The Role of Google Scholar in Evidence Reviews and Its Applicability to Grey Literature Searching

Google Scholar (GS), a commonly used web-based academic search engine, catalogues between 2 and 100 million records of both academic and grey literature (articles not formally published by commercial academic publishers). Google Scholar collates results from across the internet and is free to use. As a result it has received considerable attention as a method for searching for literature, particularly in searches for grey literature, as required by systematic reviews. The reliance on GS as a standalone resource has been greatly debated, however, and its efficacy in grey literature searching has not yet been investigated. Using systematic review case studies from environmental science, we investigated the utility of GS in systematic reviews and in searches for grey literature. Our findings show that GS results contain moderate amounts of grey literature, with the majority found on average at page 80. We also found that, when searched for specifically, the majority of literature identified using Web of Science was also found using GS. However, our findings showed moderate/poor overlap in results when similar search strings were used in Web of Science and GS (10–67%), and that GS missed some important literature in five of six case studies. Furthermore, a general GS search failed to find any grey literature from a case study that involved manual searching of organisations’ websites. If used in systematic reviews for grey literature, we recommend that searches of article titles focus on the first 200 to 300 results. We conclude that whilst Google Scholar can find much grey literature and specific, known studies, it should not be used alone for systematic review searches. Rather, it forms a powerful addition to other traditional search methods. In addition, we advocate the use of tools to transparently document and catalogue GS search results to maintain high levels of transparency and the ability to be updated, critical to systematic reviews.     

FITNESS CONSEQUENCES OF OUTCROSSING IN A SOCIAL SPIDER WITH AN INBREEDING MATING SYSTEM

Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female‐biased sex ratio, sib‐mating results in small effective populations. In such a system, high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib‐males, to a non‐nestmate within the population, or to a male from a distant population, and fitness traits of F1s were compared. We found reduced hatching success of broods from between‐population crosses, suggesting the presence of population divergence at a large geographical scale that may result in population incompatibility. However, a lack of a difference in offspring performance between inbred and outbred crosses indicates little genetic variation between populations, and could suggest recent colonization by a common ancestor. This is consistent with population dynamics of frequent colonizations by single sib‐mated females of common origin, and extinctions of populations after few generations. Although drift or single mutations can lead to population divergence at a relatively short time scale, it is possible that dynamic population processes homogenize these effects at longer time scales.     

Nutrient uptake and management under saline conditions in the xerohalophyte: Tecticornia indica (Willd.) subsp. indica

In the present investigation, we studied uptake and management of the major cations in the xerohalophyte, Tecticornia indica (Willd.) subsp. indica as subjected to salinity. Plants were grown under greenhouse conditions at various salinity levels (0, 100, 200 and 400 mM NaCl) over 110 days. At harvest, they were separated into shoots and roots then analyzed for water contents, dry weights (DW), and Na+, K+, Ca2+, and Mg2+ contents. Plants showed a growth optimum at 200 mM NaCl and much better tissue hydration under saline than non-saline conditions. At this salt concentration (200 mM NaCl), shoot Na+ content reached its highest value (7.9 mmol · g-?1 DW). In spite of such stressful conditions, salt-treated plants maintained adequate K+, Ca2+, and Mg2+ status even under severe saline conditions. This was mainly due to their aptitude to selectively acquire these essential cations and efficiently use them for biomass production.     

Impact of Feedback Phosphorylation and Raf Heterodimerization on Normal and Mutant B-Raf Signaling

