gebhart/patrepeval huggingface dataset:
Development of a new field inoculation technique to assess partial resistance in soybean to Sclerotinia sclerotiorum (2004)

The use of appropriate techniques to assess disease resistance is crucial to understanding the genetic control of host resistance to pathogens to develop resistant plant varieties. The objective of this study was to develop and evaluate a novel field-based inoculation technique for sclerotinia stem rot in soybean [Glycine max (L.) Merr.], caused by Sclerotinia sclerotiorum (Lib.) de Bary. The barley kernel inoculation technique involves stem inoculation using an infected barley kernel inserted into a wound made in the soybean stem. The damage on soybean plants is measured by the length of the lesion on inoculated stem and expressed as inoculation severity index (ISI). Soybean varieties were evaluated for 2 yr at different sites using the barley kernel inoculation technique, and compared with other controlled environment and natural infection-based techniques. The ISIs obtained at Elora, ON, were significantly correlated (r = 0.21, P = 0.021) between the 2 test years (1998 and 1999), and in 1998 with natural infection [as measured by the disease severity index, DSI] at the same location (r = 0.31; P = 0.0005). Using a small set of lines that were specifically selected over several years to respond to DSI, the correlation between the DSI from some locations and years and the ISI in 1999 was negative. The significant positive correlations obtained using soybean lines that were not previously selected for DSI suggest the potential of this technique for pre-screening the breeding material for partial resistance to sclerotinia stem rot prior to confirmation with natural infection levels as measured by DSI. This may be of value to soybean breeders trying to develop soybean lines partially resistant to sclerotinia stem rot because of the difficulty in obtaining consistent and reliable DSI scores across locations and over years. Key words: Sclerotinia stem rot, white mould, inoculation, resistance, soybean
Smoking and cancer‐related gene expression in bronchial epithelium and non‐small‐cell lung cancers (2006)

Tobacco smoking is the leading cause of lung cancer worldwide. Gene expression in surgically resected and microdissected samples of non-small-cell lung cancers (18 squamous cell carcinomas and nine adenocarcinomas), matched normal bronchial epithelium, and peripheral lung tissue from both smokers (n = 22) and non-smokers (n = 5) was studied using the Affymetrix U133A array. A subset of 15 differentially regulated genes was validated by real-time PCR or immunohistochemistry. Hierarchical cluster analysis clearly distinguished between benign and malignant tissue and between squamous cell carcinomas and adenocarcinomas. The bronchial epithelium and adenocarcinomas could be divided into the two subgroups of smokers and non-smokers. By comparison of the gene expression profiles in the bronchial epithelium of non-smokers, smokers, and matched cancer tissues, it was possible to identify a signature of 23 differentially expressed genes, which might reflect early cigarette smoke-induced and cancer-relevant molecular lesions in the central bronchial epithelium of smokers. Ten of these genes are involved in xenobiotic metabolism and redox stress (eg AKR1B10, AKR1C1, and MT1K). One gene is a tumour suppressor gene (HLF); two genes act as oncogenes (FGFR3 and LMO3); two genes are involved in matrix degradation (MMP12 and PTHLH); three genes are related to cell differentiation (SPRR1B, RTN1, and MUC7); and five genes have not been well characterized to date. By comparison of the tobacco-exposed peripheral alveolar lung tissue of smokers with non-smokers and with adenocarcinomas from smokers, it was possible to identify a signature of 27 other differentially expressed genes. These genes are involved in the metabolism of xenobiotics (eg GPX2 and FMO3) and may represent cigarette smoke-induced, cancer-related molecular targets that may be utilized to identify smokers with increased risk for lung cancer.
Poststroke neuronal rescue and synaptogenesis mediated in vivo by protein kinase C in adult brains (2008)

Global cerebral ischemia/hypoxia, as can occur during human stroke, damages brain neural networks and synaptic functions. The recently demonstrated protein kinase C (PKC) activation-induced synaptogenesis in rat hippocampus suggested the potential of PKC-mediated antiapoptosis and synaptogenesis during conditions of neurodegeneration. Consequently, we examined the effects of chronic bryostatin-1, a PKC activator, on the cerebral ischemia/hypoxia-induced impairment of synapses and neurotrophic activity in the hippocampal CA1 area and on hippocampus-dependent spatial learning and memory. Postischemic/hypoxic bryostatin-1 treatment effectively rescued ischemia-induced deficits in synaptogenesis, neurotrophic activity, and spatial learning and memory. These results highlight a neuroprotective signaling pathway, as well as a therapeutic strategy with an extended time window for reducing brain damage due to stroke by activating particular PKC isozymes.
Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening (2008)

