Miracle-dz/UniFAR-FTUs huggingface dataset:
Extreme Coexceedances in South Eastern European Stock Markets with Focus on EU Accession Countries

The aim of this paper is to investigate and document the financial contagion of the South Eastern Europe (SEE) stock markets. Using a modification of the Bae et al. (2003) coexceedance approach based on multinomial logistic regressions we model the occurrence of the large negative or positive stock returns on a given day across the SEE stock markets. Specifically, we divide the SEE stock markets on two groups based on country’s EU membership in order to allow for transmission mechanism from major EU economies stock markets to EU member countries from SEE, and in addition, transitory effect from EU member countries from SEE to accession countries from SEE region. We test the persistence, asset class and volatility effects on the likelihood of the coexceedances in both SEE groups. We find that effects differ: (i) between negative and positive coexceedances and (ii) between the EU member countries and EU accession countries stock markets from SEE. The empirical evidence for the persistence effects, asset class and volatility effects in the SEE region should draw the attention of both investors and policy makers.
Identification and characterisation of new mouse models for hearing loss

Mouse N-ethyl-N-Nitrosourea (ENU) mutagenesis programmes have been successfully employed for the identification of models of human disease, and allowed the discovery of novel gene associations. This thesis describes the characterization of two new ENU-induced mouse models of hearing loss, goya and Boycie, identified at the MRC Harwell Institute. The goya mice carry a splice site mutation in the mitogen-activated protein kinase Map3k1 gene. In addition to an eyes-open-at-birth phenotype, Map3k1goya/goya mice initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9-weeks of age. Interestingly, heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. The extra OHCs were found not to arise from aberrant control of proliferation via p27KIP1. Expression of MAP3K1 is present in a number of inner ear cell types (inner and outer hair cells, spiral ganglion and stria vascularis), and investigation of targets downstream of MAP3K1 identified increased p38 phosphorylation in these cells. The goya mutant reveals a signalling molecule involved with hair cell development and survival. Boycie mice were identified as exhibiting a high frequency progressive hearing loss with a semi-dominant mode of inheritance. Ultrastructural and morphological assessment of these mice identified interesting pathological findings, including: a consistent pattern of OHC loss in the basal and mid cochlear turns of both heterozygote and homozygote mice; thinning of the stria vascularis in similar cochlear regions; and, spiral ganglion neuron degeneration in the apical turn. The Boycie mutation was mapped to a ~3 Mb candidate interval on Chromosome 5 containing only one ENU-induced coding lesion, which is in the Orai1 gene that codes for a component of the calcium activated calcium entry (CRAC) channel. These two novel mouse models highlight the important role for ENU mutagenesis in disease gene discovery.
Investigating the effectiveness of function clone detection tool for simultaneous fixing of defects

Investigating the effectiveness of function clone detection tool for simultaneous fixing of defects Seiya NUMATA†, Norihiro YOSHIDA††, Eunjong CHOI†††, and Katsuro INOUE† † Graduate School of Information Science and Technology, Osaka University 1–5, Yamadaoka, Suita, Osaka, 565–0871, Japan †† Graduate School of Information Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan ††† Graduate School of Information Science, Nara Institute of Science and Technology 8916–5, Takayama, Ikoma, Nara, 630–0192,Japan E-mail: †{s-numata,inoue}@ist.osaka-u.ac. jp, ††yoshida@ertl.jp, †††choi@is.naist. jp
Is oral squamous cell carcinoma unique in terms of intra- and inter-tumoral heterogeneity?

Tumoral heterogeneity has become one of the important issues in cancer research and carries outmost weightage in designing personalized cancer medicine. Oral squamous cell carcinoma (OSCC) is present in unique microenvironment of oral cavity attributed to site-specific diversified tissue compositions, microbial flora, diversified carcinogenic attacks, potentially malignant disorders, epithelial turnover rate, saliva, and closeness to external environment. Such microenvironment has potential to modulate the pathogenesis of many oral pathologies including OSCC. We believe that such factors and microenvironment are unique for OSCC and cannot be found in other carcinomas of the body. Methodologies such as multiregional sequencing, single-cell genomics, genomic landscape of bulk tumor sequencing, and so on, will help in understanding OSCC uniqueness in terms of heterogeneity. If explored, it will enable us to know the attributes of heterogeneity and their magnitude in OSCC, which will benefit in designing predictable biomarker and effective therapeutic strategy.
Liquid carbon reflectivity in the mbar regime

