gebhart/patrepeval huggingface dataset:
Three New Races of the Spinach Downy Mildew Pathogen Identified by a Modified Set of Spinach Differentials (2007)

Spinach downy mildew, caused by Peronospora farinosa f. sp. spinaciae, is the most economically important disease of spinach worldwide. During the past few years, spinach cultivars resistant to the seven previously described races of P. farinosa f. sp. spinaciae were observed to be severely affected by downy mildew in both the United States and the European Union. Four new isolates of P. farinosa f. sp. spinaciae were collected from California and The Netherlands and characterized based on disease reactions on two modified sets of spinach differentials. The results led to the description of three new races of the downy mildew pathogen, designated races 8, 9, and 10. Four differential cultivars with resistance to races 1 to 7 were used to distinguish the three new races. Dolphin was susceptible to races 8 and 10 but resistant to race 9; Lion was susceptible to race 10 but resistant to races 8 and 9; Lazio was resistant to races 1 to 7 as well as races 8, 9, and 10; and Tarpy was susceptible to all three new races. The three new races also were used to evaluate the disease reactions on 43 contemporary commercial spinach cultivars in greenhouse trials. A survey of 58 isolates of P. farinosa f. sp. spinaciae collected in California and Arizona between 2004 and 2006 revealed that race 10 predominated in the areas sampled.
Electrochemical modification of everninomicin D (1980)

A. K. Ganguly, P. Kabasakalian, J. Morton, O. Sarre, A. Westcott, S. Kalliney, P. Mangiaracina and A. Papaphilippou, J. Chem. Soc., Chem. Commun., 1980, 56 DOI: 10.1039/C39800000056
Monitoring Interactions and Dynamics of Endogenous Beta-catenin With Intracellular Nanobodies in Living Cells* (2015)

β-catenin is the key component of the canonical Wnt pathway and plays a crucial role in a multitude of developmental and homeostatic processes. The different tasks of β-catenin are orchestrated by its subcellular localization and participation in multiprotein complexes. To gain a better understanding of β-catenin's role in living cells we have generated a new set of single domain antibodies, referred to as nanobodies, derived from heavy chain antibodies of camelids. We selected nanobodies recognizing the N-terminal, core or C-terminal domain of β-catenin and applied these new high-affinity binders as capture molecules in sandwich immunoassays and co-immunoprecipitations of endogenous β-catenin complexes. In addition, we engineered intracellularly functional anti-β-catenin chromobodies by combining the binding moieties of the nanobodies with fluorescent proteins. For the first time, we were able to visualize the subcellular localization and nuclear translocation of endogenous β-catenin in living cells using these chromobodies. Moreover, the chromobody signal allowed us to trace the accumulation of diffusible, hypo-phosphorylated β-catenin in response to compound treatment in real time using High Content Imaging. The anti-β-catenin nanobodies and chromobodies characterized in this study are versatile tools that enable a novel and unique approach to monitor the dynamics of subcellular β-catenin in biochemical and cell biological assays.
Inhibition of bone resrption by selctive inactivators of cysteine proteinases (1994)

Inactivators of cysteine proteinases (CPs) were tested as inhibitors of bone resorption in vitro and in vivo. The following four CP inactivators were tested: Ep475, a compound with low membrane permeability which inhibits cathepsins B, L, S, H, and calpain; Ep453, the membrane-permeant prodrug of Ep475; CA074, a compound with low membrane permeability which selectively inactivates cathepsin B; and CA074Me, the membrane-permeant prodrug of CA074. The test systems consisted of 1) monitoring the release of radioisotope from prelabelled mouse calvarial explants and 2) assessing the extent of bone resorption in an isolated osteoclast assay using confocal laser microscopy. Ep453, Ep475, and CA074Me inhibited both stimulated and basal bone resorption in vitro while CA074 was without effect; the inhibition was reversible and dose dependent. None of the inhibitors affected protein synthesis, DNA synthesis, the PTH-enhanced secretion of beta-glucuronidase, and N-acetyl-beta-glucosaminidase, or the spontaneous release of lactate dehydrogenase. Ep453, Ep475, and CA074Me dose-dependently inhibited the resorptive activity of isolated rat osteoclasts cultured on bone slices with a maximal effect at 50 microM. The number of resorption pits and their mean volume was reduced, whilst the mean surface area remained unaffected. Again, CA074 was without effect. Ep453, Ep475, and CA074Me, but not CA074, when administered subcutaneously at a dose of 60 micrograms/g body weight inhibited bone resorption in vivo as measured by an in vivo/in vitro assay, by about 20%. This study demonstrates that cathepsins B, L, and/or S are involved in bone resorption in vitro and in vivo. Whilst cathepsin L and/or S act extracellularly, and possibly intracellularly, cathepsin B mediates its effects intracellularly perhaps through the activation of other proteinases involved in subosteoclastic collagen degradation.
Derivation of Primordial Germ Cells from Human Embryonic and Induced Pluripotent Stem Cells Is Significantly Improved by Coculture with Human Fetal Gonadal Cells (2009)

