Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of BED HIV-1 Incidence Assay in Seroconverter Cohorts: Effect of Individuals with Long-Term Infection and Importance of Stable Incidence

Background Performance of the BED assay in estimating HIV-1 incidence has previously been evaluated by using longitudinal specimens from persons with incident HIV infections, but questions remain about its accuracy. We sought to assess its performance in three longitudinal cohorts from Thailand where HIV-1 CRF01_AE and subtype B′ dominate the epidemic. Design BED testing was conducted in two longitudinal cohorts with only incident infections (a military conscript cohort and an injection drug user cohort) and in one longitudinal cohort (an HIV-1 vaccine efficacy trial cohort) that also included long-term infections. Methods Incidence estimates were generated conventionally (based on the number of annual serocoversions) and by using BED test results in the three cohorts. Adjusted incidence was calculated where appropriate. Results For each longitudinal cohort the BED incidence estimates and the conventional incidence estimates were similar when only newly infected persons were tested, whether infected with CRF01_AE or subtype B′. When the analysis included persons with long-term infections (to mimic a true cross-sectional cohort), BED incidence estimates were higher, although not significantly, than the conventional incidence estimates. After adjustment, the BED incidence estimates were closer to the conventional incidence estimates. When the conventional incidence varied over time, as in the early phase of the injection drug user cohort, the difference between the two estimates increased, but not significantly. Conclusions Evaluation of the performance of incidence assays requires the inclusion of a substantial number of cohort-derived specimens from individuals with long-term HIV infection and, ideally, the use of cohorts in which incidence remained stable. Appropriate adjustments of the BED incidence estimates generate estimates similar to those generated conventionally.
L-Citrulline, But Not L-Arginine, Prevents Diabetes Mellitus–Induced Glomerular Hyperfiltration and Proteinuria in Rat

Diabetes mellitus–induced oxidative stress causes increased renal oxygen consumption and intrarenal tissue hypoxia. Nitric oxide is an important determinant of renal oxygen consumption and electrolyte transport efficiency. The present study investigates whether L-arginine or L-citrulline to promote nitric oxide production prevents the diabetes mellitus–induced kidney dysfunction. Glomerular filtration rate, renal blood flow, in vivo oxygen consumption, tissue oxygen tension, and proteinuria were investigated in control and streptozotocin-diabetic rats with and without chronic L-arginine or L-citrulline treatment for 3 weeks. Untreated and L-arginine–treated diabetic rats displayed increased glomerular filtration rate (2600±162 versus 1599±127 and 2290±171 versus 1739±138 µL/min per kidney), whereas L-citrulline prevented the increase (1227±126 versus 1375±88 µL/min per kidney). Filtration fraction was increased in untreated diabetic rats because of the increase in glomerular filtration rate but not in L-arginine– or L-citrulline–treated diabetic rats. Urinary protein excretion was increased in untreated and L-arginine–treated diabetic rats (142±25 versus 75±7 and 128±7 versus 89±7 µg/min per kidney) but not in diabetic rats administered L-citrulline (67±7 versus 61±5 µg/min per kidney). The diabetes mellitus–induced tissue hypoxia, because of elevated oxygen consumption, was unaltered by any of the treatments. L-citrulline administered to diabetic rats increases plasma L-arginine concentration, which prevents the diabetes mellitus–induced glomerular hyperfiltration, filtration fraction, and proteinuria, possibly by a vascular effect.
Calibrating Thrombin Generation in Different Samples: Less Effort with a Less Efficient Substrate

The technique of thrombin generation has been established as a promising tool for the diagnosis, risk estima- tion, and perhaps prognosis of coagulation insufficiencies. Without further experimentation an indication can be obtained if a sample donor carries the risk for haemophilia or thrombophilia, either congenital or acquired. A comparison of two different thrombin generation assays is presented, demonstrating that a currently not commercially available test allows an easier and cheaper calibration than its commercial counterpart. This is achieved by employment of a less efficient but highly specific peptide substrate for thrombin and the involvement of low amounts of analyte (plasma samples).
A Population-Based Study to Evaluate the Effectiveness of Multidisciplinary Heart Failure Clinics and Identify Important Service Components

