bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal integration between host physiology and functions of the gut microbiome
Authors: Fontaine Samantha S. , Kohl Kevin D.
Published: August 2020

Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of ‘symmorphosis’, which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities.

This article is part of the theme issue ‘The role of the microbiome in host evolution’.
Symbiotic magnetic sensing: raising evidence and beyond
Authors: Natan Eviatar , Fitak Robert Rodgers , Werber Yuval , Vortman Yoni
Published: August 2020

The identity of a magnetic sensor in animals remains enigmatic. Although the use of the geomagnetic field for orientation and navigation in animals across a broad taxonomic range has been well established over the past five decades, the identity of the magnetic-sensing organ and its structure and/or apparatus within such animals remains elusive—‘a sense without a receptor’. Recently, we proposed that symbiotic magnetotactic bacteria (MTB) may serve as the underlying mechanism behind a magnetic sense in animals—‘the symbiotic magnetic-sensing hypothesis'. Since we first presented this hypothesis, both criticism and support have been raised accordingly. Here we address the primary criticisms and discuss the plausibility of such a symbiosis, supported by preliminary findings demonstrating the ubiquity of MTB DNA in general, and specifically in animal samples. We also refer to new supporting findings, and discuss host adaptations that could be driven by such a symbiosis. Finally, we suggest the future research directions required to confirm or refute the possibility of symbiotic magnetic-sensing.

This article is part of the theme issue ‘The role of the microbiome in host evolution’.
Contemporary and historical selection in Tasmanian devils (Sarcophilus harrisii) support novel, polygenic response to transmissible cancer
Authors: Stahlke Amanda R. , Epstein Brendan , Barbosa Soraia , Margres Mark J. , Patton Austin , Hendricks Sarah A. , Veillet Anne , Fraik Alexandra K , Schönfeld Barbara , McCallum Hamish I. , Hamede Rodrigo , Jones Menna E. , Storfer Andrew , Hohenlohe Paul A.
Published: August 2020

Tasmanian devils (Sarcophilus harrisii) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independently evolved transmissible cancer suggest that transmissible cancers may be a recurrent feature in devils. Here we compared signatures of selection across temporal scales to determine whether genes or gene pathways under contemporary selection (6-8 generations) have also been subject to historical selection (65-85 million years), and test for recurrent selection in devils. First, we used a targeted sequencing approach, RAD-capture, to identify genomic regions subject to rapid evolution in approximately 2,500 devils in six populations as DFTD spread across the species range. We documented genome-wide contemporary evolution, including 186 candidate genes related to cell cycling and immune response. Then we used a molecular evolution approach to identify historical positive selection in devils compared to other marsupials and found evidence of selection in 1,773 genes. However, we found limited overlap across time scales, with historical selection detected in only 16 contemporary candidate genes, and no overlap in enriched functional gene sets. Our results are consistent with a novel, multi-locus evolutionary response of devils to DFTD. Our results can inform management actions to conserve adaptive potential of devils by identifying high priority targets for genetic monitoring and maintenance of functional diversity in managed populations.
Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships
Authors: Harder Matthew J. , Hix Julie , Reeves Wendy M. , Veeman Michael T.
Published: August 2020

Many genes are regulated by two or more enhancers that drive similar expression patterns. Evolutionary theory suggests that these seemingly redundant enhancers must have functionally important differences. In the simple ascidian chordateCiona, the transcription factor Brachyury is induced exclusively in the presumptive notochord downstream of lineage specific regulators and FGF-responsive Ets family transcription factors. Here we exploit the ability to finely titrate FGF signaling activity via the MAPK pathway using the MEK inhibitor U0126 to quantify the dependence of transcription driven by differentBrachyuryreporter constructs on this direct upstream regulator. We find that the more powerful promoter-adjacent proximal enhancer and a weaker distal enhancer have fundamentally different dose-response relationships to MAPK inhibition. The Distal enhancer is more sensitive to MAPK inhibition but shows a less cooperative response, whereas the Proximal enhancer is less sensitive and more cooperative. A longer construct containing both enhancers has a complex dose-response curve that supports the idea that the proximal and distal enhancers are moderately super-additive. We show that the overall expression loss from intermediate doses of U0126 is not only a function of the fraction of cells expressing these reporters, but also involves graded decreases in expression at the single-cell level. Expression of the endogenous gene shows a comparable dose-response relationship to the full length reporter, and we find that different notochord founder cells are differentially sensitive to MAPK inhibition. Together, these results indicate that although the twoBrachyuryenhancers have qualitatively similar expression patterns, they respond to FGF in quantitatively different ways and act together to drive high levels ofBrachyuryexpression with a characteristic input/output relationship. This indicates that they are fundamentally not redundant genetic elements.
Colour vision and information theory: the receptor noise-limited model implies optimal colour discrimination by opponent channels
Authors: Risau-Gusman Sebastián
Published: August 2020

