Evaluating gillnetting protocols to characterize lacustrine fish communities

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70 m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.

Toxicity of eosinophil MBP is repressed by intracellular crystallization and promoted by extracellular aggregation.

Eosinophils are white blood cells that function in innate immunity and participate in the pathogenesis of various inflammatory and neoplastic disorders. Their secretory granules contain four cytotoxic proteins, including the eosinophil major basic protein (MBP-1). How MBP-1 toxicity is controlled within the eosinophil itself and activated upon extracellular release is unknown. Here we show how intragranular MBP-1 nanocrystals restrain toxicity, enabling its safe storage, and characterize them with an X-ray-free electron laser. Following eosinophil activation, MBP-1 toxicity is triggered by granule acidification, followed by extracellular aggregation, which mediates the damage to pathogens and host cells. Larger non-toxic amyloid plaques are also present in tissues of eosinophilic patients in a feedback mechanism that likely limits tissue damage under pathological conditions of MBP-1 oversecretion. Our results suggest that MBP-1 aggregation is important for innate immunity and immunopathology mediated by eosinophils and clarify how its polymorphic self-association pathways regulate toxicity intra- and extracellularly.

Tubes or sheets: divergent aggregation pathways of an amphiphilic 2,7-substituted pyrene trimer

The self-assembly of an amphiphilic 2,7-linked pyrene trimer in an aqueous environment into two morphologically related forms is described. Supramolecular polymerization leads to the simultaneous formation of nanosheets and nanotubes.

Intraspecific Aggregation Alters Competitive Interactions in Experimental Plant Communities

We tested the prediction from spatial competition models that intraspecific aggregation may promote coexistence and thus maintain biodiversity with experimental communities of four annual species. Monocultures, three-species mixtures, and the four-species mixture were sown at two densities and with either random or intraspecifically aggregated distributions. There was a hierarchy of competitive abilities among the four species. The weaker competitors showed higher aboveground biomass in the aggregated distribution compared to the random distribution, especially at high density. In one species, intraspecific aggregation resulted in an 86% increase in the number of flowering individuals and a 171% increase in the reproductive biomass at high density. The competitively superior species had a lower biomass in the aggregated distribution than in the random distribution at high density. The data support the hypothesis that the spatial distribution of plants profoundly affects competition in such a way that weaker competitors increase their fitness while stronger competitors are suppressed when grown in the neighborhood of conspecifics. This implies that the spatial arrangement of plants in a community can be an important determinant of species coexistence and biodiversity.

Efficacy of patient-administered mechanical and/or chemical plaque control protocols in the management of peri-implant mucositis. A systematic review

AIM To systematically assess the efficacy of patient-administered mechanical and/or chemical plaque control protocols in the management of peri-implant mucositis (PM). MATERIAL AND METHODS Randomized (RCTs) and Controlled Clinical Trials (CCTs) were identified through an electronic search of three databases complemented by manual search. Identification, screening, eligibility and inclusion of studies was performed independently by two reviewers. Studies without professional intervention or with only mechanical debridement professionally administered were included. Quality assessment was performed by means of the Cochrane Collaboration's tool for assessing risk of bias. RESULTS Eleven RCTs with a follow-up from 3 to 24 months were included. Definition of PM was lacking or heterogeneously reported. Complete resolution of PM was not achieved in any study. One study reported 38% of patients with complete resolution of PM. Surrogate end-point outcomes of PM therapy were often reported. The choice of control interventions showed great variability. The efficacy of powered toothbrushes, a triclosan-containing toothpaste and adjunctive antiseptics remains to be established. High quality of methods and reporting was found in four studies. CONCLUSIONS Professionally- and patient-administered mechanical plaque control alone should be considered the standard of care in the management of PM. Therapy of PM is a prerequisite for the prevention of peri-implantitis.

Comparison of two protocols of periosteal distraction osteogenesis in a rabbit calvaria model

