Miracle-dz/UniFAR-FTUs huggingface dataset:
FDG-PET Response Prediction in Pediatric Hodgkin’s Lymphoma: Impact of Metabolically Defined Tumor Volumes and Individualized SUV Measurements on the Positive Predictive Value

Background: In pediatric Hodgkin’s lymphoma (pHL) early response-to-therapy prediction is metabolically assessed by (18)F-FDG PET carrying an excellent negative predictive value (NPV) but an impaired positive predictive value (PPV). Aim of this study was to improve the PPV while keeping the optimal NPV. A comparison of different PET data analyses was performed applying individualized standardized uptake values (SUV), PET-derived metabolic tumor volume (MTV) and the product of both parameters, termed total lesion glycolysis (TLG); Methods: One-hundred-eight PET datasets (PET1, n = 54; PET2, n = 54) of 54 children were analysed by visual and semi-quantitative means. SUVmax, SUVmean, MTV and TLG were obtained the results of both PETs and the relative change from PET1 to PET2 (Δ in %) were compared for their capability of identifying responders and non-responders using receiver operating characteristics (ROC)-curves. In consideration of individual variations in noise and contrasts levels all parameters were additionally obtained after threshold correction to lean body mass and background; Results: All semi-quantitative SUV estimates obtained at PET2 were significantly superior to the visual PET2 analysis. However, ΔSUVmax revealed the best results (area under the curve, 0.92; p < 0.001; sensitivity 100%; specificity 85.4%; PPV 46.2%; NPV 100%; accuracy, 87.0%) but was not significantly superior to SUVmax-estimation at PET2 and ΔTLGmax. Likewise, the lean body mass and background individualization of the datasets did not impove the results of the ROC analyses; Conclusions: Sophisticated semi-quantitative PET measures in early response assessment of pHL patients do not perform significantly better than the previously proposed ΔSUVmax. All analytical strategies failed to improve the impaired PPV to a clinically acceptable level while preserving the excellent NPV.
A Flexible Base Electrode Array for Intraspinal Microstimulation

In this paper, we report the development of a flexible base array of penetrating electrodes which can be used to interface with the spinal cord. A customizable and feasible fabrication protocol is described. The flexible base arrays were fabricated and implanted into surrogate cords which were elongated by 12%. The resulting strains were optically measured across the cord and compared to those associated with two types of electrodes arrays (one without a base and one with a rigid base connecting the electrodes). The deformation behavior of cords implanted with the flexible base arrays resembled the behavior of cords implanted with individual microwires that were not connected through a base. The results of the strain test were used to validate a 2-D finite element model. The validated model was used to assess the stresses induced by the electrodes of the three types of arrays on the cord, and to examine how various design parameters (thickness, base modulus, etc.,) impact the mechanical behavior of the electrode array. Rigid base arrays induced higher stresses on the cord than the flexible base arrays which in turn imposed higher stresses than the individual microwire implants. The developed flexible base array showed improvement over the rigid base array; however, its stiffness needs to be further reduced to emulate the mechanical behavior of individual microwire arrays without a base.
Biogenic Silver Nanoparticles and its Antifungal Activity as a New Topical Transungual Drug

Silver nanoparticles production was monitored by UVVis and TEM micrograph and they were obtained as spherical and homogenous nanoparticles with a size of ~100 nm by photon correlation spectroscopy (PCS). Silver nanoparticles, in an IC80 range of 1-2 μg/mL, showed significant antifungal activity against T. rubrum. Cytotoxicity through hemolytic activity against erythrocytes and the viability of V79 fibroblast or HL60 cells showed less toxicity than amphotericin B. The disk diffusion test showed that the silver nanoparticles exerted a similar inhibition zone that amphotericin B by a synergistic effect when added at the same time against T. rubrum culture.
Recruiting for Epigenetic Research: Facilitating the Informed Consent Process

Because the effects of epigenetic (gene-environment interaction) changes have been associated with numerous adverse health states, the study of epigenetic measures provides exciting research opportunities for biobehavioral scientists. However, recruitment for studies focusing on any aspect of genetics poses challenges. Multiple factors, including lack of knowledge regarding a research study, have been identified as barriers to recruitment. Strengthening the informed consent process through extended discussion has been found to be effective in recruiting for research studies in general, yet there is a paucity of information that focused on such a recruitment strategy for epigenetic studies. In this paper, we share our experiences with strategies to strengthen the informed consent process as well as provide samples of materials developed to heighten potential participants' understanding of epigenetics, in 4 epigenetic research studies with women from diverse backgrounds experiencing a range of health issues. The combined enrollment success rate for epigenetic studies using the process was 89% with participants representing a diverse population. We posit that carefully developed recruitment scripts provided a foundation for improving potential participants' understanding of the research project. Easy to understand illustrations of the epigenetic process provided a basis for active engagement and encouraged individual questions.
Developing predictive models for early detection of at-risk students on distance learning modules

