gebhart/patrepeval huggingface dataset:
Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus (2008)

The complete genome of the Maruca vitrata nucleopolyhedrovirus (MaviNPV) isolated from the legume pod borer, Maruca vitrata (Lepidoptera: Pyralidae), was sequenced. It was found to be 111 953 bp in length, with an overall 39 % G+C content, and contained 126 open reading frames (ORFs) encoding predicted proteins of over 50 aa. The gene content and gene order of MaviNPV have the highest similarity to those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and their shared homologous genes are 100 % collinear. In fact, MaviNPV seems to be a mini-AcMNPV that is native to Taiwan and possesses a smaller genome with fewer auxiliary genes than the AcMNPV type species. Except for one ORF (Mv74), all of the MaviNPV ORFs have homologues in the AcMNPV genome. MaviNPV is the first lepidopteran-specific baculovirus to lack homologues of vfgf and odv-e66. In addition, MaviNPV lacks the baculovirus repeat ORF (bro) gene that corresponds to AcMNPV ORF2. Five homologous regions (hrs) were located within the MaviNPV genome, and these contained a total of 44 imperfect palindromes. Phylogenetic analysis of the whole genome revealed that MaviNPV was separated from the common ancestor of AcMNPV and Bombyx mori nucleopolyhedrovirus before these two viral species diverged from each other. Moreover, replication of MaviNPV in several cell lines and an egfp-MaviNPV infection assay revealed that IPLB-LD-652Y cells are only partially permissive to MaviNPV, which supports our conclusion that MaviNPV is a distinct species of the group I lepidopteran NPVs.
Simulation of the athermal coarsening of composites structured by a uniaxial field (1998)

We report the results of a computer simulation of the evolution of structure in a two component fluid consisting of a liquid phase and a dispersed colloidal phase subjected to a uniaxial field. Our primary objective is to understand the mechanism and kinetics of coarsening and the emergence of crystallinity. Using an efficient, linear-N simulation method we report studies of systems of N=10 000 particles over the concentration range of 10–50 vol %. We present a variety of methods of characterizing the structures that emerge, including the anisotropy of the conductivity, capacitance and dipolar interaction energy, the two-dimensional pair correlation function, principal moments of the gyration tensor, velocity correlation functions, microcrystallinity and coordination number, and the optical attenuation length. We conclude that athermal coarsening is effectively driven by the presence of defect structures and that as the concentration increases, the structures progressively lose the well-known “chain” anisotropy evinced at low concentration.
Androgens and the Aging Male (2025)

In contrast to women, men do not experience a sudden cessation of gonadal function comparable to menopause. However, there is a progressive reduction in male hypothalamic-pituitary-gonadal (HPG) axis function: testosterone levels decline through both central (pituitary) and peripheral (testicular) mechanisms, and there is a loss of the circadian rhythm of testosterone secretion. The progressive decline in testosterone levels has been demonstrated in both cross-sectional and longitudinal studies, and overall at least 25% of men over age 70 meet laboratory criteria for hypogonadism (ie, testosterone deficiency). Such age-associated HPG hypofunctioning, which has been termed "andropause," is thought to be responsible for a variety of symptoms experienced by elderly men, including weakness, fatigue, reduced muscle and bone mass, impaired hematopoiesis, sexual dysfunction (including erectile dysfunction and loss of libido), and depression. Although, it has been difficult to establish correlations between these symptoms and plasma testosterone levels, there is some evidence that testosterone replacement leads to symptom relief, particularly with respect to muscle strength, bone mineral density, and erectile dysfunction. There is little evidence of a link between the HPG axis hypofunctioning and depressive illness, and exogenous androgens have not been consistently shown to have antidepressant activity. This article reviews the relationship between androgens, depression, and sexual function in aging men.
Memristive crypto primitive for building highly secure physical unclonable functions (2015)

