gebhart/patrepeval huggingface dataset:
Invited review: Body condition score and its association with dairy cow productivity, health, and welfare (2009)

The body condition score (BCS) of a dairy cow is an assessment of the proportion of body fat that it possesses, and it is recognized by animal scientists and producers as being an important factor in dairy cattle management. The scale used to measure BCS differs between countries, but low values always reflect emaciation and high values equate to obesity. The intercalving profile of BCS is a mirror image of the milk lactation profile. Cows lose condition for 50 to 100 d postcalving, because of homeorhetic changes that occur in the somatotropic axis and the sensitivity of peripheral tissues to insulin, and the upregulation of lipolytic pathways in adipose tissue. Management and feeding have little effect on early postcalving BCS loss (wk 1 to 4 postcalving) until the natural period of insulin resistance has passed and the somatotropic axis has recoupled. There is evidence, however, that management and diet can influence the timing of recoupling of the somatotropic axis and the sensitivity of peripheral tissues to insulin, and gene expression differences in adipose tissue 30 d in milk confirm an effect of energy intake on lipogenic enzymes. The BCS in which a cow calves, nadir BCS, and the amount of BCS she loses postcalving are associated with milk production, reproduction, and health. Body condition score may also be a valid indicator of animal welfare, but further research is required to determine the effect of BCS and BCS change on how a cow "feels." Although the actual strength of the association may vary, there is relative consistency in the associations among calving and nadir BCS, and BCS change on milk production, postpartum anestrous, the likelihood of a successful pregnancy and days open, the risk of uterine infection, and the risk of metabolic disorders. For many production and health variables, the association with BCS is nonlinear, with an optimum calving BCS of 3.0 to 3.25 (5-point scale); lower calving BCS is associated with reduced production and reproduction, whereas calving BCS >/=3.5 (5-point scale) is associated with a reduction in early lactation dry matter intake and milk production and an increased risk of metabolic disorders. Ongoing research into the automation of body condition scoring suggests that it is a likely candidate to be incorporated into decision support systems in the near future to aid producers in making operational and tactical decisions.
Triply Periodic Bicontinuous Structures as Templates for Photonic Crystals: A Pinch‐off Problem (2007)

Triply periodic diamond, cubic, and gyroid structures are studied as templates for the fabrication of 3D photonic crystals (see figure). The achievable backfilling volume fraction and bandgap properties are analyzed by considering the pinch-off of level surfaces. The conformal coating on such templates is found to result in incomplete filling and loss of the photonic bandgap. An attempt to solve this problem is made by using electrophoretic deposition, which results in a nearly completely filled 3D titania structure. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c0147_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Tumor-treating fields (TTFields) induce immunogenic cell death resulting in enhanced antitumor efficacy when combined with anti-PD-1 therapy (2020)

Tumor-treating fields (TTFields) are alternating electric fields in a specific frequency range (100-300 kHz) delivered to the human body through transducer arrays. In this study, we evaluated whether TTFields-mediated cell death can elicit antitumoral immunity and hence would be effectively combined with anti-PD-1 therapy. We demonstrate that in TTFields-treated cancer cells, damage-associated molecular patterns including high-mobility group B1 and adenosine triphosphate are released and calreticulin is exposed on the cell surface. Moreover, we show that TTFields treatment promotes the engulfment of cancer cells by dendritic cells (DCs) and DCs maturation in vitro, as well as recruitment of immune cells in vivo. Additionally, our study demonstrates that the combination of TTFields with anti-PD-1 therapy results in a significant decline of tumor volume and increase in the percentage of tumor-infiltrating leukocytes in two tumor models. In orthotopic lung tumors, these infiltrating leukocytes, specifically macrophages and DCs, showed elevated expression of PD-L1. Compatibly, cytotoxic T-cells isolated from these tumors demonstrated increased production of IFN-γ. In colon cancer tumors, T-cells infiltration was significantly increased following long treatment duration with TTFields plus anti-PD-1. Collectively, our results suggest that TTFields therapy can induce anticancer immune response. Furthermore, we demonstrate robust efficacy of concomitant application of TTFields and anti-PD-1 therapy. These data suggest that integrating TTFields with anti-PD-1 therapy may further enhance antitumor immunity, hence achieve better tumor control.
Adaptive channel allocation in a TIA IS-54 system (2003)