Not all students who fail or drop out would have done so if they had been offered help at the right time. This is particularly true on distance learning modules where there is no direct tutor/student contact, but where it has been shown that making contact at the right time can improve a student’s chances. This paper explores the latest work conducted at the Open University, one of Europe’s largest distance learning institutions, to identify when is the optimum time to make student interventions and to develop models to identify the at-risk students in this time frame. This work in progress is taking real time data and feeding it back to module teams as the module is running. Module teams will be indicating which of the predicted at-risk students have received an intervention, and the nature of the intervention.
An Integrated Model for Optimal Reservoir Operation for Irrigation of Multiple Crops

An integrated model is developed, based on seasonal inputs of reservoir inflow and rainfall in the irrigated area, to determine the optimal reservoir release policies and irrigation allocations to multiple crops. The model is conceptually made up of two modules. Module 1 is an intraseasonal allocation model to maximize the sum of relative yields of all crops, for a given state of the system, using linear programming (LP). The module takes into account reservoir storage continuity, soil moisture balance, and crop root growth with time. Module 2 is a seasonal allocation model to derive the steady state reservoir operating policy using stochastic dynamic programming (SDP). Reservoir storage, seasonal inflow, and seasonal rainfall are the state variables in the SDP. The objective in SDP is to maximize the expected sum of relative yields of all crops in a year. The results of module 1 and the transition probabilities of seasonal inflow and rainfall form the input for module 2. The use of seasonal inputs coupled with the LP-SDP solution strategy in the present formulation facilitates in relaxing the limitations of an earlier study, while affecting additional improvements. The model is applied to an existing reservoir in Karnataka State, India.
Development and aging of noradrenergic cell bodies and axon terminals in the chicken

Tyrosine hydroxylase activity was measured in the region of locus coeruleus, cerebellum, cervical spinal cord, lumbar sympathetic ganglia, and iris throughout most of the life span of the chicken (8 days of incubation to 5 years) to compare developmental trends in tyrosine hydroxylase activity in noradrenergic cell bodies and in axon terminals in both the central and peripheral nervous system. Fluorescence histochemistry and retrograde transport of horseradish peroxidase were used to characterize further the coeruleo‐cerebellar projections. Tyrosine hydroxylase activity was detected in the cerebellum as early as 8 days of incubation, which is the earliest stage so far reported. The greatest increase in total tyrosine hydroxylase activity in the region of the locus coeruleus and cerebellum occurred during the embryonic period. There was a more pronounced increase in the cerebellum than in the locus coeruleus region. This is in contrast to the cervical spinal cord where tyrosine hydroxylase activity increased at approximately the same rate during the embryonic and post‐hatching periods. Moreover, the cerebellum and cervical spinal cord, two locus coeruleus target sites, displayed different trends in tyrosine hydroxylase activity throughout development and aging.
A Fast Synthetic Aperture Radar Raw Data Simulation Using Cloud Computing

Synthetic Aperture Radar (SAR) raw data simulation is a fundamental problem in radar system design and imaging algorithm research. The growth of surveying swath and resolution results in a significant increase in data volume and simulation period, which can be considered to be a comprehensive data intensive and computing intensive issue. Although several high performance computing (HPC) methods have demonstrated their potential for accelerating simulation, the input/output (I/O) bottleneck of huge raw data has not been eased. In this paper, we propose a cloud computing based SAR raw data simulation algorithm, which employs the MapReduce model to accelerate the raw data computing and the Hadoop distributed file system (HDFS) for fast I/O access. The MapReduce model is designed for the irregular parallel accumulation of raw data simulation, which greatly reduces the parallel efficiency of graphics processing unit (GPU) based simulation methods. In addition, three kinds of optimization strategies are put forward from the aspects of programming model, HDFS configuration and scheduling. The experimental results show that the cloud computing based algorithm achieves 4× speedup over the baseline serial approach in an 8-node cloud environment, and each optimization strategy can improve about 20%. This work proves that the proposed cloud algorithm is capable of solving the computing intensive and data intensive issues in SAR raw data simulation, and is easily extended to large scale computing to achieve higher acceleration.
The effects of HIV type-1 viral suppression and non-viral factors on quantitative proteinuria in the highly active antiretroviral therapy era

