Transient dominance in a central African rain forest

The large-crowned emergent tree Microberlinia bisulcata dominates rain forest groves at Korup National Park, Cameroon, along with two codominants, Tetraberlinia bifoliolata and T. korupensis. M. bisulcata has a pronounced modal size frequency distribution around 110 cm stem diameter: its recruitment potential is very poor. It is a long-lived light-demanding species, one of many found in African forests. Tetraberlinia species lack modality, are more shade tolerant, and recruit better. All three species are ectomycorrhizal. M. bisulcata dominates grove basal area, even though it has similar numbers of trees (≥50 cm stem diameter) as each of the other two species. This situation presented a conundrum that prompted a long-term study of grove dynamics. Enumerations of two plots (82.5 and 56.25 ha) between 1990 and 2010 showed mortality and recruitment of M. bisulcata to be very low (both rates 0.2% per year) compared with Tetraberlinia (2.4% and 0.8% per year), and M. bisulcata grows twice as fast as the Tetraberlinia. Ordinations indicated that these three species determined community structure by their strong negative associations while other species showed almost none. Ranked species abundance curves fitted the Zipf-Mandelbrot model well and allowed “overdominance” of M. bisulcata to be estimated. Spatial analysis indicated strong repulsion by clusters of large (50 to <100 cm) and very large (≥100 cm) M. bisulcata of their own medium-sized (10 to <50 cm) trees and all sizes of Tetraberlinia. This was interpreted as competition by M. bisulcata increasing its dominance, but also inhibition of its own replacement potential. Stem coring showed a modal age of 200 years for M. bisulcata, but with large size variation (50–150 cm). Fifty-year model projections suggested little change in medium, decreases in large, and increases in very large trees of M. bisulcata, accompanied by overall decreases in medium and large trees of Tetraberlinia species. Realistically increasing very-large-tree mortality led to grove collapse without short-term replacement. M. bisulcata most likely depends on climatic events to rebuild its stands: the ratio of disturbance interval to median species' longevity is important. A new theory of transient dominance explains how M. bisulcata may be cycling in abundance over time and displaying nonequilibrium dynamics.

Tropopause level Rossby wave breaking in the Northern Hemisphere: a feature-based validation of the ECHAM5-HAM climate model

Breaking synoptic-scale Rossby waves (RWB) at the tropopause level are central to the daily weather evolution in the extratropics and the subtropics. RWB leads to pronounced meridional transport of heat, moisture, momentum, and chemical constituents. RWB events are manifest as elongated and narrow structures in the tropopause-level potential vorticity (PV) field. A feature-based validation approach is used to assess the representation of Northern Hemisphere RWB in present-day climate simulations carried out with the ECHAM5-HAM climate model at three different resolutions (T42L19, T63L31, and T106L31) against the ERA-40 reanalysis data set. An objective identification algorithm extracts RWB events from the isentropic PV field and allows quantifying the frequency of occurrence of RWB. The biases in the frequency of RWB are then compared to biases in the time mean tropopause-level jet wind speeds. The ECHAM5-HAM model captures the location of the RWB frequency maxima in the Northern Hemisphere at all three resolutions. However, at coarse resolution (T42L19) the overall frequency of RWB, i.e. the frequency averaged over all seasons and the entire hemisphere, is underestimated by 28%.The higher-resolution simulations capture the overall frequency of RWB much better, with a minor difference between T63L31 and T106L31 (frequency errors of −3.5 and 6%, respectively). The number of large-size RWB events is significantly underestimated by the T42L19 experiment and well represented in the T106L31 simulation. On the local scale, however, significant differences to ERA-40 are found in the higher-resolution simulations. These differences are regionally confined and vary with the season. The most striking difference between T106L31 and ERA-40 is that ECHAM5-HAM overestimates the frequency of RWB in the subtropical Atlantic in all seasons except for spring. This bias maximum is accompanied by an equatorward extension of the subtropical westerlies.

