Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating MCMC via Parallel Predictive Prefetching

Parallel predictive prefetching is a new framework for accelerating a large class of widely-used Markov chain Monte Carlo (MCMC) algorithms. It speculatively evaluates many potential steps of an MCMC chain in parallel while exploiting fast, iterative approximations to the target density. This can accelerate sampling from target distributions in Bayesian inference problems. Our approach takes advantage of whatever parallel resources are available, but produces results exactly equivalent to standard serial execution. In the initial burn-in phase of chain evaluation, we achieve speedup close to linear in the number of available cores.
SUZ12 is a novel putative oncogene promoting tumorigenesis in head and neck squamous cell carcinoma

The suppressor of zest 12 (SUZ12), one of the core polycomb repressive complex 2 (PRC2) components, has increasingly appreciated as a key mediator during human tumorigenesis. However, its expression pattern and oncogenic roles in head and neck squamous cell carcinoma (HNSCC) remain largely unexplored yet. Here, we sought to determine its expression pattern, clinicopathological significance and biological roles in HNSCC. Through data mining and interrogation from multiple publicly available databases, our bioinformatics analyses revealed that SUZ12 mRNA was significantly overexpressed in multiple HNSCC patient cohorts. Moreover, SUZ12 protein was markedly up‐regulated in primary HNSCC samples from our patient cohort as assessed by immunohistochemical staining and its overexpression significantly associated with cervical node metastasis and reduced overall and disease‐free survival. In the 4‐nitroquinoline 1‐oxide (4NQO)‐induced HNSCC mouse model, increased SUZ12 immunostaining was observed along with disease progression from epithelial hyperplasia to squamous cell carcinoma in tongue. Furthermore, shRNA‐mediated SUZ12 knock‐down significantly inhibited cell proliferation, migration and invasion in HNSCC cells, and resulted in compromised tumour growth in vivo. Collectively, our data reveal that SUZ12 might serve as a putative oncogene by promoting cell proliferation, migration and invasion, and also a novel biomarker with diagnostic and prognostic significance for HNSCC.
Biomechanics in Soft Mechanical Sensing: From Natural Case Studies to the Artificial World

Living beings use mechanical interaction with the environment to gather essential cues for implementing necessary movements and actions. This process is mediated by biomechanics, primarily of the sensory structures, meaning that, at first, mechanical stimuli are morphologically computed. In the present paper, we select and review cases of specialized sensory organs for mechanical sensing—from both the animal and plant kingdoms—that distribute their intelligence in both structure and materials. A focus is set on biomechanical aspects, such as morphology and material characteristics of the selected sensory organs, and on how their sensing function is affected by them in natural environments. In this route, examples of artificial sensors that implement these principles are provided, and/or ways in which they can be translated artificially are suggested. Following a biomimetic approach, our aim is to make a step towards creating a toolbox with general tailoring principles, based on mechanical aspects tuned repeatedly in nature, such as orientation, shape, distribution, materials, and micromechanics. These should be used for a future methodical design of novel soft sensing systems for soft robotics.
An Action Principle for Action-dependent Lagrangians: toward an Action Principle to non-conservative systems

In this work, we propose an Action Principle for Action-dependent Lagrangian functions by generalizing the Herglotz variational problem to the case with several independent variables. We obtain a necessary condition for the extremum equivalent to the Euler-Lagrange equation and, through some examples, we show that this generalized Action Principle enables us to construct simple and physically meaningful Action-dependent Lagrangian functions for a wide range of non-conservative classical and quantum systems. Furthermore, when the dependence on the Action is removed, the traditional Action Principle for conservative systems is recovered.
Behavioral enhancement of onshore transport by postlarval Caribbean spiny lobster (Panulirus argus)

We conducted a series of laboratory experiments to examine the orientation, settlement, and metamorphosis of Caribbean spiny lobster (Panulirus argus) pueruli (postlarvae) in response to cues characteristic of their nursery in back‐reef tropical lagoons. Our results suggest that pueruli were attracted to coastal water sources and the metabolites of red macroalgae (Laurencia spp.) when compared with oceanic water and artificial seawater treatments. Pueruli were not attracted to waterborne cues from sea grass, were repelled by hypersaline or hyposaline water, and discerned coastal cues from water collected as far as 30 km offshore from the reef. We also conducted experiments to examine the settlement behavior of pueruli in response to different substrates and hydrostatic pressures. Pueruli only settled at pressures equivalent to depths ≪5 m, which is where most settlement occurs in the field; settlement behavior was further enhanced by the presence of red macroalgae. Coastal water or artificial seawater containing red macroalgae metabolites hastened puerulus development and molting to the benthic juvenile stage by 20‐30% compared with those exposed to artificial seawater. Collectively, our results demonstrate that spiny lobster pueruli use chemical and pressure cues during onshore transport and selection of settlement habitat, highlighting the important role of behavioral responses to physical cues in the recruitment of this species.
Study of fourier transform infrared of adding metallic nanofillers on heat cure acrylic resin treated by microwave

