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Segmenting DNA sequence into words based on statistical language model
Get PDFThis paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA “words” is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised ‘probability approach to word segmentation’ method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last
Seminal Plasma Proteins
Get PDFThe ejaculated semen consists of two major components viz. sperm cells (spermatozoa) and the fluid part obtained after centrifugation called seminal plasma. The spermatozoa originate from the semniferous tubule and are suspended in the seminal plasma. The seminal plasma is composed of secretions contributed by the testis, epididymis, seminal vesicles, ampullae, prostate and bulbourethral glands. About 60-80 % of the ejaculated semen of the bull originates from these sources. Seminal plasma is a highly complex biological fluid containing proteins, amino acids, enzymes, fructose and other carbohydrates, lipids, major minerals and trace elements. Seminal plasma proteins partly originates from the blood plasma by exudation through the lumen of the male genital tract and partly are synthesized and secreted by various reproductive organs and are known as seminal plasma specific proteins. Several seminal plasma proteins of blood origin viz. prealbumin, albumin, globulin, transferring, α-antitrypsin, β-lipoprotein, β-glycoprotein, orsomucoid, kininogen, Peptide hormones, IgG, IgA and IgM have been identified and characterized. These proteins are involved in regulation of osmotic pressure and pH of seminal plasma, transport of ions, lipid and hormones. A major part of seminal plasma proteins originate from the testis, epididymis, vas deference, prostate, seminal vesicle and bulbourethral glands. The biosynthesis and secretion of these proteins is regulated by testosterone levels in the blood
A new outlook towards kidney injuries
Get PDFAcute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate immunity indicates the involvement of the pathogen. Research in this theme possesses a strong possibility in the development of therapeutic, preventive and management strategies for the acute and chronic kidney injuries
Lyme Borreliosis During Pregnancy
Get PDFOne of the authors (AL) presented a poster on 34 pregnancies of maternal Lyme borreliosis (Lb) in 1995. It was striking that untreated Lb associated with higher probability of adverse outcome but the number of patients were small and the statistical power was low. We have recently published a paper on 95 maternal Lb and the outcome of their pregnancies. Since the closure of the database for that manuscript the number of the pregnant women with Borrelia infection observed in our Centre increased to 124, and the statistical analysis strengthened our previous doubtful observations and reached significant results in important aspects by now. This series is the largest study to date on this topic. Treatment was administered parenterally to 87 (70%) women and orally to 25 (20.0%). Infection remained untreated in 12 (10%) pregnancies. Adverse outcomes were seen in 7/87 (8%), 9/25 (36%), 8/12 (67%), of the parenterally, orally treated and untreated women, respectively. In comparison to patients treated with antibiotics, untreated women had a significantly higher risk of adverse pregnancy outcomes (OR: 11.62, p<0.001). Mothers treated orally comparing to iv. treatment had an increased chance (OR: 6.28) to have an adverse outcome (p=0.001). In the adverse pregnancy outcome, the most impressive difference was between the untreated and parenterally treated women (OR: 21.44, p<0.001). The probability of adverse outcome increased by the exposition time (from the first maternal symptom to the treatment or delivery). When the exposition time has reached four months, the probability of adverse outcome increased by 33%. We had no chance to examine the bacterial invasion of the foetus. Loss of the pregnancy (N=9), small for gestational age or preterm birth (N=7) were the most prevalent adverse outcomes in our series. The other complications were heterogeneous. Our results indicate that untreated or orally treated maternal Borrelia burgdorferi s.l. infection is associated with adverse outcomes. 'Congenital Lyme disease' similar to the Hutchinson's triad in syphilis is unlikely.

