gebhart/patrepeval huggingface dataset:
Mutations at the ataxia‐telangiectasia locus and clinical phenotypes of A–T patients (2000)

Mutations at the ataxia-telangiectasia (A-T) locus on chromosome band 11q22 cause a distinctive autosomal recessive syndrome in homozygotes and predispose heterozygotes to cancer, ischemic heart disease, and early mortality. PCR amplification from genomic DNA and automated sequencing of the entire coding region (66 exons) and splice junctions detected 77 mutations (85%) in 90 A-T chromosomes. Heteroduplex analysis detected another 42 mutations at the A-T locus. Out of a total of 71 unique mutations, 50 were found only in a single family, and 51 had not been reported previously. Most (58/71, 82%) mutations were frameshift and nonsense mutations that are predicted to cause truncation of the A-T protein; the less common mutation types were missense (9/71, 13%), splicing (3/71, 4%) and one in-frame deletion, 2546 3 (1/71, 1%). The mean survival and height distribution of 134 A-T patients correlated significantly with the specific mutations present in the patients. Patients homozygous for a single truncating mutation, typically near the N-terminal end of the gene, or heterozygous for the in-frame deletion 2546 3, were shorter and had significantly shorter survival than those heterozygous for a splice site or missense mutation, or heterozygous for two truncating mutations. Alterations of the length or amino acid composition of the A-T gene product affect the A-T clinical phenotype in different ways. Mutation analysis at the A-T locus may help estimate the prognosis of A-T patients.
Vitamin B1 Functions as an Activator of Plant Disease Resistance (2005)

Vitamin B(1) (thiamine) is an essential nutrient for humans. Vitamin B(1) deficiency causes beriberi, which disturbs the central nervous and circulatory systems. In countries in which rice (Oryza sativa) is a major food, thiamine deficiency is prevalent because polishing of rice removes most of the thiamine in the grain. We demonstrate here that thiamine, in addition to its nutritional value, induces systemic acquired resistance (SAR) in plants. Thiamine-treated rice, Arabidopsis (Arabidopsis thaliana), and vegetable crop plants showed resistance to fungal, bacterial, and viral infections. Thiamine treatment induces the transient expression of pathogenesis-related (PR) genes in rice and other plants. In addition, thiamine treatment potentiates stronger and more rapid PR gene expression and the up-regulation of protein kinase C activity. The effects of thiamine on disease resistance and defense-related gene expression mobilize systemically throughout the plant and last for more than 15 d after treatment. Treatment of Arabidopsis ecotype Columbia-0 plants with thiamine resulted in the activation of PR-1 but not PDF1.2. Furthermore, thiamine prevented bacterial infection in Arabidopsis mutants insensitive to jasmonic acid or ethylene but not in mutants impaired in the SAR transduction pathway. These results clearly demonstrate that thiamine induces SAR in plants through the salicylic acid and Ca(2+)-related signaling pathways. The findings provide a novel paradigm for developing alternative strategies for the control of plant diseases.
A DNA-Based Archival Storage System (2016)

Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm3 (109 GB/mm3), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.
Dose-dependent stimulation of bone induction by basic fibroblast growth factor in rats (1991)

Implantation of demineralized bone matrix in rodents elicits a series of cellular events leading to the formation of new bone inside and adjacent to the implant. This process is believed to be initiated by an inductive protein present in bone matrix, and local growth factors may further regulate the process. We have previously shown that local application of recombinant human basic fibroblast growth factor (bFGF) in a carboxymethyl cellulose gel to demineralized bone matrix implants increases the bone yield as measured by calcium content 3 weeks after implantation in rats. We now report that this increase was seen at 3 and 4 weeks, but not earlier or later. Further, the stimulatory effect was seen with doses from 3 to 75 ng per implant. A dose of 0.6 or 380 ng did not increase the bone yield, and 1,900 ng had a marked inhibitory effect. This narrow dosage optimum may reflect the complex actions of the growth factor.
Phase Behavior of Solvent Vapor Annealed Thin Films of PS-b-P4VP(PDP) Supramolecules (2008)

