Miracle-dz/UniFAR-FTUs huggingface dataset:
Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

The autoregulatory motif of Nanog, a heterogeneously expressed core pluripotency factor in mouse embryonic stem cells, remains debated. Although recent time-lapse microscopy data provide the unparalleled ability to monitor Nanog expression at the single-cell level, the extraction of mechanistic knowledge is precluded by the lack of inference techniques suitable for noisy, incomplete and heterogeneous data obtained from proliferating cell populations. This work identifies Nanog’s autoregulatory motif from quantified time-lapse fluorescence line-age trees with STILT (Stochastic Inference on Lineage Trees), a novel particle-filter based algorithm for exact Bayesian parameter inference and model selection of stochastic models. We first verify STILT’s ability to accurately infer parameters and select the correct autoregulatory motif from simulated data. We then apply STILT to time-lapse microscopy movies of a fluorescent Nanog fusion protein reporter and reject the possibility of positive autoregulation. Finally, we use STILT for experimental design, perform in silico overexpression simulations, and experimentally validate model predictions via exogenous Nanog overexpression. We finally conclude that the protein expression dynamics and overexpression experiments strongly suggest a weak negative feedback from the protein on the DNA activation rate. We find that a simple autoregulatory mechanism can explain the observed heterogeneous Nanog dynamics. This finding has implications on the understanding of the core pluripotency network, such as supporting the ability of mESC populations to diversify their proteomic profile to respond to a spectrum of differentiation cues. Beyond this application STILT constitutes a generally applicable fully Bayesian approach for model selection of gene regulatory models on the basis of time-lapse imaging data of proliferating cell populations. STILT is freely available at: http://www.imsb. ethz.ch/research/claassen/Software/stilt—stochastic-inference-on-lineage-trees.html
Evolution and Extinction of Land Snails on Oceanic Islands

Nonmarine molluscs are the major animal group with the greatest number of recorded extinctions due to anthropogenic impacts, and that number is certainly a serious underestimate. Land snails, particularly endemic land snails of oceanic islands, are the group of molluscs that have sustained the most extinctions. Understanding their ecology and the evolutionary processes that have led to their extreme vulnerability is crucial if we are to be able to conserve these diverse and important species. Oceanic island snails tend to have low α-diversity and high β-diversity, and divergence of habitat use among related species is known to occur in some radiations of land snails on oceanic islands. Processes of speciation and ecological interaction are possible major drivers of these patterns. The ecological opportunities available at the initial stage of insular evolution and the scarcity of effective predators may have led to divergence of habitat use and high β-diversity in oceanic island snails. Fewer and less div.
Expression of Penaeus monodon lysozyme gene in prokaryocyte system and evaluation of its lytic activity

The c-type lysozyme cDNA of Penaeus monodon cloned previously in our lab (GenBank accession no. AF539466) was modified by PCR to delete the signal peptide and subcloned to pBV220 expression vector which contains P_RP_L promoter to construct the recombinant vector pBV220-lyz. pBV220-lyz was transformed to E.coli DH5α and then induced to express at 42℃. A specific band about 16kD in molecular mass was showed by SDS-PAGE analysis, which was larger than those from other species such as human, fish and insects (about 14kD). The recombinant P. monodon lysozyme existed as inclusion bodies in the cells. The inclusion bodies were collected, washed and then dissolved. And finally the target protein was dialyzed in order to recover its biological activity. Scanned and quantified by the Analysis System of Biology Image showed that the recombinant lysozyme accounted for 32% of the total cell protein, and was about 90% after purification. The biological activity of the recombinant protein was evaluated by turbidimetric assay described by Hultmark. The optimum pH and temperature of the lytic activities of the recombinant lysozyme were 6.0 and 40℃,respectively. The recombinant protein was found to possess potent lytic activities against Micrococcus lysodeikticus1-634, Vibrio alginolyticus As1.1833 and V. anguillarum E3-11. And it has some lytic activities against Edwardsiella tarda E 895205 but with little lytic activities against Aeromonas hydrophila AhG1, V. parahaemolyticus As1.1615 and E. coli DH5α. The standard lysozyme (lysozyme from chicken egg white) showed lower lytic activities against Micrococcus lysodeikticus1-634, Vibrio alginolyticus As1.1833 and V. anguillarum E3-1 compared with that of the recombinant protein. The present study suggests the potential application of the recombinant P. monodon lysozyme in aqauculture.
Inestabilidad genética y cambios en la cromatina en mutantes del complejo Tho en mitosis y meiosis de eucariotas modelo

