Miracle-dz/UniFAR-FTUs huggingface dataset:
Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians

Background Age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections. Methodology/Principal Findings By using the Human Intestinal Tract Chip (HITChip) and quantitative PCR of 16S rRNA genes of Bacteria and Archaea, we explored the age-related differences in the gut microbiota composition among young adults, elderly, and centenarians, i.e subjects who reached the extreme limits of the human lifespan, living for over 100 years. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment in facultative anaerobes, notably pathobionts. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammatory status, also known as inflammageing, as determined by a range of peripheral blood inflammatory markers. This may be explained by a remodelling of the centenarians' microbiota, with a marked decrease in Faecalibacterium prauznitzii and relatives, symbiotic species with reported anti-inflammatory properties. As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians. Conclusions/Significance We provide evidence for the fact that the ageing process deeply affects the structure of the human gut microbiota, as well as its homeostasis with the host's immune system. Because of its crucial role in the host physiology and health status, age-related differences in the gut microbiota composition may be related to the progression of diseases and frailty in the elderly population.
Interactive Effect of Smoking and NQO1 Haplotypes on Lung Cancer Risk

The role of genetic polymorphisms of NAD(P)H:quinone oxidoreductase 1 (NQO1), which is known to be related to carcinogen metabolism and oxidative status, was evaluated for lung cancer development. The genotypes of two NQO1 polymorphisms, namely, IVS1-27C>G and Ex6+40C>T, were determined in 616 lung cancer cases and 616 lung cancer-free controls and haplotypes composed of the two polymorphisms were estimated. In the evaluation of the effect of the NQO1 genotypes or diplotypes, we did not find any significant association with lung cancer risk after adjusting for body mass index and smoking status. However, when we evaluated the effect of the NQO1 diplotypes for lung cancer risk in combination with smoking, smokers without the C-T/C-T diplotype showed a significantly increased risk of lung cancer compared with nonsmokers without the C-T/C-T diplotype (adjusted OR, 2.2; 95% CI, 1.67-3.02), and smokers with the C-T/C-T diplotype showed the highest OR of lung cancer (adjusted OR, 2.7; 95% CI, 1.78-4.21). Moreover, a trend test showed an additive interaction between smoking and the NQO1 C-T/C-T diplotype (Ptrend < 0.01). The additive effect of smoking and the NQO1 C-T/C-T diplotype was more apparent in squamous cell carcinoma, although this effect was statistically significant in all lung cancer cell types (all cell types, Ptrend < 0.05). This result suggests that haplotypes of the NQO1 gene play an important role in the development of lung cancer by interaction with smoking. Graphical Abstract
Preface to the special issue on the basic linear algebra subprograms (BLAS)

The simultaneous achievement of both easy portability and high performance is one of the main challenges in the production of mathematical software. One of the most successful and far-reaching efforts in this regard has been the development of the Basic Linear Algebra Subprograms (BLAS). The BLAS provide an application programmer’s interface for fundamental operations of numerical linear algebra. Using the BLAS, programmers can express their algorithms at a higher level of abstraction, making the resulting codes easier to understand and maintain. Because the BLAS specify operations that are found at the core of many scientific applications, library developers are motivated to develop implementations that are highly efficient; indeed, highly optimized versions of the BLAS now exist for nearly every computing system. In this way, the BLAS have provided key infrastructure for both portability and performance in mathematical software. Today, the BLAS form the cornerstone of nearly every large mathematical software library. First introduced in 1979 [Lawson et al. 1979a, 1979b], the BLAS effort has not been static. Two subsequent editions of the BLAS, Level 2 (1988) [Dongarra et al. 1988a, 1988b] and Level 3 (1990) [Dongarra et al. 1990a, 1990b], were developed to embrace higher-level operations and capture much higher levels of performance. During this period, many proposals for extensions of the BLAS in a variety of directions were also made. In 1995, the BLAS Technical (BLAST) Forum was established to formally consider further expansion of the BLAS in the light of modern software, language, and hardware developments. The open forum attracted many participants from academia, government, and private industry. Among the topics discussed were overall functionality, language interfaces, sparse matrix operations, distributed-memory dense matrix operations, extended and mixed precision operations, support of interval arithmetic, and extensions to the existing BLAS. In the end, formal specifications for three sets of BLAS were developed: (1) dense and banded, (2) sparse, and (3) extended and mixed precision. The formal specification for the new standard appears in Blackford et al. [2001]. In this issue of the ACM Transactions on Mathematical Software, we have collected together a set of research contributions which provide some of the technical background behind the development of the new BLAS standard.
Discovering Lexical Information by Tagging Arabic Newspaper Text

