gebhart/patrepeval huggingface dataset:
Supernatants of acquired immunodeficiency syndrome-related Kaposi's sarcoma cells induce endothelial cell chemotaxis and invasiveness. (1991)

Kaposi's sarcoma (KS) in general, and acquired immunodeficiency syndrome-related KS (AIDS-KS) in particular, is a highly invasive and intensely angiogenic neoplasm of unknown cellular origin. We have recently established AIDS-KS cells in long term culture and reported the development of KS-like lesions in nude mice inoculated with these cells. Here, we have examined the in vitro invasiveness of basement membrane by AIDS-KS cells, as well as the effect(s) of their supernatants on the migration and invasiveness of human vascular endothelial cells. AIDS-KS cells were highly invasive in the Boyden chamber invasion assay and formed invasive, branching colonies in a 3-dimensional gel (Matrigel). Normal endothelial cells form tube-like structures on Matrigel. AIDS-KS cell-conditioned media induced endothelial cells to form invasive clusters in addition to tubes. KS-cell-conditioned media, when placed in the lower compartment of the Boyden chamber, stimulated the migration of human and bovine vascular endothelial cells across filters coated with either small amounts of collagen IV (chemotaxis) or a Matrigel barrier (invasion). Basic fibroblast growth factor could also induce endothelial cell chemotaxis and invasion in these assays. However, when antibodies to basic fibroblast growth factor were used the invasive activity induced by the AIDS-KS-cell-conditioned media was only marginally inhibited, suggesting that the large quantities of basic fibroblast growth factor-like material released by the AIDS-KS cells are not the main mediators of this effect. Specific inhibitors of laminin and collagenase IV action, which represent critical determinants of basement membrane invasion, blocked the invasiveness of the AIDS-KS cell-activated endothelial cells in these assays. These data indicate that KS cells appear to be of smooth muscle origin but secrete a potent inducer of endothelial cell chemotaxis and invasiveness which could be responsible for angiogenesis and the resulting highly vascularized lesions. These assays appear to be a model to study the invasive spread and angiogenic capacity of human AIDS-related KS and should prove useful in the identification of molecular mediators and potential inhibitors of neoplastic neovascularization.
Brexanolone as adjunctive therapy in super‐refractory status epilepticus (2017)

In an open-label cohort of limited size, brexanolone demonstrated tolerability among SRSE patients of heterogeneous etiologies and was associated with a high rate of successful TLA weaning. The results suggest the possible development of brexanolone as an adjunctive therapy for SRSE requiring pharmacological coma for seizure control. Ann Neurol 2017;82:342-352.
Progress and Challenges toward the Development of Vaccines against Avian Infectious Bronchitis (2015)

Avian infectious bronchitis (IB) is a widely distributed poultry disease that has huge economic impact on poultry industry. The continuous emergence of new IBV genotypes and lack of cross protection among different IBV genotypes have been an important challenge. Although live attenuated IB vaccines remarkably induce potent immune response, the potential risk of reversion to virulence, neutralization by the maternal antibodies, and recombination and mutation events are important concern on their usage. On the other hand, inactivated vaccines induce a weaker immune response and may require multiple dosing and/or the use of adjuvants that probably have potential safety risks and increased economic burdens. Consequently, alternative IB vaccines are widely sought. Recent advances in recombinant DNA technology have resulted in experimental IB vaccines that show promise in antibody and T-cells responses, comparable to live attenuated vaccines. Recombinant DNA vaccines have also been enhanced to target multiple serotypes and their efficacy has been improved using delivery vectors, nanoadjuvants, and in ovo vaccination approaches. Although most recombinant IB DNA vaccines are yet to be licensed, it is expected that these types of vaccines may hold sway as future vaccines for inducing a cross protection against multiple IBV serotypes.
A Fast Minimal Infrequent Itemset Mining Algorithm (2014)

A novel fast algorithm for finding quasi identifiers in large datasets is presented. Performance measurements on a broad range of datasets demonstrate substantial reductions in run-time relative to the state of the art and the scalability of the algorithm to realistically-sized datasets up to several million records.
Thrombopoietin mobilizes CD34+ cell subsets into peripheral blood and expands multilineage progenitors in bone marrow of cancer patients with normal hematopoiesis. (1998)

