Miracle-dz/UniFAR-FTUs huggingface dataset:
Base Excision Repair in Chromatin

DNA in the eukaryotic nucleus is complexed with histone and non-histone proteins into chromatin. Nucleosomes, the basic repeating unit of chromatin, not only package DNA but are also intimately involved the regulation of gene expression. All DNA transactions including replication, transcription, recombination and repair take place in such a chromatin environment. Access to packaged nucleosomal DNA in vivo is mediated at least in part by protein complexes that modify or remodel chromatin. Buried sequences in nucleosomes can also transiently become accessible to DNA binding proteins during cycles of partial, reversible unwrapping of nucleosomal DNA from the histone octamer. We have investigated the ability of the human, bifunctional DNA glycosylase, endonuclease III (hNTH1), to initiate base excision repair (BER) of discretely positioned oxidative lesions in model nucleosomes. hNTH1 was able to process a thymine glycol (Tg) lesion almost as efficiently as naked DNA, when the minor groove of the lesion faced away from the histone octamer. Lesion processing did not require or result in detectable nucleosome disruption, as assayed in gel mobility-shift experiments. Instead, hNTH1 formed a slower migrating enzyme-nucleosome ternary complex that was found to contain processed DNA. Processing of an inward-facing Tg residue located just 5 bp away from the outward-facing lesion was much reduced and processing of a sterically occluded Tg residue positioned closer to the dyad center of the nucleosome was even more reduced. Notably, processing of both inward-facing lesions was found to increase as a function of enzyme concentration. Restriction enzyme protection studies indicated that access to these inward-facing lesions did not entail nucleosomal translocation or sliding. Collectively, these observations are consistent with a model in which hNTH1 binds to lesions during cycles of reversible, partial unwrapping of nucleosomal DNA from the histone octamer core. To further investigate this partial unwrapping hypothesis, we studied the kinetics of hNTH1 processing of sterically occluded lesions in greater detail. Our results suggest that efficiency of processing of inward-facing lesions is a function of both DNA unwrapping and rewrapping rates, and enzyme affinity for the lesion. In addition, we determined that APE1 which catalyzes the second step in BER, exhibited an increasing capacity to process inward-facing furan residues as its concentration was increased. Thus as with hNTH1, we hypothesize that APE1 can capture occluded furan residues during cycles of partial DNA unwrapping. We propose that cellular regulatory factors benefit from this intrinsic, periodic exposure of nucleosomal DNA exposure in vivo, which may be amplified by the downstream recruitment of remodeling and / or modifying proteins to facilitate DNA transactions in the cell.
Local Gradient Field Feature Contrast Measure for Infrared Small Target Detection

To overcome the drawbacks of conventional methods to detect infrared (IR) small targets, including high false alarm probability and low detection rate, a novel approach to detect IR small targets based on local gradient field feature contrast measure (LGFFCM) is presented in this letter. First, the distinctive characters of the target, background, and clutter in the infrared gradient vector field (IGVF) are investigated. Next, a local contrast measure based on IGVF features was proposed. Then, an adaptive threshold method to obtain coarse detection results is proposed. Finally, a flux across the plane curve in the IGVF, which can eliminate clutter and enhance target, is defined. The experimental results indicate that the proposed approach shows superiority to other advanced approaches and can effectively and stably reduce false alarm probability and enhance detection rate.
Universality, specificity and regulation of S. cerevisiae growth rate response in different carbon s

