Ten Simple Rules for Getting Help from Online Scientific Communities

The increasing complexity of research requires scientists to work at the intersection of multiple fields and to face problems for which their formal education has not prepared them. For example, biologists with no or little background in programming are now often using complex scripts to handle the results from their experiments; vice versa, programmers wishing to enter the world of bioinformatics must know about biochemistry, genetics, and other fields. In this context, communication tools such as mailing lists, web forums, and online communities acquire increasing importance. These tools permit scientists to quickly contact people skilled in a specialized field. A question posed properly to the right online scientific community can help in solving difficult problems, often faster than screening literature or writing to publication authors. The growth of active online scientific communities, such as those listed in Table S1, demonstrates how these tools are becoming an important source of support for an increasing number of researchers. Nevertheless, making proper use of these resources is not easy. Adhering to the social norms of World Wide Web communication—loosely termed “netiquette”—is both important and non-trivial. In this article, we take inspiration from our experience on Internet-shared scientific knowledge, and from similar documents such as “Asking the Questions the Smart Way” and “Getting Answers”, to provide guidelines and suggestions on how to use online communities to solve scientific problems

Bouveret's syndrome as an unusual cause of gastric outlet obstruction: a case report

An 83 year old caucasian gentleman presented with vomiting and left sided abdominal pain. A subsequent upper GI endoscopy demonstrated a large smooth mass impacted within the duodenum. A cholecysto-duodenal fistula was discovered at laparotomy, with a large gallstone impacted in the duodenum. A diagnosis of Bouveret's syndrome was made. The management of this rare cause of gastric outlet obstruction is discussed

Security Implications of Running Windows Software on a Linux System Using Wine

Linux is considered to be less prone to malware compared to other operating systems, and as a result Linux users rarely run anti-malware. However, many popular software applications released on other platforms cannot run natively on Linux. Wine is a popular compatibility layer for running Windows programs on Linux. The level of security risk that Wine poses to Linux users is largely undocumented. This project was conducted to assess the security implications of using Wine, and to determine if any specific types of malware or malware behavior have a significant effect on the malware being successful in Wine. Dynamic analysis (both automated and manual) was applied to 30 malware samples both in a Windows environment and Linux environment running Wine. Behavior analyzed included file system, registry, and network access, and the spawning of processes, and services. The behavior was compared to determine malware success in Wine. The study results provide evidence that Wine can pose serious security implications when used to run Windows software in a Linux environment. Five samples of Windows malware were run successfully through Wine on a Linux system. No significant relationships were discovered between the success of the malware and its high-level behavior or malware type. However, certain API calls could not be recreated in a Linux environment, and led to failure of malware to execute via Wine. This suggests that particular malware samples that utilize these API calls will never run completely successfully in a Linux environment. As a consequence, the success of some samples can be determined from observing the API calls when run within a Windows environment

Applying the 3C Model to FLOSS communities

Publicado em "Collaboration and technology: 22nd International Conference, CRIWG 2016, Kanazawa, Japan, September 14-16, 2016, proceedings". ISBN 978-3-319-44798-8How learning occurs within Free/Libre Open Source (FLOSS) communities and what is the dynamics such projects (e.g. the life cycle of such projects) are very relevant questions when considering the use of FLOSS projects in a formal education setting. This paper introduces an approach based on the 3C collaboration model (communication, coordination and cooperation) to represent the collaborative learning dynamics within FLOSS communities. To explore the collaborative learning potential of FLOSS communities a number of questionnaires and interviews to selected FLOSS contributors were run. From this study a 3C collaborative model applicable to FLOSS communities was designed and discussed.Programa Operacional da Região Norte, NORTE2020, in the context of project NORTE-01-0145-FEDER-000037FCT under grant SFRH/BSAB/113890/201

Memory consolidation in the cerebellar cortex

Several forms of learning, including classical conditioning of the eyeblink, depend upon the cerebellum. In examining mechanisms of eyeblink conditioning in rabbits, reversible inactivations of the control circuitry have begun to dissociate aspects of cerebellar cortical and nuclear function in memory consolidation. It was previously shown that post-training cerebellar cortical, but not nuclear, inactivations with the GABA(A) agonist muscimol prevented consolidation but these findings left open the question as to how final memory storage was partitioned across cortical and nuclear levels. Memory consolidation might be essentially cortical and directly disturbed by actions of the muscimol, or it might be nuclear, and sensitive to the raised excitability of the nuclear neurons following the loss of cortical inhibition. To resolve this question, we simultaneously inactivated cerebellar cortical lobule HVI and the anterior interpositus nucleus of rabbits during the post-training period, so protecting the nuclei from disinhibitory effects of cortical inactivation. Consolidation was impaired by these simultaneous inactivations. Because direct application of muscimol to the nuclei alone has no impact upon consolidation, we can conclude that post-training, consolidation processes and memory storage for eyeblink conditioning have critical cerebellar cortical components. The findings are consistent with a recent model that suggests the distribution of learning-related plasticity across cortical and nuclear levels is task-dependent. There can be transfer to nuclear or brainstem levels for control of high-frequency responses but learning with lower frequency response components, such as in eyeblink conditioning, remains mainly dependent upon cortical memory storage

