bluuebunny/crossref_metadata_2025 huggingface dataset:
Medicolegal Investigations Into Deaths Due to Crush Asphyxia After Tractor Side Rollovers
Authors: Moreschi Carlo , Da Broi Ugo , Fanzutto Antonia , Cividino Sirio , Gubiani Rino , Pergher Gianfranco
Published: August 2017

Farm tractors are large, heavy, powerful vehicles with a high center of gravity. When driven carelessly on sloping, irregular, or slippery ground, tractors can overturn sideways and cause the death by crush asphyxia of the driver or passengers, especially if appropriate safety equipment is not fitted or used. The aim of this review is to focus on the diagnostic difficulties with which coroners and forensic pathologists have to cope when a confirmation of crush asphyxia after tractor side rollover is required by judicial authorities. Forensic investigations in such cases must involve the meticulous analysis of the death scene and the mechanical characteristics of the vehicle together with accurate postmortem and toxicological examination.
Reproductive competition and sexual selection
Authors: Clutton-Brock Tim
Published: August 2017

This paper traces the development of our understanding of the development of different approaches to estimating the strength of reproductive competition and sexual selection in the two sexes, based on measures of the operational sex ratio, the opportunity for sexual selection and contrasts in selection gradients between the sexes. It argues that different approaches provide complementary insights into the causes of sex differences in reproductive competition, the operation of sexual selection and the evolution of secondary sexual characters and that improvements in our understanding of the evolution of secondary sexual characters will require a more comprehensive understanding of the ways in which social and ecological conditions modify reproductive competition and development in females and males.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Estimating adult sex ratios in nature
Authors: Ancona Sergio , Dénes Francisco V. , Krüger Oliver , Székely Tamás , Beissinger Steven R.
Published: August 2017

Adult sex ratio (ASR, the proportion of males in the adult population) is a central concept in population and evolutionary biology, and is also emerging as a major factor influencing mate choice, pair bonding and parental cooperation in both human and non-human societies. However, estimating ASR is fraught with difficulties stemming from the effects of spatial and temporal variation in the numbers of males and females, and detection/capture probabilities that differ between the sexes. Here, we critically evaluate methods for estimating ASR in wild animal populations, reviewing how recent statistical advances can be applied to handle some of these challenges. We review methods that directly account for detection differences between the sexes using counts of unmarked individuals (observed, trapped or killed) and counts of marked individuals using mark–recapture models. We review a third class of methods that do not directly sample the number of males and females, but instead estimate the sex ratio indirectly using relationships that emerge from demographic measures, such as survival, age structure, reproduction and assumed dynamics. We recommend that detection-based methods be used for estimating ASR in most situations, and point out that studies are needed that compare different ASR estimation methods and control for sex differences in dispersal.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Persistent effect of sex ratios on relationship quality and life satisfaction
Authors: Grosjean Pauline , Brooks Robert C.
Published: August 2017

Convict transportation to Australia imposed heavily male-biased sex ratios in some areas, altering the convict-era mating market and generating long-running cultural effects that persist to the present day. We test whether convict-era sex ratios have altered marital and overall life satisfaction today, through their persistent effects on gender norms and household bargaining. We find that both women and men are happier, and the happiness gap within married couples is smaller in areas where convict-era sex ratios were heavily male-biased than in areas where sex ratios were historically more even. We discuss our results in light of household bargaining theory, evolutionary sexual conflict theory and the well-documented relationship between conservative attitudes and self-reported happiness.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
The potential pitfalls of studying adult sex ratios at aggregate levels in humans
Authors: Pollet Thomas V. , Stoevenbelt Andrea H. , Kuppens Toon
Published: August 2017

Human adult sex ratios have been studied extensively across the biological and social sciences. While several studies have examined adult sex ratio effects in a multilevel perspective, many studies have focused on effects at an aggregated level only. In this paper, we review some key issues relating to such analyses. We address not only nation-level analyses, but also aggregation at lower levels, to investigate whether these issues extend to lower levels of aggregation. We illustrate these issues with novel databases covering a broad range of variables. Specifically, we discuss distributional issues with aggregated measures of adult sex ratio, significance testing, and statistical non-independence when using aggregate data. Firstly, we show that there are severe distributional issues with national adult sex ratio, such as extreme cases. Secondly, we demonstrate that many ‘meaningless’ variables are significantly correlated with adult sex ratio (e.g. the max. elevation level correlates with sex ratio at US state level). Finally, we re-examine associations between adult sex ratios and teenage fertility and find no robust evidence for an association at the aggregate level. Our review highlights the potential issues of using aggregate data on adult sex ratios to test hypotheses from an evolutionary perspective in humans.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Evolution of male strategies with sex-ratio–dependent pay-offs: connecting pair bonds with grandmothering
Authors: Loo Sara L. , Hawkes Kristen , Kim Peter S.
Published: August 2017

