ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

peer-reviewedCrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks

Comparative genomics of Drosophila and human core promoters

BACKGROUND: The core promoter region plays a critical role in the regulation of eukaryotic gene expression. We have determined the non-random distribution of DNA sequences relative to the transcriptional start site in Drosophila melanogaster promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters. RESULTS: We determined the distribution of all 65,536 octamer (8-mers) DNA sequences in 10,914 Drosophila promoters and two sets of human promoters aligned relative to the transcriptional start site. In Drosophila, 298 8-mers have highly significant (p ≤ 1 × 10(-16)) non-random distributions peaking within 100 base-pairs of the transcriptional start site. These sequences were grouped into 15 DNA motifs. Ten motifs, termed directional motifs, occur only on the positive strand while the remaining five motifs, termed non-directional motifs, occur on both strands. The only directional motifs to localize in human promoters are TATA, INR, and DPE. The directional motifs were further subdivided into those precisely positioned relative to the transcriptional start site and those that are positioned more loosely relative to the transcriptional start site. Similar numbers of non-directional motifs were identified in both species and most are different. The genes associated with all 15 DNA motifs, when they occur in the peak, are enriched in specific Gene Ontology categories and show a distinct mRNA expression pattern, suggesting that there is a core promoter code in Drosophila. CONCLUSION: Drosophila and human promoters use different DNA sequences to regulate gene expression, supporting the idea that evolution occurs by the modulation of gene regulation

How U.S. Ocean Policy and Market Power Can Reform the Coral Reef Wildlife Trade

As the world’s largest importer of marine ornamental species for the aquaria, curio, home décor, and jewelry industries, the United States has an opportunity to leverage its considerable market power to promote more sustainable trade and reduce the effects of ornamental trade stress on coral reefs worldwide. Evidence indicates that collection of some coral reef animals for these trades has caused virtual elimination of local populations, major changes in age structure, and promotion of collection practices that destroy reef habitats. Management and enforcement of collection activities in major source countries such as Indonesia and the Philippines remain weak. Strengthening US trade laws and enforcement capabilities combined with increasing consumer and industry demand for responsible conservation can create strong incentives for improving management in source countries. This is particularly important in light of the March 2010 failure of the parties to the Convention on International Trade in Endangered Species (CITES) to take action on key groups of corals

EFFECTS OF STATIC STRETCHING ON MAXIMAL ISOKINETIC TORQUE

The effects of 20 seconds of agonist (AGO), antagonist (ANT) or no (NO) pre-exercise stretch on concentric (CON) and eccentric (ECC) maximal isokinetic torque produced at the knee were examined. Twelve male semi-pro rugby players performed dominant isokinetic knee extension following the specified stretch protocol. One-way Repeated Measures ANOVA revealed AGO to be significantly less (p < 0.05) than the other protocols for both CON (270 28 Nm) and ECC (309 42 Nm) torque. There was no difference between the ANT or NO for either CON (303 35 Nm and 304 38 Nm, respectively) or ECC (341 40 Nm and 33644 Nm). The results support the theory that pre-exercise agonist stretching may lead to performance decrements in maximal concentric torque production

LPS-TLR4 Signaling to IRF-3/7 and NF-κB Involves the Toll Adapters TRAM and TRIF

Toll–IL-1–resistance (TIR) domain–containing adaptor-inducing IFN-β (TRIF)–related adaptor molecule (TRAM) is the fourth TIR domain–containing adaptor protein to be described that participates in Toll receptor signaling. Like TRIF, TRAM activates interferon regulatory factor (IRF)-3, IRF-7, and NF-κB-dependent signaling pathways. Toll-like receptor (TLR)3 and 4 activate these pathways to induce IFN-α/β, regulated on activation, normal T cell expressed and secreted (RANTES), and γ interferon–inducible protein 10 (IP-10) expression independently of the adaptor protein myeloid differentiation factor 88 (MyD88). Dominant negative and siRNA studies performed here demonstrate that TRIF functions downstream of both the TLR3 (dsRNA) and TLR4 (LPS) signaling pathways, whereas the function of TRAM is restricted to the TLR4 pathway. TRAM interacts with TRIF, MyD88 adaptor–like protein (Mal)/TIRAP, and TLR4 but not with TLR3. These studies suggest that TRIF and TRAM both function in LPS-TLR4 signaling to regulate the MyD88-independent pathway during the innate immune response to LPS

