gebhart/patrepeval huggingface dataset:
Identification and Detection of <i>Phoma tracheiphila</i>, Causal Agent of Citrus Mal Secco Disease, by Real-Time Polymerase Chain Reaction (2006)

Phoma tracheiphila is the causal agent of a tracheomycotic disease of citrus called mal secco causing the dieback of twigs and branches. This pathogen is of quarantine concern; therefore, fast and reliable protocols are required to detect it promptly. A specific primer pair and a dual-labeled fluorogenic probe were used in a real-time polymerase chain reaction (PCR) with the Cepheid Smart Cycler II System (Transportable Device TD configuration) to detect this fungus in citrus samples. Real-time PCR assay was compared to modified conventional PCR assay. The sensitivity of the former was evaluated by testing P. tracheiphila DNA dilutions, and the minimum amount detectable was about 500 fg, whereas the linear quantification range was within 100 ng to 1 pg. Conventional PCR sensitivity was 10 pg. Conventional and real-time PCR successfully detected the fungus in woody samples of naturally infected lemon and artificially inoculated sour orange seedlings. Nevertheless, real-time PCR was about 10- to 20-fold more sensitive than conventional PCR, and preliminary results indicate that the former technique achieves quantitative monitoring of the fungus in tissues. Simple and rapid procedures to obtain suitable DNA samples from fungal cultures and citrus woody samples for PCR assays enable diagnosis to be completed in a short time.
Endogenous IL-1R1 Signaling Is Critical for Cognate CD4+ T Cell Help for Induction of In Vivo Type 1 and Type 2 Antipolysaccharide and Antiprotein Ig Isotype Responses to Intact <i>Streptococcus pneumoniae</i> , but Not to a Soluble Pneumococcal Conjugate Vaccine (2006)

MyD88(-/-) mice exhibit defective innate, diminished CD4(+) T cell-dependent (TD) type 1, but enhanced type 2, humoral immunity in response to intact Streptococcus pneumoniae (Pn). Because type 1 IL-1R (IL-1R1) signaling is MyD88 dependent, a role for endogenous IL-1 was determined. IL-1R1(-/-), in contrast to MyD88(-/-), mice exhibited relatively intact innate splenic cytokine expression in response to Pn. Nevertheless, IL-1R1(-/-), like MyD88(-/-), mice were more sensitive to killing with live Pn relative to wild-type controls. Although IL-1R1(-/-) mice elicited a normal T cell-independent IgM antipolysaccharide (PS) response to heat-killed Pn, the induction of PS- and protein-specific cognate, but not noncognate, TD type 1 and type 2 IgG isotypes were markedly reduced. Additionally, CD4(+) T cells from Pn-primed IL-1R1(-/-) mice failed to elicit IFN-gamma, IL-5, or IL-13 secretion upon restimulation with Pn in vitro, whereas MyD88(-/-) mice secreted normal levels of IFN-gamma and enhanced levels of IL-5 and IL-13. In contrast, IgG responses to a soluble, pneumococcal protein-PS conjugate, with or without adjuvant, showed little dependence on IL-1R1 and normal CD4(+) T cell priming. These data are the first to demonstrate a nonredundant role for endogenous IL-1 in TD induction of humoral immune responses to an intact pathogen, although not a pathogen-derived soluble conjugate, suggesting that antigenic context is a key determinant for IL-1 dependence. These data further suggest that IL-1 may be critical for preserving CD4(+) Th2 function in the presence, but not absence, of MyD88-dependent signaling via TLRs.
Phenyl versus Ethyl Transfer in the Addition of Organozinc Reagents to Aldehydes: A Theoretical Study (2003)

Warum Diethylzink die Addition von Diphenylzink an Aldehyde drastisch verbessert, wurde mit DFT-Methoden untersucht. Wechselwirkungen mit dem Phenyl-π-System im Übergangszustand (siehe Bild) führen zu einer deutlichen Bevorzugung des Phenyltransfers gegenüber dem Ethyltransfer. Auch die Gründe für die hohen ee-Werte in Reaktionen mit ZnEt2 werden angesprochen.
Chiral separation of promethazine by capillary electrophoresis with end-column amperometric detection (2001)

