gebhart/patrepeval huggingface dataset:
Plant growth-promoting rhizobacteria and root system functioning (2013)

The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.
Natural killer cells in immunodefense against infective agents (2008)

Following the discovery of innate immune receptors, the topics of innate immunity and its role in defense against infective agents have recently blossomed into very active research fields, after several decades of neglect. Among innate immune cells, natural killer (NK) cells are endowed with the unique ability to recognize and kill cells infected with a variety of pathogens, irrespective of prior sensitization to these microbes. NK cells have a number of other functions, including cytokine production and immunoregulatory activities. Major advances have recently been made in the understanding of the role of NK cells in the physiopathology of infectious diseases. The cellular and molecular mechanisms regulating the acquisition of effector functions by NK cells and their triggering upon pathogenic encounters are being unraveled. The possibility that the power of NK cells could be harnessed for the design of innovative treatments against infections is a major incentive for biologists to further explore NK cell subset complexity and to identify the ligands that activate NK cell receptors.
Near-field optical microscopy in liquids (1995)

The scanning near-field optical microscopy imaging of specimens in liquid and of cultured cells in aqueous solutions is reported. A scanning near-field optical/atomic-force microscope (SNOM-AFM) was developed, in which the scanning of an optical-fiber probe cantilever over the specimen was controlled by noncontact mode AFM (dynamic mode AFM). This imaging mode reduces damage to the probe and soft specimens. The resonant frequency of the probe cantilever decreased 20% to ≊14 kHz and the Q factor decreased by a factor of 8 to ≊30 in water, compared with these values in air, which was sufficient to perform SNOM-AFM imaging in liquid.
Recombinant platelet-derived growth factor B gene expression in porcine arteries induce intimal hyperplasia in vivo. (1993)

Platelet-derived growth factor (PDGF) B chain induces cell proliferation in vitro and is associated with arterial lesions that cause cardiovascular disease. However, it has been difficult to document the biological response to PDGF B gene expression in arteries in vivo. To determine the biologic effects of this growth factor in vivo, we have introduced an eukaryotic expression vector plasmid encoding recombinant PDGF B by direct gene transfer into porcine iliofemoral arteries using DNA liposome complexes. The presence of PDGF B plasmid DNA and expression of recombinant mRNA were confirmed by polymerase chain reaction analysis, and recombinant PDGF protein was demonstrated by immunohistochemistry. Intimal thickening was observed in porcine arteries 21 days following transfection with the recombinant PDGF B gene compared with arteries transduced with a control gene, E. coli beta-galactosidase. An eightfold increase in intimal to medial ratio was present in PDGF B gene transfected arteries compared with control transfected arteries (P = 0.001). This study suggests that expression of a recombinant PDGF B gene in vivo can play a role in the induction of intimal hyperplasia, which can lead to cardiovascular diseases.
Beta-ketoadipate enol-lactone hydrolases I and II from Acinetobacter calcoaceticus (1975)

Beta-Ketoadipate enol-lactone hydrolase catalyzes a common step in the utilization of protocatechuate and cis,cis-muconate by bacteria. Either of the two compounds elicits the synthesize of an enol-lactone hydrolase in Acinetobacter. The enol-lactone hydrolase that is induced by each compound was purified, and the properties of the proteins were compared. Both enzymes appear to be dimers with molecular weights of approximately 25,000. The amino acid compositions of the enzymes differ, and the two proteins do not cross-react serologically. The NH2-terminal amino acid residue of the protocatechuate-induced enol-lactone hydrolase (ELH I) is methionine and the NH2-terminal amino acid residue of the cis,cis-muconate-induced enol-lactone hydrolase (ELH II) is proline. Therefore, ELH I and ELH II appear to be the products of different structural genes. The serological specificity of ELH I and ELH II made it possible to demonstrate the mutually independent regulation of their synthesis in wild type cells and in constitutive mutant strains. The synthesis of ELH I is not impaired in mutant strains that cannot synthesize ELH II. The rapid characterization of mutant strains that produce ELH I or ELH II constitutively was made possible by the development of pH indicator enzyme assays that were performed with toluenized cells. cis,trans-Muconate, which does not support the growth of Acinetobacter, elicits the synthesis of the enzymes that normally are induced by cis,cis-muconate to 20% of fully induced levels.
Description and performance analysis of signature file methods for office filing (1987)

Signature files have attracted a lot of interest as an access method for text and specifically for messages in the office environment. Messages are stored sequentially in the message file, whereas their hash-coded abstractions (signatures) are stored sequentially in the signature file. To answer a query, the signature file is examined first, and many nonqualifying messages are immediately rejected. In this paper we examine the problem of designing signature extraction methods and studying their performance. We describe two old methods, generalize another one, and propose a new method and its variation. We provide exact and approximate formulas for the dependency between the false drop probability and the signature size for all the methods, and we show that the proposed method (VBC) achieves approximately ten times smaller false drop probability than the old methods, whereas it is well suited for collections of documents with variable document sizes.
Chelators in the Treatment of Iron Accumulation in Parkinson's Disease (2012)