Case Survey Studies in Software Engineering Research

Background: Given the social aspects of Software Engineering (SE), in the last twenty years, researchers from the field started using research methods common in social sciences such as case study, ethnography, and grounded theory. More recently, case survey, another imported research method, has seen its increasing use in SE studies. It is based on existing case studies reported in the literature and intends to harness the generalizability of survey and the depth of case study. However, little is known on how case survey has been applied in SE research, let alone guidelines on how to employ it properly. Aims: This article aims to provide a better understanding of how case survey has been applied in Software Engineering research. Method: To address this knowledge gap, we performed a systematic mapping study and analyzed 12 Software Engineering studies that used the case survey method. Results: Our findings show that these studies presented a heterogeneous understanding of the approach ranging from secondary studies to primary inquiries focused on a large number of instances of a research phenomenon. They have not applied the case survey method consistently as defined in the seminal methodological papers. Conclusions: We conclude that a set of clearly defined guidelines are needed on how to use case survey in SE research, to ensure the quality of the studies employing this approach and to provide a set of clearly defined criteria to evaluate such work.Comment: Accepted for presentation at ACM / IEEE International Symposium on Empirical Software Engineering and Measurement (ESEM) (ESEM '20

Simulation can offer a sustainable contribution to clinical education in osteopathy

Background: Clinical education forms a substantial component of health professional education. Increased cohorts in Australian osteopathic education have led to consideration of alternatives to traditional placements to ensure adequate clinical exposure and learning opportunities. Simulated learning offers a new avenue for sustainable clinical education. The aim of the study was to explore whether directed observation of simulated scenarios, as part replacement of clinical hours, could provide an equivalent learning experience as measured by performance in an objective structured clinical examination (OSCE).Methods:The year 3 osteopathy cohort were invited to participate in replacement of 50% of their clinical placement hours with online facilitated, video-based simulation exercises (intervention). Competency was assessed by an OSCE at the end of the teaching period. Inferential statistics were used to explore any differences between the control and intervention groups as a post-test control design.Results:The funding model allowed ten learners to participate in the intervention, with sixty-six in the control group. Only one OSCE item was significantly different between groups, that being technique selection (p = 0.038, d = 0.72) in favour of the intervention group, although this may be a type 1 error. Grade point average was moderately positively correlated with the manual therapy technique station total score (r = 0.35, p r = 0.17, p = 0.132).Conclusions:The current study provides support for further investigation into part replacement of clinical placements with directed observation of simulated scenarios in osteopathy

The Ursinus Weekly, November 7, 1974

The Great Pumpkin comes to U.C. • Course Directory Catalogue Committee formed by U.S.G.A. • Antigone is ProTheatre\u27s production • Union does it again • Criminal law featured as Forum topic • Letters to the editor: Epitaph on an Ursinus transfer • Pages from Ursinus past: A legend • Perusing Pfahler\u27s pigeons • New Economics head • Equus reviewed • Concerts: Bizarre and sublime • Record review • Nate DuPree: Can a black man find happiness at Ursinus? • Martha Franklin: A half century of service to our students and campus • Readin\u27, ritin\u27 and new math • Introducing campus leaders • Football wrapup: Swarthmore; Widener • Hockey teams win the big games! • Harriers 6-4 on seasonhttps://digitalcommons.ursinus.edu/weekly/1024/thumbnail.jp