gebhart/patrepeval huggingface dataset:
Insect Pollinated Crops, Insect Pollinators and US Agriculture: Trend Analysis of Aggregate Data for the Period 1992–2009 (2012)

In the US, the cultivated area (hectares) and production (tonnes) of crops that require or benefit from insect pollination (directly dependent crops: apples, almonds, blueberries, cucurbits, etc.) increased from 1992, the first year in this study, through 1999 and continued near those levels through 2009; aggregate yield (tonnes/hectare) remained unchanged. The value of directly dependent crops attributed to all insect pollination (2009 USD) decreased from $14.29 billion in 1996, the first year for value data in this study, to $10.69 billion in 2001, but increased thereafter, reaching $15.12 billion by 2009. The values attributed to honey bees and non-Apis pollinators followed similar patterns, reaching $11.68 billion and $3.44 billion, respectively, by 2009. The cultivated area of crops grown from seeds resulting from insect pollination (indirectly dependent crops: legume hays, carrots, onions, etc.) was stable from 1992 through 1999, but has since declined. Production of those crops also declined, albeit not as rapidly as the decline in cultivated area; this asymmetry was due to increases in aggregate yield. The value of indirectly dependent crops attributed to insect pollination declined from $15.45 billion in 1996 to $12.00 billion in 2004, but has since trended upward. The value of indirectly dependent crops attributed to honey bees and non-Apis pollinators, exclusive of alfalfa leafcutter bees, has declined since 1996 to $5.39 billion and $1.15 billion, respectively in 2009. The value of alfalfa hay attributed to alfalfa leafcutter bees ranged between $4.99 and $7.04 billion. Trend analysis demonstrates that US producers have a continued and significant need for insect pollinators and that a diminution in managed or wild pollinator populations could seriously threaten the continued production of insect pollinated crops and crops grown from seeds resulting from insect pollination.
Metabolite and hormonal response in smokers during rest and sustained exercise (1995)

To evaluate the effects of acute and chronic smoking on blood glucose homeostasis, concentrations of metabolites, and hormonal responses at rest and during submaximal exercise, seven male smokers and seven similar nonsmokers were studied after an overnight fast. Nonsmokers (NS) and chronic smokers, abstaining from smoking (CS), were tested during rest and 60 min of cycle ergometry exercise at 49.7 +/- 0.8% of VO2peak. Smokers were restudied after acutely smoking (AS) two cigarettes prior to rest and one prior to exercise. Blood glucose levels were similar among NS, CS, and AS at all times. Lactate levels were elevated in AS compared with NS during exercise (2.32 +/- 0.22 mM vs 1.81 +/- 0.11; P < 0.05), with no differences in alanine. Free fatty acid levels were initially lower at rest in CS (0.45 +/- 0.04 mM) than in either AS (0.77 +/- 0.11) or NS (0.64 +/- 0.06; p < 0.05), but no other differences were found. During exercise, CS had lower glycerol levels (0.31 +/- 0.02 mM) than either AS (0.38 +/- 0.02) or NS (0.41 +/- 0.02; P < 0.05). Nevertheless, respiratory exchange ratio values were not significantly different during steady-state rest or exercise; and insulin, glucagon, and norepinephrine levels were also similar. Smokers effectively maintained normal blood glucose levels with only minor changes in some metabolite and hormone concentrations during rest and sustained exercise.
Cloning and functional expression in Escherichia coli of the gene encoding the di- and tripeptide transport protein of Lactobacillus helveticus (1997)

The gene encoding the di- and tripeptide transport protein (DtpT) of Lactobacillus helveticus (DtpTLH) was cloned with the aid of the inverse PCR technique and used to complement the dipeptide transport-deficient and proline-auxotrophic Escherichia coli E1772. Functional expression of the peptide transporter was shown by the uptake of prolyl-[14C] alanine in whole cells and membrane vesicles. Peptide transport via DtpT in membrane vesicles is driven by the proton motive force. The system has specificity for di- and tripeptides but not for amino acids or tetrapeptides. The dtpTLH gene consists of 1,491 bp, which translates into a 497-amino-acid polypeptide. DtpTLH shows 34% identity to the di- and tripeptide transport protein of Lactococcus lactis and is also homologous to various peptide transporters of eukaryotic origin, but the similarity between these proteins is confined mainly to the N-terminal halves.
Effect of Immobilized Nerve Growth Factor on Conductive Polymers: Electrical Properties and Cellular Response (2006)