Many studies have used chemostats and gene expression microarrays to characterize the growth rate response of the buddying yeast (Saccharomyces cerevisiae) growing on glucose carbon source (Hayes et al, 2002; Pir et al, 2006; Regenberg et al, 2006; Castrillo et al, 2007; Brauer et al, 2008). These studies demonstrated a common growth rate response (GRR) in continuous exponentially growing cultures, both aerobic and anaerobic and limited by different natural nutrients as well as by auxotrophic requirements. However, in all studies the carbon source was glucose, which is highly preferred by S. cerevisiae and special in many ways (Zaman et al, 2008). Thus, it is not clear how much of the identified GRR is specific to growth on glucose (Zaman et al, 2009; Futcher, 2006) as a sole carbon source and how much of the GRR is general to growth and independent of the carbon source. In fact, Zaman et al (2009) have suggested that much of the observed common growth rate response can be due to glucose. To explore whether the common growth rate response is still going to be present in cultures grown on non–fermentable carbon source, I grew S. cerevisiae continuous cultures on ethanol carbon source and measured physiological parameters, gene expression, and metabolites. I found that the growth rate response of a large number of genes (about 1500) remains very similar on ethanol carbon source and I call this common growth rate response universal growth rate response. Genes with positive universal growth rate response include ribosomal and translation genes. Genes with negative universal growth rate response include autophagy, vacuolar and stress response genes. Remarkably, all genes having universal growth rate response are expressed periodically in the yeast metabolic cycle (YMC) (Slavov and Botstein, 2011; Slavov et al, 2011). Genes whose expression levels increase with growth rate are expressed in YMC phase with high oxygen consumption while genes whose expression levels decrease with growth rate are expressed in YMC phase with low oxygen consumption. To understand better the relationship between the
A survey of nonlinear robust optimization

Abstract Robust optimization (RO) has attracted much attention from the optimization community over the past decade. RO is dedicated to solving optimization problems subject to uncertainty: design constraints must be satisfied for all the values of the uncertain parameters within a given uncertainty set. Uncertainty sets may be modeled as deterministic sets (boxes, polyhedra, ellipsoids), in which case the RO problem may be reformulated via worst-case analysis, or as families of distributions. The challenge of RO is to reformulate or approximate robust constraints so that the uncertain optimization problem is transformed into a tractable deterministic optimization problem. Most reformulation methods assume linearity of the robust constraints or uncertainty sets of favorable shape, which represents only a fraction of real-world applications. This survey addresses nonlinear RO and includes problem formulations and applications, solution approaches, and available software with code samples.
Reproductive Allocation and Maternal Investment in Intertidal Whelks

Parental investment per offspring is a key life history trait in which offspring size and number co mbinations are balanced in order to maximise fitnes s. When food is scarce and energy for reproduction is reduced , changes in reproductive allocation can be expected. These adjustments may go on to influence the growth and survival of the
The interaction efficiency evaluation between defect and eddy current induced by different exciting coils of planar eddy current probe

This paper presents a quantitative evaluation index efficiency of eddy current and defect interaction to evaluate the eddy current distribution induced by different planar eddy current probe. Efficiency’s definition and its calculation method are presented. Eddy current induced by three different exciting coils interacting with defects having different lengths and different orientation angles is analyzed by the proposed method. Finally, the paper highlights strengths and weaknesses of the studied current probe inducers and an improving method is proposed.
Tannins and Related Compounds. CXIV. Structure of Novel Fermentation Products, Theogallinin, Theaflavonin and Desgalloyl Theaflavonin from Black Tea, and Changes of Tea Leaf Polyphenols during Fermentation

Continuing chemical examination of black tea has led to the isolation of three novel fermentation products, theogallinin (1), theaflavonin (10) and desgalloyl theaflavonin (11). The structure of 1 was established on the basis of physico-chemical evidence to be a condensation product linked through pyrogallol-pyrogallol rings in theogallin (2) and (-)-epigallocatechin 3-O-gallate (3), while 10 and 11 were characterized as B, B'-linked bisflavonoids formed by an oxidative coupling of isomyricitrin (12) and tea catechins [3 and (-)-epigallocatechin (4)]. Furthermore, high performance liquid chromatography analyses of the changes of tea polyphenols during fermentation have revealed that original tea catechins are more rapidly transformed by endogenous phenol oxidase to theasinensins (e.g.6, 8) and oolongtheanin (13) than the formerly known black tea pigments, theafiavins.
Phylogeographic patterns of Buthus scorpions (Scorpiones: Buthidae) in the Maghreb and South‐Western Europe based on CO1 mtDNA sequences

