gebhart/patrepeval huggingface dataset:
Colorimetric and Fluorescent Dual-Mode Immunoassay Based on Plasmon-Enhanced Fluorescence of Polymer Dots for Detection of PSA in Whole Blood (2019)

Although enormous efforts have been devoted to the development of new types of fluorometric immunochromatographic test strip (ICTS) with improved sensitivity over the past years, it still remains a big challenge to design ICTS with colorimetric and fluorescent bimodal signal readout for rapid yet accurate detection of cancer markers in a clinic. Scientists have tried to prepare bimodal reporters by combining fluorescent dyes with metal nanomaterials, but their fluorescence was easily quenched by metal nanomaterials through surface energy transfer, making dual colorimetric and fluorometric ICTS very difficult to be achieved. As compared to conventional fluorescent probes, semiconducting polymer dots (Pdots) exhibit extraordinary fluorescence brightness and facile surface functionalization, which are very suitable to be engineered as bimodal signal reporting reagents. Here, we integrated highly fluorescent Pdots with strongly plasmonic Au nanorods to form Pdot-Au hybrid nanocomposites with dual colorimetric and fluorescent readout abilities. We further utilized these nanohybrids in ICTS for qualitatively fast screening (colorimetry) as well as quantitatively accurate determination (fluorometry) of prostate-specific antigen (PSA) within 10 min. By taking advantage of the plasmon-enhanced fluorescence of Pdots on Au nanorods, this immunoassay possesses much better detection sensitivity of 1.07 pg/mL for PSA, which is at least 2 orders of magnitude lower than that of conventional fluorometric ICTS. Moreover, the direct detection of PSA from human whole blood collected without sample pretreatment makes this Pdot-based ICTS platform promising for on-site point-of-care diagnostics.
Risk Evaluation Method for Range of Motion after Total Hip Arthroplasty applying Monte-Carlo Simulation (2018)

Quality of Total Hip Arthroplasty (THA) is decided by the range of motion (ROM), a patient can achieve after the transplant. The ROM plays an important role to perform different daily life activities. The post-operation achievement of ROM is dependent on pre-operation plans. Surgeons plan and perform operations based on their previous experiences because of the unavailability of authentic quantitative criteria due to various limitations. This study attempts to support pre-operation planning to calculate post-operation ROM achieved by the patient in THA, alongside, the risk evaluation with respect to flexion which is the most critical ROM of hip joint.
Peripheral blood lymphocyte/monocyte ratio at diagnosis and survival in classical Hodgkin's lymphoma (2011)

The ratio of absolute lymphocyte count/absolute monocyte count at diagnosis is an independent prognostic factor for survival and provides a single biomarker to predict clinical outcomes in patients with classical Hodgkin's lymphoma.
Biological Activity of Follistatin Isoforms and Follistatin-Like-3 Is Dependent on Differential Cell Surface Binding and Specificity for Activin, Myostatin, and Bone Morphogenetic Proteins (2006)

Follistatin (FST) and FST-like-3 (FSTL3) are activin-binding and neutralization proteins that also bind myostatin. Three FST isoforms have been described that differ in tissue distribution and cell-surface binding activity, suggesting that the FST isoforms and FSTL3 may have some nonoverlapping biological actions. We produced recombinant FST isoforms and FSTL3 and compared their biochemical and biological properties. Activin-binding affinities and kinetics were comparable between the isoforms and FSTL3, whereas cell-surface binding differed markedly (FST288 > FST303 > FST315 > FSTL3). Inhibition of endogenous activin bioactivity, whether the FST isoforms were administered endogenously or exogenously, correlated closely with surface binding activity, whereas neutralization of exogenous activin when FST and FSTL3 were also exogenous was consistent with their equivalent activin-binding affinities. This difference in activin inhibition was also evident in an in vitro bioassay because FST288 suppressed, whereas FST315 enhanced, activin-dependent TT cell proliferation. Moreover, when FSTL3, which does not associate with cell membranes, was expressed as a membrane-anchored protein, its endogenous activin inhibitory activity was dramatically increased. In competitive binding assays, myostatin was more potent than bone morphogenetic proteins (BMPs) 6 and 7, and BMPs 2 and 4 were inactive in binding to FST isoforms, whereas none of the BMPs tested competed with activin for binding to FSTL3. Neutralization of exogenous BMP or myostatin bioactivity correlated with the relative abilities of the isoforms to bind cell-surface proteoglycans. These results indicate that the differential biological actions among the FST isoforms and FSTL3 are primarily dependent on their relative cell-surface binding ability and ligand specificity.
A Packaged Noise-Canceling High-Gain Wideband Low Noise Amplifier (2018)

This brief presents a bandwidth and gain enhancement technique for packaged single-ended wideband low noise amplifier (LNA) module for high-sensitivity receivers. Wide bandwidth, low noise figure (NF), and high power gain are achieved by using gate-source inductors assisted impedance matching, current reuse feed-forward noise cancellation technique, and integrated shunt peaking output buffer. Fabricated in UMC 65-nm CMOS technology, the proposed LNA packaged in quad-flat no-leads package module achieves a maximum power gain of 20.5 dB, NF of 2-2.5 dB, 3-dB bandwidth from 0.4 to 2.2 GHz, and third-order inter modulation intercept the point of -5 dBm while consuming 25 mA current (including buffer) from 1.2 V supply.
Enhanced glypican-3 expression differentiates the majority of hepatocellular carcinomas from benign hepatic disorders (2001)

BACKGROUND/AIMS Hepatocellular carcinoma (HCC) is a common malignant tumour worldwide, and its differential diagnosis from benign lesions of the liver is often difficult yet of great clinical importance. In the present study, we analysed whether glypican-3 is useful in differentiating between benign and malignant liver diseases and whether it influences the growth behaviour of HCC. METHODS Northern blot analysis and in situ hybridisation. RESULTS Northern blot analysis indicated that expression of glypican-3 mRNA was either low or absent in normal liver, in focal nodular hyperplasia (FNH), and in liver cirrhosis. In contrast, expression of glypican-3 mRNA was markedly increased in 20 of 30 and moderately increased in five of 30 HCC samples. The average increase in glypican-3 mRNA expression in HCC was significant compared with expression in normal liver (21.7-fold increase, p<0.01). In comparison with FNH or liver cirrhosis, glypican-3 mRNA expression in HCC was increased 7.2- (p<0.05) and 10.8-fold (p<0.01), respectively. In addition, pushing HCCs exhibited significantly higher glypican-3 mRNA expression than invading tumours (p<0.05). In situ hybridisation analysis demonstrated weak expression of glypican-3 mRNA in normal hepatocytes and bile ductular cells, and weak to occasionally moderate signals in hepatocytes forming nodules of liver cirrhosis and in regenerated hepatic nodules of FNH. In contrast, glypican-3 in situ hybridisation signals were intense in hepatic cancer cells with even higher levels in pushing HCCs than in invading HCCs. CONCLUSIONS These findings suggest that glypican-3, in many cases, has the potential to differentiate between benign and malignant liver diseases.
The design of an application specific interface driver for a high capacitive load (1989)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1990.
Introducción al volumen VIII, Nº2 (2014)

Este monográfico está consagrado a la discusión y reflexión sobre la fabricación de las prácticas corporales en las diversas comunidades religiosas, principalmente en Latinoamérica. Aunque no debemos dejar de advertir que si bien es cierto que la segunda parte del siglo XX y por lo menos la que va del XXI pueden ser consideradas como el «estallido del cuerpo» debido a la diversa y profusa investigación que sobre éste se ha realizado, ya desde los campos sociales, humanos, religiosos o de la salud (tiempos que han transitado desde la comprensión seria respecto al lugar que ocupa el cuerpo en la constitución de lo humano, hasta aquellos momentos estrechos y reduccionistas que no hacen otra cosa que afirmar que todo inicia y termina en el cuerpo, buscando culminar la promesa, hasta ahora incumplida de la modernidad, de liberarnos de la cárcel del alma {Heller, 1995}), no lo es menos el hecho de que este monográfico no pretende contribuir a la moda del cuerpo. Sin duda, sí creemos junto con el teólogo católico Genevieve Comeau que nos encontramos en “la sociedad de la liberación del cuerpo”, (2001); en un periodo en que éste se ha revelado como uno de los rostros relevantes en nuestra constitución como seres humanos. Tenemos a bien la idea que otorga un papel de relevancia al cuerpo y corporalidad no solo en la construcción, también en la implicación con el mundo. Ese ha sido sin duda el gran aporte de los estudios corporales en estos tiempos, develar el modo en que un cuerpo físico se articula a una subjetividad (en singular-plural) para coexistir con el Otro.
TGF-beta Family Signaling in Embryonic Stem Cells (2011)

