gebhart/patrepeval huggingface dataset:
Design and Evaluation of a Peptidyl Fluorescent Chemosensor for Divalent Zinc (1996)

The rapid analysis of trace metal cations for environmental&#13;\nand biomedical applications is particularly demanding since it&#13;\nrequires the specific recognition of a particular element in the&#13;\npresence of numerous closely related species. While remarkable&#13;\nprogress has been achieved for inorganic analytes, such as Ca^(2+), there is still a significant need for the genesis of new fluorosensors. In light of the selectivity and avidity with which proteins bind divalent metal cations, we have chosen to use a polypeptide architecture as the framework for metal ion recognition.In addition, our ability to manipulate synthetic polypeptides allows the coordinated integration of fluorescent reporters for signal transduction within a metal-binding peptidyl construct. Herein we report the design, synthesis, and evaluation of a selective fluorescent chemosensor, sensitive to nanomolar&#13;\nconcentrations of Zn^(2+).
Reaction and regrowth control of CeO2 on Si(111) surface for the silicon-on-insulator structure (1994)

The interface structure of CeO2/Si(111) grown by laser ablation in ultrahigh vacuum was investigated by, reflection high-energy electron diffraction (RHEED), high resolution transmission electron microscopy (HRTEM), and Auger electron spectroscopy (AES). The deposited film was single-crystalline CeO2. However, during the deposition, a reaction between CeO2 and Si occurred at the interface, that resulted in the formation of an oxygen deficient amorphous CeO2−x and SiO2 layer. Post annealing in oxygen atmosphere caused the regrowth of crystalline CeO2 from CeO2−x and increased of the SiO2 thickness. The modified structure of CeO2/SiO2/Si is expected to be useful as a silicon-on-insulator structure since it maintains the desirable SiO2/Si interface followed by a single-crystal insulating film lattice-matched to Si.
Tissue Doppler gated (TDOG) dynamic three‐dimensional ultrasound imaging of the fetal heart (2004)

Dynamic three-dimensional (3D) ultrasound imaging of the fetal heart is difficult due to the absence of an electrocardiogram (ECG) signal for synchronization between loops. In this study we introduce tissue Doppler gating (TDOG), a technique in which tissue Doppler data are used to calculate a gating signal. We have applied this cardiac gating method to dynamic 3D reconstructions of the heart of eight fetuses aged 20-24 weeks. The gating signal was derived from the amplitude and frequency contents of the tissue Doppler signal. We used this signal as a replacement for ECG in a 3D-volume reconstruction and visualization, utilizing techniques established in ECG-gated 3D echocardiography. The reliability of the TDOG signal for fetal cardiac cycle detection was experimentally investigated. Simultaneous recordings of tissue Doppler of the heart and continuous wave (CW) spectral Doppler of the umbilical artery (UA) were performed using two independent ultrasound systems, and the TDOG signal from one system was compared to the Doppler spectrum data from the other system. Each recording consisted of a two-dimensional (2D) sector scan, transabdominally and slowly tilted by the operator, covering the fetal heart over approximately 40 cardiac cycles. The total angle of the sweep was estimated by recording a separate loop through the center of the heart, in the elevation direction of the sweep.3D reconstruction and visualization were performed with the EchoPAC-3D software (GE Medical Systems). The 3D data were visualized by showing simultaneous cineloops of three 2D slices, as well as by volume projections running in cineloop. Synchronization of B-mode cineloops with the TDOG signal proved to be sufficiently accurate for reconstruction of high-quality dynamic 3D data. We show one example of a B-mode recording with a frame rate of 96 frames/s over 20 seconds. The reconstruction consists of 31 volumes, each with 49 tilted frames. With the fetal heart positioned 5-8 cm from the transducer, the sampling distances were approximately 0.15 mm in the beam direction, 0.33 degrees approximately 0.37 mm azimuth and 0.45 degrees approximately 0.51 mm elevation. From this single dataset we were able to generate a complete set of classical 2D views (such as four-chamber, three-vessel and short-axis views as well as those of the ascending aorta, aortic and ductal arches and inferior and superior venae cavae) with high image quality adequate for clinical use.
Fully convolutional networks for semantic segmentation (2015)

Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, exceed the state-of-the-art in semantic segmentation. Our key insight is to build “fully convolutional” networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet [20], the VGG net [31], and GoogLeNet [32]) into fully convolutional networks and transfer their learned representations by fine-tuning [3] to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves state-of-the-art segmentation of PASCAL VOC (20% relative improvement to 62.2% mean IU on 2012), NYUDv2, and SIFT Flow, while inference takes less than one fifth of a second for a typical image.
Interleukin‐8 modulates growth and invasiveness of estrogen receptor‐negative breast cancer cells (2007)

Breast cancer, especially estrogen receptor (ER)-negative breast cancer, remains hard to treat despite major advances in surgery and adjuvant therapies. The deletion of ER has been consistently associated with tumor progression, recurrence, metastasis and poor prognosis. Among other differences in biological features, ER-negative breast cancers express high levels of interleukin-8 (IL-8), whereas their ER-positive counterparts do not. IL-8 is a multi-functional cytokine with many important biological functions in tumor formation and development. We aimed to study the role(s) of IL-8 in ER-negative breast cancer progression by using RNA interference to specifically knockdown IL-8 expression in ER-negative breast cancer cell lines MDA-MB-231 and MDA-MB-468. In vitro, suppression of IL-8 led to significant reductions in cell invasion (p<0.001), but had no effects on cell proliferation or cell cycle. In vivo, suppression of IL-8 significantly reduced the microvessel density (p<0.05), and markedly reduced neutrophil infiltration into the tumors (p<0.05). In contrast to in vitro observations, suppression of IL-8 promoted tumor growth in nude mice (p<0.05). Our results imply that the complex roles of IL-8 in the regulation of ER-negative breast cancer progression may in part be related to its potent chemotactic effects on neutrophils, which in turn mediates many of the biological functions of IL-8.
A 100 nm thick InGaN/GaN multiple quantum-well column-crystallized thin film deposited on Si(111) substrate and its micromachining (2007)

A 100 nm thick InGaN/GaN multiple quantum-well column-crystallized thin film was deposited on Si(111) substrate, with InN as the interlayer, by molecular beam epitaxy. The diameter of the column crystal is about 40 nm. Transmission electron microscopy images showed clear five-period well layers. Photoluminescence measurements demonstrated a wide emission wavelength from about 500 to 800 nm with the full width at half maximum of 107 nm at room temperature. An unusual photoluminescence peak position shift was observed from the optical measurement. The selected area electron diffraction image demonstrated the hexagonal wurtzite structure of the column crystal. A self-supported GaN-based active subwavelength grating was proposed, and the active subwavelength grating structure was fabricated from the InGaN/GaN quantum-well thin film by a Si micromachining process.
Metabolomics Identifies Pyrimidine Starvation as the Mechanism of 5-Aminoimidazole-4-Carboxamide-1-β-Riboside-Induced Apoptosis in Multiple Myeloma Cells (2013)

To investigate the mechanism by which 5-aminoimidazole-4-carboxamide-1-β-riboside (AICAr) induces apoptosis in multiple myeloma cells, we conducted an unbiased metabolomics screen. AICAr had selective effects on nucleotide metabolism, resulting in an increase in purine metabolites and a decrease in pyrimidine metabolites. The most striking abnormality was a 26-fold increase in orotate associated with a decrease in uridine monophosphate (UMP) levels, indicating an inhibition of UMP synthetase (UMPS), the last enzyme in the de novo pyrimidine biosynthetic pathway, which produces UMP from orotate and 5-phosphoribosyl-α-pyrophosphate (PRPP). As all pyrimidine nucleotides can be synthesized from UMP, this suggested that the decrease in UMP would lead to pyrimidine starvation as a possible cause of AICAr-induced apoptosis. Exogenous pyrimidines uridine, cytidine, and thymidine, but not purines adenosine or guanosine, rescued multiple myeloma cells from AICAr-induced apoptosis, supporting this notion. In contrast, exogenous uridine had no protective effect on apoptosis resulting from bortezomib, melphalan, or metformin. Rescue resulting from thymidine add-back indicated apoptosis was induced by limiting DNA synthesis rather than RNA synthesis. DNA replicative stress was identified by associated H2A.X phosphorylation in AICAr-treated cells, which was also prevented by uridine add-back. Although phosphorylation of AICAr by adenosine kinase was required to induce multiple myeloma cell death, apoptosis was not associated with AMP-activated kinase activation or mTORC1 inhibition. A possible explanation for inhibition of UMP synthase activity by AICAr was a depression in cellular levels of PRPP, a substrate of UMP synthase. These data identify pyrimidine biosynthesis as a potential molecular target for future therapeutics in multiple myeloma cells.
Transducteur torique à Ultrasons Focalisés de Haute Intensité pour générer des ablations volumineuses : applications précliniques pour le traitement des métastases hépatiques de cancers colorectaux (2008)

Une sonde medicale peroperatoire de therapie ultrasonore dediee a l’ablation thermique des metastases hepatiques de cancers colorectaux (MHCCR) a ete developpee et validee au stade preclinique sur le modele porcin. L’objectif de ces travaux etait de proposer un nouvel outil complementaire a la resection chirurgicale. Un transducteur HIFU torique a imagerie integree a ete mis au point pour generer des lesions volumineuses (7cm3, 40s). Les caracteristiques de ces lesions ont ete etudiees en modelisation et lors d’essais precliniques in vivo. Des etudes de ciblage ont fait intervenir un modele pseudotumoral implante dans le foie. Ses caracteristiques acoustiques ont ete validees comme compatibles avec l’ablation par HIFU. La strategie therapeutique mise en place (parametre de tirs, approche peroperatoire, guidage echographique) a permis de traiter les pseudotumeurs avec des marges negatives. Des ablations homogenes ont egalement ete realisees au contact de vaisseaux de 8 mm de diametre dans des regions peu accessibles (confluent cavo-sus-hepatique). Puis, la sonde torique a ete utilisee comme outil pour la resection chirurgicale assistee par HIFU (RA-HIFU). La RA-HIFU apporte des ameliorations significatives en terme de controle vasculaire. Enfin, les effets des mouvements du foie in vivo sur les traitements HIFU ont ete etudies dans une methode combinee de modelisation et d’images echographiques enregistrees sur animaux. Une etude in vivo a montre que le traitement HIFU realise avec la sonde torique etait peu influence par ce type de mouvements. Une etude clinique va etre entreprise au Centre Leon Berard en utilisant la strategie de tir determinee par ces travaux
Use of laser-UV for inactivation of virus in blood products (1987)

Inactivation of virus by UV radiation was examined as a potential method for sterilization of blood products. Samples of attenuated poliovirus, platelets and plasma were uniformly irradiated with a XeCl excimer laser that delivered 40 nsec pulses of UV at 308 nm (UVB308). Intensities and exposure does were varied from 0.11 to 1.40 MW/cm2 and 0.51 to 56.0 J/cm2, respectively. In studies conducted with low intensity UVB308 (less than or equal to 0.17 MW/cm2), using exposure doses greater than or equal to 10.8 J/cm2, it was possible to inactivate poliovirus by 4 to 6 log10. Platelets irradiated with doses less than or equal to 21.5 J/cm2 exhibited minimal damage as assessed by aggregation activity and spontaneous release of serotonin. Examination of the coagulation activity of irradiated plasma indicated that exposure doses less than or equal to 21.5 J/cm2 resulted in less than 20% increase in prothrombin and partial thromboplastin times. The use of UVB308 at a higher intensity (1.4 MW/cm2) over a similar range of exposure doses did not enhance viral inactivation but did result in increased damage to platelet and plasma proteins. These results demonstrate that at 308 nm there exists a “window of efficacy” for exposure doses between 10.8 and 21.5 J/cm2 and peak intensities less than or equal to 0.17 MW/cm2 in which a hardy virus is significantly inactivated and platelets and plasma proteins are, by functional criteria, minimally affected. Increased viral inactivation cannot be accomplished with higher UV intensities and will require additional or alternate measures.
Genome-Wide Mapping of in Vivo Protein-DNA Interactions (2007)