The genus Buthus is a medium diverse scorpion genus, with 35 species distributed from Portugal and Morocco ranging eastward to Yemen in the Arabic Peninsula. The bulk of the genus’ known species diversity occurs in the Western Mediterranean area. A recent molecular study started to elucidate the patterns of diversity of this genus in the Iberian Peninsula and the Maghreb. Since then, the taxonomy of the genus has changed substantially, with several new species having been described, and with the elevation of former subspecies to species-level. In this study, we assessed the patterns of diversity of Buthus scorpions from across the Maghreb region of North Africa using CO1 DNA sequence data. Based on our dataset of 147 sequences, including 67 new sequences, we recovered four wellsupported deep clades within Buthus scorpions from the Maghreb and Southern Europe. This further strengthens the support for cryptic diversity in the Maghreb region. The broader sampling of the Maghreb permitted a better understanding of the phylogeographic structure in this area. Three clades were restricted to Morocco and appear to have originated at the Atlantic Coast of this country, while the fourth was found throughout the region. We propose a model with two colonizing events to explain the distribution patterns across the Strait of Gibraltar, with an initial colonization from North Africa to Iberia followed by a reinvasion of the Rif Mountains region in Morocco.
New binary and ternary LCD codes from matrix-product codes

ABSTRACT Linear complementary dual (LCD) codes are linear codes satisfying . Researchers have proved to construct linear codes over finite fields , q>3, is equivalent to construct LCD codes. This means that the investigation of binary and ternary LCD codes is the only remaining open problem. In this work, we propose new constructions of binary and ternary LCD codes by using matrix-product codes and prove that binary and ternary LCD codes from matrix-product codes are asymptotically good. Then we construct some new and good binary and ternary LCD codes using matrix-product matrices.
Collaborated effort against SARS‐CoV‐2 outbreak in China

Abstract A previously unknown beta coronavirus, SARS‐CoV‐2, was discovered from a cluster of patients with pneumonia of unknown cause in Wuhan since the end of 2019. Ever since the start of COVID‐19, government administrations, academic institutions, and technology enterprises are under unprecedented cooperation in controlling this outbreak from pathogen identification, epidemic situation assessment, to outbreak containment. Timely identification, isolation, and whole‐genome sequencing of SARS‐CoV‐2 have laid the foundation for effective control of this novel infection. With the increasing case numbers worldwide, more real‐time information is emerging, changing our understandings to SARS‐CoV‐2 outbreak, and nonetheless refining the outbreak control responses. The efficient management of COVID‐19 requires global collaboration and an efficient share of information.
The Species of Cladophora from Japan and its Vicinity

Title The Species of Cladophora from Japan and its Vicinity Author(s) Sakai, Yoshio Citation 北海道大學理學部海藻研究所歐文報告 = Scientific papers of the Institute of Algological Research, Faculty of Science, Hokkaido University, 5(1): 1-104 Issue Date 1964-03-13 Doc URL http://hdl.handle. net/2115/48091 Type bulletin (article) Additional Information There are other files related to this item in HUSCAP. Check the above URL. File Information 5(1)_1-104.pdf (本文)
The Sense of Syncretism in Bugis Architecture at the Traditional Houses of Towani To-Lotang Community

: The syncretism of architecture is the process of achieving the balance by each human which includes the integration, intermixture or combination related to religious activities, traditions, cultural practices and adaptations to the environment such as a building that displays a form of syncretism values between architectural concepts that are implemented into buildings on macro and micro scales. This study aims to analyze the concept of the traditional home of To-lotang in the sense of syncretism through symbols and messages. This research is a qualitative research. The data collection method of this study uses purposive sampling with direct observation in-depth interviews, sketches and documentation. The object of this research is Towani To-Lotang traditional house units located in Sidrap district, South Sulawesi. The results shows that the meaning of syncretism in Towani To-Lotang’s house has a unanimous philosophy symbolizing the unity and the messages behind the form and function of a traditional home of Towani To-Lotang symbolize the social solidarity.
The relationship between dyslipidemia and lupus nephritis in systemic lupus erythematosus patients attending a Saudi Rheumatic Center, Tabuk

