Charting the Course of Pinniped Evolution: insights from molecular phylogeny and fossil record integration

Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these two rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to-date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses however experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12-6 Ma, possibly due to changing sea-levels and/or competition with otariids (eared seals). Historical biogeographic analyses including fossil data allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.

Developing a core outcome set for the health outcomes for children and adults with congenital oesophageal atresia and/or tracheo-oesophageal fistula: OCELOT task group study protocol

INTRODUCTION

Heterogeneity in reported outcomes of infants with oesophageal atresia (OA) with or without tracheo-oesophageal fistula (TOF) prevents effective data pooling. Core outcome sets (COS) have been developed for many conditions to standardise outcome reporting, facilitate meta-analysis and improve the relevance of research for patients and families. Our aim is to develop an internationally-agreed, comprehensive COS for OA-TOF, relevant from birth through to transition and adulthood.

METHODS AND ANALYSIS

A long list of outcomes will be generated using (1) a systematic review of existing studies on OA-TOF and (2) qualitative research with children (patients), adults (patients) and families involving focus groups, semistructured interviews and self-reported outcome activity packs. A two-phase Delphi survey will then be completed by four key stakeholder groups: (1) patients (paediatric and adult); (2) families; (3) healthcare professionals; and (4) researchers. Phase I will include stakeholders individually rating the importance and relevance of each long-listed outcome using a 9-point Likert scale, with the option to suggest additional outcomes not already included. During phase II, stakeholders will review summarised results from phase I relative to their own initial score and then will be asked to rescore the outcome based on this information. Responses from phase II will be summarised using descriptive statistics and a predefined definition of consensus for inclusion or exclusion of outcomes. Following the Delphi process, stakeholder experts will be invited to review data at a consensus meeting and agree on a COS for OA-TOF.

ETHICS AND DISSEMINATION

Ethical approval was sought through the Health Research Authority via the Integrated Research Application System, registration no. 297026. However, approval was deemed not to be required, so study sponsorship and oversight were provided by Alder Hey Children's NHS Foundation Trust. The study has been prospectively registered with the COMET Initiative. The study will be published in an open access forum.

Transitional Care for Patients with Congenital Colorectal Diseases: An EUPSA Network Office, ERNICA, and eUROGEN Joint Venture

BACKGROUND

Transition of care (TOC; from childhood into adulthood) of patients with anorectal malformations (ARM) and Hirschsprung disease (HD) ensures continuation of care for these patients. The aim of this international study was to assess the current status of TOC and adult care (AC) programs for patients with ARM and HD.

METHODS

A survey was developed by members of EUPSA, ERN eUROGEN, and ERNICA, including patient representatives (ePAGs), comprising of four domains: general information, general questions about transition to adulthood, and disease-specific questions regarding TOC and AC programs. Recruitment of centres was done by the ERNs and EUPSA, using mailing lists and social media accounts. Only descriptive statistics were reported.

RESULTS

In total, 82 centres from 21 different countries entered the survey. Approximately half of them were ERN network members. Seventy-two centres (87.8%) had a self-reported area of expertise for both ARM and HD. Specific TOC programs were installed in 44% of the centres and AC programs in 31% of these centres. When comparing centres, wide variation was observed in the content of the programs.

CONCLUSION

Despite the awareness of the importance of TOC and AC programs, these programs were installed in less than 50% of the participating centres. Various transition and AC programs were applied, with considerable heterogeneity in implementation, content and responsible caregivers involved. Sharing best practice examples and taking into account local and National Health Care Programs might lead to a better continuation of care in the future.

LEVEL OF EVIDENCE

III.

The International Network on Oesophageal Atresia (INoEA) consensus guidelines on the transition of patients with oesophageal atresia-tracheoesophageal fistula

Oesophageal atresia-tracheoesophageal fistula (EA-TEF) is a common congenital digestive disease. Patients with EA-TEF face gastrointestinal, surgical, respiratory, otolaryngological, nutritional, psychological and quality of life issues in childhood, adolescence and adulthood. Although consensus guidelines exist for the management of gastrointestinal, nutritional, surgical and respiratory problems in childhood, a systematic approach to the care of these patients in adolescence, during transition to adulthood and in adulthood is currently lacking. The Transition Working Group of the International Network on Oesophageal Atresia (INoEA) was charged with the task of developing uniform evidence-based guidelines for the management of complications through the transition from adolescence into adulthood. Forty-two questions addressing the diagnosis, treatment and prognosis of gastrointestinal, surgical, respiratory, otolaryngological, nutritional, psychological and quality of life complications that patients with EA-TEF face during adolescence and after the transition to adulthood were formulated. A systematic literature search was performed based on which recommendations were made. All recommendations were discussed and finalized during consensus meetings, and the group members voted on each recommendation. Expert opinion was used when no randomized controlled trials were available to support the recommendation. The list of the 42 statements, all based on expert opinion, was voted on and agreed upon.