Background Proteinuria is associated with progressive renal disease and overall mortality in HIV-infected patients; however, the prevalence and correlates of quantitative pro-teinuria in the highly active antiretroviral therapy era are unknown. Methods Spot urine protein to creatinine (P/Cr) ratios, an accepted measure of quantitative daily proteinuria, were measured annually since 2002 in participants of the AIDS Clinical Trials Group Longitudinal Linked Randomized Trials cohort. We used linear regression models with general estimating equations to identify factors associated with the abnormal P/Cr thresholds of ≥0.2 and ≥1.0. Results Of the 2,857 participants (most of whom were receiving antiretroviral therapy) analysed, 16% and 3% had P/Cr levels ≥0.2 and ≥1.0, respectively, at first measurement. P/Cr levels did not change during a median follow-up of 3 years (interquartile range 2–4). Factors associated with P/Cr≥0.2 at any measurement included greater age, lower glomerular filtration rate, female sex, antiretroviral therapy prior to entry into parent randomized trial, HIV type-1 RNA level ≥400 copies/ ml, lower CD4+ T-cell count and history of hypertension, diabetes or hepatitis C coinfection (all P<0.04). Black race and higher non-high-density lipoprotein cholesterol levels were associated with P/Cr levels ≥1.0, but not with P/ Cr levels ≥0.2. Hepatitis B coinfection and current use of adefovir, indinavir and tenofovir were not associated with either of the P/Cr thresholds. Conclusions Both HIV-1 and non-HIV-1-related factors are associated with abnormal levels of proteinuria and identify those who are at a greater risk of worse clinical outcomes. Several of these factors are differentially associated with lower and higher proteinuria thresholds.
Superconductivity at the Two-Dimensional Limit

Superconducting Limits An electron wave function extends in three dimensions. Pairing up into Cooper pairs and reducing the temperatures can induce superconductivity in a material. How robust is an inherently three-dimensional effect when the dimensions are restricted? Qin et al. (p. 1314, published online 30 April) looked at the thickness dependence of superconductivity in thin lead films. In contrast to earlier, less direct measurements, superconductivity was robust, even down to films of only two monolayers. Superconductivity persists in lead films down to just two monolayers thick. Superconductivity in the extreme two-dimensional limit is studied on ultrathin lead films down to two atomic layers, where only a single channel of quantum well states exists. Scanning tunneling spectroscopy reveals that local superconducting order remains robust until two atomic layers, where the transition temperature abruptly plunges to a lower value, depending sensitively on the exact atomic structure of the film. Our result shows that Cooper pairs can still form in the last two-dimensional channel of electron states, although their binding is strongly affected by the substrate.
Memory performance on the California Verbal Learning Test–II: Findings from patients with focal frontal lesions

Numerous studies have suggested that frontal cortex plays a strategic, rather than an absolute, role in memory performance. Typically, frontal patients are reported to have impaired recall but normal recognition memory. A recent meta-analysis, however, has questioned this conclusion. To further investigate the role of frontal cortex in long-term memory, patients with focal frontal lesions and age- and education-matched controls were tested on a new version of the California Verbal Learning Test (CVLT–II). Frontal patients exhibited a number of deficits on this test, including overall poorer recall, an increased tendency to make intrusions, reduced semantic clustering, and impaired yes/no recognition performance. Further analysis of the error rates in the yes/no recognition task revealed that frontal patients were most likely to mistakenly endorse 2 types of distractors: semantically related words and words from an interference list. These findings are discussed with respect to the role of frontal dysfunction in false recollections and poor source memory, as well as the distinction between the roles of frontal and temporal cortex in long-term memory. (JINS, 2002, 8, 539–546.)
Binding “When” and “Where” Impairs Temporal, but not Spatial Recall in Auditory and Visual Working Memory

Information about where and when events happen seem naturally linked to each other, but only few studies have investigated whether and how they are associated in working memory. We tested whether the location of items and their temporal order are jointly or independently encoded. We also verified if spatio-temporal binding is influenced by the sensory modality of items. Participants were requested to memorize the location and/or the serial order of five items (environmental sounds or pictures sequentially presented from five different locations). Next, they were asked to recall either the item location or their order of presentation within the sequence. Attention during encoding was manipulated by contrasting blocks of trials in which participants were requested to encode only one feature to blocks of trials where they had to encode both features. Results show an interesting interaction between task and attention. Accuracy in serial order recall was affected by the simultaneous encoding of item location, whereas the recall of item location was unaffected by the concurrent encoding of the serial order of items. This asymmetric influence of attention on the two tasks was similar for the auditory and visual modality. Together, these data indicate that item location is processed in a relatively automatic fashion, whereas maintaining serial order is more demanding in terms of attention. The remarkably analogous results for auditory and visual memory performance, suggest that the binding of serial order and location in working memory is not modality-dependent, and may involve common intersensory mechanisms.
Generalized plane strain finite-element formulation for thermal and electrical buckling analysis of piezo composite beam

