Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Filter Paper Transfer of Whole-Blood and Plasma Samples for Quantifying HIV RNA in Subjects on Antiretroviral Therapy in Uganda

Background:Most HIV-infected subjects on antiretroviral therapy (ART) in resource-limited settings do not undergo virologic monitoring. There is an urgent need for cheap, accessible HIV RNA assays for early diagnosis of virologic failure. We investigated filter paper transfer (FPT) of whole blood and plasma as an alternative to standard plasma-based assays for virologic monitoring in Uganda. Methods:Whole blood (n = 306) and plasma (n = 218) from 402 subjects established on ART were spotted onto filter paper and transported to Europe for HIV RNA extraction and quantification. These results were compared to a gold standard plasma assay in Kampala. Results:Of 402 ART-treated subjects, 39 (9.7%) had viremia detectable (>500 copies/mL) by local methods. Plasma FPT showed excellent agreement with gold standard, whereas whole blood yielded a large number of false-positive viral loads. Conclusions:This is the first study to investigate the use of FPT in ART-treated subjects and demonstrates that it may provide a practical, reliable method for virologic monitoring in resource-poor settings. Plasma FPT was accurate but requires centrifuge; whole blood produced a high number of false-positive results, but these were low-level. Whole blood may be sufficiently accurate if higher HIV RNA cut-offs were used to define virologic failure.
Tissue-Engineered Skin Substitutes Using Collagen Scaffold with Amniotic Membrane Component

Human skin substitutes are needed for implantation and wound repair based on the new concept of tissue engineering in combination with biomaterials and cell biological technology. However, failure sometimes occurs when the wound healing is delayed in vivo due to acute inflammation resulting from the early degradation of the transplanted biomaterials. Accordingly, the current study modified conventional biomaterials to overcome early degradation and strong inflammation. In a conventional skin substitute, the animal origin collagenous materials have a slight antigenicity as xenogenic materials, however, the modified method was able to obtain a low antigenicity and anti-inflammation effect using atelo-collagen and an amniotic component. The tyrosine content in the developed atelo-collagen, representing the antigenicity, was reduced from 0.590% to 0.046% based on an HPLC analysis. In addition, to reduce the inflammation and foreign material reaction, an amniotic component was applied to the atelo-collagen materials. While, to enhance the wound healing, the modified skin substitute was developed as a composite matrix of an atelo-collagen scaffold with an amniotic membrane component. A quantitative analysis of hEGF in the amniotic membrane was also performed using different processing methods. Finally, a tissueengineered skin substitute was constructed by cultivating skin cells in the collagen scaffold attached to an amniotic membrane.
With Great Freedom for Inconsistent Data Comes Great Scalability Responsibility

Shared online databases, such as Google Fusion Tables or Quickbase, allow community members to collaboratively maintain and browse data. While users may believe in conflicting facts (due to conflicting sources, measurements or opinions), current online databases do not offer support for the management of data conflicts. Thus online databases could clearly benefit from technology for uncertain/incomplete databases. However, prior works on uncertain databases are of limited help when designing a conflict-aware online database, for two reasons: First, their performance degrades rapidly as the number of conflicting facts escalates, which can be the case in large user communities. Second, they were built as storage models, resulting in data models that are either non-simple or non-compact and thus may require additional, often non-trivial processing before they appear in the Frontend of an online database. To overcome these problems, we describe Ricolla; a scalable online database with built-in support for data conflict management. Ricolla allows users to model conflicting data, inspect them in a compact form and resolve inconsistencies in an “as-you-go" personalized fashion, even in the presence of a large number of conflicts. It achieves this by coordinating a novel conflict-aware data model (shown to be both compact and simple) with respective efficient query answering algorithms, that allow the system to scale to a large number of data conflicts (as evidenced by a performance comparison against Trio and MayBMS; two recent research prototypes for uncertain data). In parallel, the data model’s simplicity and compactness make it suitable for direct use by the Frontend.
High-resolution diffusion tensor imaging of the human kidneys using a free-breathing, multi-slice, targeted field of view approach