The regenerative pathways during periosteal distraction osteogenesis may be influenced by the local environment composed by cells, growth factors, nutrition and mechanical load. The aim of the present study was to evaluate the influence of two protocols of periosteal distraction on bone formation. Custom made distraction devices were surgically fixed onto the calvariae of 60 rabbits. After an initial healing period of 7 days, two groups of animals were submitted to distraction rates of 0.25 and 0.5 mm/24 h for 10 days, respectively. Six animals per group were sacrificed 10 (mid-distraction), 17 (end-distraction), 24 (1-week consolidation), 31 (2-week consolidation) and 77 days (2-month consolidation) after surgery. Newly formed bone was assessed by means of micro-CT and histologically. Expression of transcripts encoding tissue-specific genes (BMP-2, RUNX2, ACP5, SPARC, collagen I α1, collagen II α1 and SOX9) was analyzed by quantitative PCR. Two patterns of bone formation were observed, originating from the old bone surface in Group I and from the periosteum in Group II. Bone volume (BV) and bone mineral density (BMD) significantly increased up to the 2-month consolidation period within the groups (p < 0.05). Significantly more bone was observed in Group II compared to Group I at the 2-month consolidation period (p < 0.001). Expression of transcripts encoding osteogenic genes in bone depended on the time-point of observation (p < 0.05). Low level of transcripts reveals an indirect role of periosteum in the osteogenic process. Two protocols of periosteal distraction in the present model resulted in moderate differences in terms of bone formation.

An analysis of protocols and publications suggested that most discontinuations of clinical trials were not based on preplanned interim analyses or stopping rules.

OBJECTIVES To investigate the frequency of interim analyses, stopping rules, and data safety and monitoring boards (DSMBs) in protocols of randomized controlled trials (RCTs); to examine these features across different reasons for trial discontinuation; and to identify discrepancies in reporting between protocols and publications. STUDY DESIGN AND SETTING We used data from a cohort of RCT protocols approved between 2000 and 2003 by six research ethics committees in Switzerland, Germany, and Canada. RESULTS Of 894 RCT protocols, 289 prespecified interim analyses (32.3%), 153 stopping rules (17.1%), and 257 DSMBs (28.7%). Overall, 249 of 894 RCTs (27.9%) were prematurely discontinued; mostly due to reasons such as poor recruitment, administrative reasons, or unexpected harm. Forty-six of 249 RCTs (18.4%) were discontinued due to early benefit or futility; of those, 37 (80.4%) were stopped outside a formal interim analysis or stopping rule. Of 515 published RCTs, there were discrepancies between protocols and publications for interim analyses (21.1%), stopping rules (14.4%), and DSMBs (19.6%). CONCLUSION Two-thirds of RCT protocols did not consider interim analyses, stopping rules, or DSMBs. Most RCTs discontinued for early benefit or futility were stopped without a prespecified mechanism. When assessing trial manuscripts, journals should require access to the protocol.

Sphingosine 1-Phosphate Produced by Sphingosine Kinase 2 Intrinsically Controls Platelet Aggregation In Vitro and In Vivo

RATIONALE Platelets are known to play a crucial role in hemostasis. Sphingosine kinases (Sphk) 1 and 2 catalyze the conversion of sphingosine to the bioactive metabolite sphingosine 1-phosphate (S1P). Although platelets are able to secrete S1P on activation, little is known about a potential intrinsic effect of S1P on platelet function. OBJECTIVE To investigate the role of Sphk1- and Sphk2-derived S1P in the regulation of platelet function. METHODS AND RESULTS We found a 100-fold reduction in intracellular S1P levels in platelets derived from Sphk2(-/-) mutants compared with Sphk1(-/-) or wild-type mice, as analyzed by mass spectrometry. Sphk2(-/-) platelets also failed to secrete S1P on stimulation. Blood from Sphk2-deficient mice showed decreased aggregation after protease-activated receptor 4-peptide and adenosine diphosphate stimulation in vitro, as assessed by whole blood impedance aggregometry. We revealed that S1P controls platelet aggregation via the sphingosine 1-phosphate receptor 1 through modulation of protease-activated receptor 4-peptide and adenosine diphosphate-induced platelet activation. Finally, we show by intravital microscopy that defective platelet aggregation in Sphk2-deficient mice translates into reduced arterial thrombus stability in vivo. CONCLUSIONS We demonstrate that Sphk2 is the major Sphk isoform responsible for the generation of S1P in platelets and plays a pivotal intrinsic role in the control of platelet activation. Correspondingly, Sphk2-deficient mice are protected from arterial thrombosis after vascular injury, but have normal bleeding times. Targeting this pathway could therefore present a new therapeutic strategy to prevent thrombosis.

In vitro differentiation of mouse granulocytes. Programmed Cell Death: Methods and Protocols

Granulocytes are central players of the immune system and, once activated, a tightly controlled balance between effector functions and cell removal by apoptosis guarantees maximal host benefit with least possible collateral damage to healthy tissue. Granulocytes are end-differentiated cells that cannot be maintained in culture for prolonged times. Isolating primary granulocytes is inefficient and challenging when working with mice, and especially so for the lowly abundant eosinophil and basophils subtypes. Here we describe an in vitro protocol to massively expand mouse derived myeloid progenitors and to differentiate them ‘on demand’ and in large numbers into mature neutrophils or basophils.

