Miracle-dz/UniFAR-FTUs huggingface dataset:
Polyfunctional Fc-Effector Profiles Mediated by IgG Subclass Selection Distinguish RV144 and VAX003 Vaccines

RV144 vaccination induced polyfunctional antibody Fc-effector responses, whereas VAX003 vaccination increased inhibitory IgG4 antibodies. More Is Better for Protection Against HIV Recently, results from the first protective HIV phase 2B RV144 vaccine trial pointed to an unexpected signature of protection, not associated with the traditional mechanisms of vaccine-induced immunity, namely, neutralizing antibodies and killer T cell immunity. Instead, protection was associated with specific subpopulations of antibodies that were able to direct killing of HIV-infected cells. However, little is known about the properties of these killer antibodies or their biophysical features. In a new study, Chung et al. functionally profiled antibodies raised by the protective RV144 vaccine trial and its nonprotective predecessor, the VAX003 vaccine trial, both conducted in Thailand. RV144 vaccination uniquely induced antibodies capable of directing several different antiviral functions in a coordinated manner. In contrast, VAX003 vaccination predominantly induced single or uncoordinated antiviral responses. Functional coordination was regulated by the selection of antibody responses directed at vulnerable regions on the HIV envelope that were specifically tuned to enhanced functionality through the selection of a specific antibody subclass, IgG3, known to harbor strong antiviral activity. Collectively, these data suggest that vaccines able to induce broader antibody functional profiles, through the selection of more potent antibody subclasses, which target vulnerable regions of the virus, may represent a new means by which to achieve protection from HIV infection in the absence of neutralization. The human phase 2B RV144 ALVAC-HIV vCP1521/AIDSVAX B/E vaccine trial, held in Thailand, resulted in an estimated 31.2% efficacy against HIV infection. By contrast, vaccination with VAX003 (consisting of only AIDSVAX B/E) was not protective. Because protection within RV144 was observed in the absence of neutralizing antibody activity or cytotoxic T cell responses, we speculated that the specificity or qualitative differences in Fc-effector profiles of nonneutralizing antibodies may have accounted for the efficacy differences observed between the two trials. We show that the RV144 regimen elicited nonneutralizing antibodies with highly coordinated Fc-mediated effector responses through the selective induction of highly functional immunoglobulin G3 (IgG3). By contrast, VAX003 elicited monofunctional antibody responses influenced by IgG4 selection, which was promoted by repeated AIDSVAX B/E protein boosts. Moreover, only RV144 induced IgG1 and IgG3 antibodies targeting the crown of the HIV envelope V2 loop, albeit with limited coverage of breakthrough viral sequences. These data suggest that subclass selection differences associated with coordinated humoral functional responses targeting strain-specific protective V2 loop epitopes may underlie differences in vaccine efficacy observed between these two vaccine trials.
Proof Test and Fatigue of Unnotched Composite Laminates

A comprehansive Fatigue and residual strength degradation model has been used to predict the effect of proof loads (or high load) on the statisti cal fatigue behavior of composite laminates. The validity of the theoretical model is confirmed by the experimental test results. The correlation be tween the test results and the theoretical distributions of the fatigue life and the residual strength for composite specimens with or without the effect of proof loads is shown to be very good.
Beta-Estradiol , Integrins , and Synaptic Proteins

ACKNOWLEDGEMENTS Foremost, I would like to sincerely express my gratitude to my mentor Dr. James Simpkins for his continued support, encouragement, sound advice and for his strategic ideas that contributed to the betterment of my thesis work and helped me meet my timelines. This work would not have been possible without him. Also, I would like to sincerely appreciate Dr. Simpkins for his kind and compassionate nature that will always be an inspiration to me. I would like to sincerely thank my committee members Dr. Shaohua Yang and Dr. Nathalie Sumien for their kind support and guidance throughout my thesis work. I am especially grateful to Dr. Sumien for teaching me some of the basic laboratory techniques and giving me moral strength during the difficult times. I would also like to thank Dr. Ladislav Dory for his support and cooperation as my university member. I would like to thank Sue Yi for teaching me and helping me with all the animal procedures in this work. Her guidance has helped me solve many problems in my work. I also want to thank Pil Kim for teaching me some of the basic laboratory procedures and for offering me a helping hand whenever I needed. I wish to thank all the members and staff of Dr. Simpkins laboratory and all my friends at UNTHSC for providing me a friendly environment to work in. Lastly, but most importantly, I would like to thank my beloved husband Kranti for his support and encouragement that enabled me to complete this thesis. Finally, I have to thank my parents for their unconditional love and support in everything I do.
Depletion of norepinephrine, but not serotonin, reduces long-term potentiation in the dentate gyrus of rat hippocampal slices