In order to interpret animal behaviour we need to understand how they see the world. As colour discrimination is almost impossible to test directly in animals, it is important to develop theoretical models based in the properties of visual systems. One of the most successful is the receptor noise-limited (RNL) model, which depends only on the level of noise in photoreceptors and opponent mechanisms. Here optimal colour discrimination properties are obtained using information theoretical tools, for the early stages of visual systems with and without colour opponent mechanisms. For most biologically relevant conditions the optimal discrimination function of an ideal observer coincides with the one obtained with the RNL model. Many variants of the model can be cast into the same framework, which permits meaningful comparisons across species. For example, it is shown that the presence of opponency seems to be the preferred hypothesis for bees, but not for budgerigars. Since this is a consequence of the presence of oil droplets, this could also be true for most other species of birds.
Reduction of Short-Chain Fatty Acid-Producing Gut Microbiota Leads to Transition from Rapid-Eye-Movement Sleep Behavior Disorder to Parkinson’s Disease
Authors: Nishiwaki Hiroshi , Hamaguchi Tomonari , Ito Mikako , Ishida Tomohiro , Maeda Tetsuya , Kashihara Kenichi , Tsuboi Yoshio , Ueyama Jun , Shimamura Teppei , Mori Hiroshi , Kurokawa Ken , Katsuno Masahisa , Hirayama Masaaki , Ohno Kinji
Published: August 2020

Gut dysbiosis has been reported repeatedly in Parkinson’s disease (PD), but once in rapid-eye-movement sleep behavior disorder (RBD) from Germany. Abnormal aggregation of α-synuclein fibrils causing PD possibly starts from the intestine. RBD patients frequently develop PD. Early-stage gut dysbiosis that is causally associated with PD is thus expected to be observed in RBD. We analyzed gut microbiota in 26 RBD patients and 137 controls by 16S rRNA-seq. Our RBD dataset was meta-analyzed with the German RBD dataset, and was compared with gut microbiota in 223 PD patients. Unsupervised clustering of gut microbiota by LIGER, a topic model-based tool for single-cell RNA-seq analysis, revealed four enterotypes in controls, RBD, and PD. Short-chain fatty acid (SCFA)-producing bacteria were conserved in an enterotype observed in controls and RBD, whereas they were less in enterotypes observed in PD. GenusAkkermansiaand familyAkkermansiaceaewere consistently increased in both RBD in two countries and PD in five countries. No short-chain fatty acid (SCFA)-producing bacteria were significantly changed in RBD in two counties. In contrast, we previously reported that recognized and putative SCFA-producing generaFaecalibacterium,Roseburia, andLachnospiraceae ND3007 groupwere consistently decreased in PD in five countries. Increased mucin-layer-degrading genusAkkermansiapossibly accounts for the development of RBD, and an additional decrease of SCFA-producing genera is likely to be associated with the transition from RBD to PD.

Importance

Nineteen studies have been reported on gut microbiota in PD, whereas only one study has been reported in RBD from Germany. RBD has the highest likelihood ratio to develop PD. Our meta-analysis of RBD in Japan and Germany revealed increased mucin-layer-degrading genusAkkermansiain RBD. GenusAkkermansiamay increase the intestinal permeability, as we previously observed in PD patients, and make the intestinal neural plexus exposed to oxidative stress, which can lead to abnormal aggregation of prion-like α-synuclein fibrils in the intestine. In contrast to PD, SCFA-producing bacteria were not decreased in RBD. As SCFA induces Treg cells, a decrease of SCFA-producing bacteria may be a prerequisite for the development of PD. We propose that prebiotic and/or probiotic therapeutic strategies to increase the intestinal mucin layer and to increase intestinal SCFA potentially retard the development of RBD and PD.
Raven: a de novo genome assembler for long reads
Authors: Vaser Robert , Šikić Mile
Published: August 2020

We present new methods for the improvement of de novo genome assembly from erroneous long-reads incorporated into a straightforward tool called Raven (https://github.com/lbcb-sci/raven). Raven maintains similar performance for various genomes and has accuracy on par with other assemblers which support third-generation sequencing data. It is one of the fastest options while having the lowest memory consumption on the majority of benchmarked datasets.
Constitutive Androstane Receptor and Hepatitis B Virus X Protein Cooperatively Induce β-catenin-Activated Liver Tumors
Authors: Scott Jessica D. , Liu Silvia , Klatt Kevin C. , Sun Zhen , Guo Qi , Grimm Sandra L. , Coarfa Cristian , Dong Bingning , Moore David D.
Published: August 2020

Background and Aims

The xenobiotic nuclear receptor Constitutive Androstane Receptor (CAR) is essential for xenobiotic tumor promotion in mouse models. In these models, β-catenin is genetically activated in approximately 80% of tumors. Chronic Hepatitis B Virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC), and β-catenin activation is also frequently activated in HBV-associated HCCs. The goal of this research was to determine whether activation of CAR in a mouse model of chronic HBV infection would result in tumor formation and whether these tumors would display increased β-catenin activation.