The phase behavior and terrace formation of solvent (chloroform) vapor annealed thin films of asymmetric comb-shaped supramolecules consisting of a polystyrene (PS) block and a supramolecular block of poly(4-vinylpyridine) (P4VP) hydrogen bonded with pentadecylphenol (PDP) on silicon oxide (SiO2) were examined. P4VP(PDP) was found to be present at the SiO2 interface as well as the air interface, implying symmetric boundary conditions. Because of the inherent change in composition by swelling in a selective solvent, the morphology of a lamellar film could be changed to cylindrical by swelling at different vapor pressures of chloroform vapor. Swelling at a specific vapor pressure at the phase boundary between lamellar and cylindrical resulted in noncommon terrace formation behavior. The lowest terrace consisted of two wetting layers forming one lamella, the second terrace contained perpendicular lamellae, and the highest terrace consisted of parallel P4VP(PDP) cylinders. The results are presented in a morphology diagram as a function of film thickness and composition.
HLA-A, B and DRB1 allele and haplotype frequencies in volunteer bone marrow donors from the north of Parana State (2011)

There is a need to target and expand bone marrow donor campaigns in the north of Parana State. The data of this study may be used as a reference by the Instituto Nacional de Cancer/Brazilian National Bone Marrow Donor Registry to evaluate the immunogenetic profile of populations in specific regions and in the selection of bone marrow donors.
Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide Derivative Verubecestat (MK-8931)–A β-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor for the Treatment of Alzheimer’s Disease (2016)

Verubecestat 3 (MK-8931), a diaryl amide-substituted 3-imino-1,2,4-thiadiazinane 1,1-dioxide derivative, is a high-affinity β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor currently undergoing Phase 3 clinical evaluation for the treatment of mild to moderate and prodromal Alzheimer's disease. Although not selective over the closely related aspartyl protease BACE2, verubecestat has high selectivity for BACE1 over other key aspartyl proteases, notably cathepsin D, and profoundly lowers CSF and brain Aβ levels in rats and nonhuman primates and CSF Aβ levels in humans. In this annotation, we describe the discovery of 3, including design, validation, and selected SAR around the novel iminothiadiazinane dioxide core as well as aspects of its preclinical and Phase 1 clinical characterization.
Antisense Anticancer Oligonucleotide Therapeutics (2001)

Recent progress made in molecular biology, biotechnology, and genetics, especially in identifying, cloning, sequencing and characterization of normal and pathogenic genes, has led to the development of genetic therapy. Major efforts in the field can be summarized in two general approaches: gene therapy and antisense therapy. The second is to deliver to the target cells antisense molecules that target to mRNA with which they can hybridize and specifically inhibit the expression of pathogenic genes. Antisense oligonucleotides offer the possibility of specific, rational, genetic-based therapeutics. With encouraging results from preclinical and clinical studies of antisense oligonucleotides in the past decade, significant progress has been made in developing antisense therapy, with the first antisense drug now being approved for clinical use. In this article, we will discuss approaches to developing these drugs from preclinical to clinical settings. Of particular interest for the area of human cancer therapy, several cancer targets, including bcl-2, BCR-ABL, C-raf-1, Ha-ras, c-myc, PKC, PKA, p53 and MDM2, are reviewed as examples to illustrate the progress in this field and emphasize the importance of target selection and advanced antisense chemistry in the development of antisense therapy.
Single Gene Mutations in Tomato Plants Regenerated from Tissue Culture (1983)

Plants were regenerated from cultured leaf explants of an inbred variety of Lycopersicon esculentum. Seeds were collected from the regenerated plants and sown in the greenhouse. The resultant plants were then evaluated in the field. Several monogenic mutations segregated in the progeny of regenerated plants. The recovery of single gene mutations is evidence that plant tissue culture can be mutagenic. Complementation tests revealed that one mutation was located on the long arm of chromosome 10.
State-of-the-art in privacy preserving data mining (2004)

