gebhart/patrepeval huggingface dataset:
Defensins and the convergent evolution of platypus and reptile venom genes (2008)

When the platypus (Ornithorhynchus anatinus) was first discovered, it was thought to be a taxidermist's hoax, as it has a blend of mammalian and reptilian features. It is a most remarkable mammal, not only because it lays eggs but also because it is venomous. Rather than delivering venom through a bite, as do snakes and shrews, male platypuses have venomous spurs on each hind leg. The platypus genome sequence provides a unique opportunity to unravel the evolutionary history of many of these interesting features. While searching the platypus genome for the sequences of antimicrobial defensin genes, we identified three Ornithorhynchus venom defensin-like peptide (OvDLP) genes, which produce the major components of platypus venom. We show that gene duplication and subsequent functional diversification of beta-defensins gave rise to these platypus OvDLPs. The OvDLP genes are located adjacent to the beta-defensins and share similar gene organization and peptide structures. Intriguingly, some species of snakes and lizards also produce venoms containing similar molecules called crotamines and crotamine-like peptides. This led us to trace the evolutionary origins of other components of platypus and reptile venom. Here we show that several venom components have evolved separately in the platypus and reptiles. Convergent evolution has repeatedly selected genes coding for proteins containing specific structural motifs as templates for venom molecules.
Quantitative analysis of synaptic potentiation during kindling of the perforant path (1986)

Synaptic transmission was studied during the development of kindling in the pathway from entorhinal cortex (EC) to dentate gyrus (DG) of unrestrained unanesthetized rats using chronic neurophysiological techniques. Extracellular field potentials were recorded from the DG in response to activation of the perforant pathway with 0.1-ms constant current square-wave pulses. The evoked field potentials consisted of a population EPSP (a reflection of excitatory synaptic activation) and a population spike (a measure of synchronous postsynaptic discharge of granule cells). Synaptic efficacy was quantitated in this pathway by measurement of the population EPSP slope and population spike amplitude across a range of stimulus intensities from threshold to maximal evoked response. Input-output relationships for population EPSP and population spike were determined at regular intervals during the course of kindling, corresponding to the stages of evoked behavioral seizures. Increases in the population EPSP and population spike were observed after a single kindling stimulus that evoked afterdischarge (AD) when behavioral seizures were minimal. Evaluation of the input-output relationships for the group of kindled animals at the various stages of evoked behavioral seizure activity revealed that increases in the population EPSP continued to slowly evolve with repeated stimulations but that increases in the population spike were maximal after one or at most a few stimulations that evoked AD. The increases in both population EPSP and population spike persisted for the duration of the recording, i.e., through induction of generalized motor convulsions. To evaluate the translation of synaptic activation into cell discharge during kindling, we made use of the population spike/population EPSP ratio across a range of stimulus intensities. The spike/EPSP ratios revealed a dissociation of the population spike and population EPSP early in the course of kindling during class 1 seizures. Specifically, after induction of an AD, an extracellular population EPSP of a given size evoked a larger population spike than an EPSP of comparable size before the induction of an AD by kindling stimulation. The development of generalized motor convulsions (class 5 seizures) was associated with a reduction in the spike/EPSP ratio. The mechanism of this reduction in spike/EPSP ratio is uncertain, but since synaptic activation (as reflected by population EPSP) did not decline during class 5 seizures, the reduction in the spike/EPSP ratio could be consistent with increased inhibition after generalized motor convulsions, or could reflect a decrease in granule cell excitability.(ABSTRACT TRUNCATED AT 400 WORDS)
Segmentation and Feature Extraction of Panoramic Dental X-Ray Images (2010)

