Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of linear and curvilinear ultrasound probes to assess quadriceps rectus femoris muscle mass in healthy subjects and in patients with chronic respiratory disease

Introduction Ultrasound measurements of rectus femoris cross-sectional area (RFCSA) are clinically useful measurements in chronic obstructive pulmonary disease (COPD) and critically ill patients. Technical considerations as to the type of probe used, which affects image resolution, have limited widespread clinical application. We hypothesised that measurement of RFCSA would be similar with linear and curvilinear probes. Methods Four studies were performed to compare the use of the curvilinear probe in measuring RFCSA. Study 1 investigated agreement of RFCSA measurements using linear and curvilinear probes in healthy subjects, and in patients with chronic respiratory disease. Study 2 investigated the intra-rater and inter-rater agreement using the curvilinear probe. Study 3 investigated the agreement of RFCSA measured from whole and spliced images using the linear probe. Study 4 investigated the applicability of ultrasound in measuring RFCSA during the acute and recovery phases of an exacerbation of COPD. Results Study 1 showed demonstrated no difference in the measurement of RFCSA using the curvilinear and linear probes (308±104 mm2 vs 320±117 mm2, p=0.80; intraclass correlation coefficient (ICC)>0.97). Study 2 demonstrated high intra-rater and inter-rater reliability of RFCSA measurement with ICC>0.95 for both. Study 3 showed that the spliced image from the linear probe was similar to the whole image RFCSA (308±103.5 vs 263±147 mm2, p=0.34; ICC>0.98). Study 4 confirmed the clinical acceptability of using the curvilinear probe during an exacerbation of COPD. There were relationships observed between admission RFCSA and body mass index (r=+0.65, p=0.018), and between RFCSA at admission and physical activity levels at 4 weeks post-hospital discharge (r=+0.75, p=0.006). Conclusions These studies have demonstrated that clinicians can employ whole and spliced images from the linear probe or use images from the curvilinear probe, to measure RFCSA. This will extend the clinical applicability of ultrasound in the measurement of muscle mass in all patient groups.
Non-Blocking PMI Extensions for Fast MPI Startup

An efficient implementation of the Process Management Interface (PMI) is crucial to enable fast start-up of MPI jobs. We propose three extensions to the PMI specification: 1) a blocking all gather collective (PMIX_Allgather), 2) a non-blocking all gather collective (PMIX_Iallgather), and 3) a non-blocking fence (PMIX_KVS_Ifence). We design and evaluate several PMI implementations to demonstrate how such extensions reduce MPI start-up cost. In particular, when sufficient work can be overlapped, these extensions allow for a constant initialization cost of MPI jobs at different core counts. At 16,384 cores, the designs lead to a speedup of 2.88 times over the state-of-the-art start-up schemes.
Changes in Hospital Inpatient Utilization Following Health Care Reform.

OBJECTIVE To estimate the effects of 2014 Medicaid expansions on inpatient outcomes. DATA SOURCES Health Care Cost and Utilization Project State Inpatient Databases, 2011-2014; population and unemployment estimates. STUDY DESIGN Retrospective study estimating effects of Medicaid expansions using difference-in-differences regression. Outcomes included total admissions, referral-sensitive surgical and preventable admissions, length of stay, cost, and patient illness severity. FINDINGS In 2014 quarter four, compared with nonexpansion states, Medicaid admissions increased (28.5 percent, p = .006), and uninsured and private admissions decreased (-55.1 percent, p = .001, and -6.6 percent, p = .052), whereas all-payer admissions showed little change. Uninsured expansion effects were negative for preventable admissions (-24.4 percent, p = .068), length of stay (-9.3 percent, p = .039), total cost (-9.2 percent, p = .128), and illness severity (-4.5 percent, p = .397). Significant positive expansion effects were found for Medicaid referral-sensitive surgeries (11.8 percent, p = .021) and patient illness severity (2.3 percent, p = .015). Private and all-payer expansion effects for outcomes other than admission volume were small and mainly nonsignificant (p > .05). CONCLUSION Medicaid expansions did not change all-payer admission volumes, but they were associated with increased Medicaid and decreased uninsured volumes. Results suggest those previously uninsured with greater needs for inpatient services were most likely to gain coverage. Compositional changes in uninsured and Medicaid admissions may be due to selection.
Parallel Genome-Wide Fixation of Ancestral Alleles in Partially Outcrossing Experimental Populations of Caenorhabditis elegans

