gebhart/patrepeval huggingface dataset:
Diverse human extracellular RNAs are widely detected in human plasma (2016)

There is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence in plasma of many non-microRNA small-RNAs was confirmed in an independent cohort. We present comprehensive data to demonstrate the broad and consistent detection of diverse classes of circulating non-cellular small-RNAs from a large population.
Genomic Medicine and the Future of Health Care (2000)

Genomic technologies and computational advances are leading to an information revolution in biology and medicine. Simulations of molecular processes in cells and predictions of drug effects in humans will advance pharmaceutical research and speed up clinical trials. Computational prognostics and diagnostics that combine with genotyping and molecular profiling may soon cause fundamental changes in the practice of health care.
Endoglin is a component of the transforming growth factor-beta receptor system in human endothelial cells. (1992)

Endoglin, a dimeric membrane glycoprotein expressed at high levels on human vascular endothelial cells, shares regions of sequence identity with betaglycan, a major binding protein for transforming growth factor-beta (TGF-beta) that co-exists with TGF-beta receptors I and II in a variety of cell lines but is low or absent in endothelial cells. We have examined whether endoglin also binds TGF-beta and demonstrate here that the major TGF-beta 1-binding protein co-existing with TGF-beta receptors I and II on human umbilical vein endothelial cells is endoglin, as determined by specific immunoprecipitation of endoglin affinity-labeled with 125I-TGF-beta. Furthermore, endoglin ectopically expressed in COS cells binds TGF-beta 1. Competition affinity-labeling experiments showed that endoglin binds TGF-beta 1 (KD approximately 50 pM) and TGF-beta 3 with high affinity but fails to bind TGF-beta 2. This difference in affinity of endoglin for the TGF-beta isoforms is in contrast to beta-glycan which recognizes all three isoforms. TGF-beta however is binding with high affinity to only a small fraction of the available endoglin molecules, suggesting that some rate-limiting event is required to sustain TGF-beta binding to endoglin.
-Propiolactone/Ultraviolet Irradiation: A review of Its Effectiveness for Inactivation of Viruses in Blood Derivatives (1983)

The efficacy of combined beta-propiolactone/ultraviolet irradiation (betaPL/UV) for inactivation of hepatitis B virus in labile blood derivatives has been reviewed. The initial evaluations of these procedures were hampered by inadequate process control that resulted in excessive protein denaturation; furthermore, adequate evaluation of process efficacy for virus inactivation was prevented by the absence of titered hepatitis virus stocks, the lack of an animal model, and the failure to carry out controlled trials. Finally, it was not appreciated that the power of these procedures lay especially in their use in combination. These deficits have now been remedied. To permit quantitation of process efficacy, a regression analysis of the relation between virus dose and incubation period in chimpanzees has been carried out. This has provided a means of estimating virus titer and determining the accuracy of such estimates. The most recent data suggest that betaPL/UV can reduce the titer of hepatitis B virus about 10 million fold (10(-7)). The process efficacy for betaPL/UV followed by the special adsorption procedures used in preparation of a stabilized human serum containing most human serum proteins except for factor VIII, the factor IX complex, fibrinogen, and the lipoproteins was estimated as a 10(8)-fold reduction in virus titer. This degree of virus inactivation should be more than sufficient to sterilize the amounts of hepatitis B virus that could be expected in pooled human plasma that has been screened for hepatitis B surface antigen. Preliminary data also suggest that the betaPL/UV procedure effectively inactivates non-A, non-B hepatitis virus(es).
Current advances in the treatment of Alzheimer's disease: focused on considerations targeting Aβ and tau (2012)

