32 + BMOD was generally well tolerated, although associated with more reports of nausea than placebo + BMOD. The present findings support the efficacy of combined naltrexone/bupropion therapy as an adjunct to intensive BMOD for obesity.
Induction of CD8+ cytotoxic T lymphocytes by immunization with syngeneic irradiated HIV-1 envelope derived peptide-pulsed dendritic cells (1993)

Based on the evidence that CD8+ cytotoxic T cells (CTL) precursors do not appear to distinguish between virus-infected cells and viral peptide-pulsed syngeneic cells, we have developed methods for priming class I MHC molecule restricted CD8+ CTL with such peptides without using any adjuvant. We were able to prime in vivo such CTL immunity lasting at least 6 months with a single i.v. injection of syngeneic 2200-3300 rad irradiated peptide-pulsed spleen cells, and even more efficiently with a very small number of irradiated class II MHC molecule expressing splenic dendritic cells (DC). No foreign serum source was necessary during the pulsing. Interestingly, we could not generate significant CTL activity with unirradiated or low dose (< 1100 rad) irradiated spleen cells. Because even purified DC required irradiation for optimal activity, because unirradiated B cells did not significantly inhibit the immunization with DC, and because B cell depletion did not substitute for irradiation, we believe that the effect of irradiation is more to determine homing of the cells than to eliminate interference by B cells. Intravenous immunization was much more effective than s.c. or i.p. immunization. CTL generated by this method could kill both peptide-pulsed syngeneic targets and targets endogenously expressing the whole gp160 gene. Moreover, we found that we could prime CD8+ CTL with the minimal 10-residue core peptide (RGPGRAFVTI) for optimal presentation by class I MHC molecules as efficiently as the original p18. These results suggested that DC bearing antigenic peptide may prime antigen-specific CD8+ CTL in vivo. These results offer useful information for development of synthetic peptide vaccines and immunotherapy.
Synthesis of Hydroxyapatite Nanopowders via Sucrose‐Templated Sol–Gel Method (2003)

The present research describes synthesis of hydroxyapatite (HAp) nanopowders using a sol–gel route with calcium nitrate and ammonium hydrogen phosphate as calcium and phosphorous precursors, respectively. Sucrose is used as template material, and alumina is added as a dopant to study its effects on particle size and surface area. Synthesized powders are characterized using X‐ray diffractometry, BET surface‐area analysis, and transmission electron microscopy. Results show that alumina stabilizes the HAp crystalline phase. Average particle size of mesoporous HAp samples is between 30 and 50 nm with surface area of 51–60 m 2 /g.
A high performing brain–machine interface driven by low-frequency local field potentials alone and together with spikes (2015)

These findings show that LMP is an effective BMI control signal which requires minimal power to extract and can substitute for or augment impoverished spikes signals. Use of this signal may lengthen the useful lifespan of BMIs and is therefore an important step towards clinically viable BMIs.