Abstract The use of biologically active dopants in conductive polymers allows the polymer to be tailored for specific applications. The incorporation of nerve growth factor (NGF) as a co‐dopant in the electrochemical deposition of conductive polymers is evaluated for its ability to elicit specific biological interactions with neurons. The electrochemical properties of the NGF‐modified conducting polymers are studied by impedance spectroscopy and cyclic voltammetry. Impedance measurements at the neurobiologically important frequency of 1 kHz reveal that the minimum impedance of the NGF‐modified polypyrrole (PPy) film, 15 kΩ, is lower than the minimum impedance of peptide‐modified PPy film (360 kΩ). Similar results are found with NGF‐modified poly(3,4‐ethylene dioxythiophene) (PEDOT). The microstructure of the conductive polymer films is characterized by optical microscopy and electron microscopy and indicates that the NGF‐functionalized polymer surface topology is similar to that of the unmodified polymer film. Optical and fluorescence microscopy reveal that PC‐12 (rat pheochromacytoma) cells adhered to the NGF‐modified substrate and extended neurites on both PPy and PEDOT, indicating that the NGF in the polymer film is biologically active. Taken together these data indicate that the incorporation of NGF can modify the biological interactions of the electrode without compromising the conductive properties or the morphology of the polymeric film.
Identification of a novel negative role of flagellin in regulating IL‐10 production (2007)

Toll-like receptors (TLR) expressed by cells of the immune system play a central role in the generation of immune responses against pathogens. Following TLR ligation, both pro-inflammatory and anti-inflammatory mediators are produced in order to elicit an immune response that controls the microbial infection while limiting tissue damage. Among these mediators, the pro-inflammatory cytokine IL-12 and the anti-inflammatory cytokine IL-10 are known to play major roles. Here, we show that in vitro or in vivo stimulation with flagellin, the TLR5 ligand, does not result in IL-10 production. Furthermore, flagellin inhibits IL-10 production by other specific TLR ligands at the protein and mRNA levels while increasing IL-12p70 production. Several studies have linked the activation of extracellular signal-regulated kinases with IL-10 induction by TLR. We have observed that LPS-induced extracellular signal-regulated kinase activation was significantly decreased in flagellin-treated macrophages, suggesting that this pathway might play a role in the inhibition of IL-10 production observed in flagellin-treated macrophages. Flagellin-mediated IL-10 inhibition was not observed in cells that do not express TLR5, supporting that this effect is indeed TLR5-dependent. This study provides a new insight into the role of flagellin recognition by TLR5 in shaping the immune response elicited by flagellated microorganisms.
Two distinct loci affecting conversion to mucoidy in Pseudomonas aeruginosa in cystic fibrosis encode homologs of the serine protease HtrA (1996)

Conversion to a mucoid, exopolysaccharide alginate-overproducing phenotype in Pseudomonas aeruginosa is associated with chronic respiratory infections in cystic fibrosis. Mucoidy is caused by muc mutations that derepress the alternative sigma factor AlgU, which in turn activates alginate biosynthetic and ancillary regulatory genes. Here we report the molecular characterization of two newly identified genes, algW and mucD, that affect expression of mucoidy. The algW gene, mapping at 69 min, was isolated on the basis of its ability to suppress mucoidy and reduce transcription of the alginate biosynthetic gene algD. The predicted primary structure of AlgW displayed similarity to HtrA (DegP), a serine protease involved in proteolysis of abnormal proteins and required for resistance to oxidative and heat stress in enteric bacteria. Inactivation of algW on the chromosome of the wild-type nonmucoid strain PAO1 caused increased sensitivity to heat, H2O2, and paraquat, a redox cycling compound inducing intracellular levels of superoxide. This mutation also permitted significant induction of alginate production in the presence of subinhibitory concentrations of paraquat. Two new genes, mucC and mucD, were identified immediately downstream of the previously characterized portion (algU mucA mucB) of the gene cluster at 67.5 min encoding the alternative sigma factor AlgU and its regulators. Interestingly, the predicted gene product of mucD also showed similarities to HtrA. Inactivation of mucD on the PAO1 chromosome resulted in conversion to the mucoid phenotype. The mutation in mucD also caused increased sensitivity to H2O2 and heat killing. However, in contrast to algW mutants, no increase in susceptibility to paraquat was observed in mucD mutants. These findings indicate that algW and mucD play partially overlapping but distinct roles in P. aeruginosa resistance to reactive oxygen intermediates and heat. In addition, since mutations in mucD and algW cause conversion to mucoidy or lower the threshold for its induction by reactive oxygen intermediates, these factors may repress alginate synthesis either directly by acting on AlgU or its regulators or indirectly by removing physiological signals that may activate this stress response system.
Colistin inhalation therapy in cystic fibrosis patients with chronic Pseudomonas aeruginosa lung infection (1987)

