Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine bacterioplankton consortia follow deterministic, non-neutral community assembly rules

The Bermuda Atlantic Time-series Study site provided an opportunity to study bacterial community assembly processes at 2 different depths, the surface and 200 m, in the upper mesopelagic, just below the euphotic zone. Over 100 monthly bacterioplankton DNA samples, from each depth, were analyzed using 16S rRNA gene sequences parsed with the custom software package PhyloAssigner. Co-occurrence networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the 2 depths were remarkably similar, and network parameters, such as connectance, were in the same range as previously published for ecological networks. Spectral clustering applied to similarity matrices based on exact connections revealed clusters of nodal taxonomic units (NTUs) that peaked at similar times, supporting deterministic, niche-based assembly. An algorithm that used hierarchical Dirichlet processes (HDPs) to model neutral communities based on learned parameters indicated that community assembly processes fit niche-based models at the metacommunity level for both depths. However, HDP analyses restricted to SAR11, SAR86, or SAR202 NTUs supported the neutral assembly hypothesis, suggesting that neutral process models may apply within some phylogenetic domains. To understand whether phylogenetically related taxa can substitute for one another in networks, we created a new metric, phylogenetically weighted connectivity, which considered the similarity of connections among near phylogenetic neighbors. This analysis suggested that phylogenetically similar lineages share similar network connections. Overall, our findings show that niche-based community assembly models are the best fit at both depths but that the neutral model may apply at some phylogenetic scales.
Maintaining their genetic distance; limited gene flow between widely hybridising species of Geum with contrasting mating systems

Mating system transition from outcrossing to selfing frequently gives rise to sister lineages with contrasting outcrossing rates. The evolutionary fate of such lineages depends on the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, two sister species derived by mating system transition, which frequently hybridise. A draft genome was generated for G. urbanum and used to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the two species diverged 2-3 Mya, and that long term gene flow between them has been very low (M=0.04). G. rivale showed greater genetic diversity in sympatry than allopatry, but genetic divergence between species was no lower in sympatry than allopatry, providing little evidence for recent introgression. Clustering of genotypes revealed that, apart from four early generation hybrids, individuals in sympatric populations fell into two genetically distinct groups with <1% admixture that corresponded exactly to their morphological species classification. Although our data suggest limited gene flow, we observed joint segregation of two putatively introgressed SNPs in G. urbanum populations that was associated with significant morphological variation; this provides tentative evidence for rare introduction of novel genetic diversity by interspecific gene flow. Our results indicate that despite frequent hybridisation, genetic exchange between G. rivale and G. urbanum has been very limited throughout their evolutionary history.
Comparison of fatty acids in beef tissues from conventional, organic and natural feeding systems in western Canada

Turner, T. D. , Jensen, J., Pilfold, J. L. , Prema, D. , Donkor, K. K. , Cinel, B. , Thompson, D. J., Dugan, M. E. R. and Church, J. S. 2015. Comparison of fatty acids in beef tissues from conventional, organic and natural feeding systems in western Canada. Can. J. Anim. Sci. 95: 49-58. The effect of production system on intramuscular and associated trim fatty acid (FA) profiles of retail ribeye steaks from conventional and niche market organic and natural (grain- or grass-fed) beef were compared. Meat from organic grain- and grass-fed systems was leaner, containing greater proportions of polyunsaturated FA, i.e., 18:3n-3, 20:5n-3, 22:5n-3, 22:6n-3. Correspondingly, the n-6/n-3 ratios of organic grain- and grass-fed systems were 3:1, while conventional and natural grain systems had ratios of 8:1. High forage-to-grain ratio production systems increased proportions of desirable biohydrogenation intermediates (BI), including t11-18:1 and c9,t11-18:2, whereas conventional and natural grain systems elevated t10-18:1. Trim fat was similarly affected by production system, and was a relatively richer source of BI. Overall, proportions of desirable FAs, including n-3 and BI, were greater for organic grain- and grass-fed systems, emphasizing the importance of a high forage-to-grain ratio to enhance the healthfulness of beef, whereas conventional and natural grain-fed systems were largely equivalent.
Phylogenetic Analysis of the Genus Pistacia (Anacardiaceae)

