Physical constraints during Snowball Earth drive the evolution of multicellularity.

Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.

Environmental and temporal patterns in bioturbation in the Cambrian-Ordovician of Western Newfoundland.

The early Paleozoic emergence of bioturbating (sediment-dwelling and -mixing) animals has long been assumed to have led to substantial changes in marine biogeochemistry, seafloor ecology, and the preservation potential of both sedimentary and fossil archives. However, the timing of the rise of bioturbation and environmental patterns in its expansion have long been subjects of debate-resolution of which has been hampered, in part, by a paucity of high-resolution bioturbation data or of systematic investigations of facies trends in lower Paleozoic bioturbation. To address these issues, we conducted an integrated sedimentological and ichnological characterization of the Cambrian-Ordovician Port au Port succession and Cow Head Group of western Newfoundland, encompassing over 350 meters of stratigraphy logged at the centimeter to decimeter scale. We find that, across a wide range of marine facies, bioturbation does not on average exceed moderate intensities-corroborating observations from other lower Paleozoic successions indicating that the early Paleozoic development of bioturbation was a protracted process. Moreover, bioturbation intensities in the Port au Port succession and Cow Head Group are commonly characterized by considerable variability at even fine scales of stratigraphic resolution and changes in bioturbation intensity correlate strongly with variability in sedimentary facies. We observe that facies recording nearshore depositional environments and carbonate-rich lithologies are each characterized by the highest intensities of both burrowing and sediment mixing. These data highlight the need for a high-resolution and facies-specific approach to reconstructing the evolutionary history of bioturbation and suggest that average levels of bioturbation, although relatively low throughout this interval, increased notably earlier in nearshore marine settings.

Photosymbiont associations persisted in planktic foraminifera during early Eocene hyperthermals at Shatsky Rise (Pacific Ocean).

Understanding the sensitivity of species-level responses to long-term warming will become increasingly important as we look towards a warmer future. Here, we examine photosymbiont associations in planktic foraminifera at Shatsky Rise (ODP Site 1209, Pacific Ocean) across periods of global warming of differing magnitude and duration. We compare published data from the Paleocene-Eocene Thermal Maximum (PETM; ~55.9 Ma) with data from the less intense Eocene Thermal Maximum 2 (ETM2; ~54.0 Ma), and H2 events (~53.9 Ma). We use a positive relationship between test size and carbon isotope value (size-δ13C) in foraminifera shells as a proxy for photosymbiosis in Morozovella subbotinae and Acarinina soldadoensis, and find no change in photosymbiont associations during the less intense warming events, in contrast with PETM records indicating a shift in symbiosis in A. soldadoensis (but not M. subbotinae). Declines in abundance and differing preservation potential of the asymbiotic species Subbotina roesnaesensis along with sediment mixing likely account for diminished differences in δ13C between symbiotic and asymbiotic species from the PETM and ETM2. We therefore conclude that photosymbiont associations were maintained in both A. soldadoensis and M. subbotinae across ETM2 and H2. Our findings support one or both of the hypotheses that 1) changing symbiotic associations in response to warming during the PETM allowed A. soldadoensis and perhaps other acarininids to thrive through subsequent hyperthermals or 2) some critical environmental threshold value was not reached in these less intense hyperthermals.

Bite force data suggests relationship between acrodont tooth implantation and strong bite force.

Extant and extinct reptiles exhibit numerous combinations of tooth implantation and attachment. Tooth implantation ranges from those possessing roots and lying within a socket (thecodonty), to teeth lying against the lingual wall of the jawbone (pleurodonty), to teeth without roots or sockets that are attached to the apex of the marginal jawbones (acrodonty). Attachment may be ligamentous (gomphosis) or via fusion (ankylosis). Generally speaking, adaptative reasonings are proposed as an underlying driver for evolutionary changes in some forms of tooth implantation and attachment. However, a substantiated adaptive hypothesis is lacking for the state of acrodont ankylosis that is seen in several lineages of Lepidosauria, a clade that is plesiomorphically pleurodont. The convergent evolution of acrodont ankylosis in several clades of lepidosaurs suggests a selective pressure shaped the evolution of the trait. We hypothesize that acrodont ankylosis as seen in Acrodonta and Sphenodon punctatus, is an adaptation either resulting from or allowing for a stronger bite force. We analyzed bite force data gathered from the literature to show that those taxa possessing acrodont dentition possess a stronger bite force on average than those taxa with pleurodont dentition. Dietary specialists with pleurodont dentition may also possess relatively high bite forces, though body size may also play a role in their ability to bite hard. Furthermore, our results have implications for the evolution of acrodont ankylosis and potential behaviors related to strong bite force that influenced the evolution of acrodonty within Acrodonta and Rhynchocephalia.

Meta-analysis of survival prediction with Palliative Performance Scale.

This paper aims to reconcile the use of Palliative Performance Scale (PPSv2) for survival prediction in palliative care through an international collaborative study by five research groups. The study involves an individual patient data meta-analysis on 1,808 patients from four original datasets to reanalyze their survival patterns by age, gender, cancer status, and initial PPS score. Our findings reveal a strong association between PPS and survival across the four datasets. The Kaplan-Meier survival curves show each PPS level as distinct, with a strong ordering effect in which higher PPS levels are associated with increased length of survival. Using a stratified Cox proportional hazard model to adjust for study differences, we found females lived significantly longer than males, with a further decrease in hazard for females not diagnosed with cancer. Further work is needed to refine the reporting of survival times/probabilities and to improve prediction accuracy with the inclusion of other variables in the models.

Use of Palliative Performance Scale in end-of-life prognostication.