Long-term potentiation (LTP) in the hippocampus is a long-lasting enhancement of synaptic efficacy produced by a brief, high frequency repetitive stimulation of afferents. LTP has generated a great deal of interest as a candidate mechanism in learning and memory. A recent in vivo study has shown that depletion of norepinephrine (NE) or serotonin (5-hydroxytryptamine, 5-HT) reduced LTP in the dentate gyrus produced by stimulation of the perforant path. However, it was impossible to tell whether this resulted from depletion in the hippocampus, itself, or was secondary to depletion of other brain areas, and no comparison between hippocampal cell fields was done. Therefore, we have examined the effects of depletion of NE or 5-HT on LTP in the dentate and field CA1 of the isolated in vitro hippocampal slice preparation. We report here that NE depletion markedly reduces the occurrence and amplitude of LTP in the dentate, but not in field CA1. In contrast, depletion of 5- HT does not prevent occurrence of LTP in either area. Furthermore, pharmacologic data indicate that beta-receptor stimulation of adenylate cyclase is probably the mechanism of NE's action in the production of LTP in the dentate. These results suggest that endogenous hippocampal NE is more important to LTP in the dentate than is endogenous 5-HT.
Research Paper No . 2004 / 25 Indicators of Inequality and Poverty

This essay aims at a broad, main-stream account of the literature on inequality and poverty measurement in the space of income and, additionally, deals with measures of disparity and deprivation in the more expanded domain of capabilities and functionings. In addition to an introductory and a concluding part, the paper has four sections. The first of these, on measurement of income inequality, deals with preliminary concepts and definitions; a visual representation of inequality (the Lorenz curve); real-valued indices of inequality; properties of inequality indices; some specific inequality measures; and the relationship between Lorenz, welfare, and inequality orderings. The second section, on poverty, deals with the identification and aggregation exercises; properties of poverty indices; some specific poverty measures; the problem of plurality and unambiguous rankings; poverty measures and anti-poverty policy; and other issues in the measurement of poverty. The third section considers aspects of both congruence and conflict in the relationship amongst poverty, inequality, and welfare. The final substantive section advances the rationale for a more comprehensive assessment of human wellbeing than is afforded by the income perspective, it briefly reviews measurement concerns relating to generalized indices of deprivation and disparity, and it discusses the data and policy implications of the more expansive view of well-being adopted in the section.
Broad Antiretroviral Activity and Resistance Profile of the Novel Human Immunodeficiency Virus Integrase Inhibitor Elvitegravir (JTK-303/GS-9137)

ABSTRACT Integrase (IN), an essential enzyme of human immunodeficiency virus (HIV), is an attractive antiretroviral drug target. The antiviral activity and resistance profile in vitro of a novel IN inhibitor, elvitegravir (EVG) (also known as JTK-303/GS-9137), currently being developed for the treatment of HIV-1 infection are described. EVG blocked the integration of HIV-1 cDNA through the inhibition of DNA strand transfer. EVG inhibited the replication of HIV-1, including various subtypes and multiple-drug-resistant clinical isolates, and HIV-2 strains with a 50% effective concentration in the subnanomolar to nanomolar range. EVG-resistant variants were selected in two independent inductions, and a total of 8 amino acid substitutions in the catalytic core domain of IN were observed. Among the observed IN mutations, T66I and E92Q substitutions mainly contributed to EVG resistance. These two primary resistance mutations are located in the active site, and other secondary mutations identified are proximal to these primary mutations. The EVG-selected IN mutations, some of which represent novel IN inhibitor resistance mutations, conferred reduced susceptibility to other IN inhibitors, suggesting that a common mechanism is involved in resistance and potential cross-resistance. The replication capacity of EVG-resistant variants was significantly reduced relative to both wild-type virus and other IN inhibitor-resistant variants selected by L-870,810. EVG and L-870,810 both inhibited the replication of murine leukemia virus and simian immunodeficiency virus, suggesting that IN inhibitors bind to a conformationally conserved region of various retroviral IN enzymes and are an ideal drug for a range of retroviral infections.
Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