By virtue of their accumulated genetic alterations, tumor cells may acquire vulnerabilities that create opportunities for therapeutic intervention. We have devised a massively parallel strategy for screening short hairpin RNA (shRNA) collections for stable loss-of-function phenotypes. We assayed from 6000 to 20,000 shRNAs simultaneously to identify genes important for the proliferation and survival of five cell lines derived from human mammary tissue. Lethal shRNAs common to these cell lines targeted many known cell-cycle regulatory networks. Cell line-specific sensitivities to suppression of protein complexes and biological pathways also emerged, and these could be validated by RNA interference (RNAi) and pharmacologically. These studies establish a practical platform for genome-scale screening of complex phenotypes in mammalian cells and demonstrate that RNAi can be used to expose genotype-specific sensitivities.
Bandwidth-allocation schemes for variable-bit-rate MPEG sources in ATM networks (1993)

The complex traffic characteristics of variable-bit-rate (VBR) video sources makes them difficult to accommodate in asynchronous-transfer-mode (ATM) networks. To efficiently transport these services will require both an understanding of the source traffic and novel network control schemes. The performance of variable-bandwidth-allocation schemes that estimate the required bandwidth for a VBR Motion Picture Experts Group (MPEG) video source is studied using a simple prediction algorithm. The advantages of using a layered MPEG coder over the standard MPEG coder are discussed. A method for controlling a layered MPEG coder to reduce the effect of cell losses when compared to a standard MPEG coder is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Locality-Sensitive Deconvolution Networks with Gated Fusion for RGB-D Indoor Semantic Segmentation (2017)

This paper focuses on indoor semantic segmentation using RGB-D data. Although the commonly used deconvolution networks (DeconvNet) have achieved impressive results on this task, we find there is still room for improvements in two aspects. One is about the boundary segmentation. DeconvNet aggregates large context to predict the label of each pixel, inherently limiting the segmentation precision of object boundaries. The other is about RGB-D fusion. Recent state-of-the-art methods generally fuse RGB and depth networks with equal-weight score fusion, regardless of the varying contributions of the two modalities on delineating different categories in different scenes. To address the two problems, we first propose a locality-sensitive DeconvNet (LS-DeconvNet) to refine the boundary segmentation over each modality. LS-DeconvNet incorporates locally visual and geometric cues from the raw RGB-D data into each DeconvNet, which is able to learn to upsample the coarse convolutional maps with large context whilst recovering sharp object boundaries. Towards RGB-D fusion, we introduce a gated fusion layer to effectively combine the two LS-DeconvNets. This layer can learn to adjust the contributions of RGB and depth over each pixel for high-performance object recognition. Experiments on the large-scale SUN RGB-D dataset and the popular NYU-Depth v2 dataset show that our approach achieves new state-of-the-art results for RGB-D indoor semantic segmentation.
Guanine Nucleotide-Exchange Factors for Arf GTPases: Their Diverse Functions in Membrane Traffic (2004)

Small GTPases of the Arf family, by cycling between GDP-bound inactive and GTP-bound active states, play a crucial role not only in the regulation of membrane traffic and dynamics but also in rearrangement of actin cytoskeleton. The exchange of GDP for GTP on Arf is catalyzed by a family of guanine nucleotide-exchange factors (GEFs) containing a Sec7 domain. The Sec7 domain is a target of brefeldin A, which inhibits various trafficking processes and induces organelle disintegration. During the past few years, significant progress has been made in elucidating the structure and catalytic mechanism of the Sec7 domains and physiological functions of the Sec7 domain-containing Arf-GEFs. Here we review the structures and functions of Arf-GEFs by focusing on the regulation of membrane traffic.
Comparative mechanisms and rates of free radical scavenging by carotenoid antioxidants (1997)