Approach and Results

We treated transgenic mice expressing the HBV X protein (HBx) in hepatocytes with a single dose of the potent CAR agonist TCPOBOP. After 10 months, these mice developed large liver tumors that are characterized by β-catenin nuclear localization and upregulation of β-catenin targets. The β-catenin regulator FoxM1 and the oxidative stress master regulator Nrf2, both of which are CAR gene targets, were also overactivated in tumors. The CAR/HBx tumors share a conserved gene signature with HBV-related human hepatocellular carcinoma.

Conclusions

Activation of CAR in the presence of HBx results in tumors with strong β-catenin activation. The mouse model we have described reflects the gene expression patterns seen in human HBV-associated HCC and presents an attractive basis for future studies.
Deep Learning assisted Peak Curation for large scale LC-MS Metabolomics
Authors: Gloaguen Yoann , Kirwan Jennifer , Beule Dieter
Published: August 2020

Available automated methods for peak detection in untargeted metabolomics suffer from poor precision. We present NeatMS which uses machine learning to replace peak curation by human experts. We show how to integrate our open source module into different LC-MS analysis workflows and quantify its performance. NeatMS is designed to be suitable for large scale studies and improves the robustness of the final peak list.
Engineered Reproductively Isolated Species Drive Reversible Population Replacement
Authors: Buchman Anna , Shriner Isaiah , Yang Ting , Liu Junru , Antoshechkin Igor , Marshall John M. , Perry Michael W. , Akbari Omar S.
Published: August 2020

Engineered reproductive species barriers are useful for impeding gene flow and driving desirable genes into wild populations in a reversible threshold-dependent manner. However, methods to generate synthetic barriers are lacking in advanced eukaryotes. To overcome this challenge, we engineered SPECIES (SyntheticPostzygotic barriersExploitingCRISPR-basedIncompatibilities forEngineeringSpecies) to generate postzygotic reproductive barriers. Using this approach, we engineer multiple reproductively isolated SPECIES and demonstrate their threshold-dependent gene drive capabilities inD. melanogaster. Given the near-universal functionality of CRISPR tools, this approach should be portable to many species, including insect disease vectors in which confinable gene drives could be of great practical utility.

One Sentence Summary

Synthetically engineered SPECIES drive confinable population replacement.
Action Potentials and Na+ voltage-gated ion channels in Placozoa
Authors: Romanova Daria Y. , Smirnov Ivan V. , Nikitin Mikhail A. , Kohn Andrea B. , Borman Alisa I. , Malyshev Alexey Y. , Balaban Pavel M. , Moroz Leonid L.
Published: August 2020

Placozoa are small disc-shaped animals, representing the simplest known, possibly ancestral, organization of free-living animals. With only six morphological distinct cell types, without any recognized neurons or muscle, placozoans exhibit fast effector reactions and complex behaviors. However, little is known about electrogenic mechanisms in these animals. Here, we showed the presence of rapid action potentials in four species of placozoans (Trichoplax adhaerens [H1 haplotype], Trichoplax sp.[H2], Hoilungia hongkongensis [H13], and Hoilungia sp. [H4]). These action potentials are sodium-dependent and can be inducible. The molecular analysis suggests the presence of 5-7 different types of voltage-gated sodium channels, which showed substantial evolutionary radiation compared to many other metazoans. Such unexpected diversity of sodium channels in early-branched animal lineages reflect both duplication events and parallel evolution of unique behavioral integration in these nerveless animals.

Highlights

Placozoans are the simplest known animals without recognized neurons and muscles

With only six morphological cell types, placozoans showed complex & rapid behaviors

Sodium-dependent action potentials have been discovered in intact animals

Voltage-gated sodium channels (Nav) in Placozoa support a rapid behavioral integration

Placozoans have more Nav channels that any studied invertebrate animal so far

Diversification of Nav-channels highlight the unique evolution of these nerveless animals
Nonlinear System Identification of Neural Systems from Neurophysiological Signals
Authors: He Fei , Yang Yuan
Published: August 2020