Rules of teeth development align microevolution with macroevolution in extant and extinct primates

Macroevolutionary biologists have classically rejected the notion that higher-level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behaviour of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro- and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here we reframe this issue by asking whether using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro- and macroscales, whereas biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.

Reliability of resting metabolic rate between and within day measurements using the Vyntus CPX system and comparison against predictive formulas

Background: To detect longitudinal changes of resting metabolic rate (RMR) resulting from the effects of energetic stress, reliable RMR measurements are crucial. The Vyntus CPX is a new automated indirect calorimetry system for which RMR reliability has not been determined. Additionally, its agreement with common predictive RMR formulas is unknown. Aim: To determine the within and between-day reliability of RMR measurements using the Vyntus CPX system and its agreement with predictive RMR formulas. Methods: Young (31  ±  7 years) healthy participants (n = 26, 12 females, 14 males) completed three measurements of RMR, two consecutive measures on the same day, one the day before/after, all under standardised conditions. Reliability was assessed with pairwise comparisons of between-day at the same time (BDST), within day consecutive measurements (WDCM) and between-day different time (BDDT), for parameters of reliability (mean change (MC), intraclass correlation (ICC) and typical error of measurement (TEM)). Measured RMR values (kcal/day) were compared against predictive values of 4 common formulas. Results: Parameters of reliability (mean, (95% confidence interval)) were: -BDST: MC, 0.2(-2.3-2.7)% (p = 0.67); ICC, 0.92(0.84-0.97); TEM, 4.5(3.5-6.2)%. -WDCM: MC, -2.5(-6.2-1.3)% (p = 0.21); ICC, 0.88(0.74-0.88); TEM, 7.0(5.4-9.8)%. -BDDT: MC, -1.5(-4.8-1.9)% (p = 0.57); ICC, 0.90(0.76-0.95); TEM, 6.1(4.8-8.5)%. RMR_ratios (measured/predicted) were: 1.04  ±  0.14 (Nelson, p = 0.13), 1.03  ±  0.10 (Mifflin, p = 0.21), 0.98  ±  0.09 (Harris-benedict, p = 0.30), 0.95  ±  0.11 (Cunningham₁₉₈₀, p = 0.01), 1.00  ±  0.12 (Cunningham₁₉₉₁, p = 0.90) and 0.96  ±  0.13 (DXA, p = 0.03). Conclusions: The Vyntus CPX is reliable and measured RMR values agreed with four predictive formulas but are lower than Cunningham₁₉₈₀ and DXA RMR estimates for this population.

Precision of the GE Lunar Total Body-Less Head Scan for the Measurement of Three-Compartment Body Composition in Athletes

INTRODUCTION

Dual energy X-ray absorptiometry (DXA) is widely used for the assessment of lean mass (LM), fat mass (FM) and bone mineral content (BMC). When observing standardised protocols, DXA has a high level of precision for the assessment of total body composition, including the head region. However, including the head region may have limited relevance in athletes and can be problematic when positioning taller athletes who exceed scan boundaries. This study investigated the precision of a new total-body-less-head (TBLH) DXA scan for three-compartment body composition measurement in athletes, with outcomes compared to the standard total-body DXA scan.

METHODS

Precision errors were calculated from two consecutive scans with re-positioning (Lunar iDXA, GE Healthcare, Madison, WI), in male and female athletes from a range of sports. TBLH precision was determined from repeat scans in 95 athletes (male n = 55; female n = 40; age: 26.0 ± 8.5 y; body mass: 81.2 ± 20.5 kg; stature: 1.77 ± 0.11 m), and standard total-body scan precision was derived from a sub-sample of 58 athletes (male n = 19; female n = 39; age: 27.6 ± 9.9 y; body mass: 69.6 ± 14.8 kg; stature: 1.72 ± 0.94 m). Data from the sub-sample were also used to compare precision error and 3-compartment body composition outcomes between the standard total-body scan and the TBLH scan.

RESULTS

TBLH precision errors [root mean squared-standard deviation, RMS-SD (coefficient of variation, %CV)] were bone mineral content (BMC): 15.6 g (0.5%), lean mass (LM): 254.3 g (0.4%) and fat mass (FM): 199.4 g (1.3%). These outcomes compared favourably to the precision errors derived from the standard total-body scan [BMC: 12.4 g (0.4%), LM: 202.2 g (0.4%), and FM: 160.8 g (1.1%)]. The TBLH scan resulted in lower BMC (-19.5%), LM (-6.6%), and FM (-4.5%) compared to the total-body scan (BMC: 2,308 vs. 2,865 g; LM: 46,954 vs. 50,276 g; FM: 15,183 vs. 15,888 g, all p<0.005). ConclusionThe TBLH scan demonstrates high in-vivo precision comparable to that of the standard total-body scan in a heterogeneous cohort of athletes. Given the impact of head exclusion on total body composition outcomes, TBLH scans should not be used interchangeably with the standard total-body scan.

