bluuebunny/crossref_metadata_2025 huggingface dataset:
The clinical value of IL-3, IL-4, IL-12p70, IL17A, IFN-γ, MIP-1β, NLR, P-selectin, and TNF-α in differentiating bloodstream infections caused by gram-negative, gram-positive bacteria and fungi in hospitalized patients
Authors: Li Xinjun , Yuan Xiaozhou , Wang Chengbin
Published: October 2019

Early differential diagnosis of bloodstream infections (BSIs) caused by different sources and species of bacteria in hospitalized patients is crucial for the timely targeted interventions including appropriate use of antibiotics. The aim of this study was to identify 9 biomarkers for the early differentiation of gram-negative-bloodstream infection (GN-BSI), gram-positive (GP)-BSI, and fungal-BSI.

A prospective study was conducted for a total of 390 inpatients who underwent blood culture in the Chinese PLA General Hospital from September 2015 to March 2018. Patients with positive culture of a single pathogen were divided into GN-BSI, GP-BSI, and Fungal-BSI groups, and a culture-negative disease control group was also established. The serum levels of macrophage inflammatory protein 1β (MIP-1β), tumor necrosis factor α (TNF-α), interleukin (IL)-3, interferon (IFN)-γ, IL-17A, IL-4, IL-12p70, and P-selectin were detected and the NLR was calculated from routine blood test. Receiver-operating characteristic analysis was used to determine the efficacy of various indicators in the differential diagnosis of BSIs. Prediction and validation experiments on clinical patient samples (263 cases) were also performed.

The level of IL-3 in the GP-BSI group was significantly higher than those in the other 3 groups. The level of IFN-γ in the fungal-BSI group was significantly higher than those in the other 3 groups. NLR, MIP-1β, TNF-α, IL-17A, and IL3 exhibited some efficacy when distinguishing between GN-BSI and GP-BSI and NLR had the largest area under curve (AUC) (0.728), followed by MIP-1β with an AUC of 0.679. IFN-γ and IL-3 exhibited some value in differential diagnosis between GN-BSI and Fungal-BSI. IL-3, MIP-1β, TNF-α, IFN-γ, NLR, IL-17A, and IL-4 exhibited some value in distinguishing fungal-BSI and GP-BSI, with IL-3 had the largest AUC (0.722), followed by MIP-1β with an AUC of 0.703.

NLR and MIP-1β may be valuable in differentiating GN-BSI from GP-BSI in hospitalized patients. IFN-γ and IL-3 may be helpful in differential diagnosis GN-BSI and fungal-BSI. IL-3 and MIP-1β exhibited some diagnostic efficacy in distinguishing fungal-BSI and GP-BSI. Additionally, IL-3 with high serum level may be a marker for GP-BSI and IFN-γ with high serum level may be a valuable marker for the prediction of Fungal-BSI. The utility of these biomarkers to predict BSIs owing to different pathogens in hospitalized patients needs to be assessed in further studies.
Comparative Early Hemodynamic Profiles in Patients Presenting to the Emergency Department with Septic and Nonseptic Acute Circulatory Failure Using Focused Echocardiography
Authors: Lafon Thomas , Appert Alexandra , Hadj Mathilde , Bigrat Vincent , Legarcon Vincent , Claveries Paul , Goudelin Marine , Evrard Bruno , Padilla Ana Catalina Hernandez , Baisse Arthur , Vignon Philippe
Published: October 2019

Study Objective:

We evaluated the early hemodynamic profile of patients presenting with acute circulatory failure to the Emergency Department (ED) using focused echocardiography performed by emergency physicians after a dedicated training program.

Methods:

Patients presenting to the ED with an acute circulatory failure of any origin were successively examined by a recently trained emergency physician and by an expert in critical care echocardiography. Operators independently performed and interpreted online echocardiographic examinations to determine the leading mechanism of acute circulatory failure.

Results:

Focused echocardiography could be performed in 100 of 114 screened patients (55 with sepsis/septic shock and 45 with shock of other origin) after a median fluid loading of 500 mL (interquartile range: 187–1,500 mL). A hypovolemic profile was predominantly observed whether the acute circulatory failure was of septic origin or not (33/55 [60%] vs. 23/45 [51%]: P = 0.37). Although a vasoplegic profile associated with a hyperkinetic left ventricle was most frequently identified in septic patients when compared with their counterparts (17/55 [31%] vs. 5/45 [11%]: P = 0.02), early left or right ventricular failure was observed in 31% of them. Hemodynamic profiles were adequately appraised by recently trained emergency physicians, as reflected by a good-to-excellent agreement with the expert's assessment (Κ: 0.61–0.85).