Background: There is an increasing awareness of the role of dyslipidemia in lupus nephritis patients, no researchers have studied dyslipidemia in systemic lupus erythematosus (SLE) in Tabuk. In this study, we aimed to investigate the association between dyslipidemia and lupus nephritis in Tabuk, Saudi Arabia. Methods: This cross-sectional comparative longitudinal hospital-based study was conducted at a rheumatic clinic in the North West Armed Force Hospital (NWAFH) during the period April 2014–June 2015. Seventy-three patients diagnosed with SLE were invited to participate in the study. All participants were required to sign a written informed consent, following which they were interviewed using a structured questionnaire. Data collected include demographic data, clinical characteristics, fasting lipid profile, renal function tests, urine analysis, antinuclear antibody, anti-double-stranded antibodies, complement levels, serum albumin, anticardiolipin, ant bodies, and antiphospholipid antibodies. Lupus nephritis was ascertained by renal biopsy. The research was approved by the ethical committees of both the University of Tabuk and the NWAFH and data were analyzed using the Statistical Package for Social Sciences (SPSS). Results: Out of 73 patients with SLE, 86.3% were females with a mean age of 34 ± 6.4 years. Lupus nephritis was evident in 26% of the patients, proteinuria in 44.1%, high total cholesterol in 17.8%, high low-density lipoprotein in 15.1%, high triglycerides in 27.3%, and low high-density lipoproteins in 52.1%. Patients with lupus nephritis had high total cholesterol, high LDL, high TG, and low HDL than those without lupus nephritis P-value < 0.05. Conclusion: Dyslipidemia was more common among patients with SLE nephritis, and an aggressive treatment is recommended to reduce this serious complication. The relatively small size of the study group and the fact that the study was conducted at a single tertiary center are the limitations of this study. Keywords: dyslipidemia, lupus nephritis, Saudi Arabia
Direct inversion of circulation from tracer measurements – Part 2: Sensitivity studies and model recovery tests

The direct inversion of the 2D continuity equation allows for the inference of the effective meridional transport of trace gases in the middle stratosphere. This method exploits the information given by both the displacement of patterns in measured trace gas distributions and the approximate balance between sinks and horizontal as well as vertical advection. Model recovery tests show that with the current setup of the algorithm, this method reliably reproduces the circulation patterns in the entire analysis domain from 6 to 66 km altitude. Due to the regularization of the inversion, velocities above about 30 km are more likely underthan overestimated. This is explained by the fact that the measured trace gas distributions at higher altitudes generally contain less information and that the regularization of the inversion pushes results towards 0. Weaker regularization would in some cases allow a more accurate recovery of the velocity fields, but there is a price to pay in that the risk of convergence failure increases. No instance was found where the algorithm generated artificial patterns not present in the reference fields. Most information on effective velocities above 50 km is included in measurements of CH4, CO, H2O, and N2O, while CFC-11, HCFC-22, and CFC-12 constrain the inversion most efficiently in the middle stratosphere. H2O is a particularly important tracer in the upper troposphere or lower stratosphere. SF6 and CCl4 generally contain less information but still contribute to the reduction in the estimated uncertainties. With these tests, the reliability of the method has been established.
A New Type of Fuzzy-Rule-Based System With Chaotic Swarm Intelligence for Multiclassification of Pain Perception From fMRI