Automating the process of analysis of Panoramic X-Ray images is important to help dentist procedures and diagnosis. Tooth segmentation from the radiographic images and feature extraction are essential steps. The authors propose a segmentation approach based on mathematical morphology, quadtree decomposition for mask generation, thresholding, and snake models. The feature extraction stage is steered by a shape model based on Principal Component Analysis (PCA). First, the authors take the quadtree decomposition of a low-pass version of the original image and select the smallest blocks to generate a mask. Then, the original image is processed by Otsu’s thresholding. The result is improved by morphological operators and the quadtree mask is applied to address overlapping, a common problem in X-ray images. The obtained regions are searched and the larger ones are selected to find tooth candidates. The boundary of the obtained regions are extracted and aligned with the shape model in order to recognize the target tooth (molar). The selected curve is used in a search method to initialize a snake technique. Finally, morphometric data extraction is performed to obtain tooth measurements for dentist diagnosis. Experiments show the advantages of the proposed method to extract teeth from X-Ray images and discuss its drawbacks.
Identification of Suitable Reference Genes for Real-Time PCR Analysis of Statin-Treated Human Umbilical Vein Endothelial Cells (2012)

Proper data normalization in quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) is of critical importance for reliable mRNA expression analysis. Due to a diversity in putative reference genes expression stability in different in vitro models, a validation of an internal control gene should be made for each particular tissue or cell type and every specific experimental design. A few approaches have been proposed for reference gene selection, including pair-wise comparison approach and model-based approach. In this article we have assessed the expression stability of eight putative reference genes: ACTB, B2M, GADD45A, GAPDH, HPRT1, PES1, PSMC4, YWHAZ, in human umbilical vein endothelial cells (HUVEC) treated with different statins and with TNF-α. The analysis was performed with three reference gene validation programs: geNorm, NormFinder and BestKeeper. We have shown that hypoxanthine phosphoribosyltransferase 1 gene (HPRT1) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide gene (YWHAZ) are the most stably expressed genes among the analyzed ones. Furthermore, our results show that β-actin gene (ACTB) is downregulated by statins and thus should not be used as a normalizing gene in a discussed experimental setup. A ranking of candidate reference genes stability values is provided and might serve as a valuable guide for future gene expression studies in endothelial cells. This is the first report on reference gene selection for RT-qPCR applications in statin-treated HUVEC model.
Production, purification, and characterization of a fusion protein of carbonic anhydrase from <i>Neisseria gonorrhoeae</i> and cellulose binding domain from <i>Clostridium thermocellum</i> (2008)

Carbon dioxide capture technologies have the potential to become an important climate change mitigation option through sequestration of gaseous CO2. A new concept for CO2 capture involves use of immobilized carbonic anhydrase (CA) that catalyzes the reversible hydration of CO2 to HCO3(-) and H+. Cost-efficient production of the enzyme and an inexpensive immobilization system are critical for development of economically feasible CA-based CO2 capture processes. An artificial, bifunctional enzyme containing CA from Neisseria gonorrhoeae and a cellulose binding domain (CBD) from Clostridium thermocellum was constructed with a His6 tag. The chimeric enzyme exhibited both CA activity and CBD binding affinity. This fusion enzyme is of particular interest due to its binding affinity for cellulose and retained CA activity, which could serve as the basis for improved technology to capture CO2 from flue gasses.
Multivehicle Cooperative Driving Using Cooperative Perception: Design and Experimental Validation (2014)

In this paper, we present a multivehicle cooperative driving system architecture using cooperative perception along with experimental validation. For this goal, we first propose a multimodal cooperative perception system that provides see-through, lifted-seat, satellite and all-around views to drivers. Using the extended range information from the system, we then realize cooperative driving by a see-through forward collision warning, overtaking/lane-changing assistance, and automated hidden obstacle avoidance. We demonstrate the capabilities and features of our system through real-world experiments using four vehicles on the road.
Holistic approach for overlay and edge placement error to meet the 5nm technology node requirements (2018)

In this paper, we discuss the metrology methods and error budget that describe the edge placement error (EPE). EPE quantifies the pattern fidelity of a device structure made in a multi-patterning scheme. Here the pattern is the result of a sequence of lithography and etching steps, and consequently the contour of the final pattern contains error sources of the different process steps. EPE is computed by combining optical and ebeam metrology data. We show that high NA optical scatterometer can be used to densely measure in device CD and overlay errors. Large field e-beam system enables massive CD metrology which is used to characterize the local CD error. Local CD distribution needs to be characterized beyond 6 sigma, and requires high throughput e-beam system. We present in this paper the first images of a multi-beam e-beam inspection system. We discuss our holistic patterning optimization approach to understand and minimize the EPE of the final pattern. As a use case, we evaluated a 5-nm logic patterning process based on Self-Aligned-QuadruplePatterning (SAQP) using ArF lithography, combined with line cut exposures using EUV lithography.
Dynamic page migration in multiprocessors with distributed global memory (2003)