Men's provisioning of mates and offspring has been central to ideas about human evolution because paternal provisioning is absent in our closest evolutionary cousins, the great apes, and is widely assumed to result in pair bonding, which distinguishes us from them. Yet mathematical modelling has shown that paternal care does not readily spread in populations where competition for multiple mates is the common male strategy. Here we add to models that point to the mating sex ratio as an explanation for pairing as pay-offs to mate guarding rise with a male-biased sex ratio. This is of interest for human evolution because our grandmothering life history shifts the mating sex ratio from female- to male-biased. Using a difference equation model, we explore the relative pay-offs for three competing male strategies (dependant care, multiple mating, mate guarding) in response to changing adult sex ratios. When fertile females are abundant, multiple mating prevails. As they become scarce, mate guarding triumphs. The threshold for this shift depends on guarding efficiency. Combined with mating sex ratios of hunter–gatherer and chimpanzee populations, these results strengthen the hypothesis that the evolution of our grandmothering life history propelled the shift to pair bonding in the human lineage.

This article is part of the themed issue ‘Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies’.
Genotoxicity evaluation of balanced nutritional food for patients pasteurized by gamma irradiation at 4 kGy
Authors: Song Beom-Seok , Park Jong-Heum , Kim Jae-Kyung , Park Ha-Young , Kim Dong-Ho , Hong Seong-Gil , Jeong Sang-Hee
Published: August 2017

This study was conducted to evaluate the genotoxicity of balanced nutritional formular for patients containing various ingredients after gamma irradiation at 4 kGy. Since viable bacteria were not observed within the detection limit of 1 log CFU/g, a dose of 4 kGy was appropriate for the pasteurization of the formular. In a bacterial reverse mutation assay, both hot water and methanol extracts of the formular exhibited dose-independent responses, which was similar to those obtained from that of the negative control (distilled water or dimethyl sulfoxide). In a chromosomal aberration test using lung fibroblast cells of Chinese hamster, the numbers of normal chromosomes were comparable to those observed in the negative control, regardless of the treatment dose and metabolic activation system. Furthermore, no significant increases in the frequency of micronucleated polychromatic erythrocytes were observed relative to the control, when mice were fed with the formular at doses up to 2,000 mg/kg body weight. Therefore, the balanced nutritional formular for patients did not exhibit genotoxicity when pasteurization by gamma irradiation at 4 kGy.
Quality characteristics of fried fish paste with squeezed Aronia melanocarpa juice
Authors: Yun Jae-Ung , Jung Ko-Eun , Kim Dong-Hyun , Nam Ki-Ho , Sim Kil-Bo , Jang Mi-Soon
Published: August 2017

This study was carried out to investigate the quality characteristics of fried fish paste prepared with different amounts of squeezed Aronia melanocarpa juice. Squeezed Aronia melanocarpa juice (AMJ) was incorporated into fish paste at different levels (containing 2, 7, and 12 g of Aronia melanocarpa juice in 2 AMJ, 7 AMJ, and 12 AMJ, respectively) based on the total weight of water. Sugar contents and total acidity increased with increasing AMJ content. With increasing amounts of AMJ in fried fish paste, L value inside and on the surface decreased, a value increased, and b value inside decreased, whereas b value on the surface increased. pH decreased with increasing levels of AMJ. As the result of textural properties, folding test in all samples showed that AA means good flexibility. The strength, hardness, and chewiness of fried fish paste with AMJ increased while cohesiveness was not significantly different. Total polyphenol contents increased with higher levels of AMJ. DPPH radical scavenging activity was significantly higher than those of the control. In the sensory evaluation, fried fish paste containing 7 AMJ received the highest score than both the control and other samples.
Effect of pectinase treatment on extraction yield and physicochemical properties of Aronia juice
Authors: Kim Dong-Hwan , Choi Jun-Su , Lee Min-Hyung , Jang Han-Hee , Kim Han-Sol , Kim Do-Youn , Yeo Soo-Hwan , Park Heui-Dong
Published: August 2017