Pistacia is an economically important genus because it contains the pistachio crop, P. vera, which has edible seeds of considerable commercial importance. The evolutionary history of the genus and the taxonomic relationships among the species are controversial and not well understood. This study that has been conducted on this genus to refine taxonomic and evolutionary relationship utilizing different types of data (including morphology, anatomy and molecular) The studied species were the following: Pistacia aethiopica J. O. Kokwaro, P. atlantica Desf. , P. chinensis Bunge, P. eurycarpa Yaltirik, P. falcata Becc. ex Martelli, P. integerrima Stew. ex Brand. , P. khinjuk Stocks, P. lentiscus L. , P. mexicana HBK, P. mutica Fisch. & Mey. , P. palaestina Boiss. , P. terebinthus L. , P. texana Swingle, P. vera L. , and P. weinmannifolia Poiss. ex Franch. Phylogenetic analysis based on morphological data strongly supported the monophyly of Pistacia. The genus divided into two monophyletic groups. One group (Section Pistacia) contains P. atlantica, P. chinensis, P. eurycarpa, P. falcata, P. integerrima, P. khinjuk, P. mutica, P. palaestina, P. terebinthus, and P. vera while the other group (Section Lentiscus) contains P. aethiopica, P. lentiscus, P. mexicana, P. texana, and P. weinmannifolia. In anatomical analysis, all species had anomocytic stomata. In most species, the stomata density was higher on the abaxial surface than the adaxial. The ratio of abaxial to adaxial stomatal density varied from 0.0 to 1.7. Stomatal distribution may provide insights into how Pistacia species evolve in terms of leaf anatomy and respond to different climatic changes. Stomatal distribution changed (losing stomata on either surface) as the genus
The relevance of viral culture based methods for the detection of rat cytomegalovirus (RCMV all-03) in the modern era of technology

In spite of the unequivocal advantages of traditional virological methods, its utilization seems to have taken a back seat coincident with the concurrent advances in science and technology. This study examined the impact of such techniques in the groundwork identification of rat cytomegalovirus ALL-03 strain. Virus was validated in terms of its intrauterine novelty, cytopathogenicity and was identified based on morphologic criteria classical of herpesvirus. Our findings demonstrate the suitability of primary brain endothelial cells for the propagation of the virus resulting in concomitant production of cytopathic effects and formation of plaques comparable to the ones produced in established secondary cell lines. In the absence of any known sequences for molecular based detection method, such findings provided critical clues crucial for the preliminary identification of the virus. This paper concludes that conventional methods such as tissue culture and electron microscopy are still in the forefront in the field of virology and remains relevant, but should ideally be used in conjunction with more advanced methodologies for a more comprehensive evaluation of novel viruses.
Folate Absorption Across the Colon: And the Modulation of Bacterial Folate Synthesis by Diet

While assessment of folate requirements has been ba sed only on dietary intakes, folate produced by the colonic microflora can exceed amoun ts consumed in food. Bacterially synthesized folate is absorbed across the rat and p iglet colon. In vitro studies suggest, but direct evidence is lacking that folate is absorbed across the intact human colon. If indeed folate is absorbed, the amount synthesized may be suscepti ble to manipulation by fibre and prebiotics intake. We therefore performed two studies to inve stigate folate absorption across the colon. To confirm absorption across the intact human colon , in our first study, 684 nmol (320 μg) C5-glutamyl-[6S]-5-formyltetrahydrofolate was infused into the cecum of six adults and blood samples were collected. Tandem mass spectrom etry confirmed folate absorption across the colon by appearance in plasma of C5-[6S]-5-methyltetrahydrofolate, at a rate of 0.6±0. 2 nmol/h versus 7±1.2 nmol/h after intravenous inject ion of 172 nmol C5-5formyltetrahydrofolate. Since bifidobacteria are potent folate producers, i n our second study we evaluated the influence of bifidogenic oligosaccharides on coloni c folate production and host folate status, using a piglet animal model. Piglets (n=12) were r andomly assigned a milk-based formula with 5g/L inulin + 5g/L galactooligosaccharides, or 5g/L maltodextrin (control). After 28 days, the weights of colon contents (178 %) and colon tissue (37.9 %) of piglets fed oligosaccharides were greater than controls ( P=0.0003, P=0.0044, respectively). The bacterial load and fol ate contents in the colons of piglets fed oligosacchari des were greater than controls ( P=0.0022,
Growth and yield of French bean (Phaseolus vulgaris L.) under organic farming

