Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal constancy of faunal assemblages in 'mesohabitats' ― application to management?

Variations in the composition of faunal assemblages in streams are often associated with changes in areas of substrate. An observer walking along the bank finds these areas easy to distinguish and we have used these as our basic ecological unit. Essentially the unit is visually distinct from the bank and we have called it a mesohabitat to introduce a scalar dimension which the term biotope does not have and to distinguish it from microhabitats such as a leaf tip or stone surface and macrohabitats which might include the whole of a reach of river. We wished to test the hypothesis that mesohabitats support specific faunal communities which remain distinct and faithful throughout the seasons and to explore the use of such information in environmental assessment. 10 replicate faunal samples, together with associated depth and velocity measurements, were collected from each of 8 mesohabitats ('Ranunculus fast', 'Ranunculus slow', 'Silt', 'Nasturtium', 'Phragmites', 'Sand', 'Gravel fast' and 'Gravel slow') in spring, summer and autumn from a lowland weeded stream, the Mill Stream, in southern England. Analysis of variance indicated that both abundance and faunal richness varied significantly between and within mesohabitats. The most valiability was noted in 'sand', 'Ranunculus slow', and 'silt'. Variation between mesohabitats was significant for all seasons but there was a tendency for the differences to be greatest in spring samples. Multivariate techniques, DECORANA and CCA (canonical correspondence analysis) showed that in general the mesohabitats selected for study remained distinct from one another but that the degree of separation varied markedly with season. In spring when discharge was high mesohabitats showed considerable overlap on the basis of their faunal communities. As the year progressed and discharge declined so mesohabitats became more distinct. There is a continual expansion and contraction of available mesohabitat. Thus instream macrophyte beds increase at the expense of open water habitat, and marginal vegetation encroaches into the main flow. The stream therefore consists of a dynamic system of mesohabitats whose borders are best defined in low flow periods. The 'distinctness' of the mesohabitats meant that it was possible to determine their proportion along a 300 m reach of the Mill Stream. The application of these data is discussed. This information together with data on the 'quality' (species richness, faunal abundance, rarity) can be used to categorise a stream at reach level and assess the effect of management (flow changes, dredging, bank clearance and weed-cutting) on the distribution of mesohabitats and hence on the faunal assemblages associated with them. This could be considered a more useful scale than point sampling when considering fish and macrophytes as well as invertebrates.
Direct evidence of the impact of longline fishery on mortality in the Black-footed Albatross Phoebastria nigripes

Summary The incidental bycatch of seabirds in longline fisheries is one of the most striking examples of diffuse and incidental impact of human activities on vertebrate species. While there are various types of evidence of a strong impact of longline fisheries on seabirds, in particular albatrosses, the incidental bycatch mortality has never been directly linked to estimates of bycatch derived from on-board surveys. We develop a capture-recapture analysis which relates the annual probability of survival in the Black-Footed Albatross to the estimated absolute bycatch. By converting the absolute bycatch into an estimate relative to population size and using the theory of exploited populations, we show that survival probability decreases linearly with bycatch, and that the bycatch is underestimated by at least 50%, confirming suspicions based on reviews of the bycatch survey procedures, and raising further concerns about the impact of longline fisheries on seabirds.
A simple method for the extraction of reducing and non‐reducing sugars from carrot and other storage root vegetables

A procedure is described for the extraction of sucrose, glucose and fructose from storage root vegetables. An automatic domestic pressure cooker containing a circular test tube rack holding 36 tubes was used for the extraction. All water soluble sugars were extracted in 30 min at 110°C. The method is at least as efficient as those using hot ethanol and methanol: chloroform:water and is significantly more efficient in its use of time and energy.
Investigating the Roles of Tat Specific Factor 1 in Both HIV-1 and Cellular Gene Expression