In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area >/= 0.96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.
Dexmedetomidine inhibits astrocyte pyroptosis and subsequently protects the brain in in vitro and in vivo models of sepsis (2019)

Sepsis is life-threatening and often leads to acute brain damage. Dexmedetomidine, an α<sub>2</sub>-adrenoceptor agonist, has been reported to possess neuroprotective effects against various brain injury but underlying mechanisms remain elusive. In this study, in vitro and in vivo models of sepsis were used to explore the effects of dexmedetomidine on the inflammasome activity and its associated glia pyroptosis and neuronal death. In vitro, inflammasome activation and pyroptosis were found in astrocytes following lipopolysaccharide (LPS) exposure. Dexmedetomidine significantly alleviated astrocyte pyroptosis and inhibited histone release induced by LPS. In vivo, LPS treatment in rats promoted caspase-1 immunoreactivity in astrocytes and caused an increase in the release of pro-inflammatory cytokines of IL-1β and IL-18, resulting in neuronal injury, which was attenuated by dexmedetomidine; this neuroprotective effect was abolished by α<sub>2</sub>-adrenoceptor antagonist atipamezole. Dexmedetomidine significantly reduced the high mortality rate caused by LPS challenge. Our data demonstrated that dexmedetomidine may protect glia cells via reducing pyroptosis and subsequently protect neurons, all of which may preserve brain function and ultimately improve the outcome in sepsis.
On the self-similar nature of Ethernet traffic (extended version) (1994)

Demonstrates that Ethernet LAN traffic is statistically self-similar, that none of the commonly used traffic models is able to capture this fractal-like behavior, that such behavior has serious implications for the design, control, and analysis of high-speed, cell-based networks, and that aggregating streams of such traffic typically intensifies the self-similarity ("burstiness") instead of smoothing it. These conclusions are supported by a rigorous statistical analysis of hundreds of millions of high quality Ethernet traffic measurements collected between 1989 and 1992, coupled with a discussion of the underlying mathematical and statistical properties of self-similarity and their relationship with actual network behavior. The authors also present traffic models based on self-similar stochastic processes that provide simple, accurate, and realistic descriptions of traffic scenarios expected during B-ISDN deployment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fixed-Income Arbitrage: Analytical Techniques and Strategies (1993)

A Repertoire of Arbitrage Techniques. The Global Fixed-Income Securities Markets. Analytical Tools for Fixed-Income Securities. Advanced Models and Algorithms. Fixed-Income Analytics on the Trading Floor. Relative-Value Trading in Short-Maturity Instruments. Yield Spreads in the Intermediate- and Long-Maturity Sectors. Relative-Volatility Trading in Bond Options. Critical Success Factors of an Arbitrage Trading Unit. Index.
Antibody Repertoire Development in Fetal and Neonatal Piglets. I. Four VH Genes Account for 80 Percent of VH Usage During 84 Days of Fetal Life (1998)

VDJ rearrangement and VH gene usage during fetal development in 35 outbred piglets was examined by PCR amplification of VDJs; VDJs were subsequently characterized by hybridization with VH-specific gene probes and by sequencing. VDJ rearrangement was first seen in the fetal liver on day 30 of a 114-day gestation. Four VH genes (V(H)A, V(H)B, V(H)C, and V(H)E) accounted for approximately 80% of all VH gene usage regardless of gestational age, choice of piglet, or lymphoid tissue tested; D(H)A and D(H)B were used in >90% of the fetal VDJs examined. Evidence of somatic hypermutation during fetal development was not found. The proportion of the four prominent fetal VH genes did not differ significantly between cDNA and DNA, suggesting the absence of selective B cell differentiation. A comparison of recombination signal sequences, flanking sequences, and framework sequences of these fetal genes with other germline VH genes of swine offered no clue as to their selective usage. N-region additions were prominent on day 40 but not on day 30, suggesting that the onset of terminal deoxynucleotidyltransferase activity occurs after 30 days of fetal development. These collective findings indicate that the preimmune, "natural Ab" repertoire of the fetal piglet is largely restricted to the use of four nonpolymorphic and nonmutated VH genes and two nonmutated DH segments. This suggests that the preimmune repertoire of swine is either highly restricted or almost entirely determined by junctional diversity in complementarity-determining region-3.
Multiple sclerosis, seizures, and antiepileptics: role of IL-18, IDO, and melatonin (2010)