Multiprocessor architectures using point-to point interconnects and executing parallel algorithms require careful partitioning and allocation of data and processes. For a given interconnection, optimal allocation may be difficult to achieve in some cases because the data-dependent behavior of some algorithms may be impossible to predict. A mechanism called the pivot mechanism is introduced and described that controls the dynamic migration of data pages between neighboring memory modules during program execution. Flexible data migration serves the dual purpose of making algorithms less machine-specific and making possible efficient algorithm execution that is impossible to achieve by using static data allocation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cell tracking and detection of molecular expression in live cells using lipid-enclosed CdSe quantum dots as contrast agents for epi-third harmonic generation microscopy (2008)

We demonstrated that lipid-enclosed CdSe quantum dots (LEQDs) can function as versatile contrast agents in epi-detection third harmonic generation (THG) microscopy for biological applications in vivo. With epi-THG intensities 20 times stronger than corresponding fluorescence intensities from the same LEQDs under the same conditions of energy absorption, such high brightness LEQDs were proved for the abilities of cell tracking and detection of specific molecular expression in live cancer cells. Using nude mice as an animal model, the distribution of LEQD-loaded tumor cells deep in subcutaneous tissues were imaged with high THG contrast. This is the first demonstration that THG contrast can be manipulated in vivo with nanoparticles. By linking LEQDs with anti-Her2 antibodies, the expression of Her2/neu receptors in live breast cancer cells could also be easily detected through THG. Compared with fluorescence modalities, the THG modality also provides the advantage of no photobleaching and photoblinkin g effects. Combined with a high penetration 1230 nm laser, these novel features make LEQDs excellent THG contrast agents for in vivo deep-tissue imaging in the future.
Optical Filters (1952)

This survey of filters useful in optical work includes the range from ultraviolet through infrared. Descriptions of absorption filters making use of solid, liquid, and gaseous absorbers are treated in Part I. Part II contains descriptions of polarization, interference, and Christiansen types of filter as well as devices occasionally used in lieu of filters such as focal isolation and residual ray apparatus, gratings, and powder films used effectively as scatterers.
Inhibition of the Sexual Behavior of the Smaller Tea Tortrix Moth by the Sex Pheromone and Its Components (1975)

チャノコカクモンハマキの性フェロモンおよびその構成成分であるcis-9-tetradecenyl acetate (cis-9-TDA)およびcis-11-tetradecenyl acetate (cis-11-TDA)は,室内条件ガラス容器内でこのハマキガの交尾を阻害した。cis-9-TDA,cis-11-TDA,および両者の7対3混合物による90%阻害濃度は20°C, 14L-10D条件下でそれぞれ3, 0.3,および3μg/lであった。trans体による交尾阻害効果はこの条件下ではきわめて低かった。これらの化合物をほ場に均一に蒸散させた場合,cis-9-TDA, cis-11-TDA,および混合物いずれの処理の場合も処女雌トラップの雄の飛来を阻害した。しかし,これらの化合物およびtrans異性体を処女雌トラップに付置した場合には,trans異性体およびその混合物のほうがcis体よりも強く処女雌トラップの誘引性を抑え,室内条件下でもっとも強い交尾阻害を示したcis-11-TDAはむしろcis-9-TDAに劣る誘引阻害を示した。
Mutations in the carboxyl-terminal hydrophobic sequence of human cytomegalovirus glycoprotein B alter transport and protein chaperone binding (1996)

