Trait Evolution in Adaptive Radiations: Modeling and Measuring Interspecific Competition on Phylogenies

The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species. Competition is modeled as a tendency of sympatric species to evolve toward difference from one another, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We use an approximate Bayesian computation approach to estimate model parameters. We find reasonable power to detect competition in sufficiently large (20+ species) trees compared with Brownian trait evolution and with Ornstein-Uhlenbeck and early burst models. We apply the model to examine the evolution of bill morphology of Darwin’s finches and find evidence that competition affects the evolution of bill length

A centrifugally controlled circuit in the avian retina and its possible role in visual attention switching

The isthmo-optic nucleus (ION) is the main source of efferents to the retina in birds. Isthmo-optic neurons project in topographical order on amacrine cells in the ventral parts of the retina, and a subclass of these known as proprioretinal neurons project onto the dorsal retina. We propose that, through the intermediary of the amacrine target cells, activity in the isthmo-optic pathway excites ganglion cells locally in the ventral retina but inhibits those in dorsal regions. This circuit would thereby mediate centrifugally controlled switches in attention between the dorsal retina, involved in feeding, and the more ventral parts, involved in scanning for predators. This hypothesis accounts for a wide range of disparate data from behavior, comparative anatomy, endocrinology, hodology, and neurophysiolog

The Recent Cholera Outbreak in the South Mrican Gold Mining Industry

A large-scale cholera surveillance programme was introduced in South Africa in November 1973 as a result of the progressive southward spread of cholera in Africa. Moore's technique for the isolation of Salmonella paratyphi was modified for cholera detection. The method proved to be very sensitive and it was possible to detect Vibrio cholerae in main sewer lines after its casual and transient introduction by an unidentified carrier. Transmission occurred in the acc!im<:tisation centre, probably through the drinking of water contaminated after it had been drawn from the tap. Faecal contamination of the environment was demonstrated, and V. cho/erae was isolated from the floor, onto which it had been disseminated from the perianal region by means of profuse perspiration. Perpetuation of cholera was probably aided by a faecally contaminated air-humidifying water reservoir, the water of which experimentally allows survival and multiplication of V. cholerae for a week and longer. Prophylactic treatment of selected high-risk groups of people was administered in the form of doxycycline, which appeared to result in rapid termination of the epidemic. Mass vaccination of all mine personnel (20 000) was carried out to reduce the incidence of clinical cholera and the bacterial load

Derivation and validation of a prognostic model for postoperative risk stratification of critically ill patients with faecal peritonitis

Background Prognostic scores and models of illness severity are useful both clinically and for research. The aim of this study was to develop two prognostic models for the prediction of long-term (6 months) and 28-day mortality of postoperative critically ill patients with faecal peritonitis (FP). Methods Patients admitted to intensive care units with faecal peritonitis and recruited to the European GenOSept study were divided into a derivation and a geographical validation subset; patients subsequently recruited to the UK GAinS study were used for temporal validation. Using all 50 clinical and laboratory variables available on day 1 of critical care admission, Cox proportional hazards regression was fitted to select variables for inclusion in two prognostic models, using stepwise selection and nonparametric bootstrapping sampling techniques. Using Area under the receiver operating characteristic curve (AuROC) analysis, the performance of the models was compared to SOFA and APACHE II. Results Five variables (age, SOFA score, lowest temperature, highest heart rate, haematocrit) were entered into the prognostic models. The discriminatory performance of the 6-month prognostic model yielded an AuROC 0.81 (95% CI 0.76–0.86), 0.73 (95% CI 0.69–0.78) and 0.76 (95% CI 0.69–0.83) for the derivation, geographic and temporal external validation cohorts, respectively. The 28-day prognostic tool yielded an AuROC 0.82 (95% CI 0.77–0.88), 0.75 (95% CI 0.69–0.80) and 0.79 (95% CI 0.71–0.87) for the same cohorts. These AuROCs appeared consistently superior to those obtained with the SOFA and APACHE II scores alone. Conclusions The two prognostic models developed for 6-month and 28-day mortality prediction in critically ill septic patients with FP, in the postoperative phase, enhanced the day one SOFA score’s predictive utility by adding a few key variables: age, lowest recorded temperature, highest recorded heart rate and haematocrit. External validation of their predictive capability in larger cohorts is needed, before introduction of the proposed scores into clinical practice to inform decision making and the design of clinical trials

Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols

Fecal microbiota transplant (FMT) is a powerful tool used to connect changes in gut microbial composition with a variety of disease states and pathologies. While FMT enables potential causal relationships to be identified, the experimental details reported in preclinical FMT protocols are highly inconsistent and/or incomplete. This limitation reflects a current lack of authoritative guidance on reporting standards that would facilitate replication efforts and ultimately reproducible science. We therefore systematically reviewed all FMT protocols used in mouse models with the goal of formulating recommendations on the reporting of preclinical FMT protocols. Search strategies were applied across three databases (PubMed, EMBASE, and Ovid Medline) until June 30, 2020. Data related to donor attributes, stool collection, processing/storage, recipient preparation, administration, and quality control were extracted. A total of 1753 papers were identified, with 241 identified for data extraction and analysis. Of the papers included, 92.5% reported a positive outcome with FMT intervention. However, the vast majority of studies failed to address core methodological aspects including the use of anaerobic conditions (91.7% of papers lacked information), storage (49.4%), homogenization (33.6%), concentration (31.5%), volume (19.9%) and administration route (5.3%). To address these reporting limitations, we developed theGuidelines for Reporting Animal Fecal Transplant (GRAFT) that guide reporting standards for preclinical FMT. The GRAFT recommendations will enable robust reporting of preclinical FMT design, and facilitate high-quality peer review, improving the rigor and translation of knowledge gained through preclinical FMT studies.Kate R. Secombe, Ghanyah H. Al-Qadami, Courtney B. Subramaniam, Joanne M. Bowen, Jacqui Scott, Ysabella Z.A. Van Sebille ... et a

Sensory fusion in Physarum polycephalum and implementing multi-sensory functional computation

Surface electrical potential and observational growth recordings were made of a protoplasmic tube of the slime mould Physarum polycephalum in response to a multitude of stimuli with regards to sensory fusion or multisensory integration. Each stimulus was tested alone and in combination in order to evaluate for the first time the effect that multiple stimuli have on the frequency of streaming oscillation. White light caused a decrease in frequency whilst increasing the temperature and applying a food source in the form of oat flakes both increased the frequency. Simultaneously stimulating P. polycephalum with light and oat flake produced no net change in frequency, while combined light and heat stimuli showed an increase in frequency smaller than that observed for heat alone. When the two positive stimuli, oat flakes and heat, were combined, there was a net increase in frequency similar to the cumulative increases caused by the individual stimuli. Boolean logic gates were derived from the measured frequency change. © 2014

The Transplanted Appropriate Adult Scheme in China

Borrowed from England and Wales, the Chinese Appropriate Adult Scheme involves a dynamic of selective adaptation. This article analyses two salient features of the appropriate adult scheme within the Chinese context, in comparison with its counterpart in England and Wales: its complementarity of the juvenile's parent, and the passive role that appropriate adults play during pretrial interrogations. Drawing upon empirical evidence, the article argues that the transplanted Chinese appropriate adult scheme has failed to oversee the legality of interrogations, nor does it provide adequate safeguards for juvenile suspects. The concept of vulnerability that lies at the heart of the appropriate adult safeguard in England and Wales appears to be lost in translation. Rather than providing a safeguard for juveniles at their most vulnerable, the appropriate adult is more concerned with indulging the needs of the interrogators in China

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results