Ligands of transforming growth factor beta (TGF-β) family members have been implicated in the development and patho-physiological process of various organs. Embryonic stem cells (ESCs) are characterized by their ability to proliferate indefinitely and differentiated into all three germ layer cells, which are termed as pluripotency and self-renewal,respectively. For successful therapeutic application of ESCs, it is essential to understand the mechanisms underlying self-renewal and pluripotency, which involve complex networks among key factors including transcription factors, epigenetic control, microRNAs and signaling pathways. In this review, we discuss recent progress on the function of TGF beta family ligands and their canonical SMAD signaling in the maintenance of ESC' s identity.
Zinc Deficiency (1991)

Zinc deficiency occurs in individuals and populations whose diets are low in sources of readily bioavailable zinc such as red meat, and high in unrefined cereals that are rich in phytate and dietary fibers. Dietary zinc deficiency was described nearly three decades ago among the poor of the Middle East. It is now known to occur in children and adolescents from widely diverse areas including Egypt, Iran, Turkey, China, Yugoslavia, Canada, and the United States; and among pregnant women from Iran, Turkey, the United Kingdom, Australia, and the United States. Major manifestations include retarded growth and development and an increased incidence of pregnancy complications. Other manifestations may include suppressed immunity, poor healing, dermatitis, and impairments in neuropsychological functions. Precise information as to the numbers of people affected by dietary zinc deficiency is not available. Even so the nature of diets associated with zinc deficiency suggests that mild deficiency is common in some populations.
A Pruning-Based Disk Scheduling Algorithm for Heterogeneous I/O Workloads (2014)

In heterogeneous I/O workload environments, disk scheduling algorithms should support different QoS (Quality-of-Service) for each I/O request. For example, the algorithm should meet the deadlines of real-time requests and at the same time provide reasonable response time for best-effort requests. This paper presents a novel disk scheduling algorithm called G-SCAN (Grouping-SCAN) for handling heterogeneous I/O workloads. To find a schedule that satisfies the deadline constraints and seek time minimization simultaneously, G-SCAN maintains a series of candidate schedules and expands the schedules whenever a new request arrives. Maintaining these candidate schedules requires excessive spatial and temporal overhead, but G-SCAN reduces the overhead to a manageable level via pruning the state space using two heuristics. One is grouping that clusters adjacent best-effort requests into a single scheduling unit and the other is the branch-and-bound strategy that cuts off inefficient or impractical schedules. Experiments with various synthetic and real-world I/O workloads show that G-SCAN outperforms existing disk scheduling algorithms significantly in terms of the average response time, throughput, and QoS-guarantees for heterogeneous I/O workloads. We also show that the overhead of G-SCAN is reasonable for on-line execution.
What Can We Learn from Analysis of Field Asphaltenes Deposits? Enhancing Product Development Through Knowledge-Based Field-to-Lab-to-Field Approach (2019)

Abstract Recent studies revealed that solids from lab-generated deposits often exhibit compositional differences from those of field deposits, pointing to a more complex fouling process in field operations. The objective of this work was to understand and apply knowledge from field deposit characteristics in order to design and conduct laboratory experiments which yield solid deposits with comparable compositional fingerprints. This approach allows a more objective and reliable product development and recommendation strategy to be adopted for increased success in the field applications. First, oil and deposit samples from an offshore field was characterized. Second, samples of the asphaltenes extracted from oil (AEO) and from the deposit (AED) were characterized based on solubility using an Accelerated Solubility Test (AST). A customized Asphaltene Dynamic Deposition Loop (ADDL) was used in this study to simulate the precipitation and deposition of asphaltenes from the crude oil. Crude oil used in the tests was from the same well where the deposits were collected. ADDL tests were conducted at high temperature and pressure and the composition of the collected deposit from this test was compared with the deposits from the field. At last, Light Scattering Technique (LST) was applied to screen asphaltene inhibitors (AI). Four candidate chemistries were tested on LST. To confirm the efficiency, the high performer was tested on ADDL under dynamic conditions. Deposits collected from the ADDL were characterized and results showed a high degree of similarity to the field deposit. AI1 was evaluated by ADDL and it decreased the deposition in the filters by 60% and 84% at 1000 ppm. This product was selected to be tested in the field and a plant trial is ongoing.
Interleukin 1β, Tumor Necrosis Factor Alpha, and Interleukin 8 in Bronchoalveolar Lavage Fluid of Patients with Diffuse Panbronchiolitis: A Potential Mechanism of Macrolide Therapy (1996)

We measured the levels of interleukin (IL) 1 beta, tumor necrosis factor alpha, and IL-8 in bronchoalveolar lavage fluid (BALF) and sera of patients with diffuse panbronchiolitis (DPB) before and after administration of erythromycin or roxithromycin. The pretreatment levels of IL-1 beta and IL-8 were significantly higher in the BALF of patients with DPB than in the BALF of patients with sarcoidosis and controls. The tumor necrosis factor alpha level was also higher than in controls, but not statistically significant. There was a significant correlation between percentage of neutrophils and IL-8 level in the BALF of DPB patients (r = 0.509; p < 0.05) on the one hand and between IL-1 beta and IL-8 on the other (r = 0.476; p < 0.04). Treatment for 1-24 months significantly reduced BALF levels of IL-1 beta and IL-8 of DPB patients in parallel with a reduction in BALF neutrophils. The serum level of IL-8 of DPB patients was higher, albeit insignificant, than that of controls and significantly lower than that in the BALF of the same patients (p = 0.0088). Serum IL-1 beta was below the detection limit. In addition, the concentration of IL-8 in alveolar macrophages obtained from 2 volunteers before and after oral erythromycin administration also decreased ex vivo. Our results indicate that IL-8 induces the migration of neutrophils to inflammatory sites. It is possible that the macrolides impair production and/or secretion of these cytokines, ultimately reducing neutrophil accumulation in the airway.
NPXY motifs control the recruitment of the α5β1 integrin in focal adhesions independently of the association of talin with the β1 chain (1997)

With the exception of the divergent beta4 and beta8 chains, the integrin beta subunit cytoplasmic domains are short and highly conserved sequences. Consensus motifs are found among the different cytoplasmic beta chains. Experiments using chimeric receptors demonstrated that the 47 amino acids of the beta1 subunit cytoplasmic domain contain sufficient information to target integrins to adhesion plaques. Three clusters of amino acids, named cyto-1, cyto-2 and cyto-3, seem to contribute to this localization. Cyto-2 and cyto-3 exhibit NPXY motifs. At present, the exact function of these motifs remains unknown but it is likely that these sequences are involved in protein-protein interactions. Although NPXY motifs often act as internalization signals at the cytoplasmic tail of membrane receptors, our previous results showed that the two NPXY motifs are not responsible for the alpha5beta1 integrin endocytosis. Herein, we address the question of the role of the two highly conserved NPXY motifs found in the beta1 cytoplasmic domain, and which correspond to the conserved domains cyto-2 and cyto-3. We demonstrate that, within the integrin beta1 cytoplasmic tail, the two NPXY motifs are required for the recruitment of the integrin in focal adhesions. In addition, our results indicate that these two motifs control but do not belong to the talin-binding sites. Finally, the analysis of the phenotypes of NPXY mutants reveals that the interaction of talin with the beta1 cytosolic domain is not sufficient to target the integrins to focal adhesions.
<i>split ends</i>encodes large nuclear proteins that regulate neuronal cell fate and axon extension in the<i>Drosophila</i>embryo (2000)

