Miracle-dz/UniFAR-FTUs huggingface dataset:
Carotid artery recognition system: a comparison of three automated paradigms for ultrasound images.

PURPOSE The development of completely automated techniques for arterial wall segmentation and intima-media thickness measurement requires the recognition of the artery in the image frame. Conceptually, automated techniques can be thought of as the combination of two cascaded stages: artery recognition and wall segmentation. In this paper, the authors show three carotid artery recognition systems (CARS) that are fully automated. METHODS The first technique is based on a first-order derivative Gaussian edge analysis (CARSgd). The second method is based on an integrated approach (CARSia) that combines image feature extraction, fitting, and classification. The third strategy is based on signal analysis (CARSsa). The output of all the three paradigms provide tracing of the far adventitial (AD(F)). The authors validated CARSgd, CARSia, and CARSsa on a dataset of 365 longitudinal B-Mode carotid images, acquired by different sonographers. Performance evaluation of the carotid recognition process was done in three ways: (1) visual inspection by experts; (2) by measuring the Hausdorff distance (HD) between the automatic far adventitial (AD(F)) and the manually traced AD(F), and (3) by measuring the HD between AD(F) and the lumen-intima (GT(LI)) and media-adventitia (GT(MA)) borders of the arterial walls. RESULTS The average HD between AD(F) and the manual AD(F) was 1.53 ± 1.51 mm for CARSgd, 1.82 ± 3.08 mm for CARSia, and 2.56 ± 2.89 mm for CARSsa. The average HD between GT(LI) and AD(F) for CARSgd, CARSia, and CARSsa were 2.16 ± 1.16 mm, 2.71 ± 2.89 mm, and 2.66 ± 1.52 mm, respectively. The average HD between AD(F) and GT(MA) for CARSgd, CARSia, and CARSsa were 1.54 ± 1.19 mm, 1.86 ± 2.66 mm, and 1.95 ± 1.64 mm, respectively. Considering a maximum distance of 50 pixels (about 3 mm), CARSgd showed an identification accuracy of 100%, CARSia of 92%, and CARSsa of 96%. These identification accuracies were confirmed by visual inspection. All the three systems work on MATLAB, Windows OS, and on a PC based cross platform medical application written in Java called ATHEROEDGE™ with 1 s per image. CONCLUSIONS CARSgd showed very accurate AD(F) profiles coupled with a low computational burden and without the need for specific tuning. It can be thought of as a reference technique for carotid localization, to be used in automated intima-media thickness measurement strategies.
Inspiratory flow rate, not type of incentive spirometry device, influences chest wall motion in healthy individuals

This study investigated the effect of flow rates and spirometer type on chest wall motion in healthy individuals. Twenty-one healthy volunteers completed breathing trials to either two times tidal volume (2xVT) or inspiratory capacity (IC) at high, low, or natural flow rates, using a volume- or flow-oriented spirometer. The proportions of rib cage movement to tidal volume (%RC/VT), chest wall diameters, and perceived level of exertion (RPE) were compared. Low and natural flow rates resulted in significantly lower %RC/VT compared to high flow rate trials (p=0.001) at 2xVT. Low flow trials also resulted in significantly less chest wall motion in the upper anteroposterior direction than high and natural flow rates (p<0.001). At IC, significantly greater movement occurred in the abdominal lateral direction during low flow compared to high and natural flow trials (both p<0.003). RPE was lower for the low flow trials compared to high flow trials at IC and 2xVT (p<0.01). In healthy individuals, inspiratory flow (not device type) during incentive spirometry determines the resultant breathing pattern. High flow rates result in greater chest wall motion than low flow rates.
DLVM: A modern compiler infrastructure for deep learning systems

Deep learning software demands reliability and performance. However, many of the existing deep learning frameworks are software libraries that act as an unsafe DSL in Python and a computation graph interpreter. We present DLVM, a design and implementation of a compiler infrastructure with a linear algebra intermediate representation, algorithmic differentiation by adjoint code generation, domain-specific optimizations and a code generator targeting GPU via LLVM. Designed as a modern compiler infrastructure inspired by LLVM, DLVM is more modular and more generic than existing deep learning compiler frameworks, and supports tensor DSLs with high expressivity. With our prototypical staged DSL embedded in Swift, we argue that the DLVM system enables a form of modular, safe and performant frameworks for deep learning.
A genome‐wide linkage scan for cleft lip and cleft palate identifies a novel locus on 8p11‐23

Isolated or nonsyndromic cleft lip and palate (NS CLP) is a complex disorder resulting from multiple genetic and environmental factors. NS CLP has a birth prevalence of 1 per 500 in the Philippines where large families provide an opportunity for gene localization. Genotyping of 392 microsatellite repeat markers at 10 cM intervals over the genome was performed by the Center for Inherited Disease Research (CIDR) on 220 Filipino families with 567 affected and 1,109 unaffected family members genotyped. Among the most statistically significant results from analysis of the genome‐wide scan data was a 20 cM region at 8p11‐23 in which markers had LODs ≥1.0. This region on 8p11‐23 has not been found in any previous genome wide scan nor does it contain any of the candidate genes widely studied in CLP. Fine mapping in 8p11‐23 was done in the 220 families plus an additional 51 families, using SNP markers from 10 known genes (FGFR1, NRG1, FZD3, SLC8A1, PPP3CC, EPHX2, BNIP3L, EGR3, PPP2R2A, and NAT1) within the 20 cM region of 8p11‐23. Linkage and association analyses of these SNPs yield suggestive results for markers in FGFR1 (recessive multipoint HLOD 1.07) and BAG4 (recessive multipoint HLOD 1.31). © 2007 Wiley‐Liss, Inc.
Modeling of experts’ divergent prior beliefs for a sequential phase III clinical trial

Background There have been few Bayesian analyses of phase III sequential clinical trials that model divergent expert opinions in a single distribution. Purpose We used modeling of experts’ opinions to perform additional Bayesian analyses of a randomized clinical trial (designed as a sequential trial), particularly when a bimodal shape is observed. We provide an illustrative example based on a randomized trial conducted in patients aged between 65 and 75 years with multiple myeloma as the case study. Methods The main endpoint of the trial was overall survival (OS). Prior distribution of the log hazard ratio of death in the experimental versus the control arm ( θ ) was constructed based on elicitation of experts using a mixture of normal distributions estimated by the Expectation–Maximisation (EM) algorithm. At each interim and terminal analysis, the posterior probability of θ and the resulting increases in median OS in the experimental arm compared to the control were computed. The results were compared to results obtained using either skeptical, enthusiastic, or a mixture of those priors. Finally, we discuss our results in light of the frequentist approach originally designed for the trial. Results A total of 39 experts reported their opinion on the median OS in the experimental arm compared to the median control survival of 30 months. The resulting pooled distribution of the log hazard ratios exhibited a bimodal profile. When the prior mixture of the normal distribution was fitted to the data sets from the experts, 44% of the experts’ opinions were optimistic and 56% were doubtful. At the final analysis, the percentage of doubting experts dropped to 18%. This corresponded to a posterior probability of an improved OS in the experimental arm compared to the control arm of at least 0.98, regardless of the prior. These findings are in agreement with the original conclusion of the trial regarding the beneficial effect of the experimental treatment in this population. Limitations Only 39 experts among the 120 questioned physicians responded to the inquiry. Our approach was hybrid because the prior mixture was estimated using the EM algorithm, and a full Bayesian approach may have been used. Conclusions Bayesian inference allows the quantification of increased survival in terms of probability distributions and provides investigators with an additional tool in the analysis of a randomized phase III clinical trial. Using a mixture of densities appears to be a promising strategy for incorporating the bimodal profile of prior opinion, with actualization of the two components along the trial as an illustration of the evolution of opinions as data are accumulated.
Validation and Topic-driven Ranking for Biomedical Hypothesis Generation Systems

Literature underpins research, providing the foundation for new ideas. But as the pace of science accelerates, many researchers struggle to stay current. To expedite their searches, some scientists leverage hypothesis generation (HG) systems, which can automatically inspect published papers to uncover novel implicit connections. With no foreseeable end to the driving pace of research, we expect these systems will become crucial for productive scientists, and later form the basis of intelligent automated discovery systems. Yet, many resort to expert analysis to validate such systems. This process is slow, hard to reproduce, and takes time away from other researchers. Therefore, we present a novel method to validate HG systems, which both scales to large validation sets and does not require expert input. We also introduce a number of new metrics to automatically identify plausible generated hypotheses. Through the study of published, highly cited, and noise predicates, we devise a validation challenge, which allows us to evaluate the performance of a HG system. Using an in-progress system, MOLIERE, as a case-study, we show the utility of our validation and ranking methods. So that others may reproduce our results, we provide our code, validation data, and results at bit.ly/2EtVshN.
Challenges in embedded model checking — a simulator for the [mc]square model checker