Iron is an essential element in the metabolism of all cells. Elevated levels of the metal have been found in the brains of patients of numerous neurodegenerative disorders, including Parkinson's disease (PD). The pathogenesis of PD is largely unknown, although it is thought through studies with experimental models that oxidative stress and dysfunction of brain iron homeostasis, usually a tightly regulated process, play significant roles in the death of dopaminergic neurons. Accumulation of iron is present at affected neurons and associated microglia in the substantia nigra of PD patients. This additional free-iron has the capacity to generate reactive oxygen species, promote the aggregation of α-synuclein protein, and exacerbate or even cause neurodegeneration. There are various treatments aimed at reversing this pathologic increase in iron content, comprising both synthetic and natural iron chelators. These include established drugs, which have been used to treat other disorders related to iron accumulation. This paper will discuss how iron dysregulation occurs and the link between increased iron and oxidative stress in PD, including the mechanism by which these processes lead to cell death, before assessing the current pharmacotherapies aimed at restoring normal iron redox and new chelation strategies undergoing research.
Characterization of interleukin-4 receptors expressed on human renal cell carcinoma cells. (1994)

We have recently reported that a variety of solid human tumor cells express high-affinity interleukin-4 receptors (IL-4R). In this study, we have compared structural characteristics of IL-4R expressed on human renal cell carcinoma cells (RCC-WS) and the lymphoid cell lines RAJI (B-cell line) and H9 (T-cell line). In crosslinking studies, the three cell types expressed a predominant 140 kDa IL-4R band. In addition, a 70 kDa band was expressed strongly in H9 cells but only faintly on RCC-WS and RAJI cells. These different species of IL-4R were not observed when crosslinking studies were performed in the presence of excess interleukin-4 (IL-4), indicating IL-4 specificity. A polyclonal anti-IL-4R antibody immunoprecipitated the two species (140 and 70 kDa) in H9 and predominantly the 140 kDa species in RCC-WS tumor cells and RAJI cells. A faint band for the 70 kDa protein was also observed. The affinity of IL-4 binding to its receptor in RCC-WS cells was similar to the binding affinity observed in H9 and RAJI cells examined. However, the RCC tumor cells and B lymphoid cells internalized IL-4R more rapidly compared to T lymphoid cells. Although IL-4R synthesis was similarly inhibited by cycloheximide in all three cell lines, IL-4R expression was more sensitive to actinomycin D inhibition on the RCC-WS and RAJI cells than on H9 cells. Our results suggest that IL-4R expressed on RCC-WS tumor cells are structurally different from those expressed on lymphoid cells because the proportions of IL-4R subunits differ in these cells. Further studies should be performed to determine the identity and functional significance of IL-4R proteins expressed on RCC and immune cells.
Control of the Lysine Biosynthesis Sequence in Corynebacterium glutamicum as Analyzed by Overexpression of the Individual Corresponding Genes (1991)

The gene cluster that codes for feedback-resistant aspartate kinase (lysCalpha and lysCbeta) and aspartate semialdehyde dehydrogenase (asd) was cloned from a mutant strain of Corynebacterium glutamicum. Its functional analysis by subcloning, enzyme assays, and type of aspartate kinase regulation enabled the isolation of a fragment for separate expression of the feedback-resistant kinase without aspartate semialdehyde dehydrogenase expression. This was used together with other clones constructed (J. Cremer, L. Eggeling, and H. Sahm, Mol. Gen. Genet. 220:478-480, 1990) to overexpress individually each of the six genes that convert aspartate to lysine. Analysis of lysine formation revealed that overexpression of the feedback-resistant kinase alone suffices to achieve lysine formation (38 mM). Also, sole overexpression of wild-type dihydrodipicolinate synthase resulted in lysine formation but in a lower amount (11 mM). The other four enzymes had no effect on lysine secretion. With a plasmid overexpressing both relevant enzymes together, a further increase in lysine yield was obtained. This shows that of the six enzymes that convert aspartate to lysine the kinase and the synthase are responsible for flow control in the wild-type background and can be useful for construction of lysine-producing strains.
Essential Role of Yl MPO1 , a Novel Yarrowia lipolytica Homologue of Saccharomyces cerevisiae MNN4 , in Mannosylphosphorylation of N- and O-Linked Glycans (2010)