Forty patients with cystic fibrosis and chronic broncho-pulmonary Pseudomonas aeruginosa infection entered a prospective double-blind placebo-controlled study of colistin inhalation. Active treatment consisted of inhalation of colistin one million units twice daily for three months and was compared to placebo inhalations of isotonic saline. Significantly more patients in the colistin inhalation group completed the study as compared to the placebo group (18 versus 11). Colistin treatment was superior to placebo treatment in terms of a significantly better clinical symptom score, maintenance of pulmonary function and inflammatory parameters. We recommend colistin inhalation therapy for cystic fibrosis patients with chronic P. aeruginosa lung infection as a supplementary treatment to frequent courses of intravenous anti-pseudomonas chemotherapy.
MR-PDP: Multiple-Replica Provable Data Possession (2008)

Many storage systems rely on replication to increase the availability and durability of data on untrusted storage systems. At present, such storage systems provide no strong evidence that multiple copies of the data are actually stored. Storage servers can collude to make it look like they are storing many copies of the data, whereas in reality they only store a single copy. We address this shortcoming through multiple-replica provable data possession (MR-PDP): A provably-secure scheme that allows a client that stores t replicas of a file in a storage system to verify through a challenge-response protocol that (1) each unique replica can be produced at the time of the challenge and that (2) the storage system uses t times the storage required to store a single replica. MR-PDP extends previous work on data possession proofs for a single copy of a file in a client/server storage system (Ateniese et al., 2007). Using MR-PDP to store t replicas is computationally much more efficient than using a single-replica PDP scheme to store t separate, unrelated files (e.g., by encrypting each file separately prior to storing it). Another advantage of MR-PDP is that it can generate further replicas on demand, at little expense, when some of the existing replicas fail.
The Impact of User Location on Cookie Notices (Inside and Outside of the European Union) (2021)

The web is global, but privacy laws differ by country. Which set of privacy rules do websites follow? We empirically study this question by detecting and analyzing cookie notices in an automated way. We crawl 1,500 European, American, and Canadian websites from each of 18 countries. We detect cookie notices on 40 percent of websites in our sample. We treat the presence or absence of cookie notices, as well as visual differences, as proxies for differences in privacy rules. Using a series of regression models, we find that the website's Top Level Domain explains a substantial portion of the variance in cookie notice metrics, but the user's vantage point does not. This suggests that websites follow one set of privacy rules for all their users. There is one exception to this finding: cookie notices differ when accessing .com domains from inside versus outside of the EU. We highlight ways in which future research could build on our preliminary findings.
An anionic human protein mediates cationic liposome delivery of genome editing proteins into mammalian cells (2019)

Delivery into mammalian cells remains a significant challenge for many applications of proteins as research tools and therapeutics. We recently reported that the fusion of cargo proteins to a supernegatively charged (-30)GFP enhances encapsulation by cationic lipids and delivery into mammalian cells. To discover polyanionic proteins with optimal delivery properties, we evaluate negatively charged natural human proteins for their ability to deliver proteins into cultured mammalian cells and human primary fibroblasts. Here we discover that ProTα, a small, widely expressed, intrinsically disordered human protein, enables up to ~10-fold more efficient cationic lipid-mediated protein delivery compared to (-30)GFP. ProTα enables efficient delivery at low- to mid-nM concentrations of two unrelated genome editing proteins, Cre recombinase and zinc-finger nucleases, under conditions in which (-30)GFP fusion or cationic lipid alone does not result in substantial activity. ProTα may enable mammalian cell protein delivery applications when delivery potency is limiting.
An improved method for synthesis and purification of 125I or 131I labeled carrier‐free 5‐iodo‐2′‐deoxyuridine (1978)

