gebhart/patrepeval huggingface dataset:
Characterization of 26 MiniSTR Loci for Improved Analysis of Degraded DNA Samples (2007)

An additional 20 novel mini-short tandem repeat (miniSTR) loci have been developed and characterized beyond the six previously developed by our laboratory for a total of 26 non-CODIS miniSTR markers. These new markers produce short PCR products in the target range of 50-150 base pairs (bp) by moving the primer sequences as close as possible-often directly next to the identified repeat region. These candidate loci were initially screened based on their small amplicon sizes and locations on chromosomes currently unoccupied by the 13 CODIS STR loci or at least 50 Mb away from them on the same chromosome. They were sequenced and evaluated across more than 600 samples, and their population statistics were determined. The heterozygosities of the new loci were compared with those of the 13 CODIS loci and all were found to be comparable. Only five of the new loci had lower values than the CODIS loci; however, all of these were much smaller in size. This data suggests that these 26 miniSTR loci will serve as useful complements to the CODIS loci to aid in the forensic analysis of degraded DNA, as well as missing persons work and parentage testing with limited next-of-kin reference samples.
Rapid purification of grapevine RNA by a simple electrophoretic method (2015)

Research Note
Specific Glycoforms of MUC5AC and Endorepellin Accurately Distinguish Mucinous from Nonmucinous Pancreatic Cysts (2013)

Specific protein glycoforms may be uniquely informative about the pathological state of a cyst and may serve as accurate biomarkers. Here we tested that hypothesis using antibody-lectin sandwich arrays in broad screens of protein glycoforms and in targeted studies of candidate markers. We profiled 16 different glycoforms of proteins captured by 72 different antibodies in cyst fluid from mucinous and nonmucinous cysts (n = 22), and we then tested a three-marker panel in 22 addition samples and 22 blinded samples. Glycan alterations were not widespread among the proteins and were mainly confined to MUC5AC and endorepellin. Specific glycoforms of these proteins, defined by reactivity with wheat germ agglutinin and a blood group H antibody, were significantly elevated in mucinous cysts, whereas the core protein levels were not significantly elevated. A three-marker panel based on these glycoforms distinguished mucinous from nonmucinous cysts with 93% accuracy (89% sensitivity, 100% specificity) in a prevalidation sample set (n = 44) and with 91% accuracy (87% sensitivity, 100% specificity) in independent, blinded samples (n = 22). Targeted lectin measurements and mass spectrometry analyses indicated that the higher wheat germ agglutinin and blood group H reactivity was due to oligosaccharides terminating in GlcNAc or N-acetyl-lactosamine with occasional α1,2-linked fucose. The results show that MUC5AC and endorepellin glycoforms may be highly specific and sensitive biomarkers for the differentiation of mucinous from nonmucinous pancreatic cysts.
ChemInform Abstract: TOUGHENING BEHAVIOR IN SILICON CARBIDE‐WHISKER‐REINFORCED ALUMINA (1985)

Abstract Feinkörnige AlzOyMatrices werden durch Pressen einer Mischung von M203′PUIVCI′ und 20 Vol‐% SiC‐Whiskerkristallen bei 185Q°Cerhalten.
Fracture toughness is dependent on bone location—A study of the femoral neck, femoral shaft, and the tibial shaft (2000)

The fracture toughness of the right femoral neck, femoral shaft, and tibial shaft of matched cadaveric bones, ages 50 to 90 years, was compared. Results of this study indicate that tensile (GIc) and shear (GIIc) fracture toughness vary depending on bone location. The femoral neck has the greatest resistance to crack initiation for both tension and shear loading while the femoral shaft has the least. The relationship between age and the fracture toughness of the femoral neck and shaft was investigated. Gc of the femoral shaft significantly decreased with age for mode I and was nearly significant for mode II. Fracture toughness of the femoral neck did not change with age for the later decades of life. Implications of these findings are discussed. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 49, 380–389, 2000.
FORMULATION AND EVALUATION OF BILAYERED TABLET OF METFORMIN HYDROCHLORIDE AND PIOGLITAZONE HYDROCHLORIDE (2012)