The human nervous system is one of the most complicated systems in nature. Complex nonlinear behaviours have been shown from the single neuron level to the system level. For decades, linear connectivity analysis methods, such as correlation, coherence and Granger causality, have been extensively used to assess the neural connectivities and input-output interconnections in neural systems. Recent studies indicate that these linear methods can only capture a small amount of neural activities and functional relationships, and therefore cannot describe neural behaviours in a precise or complete way. In this review, we highlight recent advances in nonlinear system identification of neural systems, corresponding time and frequency domain analysis, and novel neural connectivity measures based on nonlinear system identification techniques. We argue that nonlinear modelling and analysis are necessary to study neuronal processing and signal transfer in neural systems quantitatively. These approaches can hopefully provide new insights to advance our understanding of neurophysiological mechanisms underlying neural functions. These nonlinear approaches also have the potential to produce sensitive biomarkers to facilitate the development of precision diagnostic tools for evaluating neurological disorders and the effects of targeted intervention.
A hardware/software system for electrophysiology “supersessions” in marmosets
Authors: Muthmann Jens-Oliver , Levi Aaron J. , Carney Hayden C. , Huk Alexander C.
Published: August 2020

We introduce a straightforward, robust method for recording and analyzing spiking activity over timeframes longer than a single session, with primary application to the marmoset (Callithrix jacchus). Although in theory the marmoset’s smooth brain allows for broad deployment of powerful tools in primate cortex, in practice marmosets do not typically engage in long experimental sessions akin to rhesus monkeys. This potentially limits their value for detailed, quantitative neurophysiological study. Here we describe chronically-implanted arrays with a 3D arrangement of electrodes yielding stable single and multi-unit responses, and an analytic method for creating “supersessions” combining that array data across multiple experiments. We could match units across different recording sessions over several weeks, demonstrating the feasibility of pooling data over sessions. This could be a key tool for extending the viability of marmosets for dissecting neural computations in primate cortex.
Long-read transcriptome and other genomic resources for the angiospermSilene noctiflora
Authors: Williams Alissa M. , Itgen Michael W. , Broz Amanda K. , Carter Olivia G. , Sloan Daniel B.
Published: August 2020

The angiosperm genusSileneis a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious speciesS. latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts and identify paralogous genes and alternatively spliced genes. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 17,000S. noctifloragenes and 27,000 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Further, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and three-fold larger than the 0.9-Gb genome ofS. conica, another species in the same subgenus. Karyotyping confirmed thatS. noctiflorais a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.
Susceptibility to gingipains and transcriptomic response toP. gingivalishighlights the ribosome, hypothalamus, and cholinergic neurons
Authors: Patel Sejal , Howard Derek , French Leon
Published: August 2020

Porphyromonas gingivalis, a keystone species in the development of periodontal disease, is a suspected cause of Alzheimer’s disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Proteins in the SRP-dependent cotranslational protein targeting to membrane pathway were enriched for these residues and previously associated with periodontal and Alzheimer’s disease. These ribosomal genes are up-regulated in prefrontal cortex samples with detectedP. gingivalissequences. Other differentially expressed genes have been previously associated with dementia (ITM2B, MAPI, ZNF267, andDHX37). For an anatomical perspective, we characterized the expression of theP. gingivalisassociated genes in the mouse and human brain. This analysis highlighted the hypothalamus, cholinergic neurons, and the basal forebrain. Our results suggest markers of neuralP. gingivalisinfection and link the gingipain and cholinergic hypotheses of Alzheimer’s disease.
Urinary proteome profiling for stratifying patients with familial Parkinson’s disease
Authors: Winter Sebastian Virreira , Karayel Ozge , Strauss Maximilian T , Padmanabhan Shalini , Surface Matthew , Merchant Kalpana , Alcalay Roy N. , Mann Matthias
Published: August 2020

The prevalence of Parkinson’s disease (PD) is increasing but the development of novel treatment strategies and therapeutics altering the course of the disease would benefit from specific, sensitive and non-invasive biomarkers to detect PD early. Here, we describe a scalable and sensitive mass spectrometry (MS)-based proteomic workflow for urinary proteome profiling. Our workflow enabled the reproducible quantification of more than 2,000 proteins in more than 200 urine samples using minimal volumes from two independent patient cohorts. The urinary proteome was significantly different between PD patients and healthy controls, as well as betweenLRRK2G2019S carriers and non-carriers in both cohorts. Interestingly, our data revealed lysosomal dysregulation in individuals with theLRRK2G2019S mutation. When combined with machine learning, the urinary proteome data alone was sufficient to classify mutation status and disease manifestation in mutation carriers remarkably well, identifying VGF, ENPEP and other PD-associated proteins as the most discriminating features. Taken together, our results validate urinary proteomics as a valuable strategy for biomarker discovery and patient stratification in PD.
Varying intestinal absorption curves of glucose and fat with different plasma insulin curves in different positions
Authors: Yang Junhua , Wang Ling , Song Linyang , Li Guoying , Jin Xiaobao , Tian Sumin
Published: August 2020