S. Paleari,1, D. Batani,2 R. Benocci,1 K. Shigemori,3 Y. Hironaka,3 T. Kadono,3 A. Shiroshita,3 and A. Aliverdiev 4 * 1 Dipartimento di Fisica G.Occhialini, Università di Milano Bicocca, Milan, Italy 2 University Bordeaux, CEA, CNRS, CELIA (Centre Laser Intense at Applications), UMR 5107,F-33405 Talence, France 3 Institute of Laser Engineering, Osaka University, Osaka Japan 4 IGR DSC RAS Pr. Shamilya 30A, 367030, Makhachkala, Russia * aliverdi@mail.ru
Validation of the snp panel for parentage assignment in local Russian sheep breeds

the further analysis. The mean MAF for 88 parentage SNPs was 0.380±0.091. Analysis of the SNPs’ distribution depending on theirs MAF showed that most of the SNPs (81.8 %) were informative (MAF≥  0.3). Proportion of informative SNPs differed between breeds and was 56.8 % in ROM, 63.4 % in ZBL, 71.6 % in BUB and 72.7 % in TUV. Twenty-one SNPs (23.9 %) were highly informative in all four breeds, while 37 SNPs (42.0 %), 17 SNPs (19.3 %) and 10 SNPs (11.4 %) were informative, respectively, in three, two or only one breed. Marker DU196132_525. 1 was monomor-phic in TUV (MAF = 0). Three SNPs with MAF < 0.3 (DU232924_365.1, DU501115_497.1 and DU372582_268.1) were not informative for all four breeds. Lower pairwise values of F st based on 88 SNPs with the same character of genetic relations compared with those using whole genome SNP profiles shown high flexibility of ISAG panel. PCA confirmed the low breed’s dependence of SNP panel by creating purely consolidated overlapping areas corresponding to different breeds. The prob- ability of identity for 88 SNPs ranged from 4. 32½10 -33 in TUV to 7. 48½10 -33 in BUB. Probability of exclusion was P1≥99.99 % for all four breeds. The value of P2 was the highest in TUV (P2≥99.99 %) with P2≥99.98 % for others. The value of P3 was 99.9 % for all breeds. Instead of some breed-dependent character of DNA profiles of 88 autosomal SNPs, our results confirmed the possibility of applying of ISAG panel for parentage testing in four local Russian sheep breeds.
A Tunable Protein Oscillator Controls Directional Movements In Myxococcus xanthus

Dynamic control of cell polarity is of critical importance for many aspects of cellular development and motility. In Myxococcus xanthus a three-protein module MglA, MglB and RomR, forms a polarity axis that can be rapidly inverted by the Frz chemosensory system to change the direction of movement. However, how Frz signalling provokes the polarity switch has remained unknown. Here, we show that Frz exerts spatial regulations at both cell poles. At the lagging cell pole, RomR and FrzX, a newly identified Frz regulator, form a two-component checkpoint that triggers the switch when MglA and FrzX-P concentrations are sufficiently high. At the leading cell pole, the FrzZ protein overcomes the slow unbinding of RomR to provoke fast reversals when Frz signalling is high. Mathematical modelling reveals that this architecture creates a spatiotemporal oscillator with highly tunable properties allowing a wide range of motility responses to internal and external signals.
Linking microscopic interactions with macroscopic effects

Understanding how biotic interactions impact plant community assembly is a long-standing goal in ecology, but studies of biotic interactions in this context are often limited to macro-interactions. In this issue of Journal of Vegetation Science, Sonkoly et al. synthesize current knowledge regarding the impact of cyanobacteria on terrestrial plants and show that cyanotoxins can alter germination and establishment success in grassland communities.
Single Nucleotide Polymorphisms rs2227284, rs2243283 and rs2243288 in the IL-4 Gene Show no Association with Susceptibility to Chronic Hepatitis B in a Chinese Han Population