Model checking is considered a promising approach for the verification of software for embedded systems. Generating system models that are close to real-life behavior, however, is challenging. As a result, in some approaches a model can be automatically constructed out of the assembly code along with an appropriate target simulator/debugger. The implementation of the latter is crucial for the entire verification process. To that end, this paper presents requirements and challenges that arise when implementing and verifying such a simulator for the [mc]square model checker from the RWTH Aachen University.
Revisiting Degrees of Freedom of Full-Duplex Systems with Opportunistic Transmission: An Improved User Scaling Law

It was recently studied how to achieve the optimal degrees of freedom (DoF) in a multi-antenna full-duplex system with partial channel state information (CSI). In this paper, we revisit the DoF of a multiple-antenna full-duplex system using opportunistic transmission under the partial CSI, in which a full-duplex base station having M transmit antennas and M receive antennas supports a set of half-duplex mobile stations (MSs) having a single antenna each. Assuming no self-interference, we present a new hybrid opportunistic scheduling method that achieves the optimal sum DoF under an improved user scaling law. Unlike the state-of-the-art scheduling method, our method is designed in the sense that the scheduling role between downlink MSs and uplink MSs is well-balanced. It is shown that the optimal sum DoF of 2M is asymptotically achievable provided that the number of MSs scales faster than SNRM, where SNR denotes the signal-to-noise ratio. This result reveals that, in our full-duplex system, better performance on the user scaling law can be obtained without extra CSI, compared to the prior work that showed the required user scaling condition (i.e., the minimum number of MSs for guaranteeing the optimal DoF) of SNR2M−1. Moreover, the average interference decaying rate is analyzed. Numerical evaluation is performed to not only validate our analysis but also show superiority of the proposed method over the state-of-the-art method.
Agarose and Its Derivatives as Supports for Enzyme Immobilization

Agarose is a polysaccharide obtained from some seaweeds, with a quite particular structure that allows spontaneous gelation. Agarose-based beads are highly porous, mechanically resistant, chemically and physically inert, and sharply hydrophilic. These features—that could be further improved by means of covalent cross-linking—render them particularly suitable for enzyme immobilization with a wide range of derivatization methods taking advantage of chemical modification of a fraction of the polymer hydroxyls. The main properties of the polymer are described here, followed by a review of cross-linking and derivatization methods. Some recent, innovative procedures to optimize the catalytic activity and operational stability of the obtained preparations are also described, together with multi-enzyme immobilized systems and the main guidelines to exploit their performances.
Stable Cd-Mg-Yb and Cd-Mg-Ca icosahedral quasicrystals with wide composition ranges

Stable icosahedral quasicrystals with wide composition ranges have been found in the systems Cd-Mg-Yb and Cd-Mg-Ca. The icosahedral quasicrystals form in the following composition ranges: 25-85at. %Cd, 0-60at. %Mg and 10-20at. %Yb for the Cd-Mg-Yb system; 33-85at. %Cd, 0-52at. %Mg and 10-20at. %Ca for the Cd-Mg-Ca system. An electron diffraction study confirmed that the icosahedral quasicrystals have a primitive lattice. Its quasilattice constant is proportional to a Goldschmidt atom diameter of the quasicrystals weighted by a factor of 1.75 in the range 0.5681- 0.5799nm for the Cd-Mg-Yb system and 0.5697-0.5778nm for the Cd-Mg-Ca system. The closely similar atom sizes of Cd and Mg, the valence electron ratio e / a =2.0 and the large atom sizes of Yb and Ca cause the wide composition ranges of the Cd-Mg-Yb and Cd-Mg-Ca quasicrystals. The metallurgical behaviour of the quasicrystals is discussed.
Seeking kinetic pathways relevant to the structural evolution of metal nanoparticles

Understanding the kinetic pathways that cause metal nanoparticles to structurally evolve over time is essential for predicting their shape and size distributions and catalytic properties. Consequently, we need detailed kinetic models that can provide such information. Most kinetic Monte Carlo models used for metal systems contain a fixed catalogue of atomic moves; the catalogue is largely constructed based on our physical understanding of the material. In some situations, it is possible that an incorrect picture of the overall dynamics is obtained when kinetic pathways that are relevant to the dynamics are missing from the catalogue. Hence, a computational framework that can systematically determine the relevant pathways is required. This work intends to fulfil this requirement. Examples involving an Ag nanoparticle are studied to illustrate how molecular dynamics (MD) calculations can be employed to find the relevant pathways in a system. Since pathways that are unlikely to be selected at short timescales can become relevant at longer times, the accuracy of the catalogue is maintained by continually seeking these pathways using MD. We discuss various aspects of our approach, namely, defining the relevance of atomic moves to the dynamics and determining when additional MD is required to ensure the desired accuracy, as well as physical insights into the Ag nanoparticle.
Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China

