Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequencing Metrics of Human Genomes Extracted from Single Cancer Cells Individually Isolated in a Valveless Microfluidic Device

Sequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cell (LS174T, LS180 and RKO) lines and fresh colorectal cancers are individually trapped, their genomes extracted and prepared for sequencing, using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources. In addition, most of the reads are correctly paired, with a low percentage of singletons (0.17 ± 0.06 %) and we obtain genome coverages approaching 90%. To achieve this high quality, our device design and process shows that amplification can be conducted in microliter volumes as long as extraction is in sub-nanoliter volumes. Our data also demonstrates that high quality single cell sequencing can be achieved using a relatively simple, inexpensive and scalable device.
Linear system identification of 1-dof vibratory system based on the Maximum Likelihood Estimation using the analytical solution of Fokker-Planck equation

This paper discusses a new identification method of linear single-degree-of-freedom system using Gaussian random vibration response. The propose method is based on the method of Maximum Likelihood Estimation (MLE). The likelihood function of proposed method is composed from the analytical solution of Fokker-Planck equation. The estimation formulas of unknown parameter are obtained by maximization of the original likelihood function. The obtained estimators correspond with population variance estimation of multivariate Gaussian model. Furthermore, the numerical identifications are conducted using the random vibration response by calculation result of 4th RungeKutta method. In the result, the estimation performance of the propose method is confirmed in terms of dependency of sample number and dependency of damping coefficient. Especially, the proposed method is implied the application to identification problem of large damping system. Quantification of large damping characteristic is important problem, because it is very difficult problem in conventional identification method. Moreover, the benchmark tests are conducted with Half-Power Method (HPM) based on the spectral analysis and Auto-Regressive Method (ARM) based on the time series analysis, respectively. The results of benchmark are shown in the accuracy of propose method is higher than its of HPM and ARM, respectively. Finally, the expansion to recursive estimation algorithm is conducted using MLE estimator of recurrence form. In addition, operation of the recursive algorithm is confirmed.
Structural rearrangement of TFIIS- and TFIIE/TFIIF-like subunits in RNA polymerase I transcription complexes

RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-EM structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-electron microscopy structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the TFIIE/TFIIF-like A49-A34.5 heterodimer and the TFIIS-like subunit A12.2 present in Pol I. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our work suggests a regulatory mechanism of Pol I transcription where the association of the A49-A34.5 heterodimer to Pol I is regulated by subunit A12.2, thereby explaining in vitro biochemical and kinetic data.
Copy number variant identification from Holstein dairy cattle whole-genome sequence data using a multi-sample approach

Copy number variant (CNV) identification from next generation re-sequencing (NGS) data is still in its infancy. In this study, we describe a set of CNVs identified from NGS data of 80 Holstein bulls using a multi-sample approach. In total, 847 CNV regions covering 7.36% of the bovine genome were detected. Most of the detected variants were copy number gains in comparison to the bovine reference genome UMD3.1. Some variants were found to be copy number losses or copy number gains in different samples. The CNVs were not equally distributed over the genome, which could possibly indicate CNV hotspots. Further analysis of the data will allow the creation of a validated CNV dataset that can be analyzed for associations between genomic variations and phenotypes of interest.
Disturbance of Non-Breeding Waders by Pedestrians and Boats in a Mediterranean Lagoon

Summary. Flight initiation distances (FIDs) were measured for nine wader species at the Venice lagoon (Italy), one of the most important sites for waterbirds around the Mediterranean. The response (277 instances) to boat and pedestrian disturbances caused outside the breeding season was observed. FID was positively and significantly correlated with the mean body size of the species. The correlation between FID and flock size was also positive and significant, irrespective of the type of disturbance. FID values ranged from 27.9 + 15.6 m (mean + SD, N = 32) in Common Snipe to 140.4 + 48.1 m (N = 30) in Eurasian Curlew, pooling data for both disturbance types. The same ranking was observed if pedestrian and boat disturbances were considered separately; differences were species-specific. For six species, the data allowed comparisons to be made between boat- and pedestrian-evoked FID; the observed differences were not significant. Thus, boat disturbances during the non-breeding season did not evoke a stronger response among waders, in terms of FID, compared to pedestrians. According to these results, set-back distances, expressed as mean FID + 2 SD, are suggested to reduce the effects of man-made disturbances to waterbirds at a local scale. These distances range from 59-74 m for the most confiding species (Common Snipe, Kentish Plover and Ruddy Turnstone) to 121–267 m for the most wary (Eurasian Oystercatcher, Grey Plover and Eurasian Curlew). To protect the multi-specific and often large winter roosts from disturbance caused by pedestrians or boats, a higher set-back distance, 270 m, is suggested. —Scarton, F. (2018). Disturbance of non-breeding waders by pedestrians and boats in a Mediterranean lagoon. Ardeola, 65: 209–220.
A resource competition model for seed mass variation in grasslands