Machine learning has been increasingly used in decoding brain states from functional magnetic resonance imaging (fMRI). One important application is to classify the levels of pain perception from patients’ fMRI for clinical pain assessment. However, the huge number of fMRI features and the complex relationships between fMRI and pain levels affect the performance of pain classification models heavily. In this article, we introduce a new fuzzy-rule-based hybrid optimization approach for dimension reduction and multiclassification problems using chaotic map, crow search optimization (CSO), and self-organizing fuzzy logic prototype (SOFLP). The approach is named as CCSO–SOFLP. In the proposed approach, chaotic map-based CSO is employed to find the optimal features from ultra-high-dimensional fMRI, and the fuzzy-rule-based SOFLP is employed for multiclassification of pain levels. In this sense, CSO is provided to avoid being stuck in local minima and to increase the computational performance. On the other hand, multilayer SOFLP classifier can continuously learn from new data and identify prototypes from the observed data and use them to build fuzzy rules, to define a suitable local area for each prototype, and to avoid overlapping. The proposed approach is applied on a pain-evoked fMRI data set to classify the levels of pain. Results indicate that the proposed approach can decode levels of pain and identify predictive fMRI patterns with higher accuracy and convergence speed and shorter execution time. Therefore, the new type of fuzzy-rule-based system with chaotic swarm intelligence holds great potential to predict pain perception in clinical uses.
An Expedient Synthesis of [1]Benzopyrano[b]pyridin-3-carbonitriles Catalyzed by NiCr2O4 NPs

Abstract Nickel (II) chromite nanoparticles (NiCr2O4 NPs) have been used as an efficient and reusable heterogeneous catalyst for the mild and green synthesis of [1]benzopyrano[b]pyridin-3-carbonitriles. The reaction was performed under solvent-free conditions at 70 °C. Several sustainable and economic benefits of the presented method are high yields of products, short reaction times, the use of new, highly efficient, heterogeneous and recyclable catalyst, clean conditions, and simplify practical aspects. Graphical Abstract Highlights Strategy toward a very simple and efficient synthesis of diverse [1]benzopyrano[b]pyridin-3-carbonitriles. The present methodology avoids the use of toxic catalyst. The present methodology runs in water as a green media. The use of NiCr2O4 NPs as a heterogeneous recyclable catalyst makes the protocol green and economical.
Investigating genetic aspects of the variation in the host response to gastrointestinal parasites in sheep

Analysis of data from 6-month old Scottish Blackface lambs exposed to a mixed, natural nematode infection demonstrated that the indicator traits, faecal egg counts (FEC), immunoglobulin A activity, eosinophil count, plasma pepsinogen activity and fructosamine concentration, investigated at 6 months of age were highly heritable and strongly correlated with the worm development traits. Strong negative genetic correlations (<-0.06) were often observed between worm development traits and eosinophil count, IgA activity and pepsinogen activity. A substantial genetic correlation was also observed between fructosamine concentration and worm length (0.67). However when such correlations were investigated across the 6-month time-period, the genetic correlations changed systemically and dramatically over time. These results provide an insight into the evolution of the genetic basis of the host prarasite interaction at a time when the host immune response is developing, and help to define optimal measurement ages for selection purposes. Two quantitative trait loci (QTL) studies were carried out on populations comprising different breeds and population structure; firstly a purebred Scottish Blackface flock and secondly a wide-breed cross flock developed from a resistant breed, Gulf Coast Native, and a susceptible breed, Suffolk. Both studies identified QTL associated with parasitic resistance traits, and although there is no concordance between the results, this is possibly due to the animals being infected with different nematode species. QTL such as those identified in this thesis could be utilised in a marker assisted selection scheme to increase resistance to parasitic infection. In the final study interactions between different parasite specifies within the host animal were investigated. Significant interactions were observed between Cooperia and Teladorsagia circumcincta, and T. circumcinta and Trichostrongylus vitrinus. Additionally Cooperia had a greater effect on FEC than T. circumcincta. The results from this study indicate that complex multi-parasitic relationships exist and hence when developing new control strategies it is essential to consider this background multi-parasitic infection and not simply focus on specific species.