Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring Mutual Information Between All Pairs of Variables in Subquadratic Complexity

Finding associations between pairs of variables in large datasets is crucial for various disciplines. The brute force method for solving this problem requires computing the mutual information between � N 2 � pairs. In this paper, we consider the problem of ﬁnding pairs of variables with high mutual information in sub-quadratic complexity. This problem is analogous to the nearest neighbor search, where the goal is to ﬁnd pairs among N variables that are similar to each other. To solve this problem, we develop a new algorithm for ﬁnding associations based on constructing a decision tree that assigns a hash to each variable, in a way that for pairs with higher mutual information, the chance of having the same hash is higher. For any 1  �  2, we prove that in the case of binary data, we can reduce the number of necessary mutual information computations for ﬁnding all pairs satisfying I ( X, Y ) > 2 � � from O ( N 2 ) to O ( N � ), where I ( X, Y ) is the empirical mutual information between variables X and Y . Finally, we conﬁrmed our theory by experiments on simulated and real data. The implementation of our method and experiments is publicly
T-Cell Epitopes of Mycobacterium tuberculosis Antigen 85 Complex Potential for Generating Antibody: an Immunoinformatics Study

The present study was conducted to predict T-cell epitopes of the antigen 85 complex capable of stimulating antibody generation by using immunoinformatics approaches. By applying computational biology software, the available data of the antigen 85 complex and related-epitopes would be turned into more constructive and useful scientific informations for the development of multiepitope-based anti-TB vaccine. The identification of T-cell epitopes capable of generating antibody was done by the 3DEX program, discotope analysis and PyMol program. Selected peptides having individual amino acids localized on the predicted antibody-binding sites were subjected to antigenic property analysis, including their hydrophilicity, flexibility and antigenic propensity. The 3DEX program identified 17 peptides having at least four individual amino acids located on the antigen surface. However, after homology analysis with preselected distance of 7 A and taking into account the spatial neighborship, only seven peptides of antigen 85A, 85B and 85C (3, 3 and 1 peptide(s) respectively) had individual amino acids overlapping the predicted antibody-binding site. Peptides 17838, 21780, 21275 and 36131 had an average score of antigenic propensity above 1.0. In conclusion, there are seven peptides representing T-cell epitope of antigen 85 complex that could potentially be capable of generating an antibody response. The seven peptides, P17838, P21093, P36131, P21275, P21780, P21796 and P10839, are suitable candidates for further study in order to develop a subunit-based multiepitope anti-TB vaccine.
Resolution ofChlamydial Genital Infection inB-Cell-Deficient Mice andImmunity toReinfection

Thepurposeofthisinvestigation was todetermine therelative roles ofthehumoral andcell-mediated immuneresponsesintheresolution ofchlamydial genital infection ofmiceandresistance toreinfection. Tothis end,female BALB/cmicewererendered Bcell deficient bytreatment withheterologous anti-immunoglobulin M (IgM) serum frombirth. Controls weresimilarly treated witheither normal serum or phosphate-buffered saline. Before inclusion ineachexperiment, aiti-IgM-treated micewere screened fortheabsence ofIgMin serum andforthepresenceofcell-mediated immuneresponses.Inaddition, ppleen cells fromanti-IgM-treated miceresponded toconcanavalin A andphytohemagglutinin butnottolipopolysaccharide. Bythese criteria, micewere designated Bcell deficient. B-cell-deficient miceandcontrols were inoculated intravaginally with a suspension ofmouse pnecvumonitis agent(MoPn), a Chiamydia trachomatis biovar. AllB-cell-deficient mice resolved theinfection. Additionally, no significant difference was seen inthecourseoftheinfection in B-cell-deficient micewhencompared withcontrols. Incontrast tocontrol mice, B-cell-deficient micedisplayed nodetectable antibody responsestoMoPninserum oringenital secretions. However, bothB-cell-deficient mice andcontrols developed delayed-type hypersensitivity andT-cell proliferative responsestoMoPn.When challenged 53daysafter primary infection, nosignificant difference was seenintheresistance ofB-cell-deficient micetoreinfection whencompared withthatofthecontrols. Thesedataindicate thatcell-mediated immune mechanisms play an important role intheresolution ofandresistance tochlamydial genital infection inthis model.
Catabolic Activity of Desulfotomaculum ruminis Bacteria in Media Containing Amino Acids