The derivation of germ cells from human embryonic stem cells (hESCs) or human induced pluripotent stem (hIPS) cells represents a desirable experimental model and potential strategy for treating infertility. In the current study, we developed a triple biomarker assay for identifying and isolating human primordial germ cells (PGCs) by first evaluating human PGC formation during the first trimester in vivo. Next, we applied this technology to characterizing in vitro derived PGCs (iPGCs) from pluripotent cells. Our results show that codifferentiation of hESCs on human fetal gonadal stromal cells significantly improves the efficiency of generating iPGCs. Furthermore, the efficiency was comparable between various pluripotent cell lines regardless of origin from the inner cell mass of human blastocysts (hESCs), or reprogramming of human skin fibroblasts (hIPS). To better characterize the iPGCs, we performed Real-time polymerase chain reaction, microarray, and bisulfite sequencing. Our results show that iPGCs at day 7 of differentiation are transcriptionally distinct from the somatic cells, expressing genes associated with pluripotency and germ cell development while repressing genes associated with somatic differentiation (specifically multiple HOX genes). Using bisulfite sequencing, we show that iPGCs initiate imprint erasure from differentially methylated imprinted regions by day 7 of differentiation. However, iPGCs derived from hIPS cells do not initiate imprint erasure as efficiently. In conclusion, our results indicate that triple positive iPGCs derived from pluripotent cells differentiated on hFGS cells correspond to committed first trimester germ cells (before 9 weeks) that have initiated the process of imprint erasure.
Nanocrystalline TiO2 Photocatalytic Membranes with a Hierarchical Mesoporous Multilayer Structure: Synthesis, Characterization, and Multifunction (2006)

Abstract A novel sol–gel dip‐coating process to fabricate nanocrystalline TiO 2 photocatalytic membranes with a robust hierarchical mesoporous multilayer and improved performance has been studied. Various titania sols containing poly(oxyethylenesorbitan monooleate) (Tween 80) surfactant as a pore‐directing agent to tailor‐design the porous structure of TiO 2 materials at different molar ratios of Tween 80/isopropyl alcohol/acetic acid/titanium tetraisopropoxide = R :45:6:1 have been synthesized. The sols are dip‐coated on top of a homemade porous alumina substrate to fabricate TiO 2 /Al 2 O 3 composite membranes, dried, and calcined, and this procedure is repeated with varying sols in succession. The resulting asymmetric mesoporous TiO 2 membrane with a thickness of 0.9 μm exhibits a hierarchical change in pore diameter from 2–6, through 3–8, to 5–11 nm from the top to the bottom layer. Moreover, the corresponding porosity is incremented from 46.2, through 56.7, to 69.3 %. Compared to a repeated‐coating process using a single sol, the hierarchical multilayer process improves water permeability significantly without sacrificing the organic retention and photocatalytic activity of the TiO 2 membranes. The prepared TiO 2 photocatalytic membrane has great potential in developing highly efficient water treatment and reuse systems, for example, decomposition of organic pollutants, inactivation of pathogenic microorganisms, physical separation of contaminants, and self‐antifouling action because of its multifunctional capability.
Molecular Methods for the Detection and Identification of Viral Pathogens (1995)