We provide here an overview of the new and rapidly emerging research area of privacy preserving data mining. We also propose a classification hierarchy that sets the basis for analyzing the work which has been performed in this context. A detailed review of the work accomplished in this area is also given, along with the coordinates of each work to the classification hierarchy. A brief evaluation is performed, and some initial conclusions are made.
Ex vivo expansion with stem cell factor and interleukin-11 augments both short-term recovery posttransplant and the ability to serially transplant marrow (1996)

The characterization of many cytokines involved in the control of hematopoiesis has led to intense investigation into their potential use in ex vivo culture to expand progenitor numbers. We have established the optimum ex vivo culture conditions that allow substantial amplification of transient engrafting murine stem cells and which, simultaneously, augment the ability to sustain serial bone marrow transplantation (BMT). Short-term incubation of unfractionated BM cells in liquid culture with stem cell factor (SCF) and interleukin-11 (IL-11) produced a 50-fold amplification of clonogenic multipotential progenitors (CFU-A). Following such ex vivo expansion, substantially fewer cells were required to rescue lethally irradiated mice. When transplanted in cell doses above threshold for engraftment, BM cells expanded ex vivo resulted in significantly more rapid hematopoietic recovery. In a serial transplantation model, unmanipulated BM was only able to consistently sustain secondary BMT recipients, but BM expanded ex vivo has sustained quaternary BMT recipients that remain alive and well more than 140 days after 4th degree BMT. These results show augmentation of both short-term recovery posttransplant and the ability to serially transplant marrow by preincubation in culture with SCF and IL-11.
Polyoxin D inhibits growth of zoopathogenic fungi (1983)

We demonstrated that polyoxin D at millimolar concentrations caused marked morphological alterations of the human pathogens Candida albicans and Cryptococcus neoformans. C. albicans incubated in the presence of this drug grew in long chains that were severely swollen. Polyoxin D inhibited the growth of C. neoformans and killed cells of both the yeast and the hyphal phase of C. albicans. These observations give the first evidence that polyoxin antibiotics can kill zoopathogenic fungi.
Extensive and Intimate Association of the Cytoskeleton with Forming Silica in Diatoms: Control over Patterning on the Meso- and Micro-Scale (2010)

These results reveal the importance of top down control over positioning of and within the SDV during diatom wall formation and open a new perspective for the study of the mechanism of frustule patterning as well as for the understanding of the control of membrane dynamics by the cytoskeleton.
Design and optimization on dynamic power system for self-powered integrated wireless sensing nodes (2005)

This paper presents an integrated power system for low-power wireless sensor networks with dynamic efficiency optimization technique. By adaptively resizing power transistors and adjusting switching frequency, system efficiency is enhanced significantly. Theoretical analysis is elaborated to support the proposed technique. A prototype integrated power system for self-powered photovoltaic wireless sensing node was designed and simulated with TSMC 0.35μm CMOS process. With a power range of 0.5μW to 10mW, power efficiency stays above 71%. Tolerance between theoretical and simulated optimal power transistor sizes is less than 6.7%, while that of optimal switching frequencies is less than 5%. The paper gives another solution to minimizing system power in the perspective of power processing
An Overview of Neuropathic Pain: Syndromes, Symptoms, Signs, and Several Mechanisms (2002)

Precise estimates of the prevalence of neuropathic pain are not available, but chronic neuropathic pain may be much more common than has generally been appreciated and its prevalence can be expected to increase in the future. There is considerable agreement that both peripheral and central processes contribute to many chronic neuropathic pain syndromes, and that these different mechanisms may explain the qualitatively different symptoms and signs that patients experience. The limitations of existing treatments for neuropathic pain and the inability to provide relief for many patients has stimulated ongoing studies that examine different approaches to preventing neuropathic pain.
Cross-linking of glycoprotein oligomers during herpes simplex virus type 1 entry (1996)

Herpes simplex virus (HSV) has 10 glycoproteins in its envelope. Glycoprotein B (gB), gC, gD, gH, and gL have been implicated in virus entry. We previously used chemical cross-linking to show that these five glycoproteins were close enough to each other to be cross-linked into homodimeric and hetero-oligomeric forms; hetero-oligomers of gB-gC, gC-gD, gD-gB, gH-gL, gC-gL and gD-gL were found in purified virions. To better understand the roles of these glycoproteins in viral entry, we have modified a standard HSV penetration assay to include cross-linkers. This allowed us to examine changes in associations of viral glycoproteins during the entry process. HSV-1(KOS) was adsorbed at 4 degrees C to human neuroblastoma cells (SY5Y). The temperature was raised to 37 degrees C and cells were treated with cross-linker at various times after the temperature shift. Cytoplasmic extracts were examined by Western blotting (immunoblotting) for viral glycoproteins. We found that (i) as in virus alone, the length and concentration of the cross-linking agent affected the number of specific complexes isolated; (ii) the same glycoprotein patterns found in purified virions were also present after attachment of virions to cells; and (iii) the ability to cross-link HSV glycoproteins changed as virus penetration proceeded, e.g., gB and gD complexes which were present during attachment disappeared with increasing time, and their disappearance paralleled the kinetics of penetration. However, this phenomenon appeared to be selective since it was not observed with gC oligomers. In addition, we examined the cross-linking patterns of gB and gD in null viruses K082 and KOSgD beta. Neither of these mutants, which attach but cannot penetrate, showed changes in glycoprotein cross-linking over time. We speculate that these changes are due to conformational changes which preclude cross-linking or spatial alterations which dissociate the glycoprotein interactions during the penetration events.
Solar Hot Water (2011)

[EDG Note no.68 is now superseded. See EDG Note no.83 (Dec 2015) for current information.] Solar Water Heating is increasingly the preferred water heating option for new homes and retrofits. Whether mandated by government or specified by clients, solar hot water is something that every designer needs to consider. However with so many system types and variations, choosing the right system for your project can be a challenge. This note will help you to select the right system for your design.
A Prospective, Blinded, Randomized, Controlled Clinical Trial of Topical Negative Pressure Use in Skin Grafting (2004)

Topical negative pressure has been demonstrated to improve graft take in a number of noncomparative studies. This study aimed to assess whether split-thickness skin graft take is improved qualitatively or quantitatively with topical negative pressure therapy compared with standard bolster dressings. A blinded, prospective, randomized trial was conducted of 22 adult inpatients of Liverpool Hospital between July of 2001 and July of 2002 who had wounds requiring skin grafting. After grafting, each wound half was randomized to receive either a standard bolster dressing or a topical negative pressure dressing. Skin graft assessment was performed at 2 weeks by a single observer blinded to the randomization. Two patients were lost to follow-up and were excluded from the study. There were 20 patients (12 men and eightwomen) in the study group. The median patient age was 64 years (range, 27 to 88 years), and the mean wound size was 128 cm2 (range, 35 to 450 cm2). The wound exposed subcutaneous fat in eight patients, muscle in six patients, paratenon in four patients, and deep fascia in two patients. At 2 weeks, wounds that received a topical negative pressure dressing had a greater degree of epithelialization in six cases (30 percent), the same degree of epithelialization in nine cases (45 percent), and less epithelialization in five cases (25 percent) compared with their respective control wounds. Graft quality following topical negative pressure therapy was subjectively determined to be better in 10 cases (50 percent), equivalent in seven cases (35 percent), and worse in three cases (15 percent). Although the quantitative graft take was not significant, the qualitative graft take was found to be significantly better with the use of topical negative pressure therapy (p < 0.05). Topical negative pressure significantly improved the qualitative appearance of split-thickness skin grafts as compared with standard bolster dressings.
Unexpectedly high occurrence of catalytic antibodies in MRL/lpr and SJL mice immunized with a transition-state analog: is there a linkage to autoimmunity? (1995)