Investigating the Roles of Tat Specific Factor 1 in Both HIV-1 and Cellular Gene Expression by Heather Bennett Miller Department of Molecular Genetics and Microbiology Duke University Date:_______________________ Approved: ___________________________ Mariano Garcia-Blanco, Supervisor ___________________________ Beth Sullivan, Committee Chair ___________________________ Robin Wharton ___________________________ Georgia Tomaras ___________________________ Arno Greenleaf An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2009
2009 Anesthesia & Analgesia Guide for Authors

s and should not exceed 1500 words. Pro/Con/Core Reviews present a focused review accompanied by expert commentary for and against a specific clinical topic or technique. The Core Review includes an Abstract (unstructured, maximum of 100 words), and the text of the review, which should not exceed 2500 words. It may be accompanied by figures or a video supplement. Pro/Con/Core Reviews are solicited by the Editorial Board. Book and Multimedia Reviews report current literature in perioperative medicine, critical care, and pain management. Publishers interested in having their book or multimedia material reviewed by the Journal should first contact Dr. Paul White, Section Editor for Book, Multimedia, and Meeting Reviews at paul. white@utsouthwestern.edu prior to sending the material. All books and multimedia material for review should be sent to Paul F. White, Ph.D., M.D., FANZCA, Department of Anesthesiology and Pain Management, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., RM F2.208, Dallas, TX 75390-9068. Book Reviews should not exceed 750 words. Meeting Reports are scholarly outlines of the program and content of a scientific meeting. They may be organized temporally (day by day) or thematically (topic by topic). Authors interested in submitting meeting reports should first contact Dr. Paul White, Section Editor for Book, Multimedia, and Meeting Reviews at paul.white@utsouthwestern.edu to confirm that the meeting is of general interest to the readership. Meeting reports do not have Abstracts and should not exceed 1500 words. Focused Reviews summarize recent advances in a particular field with direct application to clinical practice. They are intended to efficiently communicate new knowledge to make clinical practice safer, more efficient, and up-to-date. They are solicited by the Editorial Board. Focused Reviews contain an unstructured abstract, text, and references. They should not
Correspondence between shape and feeding habit changes throughout ontogeny of gilthead sea bream Sparus aurata L., 1758

The shape development through ontogeny of the gilthead sea bream Sparus aurata was studied by means of geometric morphometry and elliptic Fourier analysis. In parallel, observations are reported on the feeding habits of the same specimens until the end of the larval stage. Data for later stages were obtained from the literature. Sparus aurata underwent ontogenetic shifts in diet from zooplankton, selected by larvae, to mysids, errant polychaete, amphipods and isopods for juveniles, and finally to hard prey (decapods, gastropods and bivalves) in adults. The aims were: (1) to provide a complete description of shape development, from hatching to the adult stage, (2) to identify distinguishable morphological stages during ontogenesis, (3) to search for correspondence between morphological devel- opment and diet shifts, and (4) to examine the functional effect connecting shape changes to diet shifts and habitat selection. The growth trajectory obtained reflected a saturating curve made up by different sections. Each section corresponded to a developmental shape stage characterized by different allometric trends of different body regions. Indeed, these shape stages matched those based on widespread features of development. Furthermore, the size- defined limits of the shape stages closely match the feeding shifts in the development of dietary behaviour of gilthead sea bream. The different constraints underpinning this pattern of covariation are discussed by showing that the growth profile of early stages is mainly determined by organogenesis of important apparati, whereas that of later stages seems optimized to improve feeding on hard prey in complex microhabitat and swimming abilities, and to reduce predation risk.
Two new sesquiterpenes from the stems of Miliusa velutina

Abstract From the ethyl acetate extract of the stems of Miliusa velutina, seven compounds (1–7) were isolated, including two new compounds such as mivelutina A acid (1), mivelutina B acid (2) and one known compound mivelutina B methyl ester (3). For this NMR data were not known previously. Their relative structures were elucidated based on NMR spectroscopic analysis. The absolute configuartions were determined based on DFT calculations of 13C chemical shifts. All of the seven compounds were screened for their in vitro cytotoxic activities against HepG2 cell line using the SRB assay. Epoxyconiferyl alcohol (7) showed the highest potential for the cytotoxicity of cancer cell lines HepG2 with the IC50 values of 95.94 μg/mL (527 μM). Graphical Abstract
Bedtime procrastination predicts the prevalence and severity of poor sleep quality of Chinese undergraduate students

