Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of Rapamycin Sensitivity in Breast Cancer Cells

Purpose: Rapamycin inhibits the serine-threonine kinase mammalian target of rapamycin (mTOR), blocking phosphorylation of p70 S6 kinase (S6K1) and 4E-binding protein 1 (4E-BP1) and inhibiting protein translation and cell cycle progression. Rapamycin and its analogues are currently being tested in clinical trials as novel-targeted anticancer agents. Although rapamycin analogues show activity in clinical trials, only some of the treated patients respond. The purpose of this study is to identify determinants of rapamycin sensitivity that may assist the selection of appropriate patients for therapy. Experimental Design: Breast cancer cell lines representing a spectrum of aberrations in the mTOR signaling pathway were tested for rapamycin sensitivity. The expression and phosphorylation state of multiple components of the pathway were tested by Western blot analysis, in the presence and absence of rapamycin. Results: Cell proliferation was significantly inhibited in response to rapamycin in 12 of 15 breast cancer cell lines. The ratio of total protein levels of 4E-BP1 to its binding partner eukaryotic initiation factor 4E did not predict rapamycin sensitivity. In contrast, overexpression of S6K1, and phosphorylated Akt independent of phosphatase and tensin homologue deleted from chromosome 10 status, were associated with rapamycin sensitivity. Targeting S6K1 and Akt with small interfering RNA and dominant-negative constructs, respectively, decreased rapamycin sensitivity. Rapamycin inhibited the phosphorylation of S6K1, ribosomal S6 protein, and 4E-BP1 in rapamycin-resistant as well as -sensitive cells, indicating that its ability to inhibit the mTOR pathway is not sufficient to confer sensitivity to rapamycin. In contrast, rapamycin treatment was associated with decreased cyclin D1 levels in the rapamycin-sensitive cells but not in rapamycin-resistant cells. Conclusions: Overexpression of S6K1 and expression of phosphorylated Akt should be evaluated as predictors of rapamycin sensitivity in breast cancer patients. Furthermore, changes in cyclin D1 levels provide a potential pharmacodynamic marker of response to rapamycin.
Cadmium and Lead Accumulation and Distribution in the Organs of Nine Crops: Implications for Phytoremediation

Field experiments were carried out from 1999 to 2001 with nine crops (red beet, field pumpkin, chicory, common bean, barley, white cabbage, maize, alfalfa and common parsnip) to determine the cadmium and lead accumulation and distribution in the plants' organs. Based on the obtained results, species suited for phytoremediation were selected. Within the red beet, field pumpkin, chicory, common bean, white cabbage and parsnip the maximum Cd and Pb content was found in leaves. The red beet was characterized by the highest cadmium concentration ratio (shoots/roots). The red beet and common parsnip were characterized by the highest lead concentration ratios (shoots/roots). The phytoremediation efficiency of the investigated crops depended on the biomass production and the possibility of metal accumulation in harvestable organs.
What comes first the Co-authorship Network or the Citation?

For many decades citation counting has been used as the way to quantify the nebulous notion of research "quality". Indeed, in conversation the terms "research quality", "impact" or "excellence in research" are simply a reference to a scientific document's citation count. Moreover, the commonly used journal "impact" factors are simply manipulated forms of citation counting. In recent times, the word "impact" has morphed into the new 'mot du jour'. This paper investigates and discusses the association between co-authorship networks and citations of institutions within an arbitrary, but defined, subject area. The data examined is readily available and the analytical techniques employed are deliberately simple. The simplicity of this analysis is driven by the desire to show that citation counts are not explicitly related to the quality of research but that citations are a result of multifaceted author networks that are inherent in scientific endeavor. The paper presents an argument that the improved ability to conduct effective network analysis and related research shows that the notion of high citations being the same as "research quality" has run its course. Citation performance is more likely to be a result of co-authorship network dynamics rather than any perceived notion of "quality". Moreover, it is time the folly of citation counting is put to rest and that if one wants know what "impact" one is having that you need look no further than your co-authorship network and the reach it has across whatever subject area you are interested in. The discussion and results herein highlight that rather than counting citations, the "impact" of research is driven by connections through networks of people.
Analysis of viral RNA persistence in seawater by reverse transcriptase-PCR