ERNICA Consensus Conference on the Management of Patients with Long-Gap Esophageal Atresia: Perioperative, Surgical, and Long-Term Management

INTRODUCTION

 Evidence supporting best practice for long-gap esophageal atresia is limited. The European Reference Network for Rare Inherited Congenital Anomalies (ERNICA) organized a consensus conference on the management of patients with long-gap esophageal atresia based on expert opinion referring to the latest literature aiming to provide clear and uniform statements in this respect.

MATERIALS AND METHODS

 Twenty-four ERNICA representatives from nine European countries participated. The conference was prepared by item generation, item prioritization by online survey, formulation of a final list containing items on perioperative, surgical, and long-term management, and literature review. The 2-day conference was held in Berlin in November 2019. Anonymous voting was conducted via an internet-based system using a 1 to 9 scale. Consensus was defined as ≥75% of those voting scoring 6 to 9.

RESULTS

 Ninety-seven items were generated. Complete consensus (100%) was achieved on 56 items (58%), e.g., avoidance of a cervical esophagostomy, promotion of sham feeding, details of delayed anastomosis, thoracoscopic pouch mobilization and placement of traction sutures as novel technique, replacement techniques, and follow-up. Consensus ≥75% was achieved on 90 items (93%), e.g., definition of long gap, routine pyloroplasty in gastric transposition, and avoidance of preoperative bougienage to enable delayed anastomosis. Nineteen items (20%), e.g., methods of gap measurement were discussed controversially (range 1-9).

CONCLUSION

 This is the first consensus conference on the perioperative, surgical, and long-term management of patients with long-gap esophageal atresia. Substantial statements regarding esophageal reconstruction or replacement and follow-up were formulated which may contribute to improve patient care.

ERNICA Consensus Conference on the Management of Patients with Esophageal Atresia and Tracheoesophageal Fistula: Follow-up and Framework

INTRODUCTION

 Improvements in care of patients with esophageal atresia (EA) and tracheoesophageal fistula (TEF) have shifted the focus from mortality to morbidity and quality-of-life. Long-term follow-up is essential, but evidence is limited and standardized protocols are scarce. Nineteen representatives of the European Reference Network for Rare Inherited Congenital Anomalies (ERNICA) from nine European countries conducted a consensus conference on the surgical management of EA/TEF.

MATERIALS AND METHODS

 The conference was prepared by item generation (including items of surgical relevance from the European Society for Pediatric Gastroenterology Hepatology and Nutrition (ESPGHAN)-The North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) guidelines on follow-up after EA repair), item prioritization, formulation of a final list containing the domains Follow-up and Framework, and literature review. Anonymous voting was conducted via an internet-based system. Consensus was defined as ≥75% of those voting with scores of 6 to 9.

RESULTS

 Twenty-five items were generated in the domain Follow-up of which 17 (68%) matched with corresponding ESPGHAN-NASPGHAN statements. Complete consensus (100%) was achieved on seven items (28%), such as the necessity of an interdisciplinary follow-up program. Consensus ≥75% was achieved on 18 items (72%), such as potential indications for fundoplication. There was an 82% concordance with the ESPGHAN-NASPGHAN recommendations. Four items were generated in the domain Framework, and complete consensus was achieved on all these items.

CONCLUSION

 Participants of the first ERNICA conference reached significant consensus on the follow-up of patients with EA/TEF who undergo primary anastomosis. Fundamental statements regarding centralization, multidisciplinary approach, and involvement of patient organizations were formulated. These consensus statements will provide the cornerstone for uniform treatment protocols and resultant optimized patient care.

ERNICA Consensus Conference on the Management of Patients with Esophageal Atresia and Tracheoesophageal Fistula: Diagnostics, Preoperative, Operative, and Postoperative Management

INTRODUCTION

 Many aspects of the management of esophageal atresia (EA) and tracheoesophageal fistula (TEF) are controversial and the evidence for decision making is limited. Members of the European Reference Network for Rare Inherited Congenital Anomalies (ERNICA) conducted a consensus conference on the surgical management of EA/TEF based on expert opinions referring to the latest literature.

MATERIALS AND METHODS

 Nineteen ERNICA representatives from nine European countries participated in the conference. The conference was prepared by item generation, item prioritization by online survey, formulation of a final list containing the domains diagnostics, preoperative, operative, and postoperative management, and literature review. The 2-day conference was held in Berlin in October 2018. Anonymous voting was conducted via an internet-based system. Consensus was defined when 75% of the votes scored 6 to 9.