The B-Raf kinase is a Ras pathway effector activated by mutation in numerous human cancers and certain developmental disorders. Here we report that normal and oncogenic B-Raf proteins are subject to a regulatory cycle of extracellular signal-regulated kinase (ERK)-dependent feedback phosphorylation, followed by PP2A- and Pin1-dependent dephosphorylation/recycling. We identify four S/TP sites of B-Raf phosphorylated by activated ERK and find that feedback phosphorylation of B-Raf inhibits binding to activated Ras and disrupts heterodimerization with C-Raf, which is dependent on the B-Raf pS729/14-3-3 binding site. Moreover, we find that events influencing Raf heterodimerization can alter the transforming potential of oncogenic B-Raf proteins possessing intermediate or impaired kinase activity but have no significant effect on proteins with high kinase activity, such as V600E B-Raf. Mutation of the feedback sites or overexpression of the Pin1 prolyl-isomerase, which facilitates B-Raf dephosphorylation/recycling, resulted in increased transformation, whereas mutation of the S729/14-3-3 binding site or expression of dominant negative Pin1 reduced transformation. Mutation of each feedback site caused increased transformation and correlated with enhanced heterodimerization and activation of C-Raf. Finally, we find that B-Raf and C-Raf proteins containing mutations identified in certain developmental disorders constitutively heterodimerize and that their signaling activity can also be modulated by feedback phosphorylation.The Ras, Raf, MEK, and extracellular signal-regulated kinase (ERK) proteins are core components of one of the major signaling cascades regulating normal cell proliferation—the Ras pathway. Not surprising, deregulation of Ras pathway signaling is a major contributor to human cancer and has recently been linked with several developmental disorders, such as Noonan''s, LEOPARD, and cardiofaciocutaneous (CFC) syndromes (28). Given its importance to both normal and disease states, much effort has been directed toward elucidating the mechanisms that modulate Ras pathway signaling. Of all the pathway components, regulation of the Raf proteins has proved to be the most complex, involving inter- and intramolecular interactions, a change in subcellular localization, and phosphorylation and dephosphorylation events (6, 32).In mammalian cells, there are three Raf family members: A-Raf, B-Raf, and C-Raf (12). In their inactive state, all Raf proteins are found in the cytosol, with the N-terminal regulatory domain acting as an autoinhibitor of the C-terminal kinase domain (4, 5, 13). 14-3-3 dimers bind to phosphorylation sites present in both the N- and C-terminal regions and stabilize the autoinhibited state (22). To activate the Raf proteins, autoinhibition mediated by the N terminus must be relieved and the kinase domain must adopt the active catalytic conformation (6, 31, 32). Under normal signaling conditions, Ras activation helps mediate these events by recruiting the Raf proteins to the plasma membrane, which induces the release of 14-3-3 from the N-terminal binding site and facilitates phosphorylation of the Raf kinase domain (19). For the C-Raf and A-Raf proteins, phosphorylation occurs in two regions of the kinase domain, the negative-charge regulatory region (N-region) and the activation segment (4). In contrast, the N-region of B-Raf exhibits a constitutive negative charge due to increased basal phosphorylation of an activating serine site and the presence of two aspartic acid residues (18); thus, only phosphorylation of the activation segment is required. Phosphorylation of the activation segment serves both to destabilize the “inactive” catalytic conformation maintained by hydrophobic interactions between the glycine-rich loop and the activation segment and to stabilize the “active” catalytic conformation, whereas the negative charge of the N-region helps to disrupt the autoinhibitory activity of the N-terminal domain (5, 30, 31).Because the N-region of B-Raf exhibits a constitutive negative charge, B-Raf possesses higher basal kinase activity than other family members and is more susceptible to mutational activation (9, 11, 17). In particular, B-Raf is a major contributor to human cancer: somatic mutations in the B-Raf gene are detected in ∼50% of malignant melanomas and many colorectal, ovarian, and papillary thyroid carcinomas (7). Of the oncogenic mutations identified in B-Raf, the vast majority cluster to the two regions of the kinase domain responsible for maintaining the inactive catalytic conformation—the glycine-rich loop and the activation segment (31). Based on enzymatic activity, the oncogenic B-Raf proteins have been divided into three groups: those with high activity (130- to 700-fold more active than wild-type [WT] B-Raf), those with intermediate activity (64- to 1.3-fold more active), and surprisingly, those with impaired catalytic activity (0.8 to 0.3 of WT B-Raf activity) (31). Further analysis has revealed that all oncogenic B-Raf proteins heterodimerize constitutively with C-Raf and activate C-Raf in a Ras-independent manner that requires an intact C-Raf activation segment as well as the binding of 14-3-3 to the C-terminal pS621 binding site on C-Raf (11). Importantly, for the oncogenic B-Raf proteins with impaired kinase activity, the binding and activation of C-Raf are required for ERK activation in vivo (31). Interestingly, heterodimerization of B-Raf and C-Raf also occurs under normal signaling conditions; however, in this case, heterodimerization is Ras dependent and occurs at the plasma membrane following mitogen stimulation (11, 27).Once activated, either by upstream signaling or by mutational events, all Raf proteins are capable of initiating the phosphorylation cascade that results in the sequential activation of MEK and ERK. ERK then phosphorylates targets in both the cytoplasm and the nucleus that are required for cell proliferation. Strikingly, the Raf proteins themselves are also substrates of activated ERK. In regard to C-Raf, ERK-dependent feedback phosphorylation has been shown to instigate a regulatory cycle whereby phosphorylation of the feedback sites down-modulates C-Raf signaling, after which the hyperphosphorylated C-Raf protein is dephosphorylated and returned to a signaling-competent state through dephosphorylation events involving protein phosphatase 2A (PP2A) and the Pin1 prolyl-isomerase (8). For B-Raf, two ERK-dependent feedback sites, S750 and T753, have been identified, and phosphorylation of these sites has been reported to have a negative regulatory effect (3).In this study, we have further investigated the impact of feedback phosphorylation and heterodimerization on B-Raf signaling. Here we find that both normal and oncogenic B-Raf proteins are phosphorylated on four S/TP sites (S151, T401, S750, and T753) by activated ERK. Through mutational analysis, we find that phosphorylation of B-Raf at S151 inhibits binding to activated Ras, whereas phosphorylation of each of the feedback sites contributes to the disruption of B-Raf/C-Raf heterodimers. Moreover, we find that events influencing B-Raf/C-Raf heterodimerization, such as feedback phosphorylation and 14-3-3 binding, can alter the signaling activity of oncogenic B-Raf proteins possessing intermediate or impaired kinase activity as well as that of B-Raf and C-Raf proteins containing mutations identified in CFC and Noonan''s syndromes, respectively.     

