gebhart/patrepeval huggingface dataset:
Ancient Invasions: From Endosymbionts to Organelles (2004)

The acquisitions of mitochondria and plastids were important events in the evolution of the eukaryotic cell, supplying it with compartmentalized bioenergetic and biosynthetic factories. Ancient invasions by eubacteria through symbiosis more than a billion years ago initiated these processes. Advances in geochemistry, molecular phylogeny, and cell biology have offered insight into complex molecular events that drove the evolution of endosymbionts into contemporary organelles. In losing their autonomy, endosymbionts lost the bulk of their genomes, necessitating the evolution of elaborate mechanisms for organelle biogenesis and metabolite exchange. In the process, symbionts acquired many host-derived properties, lost much of their eubacterial identity, and were transformed into extraordinarily diverse organelles that reveal complex histories that we are only beginning to decipher.
Photosynthesis mimics as molecular electronic devices (1994)

As illustrated in this brief survey, the field of artificial photosynthesis has developed to the point where molecular scale photovoltaics giving high quantum yields of long-lived, energetic charge separated states can be designed using the principles governing natural photosynthesis, and then synthesized and studied. In contrast to the large progress in this area, the study of how to incorporate such devices into electrical circuits is still in its infancy. Finally, these same principles may be employed in the design of relatively sophisticated optoelectronic switches and logic elements. Although only a few prototypes have as yet been reported. The field is ripe for further development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rescue of synthetic analogs of respiratory syncytial virus genomic RNA and effect of truncations and mutations on the expression of a foreign reporter gene. (1991)

The viral genomic RNA (vRNA) of human respiratory syncytial virus is a nonsegmented negative strand that is not infectious alone. To develop methods for complementing synthetic vRNA with viral proteins, a cDNA was constructed to encode a vRNA in which all of the viral protein-coding sequences were removed and replaced with a negative-sense copy of the bacterial chloramphenicol acetyltransferase gene. Upon transfection into respiratory syncytial virus-infected cells, the synthetic vRNA was "rescued" such that it was amplified, expressed, and packaged into infectious virions. A heterologous paramyxovirus, parainfluenza virus 3, was inactive in rescue. Further internal deletions mapped the cis-acting viral sequences required for rescue to two segments totaling 105 nucleotides (nt) derived from the two vRNA ends. Rescue was unaffected by replacement of the 44-nt 3'-terminal leader region with a 50-nt sequence that is complementary to the 5' terminus and represents the 3' end of the positive-sense replicative intermediate RNA. This 5'-end complement was related to the parental leader region only near the 3' terminus (91% or 73% identical for the first 11 or 22 nt, respectively). The addition of 11 heterologous nt to the 3' end of the parental leader region ablated rescue, suggesting that the 3'-proximal conserved domain is required and cannot function from an internal site. However, deletion of the 3'-terminal 3 nt, or a double transition at positions 4 and 5, had no effect on rescue. Thus, the 3'-terminal 5 nt, although conserved between 3' ends of the negative- and positive-sense RNAs, do not appear to be essential.
Integrating Jit and 5-S Concepts for Construction Site Management: A Case Study (2003)

Both the Just-In-Time (JIT) philosophy and the 5-S concepts have been successfully implemented in the manufacturing industry to boost productivity and quality. However, construction practitioners have yet to appreciate and reap the benefits of the JIT and 5-S. This paper seeks to apply the JIT and 5-S concepts into the construction setting by identifying the similarities between them and subsequently integrating them by incorporating the 5-S concepts to operationalise the JIT philosophy. By introducing 5-S activities in the work site, the JIT system can be achieved without expending additional resources. By means of a case study, this paper shows how efficient site management can be achieved by further integrating the JIT and 5-S concepts to improve productivity and quality.
Malaria Control with Genetically Manipulated Insect Vectors (2002)

At a recent workshop, experts discussed the benefits, risks, and research priorities associated with using genetically manipulated insects in the control of vector-borne diseases.
Differential regulation of two sets of mesonephric tubules by WT-1 (1997)