RESULTS

 Fifty-two items were generated with 116 relevant articles of which five studies (4.3%) were assigned as level-1evidence. Complete consensus (100%) was achieved on 20 items (38%), such as TEF closure by transfixing suture, esophageal anastomosis by interrupted sutures, and initiation of feeding 24 hours postoperatively. Consensus ≥75% was achieved on 37 items (71%), such as routine insertion of transanastomotic tube or maximum duration of thoracoscopy of 3 hours. Thirteen items (25%) were controversial (range of scores, 1-9). Eight of these (62%) did not reach consensus.

CONCLUSION

 Participants of the conference reached significant consensus on the management of patients with EA/TEF. The consensus may facilitate standardization and development of generally accepted guidelines. The conference methodology may serve as a blueprint for further conferences on the management of congenital malformations in pediatric surgery.

Origin of Groundwater Arsenic in a Rural Pleistocene Aquifer in Bangladesh Depressurized by Distal Municipal Pumping

Across South Asia, millions of villagers have reduced their exposure to high-arsenic (As) groundwater by switching to low-As wells. Isotopic tracers and flow modeling are used in this study to understand the groundwater flow system of a semi-confined aquifer of Pleistocene (>10 kyr) age in Bangladesh that is generally low in As but has been perturbed by massive pumping at a distance of about 25 km for the municipal water supply of Dhaka. A 10- to 15-m-thick clay aquitard caps much of the intermediate aquifer (>40- to 90-m depth) in the 3-km² study area, with some interruptions by younger channel sand deposits indicative of river scouring. Hydraulic heads in the intermediate aquifer below the clay-capped areas are 1-2 m lower than in the high-As shallow aquifer above the clay layer. In contrast, similar heads in the shallow and intermediate aquifer are observed where the clay layer is missing. The head distribution suggests a pattern of downward flow through interruptions in the aquitard and lateral advection from the sandy areas to the confined portion of the aquifer. The interpreted flow system is consistent with ³H-³He ages, stable isotope data, and groundwater flow modeling. Lateral flow could explain an association of elevated As with high methane concentrations within layers of gray sand below certain clay-capped portions of the Pleistocene aquifer. An influx of dissolved organic carbon from the clay layer itself leading to a reduction of initially orange sands has also likely contributed to the rise of As.

A patient led, international study of long term outcomes of esophageal atresia: EAT 1

INTRODUCTION

Long term outcomes of esophageal atresia (OA) are poorly understood. The Federation of Esophageal Atresia and Tracheo-Esophageal Fistula support groups (EAT), a collaboration of patient support groups aimed to define patient reported long term outcomes and quality of life (QoL) in a large international cohort of OA patients.

METHODS

Questionnaires were designed focusing on patient/parent reported outcomes including surgical history, current symptomatology and quality of life. Members of support groups within EAT were invited to complete questionnaires electronically via SurveyMonkey®.

RESULTS

1100 patients from 25 countries responded to the questionnaire and 928 were analyzed. 80% had type C anatomy, 19% type A and 1% type E. Patient ages were <5 years (42%), 5-10 years (26%), 11-17 years (16%) and 18 years and older (16%). 49% of all patients reported previous dilatations which was similar across age groups. Reflux symptoms affected 58% of patients and persisted into adulthood. Dysphagia also persisted in the adult population with 50% reporting sometimes or often getting food stuck. Reflux was significantly more frequent in 'long gap' versus 'standard gap' patients (p<0.005). Respiratory symptoms and chest infections decreased in frequency with age. In children median SDS for height was -0.41 (IQR -1.4 to 0.67) and that for weight was -0.63 (-1.6 to 0.67). BMI in adults was 21.5. Quality of life was described as significantly affected by OA in 18% of patients while 25% reported no effect on QoL.

CONCLUSIONS

These results highlight the significant long term morbidity suffered by OA patients as children and into adulthood and suggest the need for quality transitional care. The patient designed and reported nature of the study gives a unique perspective to the results and emphasizes the benefits of collaboration.

Integrating Paleontological and Phylogenetic Approaches to Macroevolution

With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.

Reconstruction of limnology and microbialite formation conditions from carbonate clumped isotope thermometry

Quantitative tools for deciphering the environment of microbialite formation are relatively limited. For example, the oxygen isotope carbonate-water geothermometer requires assumptions about the isotopic composition of the water of formation. We explored the utility of using 'clumped' isotope thermometry as a tool to study the temperatures of microbialite formation. We studied microbialites recovered from water depths of 10-55 m in Pavilion Lake, and 10-25 m in Kelly Lake, spanning the thermocline in both lakes. We determined the temperature of carbonate growth and the (18)O/(16)O ratio of the waters that microbialites grew in. Results were then compared to current limnological data from the lakes to reconstruct the history of microbialite formation. Modern microbialites collected at shallow depths (11.7 m) in both lakes yield clumped isotope-based temperatures of formation that are within error of summer water temperatures, suggesting that clumped isotope analyses may be used to reconstruct past climates and to probe the environments in which microbialites formed. The deepest microbialites (21.7-55 m) were recovered from below the present-day thermoclines in both lakes and yield radioisotope ages indicating they primarily formed earlier in the Holocene. During this time, pollen data and our reconstructed water (18)O/(16)O ratios indicate a period of aridity, with lower lake levels. At present, there is a close association between both photosynthetic and heterotrophic communities, and carbonate precipitation/microbialite formation, with biosignatures of photosynthetic influences on carbonate detected in microbialites from the photic zone and above the thermocline (i.e., depths of generally <20 m). Given the deeper microbialites are receiving <1% of photosynthetically active radiation (PAR), it is likely these microbialites primarily formed when lower lake levels resulted in microbialites being located higher in the photic zone, in warm surface waters.