Background: Polymethylmethacrylate (PMMA) has been the most popular material for the construction of denture bases since 1937. This is largely due to its favourable although not ideal characteristics. Aims of the study: To study the structural characterisation using Fourier transform infrared (FTIR) of adding aluminium oxide (Al2O3) and silver nanofillers on heat cure acrylic powder treated with microwave radiation and microwave-treated PMMA powder ground by micronizer. Materials and Methods: PMMA powder was treated with microwave radiation at a power level of 360 watt for ¾ h. The obtained PMMA powder was then grinded using a domestic blender group (V). The next step is particle size reduction of the microwave-treated PMMA powder using micronizer group (M). Two concentrations of Al2O3and Ag nanoparticles (NPs) were added separately into untreated PMMA powder group (P) and microwave-treated PMMA powder group (V and M) compared with the control group. The structural characterisations of all experimental groups are determined by FTIR. The samples were divided into 15 groups, one sample for each group. Results: The FTIR analysis has confirmed that the structural behaviour of both microwave and micronizer groups showed that there were no changes in the regions of the band locations for C=C and C=O when compared with the control one. The infrared spectra of all acrylic groups with (Al2O3and Ag) NPs additives showed all of the unique peaks attributed to the PMMA. These bands appeared in the same regions of the acrylic except the carbon double bond carbon (C=C) were absent in the infrared spectrometer chart. Conclusion: The FTIR test charts provide strong evidence that there are no chemical changes in all experimental groups. Except for the C=C band from the methacrylate group did not appear in samples containing NPs, which in turn indicates that the residual monomer of these groups is remarkably decreased.
Efficient Search of Compact QC-LDPC and SC-LDPC Convolutional Codes With Large Girth

We propose a low-complexity method to find quasi-cyclic low-density parity-check block codes with girth 10 or 12 and length shorter than those designed through classical approaches. The method is extended to time-invariant spatially coupled low-density parity-check convolutional codes, permitting to achieve small syndrome former constraint lengths. Several numerical examples are given to show its effectiveness.
Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.
A unified Ruzsa-Szemerédi framework for finite-length coded caching

We review existing work on efficient schemes for finite length coded caching. The coded caching problem studies efficient ways of broadcasting in a noiseless wireless network where each user is equipped with cache of size M files and has possibly distinct demands from a library of N files. The problem is to jointly design the cache content and the transmission protocol such that, irrespective of the demand pattern, every user can decode their demanded file. Schemes were proposed that are almost information theoretically optimal and ensure that at most N/M transmissions are needed in the worst case. However, to achieve this, files need to be split into exponentially many packets that increases complexity of encoding, decoding and delay. In recent years, search for schemes that are efficient in terms of file size has gathered considerable interest. We outline a class of coded caching schemes based on Ruzsa-Szemerédi constructions. All existing schemes can be cast in this framework. We demonstrate this by casting a few existing schemes, arrived at using seemingly disparate ideas, in the Ruzsa-Szemerédi framework. We also discuss remaining open problems in tackling this important practical issue.
Geometrical-Based Modeling for Millimeter-Wave MIMO Mobile-to-Mobile Channels

A geometric multiple-input multiple-output (MIMO) channel model is proposed for millimeter-wave (mmWave) mobile-to-mobile (M2M) applications based on the two-ring reference model, where cluster-based nonisotropic scattering at both ends of the radio link is considered. The proposed model employs a few clusters of scatterers located on two rings centered on the transmitter and receiver, and intracluster azimuth spread of scatterers is further characterized according to mmWave channel characteristics. From the model, the time–frequency correlation function, power delay profile (PDP), and the Doppler power spectrum are derived. By adjusting the cluster number, cluster center position, and the degree of intracluster nonisotropic scattering, the model is adaptable to a variety of mmWave M2M scenarios. Model validation is further conducted by comparing the simulated PDPs with mmWave outdoor measurements. Based on a detailed investigation of channel correlation functions, it is found that a small number of clusters leads to high channel correlation, and the degree of intracluster nonisotropic scattering has major impact on correlation only if cluster number is small. In addition, the Doppler power spectrum is similar to the U-shaped spectrum, and several factors (e.g., small cluster number, high intracluster azimuth spread, and large antenna spacing) introduce significant fluctuations in the Doppler power spectrum. Finally, the model is implemented with directional antennas for safety related M2M scenarios, which leads to high channel correlation compared with using omnidirectional antennas. These observations and conclusions can be considered as a guidance for the mmWave M2M MIMO system design.
Crepant resolutions of Weierstrass models with torsion