Trabajo realizado en el Departamento de Genetica, Facultad de Biologia, y en el Departamento de Biologia Molecular, CABIMER, de la Universidad de Sevilla, para optar al grado de doctor en Biologia por el licenciado Maikel Castellano Pozo.
Directional Hearing in the Locust Schistocerca gregaria Forskfil (Acrididae, Orthophera)

At 2kHz, 3.5 kHz and 5 kHz the locust ear functions as a mixed pressure and pressure-gradient receiver. The ear is inherently directional at these frequencies. The directional characteristics are independent of the amount of body tissue (Figs. 6 and 7). At 15 kHz the locust ear functions mostly as a pressure receiver, and is inherently non-directional (Fig. 6d). Hearing is, however, directional at 15 kHz owing to diffraction caused by the body (Fig. 1). Auditory thresholds are influenced by the amount of body tissue at frequencies from 2 to 15 kHz (Fig. 8). At frequencies less than 6 kHz the sound conducted through the body is attenuated by 1 to 8 dB depending on the amount of body tissue. At frequencies greater than 12kHz the sound conducted through the body is attenuated by up to 18 dB, and the attenuation is only slightly influenced by body tissue (Fig. 2). The attenuation of sound conducted through the body is independent of the direction of sound, but may be affected by the amount of tissue between the ears (Fig. 4). The tissue in the body appears to act as a 'resistive' element, which introduces a phase shift in the sound conducted through the body relative to that striking the front side of the tympanum. Body tissue can set the level of sensitivity, but does not influence the receiver characteristics of the ear.
Glycerol Supplementation Effect on Biogas Production from Cattle and

Organic wastes are potential sources of biogas and high-quality bio-fertilizers. Biogas is an appealing energy product that can be used directly as a renewable alternative source of energy. Some of the most commonly used substrates for biogas production are cattle and pig manure. Technology for biogas production is an active research area. Studies on optimization of biogas production are being undertaken with a view to making the process fully cost-effective. This study was conducted to investigate the effect of glycerol supplementation on biogas yield under the respective appropriate optimum mesophilic temperatures and substrates to water dilution ratios of both cattle and pig manure substrates. Analysis of substrates and inoculum for various physico-chemical characteristics was carried out. The optimum mesophilic temperature for both cattle and pig manure substrates was determined to be 40 oC. The optimum cattle manure substrate to water dilution ratio was established to be 17.5:7.5 (m/v) and 5:20 (m/v) for pig manure substrate, respectively. On supplementing the optimum cattle manure substrate to water dilution ratio of 17.5:7.5 (m/v) with 0.1, 0.2 and 0.3 g of glycerol, the respective percentage increases in biogas yields over the control were calculated to be 6.4, 12.5 and 21.9%. Further, for the established optimum pig manure substrate to water dilution ratio of 5:20 (m/v) supplemented with 0.03, 0.05 and 0.08 g of glycerol, the respective percentage increases in biogas yields over the control were calculated to be 10.0, 17.65 and 29.6%. The study shows that, one, the upper limit of the mesophilic range (30-40 °C) gives a higher biogas yield; two, over-diluting or under-diluting substrates with water influences biogas yields; and three, glycerol which is also a by-product of biodiesel manufacturing can be advantageously utilized as a supplement to boost biogas production. Use of optimum conditions of temperature and dilution ratios would significantly improve biogas production.
A new rhamphorhynchid (Pterosauria: Rhamphorhynchidae) from the Middle/Upper Jurassic of Qinglong, Hebei Province, China

