Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine learning in SQL by translation to TensorFlow

We present sql4ml, a framework for expressing machine learning (ML) algorithms in a relational database management system (RDBMS). The user writes the objective function of an ML model as a SQL query, then sql4ml translates the query into an equivalent TensorFlow (TF) graph, which can be automatically differentiated and optimized to learn the model weights. Sql4ml makes the database a unified programming environment for feature engineering, learning/inference, and evaluating models. The proposed approach is more expressive than using ready-made ML algorithms, but abstracts away the details of the training process. We present the architecture of sql4ml and describe the method for translating an objective function in SQL to a TensorFlow representation. We show how recent ideas from Factorized ML [7] can be leveraged to efficiently move data between a database and an ML framework. Finally, we present experimental results regarding both the proposed translation and the optimization techniques for data transfer. Our results show that translation time is negligible compared to time for data processing, and that the optimization techniques achieve up to 50% improvement in the export runtime and up to 85% decrease in the size of the exported data.
Understanding and utilizing hardware transactional memory capacity

Hardware transactional memory (HTM) provides a simpler programming model than lock-based synchronization. However, HTM has limits that mean that transactions may suffer costly capacity aborts. Understanding HTM capacity is therefore critical. Unfortunately, crucial implementation details are undisclosed. In practice HTM capacity can manifest in puzzling ways. It is therefore unsurprising that the literature reports results that appear to be highly contradictory, reporting capacities that vary by nearly three orders of magnitude. We conduct an in-depth study into the causes of HTM capacity aborts using four generations of Intel's Transactional Synchronization Extensions (TSX). We identify the apparent contradictions among prior work, and shed new light on the causes of HTM capacity aborts. In doing so, we reconcile the apparent contradictions. We focus on how replacement policies and the status of the cache can affect HTM capacity. One source of surprising behavior appears to be the cache replacement policies used by the processors we evaluated. Both invalidating the cache and warming it up with the transactional working set can significantly improve the read capacity of transactions across the microarchitectures we tested. A further complication is that a physically indexed LLC will typically yield only half the total LLC capacity. We found that methodological differences in the prior work led to different warmup states and thus to their apparently contradictory findings. This paper deepens our understanding of how the underlying implementation and cache behavior affect the apparent capacity of HTM. Our insights on how to increase the read capacity of transactions can be used to optimize HTM applications, particularly those with large read-mostly transactions, which are common in the context of optimistic parallelization.
RP-HPLC Determination of Rutin and Isoquercitrin in Mulberry Leaves(Morus alba L.)

Objective:To determine the contents of rutin,and isoquercetin in mulberry leaves by HPLC. Methods:An external standard method was adopped by HPLC with Agilent TC-C18 column(250mm×4.6mm,5μm) as fixed phase,and CH3CN-CH3OH-H2O-H3PO4(100:10:340:0.3,V/V) as mobile phase. The detection wavelength was 365 nm and the flow rate was 1.0ml/ min. Results:Rutin and isoquercetin were well separated by this method. Linearities of rutin and isoquercetin were good in concentration ranges of 7.5～150μg/ml(R2=0.9995) and 7.1～142μg/ml(R2=0.9998) respectively. The average spiked recoveries are 98.79%(RSD 3.37%) and 99.01%(RSD 2.43%) and RSDs of repeatability experiments are 0.0133% and 0.0214% respectively. Conclusion:The method validation data indicate that the method is reliable and it can be used for quality control of crude drug mulberry leave and its preparation.
Dip coated TiO2 nanostructured thin film: synthesis and application

TiO2 thin film was fabricated by dip coating method using titanium IV chloride as precursor and sodium carboxymethyl cellulose as thickening as well as capping agent. Structural and morphological features of TiO2 thin film were characterized by X-ray diffractometer and field emission scanning electron microscope, respectively. Crystallinity of the film was confirmed with high-intensity peak at (101) plane, and its average crystallite size was found to be 28 nm. The ethanol-sensing properties of TiO2 thin film was studied by the chemiresistive method. Furthermore, various gases were tested in order to verify the selectivity of the sensor. Among the several gases, the fabricated TiO2 sensor showed very high selectivity towards ethanol at room temperature.
Removal of microcystin-LR from water by polymers based on N-vinylformamide structure