Results from simulations of an adaptive channel allocation (ACA) algorithm which can be implemented in a microcellular system conforming to the TIA standard IS-54 are presented. The algorithm is completely decentralized, i.e., the allocation of a channel can be done at the base without any explicit reference to other bases. The results of the simulations show that the tested algorithm would perform well and also give an increase in capacity in comparison to a fixed channel allocation (FCA).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation and characterization of porcine Müller cells. Myofibroblastic dedifferentiation in culture. (1996)

Isolated porcine Muller cells in culture undergo a phenotypic dedifferentiation to a fibroblast-like cell, which includes loss of detectable CRALBP, CA-II, and GFAP, and they acquire expression of the myoid marker alpha SMA.
The binding of some human antiendothelial cell antibodies induces endothelial cell apoptosis. (1998)

The pathogenic role of antiendothelial cell antibodies (AECA) remains unclear. They are frequently associated with antibodies to anionic phospholipids (PL), such as phosphatidylserine (PS), which is difficult to reconcile with the distribution of PL molecular species within the plasma membrane. Since it is already known that PS is transferred to the outer face of the membrane as a preclude to apoptosis, the possibility exists that apoptosis is initiated by AECA. AECA-positive/anti-PL antibody-negative sera from eight patients with systemic sclerosis (SS) and 21 control patients were evaluated. Endothelial cells (EC) were incubated with AECA and the exposure of PS was established through the binding of annexin V. Hypoploid cell enumeration, DNA fragmentation, and optical and ultrastructural analyses of EC were used to confirm apoptosis. Incubation of EC with AECA derived from six of eight patients with SS led to the expression of PS on the surface of the cells. This phenomenon was significantly more frequent in SS (P < 0.04) than in control diseases. The redistribution of plasma membrane PS preceded other events associated with apoptosis: hypoploidy, DNA fragmentation, and morphology characteristic for apoptosis. Apoptosis-inducing AECA did not recognize the Fas receptor. We conclude that AECA may be pathogenic by inducing apoptosis.
Inhibition of cell growth by a hypothalamic peptide. (1982)

A fraction purified from acetic acid extracts of porcine hypothalami was found to contain significant antimitogenic activity when tested in normal and neoplastic cell lines. Addition of this hypothalamic material (1-100 micrograms/ml) to culture media significantly inhibited [3H]thymidine incorporation into cellular DNA in several cell lines. Amino acid incorporation into pituitary proteins and uridine incorporation into RNA were also significantly reduced by this factor(s). Addition to the culture media of this hypothalamic material at 5 micrograms/ml and 50 micrograms/ml per day decreased by 17% and 36%, respectively, cell numbers of 3T6 fibroblast cell cultures. Time-response curves showed that the inhibition of [3H]thymidine incorporation into DNA in 3T6 fibroblast cells begins within 2 hr after adding this fraction to the culture medium. The inhibitory action cannot be explained by a direct cytotoxic effect since 3T6 cells labeled with 51Cr and incubated for 6 hr in the presence of this hypothalamic fraction fail to show an increase in the release of 51Cr into the medium as compared with controls. Incubation with trypsin and chymotrypsin completely abolished the antimitogenic activity of this material and pepsin decreased it. This strongly suggests that the antimitogenic activity exhibited by this fraction is due to a polypeptide(s). These observations provide evidence for the presence in the mammalian hypothalamus of an antimitogenic peptide(s) that may be involved in the regulation of cell proliferation.
Estimation and Tests of Haplotype-Environment Interaction when Linkage Phase Is Ambiguous (2003)

In the study of complex traits, the utility of linkage analysis and single marker association tests can be limited for researchers attempting to elucidate the complex interplay between a gene and environmental covariates. For these purposes, tests of gene-environment interactions are needed. In addition, recent studies have indicated that haplotypes, which are specific combinations of nucleotides on the same chromosome, may be more suitable as the unit of analysis for statistical tests than single genetic markers. The difficulty with this approach is that, in standard laboratory genotyping, haplotypes are often not directly observable. Instead, unphased marker phenotypes are collected. In this article, we present a method for estimating and testing haplotype-environment interactions when linkage phase is potentially ambiguous. The method builds on the work of Schaid et al. [2002] and is applicable to any trait that can be placed in the generalized linear model framework. Simulations were run to illustrate the salient features of the method. In addition, the method was used to test for haplotype-smoking exposure interaction with data from the Childhood Asthma Management Program.
Disulfide spacer between methotrexate and poly(D-lysine). A probe for exploring the reductive process in endocytosis. (1985)