Sensitive end-column amperometric detection has been successfully coupled to capillary electrophoresis for chiral separation of promethazine, with a carbon fiber microdisk electrode as working electrode. Baseline separation and sensitive detection were achieved under optimum conditions: 0.030 M Na2HPO4 and 0.015 M citric acid at pH = 2.50, 1.0 mM β-CD, 10 kV separation voltage, and detection potential 1.10 V (vs Ag/AgCl). The numbers of theoretical plates were higher than 700 000, and the detection limit was 5×10–8 M. On-line treatment of the electrode has also been studied and discussed.
Subideal border bases (2010)

In modeling physical systems, it is sometimes useful to construct border bases of 0-dimensional polynomial ideals which are contained in the ideal generated by a given set of polynomials. We define and construct such subideal border bases, provide some basic properties and generalize a suitable variant of the Buchberger-MÃ¶ller algorithm as well as the AVI-algorithm of Heldt, Kreuzer, Pokutta, and Poulisse to the subideal setting. The subideal version of the AVI-algorithm is then applied to an actual industrial problem.
Feasibility analysis of messages for on-chip networks using wormhole routing (2005)

The feasibility of a message in a network concerns if its timing property can be satisfied without jeopardizing any messages already in the network to meet their timing properties. We present a novel feasibility analysis for real-time (RT) and nonreal-time (NT) messages in wormhole-routed networks on chip. For RT messages, we formulate a contention tree that captures contentions in the network. For coexisting RT and NT messages, we propose a simple bandwidth partitioning method that allows us to analyze their feasibility independently.
Femoroacetabular impingement: treatment of the acetabular side. (2009)

Over the past decade, femoroacetabular impingement (FAI) has become an increasingly recognized pathomechanism that may explain why some hips that were previously considered to have normal morphology fail early in life. Subtle morphologic alterations in the acetabulum or femur, as well as the degree of hypermobility or impact on the hip, affect the potential for joint damage. The most frequent location of FAI is the anterosuperior acetabular rim, and the most critical motion is internal rotation of the hip in flexion. Because medication, activity restrictions, and physical therapy are rarely successful in treating symptoms caused by FAI, surgery has become a mainstay of treatment. Acetabular causes of FAI, called pincer FAI, can be treated by improving hip clearance. Independent of whether local or global overcoverage is present, rim reduction should be combined with labral preservation whenever possible.
cAMP-Response Element-Binding Protein Mediates Tumor Necrosis Factor-α–Induced Vascular Smooth Muscle Cell Migration (2004)

Our results suggest that p38-MAPK/CREB/Rac1 pathway plays a critical role in TNF-alpha-induced VSMC migration and may be a novel therapeutic target for vascular stenotic lesion. Migration of vascular smooth muscle cells (VSMCs) contributes to formation of vascular stenotic lesions. TNF-alpha, a potent migration factor for VSMCs, activated CREB through p38 mitogen-activated protein kinase (p38-MAPK). CREB inhibition suppressed TNF-alpha-induced VSMC migration and Rac1 expression. These results suggest p38-MAPK/CREB/Rac1 pathway mediates TNF-alpha-induced VSMC migration.
Diabetic Foot Ulcers and Their Recurrence (2017)

Foot ulceration is the most common lower-extremity complication in patients with diabetes mellitus. This review considers the pathogenesis, treatment, and management of diabetic foot ulcers, including prevention of recurrence.
The Impact of Human Immunodeficiency Virus Infection on Drug-Resistant Tuberculosis (1996)

Infection with human immunodeficiency virus (HIV) has been associated with increased rates of single- and multidrug-resistant (MDR) tuberculosis in the New York City area. In order to examine the relationship of HIV infection to drug-resistant tuberculosis in other selected regions of the United States, we established a registry of cases of culture-proven tuberculosis. Data were collected from sites participating in an NIH-funded, community-based HIV clinical trials group. All cases of tuberculosis, regardless of HIV status, which occurred between January 1992 and June 1994 were recorded. Overall, 1,373 cases of tuberculosis were evaluated, including 425 from the New York City area, and 948 from seven other metropolitan areas. The overall prevalence of resistance to one or more drugs was 20.4%, and 5.6% of isolates were resistant to both isoniazid and rifampin (MDR). In the New York City area, HIV-infected patients were significantly more likely than persons not known to be HIV-infected, to have resistance to at least one drug (37% versus 19%) and MDR (19% versus 6%). In other geographic areas, overall drug resistance was 16%, and only 2.2% of isolates were MDR. In multiple logistic regression analyses, HIV infection was shown to be a risk factor for drug-resistant tuberculosis, independent of geographic location, history of prior therapy, age, and race. We concluded that HIV infection is associated with increased rates of resistance to antituberculosis drugs in both the New York City area and other geographic areas. MDR tuberculosis is occurring predominantly in the New York City area and is highly correlated with HIV infection.
Towards efficient main-memory use for optimum tree index update (2008)