A fi eld experiment was conducted during 2007-2010 to study the effect of levels of organic manure and conventional practices on growth and yield of French bean grown organically. The trial was carried out in organic experimental block of IIHR farm, Hesaraghatta, Bangalore. The trial included four levels of organic manure nutrient and two inorganic nutrient supply treatments. The treatment which received 100 per cent recommended dose of N (RDN) through organics produced the highest pod yield (17.77 t/ha) followed by treatments which received 75 per cent RDN through organics and conventional practices (17.45 and 15.93 t/ha). Plant growth parameters such as plant height (45.5 cm), number of leaves per plant (42.9), leaf area per plant (2706 cm2), nodules per plant (43.9), pod weight per plant (160.1g) and pod length (14.7 cm) were also comparatively higher in this treatment resulting in better pod yield. Application of recommended dose of chemical fertilizer in conjunction with farm yard manure recorded higher values for growth and yield parameters like number of leaves, leaf area, dry matter production, number of pods, pod weight per plant and pod length which also resulted in signifi cantly higher pod yield as compared to the treatment which received recommended dose of chemical fertilizer only.
Comparative Transcriptome Analysis of Three Bactrocera dorsalis (Diptera: Tephritidae) Organs to Identify Functional Genes in the Male Accessory Glands and Ejaculatory Duct

Abstract The insect male accessory glands/ejaculatory duct (MAG/ED) are important tissues of the male reproductive system. The MAG/ED's functions in reproduction have been well studied in Drosophila (Diptera: Drosophilidae) but remain largely unknown in the important agricultural pest Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). In the present study, we re-assembled the transcriptome datasets of B. dorsalis's fat body, testis, and MAG/ED and compared these tissue-specific transcriptomes. Clean reads from these transcriptome data sets were de novo re-assembled and clustered into 31,782 unigenes (average 922 bp). In total, 21,306 unigenes were functionally annotated by Blasting against online databases. Comparative transcriptomic analysis identified numerous genes that were identified with the expressed tissue-bias patterns. Some MAG/ED-specific genes potentially involved in spermatozoa motility and capacitation (e.g., perlucin, glucose dehydrogenase, lipase), mating regulation (pheromone-binding protein—related protein), and immunity (lectin) were identified in B. dorsalis. The expressions of some of these genes were further validated by realtime quantitative polymerase chain reaction at transcriptional level. All of these identifications will help us to explore the physiological regulation of mating and reproduction in B. dorsalis in the future.
Adult Stem Cells in the Pathogenesis and Treatment of Endometriosis

The human endometrium is a dynamic tissue that undergoes approximately 400 cyclical episodes of proliferation, differentiation, shedding, and regeneration in a woman's reproductive lifespan. The regenerative capacity of human endometrium is likely mediated by adult stem cells. At the cellular level, endometrial mesenchymal stem/stromal cells, located in both the functionalis and basalis layers, support regeneration of the stromal vascular compartment and epithelial progenitor cells, postulated to reside in the basalis epithelium, likely regenerate the glands. Bone marrow adult stem cells, including endothelial progenitor cells, may also participate. Endometriosis can be considered an endometrial proliferative disorder due to dysregulation of the cellular and molecular regenerative processes. Endometriosis is primarily thought to occur via retrograde menstruation of endometrial debris. It is postulated that endometrial stem/progenitor cells, which have been identified in menstrual blood, are shed into the peritoneal cavity where they adhere to pelvic organs and initiate endometriotic lesions. The homing of bone-marrow-derived adult stem cells to endometriotic lesions is thought to drive progression of the disease. New drug therapies are urgently required for the treatment of endometriosis due to frequent disease recurrence with current surgical or medical treatments. Medications directly targeting endometrial stem/progenitor cells during menstruation, or following surgery, or targeting bone marrow cell trafficking, are potential targets for future therapies to manage disease initiation and progression. In this review, we will summarize the current literature on adult stem cell contributions to the development of endometriosis and will then examine the current potential therapies that may target endometrial stem/progenitor cells.
Antibody-mediated modulation of the IgM B-cell receptor (BCR) expression and signaling.