Getting a grip on the evolution of grasping in musteloid carnivorans: a three-dimensional analysis of forelimb shape

The ability to grasp and manipulate is often considered a hallmark of hominins and associated with the evolution of their bipedal locomotion and tool use. Yet, many other mammals use their forelimbs to grasp and manipulate objects. Previous investigations have suggested that grasping may be derived from digging behaviour, arboreal locomotion or hunting behaviour. Here, we test the arboreal origin of grasping and investigate whether an arboreal lifestyle could confer a greater grasping ability in musteloid carnivorans. Moreover, we investigate the morphological adaptations related to grasping and the differences between arboreal species with different grasping abilities. We predict that if grasping is derived from an arboreal lifestyle, then the anatomical specializations of the forelimb for arboreality must be similar to those involved in grasping. We further predict that arboreal species with a well-developed manipulation ability will have articulations that facilitate radio-ulnar rotation. We use ancestral character state reconstructions of lifestyle and grasping ability to understand the evolution of both traits. Finally, we use a surface sliding semi-landmark approach capable of quantifying the articulations in their full complexity. Our results largely confirm our predictions, demonstrating that musteloids with greater grasping skills differ markedly from others in the shape of their forelimb bones. These analyses further suggest that the evolution of an arboreal lifestyle likely preceded the development of enhanced grasping ability.

Constraining carbon sources and growth rates of freshwater microbialites in Pavilion Lake using (14)C analysis

This study determined the natural abundance isotopic compositions ((13)C, (14)C) of the primary carbon pools and microbial communities associated with modern freshwater microbialites located in Pavilion Lake, British Columbia, Canada. The Delta(14)C of dissolved inorganic carbon (DIC) was constant throughout the water column and consistent with a primarily atmospheric source. Observed depletions in DIC (14)C values compared with atmospheric CO(2) indicated effects due either to DIC residence time and/or inputs of (14)C-depleted groundwater. Mass balance comparisons of local and regional groundwater indicate that groundwater DIC could contribute a maximum of 9-13% of the DIC. (14)C analysis of microbial phospholipid fatty acids from microbialite communities had Delta(14)C values comparable with lake water DIC, demonstrating that lake water DIC was their primary carbon source. Microbialite carbonate was also primarily derived from DIC. However, some depletion in microbialite carbonate (14)C relative to lake water DIC occurred, due either to residence time or mixing with a (14)C-depleted carbon source. A detrital branch covered with microbialite growth was used to estimate a microbialite growth rate of 0.05 mm year(-1) for the past 1000 years, faster than previous estimates for this system. These results demonstrate that the microbialites are actively growing and that the primary carbon source for both microbial communities and recent carbonate is DIC originating from the atmosphere. While these data cannot conclusively differentiate between abiotic and biotic formation mechanisms, the evidence for minor inputs of groundwater-derived DIC is consistent with the previously hypothesized biological origin of the Pavilion Lake microbialites.

Ensembl 2009

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Ensembl 2008

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Ensembl 2007

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Ensembl 2006

The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Acute weight loss followed by an aggressive nutritional recovery strategy has little impact on on-water rowing performance

OBJECTIVES

To assess the influence of moderate, acute weight loss on on-water rowing performance when aggressive nutritional recovery strategies were used in the two hours between weigh in and racing.

METHODS

Competitive rowers (n = 17) undertook three on-water 1800 m time trials under cool conditions (mean (SD) temperature 8.4 (2.0) degrees C), each separated by 48 hours. No weight limit was imposed for the first time trial--that is, unrestricted body mass (UNR1). However, one of the remaining two trials followed a 4% loss in body mass in the previous 24 hours (WT(-4%)). No weight limit was imposed for the other trial (UNR2). Aggressive nutritional recovery strategies (WT(-4%), 2.3 g/kg carbohydrate, 34 mg/kg Na+, and 28.4 ml/kg fluid; UNR, ad libitum) were used in the first 90 minutes of the two hours between weigh in and performance trials.

RESULTS

WT(-4%) had only a small and statistically non-significant effect on the on-water time trial performance (mean 1.0 second, 95% confidence interval (CI) -0.9 to 2.8; p = 0.29) compared with UNR. This was despite a significant decrease in plasma volume at the time of weigh in for WT(-4%) compared with UNR (-9.2%, 95% CI -12.8% to -5.6%; p<0.001).