The comparative mechanisms and relative rates of nitrogen dioxide (NO2.), thiyl (RS.) and sulphonyl (RSO2.) radical scavenging by the carotenoid antioxidants lycopene, lutein, zeaxanthin, astaxanthin and canthaxanthin have been determined by pulse radiolysis. All the carotenoids under study react with the NO2. radical via electron transfer to generate the carotenoid radical cation (Car.+). In marked contrast the glutathione and 2-mercaptoethanol thiyl radicals react via a radical addition process to generate carotenoid-thiyl radical adducts [RS-Car].. The RSO2. radical undergoes both radical addition, [RSO2-Car]. and electron abstraction, Car.+. Both carotenoid adduct radicals and radical cations decay bimolecularly. Absolute rate constants for radical scavenging were in the order of approximately 10(7)-10(9) M(-1) s(-1) and follow the sequence HO(CH2)2S. > RSO2. > GS. > NO2.. Although there were some discernible trends in carotenoid reactivity for individual radicals, rate constants varied by no greater than a factor of 2.5. The mechanism and rate of scavenging is strongly dependent on the nature of the oxidising radical species but much less dependent on the carotenoid structure.
Vestibular actions on back and lower limb muscles during postural tasks in man (2003)

The vestibular system was activated by galvanic electrical stimulation in 19 normal subjects. With the head turned to one side so that the stimulating anode was on the posterior mastoid process, stimulation caused standing subjects to sway backwards in the sagittal plane. Electromyography showed bilateral activation of erector spinae, gluteus maximus, biceps femoris, soleus and intrinsic foot (toe flexor) muscles. When head direction or electrode polarity was reversed so that the anode was anterior, all those muscles became less active and the subjects swayed forwards. With the head facing forward, stimulation caused sideways sway in the coronal plane, towards the anode, with excitation of the erector spinae on the anode side and reduced activity on the cathode side. The limb muscles were activated on the side opposite the anode and showed complex responses on the anode side. Responses were detectable in the erectores spinae muscles in sitting subjects. No responses in limb muscles were detected in the sitting posture. Subject responses in erector spinae recorded at L3/L4 had latencies from 59 to 110 ms, using a 2 mA stimulus. Latencies in lower limb muscles were longer. The results suggest a role for the vestibular system and descending brain stem motor pathways to the erectores spinae muscles in the control of postural orientation of the back when sitting and standing. The conduction velocity in the motor pathway was estimated to be 13 +/- 10 m s(-1) (mean +/- S.D., n = 12 subjects).
SLIC: A Specification Language for Interface Checking (of C) (2002)

Modern software systems are built by a multitude of programmers using application program interfaces (APIs). When a software system is built using APIs, there are several classes of problems that can hamper its dependability: a client P of an API may use it improperly; an implementation L may not properly implement the API. There are many requirements on both the client and implementer of an API that are typically stated only in the documentation for the API. Currently, only a small portion of these requirements |namely, the number of arguments of a function, and the types of each argument and return value| are stated in the header file for the API and checked for agreement at call sites by the compiler. We wish to express temporal safety requirements [15] on the API, such as rules about ordering of function calls with associated constraints on the data values visible at the API boundary, and automatically check (statically or dynamically) if these requirements are satisfied by the client and the implementer of the API.
A high-flow thermopneumatic microvalve with improved efficiency and integrated state sensing (2003)

This paper reports a thermopneumatic microvalve featuring a corrugated diaphragm. A sealed cavity below the diaphragm contains a volatile fluid, the vapor pressure of which can be increased by resistive heating to deflect the diaphragm, thus closing the valve. Silicon heater grids are elevated 9 μm above the cavity floor, and the cavity is only partially filled with fluid, to increase thermal efficiency. A vacuum-sealed, capacitive pressure sensor on the floor allows direct monitoring of the cavity pressure. Pentane-filled actuators sustain a 2070 torr pressure rise above atmospheric with 500 mW input power. A device tested in situ closes with 350 mW at 1000 torr inlet pressure (venting to vacuum) and maintains closure with 30 mW input. Valves conduct 400 sccm under 1500 torr differential pressure, while maintaining leak rates as low as 10/sup -3/ sccm, yielding a dynamic range of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . A thermodynamic model has been developed that matches experimental power, pressure, and transient response data to within a few percent. This model is used to suggest an optimized structure capable of a 2000 torr pressure rise with 50 mW input and a 1 s response time. The glass-and-silicon valve structure is suitable for integration into complete microfluidic systems.
Long-Term Potentiation of Neuron-Glia Synapses Mediated by Ca 2+ -Permeable AMPA Receptors (2006)