3050 Background: Targeting the BCR signaling pathway in B-cell malignancies has been shown to be therapeutic, but inhibition of the BCR itself has remained elusive due to serum IgM (sIgM) sequence homology. A unique sequence in the extracellular domain of membrane IgM (ECD-mIgM), designated proximal domain (PD), is not expressed in sIgM. Anti-PD monoclonal antibodies (mAbs) can be used to purify ECD-mIgM for mAb generation. Here we identify an ECD-mIgM conformational epitope not detected in sIgM. Methods: High affinity anti-PD monoclonal antibodies (mAbs) were generated by proprietary immunization techniques. These mAbs are shown by ELIZA, Western blots and Scanning Immuno-Electron Microscopy (SEM) to bind to mIgM protein and mIgM+ expressing cell lines (CA 46, SU-DHL-5, CRL-1596, CRL-1432, CRL-1642). Using these high affinity anti-PD mAbs, mIgM was immune-affinity purified. Second generation mAbs detecting mIgM conformational epitopes and not reacting with sIgM in ELIZA/Western/SEM assays were collected.
The histology of grain caryopses for nutrient location: a comparative study of six cereals

Summary In this study, we compare the histological localisation of phenols and β-glucan in six cereal cross sections. The concentrations of β-glucan and total phenols in whole grain flour (WGF) were also investigated to provide their nutrient content in grams. Cross sections of durum, soft, einkorn and emmer wheat, oats and barley were stained with Azan Trichrome (ATH) and periodic acid–Schiff (PAS) to characterise the morphology and cytohistology of the living cells in the aleurone, subaleurone and germ, as well as the a-nucleated cells in the starchy endosperm. Phenol localisation in the outer layers was performed by fluorescence microscopy due to the presence of ferulic acid. β-Glucan, examined with Calcofluor White staining, was found to be located primarily in the subaleurone layer and starchy endosperm of oats and barley. Our findings shed light on why WGF nutritional value is markedly reduced when the bran is removed through milling.
Systematics of Yoania prainii (Orchidaceae: Calypsoinae).

Recently, two new genera of mycoheterotrophic orchids were described from China: Danxiaorchis Zhai, Xing & Liu (2013: e60371) and Yunorchis Liu, Zhang & Li (2015: e123382). Both were considered to be monospecific, and in each case the descriptions were accompanied by a phylogenetic analysis.
Role of Visionary Leadership in the Performance of the Employees at a Workplace: Moderating Effect of Organizational Citizenship Behavior

The purpose of this study is to explore the role of visionary leadership (VL) in the performance of the employees in an organization, with the moderating role of organizational citizenship behavior (OCB). VL enables the employees to work collectively to get the desired results. OCB is associated with job satisfaction level and the faith of the employees in their top management Data have been collected from the employees working in the service sector of Rawalpindi/Islamabad regions of Pakistan. A total of 350 questionnaires have been distributed, out of which 275 questionnaires were responded. Convenient sampling has been done to get the desired outcomes. SPSS and AMOS software have been used to test the proposed hypotheses. Results of this study have shown the significant relationships between the variables. This research will help the managers and organization to incorporate the results in their management to get the maximum output from the employees. In addition, this study has explored the VL impacts on the performance of the employees as it is a very important phenomenon at any workplace. Aus. J. Bus. Sco S. & IT. Vol 3(2), April 2017, P 62-70
Uncertainty estimation and model selection in stock assessment models with non-parametric effects on fishing mortality

