gebhart/patrepeval huggingface dataset:
Minimum weight design of axisymmetric sandwich plates (1976)

The problem of minimum weight design of laminated circular sandwich plates with axial symmetry is formulated using optimal control theory. A steepest descent algorithm is used to solve the resulting two-point boundary value problem. Inequality constraints on minimum face and core thicknesses, maximum stress levels, and maximum displacement are included. Both statically determinate and statically indeterminate plates are considered. Several examples are presented illustrating the general configuration of minimum-weight designs and the dramatic weight savings attainable.
Detection of vascular endothelial growth factor in AIDS-related primary effusion lymphomas (2000)

To the editor:

Detection of vascular endothelial growth factor in AIDS-related primary effusion lymphomas

Primary effusion lymphoma (PEL), an infrequent type of AIDS-related non-Hodgkin's lymphoma involving B lymphocytes infected with Kaposi's sarcoma-associated herpesvirus (KSHV) and often
Chemistry and Biology of DNA Containing 1,N2-Deoxyguanosine Adducts of the α,β-Unsaturated Aldehydes Acrolein, Crotonaldehyde, and 4-Hydroxynonenal (2009)

The alpha,beta-unsaturated aldehydes (enals) acrolein, crotonaldehyde, and trans-4-hydroxynonenal (4-HNE) are products of endogenous lipid peroxidation, arising as a consequence of oxidative stress. The addition of enals to dG involves Michael addition of the N(2)-amine to give N(2)-(3-oxopropyl)-dG adducts, followed by reversible cyclization of N1 with the aldehyde, yielding 1,N(2)-dG exocyclic products. The 1,N(2)-dG exocyclic adducts from acrolein, crotonaldehyde, and 4-HNE exist in human and rodent DNA. The enal-induced 1,N(2)-dG lesions are repaired by the nucleotide excision repair pathway in both Escherichia coli and mammalian cells. Oligodeoxynucleotides containing structurally defined 1,N(2)-dG adducts of acrolein, crotonaldehyde, and 4-HNE were synthesized via a postsynthetic modification strategy. Site-specific mutagenesis of enal adducts has been carried out in E. coli and various mammalian cells. In all cases, the predominant mutations observed are G-->T transversions, but these adducts are not strongly miscoding. When placed into duplex DNA opposite dC, the 1,N(2)-dG exocyclic lesions undergo ring opening to the corresponding N(2)-(3-oxopropyl)-dG derivatives. Significantly, this places a reactive aldehyde in the minor groove of DNA, and the adducted base possesses a modestly perturbed Watson-Crick face. Replication bypass studies in vitro indicate that DNA synthesis past the ring-opened lesions can be catalyzed by pol eta, pol iota, and pol kappa. It also can be accomplished by a combination of Rev1 and pol zeta acting sequentially. However, efficient nucleotide insertion opposite the 1,N(2)-dG ring-closed adducts can be carried out only by pol iota and Rev1, two DNA polymerases that do not rely on the Watson-Crick pairing to recognize the template base. The N(2)-(3-oxopropyl)-dG adducts can undergo further chemistry, forming interstrand DNA cross-links in the 5'-CpG-3' sequence, intrastrand DNA cross-links, or DNA-protein conjugates. NMR and mass spectrometric analyses indicate that the DNA interstand cross-links contain a mixture of carbinolamine and Schiff base, with the carbinolamine forms of the linkages predominating in duplex DNA. The reduced derivatives of the enal-mediated N(2)-dG:N(2)-dG interstrand cross-links can be processed in mammalian cells by a mechanism not requiring homologous recombination. Mutations are rarely generated during processing of these cross-links. In contrast, the reduced acrolein-mediated N(2)-dG peptide conjugates can be more mutagenic than the corresponding monoadduct. DNA polymerases of the DinB family, pol IV in E. coli and pol kappa in human, are implicated in error-free bypass of model acrolein-mediated N(2)-dG secondary adducts, the interstrand cross-links, and the peptide conjugates.
The Expression of Interleukin-6 (IL-6), IL-6 Receptor, and gp130-Kilodalton Glycoprotein in the Rat Decidua and a Decidual Cell Line: Regulation by 17β-Estradiol and Prolactin1 (1999)

The cytokine interleukin 6 (IL-6), a major mediator of immune and acute phase responses of the liver, has been implicated in the termination of pregnancy once expressed in the uterus. This study was undertaken to investigate the expression and regulation of genes encoding IL-6 and IL-6 receptor (IL-6R) in rat decidual tissue. Total RNA obtained from rat decidual tissue on different days of pseudopregnancy was analyzed by RT-PCR using specific primers for IL-6, IL-6R, and 130-kDa glycoprotein (gp130). Ribosomal L19 primers served as an internal control. IL-6R and gp130 were found to be expressed in the decidua throughout development, while no messenger RNA (mRNA) for IL-6 was detected. Interestingly, within several hours of culture, decidual explants acquired the ability to express IL-6. The apparent ability of decidual cells to express IL-6 and its lack of expression in vivo led us to examine whether the IL-6 gene is actively inhibited. Primary decidual cells were cultured in the presence of estradiol, progesterone, or PRL. Progesterone showed no effect, whereas estradiol and PRL reduced the level of IL-6 mRNA expression. To examine the mechanism by which these hormones inhibit IL-6 expression, we used a simian virus 40-transformed decidual cell line (GG-AD), which expresses only estrogen receptor-beta (ERbeta). Like primary decidual cells in culture, GG-AD cells express IL-6, IL-6R, and gp130 mRNA. When cultured in the presence of estradiol (0-100 ng/ml), mRNA for IL-6 and its receptor components were down-regulated in a dose-dependent manner. Estradiol also caused a dose-dependent decrease in IL-6 protein secretion into the culture medium. The inhibitory effect of estradiol on IL-6 mRNA expression was reversed by the antiestrogen ICI-164,384. Similar inhibition of IL-6 and gp130 mRNA expression was observed with PRL treatment. However, PRL had no effect on IL-6R mRNA levels. PRL inhibition of IL-6 expression was totally reversed by tyrphostin AG490, a JAK2 inhibitor. In summary, the results of this investigation indicate that IL-6 expression, which is detrimental to the maintenance of pregnancy, is inhibited in the rat decidual tissue. This inhibition is induced by PRL and estradiol, which down-regulate not only IL-6 expression, but also the expression of IL-6 receptor and signaling proteins. The results also suggest that PRL signaling to the IL-6 gene is mediated through the long form of PRL receptor and involves JAK2 activation, whereas that of estradiol can be transduced by estrogen receptor-beta.
On the capacity of a biometrical identification system (2003)

We investigate fundamental properties of biometrical identification systems. We focus on the capacity, i.e. a measure for the number of individuals that can be reliably identified. It can be expressed using standard information-theoretical concepts.
Direct detection of Brucella spp. in raw milk by PCR and reverse hybridization with 16S-23S rRNA spacer probes (1996)

The 16S-23S rRNA spacer regions of Brucella abortus, B. melitensis, and B. suis were cloned and subcloned after PCR amplification. Sequence analysis of the inserts revealed a spacer of about 800 bp with very high ( > 99%) homology among the three species examined. Two genus-specific primer pairs, BRU-P5-BRU-P8 and BRU-P6-BRU-P7, that could be used in a nested PCR format and three genus-specific DNA probes, BRU-ICG2, BRU-ICG3, and BRU-ICG4, were deduced from this spacer. The specificity and sensitivity of both primer sets and probes were examined by testing them against a collection of 18 Brucella strains and 56 strains from other relevant taxa by using PCR and the Line Probe Assay (LiPA), respectively. A method for direct detection of Brucella spp. in 1 ml of raw milk was developed on the basis of enzymatic treatment of the milk components and subsequent PCR and LiPA hybridization. After a single PCR, sensitivities of 2.8 x 10(5) and 2.8 x 10(4) CFU/ml were obtained for detection by agarose gel electrophoresis and LiPA, respectively. Nested PCR yielded a sensitivity of 2.8 x 10(2) CFU/ml for both methods.
Optical Properties of Overfire Soot in Buoyant Turbulent Diffusion Flames at Long Residence Times (1994)

The optical properties of soot were studied for the fuel-lean (overfire) region of buoyant turbulent diffusion flames in still air. Results were limited to the long residence time regime where soot structure is independent of position in the overfire region and residence time for a particular fuel. Measurements included scattering, absorption, and extinction cross sections at 514.5 nm and extinction cross sections at 632.8 and 1152 nm for flames fueled with acetylene, propylene, ethylene, and propane. The measurements were used to evaluate scattering predictions based on the Rayleigh-Debye-Gans (RDG) approximation for randomly oriented poly disperse fractal aggregates of spherical primary soot particles having constant diameters. The present soot aggregates exhibited significant departures from Rayleigh-scattering behavior at 514.5 nm, with forward scattering roughly 100 times larger than wide-angle scattering and ratios of scattering to absorption cross sections in the range 0.22–0.41, increasing with increasing propensity of the fuel to soot. The approximate RDG theory generally provided an acceptable basis to treat the optical properties of the present overfire soot aggregates, although additional measurements in the Guinier (small angle) regime are needed for a definitive evaluation of model performance.
Microencapsulation of perfumes for application in textile industry (2010)

Tese de doutoramento. Engenharia Química. Faculdade de Engenharia. Universidade do Porto. 2010
On-demand, competing gradient arrays for neutrophil chemotaxis (2013)

Neutrophils are the most abundant type of white blood cells in the circulation, protecting the body against pathogens and responding early to inflammation. Although we understand how neutrophils respond to individual stimuli, we know less about how they prioritize between competing signals or respond to combinational signals. This situation is due in part to the lack of adequate experimental systems to provide signals in controlled spatial and temporal fashion. To address these limitations, we designed a platform for generating on-demand, competing chemical gradients and for monitoring neutrophil migration. On this platform, we implemented forty-eight assays generating independent gradients and employed synchronized valves to control the timing of these gradients. We observed faster activation of neutrophils in response to fMLP than to LTB4 and unveiled for the first time a potentiating effect for fMLP during migration towards LTB4. Our observations, enabled by the new tools, challenge the current paradigm of inhibitory competition between distinct chemoattractant gradients and suggest that human neutrophils are capable of complex integration of chemical signals in their environment.
<title>Key transport protocol based on secret sharing: an application to conditional access systems</title> (2001)

In today's digital world, multimedia content is delivered to homes via the Internet, satellite, terrestrial and cable networks. Scrambling is a common approach used by conditional access systems to prevent unauthorized access to audio/visual data. The descrambling keys are securely distributed to the receivers in the same transmission channel. Their protection is an important part of the key management problem. Although public-key cryptography provides a viable solution, alternative methods are sought for economy and efficiency. This paper presents a key transport protocol based on secret sharing. It eliminates the need for a cipher, yet combines the advantages of symmetric and public-key ciphers.
Optofluidic Devices for Droplet and Cell Manipulation (2015)

The field of lab-on-a-chip offers exciting new capabilities for chemical and biological assays, including increased automation, higher throughput, heightened sensitivity of detection, and reduced sample and reagent usage. This area of study has seen remarkable progress in the last decade, with applications ranging from drug development to point-of-care diagnostics. The research presented herein focuses on the development of semiconductor-based optoelectrowetting (OEW) and optoelectronic tweezers (OET) platforms, which can respectively perform operations on droplets and cells/particles. This thesis discusses progress achieved on both OEW and OET platforms. For OEW, a novel optimization model has been developed to accurately predict the interaction of droplets, semiconductor layers, and a programmable DLP-based optical source. Consequently, parallel and arrayed droplet manipulation is now possible over a large operational area (cm Ã cm). In addition, critical droplet operations such as mixing, splitting, and dispensing have been demonstrated. As a biological application of OEW, this work will discuss the parallel, real-time, isothermal polymerase chain reaction detection of Herpes Simplex Virus Type 1 in droplet arrays. For OET, the effort in long-term culture of adherent mammalian single cells into clonal colonies will be discussed; OET surface functionalization enables large (0.5-mm-diameter) growth patches in which positioned single cells can adhere and proliferate. Lastly, the link between the OEW and OET devices and how both droplet and particle manipulation can be enabled on a unified platform will be presented.
Differential bone-forming capacity of osteogenic cells from either embryonic stem cells or bone marrow-derived mesenchymal stem cells (2010)

For more than a decade, human mesenchymal stem cells (hMSCs) have been used in bone tissue-engineering research. More recently some of the focus in this field has shifted towards the use of embryonic stem cells. While it is well known that hMSCs are able to form bone when implanted subcutaneously in immune-deficient mice, the osteogenic potential of embryonic stem cells has been mainly assessed in vitro. Therefore, we performed a series of studies to compare the in vitro and in vivo osteogenic capacities of human and mouse embryonic stem cells to those of hMSCs. Embryonic and mesenchymal stem cells showed all characteristic signs of osteogenic differentiation in vitro when cultured in osteogenic medium, including the deposition of a mineralized matrix and expression of genes involved in osteogenic differentiation. As such, based on the in vitro results, osteogenic ES cells could not be discriminated from osteogenic hMSCs. Nevertheless, although osteogenic hMSCs formed bone upon implantation, osteogenic cells derived from both human and mouse embryonic stem cells did not form functional bone, indicated by absence of osteocytes, bone marrow and lamellar bone. Although embryonic stem cells show all signs of osteogenic differentiation in vitro, it appears that, in contrast to mesenchymal stem cells, they do not possess the ability to form bone in vivo when a similar culture method and osteogenic differentiation protocol was applied.
An MDP model for optimal handover decisions in mmWave cellular networks (2016)

The new frontier in cellular networks is harnessing the enormous spectrum available at millimeter wave (mmWave) frequencies above 28 GHz. The challenging radio propagation characteristics at these frequencies, and the use of highly directional beamforming, lead to intermittent links between the base station (BS) and the user equipment (UE). In this paper, we revisit the problem of cell selection to maintain an acceptable level of service, despite the underlying intermittent link connectivity typical of mmWave links. We propose a Markov Decision Process (MDP) framework to study the properties and performance of our proposed cell selection strategy, which jointly considers several factors such as dynamic channel load and link quality. We use the Value Iteration Algorithm (VIA) to solve the MDP, and obtain the optimal set of associations. We address the multi user problem through a distributed iterative approach, in which each UE characterizes the evolution of the system based on stationary channel distribution and cell selection statistics of other UEs. Through simulation results, we show that our proposed technique makes judicious handoff choices, thereby providing a significant improvement in the overall network capacity. Further, our technique reduces the total number of handoffs, thus lowering the signaling overhead, while providing a higher quality of service to the UEs.
NestCloud: Towards practical nested virtualization (2011)

This paper describes a nested virtualization solution, which allows virtual machine monitor (VMM) with virtual machine to run within another virtual machine with low overhead. Previous nested virtualization solutions on x86 platform are mainly based on emulation, which result in poor performance and poor usability. We propose and implement NestCloud, a practical high performance nested virtualization architecture, which fully employs the hardware virtualization extensions. Furthermore, three optimizations are provided to reduce the overhead of nested guests: (1) Guest Page Fault Bypassing, which permits nested guests to handle page faults without VM Exit; (2) Virtual EPT (Extended Page Table), which eliminates unnecessary page faults introduced by shadow page table in nested VMM; (3) PV VMCS, which provides more effective VMCS accessing for nested VMM. Experimental results show that the performance of NestCloud guest is close to single level guest in both CPU-intensive and memory-intensive benchmarks. The CPU overhead is 5.22% and the memory overhead is 5.69%, which makes the nested guest of NestCloud comparable with a conventional one.
1160. Peptides. Part XVII. Synthesis of peptides and polymers of some sterically hindered amino-acids via oxazolone intermediates (1965)

D. S. Jones, G. W. Kenner, J. Preston and R. C. Sheppard, J. Chem. Soc., 1965, 6227 DOI: 10.1039/JR9650006227
Bovine Leukemia Virus-Induced Persistent Lymphocytosis in Cattle Does Not Correlate with Increased Ex Vivo Survival of B Lymphocytes (1999)

Bovine leukemia virus (BLV) is an oncogenic retrovirus associated with B-cell lymphocytosis, leukemia, and lymphosarcoma in the ovine and bovine species. We have recently reported that in sheep, BLV protects the total population of peripheral blood mononuclear cells (PBMCs) from ex vivo spontaneous apoptosis. This global decrease in the apoptosis rates resulted from both direct and indirect mechanisms which allow extension of cell survival. Although sheep are not natural hosts for BLV, these animals are prone to develop virus-induced leukemia at very high frequencies. Most infected cattle, however, remain clinically healthy. This difference in the susceptibilities to development of leukemia in these two species might be related to alterations of the apoptotic processes. Therefore, we designed this study to unravel the mechanisms of programmed cell death in cattle. We have observed that PBMCs from persistently lymphocytotic BLV-infected cows were more susceptible to spontaneous ex vivo apoptosis than cells from uninfected or aleukemic animals. These higher apoptosis rates were the consequence of an increased proportion of B cells exhibiting lower survival abilities. About one-third of the BLV-expressing cells did not survive the ex vivo culture conditions, demonstrating that viral expression is not strictly associated with cell survival in cattle. Surprisingly, culture supernatants from persistently lymphocytotic cows exhibited efficient antiapoptotic properties on both uninfected bovine and uninfected ovine cells. It thus appears that indirect inhibition of cell death can occur even in the presence of high apoptosis rates. Together, these results demonstrate that the protection against spontaneous apoptosis associated with BLV is different in cattle and in sheep. The higher levels of ex vivo apoptosis occurring in cattle might indicate a decreased susceptibility to development of leukemia in vivo.
The Importance of Accurately Measuring the Range Correlation for Range-Oversampling Processing (2012)

Abstract A fundamental assumption for the application of range-oversampling techniques is that the correlation of oversampled signals in range is accurately known. In this paper, a theoretical framework is derived to quantify the effects of inaccurate range correlation measurements on the performance of such techniques, which include digital matched filtering and those based on decorrelation (whitening) transformations. It is demonstrated that significant reflectivity biases and increased variance of estimates can occur if the range correlation is not accurately measured. Simulations and real data are used to validate the theoretical results and to illustrate the detrimental effects of mismeasurements. Results from this work underline the need for reliable calibration in the context of range-oversampling processing, and they can be used to establish appropriate accuracy requirements for the measurement of the range correlation on modern weather radars.
S0117 Development of the ipd-MHC Database (2016)

The IPD-MHC Database was released in 2003 to provide a curated database of MHC sequences from several non-human species. The system was modeled on the IPD-IMGT/HLA database but expanded to cover multiple species and nomenclature systems. The initial release contained data on non-human primates, felines, and canines. Since this time, further data on horse, sheep, swine, cattle, fish, and rats have been added. Since its release, the database has grown rapidly and now contains nearly 7.000 alleles covering more than 70 non-human species. The site averages ∼1,500 unique visitors a month, viewing ∼5,000 pages. This growth has led to several challenges in maintaining and developing the site. The bioinformatics challenges of running a locus-specific database across multiple nomenclature systems and locations have impacted the performance and sustainability of the current IPD-MHC model. In 2015, a BBSRC Bioinformatics and Biological Resources (BBR) grant (UK) was awarded to fund both essential upgrades and future expansion of IPD-MHC. Work is currently focused on the underlying database, public website, and submission procedures. The key aims of this first phase are development of a universal cross-species data submission and display tool, and streamlining and standardizing work of the nomenclature committees in curating the data. This will allow for simpler and more frequent species updates. Future developments aim to incorporate cross-species alignment, primer design tools, and incorporation of NGS data. Ultimately, this will create an improved system capable of coping with large numbers of sequence variants, genes, and species within the data set. The project is overseen by a steering committee representing key stakeholders and non-human MHC nomenclature committees. This group is also helping to develop new MHC nomenclature standards and guidelines.