In this paper we describe a system for building an Arabic lexicon automatically by tagging Arabic newspaper text. In this system we are using several techniques for tagging the words in the text and figuring out their types and their features. The major techniques that we are using are: finding phrases, analyzing the affixes of the words, and analyzing their patterns. Proper nouns are particularly difficult to identify in the Arabic language; we describe techniques for isolating them.
Eustatic sea level record for the Cenomanian (Late Cretaceous) – extension to the Western Interior Basin, USA

A combination of biostratigraphic markers (ammonites, inoceramid bivalves) and carbon isotope excursions is employed to establish a high-resolution correlation between the middle to late Cenomanian successions of the Western Interior Basin (USA) and the Anglo-Paris Basin (southern UK). Sequences identified from sedimentologic criteria in the Pueblo succession and elsewhere in the Western Interior Basin are shown to coincide precisely with globally recognized sea-level events and were therefore under eustatic control. This evidence refutes arguments that Cenomanian sequences in the Western Interior Basin were formed by local tectonic events. The interaction of longer-term tectonic movements and more rapid eustatic change may have simply enhanced the amount of erosion associated with sequence boundaries. A crossplot of radiometric ages derived from North American bentonites against an orbitally tuned time scale developed in the Anglo-Paris Basin provides support for the argument that the sequences were controlled by the 405-k.y. -long eccentricity cycle.
Verbal augmented feedback in the rehabilitation of lower extremity musculoskeletal dysfunctions: a systematic review

Background Verbal augmented feedback (VAF) is commonly used in physiotherapy rehabilitation of individuals with lower extremity musculoskeletal dysfunction or to induce motor learning for injury prevention. Its effectiveness for acquisition, retention and transfer of learning of new skills in this population is unknown. Objectives First, to investigate the effect of VAF for rehabilitation and prevention of lower extremity musculoskeletal dysfunction. Second, to determine its effect on motor learning and the stages of acquisition, retention and transfer in this population. Design Systematic review designed in accordance with the Centre for Reviews and Dissemination and reported in line with Preferred Reporting Items for Systematic Review and Meta-analysis. Method MEDLINE, Embase, PubMed and five additional databases were searched to identify primary studies with a focus on VAF for prevention and rehabilitation of lower extremity musculoskeletal dysfunction. One reviewer screened the titles and abstracts. Two reviewers retrieved full text articles for final inclusion. The first reviewer extracted data, whereas the second reviewer audited. Two reviewers independently assessed risk of bias and quality of evidence using Cochrane Collaboration’s tool and Grading of Recommendations Assessment, Development and Evaluation, respectively. Results Six studies were included, with a total sample of 304 participants. Participants included patients with lateral ankle sprain (n=76), postoperative ACL reconstruction (n=16) and healthy individuals in injury prevention (n=212). All six studies included acquisition, whereas retention was found in five studies. Only one study examined transfer of the achieved motor learning (n=36). VAF was found to be effective for improving lower extremity biomechanics and postural control with moderate evidence from five studies. Conclusion VAF should be considered in the rehabilitation of lower extremity musculoskeletal dysfunctions. However, it cannot be unequivocally confirmed that VAF is effective in this population, owing to study heterogeneity and a lack of high-quality evidence. Nevertheless, positive effects on lower extremity biomechanics and postural control have been identified. This suggests that further research into this topic is warranted where an investigation of long-term effects of interventions is required. All stages (acquisition, retention and transfer) should be evaluated.
‘Settling back’? A biographical and life-course perspective on Ireland's recent return migration

This paper uses a biographical and life-course perspective to explore some of the key narratives of return among return migrants to Ireland, focusing in particular on the themes of family, child-rearing, relationship breakdown and ‘settling down’. The ways in which return migrants use the concept of life-course transitions in order to make sense of and narrate their migration stories is explored. I argue that their narratives reflect a normative association of life stage with place, and that return migration reflects the ways in which key events in the individual life course transitions and family life cycles of 1980s emigrants have intersected with processes of economic and social transformation in Ireland. This occurs within the context of heteronormative and kinship-based ideals of Irish culture and of powerful myths of return. The data used in the paper is taken from the Narratives of Migration and Return research project, a north-south cross-border project which assembled an oral archive of 92 return migrant life narratives. In the paper, I draw on 33 of the interviews conducted in the south, which focused on the cohort of return migrants who had emigrated in the 1980s.
Performance Evaluation of H.264 Codec