It has been shown that posture could affect the rehabilitation of some diseases, and even affect the physiological metabolism and function of certain systems of the human body, including gastrointestinal absorption of glucose. Studies attributed the different gastrointestinal absorption rate in different positions to the varying rate of gastric emptying in different positions. However, it is still unknown whether the absorption rate of nutrients from the intestine varies in different positions. To verify this hypothesis, the present study was conducted using rats as subjects. After injection of glucose or chyme of safflower oil into the upper segment of jejunum of rats, curves of plasma glucose or triglyceride were drawed to evaluate and compare the potential influences on intestinal absorption by postures. We found varying intestinal absorption curves of glucose and fat with different plasma insulin curves in different positions. To be specific, the right lateral decubitus resulted in the most sharp curves, whereas the supine position the most obtuse curves with a delayed peak, both in case of glucose and fat absorption. These findings contribute to understand the position-related absorption kinetics of substances in the intestinal tract. According to this study, posture may be important for the prevention and nursing intervention of some diseases related to metabolic kinetics of glucose and lipids. It may also be important for the absorption and transport of lipophilic drugs through the mesentery lymphatic vessels.
Durable Control of HIV-1 Using aStaphylococcus aureusCas9-Expressing Lentivirus Co-Targeting Viral Latency and Host Susceptibility
Authors: Chavez Leonard R. , Reddy Nishith R. , Raymond Kyle A. , Bouzidi Mohamed S. , Desai Shivani , Dossani Zain Y. , Sperber Hannah S. , Theiler James , Korber Bette , Pillai Satish K.
Published: August 2020

CRISPR/Cas9 gene editing has the potential to revolutionize the clinical management of HIV-1 infection, and may eliminate the need for antiretroviral therapy (ART). Current gene therapies attempt to either excise HIV-1 provirus or target HIV-1 entry receptors to prevent infection of new cells. Using a viral dynamic model, we determined that combining these two interventions, in the presence or absence of ART, significantly lowers the gene editing efficacy thresholds required to achieve an HIV-1 cure. To implement this dual-targeting approach, we engineered a single lentiviral vector that simultaneously targets multiple highly-conserved regions of the provirus and the host CXCR4 coreceptor, and developed a novel coculture system enabling real-time monitoring of latent infection, viral reactivation, and infection of new target cells. Simultaneous dual-targeting depleted HIV-1-infected cells with significantly greater potency than vectors targeting either virus or host independently, highlighting its potential as an HIV-1 cure strategy.
Waiting for love but not forever: modelling the evolution of waiting time to selfing in hermaphrodites
Authors: Blüml Chantal , Ramm Steven A. , van Benthem Koen J. , Wittmann Meike J.
Published: August 2020

Although mixed mating systems involving both selfing and outcrossing are fairly common in hermaphrodites, it is unclear how they are maintained. In some species, individuals delay self-fertilization while they have not found a mating partner. The ‘waiting time’ is subject to two opposing selection pressures: waiting helps to avoid inbreeding depression in offspring by increasing the density-dependent probability to encounter a mate, but also increases the risk of dying before reproduction. In some species waiting time can vary between individuals and be heritable. We therefore used an individual-based model to explore how delayed selfing evolves in response to density and density fluctuations. We find that at high density, when individuals meet often, drift drives waiting time; at intermediate densities, strong inbreeding depression causes waiting time to increase; and at low densities, inbreeding depression is purged, and waiting time approaches zero. Positive feedback loops drive the system to either complete selfing or complete outcrossing. Fluctuating density can slow down convergence to these alternative stable states. However, mixed mating, in the sense of either a stable polymorphism in waiting times, or stable intermediate times, was never observed. Thus, additional factors need to be explored to explain the persistence of delayed selfing.
Quantity and quality of suitable matrices matter in reducing the negative effect of fragmentation on populations extinction risk
Authors: Travassos-Britto Bruno , Hohlenwerger Camila , Miranda José , Rocha Pedro Luís Bernardo da
Published: August 2020

The negative effect of fragmentation is one of the main concerns in the study of biodiversity loss in landscape ecology. The use of the matrix has been considered an important factor because it can change the relationship of a population with the configuration of the landscape. A systematic way to assess the effect of matrix quality in fragmented landscapes could lead to a better understanding of how matrices can be used to suppress the negative effect of fragmentation. We built a computational individual-based model capable of simulating bi-dimensional landscapes with three types of land cover (habitat, suitable matrix and hostile matrix) and individuals that inhabit those landscapes. We explored in which situations changes in the proportion of the suitable matrix in the landscape and the degree of usability of this suitable matrix can mitigate the negative effect of fragmentation per se. We observed that (i) an increase in the matrix quality (increases in the suitable matrix proportion and/or usability) can suppress the fragmentation effect in 47% of the simulated scenarios; (ii) the less usable the matrix is the more of it is needed to suppress the fragmentation effect; (iii) there is a level of usability below which increasing the suitable matrix proportion does cause the fragmentation effect to cease. These results point toward a landscape management that considers the similarity of the matrix to the native habitat under management. We suggest that an index to measure the usability of elements of the matrix could be an important tool to further the use of computational models in landscape management.
Risk disclosure in listed Greek companies: the effects of the financial crisis
Authors: Gonidakis Fragiskos K. , Koutoupis Andreas G. , Tsamis Anastasios D. , Agoraki Maria-Eleni K.
Published: August 2020