Background— Multidisciplinary heart failure (HF) clinics are efficacious in clinical trials. Our objectives were to compare real-world outcomes of patients with HF treated in HF clinics versus usual therapy and identify HF clinic features associated with improved outcomes. Methods and Results— The service components at all HF clinics in Ontario, Canada, were quantified using a validated instrument and categorized as high/medium/low intensity. We used propensity-scores to match HF clinic and control patients discharged alive after a HF readmission in 2006–2007. Outcomes were mortality, and both all-cause and HF readmission. Cox-proportional hazard models were used to evaluate HF clinic-level characteristics associated with improved outcomes. We identified 14 468 patients with HF, of whom 1288 were seen in HF clinics. Within 4 years of follow-up, 52.1% of patients treated at a HF clinic died versus 54.7% of control patients (P=0.02). Patients treated at HF clinics had increased readmissions (87.4% versus 86.6% for all-cause [P=0.009]; 58.7% versus 47.3% for HF related [P<0.001]). There was no difference between high, medium, or low intensity clinics in terms of mortality, all-cause, or HF readmissions. HF clinics with greater frequency of visits (>4 contacts of significant duration for 6 months) were associated with lower mortality (hazard ratio, 0.14; P<0.0001) and hospitalization (hazard ratio, 0.69; P=0.039). More intensive medication management was associated with lower all-cause (hazard ratio, 0.46; P<0.001) and HF readmission (hazard ratio, 0.42; P<0.001). Conclusions— In this real-world population-based study, we found that multidisciplinary HF clinics are associated with a decrease in mortality, but an increase in readmissions.
A Graphical Interface for Automatic Error Mining in Corpora

We present an error mining tool that is designed to help human annotators to find errors and inconsistencies in their annotation. The output of the underlying algorithm is accessible via a graphical user interface, which provides two aggregate views: a list of potential errors in context and a distribution over labels. The user can always directly access the actual sentence containing the potential error, thus enabling annotators to quickly judge whether the found candidate is indeed incorrectly labeled.
Lecture 5 : Regret Bounds for Thompson Sampling

For each round t, we defined a posterior distribution over arms a as: p t (a) = P(a = a * |H t) where a * is the best arm for the problem instance and H t is the history of rewards up to round t. By definition, the Thompson algorithm draws arm a t independently from this distribution p t. If we consider a * to be a random variable dependent on the problem instance, a t and a * are identically distributed. We will use this fact later on:
Multimodal Nondestructive Dry Cask Basket Structure and Spent Fuel Evaluation

submitted: 1. Xiao, W. , Yu, L. (2019) Nondestructive evaluation with fully non-contact ACT-SLDV guided wave system, Proceedings of SPIE 2019 Smart Structures/NDE, Nondestructive Characterization and Monitoring of Advanced Materials, Aerospace, Civil Infrastructure, and Transportation XIII
Associations of growth trajectories in infancy and early childhood with later childhood outcomes.

BACKGROUND Weight and length at birth (which represent fetal growth) and weight and length or height gain during childhood (which potentially represent catch-up growth) may be related to later health outcomes. However, methods for the assessment of such relations are complex and underdeveloped. OBJECTIVES We aimed to describe childhood weight and length or height trajectories and to relate these to later outcomes by using rash at age 6.5 y as an example. DESIGN The data came from a prospective cohort study in Belarus in 10,494 children born in 31 hospitals that participated in a cluster randomized trial of breastfeeding promotion. Weight and length or height were measured at birth, at scheduled clinic visits up to 1 y, and at 6.5 y; intermediate measures were obtained from routine child health records. Linear spline multilevel models for weight and length or height were used to estimate each child's deviance from average birth weight, birth length, weight, and length or height gain velocity in each time period. Logistic regression was used to relate the outcome (parental report of rash at 6.5 y) to these weight and length or height estimates. RESULTS The best-fitting splines for length or height and weight had knots at 3 and 12 mo, with another knot at 34 mo for height. The only relation between weight and length or height and reported rash was a positive association with weight gain velocity between 12 and 34 mo (odds ratio per SD increase in weight gain velocity: 1.11; 95% CI: 1.01, 1.22). CONCLUSION Advantages of multilevel models include no restriction to measures at arbitrary times or to individuals with complete data and allowance for measurement error. This trial was registered at isrctn.org as ISRCTN37687716.
Very low bit rate image coding using redundant dictionaries

Very low bit rate image coding is an important problem regarding applications such as storage on low memory devices or streaming data on the internet. The state of the art in image compression is to use 2-D wavelets. The advantages of wavelet bases lie in their multiscale nature and in their ability to sparsely represent functions that are piecewise smooth. Their main problem on the other hand, is that in 2-D wavelets are not able to deal with the natural geometry of images, i.e they cannot sparsely represent objects that are smooth away from regular submanifolds. In this paper we propose an approach based on building a sparse representation of images in a redundant geometrically inspired library of functions, followed by suitable coding techniques. Best N-term non- linear approximations in general dictionaries is, in most cases, a NP-hard problem and sub-optimal approaches have to be followed. In this work we use a greedy strategy, also known as Matching Pursuit to compute the expansion. Finally the last step in our algorithm is an enhancement layer that encodes the residual image: in our simulation we have used a genuine embedded wavelet codec.
Advanced amplification techniques for nanoscale CMOS in the context of IoT node sensors