Mammalian renal development undergoes two transient stages, the pronephros and the mesonephros. While the regulation of metanephric differentiation has received considerable attention, very little is known about the mode of differentiation of the mesonephros and its regulation. We have followed mesonephric differentiation to unravel the developmental mechanisms and fates of mesonephric tubules by whole-mount immunohistology using antibodies to laminin, brush border epitopes, cytokeratin-8/18, p75 neurotrophin receptor and some other renal antigens as markers. In rat and mouse embryos, two distinct sets of tubules were observed throughout mesonephric development. Four to six pairs of cranial mesonephric tubules developed as outgrowths from the Wolffian duct. The majority of tubules were caudal tubules which never fused with the Wolffian and differentiated similarly to metanephric nephrons. The murine mesonephric tubules degenerate by apoptosis, except in males where the cranial tubules become the epididymal ducts. These developmental differences between the cranial and caudal sets of tubules suggested different regulatory systems for each. Targeted disruption of the Wilms' tumour gene product, WT-1, results in renal aplasia, and a reduction in the number of mesonephric tubules (Kreidberg, J. A., Sariola, H., Loring, J., Maeda, M., Pelletier, J., Housman, D. and Jaenisch, R. (1993). Cell 74, 679-691). We therefore analysed more closely mesonephric differentiation in WT-1-deficient mice, and showed that they only develop the cranial mesonephric tubules but not the caudal ones. Thus, WT-1 appears to regulate only the development of the caudal mesonephric tubules that conceivably are formed from mesenchymal cells like the metanephric tubules. WT-1 therefore seems to be necessary for the mesenchyme to epithelium transitions at different stages of nephrogenesis.
InterStim Therapy: A Contemporary Approach to Overactive Bladder. (2009)

Overactive bladder is a common and challenging condition for the practicing obstetrician-gynecologist. The prevalence of the condition is increasing with our aging population. Although some patients respond to first-line therapy, a significant number will require sacral nerve stimulation to address the underlying neurologic condition that causes overactive bladder as well as other pelvic floor conditions. This article summarizes the epidemiology and symptomatology, office evaluation, and treatment of overactive bladder with particular emphasis on sacral nerve stimulation (SNS). SNS technique, results, and future applications are also reviewed.
The evolving treatment paradigm in myelofibrosis (2012)

Myelofibrosis (MF) is a BCR-ABL1-negative myeloproliferative neoplasm diagnosed de novo or developed from essential thrombocythemia (ET) or polycythemia vera (PV). Average survival of a patient with MF is 5-7 years. Disease complications include fatigue, early satiety, pruritus, painful splenic infarcts, infections and leukemic transformation. Allogeneic hematopoietic stem cell transplant (HSCT) is the only potentially curative option for MF, but carries a risk of treatment-related mortality and is reserved for the few high-risk patients fit enough to endure the procedure. Other traditional therapies are palliative and supported by few randomized, controlled trials; thus, novel treatment strategies are needed. Discovery of the Janus kinase 2 (JAK2) gain-of-function mutation, JAK2V617F, in the majority (50-60%) of patients with MF led to increased understanding of the biology underlying MF and the development of JAK2 inhibitors to treat MF. Recent Food and Drug Administration (FDA) approval of the first JAK2 inhibitor, ruxolitinib, signaled a new era for treatment of MF. Additional JAK2 inhibitors, such as SAR302503, may become commercially available in the near future, and their distinct pharmacologic and efficacy profiles will help determine their use across the patient population. Data on JAK2 inhibitors, their role in an evolving treatment paradigm, and future directions for treatment of MF are discussed.
Ketamine for chronic pain: risks and benefits (2013)