A heavily compressed, but nearly complete fossil skeleton recovered from the Middle/Upper Jurassic Tiaojishan Forma-tion of Mutoudeng, Qinglong County, Hebei Province, China, represents a new genus and species of long-tailed pterosaur, Qinglongopterus guoi gen. et sp. nov. The holotype and only known specimen has an estimated forelimb length of 0.18m. The new taxon is distinguished by a relatively short skull, a remarkably short pteroid with a distinctive knob-like distalexpansion, and a prepubis with a relatively slender distal process. Phylogenetic analysis demonstrates that Qinglongopter- us is a member of Rhamphorhynchidae, exhibiting many of the unique character states found in members of this clade. Qinglongopterus is strikingly similar to Rhamphorhynchus and more closely related to this taxon than to any other rham-phorhynchine, this pairing is supported by morphometric data and several synapomorphies (short, broad nasal process ofthe maxilla; forelimb length more than four times that of the hind limb; wing-phalanx one more than twice the length ofthe tibia). Qinglongopterus demonstrates that the highly derived skeletal morphology of Rhamphorhynchus, known onlyfrom the latest Jurassic (Tithonian) of Europe, had already appeared by the start of the Late Jurassic. This hints at evolu-tionary stasis in Rhamphorhynchinae, a phenomenon seemingly also present in two other clades of basal pterosaurs,Anurognathidae and Scaphognathinae, and contrasting sharply with basal monofenestratans which appear to have undergone extensive evolutionary change during the same interval.
Abiotic Stress-induced Expression of Artemisinin Biosynthesis Genes in Artemisia annua L.

The abiotic stress-induced expression pattern of three genes responsible for artemisinin accumulation was preliminarily elucidated in cultured Artemisia annua plants. The semi-quantitative RT-PCR determination showed that upon exposure to chilling, heat shock or UV light, the transcription levels of amorpha-4,11-diene synthase gene (ADS) and cytochrome P450 monooxygenase gene (CYP71AV1) were up-regulated; In contrast, under the circumstance without stress treatments, the expression levels of ADS and CYP71AV1 genes were relatively low, while the mRNA generated by the transcription of cytochrome P450 reductase gene (CPR) remained stable under pre-and post-treatments. The induced outcome by chilling stress was also supported by the measurement data from real-time fluorescent quantitative RT-PCR. Consequently, for A. annua shoots claimed by low temperature, the transcripts of ADS and CYP71AV1 genes were 11 folds and 7 folds higher than those of the control, but the CPR mRNA copy was almost equivalent to the control. Furthermore, a transient pre-chilling treatment led to an elevated artemisinin content up to 7.5~8.8 mg/g dry weight (DW), i.e., increased by 66.7%~95.6% as compared with the control, thereby providing art open space for enhanced artemisinin production by the environmental stresses.
Seasonal dynamics of soil microbial biomass C and N in two larch plantation forests with different ages in Northeastern China

Aiming to exhibit the soil fertility of larch plantation forests based on the soil microbial biomass,the soil microbial biomass C and N were observed in two soil layer(i.e.,humic layer and mineral layer) of two larch(Larix olgensis) plantation forests with different ages(nine years old: young plantation forest;forty-three years old: mature plantation forest) for one growing season in northeastern China.Meanwhile,the relationships between the seasonal dynamics of soil microbial biomass and the soil nutrient and soil water were also analyzed in this study.The results showed that microbial biomass C and N were higher in humic layer than those in mineral layer for both larch plantation forests.In humic layer,the microbial biomass C and N were higher in young plantation forest than those in mature plantation forest.In both spring and autumn,microbial biomass C and N in the same soil layer were significantly different between two plantation forests(P0.01). In humic layer,the microbial biomass C remained constant in young plantation forest through the growing season,while it reached maximum in autumn in mature plantation forest.The microbial biomass N was the highest in summer in humic layer for both plantation forests.In mineral layer,the microbial biomass C and N were the highest in autumn for both plantation forests.Microbial biomass C and N had a significant positive correlation with soil organic carbon and total nitrogen,but exhibited no significant correlation with soil water in both larch plantation forests.In addition,the microbial biomass C and N were also influenced by species composition and quantities of shrubs,and seasonal fluctuation of temperature in the stands.The above results suggested that:(1) the seasonal dynamics of soil microbial biomass C and N in the test stands were closely related with soil nutrients,and(2) the soil nutrients in young plantation forest were better than those in mature plantation forest.
The impacts of elephants on biodiversity in the Eastern Cape Subtropical Thickets