Conclusions:

Hypovolemia was predominantly identified in patients presenting to the ED with acute circulatory failure. Although vasoplegia was more frequently associated with sepsis, early ventricular dysfunction was also depicted in septic patients. Focused echocardiography seemed reliable when performed by recently trained emergency physicians without previous experience in ultrasound.
Mid-sized groups perform best in a collective decision task in sticklebacks
Authors: Ward Ashley J. W. , Webster Michael M.
Published: October 2019

Numerous studies have reported functional improvements in collective behaviour with increasing group size, however, the possibility that such improvements may saturate or even decline as group size continues to grow have seldom been tested experimentally. Here, we tested the ability of solitary three-spined sticklebacks and those in groups, ranging from 2 to 29 fish, to leave an unfavourable patch of habitat. Our results replicate the findings of previous studies at low group sizes, with the fish initially showing a reduction in their latency to leave the unfavourable habitat as group size increased. As group size continued to increase, however, latency to leave the habitat increased, so that the functional relationship between group size and latency to depart was U-shaped. Our results suggest an optimum group size in this context of between 12 and 20 fish. Underlying this group-level trend was a similar U-shaped relationship between group size and the first fish to leave the habitat, suggesting that at larger group sizes, social conformity to the behaviour of the majority can stifle the ability of fish to innovate—in this case, to induce a collective movement from the unfavourable habitat.
Why do chitons curl into a ball?
Authors: Sigwart Julia D. , Vermeij Geerat J. , Hoyer Peter
Published: October 2019

Many animals with external armour, such as hedgehogs, isopods and trilobites, curl into a protective ball when disturbed. However, in situations where predators would engulf an exposed animal whole, regardless of position, conglobation may provide limited added defence and the benefits were previously unclear. We show that polyplacophoran molluscs (chitons) are three times less likely to spend time curled into a ball in the presence of a predator. When the cue of a potential predator is present, animals instead spend significantly more time in active, high risk, high reward behaviours such as arching, balancing on the head and tail ends of their girdle and pushing the soft foot up into an exposed position. Arching increases vulnerability, but also can increase the likelihood of rapidly encountering new substratum that would allow the animal to right itself. In some other animals, the ability to roll into a ball is associated with rolling away from danger. Curling into a ball would improve mobility, to be rolled on to a safer position, but reattachment is the higher priority for chitons in the face of danger.
Always a price to pay: hibernation at low temperatures comes with a trade-off between energy savings and telomere damage
Authors: Nowack Julia , Tarmann Iris , Hoelzl Franz , Smith Steve , Giroud Sylvain , Ruf Thomas
Published: October 2019

We experimentally tested the costs of deep torpor at low temperatures by comparing telomere dynamics in two species of rodents hibernating at either 3 or 14°C. Our data show that hibernators kept at the warmer temperature had higher arousal frequencies, but maintained longer telomeres than individuals hibernating at the colder temperature. We suggest that the high-energy demand of frequent arousals is counteracted by a lower temperature differential between torpid and euthermic body temperature and that telomere length is restored during arousals when the body temperature is returned to normothermic values. Taken together, our study shows that hibernation at low body temperatures comes with costs on a cellular level and that hibernators need to actively counterbalance the shortening of telomeres.
Investigating Gut Microbiota-Host Interactions in a Microaerobic Environment
Authors: McGrath Conor , Bell Andrew , McGrath Emmanuelle , Juge Nathalie , Schüller Stephanie
Published: October 2019

The gut microbiota has an important role in maintaining intestinal health and protecting against enteric infections (colonisation resistance). Nevertheless the majority of these interactions haven't been explored, largely due to a lack of experimental model systems that can culture oxygen-sensitive commensals alongside intestinal cells. In this project, we have established a novel in vitro model system of the human intestinal epithelium (Vertical Diffusion Chamber, VDC) which also supports growth of strictly anaerobic bacteria. We have applied this system to investigate the interactions of gut symbiont Ruminococcus gnavus with a functioning mucus-producing epithelium, established using T84 and goblet-like LS174T cell lines, and its effect on infection with foodborne pathogen enteropathogenic E. coli (EPEC).

Initial work focused on identifying a culture medium that supports R. gnavus and EPEC growth whilst maintaining epithelial integrity and barrier function. This has been achieved by establishing bacterial growth curves in different media and assessing epithelial barrier function by transepithelial electrical resistance and immunofluorescence staining (IFS) of tight-junction protein occludin. Further IFS demonstrated that introduction of LS174T cells to the epithelium causes mucin secretion and facilitates colonisation by R. gnavus. Co-culture of EPEC with R. gnavus reduces numbers of viable and adherent EPEC, but only when LS174T are present.

These data indicate potential colonisation resistance activity by R. gnavus, discovered by utilising a model system that supports anaerobic culture and a functioning epithelium side-by-side. Future work will investigate colonisation resistance activity for a panel of R. gnavus strains and attempt to elucidate mechanisms behind this activity.
The anaerobic skin colonizer Staphylococcus saccharolyticus, a possible agent of prosthetic joint infections, exhibits excessive genome decay
Authors: Brüggemann Holger , Söderquist Bo
Published: October 2019

Human skin-colonizing bacteria can have double ‘personalities’, which muddles the distinction between commensals and pathogens. Coagulase-negative staphylococci (CoNS) are part of the normal skin microbiota, but some CoNS species can act as opportunistic pathogens.

The anaerobic CoNS species Staphylococcus saccharolyticus has not received much attention, although it is a frequent colonizer of human skin and associated with prosthetic joint infections. Therefore, we determined the frequencies of S. saccharolyticus on human skin and analyzed clinical and skin-derived S. saccharolyticus strains by genome sequencing and biochemical tests.

