Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical utility of complement‐dependent C3d assay in kidney recipients presenting with late allograft dysfunction

The objective of this study was to evaluate the utility of a complement‐dependent C3d assay to risk stratify donor‐specific antibodies (DSA) in a multicenter cohort of kidney recipients presenting with new‐onset clinical dysfunction. A total of 106 subjects with evidence of DSA at a mean period of 5.3 ± 5.0 years posttransplant underwent testing using C3d reagents. C3d positivity was strongly associated with both the peak and sum IgG DSA MFI, with 98.3% (n = 57/58) of strongly reactive sera (peak MFI > 10 000) eliciting a positive signal. Patients with C3d+ DSA had a higher creatinine (P = .03), more significant graft fibrosis (P = .035), and a faster rate of graft loss posttest compared to those with C3d‐ DSA (P = .05). Subanalysis of patients with low‐moderate level DSA confirmed the inferior outcome associated with C3d positivity. Despite the prognostic value of C3d as a stand‐alone test, the assay did not provide independent risk prediction after incorporation of graft fibrosis in a multivariate model (P = .94). Overall, C3d offered limited discriminatory value for strong DSA with peak IgG MFI > 10 000 and in patients where histologic data is available, but its utilization may be considered in those with low‐moderate level DSA and where an allograft biopsy is not accessible.
Waxy genes from spelt wheat: new alleles for modern wheat breeding and new phylogenetic inferences about the origin of this species.

BACKGROUND AND AIMS Waxy proteins are responsible for amylose synthesis in wheat seeds, being encoded by three waxy genes (Wx-A1, Wx-B1 and Wx-D1) in hexaploid wheat. In addition to their role in starch quality, waxy loci have been used to study the phylogeny of wheat. The origin of European spelt (Triticum aestivum ssp. spelta) is not clear. This study compared waxy gene sequences of a Spanish spelt collection with their homologous genes in emmer (T. turgidum ssp. dicoccum), durum (T. turgidum ssp. durum) and common wheat (T. aestivum ssp. aestivum), together with other Asian and European spelt that could be used to determine the origin of European spelt. METHODS waxy genes were amplified and sequenced. Geneious Pro software, DNAsp and MEGA5 were used for sequence, nucleotide diversity and phylogenetic analysis, respectively. KEY RESULTS Three, four and three new alleles were described for the Wx-A1, Wx-B1 and Wx-D1 loci, respectively. Spelt accessions were classified into two groups based on the variation in Wx-B1, which suggests that there were two different origins for the emmer wheat that has been found to be part of the spelt genetic make-up. One of these groups was only detected in Iberian material. No differences were found between the rest of the European spelt and the Asiatic spelt, which suggested that the Iberian material had a different origin from the other spelt sources. CONCLUSIONS The results suggested that the waxy gene variability present in wheat is undervalued. The evaluation of this variability has permitted the detection of ten new waxy alleles that could affect starch quality and thus could be used in modern wheat breeding. In addition, two different classes of Wx-B1 were detected that could be used for evaluating the phylogenetic relationships and the origins of different types of wheat.
The effect of light intensity and shear stress on microbial biostabilization and the community composition of natural biofilms

php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License (http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms (https://www.dovepress.com/terms.php). Research and Reports in Biology 2018:9 1–16 Research and Reports in Biology Dovepress
Equation of state for magnetized Coulomb plasmas

We have developed an analytical equation of state (EOS) for magnetized fully-ionized plasmas that cover a wide range of temperatures and densities, from low-density classical plasmas to relativistic, quantum plasma conditions. This EOS directly applies to calculations of structure and evolution of strongly magnetized white dwarfs and neutron stars. We review available analytical and numerical results for thermodynamic functions of the nonmagnetized and magnetized Coulomb gases, liquids, and solids. We propose a new analytical expression for the free energy of solid Coulomb mixtures. Based on recent numerical results, we have constructed analytical approximations for the thermodynamic functions of harmonic Coulomb crystals in quantizing magnetic fields. The analytical description ensures a consistent evaluation of all astrophysically important thermodynamic functions based on the first, second, and mixed derivatives of the free energy. Our numerical code for calculation of thermodynamic functions based on these approximations has been made publicly available. Using this code, we calculate and discuss the effects of electron screening and magnetic quantization on the position of the melting point in a range of densities and magnetic fields relevant to white dwarfs and outer envelopes of neutron stars. We consider also the thermal and mechanical structure of a magnetar envelope and argue that it can have a frozen surface which covers the liquid ocean above the solid crust.
Disparities for LGBTQ and Gender Nonconforming Adolescents