Thrombopoietin (TPO), the primary regulator of megakaryocytopoiesis, also mediates biologic effects in vitro on hematopoietic cells more primitive than those committed to the megakaryocyte (MK) lineage. To assess the spectrum of hematopoietic effects of recombinant human (rh)TPO in vivo, we evaluated its proliferative effect on bone marrow (BM) progenitor cells, its maturation effect on BM MKs, and its mobilizing effect on peripheral blood (PB) progenitor cells during a phase I clinical laboratory investigation in which rhTPO was administered to cancer patients with normal hematopoiesis. Twelve patients received a single dose of rhTPO (0.3, 0.6, 1.2, or 2.4 microg/kg of body weight) prior to chemotherapy. BM and PB samples from these patients were analyzed 1 to 2 days before (baseline) and 7 days after rhTPO administration. At higher doses (1.2-2.4 microg/kg), rhTPO produced increased concentrations of primitive CD34+Thy-1+Lin-cells (mean 2.1-fold), CD34+mpl+ cells (mean 5.2-fold), CD34+CD41+CD14- promegakaryoblasts (mean 2.9-fold), and myeloerythroid colony-forming cells (mean threefold) in BM. No significant increases in the frequency of BM colony-forming unit (CFU)-MK were observed. Elevated numbers of both immature (2N-8N) and more mature (64N and 128N) CD41+ MKs were detected in BM, with modal ploidy remaining at 16N. Higher doses of rhTPO (1.2-2.4 microg/kg) also induced increased concentrations of CD34+ cell subsets in PB, including both primitive CD34+Thy-1+Lin- (mean 8.8-fold) and MK lineage-committed CD34+CD41+CD14- cells (mean 14.6-fold) as well as various myeloerythroid colony-forming cells (mean 3.6- to 5.5-fold). These results demonstrate that rhTPO given as a single dose not only promotes proliferation and maturation of cells of the MK lineage, but also expands the pool of BM primitive hematopoietic cells. In addition, rhTPO induces mobilization of hematopoietic progenitors into peripheral circulation. The extent to which such multilineage effects on human progenitor cells will contribute to clinical efficacy remains to be determined.
Contrasting a NoC and a Traditional Interconnect Fabric with Layout Awareness (2006)

Increasing miniaturization is posing multiple challenges to electronic designers. In the context of multi-processor system-on-chips (MPSoCs), we focus on the problem of implementing efficient interconnect systems for devices which are ever more densely packed with parallel computing cores. Easily seen that traditional buses can not provide enough bandwidth, a revolutionary path to scalability is provided by packet-switched network-on-chips (NoCs), while a more conservative approach dictates the addition of bandwidth-rich components (e.g. crossbars) within the preexisting fabrics. While both alternatives have already been explored, a thorough contrastive analysis is still missing. In this paper, we bring crossbar and NoC designs to the chip layout level in order to highlight the respective strengths and weaknesses in terms of performance, area and power, keeping an eye on future scalability
A ghost story: Spatio-temporal response characteristics of an indirect-detection flat-panel imager (1999)

Spatial and temporal imaging characteristics of an amorphous silicon flat-panel imager (FPI) were investigated in terms relevant to the application of such devices in cone-beam computed tomography (CBCT) and other x-ray imaging modalities, including general radiography, fluoroscopy, mammography, radiotherapy portal imaging, and nondestructive testing. Specifically, issues of image lag (including the magnitude, spatial uniformity, temporal-frequency characteristics, and dependence upon exposure and frame time) and long-term image persistence ("ghosts") were investigated. As part of the basic characterization of the FPI, pixel dark signal and noise (magnitude, temporal stability, and spatial uniformity) as well as radiation response (signal size, linearity, gain, and reciprocity) were also measured. Image lag was analyzed as a function of frame time and incident exposure. First-frame lag (i.e., the relative residual signal in the first frame following readout of an exposure) was approximately 2-10%, depending upon incident exposure and was spatially nonuniform to a slight degree across the FPI; second-, third-, and fourth-frame lag were approximately 0.7%, 0.4%, and 0.3%, respectively (at 25% sensor saturation). Image lag was also analyzed in terms of the temporal-frequency-dependent transfer function derived from the radiation response, allowing a quantitative description of system components contributing to lag. Finally, the contrast of objects as a function of time following an exposure was measured in order to examine long-term image persistence ("ghosts"). Ghosts were found to persist up to 30 min or longer, depending upon the exposure and frame time. Two means of reducing the apparent contrast of ghost images were tested: (i) rapid scanning of the FPI at maximum frame rate, and (ii) flood-field exposure of the FPI; neither was entirely satisfactory. These results pose important considerations for application of FPIs in CBCT as well as other x-ray imaging modalities. For example in CBCT, the magnitude of image lag is such that significant artifacts in tomographic reconstructions may result if strategies are not adopted either to reduce or correct the lag between successive projections (e.g., rapid scanning between projections or iterative correction algorithms, respectively). Similarly, long-term image persistence may necessitate frequent recalibration of offset corrections.
Quality of life in multiple sclerosis (1999)

The SF-36 captures the broad effects of MS, and the results showed that patients also are bothered frequently with health problems such as bodily pain and low vitality. These problems, which are not reflected in the Expanded Disability Status Scale, should be given more attention in the treatment of MS and when evaluating interventions.
Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition (2012)

Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system's lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples.
Alternative therapies to address the unmet medical needs of patients with phenylketonuria (2015)

Standard therapy for phenylketonuria (PKU), the most common inherited disorder in amino acid metabolism, is an onerous phenylalanine-restricted diet. Adherence to this stringent diet regimen decreases as patients get older, and this lack of adherence is directly associated with cognitive and executive dysfunction and psychiatric issues. These factors emphasize the need for alternative pharmacological therapies to help treat patients with PKU. Sapropterin dihydrochloride is a synthetic form of tetrahydrobiopterin, the cofactor of phenylalanine hydroxylase that in pharmacological doses can stabilize and increase residual enzyme activity in some patients with PKU. About one-third of all patients with PKU respond to oral sapropterin. Phenylalanine ammonia lyase (PAL) is a prokaryotic enzyme that converts phenylalanine to ammonia and trans-cinnamic acid. Phase I and II trials have shown that injectable recombinant Anabaena variabilis PAL produced in Escherichia coli conjugated with PEG can reduce phenylalanine levels in subjects with PKU. The most frequently reported adverse events were injection-site reactions, dizziness and immune reactions. Additionally, oral administration of PAL and delivery of enzyme substitution therapies by encapsulation in erythrocytes are being investigated. Novel therapies for patients with PKU appear to be options to reduce phenylalanine levels, and may reduce the deleterious effects of this disorder.
Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein (1997)

The 2.1-Å resolution crystal structure of wild-type green fluorescent protein and comparison of it with the recently determined structure of the Ser-65 → Thr (S65T) mutant explains the dual wavelength absorption and photoisomerization properties of the wild-type protein. The two absorption maxima are caused by a change in the ionization state of the chromophore. The equilibrium between these states appears to be governed by a hydrogen bond network that permits proton transfer between the chromophore and neighboring side chains. The predominant neutral form of the fluorophore maximally absorbs at 395 nm. It is maintained by the carboxylate of Glu-222 through electrostatic repulsion and hydrogen bonding via a bound water molecule and Ser-205. The ionized form of the fluorophore, absorbing at 475 nm, is present in a minor fraction of the native protein. Glu-222 donates its charge to the fluorophore by proton abstraction through a hydrogen bond network, involving Ser-205 and bound water. Further stabilization of the ionized state of the fluorophore occurs through a rearrangement of the side chains of Thr-203 and His-148. UV irradiation shifts the ratio of the two absorption maxima by pumping a proton relay from the neutral chromophore’s excited state to Glu-222. Loss of the Ser-205–Glu-222 hydrogen bond and isomerization of neutral Glu-222 explains the slow return to the equilibrium dark-adapted state of the chromophore. In the S65T structure, steric hindrance by the extra methyl group stabilizes a hydrogen bonding network, which prevents ionization of Glu-222. Therefore the fluorophore is permanently ionized, causing only a 489-nm excitation peak. This new understanding of proton redistribution in green fluorescent protein should enable engineering of environmentally sensitive fluorescent indicators and UV-triggered fluorescent markers of protein diffusion and trafficking in living cells.
Expression of Her2/neu, steroid receptors (ER and PR), Ki67 and p53 in invasive mammary ductal carcinoma associated with ductal carcinoma In Situ (DCIS) Versus invasive breast cancer alone. (2005)

We demonstrated significantly different expression patterns of Her2/neu, PR and Ki67 in IDC versus IDC/DCIS. Since these molecular markers play important roles in carcinogenesis and tumor progression, IDC/DCIS could be an important subtype of mammary invasive ductal cancer. Differences in expression of the evaluated markers might suggest a higher malignant potential of invasive carcinomas alone. The lower expression of Her2/neu and Ki67 in IDC/DCIS could implicate a less malignant behavior compared to a differentiated IDC. Additionally, these results might suggest that DCIS might be a malignant preform and the interaction with neoplastic tissue could result in an aggressive type of invasive tumor.
SonarPen : an ultrasonic pointing device for an interactive TV (2004)

An interactive TV is requiring a more advanced remote controlling method than the traditional TV due to its diverse and complex functions. Many types of input technologies and interaction styles are being tested for remote pointing for an interactive TV. We introduce the SonarPen, an ultrasonic pointing device system developed for an interactive TV. It determines a cursor position from phase differences among sinusoidal signals received by three ultrasonic receivers. A common problem with phase difference methods is phase ambiguity, but we solved this problem by exploiting the directionality of an LED and discontinuity in phase difference signals. A performance evaluation of the SonarPen in comparison with other pointing devices showed that the SonarPen has a better throughput, while it has a relatively high error rate than others.
Factors Influencing Lethality of Bacillus thuringiensis kurstaki Toxin for Eggs and Larvae of Trichostrongylus colubriformis (Nematoda) (1989)