The influence of the presence of certain amino acids at different concentrations on the catabolic activity of the bacteria Desulfotomaculum ruminis was studied. Introduction of amino acids of the simple chain molecule in concentrations up to 10 g/dm 3 in the Starkey media leads to a small decrease of the sulphate conversion degree. A more significant decrease in the reaction rate is observed for amino acids with branched side chains such as valine. Moreover, it was shown that except for the D-asparagine isomer, which is not assimilable by the bacteria Desulfotomaculum ruminis, the other amino acids are a source of assimilable nitrogen. Serine meets the demands of the minimum substrates and is a source of assimilable carbon and nitrogen in the process of bacteria proliferation.
Progress towards continuous cover woodland: Ipsden estate

Increasing interest in continuous cover management of woodlands in Britain indicates the need for more study of the resulting wood production, since sales of wood remain the most important source of finance for established woodlands. Detailed enumeration data by 1 inch quarter girth (1" QG = 3.23 cm diameter) classes and records of cut are available for 22 compartments of all-aged woodlands of the Ipsden estate, Oxfordshire, together with accounts compiled on a consistent basis since 1973. Predominant species are beech, oak, ash, cherry with, usually younger, European larch, Scots pine and other conifers managed on an irregular group selection system. Average growing stock volume of material over 5" QG increased from 1080 hoppus feet per acre (96.3 m 3 ha - 1 ) in 1973 to 1800 h.ft per acre (160.4 m 3 ha - 1 ) in 2000. Cut amounted to 593 h.ft per acre (52.8 m 3 ha - 1 ). Total increment over the 27 years was 1312 h.ft per acre or 48.6 h.ft per acre per year (4.33 m 3 ha - 1 a - 1 ). An 'ideal' stand is defined. The net annual income relative to value of standing timber of this is 1.8 per cent. The current absence of simulations of growth and potential yield in mixed-age, mixed-species stands makes forecasts of volume and money yield difficult. A plausible profile of future net income suggests that net present value of the current stock lies between £1450 per acre at 2 per cent and £750 at 3 per cent, both values being substantially lower than the standing value of timber of £1670 per acre: equality occurs at 1.7 per cent. This result should be set alongside the return, without grants, of growing even-aged broadleaved stands in Britain of a little over 1 per cent in real terms.
RADIAL-GROWTH AVERAGING CRITERIA FOR RECONSTRUCTING DISTURBANCE HISTORIES FROM PRESETTLEMENT-ORIGIN OAKS

A novel dendroecological procedure was developed to elucidate canopy disturbances spanning a >300-yr period for oak (Quercus) forests of central Pennsylvania. Running comparisons of sequential 10-yr ring-width averages may effectively neutralize both short-term (i.e., drought) and long-term growth trends associated with climate while enhancing detection of abrupt and sustained radial-growth increases characteristic of canopy disturbance. Thinning-response studies revealed the conservative tendencies of overstory oak, with substantial basal area reductions (>1/3) required to attain moderate and consistently detectable growth increases. Based on empirical evidence, a minimum growth-response threshold of 25% was established to depict canopy disturbances. This is in contrast to the 50–100% sustained radial-growth release often used to detect disturbance using understory trees in closed forests. Our default threshold was adjusted higher as necessary for those trees highly correlated to climatic trends (as repr.
Creatine kinase, cell membrane and Duchenne muscular dystrophy*

In1958ProfessorSetsuroEbashifoundthatserumcreatinekinaseactivityisincreasedinpatientssufferingfromvariousmuscular dystrophies,especiallyDuchennemusculardystrophy(DMD). Heandothersproposedthatcreatinekinasepassesthroughthe cellmembraneasitisreleasedfromDMDmusclefibers. Sincethen,ithasbeenfoundthatdystrophinanddystrophin-associatedproteinsareconnectedtoseveralothercomponents, includingthebasallaminaandsubsarcolemmalcytoskeletalnetworksonthecellmembrane,whiledystrophinanchorsthese dystrophin-associatedproteinstotheactin filamentsinsidethemusclecell.InDMDmuscle,dystrophinhasbeenfoundtobe absentanddystroglycansandsarcoglycansdecreased.However,howcreatinekinasemoleculescanpassthroughtheDMD musclecellmembranestillremainsunanswered. Onthebasisofrecentfindingsonthestructureoftheproteinlayerswhichsandwichthelipidbilayerofmusclecellmembranes, thisessaystressestheimportanceoftheselipidbilayersinprotectingcreatinekinasereleasefromprotoplasmainnormalmuscle. ItfurtherindicatesthepossibilitythattheabsenceofdystrophininDMDmuscleduringmusclecontractionmayresultintemporal damagetothelipidbilayer. (MolCellBiochem190: 143-151,1999)
The isolation and genotypic characterisation of campylobacter jejuni from environmental matrices