The main objective of this study was to investigate the effects of various commercial pectin enzyme treatments on juice yield from Aronia fruits (Aronia melanocarpa) as well as changes in physicochemical properties such as pH, total acid, reducing sugar, soluble solid, total anthocyanin, total phenolic compounds, and DPPH radical scavenging activity. Different types and reaction conditions of pectinase were also investigated in order to improve extraction yield of Aronia juice. The optimal conditions of enzyme treatment were 0.1% of concentration (w/w) at 50°C for 120 min. Among enzymes used in this study, extraction yield with Rapidase Press L treatment from Aronia juice was the highest and resulted in a significant increase in juice from 51.0 to 69.1%. Rapidase C80 MAX showed 68.83% extraction yield while Plantase TCL showed 66.70% extraction yield. Reducing sugar and soluble solid contents increased after enzyme treatment. Total acids also slightly increased after enzyme reaction. No significant difference was observed in pH regardless of pectin enzyme treatment. However, enzyme treatment resulted in an increase in total phenolic compounds, total anthocyanin, and DPPH radical scavenging in Aronia juice compared to the juice prepared juice.
Effects of packaging methods on the freshness during storage of lettuce harvested in summer season of Korea
Authors: Chang Min-Sun , Lee Jung-Soo
Published: August 2017

This study was investigated the effects of maintaining the freshness and stabilization of supply and demand for lettuce (Lactuca sativa L.) by packaging methods in summer. Post-harvest lettuces were packaged by corrugated box, polypropylene (P) box, and individual wrapping using polyvinyl chloride (PVC) film. Then, the lettuce samples were stored at 2°C and evaluated the change of quality during storage. The lettuces wrapped individually with PVC film had lower weight loss rate, color change, and browning index compared to lettuces packaged by corrugated box and P box. The SPAD value and hardness were higher in lettuces wrapped individually with PVC film than other packaging methods. The lettuces wrapped individually with PVC film were showed the highest total phenolic contents and DPPH radical scavenging activity, but there were no significantly differences by packaging methods. The lettuces packaged by corrugated box were showed the inside browning after 14 days. However, the lettuces wrapped individually with PVC film were showed the best appearance. Therefore, the packaging method of wrapped individually with PVC film were effective in maintaining the freshness during 21 days and helpful for the stabilization of supply and demand for lettuce in summer.
Development of natural fermented seasoning with Flammulina velutipes powder fortified with γ-aminobutyric acid (GABA) by lactic acid fermentation
Authors: Park Eun-Jin , Lee Syng-Ook , Lee Sam-Pin
Published: August 2017

Lactic acid fermentation of Flammulina velutipes (FV) powder was optimized to produce higher content of γ -aminobutyric acid (GABA). FV powder (10%) was fermented with 0.5% yeast extract, 1% glucose, 5% mono sodium-L-glutamate (MSG) by Lactobacillus plantarum EJ2014 for 5 days at 30°C. The pH decreased from 6.1 to 4.4 for first 2 days after then increased to 6.2 for following 5 days. While the acidity increased from 0.5% to 1.3% for 2 days, after then decreased to 0.4% for 5 days. Viable cell count showed higher value of 2.2×109 CFU/mL after fermentation for 5 days. In particular, 3.54% MSG as a substrate was completely utilized during lactic acid fermentation, indicating higher 2.31% GABA content. The fermented FV powder showed higher antioxidant properties than that of un-fermented FV power. IC50 values of DPPH radical scavenging and ABTS radical scavenging activities were 1.11 mg/mL and 2.58 mg/mL, respectively. Conclusively, natural fermented seasoning from the lactic acid fermentation of 30g of FV powder and 1 g of roasted wheat bran could provide the functional ingredients with 17% GABA, probiotics and dietary fiber, which is used for health food and functional seasoning.
Spray-dried powder preparation of pumpkin sweet potato hydrolysates and its physicochemical properties
Authors: Lee Dae-Hoon , Jang Jong-Hyun , Hong Joo-Heon
Published: August 2017

This study was conducted prepare spray-dried powder using pumpkin sweet potato hydrolysates and examine the physicochemical properties of the powder. The insoluble dietary fiber and soluble dietary fiber of the pumpkin sweet potato treated by enzyme were 4.17% and 2.07%, respectively. The spray-dried pumpkin sweet potato hydrolysates was manufactured via spray-drying with different forming agents: i.e., pectin 0.1%, 0.5%, 1%, and 2.0%. The moisture contents and total starches of the spray-dried powders were approximately 1.68-2.46 and 45.32-46.51%, respectively. The color of the L and a value decreased, and that of the b and ΔE value increased. The particle size and outer topology of the spray-dried powders were 37.17-42.32 μm, and its shape was generally globular. The water absorption index of the spray-dried powder (1.74-1.91) was lower than that of the freeze-dried powder (2.15). The water solubility index of the spray-dried powder, 80.75-87.61%, was higher than that of the freeze-dried powder (70.47%). The adhesion values of spray-dried powder to epithelial HT-29 cells were 2.66-6.18% of the initial cell counts, whereas freeze-dried powder showed lower adhesive ability (1.79%). The in vitro human digestibility in the spray-dried powder was 70.09% which is very effective in digestion.
Antimicrobial activities and skin barrier improvement effect of Eruca sativa extract
Authors: Kim Bora , Kim Hyun-Soo
Published: August 2017