The anaesthetic ketamine is used to treat various chronic pain syndromes, especially those that have a neuropathic component. Low dose ketamine produces strong analgesia in neuropathic pain states, presumably by inhibition of the N-methyl-D-aspartate receptor although other mechanisms are possibly involved, including enhancement of descending inhibition and anti-inflammatory effects at central sites. Current data on short term infusions indicate that ketamine produces potent analgesia during administration only, while three studies on the effect of prolonged infusion (4-14 days) show long-term analgesic effects up to 3 months following infusion. The side effects of ketamine noted in clinical studies include psychedelic symptoms (hallucinations, memory defects, panic attacks), nausea/vomiting, somnolence, cardiovascular stimulation and, in a minority of patients, hepatoxicity. The recreational use of ketamine is increasing and comes with a variety of additional risks ranging from bladder and renal complications to persistent psychotypical behaviour and memory defects. Blind extrapolation of these risks to clinical patients is difficult because of the variable, high and recurrent exposure to the drug in ketamine abusers and the high frequency of abuse of other illicit substances in this population. In clinical settings, ketamine is well tolerated, especially when benzodiazepines are used to tame the psychotropic side effects. Irrespective, close monitoring of patients receiving ketamine is mandatory, particularly aimed at CNS, haemodynamic, renal and hepatic symptoms as well as abuse. Further research is required to assess whether the benefits outweigh the risks and costs. Until definite proof is obtained ketamine administration should be restricted to patients with therapy-resistant severe neuropathic pain.
Pterostilbene production by microorganisms expressing resveratrol O-methyltransferase (2014)

Pterostilbene (3,5-dimethoxy-4′-hydroxyl-trans-stilbene)—a derivative of resveratrol—is a natural dietary compound and the primary antioxidant component in berries. Pterostilbene has significant advantages over resveratrol in bioavailability, half-life in the body, cellular uptake, oral absorption and metabolic stability. Here, we expressed the resveratrol O-methyltransferase (ROMT) gene (VvROMT) from grape (Vitis vinifera) in Escherichia coli and Saccharomyces cerevisiae and confirmed its specific ability to catalyze the production of pterostilbene from resveratrol. By co-expressing an additional two genes from the resveratrol biosynthetic pathway—4-coumarate CoA-ligase (4CL) and stilbene synthase (STS)—a large amount of pterostilbene was produced, with a trace amount of pinostilbene detected. To understand the molecular basis of the catalytic activity, four key amino acid residues were identified in a 3D-model of VvROMT and mutagenized and assayed for augmented catalytic activity. Our results demonstrate the potential utility of the engineered microorganisms for pterostilbene production and provide protein engineering targets that will hopefully lead to increased activity of the ROMT enzyme.
Antibody-Mediated Targeting of Replication-Competent Retroviral Vectors (2003)

Replication-competent murine leukemia virus (MLV) vectors can be engineered to achieve high efficiency gene transfer to solid tumors in vivo and tumor-restricted replication, however their safety can be further enhanced by redirecting tropism of the virus envelope. We have therefore tested the targeting capability and replicative stability of ecotropic and amphotropic replication-competent retrovirus (RCR) vectors containing two tandem repeats from the immunoglobulin G-binding domain of Staphylococcal protein A inserted into the proline-rich "hinge" region of the envelope, which enables modular use of antibodies of various specificities for vector targeting. The modified envelopes were efficiently expressed and incorporated into virions, were capable of capturing monoclonal anti-HER2 antibodies, and mediated efficient binding of the virus-antibody complex to HER2-positive target cells. While infectivity was markedly reduced by pseudotyping with targeted envelopes alone, coexpression of wild-type envelope rescued efficient cellular entry. Both ecotropic and amphotropic RCR vector/anti-HER2 antibody complexes achieved significant enhancement of transduction on murine target cells overexpressing HER2, which could be competed by preincubation with excess free antibodies. Interestingly, HER2-expressing human breast cancer cells did not show enhancement of transduction despite efficient antibody-mediated cell surface binding, suggesting that target cell-specific parameters markedly affect the efficiency of post-binding entry processes. Serial replication of targeted vectors resulted in selection of Z domain deletion variants, but reduction of the overall size of the vector genome enhanced its stability. Application of antibody-mediated targeting to the initial localization of replication-competent virus vectors to tumor sites will thus require optimized target selection and vector design.
Regulation of Neurogenesis in Adult Mouse Hippocampus by cAMP and the cAMP Response Element-Binding Protein (2002)