Human cytomegalovirus glycoprotein B (gB) plays a role in the fusion of the virion envelope with the host cell membrane and in syncytium formation in infected cells. Hydrophobic sequences at the carboxyl terminus, amino acids (aa) 714 to 771, anchor gB in the lipid bilayer, but the unusual length of this domain suggests that it may serve another role in gB structure. To explore the function(s) of this region, we deleted aa 717 to 747 (gB deltaI mutation), aa 751 to 771 (gB deltaII mutation), and aa 717 to 772 (gB deltaI-II mutation) and constructed a substitution mutation, Lys-748 to Val (Lys748Val)-Asn749Ala-Pro750Ile (gB KNPm). Mutated forms of gB were expressed in U373 glioblastoma cells and subjected to analysis by flow cytometry, confocal microscopy, and immunoprecipitation. Mutations gB deltaI-II and gB deltaII alone caused secretion of gB into the medium, confirming that aa 751 to 771 function as a membrane anchor. In contrast, mutations gB deltaI and gB KNPm blocked cell surface expression and arrested gB transport in the endoplasmic reticulum (ER). Detailed examination of gB deltaI and gB KNPm with a panel of monoclonal antibodies showed that the mutated forms were indistinguishable from wild-type gB in conformation and formed oligomers; however, they remained sensitive to endoglycosidase H and did not undergo endoproteolytic cleavage. Analysis of protein complexes formed by gB and molecular chaperones in the ER showed that calnexin and calreticulin, lectin-like chaperones, bound equal amounts of uncleaved wild-type gB, gB deltaI, and gB KNPm, but the glucose-regulated proteins 78 (BiP) and 94 formed stable complexes only with the mutated forms, causing their retention in the ER. Our studies show that aa 714 to 750 are key residues in the architecture of gB molecules and that the ER chaperones, which facilitate gB folding and monitor the quality of glycoproteins, detect subtle changes in folding intermediates that are conferred by mutations in this region.
Further improvement on synchronization stability of complex networks with coupling delays (2008)

This paper revisits the problem of synchronization stability for general complex dynamical networks with coupling delays. A new delay-dependent criterion is derived by introducing a new kind of Lyapunov–Krasovskii functional and is formulated in terms of a linear matrix inequality, which can be readily solved via standard software. This new criterion based on a delay fractioning approach is proved to be much less conservative and the conservatism could be notably reduced by thinning the delay fractioning. Furthermore, the resulting criterion is further extended to the synchronization stability analysis of complex dynamical networks with time-varying structured uncertainties. Two numerical examples are provided to show the effectiveness and advantage of the proposed results.
TGF-β1 signaling and Krüppel-like factor 10 regulate bone marrow–derived proangiogenic cell differentiation, function, and neovascularization (2011)

Emerging evidence demonstrates that proangiogenic cells (PACs) originate from the BM and are capable of being recruited to sites of ischemic injury where they contribute to neovascularization. We previously determined that among hematopoietic progenitor stem cells, common myeloid progenitors (CMPs) and granulocyte-macrophage progenitor cells (GMPs) differentiate into PACs and possess robust angiogenic activity under ischemic conditions. Herein, we report that a TGF-β1-responsive Krüppel- like factor, KLF10, is strongly expressed in PACs derived from CMPs and GMPs, ∼ 60-fold higher than in progenitors lacking PAC markers. KLF10(-/-) mice present with marked defects in PAC differentiation, function, TGF-β responsiveness, and impaired blood flow recovery after hindlimb ischemia, an effect rescued by wild-type PACs, but not KLF10(-/-) PACs. Overexpression studies revealed that KLF10 could rescue PAC formation from TGF-β1(+/-) CMPs and GMPs. Mechanistically, KLF10 targets the VEGFR2 promoter in PACs which may underlie the observed effects. These findings may be clinically relevant because KLF10 expression was also found to be significantly reduced in PACs from patients with peripheral artery disease. Collectively, these observations identify TGF-β1 signaling and KLF10 as key regulators of functional PACs derived from CMPs and GMPs and may provide a therapeutic target during cardiovascular ischemic states.
Single stage, high power factor, lamp ballast (2002)

Unlike conventional ballasts requiring two cascaded stages, a new lamp ballast achieves near unity input power factor and high frequency sinusoidal lamp current in a single power conversion stage. A new discontinuous inductor current mode (DICM) of input inductor makes this possible by separating the input current shaping from high frequency output lamp ballasting function. The high efficiency is further enhanced by soft switching improvement, which is provided naturally through lagging current of the output resonant matching network. Design equations and experimental results verify all the advantages of the new lamp ballast.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
[Thyroid function in depressed patients]. (1996)