Eruca sativa is a rocket plant and a member of the Brassicaceae, which is considered to be an important chemo-preventive plant family. Although Eruca sativa has positive biological effects, the effect of Eruca sativa extract (ES) on improvement of skin barrier function has not been reported. In this study, we investigated the applicability of functional materials by examining a variety of physiological activities of Eruca sativa extract. ES showed anti-microbial activities against Bacillus subtilis, Escherichia coli, and Candida albicans. In particular, antimicrobial activities of ES against B. subtilis was the highest. Additionally, immunohistochemical analysis of protein marker related to keratinocyte differentiation was determined. The treatment by ES (50 mg/L) showed a significant increase of involucrin expression compared with treatment by 0.1% DMSO as a control in skin equivalents, the ES-treated group showed similar level in the expression of involucrin compared to the group treated with the same concentration of WY14643 in EpiDerm™, a three-dimensional model of skin equivalents. These results indicate that ES promotes the expression of protein related to barrier properties of the skin. Therefore, ES may be an effective ingredient for skin barrier improvement.
Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies
Authors: Meyers Lindsay , Ginocchio Christine C. , Faucett Aimie N. , Nolte Frederick S. , Gesteland Per H. , Leber Amy , Janowiak Diane , Donovan Virginia , Dien Bard Jennifer , Spitzer Silvia , Stellrecht Kathleen A. , Salimnia Hossein , Selvarangan Rangaraj , Juretschko Stefan , Daly Judy A. , Wallentine Jeremy C. , Lindsey Kristy , Moore Franklin , Reed Sharon L. , Aguero-Rosenfeld Maria , Fey Paul D. , Storch Gregory A. , Melnick Steve J. , Robinson Christine C. , Meredith Jennifer F. , Cook Camille V. , Nelson Robert K. , Jones Jay D. , Scarpino Samuel V. , Althouse Benjamin M. , Ririe Kirk M. , Malin Bradley A. , Poritz Mark A.
Published: August 2017

Health-care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are pathogen-specific. We describe a system, FilmArray®Trend, for rapid disease reporting that is syndrome-based but pathogen-specific. Results from a multiplex molecular diagnostic test are sent directly to a cloud database.www.syndromictrends.compresents these data in near real-time. Trend preserves patient privacy by removing or obfuscating patient identifiers. We summarize the respiratory pathogen results, for 20 organisms from 344,000 patient samples acquired as standard of care testing over the last four years from 20 clinical laboratories in the United States. The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks and adenovirus and bacterial pathogens show constant detection over the year. Interestingly, the rate of pathogen co-detections, on average 7.7%, matches predictions based on the relative abundance of organisms present.
Inferring proteome dynamics during yeast cell cycle using gene expression data
Authors: Kuchta Krzysztof , Towpik Joanna , Biernacka Anna , Kutner Jan , Kudlicki Andrzej , Ginalski Krzysztof , Rowicka Maga
Published: August 2017

Protein levels are most relevant physiologically, but measuring them genome-wide remains a challenge. In contrast, mRNA levels are much easier and less expensive to measure globally. Therefore, RNA levels are typically used to infer the corresponding protein levels. The steady-state condition (assumption that protein levels remain constant) is typically used to calculate protein abundances, as it is mathematically very convenient, even though it is often clear that it is not satisfied for proteins of interest. Here, we propose a simple, yet very effective, method to estimate genome wide protein abundances, which does not require the assumption that protein levels remain constant, and thus allows us to also predict proteome dynamics. Instead, we assume that the system returns to the baseline at the end of experiments; such an assumption is satisfied in many time-course experiments and in all periodic conditions (e.g. cell cycle). The approach only requires availability of gene expression and protein half-life data. As proof-of-concept, we calculated the predicted proteome dynamics for the budding yeast proteome during the cell cycle, which can be conveniently browsed online. The approach was validated experimentally by verifying that the predicted protein concentration changes were consistent with measurements for all proteins tested. Additionally, if proteomic data are also available, our approach can be used to predict how half-lives change in response to posttranslational regulation. We illustrated this application of our method withde novoprediction of changes in the degradation rate of Clb2 in response to post-translational modifications. The predicted changes were consistent with earlier observations in the literature.
Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)
Authors: Westbury Michael , Hartmann Stefanie , Barlow Axel , Wiesel Ingrid , Leo Viyanna , Welch Rebecca , Parker Daniel M , Sicks Florian , Ludwig Arne , Dalén Love , Hofreiter Michael
Published: August 2017