Physical unclonable functions (PUFs) exploit the intrinsic complexity and irreproducibility of physical systems to generate secret information. The advantage is that PUFs have the potential to provide fundamentally higher security than traditional cryptographic methods by preventing the cloning of devices and the extraction of secret keys. Most PUF designs focus on exploiting process variations in Complementary Metal Oxide Semiconductor (CMOS) technology. In recent years, progress in nanoelectronic devices such as memristors has demonstrated the prevalence of process variations in scaling electronics down to the nano region. In this paper, we exploit the extremely large information density available in nanocrossbar architectures and the significant resistance variations of memristors to develop an on-chip memristive device based strong PUF (mrSPUF). Our novel architecture demonstrates desirable characteristics of PUFs, including uniqueness, reliability, and large number of challenge-response pairs (CRPs) and desirable characteristics of strong PUFs. More significantly, in contrast to most existing PUFs, our PUF can act as a reconfigurable PUF (rPUF) without additional hardware and is of benefit to applications needing revocation or update of secure key information.
Dna2 is a structure-specific nuclease, with affinity for 5′-flap intermediates (2009)

Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5'-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5'-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of approximately 5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing.
Paclitaxel liposome aerosol treatment induces inhibition of pulmonary metastases in murine renal carcinoma model. (2001)

The present studies were undertaken to evaluate the pulmonary pharmacokinetics and therapeutic efficacy of paclitaxel (PTX) administered by aerosol. PTX was encapsulated into dilauroylphosphatidylcholine liposomal formulations (PTX-DLPC). The deposition and clearance of PTX-DLPC in the lungs administered by aerosol or i.v. at comparative doses was performed, and PTX was quantitatively determined in tissue extracts by high-performance liquid chromatography analysis. The murine renal carcinoma (Renca) pulmonary metastases model was used to determine the therapeutic effect of drug formulation administered by aerosol. PTX-DLPC aerosols were generated with the Aero-Mist jet nebulizer (cis-USA). The most effective schedule of treatment was when mice inhaled the drug for 30 min 3 days per week. There was a significant reduction of the lung weights and reduced number of visible tumor foci on the lung surfaces of mice treated with PTX aerosol (P < 0.004 and P < 0.01, respectively) compared with control groups. Inhalation of PTX-DLPC also led to prolonged survival in mice inoculated with Renca cells. The results of the present studies demonstrate the therapeutic potential of aerosol technology for lung cancer treatment.
An Experimental Study to Evaluate the Fluobeam 800 Imaging System for Fluorescence-Guided Lymphatic Imaging and Sentinel Node Biopsy (2012)

This is the first study analyzing the feasibility of the Fluobeam 800 imaging system allowing transcutaneous real-time imaging. It enables detection of the SLN by fluorescence retention with increased detection depth and resolution. After fixation to the ceiling, the ergonomics advanced for simultaneous field navigation and dissection. The new system can be applied for lymphatic imaging for lympatico-reconstructive surgery and SLN biopsy.
Genetic Mosaicism in Adult Mice of Quadriparental Lineage (1965)

Genetic mosaic mice can be produced by aggregating, during cleavage stages, the blastomeres of two embryos of different genotype into a single cluster, and by transferring the developing aggregates to the uterus of a surrogate mother. Substantial numbers of such composite embryos survive past birth. Among the living adult mosaic mice are individuals within which cells of markedly different immunogenetic constitution coexist. Through the incorporation of appropriate genetic markers into mosaics, many new possibilities now present themselves for analysis of biological problems during embryonic as well as adult life.
Maleimide polymers. I. A polymeric color reaction (1973)