The work describes the results of experiments aimed at developing a new method using synthetic polymers to remove microcystins from water. Three hydrophilic polymers were synthesized based on a N -vinylformamide (NVF) structure cross-linked with divinylbenzene (DVB): p(NVF-co-DVB), p(VAm-co-DVB), and, after reaction with glutaraldehyde (GA), p(VAm-co-DVB)GA. The physicochemical characteristics of the resulting polymers were determined by measuring element content, specific surface area, total pore volume and the positive zeta potential of the surface. All the tested polymers showed more than 99.5% adsorption of microcystin-LR (MC-LR) in aqueous solution during 15 min of incubation. Desorption of MC-LR from the complexes formed with polymers depended on the type of polymer and the solvent and ranged from 0 to 22.8%. The yield from application of a field of acoustic waves to methanol solution freed from the MC-LR–p(NVF-co-DVB) complex was 25.1% MC-LR. These results suggest the occurrence of strong bonds in the complex, bonds formed through physical interaction between the negative resultant charge of the MC-LR molecule and the positive charge of the polymer surface. The MC-LR adsorption capacity of the polymer depended on the dose of the toxin: 99.5% at a MC-LR: polymer ratio of 1:1,000 (w/w) and 98.6% at a 1:100 ratio.
Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution

Skeletal myofibers are the main components of skeletal muscle which is the largest tissue in the body. Myofibers are highly adaptive in nature and they can vary in different biological and disease conditions. Therefore, transcriptional and epigenetic studies on myofibers are crucial to discover how chromatin alterations occur in the skeletal muscle under different conditions. However, due to the heterogenous nature of skeletal muscle, studying myofibers in isolation proves to be a challenging task. Single cell sequencing has permitted for the study of the epigenome of isolated myonuclei. While this provides sequencing with high dimensionality, the sequencing depth is lacking, which makes comparisons between different biological conditions difficult. Here we report the first implementation of single myofiber ATAC-Seq, which permits for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological, physical and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers. This technique can lead to wide application in identifying chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.
The contribution of genetic and environmental effects to Bergmann’s rule and Allen’s rule in house mice

Distinguishing between genetic, environmental, and genotype-by-environment effects is central to understanding geographic variation in phenotypic clines. Two of the best-documented phenotypic clines are Bergmann’s rule and Allen’s rule, which describe larger body sizes and shortened extremities in colder climates, respectively. Although numerous studies have found inter- and intraspecific evidence for both ecogeographic patterns, we still have a poor understanding of the extent to which these patterns are driven by genetics, environment, or both. Here, we measured the genetic and environmental contributions to Bergmann’s rule and Allen’s rule across introduced populations of house mice (Mus musculus domesticus) in the Americas. First, we documented clines for body mass, tail length, and ear length in natural populations, and found that these conform to both Bergmann’s rule and Allen’s rule. We then raised descendants of wild-caught mice in the lab and showed that these differences persisted in a common environment and are heritable, indicating that they have a genetic basis. Finally, using a full-sib design, we reared mice under warm and cold conditions. We found very little plasticity associated with body size, suggesting that Bergmann’s rule has been shaped by strong directional selection in house mice. However, extremities showed considerable plasticity, as both tails and ears grew shorter in cold environments. These results indicate that adaptive phenotypic plasticity as well as genetic changes underlie major patterns of clinal variation in house mice and likely facilitated their rapid expansion into new environments across the Americas.
MMMVI: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Wastewater Samples

Motivation SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Variants of Concern (VOCs) and Variants of Interest (VOIs) are lineages that represent a greater risk to public health, and can be differentiated from the wildtype virus based on unique profiles of signature mutations. Metagenomic sequence analysis of wastewater represents an emerging form of surveillance that can capture early signal for these variants in a community prior to detection through public health testing or genomic surveillance activities. However, because multiple viral genomes are likely to be present in a metagenomic sample, additional analytical scrutiny of the sequencing reads beyond variant calling is needed to increase confidence in diagnostic determinations. Results Where multiple signature mutations are present on a given read, they can be used as enhanced biomarkers to confirm the presence of a VOC/VOI in the sample. We have developed MMMVI, a tool to aggregate and report on the likely presence of a VOC/VOI in a set of metagenomic reads based on the detection of reads bearing multiple signature mutations. Availability MMMVI is implemented in Python, and is available under the MIT licence from https://github.com/dorbarker/voc-identify/ Contact dillon.barker@canada.ca
Dynamic autonomic nervous system patterns differentiate human emotions and manifest in resting physiology