With an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as ‘near threatened’ by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.
Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships
Authors: Prasanna Arun N. , Gerber Daniel , Teeratas Kijpornyongpan , Aime M. Catherina , Doyle Vinson , Nagy Laszlo G.
Published: August 2017

Resolving deep divergences in the fungal tree of life remains a challenging task even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts (Pucciniomycotina), smuts (Ustilaginomycotina) and mushroom forming fungi (Agaricomycotina) represent a particularly challenging situation that posed problems to both traditional multigene and genome-scale phylogenetic studies. Here, we address basal Basidiomycota relationships using three different phylogenomic datasets, concatenated and gene tree-based analyses and examine the contribution of several potential sources of uncertainty, including fast-evolving sites, putative long-branch taxa, model violation and missing data. We inferred conflicting results with different datasets and under different models. Fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and Astral analyses. The most conserved datasets grouped rusts with mushroom forming fungi, although this relationship proved labile, sensitive to model choice, different data subsets and missing data. Excluding putative long branch taxa, genes with the highest proportions of missing data and/or genes with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play too. Our analyses suggest that topologies uniting smuts with mushroom forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for rusts, smuts and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of the tree space that is difficult to access using both concatenation and gene tree based approaches. Thus, basal Basidiomycota relationships remain unresolved and might represent a phylogenetic problem that remains contentious even in the genomic era.
Functional consequences of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals
Authors: Coleman Jonathan R. I. , Bryois Julien , Gaspar Héléna A. , Jansen Philip R. , Savage Jeanne , Skene Nathan , Plomin Robert , Muñoz-Manchado Ana B. , Linnarsson Sten , Crawford Greg , Hjerling-Leffler Jens , Sullivan Patrick F. , Posthuma Danielle , Breen Gerome
Published: August 2017

Variance in IQ is associated with a wide range of health outcomes, and 1% of the population are affected by intellectual disability. Despite a century of research, the fundamental neural underpinnings of intelligence remain unclear. We integrate results from genome-wide association studies (GWAS) of intelligence with brain tissue and single cell gene expression data to identify tissues and cell types associated with intelligence. GWAS data for IQ (N = 78,308) were meta-analyzed with an extreme-trait cohort of 1,247 individuals with mean IQ ∼170 and 8,185 controls. Genes associated with intelligence implicate pyramidal neurons of the somatosensory cortex and CA1 region of the hippocampus, and midbrain embryonic GABAergic neurons. Tissue-specific analyses find the most significant enrichment for frontal cortex brain expressed genes. These results suggest specific neuronal cell types and genes may be involved in intelligence and provide new hypotheses for neuroscience experiments using model systems.
A synthetic biology approach to probing nucleosome symmetry
Authors: Ichikawa Yuichi , Connelly Caitlin F. , Appleboim Alon , Miller Thomas C. , Jacobi Hadas , Abshiru Nebiyu A. , Chou Hsin-Jung , Chen Yuanyuan , Sharma Upasna , Zheng Yupeng , Thomas Paul M. , Chen Hsiuyi V. , Bajaj Vineeta , Müller Christoph W. , Kelleher Neil L. , Friedman Nir , Bolon Daniel N. , Rando Oliver J. , Kaufman Paul D.
Published: August 2017

The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.
The chromosomal basis of species initiation:Prdm9as an anti-speciation gene
Authors: Forsdyke Donald R.
Published: August 2017