This article addresses the use of nucleic acid amplification technology, specifically polymerase chain reaction (PCR), for the detection of viral nucleic acids in tissue specimens. Two different approaches are being used for the detection of viral DNA in tissue by PCR, solution PCR and in situ PCR (ISPCR). Solution PCR is the classic form of the procedure that uses DNA isolated from cells or tissue as target. ISPCR is where target DNA amplification occurs in the cell or tissue and the amplified product is visualized within the context of the intact specimen.Solution PCR is a very powerful technique for detection of viruses in tissue. While solution PCR does not afford target localization capability, it is a well researched and highly utilized procedure that can be readily adapted to routine use in a clinical laboratory. Unfortunately, the inherent difficulties associated with ISPCR obviates its use in the clinical laboratory. At present, ISPCR is in the developmental stages and its use should be restricted to the research laboratory. (The J Histotechnol 18:225, 1995)
Predictors of onset of facial pain and temporomandibular disorders in early adolescence (2006)

There are few prospective studies assessing risk factors for onset of temporomandibular (TMD) pain disorders in any age group. The aim of this prospective cohort study was to identify risk factors for onset of clinically significant TMD pain (i.e., pain meeting research diagnostic criteria for myofascial pain and/or arthralgia) during early adolescence. Subjects were 1,996 boys and girls, initially 11 years old, randomly selected from a large nonprofit health care system. Subjects completed a baseline telephone interview and were followed up with mailed questionnaires every 3 months for 3 years. At baseline and all follow ups, subjects were asked to report the presence of facial pain in the past 3 months. Subjects reporting a first onset of facial pain received a standardized clinical examination. In multivariate analyses, baseline predictors of clinically significant pain included female gender [Odds Ratio (OR)=2.0, 95% Confidence Interval (CI)=1.2-3.3] and negative somatic and psychological symptoms including somatization (OR=1.8, CI=1.1-2.8), number of other pain complaints (OR=3.2, CI=1.7-6.1) and life dissatisfaction (OR=4.1, CI=1.9-9.0). Many of the risk factors for onset of clinically significant TMD pain in adolescents are similar to risk factors for onset of TMD and other pain problems in adults, as well as risk factors for onset of other pain conditions in adolescents. These findings suggest that the development of TMD pain in adolescence may reflect an underlying vulnerability to musculoskeletal pain that is not unique to the orofacial region.
Enteral Versus Parenteral Feeding Effects on Septic Morbidity After Blunt and Penetrating Abdominal Trauma (1992)

To investigate the importance of route of nutrient administration on septic complications after blunt and penetrating trauma, 98 patients with an abdominal trauma index of at least 15 were randomized to either enteral or parenteral feeding within 24 hours of injury. Septic morbidity was defined as pneumonia, intra-abdominal abscess, empyema, line sepsis, or fasciitis with wound dehiscence. Patients were fed formulas with almost identical amounts of fat, carbohydrate, and protein. Two patients died early in the study. The enteral group sustained significantly fewer pneumonias (11.8% versus total parenteral nutrition 31.%, p less than 0.02), intra-abdominal abscess (1.9% versus total parenteral nutrition 13.3%, p less than 0.04), and line sepsis (1.9% versus total parenteral nutrition 13.3%, p less than 0.04), and sustained significantly fewer infections per patient (p less than 0.03), as well as significantly fewer infections per infected patient (p less than 0.05). Although there were no differences in infection rates in patients with injury severity score less than 20 or abdominal trauma index less than or equal to 24, there were significantly fewer infections in patients with an injury severity score greater than 20 (p less than 0.002) and abdominal trauma index greater than 24 (p less than 0.005). Enteral feeding produced significantly fewer infections in the penetrating group (p less than 0.05) and barely missed the statistical significance in the blunt-injured patients (p = 0.08). In the subpopulation of patients requiring more than 20 units of blood, sustaining an abdominal trauma index greater than 40 or requiring reoperation within 72 hours, there were significantly fewer infections per patient (p = 0.03) and significantly fewer infections per infected patient (p less than 0.01). There is a significantly lower incidence of septic morbidity in patients fed enterally after blunt and penetrating trauma, with most of the significant changes occurring in the more severely injured patients. The authors recommend that the surgeon obtain enteral access at the time of initial celiotomy to assure an opportunity for enteral delivery of nutrients, particularly in the most severely injured patients.
QAM Vector Signal Generation by Optical Carrier Suppression and Precoding Techniques (2015)