Whether activity in the autonomic nervous system differs during distinct emotions remains controversial. We obtained continuous multichannel recordings of autonomic nervous system activity in healthy adults during a video-based emotional reactivity task. Dimensionality reduction revealed five principal components in the autonomic time series data, and these modes of covariation differentiated periods of baseline from those of video-viewing. Unsupervised clustering of the principal component time series data uncovered separable autonomic states that distinguished among the five emotion-inducing trials. These autonomic states were also detected in baseline physiology but were intermittent and of smaller magnitude. Our results suggest the autonomic nervous system assembles dynamic activity patterns during emotions that are similar across people and are present even during undirected moments of rest. One Sentence Summary Dynamic autonomic patterns distinguish among emotions and are evident in resting physiology.
Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

DNA metabarcoding approaches to analyse complex mixtures of pollen has become the standard in pollination biology, especially in the light of recent threats affecting pollination. In spite of the increasing adoption of High Throughput Sequencing (HTS) approaches, these studies generate huge numbers of raw reads, some of which might be associated to false positives or infrequently recorded species with potentially little biological information. If these reads are not discarded (i.e. pruned), they can lead to changes in the ecological findings and lead to biased conclusions. In this study we reviewed 42 papers in the recent pollen DNA metabarcoding literature and focused on the type of pruning applied. We also tested whether the different types of those cut off threshold may leave a mark on the DNA metabarcoding data. To do so, we compared for the first time community composition, species richness and networks of species interactions (i.e. Connectace, Modularity, Connectivity and Shannon entropy) associated with the most relevant ways of treating HTS outputs: no cut (no reads filtering), or cutting levels obtained as proportional 1% of sample total reads, or as fixed amount of 100 reads, or from ROC (Receiver operator characteristic). Results clearly indicated that pruning type shapes species composition and that to apply or not a threshold dramatically impacts ecological indices, potentially increasing the risk of misinterpreting DNA metabarcoding data under an ecological point of view. Given the high methodological heterogeneity from the revised literature, we discuss in what conditions filtering types may be more appropriate, and also recommend to biologically justify the pruning threshold when analysing DNA metabarcoding raw reads, and to develop shared approaches to make future studies more comparable.
Increased Sensitivity of SARS-CoV-2 to Type III Interferon in Human Intestinal Epithelial Cells

SARS-CoV-2 infection is not restricted to the respiratory tract and a large number of COVID-19 patients experience gastrointestinal distress. Interferons are key molecules produced by the cell to combat virus infection. ABSTRACT The coronavirus SARS-CoV-2 caused the COVID-19 global pandemic leading to 5.3 million deaths worldwide as of December 2021. The human intestine was found to be a major viral target which could have a strong impact on virus spread and pathogenesis since it is one of the largest organs. While type I interferons (IFNs) are key cytokines acting against systemic virus spread, in the human intestine type III IFNs play a major role by restricting virus infection and dissemination without disturbing homeostasis. Recent studies showed that both type I and III IFNs can inhibit SARS-CoV-2 infection, but it is not clear whether one IFN controls SARS-CoV-2 infection of the human intestine better or with a faster kinetics. In this study, we could show that type I and III IFNs both possess antiviral activity against SARS-CoV-2 in human intestinal epithelial cells (hIECs); however, type III IFN is more potent. Shorter type III IFN pretreatment times and lower concentrations were required to efficiently reduce virus load compared to type I IFNs. Moreover, type III IFNs significantly inhibited SARS-CoV-2 even 4 h postinfection and induced a long-lasting antiviral effect in hIECs. Importantly, the sensitivity of SARS-CoV-2 to type III IFNs was virus specific since type III IFN did not control VSV infection as efficiently. Together, these results suggest that type III IFNs have a higher potential for IFN-based treatment of SARS-CoV-2 intestinal infection compared to type I IFNs. IMPORTANCE SARS-CoV-2 infection is not restricted to the respiratory tract and a large number of COVID-19 patients experience gastrointestinal distress. Interferons are key molecules produced by the cell to combat virus infection. Here, we evaluated how two types of interferons (type I and III) can combat SARS-CoV-2 infection of human gut cells. We found that type III interferons were crucial to control SARS-CoV-2 infection when added both before and after infection. Importantly, type III interferons were also able to produce a long-lasting effect, as cells were protected from SARS-CoV-2 infection up to 72 h posttreatment. This study suggested an alternative treatment possibility for SARS-CoV-2 infection.
The structures, electronic and magnetic properties of the FeMg n –1O n and Fe2Mg n –2O n (n = 1–8) clusters