Mechanisms initiating a branching process that can lead to new species are broadly classified as chromosomal and genic. Chromosomal mechanisms are supported by breeding studies involving exchanges of individual chromosomes or their segments between mouse subspecies. There are also studies of the rapidly mutating mousePR/SET-domain 9(prdm9) gene, which encodes PRDM9, a protein targeting DNA recombination hotspots. When PRDM9 is bound symmetrically with equal strength, the meiotic repair of mutations in one parental strand, based on information on the allelic strand (conversion), would seem to be unbiased in discriminating between strands. So mismatches detected between pairing paternal and maternal DNA strands (heteroduplexes) undergo unbiased conversions (to homoduplexes). This leaves uncertainty on whether a mutation has been corrected or compounded. However, it has been hypothesized that tagging of mismatch regions, so that both strands are epigenetically marked as uncertain, would make it possible over numerous generations for mutations to be corrected (biased conversions) wheneverasymmetryis detected. Thus, variation would decrease and members of a species would remain within its bounds. Intriguingly, new experimental studies show that, when chromosomally interpreted, PRDM9 also works throughasymmetricalepigenetic labelling to confine members to species bounds. To the extent that the experimentally observed and hypothetical anti-speciation asymmetries can be related, chromosomal mechanisms are further supported.
Estimating Excitatory and Inhibitory Synaptic Conductances from Spike Trains using a Recursive Bayesian Approach
Authors: Lankarany Mila
Published: August 2017

Inference of excitatory and inhibitory synaptic conductances (SCs) from the spike trains is poorly addressed in the literature due to the complexity of the problem. As recent technological advancements make recording spikes from multiple (neighbor) neurons of a behaving animal (in some rare cases from humans) possible, this paper tackles the problem of estimating SCs solely from the recorded spike trains. Given an ensemble of spikes corresponding to population of neighbor neurons, we aim to infer the average excitatory and inhibitory SCs underlying the shared neural activity. In this paper, we extended our previously established Kalman filtering (KF)–based algorithm to incorporate the voltage-to-spike nonlinearity (mapping from membrane potential to spike rate). Having estimated the instantaneous spike rate using optimal linear filtering (Gaussian kernel), our proposed algorithm uses KF followed by expectation maximization (EM) algorithm in a recursive fashion to infer the average SCs. As the dynamics of SCs and membrane potential is included in our model, the proposed algorithm, unlike other related works, considers different sources of stochasticity, i.e., the variabilities of SCs, membrane potential, and spikes. Moreover, it is worth mentioning that our algorithm is blind to the external stimulus, and it performs only based on observed spikes. We validate the accuracy and practicality of our technique through simulation studies where leaky integrate and fire (LIF) model is used to generate spikes. We show that the estimated SCs can precisely track the original ones. Moreover, we show that the performance of our algorithm can be further improved given enough number of trials (spikes). As a rule of thumb, 50 trials of neurons with the average firing rate of 5 Hz can guarantee the accuracy of our proposed algorithm.
A Prototype for Modular Cell Engineering
Authors: Wilbanks Brandon , Layton Donovan S. , Garcia Sergio , Trinh Cong T.
Published: August 2017

When aiming to produce a target chemical at high yield, titer, and productivity, various combinations of genetic parts available to build the target pathway can generate a large number of strains for characterization. This engineering approach will become increasingly laborious and expensive when seeking to develop desirable strains for optimal production of a large space of biochemicals due to extensive screening. Our recent theoretical development of modular cell (MODCELL) design principles can offer a promising solution for rapid generation of optimal strains by coupling a modular cell and exchangeable production modules in a plug-and-play fashion. In this study, we experimentally validated some designed properties of MODCELL by demonstrating: i) a modular (chassis) cell is required to couple with a production module, a heterologous ethanol pathway, as a testbed, ii) degree of coupling between the modular cell and production modules can be modulated to enhance growth and product synthesis, iii) a modular cell can be used as a host to select an optimal pyruvate decarboxylase (PDC) of the ethanol production module and to help identify a hypothetical PDC protein, and iv) adaptive laboratory evolution based on growth selection of the modular cell can enhance growth and product synthesis rates. We envision that the MODCELL design provides a powerful prototype for modular cell engineering to rapidly create optimal strains for synthesis of a large space of biochemicals.
Rap1 acts via multiple mechanisms to position Canoe/Afadin and adherens junctions and mediate apical-basal polarity establishment
Authors: Bonello Teresa T. , Perez-Vale Kia Z. , Sumigray Kaelyn D. , Peifer Mark
Published: August 2017

Epithelial apical-basal polarity drives assembly and function of most animal tissues. Polarity initiation requires cell-cell adherens junction assembly at the apical-basolateral boundary. The mechanisms underlying this remain key issues. Drosophila embryos provide a superb model, as 6000 polarized cells assemble simultaneously. Current data place the actin-junctional linker Canoe (mammalian Afadin’s homolog) at the top of the polarity hierarchy, where it directs Bazooka/Par3 and adherens junctions positioning. Here we define mechanisms regulating Canoe localization/function. Spatial organization of Canoe is multifaceted, involving membrane-localization, recruitment to nascent junctions and macromolecular assembly into cables at tricellular junctions. Our data suggest apical activation of the small GTPase Rap1 regulates all three events, but support multiple modes of regulation. The Rap1GEF Dizzy/PDZ-GEF is critical for Canoe tricellular junction enrichment but not apical retention. Canoe’s Rap1-interacting RA-domains mediate adherens junction and tricellular junction recruitment but are dispensable for membrane-localization. Our data also support a role for Canoe-multimerization. These multifactorial inputs all shape Canoe localization, correct Bazooka/Par3 and adherens junction positioning, and thus apical-basal polarity. We integrate existing data into a new polarity establishment model.

Abbreviations used

α-cat, alpha-catenin; β-cat, beta-catenin; AJ, adherens junction; Arm, Armadillo; Baz, Bazooka; CA, constitutively active; Cno, Canoe; DE-cad,DrosophilaE-cadherin; Dzy, Dizzy; GAP, GTPase activating protein; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factor; GFP, green fluorescent protein; GTP, guanosine triphosphate; IF, immunofluorescence; MIP, maximum intensity projection; RA, Ras-associated; RFP, red fluorescent protein; SAJ, spot adherens junction; shRNA, short hairpin RNA; TCJ, tricellular junction; WT, wildtype
A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals
Authors: Marcovitz Amir , Turakhia Yatish , Gloudemans Michael , Braun Benjamin A. , Chen Heidi I. , Bejerano Gill
Published: August 2017

Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. The extent to which genomic molecular convergence, and the extent to which coding mutations underlie this convergent phenotypic evolution remain unknown. Using a novel test, we ask which group of functionally coherent genes is most affected by convergent amino acid substitutions between phenotypically convergent lineages. This most affected sets reveals 75 novel coding convergences in important genes that pattern a highly adapted organ: the cochlea, skin and lung in echolocating, aquatic and high-altitude mammals, respectively. Our test explicitly requires the enriched converged term to not be simultaneously enriched for divergent mutations, and correctly dismisses relaxation-based signals, such as those produced by vision genes in subterranean mammals. This novel test can be readily applied to birds, fish, flies, worms etc., to discover more of the fascinating contribution of protein coding convergence to phenotype convergence.
Anju Pharmaceuticals: riding the herbal wave
Authors: Attri Rekha
Published: August 2017

Subject area

Marketing management, consumer behaviour, digital marketing.

Study level/applicability

This case can be used for students studying marketing management courses and also for elective courses on consumer behaviour, digital marketing and strategic management in an MBA programme.

Case overview

This case is about Anju Pharmaceuticals which dealt in the manufacture and sale of ayurvedic/herbal products such as Panchsudha, Zalim Lotion, Ruz, Vama, Mekado etc. in Madhya Pradesh, India. Started in the year 1983, the company had still not been able to make a mark in the market. For quite some time now Mitesh, the third-generation proprietor of the company, was continuously reading articles which discussed how there has been a positive shift in the consumer preferences for products having herbal ingredients. Indian fast-moving consumer goods (FMCG) companies such as Patanjali, Dabur, Marico were banking on herbal components in their various key products such as toothpaste, shampoo and hair oil to expand their market share and some of these Indian companies seemed to be growing faster than bigger multinationals including Hindustan Unilever and Procter & Gamble. With the changes in consumer perception towards herbal products, Mitesh was hopeful that if he could gear up his distribution it would result in improving the bottom-line of the company. He had also started receiving queries from interested clients for third-party manufacturing and packaging of the ayurvedic products under the desired brand name. Mitesh was very much aware that to improve his bottom-line, just relying on efficient distribution would not suffice and he would need to come up with strategic alliances and newer ways of doing the business rather than just following what had been the norm for the last few years. The idea of becoming a third-party manufacturer somehow did not excite Mitesh because he felt that by going in for third-party manufacturing he would never be able to establish the brand identity of Anju Pharmaceuticals. He wanted his company to ride the FMCG herbal wave but how and at what cost were the big questions facing him.

Expected learning outcomes

After the successful completion of this case, the readers would be able to accomplish the following: gain insights into the problems faced by small businesses when they want to scale up their business. Get insights into the challenges/difficulties of adopting e-commerce by a small organization. Be aware of the changing consumer preferences for herbal and ayurvedic products and how companies are gearing up to cash on to the changing market opportunities. Comprehend the problem situation. Suggest ways of taking advantage of the current scenario to expand and grow the business.