Analysis of skin samples from volunteers identified S. saccharolyticus on the forehead and in the elbow pit in approx. 20% of the samples. Genome sequencing revealed an unexpected feature of S. saccharolyticus: extensive genome decay, with over 300 pseudogenes, indicating ongoing reductive evolution. Many genes of the core metabolism are not functional, rendering the species auxotrophic for several amino acids, which could explain its slow growth, and the need for fastidious growth conditions.

In an attempt to evaluate the virulence potential of S. saccharolyticus, we determined abundantly secreted proteins: these included stress response proteins such as heat shock- and oxidative stress-related factors, as well as immunodominant staphylococcal surface antigens. The strains secrete lipases and a hyaluronic acid lyase; hyaluronidase as well as urease activities were detected with biochemical assays.

Our study revealed that S. saccharolyticus has adapted its genome, possibly due to a recent change of habitat; moreover, the data imply that the species has tissue-invasive potential and might cause prosthetic joint infections.
Survival strategies of Clostridium difficile to fluctuating concentrations of oxygen
Authors: Martins Maria Carlos , Salgueiro Bruno , Carlos Filipe , Romão Célia , Frazão Carlos , Teixeira Miguel
Published: October 2019

Oxygen and reactive oxygen species (ROS) can react with multiple cellular components, leading to the inactivation of a plethora of metabolic pathways. Therefore, organismshave systems to sense and eliminate O2 and ROS, contributing to their survival in the adverse host environment.

Clostridium difficileP28 is an anaerobic pathogenic bacterium that contains in its genome a flavodiiron protein (FDP) and a rubrerythrin (Rbr),that are putatively involved in the detoxification pathways used by this organism.

Flavodiiron proteins are widespread in all life domains, with a crucial role in O2detoxification, through its reduction directly to water. FDPs are cytoplasmic enzymes with a minimal structural unit composed by two main domains, a metallo-β-lactamase domain, containing the catalytic diiron site, and a flavodoxin domain having a flavin mononucleotide. Rubrerythrins are generally considered to act as NADH-linked hydrogen peroxide reductases, thus eliminating this ROS, and are composed by two iron sites:a diiron center and a rubredoxin-like FeCys4 center.

In this work with characterized biochemically, spectroscopically, structurally and kinetically the FDP and Rbr and their twoputative redox partners, a High Molecular Weight Rubredoxin (HRb) and a Rubredoxin (Rd). We confirmed theexistence of direct electron transfer betweenHRb, Rd and FDP and also between HRb, Rd and Rbr. In addition, we alsoestablished the reaction rates for the reduction, by FDP, of O2(0.43s-1) and H2O2 (0.06s-1) and for the reduction of H2O2by Rbr (1.53s-1). The enzymatic activity of Rbr towards O2 was also investigated.

Romão, C.V., et al, 2016.JBIC., 21:39-52.

Martins, M.C., et al., 2019. FRBM, in press.
The role of metalloenzymes for the survival of the anaerobe Clostridium difficile during infection
Authors: Folgosa Filipe , Alves Catarina , Martins Maria C. , Teixeira Miguel
Published: October 2019

Clostridium difficile is the most prevalent pathogen among all healthcare-associated infections. This anaerobic bacterium can colonize the human gut, typically following agents that disrupt the normal gut microbiota, like antibiotics. In the gut, C. difficile is subjected to oxygen, which it has to eliminate for survival. Its genome encodes for two flavodiiron proteins, capable to reduceoxygen to water. Besides, some FDPs also reduce NO to N2O, an important feature as a resistance mechanism towards the human innate immune system[1,2]. Flavodiiron enzymes are constituted by a minimal core of two domains: a metallo-β-lactamase-like one, harboring the catalytic center, followed by a short-chain flavodoxin[1,2]. More complex FDPs exist, with multiple extra domains and redox centers[1,2]. C. difficile contains a ‘classical’ FDP, and a very complex one, with an extra short-type rubredoxin domain followed by an NADH:rubredoxin oxidoreductase-like one[3]. The biochemical, redox and spectroscopic studies demonstrated that this enzyme receives electrons directly from NADH, reducing its substrates, precluding the need for extra partners. This FDP is selective for O2 (16s-1), almost 10x higher than with NO. The reactivity towards hydrogen peroxide, as an H2O2 reductase with formation of water, with a non-negligible turnover (2s-1) is a novelty in the field of FDPs. Site directed mutants revealed that the rubredoxin-like center is essential for electron transfer from NADH to the catalytic center.

[1] Martins et al, Free Rad. Biol. Med., in press, 2019.

[2] Romão et al, J. Biol.Inorg. Chem., 21,39-52, 2016.