By examining experiences of household dysfunction and abuse, disparities in patterns of adversity (such as polyvictimization) for LGBTQ and gender nonconforming adolescents are identified in this study. OBJECTIVES: To identify patterns of childhood adversity in a sample of adolescents and assess disparities in these experiences for lesbian, gay, bisexual, transgender, and questioning adolescents and by level of gender nonconformity. METHOD By using the cross-sectional, statewide, anonymous 2016 Minnesota Student Survey, 81 885 students were included in the current study (50.59% male; mean age = 15.51). Participants were enrolled in grades 9 and 11 in a total of 348 schools. RESULTS: Four patterns of childhood adversity were identified with sex-stratified latent class analyses (entropy = 0.833 males; 0.833 females), ranging from relatively low levels of abuse (85.3% males; 80.1% females) to polyvictimization (0.84% males; 1.98% females). A regression analysis showed that compared with heterosexual adolescents, gay, lesbian, bisexual, and questioning adolescents were more likely to be classified into profiles characterized by polyvictimization (odds ratio [OR] 1.81–7.53) and psychological and/or physical abuse (OR 1.29–3.12), than no or low adversity. Similarly, compared with nontransgender adolescents, transgender adolescents were more likely to be classified into profiles characterized by patterns of polyvictimization (OR 1.49–2.91) and psychological and/or physical abuse (OR 1.23–1.96). A higher level of gender nonconformity predicted a higher likelihood of being classified into each adversity profile compared with the no or low adversity profile (OR 1.14–1.45). CONCLUSIONS: Sexual minority adolescents and adolescents with high levels of gender nonconformity are vulnerable to experience adversity. The disparities for lesbian, gay, bisexual, transgender, and questioning adolescents and adolescents with high gender nonconformity highlight the variation in patterns of childhood adversity that these youth are at risk of experiencing. The findings reveal the need for further research on the benefits and harm of screening for childhood adversity by physicians and pediatricians.
Barakat syndrome revisited

Barakat syndrome also known as HDR syndrome (Online Mendelian Inheritance in Man [OMIM] 146255), was first described by Barakat et al. in . It is a rare genetic disorder characterized by the triad of hypoparathyroidism “H,” sensorineural deafness “D,” and renal disease “R. ” The defect is caused by deletions in chromosome 10p14 or mutations in the GATA3 gene. Although the syndrome has been phenotypically defined by this triad the literature identifies cases with different components with, or without GATA3 defects making the definition of the syndrome confusing. We analyzed 180 cases and attempted to define the phenotype of the syndrome and suggest guidelines for diagnosis. We suggest that the diagnosis could be confirmed in patients who have all three components, and in those who have two components with a positive family history. GATA3 testing is optional to establish the diagnosis in these patients. The syndrome should be considered in patients with isolated “D” where other causes of “D” have been excluded and those with isolated “R,” especially if there is family history of any of these components. In these instances, confirmatory GATA3 testing is indicated to confirm the diagnosis. In patients with nonsurgical “H,” where “D” and “R” have been conclusively ruled out GATA3 studies are not needed as none of these patients were shown to be GATA3 haploinsufficient. Only 64.4% of patients in our review had “HDR. ” Some findings might have not been recognized or may could have appeared later in life, but it is evident that this syndrome is genotypically heterogeneous.
Out of Africa: origins of the Taenia tapeworms in humans

Phylogenetic and divergence date analyses indicate that the occurrence of Taenia tapeworms in humans pre–dates the development of agriculture, animal husbandry and domestication of cattle (Bos spp.) or swine (Sus scrofa). Taeniid tapeworms in Africa twice independently colonized hominids and the genus Homo prior to the origin of modern humans. Dietary and behavioural shifts, from herbivory to scavenging and carnivory, as early Homo entered the carnivore guild in the Pliocene/Pleistocene, were drivers for host switching by tapeworms to hominids from carnivores including hyaenids and felids. Parasitological data provide a unique means of elucidating the historical ecology, foraging behaviour and food habits of hominids during the diversification of Homo spp.
Glucose Hypometabolism in Hippocampal Subdivisions in Alzheimer's Disease: A Pilot Study Using High-Resolution 18F-FDG PET and 7.0-T MRI

Background and Purpose Atrophy of the hippocampus is an important clinical diagnostic marker of Alzheimer's disease (AD), and so assessments of hippocampal activity and its subdivisions might provide invaluable information. This study compared the glucose metabolism of hippocampal subdivisions in mild-AD patients and healthy controls. Methods High-resolution T2*-weighted gradient-echo magnetic resonance imaging (MRI) images and 18F-fluorodeoxyglucose (FDG) positron-emission tomography (PET) images were acquired using 7.0-T MRI and high-resolution research tomograph FDG-PET, respectively, in 9 early-stage AD patients and 10 healthy subjects. The hippocampal body was divided into three equal parts (anterior, middle, and posterior), and in each part a region of interest (ROI) was drawn over the cornus ammonis (CA)1, CA2/3, CA4/dentate gyrus (DG), and subiculum. The standardized uptake values of the hippocampal subdivisions were calculated for each ROI as ratios relative to the pons standardized uptake value. Statistical analysis was conducted using the Mann-Whitney U test. Results Patients with early-stage AD patients showed significantly less metabolic activity than healthy controls focally in the middle (p=0.050) and posterior (p=0.034) CA2/3 regions of the right hippocampus, and significantly less activity throughout the left hippocampal body in the anterior CA2/3 (p=0.027) and CA4/DG (p=0.027) regions, the middle CA1 region (p=0.011), and the posterior CA1 (p=0.034), CA2/3 (p=0.007), and CA4/DG (p=0.014) regions. Conclusions It was possible to use high-resolution PET-MRI fusion images to identify hippocampus subdivisions and assess glucose metabolism in the subfields. Reductions in metabolic activity were found to vary along the hippocampal axis in early-stage AD patients.
Mid-Infrared and Visible Photometry of Galaxies: Anomalously Low Polycyclic Aromatic Hydrocarbon Emission from Low-Luminosity Galaxies

The Spitzer Space Telescope First Look Survey Infrared Array Camera (IRAC) near- and mid-infrared imaging data partially overlap the Sloan Digital Sky Survey (SDSS), with 313 visible-selected (r < 17.6 mag) SDSS main sample galaxies in the overlap region. The 3.5 and 7.8 μm properties of the galaxies are investigated in the context of their visible properties, where the IRAC [3.5] magnitude primarily measures starlight and the [7.8] magnitude primarily measures polycyclic aromatic hydrocarbon (PAH) emission from the interstellar medium. As expected, we find a strong inverse correlation between [3.5]-[7.8] and visible color; galaxies red in visible colors ("red galaxies") tend to show very little dust and molecular emission (low PAH-to-star ratios), and galaxies blue in visible colors ("blue galaxies," i.e., star-forming galaxies) tend to show large PAH-to-star ratios. Red galaxies with high PAH-to-star ratios tend to be edge-on disks reddened by dust lanes. Simple attenuation corrections inferred in the visible bring the visible colors of these galaxies in line with those of face-on disks; i.e., PAH emission is closely related to attenuation-corrected star formation rates inferred in the visible. Blue galaxies with anomalously low PAH-to-star ratios are all low-luminosity star-forming galaxies. There is some weak evidence in this sample that the deficiency in PAH emission for these low-luminosity galaxies may be related to emission-line metallicity.
Specific pre‐cleavage and post‐cleavage complexes involved in the formation of SV40 late mRNA 3′ termini in vitro.