We review available information on the impact of elephants on the Subtropical Thickets of the Eastern Cape province as a contribution to the current debate around biodiversity and the need to manage elephant populations. This ecologically diverse region historically supported an abundance of elephants that was incrementally reduced to a single population limited to the Addo Elephant National Park (AENP). The results of research on elephant impacts associated with this population has shown that these animals influence many ecological processes, and patterns, including soil features, landscape patchiness and plant biomass and diversity. Furthermore, elephants influence insect, bird and antelope abundances and reduce browse availability for black rhinoceros. We conclude that elephants affect biodiversity at all levels investigated but that further research is necessary to identify the mechanisms responsible. Of specific concern is the observation that the AENP represents the only current example where elephants may be driving many endemic plants to extinction. This suggests that managing elephant impacts in Subtropical Thickets, specifically, is a matter of urgency.
Resistance Identification of Wheat Germplasm Resourcesto Macrosiphum avenae

From 1999 to 2002, 468 wheat germplasm resources from home and abroad were collected. Using fuzzy identify technique, their resistance to Macrosiphum avenae Fabficius was identified in Linfen,the main wheat production area in shanxi. Results show that there is significant differences of resistance to Macrosiphum avenae Fabficius between these wheat varieties . Among them, eleven wheat varieties are high resistance to Macrosiphum avenae Fabficius, and sixty-three middle.These wheat germplasm resources could be used in breeding.
L'évaluation (de l'évaluation)+ de la diversité lexicale

Les mesures de diversité lexicale sont systématiquement évaluées du point de vue de leur robustesse, mais rarement et peu rigoureusement quant à leur sensibilité. Cette contribution propose une méthodologie d'évaluation de la sensibilité basée sur une technique de génération de données textuelles permettant de contrôler artificiellement leur degré de diversité lexicale. La démarche est illustrée par la comparaison entre deux mesures basées sur deux façons différentes – et opposées – d'exploiter le principe de ré-échantillonnage pour l'évaluation de la diversité lexicale
Research Advancement of Nutritional Characteristics and Functions of Common Edible Oils

Common edible oils consists of olive oil,peanut oil,soybean oil,tea oil,sesame oil and so on,which are different in their compositions and contents of fatty acids,especially some unsaturated fatty acids such as oleic acid,linoleic acid and linolenic acid vary markedly.The monounsaturated fatty acids(MUFA) in the olive oil and tea oil is up to 70%,oleic acid accounts for about 40% in peanut oil,the polyunsaturated fatty acids(PUFA) in soybean oil is enriched,linolenic acid is its major unsaturated fatty acid,and the linoleic acid content in sesame oil accounts for more than 40%. These oils provide not only energy and essential fatty acids,but also fat-soluble vitamins and phytochemicals.Moreover,some kinds of cooking oils are proved to improve dyslipidemia.
Antineoplastic effects of peroxisome proliferator activated receptorγ agonists

The peroxisome proliferators-activated receptor γ (PPARγ) is a member of the NHR superfamily. PPARγ ligands can inhibit growth, induce apoptosis, and cause differentiation of cancer cells in vitro and in xenografts; and this can be enhanced by retinoids and NSAIDs. This paper reviews PPARγ-induced antineoplastic signaling pathways, and summaries the antineoplastic effects of PPARγ agonists in different cancer cell lines, animal models, and so on.
Research Progress on Chinese Medicinal Material Aurea Helianthus

Aurea Helianthus is a kind of annual herb in Malvaceae Abelmoschus and it is one of the endangered plants. Its main effects are antipyretic,antiinflammatory,analgesic and it has the functions of blood lipid regulation,tumor cells inhibition,immune regulation,and antioxidation and so on. It is a kind of high medicinal valuable plants. This article analyzes and summarizes its resource distribution,main constituents and biological activity on the base of the related literatures in recent years. This article provides the references for Aurea Helianthus' further study and development.
STUDIES IN THE CLASSIFICATION AND NOMENCLATURE OF THE BACTERIA X. SUBGROUPS AND GENERA OF THE MYXOBACTERIALES AND SPIROCHAETALES