The downscaling of the CMOS technology and the demand for low power impose new challenges on the design of mixed-mode integrated circuits, such as analog to digital converters. Consequently, the amplifier, which is one of the building blocks, has been the subject of extensive development. This paper presents recent advances in low-power technique options for the design of amplifiers within the context of sensor nodes for the Internet-of-Things (IoT). Some of the most promising energy-efficient amplification techniques, either in continuous-time and discrete-time domains, are reviewed.
Ultrasound patterning technologies for studying vascular morphogenesis in 3D

ABSTRACT Investigations in this report demonstrate the versatility of ultrasound-based patterning and imaging technologies for studying determinants of vascular morphogenesis in 3D environments. Forces associated with ultrasound standing wave fields (USWFs) were employed to non-invasively and volumetrically pattern endothelial cells within 3D collagen hydrogels. Patterned hydrogels were composed of parallel bands of endothelial cells located at nodal regions of the USWF and spaced at intervals equal to one half wavelength of the incident sound field. Acoustic parameters were adjusted to vary the spatial dimensions of the endothelial bands, and effects on microvessel morphogenesis were analyzed. High-frequency ultrasound imaging techniques were used to image and quantify the spacing, width and density of initial planar cell bands. Analysis of resultant microvessel networks showed that vessel width, orientation, density and branching activity were strongly influenced by the initial 3D organization of planar bands and, hence, could be controlled by acoustic parameters used for patterning. In summary, integration of USWF-patterning and high-frequency ultrasound imaging tools enabled fabrication of vascular constructs with defined microvessel size and orientation, providing insight into how spatial cues in 3D influence vascular morphogenesis. Summary: Acoustic patterning techniques provide a non-invasive method to direct the spatial organization of endothelial cells within 3D collagen hydrogels and, in turn, control microvessel morphogenesis.
Organization of the murine and human interleukin-7 receptor genes: two mRNAs generated by differential splicing and presence of a type I-interferon-inducible promoter

To better understand the regulation of interleukin-7 receptor (IL-7R) expression, we have pursued a detailed analysis of the structure of the murine and human IL-7R genes. The genes consist of eight exons, the sizes of which are conserved in mouse and human cells, spread out over 24 kbp (murine) and 19 kbp (human). A differential splicing event results in an mRNA encoding a secreted form of the human IL-7R gene. Primer extension and S1 nuclease analysis show a single transcriptional start site for the murine IL-7R gene. The 5'-flanking region of the murine IL-7R gene contains TATA- and CAAT-like sequences. The promoter region also contains a functional interferon regulatory element, to which the interferon-induced nuclear factors IRF-1 and IRF-2 are capable of binding and which is able to confer interferon-inducible expression on a heterologous gene. There are also potential binding sites for the transcription factors AP-1 and AP-2 as well as multiple glucocorticoid response elements. A fusion gene containing 2.5 kb of murine IL-7R 5' regulatory sequence linked to the bacterial chloramphenicol acetyltransferase gene directed expression of chloramphenicol acetyltransferase activity in murine pre-B-cell line 70Z/3 but not in the mouse fibroblast cell line NIH 3T3. Comparison of the murine and human IL-7R exon/intron boundaries with those of other hematopoietin receptor superfamily members whose exon/intron boundaries are also known reveals a conserved evolutionary structure.
Group extinction heuristics in evolution strategy

In this paper, we propose a new heuristics called “group extinction”. The heuristics is inspired by the existence of the extinction in the nature that groups of individuals, which have been consuming a large amount of the ecological resources, are not always the best groups in the evolutionary process. Ideally, these groups should be forced to become extinct such that the resources they use can be released to the other individuals or groups. In the context of optimization, the motivation of using the group extinction is to reduce the computational resources used by groups of candidate solutions that do not have any significant contribution to the overall performances of the optimization algorithms. The proposed heuristics is tested in the well-known framework of evolution strategy and their performances on the common unimodal and multimodal optimization problems are investigated. Experimental results show that using the group extinction heuristics can significantly reduce the average numbers of function evaluations to reach the optima, in particular when large populations are used.
A lightweight interactive debugger for haskell

This paper describes the design and construction of a Haskell source-level debugger built into the GHCi interactive environment. We have taken a pragmatic approach: the debugger is based on the traditional stop-examine-continue model of online debugging, which is simple and intuitive, but has traditionally been shunned in the context of Haskell because it exposes the lazy evaluation order. We argue that this drawback is not as severe as it may seem, and in some cases is an advantage. The design focuses on availability: our debugger is intended to work on all programs that can be compiled with GHC, and without requiring the programmer to jump through additional hoops to debug their program. The debugger has a novel approach for reconstructing the type of runtime values in a polymorphic context. Our implementation is light on complexity, and was integrated into GHC without significant upheaval.
Partial Observation vs. Blind Tracking through Occlusion