Complexes form between processing factors present in a crude nuclear extract from HeLa cells and a simian virus 40 (SV40) late pre‐mRNA which spans the polyadenylation [poly(A)] site. A specific ‘pre‐cleavage complex’ forms on the pre‐mRNA before cleavage. Formation of this complex requires the highly conserved sequence AAUAAA: it is prevented by mutations in AAUAAA, and by annealing DNA oligonucleotides to that sequence. After cleavage, the 5′ half‐molecule is found in a distinct ‘post‐cleavage complex’. In contrast, the 3′ half‐molecule is released. After cleavage and polyadenylation, polyadenylated RNA also is released. De novo formation of the post‐cleavage complex requires AAUAAA and a nearby 3′ terminus. Competition experiments suggest that a component which recognizes AAUAAA is required for formation of both pre‐ and post‐cleavage complexes.
Controlling the Charging of Electric Vehicles with Neural Networks

We propose and evaluate controllers for the coordination of the charging of electric vehicles. The controllers are based on neural networks and are completely de-centralized, in the sense that the charging current is completely decided by the controller itself. One of the versions of the controllers does not require any outside communication at all. We test controllers based on two different architectures of neural networks-the feed-forward networks and the echo state networks. The networks are optimized by either an evolutionary algorithm (CMA-ES) or by a gradient-based method. The results of the different architectures and the different optimization algorithms are compared in a realistic scenario. We show that the controllers are able to charge the cars while keeping the peak consumptions almost the same as when no charging is performed. Moreover, the controllers fill the valleys of the consumption thus reducing the difference between the maximum and minimum consumption in the grid.
Combined therapy for critical limb ischaemia: Biomimetic PLGA microcarriers potentiates the pro‐angiogenic effect of adipose tissue stromal vascular fraction cells

We propose a regenerative solution in the treatment of critical limb ischaemia (CLI). Poly‐lactic/glycolic acid microcarriers were prepared and coated with laminin to be sterilized through γ‐irradiation of 25 kGy at low temperature. Stromal vascular fraction (SVF) cells were extracted through enzymatic digestion of adipose tissue. Streptozotocin‐induced diabetic mice underwent arteriotomy and received an administration of SVF cells combined or not with biomimetic microcarriers. Functional evaluation of the ischaemic limb was then reported, and tissue reperfusion was evaluated through fluorescence molecular tomography. Microcarriers were stable and functional after γ‐irradiation until at least 12 months of storage. Mice that received an injection of SVF cells in the ischaemic limb have 22% of supplementary blood supply within this limb 7 days after surgery compared with vehicle, whereas no difference was observed at Day 14. With the combined therapy, the improvement of blood flow is significantly higher compared with vehicle, of about 31% at Day 7 and of about 11% at Day 14. Injection of SVF cells induces a significant 27% decrease of necrosis compared with vehicle. This effect is more important when SVF cells were mixed with biomimetic microcarriers: −37% compared with control. Although SVF cells injection leads to a non‐significant 22% proprioception recovery, the combined therapy induces a significant recovery of about 27% compared with vehicle. We show that the combination of SVF cells from adipose tissue with laminin‐coated poly‐lactic/glycolic acid microcarriers is efficient for critical limb ischaemia therapy in a diabetic mouse model.
Convergence diagnostics for stochastic gradient descent with constant learning rate

Many iterative procedures in stochastic optimization exhibit a transient phase followed by a stationary phase. During the transient phase the procedure converges towards a region of interest, and during the stationary phase the procedure oscillates in that region, commonly around a single point. In this paper, we develop a statistical diagnostic test to detect such phase transition in the context of stochastic gradient descent with constant learning rate. We present theory and experiments suggesting that the region where the proposed diagnostic is activated coincides with the convergence region. For a class of loss functions, we derive a closed-form solution describing such region. Finally, we suggest an application to speed up convergence of stochastic gradient descent by halving the learning rate each time stationarity is detected. This leads to a new variant of stochastic gradient descent, which in many settings is comparable to state-of-art.
Modeling Soft-Error Propagation in Programs