Poly(D-lysine) is taken up avidly by cultured cells through adsorptive endocytosis and can serve as a carrier to increase cellular uptake of other molecules. While direct conjugation of methotrexate to poly(D-lysine) yields a conjugate devoid of cytotoxic effects because poly(D-lysine) is not digested in lysosomes, the indirect conjugation using a triglycine spacer or a disulfide spacer strongly inhibits the growth of both the wild type and the methotrexate transport-defective Chinese hamster ovary cells. Cell treatment with 3 mM NH4Cl or 50 micrograms/ml leupeptin prevents the effect of conjugate with the triglycine spacer, but not of conjugate with the disulfide spacer. On the other hand, preincubation with 2-mercaptoethanol abolishes the effect of the drug-disulfide conjugate in the methotrexate transport-defective mutant, but not the effect of the drug-triglycine conjugate. The disulfide conjugate shows an identical cytotoxic effect in alpha-minimal essential medium and RPMI 1640 media, even though cells grown in the latter have only half the glutathione content as cells grown in the former medium. We conclude that the reductive process through which methotrexate is released from the disulfide spacer (a) occurs inside cells and not at the cell surface, (b) requires neither acid pH nor lysosomal enzymes, and (c) is not mediated by a glutathione-disulfide exchange reaction requiring high glutathione concentrations. Although the cellular compartment in which this reductive process occurs is not yet identified, there are reasons to assume that it is prelysosomal.
Chemical Composition and Antimicrobial Activity of Essential Oil of Citrus limettioides Tanaka (2012)

The present study is aimed to isolate the essential oil of Citrus limettioides and analyze its chemical composition and antimicrobial potential. Methods: The essential oil (EO) isolated by hydro-distillation from the peel of fully matured ripen fruits of Citrus limettioides Tanaka and analysed by Gas Chromatography-Mass Spectrometry (GC-MS). The antifungal activity in terms of zone of inhibition and minimum inhibitory concentration (MIC) of the essential oil was tested against ten food borne fungal strains and ten bacterial strains. The EO was also examined for any possible toxicity or adverse effect resulting from its consumption. Results: Fourteen different components were identified constituting approximately 99% of the oil. The major components were dl-limonene (89.089%), -myrcene (2.933%), ()-linalool (2.927%), -pinene (0.865%), (E)-citral (0.749%) etc. According to disc diffusion assay and broth micro-dilution method showed that EO has a wide spectrum of antimicrobial activity against the tested strains with their MIC ranging from 3.12 l/ml to50 l/ml. Conclusion: It can be concluded that EO of Citrus limettioides can be used in skincare formulations for acne control, in treatment of various infectious diseases like typhoid fever, food poisoning, inflammation, sepsis, endocarditis, bladder, prostate and epididymal infections. Along with this it can also be used as safer and alternative means of food preservation. No serious or life-threatening side effects were observed on the haematological and biochemical parameters of mice fed with specific dose of EO of Citrus limettioides, therefore the EO can be recommended as safe fumigant for preservation of food commodities.
Genetic Analysis of Salt Tolerance in Arabidopsis: Evidence for a Critical Role of Potassium Nutrition (1998)

A large genetic screen for sos (for salt overly sensitive) mutants was performed in an attempt to isolate mutations in any gene with an sos phenotype. Our search yielded 28 new alleles of sos1, nine mutant alleles of a newly identified locus, SOS2, and one allele of a third salt tolerance locus, SOS3. The sos2 mutations, which are recessive, were mapped to the lower arm of chromosome V, approximately 2.3 centimorgans away from the marker PHYC. Growth measurements demonstrated that sos2 mutants are specifically hypersensitive to inhibition by Na+ or Li+ and not hypersensitive to general osmotic stresses. Interestingly, the SOS2 locus is also necessary for K+ nutrition because sos2 mutants were unable to grow on a culture medium with a low level of K+. The expression of several salt-inducible genes was superinduced in sos2 plants. The salt tolerance of sos1, sos2, and sos3 mutants correlated with their K+ tissue content but not their Na+ tissue content. Double mutant analysis indicated that the SOS genes function in the same pathway. Based on these results, a genetic model for salt tolerance mechanisms in Arabidopsis is presented in which SOS1, SOS2, and SOS3 are postulated to encode regulatory components controlling plant K+ nutrition that in turn is essential for salt tolerance.
Expression of selected human HOX-2 genes in B/T acute lymphoid leukemia and interleukin-2/interleukin-1 beta-stimulated natural killer lymphocytes (1992)