H.264/AVC is the most popular standard of video compression and decompression today, encapsulating all the advantages of MPEG as well as VCEG, both of them having their own independent codecs. The software used for compression and decompression is JM [Joint Video Team (JVT) of ISO/IEC MPEG & ITUT-T VCEG] version 18.2. This paper is a study of H.264 codec. The yuv file is first encoded to h.264 format. Some other output files are also generated, which are useful for overall analysis of the input yuv file or sequence. These files help us to analyze parameters like PSNR, sequence parameter set, picture parameter set, information about different frames as regards slices and macroblocks. In this paper, all the three profiles (baseline, main and extended) are operated for the sequence (foreman_part_qcif.yuv) with one reference frame. A quantization parameter for the I, P and B slices is taken as 30. The graph of bitrate vs. PSNR (rate distortion curves) in all the three profiles show a striking similarity as can be seen in figures shown below. Keywords-H.264, PSNR, compression, decompression, profiles, Performance et. al.
Interplanetary magnetic field control of the ionospheric field‐aligned current and convection distributions

Patterns of the high‐latitude ionospheric convection and field‐aligned current (FAC) are a manifestation of the solar wind‐magnetosphere‐ionosphere coupling. By observing them we can acquire information on magnetopause reconnection, a process through which solar wind energy enters the magnetosphere. We use over 10 years of magnetic field and convection data from the CHAMP satellite and Super Dual Auroral Radar Network radars, respectively, to display combined distributions of the FACs and convection for different interplanetary magnetic field (IMF) orientations and amplitudes. During southward IMF, convection follows the established two‐cell pattern with associated Region 1 and Region 2 FACs, indicating subsolar reconnection. During northward IMF, superposed on a weak two‐cell pattern there is a reversed two‐cell pattern with associated Region 0 and Region 1 FACs on the dayside, indicating lobe reconnection. For dominant IMF Bx, the sign of Bz determines whether lobe or subsolar reconnection signatures will be observed, but Bx will weaken the signatures compared to pure northward or southward IMF. When the IMF rotates from northward to duskward or dawnward, the distinct reversed and forward two‐cell patterns start to merge into a distorted two‐cell pattern. This is in agreement with the IMF By displacing the reconnection location from the open lobe field lines to closed dawn or dusk field lines, even though IMF Bz>0. As the IMF continues to rotate southward, the distorted pattern transforms smoothly to that of the symmetric two‐cell pattern. While the IMF direction determines the configuration of the FACs and convection, the IMF amplitude affects their intensity.
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts

Endosymbionts, which are widely observed in nature, have undergone reductive genome evolution because of their long-term intracellular lifestyle. Here we compared the complete genome sequences of two different endosymbionts, Buchnera and a protist mitochondrion, with their close relatives to study the evolutionary rates of functional genes in endosymbionts. The results indicate that the rate of amino acid substitution is two times higher in symbionts than in their relatives. This rate increase was observed uniformly among different functional classes of genes, although strong purifying selection may have counterbalanced the rate increase in a few cases. Our data suggest that, contrary to current views, neither the Muller's ratchet effect nor the slightly deleterious mutation theory sufficiently accounts for the elevated evolutionary rate. Rather, the elevated evolutionary rate appears to be mainly due to enhanced mutation rate, although the possibility of relaxation of purifying selection cannot be ruled out.
The 11-Yr Solar Cycle in ERA-40 Data: An Update to 2008

Abstract Multiple linear regression is used to diagnose the signal of the 11-yr solar cycle in zonal-mean zonal wind and temperature in the 40-yr ECMWF Re-Analysis (ERA-40) dataset. The results of previous studies are extended to 2008 using data from ECMWF operational analyses. This analysis confirms that the solar signal found in previous studies is distinct from that of volcanic aerosol forcing resulting from the eruptions of El Chichon and Mount Pinatubo, but it highlights the potential for confusion of the solar signal and lower-stratospheric temperature trends. A correction to an error that is present in previous results of Crooks and Gray, stemming from the use of a single daily analysis field rather than monthly averaged data, is also presented.
Fixed-Size Least Squares Support Vector Machines: Scala Implementation for Large Scale Classification

We propose FS-Scala, a flexible and modular Scala based implementation of the Fixed Size Least Squares Support Vector Machine (FS-LSSVM) for large data sets. The framework consists of a set of modules for (gradient and gradient free) optimization, model representation, kernel functions and evaluation of FS-LSSVM models. A kernel based Fixed-Size Least Squares Support Vector Machine (FS-LSSVM) model is implemented in the proposed framework, while heavily leveraging the parallel computing capabilities of Apache Spark. Global optimization routines like Coupled Simulated Annealing (CSA) and Grid Search are implemented and used to tune the hyper-parameters of the FS-LSSVM model. Finally, we carry out experiments on benchmark data sets and evaluate the performance of various kernel based FS-LSSVM models.
Genome Studies on Nematophagous and Entomogenous Fungi in China

The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper.
Cooperative control in HNMSim — A 3D hybrid networked MAS simulator

A multi-purpose 3D simulator named HNMSim (hybrid networked multi-agent system (MAS) simulator) with application in cooperative control is presented in this paper. Based on USARSim (Unified system for automation and robot simulation) [37], Unreal Engine [33], LabView [17], Matlab [20] and OMNet++ [22], this simulator creates a high-fidelity simulation environment for networked MAS. To provide assistant in research and education, we present three interfaces based on LabView, Matlab and OMNet++, respectively. The system structure (hardware-in-the-loop simulation) and design methodology are also briefly described. In addition, the network simulation is highlighted. Furthermore, we show its wide applications in networked MAS by demonstrating its usage in distributed formation control, distributed coverage control and search problem using multiple UAVs/UGVs.
Duration mismatch compensation for i-vector based speaker recognition systems

Speaker recognition systems trained on long duration utterances are known to perform significantly worse when short test segments are encountered. To address this mismatch, we analyze the effect of duration variability on phoneme distributions of speech utterances and i-vector length. We demonstrate that, as utterance duration is decreased, number of detected unique phonemes and i-vector length approaches zero in a logarithmic and non-linear fashion, respectively. Assuming duration variability as an additive noise in the i-vector space, we propose three different strategies for its compensation: i) multi-duration training in Probabilistic Linear Discriminant Analysis (PLDA) model, ii) score calibration using log duration as a Quality Measure Function (QMF), and iii) multi-duration PLDA training with synthesized short duration i-vectors. Experiments are designed based on the 2012 National Institute of Standards and Technology (NIST) Speaker Recognition Evaluation (SRE) protocol with varying test utterance duration. Experimental results demonstrate the effectiveness of the proposed schemes on short duration test conditions, especially with the QMF calibration approach.
Impurity sources Of F−, Cl−, NO3 − and SO4 2− in Greenland and Antarctic precipitation

Five polar impurity sources are proposed: anthropogenic NO3− and SO42− in recent Greenland but not Antarctic snow; marine aerosols, the dominant Cl− source; volcanic eruptions, which produce detectable but variable peaks in SO42−, F−, and/or Cl− concentrations; biogenic sulfurous gases from soil and coastal waters, the dominant source for SO42− in nonvolcanic strata; an unidentified source of background nitrate which is more active in the northern hemisphere and which displays a summer concentration maximum. Solar activity and supernova events do not modulate NO3− concentrations in Greenland snow.
Multi-antenna cell constellations for interference management in dense urban areas

The aim of this paper is to present and propose different multi-antenna cell constellations based on outdoor distributed antenna system implementation. The idea of the outdoor DAS is to reduce interference in dense urban areas in order to achieve very high signal-to-interference-ratios (SIR) which defines the data throughput available to the user. Moreover, the SIR distribution over the network coverage area has to be as constant as possible in order to keep throughput in maximum and constant. Analysis of different multi-antenna constellations are presented and interference behavior is compared to independent small cell i.e. micro/pico/femto cells. The obtained results show superior SIR distribution for multi-antenna layout compared to independent small cells. Strategic antenna placement and configuration of eight antennas per cell result in average SIR of 23 dB over the cell coverage area.