Alzheimer's disease (AD) is a neurodegenerative disorder that impairs mainly the memory and cognitive function in elderly. Extracellular beta amyloid deposition and intracellular tau hyperphosphorylation are the two pathological events that are thought to cause neuronal dysfunction in AD. Since the detailed mechanisms that underlie the pathogenesis of AD are still not clear, the current treatments are those drugs that can alleviate the symptoms of AD patients. Recent studies have indicated that these symptom-reliving drugs also have the ability of regulating amyloid precursor protein processing and tau phosphorylation. Thus the pharmacological mechanism of these drugs may be too simply-evaluated. This review summarizes the current status of AD therapy and some potential preclinical considerations that target beta amyloid and tau protein are also discussed.
Multicentric Castlemanʼs disease in HIV infection (1996)

MCD associated with HIV infection is a distinct clinico-pathological entity that can be differentiated from other types of HIV-associated systemic lymphoproliferative disorders. It is very similar to MCD observed in non-HIV-infected patients, except for the high prevalence of pulmonary symptoms and for the stronger association with Kaposi's sarcoma. Single-agent chemotherapy with vinblastine is effective and may prolong survival.
Sex-specific hippocampus-dependent cognitive deficits and increased neuronal autophagy in DEspR haploinsufficiency in mice (2008)

Aside from abnormal angiogenesis, dual endothelin-1/VEGF signal peptide-activated receptor deficiency (DEspR(-/-)) results in aberrant neuroepithelium and neural tube differentiation, thus elucidating DEspR's role in neurogenesis. With the emerging importance of neurogenesis in adulthood, we tested the hypothesis that nonembryonic-lethal DEspR haploinsufficiency (DEspR(+/-)) perturbs neuronal homeostasis, thereby facilitating aging-associated neurodegeneration. Here we show that, in male mice only, DEspR-haploinsufficiency impaired hippocampus-dependent visuospatial and associative learning and induced noninflammatory spongiform changes, neuronal vacuolation, and loss in the hippocampus, cerebral cortex, and subcortical regions, consistent with autophagic cell death. In contrast, DEspR(+/-) females exhibited better cognitive performance than wild-type females and showed absence of neuropathological changes. Signaling pathway analysis revealed DEspR-mediated phosphorylation of activators of autophagy inhibitor mammalian target of rapamycin (mTOR) and dephosphorylation of known autophagy inducers. Altogether, the data demonstrate DEspR-mediated diametrical, sex-specific modulation of cognitive performance and autophagy, highlight cerebral neuronal vulnerability to autophagic dysregulation, and causally link DEspR haploinsufficiency with increased neuronal autophagy, spongiosis, and cognitive decline in mice.
Overview literature on atomic force microscopy (AFM) : Basics and its important applications for polymer characterization (2006)

Atomic force microscopy (AFM) is a relatively new technique used for the surface characterization of polymers. It is capable of producing images of a non-conducting polymer surface without any chemical etching or staining. The unique feature of this technique as compared to other microscopy techniques is that we can study the mechanical properties of the polymer surface and it also does not involve the use of electron beam radiation that damages the polymer surface. This paper describes the various applications of atomic force microscopy like evaluation of mechanical properties, determining the chemical composition, studying photo-oxidative degradation of polymers, measuring the surface adhesion forces, studying the thermal phase transitions in polymers and determining the molecular weight and polydispersity index of polymer brushes. These applications have been elucidated with suitable examples. IPC Code: G01N13/16 The chemical properties and topography of polymer surfaces determine the functionality for a wide range of materials such as adhesives, protective coatings, and thin films for packaging, paints and lubricants. Surface and interface properties are becoming increasingly important. Scanning electron microscopy and transmission electron microscopy are the most frequently used techniques for surface characterization. These techniques use electron beam as the source of irradiation of the polymer sample. There is a possibility of damaging the polymer sample due to electron beam. Moreover; these techniques provide only two-dimensional images of the polymer surface. A new technique known as Atomic Force Microscopy (AFM) for the surface characterization of the polymer surfaces has been developed. This technique is based on the interatomic forces and is a relatively nondestructive technique as compared to scanning electron microscopy and transmission electron microscopy. It is also capable of three-dimensional mapping of the surface.
An alternative subspace approach to EEG dipole source localization (2004)