Infection by Campylobacter is the most notified gastrointestinal disease in New Zealand. Reliable recovery and identification of campylobacters is challenging. Improved and validated methods are needed to increase the power of subtyping and epidemiological studies to trace the sources and transmission routes of Campylobacter. An enrichment-PCR method for the isolation and detection of C. jejuni and C. coli was developed and sensitivity levels determined in 13 environmental matrices, including animal faeces, food and water. Less than ten cells per sample of either C. jejuni or C. coli could be detected, except for rabbit faeces where the minimum number of cells detected per sample was greater than ten cells for C. coli (range 3-32 cells). The sensitivity of the method was comparable to that determined for the conventional methods in the same matrices. Application of the method to retail chicken carcasses (n =204) determined a prevalence of 27.5% C. jejuni and 1% C. coli. River water assays (n = 293) found 55.3% of samples to contain C. jejuni and 4.1% C. coli. Furthermore, the enrichment-PCR assay was shown to identify up to three subtypes in individual water samples. It was proposed that the identification of non-dominant subtypes carried by a chicken carcass may aid the identification of subtypes implicated in human cases of campylobacteriosis. An average of twenty-three C. jejuni isolates from each of ten retail chicken carcass were subtyped by PFGE using the two restriction enzymes SmaI and KpnI. Fifteen subtypes, in total, were identified from the ten carcasses. One subtype was identified on three carcasses. Five carcasses carried a single subtype, three carcasses carried two subtypes each and two carcasses carried three subtypes each. Some of the subtypes carried by an individual carcass were shown to be clonally related raising the question of in vivo recombination events during host passage. Comparison of C. jejuni subtypes from chickens with those isolated from human clinical cases revealed three of the fifteen subtypes correlated with those from human cases. None of the minority subtypes were identified in human case isolate data, suggesting that the lack of identification of non-dominant subtypes from chicken carcasses may not hinder the investigation of campylobacteriosis outbreaks. Chapter
Pigment Composition in the Reaction Center Complex from the Thermophilic Green Sulfur Bacterium, Chlorobium tepidum: Carotenoid Glucoside Esters, Menaquinone and Chlorophylls

Distribution of pigments in the reaction center (RC) complex, chlorosomes and chlorosome-free membranes prepared from the green sulfur bacterium, Chlorobium tepidum, was analyzed. The RC complex contained approximately 40 molecules of bacteriochlor ophyll (BChl) a per P840, half of which are estimated to be in the Fenna-Matthews-Olson (FMO) protein. Carotenes (2 molecules per P840) occupied only one third of the total carotenoids. The remaining carotenoids (4 to 5 molecules per P840) were OH-chlorobactene glucoside ester and OH-/-carotene glucoside ester. Dihydrochlorobactene was decreased compared with cellular carotenes. Furthermore, approximately 9 C670 and 1 menaquinone-7 per P840 were also found. BChl c and carotenes, whose major component is chlorobactene, were found mainly in chlorosomes, and two kinds of carotenoid glucoside esters were observed in chlorosome-free membranes.
Role of the Elicitor Compound Methyl Salicylate in Enhancing Allelopathic Potential of Rice for Sustainable Weed Management