Purpose

The purpose of this study is to investigate risk disclosure in listed Greek companies. The effects of the financial crisis were also considered.

Design/methodology/approach

This study aimed to determine the risk-reporting practices of Greek’s non-financial companies listed on the Athens Stock Exchange through a content analysis of their annual reports.

Findings

Risk identification and anticipation protect businesses and create shareholder value. In recent years, particularly since the economic crisis, risk has become one of the most important business issues. This study concluded that during the crisis, there was an increase in disclosure. Financial, personnel and legal risks were the most reported types of risk. This study also found liquidity to be a very important issue.

Research limitations/implications

Content analysis has limitations because subjectivity cannot be eliminated. This study measured only the quantity, not the quality, of risk disclosure. The quality of risk reporting will be examined in future research.

Originality/value

This is the first study on risk disclosure in the non-financial companies listed on the Athens Stock Exchange to conduct a content analysis of the corporate annual reports.
Impact of relational communication on buyer–supplier relationship satisfaction: role of trust and commitment
Authors: Agarwal Upasna A. , Narayana Sushmita A.
Published: August 2020

Purpose

The present study aims to examine the impact of relational communication, operationalized in terms of information sharing, quality and frequency of information, on buyer's trust and relationship satisfaction in a buyer–vendor relationship. The study also tests the mediating role of trust and the moderating role of relationship commitment in relational communication and satisfaction relationship.

Design/methodology/approach

The data for the study were collected through a questionnaire survey from 321 managers of the different firms who were directly or indirectly involved in making procurement or purchasing decision in the firm and were familiar with the firm's supplier relationships.

Findings

Relational communication was found to be positively related to relational satisfaction and trust partially mediated this relationship. Further, relationship commitment moderated relational communication-satisfaction relationship, such that the positive affect of relational communication on relational satisfaction was accentuated when buyer experienced higher relationship commitment towards the supplier.

Research limitations/implications

Using single source, self-reported questionnaire data and cross-sectional research design are the limitations of this study. Studies in future should consider a dyadic perspective. The study outlines the need to explore investments and strategies in enhancing relational communication in buyer–vendor relationships.

Originality/value

Anchored in theoretical foundations of social exchange theory, the study integrates and tests behavioral aspects of buyer–vendor relationship. Testing an integrated model with direct and indirect effects of relational communication on relationship satisfaction in buyer–vendor is a significant contribution of the research. The study also contributes by examining relational exchanges in buyer-vendor relationships in India, an underrepresented context in buyer–supplier relationship (BSR) literature.
Dr. Lal Pathlabs (A)
Authors: Mathur Ajeet
Published: August 2020

Diagnostics services in India were growing at 20% annually with billing of USD 3.4 billion. With WTO's GATS, foreign competition was arising. Dr. Lal PathLabs had formidable brand recognition and Dr. Arvind Lal was wondering whether to accept private equity and induct management professionals to keep pace with competitors through acquisitions or greenfield or sell out. He worried over loss of proprietary control. The industry practice of incentivizing doctors for referrals meant that acquisitions brought perverse incentive systems. The choice of compromising ethics or inventing another business model had to be made alongside whether to expand in India or abroad.
Dr. Lal Pathlabs (B)
Authors: Mathur Ajeet
Published: August 2020

India's diagnostics business valued at USD 10 billion was growing at 20% annually. Several players with different business models competed. Dr. Lal PathLabs, the world's largest histopathology centre led with a menu of 3,500 tests, 1,600 collection centres and 7,000 pick-up points. Its Initial Public Offer had been oversubscribed 33.41 times and the team at Dr. Lal PathLabs was excited about expanding its international footprint. Two overseas companies were incorporated in Netherlands and Nepal. Yet, there were enormous unmet needs in India alongside potential for public-private partnerships. Trade-offs over portfolio choice and regional versus international footprint needed thinking through.
Dr. Janel Jeyapaul v. SRM University: Private Organisations and Public Rights
Authors: Pathak Akhileshwar
Published: August 2020