Comparative efficacy of seven psychotherapeutic interventions for patients with depression: a network meta-analysis

BACKGROUND Previous meta-analyses comparing the efficacy of psychotherapeutic interventions for depression were clouded by a limited number of within-study treatment comparisons. This study used network meta-analysis, a novel methodological approach that integrates direct and indirect evidence from randomised controlled studies, to re-examine the comparative efficacy of seven psychotherapeutic interventions for adult depression. METHODS AND FINDINGS We conducted systematic literature searches in PubMed, PsycINFO, and Embase up to November 2012, and identified additional studies through earlier meta-analyses and the references of included studies. We identified 198 studies, including 15,118 adult patients with depression, and coded moderator variables. Each of the seven psychotherapeutic interventions was superior to a waitlist control condition with moderate to large effects (range d = -0.62 to d = -0.92). Relative effects of different psychotherapeutic interventions on depressive symptoms were absent to small (range d = 0.01 to d = -0.30). Interpersonal therapy was significantly more effective than supportive therapy (d = -0.30, 95% credibility interval [CrI] [-0.54 to -0.05]). Moderator analysis showed that patient characteristics had no influence on treatment effects, but identified aspects of study quality and sample size as effect modifiers. Smaller effects were found in studies of at least moderate (Δd = 0.29 [-0.01 to 0.58]; p = 0.063) and large size (Δd = 0.33 [0.08 to 0.61]; p = 0.012) and those that had adequate outcome assessment (Δd = 0.38 [-0.06 to 0.87]; p = 0.100). Stepwise restriction of analyses by sample size showed robust effects for cognitive-behavioural therapy, interpersonal therapy, and problem-solving therapy (all d>0.46) compared to waitlist. Empirical evidence from large studies was unavailable or limited for other psychotherapeutic interventions. CONCLUSIONS Overall our results are consistent with the notion that different psychotherapeutic interventions for depression have comparable benefits. However, the robustness of the evidence varies considerably between different psychotherapeutic treatments.

Genetic of catecholaminergic polymorphic ventricular tachycardia: basic concepts.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a cardiac channelopathy characterized by altered intracellular calcium handling resulting in ventricular arrhythmias and high risk of cardiac sudden death in young cases with normal structural hearts. Patients present with exertional syncope and the trademark dysrhythmia is polymorphic and/or bidirectional ventricular tachycardia during exercise or adrenergic stimulation. Early detection of CPVT is crucial because opportune medical intervention prevents sudden cardiac death. Mutations in the ryanodine receptor RYR2 explain nearly 70% of the CPVT cases and cause the autosomic dominant form of the disease. Mutations in calsequestrin 2 causes a recessive form and explain less than 5% of all cases. Genetic screening in CPVT, besides providing early detection of asymptomatic carriers at risk, has provided important insights in the mechanism underlying the disease. Mutational analysis of RYR2 has been a challenge due to the large size of the gene, 105 exons encoded for 4,967 amino-acids. In this review we analyze general concepts of the disease, differential diagnosis and strategies for genetic screening.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Growth Codes: Intermediate Performance Analysis and Application to Video

Growth codes are a subclass of Rateless codes that have found interesting applications in data dissemination problems. Compared to other Rateless and conventional channel codes, Growth codes show improved intermediate performance which is particularly useful in applications where partial data presents some utility. In this paper, we investigate the asymptotic performance of Growth codes using the Wormald method, which was proposed for studying the Peeling Decoder of LDPC and LDGM codes. Compared to previous works, the Wormald differential equations are set on nodes' perspective which enables a numerical solution to the computation of the expected asymptotic decoding performance of Growth codes. Our framework is appropriate for any class of Rateless codes that does not include a precoding step. We further study the performance of Growth codes with moderate and large size codeblocks through simulations and we use the generalized logistic function to model the decoding probability. We then exploit the decoding probability model in an illustrative application of Growth codes to error resilient video transmission. The video transmission problem is cast as a joint source and channel rate allocation problem that is shown to be convex with respect to the channel rate. This illustrative application permits to highlight the main advantage of Growth codes, namely improved performance in the intermediate loss region.

Fish Faunal Resurgence in Lake Nabugabo, East Africa

In Lake Nabugabo, Uganda, a small satellite of the equatorial Lake Victoria, approximately 50% of the indigenous fish species disappeared from the open waters subsequent to establishment of the introduced predatory Nile perch (Lates niloticus). However, several of these species persisted in wetland refugia. Over the past decade, Nile perch in Lake Nabugabo have been intensively fished. Herein we report a resurgence of some indigenous species in open waters. In a multiyear study, we used annual transects in inshore and offshore waters of exposed (no wetland) and wetland habitats to document the pattern of resurgence. In 1995, haplochromine cichlids were largely confined to inshore areas, particularly wetland ecotones, and were rare in Nile perch stomachs, as were most other indigenous species. By 2000 haplochromine cichlids were abundant in inshore and offshore areas of both exposed and wetland transects. Several indigenous noncichlids also reappeared in the main lake, including three of the four original mormyrid species. Between 1995 and 1999, there was a dramatic increase in the proportion of haplochromines in the diet of Nile perch. When haplochromines were rare (1995), Nile perch switched from an invertebrate-dominated diet to piscivory at a large size (30 cm total length). In 2000, however, Nile perch were strongly piscivorous by 5–10 cm total length. The pattern of faunal loss and recovery in Lake Nabugabo demonstrates the importance of refugia in providing the seeds of resurgence and provides a model with which to understand some changes in Lake Victoria.