BACKGROUND: Current literature suggests clinicians are not accurate in prognostication when estimating survival times of palliative care patients. There are reported studies in which the Palliative Performance Scale (PPS) is used as a prognostic tool to predict survival of these patients. Yet, their findings are different in terms of the presence of distinct PPS survival profiles and significant covariates. OBJECTIVE: This study investigates the use of PPS as a prognostication tool for estimating survival times of patients with life-limiting illness in a palliative care unit. These findings are compared to those from earlier studies in terms of PPS survival profiles and covariates. METHODS: This is a retrospective cohort study in which the admission PPS scores of 733 palliative care patients admitted between March 3, 2000 and August 9, 2002 were examined for survival patterns. Other predictors for survival included were age, gender, and diagnosis. RESULTS: Study findings revealed that admission PPS score was a strong predictor of survival in patients already identified as palliative, along with gender and age, but diagnosis was not significantly related to survival. We also found that scores of PPS 10% through PPS 50% led to distinct survival curves, and male patients had consistently lower survival rates than females regardless of PPS score. CONCLUSION: Our findings differ somewhat from earlier studies that suggested the presence of three distinct PPS survival profiles or bands, with diagnosis and noncancer as significant covariates. Such differences are likely attributed to the size and characteristics of the patient populations involved and further analysis with larger patient samples may help clarify PPS use in prognosis.

Diffuse lamellar keratitis complicating laser in situ keratomileusis: post-marketing surveillance of an emerging disease in British Columbia, Canada, 2000-2002.

PURPOSE: To describe a surveillance system and summarize data between January 2000 and December 2002 regarding diffuse lamellar keratitis (DLK), a complication of laser in situ keratomileusis (LASIK) surgery. SETTING: Community-based clinics in British Columbia, Canada, in which LASIK surgery is performed. METHODS: Monthly, all clinics in which LASIK is performed reported the number of LASIK procedures and nonnominal cases of DLK (by grade and onset date) to the British Columbia Centre for Disease Control. Diffuse lamellar keratitis outbreaks were investigated, and prevention and control measures were recommended. RESULTS: From 2000 to 2002, approximately 72,000 LASIK procedures were performed, with a mean DLK incidence rate of 0.67% (95% confidence interval, 0.61-0.73). The overall proportion of DLK cases attributed to outbreaks was 64%, decreasing from 72% in 2000 to 40% in 2003. CONCLUSIONS: An effective DLK surveillance program was implemented at all laser refractive clinics in British Columbia. Reported DLK incidence was 0.67 cases per 100 procedures, with 64% occurring in outbreaks.

Sensing the heat stress by Mammalian cells.

BACKGROUND: The heat-shock response network controls the adaptation and survival of the cell against environmental stress. This network is highly conserved and is connected with many other signaling pathways. A key element of the heat-shock network is the heat-shock transcription factor-1 (HSF), which is transiently activated by elevated temperatures. HSF translocates to the nucleus upon elevated temperatures, forming homotrimeric complexes. The HSF homotrimers bind to the heat shock element on the DNA and control the expression of the hsp70 gene. The Hsp70 proteins protect cells from thermal stress. Thermal stress causes the unfolding of proteins, perturbing thus the pathways under their control. By binding to these proteins, Hsp70 allows them to refold and prevents their aggregation. The modulation of the activity of the hsp70-promoter by the intensity of the input stress is thus critical for cell's survival. The promoter activity starts from a basal level and rapidly increases once the stress is applied, reaches a maximum level and attenuates slowely back to the basal level. This phenomenon is the hallmark of many experimental studies and of all computational network analysis. RESULTS: The molecular construct used as a measure of the response to thermal stress is a Hsp70-GFP fusion gene transfected in Chinese hamster ovary (CHO) cells. The time profile of the GFP protein depends on the transient activity, Transient(t), of the heat shock system. The function Transient(t) depends on hsp70 promoter activity, transcriptional regulation and the translation initiation effects elicited by the heat stress. The GFP time profile is recorded using flow cytometry measurements, a technique that allows a quantitative measurement of the fluorescence of a large number of cells (104). The GFP responses to one and two heat shocks were measured for 261 conditions of different temperatures and durations. We found that: (i) the response of the cell to two consecutive shocks (i.e., no recovery time in between shocks) depends on the order of the input shocks, that is the shocks do not commute; (ii) the responses may be classified as mild or severe, depending on the temperature level and the duration of the heat shock and (iii) the response is highly sensitive to small variations in temperature. CONCLUSIONS: We propose a mathematical model that maps temperature into the transient activity using experimental data that describes the time course of the response to input thermal stress. The model is built on thermotolerance without recovery time, sharp sensitivity to small variations in temperature and the existence of mild and severe classes of stress responses. The theoretical predictions are tested against experimental data using a series of double-shock inputs. The theoretical structure is represented by a sequence of three cascade processes that transform the input stress into the transient activity. The structure of the cascade is nonlinear-linear-nonlinear (NLN). The first nonlinear system (N) from the NLN structure represents the amplification of small changes in the environmental temperature; the linear system (L) represents the thermotolerance without recovery time, whereas the last system (N) represents the transition of the cell's response from a mild to a severe shock.

Hardware accelerator for genomic sequence alignment.

To infer homology and subsequently gene function, the Smith-Waterman algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain billions of sequences, this algorithm becomes computationally expensive. Consequently, in this paper, we focused on accelerating the Smith-Waterman algorithm by modifying the computationally repeated portion of the algorithm by FPGA hardware custom instructions. These simple modifications accelerated the algorithm runtime by an average of 287% compared to the pure software implementation. Therefore, further design of FPGA accelerated hardware offers a promising direction to seeking runtime improvement of genomic database searching.