Abstract Objective Bedtime procrastination is a type of unhealthy sleep behavior, but whether it affects sleep quality remains unknown. The current study aimed to examine the relationship between bedtime procrastination and poor sleep quality among Chinese college students. Participants: A total of 1550 Chinese undergraduates participated and effectively completed the study. Methods: This cross-sectional study collected information on bedtime procrastination and self-reported sleep quality via the Bedtime Procrastination Scale and the Pittsburgh Sleep Quality Index. Results: The prevalence of poor sleep quality was 39.42% among Chinese undergraduates. Age, education, and bedtime procrastination independently predicted the prevalence of poor sleep quality. Bedtime procrastination was a unique contributor to the severity of poor sleep quality. Conclusions: This study highlighted the independent associations between bedtime procrastination and the prevalence and severity of self-reported poor sleep quality. These findings may be helpful in designing effective measures to improve the sleep quality of college students.
Evidence for Hybrid Origin and Segmental Allopolyploidy in Eutetraploid and Aneutetraploid Lepisorus thunbergianus (Polypodiaceae)

Abstract Several cytotypes (polyploids and aneuploids) have been reported in Lepisorus thunbergianus. The relationships between these cytotypes within the species remain poorly understood. We studied populations in an area where various cytotypes of L. thunbergianus as well as two diploid species, L. angustus and L. onoei, candidate parental species that may be involved in allopolyploid origins of L. thunbergianus polyploids, occur. We determined the ploidy levels of sampled materials by direct chromosome counting and flow cytometry. We elucidated the origins of L. thunbergianus polyploids by analyzing allozyme polymorphisms, and in addition, we examined the occurrence of segmental allopolyploidy by comparing allelic variation between polyploids and their parental diploids. Six cytotypes, i.e. one diploid (2n = 50), two triploid (2n = 75 and 76) and three tetraploid (2n = 100, 101, and 102) cytotypes, were observed in L. thunbergianus, and the two diploid species, L. angustus (2n =52) and L. onoei (2n =50) were confirmed to include a single cytotype each. Allozyme analyses indicated that the tetraploid (2n =100) and hypertetraploid (2n = 102) of L. thunbergianus originated by allopolyploidy between diploid L. thunbergianus (2n = 50) and diploid L. angustus (2n = 52), since the polyploids shared alleles with these two diploids that were unique to each diploid. The allozyme patterns excluded the possibility that L. thunbergianus polyploids originated from L. onoei. The unbalanced heterozygosity and homozygosity found in the tetraploid and the hypertetraploid of L. thunbergianus indicated their segmental allopolyploidy.
RNA-Seq Transcriptome Analysis Reveals Long Terminal Repeat Retrotransposon Modulation in Human Peripheral Blood Mononuclear Cells after In Vivo Lipopolysaccharide Injection