The Apis mellifera filamentous virus genome

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family.

The Impact of Whaling on the Ocean Carbon Cycle: Why Bigger Was Better

Background: Humans have reduced the abundance of many large marine vertebrates, including whales, large fish, and sharks, to only a small percentage of their pre-exploitation levels. Industrial fishing and whaling also tended to preferentially harvest the largest species and largest individuals within a population. We consider the consequences of removing these animals on the ocean's ability to store carbon. Methodology/Principal Findings: Because body size is critical to our arguments, our analysis focuses on populations of baleen whales. Using reconstructions of pre-whaling and modern abundances, we consider the impact of whaling on the amount of carbon stored in living whales and on the amount of carbon exported to the deep sea by sinking whale carcasses. Populations of large baleen whales now store 9.1 x 10(6) tons less carbon than before whaling. Some of the lost storage has been offset by increases in smaller competitors; however, due to the relative metabolic efficiency of larger organisms, a shift toward smaller animals could decrease the total community biomass by 30% or more. Because of their large size and few predators, whales and other large marine vertebrates can efficiently export carbon from the surface waters to the deep sea. We estimate that rebuilding whale populations would remove 1.6 x 10(5) tons of carbon each year through sinking whale carcasses. Conclusions/Significance: Even though fish and whales are only a small portion of the ocean's overall biomass, fishing and whaling have altered the ocean's ability to store and sequester carbon. Although these changes are small relative to the total ocean carbon sink, rebuilding populations of fish and whales would be comparable to other carbon management schemes, including ocean iron fertilization.

ODP Site 162-980 age model and color reflectance record of sediments from ODP Leg 162 sites

Sediment spectral reflectance measurements were generated aboard the JOIDES Resolution during Ocean Drilling Program Leg 162 shipboard operations. The large size of the raw data set (over 1.3 gigabytes) and limited computer hard disk storage space precluded detailed analysis of the data at sea, although broad band averages were used as aids in developing splices and determining lithologic boundaries. This data report describes the methods used to collect these data and their shipboard and postcruise processing. These initial results provide the basis for further postcruise research.

Age determination of Lake Melkoe sediments

The formation of Lake Melkoe (64°51'30''N, 175°14'E, altitude 36 m), one of the largest lakes of the Anadyr Lowland, is related to the moraine left by the Tyellakh Glacier, which originated on the Pekul'nei Ridge. The lake (6 km long and 4.4 km wide) extends in the northwestern direction. The Kholmy Priozernye moraine (16 km long along the arc, 1.5 km wide, and 92-103 masl) surrounds the lake in the west and south. The lake coasts are covered by sand with pebbles and shingle. The flat lake bottom dips toward its central part to a depth of 160 cm. In distinction from many other lakes of the Anadyr Lowland, the thickness of the upper layer of water-saturated sediments overlying compact aleurites in Lake Melkoe is only 5-6 cm. Such a peculiarity of the bottom is explained by the large size of the lake, low sedimentation rates, and frequent storms caused by strong winds. Regional and local vegetation corresponds to a mosaic tundra represented by high shrubs Pinus pumila, Duschekia fruticosa , and hummocky Betula - Ericales - Eriophorum communities. Pinus pumila and Alnus form thickets on the banks of the Anadyr River, coasts of lakes, and moraine slopes.