A toxin from Bacillus thuringiensis kurstaki was lethal to eggs and first- and second-stage larvae of the ruminant nematode Trichostrongylus colubriformis. Sheathed and exsheathed third-stage larvae were also killed by the toxin. However, susceptibility of the ova to the toxin decreased after several hours of development. Heating at 65 C for 1 hr or freezing at 0 C for 3 mo did not affect stability of the toxin. Ovicidal activity of the toxin was not altered by treatment with 13 microbial or mammalian enzymes, but toxicity was reduced by the antibiotics streptomycin or penicillin G and the enzyme inhibitor L-1-tosylamide 2-phenylethylchloromethyl ketone. Cuprous, ferrous, and zinc chlorides also inhibited the ovicidal activity of the toxin. Increased osmolarity of the assay media or solubilization of the toxin from pH 3 to 11 had no effect on toxicity for eggs. The membrane agents sodium vanadate and 4,4'-diisothiocyano-2,2' disulfonic acid stilbene increased (9-fold) and decreased (333-fold) toxicity, respectively. N-acetylneuraminic acid was the only tested sugar that reduced the toxicity of B. t. kurstaki.
Cysteine, cystine or N-acetylcysteine supplementation in parenterally fed neonates (2006)

Available evidence from RCTs shows that routine short-term cysteine chloride supplementation of cysteine-free PN in preterm infants improves nitrogen balance.However, there is insufficient evidence to assess the risks of cysteine supplementation, especially regarding metabolic acidosis, which has been reported during the first two weeks of cysteine chloride administration. Available evidence from a large RCT trial does not support routine N-acetylcysteine supplementation of cysteine-containing PN in extremely low birth weight infants. A large RCT would be required to assess whether routine prolonged cysteine supplementation of cysteine-free PN affects growth and short and long-term neonatal outcomes in very low birth weight infants.
HIV-1 Nomenclature Proposal (2000)

A clear and consistent genetic classification of human immunodeficiency virus-type 1 (HIV-1) strains continues to be of great utility in epidemiological tracking of the AIDS pandemic and in vaccine design. It also provides a foundation for detecting any biological differences that may have evolved
HIV-1 Resistance to the Capsid-Targeting Inhibitor PF74 Results in Altered Dependence on Host Factors Required for Virus Nuclear Entry (2015)

The HIV-1 capsid plays critical roles in early steps of infection and is an attractive target for therapy. Here we show that selection for resistance to a capsid-targeting small molecule inhibitor can result in viral dependence on the compound. The mutant virus was debilitated in primary T cells and macrophages--cellular targets of infection in vivo. The mutations also altered the virus's dependence on cellular factors that are normally required for HIV-1 entry into the nucleus. This work provides new information regarding mechanisms of HIV-1 resistance that should be useful in efforts to develop clinically useful drugs targeting the HIV-1 capsid.
Fluorescence Probes for Membrane Potentials Based on Mesoscopic Electron Transfer (2007)

A new type of voltage-sensitive dye is proposed based on the electric-field dependence of electron transfer. These dyes contain an electron donor-acceptor pair in which intramolecular electron transfer competes with fluorescence emission, converting changes in electric field to those in fluorescence intensity. With electron-transfer distance of nanometers, theoretical analysis shows that these dyes can have high sensitivity to neuron action potentials with high fluorescence quantum yield, allowing for fast optical neuroimaging with large signal-to-noise ratio.
Novel Role of the Small GTPase Rheb: Its Implication in Endocytic Pathway Independent of the Activation of Mammalian Target of Rapamycin (2005)

The Ras-homologous GTPase Rheb that is conserved from yeast to human appears to be involved not only in cell growth but also in nutrient uptake. Recent biochemical analysis revealed that tuberous sclerosis complex (TSC), a GTPase-activating protein (GAP), deactivates Rheb and that phosphatidylinositol 3'-kinase (PI3k)-Akt/PKB kinase pathway activates Rheb through inhibition of the GAP-mediated deactivation. Although mammalian target of rapamycin (mTOR) kinase is implicated in the downstream target of Rheb, the direct effector(s) and exact functions of Rheb have not been fully elucidated. Here we identified that Rheb expression in cultured cells induces the formation of large cytoplasmic vacuoles, which are characterized as late endocytic (late endosome- and lysosome-like) components. The vacuole formation required the GTP form of Rheb, but not the activation of the downstream mTOR kinase. These results suggest that Rheb regulates endocytic trafficking pathway independent of the previously identified mTOR pathway. The physiological roles of the two Rheb-dependent signaling pathways are discussed in terms of nutrient uptake and cell growth or cell cycle progression.