Abstract Although the key role of human homeobox (HOX) genes in development is well established, their function in adult cells is still under scrutiny. We have analyzed, in normal adult blood cell subpopulations, acute lymphoid leukemia (ALL) cells lines, and primary blasts, the RNA expression of all HOX-2 cluster genes (5′-2.5, 2.4, 2.3, 2.2, 2.1, 2.6, 2.7, 2.8, 2.9, 3′) and nine genes in the HOX-1, -3, and -4 cluster by Northern blotting, RNAse protection, and/or reverse transcriptase polymerase chain reaction (RT-PCR). The analyzed HOX-1, -3, and -4 genes were never expressed in all tested cell populations. Natural killer (NK) cells activated in interleukin-2 (IL-2)/IL-1 beta-treated cultures exhibit a gradually increasing, abundant expression of three HOX-2 genes (2.2, 2.6, 2.8), while three other genes (2.3, 2.1, 2.7) are expressed at a lower level at late culture times. However, no HOX-2 gene is expressed in quiescent lymphocytes (NK, B and T [T-cell receptor (TCR) alpha/beta, gamma/delta lymphocytes, thymocytes] cells), granulocytes, and monocytes. In B- and T-ALL cell lines, HOX-2 genes are expressed according to different patterns: (1) widespread transcription (seven of nine genes, including 2.3 and 2.6) in the Peer line bearing the TCR gamma/delta; (2) expression of 2.5, 2.2, and 2.6 in the SEZ 627 line, which derives from an HTLV-1+ T-helper leukemia; (3) transcription of 2.3 and 2.6 in both the T-ALL CEM line and four B- ALL lines (interestingly, CALLA- B-ALL lines are constantly 2.3/2.6 RNA+); (4) no HOX-2 gene expression was detected in one T- and two B- ALL lines. Primary blasts from five T- and five pre-B-ALL showed selective expression of one or more HOX-2 genes, namely 2.5, 2.2, 2.6, and 2.7. Our data are compatible with the hypothesis that selected HOX- 2 genes play a role in the IL-2/IL-1 beta-induced activation and/or proliferation of normal NK lymphocytes and possibly in the oncogenetic process of some T- and B-ALL.
Characterization of Cytochrome P450 3A Inactivation by Cannabidiol:  Possible Involvement of Cannabidiol-Hydroxyquinone as a P450 Inactivator (1998)

Cannabidiol (CBD) is a major constituent of marijuana and a potent inhibitor of P450-mediated hepatic drug metabolism. Mouse P450 3A11 metabolism of [14C]CBD resulted in the formation of radiolabeled P450, which after digestion with lysyl endopeptidase C (Lys-C) and HPLC resolution of peptides, revealed one major broadly eluting peak of radioactivity. Electrophoresis/autoradiography of this peak identified several peptide bands, one of which was predominantly radiolabeled and had an apparent molecular mass of approximately 6 kDa. Amino-terminal sequence determination of this band revealed the presence of two peptides whose sequences identified them as Ala344-Lys379 and Gly426-Lys454. To characterize the reactive species that may be generated during P450 3A11-catalyzed CBD metabolism, reduced glutathione (GSH) was used as a trapping agent for possible electrophilic metabolites. Incubation of P450 3A11 in the presence of cofactors NADPH, CBD, and [3H]GSH resulted in the formation of a radiolabeled product which was absent in incubations lacking any of the cofactors. The UV absorption spectra of this compound indicated absorbances at approximately 220, 275, and 350 nm, and mass spectral analysis revealed prominent ions at m/z 634, 599, 505, 402, and 359, ions consistent with that of a GSH adduct of CBD-hydroxyquinone. A synthetic CBD-hydroxyquinone-GSH adduct was also prepared and had UV absorption and mass spectra nearly identical to that of the P450-mediated CBD-GSH adduct. CBD-hydroxyquinone formation may be the penultimate oxidative step involved in CBD-mediated modification and inactivation of P450 3A11.
Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. (1990)