We numerically and experimentally investigate and compare photonic constant- and multi-amplitude quadrature-amplitude-modulation (QAM) vector signal generation at radio frequency (RF) bands enabled by a Mach-Zehnder modulator (MZM)-based optical carrier suppression (OCS) modulation. In order to attain an electrical vector RF signal displaying multi-amplitude QAM modulation, such as 8 QAM and 16 QAM, after square-law photodiode detection, the driving RF signal carrying multiamplitude QAM transmitter data, should be both amplitude- and phase-precoded before used to drive the MZM. However, for constant-amplitude QAM modulation, such as quadrature-phase-shift-keying (QPSK), only phase precoding is needed. We experimentally demonstrate 1-GBd vector signal generation at 12 GHz enabled by an MZM-based OSC modulation, adopting QPSK, 8 QAM, and 16 QAM modulation, respectively. We also experimentally compare the bit error rate performance of the three different vector signals, and the QPSK case is the best, while the 16 QAM case is the worst.
Establishment and characterization of a chicken hepatocellular carcinoma cell line, LMH. (1987)

A hepatocellular carcinoma cell line, LMH, has been established from a hepatocellular carcinoma induced in a male leghorn chicken by diethylnitrosamine. The cell line is characterized by well-differentiated morphological and biochemical features including the expression of glucose-6-phosphatase and canalicular ATPase activities and triploid karyotype with six marker chromosomes. The cells have been continuously propagated in culture for 5 yr and are now at about the 120th passage. Morphological change occurred in culture associated with gradual increase in growth rate at about the 40th passage. However, the biochemical and chromosomal features remained constant. This is the first established domestic fowl epithelial cell line and will allow comparative investigation of a number of parameters relevant to chicken hepatocarcinogenesis.
Activation of somatostatin receptors attenuates pulmonary fibrosis (2007)

We conclude that SOM230 attenuates bleomycin induced pulmonary fibrosis in mice and human lung fibroblasts activation. This study points to a potential new approach for treating pulmonary fibrotic disorders.
Recognizing substrings of LR(k) languages in linear time (1994)

LR parsing techniques have long been studied as being efficient and powerful methods for processing context-free languages. A linear-time algorithm for recognizing languages representable by LR(k) grammars has long been known. Recognizing substrings of a context-free language is at least as hard as recognizing full strings of the language, since the latter problem easily reduces to the former. In this article we present a linear-time algorithm for recognizing substrings of LR(k) languages, thus showing that the substring recognition problem for these languages is no harder than the full string recognition problem. An interesting data structure, the Forest-Structured Stack, allows the algorithm to track all possible parses of a substring without loosing the efficiency of the original LR parser. We present the algorithm, prove its correctness, analyze its complexity, and mention several applications that have been constructed.
Cytokines and Chemokines as Regulators of Skeletal Muscle Inflammation: Presenting the Case of Duchenne Muscular Dystrophy (2013)

Duchenne muscular dystrophy is a severe inherited muscle disease that affects 1 in 3500 boys worldwide. Infiltration of skeletal muscle by inflammatory cells is an important facet of disease pathophysiology and is strongly associated with disease severity in the individual patient. In the chronic inflammation that characterizes Duchenne muscle, cytokines and chemokines are considered essential activators and recruiters of inflammatory cells. In addition, they provide potential beneficiary effects on muscle fiber damage control and tissue regeneration. In this review, current knowledge of cytokine and chemokine expression in Duchenne muscular dystrophy and its relevant animal disease models is listed, and implications for future therapeutic avenues are discussed.
Cell Survival Promoted by the Ras-MAPK Signaling Pathway by Transcription-Dependent and -Independent Mechanisms (1999)