A systematic review on the innervation of peri-implant tissues with special emphasis on the influence of implant placement and loading protocols

OBJECTIVES To systematically review the available literature on the influence of dental implant placement and loading protocols on peri-implant innervation. MATERIAL AND METHODS The database MEDLINE, Cochrane, EMBASE, Web of Science, LILACS, OpenGrey and hand searching were used to identify the studies published up to July 2013, with a populations, exposures and outcomes (PEO) search strategy using MeSH keywords, focusing on the question: Is there, and if so, what is the effect of time between tooth extraction and implant placement or implant loading on neural fibre content in the peri-implant hard and soft tissues? RESULTS Of 683 titles retrieved based on the standardized search strategy, only 10 articles fulfilled the inclusion criteria, five evaluating the innervation of peri-implant epithelium, five elucidating the sensory function in peri-implant bone. Three included studies were considered having a methodology of medium quality and the rest were at low quality. All those papers reported a sensory innervation around osseointegrated implants, either in the bone-implant interface or peri-implant epithelium, which expressed a particular innervation pattern. Compared to unloaded implants or extraction sites without implantation, a significant higher density of nerve fibres around loaded dental implants was confirmed. CONCLUSIONS To date, the published literature describes peri-implant innervation with a distinct pattern in hard and soft tissues. Implant loading seems to increase the density of nerve fibres in peri-implant tissues, with insufficient evidence to distinguish between the innervation patterns following immediate and delayed implant placement and loading protocols. Variability in study design and loading protocols across the literature and a high risk of bias in the studies included may contribute to this inconsistency, revealing the need for more uniformity in reporting, randomized controlled trials, longer observation periods and standardization of protocols.

Discrepancies in Outcome Reporting Exist Between Protocols and Published Oral Health Cochrane Systematic Reviews

OBJECTIVES To assess discrepancies in the analyzed outcomes between protocols and published reviews within Cochrane oral health systematic reviews (COHG) on the Cochrane Database of Systematic Reviews (CDSR). STUDY DESIGN AND SETTING All COHG systematic reviews on the CDSR and the corresponding protocols were retrieved in November 2014 and information on the reported outcomes was recorded. Data was collected at the systematic review level by two reviewers independently. RESULTS One hundred and fifty two reviews were included. In relation to primary outcomes, 11.2% were downgraded to secondary outcomes, 9.9% were omitted altogether in the final publication and new primary outcomes were identified in 18.4% of publications. For secondary outcomes, 2% were upgraded to primary, 12.5% were omitted and 30.9% were newly introduced in the publication. Overall, 45.4% of reviews had at least one discrepancy when compared to the protocol; these were reported in 14.5% reviews. The number of review updates appears to be associated with discrepancies between final review and protocol (OR: 3.18, 95% CI: 1.77, 5.74, p<0.001). The risk of reporting significant results was lower for both downgraded outcomes [RR: 0.52, 95% CI: 0.17, 1.58, p = 0.24] and upgraded or newly introduced outcomes [RR: 0.77, 95% CI: 0.36, 1.64, p = 0.50] compared to outcomes with no discrepancies. The risk of reporting significant results was higher for upgraded or newly introduced outcomes compared to downgraded outcomes (RR = 1.19, 95% CI: 0.65, 2.16, p = 0.57). None of the comparisons reached statistical significance. CONCLUSION While no evidence of selective outcome reporting was found in this study, based on the present analysis of SRs published within COHG systematic reviews, discrepancies between outcomes in pre-published protocols and final reviews continue to be common. Solutions such as the use of standardized outcomes to reduce the prevalence of this issue may need to be explored.

The temporal evolution of nonverbal synchrony in outpatient psychotherapy: An aggregation of single-case studies