Mannosylphosphorylation of N- and O-glycans, which confers negative charges on the surfaces of cells, requires the functions of both MNN4 and MNN6 in Saccharomyces cerevisiae. To identify genes relevant to mannosylphosphorylation in the dimorphic yeast Yarrowia lipolytica, the molecular functions of five Y. lipolytica genes showing significant sequence homology with S. cerevisiae MNN4 and MNN6 were investigated. A set of mutant strains in which Y. lipolytica MNN4 and MNN6 homologues were deleted underwent glycan structure analysis. In contrast to S. cerevisiae MNN4 (ScMNN4), the Y. lipolytica MNN4 homologue, MPO1 (YlMPO1), encodes a protein that lacks the long KKKKEEEE repeat domain at its C terminus. Moreover, just a single disruption of YlMPO1 resulted in complete disappearance of the acidic sugar moiety in both the N- and O-linked glycan profiles. In contrast, even quadruple disruption of all ScMNN6 homologues, designated YlKTR1, YlKTR2, YlKTR3, and YlKTR4, resulted in no apparent reduction in acidic sugar moieties. These findings strongly indicate that YlMpo1p performs a significant role in mannosylphosphorylation in Y. lipolytica with no involvement of the Mnn6p homologues. Mutant strains harboring the YlMPO1 gene disruption may serve as useful platforms for engineering Y. lipolytica glycosylation pathways for humanized glycans without any yeast-specific acidic modifications.
Toxoplasma gondii: cloning, sequencing, expression, and antigenic characterization of ROP2, GRA5 and GRA7 (2008)

Toxoplasma gondii is an intracellular obligate protozoan, which infects humans and warm-blooded animals. The aim of the present study was to clone the rop2, gra5 and gra7 genes from T. gondii RH strain and to produce recombinant proteins. The rop2, gra5 and gra7 gene fragments produced by polymerase chain reaction were cloned into the pET102/D-TOPO vector which contains thioredoxin and polyhistidine tags at the C- and N-ends, respectively, and is expressed in Escherichia coli BL21(DE-3). The expression fusion proteins were found almost entirely in the insoluble form in the cell lysate. These recombinant proteins were purified with an Ni-NTA column. Concentrations of the recombinant antigens produced in the E. coli BL21-star ranged from 300 to 500 microg/ml growth media, which was used to immunize rabbits. We observed an identity ranging from 96 to 97% when nucleotide sequences were compared to GenBank database sequences. Immunocharacterization of proteins was made by indirect immunofluorescence assay. These proteins will be used for serodiagnosis and vaccination.
Enumeration of leukocyte infiltration in solid tumors by confocal laser scanning microscopy (2006)

From these results we conclude that this method may be of considerable use for the enumeration of cells in tissues. Furthermore, since it can be performed by laboratory technical staff, less time input is required by the pathologist in assessing the degree of leukocyte infiltration into tumors.
Diabetic Diarrhea and Steatorrhea (1970)

Aerobic bacterial cultures of upper gastrointestinal aspirates were performed in 10 patients with diabetes mellitus and gastrointestinal disturbances. All but one had diarrhea, five also had steatorrhea. "Normal" bacterial growth as previously defined was encountered in seven patients. One of the three patients with excessive bacterial growth had gastric atony without diarrhea. Two patients with diabetic diarrhea and steatorrhea had excessive small-intestinal bacterial growth (106 to 107 colony-forming units (cfu)/ml). Their diarrhea and steatorrhea were controlled by antibiotics selected according to the sensitivities of the recovered organisms. Thus, these two patients, in contrast to the remainder of the group, represented another variant of the blind-loop syndrome responsive to antibiotic treatment.
The pharmacokinetics and pharmacodynamics of monoclonal antibodies--mechanistic modeling applied to drug development. (2007)

The pharmacology of therapeutic monoclonal antibodies (mAbs) is complex and dependant on both the structure of the antibody and the physiological system that it targets. Patient exposure and responses to mAbs are also related to the structure and activity of mAbs. Furthermore, the pharmacokinetics and pharmacodynamics of mAbs are often inter-related. Pharmacokinetic and pharmacodynamic modeling have been used to elucidate or support the mechanisms of antibodies in development and can be used to identify appropriate dose regimens. Consequently, pharmacokinetic and pharmacodynamic modeling often plays a larger role during the development of therapeutic mAbs than for small molecules.
Galectins in Disease and Potential Therapeutic Approaches (2012)

The Galectin protein family includes 15 members that are characterized by galactose binding domains and are widely expressed in diverse cell types. Galectins are found in multiple intracellular compartments and are secreted into the extracelluar space. There has been an explosion in information on these fascinating proteins in pathological states, particularly inflammation, fibrosis, and cancer. This book, in conjunction with an international conference, attempts to cover the key areas of galectin-dependent disease and review the approaches to developing pharmaceutical approaches to treatment. The time is right for major efforts to advance galectin-based therapies into multiple human diseases.
Potently neutralizing human antibodies that block SARS-CoV-2 receptor binding and protect animals (2020)