Fractional anisotropy (FA) obtained by diffusion tensor imaging (DTI) can be used to image the kidneys without any contrast media. FA of the medulla has been shown to correlate with kidney function. It is expected that higher spatial resolution would improve the depiction of small structures within the kidney. However, the achievement of high spatial resolution in renal DTI remains challenging as a result of respiratory motion and susceptibility to diffusion imaging artefacts. In this study, a targeted field of view (TFOV) method was used to obtain high‐resolution FA maps and colour‐coded diffusion tensor orientations, together with measures of the medullary and cortical FA, in 12 healthy subjects. Subjects were scanned with two implementations (dual and single kidney) of a TFOV DTI method. DTI scans were performed during free breathing with a navigator‐triggered sequence. Results showed high consistency in the greyscale FA, colour‐coded FA and diffusion tensors across subjects and between dual‐ and single‐kidney scans, which have in‐plane voxel sizes of 2 × 2 mm2 and 1.2 × 1.2 mm2, respectively. The ability to acquire multiple contiguous slices allowed the medulla and cortical FA to be quantified over the entire kidney volume. The mean medulla and cortical FA values were 0.38 ± 0.017 and 0.21 ± 0.019, respectively, for the dual‐kidney scan, and 0.35 ± 0.032 and 0.20 ± 0.014, respectively, for the single‐kidney scan. The mean FA between the medulla and cortex was significantly different (p < 0.001) for both dual‐ and single‐kidney implementations. High‐spatial‐resolution DTI shows promise for improving the characterization and non‐invasive assessment of kidney function. © 2014 The Authors. NMR in Biomedicine published by John Wiley & Sons, Ltd.
Sensor pillow and bed sheet system: Unconstrained monitoring of respiration rate and posture movements during sleep

In this paper, we have developed a low-cost sleep monitoring system for patient based on polysomnography which will be useful for patient communication with healthcare personals and/or relatives. In particular, we have presented the sensor pillow and bed sheet system that employs wireless networks based on low-cost ZigBee technology and a sensor array of force sensitive resistors (FSR) based on polymer thick film (PTF) device, for classifying and specifically verifying the respiration rate during sleep. This paper also proposes a simple motion model that explains the change of head and body pressure distribution. In addition, we can detect some physiological parameters during the sleep stages and wakefulness as well as record respiration rate as related to different physiological factors. The integration of this sensor system and wireless technology with computer software could make this healthcare monitoring system a commercial product valuable for point-of-care applications.
Protein structure and dynamics at high pressure 1

The effect of pressure on the structure and dynamics of proteins is discussed in the framework of the pressure-temperature stability phase diagram. The elastic (reversible) properties, thermal expansion, compressibility and heat capacity, are correlated with the entropy, volume, and the coupling between entropy and volume fluctuations respectively. The experimental approaches that can be used to measure these quantities are reviewed. The plastic (conformational) changes reflect the changes in these properties in the cold, pressure and heat denaturation. ß 1998 Elsevier Science B.V. All rights reserved.
Revascularization and bone remodeling of frozen allografts stimulated by intramedullary sustained delivery of FGF‐2 and VEGF

Frozen bone allografts are susceptible to nonunion and fracture due to limited revascularization and incomplete bone remodeling. We aim to revascularize bone allografts by combining angiogenesis from implanted arteriovenous (AV) bundles with delivery of fibroblast growth factor (FGF‐2) and/or vascular endothelial growth factor (VEGF) via biodegradable microspheres. Rat femoral diaphyseal allografts were frozen at −80°C, and heterotopically transplanted over a major histocompatibility mismatch. A saphenous AV bundle was inserted into the intramedullary canal. Growth factor was encapsulated into microspheres and inserted into the graft, providing localized and sustained drug release. Forty rats were included in four groups: (I) phosphate‐buffered saline, (II) FGF‐2, (III) VEGF, and (IV) FGF‐2 + VEGF. At 4 weeks, angiogenesis was measured by the hydrogen washout method and microangiography. Bone remodeling was evaluated by quantitative histomorphometry and histology. Bone blood flow was significantly higher in groups III and IV compared to control (p < 0.05). Similarly, bone remodeling was higher in VEGF groups. FGF‐2 had little effect on allograft revascularization. No synergistic effect was observed with use of both cytokines. Delivered in microspheres, VEGF proved to be a potent angiogenic cytokine, increasing cortical bone blood flow and new bone formation in frozen allografts revascularized with an implanted AV bundle. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 29: 1431–1436, 2011
Mechanical Response of Plectonemic DNA: An Analytical Solution

