gebhart/patrepeval huggingface dataset:
Evolution in Action: Plants Resistant to Herbicides (2010)

Modern herbicides make major contributions to global food production by easily removing weeds and substituting for destructive soil cultivation. However, persistent herbicide selection of huge weed numbers across vast areas can result in the rapid evolution of herbicide resistance. Herbicides target specific enzymes, and mutations are selected that confer resistance-endowing amino acid substitutions, decreasing herbicide binding. Where herbicides bind within an enzyme catalytic site very few mutations give resistance while conserving enzyme functionality. Where herbicides bind away from a catalytic site many resistance-endowing mutations may evolve. Increasingly, resistance evolves due to mechanisms limiting herbicide reaching target sites. Especially threatening are herbicide-degrading cytochrome P450 enzymes able to detoxify existing, new, and even herbicides yet to be discovered. Global weed species are accumulating resistance mechanisms, displaying multiple resistance across many herbicides and posing a great challenge to herbicide sustainability in world agriculture. Fascinating genetic issues associated with resistance evolution remain to be investigated, especially the possibility of herbicide stress unleashing epigenetic gene expression. Understanding resistance and building sustainable solutions to herbicide resistance evolution are necessary and worthy challenges.
Structural bone-grafting for early atraumatic avascular necrosis of the femoral head. (1991)

Between 1970 and 1987, nineteen patients, thirty-one to fifty-five years old, had twenty core-decompression procedures with corticocancellous bone-grafting for Stage-I or II atraumatic avascular necrosis of the femoral head. A tibial autogenous graft was used in three hips; a fibular autogenous graft, in seven hips; and a fibular allograft, in ten hips. Treatment was considered to have failed when there was clinical or roentgenographic evidence of progression of the necrosis. Eighteen patients who had a minimum follow-up of two years (average, eight years; range, two to nineteen years) were asymptomatic, with no evidence of progression of the necrosis or collapse of the affected segment. In two hips, the necrotic segment of the femoral head collapsed within one year after the operation, and a replacement arthroplasty was carried out.
All-fiber anamorphic core-shape transitions (2006)

We demonstrate low-loss anamorphic transitions between circular and rectangular fiber cores with aspect ratios up to 5:1, and hence improved coupling from a diode laser by using only a spherical lens. Differential hole pressurization and localized heating of a stock photonic crystal fiber inflates the holes at different rates. Some holes are plugged in the fiber end face where pressure is applied, so they remain at ambient pressure. Alternatively, holes of different sizes expand at different rates because the effective pressure due to surface tension differs.
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010)

FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
Bone and joint complications in patients with hereditary hemochromatosis: a cross-sectional study of 93 patients (2020)

Future investigations should focus on pathogenesis and early identification of patients at risk of developing bone and joint complications secondary to HH.
THE ROLE OF COMPLEMENT IN THE PATHOGENESIS OF EXPERIMENTAL ALLERGIC ENCEPHALOMYELITIS (1989)

The role of complement in the pathogenesis of demyelination and inflammation has been investigated in a synergistic model of acute experimental allergic encephalomyelitis (EAE) in the Lewis rat. Depletion of serum complement with cobra venom factor (CVF) suppressed the clinical expression of acute inflammatory EAE induced either by immunization with 50 micrograms guinea pig basic protein (MBP) in Freund's complete adjuvant, or by the passive transfer of 10(7), but not 5 X 10(7) MBP activated spleen cells. Despite the suppression of clinical disease in actively induced EAE, treatment with CFF only had a significant effect on the severity of CNS inflammation in early disease (12 days postimmunization) when the number of inflammatory foci was reduced by 35%. Three days later this difference had resolved and no significant difference could be detected in the severity of CNS inflammation, although control animals exhibited severe disease, the CVF treated group being clinically normal. Demyelination in these models is initiated by systemic injection of the antimyelin oligodendrocyte glycoprotein (MOG) monoclonal antibody, 8-18C5, which in vitro lyses oligodendrocytes in a dose, Fc and complement-dependent manner and in vivo induces extensive CNS demyelination in rats with EAE. Treatment with CVF reduced the ability of this antibody to initiate demyelination in vivo and furthermore, its F(ab)2' fragment had no effect on the clinical course of EAE and was unable to initiate demyelination in normal animals. Complement-dependent mechanisms are therefore involved both in the clinical expression of acute inflammatory lesions and in the pathogenesis of antibody-mediated demyelination in EAE.
Rational Design of Novel Antimicrobials:  Blocking Purine Salvage in a Parasitic Protozoan (1998)

All parasitic protozoa obtain purine nucleotides solely by salvaging purine bases and/or nucleosides from their host. This observation suggests that inhibiting purine salvage may be a good way of killing these organisms. To explore this idea, we attempted to block the purine salvage pathway of the parasitic protozoan Tritrichomonas foetus. T. foetus is a good organism to study because its purine salvage depends primarily on a single enzyme, hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase), and could provide a good model for rational drug design through specific enzyme inhibition. Guided by the crystal structure of T. foetus HGXPRTase, we used structure-based drug design to identify several non-purine compounds that inhibited this enzyme without any detectable effect on human HGPRTase. One of these compounds, 4-[N-(3, 4-dichlorophenyl)carbamoyl]phthalic anhydride (referred to as TF1), was selected for further characterization. TF1 was shown to be a competitive inhibitor of T. foetus HGXPRTase with respect to both guanine (in the forward reaction; Ki = 13 microM) and GMP (in the reverse reaction; Ki = 10 microM), but showed no effect on the homologous human enzyme at concentrations of up to 1 mM. TF1 inhibited the in vitro growth of T. foetus with an EC50 of approximately 40 microM. This inhibitory effect was associated with a decrease in the incorporation of exogenous guanine into nucleic acids, and could be reversed by supplementing the growth medium with excess exogenous hypoxanthine or guanine. Thus, rationally targeting an essential enzyme in a parasitic organism has yielded specific enzyme inhibitors capable of suppressing that parasite's growth.
A rapid method of collecting taste tissue from rats and mice (1989)

Journal Article A rapid method of collecting taste tissue from rats and mice Get access Andrew I. Spielman, Andrew I. Spielman 4 1Monell Chemical Senses CenterPhiladelphia, PA 19104, USA2University of PennsylvaniaPhiladelphia, PA 19104, USA 4To whom requests for reprints should be addressed at Department of Oral Medicine and Pathology, College of Dentistry, New York University, 345 E. 24th St., New York, NY 10010, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Joseph G. Brand, Joseph G. Brand 1Monell Chemical Senses CenterPhiladelphia, PA 19104, USA2University of PennsylvaniaPhiladelphia, PA 19104, USA3Veterans Administration Medical CenterPhiladelphia, PA 19104, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Linda Wysocki Linda Wysocki 1Monell Chemical Senses CenterPhiladelphia, PA 19104, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Chemical Senses, Volume 14, Issue 6, December 1989, Pages 841–846, https://doi.org/10.1093/chemse/14.6.841 Published: 01 December 1989 Article history Received: 08 April 1989 Accepted: 26 July 1989 Published: 01 December 1989
Highly Luminescent InP/GaP/ZnS Nanocrystals and Their Application to White Light-Emitting Diodes (2012)

Highly stable and luminescent InP/GaP/ZnS QDs with a maximum quantum yield of 85% were synthesized by in situ method. The GaP shell rendered passivation of the surface and removed the traps. TCSPC data showed an evidence for the GaP shell. InP/GaP/ZnS QDs show better stability than InP/ZnS. We studied the optical properties of white QD-LEDs corresponding to various QD concentrations. Among various concentrations, the white QD-LEDs with 0.5 mL of QDs exhibited a luminous efficiency of 54.71 lm/W, Ra of 80.56, and CCT of 7864 K.
Hepatitis C Virus F Protein Is a Short-Lived Protein Associated with the Endoplasmic Reticulum (2002)

Hepatitis C virus (HCV) F protein is a newly discovered HCV gene product that is expressed by translational ribosomal frameshift. Little is known about the biological properties of this protein. By performing pulse-chase labeling experiments, we demonstrate here that the F protein is a labile protein with a half-life of <10 min in Huh7 hepatoma cells and in vitro. The half-life of the F protein could be substantially increased by proteasome inhibitors, suggesting that the rapid degradation of the F protein is mediated by the proteasome pathway. Further immunofluorescence staining and subcellular fractionation experiments indicate that the F protein is primarily associated with the endoplasmic reticulum. This subcellular localization is similar to those of HCV core and NS5A proteins, raising the possibility that the F protein may participate in HCV morphogenesis or replication.
Sodium azide mutagenesis: preferential generation of A.T-->G.C transitions in the barley Ant18 gene. (1993)

The molecular basis for the absence of anthocyanins and proanthocyanidins in four independent sodium azide-induced ant18 mutants of barley was examined by sequencing the gene encoding dihydroflavonol 4-reductase in these mutants. Sodium azide generated 21 base substitutions, which corresponds to 0.17% of the 12,704 nucleotides sequenced. Of the substitutions, 86% were nucleotide transitions, and 14% were transversions. A.T-->G.C base pair transitions were about 3 times more frequent than G.C-->A.T transitions. No deletions or mutation hot spots were found. The absence of dihydroflavonol 4-reductase activity in ant18-159, ant18-162, and ant18-164 plants is caused by missense mutations in the respective genes. By using microprojectile bombardment, a plasmid harboring the wild-type Ant18 gene was introduced into ant18-161 mutant cells and resulted in the development of anthocyanin pigmentation, which demonstrates that the mutation is corrected by expression of the introduced gene. On the other hand, a plasmid derivative with the two ant18-161-specific base transitions at the 5' splice site of intron 3 prevented complementation. It is concluded that the absence of detectable mRNA for dihydroflavonol 4-reductase in ant18-161 cells is due to the mutations in the pre-mRNA splice donor site.
Motion planning for concentric tube robots using mechanics-based models (2011)

Concentric tube robots have the potential to enable new minimally invasive surgical procedures by curving around anatomical obstacles to reach difficult-to-reach sites in body cavities. Planning motions for these devices is challenging in part due to their complex kinematics; concentric tube robots are composed of thin, pre-curved, telescoping tubes that can achieve a variety of shapes via extension and rotation of each of their constituent tubes. We introduce a new motion planner to maneuver these devices to clinical targets while minimizing the probability of colliding with anatomical obstacles. Unlike prior planners for these devices, we more accurately model device shape using mechanics-based models that consider torsional interaction between the tubes. We also account for the effects of uncertainty in actuation and predicted device shape. We integrate these models with a sampling-based approach based on the Rapidly-Exploring Roadmap to guarantee finding optimal plans as computation time is allowed to increase. We demonstrate our motion planner in simulation using a variety of evaluation scenarios including an anatomy-based neurosurgery case that requires maneuvering to a difficult-to-reach brain tumor at the skull base.
Hole-conductor-free perovskite organic lead iodide heterojunction thin-film solar cells: High efficiency and junction property (2014)

Efficient hole-conductor-free organic lead iodide thin film solar cells have been fabricated with a sequential deposition method, and a highest efficiency of 10.49% has been achieved. Meanwhile, the ideal current-voltage model for a single heterojunction solar cell is applied to clarify the junction property of the cell. The model confirms that the TiO2/CH3NH3PbI3/Au cell is a typical heterojunction cell and the intrinsic parameters of the cell are comparable to that of the high-efficiency thin-film solar cells.
Differentiation‐stage specific expression of oncoprotein 18 in human and rat prostatic adenocarcinoma (1995)

Oncoprotein 18 (Op18) is an intracellular phosphoprotein that has been shown to be overexpression in a number of human malignancies. In the present report we have studied the pattern of Op18 expression on normal, hyperplastic, and malignant prostatic tissue as well as in rat prostatic tumor lines. One of the objectives of the present work was to establish whether the level of Op18 expression can be used as a prognostic marker in human prostatic adenocarcinoma. To that end, sections from normal, hyperplastic, and malignant human prostatic tissue were examined by immunohistochemistry for expression of Op18. In the normal and hyperplastic prostate, Op18 expression was observed in basal glandular epithelial cells, whereas the columnar luminal epithelial cells were not stained by the anti Op18 antibodies. In highly differentiated prostatic cancers occasional epithelial cells were stained, while in poorly differentiated tumors most of the epithelial cells contained Op18 immunoreactivity. The staining pattern was similar in the primary prostatic tumor and in the regional lymph node metastases. Most importantly, a limited survey of prostatic cancer patient samples (n = 40) showed a significant correlation between the fraction of Op18 immunoreactive cells and survival. Studies of a rat prostatic tumor model, showed that only a few cells were stained in the highly differentiated Dunning R3327PAP tumor, while most cells were stained in the anaplastic AT1 rat prostatic tumor. Interestingly, castration of rats resulted in an increased Op18 immunoreactivity, within 14 days, in the highly differentiated rat R3327PAP prostatic tumor. In conclusion, the level of Op18 expression seems to be related to cellular differentiation, histological grade, and survival in prostatic cancers. These findings show that Op18 immunoreactivity may be useful as a prognostic marker in prostatic cancer. In addition it may help in the differentiation between highly differentiated prostatic tumors and non-malignant conditions.
Analysis of IL-1 and TNF-alpha gene expression in human rheumatoid synoviocytes and normal monocytes by in situ hybridization. (1990)

Abstract Human IL-1 alpha, IL-1 beta, and TNF-alpha mRNA expression was examined in peripheral blood monocytes (PBM) from normal individuals and in primary synoviocytes isolated from patients with rheumatoid arthritis by Northern blot and in situ hybridization. Cells cultured in the presence or absence of LPS were analyzed using in vitro synthesized 35S-labeled sense or antisense RNA probes to determine the relative abundance and the cell type expressing each of the mRNA for these potent inflammatory mediators. The results indicated that 72% of the LPS-stimulated PBM expressed detectable levels of IL-1 alpha mRNA, 89% IL-1 beta mRNA, and 10% TNF-alpha transcripts. Thus, the majority of activated PBM produced both IL-1 alpha and IL-1 beta. Experiments combining immunofluorescence for IL-1 beta protein with in situ hybridization for TNF-alpha mRNA demonstrated that monocytes expressing TNF-alpha mRNA also produced IL-1 beta. Primary synoviocytes from four patients with RA were also examined for the mRNA expression of each cytokine. Northern blot analyses of total RNA isolated from 0 to 72 h after LPS- or mock-stimulation showed that IL-1 beta mRNA was the most abundantly expressed, followed by TNF-alpha. In situ hybridization revealed that IL-1 beta and TNF-alpha transcripts were detected exclusively in synovial tissue macrophages. IL-1 alpha mRNA was not detected in these cultures by either method.
Fixation of osteochondral fractures: Fibrin sealant tested in dogs (1985)

Standardized osteochondral fractures in the left femoral condyle in 19 adult mongrel dogs were fixed with either fibrin sealant or Kirschner wire. Adaptation and mechanical strength after 4, 7 or 8, and 14 days were compared with an in vitro study of the initial strength of the fibrin sealant in osteochondral fractures. After 4 days, the maximum tensile strength was increased in the fibrin sealed group, whereas no difference in energy absorption at failure was found. Although the initial strength of the fibrin bond was low, the tendency to displacement was less in this group. Our results suggest that fibrin sealant can be used for fixation of small osteochondral fragments, provided that immobilisation is sufficient.
Src-mediated coupling of focal adhesion kinase to integrin αvβ5 in vascular endothelial growth factor signaling (2002)

Vascular endothelial growth factor (VEGF) promotes vascular permeability (VP) and neovascularization, and is required for development. We find that VEGF-stimulated Src activity in chick embryo blood vessels induces the coupling of focal adhesion kinase (FAK) to integrin alpha(v)beta5, a critical event in VEGF-mediated signaling and biological responsiveness. In contrast, FAK is constitutively associated with beta1 and beta3 integrins in the presence or absence of growth factors. In cultured endothelial cells, VEGF, but not basic fibroblast growth factor, promotes the Src-mediated phosphorylation of FAK on tyrosine 861, which contributes to the formation of a FAK/alpha(v)beta5 signaling complex. Moreover, formation of this FAK/alpha(v)beta5 complex is significantly reduced in pp60c-src-deficient mice. Supporting these results, mice deficient in either pp60c-src or integrin beta5, but not integrin beta3, have a reduced VP response to VEGF. This FAK/alpha(v)beta5 complex was also detected in epidermal growth factor-stimulated epithelial cells, suggesting a function for this complex outside the endothelium. Our findings indicate that Src can coordinate specific growth factor and extracellular matrix inputs by recruiting integrin alpha(v)beta5 into a FAK-containing signaling complex during growth factor-mediated biological responses.
Differential growth kinetics are exhibited by human immunodeficiency virus type 1 TAR mutants (1994)