The COVID-19 pandemic is a major threat to global health for which there are only limited medical countermeasures, and we lack a thorough understanding of mechanisms of humoral immunity <sup>1,2</sup> . From a panel of monoclonal antibodies (mAbs) targeting the spike (S) glycoprotein isolated from the B cells of infected subjects, we identified several mAbs that exhibited potent neutralizing activity with IC <sub>50</sub> values as low as 0.9 or 15 ng/mL in pseudovirus or wild-type ( <i>wt</i> ) SARS-CoV-2 neutralization tests, respectively. The most potent mAbs fully block the receptor-binding domain of S (S <sub>RBD</sub> ) from interacting with human ACE2. Competition-binding, structural, and functional studies allowed clustering of the mAbs into defined classes recognizing distinct epitopes within major antigenic sites on the S <sub>RBD</sub> . Electron microscopy studies revealed that these mAbs recognize distinct conformational states of trimeric S protein. Potent neutralizing mAbs recognizing unique sites, COV2-2196 and COV2-2130, bound simultaneously to S and synergistically neutralized authentic SARS-CoV-2 virus. In two murine models of SARS-CoV-2 infection, passive transfer of either COV2-2916 or COV2-2130 alone or a combination of both mAbs protected mice from severe weight loss and reduced viral burden and inflammation in the lung. These results identify protective epitopes on the S <sub>RBD</sub> and provide a structure-based framework for rational vaccine design and the selection of robust immunotherapeutic cocktails.
Enhanced prostate cancer gene transfer and therapy using a novel serotype chimera cancer terminator virus (Ad.5/3-CTV) (2013)

Few options are available for treating patients with advanced prostate cancer (PC). As PC is a slow growing disease and accessible by ultrasound, gene therapy could provide a viable option for this neoplasm. Conditionally replication-competent adenoviruses (CRCAs) represent potentially useful reagents for treating PC. We previously constructed a CRCA, cancer terminator virus (CTV), which showed efficacy both in vitro and in vivo for PC. The CTV was generated on a serotype 5-background (Ad.5-CTV) with infectivity depending on Coxsackie-Adenovirus Receptors (CARs). CARs are frequently reduced in many tumor types, including PCs thereby limiting effective Ad-mediated therapy. Using serotype chimerism, a novel CTV (Ad.5/3-CTV) was created by replacing the Ad.5 fiber knob with the Ad.3 fiber knob thereby facilitating infection in a CAR-independent manner. We evaluated Ad.5/3-CTV in comparison with Ad.5-CTV in low CAR human PC cells, demonstrating higher efficiency in inhibiting cell viability in vitro. Moreover, Ad.5/3-CTV potently suppressed in vivo tumor growth in a nude mouse xenograft model and in a spontaneously induced PC that develops in Hi-myc transgenic mice. Considering the significant responses in a Phase I clinical trial of a non-replicating Ad.5-mda-7 in advanced cancers, Ad.5/3-CTV may exert improved therapeutic benefit in a clinical setting.
Amino acids necessary for DNA contact and dimerization imply novel motifs in the papillomavirus E2 trans-activator. (1992)

The bovine papillomavirus E2 protein regulates viral transcription by binding as a dimer to the DNA sequence ACCGN4CGGT. The dimerization and DNA-binding properties are localized within its carboxy-terminal 85 amino acids (325-410). Utilizing random mutagenesis coupled with phenotypic selection in yeast, functionally important amino acids in the DNA-binding domain were identified. Four trans-activation defective point mutants within a short segment (amino acids 337-344) were DNA binding defective but dimeric. The mutation of a conserved tryptophan to serine also eliminated DNA binding, but loss of dimerization was implicated because addition of dimeric monoclonal antibody complemented this defect. A simple assay for E2 dimerization was developed using UV irradiation to produce an interchain cross-link within a dimer. No heterodimeric complexes were formed when pools of E2 of varying lengths were mixed, and only proteins with tryptophan at position 360 could be UV cross-linked. Peptide mapping of irradiated E2 protein localized the cross-link to an 18-amino-acid region bracketing this tryptophan. Substitutions for this tryptophan demonstrated the requirement for a hydrophobic residue at this position, but surprisingly, even alanine was functional. Replacement of this tryptophan with three polar amino acids or glycine eliminated DNA-binding activity, but addition of dimeric monoclonal antibody restored this function. The amino acids that were identified as being involved in DNA contact and dimerization imply that these functions are mediated by novel binding motifs.
Two novel compressed-sensing algorithms for NBI detection in OFDM systems (2010)

We propose two novel algorithms based on compressed-sensing theory to estimate and cancel narrow band interference (NBI) in orthogonal frequency division multiplexing (OFDM) systems. Simulation results demonstrate the effectiveness of our proposed algorithms in estimating the NBI frequency support and approaching the performance with no NBI.