We described the HERV and MaLR transcriptome in PBMCs, finding that about 8.4% of the LTR retrotransposon loci were expressed and identifying the betaretrovirus-like HERVs as those with the highest percentage of expressed loci. We found 4,607 HERV and MaLR loci that were modulated as a result of in vivo stimulation with LPS. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV and MaLR loci as differentially expressed, checking their genomic context of insertion and observing a general colocalization with genes that are involved and modulated in the immune response, as a consequence of LPS stimulation. The analyses of HERV and MaLR expression and modulation show that these LTR retrotransposons are expressed in PBMCs and regulated in inflammatory settings. The similar regulation of HERVs/MaLRs and genes after LPS stimulation suggests possible interactions of LTR retrotransposons and the immune host response. ABSTRACT Human endogenous retroviruses (HERVs) and mammalian apparent long terminal repeat (LTR) retrotransposons (MaLRs) are retroviral sequences that integrated into germ line cells millions of years ago. Transcripts of these LTR retrotransposons are present in several tissues, and their expression is modulated in pathological conditions, although their function remains often far from being understood. Here, we focused on the HERV/MaLR expression and modulation in a scenario of immune system activation. We used a public data set of human peripheral blood mononuclear cells (PBMCs) RNA-Seq from 15 healthy participants to a clinical trial before and after exposure to lipopolysaccharide (LPS), for which we established an RNA-Seq workflow for the identification of expressed and modulated cellular genes and LTR retrotransposon elements. IMPORTANCE We described the HERV and MaLR transcriptome in PBMCs, finding that about 8.4% of the LTR retrotransposon loci were expressed and identifying the betaretrovirus-like HERVs as those with the highest percentage of expressed loci. We found 4,607 HERV and MaLR loci that were modulated as a result of in vivo stimulation with LPS. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV and MaLR loci as differentially expressed, checking their genomic context of insertion and observing a general colocalization with genes that are involved and modulated in the immune response, as a consequence of LPS stimulation. The analyses of HERV and MaLR expression and modulation show that these LTR retrotransposons are expressed in PBMCs and regulated in inflammatory settings. The similar regulation of HERVs/MaLRs and genes after LPS stimulation suggests possible interactions of LTR retrotransposons and the immune host response.
Seasonal changes in the histology of the gonads and dorsal skin of the fathead minnow, Pimephales promelas

In central Saskatchewan gonad weights of male and female fathead minnows reach peak values between June 1 and July 31. The precise timing of the peak seems to be determined by local weather (temperature). Gonad histology shows a predominance of early gametogenic stages during winter with gametogene sis being completed in the spring. The histology of the dorsal skin is similar in both sexes during the nonbreeding season but males develop a dorsal pad during the breeding season. Pad development involves seasonal changes in epidermal thickness, mucous cell number, and dermal connective tissue thickness. Males also lose their alarm substance cells briefly during the peak breeding period.
Moderate Alcohol Consumption Targets S100β+ Vascular Stem Cells and Attenuates Injury-Induced Neointimal Hyperplasia.

BACKGROUND Stem cells present in the vessel wall may be triggered in response to injurious stimuli to undergo differentiation and contribute to vascular disease development. Our aim was to determine the effect of moderate alcohol (EtOH) exposure on the expansion and differentiation of S100 calcium-binding protein B positive (S100β+ ) resident vascular stem cells and their contribution to pathologic vessel remodeling in a mouse model of arteriosclerosis. METHODS AND RESULTS Lineage tracing analysis of S100β+ cells was performed in male and female S100β-eGFP/Cre/ERT2-dTomato transgenic mice treated daily with or without EtOH by oral gavage (peak BAC: 15mM or 0.07%) following left common carotid artery ligation for 14 days. Carotid arteries (ligated or sham-operated) were harvested for morphological analysis and confocal assessment of fluorescent-tagged S100 β + cells in FFPE carotid cross sections. Ligation-induced carotid remodeling was more robust in males than in females. EtOH-gavaged mice had less adventitial thickening and markedly reduced neo-intimal formation compared to controls, with a more pronounced inhibitory effect in males compared to females. There was significant expansion of S100β + marked cells in vessels post-ligation, primarily in the neo-intimal compartment. EtOH treatment reduced the fraction of S100β + cells in carotid cross-sections, concomitant with attenuated remodeling. In vitro, EtOH attenuated Sonic Hedgehog-stimulated myogenic differentiation (as evidenced by reduced calponin and myosin heavy chain expression) of isolated murine S100β + vascular stem cells. CONCLUSIONS These data highlight resident vascular S100β + stem cells as a novel target population for alcohol, and suggest that regulation of these progenitors in adult arteries, particularly in males, may be an important mechanism contributing to the anti-atherogenic effects of moderate alcohol consumption.
Characterization of aberrant pathways activation and immune microenviroment of BK virus associated nephropathy