Objective: The authors quantified nonverbal synchrony—the coordination of patient's and therapist's movement—in a random sample of same-sex psychotherapy dyads. The authors contrasted nonverbal synchrony in these dyads with a control condition and assessed its association with session-level and overall psychotherapy outcome. Method: Using an automated objective video analysis algorithm (Motion Energy Analysis; MEA), the authors calculated nonverbal synchrony in (n = 104) videotaped psychotherapy sessions from 70 Caucasian patients (37 women, 33 men, mean age = 36.5 years, SD = 10.2) treated at an outpatient psychotherapy clinic. The sample was randomly drawn from an archive (N = 301) of routinely videotaped psychotherapies. Patients and their therapists assessed session impact with self-report postsession questionnaires. A battery of pre- and postsymptomatology questionnaires measured therapy effectiveness. Results: The authors found that nonverbal synchrony is higher in genuine interactions contrasted with pseudointeractions (a control condition generated by a specifically designed shuffling procedure). Furthermore, nonverbal synchrony is associated with session-level process as well as therapy outcome: It is increased in sessions rated by patients as manifesting high relationship quality and in patients experiencing high self-efficacy. Higher nonverbal synchrony characterized psychotherapies with higher symptom reduction. Conclusions: The results suggest that nonverbal synchrony embodies the patients' self-reported quality of the relationship and further variables of therapy process. This hitherto overlooked facet of therapeutic relationships might prove useful as an indicator of therapy progress and outcome. (PsycINFO Database Record (c) 2015 APA, all rights reserved)

Information-centric communication in mobile and wireless networks

Information-centric networking (ICN) is a new communication paradigm that has been proposed to cope with drawbacks of host-based communication protocols, namely scalability and security. In this thesis, we base our work on Named Data Networking (NDN), which is a popular ICN architecture, and investigate NDN in the context of wireless and mobile ad hoc networks. In a first part, we focus on NDN efficiency (and potential improvements) in wireless environments by investigating NDN in wireless one-hop communication, i.e., without any routing protocols. A basic requirement to initiate informationcentric communication is the knowledge of existing and available content names. Therefore, we develop three opportunistic content discovery algorithms and evaluate them in diverse scenarios for different node densities and content distributions. After content names are known, requesters can retrieve content opportunistically from any neighbor node that provides the content. However, in case of short contact times to content sources, content retrieval may be disrupted. Therefore, we develop a requester application that keeps meta information of disrupted content retrievals and enables resume operations when a new content source has been found. Besides message efficiency, we also evaluate power consumption of information-centric broadcast and unicast communication. Based on our findings, we develop two mechanisms to increase efficiency of information-centric wireless one-hop communication. The first approach called Dynamic Unicast (DU) avoids broadcast communication whenever possible since broadcast transmissions result in more duplicate Data transmissions, lower data rates and higher energy consumption on mobile nodes, which are not interested in overheard Data, compared to unicast communication. Hence, DU uses broadcast communication only until a content source has been found and then retrieves content directly via unicast from the same source. The second approach called RC-NDN targets efficiency of wireless broadcast communication by reducing the number of duplicate Data transmissions. In particular, RC-NDN is a Data encoding scheme for content sources that increases diversity in wireless broadcast transmissions such that multiple concurrent requesters can profit from each others’ (overheard) message transmissions. If requesters and content sources are not in one-hop distance to each other, requests need to be forwarded via multi-hop routing. Therefore, in a second part of this thesis, we investigate information-centric wireless multi-hop communication. First, we consider multi-hop broadcast communication in the context of rather static community networks. We introduce the concept of preferred forwarders, which relay Interest messages slightly faster than non-preferred forwarders to reduce redundant duplicate message transmissions. While this approach works well in static networks, the performance may degrade in mobile networks if preferred forwarders may regularly move away. Thus, to enable routing in mobile ad hoc networks, we extend DU for multi-hop communication. Compared to one-hop communication, multi-hop DU requires efficient path update mechanisms (since multi-hop paths may expire quickly) and new forwarding strategies to maintain NDN benefits (request aggregation and caching) such that only a few messages need to be transmitted over the entire end-to-end path even in case of multiple concurrent requesters. To perform quick retransmission in case of collisions or other transmission errors, we implement and evaluate retransmission timers from related work and compare them to CCNTimer, which is a new algorithm that enables shorter content retrieval times in information-centric wireless multi-hop communication. Yet, in case of intermittent connectivity between requesters and content sources, multi-hop routing protocols may not work because they require continuous end-to-end paths. Therefore, we present agent-based content retrieval (ACR) for delay-tolerant networks. In ACR, requester nodes can delegate content retrieval to mobile agent nodes, which move closer to content sources, can retrieve content and return it to requesters. Thus, ACR exploits the mobility of agent nodes to retrieve content from remote locations. To enable delay-tolerant communication via agents, retrieved content needs to be stored persistently such that requesters can verify its authenticity via original publisher signatures. To achieve this, we develop a persistent caching concept that maintains received popular content in repositories and deletes unpopular content if free space is required. Since our persistent caching concept can complement regular short-term caching in the content store, it can also be used for network caching to store popular delay-tolerant content at edge routers (to reduce network traffic and improve network performance) while real-time traffic can still be maintained and served from the content store.