Response-guided neoadjuvant sacituzumab govitecan for localized triple-negative breast cancer: results from the NeoSTAR trial.

BACKGROUND: Sacituzumab govitecan (SG), a novel antibody-drug conjugate (ADC) targeting TROP2, is approved for pre-treated metastatic triple-negative breast cancer (mTNBC). We conducted an investigator-initiated clinical trial evaluating neoadjuvant (NA) SG (NCT04230109), and report primary results. PATIENTS AND METHODS: Participants with early-stage TNBC received NA SG for four cycles. The primary objective was to assess pathological complete response (pCR) rate in breast and lymph nodes (ypT0/isN0) to SG. Secondary objectives included overall response rate (ORR), safety, event-free survival (EFS), and predictive biomarkers. A response-guided approach was utilized, and subsequent systemic therapy decisions were at the discretion of the treating physician. RESULTS: From July 2020 to August 2021, 50 participants were enrolled (median age = 48.5 years; 13 clinical stage I disease, 26 stage II, 11 stage III). Forty-nine (98%) completed four cycles of SG. Overall, the pCR rate with SG alone was 30% [n = 15, 95% confidence interval (CI) 18% to 45%]. The ORR per RECIST V1.1 after SG alone was 64% (n = 32/50, 95% CI 77% to 98%). Higher Ki-67 and tumor-infiltrating lymphocytes (TILs) were predictive of pCR to SG (P = 0.007 for Ki-67 and 0.002 for TILs), while baseline TROP2 expression was not (P = 0.440). Common adverse events were nausea (82%), fatigue (76%), alopecia (76%), neutropenia (44%), and rash (48%). With a median follow-up time of 18.9 months (95% CI 16.3-21.9 months), the 2-year EFS for all participants was 95%. Among participants with a pCR with SG (n = 15), the 2-year EFS was 100%. CONCLUSIONS: In the first NA trial with an ADC in localized TNBC, SG demonstrated single-agent efficacy and feasibility of response-guided escalation/de-escalation. Further research on optimal duration of SG as well as NA combination strategies, including immunotherapy, are needed.

Ultrafast, broadband and tunable terahertz reflector and neutral density filter based on high resistivity silicon.

We report THz transmission and reflection properties of an ultrafast optically excited highly resistive silicon wafer. Amplified Ti:Sapphire femtosecond laser pulses at 800 nm were used to create fluence-dependent carrier density on the front surface of the wafer which modifies the dielectric properties at the THz frequencies. Time-resolved experiments in the optical pump-THz probe configuration were conducted in which THz pulses reflected off from the surface at 0° and 45° angles of incidence make it possible to measure the pump-fluence dependent ultrafast evolution of the reflection and transmission coefficients in 0.5-6 THz range. An analytical model, where both the Drude contributions from the photo-excited electrons and holes account for the change of the dielectric constant of the photo-excited silicon, has been used to evaluate the THz reflection and transmission coefficients at steady state. Thus obtained results match well with the experimental results and demonstrate an all-optical means to convert a silicon wafer into an ultrafast, tunable and broadband neutral density filter or reflector in the THz frequency range.

Implementing surgical mentorship in a resource-constrained context: a mixed methods assessment of the experiences of mentees, mentors, and leaders, and lessons learned.

BACKGROUND: A well-qualified workforce is critical to effective functioning of health systems and populations; however, skill gaps present a challenge in low-resource settings. While an emerging body of evidence suggests that mentorship can improve quality, access, and systems in African health settings by building the capacity of health providers, less is known about its implementation in surgery. We studied a novel surgical mentorship intervention as part of a safe surgery intervention (Safe Surgery 2020) in five rural Ethiopian facilities to understand factors affecting implementation of surgical mentorship in resource-constrained settings. METHODS: We designed a convergent mixed-methods study to understand the experiences of mentees, mentors, hospital leaders, and external stakeholders with the mentorship intervention. Quantitative data was collected through a survey (n = 25) and qualitative data through in-depth interviews (n = 26) in 2018 to gather information on (1) intervention characteristics including areas of mentorship, mentee-mentor relationships, and mentor characteristics, (2) organizational context including facilitators and barriers to implementation, (3) perceived impact, and (4) respondent characteristics. We analyzed the quantitative and qualitative data using frequency analysis and the constant comparison method, respectively; we integrated findings to identify themes. RESULTS: All mentees (100%) experienced the intervention as positive. Participants perceived impact as: safer and more frequent surgical procedures, collegial bonds between mentees and mentors, empowerment among mentees, and a culture of continuous learning. Over 70% of all mentees reported their confidence and job satisfaction increased. Supportive intervention characteristics included a systems focus, psychologically safe mentee-mentor relationships, and mentor characteristics including generosity with time and knowledge, understanding of local context, and interpersonal skills. Supportive organizational context included a receptive implementation climate. Intervention challenges included insufficient clinical training, inadequate mentor support, and inadequate dose. Organizational context challenges included resource constraints and a lack of common understanding of the intervention. CONCLUSION: We offer lessons for intervention designers, policy makers, and practitioners about optimizing surgical mentorship interventions in resource-constrained settings. We attribute the intervention's success to its holistic approach, a receptive climate, and effective mentee-mentor relationships. These qualities, along with policy support and adapting the intervention through user feedback are important for successful implementation.

Springs ecosystem classification.

Springs ecosystems are globally abundant, geomorphologically diverse, and bio-culturally productive, but are highly imperiled by anthropogenic activities. More than a century of scientific discussion about the wide array of ecohydrological factors influencing springs has been informative, but has yielded little agreement on their classification. This lack of agreement has contributed to the global neglect and degradation of springs ecosystems by the public, scientific, and management communities. Here we review the historical literature on springs classification variables, concluding that site-specific source geomorphology remains the most diagnostic approach. We present a conceptual springs ecosystem model that clarifies the central role of geomorphology in springs ecosystem development, function, and typology. We present an illustrated dichotomous key to terrestrial (non-marine) springs ecosystem types and subtypes, and describe those types. We identify representative reference sites, although data limitations presently preclude selection of continentally or globally representative reference springs of each type. We tested the classification key using data from 244 randomly selected springs of 13 types that were inventoried in western North America. The dichotomous key correctly identified springs type in 87.5% of the cases, with discrepancies primarily due to differentiation of primary vs. secondary typology, and insufficient inventory team training. Using that information, we identified sources of confusion and clarified the key. Among the types that required more detailed explanation were hypocrenes, springs in which groundwater is expressed through phreatophytic vegetation. Overall, springs biodiversity and ecosystem complexity are due, in part, to the co-occurrence of multiple intra-springs microhabitats. We describe microhabitats that are commonly associated with different springs types, reporting at least 13 microhabitats, each of which can support discrete biotic assemblages. Interdisciplinary agreement on basic classification is needed to enhance scientific understanding and stewardship of springs ecosystems, the loss and degradation of which constitute a global conservation crisis.

High mutational rates of large-scale duplication and deletion in Daphnia pulex.

Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.

Emulating natural wetlands oxygen conditions for the removal of N and P in agricultural wastewaters.

The aim of this research was to evaluate a constructed wetland system (CW) operated under aerobic-anoxic-aerobic conditions to remove C, N and P from water with high concentrations of the last two nutrients. A series of three CW were operated continuously for 190 days. An aerobic vertical CW was used in the first and third stages and an anoxic horizontal CW was used in the second stage. The total nitrogen (TN) removal efficiency was 70 ±â€¯1.5%. Similar removal efficiency behavior was observed in others nitrogen compounds, where a removal of 85 ±â€¯1.5% for NO3--N and 97 ±â€¯2.2% for NH3+N were achieved. The combination of different oxygen conditions enhanced oxidation of nitrates and the assimilation of ammonium by vegetation. On the other hand, 54 ±â€¯6.5% total phosphorus (TP) was removed in the entire system, which is higher than the reported in several investigations, including mechanized and controlled systems such as activated sludge. The phosphorous removal efficiency was attributed to the adequate design and configuration of CW, which facilitated dissolved oxygen (DO) conditions required for phosphorus capture. Despite in this investigation the CW was not designed for an optimal removal of organic matter the removal efficiency of this parameter was 64 ±â€¯7.5%. The successful results suggest that the combination of aerobic-anoxic-aerobic stages is a technically suitable option for the treatment of agricultural wastewater with high content of N and P.

Forest restoration as a strategy to mitigate climate impacts on wildfire, vegetation, and water in semiarid forests.