CONCLUSIONS

Acute weight loss of up to 4% over 24 hours, when combined with aggressive nutritional recovery strategies, can be undertaken with minimal impact on on-water rowing performance, at least in cool conditions.

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Ensembl 2004

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Ensembl 2002: accommodating comparative genomics

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

The Ensembl genome database project

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Beta-hydroxy-beta-methylbutyrate (HMB) supplementation does not affect changes in strength or body composition during resistance training in trained men

This investigation evaluated the effects of oral beta-hydroxy-beta-methylbutyrate (HMB) supplementation on training responses in resistance-trained male athletes who were randomly administered HMB in standard encapsulation (SH), HMB in time release capsule (TRH), or placebo (P) in a double-blind fashion. Subjects ingested 3 g x day(-1) of HMB or placebo for 6 weeks. Tests were conducted pre-supplementation and following 3 and 6 weeks of supplementation. The testing battery assessed body mass, body composition (using dual energy x-ray absorptiometry), and 3-repetition maximum isoinertial strength, plus biochemical parameters, including markers of muscle damage and muscle protein turnover. While the training and dietary intervention of the investigation resulted in significant strength gains (p < .001) and an increase in total lean mass (p = .01), HMB administration had no influence on these variables. Likewise, biochemical markers of muscle protein turnover and muscle damage were also unaffected by HMB supplementation. The data indicate that 6 weeks of HMB supplementation in either SH or TRH form does not influence changes in strength and body composition in response to resistance training in strength-trained athletes.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Prevalence and significance of gallbladder abnormalities seen on sonography in intensive care unit patients

OBJECTIVE

We evaluated sonographic abnormalities of the gallbladder other than acalculous cholecystitis across a broad range of intensive care unit (ICU) patients.

SUBJECTS AND METHODS

Fifty-five consecutive patients (age range, 18-94 years old; mean age, 56 years; 33 men, 22 women), who were admitted to the ICU with a variety of diagnoses, underwent sonography of the gallbladder twice a week. Patients with gallbladder calculi were excluded from the study. The gallbladder was examined for the recognized sonographic features of acalculous cholecystitis: gallbladder wall thickening, gallbladder distention, intramural gallbladder lucencies (striated gallbladder wall), pericholecystic fluid, gallbladder sludge, and Murphy's sign. These findings were correlated with clinical and laboratory parameters that are associated with acalculous cholecystitis: fever, WBC, liver function tests, levels of serum bilirubin, mechanical ventilation status, and administration of parenteral nutrition, narcotic analgesics, antibiotics, and pressor agents.

RESULTS

Eleven of the 55 patients were found to have gallbladder calculi and were excluded from the study. Thirty-seven (84%) of the remaining 44 patients had at least one sonographic abnormality while in the ICU. Twenty-five (57%) of the 44 patients had as many as three abnormalities found on sonography, and six (14%) of 44 patients had four or five sonographic findings of gallbladder abnormalities while in the ICU. No statistically significant correlation was found among any of these sonographic abnormalities and the clinical and laboratory parameters.

CONCLUSION

Gallbladder abnormalities are frequently seen on sonography in ICU patients, even if these patients are not suspected of having acalculous cholecystitis; therefore, sonography appears to be of limited value in diagnosing acalculous cholecystitis in ICU patients.

Models of local behavior of DNA electrophoresis peak parameters

Many base calling algorithms implicitly or explicitly rely on predictions of local sequence parameters such as amplitude, peak time and peak width. For example, an algorithm may search for the next peak about a predicted peak time formed by adding the mean peak separation to the last position measurement. In this paper, covariance models are presented which characterize the dependence of peak parameters on those of other peaks. Based on experimental measurements, the model features an exponential decay in peak time jitter covariance with respect to base separation. Both peak amplitude and peak width are modelled as being uncorrelated with those of adjacent bases. In the model, linear expressions are given to describe the growth in peak time jitter and peak width as a function of base position while other parameters, such as amplitude variance, are modeled by constants. Together, these results form a simple model which may be used in the derivation of new sequencing algorithms or in simulations for the testing of such algorithms. We suggest that the correlation of the peak times is related to the Kuhn length of the single-stranded DNA fragments.

GLUT1 glucose transporter expression in colorectal carcinoma: a marker for poor prognosis

BACKGROUND

Malignant cells exhibit increased glycolytic metabolism, and in many cases increased glucose transporter gene expression. The authors hypothesized that GLUT1 glucose transporter expression is increased in colorectal carcinoma, and that the degree of expression might have prognostic significance.

METHODS

GLUT1 glucose transporter immunostaining was studied in normal colon and benign colon adenomas and in 112 colorectal carcinomas from patients for whom long term clinical outcome was known.