ABSTRACT The structures, electronic and magnetic properties of the FeMg n –1O n and Fe2Mg n –2O n (n = 1–8) clusters have been investigated by using first principles. For ground-state Fe2Mg n –2O n clusters, they display a compromise that the Fe atoms prefer to exhibit the least coordination number and approach each other. Fe substitution can improve the structural stability of the Mg n O n clusters. The FeO, FeMg4O5, Fe2Mg2O4, Fe2Mg5O7 clusters show more chemical stability than the neighbors. The Fe–O bonds in the FeMg n –1O n and Fe2Mg n –2O n clusters display covalent bond properties. For FeO, FeMgO2, FeMg2O3, FeMg4O5, Fe2O2, Fe2MgO3 and Fe2Mg3O5 clusters, the Fe atoms maintain higher spin densities while others are (almost) zero.
Fire for Zeus: using Virtual Reality to explore meaning and experience at Mount Kasios

ABSTRACT From the Bronze Age onwards, summits of mountains in the East Mediterranean were sacred; many to the Greek sky-god Zeus – making a symbolic connection between the abstract sky and the physically highest point. In some cases, sacredness extends through to the Christian period, such as at Mount Kasios, which sits on the Syrian-Turkish border, and which is inaccessible for archaeological research. In this paper, we explore interactions with and representations of Mount Kasios by different groups at different times, and how these sources can help reconstruct ancient meanings and experiences of the mountain. Myth, archaeology, and landscape are mobilized to inform the construction and interrogation of two digital models in GIS and Virtual Reality (VR) designed to elicit a feeling of awe. Such ‘virtual phenomenology’ offers a means to explore a contested contemporary landscape, and to engage with ancient experiences and atmospheres of this holy mountain.
Effect of sulfate on crystal phase transition and crystal growth of titanium dioxide in metatitanic acid calcination

ABSTRACT In order to investigate the effect of sulfate in metatitanic acid on crystal transition and crystal growth of TiO2 during the calcination of metatitanic acid from sulfate process, ammonia was used to remove sulfate in metatitanic acid in this study. TG-DTA, XRD and SEM were used to analyse the crystal phase transition and crystal morphologies. Experiments showed that removal of sulfate will be beneficial to crystal transition and growth. In calcination of desulfurized metatitanic acid, both the solid-state crystallization and the phase transition from anatase to rutile have been advanced by 50°C as compared to the control samples without desulfurization treatment. Moreover, the temperature can be reduced by 60°C to achieve the same rutile conversion rate of 97.6%, and the particle size can be reduced by 70 nm. The reduction in calcination temperature greatly alleviates the sintering tendency of TiO2 and aid to produce TiO2 crystals of even size.
Coenzyme Q10 and the exclusive club of diseases that show a limited response to treatment

ABSTRACT Introduction: Coenzyme Q10 (CoQ10) is a ubiquitous organic molecule with a significant role in the mitochondrial electron transport chain (ETC). As a result of its role in such an important biological process, CoQ10 deficiency has been implicated in the pathogenesis of numerous diseases such as Parkinson’s disease (PD) and multiple sclerosis (MS). This has led to multiple attempts to use CoQ10 supplementation as a treatment or pre-treatment with varying degrees of success. Areas covered: The present review will identify evidence of mitochondrial dysfunction in MS, PD and mitochondrial ETC disorders. In addition, the inability of Co10 supplementation to elicit significant clinical outcome in these disorders and possible flaws in these studies will be discussed. The databases utilized for this review were the Web of science and PubMed, with inclusive dates (1957–2021). Expert opinion: A lack of improved neurological outcome in these disorders post treatment with CoQ10 may be attributable to the limited ability of CoQ10 to cross the blood–brain barrier. Thus, CoQ10 alternatives should also be considered. Other factors including time of disease diagnosis, dosage, administration, and duration of CoQ10 therapy may have a significant influence on the efficacy of this treatment.
Distribution of electromagnetic energy density in a dispersive and dissipative metamaterial

The distribution of electromagnetic energy density in a dispersive and dissipative metamaterial consisting of arrays of wires and split-ring resonators is obtained, using a simple approach. We show energy stored in the system can be regarded to consist of energy density of electric and magnetic fields plus energy density terms related to response of the medium. To derive energy density formulas of the medium, we compare equations of motion of polarization and magnetization of the system with corresponding differential equations of appropriate RLC circuits.
Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification

Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.