Stem cell dynamics in vivo are often being studied by lineage tracing methods. Our laboratory has previously developed a retrospective method for reconstructing cell lineage trees from somatic mutations accumulated in microsatellites. This method was applied here to explore different aspects of stem cell dynamics in the mouse colon without the use of stem cell markers. We first demonstrated the reliability of our method for the study of stem cells by confirming previously established facts, and then we addressed open questions. Our findings confirmed that colon crypts are monoclonal and that, throughout adulthood, the process of monoclonal conversion plays a major role in the maintenance of crypts. The absence of immortal strand mechanism in crypts stem cells was validated by the age-dependent accumulation of microsatellite mutations. In addition, we confirmed the positive correlation between physical and lineage proximity of crypts, by showing that the colon is separated into small domains that share a common ancestor. We gained new data demonstrating that colon epithelium is clustered separately from hematopoietic and other cell types, indicating that the colon is constituted of few progenitors and ruling out significant renewal of colonic epithelium from hematopoietic cells during adulthood. Overall, our study demonstrates the reliability of cell lineage reconstruction for the study of stem cell dynamics, and it further addresses open questions in colon stem cells. In addition, this method can be applied to study stem cell dynamics in other systems.
An assessment of the ship drag penalty arising from light calcareous tubeworm fouling

Abstract A test coupon coated with light calcareous tubeworm fouling was scanned, scaled and reproduced for wind-tunnel testing to determine the equivalent sand grain roughness ks. It was found that this surface had a ks = 0.325 mm, substantially less than the previously reported values for light calcareous fouling. This result was used to predict the drag on a fouled full scale ship. To achieve this, a modified method for predicting the total drag of a spatially developing turbulent boundary layer (TBL), such as that on the hull of a ship, is presented. The method numerically integrates the skin friction over the length of the boundary layer, assuming an analytical form for the mean velocity profile of the TBL. The velocity profile contains the roughness (fouling) information, such that the prediction requires only an input of ks, the free-stream velocity (ship speed), the kinematic viscosity and the length of the boundary layer (the hull length). Using the equivalent sandgrain roughness height determined from experiments, a FFG-7 Oliver Perry class frigate is predicted to experience a 23% increase in total resistance at cruise, if its hull is coated in light calcareous tubeworm fouling. A similarly fouled very large crude carrier would experience a 34% increase in total resistance at cruise.
A Simple Relationship for High Efficiency–Gradient Uniformity Tradeoff in Multilayer Asymmetric Gradient Coils for Magnetic Resonance Imaging

High-quality gradient coils are pivotal to advances in magnetic resonance imaging (MRI). We have studied the influence of coil dimensions and target requirements in multilayer, asymmetric, transverse gradient coils. We developed a simple linear function that defines the optimal coil length to produce a maximum figure of merit given an imaging region size and location, coil radius, and gradient nonuniformity. Our method, based on the linear function, yields high-quality solutions. The method introduces two torque/force minimization strategies in order to obtain asymmetric transverse gradient coils that balance minimum torque with a maximum figure of merit. High-performance head, asymmetric gradient coils with simple current patterns and minimum torque can be tailored to a specific magnet design, as we illustrate
High Water Absorbents from Lignocelluloses. II. Novel Soil Conditioners for Sandy Soil from Lignocellulosic Wastes