The cAMP cascade, including the cAMP response element-binding protein (CREB), is known to play an important role in neuronal survival and plasticity. Here the influence of this cascade on neurogenesis in adult hippocampus was determined. Activation of the cAMP cascade by administration of rolipram, an inhibitor of cAMP breakdown, increased the proliferation of newborn cells in adult mouse hippocampus. In addition, rolipram induction of cell proliferation resulted in mature granule cells that express neuronal-specific markers. Increased cell proliferation is accompanied by activation of CREB phosphorylation in dentate gyrus granule cells, suggesting a role for this transcription factor. This possibility is supported by studies demonstrating that cell proliferation is decreased in conditional transgenic mice that express a dominant negative mutant of CREB in hippocampus. The results suggest that the cAMP-CREB cascade could contribute to the actions of neurotransmitters and neurotrophic factors on adult neurogenesis.
Randomized trial of the anti-FGF23 antibody KRN23 in X-linked hypophosphatemia (2014)

KRN23 increased TmP/GFR, serum Pi, and serum 1,25(OH)2D. The positive effect of KR23 on serum Pi and its favorable safety profile suggest utility for KRN23 in XLH patients. Trial registration. Clinicaltrials.gov NCT00830674. Funding. Kyowa Hakko Kirin Pharma, Inc.
Export of protein in Escherichia coli: a novel mutation in ompC affects expression of other major outer membrane proteins (1987)

A mutation within the ompC structural gene of Escherichia coli K-12 which affects expression of outer membrane proteins was characterized. The mutation consisted of a 6-base-pair deletion near the 3' end of the gene which removed the amino acids Val-300 and Gly-301 of the mature coding sequence but otherwise left the reading frame intact. The deletion occurred within a region highly conserved among the porins. No protein product was detected from a single copy of the mutant gene. The mutation caused a trans-dominant decrease in the expression of a wild-type ompC allele. The mutation caused a similar decrease in the amounts of OmpA, OmpF, LamB, and Lc proteins, yet it did not appear to affect the minor outer membrane proteins. It had no significant effect on transcription from either ompF or ompC promoters as measured with lacZ operon fusions. The effects of the mutation on other proteins were completely eliminated when the signal sequence was disrupted so that the mutant protein no longer interacted with the secretion machinery of the cell but instead accumulated as precursor in the cytoplasm. A model is proposed involving the translocation of proteins to the outer membrane and the importance of protein conformation in this process.
The University of Manitoba Microwave Imaging Repository: A Two-Dimensional Microwave Scattering Database for Testing Inversion and Calibration Algorithms [Measurements Corner] (2011)

We present a repository of multi-static, near-field microwave scattering measurements. The data are presented both raw (uncalibrated), and calibrated with a scattered-field calibration. Measurements were taken with 24 co-resident Vivaldi antennas in a single plane, inside an air-filled microwave tomography system. The antennas were linearly polarized in the vertical direction, and we intended for the two-dimensional transverse magnetic (scalar) approximation to apply. Data are presented for seven targets, both metallic and dielectric, with varying geometrical complexity. Data from simple geometric targets, useful for calibration using analytic equations, are given. The repository is available from the Web site: http://www.ece.umanitoba.ca/lovetri/EMILab/index.html.
Antimitotic Antifungal Compound Benomyl Inhibits Brain Microtubule Polymerization and Dynamics and Cancer Cell Proliferation at Mitosis, by Binding to a Novel Site in Tubulin (2004)