Background Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. Methodology and Findings Twenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n = 1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5–20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%. Conclusions These results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.
Stringency of synthetic promoter sequences in Clostridium revealed and circumvented by tuning promoter library mutation rates

Collections of characterized promoters of different strengths are key resources for synthetic biology, but are not well established for many important organisms, including industrially-relevant Clostridium spp. When generating promoters, reporter constructs are used to measure expression, but classical fluorescent reporter proteins are oxygen-dependent and hence inactive in anaerobic bacteria like Clostridium. We directly compared oxygen-independent reporters of different types in Clostridium acetobutylicum and found that glucuronidase (GusA) from E. coli performed best. Using GusA, a library of synthetic promoters was first generated by a typical approach entailing complete randomization of a constitutive thiolase gene promoter (Pthl) except for the consensus -35 and -10 elements. In each synthetic promoter, the chance of each degenerate position matching Pthl was 25%. Surprisingly, none of the synthetic promoters from this library were functional in C. acetobutylicum, even though they functioned as expected in E. coli. Next, instead of complete randomization, we specified lower promoter mutation rates using oligonucleotide primers synthesized using custom mixtures of nucleotides. Using these primers, two promoter libraries were constructed in which the chance of each degenerate position matching Pthl was 79% or 58%, instead of 25% as before. Synthetic promoters from these ‘stringent’ libraries functioned well in C. acetobutylicum, covering a wide range of strengths. The promoters functioned similarly in the distantly-related species Clostridium sporogenes, and allowed predictable metabolic engineering of C. acetobutylicum for acetoin production. Besides generating the desired promoters and demonstrating their useful properties, this work indicates an unexpected ‘stringency’ of promoter sequences in Clostridium, not reported previously. GRAPHICAL ABSTRACT
Complete genome sequence of Thioalkalivibrio sp. K90mix

Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.
Impact of Mutations in the Hemagglutinin of H10N7 Viruses Isolated from Seals on Virus Replication in Avian and Human Cells

Wild birds are the reservoir for low-pathogenic avian influenza viruses, which are frequently transmitted to domestic birds and occasionally to mammals. In 2014, an H10N7 virus caused severe mortality in harbor seals in northeastern Europe. Although the hemagglutinin (HA) of this virus was closely related to H10 of avian H10N4 virus, it possessed unique nonsynonymous mutations, particularly in the HA1 subunit in or adjacent to the receptor binding domain and proteolytic cleavage site. Here, the impact of these mutations on virus replication was studied in vitro. Using reverse genetics, an avian H10N4 virus was cloned, and nine recombinant viruses carrying one of eight unique mutations or the complete HA from the seal virus were rescued. Receptor binding affinity, replication in avian and mammalian cell cultures, cell-to-cell spread, and HA cleavability of these recombinant viruses were studied. Results show that wild-type recombinant H10N4 virus has high affinity to avian-type sialic acid receptors and no affinity to mammalian-type receptors. The H10N7 virus exhibits dual receptor binding affinity. Interestingly, Q220L (H10 numbering) in the rim of the receptor binding pocket increased the affinity of the H10N4 virus to mammal-type receptors and completely abolished the affinity to avian-type receptors. No remarkable differences in cell-to-cell spread or HA cleavability were observed. All viruses, including the wild-type H10N7 virus, replicated at higher levels in chicken cells than in human cells. These results indicate that H10N7 acquired adaptive mutations (e.g., Q220L) to enhance replication in mammals and retained replication efficiency in the original avian host.
On the formulation, parameter identification and numerical integration of the EMMI model :plasticity and isotropic damage.

In this report we present the formulation of the physically-based Evolving Microstructural Model of Inelasticity (EMMI) . The specific version of the model treated here describes the plasticity and isotropic damage of metals as being currently applied to model the ductile failure process in structural components of the W80 program . The formulation of the EMMI constitutive equations is framed in the context of the large deformation kinematics of solids and the thermodynamics of internal state variables . This formulation is focused first on developing the plasticity equations in both the relaxed (unloaded) and current configurations. The equations in the current configuration, expressed in non-dimensional form, are used to devise the identification procedure for the plasticity parameters. The model is then extended to include a porosity-based isotropic damage state variable to describe the progressive deterioration of the strength and mechanical properties of metals induced by deformation . The numerical treatment of these coupled plasticity-damage constitutive equations is explained in detail. A number of examples are solved to validate the numerical implementation of the model.