The large variation in seed mass among species inspired a vast array of theoretical and empirical research that attempt to explain this variation. So far, seed mass variation was explained by two classes of models, the first focused on coexistence of species varying in seed mass within communities, while the second focused on variation in seed mass between communities along environmental gradients. Here, we develop a mechanistic resource competition model capable of simultaneously explaining variation in seed mass within and between communities. We use the model to investigate how differences in seed mass among species interact with light asymmetry and growth allometry to determine the relative fitness (relative reproductive success) of large- vs. small-seeded species within communities, and how such interactions are translated into patterns of seed mass variation along gradients of resource availability and disturbance. Under the framework of the model, growth allometry increases the relative fitness of small seeded species while light asymmetry increases the relative fitness of large seeded species. Increasing resource availability increases the fitness of large-seeded species by increasing the relative importance of light competition. In contrast, disturbance increases the fitness of small seeded species due to a combination of different mechanisms operating simultaneously. Resource availability and disturbance also influence the magnitude of within-community differences in fitness (and therefore, the potential for species coexistence). The observed patterns are consistent with empirically observed responses of species diversity to resource availability, disturbance and their interaction (e.g. the unimodal diversity response to resource availability and the 'grazing reversal hypothesis').
Mathematical modelling of immune response to the Lyme disease

We seek to understand the bull’s-eye rash pattern in the skin during the early stage of Lyme disease. By considering a PDE model incorporating the classical Keller-Segel chemotaxis term, we create a model not too complicated but is able to produce different spatial patterns. We investigate the effect of different parameters on the skin rash pattern. We present numerical simulation results that illustrate the impact of different parameters. We find that the engulfment rate of macrophages and the infection rate of the macrophage cells are the two key factors that produces different rash patterns. The implication of our result on the disease treatment is also discussed. Mathematics Subject Classification: 35B36
DETERMINE SIMULATION MODEL OF ELECTRONIC CONTROL SYSTEM FOR DIRECT INJECTION COMPRESSION COMBUSTION ENGINE

The aim of this research is to determine a simulation of an electric control unit (ECU) for direct injection compression ignition combustion engine, in order to improve an engine performance and reduced fuel consumption. The simulation comprises thermodynamic model for determining engine parameters according to Spray Penetration Mixing Length, and imposes in Matlab and Simulink. This model allows closed loop control interferences with Arduino MEGA-2560 to manage amount of injected fuel and start of injection that, could be lead to obtain the optimum thermodynamic energy. The results of thermodynamic model show that, the engine parameters can be related linearly, and matching the other published researches on the same conditions and specifications. The results of (ECU) show synchronization between desired and output signals and appear more accuracy when compared with other methods.
Passenger Intentions towards Halal Food in Low Cost Carriers: Key Influencing Factors

(CC BY-NC 4.0) This article is licensed to you under a Creative Commons Attribution-NonCommercial 4.0 International License. When you copy and redistribute this paper in full or in part, you need to provide proper attribution to it to ensure that others can later locate this work (and to ensure that others do not accuse you of plagiarism). You may (and we encourage you to) adapt, remix, transform, and build upon the material for any non-commercial purposes. This license does not permit you to use this material for commercial purposes. PASSENGER INTENTIONS TOWARDS HALAL FOOD IN LOW COST CARRIERS: KEY INFLUENCING FACTORS
The padloper’s tortuous path (Chelonia: Testudinidae): Two genera, not one