[3] Folgosa et al, Sci.Rep., 8, 10164, 2018.
ICTV Virus Taxonomy Profile: Caliciviridae
Authors: Vinjé Jan , Estes Mary K. , Esteves Pedro , Green Kim Y. , Katayama Kazuhiko , Knowles Nick J. , L’Homme Yvan , Martella Vito , Vennema Harry , White Peter A. ,   ICTV Report Consortium
Published: October 2019

The family Caliciviridae includes viruses with single-stranded, positive-sense RNA genomes of 7.4–8.3 kb. The most clinically important representatives are human noroviruses, which are a leading cause of acute gastroenteritis in humans. Virions are non-enveloped with icosahedral symmetry. Members of seven genera infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus and Vesivirus), members of two genera infect birds (Bavovirus and Nacovirus), and members of two genera infect fish (Minovirus and Salovirus). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caliciviridae, which is available at ictv.global/report/caliciviridae.
Reptile-like physiology in Early Jurassic stem-mammals
Authors: Newham Elis , Gill Pamela G. , Brewer Philippa , Benton Michael J. , Fernandez Vincent , Gostling Neil J. , Haberthür David , Jernvall Jukka , Kankanpää Tuomas , Kallonen Aki , Navarro Charles , Pacureanu Alexandra , Zeller-Plumhoff Berit , Richards Kelly , Robson-Brown Kate , Schneider Philipp , Suhonen Heikki , Tafforeau Paul , Williams Katherine , Corfe Ian J.
Published: October 2019

There is uncertainty regarding the timing and fossil species in which mammalian endothermy arose, with few studies of stem-mammals on key aspects of endothermy such as basal or maximum metabolic rates, or placing them in the context of living vertebrate metabolic ranges. Synchrotron X-ray imaging of incremental tooth cementum shows two Early Jurassic stem-mammals,MorganucodonandKuehneotherium, had lifespans (a basal metabolic rate proxy) considerably longer than comparably sized living mammals, but similar to reptiles.Morganucodonalso had femoral blood flow rates (a maximum metabolic rate proxy) intermediate between living mammals and reptiles. This shows maximum metabolic rates increased evolutionarily before basal rates, and that contrary to previous suggestions of a Triassic origin, Early Jurassic stem-mammals lacked the endothermic metabolism of living mammals.

One Sentence Summary

Surprisingly long lifespans and low femoral blood flow suggest reptile-like physiology in key Early Jurassic stem-mammals.
pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing
Authors: Thutkawkorapin Jessada , Eisfeldt Jesper , Tham Emma , Nilsson Daniel
Published: October 2019

Background

DNA damage accumulates over the course of cancer development. The often-substantial amount of somatic mutations in cancer poses a challenge to traditional methods to characterize tumors based on driver mutations. However, advances in machine learning technology can take advantage of this substantial amount of data.

Results

We developed a command line interface python package, pyCancerSig, to perform sample profiling by integrating single nucleotide variation (SNV), structural variation (SV) and microsatellite instability (MSI) profiles into a unified profile. It also provides a command to decipher underlying cancer processes, employing an unsupervised learning technique, Non-negative Matrix Factorization, and a command to visualize the results. The package accepts common standard file formats (vcf, bam). The program was evaluated using a cohort of breast- and colorectal cancer from The Cancer Genome Atlas project (TCGA). The result showed that by integrating multiple mutations modes, the tool can correctly identify cases with known clear mutational signatures and can strengthen signatures in cases with unclear signal from an SNV-only profile.

Conclusions

pyCancerSig has demonstrated its capability in identifying known and unknown cancer processes, and at the same time, illuminates the association within and between the mutation modes.
High-speed quantitative optical imaging of absolute metabolism in the rat cortex
Authors: Wilson R. H. , Crouzet C. , Torabzadeh M. , Bazrafkan A. , Maki N. , Tromberg B. J. , Akbari Y. , Choi B.
Published: October 2019

Quantitative measures of blood flow and metabolism are essential for improved assessment of brain health and response to ischemic injury. In this report, we demonstrate a multimodal technique for measuring the cerebral metabolic rate of oxygen (CMRO2) in the rodent brain on an absolute scale (μM O2 / min). We use laser speckle imaging (LSI) at 809 nm and spatial frequency domain imaging (SFDI) at 655 nm, 730 nm, and 850 nm to obtain spatiotemporal maps of cerebral blood flow (CBF), tissue absorption (μa), and tissue scattering (μs’). Knowledge of these three values enables calculation of a characteristic blood flow speed, which in turn is input to a mathematical model with a “zero-flow” boundary condition to calculate absolute CMRO2. We apply this method to a rat model of cardiac arrest (CA) and cardiopulmonary resuscitation. With this model, the zero-flow condition occurs during entry into CA. The CMRO2 values calculated with our method are in good agreement with those measured with magnetic resonance (MR) and positron emission tomography (PET) by other groups. Our technique provides a quantitative metric of cerebral metabolism that can potentially be used for comparison between animals and longitudinal monitoring of a single animal over multiple days, to assess differences in baseline metabolism and track recovery of metabolism in survival studies following ischemia and reperfusion.
Functions for Cdc42p BEM Adaptors in Regulating a Differentiation-Type MAP Kinase Pathway
Authors: Basu Sukanya , González Beatriz , Li Boyang , Kimble Garrett , Kozminski Keith G. , Cullen Paul J.
Published: October 2019

Rho GTPases regulate cell polarity and signal transduction pathways to control morphogenetic responses in different settings. In yeast, the Rho GTPase Cdc42p regulates cell polarity, and through the p21-activated kinase Ste20p, Cdc42p also regulates mitogen-activated protein kinase (MAPK) pathways (mating, filamentous growth or fMAPK, and HOG). Although much is known about how Cdc42p regulates cell polarity and the mating pathway, how Cdc42p regulates the fMAPK pathway is not clear. To address this question, Cdc42p-dependent MAPK pathways were compared in the filamentous (∑1278b) strain background. Each MAPK pathway showed a unique activation profile, with the fMAPK pathway exhibiting slow activation kinetics compared to the mating and HOG pathways. A previously characterized version of Cdc42p, Cdc42pE100A, that is specifically defective for fMAPK pathway signaling, was defective for interaction with Bem4p, the pathway-specific adaptor for the fMAPK pathway. Corresponding residues in Bem4p were identified that were required for interaction with Cdc42p and fMAPK pathway signaling. The polarity adaptor Bem1p also regulated the fMAPK pathway. In the fMAPK pathway, Bem1p recruited Ste20p to the plasma membrane, cycled between an open and closed conformation, and interacted with the GEF for Cdc42, Cdc24p. Bem1p also regulated effector pathways in different ways, behaving as a multi-functional adaptor in some pathways and an inert scaffold in others. Genetic suppression tests showed that Bem4p and Bem1p regulate the fMAPK pathway in an ordered sequence. Collectively, the study demonstrates unique and sequential functions for Rho GTPase adaptors in regulating MAPK pathways.

HIGHLIGHTS

Comparing Cdc42p-dependent MAPK pathways showed that the fMAPK pathway had slow activation kinetics compared to the mating and HOG pathways.

A collection ofcdc42alleles was tested for MAPK pathway functions.

§ Cdc42pE100A, previously characterized as being specifically defective for fMAPK signaling, showed reduced interaction with the fMAPK pathway adaptor Bem4p.

§ Corresponding residues in Bem4p were identified that were required for interaction with Cdc42p and fMAPK signaling.

The polarity adaptor Bem1p regulated the fMAPK pathway.

§ Bem1p regulated the fMAPK pathway by recruiting Ste20p to the plasma membrane, cycling between an open and closed conformation, and interacting with the Cdc42p GEF, Cdc24p.

Different domains of Bem1p had different roles in regulating effector pathways.

§ Bem1p may function as a multi-functional adaptor in some pathways and an inert scaffold in others.

Bem4p and Bem1p regulated the fMAPK pathway in an ordered sequence.

§ The data support a model where Bem4p recruits Cdc24p to GDP-Cdc42p, and Bem1p directs GTP-Cdc42p to Ste20p at the plasma membrane.

§ The bud-site GTPase Rsr1p regulates Cdc24p in the fMAPK pathway but does not initiate signaling.
Detection and characterization of copy number variants based on whole-genome sequencing by DNBSEQ platforms
Authors: Rao Junhua , Peng Lihua , Chen Fang , Jiang Hui , Geng Chunyu , Zhao Xia , Liu Xin , Liang Xinming , Mu Feng
Published: October 2019

Background

Next-generation sequence (NGS) has rapidly developed in past years which makes whole-genome sequencing (WGS) becoming a more cost- and time-efficient choice in wide range of biological researches. We usually focus on some variant detection via WGS data, such as detection of single nucleotide polymorphism (SNP), insertion and deletion (Indel) and copy number variant (CNV), which playing an important role in many human diseases. However, the feasibility of CNV detection based on WGS by DNBSEQ™ platforms was unclear. We systematically analysed the genome-wide CNV detection power of DNBSEQ™ platforms and Illumina platforms on NA12878 with five commonly used tools, respectively.

Results

DNBSEQ™ platforms showed stable ability to detect slighter more CNVs on genome-wide (average 1.24-fold than Illumina platforms). Then, CNVs based on DNBSEQ™ platforms and Illumina platforms were evaluated with two public benchmarks of NA12878, respectively. DNBSEQ™ and Illumina platforms showed similar sensitivities and precisions on both two benchmarks. Further, the difference between tools for CNV detection was analyzed, and indicated the selection of tool for CNV detection could affected the CNV performance, such as count, distribution, sensitivity and precision.

Conclusion

The major contribution of this paper is providing a comprehensive guide for CNV detection based on WGS by DNBSEQ™ platforms for the first time.
Deep residual neural networks resolve quartet molecular phylogenies
Authors: Zou Zhengting , Zhang Hongjiu , Guan Yuanfang , Zhang Jianzhi
Published: October 2019

Phylogenetic inference is of fundamental importance to evolutionary as well as other fields of biology, and molecular sequences have emerged as the primary data for this task. Although many phylogenetic methods have been developed to explicitly take into account substitution models of sequence evolution, such methods could fail due to model misspecification and insufficiency, especially in the face of heterogeneities in substitution processes across sites and among lineages. In this study, we propose to infer topologies of four-taxon trees using deep residual neural networks, a machine learning approach needing no explicit modeling of the subject system and having a record of success in solving complex non-linear inference problems. We train residual networks on simulated protein sequence data with extensive amino acid substitution heterogeneities. We show that the well-trained residual network predictors can outperform existing state-of-the-art inference methods such as the maximum likelihood method on diverse simulated test data, especially under extensive substitution heterogeneities. Reassuringly, residual network predictors generally agree with existing methods in the trees inferred from real phylogenetic data with known or widely believed topologies. We conclude that deep learning represents a powerful new approach to phylogenetic reconstruction, especially when sequences evolve via heterogeneous substitution processes. We present our best trained predictor in a freely available program namedPhylogenetics byDeepLearning (PhyDL,https://gitlab.com/ztzou/phydl).
PINOT: An Intuitive Resource for Integrating Protein-Protein Interactions
Authors: Tomkins JE , Ferrari R , Vavouraki N , Hardy J , Lovering RC , Lewis PA , McGuffin LJ , Manzoni C
Published: October 2019

The past decade has seen the rise of omics data, for the understanding of biological systems in health and disease. This wealth of data includes protein-protein interaction (PPI) derived from both low and high-throughput assays, which is curated into multiple databases that capture the extent of available information from the peer-reviewed literature. Although these curation efforts are extremely useful, reliably downloading and integrating PPI data from the variety of available repositories is challenging and time consuming.

We here present a novel user-friendly web-resource called PINOT (Protein Interaction Network Online Tool; available at http://www.reading.ac.uk/bioinf/PINOT/PINOT_form.html) to optimise the collection and processing of PPI data from the IMEx consortium associated repositories (members and observers) and from WormBase for constructing, respectively, human and C. elegans PPI networks.

Users submit a query containing a list of proteins of interest for which PINOT will mine PPIs. PPI data is downloaded, merged, quality checked, and confidence scored based on the number of distinct methods and publications in which each interaction has been reported. Examples of PINOT applications are provided to highlight the performance, the ease of use and the potential applications of this tool.

PINOT is a tool that allows users to survey the literature, extracting PPI data for a list of proteins of interest. The comparison with analogous tools showed that PINOT was able to extract similar numbers of PPIs while incorporating a set of innovative features. PINOT processes both small and large queries, it downloads PPIs live through PSICQUIC and it applies quality control filters on the downloaded PPI annotations (i.e. removing the need of manual inspection by the user). PINOT provides the user with information on detection methods and publication history for each of the downloaded interaction data entry and provides results in a table format that can be easily further customised and/or directly uploaded in a network visualization software.
The impact of online reputation on hotel profitability
Authors: Anagnostopoulou Seraina C. , Buhalis Dimitrios , Kountouri Ioanna L. , Manousakis Eleftherios G. , Tsekrekos Andrianos E.
Published: October 2019

Purpose

The purpose of this study is to quantify the impact of online customer reputation on financial profitability.

Design/methodology/approach

Online reputation is captured by extracting the most recurring textual themes associated with customer satisfaction and dissatisfaction, expressed within positive vs negative online guest reviews on Booking.com. Latent semantic analysis is used for textual analysis. Proxies of overall financial performance are manually constructed for the sample hotels, using financial data from the Financial Analysis Made Easy (FAME) database. Ordinary least squares is used to gauge the effect of online customer reputation on financial profitability.

Findings

Empirical findings indicate that recurring textual themes from positive online reviews (in contrast to negative reviews) exhibit a higher degree of homogeneity and consensus. The themes repeated in positive, but not in negative reviews, are found to significantly associate with hotel financial performance. Results contribute to the discussion about the measurable effect of online reputation on financial performance.

Originality/value

Contemporary quantitative methods are used to extract online reputation for a sample of UK hotels and associate this reputation with bottom-line financial profitability. The relationship between online reputation, as manifested within hotel guest reviews, and the financial performance of hotels is examined. Financial profitability is the result of revenues, reduced by the costs incurred in order to be able to offer a given level of service. Previous studies have mainly focused on basic measures of performance, i.e. revenue generation, rather than bottom-line profitability. By combining online guest reviews from travel websites (Booking.com) with financial measures of enterprise performance (FAME), this study makes a meaningful contribution to the strategic management of hotel businesses.
Predicting intentions to visit microbreweries and investigating beerscape
Authors: Carr Allison , Shin Yeon Ho , Severt Kimberly
Published: October 2019

Purpose

This study aims to examine the predictors of microbrewery consumers’ intentions to visit microbreweries using an extended theory of planned behavior (TPB) and to assess the gaps between attribute importance and performance by performing importance-performance analysis (IPA) on the beerscape measure.

Design/methodology/approach

A self-administered questionnaire was administered to visitors of microbreweries within a southern US state. A total of 200 responses were selected based on completion and were analyzed using structural equation modeling and an IPA analysis.

Findings

Self-identity, attitude and perceived behavioral controls were found to be significant predictors of microbrewery consumers’ intentions. The subjective norm was insignificant following the addition of self-identity. Furthermore, the beerscape was not a significant predictor of microbrewery consumers’ attitudes. The IPA found that microbreweries should improve beer value, beer cost, variety of beers and the embodiment of local culture in the atmosphere.

Originality/value

To the researcher’s knowledge, this is the first quantitative study to successfully apply the TPB framework and develop the beerscape in the microbrewery context. The results of this study provide useful information to microbrewery owners and operators, which ultimately helps them serve their consumers more effectively.
Creating a development force in Swedish healthcare
Authors: Kahm Therese , Ingelsson Pernilla
Published: October 2019

Purpose

The purpose of this paper is to present the results from a study that investigates first-line healthcare managers’ views on their role and the conditions that influence their ability to drive improvement work based on Lean.

Design/methodology/approach

A questionnaire was sent to all first-line managers in a healthcare organization to investigate their views on their role, conditions and ability to create change according to Lean. The results from four of the questions are presented, which focus on how crucial they consider their role to be for managing improvement work based on Lean, what work tasks their time is spent on, what factors they consider to be important to their ability to drive change and what factors best describe what Lean provides.

Findings

The results show that first-line managers claim that their role is crucial in improvement work, but when they defined their work tasks, the time spent on improvements was not frequently described. Time, support from coworkers, and a clear vision and clear goals were the three factors that they considered to be most important to their ability to drive improvement work. Considering their leadership, Lean contributed to the structure with tools and supportive methods.

Originality/value

The questions can be used separately or as part of the entire questionnaire before and along a Lean process to obtain a better understanding of how to create a sustainable Lean approach in healthcare. Understanding the factors that first-line managers consider supporting their ability in improvement work and what they consider Lean provides is important in creating a development force in Swedish healthcare.
Effectiveness of frequent inventory audits in retail stores: an empirical evaluation
Authors: Ishfaq Rafay , Raja Uzma
Published: October 2019

Purpose

The purpose of this paper is to focus on the effectiveness of the inventory audit process to manage operational issues related to inventory errors in retail stores. An evaluation framework is proposed based on developing an error profile of store inventory using product attributes and inventory information.

Design/methodology/approach

A store inventory error profile is developed using data on price, sales, popularity, replenishment cycle, inventory levels and inventory errors. A simulation model of store inventory management system grounded in empirical data is used to evaluate the effectiveness of the inventory audit process in a high SKU-variety retail store. The framework is tested using a large transaction data set comprised of over 200,000 records for 7,400 SKUs.

Findings

The results show that store inventory exhibits different inventory error profile groups that would determine the effectiveness of store inventory audits. The results also identify an interaction effect between store inventory policies and replenishment process that moderates the effectiveness of inventory audits.

Research limitations/implications

The analysis is based on data collected from a single focal firm and does not cover all the different segments of the retail industry. However, the evaluation framework presented in the paper is fully generalizable to different retail settings offering opportunity for additional studies.

Practical implications

The findings about the role of different error profile groups and the interaction effect of store audits with inventory and store replenishments would help retailers incorporate a more effective inventory audit process in their stores.

Originality/value

This paper presents a novel approach that uses store inventory profiles to evaluate the effectiveness of inventory audits. Unlike previous papers, it is the first empirical study in this area that is based on inventory error data gathered from multiple audits that identify the interaction effect of inventory policy and replenishments on the inventory audit process.
Dynamic positioning matters: uncovering its fundamental role in organization’s innovation performance
Authors: Wang Jingbei , Yang Naiding , Guo Min
Published: October 2019

Purpose

This paper aims to propose the following questions: How does dynamic positioning influence organization’s innovation performance? Does knowledge base mediate the relationship between them?

Design/methodology/approach

The empirical setting of this study is the smartphone collaboration network from 2004 to 2017; the authors selected one-site schemes and data of patents from the Derwent Innovation Database. Furthermore, the authors adopted the negative binomial model with random effects to test the hypotheses.

Findings

The regression results show that organization’s dynamic positioning has an inverted-U-shaped relationship with its exploratory innovation. Similarly, organization’s dynamic positioning has an inverted-U-shaped relationship with its exploitative innovation. Besides, knowledge base mediates the relationship between dynamic positioning and organization’s innovation performance.

Originality/value

This study empirically confirms the relationship between dynamic positioning and organization’s innovation performance by separately examining exploratory and exploitative innovation. Furthermore, this study provides a contribution to the literature linking dynamic positioning and organization’s innovation performance by investigating the mediating role of knowledge base.
Servitization and business performance: the moderating effects of environmental uncertainty
Authors: Zhang Ying , Wang Longwei , Gao Jie , Li Xin
Published: October 2019

Purpose

To obtain in-depth explanations of the effects of servitization, this paper aims to analyse the benefits and costs at different servitization levels. The authors also investigate the moderating roles of demand uncertainty and technological turbulence on such effects.

Design/methodology/approach

The authors use the resource-based view (RBV) and transaction cost economics (TCE) to analyse the varying benefits and costs associated with servitization at its different levels and proposes the hypotheses. Then they use the survey data of 239 Chinese manufacturing firms to empirically test these hypotheses.

Findings

The interplay among service benefits, adjustment costs and coordination costs results in a nonlinear relationship between servitization and business performance. A negative servitization–performance relationship is observed at low levels of servitization as adjustment costs would be dominant. At moderate servitization levels, a positive relationship is observed because service benefits increase substantially and outweigh the increase in adjustment and coordination costs. As servitization levels further increase, coordination costs become dominant and a negative servitization–performance relationship reappears. The study further shows the significant moderating role of demand uncertainty and the insignificant moderating role of technological turbulence.

Research limitations/implications

This study provides a nuanced understanding of the curvilinear effects of servitization on business performance in response to the calls for detailed insights from quantitative studies.