This paper presents a framework for multi-object t racking from a single fixed camera. The region-based representations of each object are tracked and p redicted using a Kalman filter. A scene model is created to help predict and interpret the occluded or exiting objects. Unlike the traditional blind tracking during occlusion, the object states are updated using partial observations whenever available. The observability of each object depends on the predictive measurement of the object, the foreground region measurement, and p erhaps the scene model. This makes the a lgorithm m ore robust i n terms of both qualitative a nd quantitative criteria.
7A-3 Optimal Pulse Sequences for the Suppression of Memoryless Tissue Harmonics

In current methods for contrast-enhanced ultrasound such as phase inversion (PI), the achievable contrast-to-tissue ratio (CTR) is limited by the nonlinear propagation of sound in tissue. A fundamental difference between sound propagation nonlinearity and contrast agent oscillation nonlinearity, however, is the different scale of the nonlinear memory of both effects. To exploit this difference, this paper proposes an optimization approach for the determination of pulses for contrast agent imaging which enhance the signal components originating from contrast agents while suppressing signal components originating from nonlinear sound propagation. For this determination, no exact model of microbubble oscillation and sound propagation is necessary. To validate the obtained pulses for contrast agent imaging, a commercial ultrasound scanner was programmed and imaging on a tissue mimicking phantom was conducted. The proposed sequences allowed for an improvement of the CTR of 14.1 dB in comparison with phase inversion.
Quantal time asymmetry: mathematical foundation and physical interpretation

For a quantum theory that includes exponentially decaying states and Breit–Wigner resonances, which are related to each other by the lifetime–width relation , where τ is the lifetime of the decaying state and Γ is the width of the resonance, one has to go beyond the Hilbert space and beyond the Schwartz–Rigged Hilbert Space of the Dirac formalism. One has to distinguish between prepared states, using a space , and detected observables, using a space , where −(+) refers to analyticity of the energy wavefunction in the lower (upper) complex energy semiplane. This differentiation is also justified by causality: a state needs to be prepared first, before an observable can be measured in it. The axiom that will lead to the lifetime–width relation is that Φ+ and Φ− are Hardy spaces of the upper and lower semiplane, respectively. Applying this axiom to the relativistic case for the variable leads to semigroup transformations into the forward light cone (Einstein causality) and a precise definition of resonance mass and width.
Visual Analytics Challenges

One of the most important challenges of the emerging Information Age is to effectively utilize the immense wealth of data and information acquired, computed and stored by modern information systems. On the one hand, the intelligent use of available data volumes and information extracted thereof offers large potential to realize technological progress and business success. On the other hand, there exists the severe danger that users and analysts get lost in irrelevant, or inappropriately processed or presented information, a problem, which is generally called the information overload problem. Visual Analytics is an emerging research discipline developing technology to make the best possible use of huge information loads in a wide variety of applications. The basic idea is to appropriately combine the strengths of intelligent automatic data analysis with the visual perception and analysis capabilities of the human user. In this paper, we will outline the most important challenges of the young research field.
Physical activity reduces hippocampal atrophy in elders at genetic risk for Alzheimer's disease

We examined the impact of physical activity (PA) on longitudinal change in hippocampal volume in cognitively intact older adults at varying genetic risk for the sporadic form of Alzheimer's disease (AD). Hippocampal volume was measured from structural magnetic resonance imaging (MRI) scans administered at baseline and at an 18-month follow-up in 97 healthy, cognitively intact older adults. Participants were classified as High or Low PA based on a self-report questionnaire of frequency and intensity of exercise. Risk status was defined by the presence or absence of the apolipoprotein E-epsilon 4 (APOE-ε4) allele. Four subgroups were studied: Low Risk/High PA (n = 24), Low Risk/Low PA (n = 34), High Risk/High PA (n = 22), and High Risk/Low PA (n = 17). Over the 18 month follow-up interval, hippocampal volume decreased by 3% in the High Risk/Low PA group, but remained stable in the three remaining groups. No main effects or interactions between genetic risk and PA were observed in control brain regions, including the caudate, amygdala, thalamus, pre-central gyrus, caudal middle frontal gyrus, cortical white matter (WM), and total gray matter (GM). These findings suggest that PA may help to preserve hippocampal volume in individuals at increased genetic risk for AD. The protective effects of PA on hippocampal atrophy were not observed in individuals at low risk for AD. These data suggest that individuals at genetic risk for AD should be targeted for increased levels of PA as a means of reducing atrophy in a brain region critical for the formation of episodic memories.