The Role of Currents and Waves in the Dispersal of Submersed Angiosperm Seeds and Seedlings

We tested the hypothesis that currents, waves, and sediment grain size affect the dispersal of seeds and seedlings of the submersed angiosperms Ruppia maritima, Potamogeton perfoliatus and Stuckenia pectinata. Seed settling velocities and initiation of motion of seeds and seedlings and distance transported were quantified on four sediment types under a range of currents and waves in a flume. The rapid settling velocities of R. maritima and S. pectinata seeds and the increased settling velocity of P. perfoliatus in currents above 8 cm/second suggest that primary dispersal of these species is localized to the general area colonized by their parents. Once settled within a bed, seeds are exposed to weak currents and waves, and are likely to be subject to sediment deposition which may further limit dispersal. In contrast, in restoration projects, the absence of vegetation is likely to make seeds more vulnerable to grazing and transport, and may contribute to the lack of plant establishment. If seeds germinate without being buried, they are susceptible to secondary dispersal at relatively low current velocities and small wave heights due to the drag exerted on the cotyledon. Sand grains tend to stick to the seed coat and rootlet of P. perfoliatus seedlings, perhaps a mechanism to reduce the chances of being displaced following germination. These data reveal the close links between sediment, water flow, and submersed angiosperm seedling establishment; these parameters should be considered when using seeds for restoration of submersed angiosperms.     

Mechanical loading modulates chondrocyte primary cilia incidence and length

The pathways by which chondrocytes of articular cartilage sense their mechanical environment are unclear. Compelling structural evidence suggests that chondrocyte primary cilia are mechanosensory organelles. This study used a 3D agarose culture model to examine the effect of compressive strain on chondrocyte cilia. Chondrocyte/agarose constructs were subjected to cyclic compression (0–15%; 1 Hz) for 0.5–48 h. Additional constructs were compressed for 48 h and allowed to recover for 72 h in uncompressed free‐swelling conditions. Incidence and length of cilia labelled with anti‐acetylated α‐tubulin were examined using confocal microscopy. In free‐swelling chondrocytes, these parameters increased progressively, but showed a significant decrease following 24 or 48 h compression. A 72 h recovery partially reversed this effect. The reduced cilia incidence and length were not due to increased cell division. We therefore propose that control of primary cilia length is an adaptive signalling mechanism in response to varying levels and duration of mechanical loads during joint activity.     

Dynamic neuroplasticity after human prefrontal cortex damage

Memory and attention deficits are common after prefrontal cortex (PFC) damage, yet people generally recover some function over time. Recovery is thought to be dependent upon undamaged brain regions, but the temporal dynamics underlying cognitive recovery are poorly understood. Here, we provide evidence that the intact PFC compensates for damage in the lesioned PFC on a trial-by-trial basis dependent on cognitive load. The extent of this rapid functional compensation is indexed by transient increases in electrophysiological measures of attention and memory in the intact PFC, detectable within a second after stimulus presentation and only when the lesioned hemisphere is challenged. These observations provide evidence supporting a dynamic and flexible model of compensatory neural plasticity.     

Identification of potent and reversible cruzipain inhibitors for the treatment of Chagas disease

Identification of potent and reversible cruzipain inhibitors for the treatment of Chagas disease is described. The identified inhibitors bearing an amino nitrile warhead in P1 exhibit low nanomolar in vitro potency against cruzipain. Further SAR in P2 portion led to the identification of compounds, such as 26, that have a unique selectivity profile against other cysteine proteases and offering new opportunities for safer treatment of Chagas disease.     

Novel benzofuran derivatives with dual 5-HT1A receptor and serotonin transporter affinity

Several benzofuran derivatives linked to a 3-indoletetrahydropyridine through an alkyl chain were prepared and evaluated for serotonin transporter and 5-HT_1A receptor affinities. Their design, synthesis and structure–activity relationships are described.