Abstract Certain copolymers of maleimide and N ‐substituted maleimides yield brilliant colors when treated with sufficiently strong basic reagents under nonhydrolytic conditions. For color generation, the copolymer must be capable of HX elimination. The chromophores which account for color probably result from the ionization of acidic protons in structures involving one or more double bonds conjugated with imide carbonyl. The analogy to the color reactions of aconitylanil is pointed out. Spectra covering the range of 330–700 mμ are presented for a number of copolymer–amine color‐generating systems. The colors produced in base with radical‐initiated polymaleimide and imidazole‐initiated poly‐ N ‐alkylmaleimides as well as the absence of color with anionic polymaleimide and radical poly‐ N ‐alkylmaleimides are discussed in light of what is known about their polymerization kinetics and mechanisms. Corresponding maleic anhydride copolymer systems are mentioned.
Chiral porous organic frameworks for asymmetric heterogeneous catalysis and gas chromatographic separation (2014)

Three chiral robust diene-based porous organic frameworks (POFs) are prepared. POF- is shown to be an efficient heterogeneous catalyst after metallation for asymmetric conjugation addition with up to 93% ee, and it can also function as a new chiral stationary phase for gas chromatographic separation of racemates.
Characterization of the Single-Strand-Specific BPV-1 Origin Binding Protein, SPSF I, as the Hela Pur Factor (1996)

SPSF I and II are two cellular proteins which bind specifically to single-stranded DNA. SPSF I and II binding sites are found in the minimal origin of replication of BPV-1 DNA and near the P2 promoter of the cellular c-myc gene. DNA-binding properties of the two proteins to single-stranded oligonucleotides of different lengths and sequences were quantified by determination of DNA-binding constants. The binding constant of SPSF proteins to the lower strand of the BPV-1 origin was determined to be 1.5 x 10(-10) M-1. Peptide sequences derived from purified SPSF I and II revealed the identity of at least one of the SPSF proteins with the so-called HeLa Pur alpha factor. The HeLa Pur alpha factor was identified previously by virtue of its capacity to bind to purine-rich strands of the PUR element found in initiation zones of DNA replication [Bergemann, A.D., Ma,Z.-W. and Johnson, E.M. (1992) Mol. Cell. Biol. 12, 5673-5682]. Expression of the Pur cDNA confirmed the identity of the Pur alpha protein with the 42 kDa SPSF I protein. Analysis of several Pur alpha cDNA clones revealed the existence of an extended 3'-untranslated region in all Pur mRNAs.
E-selectin up-regulation allows for targeted drug delivery in prostate cancer. (2003)

We have used the Eos Hu03 GeneChip array, which represents over 92% of the transcribed human genome, to measure gene expression in a panel of normal and diseased human tissues. This analysis revealed that E-selectin mRNA is selectively overexpressed in prostate cancer epithelium, a finding that correlated strongly with E-selectin protein expression as assessed by immunohistochemistry. Antibodies against E-selectin that blocked function failed to impede cancer cell growth, suggesting that overexpression of E-selectin was not essential for cell growth. However, a novel auristatin E-based antibody drug conjugate (ADC), E-selectin antibody valine-citrulline monomethyl-auristatin E, was a potent and selective agent against E-selectin-expressing cancer cell lines in vitro, with the degree of cytotoxicity varying with surface antigen density. Interestingly, sensitivity to the ADC differed among cell lines from different tissues expressing similar amounts of E-selectin and was found to correlate with sensitivity to free auristatin E. Furthermore, E-selectin-expressing tumors grown as xenografts in severe combined immunodeficient mice were responsive to treatment with E-selectin antibody valine-citrulline monomethyl-auristatin E in vivo, with more than 85% inhibition of tumor growth observed in treated mice. These findings demonstrate that an E-selectin-targeting ADC has potential as a prostate cancer therapy and validates a genomics-based paradigm for the identification of cancer-specific antigens suitable for targeted therapy.
DNA-directed alkylating agents. 4. 4-Anilinoquinoline-based minor groove directed aniline mustards (1991)