Interactions between neurons and glial cells in the brain may serve important functions in the development, maintenance, and plasticity of neural circuits. Fast neuron-glia synaptic transmission has been found between hippocampal neurons and NG2 cells, a distinct population of macroglia-like cells widely distributed in the brain. We report that these neuron-glia synapses undergo activity-dependent modifications analogous to long-term potentiation (LTP) at excitatory synapses, a hallmark of neuronal plasticity. However, unlike the induction of LTP at many neuron-neuron synapses, both induction and expression of LTP at neuron-NG2 synapses involve Ca2+-permeable AMPA receptors on NG2 cells.
Janus kinase inhibitor INCB20 has antiproliferative and apoptotic effects on human myeloma cellsin vitroandin vivo (2009)

Protein tyrosine kinases of the Janus kinase (JAK) family are associated with many cytokine receptors, which, on ligand binding, regulate important cellular functions such as proliferation, survival, and differentiation. In multiple myeloma, JAKs may be persistently activated due to a constant stimulation by interleukin (IL)-6, which is produced in the bone marrow environment. INCB20 is a synthetic molecule that potently inhibits all members of the JAK family with a 100- to 1,000-fold selectivity for JAKs over >70 other kinases. Treatment of multiple myeloma cell lines and patient tumor cells with INCB20 resulted in a significant and dose-dependent inhibition of spontaneous as well as IL-6-induced cell growth. Importantly, multiple myeloma cell growth was inhibited in the presence of bone marrow stromal cells. The IL-6 dependent cell line INA-6 was particularly sensitive to the drug (IC50<1 micromol/L). Growth suppression of INA-6 correlated with an increase in the percentage of apoptotic cells and inhibition of signal transducer and activator of transcription 3 phosphorylation. INCB20 also abrogated the protective effect of IL-6 against dexamethasone by blocking phosphorylation of SHP-2 and AKT. In contrast, AKT phosphorylation induced by insulin-like growth factor-I remained unchanged, showing selectivity of the compound. In a s.c. severe combined immunodeficient mouse model with INA-6, INCB20 significantly delayed INA-6 tumor growth. Our studies show that disruption of JAKs and downstream signaling pathways may both inhibit multiple myeloma cell growth and survival and overcome cytokine-mediated drug resistance, thereby providing the preclinical rationale for the use of JAK inhibitors as a novel therapeutic approach in multiple myeloma.
An annotation-aware Java virtual machine implementation (2000)

The Java bytecode language lacks expressiveness for traditional compiler optimizations, making this portable, secure software distribution format inefficient as a program representation for high performance. This inefficiency results from the underlying stack model, as well as the fact that many bytecode operations intrinsically include sub-operations (e.g. iaload includes the address computation, array bounds checks and the actual load of the array element). The stack model, with no operand registers and limiting access to the top of the stack, prevents the re-use of values and bytecode re-ordering. In addition, the language has no mechanism to indicate which sub-operations in the Java bytecode stream are redundant or subsumed by previous ones. As a consequence, the Java bytecode language inhibits the expression of important compiler optimizations, including register allocation and instruction scheduling. The Java bytecode stream generated by a Java bytecode compiler is a significantly under-optimized program representation. The most common solution to overcome this inefficiency is the use of a just-in-time (JIT) compiler to not only generate native code, but perform optimization as well. However, the latter is a time-consuming operation in an already time-constrained translation process. In this paper we present an alternative to an optimizing JIT compiler that makes use of code annotations generated by a Java bytecode compiler. These annotations carry information concerning compiler optimizations. During the translation process, an annotation-aware Java Virtual Machine (JVM) system then uses this information to produce high-performance native code without performing much of the necessary analyses or transformations. We describe the implementation of a prototype of an annotation-aware JVM consisting of an annotation-aware JIT compilation system. We conclude the paper showing performance results comparing our system with other JVMs running on SPARC architecture. Copyright © 2000 John Wiley & Sons, Ltd.
Reduction of Titanium(IV)-Phosphinimide Complexes:  Routes to Ti(III) Dimers, Ti(IV)-Metallacycles, and Ti(II) Species (2004)