Rice production suffers a major setback through weed pressure world wide. In the present study, exogenous ap- plication of elicitor compound methyl salicylate (MeSA), at different concentration, (0.1, 0.2, 0.3mM MeSA) was made as a foliar spray and its effect on allelopathic potential of rice genotypes was assessed. The experiment was conducted in a split-plot design with the weedy and weed-free treatments in the main plot and three genotypes as the sub-plot treatment with the foliar application of MeSA.Methyl jasmonate (MeJA) and methyl salicylate (MeSA) are important signaling mol- ecules that induce plant defense against insect herbivores and microbial pathogens. We tested the hypothesis that allelopathy is an inducible defense mechanism, and that the MeSA signaling pathways may activate allelochemicals release. MeSA was found to improve the competitive ability of the genotypes by suppressing weed biomass through enhancements in phenolic acid content (viz. caffeic, o-coumaric and syringic acid) and also in plant growth without any detrimental effect on the host plant, showing that application of MeSA resulted in enhancement of phytotoxic potential of rice genotypes. Spraying of rice plants with 0.2 mM MeSA resulted in highest inhibition of weed dry weight in all the genotypes. Application of MeSA increased also increases Shoot dry matter, grain yield, as well as PAL activity. These results suggest that allelopathy may be an active defense mechanism, and that plant signaling compounds are potentially valuable in its regulation.
A new record of root rot of broad bean (Vicia faba) from the Sudan

Summary Fusarium solani f. sp. fabae Yu & Fang was isolated from root-rotted field bean (Vicia faba)plants at the Research Farm, Hudeiba Agricultural Research Station, Northern Province, Sudan. This is the first record of this fungus on field beans in the Sudan. Cultural and morphological characteristics of the fungus on potato-dextrose agar (PDA) and the symptoms caused are described.
Aboveground phytomass productivity and morphological variability of Tunisian accessions of Cenchrus ciliaris L.

This study assessed the aboveground aerial phytomass produced by 47 accessions of Cenchrus ciliaris L. locally collected in the arid zone of Tunisia and classified into six eco-geographic groups. The extent of genetic variation in five morphologic parameters was examined. Correlations among all parameters were also analysed. For three years, phytomass of these accessions was cut and measured for three cutting periods characterised by different rainfall features. In 1998 the mean of the phytomass productivity was 199.1g DM (Dry Matter) plant–1. The productivity in 1999 was 81.0g DM plant–1, but in 2000 the productivity was only 21.6g DM plant–1. Positive correlations were found between dry matter and all morphological parameters, especially tuft diameter (r = 0.670) and tuft height (r = 0.637). Principal components analysis was carried out on all variables. For both dry matter and phenology, individuals differentiated strongly, but irrespective of their accession or eco-geographic origin.
Sources of error with in vitro digestibility assay of pasture feeds

A series of experiments was undertaken to determine population statistics for in vitro organic matter digestibility (in vitro OMD) data and to examine the effects of basal diet, donor animal and precollection fasting interval on the activity and specificity of rumen fluid inoculum. The experiments utilized wether sheep, a diverse set of pasture grass and legume feeds prominent in the Australian subtropics and the Tilley and Terry in vitro digestibility procedure running under the operating pressure of a practicing feeds evaluation laboratory. The standard errors of in vitro OMD estimates for within and between batch runs were ±0·88 × 10−2 and 0·62 × 10−2, respectively. These error terms were used to develop protocols to accept, reject or scale raw in vitro OMD data. Differences between donor animals in the activity of rumen fluid were highly significant. Extending the precollection fasting interval beyond 16 h was associated with a substantial decline in inoculum activity. An in vitro-in vivo calibration relationship based on fifteen test feeds and using lucerne (Medicago sativa) as basal diet was described by the linear model y = 1·3 x-0·195±4·9 × 10−2r= 0·79 (y =in vivo OMD, x =in vitro OMD). Despite large effects of basal diet on both the absolute values and relative ranking of test feeds, neither the RSD nor r values were improved using alternative diets to Lucerne chaff. The results highlight the need to formally standardize the analytical and biological components of the in vitro digestibility procedure to safeguard the integrity of data.
Growth and visual quality of weeping fig in relation to shading conditions

The aim of this study was to evaluate the growth and visual quality of weeping fig (Ficus benjamina L.) ‘Danielle’ in relation to different shading conditions (reductions of 50, 58, 66, 80 and 86% of the incident irradiation outside of the greenhouse). The increase of shading from 50 to 86% resulted in a reduction of the daily growth rate of approximately 42%; this reduction was proportional in both the shoots and roots. Shading, modifying certain biometric characteristics of the canopy (e.g. internode length, first-order insertion angle on the main stem, leaf number and unit leaf area), affected the visual quality of the plants. In particular the more-shaded plants (86%) exhibited a more open canopy and thus a reduced foliage density (19% compared to the 50% shaded plants). This reduction was mainly related to the modification of the insertion angle of first-ordered branches, which increased from 38.6° to 46.4° as the shading level increased. Additionally, the highest shading level (86%) resulted in a greater unit leaf area that compensated for the reduction of the leaf number (40%) in terms of the total leaf area. Furthermore, the highest shading level positively influenced certain parameters, such as the plant shape (lower height/width ratio) and leaf characteristics (greater unit area, flat stereometry and dark green colour), which are important parameters in determining the visual quality of ornamental foliage plants. Our results showed that the choice of shading level for weeping fig production could consider besides the effects on growth and indoor acclimatisation, also those on plants visual quality responding to defined market requirements.
Sex-specific Growth in Alpine Chamois