A series of 4-anilinoquinoline-linked aniline mustards of widely varying mustard reactivity were prepared and evaluated for their antitumor activity. The compounds were designed as minor grove binding agents, where the aniline mustard ring is itself part of the DNA-binding ligand. While there was a general trend for cytotoxicity to correlate with mustard reactivity, this was much less pronounced than with untargeted mustards. The compounds were much more cytotoxic than the parent diols, and were also at least 10-fold more cytotoxic than the corresponding aniline mustards themselves. Comparative cell line studies suggested that the mechanism of cytotoxicity varied with mustard reactivity. The most reactive mustards cross-linked DNA, while cell killing by the less reactive compounds appeared to be by the formation of bulky monoadducts. The compounds were active but not particularly dose-potent against P388 leukemia in vivo. The modest potency may be related to their poor aqueous solubility, since the more soluble methyl quaternary salts were equally active at much lower doses.
Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold (2006)

The design of enzymes with new functions and properties has long been a goal in protein engineering. Here, we report a strategy to change the catalytic activity of an existing protein scaffold. This was achieved by simultaneous incorporation and adjustment of functional elements through insertion, deletion, and substitution of several active site loops, followed by point mutations to fine-tune the activity. Using this approach, we were able to introduce beta-lactamase activity into the alphabeta/betaalpha metallohydrolase scaffold of glyoxalase II. The resulting enzyme, evMBL8 (evolved metallo beta-lactamase 8), completely lost its original activity and, instead, catalyzed the hydrolysis of cefotaxime with a (kcat/Km)app of 1.8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100.
Invited Review: Methods for the Screening, Isolation, and Characterization of Exopolysaccharides Produced by Lactic Acid Bacteria (2005)

The ability to produce exopolysaccharides (EPS) is widespread among lactic acid bacteria (LAB), although the physiological role of these molecules has not been clearly established yet. Some EPS confer on LAB a "ropy" character that can be detected in cultures that form long strands when extended with an inoculation loop. When EPS are produced in situ during milk fermentation they can act as natural biothickeners, giving the product a suitable consistency, improving viscosity, and reducing syneresis. In addition, some of these EPS may have beneficial effects on human health. The increasing demand by consumers of novel dairy products requires a better understanding of the effect of EPS on existing products and, at the same time, the search for new EPS-producing strains with desirable properties. The use of genetically modified organisms capable of producing high levels of EPS or newly designed biopolymers is still very limited. Therefore, exploration of the biodiversity of wild LAB strains from natural ecological environments is currently the most suitable approach to search for the desired EPS-phenotype. The screening of ropy strains and the isolation and characterization of EPS responsible for this characteristic have led to the application over the past years of a wide variety of techniques. This review summarizes the available information on methods and procedures used for research on this topic. The information provided deals with methods for screening of EPS-producing LAB, detection of the ropy phenotype, and the physicochemical and structural characterization of these molecules, including parameters related to their viscosifying properties. To our knowledge, this is the first compilation of methods available for the study of EPS produced by LAB.
2D-PCR: a method of mapping DNA in tissue sections (2009)

A novel approach was developed for mapping the location of target DNA in tissue sections. The method combines a high-density, multi-well plate with an innovative single-tube procedure to directly extract, amplify, and detect the DNA in parallel while maintaining the two-dimensional (2D) architecture of the tissue. A 2D map of the gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was created from a tissue section and shown to correlate with the spatial area of the sample. It is anticipated that this approach may be easily adapted to assess the status of multiple genes within tissue sections, yielding a molecular map that directly correlates with the histology of the sample. This will provide investigators with a new tool to interrogate the molecular heterogeneity of tissue specimens.
Cancer-testis antigen MAGEC2 promotes proliferation and resistance to apoptosis in Multiple Myeloma (2015)