RESULTS

GLUT1 immunostaining was absent in normal colorectal epithelium and tubular adenomas, and absent or only weakly apparent in tubulovillous adenomas. The majority of carcinomas (101 of 112; 90%) had GLUT1 immunostaining. Tumors from 92 patients had low GLUT1 expression (< 50% of cells were GLUT1 positive) and 19 of these patients (21%) died of disease during follow-up. In contrast, tumors from 20 patients had high GLUT1 expression (> 50% of cells were GLUT1 positive) and 9 of these patients (45%) died of disease during follow-up. Disease specific mortality was greater in patients with high GLUT1 tumors (relative risk of 2.4; P=0.02). In a multivariate analysis to assess whether high GLUT1 staining correlated with increased mortality independently of Dukes stage, the risk of death from colon carcinoma in the group with high GLUT1 staining was 2.3 times that in the group with low GLUT1 staining, a difference that approached statistical significance (P=0.07).

CONCLUSIONS

GLUT1 glucose transporter expression is associated strongly with neoplastic progression in the colon, and assessment of the extent of GLUT1 immunostaining in colorectal carcinoma identifies patients with a poorer prognosis.

GLUT1 glucose transporter expression in colorectal carcinoma: a marker for poor prognosis

BACKGROUND

Malignant cells exhibit increased glycolytic metabolism, and in many cases increased glucose transporter gene expression. The authors hypothesized that GLUT1 glucose transporter expression is increased in colorectal carcinoma, and that the degree of expression might have prognostic significance.

METHODS

GLUT1 glucose transporter immunostaining was studied in normal colon and benign colon adenomas and in 112 colorectal carcinomas from patients for whom long term clinical outcome was known.

RESULTS

GLUT1 immunostaining was absent in normal colorectal epithelium and tubular adenomas, and absent or only weakly apparent in tubulovillous adenomas. The majority of carcinomas (101 of 112; 90%) had GLUT1 immunostaining. Tumors from 92 patients had low GLUT1 expression (< 50% of cells were GLUT1 positive) and 19 of these patients (21%) died of disease during follow-up. In contrast, tumors from 20 patients had high GLUT1 expression (> 50% of cells were GLUT1 positive) and 9 of these patients (45%) died of disease during follow-up. Disease specific mortality was greater in patients with high GLUT1 tumors (relative risk of 2.4; P=0.02). In a multivariate analysis to assess whether high GLUT1 staining correlated with increased mortality independently of Dukes stage, the risk of death from colon carcinoma in the group with high GLUT1 staining was 2.3 times that in the group with low GLUT1 staining, a difference that approached statistical significance (P=0.07).

CONCLUSIONS

GLUT1 glucose transporter expression is associated strongly with neoplastic progression in the colon, and assessment of the extent of GLUT1 immunostaining in colorectal carcinoma identifies patients with a poorer prognosis.

Mesenteric fibromatosis in Crohn's disease

We have seen two patients with Crohn's disease and mesenteric fibromatosis, the least common form of desmoid tumor. Although both gastrointestinal and nongastrointestinal tumors are relatively common in Crohn's disease, this type of tumor has not been seen in > 1,650 patients operated on for this condition. As the only common factor in the two male patients discussed in this article was previous intestinal resections, surgical trauma may be a predisposing factor in the occurrence of these desmoid tumors. We will continue to search for other examples in patients with Crohn's disease.

MR contrast material for vascular enhancement: value of superparamagnetic iron oxide

OBJECTIVE

The purpose of this study were to quantify abdominal vascular enhancement and to prove the feasibility of iron oxide-enhanced MR angiography in humans using three doses of superparamagnetic iron oxide agent AMI 227.

SUBJECTS AND METHODS

Sixteen patients randomly received either 0.8, 1.1, or 1.7 mg Fe/kg of ultrasmall superparamagnetic iron oxide agent AMI 227. T1-weighted breath-hold gradient-echo images were obtained before and 45 min after i.v. administration of AMI 227. Signal intensity was measured in the aorta, the inferior vena cava, the portal vein, and muscle on unenhanced and contrast-enhanced images. Signal-to-noise ratios and enhancement [(SNR after contrast-SNR before contrast) / SNR before contrast] were calculated. Vessels were visually graded before and after administration of AMI 227.

RESULTS

All vessels showed statistically significant enhancement 45 min. after administration of AMI 227 by both qualitative and quantitative measures (p < .001). There was no significant increase in noise or signal intensity of muscle after contrast material was administered. The amount of enhancement was not statistically significantly different among the three doses.

CONCLUSIONS

AMI 227, which is currently in phase III clinical trials, demonstrates significant vascular enhancement and may prove useful as an MR angiographic contrast agent.

Capital planning: investing in excellence

Graham Slater and Kate Del Bravo describe the priorities considered and work undertaken by SETRHA to develop its capital investment strategy. Although the underlying concepts are straightforward, it represents a significant development beyond traditional NHS approaches to planning, embraces the NHS market reforms, and has reduced capital aspirations for the same service objectives by some 300m pounds.

Management of chondrosarcoma including modular ceramic and alumina prosthetic replacement

Forty-one cases of chondrosarcoma from varying sites throughout the body, and treated exclusively by one of the authors (R.L.H.) from 1972 to 1990 were reviewed. The symptoms, signs, location of tumours, treatment and progress are presented. Particular attention was paid to modular bone replacement techniques. Excision and reconstruction of the bone or joint were carried out in 17 femora, five tibia and six humeri. Comparison between this method of management and other techniques is discussed. Titanium and alumina prostheses for the hip, femur, tibia, shoulder and humerus have been designed by the senior author. These are both inert and modular, and have been found to be superior to other methods of treatment in both function and cosmesis. They do not possess the same potential donor infection risks and other disadvantages of allograft replacement. Immediate postoperative weight bearing and mobilization are possible with these systems. The Huckstep prostheses allow for bony ingrowth into their porous coated alumina sleeves, spacers and stems. In addition, the titanium alloy locking component for the femoral stems has an elasticity half that of other metal alloys and this was found to minimize stress shielding.

Clinicopathologic correlations of ABO and Rhesus blood type in colorectal cancer

There is no specific association established between colorectal cancer and blood group type. In this study, the distribution of ABO and Rh blood groups was studied in 838 patients with colorectal cancer. There was no difference in distribution of ABO blood groups between patients who were Rh+ and Rh-. There was no difference in ABO blood group or Rh factor and tumor location. The highest A/O ratio was found in rectal cancer. Although there was no difference in stage distribution for each ABO blood group, there was a significant difference between the Rh+ and Rh- groups (P < 0.037). It is not clear, however, whether the prognosis is different between the two groups since there were more early tumors as well as incurable tumors in the Rh- group. All patients with synchronous cancer were Rh+. Further studies on blood group antigens are needed to elucidate the relationship between these antigens and colorectal cancer.

Small bowel length in Crohn's disease

The length of the small intestine in patients with Crohn's disease who are referred for surgery has not been well studied. In this report, 25 patients with Crohn's disease who were being operated on for the first time had their small intestine measured at the time of surgery. The mean length of small intestine in this group was 501 cm, which was not different from a group of patients without Crohn's disease who were being operated on for other problems. In the group of patients with Crohn's disease, as well as the entire group, there was a correlation between increasing height and longer small bowel length. No other parameters investigated, including weight, surface area, age, sex, and duration of disease, correlated with bowel length. The results of this study are somewhat encouraging to patients with Crohn's disease, since these patients do not start off with a shortened bowel prior to surgery.

Synchronous carcinoma of the colon and rectum

Reports on the incidence of synchronous carcinoma of the colon and rectum have varied from 2 to 11 per cent. The variability is a result of a lack of uniformity in criteria of diagnosis, differences in the population studied and differences in time period used. In this study, we evaluated the incidence and distribution of synchronous lesions during a recent time period before the use of colonoscopy became widespread. We reviewed the records of all patients with newly diagnosed adenocarcinoma of the colon and rectum who were operated upon at our institution between 1976 and 1981. In a total group of 1,000 patients of which 52 per cent were men, there were 54 patients or 5.4 per cent who had synchronous carcinomas. The group of patients with synchronous carcinomas were older than the group with nonsynchronous carcinomas (72.4 versus 68.8 years). There was also a higher incidence of associated benign polyps in the group with synchronous carcinomas (70 versus 30 per cent for a nonsynchronous carcinomas). The anatomic distribution of carcinomas of the colon and rectum in the group with synchronous lesions (111 in total) revealed a higher percentage of carcinomas located on the right side (29.7 versus 22.5 per cent), although the difference did not reach statistical significance. Synchronous carcinomas were located in nonadjacent segments of the colon in 37 per cent. There was no difference in stage between the groups with and without synchronous carcinomas. The preoperative identification of synchronous lesions by either colonoscopy or barium enema is important for the proper treatment of patients with carcinoma of the colon and rectum. Failure to locate these tumors may lead to the demise of the patient.

Ultrasonic mucosal proctectomy in patients with ulcerative colitis

A technique for performing mucosal proctectomy in patients with ulcerative colitis using ultrasonic fragmentation is described. Twenty-eight patients undergoing colectomy and ileoanal anastomosis were studied. Removal of the mucosal layer of the distal rectum was performed using a titanium probe vibrating at 23 kHZ with an amplitude of 300 microns. This method produces complete mucosal destruction and the resulting debris and irrigating fluid is removed through the hollow central portion of the probe. Healing of the ileoanal anastomosis does not appear to be adversely affected by the use of this technique. Because ultrasonic fragmentation is not dependent on the integrity of the submucosal plane, it may be advantageous in those cases in which severe inflammation and submucosal scarring make manual dissection of the rectal mucosa difficult to perform.