An emerging class of database applications is characterized by frequent updates of low-dimensional data, e.g. coming from sensors that sample continuous real world phenomena. Traditional persistency requirements can be weakened in this setting of frequent updates, emphasizing a role of the main-memory in external storage index structures and enabling a higher update throughput. Moreover, in order for an index to be suitable for practical applications, efficient past-state queries should be supported without significantly penalizing other operations. These issues are not adequately addressed in the database research. We report on the R R -tree---our first step towards resolving them. Based on this, we outline a number of concrete short-term and more abstract longer-term future research directions.
Results of high-dose therapy for 1000 patients with multiple myeloma: durable complete remissions and superior survival in the absence of chromosome 13 abnormalities (2000)

High-dose therapy (HDT) has increased complete remission (CR) rates and survival in multiple myeloma (MM). We now report on continuous CR (CCR) and associated prognostic factors in 1000 consecutive patients receiving melphalan-based tandem HDT. Five-year CCR was 52% among 112 CR patients without chromosome 13 (▵13) abnormalities and with beta-2-microglobulin ≤ 2.5 mg/L, C-reactive protein ≤ 4 mg/L, and pre-HDT standard chemotherapy ≤ 12 months. Of all 390 CR patients without ▵13 abnormalities, 35% enjoyed 5-year CCR but none of 54 with ▵13 abnormalities. ▵13 abnormalities, present in overall 16%, reduced 5-year event-free survival from 20% to 0% and overall survival from 44% to 16% (both P < .0001). CR and a second HDT cycle applied within 6 months both extended event-free and overall survival significantly, justifying further pursuit of HDT, especially toward curing non-▵13 MM.
Novel ring transformations of 5-cyanouracils into 2-thiocytosines, 2,4-diaminopyrimidines, and pyrimido[4,5-d]pyrimidines by the reaction with thioureas and guanidines (1990)

The reaction of 5-cyanouracils with thioureas and guanidines causes novel pyrimidine-to-pyrimidine ring transformations. Thus, 1,3-disubstituted 5-cyanouracils (1) react with thiourea and guanidines to give the corresponding 5-carbamoyl-2-thiocytosines (2) and 2,4-diamino-5-carbamoylpyrimidines (5), respectively. On the other hand, 5-cyanouracils (8) possessing a phenyl group at the 1-position react with thioureas to give 7-aminopyrimido[4,5-d]pyrimidine-2,4-diones (9).
Psychophysical support for a two-dimensional view interpolation theory of object recognition. (1992)

Does the human brain represent objects for recognition by storing a series of two-dimensional snapshots, or are the object models, in some sense, three-dimensional analogs of the objects they represent? One way to address this question is to explore the ability of the human visual system to generalize recognition from familiar to unfamiliar views of three-dimensional objects. Three recently proposed theories of object recognition--viewpoint normalization or alignment of three-dimensional models [Ullman, S. (1989) Cognition 32, 193-254], linear combination of two-dimensional views [Ullman, S. & Basri, R. (1990) Recognition by Linear Combinations of Models (Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge), A. I. Memo No. 1152], and view approximation [Poggio, T. & Edelman, S. (1990) Nature (London) 343, 263-266]--predict different patterns of generalization to unfamiliar views. We have exploited the conflicting predictions to test the three theories directly in a psychophysical experiment involving computer-generated three-dimensional objects. Our results suggest that the human visual system is better described as recognizing these objects by two-dimensional view interpolation than by alignment or other methods that rely on object-centered three-dimensional models.
Identification of the RNA region transferred from a representative primer, β-globin mRNA, to influenza mRNA during in vitro transcription (1980)

Capped eukaryotic mRNAs strongly stimulate influenza viral RNA transcription in vitro and donate their cap and also additional nucleotides to the viral transcripts (1). To identify which bases of a given primer mRNA are transferred, we synthesized influenza viral mRNA using a primer rabbit globin mRNA (enriched in beta-globin mRNA) which had been labeled in vitro to high specific activity with 125I. We show that during transcription the same 125I-labeled oligonucleotides were transferred to the 5' termini of each of the eight viral mRNA segments. The predominant sequence, representing 75 percent of the transferred oligonucleotides, was identical to the first 13 nucleotides at the 5' end of beta-globin mRNA (m7G5'ppp5'm6AmC(m)ACUUGCUUUUG). Because only the C-residues are labeled with 125I, these results indicate that either the first 12, 13 or 14 5' terminal bases of beta-globin mRNA were transferred to the viral mRNAs. 125I-labeled oligonucleotides recovered from the viral mRNA in minor yields indicated that shorter 5' terminal pieces of beta-globin mRNA were sometimes transferred and that G was probably the first base inserted by transcription.
A 1Mb DRAM with 3-dimensional stacked capacitor cells (1985)

A 1Mb DRAM employing 26.46μ^2 cells with 55fF capacitance will be reported.
3‐Nitropropionic acid induces autophagy by forming mitochondrial permeability transition pores rather than activatiing the mitochondrial fission pathway (2012)

There was a direct correlation between formation of mitochondrial permeability transition pores and autophagy induced by 3NP treatment. Activation of autophagy preceded the apoptotic process and was mediated, at least partly, by formation of reactive oxygen species and mitochondrial permeability transition pores.
Thyrotropin-Independent Induction of Thyroid Endoderm from Embryonic Stem Cells by Activin A (2008)

To model the differentiation of thyroid epithelial cells, we examined embryoid bodies derived from undifferentiated murine embryonic stem cells treated with activin A to induce endoderm differentiation, the germ layer from which thyroid cells occur. The resulting endodermal cells were then further exposed to TSH and/or IGF-I for up to 21 d. Oct-4 and REX1 expression, required to sustain stem cell self-renewal and pluripotency, were appropriately down-regulated, whereas GATA-4, and alpha-fetoprotein, both endodermal-specific markers, increased as the embryonic stem cells were exposed to activin A. By d 5 culture, TSH receptor (TSHR) and sodium iodide symporter (NIS) gene and protein expression were markedly induced. Cells isolated by the fluorescence-activated cell sorter simultaneously expressed not only TSHR and NIS proteins but also PAX8 mRNA, an expression pattern unique to thyroid cells and expected in committed thyroid progenitor cells. Such expression continued until d 21 with no influence seen by the addition of TSH or IGF-I. The sequence of gene expression changes observed in these experiments demonstrated the emergence of definitive thyroid endoderm. The activin A induction of thyroid-specific markers, NIS and TSHR, occurred in the absence of TSH stimulation, and, therefore, the emergence of thyroid endoderm in vitro paralleled the emergence of thyroid cells in TSHR-knockout mice. Activin A is clearly a major regulator of thyroid endoderm.
Decrease of Tissue Angiotensin I-Converting Enzyme Activity upon Feeding Sour Milk in Spontaneously Hypertensive Rats (1996)

Blood pressure increases were inhibited by feeding a diet containing sour milk fermented by a starter containing Lactobacillus helveticus and Saccharomyces cerevisiae to spontaneously hypertensive rats. In rats fed with the sour milk, the angiotensin I-converting enzyme activity of the aorta was significantly lower than that of rats fed with the control commercial diet.
Ratchetlike Slip Angle Anisotropy on Printed Superhydrophobic Surfaces (2011)

The fabrication and properties of superhydrophobic surfaces that exhibit ratchet-like anisotropic slip angle behavior is described. The surface is composed of arrays of poly(dimethylsiloxane) (PDMS) posts fabricated by a type of 3D printing. By controlling the dispense parameters, regular arrays of asymmetric posts were deposited such that the slope of the posts was varied from 0 to 50 relative to the surface normal. Advancing and receding contact angles as well as slip angles were measured as a function of the post slope and droplet volume. Ratchetlike slip angle anisotropy was observed on surfaces composed of sloped features. The maximum slip angle difference (for a 180° tilt angle variation) was 32° for 20 μL droplets on surfaces with posts fabricated with a slope of 50°. This slip angle anisotropy is attributed to an increase in the triple contact line (TCL) length as the droplet is tilted in a direction against the post slope whereas the TCL decreases continuously when the drop travels in a direction parallel to the post slope. The increasing length of the TCL creates an increased energy barrier that accounts for the higher slip angles in this direction.
Low Plasma Antioxidant Activity Is Associated With High Lesion Volume and Neurological Impairment in Stroke (2000)

These data suggest that the antioxidant activity of plasma may be an important factor providing protection from neurological damage caused by stroke-associated oxidative stress.
TSV aware timing analysis and diagnosis in paths with multiple TSVs (2014)

3D-IC test becomes a challenge with the increasing number of TSVs and demands for effective 3D aware test techniques. In this work, we propose a timing aware model to capture delay variations on a path due to resistive open TSVs. The key idea is to analytically model delay and apply our correlation-based resistive open TSV detection method to attain path delay fault coverage. We propose two methods to investigate timing variation introduced by resistive open TSVs in a critical path delay with multiple TSVs. Method I computes the correlation of multiple TSVs in a path to overall path delay to determine if TSVs are the source of the introduced delay. Method II pinpoints which TSV is faulty by computing the delay fault coverage of each TSV in a path with multiple TSVs. Our results indicate the accuracy of our proposed method and promotes early identification of resistive open defects TSVs.
Automated Broadband High-Dynamic-Range Nonlinear Distortion Measurement System (2010)

This paper presents an intermodulation distortion measurement system based on automated feedforward cancellation that achieves 113 dB of broadband spurious-free dynamic range for discrete tone separations down to 100 Hz. For 1-Hz tone separation, the dynamic range is 106 dB, limited by carrier phase noise. A single-tone cancellation formula is developed requiring only the power of the probing signal and the power of the combined probe and cancellation signal so that the phase shift required for cancellation can be predicted. The technique is applied to a two-path feedforward cancellation system in a bridge configuration. The effects of reflected signals and of group delay on system performance is discussed. Spurious frequency content and interchannel coupling are analyzed with respect to system linearity. Feedforward cancellation and consideration of electromagnetic radiation coupling and reverse-wave isolation effects extends the dynamic range of spectrum and vector analyzers by at least 40 dB. Application of the technique to the measurement of correlated and uncorrelated nonlinear distortion of an amplified wideband code-division multiple-access signal is presented.
Mission (im)possible – mapping the brain becomes a reality (2014)

Charting and understanding the full wiring diagram of complex neuronal structures such as the central nervous system or the brain (Connectomics) is one of the big remaining challenges in life sciences. Although at first it appears nearly impossible to map out a full diagram of, e.g., a mouse brain with sufficient resolution to identify each and every connection between neurons, recent technological advances move such an ambitious undertaking into the realms of possibility without spending decades at a microscope. However there are still many challenges to address in order to pave the way for fast and systematic neurobiological understanding of whole networks. These challenges range from a more robust and reproducible sample preparation to automated image data acquisition, more efficient data storage strategies and powerful data analysis tools. Here we will review novel imaging techniques developed for the challenge of mapping out the full connectome of a nervous system, brain or eye to name just a few examples. The imaging techniques reviewed cover light sheet illumination methods, single and multi-beam scanning electron microscopy, and we will briefly mention the possible combination of both light and electron microscopy. In particular we will review 'clearing' and in vivo methods that can be performed with light sheet fluroescence microscopes such as the ZEISS Lightsheet Z.1. We will then focus on scanning electron microscopy with single and multi-beam instruments including methods such as serial blockface imaging and array tomography methods.
Excavation of methane hydrate using COIL (2006)

Methane hydrate is a energy resource distributed even in the resource-less countries such as Japan and India. The energy is necessary to extract the methane from the methane hydrate and COIL is the unique solution for the extraction tool, because fuels of COIL can be produced from the natural energy without the fossil energy resources. The experimental results of laser light-methane hydrate interaction, multi kW laser light transmission through 1 km optical fiber, and the estimation of the extracted methane by radiation of the multi hundreds kW COIL output on the methane hydrate layer, will be reported.