Experimental evolution studies, coupled with new advances in DNA sequencing technology, have become a powerful tool for exploring how populations respond to selection at the genomic level. Recent experiments in microbes typically have found evidence for multiple novel mutations, which are usually fixed. In contrast, in animal model systems, evolutionary responses seem to involve more modest changes in the frequencies of pre-existing alleles, probably because these populations outcross and are usually initialized with greater levels of standing variation. In this experiment, I used whole-genome resequencing to estimate allele frequencies and look for novel substitutions in experimentally evolved populations of Caenorhabditis elegans. These populations were founded with a fixed pair of deleterious mutations introgressed into multiple wild genetic backgrounds and allowed to evolve for 50 generations with a mixed mating system. There is evidence for some recombination between ancestral haplotypes, but selective sweeps seem to have resulted in the fixation of large chromosomal segments throughout most of the genome. In addition, a few new mutations were detected. Simulations suggest that strong selection and low outcrossing rates are likely explanations for the observed outcomes, consistent with earlier work showing large fitness increases in these populations over 50 generations. These results also show clear parallels to population genetic patterns in C. elegans in nature: recent selective sweeps, high linkage disequilibrium, and low effective recombination rates. Thus, the genomic consequences of selection depend heavily on the biology of the organism in question, including its mating system and levels of genetic variation.
Sustained treatment effect in attention-deficit/hyperactivity disorder: focus on long-term placebo-controlled randomized maintenance withdrawal and open-label studies

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder that often persists throughout life. Approximately two-thirds of patients with a childhood diagnosis of ADHD continue to experience clinically significant symptoms into adulthood. Nevertheless, most of these individuals consider themselves “well,” and a vast majority discontinue medication treatment during adolescence. As evidence concerning the adult presentation of ADHD becomes more widely accepted, increasing numbers of physicians and patients will face decisions about the benefits and risks of continuing ADHD treatment. The risks associated with psychostimulant pharmacotherapy, including abuse, dependence, and cardiovascular events, are well understood. Multiple clinical trials demonstrate the efficacy of psychostimulants in controlling ADHD symptoms in the short term. Recent investigations using randomized withdrawal designs now provide evidence of a clinically significant benefit with continued long-term ADHD pharmacotherapy and provide insight into the negative consequences associated with discontinuation. Because many patients lack insight regarding their ADHD symptoms and impairments, they may place a low value on maintaining treatment. Nevertheless, for patients who choose to discontinue treatment, physicians can remain a source of support and schedule follow-up appointments to reassess patient status. Medication discontinuation can be used as an opportunity to help patients recognize their most impairing symptoms, learn and implement behavioral strategies to cope with ADHD symptoms, and understand when additional supportive resources and the resumption of medication management may be necessary.
NAPA C: compiling for a hybrid RISC/FPGA architecture

Hybrid architectures combining conventional processors with configurable logic resources enable efficient coordination of control with datapath computation. With integration of the two components on a single device, loop control and data-dependent branching can be handled by the conventional processor. While regular datapath computation occurs on the configurable hardware. This paper describes a novel pragma-based approach to programming such hybrid devices. The NAPA C language provides pragma directives so that the programmer (or an automatic partitioner) can specify where data is to reside and where computation is to occur with statement-level granularity. The NAPA C compiler, targeting National Semiconductor's NAPA1000 chip, performs semantic analysis of the pragma-annotated program and co-synthesizes a conventional program executable combined with a configuration bit stream for the adaptive logic. Compiler optimizations include synthesis of hardware pipelines from pipelineable loops.
Parallel Adaptive Spectral Element Schemes for simulation of Geophysical Flows

The Navier-Stokes equations govern the dynamics of many geophysical flows [4],[8],[6]. Numerical simulation of these equations gives insight into the dynamics of fluids for vast ranges of length and time scales where physical experiments and theory are intractable. However, the complex nature of these flows still makes numerical simulation challenging. For example flows may experience fronts or sharp features arising from physical properties such as phase changes, and thermal boundary layers (see figure 1). The development of efficient computational algorithms to resolve complex flow structures is an active topic of research. In this prospectus, I introduce the fundamental tools used for modeling fluid flow, and outline three efficient computational techniques that show promise for modeling geophysical fluid behavior. Namely, I will discuss high order methods, adaptive mesh refinement schemes, and parallel algorithms, as examined in the papers of [1], [2] and [3] respectively.
Modeling of the signal formation in SiC sensors for measurements of the radiation spectrum in nuclear energy

The modeling methodology of the signal formation in SiC sensors is presented. The modeling uses two approaches: the first one is the integrated approach whereas the second is the analytical approach. The sensor response is obtained from both approaches: this is the usual solution of the forward problem. Moreover, the response function of the sensor is evaluated by means of the analytical approach and it can be used to solve the inverse problem: recovering the primary radiation spectrum using the response of the sensor. Additionally, the response function returns information about the signal formation in the sensor such as the shape of the response formed by particles with a specific energy. Results obtained by simulations are then compared with experimental data.
Molecule-Independent Electrical Switching in Pt/Organic Monolayer/Ti Devices