Climate change and wildfire are interacting to drive vegetation change and potentially reduce water quantity and quality in the southwestern United States, Forest restoration is a management approach that could mitigate some of these negative outcomes. However, little information exists on how restoration combined with climate change might influence hydrology across large forest landscapes that incorporate multiple vegetation types and complex fire regimes. We combined spatially explicit vegetation and fire modeling with statistical water and sediment yield models for a large forested landscape (335,000 ha) on the Kaibab Plateau in northern Arizona, USA. Our objective was to assess the impacts of climate change and forest restoration on the future fire regime, forest vegetation, and watershed outputs. Our model results predict that the combination of climate change and high-severity fire will drive forest turnover, biomass declines, and compositional change in future forests. Restoration treatments may reduce the area burned in high-severity fires and reduce conversions from forested to non-forested conditions. Even though mid-elevation forests are the targets of restoration, the treatments are expected to delay the decline of high-elevation spruce-fir, aspen, and mixed conifer forests by reducing the occurrence of high-severity fires that may spread across ecoregions. We estimate that climate-induced vegetation changes will result in annual runoff declines of up to 10%, while restoration reduced or reversed this decline. The hydrologic model suggests that mid-elevation forests, which are the targets of restoration treatments, provide around 80% of runoff in this system and the conservation of mid- to high-elevation forests types provides the greatest benefit in terms of water conservation. We also predict that restoration treatments will conserve water quality by reducing patches of high-severity fire that are associated with high sediment yield. Restoration treatments are a management strategy that may reduce undesirable outcomes for multiple ecosystem services.

Seroprevalence of anti-Toxoplasma gondii IgG antibody and risk factors among abattoir workers in Uyo, Southern Nigeria.

CONTEXT: The asymptomatic nature of toxoplasmosis with its severe consequences, especially in populations with high HIV infection rate, makes it a disease of public health importance. Being a zoonosis, Toxoplasma gondii infection may be high among people who work with animals. Thus, there is the need to determine the prevalence of the infection among abattoir workers in Uyo, where HIV prevalence rate is in double digits, which could lead to reactivation of toxoplasmosis in those with immunosuppression. AIM: To determine the prevalence and associated risk factors of T. gondii infection in abattoir workers in Uyo. SETTINGS AND DESIGN: A descriptive cross-sectional study that was conducted among persons who work with livestock and birds, in Uyo and its environs. METHODOLOGY: The study was conducted among 339 workers in abattoirs in Uyo and its environs. Data were collected using interviewer-administered questionnaire and detection of IgG antibodies to T. gondii using ELISA technique and HIV testing using the national algorithm. Data were analyzed using STATA statistical software version 20, and statistically significant level was set at P < 0.05. RESULTS: The seroprevalence of T. gondii IgG antibodies among the study participants was 55.8%. At a univariate level, many factors were associated with T. gondii seropositivity; they were age, sex, level of education, ethnicity, occupation in the abattoir, type of animal exposure, always washing hands before eating in the workplace, and taking of raw/unpasteurized milk. However, after multivariate analysis, participants exposed to poultry, butchers/raw meat sellers, and those who had worked for more than 5 years in abattoirs were at a greater risk of being T. gondii IgG seropositive; odds ratio (OR) 5.46 [confidence interval (CI) 1.88, 15.86]; OR 1.89 (CI 1.14, 3.14), and OR 1.25 (CI 1.25, 6.42), respectively. CONCLUSION: T. gondii IgG seroprevalence is high among abattoir workers in Uyo, and there is a need for Akwa Ibom State government to establish enlightenment and prevention programs for these occupationally exposed and other populations at risk of infection.

Dynamics of Tissue-Induced Alignment of Fibrous Extracellular Matrix.

Aligned fibers of extracellular matrix (ECM) affect the direction, efficiency, and persistence of migrating cells. To uncover the mechanisms by which multicellular tissues align their surrounding ECM before migration, we used an engineered three-dimensional culture model to investigate the dynamics of ECM alignment around tissues of defined geometry. Analysis of ECM alignment over time revealed that tissues rapidly reorganize their surrounding matrix, with a characteristic time that depends on the type of cell and the initial tissue geometry. We found that matrix metalloproteinase activity is not required for matrix alignment before cell migration. Instead, alignment is driven by Rho-mediated cytoskeletal contractility and accelerated by propagation of tension through intercellular adhesions. Our data suggest that multicellular tissues align their surrounding matrix by pulling collectively to exert strain, which is primarily a physical process. Consistently, the pattern of matrix alignment depends on tissue geometry and the resulting distribution of mechanical strain, with asymmetric tissues generating a higher degree of matrix alignment along their longest axes. The rapid ability of multicellular tissues to physically remodel their matrix enables their constituent cells to migrate efficiently along aligned fibers and to quickly change their direction according to other microenvironmental cues, which is important for both normal and disease processes.

Common transcriptional mechanisms for visual photoreceptor cell differentiation among Pancrustaceans.

A hallmark of visual rhabdomeric photoreceptors is the expression of a rhabdomeric opsin and uniquely associated phototransduction molecules, which are incorporated into a specialized expanded apical membrane, the rhabdomere. Given the extensive utilization of rhabdomeric photoreceptors in the eyes of protostomes, here we address whether a common transcriptional mechanism exists for the differentiation of rhabdomeric photoreceptors. In Drosophila, the transcription factors Pph13 and Orthodenticle (Otd) direct both aspects of differentiation: rhabdomeric opsin transcription and rhabdomere morphogenesis. We demonstrate that the orthologs of both proteins are expressed in the visual systems of the distantly related arthropod species Tribolium castaneum and Daphnia magna and that their functional roles are similar in these species. In particular, we establish that the Pph13 homologs have the ability to bind a subset of Rhodopsin core sequence I sites and that these sites are present in key phototransduction genes of both Tribolium and Daphnia. Furthermore, Pph13 and Otd orthologs are capable of executing deeply conserved functions of photoreceptor differentiation as evidenced by the ability to rescue their respective Drosophila mutant phenotypes. Pph13 homologs are equivalent in their ability to direct both rhabdomere morphogenesis and opsin expression within Drosophila, whereas Otd paralogs demonstrate differential abilities to regulate photoreceptor differentiation. Finally, loss-of-function analyses in Tribolium confirm the conserved requirement of Pph13 and Otd in regulating both rhabdomeric opsin transcription and rhabdomere morphogenesis. Taken together, our data identify components of a regulatory framework for rhabdomeric photoreceptor differentiation in Pancrustaceans, providing a foundation for defining ancestral regulatory modules of rhabdomeric photoreceptor differentiation.

Frequency resolved cross-correlation between optical and terahertz pulses: application to ultrashort laser pulse characterization.

We have analyzed both theoretically and experimentally the spectrum of the optical pulses produced by the interaction of optical and THz pulses in a ZnTe crystal. Recorded as a function of the delay between the two pulses, the resulting spectrogram can be viewed as a frequency resolved cross-correlation between the optical and THz pulses making it possible to characterize the optical pulse.

Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex.

Despite much theoretical work, the molecular-genetic causes and evolutionary consequences of asexuality remain largely undetermined. Asexual animal species are rare, evolutionarily short-lived, and thought to suffer mutational meltdown as a result of lack of recombination. Whole-genome analysis of 11 sexual and 11 asexual genotypes of Daphnia pulex indicates that current asexual lineages are in fact very young, exhibit no signs of purifying selection against accumulating mutations, and have extremely high rates of gene conversion and deletion. The reconstruction of chromosomal haplotypes in regions containing SNP markers associated with asexuality (chromosomes VIII and IX) indicates that introgression from a sister species, Daphnia pulicaria, underlies the origin of the asexual phenotype. Silent-site divergence of the shared chromosomal haplotypes of asexuals indicates that the spread of asexuality is as recent as 1,250 y, although the origin of the meiosis-suppressing element or elements could be substantially older. In addition, using previous estimates of the gene conversion rate from Daphnia mutation accumulation lines, we are able to age each asexual lineage. Although asexual lineages originate from wide crosses that introduce elevated individual heterozygosities on clone foundation, they also appear to be constrained by the inbreeding-like effect of loss of heterozygosity that accrues as gene conversion and hemizygous deletion expose preexisting recessive deleterious alleles of asexuals, limiting their evolutionary longevity. Our study implies that the buildup of newly introduced deleterious mutations (i.e., Muller's ratchet) may not be the dominant force imperiling nonrecombining populations of D. pulex, as previously proposed.

Using 'candidacy' as a framework for understanding access to mainstream psychological treatment for people with intellectual disabilities and common mental health problems within the English Improving Access to Psychological Therapies service.