As technology scales to lower feature sizes, devices become more susceptible to soft errors. Soft errors can lead to silent data corruptions (SDCs), seriously compromising the reliability of a system. Traditional hardware-only techniques to avoid SDCs are energy hungry, and hence not suitable for commodity systems. Researchers have proposed selective software-based protection techniques to tolerate hardware faults at lower costs. However, these techniques either use expensive fault injection or inaccurate analytical models to determine which parts of a program must be protected for preventing SDCs. In this work, we construct a three-level model, TRIDENT, that captures error propagation at the static data dependency, control-flow and memory levels, based on empirical observations of error propagations in programs. TRIDENT is implemented as a compiler module, and it can predict both the overall SDC probability of a given program and the SDC probabilities of individual instructions, without fault injection. We find that TRIDENT is nearly as accurate as fault injection and it is much faster and more scalable. We also demonstrate the use of TRIDENT to guide selective instruction duplication to efficiently mitigate SDCs under a given performance overhead bound.
Dynamic model of queue management based on resource allocation in telecommunication networks

A dynamic management model based on the allocation of resources in a telecommunication network is proposed in the article. The solution for the optimization problem presented in this model assumes optimal aggregation of the Hows in accordance with the values of their classes, as well as the subsequent optimal allocation of the network resource to the queues formed on the interface of the network router. The novelty of the model lies in considering the dynamic nature of the change in the state of the interface described by the nonlinear differential equations of the network state on the basis of the Pointwise Stationary Fluid Flow Approximation (PSFFA).
RANS Equations with Reynolds Stress Closure Can Be Ill-Conditioned

Reynolds-averaged Navier-Stokes (RANS) simulations with turbulence models continue to play important roles in industrial flow simulations as high-fidelity simulations are prohibitively expensive for such flows. Commonly used linear eddy viscosity models are intrinsically unable to handle flows with non-equilibrium turbulence (e.g., flows with massive separation). Reynolds stress models, on the other hand, are plagued by their lack of robustness and stability. Recent studies found that even substituting Reynolds stresses from DNS databases (with errors below 0.5%) into RANS equations leads to grossly inaccurate velocities. Such an observation is not only disturbing for the recently emerging data-driven Reynolds stress models but also relevant for traditional, equation-based models. This observation cannot be explained by the global matrix condition number of the discretized RANS equations. In this work, we propose a metric based on local condition numbers for a priori evaluation of the stability of Reynolds stress models. Numerical tests on turbulent channel flows at various Reynolds numbers suggest that the proposed metric can adequately explain observations in previous studies, i.e., decreased model stability with increasing Reynolds number, and better stability of the implicit treatment of Reynolds stress compared to the explicit treatment.
Investigating Backtranslation in Neural Machine Translation

A prerequisite for training corpus-based machine translation (MT) systems – either Statistical MT (SMT) or Neural MT (NMT) – is the availability of high-quality parallel data. This is arguably more important today than ever before, as NMT has been shown in many studies to outperform SMT, but mostly when large parallel corpora are available; in cases where data is limited, SMT can still outperform NMT. Recently researchers have shown that back-translating monolingual data can be used to create synthetic parallel corpora, which in turn can be used in combination with authentic parallel data to train a highquality NMT system. Given that large collections of new parallel text become available only quite rarely, backtranslation has become the norm when building state-of-the-art NMT systems, especially in resource-poor scenarios. However, we assert that there are many unknown factors regarding the actual effects of back-translated data on the translation capabilities of an NMT model. Accordingly, in this work we investigate how using back-translated data as a training corpus – both as a separate standalone dataset as well as combined with human-generated parallel data – affects the performance of an NMT model. We use incrementally larger amounts of back-translated data to train a range of NMT systems for German-to-English, and analyse the resulting translation performance.