Meaningful call combinations and compositional processing in the Southern Pied Babbler

Language’s expressive power is largely attributable to its compositionality: meaningful words are combined into larger/higher-order structures with derived meaning. Despite its importance, little is known regarding the evolutionary origins and emergence of this syntactic ability. Whilst previous research has demonstrated a rudimentary capability to combine meaningful calls in primates, due to a scarcity of comparative data, it is unclear whether analogue forms might also exist outside of primates. Here we address this ambiguity and provide evidence for rudimentary compositionality in the discrete vocal system of a social passerine, the pied babbler (Turdoides bicolor). Natural observations and predator presentations revealed babblers produce acoustically distinct alert calls in response to close, low-urgency threats, and recruitment calls when recruiting group members during locomotion. Upon encountering terrestrial predators both vocalisations are combined into a ‘mobbing-sequence’, potentially to recruit group members in a dangerous situation. To investigate whether babblers process the sequence in a compositional way, we conducted systematic experiments, playing back the individual calls in isolation, as well as naturally occurring and artificial sequences. Babblers reacted most strongly to mobbing-sequence playbacks, showing a greater attentiveness and a quicker approach to the loudspeaker, compared to individual calls or control sequences. We conclude the sequence constitutes a compositional structure, communicating information on both the context and the requested action. Our work supports previous research suggesting combinatoriality as a viable mechanism to increase communicative output, and indicates that the ability to combine and process meaningful vocal structures, a basic syntax, may be more widespread than previously thought

BRAF Mutation in Colorectal Cancer

The BRAF mutant colorectal cancer subgroup is a small population with unique clinicopathological and molecular features. This subgroup has been associated with particularly poor prognosis and advanced disease. The poor response of these patients to available treatments has driven much of the effort in trialling combination targeted treatments involving BRAF and MEK inhibitors. Most recently, an observed survival benefit with intensive triplet chemotherapy agents would encourage its use as first-line treatment in suitable candidates given that few of these patients proceed to second- or third-line treatments

Teaching genomics to life science undergraduates using cloud computing platforms with open datasets

The final year of a biochemistry degree is usually a time to experience research. However, laboratory-based research projects were not possible during COVID-19. Instead, we used open datasets to provide computational research projects in metagenomics to biochemistry undergraduates (80 students with limited computing experience). We aimed to give the students a chance to explore any dataset, rather than use a small number of artificial datasets (~60 published datasets were used). To achieve this, we utilized Google Colaboratory (Colab), a virtual computing environment. Colab was used as a framework to retrieve raw sequencing data (analyzed with QIIME2) and generate visualizations. Setting up the environment requires no prior experience; all students have the same drive structure and notebooks can be shared (for synchronous sessions). We also used the platform to combine multiple datasets, perform a meta-analysis, and allowed the students to analyze large datasets with 1000s of subjects and factors. Projects that required increased computational resources were integrated with Google Cloud Compute. In future, all research projects can include some aspects of reanalyzing public data, providing students with data science experience. Colab is also an excellent environment in which to develop data skills in multiple languages (e.g., Perl, Python, Julia)

Local Treatment Options for Unresectable Liver Metastases in Colorectal Cancer

Despite the increase in effectiveness of systemic therapy, cure for colorectal cancer with liver metastases (CRLM) is rarely achieved without surgical resection, with less than 20% of patients initially suitable for surgery. Liver-directed therapies are continually being investigated in the hope of improving cure rates in patients with unresectable liver metastases. These modalities include selective internal radiation therapy (SIRT), radiofrequency ablation (RFA), transarterial chemoembolization (TACE) and hepatic artery infusion (HAI) chemotherapy. While there is evidence of activity for all these treatments, they are somewhat lacking in high level randomized, controlled trial evidence (RCT) with appropriate control arms relevant to current standard of care. This review examines the efficacy and safety of these treatments in unresectable CRLM

Astro2020 White Paper: A Direct Measure of Cosmic Acceleration

Nearly a century after the discovery that we live in an expanding Universe, and two decades after the discovery of accelerating cosmic expansion, there remains no direct detection of this acceleration via redshift drift - a change in the cosmological expansion velocity versus time. Because cosmological redshift drift directly determines the Hubble parameter H(z), it is arguably the cleanest possible measurement of the expansion history, and has the potential to constrain dark energy models (e.g. Kim et al. 2015). The challenge is that the signal is small - the best observational constraint presently has an uncertainty several orders of magnitude larger than the expected signal (Darling 2012). Nonetheless, direct detection of redshift drift is becoming feasible, with upcoming facilities such as the ESO-ELT and SKA projecting possible detection within two to three decades. This timescale is uncomfortably long given the potential of this cosmological test. With dedicated experiments it should be possible to rapidly accelerate progress and detect redshift drift with only a five-year observational baseline. Such a facility would also be ideal for precision radial velocity measurements of exoplanets, which could be obtained as a byproduct of the ongoing calibration measurements for the experiment.Comment: White paper submitted to the Astro2020 Decadal Survey. 6 page