In the present study, we investigate a new approach to electroencephalography (EEG) three-dimensional (3D) dipole source localization by using a non-recursive subspace algorithm called FINES. In estimating source dipole locations, the present approach employs projections onto a subspace spanned by a small set of particular vectors (FINES vector set) in the estimated noise-only subspace instead of the entire estimated noise-only subspace in the case of classic MUSIC. The subspace spanned by this vector set is, in the sense of principal angle, closest to the subspace spanned by the array manifold associated with a particular brain region. By incorporating knowledge of the array manifold in identifying FINES vector sets in the estimated noise-only subspace for different brain regions, the present approach is able to estimate sources with enhanced accuracy and spatial resolution, thus enhancing the capability of resolving closely spaced sources and reducing estimation errors. The present computer simulations show, in EEG 3D dipole source localization, that compared to classic MUSIC, FINES has (1) better resolvability of two closely spaced dipolar sources and (2) better estimation accuracy of source locations. In comparison with RAP-MUSIC, FINES' performance is also better for the cases studied when the noise level is high and/or correlations among dipole sources exist.
Combining greyvalue invariants with local constraints for object recognition (1996)

This paper addresses the problem of recognizing objects in large image databases. The method is based on local characteristics which are invariant to similarity transformations in the image. These characteristics are computed at automatically detected keypoints using the greyvalue signal. The method therefore works on images such as paintings for which geometry based recognition fails. Due to the locality of the method, images can be recognized being given part of an image and in the presence of occlusions. Applying a voting algorithm and semi-local constraints makes the method robust to noise, scene clutter and small perspective deformations. Experiments show an efficient recognition for different types of images. The approach has been validated on an image database containing 1020 images, some of them being very similar by structure, texture or shape.
Exploiting High Dimensional Video Features Using Layered Gaussian Mixture Models (2006)

Analysis of video data usually requires training classifiers in high dimensional feature spaces. This paper proposes a layered Gaussian mixture model (LGMM) to exploit high dimensional features for classifying various shots in video. LGMM decomposes a high dimensional feature space by building a pyramid structure and estimating the distribution of local partitions in each layer using Gaussian mixtures from the bottom of the pyramid to the top. We reduce the dimension of features in each local region at a lower layer by projecting them onto the estimated Gaussian components. These projected feature vectors are then used to estimate the Gaussian mixture models at a upper layer. The final dimension of the feature is adjustable by choosing the number of Gaussians at the top layer of the pyramid. We demonstrate the proposed method using motion features to classify video shots. The proposed method is independent from low level features and can be extended to other classification tasks
Large-Scale Silicon Photonic Circuits for Optical Phased Arrays (2014)

We review recent advances in integrated large-scale optical phased arrays. The design and fabrication of large-scale optical phased arrays using silicon photonic circuits are discussed from device designs including the directional couplers, thermo-optic phase shifters, and optical nanoantennas, to system studies including phased array synthesis and noise analysis. By taking advantage of the well-developed silicon complementary metal-oxide-semiconductor (CMOS) fabrication technology, several large-scale integrated silicon photonic phased arrays are demonstrated, including two passive-phased arrays (64 × 64 and 32 × 32) with the ability to generate complex holographic images, an 8 × 8 active phased array for dynamic optical beamforming, and an 8 × 8 active antenna array with amplitude apodization. These optical phased array demonstrations, with up to 12 000 integrated optical elements, represent the largest and densest silicon photonic circuits demonstrated to date.
Particle image velocimetry studies on the swirling flow structure in the vortex gripper (2012)