Supplementary materials

Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 8: Marketing.
What happens “NEXT”?
Authors: Taneja Girish
Published: August 2017

Subject area

The case has been designed specifically for a Brand Management course. However, it can be used for a basic course in marketing management.

Study level/applicability

The case has been developed for the students of MBA or Executive MBA. The case needs to be taught after the students have understood the concepts of the marketing mix, segmentation, targeting and the basics of marketing strategy to ensure effective learning.

Case overview

The case discusses the entrepreneurial journey of Parminder Sandhu. Sandhu initiated an entrepreneurial venture by launching a brand of perfume in India. Parminder, with his business partner Arun, got the idea of using the brand name “Next” from Next Plc store while travelling around in the UK. Subsequently, “Next Care” successfully launched two product lines “Next” and “English Leather” and offered 51 SKUs. “Next Care” became the third highest selling perfume brand firm in India. “Next Care” suffered a setback when one of their factories was raided by “Lacoste” and had to stop production of one brand extension “Nextcare Crocodile” due to the deceptively similar logo. Parminder learned that “Next Plc” was planning to open its stores and may launch the NXT brand of perfumes in India. Sandhu, Mahajan and Wadhawan have been debating whether they should continue with the “Next” brand name.

Expected learning outcomes

The expected learning outcomes are as follows: to appreciate the marketing and legal perspective of a brand name; to introduce the concept of deceptively similar brands and implications of the same on the business; and to understand the process of brand name registration.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 8: Marketing.
Kannada movie industry in India: strategies for survival
Authors: Kidiyoor Gururaj H. , Yatgiri Prashant V.
Published: August 2017

Subject area

Strategy.

Study level/applicability

This case can be used on a strategic management course in the second year of an MBA programme, any special elective course on the media and entertainment industry and in executive education programmes to demonstrate the application of strategic management concepts and frameworks.

Case overview

The Indian film industry was the largest in the world and the seventh largest in terms of revenue. Significant number of movies were made in languages such as Bengali, Marathi, Telugu, Tamil, Malayalam and Kannada, with Hindi commanding the highest number. The film industry in Karnataka made movies in the Kannada language. The industry was plagued by a host of issues with the industry contributing just 2 per cent of the revenues and box office success rate at just around 25 per cent. The state government had set up Karnataka Chalanachitra Academy with the objective of promotion and development of the movie industry in Karnataka. The Chairman of the academy, Shailesh Singh, was extremely concerned about the poor success rate of Kannada movies and was contemplating various options of reviving the ailing Kannada movie industry.

Expected learning outcomes

The expected learning outcomes are as follows: application of strategic management frameworks in the context of the movie industry; analysis of industry issues from the long-term and short-term perspectives; study of different entities in the movie industry and the roles they play and their interdependence; applying learning to suggest survival strategies in an extremely competitive market; and insights into the role of government in the media/entertainment industry.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 11: Strategy.
HFCL: valuing a high growth company
Authors: Kastia Alok
Published: August 2017

Subject area

Finance.

Study level/applicability

This case can be taught in the Finance area as a part of the course on “Valuation” in a postgraduate program. MBA/EMBA/MBF.

Case overview

Himachal Futuristic Communications Ltd. (HFCL) discontinued all of its old products and entered into manufacturing of telecom products for mobile telephony and turnkey projects. This complete change in product line was like a re-birth for the company. HFCL grew tremendously between FY 2012 and FY 2015. Its sales grew from Rs 2,638m in FY 2012 to Rs 26,129m in FY 2015, an increase of 114 per cent CAGR (compound annual growth rate). HFCL stock price increased from Rs 11.75 in March 2012 to Rs 19.90 in September 2014 because of this tremendous growth. The stock price came down to Rs 13.35 in March 2015, as the market was sceptical about HFCL sustaining this growth. In March 2015, Choudhary, an equity analyst, was wondering how to value this high growth company. If somehow he could ascertain the intrinsic value of the stock properly, he would be able to appropriately advise his clients about the HFCL stock.

Expected learning outcomes

The case learning objectives are as follows: to scan the competitive landscape of telecom equipment manufacturing industry and gauge the competitive advantages enjoyed by HFCL; to size the potential market of the industry and predict the level of sustained profitability for HFCL; to develop multiple scenarios based on key drivers and compile projected financial statements for each scenario; and to value the company using the scenario-based discounted cash flow technique by assigning probabilistic weights to each scenario.

Supplementary Materials

Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 1: Accounting and finance.