The present work focuses on the formulation of bilayered tablet of Metformin Hydrochloride sustained release (SR) 500 mg and Pioglitazone Hydrochloride immediate release (IR) 15mg. Sustained release matrix layer of Metformin Hydrochloride were formulated using Hydroxyl propyl methyl cellulose (HPMC K100M) and Microcrystalline cellulose (MCC PH-101) in different combinations by wet granulation technique to meet Indian Pharmacopoeia (IP) 2010 specification. Immediate release layer of Pioglitazone Hydrochloride was formulated using sodium starch glycolate (SSG) as superdisintegrant. The formulated tablets were evaluated for thickness, weight variation test, hardness test, friability test and drug content. In vitro dissolution studies were carried out in 6.8 phosphate buffer as described in the IP 2010 monograph. The kinetic modeling of in vitro dissolution profiles revealed diffusion release mechanism. The stability studies revealed no significant changes in physical and chemical properties for the optimized formulation.
Functional Characterization of the Major Late Promoter of Mouse Adenovirus Type 1 (1997)

During the late phase of adenovirus infection, the major late promoter (MLP) controls the regulated expression of the genes that encode most viral structural proteins. Recently, the region of the genome of mouse adenovirus type 1 (MAV-1), predicted to contain the MLP, was sequenced and compared to that of the human virus MLP. The general organization of the transcriptional elements of the putative MAV-1 MLP is similar to that of the human virus counterpart, with some interesting differences. We wished to investigate the function of the predicted MLP of MAV-1 and to determine the significance of the differences found in the MAV-1 MLP. To test the activity of the predicted MLP of MAV-1, both Northern blot and primer extension analyses were performed on intracellular RNA isolated from cells infected with MAV-1. The results show that late RNA can be detected 48 hr postinfection and increases up to 6 days p.i. Primer extension analysis revealed that the major start sites of transcription are 28 and 31 nt downstream of the first T residue of the predicted TATA box. To analyze the functional significance of the predicted transcriptional elements, a transient transfection system, using the firefly luciferase gene controlled by the MAV-1 MLP sequence, was established. The predicted MLP sequence was capable of directing luciferase gene expression, to a level some 60% of that of the human virus MLP. Mutations were created in the inverted CAAT box, the SP1 site, and the TATA box, either singly or in combination. Each single-element mutation causes a marked reduction in luciferase gene expression, with the SP1 mutation showing the greatest effect. Double mutations were even more deficient, suggesting a level of functional redundancy among the various transcriptional elements. Finally, the putative SP1-binding site was examined by gel mobility shift assay and shown to interact with purified SP1 protein specifically, supporting the functional significance of this transcriptional element. These findings contribute to a better understanding of gene expression in MAV-1 and to its development as an appropriate model for the study of the molecular basis of pathogenesis in a natural host animal.
Magnetic resonance and near infrared spectroscopy for investigation of perinatal hypoxic-ischaemic brain injury. (1989)

Hypoxic-ischaemic injury to the brain is an important cause of perinatal death and seems to be the commonest cause of permanent neurodevelopmental disability in newborn infants who survive after intensive care. If this type of brain injury is to be prevented and treatment put on a rational basis, non-invasive methods are required for defining its mechanisms. This review has considered two such methods: magnetic resonance spectroscopy and near infrared spectroscopy. Magnetic resonance spectroscopy is used to measure, in brain tissue, the concentrations of the 'high energy' phosphorus metabolites that are dependent for their synthesis on the processes of oxidative phosphorylation. Intracellular pH can also be measured. Normal maturational changes in the brain have been defined and abnormalities detected in a range of conditions where hypoxic-ischaemic injury was suspected to have occurred. In laboratory animals the acute effects of curtailment of oxygen supply to the brain ('primary' energy failure) have been observed, and the effects of two commonly used treatments, infusions of sodium bicarbonate and glucose, have been tested. After resuscitation of newborn infants from severe intrapartum asphyxia, a latent period has often been noted before energy failure became detectable. This 'secondary' energy failure is due to a variety of damaging reactions initiated by the acute hypoxicischaemic episode and reperfusion of the brain. It is possible that in the future irreversible injury to brain cells following the episode may be prevented or ameliorated by the prompt use of cerebroprotective agents. The extent of abnormalities detected by magnetic resonance spectroscopy has prognostic implications: evidence of severe energy failure in the first days of life was regularly associated with subsequent death or with severe neurodevelopmental impairments. Many technical developments in magnetic resonance spectroscopy are under way, particularly employing proton (1H) spectroscopy, which will allow the intracerebral concentrations of a wide range of metabolites, including neurotransmitters, to be measured. The combination of spectroscopy with magnetic resonance imaging will permit quantitative data to be obtained from selected volumes within the brain. Near infrared spectroscopy is used to make observations at the cotside of the intracerebral concentrations of the chromophores oxyhaemoglobin, deoxyhaemoglobin, and oxidised cytochrome aa3, and it therefore provides information complementary to that obtained by magnetic resonance spectroscopy. Measurements can also be made of cerebral blood flow, cerebral blood volume, and other haemodynamic indices; in addition, the rea
Poly(<i>N</i>-vinylpyrrolidone) Bearing Covalently Attached Cyclodextrin via Click-Chemistry: Synthesis, Characterization, and Complexation Behavior with Phenolphthalein (2010)

We report about modification of poly(N-vinylpyrrolidone) (PVP) with monofunctional β-cyclodextrin (βCD) via click-chemistry. The modification was carried out by copper(I)-catalyzed microwave-assisted Huisgen-type cycloaddition of 3-propargyl-N-vinylpyrrolidone (2a) and mono(6-azido-6-deoxy)-β-cyclodextrin (3). We synthesized a copolymer (5) carrying CD moieties which has the same composition as the applied molar ratio of monomers. Complexation experiments of the obtained polymer (5) with phenolphthalein (PP) showed a lower binding constant compared to βCD caused by sterical effects of the polymer coil.
Potential benefits of distributed generators to power systems (2011)

With the growing awareness of environmental protection, energy savings, and economic scenarios, distributed generators (DGs) have been playing an increasingly important role in power systems (PSs) all over the world. DGs applications in and potential impacts on PSs have been paid more and more attention in recent years. However, the potential benefits of DGs on PSs have not yet been systematically examined by qualitative and quantitative analysis in most existing literatures. A proper understanding of these is important for the extensive applications of DGs in PSs. Given this background, various benefits of DGs on PSs are presented and analyzed in this work. Benefits of employing DGs are classified and outlined in detail. Moreover, new developments, characteristics, applications, and algorithms associated with DGs in power systems are clarified.
Selective modulation of specific protein kinase C (PKC) isoforms in primary human megakaryocytic vs. erythroid cells (1999)

We have investigated the pattern of expression of classical (alpha, betaI, betaII, gamma), novel (delta) and atypical (zeta) protein kinase C (PKC) isoforms during the course of human hematopoietic differentiation along the closely related megakaryocytic and erythroid lineages. Using in situ immunofluorescence analysis, freshly isolated human pluripotent CD34+ hematopoietic progenitor cells expressed detectable amounts of all the PKC isoforms investigated. On the other hand, clear-cut differences in terms of PKC staining were noticed between cells belonging to the erythroid and megakaryocytic lineages, obtained after 9 days of serum-free liquid culture in the presence of specific growth factors. Specifically, 1) erythroid cells showed a very weak expression of PKC-alpha, -betaI, -betaII, and -gamma, while megakaryocytes showed an enhanced expression of all classical PKC isoforms, predominantly confined to the cytoplasm; 2) the expression of PKC-delta increased in the cytoplasmic and nuclear compartments of both erythroid and megakaryocytic cells with respect to CD34+ cells; and 3) atypical PKC-zeta isoform showed a striking accumulation in the nucleus during both erythroid and megakaryocytic differentiation.
MicroRNA-9 Controls the Expression of Granuphilin/Slp4 and the Secretory Response of Insulin-producing Cells (2006)