In this article, particle image velocimetry was used to measure the two-dimensional flow field for vortex gripper. The vortex gripper was divided into two parts for respective research, including vortex cup and the gas film gap. In the part of vortex cup, the tangential velocity increases gradually, and the velocity decreases intensely in the vicinity of the vortex cup’s wall after it reaches maximum. In addition, the velocity decreases gradually with the increase of the gas film gap. In the part of gas film gap, the tangential velocity increases to maximum along the radial direction first; after the air flows into the gas film gap due to the viscous impedance, it decreases gradually. When the gas film gap’s thickness is smaller, the velocity almost decreases to zero at the external edge of the skirt. However, when the gas film gap increases to a certain thickness, the velocity does not decrease to zero, and the flow air still keeps a certain speed out of it. The velocity decreases gradually with the increase of the gas film gap. The radial velocity in the vortex cup and the gas film gap is of very small order of magnitude comparing with the average velocity and tangential velocity. The analysis of the Reynolds number shows that the flow in the vortex cup is the turbulent flow, and at the part of the gas film gap, the Reynolds number increases with the increase of the gas film gap, and the flow changes from the laminar flow to the turbulent flow. Through the particle image velocimetry experiment, the vortex gripper’s internal flow structure is studied. It is the theory support of the computational fluid dynamics simulation study for vortex gripper and the structure optimization in the future work.
The 14-3-3σ gene promoter is methylated in both human melanocytes and melanoma (2009)

14-3-3sigma is hypermethylated in human melanoma in a cell-linage specific manner. Spontaneous demethylation and re-expression of 14-3-3sigma is a rare event in melanoma, indicating 14-3-3sigma might have a tentative role in the pathogenesis of melanoma.
Development of a Freeze-Dried, Heat-Stable Influenza Subunit Vaccine Formulation (2016)

An influenza pandemic remains a major public health concern. A key strategy to prevent a pandemic is to stockpile and pre-position stable influenza vaccine to allow rapid deployment in response to an outbreak. However, most influenza vaccines today are formulated as liquids that are stable only within a temperature range of 2°C to 8°C and require use of a cold chain, making vaccine transportation, distribution, and storage complicated and expensive, particularly for developing countries. To support the National Strategy for Pandemic Influenza preparedness in the United States and internationally, we developed two lead dry formulations of stable H1N1 influenza subunit vaccines using freeze-drying technology. The stable formulations contain an excipient combination of a disaccharide, such as sucrose or trehalose, and glycine, in addition to a surfactant and phosphate buffer. The freeze-dried vaccines were shown to be safe and remained immunogenic in an in vivo study in mice. Moreover, the lead formulations demonstrated no significant loss of activity after 40 months at storage temperatures of 25°C and 37°C. This stability can be particularly attractive as it could eliminate the need to use a cold chain for vaccine deployment and facilitate integration of vaccine distribution with general drug distribution where appropriate. These freeze-dried thermostable influenza subunit vaccines could also reduce the frequency of vaccine stockpile turnover, offering a cost-effective option for pandemic preparedness.
TGF-β/SMAD Pathway and Its Regulation in Hepatic Fibrosis (2016)

Transforming growth factor-beta1 (TGF-β1), a key member in the TGF-β superfamily, plays a critical role in the development of hepatic fibrosis. Its expression is consistently elevated in affected organs, which correlates with increased extracellular matrix deposition. SMAD proteins have been studied extensively as pivotal intracellular effectors of TGF-β1, acting as transcription factors. In the context of hepatic fibrosis, SMAD3 and SMAD4 are pro-fibrotic, whereas SMAD2 and SMAD7 are protective. Deletion of SMAD3 inhibits type I collagen expression and blocks epithelial-myofibroblast transition. In contrast, disruption of SMAD2 upregulates type I collagen expression. SMAD4 plays an essential role in fibrosis disease by enhancing SMAD3 responsive promoter activity, whereas SMAD7 negatively mediates SMAD3-induced fibrogenesis. Accumulating evidence suggests that divergent miRNAs participate in the liver fibrotic process, which partially regulates members of the TGF-β/SMAD signaling pathway. In this review, we focus on the TGF-β/SMAD and other relative signaling pathways, and discussed the role and molecular mechanisms of TGF-β/SMAD in the pathogenesis of hepatic fibrosis. Moreover, we address the possibility of novel therapeutic approaches to hepatic fibrosis by targeting to TGF-β/SMAD signaling.
Circulating cytokines in sickle cell patients during steady state (1994)

Plasma levels of GM-CSF, IL-3, IL-6 and IL-1 (alpha,beta) were investigated in steady-state sickle cell patients. We find that SS patients with low levels of HbF (< 9% [LFSS]) are characterized by elevated plasma GM-CSF, whereas in patients with high levels of HbF (HFSS), GM-CSF is not detectable. In contrast, HFSS patients exhibited increased plasma IL-3 (m = 84.8 +/- 57 pg/ml), whereas LFSS patients had lower or no detectable plasma IL-3, IL-1(alpha,beta) and IL-6 were also detected in plasma from some SS patients, but there was no correlation with HbF levels. Normal controls tested negative for all cytokines, except for one individual positive for IL-3. These results are compatible with a model in which the level of haemopoietic stress determines the level of participation of GM-CSF or IL-3 in the regulation of SS circulating BFU-E.
Transmission of directly modulated 2.5-Gb/s signals over 250-km of nondispersion-shifted fiber by using a spectral filtering method (1996)

We demonstrate 250-km nondispersion-shifted fiber transmission of directly modulated 2.5-Gb/s signals. The chirping-induced power penalty is reduced by using a spectral filter whose transmission peak is tuned to "mark" wavelength of the modulated laser output. A well-known intensity modulation with a sufficiently high extinction ratio is used to suppress the intersymbol interference induced by nonuniform frequency modulation response of semiconductor lasers. The observed results are explained theoretically by using eye closure penalty.
Non-adherence to medication in patients with psychotic disorders: epidemiology, contributing factors and management strategies (2013)

Although non-adherence is common across all branches of medicine, psychotic disorders pose additional challenges that increase its risk. Despite the importance of non-adherence, clinicians generally spend too little time on assessing and addressing adherence attitudes and behaviors. Importantly, how adherence is measured significantly impacts the findings, and the most frequently employed methods of asking patients or judging adherence indirectly based on efficacy or tolerability information have poor validity. Novel technologies are being developed that directly assess adherence and that can also be used to both provide real-time feedback to clinicians and serve as an intervention with patients. Several treatments are available that can positively impact adherence. Among psychosocial interventions, those combining multiple approaches and involving multiple domains seem to be most effective. Although long-acting injectable antipsychotics are theoretically a very powerful tool to assure adherence and signal non-adherence, recent results from randomized controlled trials failed to show superiority compared to oral antipsychotics. These data are in contrast to nationwide cohort studies and mirror-image studies, which arguably include more representative patients receiving long-acting antipsychotics in clinical practice. This disconnect suggests that traditional randomized controlled trials are not necessarily the best way to study interventions that are thought to work via reducing non-adherence. Clearly, non-adherence is likely to remain a major public health problem despite treatment advances. However, increasing knowledge about factors affecting adherence and leveraging novel technologies can enhance its early assessment and adequate management, particularly in patients with psychotic disorders.
Aluminum metallization—Advantages and limitations for integrated circuit applications (1969)

The advantages and limitations of aluminum metallization are reviewed and compared with other systems used for integrated circuits. Metallization system properties of particular importance are summarized, including initial physical and chemical properties of the system which define potential performance and reliability considerations. The special requirements for MOS arrays and for multilevel-metallized integrated circuits are described. Recently available knowledge of aluminum metallization process technology and of metallization-related failure mechanisms is reviewed, and new results of experimental studies are presented. It is concluded that aluminum will continue to be the most widely used metallization material, not only for single-level metallized integrated circuits, but also for multilevel LSI arrays.