Electronic devices comprising a Langmuir−Blodgett molecular monolayer sandwiched between planar platinum and titanium metal electrodes functioned as switches and tunable resistors over a 102−105 Ω range under current or voltage control. Reversible hysteretic switching and resistance tuning was qualitatively similar for three very different molecular species, indicating a generic switching mechanism dominated by electrode properties or electrode/molecule interfaces, rather than molecule-specific behavior.
A limited lupus anti-spliceosomal response targets a cross-reactive, proline-rich motif.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of large amounts of characteristic autoantibodies. Anti-Sm and anti-nRNP (also known as anti-spliceosome) autoantibodies are among these. Previous epitope mapping of anti-spliceosomal antibodies has identified multiple antigenic determinants within this complex immune response. In this report we describe an SLE patient with a relatively simple, long-lasting anti-spliceosomal response. In the earliest serum sample tested the autoimmune response appeared restricted to the similar peptides PPPGMR(P,G)P of Sm B/B', PAPGMRPP of nRNP C, and PPPGMIPP of nRNP A. Unlike all the other tested lupus patients with anti-spliceosomal autoantibodies, in this patient these proline-rich epitopes remained the primary target for humoral autoimmunity in subsequent serum samples collected over many years. Absorption of anti-PAPGMRPP antibodies also removed binding to PPPGMR(P,G)P and PPPGMIPP. Isolated antibodies to PAPGMRPP were capable of binding Sm B/B', nRNP C and nRNP A by Western blot. For this particular SLE patient the autoimmune response observed against these three proteins is a single cross-reactive response against a similar proline-rich motif. Also, this patient has failed to undergo the B cell epitope spreading, typically observed in the naturally arising autoimmune response against the spliceosome in human lupus patients.
A method for predicting personalized pelvic motion based on body meta-features for gait rehabilitation robot

Training for balancing, which is governed by the motion of pelvis and thorax, is a key for gait rehabilitation. COWALK, which is a gait rehabilitation robot under development in our institute, is capable of pelvic motion training. In this paper, we describe a statistical method to generate pelvic motion which is considered to fit each person, i.e., personalized pelvic motion. We measured 14 anthropometric features of human and captured gait motion using an optical motion capture system from 113 healthy subjects. We setup a database of gait motion and body measurements; we define a 4 dimensional compact vector representation of pelvic motion, and body meta-feature, which is a weighted linear combination of the anthropometric measurements, to maximize statistical correlation between the former and the latter. To synthesize a personalized pelvic motion for a new subject, we search for k nearest neighbors in the space of body meta-feature (k-NN algorithm), and average the pelvic motions of them. We validate the algorithm using the database of 113 subjects by excluding each person, synthesizing a personalized pelvic motion for the subject, and comparing it with actual motion of the subject.
Correction for frequency-dependent hydrophone response to nonlinear pressure waves using complex deconvolution and rarefactional filtering: application with fiber optic hydrophones

Nonlinear acoustic signals contain significant energy at many harmonic frequencies. For many applications, the sensitivity (frequency response) of a hydrophone will not be uniform over such a broad spectrum. In a continuation of a previous investigation involving deconvolution methodology, deconvolution (implemented in the frequency domain as an inverse filter computed from frequency-dependent hydrophone sensitivity) was investigated for improvement of accuracy and precision of nonlinear acoustic output measurements. Timedelay spectrometry was used to measure complex sensitivities for 6 fiber-optic hydrophones. The hydrophones were then used to measure a pressure wave with rich harmonic content. Spectral asymmetry between compressional and rarefactional segments was exploited to design filters used in conjunction with deconvolution. Complex deconvolution reduced mean bias (for 6 fiber-optic hydrophones) from 163% to 24% for peak compressional pressure (p+), from 113% to 15% for peak rarefactional pressure (p-), and from 126% to 29% for pulse intensity integral (PII). Complex deconvolution reduced mean coefficient of variation (COV) (for 6 fiber optic hydrophones) from 18% to 11% (p+), 53% to 11% (p-), and 20% to 16% (PII). Deconvolution based on sensitivity magnitude or the minimum phase model also resulted in significant reductions in mean bias and COV of acoustic output parameters but was less effective than direct complex deconvolution for p+ and p-. Therefore, deconvolution with appropriate filtering facilitates reliable nonlinear acoustic output measurements using hydrophones with frequency-dependent sensitivity.
Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree.