A person can approach the High Court directly under Article 226 for a violation of a Fundamental Right. The Fundamental Rights, however, are available only against the bodies which are ‘state’ within Article 12 of the Constitution. The judgement of the Supreme Court in Dr. Janet Jeyapaul v. SRM University extends the ambit of Article 226 to all bodies, whether governmental or private, which are performing ‘public function’ or ‘public duty’. Imparting education is taken to be a public function. The judgement opens new dimensions of constitutional law
The Ajay Hasia Case: Society and the Fundamental Rights
Authors: Pathak Akhileshwar
Published: August 2020

Ajay Hasia and few others failed to secure admission to Regional Engineering College, Srinagar. They challenged before the Supreme Court that the admission process was arbitrary and violative of the Fundamental Right of equality in Article 14 of the Constitution. The right, however, is available only against the ‘state’ as defined in Article 12. The definition of ‘state’ includes ‘other authorities.’ The term ‘other authorities’ has been subject to judicial interpretation and come to include instrumentality or agency of the government. The Ajay Hasia Case consolidated the developing law and formulated that not only the bodies created by an Act but also bodies created under a law, like societies under the Societies Registration Act can be ‘other authorities’.
Rajan Overseas: An Entrepreneurial Quest for Growth
Authors: Singla Chitra , Yadav Akshay , Gomkale Advait , Acharya Aditya Shekhar
Published: August 2020

Rajan Overseas was founded by Rajan Makhija in the year 2014. It was into export of handloom products like rugs, throws, etc. Makhija wanted the company to grow from INR 7.6 crores to 100 crores in the next five years. However, the plan hit a roadblock as one of the largest customer of Makhija wanted him to sign an exclusive contract. Makhija was evaluating various growth options in the light of this new hurdle. The case can be taught in courses on entrepreneurship, internationalization and strategy for SMEs to teach topics related to effectuation and challenges of international business.
Accidental Entrepreneurs: Kwench Library Solutions
Authors: Monippally MM
Published: August 2020

Kwench Library Solutions (Kwench), a Mumbai-based start-up that offered library services to corporate clients, looked anxiously for angel funding to establish itself and expand to other parts of the country. The time – the first few months of the 2008–09 global recession – was particularly bad. The angel investors who came forward valued the start-up at one third of what the promoters had confidently expected. Their valuation was unacceptable, but spurning their offer was fraught with additional risks. The promoters, who had given up high-paying corporate jobs and invested heavily in the start-up, had to find a way out.
Ryan's Dilemma
Authors: Vohra Neharika , Agarwalla Smriti , Basoya Snehil
Published: August 2020

The case narrates the experiences of a fresh MBA graduate, Ryan, from a top business school in India. After graduating, he joined his traditional family business with the aim to transform it, accelerate growth and start a new business line. Ryan starts several initiatives over one year but his efforts are met with failure. The case focuses on the decisions he takes and the difficulties he has in making career choices. The case lends itself to discussion on taking charge of a business, change management, training next generation family business leaders and career choices by young management graduates.
Kolkata Port Trust: A Turnaround Story
Authors: Bandyopadhyay Tathagata , Raghuram G. , Sharma Yashoverman , Shukla Niraja
Published: August 2020

Kolkata Port (KoPT) had achieved a turnaround from having made a loss of Rs 7.5 crores (cr) in the year 2000–01 to a net surplus of Rs 465.1 cr in the year 2006–07. A variety of initiatives had been taken during the intervening years with a focus on tariff rationalization, revenues from alternate sources, infrastructure development and productivity improvements. While these had yielded results, there was a fundamental issue of operational complexity and inability to compete due to the locational disadvantage. KoPT was a riverine port with two locations, 232 kms and 115 kms upstream on the Hooghly with draft limitations.

Two significant studies having implications for future strategies of KoPT had recently been submitted in March and November 2007. The top management of the port, including the Chairman who was responsible for driving many of the initiatives, was concerned that it may not be possible to achieve long term sustainable growth continuing with the strategies used so far. A well thought out future roadmap, breaking away from the present thinking, was essential sustained growth.
Container Train Operations: Introducing Competition (A)
Authors: Raghuram G , Gangwar Rachna , Morris Sebastian , Pandey Ajay
Published: August 2020

In May 2005, the Committee on Infrastructure took a decision that the Ministry of Railways, in consultation with Planning Commission, would prepare a policy for permitting private and public sector operators to run container trains through the Indian Railways (IR) network. CONCOR, a listed subsidiary of IR, was the only container train operator at that time. RITES, another subsidiary of IR, was awarded a study to prepare a scheme towards this. RITES submitted its final report in September 2005. The recommendations of the report included entry requirements, classification of routes into various categories based on existing and anticipated traffic volume, regulating entry for each route and minimum traffic commitment by the operators. The representatives of the Planning Commission, Ministry of Railways, Ministry of Commerce and Industry, and Ministry of Shipping were to meet in October 2005 to discuss the RITES recommendations to work towards framing a policy document for running container trains by private and public sector operators on the IR network. This case provides a background for this meeting.
The Yumana Expressway
Authors: Raghuram G , Mehta Pranav
Published: August 2020