Abstract Studying between-sex differences in body growth has strong implications for understanding life-history tactics of animals. We used age and carcass mass data from 2,312 female and 2,622 male alpine chamois (Rupicapra rupicapra) harvested in the French Alps to model the sex-specific body growth patterns of this species. Males were heavier (asymptotic body mass: 29.6 kg) than females (22.3 kg), with an adult sexual size dimorphism of 32.4%. Sexual size dimorphism originated from both differences in body growth after 1.5 years of age and differences in length of the growth period. Females reached asymptotic body mass almost 3 years earlier (3.5 years) than males (6.2 years). We also found that females 1st reproduced before achieving asymptotic growth, at 78% of their asymptotic body mass. Between-sex differences in growth patterns in this species are most likely due to stronger selection pressure for larger size in males than in females due to intrasexual competition.
Specific expression of the gibberellin 3β-hydroxylase gene, HvGA3ox2, in the epithelium is important for Amy1 expression in germinating barley seeds

We have cloned gibberellin (GA) 3b-hydroxylase cDNA, (HvGA3ox), a homolog of the rice gene OsGA3ox from germinating barley seeds. HvGA3ox cDNA was expressed in Escherichia coli as a fusion protein capable of oxidizing GA9 to GA4 and GA20 to GA1. Deduced amino acid sequence analysis showed that HvGA3ox was identical to HvGA3ox2, which shares a high homology with the OsGA3ox2 isoform that plays an important role for induction of a-amylase in germinating rice seeds. Northern blot analysis showed that HvGA3ox2 gene was expressed only in germinating seeds, not in other organs. Typical feedback regulation was not observed in seedling treated with either biologically active GA (GA 3 ) or uniconazole, an inhibitor of GA biosynthesis. HvGA3ox2 mRNA was detected from 12 h after imbibition just before expression of a-amylase gene, Amy1. In situ hybridization of germinating seeds revealed that HvGA3ox2 mRNA was localized in the epithelium up to at least 3 days after imbibition. Our results suggest that GA biosynthesis in epithelium is important for expression of a-amylase in germinating barley seeds, and that HvGA3ox2 encodes the key enzyme of this event.
Addressing Technical Replicate Variance in Omics Data Analysis

[1] Liu, X. et al. (2006) Probe-level measurement error improves accuracy in detecting differential gene expression. Bioinformatics, 22 (17), 2107–2113 [2] Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3(1), 3 [3] Anderson, J. C. et al. (2014) Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against pseudomonas syringae. Proc. Natl. Acad. Sci. U. S. A. , 111 (18), 6846–6851 [4] Böttcher, C. , et al. (2009) The multifunctional enzyme CYP71B15 (Phytoalexin Deficient 3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3acetonitrile metabolic network of Arabidopsis thaliana. Plant Cell, 21 (6), 1830–1845 [5] Sanguinetti, G. et al. (2005) Accounting for probe-level noise in principal component analysis of microarray data. Bioinformatics, 21 (19), 3748–3754 [6] Glaab, E. , et al. (2010) vrmlgen: An R package for 3D data visualization on the web. J. Stat. Soft. , 36 (8), 1–18 Omics datasets often contain technical replicates, included to account for technical noise in the measurement process. Summarizing these replicates using robust averages may help to reduce the influence of noise on downstream data analysis, but the information on the variance across replicate measurements is lost for subsequent analyses. We present RepExplore, a web-service to exploit the information captured in the technical replicate variance to provide more robust differential abundance statistics and principal component analyses for omics datasets. A fully automated data processing pipeline and interactive ranking tables and 2D and 3D visualizations further facilitate the interpretation of complex experimental data. Introduction 1