split ends (spen) encodes nuclear 600 kDa proteins that contain RNA recognition motifs and a conserved C-terminal sequence. These features define a new protein family, Spen, which includes the vertebrate MINT transcriptional regulator. Zygotic spen mutants affect the growth and guidance of a subset of axons in the Drosophila embryo. Removing maternal and zygotic protein elicits cell-fate and more general axon-guidance defects that are not seen in zygotic mutants. The wrong number of chordotonal neurons and midline cells are generated, and we identify defects in precursor formation and EGF receptor-dependent inductive processes required for cell-fate specification. The number of neuronal precursors is variable in embryos that lack Spen. The levels of Suppressor of Hairless, a key transcriptional effector of Notch required for precursor formation, are reduced, as are the nuclear levels of Yan, a transcriptional repressor that regulates cell fate and proliferation downstream of the EGF receptor. We propose that Spen proteins regulate the expression of key effectors of signaling pathways required to specify neuronal cell fate and morphology.
RNA Interference Reveals That EndogenousXenopus MinK-related Peptides Govern Mammalian K+ Channel Function in Oocyte Expression Studies (2003)

The physiological properties of most ion channels are defined experimentally by functional expression of their pore-forming alpha subunits in Xenopus laevis oocytes. Here, we cloned a family of Xenopus KCNE genes that encode MinK-related peptide K(+) channel beta subunits (xMiRPs) and demonstrated their constitutive expression in oocytes. Electrophysiological analysis of xMiRP2 revealed that when overexpressed this gene modulates human cardiac K(+) channel alpha subunits HERG (human ether-a-go-go-related gene) and KCNQ1 by suppressing HERG currents and removing the voltage dependence of KCNQ1 activation. The ability of endogenous levels of xMiRP2 to contribute to the biophysical attributes of overexpressed mammalian K(+) channels in oocyte studies was assessed next. Injection of an xMiRP2 sequence-specific short interfering RNA (siRNA) oligo reduced endogenous xMiRP2 expression 5-fold, whereas a control siRNA oligo had no effect, indicating the effectiveness of the RNA interference technique in Xenopus oocytes. The functional effects of endogenous xMiRP2 silencing were tested using electrophysiological analysis of heterologously expressed HERG channels. The RNA interference-mediated reduction of endogenous xMiRP2 expression increased macroscopic HERG current as much as 10-fold depending on HERG cRNA concentration. The functional effects of human MiRP1 (hMiRP1)/HERG interaction were also affected by endogenous xMiRP2. At high HERG channel density, at which the effects of endogenous xMiRP2 are minimal, hMiRP1 reduced HERG current. At low HERG current density, hMiRP1 paradoxically up-regulated HERG current, a result consistent with hMiRP1 rescuing HERG from suppression by endogenous xMiRP2. Thus, endogenous Xenopus MiRP subunits contribute to the base-line properties of K(+) channels like HERG in oocyte expression studies, which could explain expression level- and expression system-dependent variation in K(+) channel function.
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration (2020)

The integration of genomic metadata is, at the same time, an important, difficult, and well-recognized challenge. It is important because a wealth of public data repositories is available to drive biological and clinical research; combining information from various heterogeneous and widely dispersed sources is paramount to a number of biological discoveries. It is difficult because the domain is complex and there is no agreement among the various metadata definitions, which refer to different vocabularies and ontologies. It is well-recognized in the bioinformatics community because, in the common practice, repositories are accessed one-by-one, learning their specific metadata definitions as result of long and tedious efforts, and such practice is error-prone. In this paper, we describe META-BASE, an architecture for integrating metadata extracted from a variety of genomic data sources, based upon a structured transformation process. We present a variety of innovative techniques for data extraction, cleaning, normalization and enrichment. We propose a general, open and extensible pipeline that can easily incorporate any number of new data sources, and propose the resulting repository-already integrating several important sources-which is exposed by means of practical user interfaces to respond biological researchers' needs.