The antifungal agent benomyl [methyl-1-(butylcarbamoyl)-2-benzimidazolecarbamate] is used throughout the world against a wide range of agricultural fungal diseases. In this paper, we investigated the interaction of benomyl with mammalian brain tubulin and microtubules. Using the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid, benomyl was found to bind to brain tubulin with a dissociation constant of 11.9 +/- 1.2 microM. Further, benomyl bound to at a novel site, distinct from the well-characterized colchicine and vinblastine binding sites. Benomyl altered the far-UV circular dichroism spectrum of tubulin and reduced the accessibility of its cysteine residues to modification by 5,5'-dithiobis-2-nitrobenzoic acid, indicating that benomyl binding to tubulin induces a conformational change in the tubulin. Benomyl inhibited the polymerization of brain tubulin into microtubules, with 50% inhibition occurring at a concentration of 70-75 microM. Furthermore, it strongly suppressed the dynamic instability behavior of individual brain microtubules in vitro as determined by video microscopy. It reduced the growing and shortening rates of the microtubules but did not alter the catastrophe or rescue frequencies. The unexpected potency of benomyl against mammalian microtubule polymerization and dynamics prompted us to investigate the effects of benomyl on HeLa cell proliferation and mitosis. Benomyl inhibited proliferation of the cells with an IC(50) of 5 microM, and it blocked mitotic spindle function by perturbing microtubule and chromosome organization. The greater than expected actions of benomyl on mammalian microtubules and mitosis together with its relatively low toxicity suggest that it might be useful as an adjuvant in cancer chemotherapy.
Conjugates of Double-Stranded Oligonucleotides with Poly(ethylene glycol) and Keyhole Limpet Hemocyanin: A Model for Treating Systemic Lupus Erythematosus (1994)

Two types of oligonucleotides were synthesized with linker groups attached at the 5'-end. Both were repeating dimers of deoxyribocytidine and deoxyriboadenosine. A 20-mer was prepared with a thiol-containing linker, masked as a disulfide, and a 50-mer was prepared with a vicinal diol-containing linker. A tetraiodoacetylated poly(ethylene glycol) (PEG) derivative was synthesized and reacted with the thiol-containing 20-mer to provide an oligonucleotide PEG conjugate of precisely four oligonucleotides on each PEG carrier. The vicinal diol on the 50-mer was oxidized to an aldehyde and conjugated to keyhole limpet hemocyanin (KLH) to provide an oligonucleotide-KLH conjugate by reductive alkylation. The conjugates were annealed with complementary (TG)n strands. While the double-stranded oligonucleotide-KLH conjugate is an immunogen, eliciting the synthesis of antibodies against oligonucleotides, the PEG conjugate has the biological property of specifically suppressing (tolerizing) B cells which make antibodies against the immunizing oligonucleotide.
Spore Display Using Bacillus thuringiensis Exosporium Protein InhA (2009)

A new spore display method is presented that enables recombinant proteins to be displayed on the surface of Bacillus spores via fusion with InhA, an exosporium component of Bacillus thuringiensis. The green fluorescent protein and beta-galactosidase as model proteins were fused to the C-terminal region of InhA, respectively. The surface expression of the proteins on the spores was confirmed by flow cytometry, confocal laser scanning microscopy, measurement of the enzyme activity, and an immunogold electron microscopy analysis. InhA-mediated anchoring of foreign proteins in the exosporium of Bacillus spores can provide a new method of microbial display, thereby broadening the potential for novel applications of microbial display.
Rational Drug Design: The Proteinase Inhibitors (1994)

Human immunodeficiency virus (HIV) proteinase is a promising target for the rational development of drugs against the acquired immunodeficiency syndrome (AIDS), since this enzyme is necessary for viral maturation, and its inhibition could lead to cessation of viral replication. Rational drug design combines chemical synthesis of compounds with structure determination methods, including protein crystallography. When the crystal structure of the HIV proteinase was determined, many research laboratories began designing drugs that would be effective inhibitors of the enzyme, and many such inhibitors were produced. Once that work was initiated, refined, and completed in the laboratory, other issues, such as specificity and bioavailability, became important. The clinical utility of such compounds is the final and most important consideration. Analysis of many agents for which structural formulas have been determined, and comparison of such formulas, provide valuable lessons for the continuing work on this enzyme and for future programs of rational drug design.
Coded aperture spectroscopy with denoising through sparsity (2012)

We compare noise and classification metrics for three aperture codes in dispersive spectroscopy. In contrast with previous theory, we show that multiplex codes may be advantageous even in systems dominated by Poisson noise. Furthermore, ill-conditioned codes with a regularized estimation strategy are shown to perform competitively with well-conditioned codes.