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically, and we derive formulas for the contact pressure, twisting moment, and geometrical parameters of the supercoiled region. We apply our model to magnetic tweezer experiments of a DNA molecule subjected to a tensile force and a torque and extract mechanical and geometrical quantities from the linear part of the experimental response curve. These reconstructed values are derived in a self-contained manner and are found to be consistent with those available in the literature.
BPR success or failure?: a business process reengineering project in the financial services industry

Business process reengineering (BPR) has attracted much interest in the academic and practitioner literature. The interest has been sparked not least by stories of dramatic success in business process improvement. The success stories stand in contrast to the supposed high failure rates associated with BPR. One stream of research on BPR has focused on those factors correlated with BPR success (or failure). In much of this literature, however, researchers have tended to assume that the factors can be readily identified and that “success” or “failure” is relatively easy to determine. In contrast, this paper reports on a BPR project where those involved disagreed on the most important factors. Moreover, the extent to which the project was successful was somewhat unclear. The project was regarded as a success by some of the participants, but not by others. This paper can be seen as one response to the call for more empirical in-depth case studies concerning the implementation of BPR in practice. The BPR project was one that involved redesigning the main accounting processes within one organization in the New Zealand financial services industry.
An update on the use of natalizumab in the treatment of multiple sclerosis: appropriate patient selection and special considerations

In the context of an increasing repertoire of multiple sclerosis (MS) therapeutics, choosing the appropriate treatment for an individual patient is becoming increasingly challenging. Natalizumab, a humanized monoclonal antibody directed against alpha4beta1 integrin, has proven short-term and long-term efficacies in terms of relapse rate reduction, prevention of disability progression, and reduction of magnetic resonance imaging-detectable activity. It is well tolerated and has further been shown to improve patients’ quality of life. Its use is limited by the risk of progressive multifocal leukoencephalopathy (PML), which occurs at an overall incidence of 3.78 cases per 1,000 patients. Three major risk factors for the occurrence of natalizumab-associated PML have been identified: John Cunningham virus (JCV) seropositivity, prior use of immunosuppressants, and treatment duration ≥2 years. Therefore, in patients considered for natalizumab therapy, as well as in patients receiving natalizumab, effective control of MS activity has to be balanced against the risk of an opportunistic central nervous system infection associated with a high risk of significant morbidity or death. Discontinuation of natalizumab is an issue in daily clinical practice, since it is an option to reduce the PML risk. However, after cessation of natalizumab therapy, currently, there is no approved strategy for avoiding postnatalizumab disease reactivation available. In this paper, short-term and long-term safety and efficacy data are reviewed. Issues in daily clinical practice, such as selection of patients, monitoring of patients, and natalizumab discontinuation, are discussed.
A Dynamic Channel Assignment Algorithm for OFDMA Systems

In this paper, we propose a heuristic dynamic channel assignment (DCA) algorithm to achieve the tradeoff between system throughput and fairness in downlink OFDMA systems. The proposed algorithm is divided into two stages: first, a proportional fairness is taken into account with quality-of- service (QoS) guaranteed to users for the system to accommodate as many users as possible; second, the remaining subcarriers are assigned for system throughput to be maximized. Numerical results reveal that a good tradeoff between system throughput and fairness is achieved. Furthermore, as a performance measure, the probability of outage is significantly reduced when compared to the optimal water-filling algorithm.
NONPARAMETRIC BAYES KERNEL-BASED PRIORS FOR FUNCTIONAL DATA ANALYSIS