The human immunodeficiency virus type 1 (HIV-1) TAR element is critical for the activation of gene expression by the transactivator protein, Tat. Mutagenesis has demonstrated that a stable stem-loop RNA structure containing both loop and bulge structures transcribed from TAR is the major target for tat activation. Though transient assays have defined elements critical for TAR function, no studies have yet determined the role of TAR in viral replication because of the inability to generate viral stocks containing mutations in TAR. In the current study, we developed a strategy which enabled us to generate stable 293 cell lines which were capable of producing high titers of different viruses containing TAR mutations. Viruses generated from these cell lines were used to infect both T-lymphocyte cell lines and peripheral blood mononuclear cells. Viruses containing TAR mutations in either the upper stem, the bulge, or the loop exhibited dramatically decreased HIV-1 gene expression and replication in all cell lines tested. However, we were able to isolate lymphoid cell lines which stably expressed gene products from each of these TAR mutant viruses. Though the amounts of virus in these cell lines were roughly equivalent, cells containing TAR mutant viruses were extremely defective for gene expression compared with cell lines containing wild-type virus. The magnitude of this decrease in viral gene expression was much greater than previously seen in transient expression assays using HIV-1 long terminal repeat chloramphenicol acetyltransferase gene constructs. In contrast to the defects in viral growth found in T-lymphocyte cell lines, several of the viruses containing TAR mutations were much less defective for gene expression and replication in activated peripheral blood mononuclear cells. These results indicate that maintenance of the TAR element is critical for viral gene expression and replication in all cell lines tested, though the cell type which is infected is also a major determinant of the replication properties of TAR mutant viruses.
Overexpression of epidermal growth factor receptor in human head and neck squamous carcinoma cell lines correlates with matrix metalloproteinase-9 expression andin vitro invasion (2000)

Numerous reports have shown an association between overexpression of the epidermal growth factor receptor (EGFR), and poor prognosis in head and neck squamous cell carcinomas (HNSCC), however, the underlying mechanisms are still unclear. In the present study, we set out to determine whether EGFR expression was associated with in vitro invasive capacity in a panel of four established and ten newly derived HNSCC lines. Ten of the cell lines expressed high levels of EGFR as determined by a ligand-binding assay and dot blot analysis, whereas the remaining four showed weak overexpression or normal levels of EGFR. The ability of cells to invade through Matrigel was found to be higher in the EGFR overexpressing cell lines (p < 0. 0001). Expression levels of matrix metalloproteinases (MMP-1, MMP-2, MMP-3, MMP-7, MMP-9, MMP-10, MMP-11, MMP-13, MT1-MMP) and tissue inhibitors of MMP (TIMP-1, TIMP-2) were evaluated by semiquantitative RT-PCR, substrate zymography and western blot. We found a strong positive correlation between EGFR levels and the expression of MMP-9 mRNA (r(2) = 0.95; p < 0.0001), MMP-9 enzyme activity (r(2) = 0.8099; p < 0.0001) and an inverse correlation with TIMP-1 (r(2) = 0.48; p = 0.0059). In six selected HNSCC lines, in vitro invasion was assayed in the presence of an anti-EGFR monoclonal antibody, ICR62. A significant reduction of invasion in four selected EGFR-overexpressing cell lines was found with 30 nM ICR62 (from 50% to 70%; p < 0.001) but there was no effect in two cell lines with normal EGFR levels. Our results show that the in vitro invasive phenotype of HNSCC lines correlates with high EGFR and MMP-9 expression, and it is therefore suggested that the EGFR signaling pathway might play an important role in the invasive behavior of HNSCC via specific upregulation of MMP-9 and downregulation of TIMP-1.