ABSTRACT Since 1957, all padlopers were considered Homopus, which was an anomaly, because only two species have four claws on the front and hind limbs. The revival of the genus Chersobius for the five-toed species (signatus, boulengeri and solus) now limits Homopus to the four-toed species (areolatus and femoralis). Molecular data indicate that Homopus is paraphyletic with two well-supported clades: the four-toed Homopus in one clade and the five-toed Chersobius together with Chersina angulata in a second clade. There are numerous distinct morphological and ecological differences between the genera. All Chersobius species have a single, large inguinal scute, whereas the number is variable in Homopus. The midline pectoral scute of Chersobius is consistently longer, and the nuchal scute shorter, than in Homopus. The fourth to fifth vertebral suture is narrow in Homopus and broad in Chersobius. Forelimb scales also differ with 3–4 large rows and 5–6 smaller rows, respectively, in Homopus and Chersobius. Chersobius males have a plastral concavity and Homopus males not. Two Chersobius species (C. signatus and C. boulengeri) are distinguishable from Homopus by having 12 or more marginal scutes, whereas Homopus species have 11 or fewer. The glans penes are respectively V-shaped and heart-shaped in Homopus and Chersobius. Ecological differences include that Chersobius species are rupicolous and inhabit arid regions, whereas Homopus species inhabit more mesic habitats. Homopus females produce multi-egg clutches and tend to be bigger compared to single-egg clutching Chersobius females. Females of all species are larger than conspecific males, and all males have larger shell openings than females have. ZooBank—urn:lsid:zoobank.org:pub: 18229454-6662-46F3-8B15-836BF2AC38EB
Evidence from asymmetric adjustment and causality between consumer and producer prices in the four selected European economies

This paper examines Granger-causality between consumer price index (CPI) and producer price index (PPI) in Germany, United Kingdom, France and Italy, based on a Momentum Threshold Vector Error Correction Model (M-TVECM) with asymmetric adjustment process. Our study introduces theoretical ground of price rigidity to the CPI-PPI relation and allows for threshold cointegration. The findings indicate CPI and PPI is cointegrated in an asymmetric manner in all countries. The M-TVECM suggests, for Germany and Italy, producer prices are relatively sticky downward in response to a decrease in consumer prices than increase. Consumer prices are sticky in response to either an increase or a decrease in producer prices in all countries except for United Kingdom that shows upward rigidity of consumer prices. For France and United Kingdom, we find evidence of sticky downward producer prices in response to a decrease in consumer prices. Causality test indicates 'production chain view' is relevant only in the short run, and 'demand-pull view' is relatively relevant in the long run for the four countries. JEL classification codes: C12; C22; E31, O52
A phylogeny and genus-level revision of the African file snakes Gonionotophis Boulenger (Squamata: Lamprophiidae)

ABSTRACT The sub-Saharan African file snake genus Gonionotophis is currently comprised of 15 species. However, the concept of this genus has been confounded by morphological and genetic differences between the constituent taxa. Due to the dearth of DNA samples, a taxonomic assessment has been impractical to date. We therefore sequenced two mitochondrial and one nuclear marker (16S, cyt b, and c-mos) from 45 samples representing ten species of Gonionotophis to construct a molecular phylogeny using Bayesian and likelihood approaches. Four divergent and well-supported clades were recovered, including: (1) grantii + brussauxi; (2) poensis + stenophthalmus; (3) nyassae; and (4) capensis, chanleri, crossi, guirali and savorgnani. Based on these results and morphological data, the genus Gonionotophis is restricted to the first clade, Mehelya is resurrected for the species in the second clade, and new genera are described for the remaining two clades. ZooBank—urn:lsid:zoobank.org:pub:A82CFAD6-E2E0-439E-90BB-9224E225426B
Bed Measuring Estimate Blood Volume and Cardiac Output With TFT Display Equipped With Data Storage (SpO2 and BPM)

Article Info Abstract Article History: Received June 9, 2019 Revised July 20, 2020 Accepted Jan 11, 2020 BED for measuring EBV and CO are the tools used to monitor the condition of preoperative patients. The Estimation Blood Volume (EBV) is a calculation to determine the approximate volume of blood in the human body and CO is the amount of blood volume pumped by the heart per minute the calculation of EBV used uses weight, height and gender. CO calculations utilize BPM multiplied by standard Stroke Volume. In this section the author discusses oxygen saturation in the blood using different wavelengths of red LED light and infrared captured by the photodiode. The author also discusses BPM to monitor minute heart rates. The design of this measuring instrument uses MAX30100 sensor, Arduino Mega , Arduino Nano and TFT LCD. Data from the MAX30100 sensor enters the Arduino minimum system, then is processed to produce a percentage of SpO2 values which are then displayed on the TFT LCD. In the module, the data displayed can be stored and displayed again so that patient data can be traced. Testing is done by comparing the module with a standard measuring instrument that produces the biggest error of 2.80% on BPM and 0.95% on SpO2.
Direct evidence for a membrane deforming motif in endophilin