We focus on developing nonparametric Bayes methods for collections of dependent random functions, allowing individual curves to vary flexibly while adaptively borrowing information. A prior is proposed, which is expressed as a hierarchical mixture of weighted kernels placed at unknown locations. The induced prior for any individual function is shown to fall within a reproducing kernel Hilbert space. We allow flexible borrowing of information through the use of a hierarchical Dirichlet process prior for the random locations, along with a functional Dirich- let process for the weights. Theoretical properties are considered and an efficient MCMC algorithm is developed, relying on stick-breaking truncations. The meth- ods are illustrated using simulation examples and an application to reproductive hormone data.
The Application of Cohesion Parameters to Wetting and Adhesion—A Review

Abstract Cohesion parameters are quantities with dimensions of (pressure)1/2 which describe the extent of cohesion within condensed phases. Although the Hildebrand solubility parameter was originally intended to describe the solution properties of liquids which did not undergo any significant mutual chemical interaction, similar cohesion parameters may be applied to the description and prediction of interfacial properties of a wide range of materials. This review outlines the application of cohesion parameters to wetting and adhesion.
Characteristics of Carbon Material Formation on SBA-15 and Ni-SBA-15 Templates by Acetylene Decomposition and Their Bioactivity Effects

Carbon spheres and tubes were formed from acetylene decomposition on SBA-15 and Ni-SBA-15 at 650–850 °C. At 650 °C, the decomposed carbons covered the surface of the support, and no carbon spheres and filament materials were formed. Carbon sphere formation occurred at 750 °C–850 °C; with diameters ranging from 0.8 μm–1.1 μm. For Ni-SBA-15, the diameters of the spheres and filaments were 0.8 μm and 62 nm, respectively, at 650 °C. At 750 °C, the diameter of the ball carbon materials ranged from 0.7 μm–0.8 μm, the diameter of the carbon tubes formed was 120–130 nm, and their pore diameter was 8.0 nm–11 nm. At 850 °C, the diameters of ball carbon materials and carbon tubes were similar to those of the materials at the formation temperature, 750 °C. Si, O and C were the main constituents of SBA-15; Ni-SBA-15 and carbon material formation supports. High-ring PAHs (such as BaP (five rings); IND (six rings); DBA (five rings) and B[ghi]P (six rings)) exist in carbon materials. SBA-15 revealed insignificant cytotoxicity, but Ni-SBA-15 inhibited the proliferation of human lung cancer cells (A549). Less inhibition on cell viability and reactive oxidative species (ROS) generation on A549 were determined for carbon material formation on the Ni-SBA-15 compared to the Ni-SBA-15.
The incremental garbage collection of processes

This paper investigates some problems associated with an argument evaluation order that we call “future” order, which is different from both call-by-name and call-by-value, In call-by-future, each formal parameter of a function is bound to a separate process (called a “future”) dedicated to the evaluation of the corresponding argument. This mechanism allows the fully parallel evaluation of arguments to a function, and has been shown to augment the expressive power of a language. We discuss an approach to a problem that arises in this context: futures which were thought to be relevant when they were created become irrelevant through being ignored in the body of the expression where they were bound. The problem of irrelevant processes also appears in multiprocessing problem-solving systems which start several processors working on the same problem but with different methods, and return with the solution which finishes first. This parallel method strategy has the drawback that the processes which are investigating the losing methods must be identified, stopped, and re-assigned to more useful tasks.
Molecular Dynamics in 1- and 2-D Confinement as Studied for the Case of Poly(Cis-1,4-Isoprene)

Broadband Dielectric Spectroscopy (BDS) is used to probe the molecular dynamics of Type A polymer, poly(cis-1,4-isoprene), when confined in the 1-dimensional (1D) exploring space of thin layers and the 2-dimensional (2D) constraining geometry of unidirectional anodic aluminum oxide (AAO) nanopores. For both cases, it was observed that the structural relaxation remains bulk-like in its mean relaxation rate, although the distribution of its relaxation times is broadened in 2D confinement. Furthermore, the fluctuation of the end-to-end vector is interrupted, with the 1D case being relatively less pronounced. By this clear-cut comparison, it is demonstrated that the effects of confinement on molecular dynamics depend, inter alia, on the dimensionality of the restricting space.
Effects of proinflammatory cytokines and bacterial toxins on neutrophil rheologic properties.