Cancer-testis antigens belonging to the MAGE family of genes, such as MAGEC2, are commonly and specifically expressed in Multiple Myeloma (MM) and are associated with a more aggressive clinical course and chemotherapy resistance. MAGEC2 is thought to be an excellent candidate for cancer immunotherapy; however, the biological role of MAGEC2 in MM has remained unclear. We investigated the biological role of MAGEC2 in myeloma cells determining the effect of MAGEC2 knockdown on proliferation and apoptosis. Loss of MAGEC2 resulted in reduced proliferation, viability, and anchorage-independent growth of myeloma cells irrespective of the functional status of TP53 (p53). The anti-proliferative effect of MAGEC2 silencing was due to a decrease of cells in the S phase, cell cycle delay at both G0/G1 and/or G2/M, and an increase in the sub-G0/G1 diploid population related to apoptotic cell death. Importantly, overexpression of short hairpin (sh)RNA-refractory MAGEC2 rescued the anti-proliferative effect of mRNA knockdown and protected cells from apoptotic cell death. Our findings support a TP53-independent role of MAGEC2 in promoting the survival of myeloma cells suggesting that MAGEC2-specific immunotherapies have the potential to eradicate the most malignant cells within the myeloma tumour bulk leading to durable clinical responses.
Cytotoxicity, Hemolysis, and Acute in Vivo Toxicity of Dendrimers Based on Melamine, Candidate Vehicles for Drug Delivery (2004)

A small library of dendrimers was prepared from a common precursor that is available in 5 g scale in five linear steps at 56% overall yield. The precursor is a generation three dendrimer that displays 48 peripheral sites by incorporating AB4 surface groups. Manipulation of these sites provided six dendrimers that vary in the chemistry of the surface group (amine, guanidine, carboxylate, sulfonate, phosphonate, and PEGylated) that were evaluated for hemolytic potential and cytotoxicity. Cationic dendrimers were found to be more cytotoxic and hemolytic than anionic or PEGylated dendrimers. The PEGylated dendrimer was evaluated for acute toxicity in vivo. No toxicity--neither mortality nor abnormal blood chemistry based on blood urea nitrogen levels or alanine transaminase activity--was observed in doses up to 2.56 g/kg i.p. and 1.28 g/kg i.v.
Application of Nazarov cyclization to access [6-5-6] and [6-5-5]tricyclic core embedded new heterocycles: an easy entry to structures related to Taiwaniaquinoids (2009)

A concise and general route to synthesize a new class of [6-5-6] tricyclic core embedded polyheterocycles has been accomplished using diastereoselective Nazarov cyclization with an overall yield of 35-40%. Versatility of this synthetic route has also been demonstrated by accessing a variety of [6-5-5] tricyclic core incorporated polycycles. It was observed that the efficiency of cyclization depends upon the impact of polarization on the reacting systems. Amongst the various Lewis and Brønsted acids screened for cyclization, triflic acid was found to be the most effective catalyst.
Preclinical studies with IRX‐2 and thymosin α1 in combination therapy (2010)

Thymosin alpha1 (Talpha1) is a 28 amino acid biologically active protein with pleiotropic immune enhancing activity. IRX-2 is a primary cell-derived biologic containing multiple cytokines that enhance dendritic cell maturation, promote T-cell growth and differentiation, and inhibit tumor-mediated apoptosis of T cells. IRX-2 is being developed as an immunotherapeutic agent as a novel T-cell adjuvant platform for vaccines as well. Based on their biological activities, thymosin alpha1 and IRX-2 were predicted to exhibit synergistic effects when evaluated in animal and human studies. In animal studies, the combination of IRX-2 and Talpha1 (IRX-3) increased T-cell numbers compared to either alone during recovery from hydrocortisone mediated reduction. IRX-3 further enhanced reduction in tumor burden following chemotherapy compared to IRX-2. Based on these studies, IRX-3 is predicted to be especially important in a setting where reversal of immune suppression due to the presence of tumor, irradiation, and/or chemotherapy is likely to be an important factor in cytokine activity.
Flow cytometry for enrichment and titration in massively parallel DNA sequencing (2009)

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols.