gebhart/patrepeval huggingface dataset:
High Frequency Stimulation of the Subthalamic Nucleus Increases the Extracellular Contents of Striatal Dopamine in Normal and Partially Dopaminergic Denervated Rats (2001)

The subthalamic nucleus (STN) has come under focus in Parkinson disease (PD) because of recent advances in the understanding of the functional organization of the basal ganglia in normal and pathological conditions. Manipulations of the STN have been described to compensate for some imbalance in motor output of the basal ganglia in animal models of PD and have been proposed as a potential therapeutic target in humans. Indeed, high frequency stimulation (HFS) (130 Hz) of the STN has beneficial effects in severe parkinsonian patients but the precise mechanisms underlying these clinical results remain to be elucidated. To date, very little is known concerning the effect of HFS-STN on striatal dopaminergic transmission. Since it has been reported that dopaminergic medication may be reduced in PD patients under HFS-STN, our goal was to study the effect of HFS-STN on striatal dopamine (DA) transmission by using intracerebral microdialysis in normal and partially DA denervated rats. Our results show that HFS STN induces a significant increase of extracellular DA in the striatum of normal and partially DA lesioned rats while striatal extracellular levels of DOPAC were not affected. We conclude that HFS-STN acts directly and/or indirectly on striatal DA levels in control or partially DA lesioned rats.
Genetically modified plants and human health (2008)

Genetically modified (or GM) plants have attracted a large amount of media attention in recent years and continue to do so. Despite this, the general public remains largely unaware of what a GM plant actually is or what advantages and disadvantages the technology has to offer, particularly with regard to the range of applications for which they can be used. From the first generation of GM crops, two main areas of concern have emerged, namely risk to the environment and risk to human health. As GM plants are gradually being introduced into the European Union there is likely to be increasing public concern regarding potential health issues. Although it is now commonplace for the press to adopt 'health campaigns', the information they publish is often unreliable and unrepresentative of the available scientific evidence. We consider it important that the medical profession should be aware of the state of the art, and, as they are often the first port of call for a concerned patient, be in a position to provide an informed opinion. This review will examine how GM plants may impact on human health both directly - through applications targeted at nutrition and enhancement of recombinant medicine production - but also indirectly, through potential effects on the environment. Finally, it will examine the most important opposition currently facing the worldwide adoption of this technology: public opinion.
Scleroderma lung disease (2013)

Systemic sclerosis (SSc) is a systemic autoimmune disease that is characterised by endothelial dysfunction resulting in a small-vessel vasculopathy, fibroblast dysfunction with resultant excessive collagen production and fibrosis, and immunological abnormalities. The classification of SSc is subdivided based on the extent of skin involvement into diffuse cutaneous sclerosis (dcSSc), limited cutaneous sclerosis (lcSSc) or SSc sine scleroderma [1]. While virtually any organ system may be involved in the disease process, fibrotic and vascular pulmonary manifestations of SSc, including interstitial lung disease (ILD) and pulmonary hypertension (PH), are the leading cause of death. As new therapies targeting these pulmonary conditions emerge, early recognition of lung involvement is essential for the care of these patients. In this article we review the direct and indirect pulmonary manifestations of SSc and recent therapeutic trials that have attempted to target these manifestations.

When a patient with SSc disease presents with signs or symptoms referring to the chest, a number of potential disorders must be considered (table 1) for: direct pulmonary involvement (ILD with or without PH or pulmonary arterial hypertension (PAH), airways disease and pleural involvement); indirect pulmonary complications (aspiration, infection, drug toxicity, malignancy, respiratory muscle weakness, restrictive lung disease from chest wall involvement and lung disease secondary to cardiac involvement); combinations of direct and indirect pulmonary manifestations; and other lung diseases not related to SSc (chronic obstructive pulmonary disease/emphysema, asthma and lung nodules).

View this table:

Table 1. Pulmonary involvement in systemic sclerosis 

In scleroderma, the two most common types of direct pulmonary involvement are ILD and PH, which together account for 60% of SSc-related deaths [2]. While certain pulmonary manifestations may occur more commonly in a subset of SSc ( i.e. ILD is more common in dcSSc while PH is more common in lcSSc) [3], all of the known pulmonary manifestations reported have been described in each of …
Self-alignment trench-pole writer (1999)

We have succeeded in designing, fabricating, and testing self-alignment trench-pole write heads. 1 /spl mu/m narrow track heads were fabricated by a newly developed self-alignment trench process and showed large overwrite of over 40 dB for low-noise high coercivity media with Hc=2800 Oe, even with a large throat height of 3 /spl mu/m. This trench pole writer showed high potential for submicrometer narrow track application.
Oral Immunogenicity of Human Papillomavirus-Like Particles Expressed in Potato (2003)

Human papillomavirus-like particles (HPV VLPs) have shown considerable promise as a parenteral vaccine for the prevention of cervical cancer and its precursor lesions. Parenteral vaccines are expensive to produce and deliver, however, and therefore are not optimal for use in resource-poor settings, where most cervical HPV disease occurs. Transgenic plants expressing recombinant vaccine immunogens offer an attractive and potentially inexpensive alternative to vaccination by injection. For example, edible plants can be grown locally and can be distributed easily without special training or equipment. To assess the feasibility of an HPV VLP-based edible vaccine, in this study we synthesized a plant codon-optimized version of the HPV type 11 (HPV11) L1 major capsid protein coding sequence and introduced it into tobacco and potato. We show that full-length L1 protein is expressed and localized in plant cell nuclei and that expression of L1 in plants is enhanced by removal of the carboxy-terminal nuclear localization signal sequence. We also show that plant-expressed L1 self-assembles into VLPs with immunological properties comparable to those of native HPV virions. Importantly, ingestion of transgenic L1 potato was associated with activation of an anti-VLP immune response in mice that was qualitatively similar to that induced by VLP parenteral administration, and this response was enhanced significantly by subsequent oral boosting with purified insect cell-derived VLPs. Thus, papillomavirus L1 protein can be expressed in transgenic plants to form immunologically functional VLPs, and ingestion of such material can activate potentially protective humoral immune responses.
Gene expression profiles in rice gametes and zygotes: identification of gamete-enriched genes and up- or down-regulated genes in zygotes after fertilization (2013)

In angiosperms, fertilization and subsequent zygotic development occur in embryo sacs deeply embedded in the ovaries; therefore, these processes are poorly elucidated. In this study, microarray-based transcriptome analyses were conducted on rice sperm cells, egg cells, and zygotes isolated from flowers to identify candidate genes involved in gametic and/or early zygotic development. Cell type-specific transcriptomes were obtained, and up- or down-regulated genes in zygotes after fertilization were identified, in addition to genes enriched in male and female gametes. A total of 325 putatively up-regulated and 94 putatively down-regulated genes in zygotes were obtained. Interestingly, several genes encoding homeobox proteins or transcription factors were identified as highly up-regulated genes after fertilization, and the gene ontology for up-regulated genes was highly enriched in functions related to chromatin/DNA organization and assembly. Because a gene encoding methyltransferase 1 was identified as a highly up-regulated gene in zygotes after fertilization, the effect of an inhibitor of this enzyme on zygote development was monitored. The inhibitor appeared partially to affect polarity or division asymmetry in rice zygotes, but it did not block normal embryo generation.
Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes (2008)

Mosquito-borne viruses cause significant levels of morbidity and mortality in humans and domesticated animals. Maintenance of mosquito-borne viruses in nature requires a biological transmission cycle that involves alternating virus replication in a susceptible vertebrate and mosquito host. Although the vertebrate infection is acute and often associated with disease, continual transmission of these viruses in nature depends on the establishment of a persistent, nonpathogenic infection in the mosquito vector. An antiviral RNAi response has been shown to limit the replication of RNA viruses in flies. However, the importance of the RNAi pathway as an antiviral defense in mammals is unclear. Differences in the immune responses of mammals and mosquitoes may explain why these viruses are not generally associated with pathology in the invertebrate host. We identified virus-derived small interfering RNAs (viRNAs), 21 nt in length, in Aedes aegypti infected with the mosquito-borne virus, Sindbis (SINV). viRNAs had an asymmetric distribution that spanned the length of the SINV genome. To determine the role of viRNAs in controlling pathogenic potential, mosquitoes were infected with recombinant alphaviruses expressing suppressors of RNA silencing. Decreased survival was observed in mosquitoes in which the accumulation of viRNAs was suppressed. These results suggest that an exogenous siRNA pathway is essential to the survival of mosquitoes infected with alphaviruses and, thus, the maintenance of these viruses in nature.
Cyber Security Risk Assessment for Industrial Automation Platform (2015)

Due to the fact that the cyber security risks exist in industrial control system, risk assessment on Industrial Automation Platform (IAP) is discussed in this paper. The cyber security assessment model for IAP is built based on relevant standards at abroad. Fuzzy analytic hierarchy process and fuzzy comprehensive evaluation method based on entropy theory are utilized to evaluate the communication links' risk of IAP software. As a result, the risk weight of communication links which have impacts on platform and the risk level of this platform are given for further study on protective strategy. The assessment result shows that the methods used can evaluate this platform efficiently and practically.
Correlation of in vivo and in vitro functions of fresh and stored human platelets (2000)

It is possible to freeze platelets and retain in vivo efficacy if the cryopreservative DMSO is included in the preparation. In vitro responses were greatly reduced by all of the storage protocols, but it may not be necessary to retain 100 percent in vitro function to have a platelet substitute or storage product that functions satisfactorily in vivo.
Spectroscopic and dynamic light scattering studies of the interaction between pterodontic acid and bovine serum albumin (2012)

Pterodontic acid (PA) has been isolated from Laggera pterodonta, a Chinese herbal medicine, and shown to possess antibacterial activity in vitro. To facilitate its preclinical development, the interaction between PA and bovine serum albumin (BSA) was studied using a fluorescence quenching technique, ultraviolet–visible spectrophotometry and dynamic light scattering (DLS). At temperatures of 297 K and 310 K and an excitation wavelength of 282 nm, the fluorescence intensity of BSA decreased significantly with increasing concentration of PA attributed to the formation of a PA–BSA complex. The apparent binding constant, number of binding sites and corresponding thermodynamic parameters were calculated and the main intermolecular attraction shown to result from hydrogen bonding and van der Waals forces. Synchronous fluorescence spectrometry revealed that the binding site in the complex approached the microenvironment of Trp and three-dimensional fluorescence spectroscopy showed the binding induced conformational changes in BSA. Using DLS, increasing PA concentration was shown to cause a gradual increase in hydrodynamic diameter and significant aggregation of the complex.
MicroTar: predicting microRNA targets from RNA duplexes (2006)

MicroTar achieves better sensitivity than previously reported predictions when tested on three distinct datasets of experimentally-verified miRNA-target interactions in C. elegans, Drosophila, and mouse.
Effects of technology scaling on the SET sensitivity of RF CMOS Voltage-controlled oscillators (2005)

We analyze single-event transient (SET) effects in a high-speed voltage-controlled oscillator (VCO) design that is applicable to mixed-signal RF operations. Our study shows that the sensitivity of this type of circuit topologies exhibits a strong correlation to: the minimum feature size of the technology in use, the range of oscillating frequencies that the circuit is designed to achieve and the frequency at which the VCO is operating. We also determine that current-starved VCOs have an optimal functional range for improved radiation tolerance, located at the upper segment of their voltage-to-frequency transfer characteristic, where exposition to low LET ions become of no consequence on the operation of the circuit. More importantly, we show that derating the frequency of such VCO designed in a state-of-the-art technology does not compensate for the increased radiation vulnerability at that node. If not properly accounted for, the performance overhead that the newer technology provides is shown to severely penalize the radiation hardness of the circuit.
Molecular profiling and characterization of luminal‐like and basal‐like <i>in vivo</i> breast cancer xenograft models (2009)

The number of relevant and well-characterized cell lines and xenograft models for studying human breast cancer are few, and may represent a limitation for this field of research. With the aim of developing new breast cancer model systems for in vivo studies of hormone dependent and independent tumor growth, progression and invasion, and for in vivo experimental therapy studies, we collected primary mammary tumor specimens from patients, and implanted them in immunodeficient mice. Primary tumor tissue from 29 patients with breast cancer was implanted subcutaneously with matrigel in SCID mice, in the presence of continuous release of estradiol. The tumors were transferred into new animals when reaching a diameter of 15mm and engrafted tumors were harvested for morphological and molecular characterization from passage six. Further, gene expression profiling was performed using Agilent Human Whole Genome Oligo Microarrays, as well as DNA copy number analysis using Agilent Human Genome CGH 244K Microarrays. Of the 30 primary tumors implanted into mice (including two implants from the same patient), two gave rise to viable tumors beyond passage ten. One showed high expression levels of estrogen receptor-alpha protein (ER) while the other was negative. Histopathological evaluation of xenograft tumors was carried out at passage 10-12; both xenografts maintained the morphological characteristics of the original tumors (classified as invasive grade III ductal carcinomas). The genomic profile of the ER-positive xenograft tumor resembled the profile of the primary tumor, while the profile obtained from the ER-negative parental tumor was different from the xenograft. However, the ER-negative parental tumor and xenograft clustered on the same branch using unsupervised hierarchical clustering analysis on RNA microarray expression data of "intrinsic genes". A significant variation was observed in the expression of extracellular matrix (ECM)-related genes, which were found downregulated in the engrafted tumors compared to the primary tumor. By IHC and qRT-PCR we found that the downregulation of stroma-related genes was compensated by the overexpression of such molecules by the mouse host tissue. The two established breast cancer xenograft models showed different histopathological characteristics and profound diversity in gene expression patterns that in part can be associated to their ER status and here described as basal-like and luminal-like phenotype, respectively. These two new breast cancer xenografts represent useful preclinical tools for developing and testing of new therapies and improving our knowledge on breast cancer biology.
Light sheet based imaging flow cytometry on a microfluidic platform (2013)

We propose a light sheet based imaging flow cytometry technique for simultaneous counting and imaging of cells on a microfluidic platform. Light sheet covers the entire microfluidic channel and thus omits the necessity of flow focusing and point scanning based technology. Another advantage lies in the orthogonal detection geometry that totally cuts-off the incident light, thereby substantially reducing the background in the detection. Compared to the existing state-of-art techniques the proposed technique shows marked improvement. Using fluorescently-coated Saccharomyces cerevisiae cells we have recorded cell counting with throughput as high as 2,090 cells/min in the low flow rate regime and were able to image the individual cells on-the-go. Overall, the proposed system is cost-effective and simple in channel geometry with the advantage of efficient counting in operational regime of low laminar flow. This technique may advance the emerging field of microfluidic based cytometry for applications in nanomedicine and point of care diagnostics.
Genetic changes in prostate cancer (1997)

Recent advances in molecular biology have allowed us to understand that it is the accumulation of genetic alterations which leads to each step of tumor genesis. What the specific alterations may be, however, often varies with each neoplasm. Prostate cancer is somewhat unique in its presentation to the pathologist of a bewildering array of histologies difficult to assign to diagnostic categories and contributing to misinterpretations of underlying molecular events. As with any malignancy, It is of utmost importance to thoroughly analyze and record the genetic aberrations found in prostate cancer with the objective of correlation to the pathology and natural history of the disease. Multiple ontogeny and tumor suppressor genes have been investigated in both clinical and latent cancers using conventional mutational analyses. To probe deeper Into these genes and to uncover novel molecular events, genomic tumor DNA were examined using restriction landmark genomic scanning (RLGS), a method which allows the Identification and comparison of specific genetic alterations within large segments and multiple samples of DNA at a time. This article reviews what has been identified based on numerous molecular studies, focusing on the genetic alterations peculiar to human prostate cancer.
Atomic layer deposition of molybdenum oxide using bis(tert-butylimido)bis(dimethylamido) molybdenum (2013)