Upon testing the ability of several strains of mice to elicit esterolytic antibodies after immunization with a p-nitrobenzyl phosphonate hapten, we have found that the occurrence of catalytic antibodies in SJL and MRL/lpr autoimmune mice is dramatically higher than in normal mouse strains (e.g., the wild-type MRL/++ or BALB/c). Fewer than 10 catalytic clones are usually obtained from a single fusion of lymphocytes taken from normal mice, whereas several hundred catalytic clones are obtained in SJL or MRL/lpr mice. Differences in the numbers of hapten-binding clones do not account for the high occurrences of catalytic clones in these strains. This phenomenon prevailed in the early responses; in both SJL and MRL/lpr mice a significant decline in the appearance of catalytic clones was observed after multiple immunizations. Esterolytic antibodies were not found in MRL/lpr mice immunized with haptens that do not mimic the transition state for the hydrolysis of the ester substrate (e.g., with a substrate analog). The catalytic antibodies manifest high specificity to the antigen and variability in their binding and catalytic properties. The use of autoimmunity-prone mice may greatly expand the repertoire of catalytic clones elicited against a transition-state analog hapten. More intriguing is the possible linkage between autoimmunity and the appearance of catalytic antibodies. These results suggest that there is normally a selection against the expression of certain variable genes encoding antibodies with catalytic activity.
Efficient Transduction of Mammalian Cells by a Recombinant Baculovirus Having the Vesicular Stomatitis Virus G Glycoprotein (1997)

Baculovirus vectors recently have been shown to be capable of efficient transduction of human hepatoma cells and primary hepatocytes in culture. This paper describes the generation of a novel recombinant baculovirus (VGZ3) in which the vesicular stomatitis virus glycoprotein G (VSV G) is present in the viral envelope. The gene encoding VSV G was inserted into the baculovirus genome under the control of the polyhedrin promoter such that it was expressed at very high levels in infected insect cells but not in mammalian cells. Expression of the lacZ reporter gene was driven by a promoter that is functional in mammalian cells (the Rous sarcoma virus long terminal repeat). We show by Western analysis that VSV G protein was present in purified baculovirus preparations. A VSV G monoclonal antibody blocked transduction of mammalian cells by VGZ3. This virus was morphologically distinct from baculovirus lacking VSV G, with virions adopting an oval rather than rod-shaped morphology. VGZ3 transduced human hepatoma cells in vitro at an efficiency roughly 10-fold greater than baculovirus lacking VSV G (the virus Z4). VGZ3 was also capable of transducing cell lines that could not be transduced efficiently by Z4. We provide evidence that VSV G protein may enhance transduction by increasing the efficiency of escape of baculovirus from intracellular vesicles rather than by increasing cell binding or uptake of the virus. The possible use of this and related baculoviruses in gene therapy is discussed.
Automatic code generation for heterogeneous multiprocessors (2002)

This paper describes the use of Ptolemy to automatically generate code for heterogeneous multiprocessor systems. The framework presented lets the designer migrate from simulation to code generation while developing an application that is specified by constructing a dataflow graph. From primitive send and receive actors, the framework can automatically construct three classes of interprocessor communication (IPC) interfaces. The first type of interface uses a synchronous dataflow (SDF) parallel scheduler to partition and schedule the graph across the available processors. The second type of interface allows hierarchical use of cooperating schedulers within an application. Finally, the third interface uses the send and receive actors as an interface between code generation and simulation systems in Ptolemy. To illustrate the framework, we present an example of a heterogeneous architecture consisting of a workstation with multiple Motorola 56001 processors. We present the relative strengths and weaknesses of each type of interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>