Abstract Consistently high yields (up to 95%) of carrier‐free 5‐iodo‐2′‐deoxyuridine‐ 125 I (or 131 I) can be obtained by iodination of 2′‐deoxyuridine at varying concentrations of radioactive NaI (1–10 mCi), as long as the molarity of deoxyuridine in the reaction mixture is kept at or above 10 −2 M. At lower deoxyuridine molarities the reaction yield is significantly reduced. Several different purification procedures (Biogel P‐2 400 mesh or Sephadex G‐10 column chromatography, paper chromatography with water‐saturated ethyl acetate or water‐saturated butanol) are described. The two column chromatography systems yield iododeoxyuridine of &gt; 95% chemical and radiochemical purity. The two paper chromatography systems are somewhat more involved, but yield 125 I or 131 I labeled 5‐iodo‐2′‐deoxyuridine of &gt; 99% chemical and radiochemical purity.
Transient immunomodulation with anti-CD40 ligand antibody and CTLA4Ig enhances persistence and secondary adenovirus-mediated gene transfer into mouse liver (1997)

Although recombinant adenovirus vectors offer a very efficient means by which to transfer genetic information into cells in vivo, antigen-dependent immunity limits the duration of gene expression and prevents retreatment. Recombinant murine CTLA4Ig and anti-CD40 ligand antibody block costimulatory interactions between T cells and antigen presenting cells. We previously reported that murine CTLA4Ig prolongs adenoviral-mediated gene transfer, but does not allow for secondary expression after readministration of the vector. In studies described here, when anti-CD40 ligand and recombinant murine CTLA4Ig were coadministered around the time of primary vector administration (i) prolonged adenovirus-mediated gene expression (length of experiment up to 1 year) from the livers of >90% of treated mice was observed, and (ii) secondary adenovirus-mediated gene transfer was achieved in >50% of the mice even after the immunosuppressive effects of these agents were no longer present. Nearly two-thirds of these mice had persistent secondary gene expression lasting for at least 200-300 days. Neither agent alone allowed transduction after secondary vector administration. Treated mice had decreased immune responses to the vector as shown by markedly decreased production of neutralizing antibodies, diminished spleen proliferation responses and IFN-gamma production in vitro, and reduced T cell infiltrates in the liver. These results suggest that it may be possible to obtain persistence as well as secondary adenoviral-mediated gene transfer with transient immunosuppressive therapies.
Surface-produced alignment of liquid crystals (1973)

The surface-generated orienting forces acting on liquid crystals (LC's) result from physicochemical processes, e.g., hydrogen bonding, Van der Waal's interactions, or dipolar interactions, and from mechanical interactions as a result of the LC's anisotropic elasticity. For flat, untextured surfaces, the physicochemical processes prevail, while for textured surfaces, the anisotropic elastic interactions must also be considered. These sometimes competing processes are compared quantitatively, and the various orienting techniques and materials are discussed. It is shown that although both physicochemical and anisotropic elastic interactions are important, the former will typically predominate.
Vaccination with the major secretory protein of Legionella pneumophila induces cell-mediated and protective immunity in a guinea pig model of Legionnaires' disease. (1989)