Characters those of the order. The following generic names have been used for organisms of this group. Polyangium Link, 1795 Stigmatella Berkeley and Curtiss, 1857, p. 70 Chondromyces Berkeley and Curtiss, 1857, p. 313 Cystobacter Schroeter, 1886, p. 170 Myxobacter Thaxter, 1892, p. 403 Myxococcus Thaxter, 1892, p. 403 Myxobotrys Zukal, 1896, p. 346 The genera may be differentiated by the following key:
Nosema Apis and Dysentery of the Honeybee

SUMMARYSevere winter losses of honeybee colonies and poor growth or dwindling in spring were associated with dysentery. They were not caused simply by an enzootic infection with Nosema apis. Infection, although it is common, is usually slight in most colonies, and is spread by dysentery, but it is not the primary cause.
The Investigation on the Patents and Properties of Transgenic Bt/CpTI Rice

Rice is one of the most important food crops in the world.Since experiment of transgenic rice first succeeded in 1988,it has been deeply studied and applied to many fields,especially in insect-resistance,disease-resistance,herbicide-tolerance,resistance to adverse conditions,and improving the rice qualities. In the development of transgenic rice,many patents were involved.Through investigation on the patents and properties related to the transgenic rice,the main conclusions were drawn that the patents and properties belonging to the foreign organization hold the development of the transgenic rice by Chinese scientists. The reasons and effects are discussed and the solutions are proposed in this article.
Thrombocytosis and CA125 as Predictor of Malignancy in Gynaecological Pelvic Mass

Background: Pelvic masses are common in women & can present at any age of woman life, it could be benign or malignant mass and may originate from gynecological organs like cervix, uterus, uterine adnexia, or from other pelvic organs like intestine, bladder, ureters, skeletal muscle, and bone.Objective: We attempted to determine the increasing of platelet counts(> 450.000 /micro liter) and CA125serum level (> 35 U/mL) as useful tools for predicting and confirming malignancy in gynecological pelvic mass.Patients and methods: A prospective unmatched hospital based case-control study carried out at Baghdad Teaching Hospital, about 126 women were enrolled in our study, divided into two groups 60 women were control group (free of gynecological pelvic mass). The other group includes 66 women above 15 years old with gynecological pelvic mass were all candidate for laparotomy.Results: Serum CA125 and blood platelets count were tested for validity when used as a test to predict a diagnosis of malignancy in gynecological pelvic mass differentiating it from benign gynecological pelvic mass. Both tests showed a very high validity in diagnosis, with serum CA125 showing a marginally higher validity.All studied subjects with a blood platelets count ≥ 385.000 and CA 125≥ 41.7were malignant, while everybody below this cut-off value was benign or healthy.Conclusion: Both blood platelet count (≥385 X 103microlitter) &serum level of CA125 (≥41.7 U/mL) are useful predictor tools to confirm malignancy in gynecological pelvic mass.
Sequence Analysis of Mitochondrial 16S rRNA Gene of Three Species of Macrobrachium

In order to understand the molecular genetic differences among three species of Macrobrachium,i.e.,M.rosenbergii,M.nipponensis,and M.qilianensis,2 individuals of each species were collected and their mitochondrial 16S rRNA gene segment sequences were obtained by using the method of PCR amplification and sequencing.After alignment,297 base pairs of consensus sequences of 16S rRNA were used.Fourty-seven variable sites were detected,accounting for 15.8% of total sequence.The average base pair contents of three species of Macrobrachium are T(37.7%),C(10.9%),A(29.8%),and G(21.6%),respectively.The individual difference is 3% within M.rosenbergii,and is 0.7% within M.nipponensis and M.qilianensis. The species differences are between 0 and 0.7% for M.nipponensis and M.qilianensis,but for M.rosenbergii,the values are between 13.1% and 14.8% for M.nipponensis and M.qilianensis. Phylogenetic tree(NJ) shows that M.rosenbergii constitutes one monophyletic group,but M.nipponensis and M.qilianensis constitutes the other monophyletic group.This result suggested that M.nipponensis and M.qilianensis are close related species,and their difference may be at subspecies level.