Abstract Objective To investigate the relationship between single nucleotide polymorphisms (SNPs) of the interleukin-4 (IL-4) gene and outcome of hepatitis B virus (HBV) infection in a Chinese Han population. Methods Total of 501 patients with chronic hepatitis B virus (HBV) infection and 301 controls with selflimiting HBV infection were studied. Three tag SNPs in the IL-4 gene (rs2227284G/T, rs2243283C/G and rs2243288A/G) were genotyped by the Multiplex snapshot technique. The genotype and allele frequencies were calculated and analyzed. Results The three SNPs showed no significant genotype/allele associations with chronic HBV infection. Overall allele P values were: rs2227284, P = 0.655, odds ratio (OR) [95% confidence interval (CI)] = 1.070 (0.793-1.445); rs2243283, P = 0.849, OR (95% CI) = 0.976 (0.758-1.257); rs2243288, P = 0.659, OR (95% CI) = 1.060 (0.818-1.375). Overall genotype P values were: rs2227284, P = 0.771; rs2243283, P = 0.571; rs2243288, P = 0.902. There were no statistically significant differences between patients with chronic HBV infection and controls. Haplotypes generated by these three SNPs also had no significant differences between the two groups. Conclusions The three tag SNPs of IL-4 were not associated with the outcome of HBV infection in the Han Chinese population.
Efecto del manejo de las malezas en macadamia sobre la población del barrenador de la nuez Ecdytolopha torticornis Meyrick (Lep: Tortricidae).

The effect of three weed management systems -macadamia husk as a mulch, bare ground and weeds growing freely - on the population ofthe nutborer, Ecdytolopha torticornis, were studied from June to September 1992 at Oriente Farm, Turrialba, Costa Rica. The smallest number of the nutborer's eggs was recorded on the bare ground treatment, followed by the unweeded treatment and the husk treatment. Although the macadamia husk as a mulch has been used to sol ve the problem of residues from nut processing, the results suggest that the use of this practice might increase the nutborer population by concentrating odours which could attract the adults, or by disrupting the parasitoid or predator population. There is a need for testing other mulches such as plastics, other plant residues, sawdust and others, and to study alternative weed management systems, including the use of cover crops in the mid-rows.
Physiological Characterization of Dubska Pramenka

Scientific knowledge about the predispositions of Bosnian native breeds of sheep (Dubska) for the production of milk and milk products until recently were quite sparse and very scarce. Therefore, the aim of this study was to investigate the biochemical indicators and serum minerals, for monitoring the nutritional status. Until now subject research did not include testing of the effect of biochemical parameters and hormonal status of the blood of sheep on the quality of milk and milk products. Persistence of this connection is justified by the fact that most of the ingredients of milk just derived from the blood. The main objective of this research was to explore metabolic parameters of sheep’s blood, and their relative importance on the quality and quantity of milk components. The study included a total of 127 sheep blood samples from two different areas (Livno and Travnik) in summer feeding period (July, August and September). The animals were marked with the appropriate number of ear tags on the basis of which we always took samples from the same animals through different periods. In sheep blood serum, the concentration of biochemical parameters (glucose, cholesterol, triglycerides, total protein, albumin, urea, AST, ALT, AP, GGT, LDH, calcium, phosphorus and magnesium) and metabolic hormones (triiodothyronine, thyroxine, and insulin cortisol), and samples of milk: milk parameters (milk fat, lactose and protein) as well as fatty acid composition of the milk. The concentrations of blood biochemical parameters were determined by spectrophotometry with automated analysis with ready-made package of slides. Concentrations of metabolic hormones (T3, T4, cortisol and insulin) in the serum were determined by ELISA method. The percentages of fat, protein and lactose in milk were determined by infrared spectrophotometry. Fatty acids in milk were determined by gas chromatography (GC). Our research showed hypoglicemia, mild hypoproteinemia and hypoalbuminemia probably due to nutritional deificiencies during lactation period. Negative energy balance could be responsabile for changes found in the cholesterol concentration as well as in the activity of ALT, AST, GGT, LDH. Significant differences in milk fat and milk protein, as well as fatty acids composition were determined between localities and season sampling. In general, our results showed varriation of blood biochemistry and milk quality. Due to differencies in climate, botanical differences of soil and pasture these variations are considered to be acceptable. Statistical analysis was performed using the software package SPSS 15.00 (for biochemical paramters and parameters of milk) and 21.00 (for metabolic hormones and fatty acid composition of the milk).
Strong functional constraint at residues in HIV-1 Gag are predicted by measures of evolutionary rather than population-level genetic conservation