It was December 13, 2010. The Government of Uttar Pradesh announced their plan to urbanize the entire area along the Yamuna Expressway (YE) in order to prevent haphazard growth of urban sprawls on the flanks of the YE. The YE was conceived in 1997 as a dream project of Ms Mayawati, the then Chief Minister of Uttar Pradesh, with the idea of reducing the travel time between Delhi (and the larger National Capital Region) and Agra. It was a 165 km long expressway and was proposed to run from Greater Noida to Agra via Mathura. Amidst issues concerning land acquisition, and various protests and litigations, the deadline for completion of the project had extended beyond its original completion date of February 8, 2010 to April 2013. Meanwhile, the project cost had escalated from Rs 2500 crore (cr) in the year 2000 to about Rs 10,000 cr as of December 2010. By then, about 80% work on the expressway had been completed. The project was finally expected to be completed around April 2011. This was, however, subject to the pending court judgements and mitigation of risks as perceived by Jaypee Infratech, the concessionaire of the project.
A hybrid computational method for optimization design of bistable compliant mechanism
Authors: Chau Ngoc Le , Tran Ngoc Thoai , Dao Thanh-Phong
Published: August 2020

Purpose

Compliant mechanism has been receiving a great interest in precision engineering. However, analytical methods involving their behavior analysis is still a challenge because there are unclear kinematic behaviors. Especially, design optimization for compliant mechanisms becomes an important task when the problem is more and more complex. Therefore, the purpose of this study is to design a new hybrid computational method. The hybridized method is an integration of statistics, numerical method, computational intelligence and optimization.

Design/methodology/approach

A tensural bistable compliant mechanism is used to clarify the efficiency of the developed method. A pseudo model of the mechanism is designed and simulations are planned to retrieve the data sets. Main contributions of design variables are analyzed by analysis of variance to initialize several new populations. Next, objective functions are transformed into the desirability, which are inputs of the fuzzy inference system (FIS). The FIS modeling is aimed to initialize a single-combined objective function (SCOF). Subsequently, adaptive neuro-fuzzy inference system is developed to modeling a relation of the main geometrical parameters and the SCOF. Finally, the SCOF is maximized by lightning attachment procedure optimization algorithm to yield a global optimality.

Findings

The results prove that the present method is better than a combination of fuzzy logic and Taguchi. The present method is also superior to other algorithms by conducting non-parameter tests. The proposed computational method is a usefully systematic method that can be applied to compliant mechanisms with complex structures and multiple-constrained optimization problems.

Originality/value

The novelty of this work is to make a new approach by combining statistical techniques, numerical method, computational intelligence and metaheuristic algorithm. The feasibility of the method is capable of solving a multi-objective optimization problem for compliant mechanisms with nonlinear complexity.
Black Lives Matter in sport…?
Authors: Hylton Kevin
Published: August 2020

Purpose

In this invited professional insight paper the author draws parallels between recent debates on racism, Black Lives Matter and related research in sport and cognate domains.

Design/methodology/approach

Drawing on Critical Race Theory (CRT) the paper contends that 1) sport is a contested site, 2) sport is a microcosm of society 3) “race” and everyday racism are central to our understanding of sport. It overlays this critique with a recognition of the dynamic and multi-dimensional nature of racisms.

Findings

While the deaths of Black lives are being mourned it is argued that our attention can also become distracted by narrow manifestations of racism (overt). Such approaches leave key stakeholders efforts focused on the individual to the detriment of challenging systemic policies, practices and dispositions that entrench racism. The color-coded racism of past decades is still with us but in addition to this, our critiques and activism require continued surveillance of cultural, institutional and structural arrangements in the everyday that remain nebulous, complex and difficult to challenge.

Research limitations/implications

This is a viewpoint paper. The author draws on previous original empirical work and current insights to draw parallels between sport, Black Lives Matter and broader social contexts. Due to limitations in the extant literature in regard to the section on cycling and ethnicity, examples are drawn primarily from the US and UK.

Practical implications

This focus on sport and leisure past times demonstrates that the Black experience of “race” and racism transcends social boundaries and cannot be perceived as restricted to narrow social domains.

Social implications

Racisms are embedded in society and therefore its cultural products of which sport is a significant one should not be marginalised in antiracism efforts and activist scholarship.

Originality/value

This paper draws on the author's original published research and current insights. The paper makes a contribution to the development of critical race theorising to the sociology of sport, and broader ethnic and racial studies.