A mechanism by which the Ras-mitogen-activated protein kinase (MAPK) signaling pathway mediates growth factor-dependent cell survival was characterized. The MAPK-activated kinases, the Rsks, catalyzed the phosphorylation of the pro-apoptotic protein BAD at serine 112 both in vitro and in vivo. The Rsk-induced phosphorylation of BAD at serine 112 suppressed BAD-mediated apoptosis in neurons. Rsks also are known to phosphorylate the transcription factor CREB (cAMP response element-binding protein) at serine 133. Activated CREB promoted cell survival, and inhibition of CREB phosphorylation at serine 133 triggered apoptosis. These findings suggest that the MAPK signaling pathway promotes cell survival by a dual mechanism comprising the posttranslational modification and inactivation of a component of the cell death machinery and the increased transcription of pro-survival genes.
Involvement of CD100, a lymphocyte semaphorin, in the activation of the human immune system via CD72: implications for the regulation of immune and inflammatory responses (2003)

CD100/Sema4D belongs to the semaphorin family, factors known to act as repulsive cues for axons during neuronal development. Mouse CD100 plays a crucial role in both humoral and cellular immunity through ligation of the lymphocyte receptor, CD72. It remains controversial, however, whether human CD100 can function through human CD72 in a manner similar to mouse CD100. To determine the function of human CD100, we generated a recombinant soluble human CD100 protein comprised of the extracellular region of human CD100 fused to the human IgG1 Fc region (hCD100-Fc). hCD100-Fc specifically binds to cells expressing human CD72. As observed previously in the mouse, hCD100-Fc induces the tyrosine dephosphorylation of human CD72, leading to the dissociation of SHP-1 from the CD72 cytoplasmic tail. Consistent with findings for mouse CD100, hCD100-Fc exerts a co-stimulatory effect on B cells and dendritic cells that are stimulated with anti-CD40 mAb. Furthermore, both hCD100-Fc and anti-human CD72 agonistic mAb induce the production of the pro-inflammatory cytokines tumor necrosis factor-alpha, IL-6 and IL-8, even in the absence of anti-CD40 mAb. Collectively, our findings not only demonstrate that human CD100, interacting with human CD72, can function as a ligand in a manner similar to mouse CD100, but also suggest the involvement of human CD100 in inflammatory responses.
An Arg-Gly-Asp sequence within thrombin promotes endothelial cell adhesion. (1991)

Thrombin, in addition to its central role in hemostasis, possesses diverse cellular bioregulatory functions implicated in wound healing, inflammation, and atherosclerosis. In the present study we demonstrate that thrombin molecules modified either at the procoagulant or catalytic sites induce endothelial cell (EC) adhesion, spreading, and cytoskeletal reorganization. The most potent adhesive thrombin analogue (NO2-alpha-thrombin) was obtained by nitration of tyrosine residues. The cell adhesion promoting activity of NO2-alpha-thrombin was blocked upon the formation of thrombin-antithrombin III (ATIII) complexes and by antiprothrombin antibodies, but was unaffected by hirudin. Arg-Gly-Asp-containing peptides, fully inhibited EC adhesion to NO2-alpha-thrombin, while synthetic peptides corresponding to thrombin "Loop B" mitogenic site and the thrombin-derived chemotactic fragment "CB67-129", were uneffective. Immunofluorescence studies indicated that EC adhesion to NO2-alpha-thrombin was followed by cell spreading, actin microfilament assembly, and formation of focal contacts. By the use of specific antibodies, the vitronectin (vn) receptor (alpha v beta 3) was found to be localized in clusters upon cell adhesion to NO2-alpha-thrombin. An anti alpha v beta 3 antibody blocked EC adhesion and spreading while antifibronectin (fn) receptor (alpha 5 beta 1) antibodies were uneffective. While native thrombin exhibited a very low cell attachment activity, thrombin that was incubated at 37 degrees C before coating of plastic surfaces induced EC attachment and spreading. We propose that under certain conditions the naturally hindered RGD domain within thrombin is exposed for interaction with alpha v beta 3 on EC. This in turn promotes cell adhesion, spreading, and reorganization of cytoskeletal elements, which may altogether contribute to repair mechanisms in the disturbed vessel wall. This study defines a new biological role of thrombin and characterizes a new recognition mechanism on EC for this molecule.