OBJECTIVE To examine the changes in neutrophil deformability, aggregation, and adherence in response to stimulation with proinflammatory cytokines and bacterial toxins. DESIGN Prospective, randomized trial. SETTING Research laboratory. SUBJECTS Neutrophils isolated from healthy volunteers. INTERVENTIONS Neutrophils were exposed to tumor necrosis factor (TNF)-alpha, interleukin (IL)-1beta, IL-8, their combination, endotoxin (LPS), lipoteichoic acid (LTA), and staphyloccocal enterotoxin B (SEB). Neutrophil deformability was measured as percent neutrophils filtered through 5-microm diameter filters. Aggregation was measured using a platelet aggregometer. Adherence was determined by examining the binding of neutrophils to albumin-coated latex beads. MEASUREMENTS AND MAIN RESULTS Exposure to TNF-alpha and IL-1beta led to significant decreases in neutrophil filterability, which was attenuated by cytochalasin D pretreatment. LPS and LTA also decreased deformability, suggesting that these toxins directly stimulated neutrophils independent of cytokines. IL-8 and SEB did not significantly affect neutrophil deformability. TNF-alpha and LPS were associated with significant neutrophil aggregation, which was inhibited by pretreatment with anti-CD18 antibodies. Neutrophil aggregation was not affected by IL-1beta, LTA, or SEB. TNF-alpha, IL-8, and LPS increased neutrophil adherence, which also was attenuated by pretreatment with anti-CD18 antibodies. IL-1beta, LTA, and SEB did not significantly affect neutrophil adherence. CONCLUSIONS Cytokines and bacterial toxins differ in their effects on neutrophil deformability, aggregation, and adherence. Of the cytokines examined, TNF-alpha appears to have the greatest direct effects on neutrophil rheology. Similarly, endotoxin appears to have greater direct effects on neutrophil rheology than the Gram-positive bacterial toxins, LTA, and staphylococcal enterotoxins.
Optimum/sub-optimum detectors for multi-branch dual-hop amplify-and-forward cooperative diversity networks with limited CSI

We study the optimum maximum-likelihood (ML) detection and sub-optimum detection for a multi-branch dual-hop cooperative diversity network with limited channel state information (CSI). Compared to the full CSI strategy, the signalling overhead at each relay involved with the limited CSI is reduced by 50%. We derive optimum ML detection with the limited CSI, which involves numerical integral evaluations. We also propose two closed-form sub-optimum detection rules of low complexity. It is shown that the first sub-optimum detection has almost identical performance to the optimum ML detection when Gaussianity in the added noise dominates, and the second sub-optimum detection has almost identical performance to the optimum ML detection when non-Gaussianity dominates. Finally, we propose a hybrid sub-optimum detection and demonstrate that its performance is almost identical to that of the optimum ML detection for general cases.
Development of Self-Decontaminating Textiles With Microporous Membranes

Abstract : Recently a number of compounds have been synthesized that can catalytically break down chemical warfare agents including G-type agents, VX and mustard. These compounds, including enzymes and polyoxometalates display significant level of hydrolytic and/or oxidative activity against a wide spectrum of chemical warfare agents. Multispectral protection could be achieved if appropriate catalysts were combined into a clothing system. However, these compounds have been difficult to incorporate into textiles for use in self-decontaminating chemical protective clothing, as their reactivity is severely impacted by the method of attachment onto and into fabrics. We now report a breakthrough in the technology of fiber spinning that has enabled us for the first time to incorporate these catalysts directly into microporous membranes. The new microporous membranes have been developed at the U.S. Army Natick Soldier Center using the process of electrospinning. By electrostatically producing nanofibers from polymer/solvent spinning solutions at room temperature through the application of a high voltage electric field, we have demonstrated increased activity of the original catalyst alone in solution by incorporating the same catalysts in the nanofibers of these new membranes. Activities of enzymes, derivatized enzymes and inorganic catalysts are discussed. Durability of the catalyst with respect to daily use conditions is considered. Manufacturability of these new reactive membranes will be forecast.