gebhart/patrepeval huggingface dataset:
Data Transmission Using Wavelength-Selective Spatial Routing for Photonic Interconnection Networks (2011)

Wavelength-selective spatial routing is proposed for photonic networks and demonstrated on an electro-optic microring switch. This technique yields greater path diversity in photonic networks, enabling improved overall network performance.
Apolipoprotein C-III displacement of apolipoprotein E from VLDL: effect of particle size (1999)

ApoC-III and apoE are important determinants of intravascular lipolysis and clearance of triglyceride-rich chylomicrons and VLDL from the blood plasma. Interactions of these two apolipoproteins were studied by adding purified human apoC-III to human plasma at levels observed in hypertriglyceridemic subjects and incubating under specific conditions (2 h, 37 degrees C). As plasma concentrations of apoC-III protein were increased, the contents in both VLDL and HDL were also increased. Addition of apoC-III at concentrations up to four times the intrinsic concentration resulted in the decreasing incremental binding of apoC-III to VLDL while HDL bound increasing amounts without evidence of saturation. No changes were found in lipid content or in particle size of any lipoprotein in these experiments. However, distribution of the intrinsic apoE in different lipoprotein particles changed markedly with displacement of apoE from VLDL to HDL. The fraction of VLDL apoE that was displaced from VLDL to HDL at these high apoC-III concentrations varied among individuals from 20% to 100% its intrinsic level. The proportion of VLDL apoE that was tightly bound (0% to 80%) was found to be reproducible and to correlate with several indices of VLDL particle size. In the group of subjects studied, strongly adherent apoE was essentially absent from VLDL particles having an average content of less than 50,000 molecules of triglyceride. Addition of apoC-III to plasma almost completely displaces apoE from small VLDL particles. Larger VLDL contain tightly bound apoE which are not displaced by increasing concentration of apoC-III.
Spontaneously Occurring Tumors of Companion Animals as Models for Human Cancer (2000)

Spontaneous tumors in companion animals (dog and cat) offer a unique opportunity as models for human cancer biology and translational cancer therapeutics. The relatively high incidence of some cancers, similar biologic behavior, large body size, comparable responses to cytotoxic agents, and shorter overall lifespan are the factors that contribute to the advantages of the companion animal model. The tumor types that offer the best comparative interest include lymphoma/leukemia, osteosarcoma, STS, melanoma, and mammary tumors. With the increase in new therapeutic agents (traditional chemotherapy, gene therapy, biologic agents, etc.), the companion animal model can provide useful populations to test new agents where efficacy and toxicity can be examined.
DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. (1994)

Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins. A method for the reassembly of genes from their random DNA fragments, resulting in in vitro recombination is reported. A 1-kb gene, after DNase I digestion and purification of 10- to 50-bp random fragments, was reassembled to its original size and function. Similarly, a 2.7-kb plasmid could be efficiently reassembled. Complete recombination was obtained between two markers separated by 75 bp; each marker was located on a separate gene. Oligonucleotides with 3' and 5' ends that are homologous to the gene can be added to the fragment mixture and incorporated into the reassembled gene. Thus, mixtures of synthetic oligonucleotides and PCR fragments can be mixed into a gene at defined positions based on homology. As an example, a library of chimeras of the human and murine genes for interleukin 1 beta has been prepared. Shuffling can also be used for the in vitro equivalent of some standard genetic manipulations, such as a backcross with parental DNA. The advantages of recombination over existing mutagenesis methods are likely to increase with the numbers of cycles of molecular evolution.
Carotenoid‐binding proteins of photosystem II (1993)

The distribution of the photosynthetic pigments of the chlorophyll-binding proteins or photosystem-II membranes, isolated from dark-adapted maize leaves was determined. Most (80%) of a xanthophyll, violaxanthin, was found in the three minor chlorophyll-a/b proteins CP24, CP26 and CP29 whose function is unknown. Violaxanthin is the precursor of zeaxanthin, which is involved in dissipating excess excitation energy into heat [Demmig-Adams, B. (1991) Biochim. Biophys. Acta 1020, 1-24] under conditions of high transmembrane pH gradient [Gilmore, A. M. & Yamamoto, H. Y. (1992) Proc. Natl Acad. Sci. USA 89, 1899-1903]. We propose that a role for the minor photosystem-II chlorophyll-a/b proteins is the regulation of energy transfer to the reaction centre. It was also confirmed that the photosystem II reaction centre (D1-D2-cytochrome b559) contains beta-carotene as the only carotenoid. However, the two other chlorophyll-a-binding proteins of photosystem II, CP47 and CP43, bind not only beta-carotene, but also the xanthophyll lutein, previously thought to be restricted to chlorophyll-a/b proteins.
Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome (2012)

Cockayne syndrome (CS) is a human premature aging disorder associated with neurological and developmental abnormalities, caused by mutations mainly in the CS group B gene (ERCC6). At the molecular level, CS is characterized by a deficiency in the transcription-couple DNA repair pathway. To understand the role of this molecular pathway in a pluripotent cell and the impact of CSB mutation during human cellular development, we generated induced pluripotent stem cells (iPSCs) from CSB skin fibroblasts (CSB-iPSC). Here, we showed that the lack of functional CSB does not represent a barrier to genetic reprogramming. However, iPSCs derived from CSB patient's fibroblasts exhibited elevated cell death rate and higher reactive oxygen species (ROS) production. Moreover, these cellular phenotypes were accompanied by an up-regulation of TXNIP and TP53 transcriptional expression. Our findings suggest that CSB modulates cell viability in pluripotent stem cells, regulating the expression of TP53 and TXNIP and ROS production.
RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression (2015)

RNA utilizes many different mechanisms to control gene expression. Among the regulatory elements that respond to external stimuli, riboswitches are a prominent and elegant example. They consist solely of RNA and couple binding of a small molecule ligand to the so-called "aptamer domain" with a conformational change in the downstream "expression platform" which then determines system output. The modular organization of riboswitches and the relative ease with which ligand-binding RNA aptamers can be selected in vitro against almost any molecule have led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology over the past decade. This review highlights proof-of-principle applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression in pro- and eukaryotes. It then focuses on strategies and parameters to identify aptamers that can be integrated into synthetic riboswitches that are functional in vivo, before finishing with a reflection on how to improve the regulatory properties of engineered riboswitches, so that we can not only further expand riboswitch applicability, but also finally fully exploit their potential as control elements in regulating gene expression.
215. Placental expression of uncoupling protein-2 is reduced by glucocorticoid treatment in late pregnancy: implications for placental oxidative stress (2008)

Placental oxidative stress plays a key role in the pathophysiology of placenta-related disorders in humans, most notably in preeclampsia (PE) and intrauterine growth restriction (IUGR). Protection from oxidative stress is provided by antioxidant enzymes including superoxide dismutase-1 and 2 (SOD-1 and –2) and catalase (CAT), which convert reactive oxygen species (ROS) to inert products. It has also been proposed that uncoupling protein-2 (UCP2) may limit oxidative stress by reducing ROS production, but little is known of UCP2 expression in placenta. Here we measured placental UCP2, SOD-1, SOD-2 and CAT mRNA expression (by qRT–PCR) in normal gestation and after glucocorticoid-induced IUGR. The latter was included because glucocorticoids can increase oxidative stress in other tissues, and placental glucocorticoid exposure is elevated in both PE and IUGR. Placentas were collected on days 16 and 22 of normal pregnancy (term = day 23) and on day 22 after dexamethasone treatment (0.75 mg/mL in drinking water from day 13). The two morphologically-distinct regions of the placenta, the junctional (JZ) and labyrinth (LZ) zones, were analysed separately because effectively all growth occurs in the LZ over this period. Expression of UCP2 in LZ exceeded that in JZ (P &lt; 0.001) and increased in both zones between days 16 and 22 (LZ: 2.0-fold; JZ: 3.2-fold). Dexamethasone treatment reduced UCP2 in LZ (44%; P &lt; 0.05) but not in JZ. SOD1 and SOD2 increased with gestational age in LZ (P &lt; 0.01) and JZ (P &lt; 0.05), but neither were affected by dexamethasone. CAT expression was higher (2.4-fold, P &lt; 0.001) in LZ compared with JZ but did not change with gestational age or dexamethasone. In summary, these data suggest that endogenous protection against oxidative stress increases in the rat placenta during late pregnancy. Moreover, this protection may be compromised by reduced placental UCP2 expression in a model of glucocorticoid-induced IUGR.
Digital predistortion based on envelope feedback (2012)

A new digital predistortion (DPD) technique based on envelope feedback is proposed for linearization of power amplifiers (PAs). Unlike conventional DPD techniques that need frequency down converters (FDCs) in the feedback path to recover the complex envelope of the PA output, the proposed technique does not need an FDC. Instead it employs two envelope detectors, estimating the envelope of the PA output and that of the difference signal between the PA input and the PA output. It is shown that the complex envelope of the PA output can be estimated from the two envelope feedbacks if the sign of the phase distortion of the AM-PM characteristic remains the same for all PA input magnitudes. Simulation results show that the performance of the proposed DPD is comparable to the conventional DPD employing an FDC.
Lossless data compression for short duration 3D frames in positron emission tomography (2005)

H/sub 2/O/sup 15/ 3D bolus studies and other dynamic 3D protocols in positron emission tomography (PET) require frame durations of five seconds or less as the protocol begins, with required frame durations increasing as the study progresses. A goal in PET acquisition is sustained 3D frame duration of ten seconds, with shorter frame durations allowed for a limited time. Transfer of projection arrays to an acquisition hard disk is a major limit of frame duration. Data compression can be used to increase the effective disk throughput and therefore decrease the sustained frame duration. The authors discuss the use of lossless compression hardware in a modern PET 3D acquisition system. The hardware uses an implementation of Lempel-Ziv compression with an estimated sustained throughput of 20 megabytes per second and compression ratios of 3 to 10 for short duration 3D projections arrays. Compression use can decrease the minimum sustainable frame duration to less than 10 seconds for an ECAT EXACT HR.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tensile properties of the supraspinatus tendon (1995)

The tensile properties of the supraspinatus tendon were investigated in 11 shoulders from fresh cadavers. The tendon was divided into three longitudinal strips: anterior, middle, and posterior. Each specimen was mounted on a materials testing machine, with four fluorescent markers placed on both surfaces of the tendon strip. The positions of these markers were recorded during the test by two synchronized video cameras. Load-deformation and strain curves were determined, and the stress-strain curve, strength, and modulus of elasticity were calculated. The posterior strip was thinner in cross section than the others (p = 0.0355). The ultimate load and ultimate stress were significantly greater in the anterior strip (16.5 +/- 7.1 MPa) than in the middle (6.0 +/- 2.6 MPa) and posterior (4.1 +/- 1.3 MPa) strips (p < 0.0001). The modulus of elasticity also was significantly greater in the anterior strip (p < 0.0001), but there was no significant difference between the superficial and deep surfaces. It is concluded that the anterior portion of the supraspinatus tendon is mechanically stronger than the other portions, and it seems to perform the main functional role of the tendon.
Photofrin photodynamic therapy for treatment of AIDS-related cutaneous Kaposi‚s sarcoma (1999)

Photofrin is effective palliative treatment for HIV-associated Kaposi's sarcoma.
Hematopoietic stem cell compartment: Acute and late effects of radiation therapy and chemotherapy (1995)

The bone marrow is an important dose-limiting cell renewal tissue for chemotherapy, wide-field irradiation, and autologous bone marrow transplantation. Over the past 5-10 years a great deal has been discovered about the hematopoietic stem cell compartment. Although the toxicity associated with prolonged myelosuppression continues to limit the wider use of chemotherapy and irradiation, ways are being discovered to circumvent this toxicity such as with the increasing use of cytokines. This review describes what is known of how chemotherapy and irradiation damage stem cells and the microenvironment, how cytokines protect hematopoietic cells from radiation damage and speed marrow recovery after chemotherapy or marrow transplantation, and how various types of blood marrow cells contribute to engraftment and long-term hematopoiesis after high doses of cytotoxic agents and/or total body irradiation.
Analysis and optimization of intensity noise reduction in spectrum-sliced WDM systems using a saturated semiconductor optical amplifier (2002)

Theoretical and experimental results on the reduction of the intensity noise in spectrum-sliced wavelength-division-multiplexing systems using a saturated semiconductor optical amplifier (SOA) are presented. The influence of the injected current and the input power to the saturated SOA on the noise reduction and its bandwidth are studied. The optimum condition for a high noise suppression ratio and a large bandwidth is derived. For the optimum operation of the SOA, an increase of 13.5 dB in the intensity-noise-limited signal-to-noise ratio for a bitrate of 2.488 Gb/s and of 17.5 dB for a bitrate of 622 Mb/s are obtained experimentally in a single-stage SOA.
A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family (2009)

CHS1/LYST, the causative protein of the Chediak-Higashi syndrome (CHS), belongs to the BEACH (named after BEige And Chediak-Higashi) family, which includes various large proteins sharing the same C-terminal domain architecture [a PH (Pleckstrin homology)-BEACH domain followed by WD repeats). Members of the BEACH family are generally defined as vesicle-trafficking regulatory proteins, but their functions remain to be determined at the molecular level. Here, using a panel of sensitive methods of sequence analysis, we show that the N-terminal regions of BEACH proteins contain an as yet not described domain, which shares striking similarities with clostridial neurotoxins and defines a novel family within the concanavalin A (ConA)-like lectin superfamily. These results suggest that the BEACH ConA-like lectin domain could be involved in oligosaccharide binding associated with protein traffic and sorting along the secretory pathway, especially in relation with components of the vesicle fusion machinery.
Identification of a surface-exposed immunodominant epitope on outer membrane protein P1 of Haemophilus influenzae type b (1991)

Eight murine monoclonal antibodies (MAbs) directed against outer membrane protein P1 of Haemophilus influenzae type b were generated and characterized. Seven of the eight MAbs reacted with recombinant P1 and purified P1 protein from H. influenzae type b strains MinnA and 1613; MAb P1.8 was specific for the latter strain. A panel of 32 nontypeable and 140 encapsulated Haemophilus strains recovered worldwide representing the major clonal families of serotypes a, b, and d was used to evaluate the distribution among Haemophilus strains of the epitopes identified by the P1-specific MAbs. The epitope reactive with the seven MAbs which recognized P1 from strains MinnA and 1613 was shared by 92% of the encapsulated Haemophilus isolates tested. The epitope is present in the H. influenzae type b strains from clonal families commonly recovered from cases of invasive disease in North America and Europe. A series of nested 5' and 3' deletions of the P1 gene were constructed and analyzed to localize the determinants on P1 recognized by the MAbs. MAbs P1.2, P1.4, P1.5, P1.6, and P1.7 recognized an epitope localized to the carboxy-terminal portion of P1. Murine MAbs P1.1 and P1.3 and two human MAbs, HiH-7 and HiH-10, recognized a complex epitope which was partially localized to the carboxy-terminal portion of the P1 protein. These data indicate that an immunodominant surface-exposed epitope is present on the carboxy-terminal portion of the P1 protein of type b Haemophilus isolates responsible for the majority of invasive disease in North America.
A Portfolio Performance Index (2000)

Fund managers may sensibly be averse to earning a time-averaged portfolio return that is less than the average return of some designated benchmark. When a portfolio is expected to earn a higher average return than the benchmark return, the probability that it will not approaches zero asymptotically at a computable exponential decay rate. The probability decay rate is thus proposed here as a new portfolio “performance index.” In the widely analyzed special case in which returns are normally distributed, the new performance-index-maximizing portfolio is the same as the popular Sharpe-ratio-maximizing portfolio. The results of the two approaches generally differ, however, because of nonnormal levels of skewness and/or kurtosis in the portfolio attributable to large asymmetrical economic shocks or investments in options and other derivative securities. An illustrative example will show that the new index is easy to implement and, consistent with empirical evidence on portfolio choice, favors investments with positively skewed returns.
Developing the next generation cockpit display system (2002)

The goal of advanced cockpit display systems is to present large amounts of information quickly and in an understandable format, enabling the aviator to improve mission performance. Wright Laboratory is developing a program to dramatically improve current display systems. Current front-line cockpit display systems utilize low-resolution analog video to present two dimensional (2-D) images on many separate displays. The future cockpit will be capable of integrating large picture digital video with three dimensional (3-D) and 2-D color images. This system will be capable of rendering icons, maps, and world-views. It will be compatible with head mounted displays and multiple large displays to improve war-planning and combat aviator situational awareness. We are developing a massively parallel 3D renderer which will be capable of updating 500,000 3-D triangles per second with shading, lighting, transparency, texture mapping, and hidden surface removal. The renderer design, based on a University of North Carolina pixel planes design, employs a massively parallel architecture. The rendering system will be small enough to fit on one board, extensible to dual-seat configuration, and capable of up to eight windows per display channel.
Cross-Reactive T-Cell Responses to the Nonstructural Regions of Dengue Viruses among Dengue Fever and Dengue Hemorrhagic Fever Patients in Malaysia (2007)

Dengue virus infections are a major cause of morbidity and mortality in tropical and subtropical areas in the world. Attempts to develop effective vaccines have been hampered by the lack of understanding of the pathogenesis of the disease and the absence of suitable experimental models for dengue viral infection. The magnitude of T-cell responses has been reported to correlate with dengue disease severity. Sixty Malaysian adults with dengue viral infections were investigated for their dengue virus-specific T-cell responses to 32 peptides antigens from the structural and nonstructural regions from a dengue virus isolate. Seventeen different peptides from the C, E, NS2B, NS3, NS4A, NS4B, and NS5 regions were found to evoke significant responses in a gamma interferon enzyme-linked immunospot (ELISPOT) assay of samples from 13 selected patients with dengue fever (DF) and dengue hemorrhagic fever (DHF). NS3 and predominantly NS3(422-431) were found to be important T-cell targets. The highest peaks of T-cell responses observed were in responses to NS3(422-431) and NS5(563-571) in DHF patients. We also found almost a sevenfold increase in T-cell response in three DHF patients compared to three DF patient responses to peptide NS3(422-431). A large number of patients' T cells also responded to the NS2B(97-106) region. The ELISPOT analyses also revealed high frequencies of T cells that recognize both serotype-specific and cross-reactive dengue virus antigens in patients with DHF.
Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization (1993)

Human cDNAs for cytosolic and mitochondrial serine hydroxymethyltransferase (SHMT) were cloned by functional complementation of an Escherichia coli glyA mutant with a human cDNA library. The cDNA for the cytosolic enzyme encodes a 483-residue protein of M(r) 53,020. The cDNA for the mitochondrial enzyme encodes a mature protein of 474 residues of M(r) 52,400. The deduced protein sequences share a high degree of sequence identity to each other (63%), and the individual isozymes are highly homologous to the analogous rabbit liver cytosolic (92% identity) and mitochondrial (97% identity) SHMT isozymes (Martini, F., Angelaccio, S., Pascarella, S., Barra, D., Bossa, F., and Schirch, V. (1987) J. Biol. Chem. 262, 5499-5509; Martini, F., Maras, B., Tanci, P., Angelaccio, S., Pascarella, S., Barra, D., Bossa, F., and Schirch, V. (1989) J. Biol. Chem. 264, 8509-8519). SHMT is a highly conserved protein with the human isozymes retaining about 43% sequence identity with the E. coli protein. The human cytosolic and mitochondrial SHMT genes were localized to chromosome regions 17p11.2 and 12q13, respectively. The high degree of nucleotide sequence identity between the two isozymes, and the presence of keratin genes in both chromosomal regions, is consistent with these regions of chromosome 12 and 17 arising by a duplication event.