Late Cretaceous dinoflagellate cysts of ODP Hole 120-748C

At Ocean Drilling Program Hole 748C in the Southern Indian Ocean, a total of 171 Late Cretaceous dinoflagellate taxa were encountered in 38 productive samples from Cores 120-748C-27R through 120-748C-62R (407-740 mbsf). Four provisional dinoflagellate assemblage zones and five subzones were recognized based on the character of the dinoflagellate flora and the first/last occurrences of some key species. Isabelidinium korojonense and Nelsoniella aceras occur in Zone A together with Oligosphaeridium pulcherrimum and Trithyrodinium suspect urn. Zone B was delineated by the total range of Odontochitina cribropoda. Zone C was separated from Zone B by the presence of Satyrodinium haumuriense, and Zone D is dominated by new taxa. The dinocyst assemblages bear a strong affinity to Australian assemblages. Paleoenvironmental interpretations based mainly on dinocysts suggest that during the ?Santonian-Campanian to the Maestrichtian this portion of the Kerguelen Plateau was a shallow submerged plateau, similar to nearshore to offshore to upper slope environments with water depths of tens to hundreds of meters, but isolated from the major continents of the Southern Hemisphere. Starting perhaps in the late Cenomanian (Mohr and Gee, 1992, doi:10.2973/odp.proc.sr.120.196.1992), the Late Cretaceous transgression over the plateau reached its maximum during the late Campanian. The plateau may have been exposed above sea level and subjected to weathering during the latest Maestrichtian. The studied dinocyst assemblages characterized by species of Amphidiadema, Nelsoniella, Satyrodinium, and Xenikoon together with abundant Chatangiella (the large-size species) and Isabelidinium suggest that a South Indian Province (tentatively named the Helby suite) may have existed during the Campanian-Maestrichtian in comparison with the other four provinces of Lentin and Williams. One new genus, three new species, and two new subspecies of dinocysts are described.

Biostratigraphy and Sr isotopic composition of sediments from DSDP Legs 12, 14, 15, 17, 20-22, and 30

We present the data used to construct the Cenozoic and Cretaceous portion of the Phanerozoic curve of seawater 87Sr/86Sr that had been given in summary form by W.H. Burke co-workers. All Cenozoic samples (128) and 22 Cretaceous samples are foram-nannofossil oozes and limestones from DSDP cores distributed among 13 sites in the Atlantic, Pacific and Indian Oceans, and the Caribbean Sea. Non-DSDP Cretaceous samples (126) include limestone, anhydrite and phosphate samples from North America, Europe and Asia. Determination of the 87Sr/86Sr value of seawater at particular times in the past is based on comparison of ratios derived from coeval marine samples from widely separated geographic areas. These samples are characterized by a wide variety of diagenetic and burial histories. The large size and cosmopolitan nature of the data set decreases the likelihood that, among coeval data, systematic error has been introduced by a similar pattern of diagenetic alteration of the ratios. There is good clustering of data points throughout the Cenozoic and Cretaceous curve. The consistency of data is illustrated by Cenozoic and Cretaceous data plots that include a separate symbol for each DSDP site and non-DSDP sample location. More than 98% of the data points are enclosed by upper and lower lines that define a narrow band. For any given time, the correct seawater ratio probably lies within this band. A line drawn within the band represents our estimate of the actual seawater ratio as a function of time. The general configuration of the Cenozoic and Cretaceous curve appears to be strongly influenced by the history of plate interactions and sea-floor spreading. Specific rises and falls in the 87Sr/86Sr of seawater, however, may be caused by a variety of factors such as variation in lithologic composition of the crust exposed to weathering, configuration and topographic relief of continents, volcanic activity, rate of sea-floor spreading, extent of continental inundation by epeiric seas, and variations in both climate and paleooceanographic conditions. Many or all of these factors are probably related to global tectonic processes, yet their combined effect on the temporal variation of seawater 87Sr/86Sr can complicate a direct platetectonic interpretation for portions of the seawater curve.

Stable isotope record of Globorotalia inflata

We sampled the upper water column for living planktic foraminifera along the SW-African continental margin. The species Globorotalia inflata strongly dominates the foraminiferal assemblages with an overall relative abundance of 70-90%. The shell delta18O and delta13C values of G. inflata were measured and compared to the predicted oxygen isotope equilibrium values (delta18O(eq)) and to the carbon isotope composition of the total dissolved inorganic carbon (delta13C(DIC)) of seawater. The delta18O of G. inflata reflects the general gradient observed in the predicted delta18O(eq) profile, while the delta13C of G. inflata shows almost no variation with depth and the reflection of the delta13C(DIC) in the foraminiferal shell seems to be covered by other effects. We found that offsets between delta18O(shell) and predicted delta18O(eq) in the surface mixed layer do not correlate to changes in seawater [CO3[2-]]. To calculate an isotopic mass balance of depth integrated growth, we used the oxygen isotope composition of G. inflata to estimate the fraction of the total shell mass that is grown within each plankton tow depth interval of the upper 500 m of the water column. This approach allows us to calculate the DELTA delta13C(interval added-DIC); i.e. the isotopic composition of calcite that was grown within a given depth interval. Our results consistently show that the DELTA delta13C(IA-DIC) correlates negatively with in situ measured [CO3[2-]] of the ambient water. Using this approach, we found DELTA delta13C(IA-DIC)/[CO3[2-]] slopes for G. inflata in the large size fraction (250-355 µm) of -0.013 per mil to 0.015 per mil (µmol/kg)**-1 and of -0.013 per mil to 0.017 per mil (µmol/kg)**-1 for the smaller specimens (150-250 µm). These slopes are in the range of those found for other non-symbiotic species, such as Globigerina bulloides, from laboratory culture experiments. Since the DELTA delta13C(IA-DIC)/[CO3[2-]] slopes from our field data are nearly identical to the slopes established from laboratory culture experiments we assume that the influence of other effects, such as temperature, are negligibly small. If we correct the delta13C values of G. inflata for a carbonate ion effect, the delta13C(shell) and delta13C(DIC) are correlated with an average offset of 2.11.