It is important to determine the stability of naked viral RNA in seawater, since false-positive results can occur when reverse transcriptase-PCR (RT-PCR) is used to detect viruses if the RT-PCR amplifies free RNA instead of RNA from intact viruses. An acid guanidinium thiocyanate-phenol-chloroform method was used to extract total RNA from a filtered poliovirus cell culture suspension. The sensitivity of detection in this viral RNA study was 600 fg when RT-PCR was used. The extracted total RNA was seeded into filtered and unfiltered seawater, and the resulting preparations were incubated at 4 degrees C and at room temperature (23 +/- 1 degrees C). Our results showed that the seeded RNA was more stable in filtered seawater than in unfiltered seawater at both temperatures. The viral RNA could not be detected by the RT-PCR after 2 days of incubation in unfiltered seawater and after 28 days of incubation in filter-sterilized seawater. Therefore, because of the relatively short life of viral RNA in natural water, the detection of virus in environmental samples by the RT-PCR was mainly due to the presence of well-protected viral particles and not due to the presence of naked viral RNA.
Approximate Zero-Variance Importance Sampling for Static Network Reliability Estimation

We propose a new Monte Carlo method, based on dynamic importance sampling, to estimate the probability that a given set of nodes is connected in a graph (or network) where each link is failed with a given probability. The method generates the link states one by one, using a sampling strategy that approximates an ideal zero-variance importance sampling scheme. The approximation is based on minimal cuts in subgraphs. In an asymptotic rare-event regime where failure probability becomes very small, we prove that the relative error of our estimator remains bounded, and even converges to 0 under additional conditions, when the unreliability of individual links converges to 0. The empirical performance of the new sampling scheme is illustrated by examples.
Tip Vortex Formation and Evolution to the Near Wake of a Rotor in Forward Flight

Realistic models of the formation, structure and evolution of tip vortices are essential to predict rotor blade aeroacoustics. Velocity measurements are reported here on tip vortex formation and evolution to the near wake from a teetering, untwisted, square-tipped, two-bladed NACA0015 rotor in low-speed forward flight. Given assured periodicity and appropriate measurement techniques, vortex formation results confirm observations made in the 1980s. Circumferential velocity profiles are observed as early as x/c = 0.47, growing in strength and core radius up to x/c of 1.06. The profiles of circumferential velocity manifest the rollup of discrete vortex filaments. The effect of seed particle dynamics on the accuracy of vortex measurements in the near wake is studied to verify accuracy. The wake structure and the tip vortex properties up to 488° of wake age are presented. Harmonic variations are seen in the tip vortex core axial velocity. A strong spanwise velocity is seen on the pressure and suction sides of the blade. The core axial velocity appears to approach tip speed at origin, and the core circumferential velocity remains constant for a large distance after formation. The equations of motion describing seed particle motion in a 2D vortex were numerically integrated to quantify the velocity error of LDV measurements of the near-wake vortex characteristics due to seed particle dynamics. For a vortex strength of 0.75 m/s typical of rotor tests at a tip Mach number of 0.15, the error in circumferential velocity error due to lag of particles between 1 and 5μm, is seen to have an upper bound of 2%.
Delineation of multiple subpopulations of natural killer cells in rhesus macaques