Uncertainty estimation and model selection in stock assessment models with non-parametric effects on fishing mortality Leire Citores*, Leire Ibaibarriaga, and Ernesto Jardim AZTI-Tecnalia, Marine Research Unit, Txatxarramendi Ugartea z/g, 48395 Sukarrieta, Basque Country, Spain BCAM Basque Center for Applied Mathematics, Applied Statistics, Mazarredo 14, E48009 Bilbao, Basque Country, Spain Sustainable Resources Directorate, Water and Marine Resources Unit, European Commission Joint Research Center (JRC), Via Enrico Fermi 2749, 21027 Ispra (VA), Italy *Corresponding author: tel: þ34 667 174 393; fax: þ34 946 572 555; e-mail: lcitores@azti.es
AnÁlise ovAriAnA do AriAcó, lutjanus synagris (Actinopterygii: lutjAnidAe), e considerAções sobre suA reprodução no est Ado do ceArÁ

Some aspects of the reproductive biology in females of lane snapper, Lutjanus synagris , were studied with the objective to describing macroscopically the gonads, addressing their stages of sexual maturity and histological organization, including the maturity stages of germinative cells. These descriptions give a support to fisheries biology investigations. A total of 272 females, collected monthly between May, 2000 and April, 2001, in Mucuripe Bay, Fortaleza, Brazil, were macroscopically evaluated, out of which 60 females were selected to provide ovarian material and histological sections. The stages of ovarian development based on morphology were defined as: A – immature, B – in maturation, C – mature and D – spent. The oocyte development phases were defined as: young germinative cells, pre-vitellogenic oocyte, final vitellogenic oocyte and mature oocyte. The female’s mean length at first sexual maturity was estimated as 21.5 cm FL and 23.4 TL. The species presents multiple spawning, yet with a period of major reproductive activity from January to April, and less intensive one, from August to December.
Comparative Study Between Different Types of Media used for the Isolation of Uropathogens with Special Reference to E.coli

Escherichia coli is the greatest cause of primary urinary tract infections. The present study aimed Urinary tract infection in female with special reference Escherichia coli and its antibiotic susceptibility pattern. A total of 100 urine samples were collected from different hospitals of Allahabad. The samples were cultured on Cystein lysine electrolytes deficiency media, MacConkey’s agar, Nutrient agar and Hicrome UTI agar media. Based on the results it was found that different media had different properties and Hicrome UTI agar was the best and convenient media for the isolation of Escherichia coli and other uropathogens. Further it was also observed that Escherichia coli was the most common organism for UTI in female.
Changes in function and ultrastructure of striatal dopaminergic terminals that regenerate following partial lesions of the SNpc

Following partial substantia nigra lesions, remaining dopaminergic neurones sprout, returning terminal density in the dorsal striatum to normal by 16 weeks. This suggests regeneration and maintenance of terminal density is regulated to release appropriate levels of dopamine. This study examined the structure and function of these reinnervated terminals, defining characteristics of dopamine uptake and release, density and affinity of the dopamine transporter (DAT) and ultrastructural morphology of dopamine terminals in the reinnervated dorsal striatum. Finally, rotational behaviour of animals in response to amphetamine was examined 4 and 16 weeks after substantia nigra pars compacta (SNpc) lesions. Dopamine transport was markedly reduced 16 weeks after lesioning along with reduced density and affinity of DAT. Rate of dopamine release and peak concentration, measured electrochemically, was similar in lesioned and control animals, while clearance was prolonged after lesioning. Ultrastructurally, terminals after lesioning were morphologically distinct, having increased bouton size, vesicle number and mitochondria, and more proximal contacts on post‐synaptic cells. After 4 weeks, tendency to rotate in response to amphetamine was proportional to lesion size. By 16 weeks, rotational behaviour returned to near normal in animals where lesions were less than 70%, although some animals demonstrated unusual rotational patterns at the beginning and end of the amphetamine effect. Together, these changes indicate that sprouted terminals are well compensated for dopamine release but that transport mechanisms are functionally impaired. We discuss these results in terms of implications for dyskinesia and other behavioural states.