The human immunodeficiency virus (HIV) integration protein, a potential target for selective antiviral therapy, was expressed in Escherichia coli. The purified protein, free of detectable contaminating endonucleases, selectively cleaved double-stranded DNA oligonucleotides that mimic the U3 and the U5 termini of linear HIV DNA. Two nucleotides were removed from the 3' ends of both the U5 plus strand and the U3 minus strand; in both cases, cleavage was adjacent to a conserved CA dinucleotide. The reaction was metal-ion dependent, with a preference for Mn2+ over Mg2+. Reaction selectivity was further demonstrated by the lack of cleavage of an HIV U5 substrate on the complementary (minus) strand, an analogous substrate that mimics the U3 terminus of an avian retrovirus, and an HIV U5 substrate in which the conserved CA dinucleotide was replaced with a TA dinucleotide. Such an integration protein-mediated cleavage reaction is expected to occur as part of the integration event in the retroviral life cycle, in which a double-stranded DNA copy of the viral RNA genome is inserted into the host cell DNA.
Enhancing Effect of Vaxfectin on the Ability of a Japanese Encephalitis DNA Vaccine to Induce Neutralizing Antibody in Mice (2003)

Vaxfectin, a recently developed adjuvant, was evaluated for its enhancing effect on immunogenicity of a Japanese encephalitis (JE) DNA vaccine plasmid encoding the JE virus premembrane (prM) and envelope (E) genes (designated pcJEME), using BALB/c and ICR mice. Formulation of pcJEME with Vaxfectin provided > or =8-fold higher neutralizing antibody titers than those induced by pcJEME alone and reduced the amount of pcJEME to one-tenth to induce comparable levels of neutralizing antibody. Use of Vaxfectin did not alter a Th1 type IgG isotype immune response (IgG1 < IgG2a) induced by pcJEME in mice. These results indicate that Vaxfectin has an ability to enhance immunogenicity of pcJEME and is considered as a useful adjuvant for DNA vaccines in murine experimental models.
Isolation and characterization of beta-glucan receptors on human mononuclear phagocytes. (1991)

beta-glucan receptors, with ligand specificity for yeast and fungal carbohydrate polymers, have been studied as phagocytic receptors of human monocytes. To characterize their structure, binding studies were carried out with human U937 cells and a rabbit IgG anti-Id that recognizes epitopes on monocyte beta-glucan receptors. Unstimulated U937 cells specifically bound large amounts of the anti-Id, but almost none of the control anti-isotype. At saturation, the number of anti-Id molecules bound per U937 cell was 2.6 x 10(6) with an apparent Ka of 1.9 x 10(7) M-1. Immunoprecipitates from detergent lysates of surface-radioiodinated U937 cells contained only two membrane proteins with antigenic specificity for the anti-Id, one having a mol wt of 180 kD and the other 160 kD. Both proteins were disulfide-linked and presented, after reduction, as five polypeptides of 95, 88, 60, 27, and 20 kD. Detergent lysates of unlabeled U937 cells, purified by affinity chromatography on anti-Id-Sepharose, yielded the same two nonreduced proteins and five reduction products in slab gels stained with Coomassie blue. In Western blots probed with the anti-Id, the most immunoreactive nonreduced and reduced affinity-purified products were the 160 and 20 kD molecules, respectively. Immunoblots of two-dimensional gels showed the 180 and 160 kD proteins to express a common epitope through disulfide linkage to the 20 kD polypeptide. By immunoblot analysis, U937 cell glucan-binding proteins from detergent lysates contained two cell proteins antigenic for the anti-Id that were indistinguishable from affinity-purified molecules in size and subunit composition. Studies of affinity-purified proteins from detergent lysed human monocytes were characterized by immunoblot analysis and found to be identical to U937 cell beta-glucan receptors. They consisted of two disulfide-linked proteins, with mol wt of 180 and 160 kD, and had in common a 20 kD polypeptide with the anti-Id epitope.