In the context of transplantation with the use of immunosuppressive drugs, BK virus infection has become the main cause of BK virus nephropathy(BKVN) in renal transplant recipients(KTRs). More importantly, BKVN may cause further allograft dysfunction and loss. However, the role of the immune microenvironment in the pathogenesis of BKVN remains unknown. Therefore, we collected microarray data of KTRs to elucidate the immune characteristics of BKVN. Via the CIBERSORT, we found that BKVN had relatively more activated memory CD4 T cells. Immunostaining showed that CD4+ and CD8+cells were significantly different between BKVN and stable allografts(STAs). In addition, the expression of immune-related genes(antigen presentation, cytotoxicity, and inflammation) was significantly higher in BKVN than in STAs. The results of gene set enrichment analysis(GSEA) and single-sample GSEA(ssGSEA) indicated that immune cell-,cytokine-,chemokine-, and inflammation-related pathways were significantly activated in BKVN, while metabolism- and renal development-related pathways were significantly downregulated in BKVN. In addition, the immune microenvironments of the peripheral blood in patients with BK viremia(BKV) or transplant kidney biopsy(TKB) with BKVN may be different. Overall, the immune microenvironment may play important roles in the occurrence and development of BKVN and provide a theoretical basis for preventing the occurrence of BKVN and finding novel treatments.
Spheroid Trapping and Calcium Spike Estimation Techniques toward Automation of 3D Culture

We present a spheroid trapping device, compatible with traditional tissue culture plates, to confine microtissues in a small area and allow suspension cultures to be treated like adherent cultures with minimal loss of spheroids due to aspiration. We also illustrate an automated morphology-independent procedure for cell recognition, segmentation, and a calcium spike detection technique for high-throughput analysis in 3D cultured tissue. Our cell recognition technique uses a maximum intensity projection of spatial-temporal data to create a binary mask, which delineates individual cell boundaries and extracts mean fluorescent data for each cell through a series of intensity thresholding and cluster labeling operations. The temporal data are subject to sorting for imaging artifacts, baseline correction, smoothing, and spike detection algorithms. We validated this procedure through analysis of calcium data from 2D and 3D SHSY-5Y cell cultures. Using this approach, we rapidly created regions of interest (ROIs) and extracted fluorescent intensity data from hundreds of cells in the field of view with superior data fidelity over hand-drawn ROIs even in dense (3D tissue) cell populations. We sorted data from cells with imaging artifacts (such as photo bleaching and dye saturation), classified nonfiring and firing cells, estimated the number of spikes in each cell, and documented the results, facilitating large-scale calcium imaging analysis in both 2D and 3D cultures. Since our recognition and segmentation technique is independent of morphology, our protocol provides a versatile platform for the analysis of large confocal calcium imaging data from neuronal cells, glial cells, and other cell types.
Two Studies Investigating Associations Between Sexual Assault Victimization History and Bystander Appraisals of Risk

Across two studies, we examined sexual assault history and bystander appraisals of risk and the moderating roles of danger cue salience (Study 1) and alcohol intoxication (Study 2) in women. Participants (Study 1 = 148, Study 2 = 64) read vignettes ending with cues of nonconsensual sexual activity and an opportunity to intervene. Participants also completed self-report measures of vignette appraisals and history of sexual assault victimization. Across both studies, sexual assault victimization was unassociated with bystander risk appraisals. Alcohol intoxication and subtlety of nonconsent cues did not interact with sexual assault victimization history to influence appraisals of dangerousness.
Forest Traders

plifications of the real diversity in the world of Islam and a most dogmatic and narrow understanding of the core principles and spirit of Islam. A native American or European ethnographer, in my estimation, would have about the same disadvantages as Ahmed if they were to study the Pushtuns or the Berbers of North Africa. Ahmed’s implicit invocation of universalist Islamic theology in support of a foggy new methodological approach is not only counterproductive but plays right into the hands of instruments of exploitation, among them the self-appointed “clergy” (or ulema, Arabic, those who know) of Islam.