To review the treatment and mechanisms underlying the increased prevalence of seizures associated with multiple sclerosis (MS). We carried out an extensive review of the literature pertaining to seizures in MS. We propose that an increase in interleukin-18, and its associated induction of indoleamine 2, 3-dioxygenase and quinolinic acid, mediates seizure activity in MS at least in part via an increase in interferon-gamma (IFNg). Increased kynurenine pathway activity decreases the availability of serotonin and melatonin. Increases in blood-brain barrier and circumventricular organ permeability are linked to these changes. Antiepileptic drugs modulate wider MS symptomatology, interacting with melatonin and vitamin D3. This manuscript provides a framework for the wider understanding and treatment of seizures in MS and wider MS symptomatology.
Discovery and Characterization of Novel Cyclotides Originated from Chimeric Precursors Consisting of Albumin-1 Chain a and Cyclotide Domains in the Fabaceae Family (2011)

The tropical plant Clitoria ternatea is a member of the Fabaceae family well known for its medicinal values. Heat extraction of C. ternatea revealed that the bioactive fractions contained heat-stable cysteine-rich peptides (CRPs). The CRP family of A1b (Albumin-1 chain b/leginsulins), which is a linear cystine knot CRP, has been shown to present abundantly in the Fabaceae. In contrast, the cyclotide family, which also belongs to the cystine knot CRPs but with a cyclic structure, is commonly found in the Rubiaceae, Violaceae, and Cucurbitaceae families. In this study, we report the discovery of a panel of 15 heat-stable CRPs, of which 12 sequences (cliotide T1-T12) are novel. We show unambiguously that the cliotides are cyclotides and not A1bs, as determined by their sequence homology, disulfide connectivity, and membrane active properties indicated by their antimicrobial activities against Escherichia coli and cytotoxicities to HeLa cells. We also show that cliotides are prevalent in C. ternatea and are found in every plant tissue examined, including flowers, seeds, and nodules. In addition, we demonstrate that their precursors are chimeras, half from cyclotide and the other half from Albumin-1, with the cyclotide domain displacing the A1b domain in the precursor. Their chimeric structures likely originate from either horizontal gene transfer or convergent evolution in plant nuclear genomes, which are exceedingly rare events. Such atypical genetic arrangement also implies a different mechanism of biosynthetic processing of cyclotides in the Fabaceae and provides new understanding of their evolution in plants.
Study of the Assembly of Vesicular Stomatitis Virus N Protein: Role of the P Protein (2000)

To derive structural information about the vesicular stomatitis virus (VSV) nucleocapsid (N) protein, the N protein and the VSV phosphoprotein (P protein) were expressed together in Escherichia coli. The N and P proteins formed soluble protein complexes of various molar ratios when coexpressed. The major N/P protein complex was composed of 10 molecules of the N protein, 5 molecules of the P protein, and an RNA. A soluble N protein-RNA oligomer free of the P protein was isolated from the N/P protein-RNA complex using conditions of lowered pH. The molecular weight of the N protein-RNA oligomer, 513,879, as determined by analytical ultracentrifugation, showed that it was composed of 10 molecules of the N protein and an RNA of approximately 90 nucleotides. The N protein-RNA oligomer had the appearance of a disk with outer diameter, inner diameter, and thickness of 148 +/- 10 A, 78 +/- 9 A, and 83 +/- 8 A, respectively, as determined by electron microscopy. RNA in the complexes was protected from RNase digestion and was stable at pH 11. This verified that N/P protein complexes expressed in E. coli were competent for encapsidation. In addition to coexpression with the full-length P protein, the N protein was expressed with the C-terminal 72 amino acids of the P protein. This portion of the P protein was sufficient for binding to the N protein, maintaining it in a soluble state, and for assembly of N protein-RNA oligomers. With the results provided in this report, we propose a model for the assembly of an N/P protein-RNA oligomer.