OBJECTIVES We analyzed the extent to which comparative effectiveness research (CER) organizations share terms for designs, analyzed coverage of CER designs in Medical Subject Headings (MeSH) and Emtree, and explored whether scientists use CER design terms. METHODS We developed local terminologies (LTs) and a CER design terminology by extracting terms in documents from five organizations. We defined coverage as the distribution over match type in MeSH and Emtree. We created a crosswalk by recording terms to which design terms mapped in both controlled vocabularies. We analyzed the hits for queries restricted to titles and abstracts to explore scientists' language. RESULTS Pairwise LT overlap ranged from 22.64% (12/53) to 75.61% (31/41). The CER design terminology (n = 78 terms) consisted of terms for primary study designs and a few terms useful for evaluating evidence, such as opinion paper and systematic review. Patterns of coverage were similar in MeSH and Emtree (gamma = 0.581, P = 0.002). CONCLUSIONS Stakeholder terminologies vary, and terms are inconsistently covered in MeSH and Emtree. The CER design terminology and crosswalk may be useful for expert searchers. For partially mapped terms, queries could consist of free text for modifiers such as nonrandomized or interrupted added to broad or related controlled terms.
Quantum optics in photonic crystals

We survey basic quantum optical processes that undergo modifications in photonic crystals doped with resonant atoms: (a) Solitons and multi-dimensional localized 'bullets' propagating at photonic band gap frequencies. These novel entities differ substantially from solitons in Kerr-nonlinear photonic crystals. (b) Giant photon-photon cross-coupling that can give rise to fully entangled two-photon states. We conclude that doped photonic crystals have the capacity to form efficient networks for high-fidelity classical and quantum optical communications.
Near Infrared Investigation of Polypropylene–Clay Nanocomposites for Further Quality Control Purposes—Opportunities and Limitations

Polymer nanocomposites are usually characterized using various methods, such as small angle X-ray diffraction (XRD) or transmission electron microscopy, to gain insights into the morphology of the material. The disadvantages of these common characterization methods are that they are expensive and time consuming in terms of sample preparation and testing. In this work, near infrared spectroscopy (NIR) spectroscopy is used to characterize nanocomposites produced using a unique twin-screw mini-mixer, which is able to replicate, at ~25 g scale, the same mixing quality as in larger scale twin screw extruders. We correlated the results of X-ray diffraction, transmission electron microscopy, G′ and G″ from rotational rheology, Young’s modulus, and tensile strength with those of NIR spectroscopy. Our work has demonstrated that NIR-technology is suitable for quantitative characterization of such properties. Furthermore, the results are very promising regarding the fact that the NIR probe can be installed in a nanocomposite-processing twin screw extruder to measure inline and in real time, and could be used to help optimize the compounding process for increased quality, consistency, and enhanced product properties.
Performance of CUDA Virtualized Remote GPUs in High Performance Clusters

In a previous work we presented the architecture of rCUDA, a middleware that enables CUDA remoting over a commodity network. That is, the middleware allows an application to use a CUDA-compatible Graphics Processor (GPU) installed in a remote computer as if it were installed in the computer where the application is being executed. This approach is based on the observation that GPUs in a cluster are not usually fully utilized, and it is intended to reduce the number of GPUs in the cluster, thus lowering the costs related with acquisition and maintenance while keeping performance close to that of the fully-equipped configuration. In this paper we model rCUDA over a series of high throughput networks in order to assess the influence of the performance of the underlying network on the performance of our virtualization technique. For this purpose, we analyze the traces of two different case studies over two different networks. Using this data, we calculate the expected performance for these same case studies over a series of high throughput networks, in order to characterize the expected behavior of our solution in high performance clusters. The estimations are validated using real 1 Gbps Ethernet and 40 Gbps InfiniBand networks, showing an error rate in the order of 1% for executions involving data transfers above 40 MB. In summary, although our virtualization technique noticeably increases execution time when using a 1 Gbps Ethernet network, it performs almost as efficiently as a local GPU when higher performance interconnects are used. Therefore, the small overhead incurred by our proposal because of the remote use of GPUs is worth the savings that a cluster configuration with less GPUs than nodes reports.
Face Recognition for Annotation in Media Asset Management Systems

The goal of this thesis was to evaluate alternatives to the Wawo face recognition (fr) library, used by the company CodeMill AB in an application for video-based fr, implemented as a plugin to the media asset management system Vidispine. The aim was to improve the fr performance of the application, and the report tried to compare the performance of recent versions of Open Source Biometrics Recognition (OpenBR) and Open Source Computer Vision (OpenCV ) to Wawo.For comparison of the fr systems, roc curves and area under roc curves (auc) metrics were used. Two different test videos were used: one simpler shot with webcam and one excerpt from a tv music show. The results are somewhat inconclusive; the Wawo system had technical diffculties with the biggest test case. However, it performed better than OpenBR in the two other cases (comparing auc values), which leads to the conclusion that Wawo would have outperformed the other systems for all test cases if it had worked. Finally, the comparison shows that OpenBR is better than OpenCV for two of the three test cases.