We perform the first computation of the Euler characteristics of all crepant resolutions of Weierstrass models for elliptic n-folds with torsion Z/2Z, Z/3Z, and Z/2Z⊕Z/2Z, in terms of n and the base, using a strategy valid for any singular fibration of projective hypersurfaces that admits a nice crepant resolution. We resolve our Weierstrass models while preserving the base (in particular, non-normal crossings in the discriminant locus), and study collisions to retrieve singular, possibly non-Kodaira fibers. Significant exposition is included (at the level of an intermediate course in algebraic geometry) with a focus on computation, spanning from the classic theory of elliptic surfaces up to recent analytic pushforward formulas in intersection theory. Applications to string theory (via gauge groups in F-theory) and Calabi-Yau geometry (via Hodge numbers in the threefold case) are also discussed.
25‐Hydroxyvitamin D Threshold for the Effects of Vitamin D Supplements on Bone Density: Secondary Analysis of a Randomized Controlled Trial

Most trials of vitamin D supplementation have shown no benefits on bone mineral density (BMD), although severe vitamin D deficiency causes osteomalacia, which is associated with profound BMD deficits. Recently, the ViDA‐BMD study from New Zealand demonstrated a threshold of baseline 25‐hydroxyvitamin D (25OHD; 30 nmol/L) below which vitamin D supplementation did benefit BMD. We have now reexamined data from a similar trial in Aberdeen to determine whether a baseline 25OHD threshold of 30 nmol/L is also observed in that database. The Aberdeen study recruited 305 postmenopausal women in late winter and randomized them to receive placebo, vitamin D 400 IU/d, or vitamin D 1000 IU/d over 1 year. As previously reported, BMD loss at the hip was reduced by vitamin D 1000 IU/d only, and there was no significant treatment effect of either dose at the lumbar spine. In the present analysis, when the trial participants were grouped according to whether their baseline 25OHD was ≤30 nmol/L or above this threshold, significant treatment effects were apparent at both the spine and hip in those with baseline 25OHD ≤30 nmol/L, but no significant effects were apparent in those with baseline 25OHD above this level. There was evidence of a similar threshold for effects on parathyroid hormone, but no groups showed changes in bone turnover markers during the study. It is concluded that vitamin D supplements only increase bone density in adults with nadir 25OHD ≤30 nmol/L. This moves us further toward a trial‐based definition of vitamin D deficiency in adults with adequate calcium intakes and suggests that supplement use should be targeted accordingly. Future trials of vitamin D supplementation should focus on individuals with 25OHD concentrations in this range. © 2018 American Society for Bone and Mineral Research.
Corynebacterium diphtheriae: a PTS view to the genome.

We have surveyed the publicly available genome sequence of Corynebacterium diphtheriae (www.sanger.ac.uk) to identify components of the phosphotransferase system (PTS), which plays a central role in carbon metabolism in many bacteria. Three gene loci were found to contain putative pts genes. These comprise: (i) the genes of the general phosphotransferases enzyme I (ptsI) and HPr (ptsH), a fructose-specific enzyme IIABC permease (fruA), and a fructose 1-phosphate kinase (fruK); (ii) a gene that encodes an enzyme IIAB of the fructose/mannitol family, and a novel HPr-like gene, ptsF, that encodes an HPr domain fused to a domain of unknown function; (iii) and a gene for a glucose-specific enzyme IIBCA (ptsG). A search for genes that may be putative PTS-targets or that may operate in general carbon regulation revealed a possible regulatory gene encoding an antiterminator protein downstream from ptsG. Furthermore, genes were detected encoding glycerol kinase, glucose kinase, and a homologue of the global activator of carbon catabolite repression in Escherichia coli, CAP. The possible significance of these observations in carbon metabolism and the novel features of the detected genes are discussed.
The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe

The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris , consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus , L. kosswigi , L. lantzi , L. schmidtleri and a more restricted L. vulgaris . The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.
Usefulness Of Tei Index In Patients With Heart Failure

Background: Tei index is a Doppler derived myocardial performance index. It is a measure of combined systolic and diastolic myocardial performance of both the left and right ventricles. Incidence of heart failure (HF) is increasing globally. Systolic and diastolic dysfunctions frequently co-exist in HF hence a combined measure of left ventricular chamber performance may be more reflective of overall cardiac dysfunction than systolic or diastolic measures alone.Method: Ninety newly presenting patients with HF in New York Heart Association (NYHA) Class II to IV and ninety age and sex matched normal controls were recruited consecutively in the Cardiac Care Unit, Obafemi Awolowo University Teaching Hospitals Complex (OAUTHC), Ile-Ife, Nigeria. Using conventional 2–D and Doppler echo techniques, parameters assessed were; isovolumic relaxation time (IVRT), isovolumic contraction time (IVCT), ejection time (ET) and ejection fraction (EF). Tei index was obtained with the formula IVCT + IVRT/ET. Result: Mean Tei index (TI) of patients was significantly higher than that of controls (0.861 ± 0.501 vs. 0.36 ± 0.07; p = 0.0001). TI ranged 0.33 to 1.938 in patients and 0.29 to 0.43 in controls. There was an inverse relationship between TI and EF. As TI increased, EF decreased (r = −0.322, p = 0.002). There were significant differences between mean TI of patients in each of NYHA class II, III and IV and mean TI of controls (p = <0.0001 for all three comparisons). Comparison of mean Tei indices of patients in NYHA Classes II, III and IV by means of ANOVA showed statistically significant difference between all three groups (p=0.000). Conclusion: Tei index is a simple reproducible myocardial performance index which can reasonably separate normal controls (low and narrow TI) from patients with HF (high and wide TI). It shows significant difference with HF severity and an inverse relationship with EF.
Management Strategies for Adverse Events Associated With EGFR TKIs in Non–Small Cell Lung Cancer

New advances in the treatment of non–small cell lung cancer (NSCLC) have afforded patients longer progression-free survival times, but these therapies are also associated with specific side effects that may not be seen with chemotherapy or radiotherapy. One class of agents includes the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), which have been shown to be efficacious in patients whose tumors harbor EGFR-activating mutations. Certain adverse effects, particularly rash and diarrhea, as well as mucositis/stomatitis, paronychia, ocular disorders, and interstitial lung disease, are seen with this class as a function of their mechanism of action. This review presents the suggested pathogenesis of these toxicities as well as specific management strategies to assist advanced practitioners in helping patients receive the full benefit of treatment with EGFR TKIs.
Impact of comprehensive cardiovascular risk reduction programme on risk factor clustering associated with elevated blood pressure in an Indian industrial population

Background & objectives: Cardiovascular risk factors clustering associated with blood pressure (BP) has not been studied in the Indian population. This study was aimed at assessing the clustering effect of cardiovascular risk factors with suboptimal BP in Indian population as also the impact of risk reduction interventions. Methods: Data from 10543 individuals collected in a nation-wide surveillance programme in India were analysed. The burden of risk factors clustering with blood pressure and coronary heart disease (CHD) was assessed. The impact of a risk reduction programmme on risk factors clustering was prospectively studied in a sub-group. Results: Mean age of participants was 40.9 ± 11.0 yr. A significant linear increase in number of risk factors with increasing blood pressure, irrespective of stratifying using different risk factor thresholds was observed. While hypertension occurred in isolation in 2.6 per cent of the total population, co-existence of hypertension and >3 risk factors was observed in 12.3 per cent population. A comprehensive risk reduction programme significantly reduced the mean number of additional risk factors in the intervention population across the blood pressure groups, while it continued to be high in the control arm without interventions (both within group and between group P<0.001). The proportion of ‘low risk phenotype’ increased from 13.4 to 19.9 per cent in the intervention population and it was decreased from 27.8 to 10.6 per cent in the control population (P<0.001). The proportion of individuals with hypertension and three more risk factors decreased from 10.6 to 4.7 per cent in the intervention arm while it was increased from 13.3 to 17.8 per cent in the control arm (P<0.001). Interpretation & conclusions: Our findings showed that cardiovascular risk factors clustered together with elevated blood pressure and a risk reduction programme significantly reduced the risk factors burden.