BACKGROUND: The Improving Access to Psychological Therapies (IAPT) service was established to address common mental health problems among the English population in a timely manner in order to counter the social and economic disadvantage accompanying such difficulties. Using the concept of candidacy, we examined how the legitimacy of claims by people with intellectual disabilities to use this service is facilitated or impeded. METHOD: We used a sequential mixed methods design. We completed 21 interviews with a range of stakeholders, including people with intellectual disabilities and their carers. Themes from the interviews were used to design an online survey questionnaire that was returned by 452 staff from IAPT and specialist intellectual disability services. RESULTS: Using the candidacy framework, we noted that eligibility and access to IAPT were achieved through dynamic and iterative processes of negotiation involving people with intellectual disabilities and their supporters on one side and IAPT staff and service structures on the other. Barriers and facilitators were apparent throughout the seven dimensions of candidacy (identification, navigation, permeability of services, appearances, adjudications, offers and resistance and operating conditions) and were linked to discourses relating to the character and purpose of IAPT and specialist intellectual disability services. CONCLUSIONS: Opportunities exist for some people with intellectual disabilities to assert their candidacy for IAPT input, although there are barriers at individual, professional, organisational and structural levels. More attention needs to be paid to how principles of inclusiveness are operationalised within IAPT teams and to the mental health facilitation role of specialist intellectual disability staff.

Chemoprotective effect of Vernonia amygdalina Del. (Astereacea) against 2-acetylaminofluorene-induced hepatotoxicity in rats.

Natural products possessing antioxidant properties play a very crucial role in ameliorating deleterious effects of reactive oxygen species. This study investigated the chemoprotective properties of methanolic extract of Vernonia amygdalina (MEVA) in an experimental model of hepatic oxidative damage induced by 2-acetylaminofluorene (2-AAF). Rats were divided into six groups. Groups 1 and 2 received saline and dimethyl sulfoxide, respectively, and served as controls. Group 3 received MEVA at a dose of 250 mg/kg, while groups 5 and 6 were pretreated for 14 days with MEVA at 250 mg/kg and 500 mg/kg doses before coadministration with 2-AAF at 100 mg/kg for another 7 days. 2-AAF was administered to group 4 for the last 7 days. Animals were killed 24 h after the last administration of 2-AAF. 2-AAF significantly (p < 0.05) induced marked hepatic damage as revealed by increased activities of serum enzymes such as alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and γ-glutamyl transferase and bilirubin concentration. 2-AAF also elicited decrease in the activities of antioxidant enzymes such as superoxide dismutase, catalase, glutathione-S-transferase, and glutathione peroxidase, depletion of reduced glutathione, and increase in malondialdehyde levels. The activities of glucose-6-phosphatase and 5'-nucleotidase were also depleted. MEVA at 250 mg/kg and 500 mg/kg significantly (p < 0.05) ameliorated the oxidative damage, functional impairments, and histopathological changes associated with 2-AAF toxicity by reducing the activities of serum enzymes, upregulating the antioxidant defense enzymes and glutathione with decrease in malondialdehyde level. In this study, the revealed ameliorative and hepatoprotective effects of MEVA against 2-AAF-induced toxicity may be due to its antioxidant and free-radical scavenging activities, thus suggesting its usefulness as a possible chemoprophylactic agent.

Evolutionary history and leaf succulence as explanations for medicinal use in aloes and the global popularity of Aloe vera.

BACKGROUND: Aloe vera supports a substantial global trade yet its wild origins, and explanations for its popularity over 500 related Aloe species in one of the world's largest succulent groups, have remained uncertain. We developed an explicit phylogenetic framework to explore links between the rich traditions of medicinal use and leaf succulence in aloes. RESULTS: The phylogenetic hypothesis clarifies the origins of Aloe vera to the Arabian Peninsula at the northernmost limits of the range for aloes. The genus Aloe originated in southern Africa ~16 million years ago and underwent two major radiations driven by different speciation processes, giving rise to the extraordinary diversity known today. Large, succulent leaves typical of medicinal aloes arose during the most recent diversification ~10 million years ago and are strongly correlated to the phylogeny and to the likelihood of a species being used for medicine. A significant, albeit weak, phylogenetic signal is evident in the medicinal uses of aloes, suggesting that the properties for which they are valued do not occur randomly across the branches of the phylogenetic tree. CONCLUSIONS: Phylogenetic investigation of plant use and leaf succulence among aloes has yielded new explanations for the extraordinary market dominance of Aloe vera. The industry preference for Aloe vera appears to be due to its proximity to important historic trade routes, and early introduction to trade and cultivation. Well-developed succulent leaf mesophyll tissue, an adaptive feature that likely contributed to the ecological success of the genus Aloe, is the main predictor for medicinal use among Aloe species, whereas evolutionary loss of succulence tends to be associated with losses of medicinal use. Phylogenetic analyses of plant use offer potential to understand patterns in the value of global plant diversity.

Computer control of drug delivery by continuous intravenous infusion: bridging the gap between intended and actual drug delivery.