We develop a generalized plane strain (GPS) finite element formulation to predict the critical buckling voltage and temperature of a piezo composite beam in more generality than the cases characterized by plane strain and plane stress assumptions. This generalized plane strain formulation represents the two-dimensional finite element model as closely as possible to the three-dimensional finite element model. It is similar to the plane strain formulation that reduces a three-dimensional stress-strain relation to a two-dimensional one, but in contrast with most GPS formulations in the literature, it does not include out of plane degrees of freedom. In our formulation the reduced two-dimensional stress-strain relation incorporates the effect of allowed/applied strain"0 in the dimension not included in the two-dimensional model. Further, since the goal is to deal with thermal and electrical buckling analysis, an initial strain vector is incorporated in the formulation. A finite element solver based on an eight-node quadrilateral element was developed under the new formulation, and its results show good agreement with those reported by Varelis and Saravanos (2004) and those obtained with ANSYS. The critical electrical and thermal buckling loads for examples other than those characterized by plane stress and plane strain were analyzed, and it was found that they are significantly influenced by , the parameter controlling the out-of-plane strains. Finite element analysis of smart structures has attracted much attention in recent years due to its wide range of applications. A significant amount of research has gone into the analysis of piezo composite structures. A number of finite element (FE) models have been proposed for the analysis of smart structures; and a detailed survey is given in [Benjeddou 2000]. One of the main problems addressed is the buckling analysis of smart structures. Three-dimensional beam models can be simulated using two-dimensional in-plane elements by considering only the longitudinal cross-section of the three-dimensional beam model. The boundary conditions and the loading conditions can be simulated more accurately in this two-dimensional model than in the one-dimensional beam element model. Still, the two-dimensional analysis of the beam is based on either the plane stress or plane strain assumption, and cases outside these assumptions cannot be handled by two-dimensional in-plane elements. The generalized plane strain formulation can be used to model cases other than plane stress and plane strain at the cost of additional degrees of freedom. The generalized plane strain formulation has been discussed extensively in the literature and has been used for several applications. Most composite problems are generalized plane strain in nature, and they
Sexual and demographic risk factors for herpes simplex type 1 and 2 in women attending an antenatal clinic

Objective: To establish risk factors for the presence of HSV-2 and HSV-1 infections in pregnant women. Design, population, and setting: A prospective study of 3306 women attending the antenatal department Westmead Hospital, Sydney, between June 1995 and April 1998. Methods: Women completed a self administered questionnaire to establish risk factors for the presence of HSV-2 and HSV-1. Sera were tested for antibodies to HSV-2 and HSV-1. Data were analysed using spss and sas. Main outcome measures: Seroprevalence of and risk factors for HSV-2 and HSV-1. Results: 375 (11.3% (95% CI 10.3–12.5)) women were HSV-2 antibody positive. Increasing age, Asian country of birth, lower education level, public hospital status, confirmed genital herpes, a partner with genital herpes, early age of first sex, more than one lifetime sexual partner, and previous chlamydia infection were independently associated with HSV-2 seropositivity. Of 408 women tested for HSV-1 antibodies, 323 (79.2% (95% CI 74.9–83.0)) were positive. Oral herpes, oral blisters or sores, and being HSV-2 seropositive were independently associated with HSV-1 seropositive status. When the logistic regression model was rerun without HSV-2 status, parity of two or more and one or more sexual partners in the past 3 months were significant predictors of HSV-1 seropositivity. Conclusions: The presence of antibodies to HSV-2 and HSV-1 is related to a number of sexual and demographic risk factors. Public health campaigns directed at encouraging young people to delay the onset of sexual activity and reduce the number of sexual partners need to be evaluated. However, the possible availability of an HSV-2 vaccine that is able to protect over 70% of women offers the best hope for control of genital herpes.
The Src Kinase Lck Facilitates Assembly of HIV-1 at the Plasma Membrane1

HIV type 1 (HIV-1) assembly and egress are driven by the viral protein Gag and occur at the plasma membrane in T cells. Recent evidence indicates that secretory vesicles and machinery are essential components of virus packaging in both T cells and macrophages. However, the pathways and cellular mediators of Gag targeting to the plasma membrane are not well characterized. Lck, a lymphoid specific Src kinase critical for T cell activation, is found in the plasma membrane as well as various intracellular compartments and it has been suggested to influence HIV-1 replication. To investigate Lck as a potential regulator of Gag targeting, we assessed HIV-1 replication and Gag-induced virus-like particle release in the presence and absence of Lck. Release of HIV-1 and virus-like particles was reduced in the absence of Lck. This decrease in replication was not due to altered HIV-1 infection, transcription or protein translation. However, in T cells lacking Lck, HIV-1 accumulated intracellularly. In addition, expressing Lck in HeLa cells promoted HIV-1 Gag plasma membrane localization. Palmitoylation of the Lck unique domain, which is essential for directing Lck to the plasma membrane, was critical for its effect on HIV-1 replication. Furthermore, HIV-1 Gag directly interacted with the Lck unique domain in the context of infected cells. These results indicate that Lck plays a key role in targeting HIV-1 Gag to the plasma membrane in T cells.