The hypothalamic genesis of obesity
No full textThe theories on obesity genesis shifted during the past years from the simple conception of "just overeating" to data supporting the diencephalic origin of the disease. Summarized findings on this issue are displayed
Calorific values and ash contents of different organs of Masson pine (Pinus massoniana) in southern China
Get PDFCalorific values of plants are important indices for evaluating and reflecting material cycle and energy conversion in forest ecosystems. Based on the data of Masson Pine (Pinus massoniana) in southern China, the calorific values (CVs) and ash contents (ACs) of different plant organs were analyzed systematically using hypothesis test and regression analysis in this paper. The results show: (i) the CVs and ACs of different plant organs are almost significantly different, and the order by AFCV (ash-free calorific value) from the largest to the smallest is foliage (23.55 kJ/g), branches (22.25 kJ/g), stem bark (21.71 kJ/g), root (21.52 kJ/g) and stem wood (21.35 kJ/g); and the order by AC is foliage (2.35%), stem bark (1.44%), root (1.42%), branches (1.08%) and stem wood (0.33%); (ii) the CVs and ACs of stem woods on top, middle and lower sections are significantly different, and the CVs are increasing from top to lower sections of trunk while the ACs are decreasing; (iii) the mean GCV (gross calorific value) and AFCV of aboveground part are larger than those of belowground part (roots), and the differences are also statistically significant; (iv) the CVs and ACs of different organs are related, to some extent, to diameter, height and origin of the tree, but the influence degrees of the factors on CVs and ACs are not the same
Modeling Compatible Single-Tree Aboveground Biomass Equations of Masson Pine (Pinus massoniana) in South China
Get PDFIn the background of facing up to the global climate change, it is becoming the inevitable demand to add forest biomass estimation to national forest resource monitoring. The biomass equations to be developed for forest biomass estimation should be compatible with volume equations. Based on the tree volume and aboveground biomass data of Masson pine (Pinus Massoniana Lamb.) in south China, the one, two and three-variable aboveground biomass equations and biomass conversion functions compatible with tree volume equations were constructed using the error-in-variable simultaneous equations in this paper. The results showed: (i) the prediction precision of aboveground biomass estimates from one variable equation was more than 95%; (ii) the regressions of aboveground biomass equations improved slightly when tree height and crown width were used together with diameter on breast height, although the contributions to regressions were statistically significant; (iii) for biomass conversion function on one variable, the conversion factor was decreased with growing diameter, but for conversion function on two variables, the factor was increased with growing diameter while decreased with growing tree height
Hydrologic and climate trends for the Coldwater River watershed in south-central British Columbia, Canada
Get PDFHistorical trends in streamflow and climate were investigated for the Coldwater River watershed in south-central British Columbia, Canada. Temporal increases in rainfall and total precipitation during the spring, summer, and autumn periods, as well as on an annual basis, at the city of Merritt near the mouth of the watershed, and year-round temperature increases at this site, compare with declining summertime and annual streamflows at the nearby Merritt hydrometric station on the Coldwater River. Declining summer flows at this site could reflect the dominance of temporally increasing evaporation that is offsetting increased precipitation over the same periods of the hydrologic year. Alternatively, increased water abstractions, altered regulation regimes, and/or land use changes in the watershed may also play significant/dominant roles. The relative absence of any coherent hydrological temporal patterns at the upstream Brookmere hydrometric station on the Coldwater River suggests that the net effects of warming temperatures, increasing precipitation, and any anthropogenic drivers over the past four decades are in approximate balance
The Diet of the Rhinolophidae in the “Kabylia of the Babors” Region, Northern Algeria
No full textMany bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one species to another
Weight matrix based identification of terpene synthases conserved motifs in Arabidopsis thaliana proteome
Get PDFTerpenes comprise the most diverse collection of natural products. Out of more than 30,000 individual terpenoids identified, at least half are synthesized by plants. A relatively small, but quantitatively significant, number of terpenoids are involved in primary plant metabolism. However, the vast majorities are classified as secondary metabolites; compounds not required for plant growth and development but presumed to have an ecological function in communication or defense and are widely used in industrial applications. Terpene hydrocarbon scaffolds are generated by the action of the mechanistically intriguing family of mono-, sesqui-, and diterpene synthases collectively termed as terpene synthases, that catalyze multistep reactions with diphosphorylated substrates of 10 (geranyl diphosphate), 15 (farnesyl diphosphate) or 20 (geranylgeranyl diphosphate) carbons. In the studied work, we performed a computational study on proteome wide identification of terpene synthase motifs in Arabidopsis thaliana proteome on the basis of weight matrix approach. We have developed an optimal weight matrix for the identification of terpene synthase motifs in the plant’s proteome. Weight matrix was constructed by aligning orthologous sequences of known terpene synthases originated from diverse plant species viz., Abies grandis, Nicotiana tobaccum etc. Sequences of detected domains & motifs were retrieved through SwissProtKB/NCBI on the basis of specific conservation IDs of Prosite, Pfam, Interpro, Prodom, COG, TIGR databases, while position specific scoring matrices were made through MEME, MotifSampler, PossuMsearch tools. Weight matrix based search of conserved motifs in the proteome of A. thaliana was done through ESA, Lahead and Simple algorithm based search tools of PossuMsearch biosuite in Linux system. Prediction was first validated by using positive control data set and optimized the method to reach prediction accuracy upto >90%. After tool performance evaluation, prediction was made on whole proteome at specific threshold/score value. Significant results were found in A. thaliana with motif similarity ranges from 80% to 100%. This proteome wide search model paves the path to identify more terpene synthases genes in A. thaliana, as well as in other plant systems