Direct Evidence for a Membrane Deforming M otif in Endophilin: Implications Beyond Synaptic Vesicle Recycling Khashayar Farsad 2003 Effective neurotransmission is dependent on fast, reproduceable synaptic vesicle recycling. The synaptic vesicle recycling process is a complex event involving both protein-protein, as well as protein-lipid interactions. A central part o f the retrieval process o f synaptic vesicles lies in the ability o f soluble proteins to deform the plasma membrane into a nascent bud which will eventually reform a fully competent synaptic vesicle upon fission. This process involves clathrin-coat proteins, which form a protein scaffold around the vesicle bud, as well as proteins which have more recently been thought to be involved in generating the high curvature membranes present at the tubular neck o f the nascent vesicle bud. Endophilin 1, a protein highly enriched in the pre-synaptic neuronal subcompartment has been implicated in many stages o f synaptic vesicle retrieval. The following work represents evidence o f a direct role for endophilin in tubular membrane R eproduced with perm ission of the copyright owner. Further reproduction prohibited without perm ission. deformation, which may play an important part in the regeneration o f synaptic vesicles. This behavior o f endophilin complements that o f one o f its major pre-synaptic binding partners, dynamin, a large GTPase strongly implicated in the fission process o f endocytosis. Endophilin forms a coordinated complex with dynamin along membrane tubules, and stabilizes these membrane tubules against the biomechanical changes imparted by dynamin to the membrane in a GTP-dependent manner. The membrane deforming motif in endophilin comprises a putative amphipathic helical region. This motif is conserved in amphiphysin, another major pre-synaptic dynamin binding partner implicated in synaptic vesicle recycling, and in another endophilin-related protein localized to the Golgi complex. Membrane deforming amphipathic helices have since been found in other proteins localized to additional cellular subcompartments, implicating this type o f membrane interaction in diverse functions within the cell. R eproduced with perm ission of the copyright owner. Further reproduction prohibited without perm ission.
Peripheral blood DNA methylation and autism spectrum disorder

Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size, and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12×10−7. Seven CpGs showed differences at p < 1×10−5 and 48 at 1×10−4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpGs hits, which was consistent across EWAS and meQTL discovery p-value thresholds. Conclusions We report the largest case-control EWAS study of ASD to date. No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the 7 sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD.
Investigation of gene expression diversity in Hypericum spp. before and after flowering under different nitrogen fertilization levels

The traditional medicinal herb, Hypericum perforatum L. has been popular for its pharmaceutical and coloring wealth since the ancient era. A secondary metabolite from the group of naphthodianthrones in Hypericum spp . named hypericin is responsible for the antidepression, anticancer, and antiviral characteristics of this herb. It has been found that several genes are involved in the biosynthesis pathway of hypericin. The hyp-1 gene is participating in this biosynthesis path through the conversion of emodin to hypericin. The naphthodianthrones (hypericin and pseudohypericin) in Hypericum are synthesized through the polyketide pathway. In the plants, the enzyme complexes named polyketide synthase (PKS) catalyzes the reactions of polyketide pathways. The genes HpPKS1 and HpPKS2 are encoding PKS enzyme complexes. In this research, the relative expression of hyp-1 , HpPKS1, and HpPKS2 genes was compared in root and leaves of Hypericum perforatum and H. androsaemum L. , before and after flowering under urea fertilization at 24, 48 and 72 hours after irrigation. The highest expression level of all three genes was observed after flowering in the samples of H. perforatum that were fertilized 72 hours after irrigation by 1 g l -1 urea ( hyp-1 in roots; HpPKS1 and HpPKS2 in leaves). The relative expression of hyp-1 in the root was greater than in the leaves, but HpPKS1 and HpPKS2 expression in leaves was higher than in root. The relative expression of all three genes in H. perforatum was higher than in H. androsaemum . By increasing the interval between urea fertilization and irrigation, the relative expression of genes had an increasing trend, also by increasing the amount of urea fertilizer, relative gene expression was increased.