Insulin release from pancreatic beta-cells plays an essential role in blood glucose homeostasis. Several proteins controlling insulin exocytosis have been identified, but the factors determining the expression of the components of the secretory machinery of beta-cells remain largely unknown. MicroRNAs are newly discovered small non-coding RNAs acting as repressors of gene expression. We found that overexpression of mir-9 in insulin-secreting cells causes a reduction in exocytosis elicited by glucose or potassium. We show that mir-9 acts by diminishing the expression of the transcription factor Onecut-2 and, in turn, by increasing the level of Granuphilin/Slp4, a Rab GTPase effector associated with beta-cell secretory granules that exerts a negative control on insulin release. Indeed, electrophoretic mobility shift assays, chromatin immunoprecipitation, and transfection experiments demonstrated that Onecut-2 is able to bind to the granuphilin promoter and to repress its transcriptional activity. Moreover, we show that silencing of Onecut-2 by RNA interference increases Granuphilin expression and mimics the effect of mir-9 on stimulus-induced exocytosis. Our data provide evidence that in insulin-producing cells adequate levels of mir-9 are mandatory for maintaining appropriate Granuphilin levels and optimal secretory capacity.
Priming by airborne signals boosts direct and indirect resistance in maize (2006)

Plants counteract attack by herbivorous insects using a variety of inducible defence mechanisms. The production of toxic proteins and metabolites that instantly affect the herbivore's development are examples of direct induced defence. In addition, plants may release mixtures of volatile organic compounds (VOCs) that indirectly protect the plant by attracting natural enemies of the herbivore. Recent studies suggest that these VOCs can also prime nearby plants for enhanced induction of defence upon future insect attack. However, evidence that this defence priming causes reduced vulnerability to insects is sparse. Here we present molecular, chemical and behavioural evidence that VOC-induced priming leads to improved direct and indirect resistance in maize. A differential hybridization screen for inducible genes upon attack by Spodoptera littoralis caterpillars identified 10 defence-related genes that are responsive to wounding, jasmonic acid (JA), or caterpillar regurgitant. Exposure to VOCs from caterpillar-infested plants did not activate these genes directly, but primed a subset of them for earlier and/or stronger induction upon subsequent defence elicitation. This priming for defence-related gene expression correlated with reduced caterpillar feeding and development. Furthermore, exposure to caterpillar-induced VOCs primed for enhanced emissions of aromatic and terpenoid compounds. At the peak of this VOC emission, primed plants were significantly more attractive to parasitic Cotesia marginiventris waSPS. This study shows that VOC-induced priming targets a specific subset of JA-inducible genes, and links these responses at the molecular level to enhanced levels of direct and indirect resistance against insect attack.
A Polymorphism in the <b> <i>CDKN1B</i> </b> Gene Is Associated with Increased Risk of Hereditary Prostate Cancer (2004)

The loss of cell cycle control is believed to be an important mechanism in the promotion of carcinogenesis. CDKN1B (p27) belongs to the Cip/Kip family and functions as an important cell cycle gatekeeper. Several lines of evidence from clinical studies and laboratory experiments demonstrate that CDKN1B is an important tumor suppressor gene in prostate cancer etiology. In addition, a case-control study has shown that the 326T/G (V109G) polymorphism in CDKN1B is associated with advanced prostate cancer. In light of the evidence for linkage between the chromosomal location of the CDKN1B gene (12p13) and prostate cancer susceptibility in several hereditary prostate cancer (HPC) populations, we hypothesized that sequence variants of CDKN1B play a role in HPC. To test this hypothesis, we first resequenced this gene in 96 HPC probands to identify germ-line mutations and sequence variants. We then genotyped the identified sequence variants among all family members of 188 HPC families and tested for their cosegregation with prostate cancer. In total, 10 sequence variants were identified, including three nonsynonymous changes. A family-based test, which is free from the effects of population stratification, revealed a significant association between single nucleotide polymorphism (SNP) -79C/T and prostate cancer (with a nominal P of 0.0005). The C allele of -79C/T was overtransmitted from parents to their affected offspring. Evidence for this association was primarily contributed by affected offspring whose age at diagnosis was <65 years. Together with the previous association study in a sporadic prostate cancer population, our new findings additionally suggest that germ-line variants of this gene play a role in prostate cancer susceptibility.
Advances in Technology—Redefining Large Shared Storage Systems (2007)

With the adoption of high definition (HD) and its commensurate requirement for increased storage capacity and bandwidth, the need for scalability has increased. Because of its deterministic performance and dual-ported redundancy, Fiber Channel is the leading technology for storage connection and storage area network (SAN) development (see Annex 2 SAN Storage Interfaces). By applying the latest advances in Fiber Channel technology, larger, more capable, and more redundant systems can be built to meet this need.
Stem cells are units of natural selection for tissue formation, for germline development, and in cancer development (2015)

It is obvious that natural selection operates at the level of individuals and collections of individuals. Nearly two decades ago we showed that in multi-individual colonies of protochordate colonial tunicates sharing a blood circulation, there exists an exchange of somatic stem cells and germline stem cells, resulting in somatic chimeras and stem cell competitions for gonadal niches. Stem cells are unlike other cells in the body in that they alone self-renew, so that they form clones that are perpetuated for the life of the organism. Stem cell competitions have allowed the emergence of competitive somatic and germline stem cell clones. Highly successful germline stem cells usually outcompete less successful competitors both in the gonads of the genotype partner from which they arise and in the gonads of the natural parabiotic partners. Therefore, natural selection also operates at the level of germline stem cell clones. In the colonial tunicate Botryllus schlosseri the formation of natural parabionts is prevented by a single-locus highly polymorphic histocompatibility gene called Botryllus histocompatibility factor. This limits germline stem cell predation to kin, as the locus has hundreds of alleles. We show that in mice germline stem cells compete for gonad niches, and in mice and humans, blood-forming stem cells also compete for bone marrow niches. We show that the clonal progression from blood-forming stem cells to acute leukemias by successive genetic and epigenetic events in blood stem cells also involves competition and selection between clones and propose that this is a general theme in cancer.
Comparative analysis of global gene expression profiles between diabetic rat wounds treated with vacuum‐assisted closure therapy, moist wound healing or gauze under suction (2008)

How differential gene expression affects wound healing is not well understood. In this study, Zucker diabetic fatty (fa/fa) male inbred rats were used to investigate gene expression during wound healing in an impaired wound-healing model. Whole genome microarray surveys were used to gain insight into the biological pathways and healing processes in acute excisional wounds treated with vacuum-assisted closure (V.A.C.). Therapy, moist wound healing (MWH) or gauze under suction (GUS). Global gene expression analyses after 2 days of healing indicated major differences with respect to both number of genes showing fold changes and pathway regulation between the three different wound treatments. Statistical analysis of expression profiles indicated that 5072 genes showed a >1.6-fold change with V.A.C. Therapy compared with 3601 genes with MWH and 3952 genes with GUS. Pathways and related genes associated with the early phases of wound healing diverged between treatment groups. For example, pathways involving angiogenesis, cytoskeletal regulation and inflammation were associated with elevated gene expression following V.A.C. Therapy. This study is the first to assess wound healing by whole genome interrogation in a diabetic rat model treated with different healing modalities.
Experimental Lyme Disease in Dogs Produces Arthritis and Persistent Infection (1993)

Lyme disease was reproduced in specific pathogen-free beagle dogs by exposure to Borrelia burgdorferi-infected ticks (Ixodes dammini). Seroconversion and disease frequency were higher after exposure to infected adult ticks than to infected nymphs. Young pups developed clinical disease more readily than older dogs. The incubation period lasted 2-5 months. Acute recurrent lameness with fibrinopurulent arthritis was the dominant clinical sign. Dogs recovered but developed persistent mild polyarthritis. B. burgdorferi persisted in recovered dogs for at least 1 year. Isolation of B. burgdorferi and detection by polymerase chain reaction was most successful from skin biopsies at the site of the tick bite. Antibody to B. burgdorferi antigens was first detected by ELISA and Western blots by 4-6 weeks after exposure. High serum levels persisted during 17 months of observation. In contrast to infection from ticks, inoculation of dogs with cultured B. burgdorferi resulted in seroconversion with a shorter duration of antibody persistence and no clinical disease.
<title>Electronic display system for computational holography</title> (1990)

We present an electro-optical apparatus capable of displaying a computer generated hologram (CGH) in real time. The CGH is calculated by a supercomputer, read from a fast frame buffer, and transmitted to a high-bandwidth acousto-optic modulator (AOM). Coherent light is modulated by the AOM and optically processed to produce a three-dimensional image with horizontal parallax.