We have examined the capacity of the major secretory protein (MSP) of Legionella pneumophila to induce humoral, cell-mediated, and protective immunity in a guinea pig model of Legionnaires' disease. MSP was purified to homogeneity by ammonium sulfate precipitation, molecular sieve chromatography, and ion-exchange chromatography. The purified MSP was nonlethal and nontoxic to guinea pigs upon subcutaneous administration. Guinea pigs immunized with a sublethal dose of aerosolized L. pneumophila or a subcutaneous dose of MSP developed a strong cell-mediated immune response to MSP. Such guinea pigs exhibited marked splenic lymphocyte proliferation and cutaneous delayed-type hypersensitivity to MSP in comparison with control animals. Guinea pigs immunized with MSP also developed a strong humoral immune response to MSP, as assayed by an ELISA. The median reciprocal antibody titer was 362 (range 45 to greater than 2,048) for immunized animals compared with less than 8 for controls. In contrast, guinea pigs immunized with a sublethal dose of L. pneumophila failed to develop anti-MSP antibody. Guinea pigs immunized with MSP and then challenged with a lethal aerosol dose of L. pneumophila exhibited highly significant protective immunity in each of five consecutive experiments. MSP induced protective immunity in dose-dependent fashion (40 greater than 10 greater than 2.5 greater than 0.6 micrograms MSP); vaccination with two doses of as little as 2.5 micrograms MSP induced significant protective immunity (p = 0.01, Fisher's Exact Test, two-tailed). Altogether, 21 (81%) of 26 animals immunized with 40 micrograms MSP survived challenge compared with 0 (0%) of 26 sham-immunized control animals (p = 7 x 10(-10), Fisher's Exact Test, two-tailed). MSP-immunized but not control guinea pigs were able to limit L. pneumophila multiplication in their lungs. This study demonstrates that (a) guinea pigs sublethally infected with L. pneumophila develop a strong cell-mediated immune response to MSP; (b) guinea pigs immunized with MSP develop a strong humoral and cell-mediated immune response to MSP; (c) guinea pigs immunized with MSP develop a very high level of protective immunity to lethal aerosol challenge with L. pneumophila; and (d) MSP-immunized animals are able to limit L. pneumophila multiplication in their lungs. MSP, an extracellular protein of an intracellular pathogen, has potential as a vaccine for the prevention of Legionnaires' disease. Secretory molecules of other intracellular pathogens may also have vaccine potential.
Hydrogen Peroxide Fluxes and Compartmentalization inside Growing Escherichia coli (2001)

Escherichia coli generates about 14 microM hydrogen peroxide (H(2)O(2)) per s when it grows exponentially in glucose medium. The steady-state intracellular concentration of H(2)O(2) depends on the rates at which this H(2)O(2) is dissipated by scavenging enzymes and by efflux from the cell. The rates of H(2)O(2) degradation by the two major scavenging enzymes, alkyl hydroperoxide reductase and catalase, were quantified. In order to estimate the rate of efflux, the permeability coefficient of membranes for H(2)O(2) was determined. The coefficient is 1.6 x 10(-3) cm/s, indicating that permeability is substantial but not unlimited. These data allowed internal H(2)O(2) fluxes and concentrations to be calculated. Under these growth conditions, Ahp scavenges the majority of the endogenous H(2)O(2), with a small fraction degraded by catalase and virtually none persisting long enough to penetrate the membrane and exit the cell. The robust scavenging activity maintains the H(2)O(2) concentration inside glucose-grown cells at <10(-7) M, substantially below the level (10(-6) M) at which toxicity is evident. When extracellular H(2)O(2) is present, its flux into the cell can be rapid, but the internal concentration may still be an order of magnitude lower than that outside. The presence of such gradients was confirmed in experiments that revealed different degrees of oxidative stress in cocultured scavenger-deficient mutants. The limited permeability of membranes to H(2)O(2) rationalizes the compartmentalization of scavenging systems and predicts that bacteria that excrete redox-cycling drugs do not experience the same H(2)O(2) dose that they impose on their competitors.
Genome‐wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion (2008)

Deletion of 17p (TP53) identifies a rare subset of chronic lymphocytic leukaemia (17p- CLL) with aggressive behaviour. Genome-wide DNA-profiling was performed to investigate 18 patients with 17p- CLL. All cases had multiple copy-number (CN) changes. Among the several recurrent CN changes identified, 8q24.13-q24.1-gain (MYC), 8p-loss (TNFRSF10A/B, also known as TRAIL1/2) and 2p16.1-p14-gain (REL/BCL11A) appeared frequently represented. 8p-loss and 2p16.1-p14-gain also appeared clinically relevant and predicted significant shorter time from diagnosis to treatment (8p-loss) and overall survival (8p-loss and 2p16.1-p14-gain, P < 0.05). These observations document a highly unstable genome in 17p- CLL and suggest that additional genes outside the TP53 locus may be important for tumour behaviour.