Acknowledgments We would like to thank all staff at IIID, Murdoch University Australia. NH&MRC APP 1012178 project grant Background HIV variation remains a central barrier to an effective vaccine. Immune escape contributes significantly to intraand inter-individual HIV diversity (1). Accumulation of certain escape mutations at the population level has been suggested by i. HLA allele associations with subtype consensus residues (2) ii. Correlation between HLA allele frequency and frequency of associated viral escape mutants across diverse populations (3) and iii. Persistence of high fitness escape mutants following transmission (4). Some conserved residues may thus represent “immunologically silent” sites not subject to immune selection, rather than sites of high structural/functional constraint. We utilized known phylogenetic relationships between HIV-1 and SIVs in their natural primate hosts to identify possible sites of deeper evolutionary conservation (“high EvC”) that are distinct from sites of HIV-1/human specific conservation only (Figure 1).
DISTRIBUTION AND POPULATION STRUCTURE OF THE INVASIVE AMPHIPOD GMELINOIDES FASCIATUS (STEBBING) IN LAKE ONEGO

Since the middle of the ХХ century, the rapid spread of exotic species and their successful penetration in natural and artificial ecosystems has led to significant environmental changes all over the world [1, 2]. As it was pointed out by many researchers, biological invasion by alien species is one of the main threats to biodiversity [3, 4, 5, 6, 7]. Gmelinoides fasciatus (Stebbing 1899) attracts special attention due to the fact that it is the most successful alien species among other invaders in aquatic ecosystems in Eurasia. This invasive amphipod of Baikalian origin was first recorded in Lake Onego in 2001 by Berezina and Panov [8]. The results of the present study indicate that the invader significantly expanded its areal in Lake Onego during the last 15 years. At present amphipod G. fasciatus is dominant on the biomass among macrozoobenthos community in littoral biotopes of some islands and east part of the Lake. In Lake Onego the invader has a one-year life cycle with the generations of the previous and current year. Seasonal dynamics of the amphipod abundance in Lake Onego has two peaks during the vegetation period. According to our data G. fasciatus successfully reproduces in the new environment and shows stable sexual structure with sex ratio of approximately 1:1. Female fecundity of the amphipod in the Lake varied from 3 to 22 eggs per female, the average variation of fertility is 9 eggs per female. Revealed data of G. fasciatus abundance and biomass in Lake Onego are comparable with those for other water bodies where this amphipod species was successfully established earlier.
Defining the anti-apoptotic function of the survival of motor neuron (SMN) protein and assessment of a novel therapy for the treatment of spinal muscular atrophy (SMA)

Spinal muscular atrophy (SMA) is a neurodegenerative disorder primarily affecting motor neurons. This untreatable disease is caused by the absence of a functional survival of motor neuron 1 (SMN1) gene, which leads to a critical reduction in fulllength survival of motor neuron (SMN) protein. The multifunctional SMN protein is important in the biogenesis of small nuclear ribonuclear proteins, pre-mRNA splicing and motor neuron viability. However, the precise functions of the SMN protein in promoting neuronal survival are yet to be completely understood. To this end, the aims of this project were to elucidate the pro-survival role(s) of the SMN protein and assess a novel therapeutic approach for the delivery of recombinant SMN protein into cells. Therefore, the hypotheses of this project stated that the SMN protein plays an important role in regulating apoptosis, and successful delivery of the SMN protein to cells can be achieved using a cell-penetrating peptide (CPP). To elucidate the pro-survival functions of the SMN protein, a novel in vitro apoptotic cell death model was established. Using differentiated human SH-SY5Y neuroblastoma cells, a predominately apoptotic cell death was induced through the inhibition of the PI3-kinase/Akt survival pathway. Results from these experiments revealed that SMN over-expression protected SH-SY5Y cells from a caspase-dependent apoptotic cell death. Further, SMN over-expression blocked calpain-mediated activation and cleavage of the caspase-3 protein. The demonstration of this previously unknown mechanism has identified a pathway activated by the SMN to block apoptosis.
Rv1886c Gene Expression for the Production of Mycobacterium tuberculosis Major Secreted Protein Antigen 85B in Escherichia coli

Tuberculosis (TB) is one of the major infectious diseases that cause health problems worldwide. Antigen 85B is a secreted protein of the infectious strain Mycobacterium tuberculosis. Our main focus is on production of proteins as a booster vaccine to replace the traditional Mycobacterium bovis bacillus Calmetter-Guerin (BCG) vaccine formula. The main challenge is to express a high yield of an active recombinant protein in native soluble form. To the extent of our knowledge, the cultivation conditions, such as optimal temperature, for overexpressing soluble Ag85B protein of the gene Rv1886c, have never been reported. This study showed for the first time the optimizing culturing conditions for inducing expression of soluble Ag85B protein by isopropyl β-D-1-thiogalactopyranoside (IPTG) in Escherichia coli BL21 (DE3) pLysS. Protein yields were higher at a low temperature of 25 °C (for 12 h), compared to those at a high temperature of 37 °C (for 5 h). To conclude, low temperature is associated with slow expression which allows the protein to adopt a well-folded conformation and provides a high yield of soluble recombinant protein.
Design of flavonoid microparticles with channel forming properties to improve oxidative stability of sunflower oil

For about a century, scientists and food technologists were puzzled trying to understand the chemistry of lipid oxidation and striving to find strategies to protect the unsaturated fatty acids in foods. For more than fifty years ago, it the free radical theory was accepted to explain the basic reaction mechanism and the involvement of product lipid hydroperoxides in autocatalysis of the reaction. Antioxidants were identified as components that are able, when present in micromolar concentrations, to provide significant protection and prolong the induction period of oxidizing fatty acids. Certain other compounds, defined as synergists, did not present antioxidant properties per se but were able to potentiate and improve the efficiency of antioxidants. The role of antioxidants and their protection efficacy were associated with a number of paradoxes pointing to a lack of proper understanding. Recently, oxidizing lipid systems have been defined as micro- or nano-emulsions wherein the oxidation and antioxidation sites are the interfaces between lipids and water. This new paradigm is expected to lead to significant progress in the understanding of the role of synergists and the potentiation of antioxidants actions. The article by Morelo et al. [1] in this issue of the European Journal of Lipid science & Technology is discussing a new idea for the addition of antioxidants to oxidizing fatty acids in a bulk oil model. Two flavonoid antioxidants, quercetin and epicatechin, were encapsulated in an oil insoluble carbohydrate polymer (inulin) and further covered with an oil-soluble soy protein isolate polymer by spray drying. Heating of these microencapsulates lead to the formation of channels within the particles that will aid the diffusion of the antioxidants to the lipid medium. As a proof of principle, the antioxidant potencies of the microparticles containing quercetin and epicatechin were tested in sunflower oil using the Rancimat at 60 °C. This work can be a start for new designs where not only antioxidants but also sensitive lipids and vitamins can be microencapsulated for protection.
Isolation and Characterization of Fusarium moniliforme var. subglutinans from Malformed Mango

Mango malformation occurs in most mango growing regions of the world. Floral and vegetative malformation have been reported. There is general agreement that the fungal pathogen Fusarium moniliforme var. subglutinans or Fusarium subglutinans is the causal agent. Healthy and malformed samples of both floral and vegetative tissues were collected from different varieties of mango grown in several locations to verify the association of F.moniliforme with mango malformation disease in Pakistan. The fungus was isolated and cultured. Frequency of fungal association with the disease ranged between 90- 94%, There was less recovery of fungus from asymptomatic tissue (12- 15%). There was no difference among the commercial mango varieties in the level of susceptibility to this disease. However, seedling germplasm and land races showing resistance to mango malformation were identified. The in vitro growth characters of the fungus were determined on different culture media, at varying temperatures, light and pH conditions. Mycelial growth on potato dextrose agar was better than nine other media tested. At pH 7.00, the ideal temperature for growth was between 25-30° C. Normally, the malformation is not controlled by fungicide application. The in vitro sensitivity of fungus to six fungicides at three concentrations was determined to seek potential means of chemical control.