Molybdenum trioxide films have been deposited using thermal atomic layer deposition techniques with bis(tert-butylimido)bis(dimethylamido)molybdenum. Films were deposited at temperatures from 100 to 300 °C using ozone as the oxidant for the process. The Mo precursor was evaluated for thermal stability and volatility using thermogravimetric analysis and static vapor pressure measurements. Film properties were evaluated with ellipsometry, x-ray photoelectron spectroscopy, secondary ion mass spectroscopy, and secondary electron microscopy. The growth rate per cycle was determined to extend from 0.3 to 2.4 Å/cycle with &lt;4% nonuniformity (1-sigma) with-in-wafer across a 150 mm wafer for the investigated temperature range.
Real-Time Probing of Membrane Transport in Living Microbial Cells Using Single Nanoparticle Optics and Living Cell Imaging (2004)

Membrane transport plays a leading role in a wide spectrum of cellular and subcellular pathways, including multidrug resistance (MDR), cellular signaling, and cell-cell communication. Pseudomonas aeruginosa is renowned for its intriguing membrane transport mechanisms, such as the interplay of membrane permeability and extrusion machinery, leading to selective accumulation of specific intracellular substances and MDR. Despite extensive studies, the mechanisms of membrane transport in living microbial cells remain incompletely understood. In this study, we directly measure real-time change of membrane permeability and pore sizes of P. aeruginosa at the nanometer scale using the intrinsic color index (surface plasmon resonance spectra) of silver (Ag) nanoparticles as the nanometer size index probes. The results show that Ag nanoparticles with sizes ranging up to 80 nm are accumulated in living microbial cells, demonstrating that these Ag nanoparticles transport through the inner and outer membrane of the cells. In addition, a greater number of larger intracellular Ag nanoparticles are observed in the cells as chloramphenicol concentration increases, suggesting that chloramphenicol increases membrane permeability and porosity. Furthermore, studies of mutants (nalB-1 and DeltaABM) show that the accumulation rate of intracellular Ag nanoparticles depends on the expression level of the extrusion pump (MexAB-OprM), suggesting that the extrusion pump plays an important role in controlling the accumulation of Ag nanoparticles in living cells. Moreover, the accumulation kinetics measured by Ag nanoparticles are similar to those measured using a small fluorescent molecule (EtBr), eliminating the possibility of steric and size effects of Ag nanoparticle probes. Susceptibility measurements also suggest that a low concentration of Ag nanoparticles (1.3 pM) does not create significant toxicity for the cells, further validating that single Ag nanoparticles (1.3 pM) can be used as biocompatible nanoprobes for the study of membrane transport kinetics in living microbial cells.
On the Practical use of Variable Elimination in Constraint Optimization Problems: 'Still-life' as a Case Study (2005)

Variable elimination is a general technique for constraint processing. It is often discarded because of its high space complexity. However, it can be extremely useful when combined with other techniques. In this paper we study the applicability of variable elimination to the challenging problem of finding still-lifes. We illustrate several alternatives: variable elimination as a stand-alone algorithm, interleaved with search, and as a source of good quality lower bounds. We show that these techniques are the best known option both theoretically and empirically. In our experiments we have been able to solve the n=20 instance, which is far beyond reach with alternative approaches.
SYNTHESIS AND IN VITRO ANTITUMOR ACTIVITY OF BENZIMIDAZOLE DERIVATIVES (2017)

One of the most important goals in medicinal chemistry is the development of new heterocyclic compounds with antitumor activity. Thus, a novel series of Schiff bases 1-11, the derivatives of 2-aryl-1H-benzimidazole has been synthesized and evaluated for their cytotoxic activity against the cells of human cancer cell lines, namely K-562 (myelogenous leukemia) and HL-60 (promyelocytic leukemia). Among the compounds tested against K-562 cell line, compounds 1, 7 and 10 showed potent activity and the compound 5 exhibited better activity against HL-60 cell line.