Practical implications

The findings provide guidance on the degree to which the manufacturing firm should extend its service businesses based on demand and technological environments.

Originality/value

This is one of the pioneering empirical studies applying RBV and TCE to examine the varying benefits and costs across different servitization levels. The findings provide insight into the ongoing discussion about “service paradox” and “deservitization”.
Distrust issues in business-to-business e-procurement decisions
Authors: Truong Dothang
Published: October 2019

Purpose

Despite the important role of distrust in predicting the intention to use, existing literature has not studied the impact of distrust on the buyer’s integration with suppliers and their e-procurement usage in the B2B context, creating major gaps in the e-procurement theory. The purpose of this paper is to fill the gaps in the literature by examining the role and impact of distrust in the e-procurement context.

Design/methodology/approach

Data were collected through a web-based survey of purchasing professionals in the USA. ANOVA was used to compare the level of distrust among companies. In addition, the measurement model and hypotheses were tested using the structural equation modeling method.

Findings

Empirical findings indicate if buyers have uncertainty or negative expectation on the reliability and capability of the supplier in e-procurement systems, they would tend to hesitate to use e-procurement for purchasing. Furthermore, distrust also inhibits buyers from strengthening the supplier integration through sharing operational and logistics information and collaborating in new product development and purchasing process.

Research limitations/implications

This paper discovers the vital role of distrust in the e-procurement context. Distrust has a significant impact on a company’s cooperation and commitment with business partners. Additionally, to improve the supplier integration, it is important not only to use e-procurement applications but also to have a mechanism to lower the buyers’ distrust level in e-procurement systems.

Practical implications

Realizing the important role of distrust, e-procurement vendors could improve the supplier selection process by allowing buyers to review the supplier’s reliability and capability, and to interact with the supplier before making any online purchase. Vendors could also build a better supplier verification system and collaborative mechanism to reduce buyers’ distrust issues.

Originality/value

Despite the important role of distrust in predicting the intention to use, existing literature has not studied the impact of distrust on the buyer’s integration with suppliers and their e-procurement usage in the B2B context, creating major gaps in the e-procurement theory. This paper fills the gaps in the literature by examining the role and impact of distrust in the e-procurement context.
Public sector entrepreneurship in South Africa
Authors: Urban Boris , Nkhumishe Mmapoulo Lindah
Published: October 2019

Purpose

Many unanswered questions remain regarding the authors’ understanding of how entrepreneurship can be fostered in the public sector. To fill this knowledge gap, the purpose of this paper is to conduct an empirical investigation to determine the relationship between different organisational factors and entrepreneurial orientation (EO) in the South African public sector.

Design/methodology/approach

Primary data are sourced from middle-level managers at municipalities in the three largest provinces across South Africa. Hypotheses are statistically tested using regression analyses.

Findings

Results reveal that the organisational antecedents of structure and culture explain a significant amount of variation in the EO dimensions of innovativeness, risk taking and proactiveness. Additionally, the findings on organisational rewards converge with an emerging stream of research which highlights that while rewards works well to motivate individuals in the private sector, they are negatively correlated with entrepreneurship in the public sector.

Research limitations/implications

The study implications relate to the efficiency and effectiveness of service delivery of municipalities in South Africa. Due to increases in community protest actions, it is necessary not only to maximise efficiency in the provision of services, but also to innovate and be proactive in order to achieve more with less resources.

Originality/value

By investigating previously unrelated factors in the public sector, the authors create closer conceptual and empirical links between the role of organisational factors and each of the EO dimensions. Furthermore, the study takes place in a relatively under-researched entrepreneurship and public sector context.
CEO compensation, portfolio holdings and strategic investments
Authors: Lord Richard A. , Saito Yoshie , Nicholson Joseph R. , Dugan Michael T.
Published: October 2019

Purpose

The purpose of this paper is to examine the relationship of CEO compensation plans and the risk of managerial equity portfolios with the extent of strategic investments in advertising, capital expenditures and research and development (R&D). The elements of compensation are salary, bonuses, options and restricted stock grants. The authors proxy the design of CEO equity portfolios by the price performance sensitivity of the holdings and the portfolio deltas.

Design/methodology/approach

The authors use the components of executive compensation and portfolio risk as the dependent variables, regressing these against measures for the level of strategic investment. The authors test for non-linear relationships between the components of CEO compensation and strategic investments. The sample is a broad cross-section from 1992 to 2016.

Findings

The authors find strong support for non-linear relationships of capital expenditures and R&D with CEO bonuses, option grants and restricted stock grants. There are very complex relationships between the components of executive compensation and R&D expenditures, but little evidence of a relationship with advertising expenditures. The authors also find strong complex relationships in the design of CEO equity portfolios with advertising and R&D.

Originality/value

Little earlier research has considered advertising, capital expenditures and R&D in a unified framework. Also, testing for non-linear associations provides much greater insight into the relationship between the components of executive compensation and strategic investment. The findings represent a valuable incremental contribution to the executive compensation literature. The results also have normative policy implications for compensation committees’ design of optimal annual CEO compensation packages to incentivize or discourage particular strategic investment behavior.