Abstract Investigations have continued for economical utilization of lignocellulosic wastes, which represents one of the environmental problems facing the third world countries. The use of sugar-cane bagasse, rice straw, and waste paper as cellulose-containing waste stuff for obtaining soil conditioners is the basic aim of this work. The grafted lignocellulosic wastes were evaluated as soil conditioner in comparison with conventional conditioners (organic fertilizers and bentonite). The benefit of such materials as soil conditioners were evaluated by studying their effect on volume distribution of pores in sandy soil (drainable pores, water holding pores, and fine capillary pores), available moisture, air-filled porosity, and water-stable structural units.
Effects of a glucose meal on energy metabolism in patients with cirrhosis before and after liver transplantation.

HYPOTHESIS Liver transplantation results in hepatic denervation. This may produce alterations of liver energy and substrate metabolism, which may contribute to weight gain after liver transplantation. DESIGN Prospective clinical study. SETTING Liver transplantation clinics in a university hospital. PATIENTS Seven nondiabetic patients with cirrhosis were recruited while on a waiting list for liver transplantation. Seven healthy subjects were recruited as controls. INTERVENTION Orthotopic liver transplantation. MAIN OUTCOME MEASURES Evaluation of energy and substrate metabolism after ingestion of a glucose load with indirect calorimetry was performed before, 2 to 6 weeks after, and 5 to 19 months after transplantation. Whole-body glucose oxidation and storage and glucose-induced thermogenesis were calculated. RESULTS Patients with cirrhosis had modestly elevated resting energy expenditure and normal glucose-induced thermogenesis and postprandial glucose oxidation and storage. These measures remained unchanged after liver transplantation despite a significant increase in postprandial glycemia. Patients, however, gained an average of 3 kg of body weight after 5 to 19 months compared with their weight before transplantation. CONCLUSION Liver denervation secondary to transplantation does not lead to alterations of energy metabolism after ingestion of a glucose load.
The microwave absorption in diamond windows

An absorption investigation of a number of diamond disks for output windows of megawatt gyrotrons in the range of frequencies 50-180 GHz is carried out. It was found out that after high temperature brazing, the disks' surfaces obtain an additional number of free charge carriers in a thin, <</spl lambda/, surface layer leading to additional absorption. This additional absorption leads both to the overheating of the surfaces and to surface discharges. Its value may account for a significant part of the total window losses. So the superfluous losses in the thin surfaces layers were investigated and a method for its calculation was developed. By using this technique the loss tangent measurements of diamond disk were carried out in a wide range of frequencies. The loss tangent frequency dependencies, with an approximation of the experimental data to a l/f function, are presented. We used an open Fabry-Perot resonator for loss tangent measurements at the resonance frequencies of the disks.
Asymptotic Properties of Adaptive designs for Clinical Trials with delayed Response

For adaptive clinical trials using a generalized Friedman's urn design, we derive the limiting distribution of the urn composition under staggered entry and delayed response. The stochastic delay mechanism is assumed to depend on both the treatment assigned and the patient's response. A very general setup is employed with K treatments and L responses. When L = K = 2, one example of a generalized Friedman's urn design is the randomized playthe-winner rule. An application of this rule occurred in a clinical trial of depression, which had staggered entry and delayed response. We show that maximum likelihood estimators from such a trial have the usual asymptotic properties.
Superficial modification in recycled PET by plasma etching for food packaging

An oxygen plasma treatment has been used to improve the adhesion of amorphous hydrogenated car- bon (a-C:H) films onto surfaces of recycled poly(ethylene terephthalate) (PET). Modifications produced by the oxygen plasma on the PET surface in chemical bonds and morphol- ogy were investigated by X-ray photoelectron spectroscopy and atomic force microscopy, respectively. Contact angle measurements were used to study the changes in the sur- face wettability. Adhesion of the a-C:H film onto the PET surface was investigated by the tape test method. It was observed that the improvement in film adhesion is in good correlation with the increase in surface roughness, due to plasma etching, and with the appearance of oxygen-related functional groups at the surface. The results of this study indicate that a-C:H-coated recycled PET can be used in food packaging. The a-C:H film could be used as a functional barrier to reduce or prevent migration of contaminants from the polymer to the package content. V C 2009 Wiley Periodicals,
An Algorithm for Performance-Driven Placement of Cell-Based ICs

In this paper we describe an efficient algorithm for obtaining a placement of cell-based ICs subject to performance constraints. Using sophisticated mathematical techniques, we are able to solve large problems quickly and effectively. The algorithm is very simple and elegant, making it easy to implement. In addition, it yields good results as we show on a set of real examples. On the average, we are able to make 20% improvement in the wire delay of these examples with little or no impact on the total Steiner tree wirelength. The acronym RITUAL represents the key idea of our technique: Residual Iterative Technique for Updating All Lagrange multipliers.
Urbanization dramatically altered the water balances of a paddy field dominated basin in Southern China

Abstract. Rice paddy fields provide important ecosystem services (e.g., food production, water retention, carbon sequestration) to a large population globally. However, these benefits are diminishing as a result of rapid environmental and socioeconomic transformations, characterized by population growth, urbanization, and climate change in many Asian countries. This case study examined the responses of stream flow and watershed water balances to the decline of rice paddy fields due to urbanization in the Qinhuai River basin in southern China, where massive industrialization has occurred during the past 3 decades. We found that stream flow increased by 58 % and evapotranspiration (ET) decreased by 23 % during 1986–2013 as a result of a three-fold increase in urban areas and a reduction of rice paddy fields by 27 %. Both high flows and low flows increased significantly by about 28 % from 2002 to 2013. The increases in stream flow were consistent with the decreases in ET and leaf area index monitored by independent remote sensing MODIS (Moderate Resolution Imaging Spectroradiometer) data. Attribution analysis, based on two empirical models, indicated that land-use/land-cover change contributed about 82–108 % of the observed increase in stream flow from 353 ± 287 mm yr−1 during 1986–2002 to 556 ± 145 during 2003–2013. We concluded that the reduction in ET was largely attributed to the conversion of cropland to urban use. The effects of land-use change overwhelmed the effects of regional climate warming and climate variability. Converting traditional rice paddy fields to urban use dramatically altered land surface conditions from an artificial wetland-dominated landscape to an urban land-use- dominated one, and thus was considered an extreme type of contemporary hydrologic disturbance. The ongoing large-scale urbanization of the rice paddy-dominated regions, in humid southern China and East Asia, will likely elevate storm-flow volume, aggravate flood risks, and intensify urban heat island effects. Understanding the connection between land-use/land-cover change and changes in hydrological processes is essential for better management of urbanizing watersheds in the rice paddy-dominated landscape.
Counterfactual Thinking Deficit in Huntington’s Disease

Background and Objective Counterfactual thinking (CFT) refers to the generation of mental simulations of alternatives to past events, actions and outcomes. CFT is a pervasive cognitive feature in every-day life and is closely related to decision-making, planning and problem-solving – all of which are cognitive processes linked to unimpaired frontal lobe functioning. Huntington’s Disease (HD) is a neurodegenerative disorder characterised by motor, behavioral and cognitive dysfunctions. Because an impairment in frontal and executive functions has been described in HD, we hypothesised that HD patients may have a CFT impairment. Methods Tests of spontaneous counterfactual thoughts and counterfactual-derived inferences were administered to 24 symptomatic HD patients and 24 age- and sex-matched healthy subjects. Results Our results show a significant impairment in the spontaneous generation of CFT and low performance on the Counterfactual Inference Test (CIT) in HD patients. Low performance on the spontaneous CFT test significantly correlates with impaired attention abilities, verbal fluency and frontal lobe efficiency, as measured by Trail Making Test – Part A, Phonemic Verbal Fluency Test and FAB. Conclusions Spontaneous CFT and the use of this type of reasoning are impaired in HD patients. This deficit may be related to frontal lobe dysfunction, which is a hallmark of HD. Because CFT has a pervasive role in patients’ daily lives regarding their planning, decision making and problem solving skills, cognitive rehabilitation may improve HD patients’ ability to analyse current behaviors and future actions.