BACKGROUND: Intravenous drug infusion driven by syringe pumps may lead to substantial temporal lags in achieving steady-state delivery at target levels when using very low flow rates ("microinfusion"). This study evaluated computer algorithms for reducing temporal lags via coordinated control of drug and carrier flows. METHODS: Novel computer control algorithms were developed based on mathematical models of fluid flow. Algorithm 1 controlled initiation of drug infusion and algorithm 2 controlled changes to ongoing steady-state infusions. These algorithms were tested in vitro and in vivo using typical high and low dead volume infusion system architectures. One syringe pump infused a carrier fluid and a second infused drug. Drug and carrier flowed together via a manifold through standard central venous catheters. Samples were collected in vitro for quantitative delivery analysis. Parameters including left ventricular max dP/dt were recorded in vivo. RESULTS: Regulation by algorithm 1 reduced delivery delay in vitro during infusion initiation by 69% (low dead volume) and 78% (high dead volume). Algorithmic control in vivo measuring % change in max dP/dt showed similar results (55% for low dead volume and 64% for high dead volume). Algorithm 2 yielded greater precision in matching the magnitude and timing of intended changes in vivo and in vitro. CONCLUSIONS: Compared with conventional methods, algorithm-based computer control of carrier and drug flows can improve drug delivery by pump-driven intravenous infusion to better match intent. For norepinephrine infusions, the amount of drug reaching the bloodstream per time appears to be a dominant factor in the hemodynamic response to infusion.

Extensive error in the number of genes inferred from draft genome assemblies.

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

Extraordinary genome stability in the ciliate Paramecium tetraurelia.

Mutation plays a central role in all evolutionary processes and is also the basis of genetic disorders. Established base-substitution mutation rates in eukaryotes range between ∼5 × 10(-10) and 5 × 10(-8) per site per generation, but here we report a genome-wide estimate for Paramecium tetraurelia that is more than an order of magnitude lower than any previous eukaryotic estimate. Nevertheless, when the mutation rate per cell division is extrapolated to the length of the sexual cycle for this protist, the measure obtained is comparable to that for multicellular species with similar genome sizes. Because Paramecium has a transcriptionally silent germ-line nucleus, these results are consistent with the hypothesis that natural selection operates on the cumulative germ-line replication fidelity per episode of somatic gene expression, with the germ-line mutation rate per cell division evolving downward to the lower barrier imposed by random genetic drift. We observe ciliate-specific modifications of widely conserved amino acid sites in DNA polymerases as one potential explanation for unusually high levels of replication fidelity.

Vascular Dilation, Tachycardia, and Increased Inotropy Occur Sequentially with Increasing Epinephrine Dose Rate, Plasma and Myocardial Concentrations, and cAMP.

BACKGROUND: While epinephrine infusion is widely used in critical care for inotropic support, there is no direct method to detect the onset and measure the magnitude of this response. We hypothesised that surrogate measurements, such as heart rate and vascular tone, may indicate if the plasma and tissue concentrations of epinephrine and cAMP are in a range sufficient to increase myocardial contractility. METHODS: Cardiovascular responses to epinephrine infusion (0.05-0.5 mcgkg(-1)min(-1)) were measured in rats using arterial and left ventricular catheters. Epinephrine and cAMP levels were measured using ELISA techniques. RESULTS: The lowest dose of epinephrine infusion (0.05 mcgkg(-1)min(-1)) did not raise plasma epinephrine levels and did not lead to cardiovascular response. Incremental increase in epinephrine infusion (0.1 mcgkg(-1)min(-1)) elevated plasma but not myocardial epinephrine levels, providing vascular, but not cardiac effects. Further increase in the infusion rate (0.2 mcgkg(-1)min(-1)) raised myocardial tissue epinephrine levels sufficient to increase heart rate but not contractility. Inotropic and lusitropic effects were significant at the infusion rate of 0.3 mcgkg(-1)min(-1). Correlation of plasma epinephrine to haemodynamic parameters suggest that as plasma concentration increases, systemic vascular resistance falls (EC50=47 pg/ml), then HR increases (ED50=168 pg/ml), followed by a rise in contractility and lusitropy (ED50=346 pg/ml and ED50=324 pg/ml accordingly). CONCLUSIONS: The dose response of epinephrine is distinct for vascular tone, HR and contractility. The need for higher doses to see cardiac effects is likely due to the threshold for drug accumulation in tissue. Successful inotropic support with epinephrine cannot be achieved unless the infusion is sufficient to raise the heart rate.