Natural killer (NK) cells in rhesus macaques have been variably defined as CD3− CD16+ or CD3− CD8+, although only limited efforts have been made to validate these definitions rigorously. To better understand the role of NK cells in macaque disease models, we undertook a multiparameter analysis of macaque NK cells employing four‐colour flow cytometry and a panel of lineage‐specific and non‐lineage‐specific lymphocyte markers. Using this approach, we identified two distinct populations of candidate NK cells: a major CD8bright CD16+ population and a minor CD8bright CD16− population. Further analysis of the major and minor NK cell populations revealed the expression of multiple markers characteristic of NK cells, including CD2, CD7, CD16, CD161, NKG2A and granzyme B. In addition, a CD56+ subset of cells within the minor rhesus NK population was identified which expressed chemokine and lymph node homing receptors similar to those expressed by the CD56bright NK cell population identified in humans. Cytolytic assays confirmed that the phenotypically defined rhesus NK cells lysed NK‐susceptible target cells. Our observations support the existence of several distinct subpopulations of rhesus macaque NK cells, which have significant phenotypic and functional similarities to their human counterparts. These improved immunophenotypic definitions of macaque NK cells should facilitate future analysis of innate immune responses in rhesus macaques and the role of NK cells in AIDS pathogenesis in Simian immunodeficiency virus (SIV)‐infected macaques.
Periodontal Disease: A Covert Source of Inflammation in Chronic Kidney Disease Patients

The prevalence of atherosclerotic complications (myocardial infarction, stroke, and sudden death) is increased in end-stage renal disease (ESRD) patients, especially in haemodialysis patients. Increasing evidence suggests that both in general population and in dialysis patients, systemic inflammation plays a dominant role in the pathogenesis of atherosclerotic complications. In general population, also, evidence shows that moderate to severe periodontitis can contribute to inflammatory burden by increasing serum CRP levels and may increase the prevalence of atherosclerotic events. Moreover, the results of some new interventional studies reveal that effective phase I periodontal therapy may decrease serum CRP levels, the most important acute phase protein, monitored as a systemic marker of inflammation and endothelial dysfunction as well, used as an initial predictor of atherosclerotic events. Considering that moderate to severe periodontal diseases have a higher prevalence in CKD and in dialysis population and that periodontal examination is not part of the standard medical assessment, destructive periodontitis might be an ignored source of systemic inflammation in end-stage renal disease patients and may add to the chronic inflammatory status in CKD.
The role of cyclin B in meiosis I

In clams, fertilization is followed by the prominent synthesis of two cyclins, A and B. During the mitotic cell cycles, the two cyclins are accumulated and then destroyed near the end of each metaphase. Newly synthesized cyclin B is complexed with a small set of other proteins, including a kinase that phosphorylates cyclin B in vitro. While both cyclins can act as general inducers of entry into M phase, the two are clearly distinguished by their amino acid sequences (70% nonidentity) and by their different modes of expression in oocytes and during meiosis. In contrast to cyclin A, which is stored solely as maternal mRNA, oocytes contain a stockpile of cyclin B protein, which is stored in large, rapidly sedimenting aggregates. Fertilization results in the release of cyclin B to a more disperse, soluble form. Since the first meiotic division in clams can proceed even when new protein synthesis is blocked, these results strongly suggest it is the fertilization- triggered unmasking of cyclin B protein that drives cells into meiosis I. We propose that the unmasking of maternal cyclin B protein allows it to interact with cdc2 protein kinase, which is also stored in oocytes, and that the formation of this cyclin B/cdc2 complex generates active M phase-promoting factor.
Treatment of abdominal aortic aneurysms with transfemoral placement of stent-grafts: complications and secondary radiologic intervention.

PURPOSE To determine the rate of complications of transluminally placed endovascular stent-grafts in patients with abdominal aortic aneurysms and to assess efficacy of secondary radiologic intervention. MATERIALS AND METHODS In 28 patients, covered nitinol stents were implanted. Frequency and outcome of complications were evaluated after stent-graft placement (mean follow-up, 8.2 months). RESULTS In 27 patients, 11 tube and 16 bifurcated grafts were implanted successfully. In one (4%) patient, distal migration of a bifurcated graft necessitated conversion to standard open repair. Technical success rates (successful deployment of the device and complete exclusion of the aneurysm at intraoperative angiography) for bifurcated and tube grafts were 24% (four of 17 patients) and 91% (10 of 11 patients). After surgery, leaks were seen in six bifurcated and five tube grafts. After secondary intervention, the final exclusion rate for bifurcated and tube grafts was 88% (15 of 17 patients) and 100% (11 of 11 patients), respectively; the overall success rate was 93% (26 of 28 patients) for exclusion of aortic abdominal aneurysms. Stent-graft thrombosis necessitated local thrombolysis in one patient. Overlapping of accessory renal arteries occurred in two patients. CONCLUSION Complications after stent-graft placement in abdominal aortic aneurysms are frequent. Secondary radiologic intervention is successful in most cases.
Relationship of health‐related quality of life to treatment adherence and sustained response in chronic hepatitis C patients