This preliminary report compares the FT3, FT4, TSH basal levels and FT4/FT3 ration of depressed patients (DSM III-R criteria) with those of a healthy control group. Authors have also studied thyroid parameters in function of some clinical depression data (polarity, intensity and endogenous character) and other factors as age and sex. 81 depressed patients (31 men, 50 women), with mean age of 44.85 years were studied. 44 patients suffered of an endogenous depression and 37 of a non endogenous depression (Newcastle criteria). 60 patients had an unipolar depression while 21 patients had a bipolar depression. The control group was constituted of 36 healthy subjects (20 men, 16 women), with mean age of 40.94 years. There is no significant difference between the two groups for sex and age, besides the different size of the two groups. FT3 mean of depressed patients was 4.39 pmol/l. There was a significant difference between unipolar group FT3 mean (4.51 +/- 1.01 pmol/l) and bipolar FT3 mean (4.03 +/- 0.91 pmol/l; t = 2.02, p < 0.05). Depression intensity was correlated negatively to FT3 mean (r = -0.23; t = 2.10, p < 0.005). FT4 mean in the depressed group was 12.62 +/- 4.14 pmol/l. The only significative result for FT4 was its correlation to TSH levels (r = -0.36; t = 3.43, p < 0.001). TSH mean in depressed patients was 1.43 +/- 0.85 microIU/ml. When we have compared these results with those of control group we concluded that FT3 and TSH levels were significantly lower in the depressed group (FT3: t = 4.83, p < 0.0001; TSH; t = 2.44 p < 0.02) and that FT4 was slightly but not significantly increased in the depressed group. FT3 decrease and the slight FT4 increase in depression may be the consequence of a metabolic deviation of FT4 transformation into FT3. Its link with intensity and polarity of depression suggests that it can be considered as a biological marker of this disease.
PNU-120596, a positive allosteric modulator of α7 nicotinic acetylcholine receptors, reverses a sub-chronic phencyclidine-induced cognitive deficit in the attentional set-shifting task in female rats (2011)

The α7 nicotinic acetylcholine receptors (nAChRs) have been highlighted as a target for cognitive enhancement in schizophrenia. Adult female hooded Lister rats received sub-chronic phencyclidine (PCP) (2 mg/kg) or vehicle i.p. twice daily for 7 days, followed by 7 days' washout. PCP-treated rats then received PNU-120596 (10 mg/kg; s.c.) or saline and were tested in the attentional set-shifting task. Sub-chronic PCP produced a significant cognitive deficit in the extra-dimensional shift (EDS) phase of the task (p < 0.001, compared with vehicle). PNU-120596 significantly improved performance of PCP-treated rats in the EDS phase of the attentional set-shifting task (p < 0.001). In conclusion, these data demonstrate that PNU-120596 improves cognitive dysfunction in our animal model of cognitive dysfunction in schizophrenia, most likely via modulation of α7 nACh receptors.
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. (1999)

The C programs used in our analysis are available upon request.
ABO3-based photocatalysts for water splitting (2012)

ABO3-based photocatalysts for water splitting were systematically reviewed in this manuscript. Crystal structure and chemical composition characteristics of ABO3 materials were briefly introduced to guide the modification of ABO3-based photocatalysts. The ABO3-based photocatalysts were then reviewed in detail and divided into four groups based on the employed modification strategies, i.e., chemical component adjustment, micro-/nano-structure adjustment, local lattice structure adjustment, and application of the modification strategy of ABO3 photocatalysts in designing AxByOz photocatalysts. In this section, the recent research works on ABO3-based photocatalysts in our group were presented. Finally, application of ABO3 photocatalysts in Z-scheme systems for overall water splitting was introduced. This review summarized the development of ABO3-based photocatalysts and showed the values and possible direction of future research, thereby offering a guide for photocatalytic water splitting.
Nematode Chemotaxis and Possible Mechanisms of Host/Prey Recognition (1984)

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for ...Read More