gebhart/patrepeval huggingface dataset:
Molecular cytogenetics by polymerase catalyzed amplification or in situ labelling of specific nucleic acid sequences (1993)

The Polymerase Chain Reaction (PCR) can be performed on isolated cells or chromosomes and the product can be analyzed by DNA technology or by FISH to test metaphases. The authors have good experiences analyzing aberrant chromosomes by FACS sorting, PCR with degenerated primers and painting of test metaphases with the PCR product. They also utilize polymerases for PRimed IN Situ labelling (PRINS) of specific nucleic acid sequences. In PRINS oligonucleotides are hybridized to their target sequences and labeled nucleotides are incorporated at the site of hybridization with the oligonucleotide as primer. PRINS may eventually allow the study of individual genes, gene expression and even somatic mutations (in mRNA) in single cells.
A “Chiral Aldehyde” Equivalent as a Building Block Towards Biologically Active Targets (2004)

Chiral gamma-aryloxybutenolides, readily accessible through dynamic kinetic asymmetric transformation (DYKAT) of racemic acyloxybutenolides, were utilized as "chiral aldehyde" building blocks for intermolecular cycloadditions and Michael reactions. Unprecedented selectivity in trimethylenemethane cycloadditions with this building block allowed an efficient synthesis of a novel metabotropic glutamate receptor 1 antagonist in development by the Bayer corporation. These studies further inspired work that culminated in the total synthesis of (+)-brefeldin A, a natural product with a range of significant biological properties. All of the stereochemistry in this target molecule was derived from two palladium-catalyzed asymmetric allylic alkylation reactions. The trans-alkenes were synthesized by a Julia olefination and a ruthenium-catalyzed trans-hydrosilylation-protodesilylation protocol. The route to (+)-brefeldin A lends itself to analogue syntheses and was completed in 18 steps in 6 % overall yield.
Intramammary Response to Modified Intramammary Devices (1992)

Twenty-five cows in three experiments were used to evaluate the following intramammary devices: abraded surfaces; abraded and sulfur hexafluoride-coated; abraded, sulfur hexafluoride-coated, and weighted; and smooth surfaces and weighted. The objectives of the experiments were 1) to determine whether coating the abraded intramammary devices prevented amorphous deposits and bacterial adherence on the devices, 2) to determine whether addition of weight to devices increased the concentration of somatic cells in milk, and 3) to evaluate milk production and response of mammary epithelial cells to the devices. Milk SCC and NAGase (EC 3.2.1.30) from quarters fitted with devices were increased in quarter bucket and stripping milk, but increases were similar among all devices. Macrophages were the predominate cell type in quarter milk before insertion and neutrophils after insertion. Moderate to heavy deposits of amorphous material were observed on all devices, regardless of time residing in the gland. Approximately 50% of the devices were colonized after intramammary inoculation with Corynebacterium bovis. Milk production in control quarters and in quarters with devices were similar. Neither coating with sulfur hexafluoride nor addition of weight to devices reduced amorphous deposits or bacterial adherence or enhanced milk somatic cell response.
Physiological Measurements for Evaluation of Human-Environment System (2006)

We review several physiological measurements for evaluation of human-environment systems, and discuss several relatively simple and useful methods focusing on those for evaluation of the autonomic and central nervous system. The methods used to evaluate the autonomic nervous system include blood pressure, electrodermal activity and electrogastrogram. In order to evaluate the central nervous system, we selected electroencephalogram, event-related potential and evoked potential. We demonstrate the examples of the studies which were conducted to evaluate the light environment, sound environment and mental work by using these parameters.
Subdermal estradiol pellets following hysterectomy and oophorectomy. Effect upon serum estrone, estradiol, luteinizing hormone, follicle-stimulating hormone, corticosteroid binding globulin-binding capacity, testosterone-estradiol binding globulin-binding capacity, lipids, and hot flushes. (1980)

Subderman estradiol (E2) pellets (25 mg) were inserted immediately after hysterectomy and oophorectomy in 22 menstruating women, ages 29 to 50 years. Serum samples were obtained daily for 7 days, weekly for 4 weeks, and at monthly intervals for 6 months. Although there was significant variation between patients, E2 levels remained within the follicular phase range, averaging 50 to 70 pg/ml for 3 months, and then slowly declining to a mean of 37 pg/ml at 6 months, when new pellets were inserted. Over the entire study period, the E2:estrone (E1) ratio was greater than unity. Subdermal E2 pellets limited the rise in luteinzing hormone (LH) and follicle-stimulating hormone (FSH) after gonadectomy and the levels of LH and FSH 6 months after the insertion of E2 pellets were significantly lower (p < 0.01) than in 20 postmenopausal women who had undergone oophorectomy and whose serum E2 levels were less than 20 pg/ml. Serum corticosteroid binding globulin-binding capacity (CBG-BC) and serum testosterone-estradiol binding globulin-binding capacity (TeBG-BC) remained unchanged with E2 pellets. Although high-density lipoprotein-cholesterol increased significantly (p < 0.05), low-density lipoprotein-cholesterol, total cholesterol, and triglycerides were unaffected, except for a rise in triglycerides in three older women with diabetes mellitus and hypertension. There were no complaints of severe hot flushes. Women who had vasomotor symptaoms had mild or moderate flushes that occurred at 5 or 6 months after replacements of the pellets. Thus, E2 pellets are an effective form of parenteral estrogen replacement therapy and offer both practical and theorteical advantages over other forms of estrogen.
Analysis of cell wall carbohydrates (neutral sugars) from ascomycetous and basidiomycetous yeasts with and without derivatization. (1993)

The presence or absence of fucose, galactose, rhamnose, and xylose as well as the ratio of glucose to mannose after hydrolysis of purified yeast cell walls are valuable characters to assign yeasts or yeast states of Ascomycetes and Basidiomycetes phylogenetically. The coupling of pellicular anion-exchange resins (Dionex CarboPac PA-1) with pulsed amperometric detection provides a simple, quick, selective, and sensitive method for the analysis of yeast cell wall carbohydrates. Phragmobasidial smut fungi of monocotyledonous (Ustilago s. str., Sporisorium) and dicotyledonous (Microbotryum, Sphacelotheca) host plants cluster in two different, phylogenetically distinct yeast types, the Microbotryum type and the Ustilago type. In contrast, all smut fungi with simple holobasidia (Entyloma, Melanotaenium) from monocots and dicots investigated so far, exhibit a cell wall carbohydrate spectrum characteristic for the Ustilago type. Ustilentyloma fluitans, although a phragmobasidial smut fungus on grasses, whose smut spores and parasitic symptoms resemble Entyloma species, display the neutral sugar pattern of the Microbotryum type. The close phylogenetic relationship between the Graphiolales, Ustilaginales s. str. (phragmobasidial smuts of monocots), and Exobasidiales was substantiated further by additional strains. The presence of xylose and balanced amounts of glucose and mannose is characteristic for yeast states of the Dacrymycetaceae. The production of extracellular amyloid compounds (EAC) as well as the cell wall carbohydrate pattern point to a Tremella type affinity of Atractogloea stillata, Itersonilia perplexans, and Sterigmatosporidium polvmorphum. A meiosporangial evolution starting from coccal yeast basidia (Sterigmatosporidium) via transversely (auricularioid) septate (Atractogloea) to longitudinally divided phragmobasidia (Tremella) and simple holobasidia (Cystofilobasidium) was substantiated further within the Tremella type. The complex holobasidia (Collybia) of the Homobasidiomycetes evolved polyphyletically from longitudinally septate phragmobasidia via partially divided holobasidia (Carcinoryces). On the basis of the cell wall carbohydrate composition of approximately 250 yeasts and yeast stages of Ascomycetes and Basidiomycetes, seven distinct yeast types are described and interpreted phylogenetically.
Die Aktin und Myosin ähnliche Proteine im Kalbsthymuszellkern (1964)

Journal Article Die Aktin und Myosin ähnliche Proteine im Kalbsthymuszellkern Get access Von TSUYOSHI OHNISHI, Von TSUYOSHI OHNISHI *Aus der Abteilung für Physik, Naturwissenschaftliche Fakultat, Universität Nagoya Search for other works by this author on: Oxford Academic PubMed Google Scholar HIROE KAWAMURA, HIROE KAWAMURA *Aus der Abteilung für Physik, Naturwissenschaftliche Fakultat, Universität Nagoya Search for other works by this author on: Oxford Academic PubMed Google Scholar YOSHIMI TANAKA YOSHIMI TANAKA **und Obermittelschuls Nagakute, Aichi Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 56, Issue 1, July 1964, Pages 6–15, https://doi.org/10.1093/oxfordjournals.jbchem.a127959 Published: 01 July 1964 Article history Received: 30 October 1963 Published: 01 July 1964
Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability (1994)

The energetics of alkane dissolution and partition between water and organic solvent are described in terms of the energy of cavity formation and solute-solvent interaction using scaled particle theory. Thermodynamic arguments are proposed that allow comparison of experimental measurements of the surface area with values calculated from an all-atom representation of the solute. While the surface tension relating to the accessible surface is shape dependent, it is found that for the molecular surface it is not. This model rationalizes the change in surface tension between the microscopic (20-30 cal/mol/A2) and macroscopic (70-75 cal/mol/A2) regimes without the need to invoke Flory-Huggins theory or to apply other corrections. The difference in the values arises (i) to a small extent as a result of the curvature dependence of surface tension and (ii) to a large extent due to the difference in the molecular surface derived from the experiment and that calculated from an extended all-atom model. The model suggests that the primary driving force for alkane association in water is due to the tendency of water to reduce the solute cavity surface. It is argued that to model the energetics of alkane association, the surface tension should be related to the molecular surface (rather than the accessible surface) with a surface tension near the macroscopic limit for water. This model is compared with results from theoretical simulations of the hydrophobic effect for two well-studied systems. The implications for antibody-antigen interactions and the effect of hydrophobic amino acid deletion on protein stability are discussed. The approach can be used to model the solute cavity formation energy in solution as a first step in the continuum modelling of biomolecular interactions.
Classification of Laser Induced Fluorescence spectra from normal and malignant tissues using Learning Vector Quantization neural network in bladder cancer diagnosis (2008)

In the present work we discuss the potential of recently developed classification algorithm, learning vector quantization (LVQ), for the analysis of laser induced fluorescence (LIF) spectra, recorded from normal and malignant bladder tissue samples. The algorithm is prototype based and inherently regularizing, which is desirable, for the LIF spectra because of its high dimensionality and features being settled at widely spaced intervals (sparseness). We discuss the effect of different parameters influencing the performance of LVQ in LIF data classification. Further, we compare and cross validate the classification accuracy of LVQ with other classifiers (eg. SVM and multi layer perception) for the same data set. Good agreement has been obtained between LVQ based classification of spectroscopy data and histopathology results which demonstrate the use of LVQ classifier in bladder cancer diagnosis.
A probabilistic model for detecting coding regions in DNA sequences (1994)

A probabilistic model is presented to predict whether or not an anonymous sequence of DNA contains exons. The method is shown to be at least as reliable as Grail, a well-known neural network solution to the problem, and to be significantly more amenable to customization for specific prediction problems.
Hardness of Al-based quasicrystals evaluated via cluster-plus-glue-atom model (2014)

In this paper, the hardness of ternary Al-based quasicrystals was assessed through an application of the cluster-plus-glue-atom model. In this model, any structure is decomposed into a first-neighbour strongly bonded cluster part and second-neighbour weakly bonded glue-atom part so that the overall structural information is condensed into a local structural unit [cluster](glue atom)x. For quasicrystals, the averaged local units are formulated as [icosahedron] TM0,1(Transition Metal) and could be visualized as single icosahedron packing. Then, the hardness of quasicrystals was related to the rupture of weak inter-cluster bonds. Typically, theoretical hardness values of 8–9 GPa were obtained using 19 broken inter-cluster bonds, which accounts for about half of all the surface bonds of an icosahedron in the Mackay-type environment. The unit cluster formulas would act as rigid units during deformation and cracking.
Endmill Condition Monitoring and Failure Forecasting Method for Curvilinear Cuts of Non-Constant Radii (2007)

In this paper, an endmill condition monitoring technique is presented for curvilinear cutting. This algorithm operates without the need for prior knowledge of cutting conditions, tool type, cut curvature, cut direction, or directional rate of change. This technique is based on an autoregressive-type monitoring algorithm which is used to track the tool’s condition using a tri-axial accelerometer. Accelerometer signals are monitored due to the sensors relatively low cost and since use of the sensor does not limit the machining envelope. To demonstrate repeatability, eight life tests were conducted. The technique discussed herein successfully prognosis impending fracture or meltdown due to wear in all cases, providing sufficient time to remove the tools before failure is realized. Furthermore, the algorithm produces similar trends capable of forecasting failure, regardless of tool type and cut geometry. Success is seen in all cases without requiring algorithm modifications or any prior information regarding the tool or cutting conditions.
Effect of Tumor Necrosis Factor on the Human Fibrinolytic System (1990)

At the request of the authors, the following is a correction of reference 4 cited in the report "Effect of Tumor Necrosis Factor on the Human Fibrinolytic System" by Silverman et al (J Clin Oncol 8:468–475, 1990): Reference 4. Helson L, Green S, Carswell EA, et al: Effect of tumor necrosis factor on cultured human melanoma cells. Science 258:731–732, 1975.
Violation of a new Wigner inequality with high angular momenta (2013)

In the study of systems that cannot be described classically, the Wigner inequality, has received only a small amount of attention. In this paper we extend the Wigner inequality - originally derived in 1969 - and show how it may be used to contradict local realism with only coincidence detections in the absence of two-outcome measurements - that is, for any system where only one possible result of a pair of potential outcomes can be registered. It thus encapsulates a much broader class of measurement schemes than could previously violate a local-realistic inequality. This is possible due to an assumption of "extended fairness" on the measurement outcomes, which we posit is highly plausible. We then apply this inequality to a recently constructed setup with access to entangled pairs of photons with very high angular momenta, in which no previously derived local-realistic inequality could successfully be used without making very broad assumptions. To our knowledge this experiment constitutes a violation of local realism with the largest quanta to date. We thus demonstrate the versatility of this inequality under very lossy conditions.
BASIC—ALIMENTARY TRACT Amphiregulin-Deficient Mice Develop Spasmolytic Polypeptide Expressing Metaplasia and Intestinal Metaplasia (2009)

Background & Aims: The loss of parietal cells from the fundic mucosa leads to the emergence of metaplastic lineages associated with an increased susceptibility to neoplastic transformation. Both intestinal metaplasia (IM) and spasmolytic polypeptide (TFF2/ SP) expressing metaplasia (SPEM) have been identified in human stomach, but only SPEM is present in most mouse models of gastric metaplasia. We previously determined that loss of amphiregulin (AR) promotes SPEM induced by acute oxyntic atrophy. We have now examined whether SPEM in the AR / mouse predisposes the stomach to gastric neoplasia. Methods: Gross pathology of 18-month-old wildtype, AR / , and TGF- / mice were examined. Ki67, -catenin, Pdx-1, TFF3, and TFF2/SP expression was analyzed by immunohistochemistry. Metaplastic gastric mucosa was analyzed by dual immunostaining for TFF2/SP with MUC2 or TFF3. Results: By 18 months of age, more than 70% of AR / mice developed SPEM while 42% showed goblet cell IM labeled with MUC2, TFF3, and Pdx-1. A total of 28% had invasive gastric lesions in the fundus. No antral abnormalities were observed in AR / mice. Metaplastic cell lineages in AR / mice showed increases in cell proliferation and cytosolic -catenin expression. Dual staining for TFF2/SP with MUC2 or TFF3 showed glands containing both SPEM and IM with intervening cells expressing both TFF2/SP and MUC2 or TFF2/SP and TFF3. Conclusions: AR / mice develop SPEM, which gives rise to goblet cell IM and invasive fundic dysplastic lesions. The AR / mouse represents the first mouse model for spontaneous development of fundic SPEM with progression to IM.
Melatonin, melatonin isomers and stilbenes in <scp>I</scp>talian traditional grape products and their antiradical capacity (2012)

Although polyphenols represent the paradigm of the health-promoting effects ascribed to grape products, recently, attention has been paid to dietary melatonin, significantly present in Mediterranean foods. In this work, we measured melatonin, its isomers, stilbenes (trans- and cis-resveratrol and their glucosides, piceids) and total polyphenols in some different grape products (red, white and dessert wines, grape juices and Modena balsamic vinegars) of distinct Italian areas. We also evaluated their antiradical activity by DPPH(·) and ABTS(·+) assays. For indoleamine analysis, the separation was carried out on a 1.7-μm C18 BEH column and the detection performed by means of mass spectrometry with electrospray ionization in positive ion mode with multiple reaction monitoring. The confirmation of the peak identity was accomplished by injection into the high-resolution system (Orbitrap) using accurate mass measurements (error below 1.0 ppm). Mass spectrometry analyses revealed, for the first time, the presence of melatonin in dessert wines and balsamic vinegars, as well as the occurrence of three different melatonin isomers in grape products.
LUT-Based Hierarchical Reversible Logic Synthesis (2018)

We present a synthesis framework to map logic networks into quantum circuits for quantum computing. The synthesis framework is based on lookup-table (LUT) networks, which play a key role in conventional logic synthesis. Establishing a connection between LUTs in an LUT network and reversible single-target gates in a reversible network allows us to bridge conventional logic synthesis with logic synthesis for quantum computing, despite several fundamental differences. We call our synthesis framework LUT-based hierarchical reversible logic synthesis (LHRS). Input to LHRS is a classical logic network representing an arbitrary Boolean combinational operation; output is a quantum network (realized in terms of Clifford+T gates). The framework allows one to account for qubit count requirements imposed by the overlying quantum algorithm or target quantum computing hardware. In a fast first step, an initial network is derived that only consists of single-target gates and already completely determines the number of qubits in the final quantum network. Different methods are then used to map each single-target gate into Clifford+T gates, while aiming at optimally using available resources. We demonstrate the versatility of our method by conducting a design space exploration using different parameters on a set of large combinational benchmarks. On the same benchmarks, we show that our approach can advance over the state-of-the-art hierarchical reversible logic synthesis algorithms.
P3526Heart Failure hospitalization and mortality in non-valvular Atrial Fibrillation: The ENGAGE-AF TIMI 48 Trial (2019)

Abstract Introduction Atrial Fibrillation (AF) is associated with increased risk of cardiovascular (CV) morbidity and mortality. Heart Failure (HF) represents the most common CV complication, more common than thromboembolic events. Purpose We aimed to determine clinical factors associated with HF hospitalization and mortality in a contemporary cohort of patients with AF without previous history of HF. Methods The Effective Anticoagulation with Factor Xa Next Generation in AF–Thrombolysis in Myocardial Infarction 48 (ENGAGE-AF TIMI 48) study tested the oral factor Xa inhibitor edoxaban in comparison with warfarin for the prevention of stroke or systemic embolism, in 21,105 patients with AF. We assessed the composite endpoint of HF hospitalization, death due to HF or sudden cardiac death in 8981 patients without a history of HF. Cox proportional hazard models were used to evaluate the significant clinical predictors associated with the endpoint of interest. Results Over a median follow-up of 2.8 years, 589 patients (6.5%) experienced the composite endpoint. Older patients, cardiovascular risk factors (hypertension, diabetes, heart valve disease), history of stroke and coronary artery disease, impaired renal function (ClCr ≤50 ml/min), heart rate at baseline and diuretic use were associated with increased risk of the composite endpoint (model c-statistic 0.66) (Figure 1). Outcomes were not affected by randomization to edoxaban or warfarin. In patients with available cardiac-derived biomarkers, elevated levels of both NT-proBNP and Troponin I were significantly associated with the endpoint after adjustment for the clinical predictors (Figure 1). The addition of the biomarkers to clinical predictors enhanced risk estimation (c-statistics 0.69, NRI 0.40, IDI 0.01, all p<0.001 for NT-proBNP and c-statistics 0.70, NRI 0.43, IDI 0.03, all p<0.001 for Troponin I). Figure 1 Conclusions HF hospitalization and mortality are important complications in AF patients without a history of HF. The addition of cardiac biomarkers to clinical characteristics enhances risk estimation. These findings may improve risk stratification.