Benthic foraminifera of the central Indian Ocean

Late Oligocene to late Pliocene vertical water-mass stratification along depth traverses in the northern Indian Ocean is depicted in this paper by benthic foraminifer index faunas. During most of this time, benthic faunas indicate well-oxygenated, bottom-water conditions at all depths except under the southern Indian upwelling and in the Pliocene in the southern Arabian Sea. Faunas suggest the initiation of lower oxygen conditions at intermediate depths in the northern Indian Ocean beginning in Oligocene Zone P21a. Lower oxygen conditions intensified during primary productivity pulses, possibly related to increased upwelling vigor, in the latest Oligocene and throughout most of the late middle through late Miocene. During times of elevated primary production, there may be more oxygen flux into sedimentary pore waters and the shallow infaunal habitat may become more oxygenated. One criterion for locating the source of "new" water masses is vertical homogeneity of benthic foraminifer indexes for well-oxygenated water masses from intermediate through abyssal depths. In the northern Mascarene Basin, this type of faunal homogeneity with depth corroborates the proposal that the northern Indian Ocean was an area of sinking well-oxygenated waters through most of the Miocene before Zone N17. Oxygenated, possibly "new" intermediate-water masses in the low- to middle-latitude Mascarene and Central Indian basins first developed in the late Oligocene. These well-oxygenated waters were probably more fertile than the Antarctic Intermediate Waters (AAIW) that cover intermediate depths in these areas today. Production of intermediate waters more similar to modern AAIW is indicated by the sparse benthic population of epifaunal rotaloid species in the northern Mascarene Basin during middle Miocene Zone N9 and from early through late Pliocene time. Deep-water characteristics are more difficult to interpret because of the extensive redeposition at the deeper sites. Redeposited intermediate, rather than shallow, water fossils and erosion from north to south in the Mascarene Basin are incompatible with the sluggish circulation from south to north through the western Indian Ocean basins today. Such erosion could result from the vigorous sinking of an intermediate-depth water mass of northern origin. Before late Oligocene Zone P22, benthic faunas indicate a twofold subdivision of the troposphere, with the boundary between upper and lower well-oxygenated water masses located from 2500-3000 mbsl. No characteristic bottom-water fauna developed before the end of late Oligocene Zone P22. Deep and abyssal benthic indexes suggest the development of water masses similar to those of the present day in the latest Miocene. Faunas containing deep-water benthic indexes, including the uvigerinids, suggestive of a water mass similar to modern Indian Deep Water (IDW), appeared during the late Miocene in the northern Mascarene and Central Indian basins. In the early Pliocene, this deep-water fauna was found only in the Central Indian Basin, whereas a fauna typical of modern Antarctic Bottom Water (AABW) spread through deep waters at 2800 mbsl in the Mascarene Basin. By late Pliocene Zone N21, however, deep-water faunas similar to their modern analogs were developed in both the eastern and western basins. Abyssal faunas, studied only in the Mascarene Basin, show more or less similarity to those under modern AABW. Bottom-water faunas containing Nuttallides umbonifera or Epistominella exiguua were first differentiated at the end of Zone P22, then appeared episodically during the early Miocene. These AABW-type faunas reappeared and migrated updepth into deep waters during the glacial episodes at the end of the Miocene and at the beginning of the Pliocene. By late Pliocene Zone N21, however, a bottom-water fauna similar to that under eastern Indian Bottom Water (IBW) developed in the Mascarene Basin. Modern bottom-water characteristics of the Mascarene Basin must have developed after ZoneN21.