Interferon therapy may exacerbate health‐related quality of life (HRQL) deficits associated with hepatitis C virus (HCV) early in the course of therapy. Treatment with polyethylene glycol–modified interferon (peginterferon) alfa‐2a (40 kd) provides improved sustained response over interferon alfa‐2a, but its effect on HRQL is unknown. The objective of this study was to (1) evaluate the effect of sustained virologic response on HRQL in patients with HCV and (2) determine whether impairment of HRQL during treatment contributes to early treatment discontinuation. Data consisted of a pooled secondary analysis of patients (n = 1,441) across 3 international, multicenter, open‐label, randomized studies that compared peginterferon alfa‐2a (40 kd) with interferon alfa‐2a. ANCOVA was used to examine the effect of sustained virologic response on HRQL. Repeated‐measures mixed‐models ANCOVA was used to compare Fatigue Severity Scale (FSS) and SF‐36 scores during treatment by treatment group. Logistic regression analysis was used to examine the association between changes at baseline in on‐treatment HRQL and early treatment discontinuation. Sustained virologic response was associated with marked improvements from baseline to end of follow‐up in all subjects, including patients with cirrhosis. During treatment, patients receiving peginterferon alfa‐2a (40 kd) had statistically significantly better scores on both the SF‐36 and FSS. Baseline to 24‐week changes in fatigue and SF‐36 mental and physical summary scores significantly predicted treatment discontinuation. In conclusion, sustained virologic response is associated with improvements in quality of life in patients with or without advanced liver disease. This parameter may be an important consideration in maximizing treatment adherence.
Elasticity of particle assemblies as a measure of the surface energy of solids

A theory is suggested to explain the elasticity of particle assemblies. It is shown that a regular cubic packing of spheres has an effective Young’s modulus that depends on the contacts between individual particles. In particular, it is noted that the effective modulus depends on the interfacial attractive energy between the spheres, and thus provides a direct method for measuring the surface energy of solids. However, most particle assemblies are neither cubic nor regular. The problem is to describe the properties of these real systems in terms of the packing of the grains. Theoretically, it is shown that the modulus of a powder compact should vary as the fourth power of the particle packing fraction. This result has been verified experimentally and has been used to determine the surface energies of zirconia, titania, alumina, and silica powders. The measured values were sometimes much lower than expected from theoretical calculations of surface energy. Experiment has shown that such discrepancies result from contamination of the solid surfaces.
Development of Rare Earth Metal Iron Oxides as Mixed Ionic and Electronic Conductors

In recent years there has been an increasing interest in finding a new and less energy demanding alternative to cryogenic distillation in the production of pure oxygen gas. The use of oxygen permeable membranes has been considered a preferable alternative, and extensive studies into candidate materials for use in these membranes, performed. Problems concerning cationic demixing and breakdown of the material structure has been reported for many of these materials were oxygen is transported through oxygen vacancies usually requiring an operating temperature above 800°C. Lately, an increasing interest in materials that can transport oxygen through oxygen interstitials instead of vacancies has emerged, since oxygen interstitials can be transported at temperatures below 600°C where cationic diffusion is usually prevented. A study of the oxygen storage ability of rare earth ferrites has recently been reported, where an oxygen storage ability of an x=0.5, and a good cycling ability has been found for LuFe2O4. A problem with the use of rare earth ferrites for this purpose is that the powder preparation route involves metallic iron as one of the precursors, requiring the use of a glove box in the preparation of the material. In this study, phase pure powder of another rare earth ferrite, YbFe2O4 has been performed from a conventional solid state synthesis route. Strong indications of the possibility of obtaining the material from a sol-gel synthesis route is also reported. Heat treatment of the material in oxygen atmosphere resulting in an oxygen rich phase, YbFe2O4.5, was quantified from in situ TGA measurements, while an ex. situ heat treatment performed under oxidizing and reducing conditions strongly indicates a good cycling ability of the material. The increase in the oxygen content during heat treatment in oxygen atmosphere took place below 500°C, and is therefore expected to originate from oxygen interstitials being implemented in the structure. A significant change in structure is also observed after heat treatment in oxygen atmosphere, emphasizing this theory. Indications of a p-type conductivity from a van der Pauw measurement is also reported. The new and more convenient powder preparation route, significantly increases the potential of rare earth ferrites for use in oxygen permeable membranes, and a further investigation into their reported multiferroic properties. A replacement of Lu with Yb in the material significantly decreases the material cost, and therefore the use of these materials in up-scale production.
Chronic demyelinating hypertrophic brachial plexus neuropathy

A patient with unilateral, painless, chronic progressive upper limb sensorimotor deficit showed electrophysiological evidence of a focal demyelinating neuropathy with almost complete conduction block across the brachial plexus. Magnetic resonance imaging disclosed marked brachial plexus hypertrophy. Intravenous immunoglobulin led to fast and complete recovery, maintained by intermittent perfusions. Hypertrophic brachial plexus neuropathy can be a presentation of focal chronic inflammatory demyelinating polyradiculoneuropathy. Objective and quantitative assessment of hand function is useful to evaluate treatment results and to optimize treatment regimens. © 2000 John Wiley & Sons, Inc. Muscle Nerve 23: 283–288, 2000.
The Social Networks of Homeless Youth Experiencing Intimate Partner Violence

While there is a growing body of research on intimate partner violence (IPV) experienced by the housed youth population, a limited amount is known about IPV experienced by homeless youth. To our knowledge, no previous studies have examined how homeless youths’ experience of IPV is related to their social network, even though the social networks of homeless youth have been shown to be significant indicators of health and mental health. The purpose of this study is to understand the relationship between IPV, gender, and social networks among a sample of 386 homeless youth in Los Angeles, California. Results revealed that one fifth of the sample experienced IPV in the past year. Stratified regression models revealed that IPV was not significantly related to any measure of male social networks; however, females who experienced IPV had more male friends (β = 2.03, SE = 0.89, p < .05) than females who did not experience IPV. Female homeless youth who witnessed family violence during childhood had more male friends (β = 2.75, SE = 1.08, p < .05), but those who experienced sexual abuse during childhood had fewer male friends (β = −2.04, SE = 0.93, p < .05). Although there was no significant difference in the rate of IPV victimization across genders, the context of this abuse appears to be drastically different. The results suggest that females with more male friendships are at greater risk for exposure to IPV. To date, there are few effective youth-targeted IPV prevention programs and none have been shown to be effective with homeless youth. These results provide insight into future program development.
An Efficient CSI Feedback Scheme for MIMO-OFDM Wireless Systems

For antenna-array-based multiple-input multiple- output orthogonal-frequency-division-multiplexing (MIMO-OFDM) wireless systems, gain in channel throughput reduced through sufficient feedback of the channel state information (CSI) is significant, particularly when the number of transmit antennas is larger than the number of receive antennas. In this letter, we demonstrate that, in such scenarios, (1) the CSI of each OFDM sub-carrier can be parameterized into a short bit stream by a proposed low-complexity QR decomposition on the corresponding MIMO channel matrix, (2) the overall CSI can be reliably represented by a proposed parameter interpolation on the above bit streams of only a fraction of sub-carriers, and (3) a MIMO-OFDM system with a low-rate CSI feedback parameterized above can provide a channel throughput comparable to the channel capacity.