Early growth response gene-2 (Egr-2) regulates the development of B and T cells

The study was supported by Arthritis Research UK. Copyright @ 2011 Li et al.BACKGROUND: Understanding of how transcription factors are involved in lymphocyte development still remains a challenge. It has been shown that Egr-2 deficiency results in impaired NKT cell development and defective positive selection of T cells. Here we investigated the development of T, B and NKT cells in Egr-2 transgenic mice and the roles in the regulation of distinct stages of B and T cell development. METHODS AND FINDINGS: The expression of Egr1, 2 and 3 were analysed at different stages of T and B cell development by RT-PCT and results showed that the expression was strictly regulated at different stages. Forced expression of Egr-2 in CD2+ lymphocytes resulted in a severe reduction of CD4+CD8+ (DP) cells in thymus and pro-B cells in bone marrow, which was associated with reduced expression of Notch1 in ISP thymocytes and Pax5 in pro-B cells, suggesting that retraction of Egr-2 at the ISP and pro-B cell stages is important for the activation of lineage differentiation programs. In contrast to reduction of DP and pro-B cells, Egr-2 enhanced the maturation of DP cells into single positive (SP) T and NKT cells in thymus, and immature B cells into mature B cells in bone marrow. CONCLUSIONS: Our results demonstrate that Egr-2 expressed in restricted stages of lymphocyte development plays a dynamic, but similar role for the development of T, NKT and B cells.This article is provided by the Brunel Open Access publishing fund

The T3SS effector EspT defines a new category of invasive enteropathogenic E. coli (EPEC) which form intracellular actin pedestals.

Enteropathogenic Escherichia coli (EPEC) strains are defined as extracellular pathogens which nucleate actin rich pedestal-like membrane extensions on intestinal enterocytes to which they intimately adhere. EPEC infection is mediated by type III secretion system effectors, which modulate host cell signaling. Recently we have shown that the WxxxE effector EspT activates Rac1 and Cdc42 leading to formation of membrane ruffles and lamellipodia. Here we report that EspT-induced membrane ruffles facilitate EPEC invasion into non-phagocytic cells in a process involving Rac1 and Wave2. Internalized EPEC resides within a vacuole and Tir is localized to the vacuolar membrane, resulting in actin polymerization and formation of intracellular pedestals. To the best of our knowledge this is the first time a pathogen has been shown to induce formation of actin comets across a vacuole membrane. Moreover, our data breaks the dogma of EPEC as an extracellular pathogen and defines a new category of invasive EPEC

Risk behaviors in a rural community with a known point-source exposure to chronic wasting disease

<p>Abstract</p> <p>Background</p> <p>The emergence and continuing spread of Chronic Wasting Disease (CWD) in cervids has now reached 14 U.S. states, two Canadian provinces, and South Korea, producing a potential for transmission of CWD prions to humans and other animals globally. In 2005, CWD spread for the first time from the Midwest to more densely populated regions of the East Coast. As a result, a large cohort of individuals attending a wild game feast in upstate New York were exposed to a deer that was subsequently confirmed positive for CWD.</p> <p>Methods</p> <p>Eighty-one participants who ingested or otherwise were exposed to a deer with chronic wasting disease at a local New York State sportsman's feast were recruited for this study. Participants were administered an exposure questionnaire and agreed to follow-up health evaluations longitudinally over the next six years.</p> <p>Results</p> <p>Our results indicate two types of risks for those who attended the feast, a <it>Feast Risk </it>and a G<it>eneral Risk</it>. The larger the number of risk factors, the greater the risk to human health if CWD is transmissible to humans. Long-term surveillance of feast participants exposed to CWD is ongoing.</p> <p>Conclusion</p> <p>The risk data from this study provide a relative scale for cumulative exposure to CWD-infected tissues and surfaces, and those in the upper tiers of cumulative risk may be most at risk if CWD is transmissible to humans.</p

Geomorphological evolution of a debris‐covered glacier surface

There exists a need to advance our understanding of debris‐covered glacier surfaces over relatively short timescales due to rapid, climatically induced areal expansion of debris cover at the global scale, and the impact debris has on mass balance. We applied unpiloted aerial vehicle structure‐from‐motion (UAV‐SfM) and digital elevation model (DEM) differencing with debris thickness and debris stability modelling to unravel the evolution of a 0.15 km2 region of the debris‐covered Miage Glacier, Italy, between June 2015 and July 2018. DEM differencing revealed widespread surface lowering (mean 4.1 ± 1.0 m a‐1; maximum 13.3 m a‐1). We combined elevation change data with local meteorological data and a sub‐debris melt model, and used these relationships to produce high resolution, spatially distributed maps of debris thickness. These maps were differenced to explore patterns and mechanisms of debris redistribution. Median debris thicknesses ranged from 0.12 to 0.17 m and were spatially variable. We observed localized debris thinning across ice cliff faces, except those which were decaying, where debris thickened. We observed pervasive debris thinning across larger, backwasting slopes, including those bordered by supraglacial streams, as well as ingestion of debris by a newly exposed englacial conduit. Debris stability mapping showed that 18.2–26.4% of the survey area was theoretically subject to debris remobilization. By linking changes in stability to changes in debris thickness, we observed that slopes that remain stable, stabilize, or remain unstable between periods almost exclusively show net debris thickening (mean 0.07 m a‐1) whilst those which become newly unstable exhibit both debris thinning and thickening. We observe a systematic downslope increase in the rate at which debris cover thickens which can be described as a function of the topographic position index and slope gradient. Our data provide quantifiable insights into mechanisms of debris remobilization on glacier surfaces over sub‐decadal timescales, and open avenues for future research to explore glacier‐scale spatiotemporal patterns of debris remobilization

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio