miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on certain types of tissues, such as archived tumor tissues, or tissues associated with mitochondrial function, such as kidney tissue [1]. We propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses. Our software package is available at https://bioconductor.org/packages/miQC.     

Transducers: an emerging probabilistic framework for modeling indels on trees

Contact: ihh{at}berkeley.edu Associate Editor: Alex Bateman     

Delayed luminescence: an experimental protocol for Chinese herbal medicines

In Chinese medicine, raw herbal materials are used in processed and unprocessed forms aiming to meet the different requirements of clinical practice. To assure the chemical quality and therapeutic properties of the herbs, fast and integrated systematic assays are required. So far, such assays have not been established. Delayed luminescence (DL) refers to a decaying long‐term ultraweak photon emission after exposure to light. Its decay kinetics under certain conditions may be a sensitive indicator reflecting the internal structural and chemical/physiological state of a biological system. DL measurements have been used in many applications for quality control. However, relatively little research has been reported on dried plant material such as Chinese herbs. The objective of the present study is to establish a protocol for direct and rapid DL measurements of dried Chinese herbal materials, including the determination of the dependence on: (a) the optimal excitation time utilizing a white light source; (b) the optimal size of the grinded herbal particle; and (c) the humidity conditions before and during measurement. Results indicate that stable and reproducible curves of DL photon emission depend mainly on the water content of herbal materials. To investigate the application of the established DL measurement protocol, non‐processed and processed Aconitum (Aconitum carmichaelii Debx.), wild and cultivated rhubarb (Rheum palmatum L.) and ginseng (Panax ginseng C.A.Mey) of different ages were measured using DL. The results suggest that DL technology is a potential tool for assessment of dried Chinese herb qualities. The results warrant a further exploration of this technique in relation to therapeutic properties of the herbs. Copyright © 2016 John Wiley & Sons, Ltd.     

PACBERG: an adaptive program for controlling the blood sugar

PACBERG, a new computer program for automatically controlling (clamping) the blood sugar is described. The plasma glucose concentration is maintained at steady basal (euglycemic) or elevated (hyperglycemic) levels during various insulin infusions. To accomplish this, a minimal mathematical model of glucose kinetics is implemented on a minicomputer. From the measured time course of plasma glucose concentration, using the model, the program estimates the insulin-dependent increase in fractional disappearance rate of glucose (X). In addition the program calculates the rate of exogenous glucose infusion (INF) which must be infused in order to maintain the desired glucose concentration. The program successfully clamps glucose at desired basal or elevated levels. Furthermore, the variable X, provided as the PACBERG studies proceed, is a real-time measure of insulin action which can be used to calculate insulin sensitivity (SI). PACBERG was written in BASIC, but can also be implemented on programmable calculators.     

Dynamic adaptive binning: an improved quantification technique for NMR spectroscopic data

The interpretation of nuclear magnetic resonance (NMR) experimental results for metabolomics studies requires intensive signal processing and multivariate data analysis techniques. A key step in this process is the quantification of spectral features, which is commonly accomplished by dividing an NMR spectrum into several hundred integral regions or bins. Binning attempts to minimize effects from variations in peak positions caused by sample pH, ionic strength, and composition, while reducing the dimensionality for multivariate statistical analyses. Herein we develop an improved novel spectral quantification technique, dynamic adaptive binning. With this technique, bin boundaries are determined by optimizing an objective function using a dynamic programming strategy. The objective function measures the quality of a bin configuration based on the number of peaks per bin. This technique shows a significant improvement over both traditional uniform binning and other adaptive binning techniques. This improvement is quantified via synthetic validation sets by analyzing an algorithm’s ability to create bins that do not contain more than a single peak and that maximize the distance from peak to bin boundary. The validation sets are developed by characterizing the salient distributions in experimental NMR spectroscopic data. Further, dynamic adaptive binning is applied to a ¹H NMR-based experiment to monitor rat urinary metabolites to empirically demonstrate improved spectral quantification.     

Metamorphosis inhibition: an alternative rearing protocol for the newt, Cynops pyrrhogaster

The newt is an indispensable model animal, of particular utility for regeneration studies. Recently, a high-throughput transgenic protocol was established for the Japanese common newt, Cynops pyrrhogaster. For studies of regeneration, metamorphosed animals may be favorable; however, for this species, there is no efficient protocol for maintaining juveniles after metamorphosis in the laboratory. In these animals, survival drops drastically after metamorphosis as their foraging behaviour changes to adapt to a terrestrial habitat, making feeding in the laboratory with live or moving foods more difficult. To elevate the efficiency of laboratory rearing of this species, we examined metamorphosis inhibition (Ml) protocols to bypass the period (four months to two years after hatching) in which the animal feeds exclusively on moving foods. We found that approximately 30% of animals survived after 2-year Ml, and that the survivors continuously grew, only with static food while maintaining their larval form and foraging behaviour in 0.02% thiourea (TU) aqueous solution, then metamorphosed when returned to a standard rearing solution even after 2-year-MI. The morphology and foraging behavior (feeding on static foods in water) of these metamorphosed newts resembled that of normally developed adult newts. Furthermore, they were able to fully regenerate amputated limbs, suggesting regenerative capacity is preserved in these animals. Thus, controlling metamorphosis with TU allows newts to be reared with the same static food under aqueous conditions, providing an alternative rearing protocol that offers the advantage of bypassing the critical period and obtaining animals that have grown sufficiently for use in regeneration studies.     

Demodulation methods for an adaptive neural encoder model

An adaptive version of the integrate and fire-at-threshold model for the neural coding process is presented. The encoder transforms stimulus intensity information into sequences of identical membrane depolarization spikes, their times of occurrence defining a modulated point process. Several theoretical decoding schemes are then introduced and their performance analyzed. These implement simple, recursive parameter estimation algorithms and their output reproduces reliably; the encoded time-varying stimulus level.     

Management of the infertile couple: an evidence-based protocol

Background

Infertility is defined as inability of a couple to conceive naturally after one year of regular unprotected sexual intercourse. It remains a major clinical and social problem, affecting perhaps one couple in six. Evaluation usually starts after 12 months; however it may be indicated earlier. The most common causes of infertility are: male factor such as sperm abnormalities, female factor such as ovulation dysfunction and tubal pathology, combined male and female factors and unexplained infertility.

Objectives

The aim of this study is to provide the healthcare professionals an evidence-based management protocol for infertile couples away from medical information overload.

Methods

A comprehensive review where the literature was searched for "Management of infertility and/or infertile couples" at library website of University of Bristol (MetaLib) by using a cross-search of different medical databases besides the relevant printed medical journals and periodicals. Guidelines and recommendations were retrieved from the best evidence reviews such as that from the American College of Obstetricians and Gynaecologists (ACOG), American Society for Reproductive Medicine (ASRM), Canadian Fertility and Andrology Society (CFAS), and Royal College of Obstetricians and Gynaecologists (RCOG).

Results

A simple guide for the clinicians to manage the infertile couples.

Conclusions

The study deploys a new strategy to translate the research findings and evidence-base recommendations into a simplified focused guide to be applied on routine daily practice. It is an approach to disseminate the recommended medical care for infertile couple to the practicing clinicians.

     

Microvillar Ca++ signaling: A new view of an old problem

Proceeding from the recent finding that the main components of the Ca⁺⁺ signal pathway are located in small membrane protrusions on the surface of differentiated cells, called microvilli, a novel concept of cellular Ca⁺⁺ signaling was developed. The main features of this concept can be summarized as follows: Microvilli are formed on the cell surface of differentiating or resting cells from exocytic membrane domains, growing out from the cell surface by elongation of an internal bundle of actin filaments. The microvillar tip membranes contain all functional important proteins synthesized such as ion channels and transporters for energy-providing substrates and structural components, which are, in rapidly growing undifferentiated cells, distributed over the whole cell surface by lateral diffusion. The microvillar shaft structure, a bundle of actin filaments, forms a dense cytoskeletal matrix tightly covered by the microvillar lipid membrane and represents an effective diffusion barrier separating the microvillar tip compartment (entrance compartment) from the cytoplasm. This diffusion barrier prevents the passage of low molecular components such as Ca⁺⁺ glucose and other relevant substrates from the entrance compartment into the cytoplasm. The effectiveness of the actin-based diffusion barrier is modulated by various signal pathways and effectors, most importantly, by the actin-depolymerizing/reorganizing activity of the phospholipase C (PLC)-coupled Ca⁺⁺ signaling. Moreover, the microvillar bundle of actin filaments plays a dual role in Ca⁺⁺ signaling. It combines the function of a diffusion barrier, preventing Ca⁺⁺ influx into the resting cell, with that of a high-affinity, ATP-dependent, and IP₃-sensitive Ca⁺⁺ store. Activation of Ca⁺⁺ signaling via PLC-coupled receptors simultaneously empties Ca⁺⁺ stores and activates the influx of external Ca⁺⁺. The presented concept of Ca⁺⁺ signaling is compatible with all established data on Ca⁺⁺ signaling. Properties of Ca⁺⁺ signaling, that could not be reconciled with the basic principles of the current hypothesis, are intrinsic properties of the new concept. Quantal Ca⁺⁺ release, Ca⁺⁺-induced Ca⁺⁺ release (CICR), the coupling phenomen between the filling state of the Ca⁺⁺ store and the activity of the Ca⁺⁺ influx pathway, as well as the various yet unexplained complex kinetics of Ca⁺⁺ uptake and release can be explained on a common mechanistic basis. J. Cell. Physiol. 180:19–34, 1999. © 1999 Wiley-Liss, Inc.     