Forecasting cosmic acceleration measurements using the Lyman-α\alpha forest

We present results from end-to-end simulations of observations designed to constrain the rate of change in the expansion history of the Universe using the redshift drift of the Lyman-$\alpha$ forest absorption lines along the lines-of-sight toward bright quasars. For our simulations we take Lyman-$\alpha$ forest lines extracted from Keck/HIRES spectra of bright quasars at $z>3$, and compare the results from these real quasar spectra with mock spectra generated via Monte Carlo realizations. We use the results of these simulations to assess the potential for a dedicated observatory to detect redshift drift, and quantify the telescope and spectrograph requirements for these observations. Relative to Liske et al. (2008), two main refinements in the current work are inclusion of quasars from more recent catalogs and consideration of a realistic observing strategy for a dedicated redshift drift experiment that maximizes $\dot{v}/\sigma_{\dot{v}}$. We find that using a dedicated facility and our designed observing plan, the redshift drift can be detected at $3\sigma$ significance in 15 years with a 25m telescope, given a spectrograph with long term stability with $R=50,000$ and 25% total system efficiency. To achieve this significance, the optimal number of targets is four quasars, with observing time weighted based upon $\dot{v}/\sigma_{\dot{v}}$ and object visibility. This optimized strategy leads to a 9% decrease in the telescope diameter or a 6% decrease in the required time to achieve the same S/N as for the idealized case of uniformly distributing time to the same quasars.Comment: 13 pages, 12 figures, accepted for publication in MNRA

Astro2020 Project White Paper: The Cosmic Accelerometer

We propose an experiment, the Cosmic Accelerometer, designed to yield velocity precision of $\leq 1$ cm/s with measurement stability over years to decades. The first-phase Cosmic Accelerometer, which is at the scale of the Astro2020 Small programs, will be ideal for precision radial velocity measurements of terrestrial exoplanets in the Habitable Zone of Sun-like stars. At the same time, this experiment will serve as the technical pathfinder and facility core for a second-phase larger facility at the Medium scale, which can provide a significant detection of cosmological redshift drift on a 6-year timescale. This larger facility will naturally provide further detection/study of Earth twin planet systems as part of its external calibration process. This experiment is fundamentally enabled by a novel low-cost telescope technology called PolyOculus, which harnesses recent advances in commercial off the shelf equipment (telescopes, CCD cameras, and control computers) combined with a novel optical architecture to produce telescope collecting areas equivalent to standard telescopes with large mirror diameters. Combining a PolyOculus array with an actively-stabilized high-precision radial velocity spectrograph provides a unique facility with novel calibration features to achieve the performance requirements for the Cosmic Accelerometer

Can we accurately report PTEN status in advanced colorectal cancer?

BACKGROUND: Loss of phosphatase and tensin homologue (PTEN) function evaluated by loss of PTEN protein expression on immunohistochemistry (IHC) has been reported as both prognostic in metastatic colorectal cancer and predictive of response to anti-EGFR monoclonal antibodies although results remain uncertain. Difficulties in the methodological assessment of PTEN are likely to be a major contributor to recent conflicting results. METHODS: We assessed loss of PTEN function in 51 colorectal cancer specimens using Taqman® copy number variation (CNV) and IHC. Two blinded pathologists performed independent IHC assessment on each specimen and inter-observer variability of IHC assessment and concordance of IHC versus Taqman® CNV was assessed. RESULTS: Concordance between pathologists (PTEN loss vs no loss) on IHC assessment was 37/51 (73%). In specimens with concordant IHC assessment, concordance between IHC and Taqman® copy number in PTEN loss assessment was 25/37 (68%). CONCLUSION: Assessment PTEN loss in colorectal cancer is limited by the inter-observer variability of IHC, and discordance of CNV with loss of protein expression. An understanding of the genetic mechanisms of PTEN loss and implementation of improved and standardized methodologies of PTEN assessment are required to clarify the role of PTEN as a biomarker in colorectal cancer