Longer First Introns Are a General Property of Eukaryotic Gene Structure

While many properties of eukaryotic gene structure are well characterized, differences in the form and function of introns that occur at different positions within a transcript are less well understood. In particular, the dynamics of intron length variation with respect to intron position has received relatively little attention. This study analyzes all available data on intron lengths in GenBank and finds a significant trend of increased length in first introns throughout a wide range of species. This trend was found to be even stronger when using high-confidence gene annotation data for three model organisms (Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster) which show that the first intron in the 5′ UTR is - on average - significantly longer than all downstream introns within a gene. A partial explanation for increased first intron length in A. thaliana is suggested by the increased frequency of certain motifs that are present in first introns. The phenomenon of longer first introns can potentially be used to improve gene prediction software and also to detect errors in existing gene annotations

A methodology to estimate the potential to move inpatient to one day surgery

BACKGROUND: The proportion of surgery performed as a day case varies greatly between countries. Low rates suggest a large growth potential in many countries. Measuring the potential development of one day surgery should be grounded on a comprehensive list of eligible procedures, based on a priori criteria, independent of local practices. We propose an algorithmic method, using only routinely available hospital data to identify surgical hospitalizations that could have been performed as one day treatment. METHODS: Moving inpatient surgery to one day surgery was considered feasible if at least one surgical intervention was eligible for one day surgery and if none of the following criteria were present: intervention or affection requiring an inpatient stay, patient transferred or died, and length of stay greater than four days. The eligibility of a procedure to be treated as a day case was mainly established on three a priori criteria: surgical access (endoscopic or not), the invasiveness of the procedure and the size of the operated organ. Few overrides of these criteria occurred when procedures were associated with risk of immediate complications, slow physiological recovery or pain treatment requiring hospital infrastructure. The algorithm was applied to a random sample of one million inpatient US stays and more than 600 thousand Swiss inpatient stays, in the year 2002. RESULTS: The validity of our method was demonstrated by the few discrepancies between the a priori criteria based list of eligible procedures, and a state list used for reimbursement purposes, the low proportion of hospitalizations eligible for one day care found in the US sample (4.9 versus 19.4% in the Swiss sample), and the distribution of the elective procedures found eligible in Swiss hospitals, well supported by the literature. There were large variations of the proportion of candidates for one day surgery among elective surgical hospitalizations between Swiss hospitals (3 to 45.3%). CONCLUSION: The proposed approach allows the monitoring of the proportion of inpatient stay candidates for one day surgery. It could be used for infrastructure planning, resources negotiation and the surveillance of appropriate resource utilization

DFT-inspired methods for quantum thermodynamics

In the framework of quantum thermodynamics, we propose a method to quantitatively describe thermodynamic quantities for out-of-equilibrium interacting many-body systems. The method is articulated in various approximation protocols which allow to achieve increasing levels of accuracy, it is relatively simple to implement even for medium and large number of interactive particles, and uses tools and concepts from density functional theory. We test the method on the driven Hubbard dimer at half filling, and compare exact and approximate results. We show that the proposed method reproduces the average quantum work to high accuracy: for a very large region of parameter space (which cuts across all dynamical regimes) estimates are within 10% of the exact results

Convolutional neural networks at the interface of physical and digital data

Electron and X-ray interactions with matter can be recorded as digital images, which are signal acquisition mechanisms often used to investigate materials microstructure. Recently, the ability to quickly acquire large datasets at high resolution has created new challenges in areas that rely upon image-based information. The proposed analysis schemes employ Convolutional Neural Networks as the core algorithm in the reconnaissance of expected events from data gathered in two regimes: experimentally and by simulation. At the interface of physical and digital datasets, we propose classification schemes that exploit complex geometrical structure from scientific images through different machine learning packages, such as MatConvNet and TensorFlow. Our results show correct classification rates over 90% considering thousands of samples from four image modalities: cryo-electron microscopy, X-ray diffraction, X-ray scattering and X-ray microtomography. Our main contributions are: (a) developing algorithms designed for data that stem from physical experiments; (b) building new software to constrain parameter space, particularly given new hardware; and (c) testing different CNN models for classification of scientific images

Comparative Genomic Insights Into the Biosynthesis and Regulation of Mycobacterial Siderophores

Iron is essential for nearly all biological events. Siderophores are indispensable for most organisms to obtain iron from iron-limiting milieus. This holds particularly true for pathogens such as the causative agent of tuberculosis – Mycobacterium tuberculosis. The categories of mycobacterial siderophores, their biosynthesis and regulation are summarized here. The siderophore biosynthesis and regulation differences between the pathogenic and non-pathogenic mycobacteria are highlighted from comparative genomic perspective, with an aim to find clues for drug or drug target within siderophore metabolism

Improving collaboration between ecosystem service communities and the IPBES science-policy platform

The end of the first working program of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) provided an opportunity to draw lessons from its work. This perspective paper captures insights from ecosystem services (ES) researchers and practitioners, largely drawing from the Europeancontext (referred to herein as ‘ES community’), on this key science–policy interface. We synthesize reflections from a workshop on how (i) IPBES can engage the ES community; (ii) the ES community can engage with IPBES; and (iii) individual scientists can contribute. We note that IPBES constitutes a great advancement towards multidisciplinarity and inclusivity in ES research and practice. Key reflections for IPBES are that funding and visibility at ES research events could be improved, the contribution and selection processes could be more transparent, and communication with experts improved. Key reflections for the ES community include a need to improvepolicy-relevance by integrating more social scientists, researchers from developing countries, early-career scientists and policy-makers. Key reflections directed towards individual scientists include contributing (pro)actively to science–policy inter-face initiatives such as IPBES and increasing transdisciplinary research. These reflections intend to contribute to the awareness of challenges and opportunities for institutions, groups and individuals working on ES