The redox chemistry of phosphinimide-containing group IV metal complexes has been investigated. Reaction of the simple phosphinimide species CpTi(NPR3)Cl2 (R = Me 1, i-Pr 2) with Mg affords complexes formulated as [CpTiCl(μ-NPR3)]2 (R = Me 3, i-Pr 4). In contrast, CpTi(NPt-Bu3)Cl2 (5) is reduced by Mg to a putative Ti(II) species that can be intercepted by a variety of reagents including 2,3-dimethyl-1,3-butadiene, diphenylacetylene, phenylacetylene, bis(trimethylsilyl)acetylene, ethylene, and propylene to give monometallic metallacyclic complexes. In this fashion, the Ti(IV) metallacycles CpTi(NPt-Bu3)(CH2C(Me)C(Me)CH2), 6, CpTi(NPt-Bu3)(CPh)4, 7, CpTi(NPt-Bu3)(C(Ph)CHC(Ph)CH), 8, CpTi(NPt-Bu3)(η2-C2(SiMe3)2), 9, CpTi(NPt-Bu3)(CH2)4, 10, CpTi(NPt-Bu3)(CH2CHMe)2, 15, and CpTi(NPt-Bu3)(CH2)2(CPh)2, 16, were prepared. Related intramolecular formation of metallacycle complexes was achieved upon reduction of Cp‘Ti(t-Bu2(2-C6H4Ph)PN)Cl2 (Cp‘ = Cp 18, Cp* 19). The products [Cp‘Ti(NPtBu2(2-C6H4Ph)] (Cp‘ = Cp 20, Cp* 21) contained η6-interactions between Ti and the 2-phenyl substituent of the biphenyl unit. While Ti(II)-phosphinimide complexes have proven difficult to handle due to their reactivity, an unequivocal example of a Ti(II) species was obtained via reduction of Cp*Ti(NPt-Bu3)Cl2 (11) with Mg in the presence of CO, affording the species Cp*Ti(NPt-Bu3)(CO)2 (22). X-ray data for 4, 6, 7, 9, 10, 15, and 17−22 are reported.
Lithographic flare measurements of EUV full-field projection optics (2003)

We demonstrate direct flare measurements of 4-mirror projection optics in the Engineering Test Stand (ETS) using a conventional resist clearing method (the Kirk method). Two extreme UV lithographic projection optics, one with higher flare than the other, have been characterized and the results compared. The measured results have also been compared to analytical calculations based on measured mirror roughness and the extended point spread function. Full-field flare across the 24 mm field width has been measured, and we have verified that flare is constant across the field for EUV lithography as predicted. Horizontal (H) and vertical (V) flare bias has been observed and the cause of the H-V flare bias has been investigated. The main cause has been identified to be anisotropic mirror polishing. Simulations with the 2D Power Spectral density function have confirmed the experimental results.
Amyloid, dementia and Alzheimer's disease. (1992)

Senile plaques (SP) and neurofibrillary tangles (NFT) are the major histopathological changes that occur in Alzheimer's disease (AD). How these two different types of lesions are related to each other and to the dementia of AD is unknown. Recent studies lead to paradoxical conclusions: NFT and neuronal alterations such as synapse loss are much more closely related to the symptoms of dementia than are SP. However, mutations in the beta-amyloid protein of SP have been found in some patients with familial AD, suggesting that an abnormality in amyloid causes the development of SP, NFT and AD dementia. Examination of transgenic animals that produce amyloid precursor protein (APP), or altered forms of APP, may lead to the development of an animal model of AD, and ultimately to answers that link amyloid production to neuronal alterations, and cognitive impairments.
Low subthreshold slope in junctionless multigate transistors (2010)

The improvement of subthreshold slope due to impact ionization is compared between “standard” inversion-mode multigate silicon nanowire transistors and junctionless transistors. The length of the region over which impact ionization takes place, as well as the amplitude of the impact ionization rate are found to be larger in the junctionless devices, which reduces the drain voltage necessary to obtain a sharp subthreshold slope.