Comparison of a kayaking ergometer protocol with an arm crank protocol for evaluating peak oxygen consumption

The purpose of this study was to compare a kayak ergometer protocol with an arm crank protocol for determining peak oxygen consumption (V(.-)O2). On separate days in random order, 10 men and 5 women (16-24 years old) with kayaking experience completed the kayak ergometer protocol and a standardized arm crank protocol. The kayak protocol began at 70 strokes per minute and increased by 10 strokes per minute every 2 minutes until volitional fatigue. The arm crank protocol consisted of a crank rate of 70 revolutions per minute, initial loading of 35 W and subsequent increases of 35 W every 2 minutes until volitional fatigue. The results showed a significant difference (p < 0.01) between the kayak ergometer and the arm crank protocols for relative peak V(.-)O2 (47.5 +/- 3.9 ml x kg(-1) x min(-1) vs. 44.2 +/- 6.2 ml x kg(-1) x min(-1)) and absolute peak V(.-)O2 (3.38 L x min(-1) +/- 0.53 vs. 3.14 +/- 0.64 L x min(-1)). The correlation between kayak and arm crank protocol was 0.79 and 0.90, for relative and absolute V(.-)O2 peak, respectively (both p < 0.01). The higher peak V(.-)O2 on the kayak ergometer may be due to the greater muscle mass involved compared to the arm crank ergometer. The kayak ergometer protocol may therefore be more specific to the sport of kayaking than an arm crank protocol.     

Task partitioning in swarms of robots: an adaptive method for strategy selection

Task partitioning is the decomposition of a task into two or more sub-tasks that can be tackled separately. Task partitioning can be observed in many species of social insects, as it is often an advantageous way of organizing the work of a group of individuals. Potential advantages of task partitioning are, among others: reduction of interference between workers, exploitation of individuals?? skills and specializations, energy efficiency, and higher parallelism. Even though swarms of robots can benefit from task partitioning in the same way as social insects do, only few works in swarm robotics are dedicated to this subject. In this paper, we study the case in which a swarm of robots has to tackle a task that can be partitioned into a sequence of two sub-tasks. We propose a method that allows the individual robots in the swarm to decide whether to partition the given task or not. The method is self-organized, relies on the experience of each individual, and does not require explicit communication between robots. We evaluate the method in simulation experiments, using foraging as testbed. We study cases in which task partitioning is preferable and cases in which it is not. We show that the proposed method leads to good performance of the swarm in both cases, by employing task partitioning only when it is advantageous. We also show that the swarm is able to react to changes in the environmental conditions by adapting the behavior on-line. Scalability experiments show that the proposed method performs well across all the tested group sizes.     

Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation

The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20?pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83?pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168?kb. Paired BAC-end reads representing ～0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).     

ParDOCK: an all atom energy based Monte Carlo docking protocol for protein-ligand complexes

We report here an all-atom energy based Monte Carlo docking procedure tested on a dataset of 226 protein-ligand complexes. Average root mean square deviation (RMSD) from crystal conformation was observed to be approximately 0.53 A. The correlation coefficient (r(2)) for the predicted binding free energies calculated using the docked structures against experimental binding affinities was 0.72. The docking protocol is web-enabled as a free software at www.scfbio-iitd.res.in/dock.     

Tetanus neurotoxin: conformational plasticity as an adaptive strategy

Tetanus neurotoxin (TeNT) secreted by Clostridium tetani is the causative agent of the spastic paralysis distinctive of human tetanus. TeNT is structurally related to the family of botulinum neurotoxins (BoNTs) produced by Clostridium botulinum that cause flaccid paralysis by disabling synaptic exocytosis at peripheral cholinergic neurons. By contrast, TeNT targets the central nervous system (CNS) by hijacking receptors for neurotrophic factors to enter peripheral neurons thereby being sorted into non‐acidifying endosomes, trafficking via retrograde axonal transport organelles, and entering spinal inhibitory interneurons after transcytosis (Fig 1 A). In this issue of EMBO Reports, Masuyer et al 1 describe the structural plasticity of individual TeNT domains in the context of the holotoxin in response to environmental pH, a key factor modulating TeNT fate and action. Through the concerted use of X‐ray crystallography, single particle cryo‐EM, and small angle X‐ray scattering (SAXS), the authors provide snapshots of conformational transitions that may underlie the productive path of TeNT from its entry in the peripheral nervous system (PNS) to its ultimate site of action on central glycinergic synapses.