bluuebunny/crossref_metadata_2025 huggingface dataset:
Synergies analysis produces consistent results between motion analysis laboratories
Authors: MacWilliams Bruce A. , McMulkin Mark L. , Rozumalski Adam , Schwartz Michael H.
Published: October 2020

Aim

The dynamic motor control index during walking (walk-DMC) has been shown to be related to patient outcomes and there has been an increasing interest from motion analysis centers regarding using this metric in their own practice. However, the methods for computing the index reported in the literature are not consistent. Here we propose a standardized method and investigate if this leads to results that are consistent between laboratories.

Method

Comparisons of typically developing controls are made between three independent motion analysis centers. Comparisons are also made between the proposed and previously published methods. A program script to compute thewalk-DMCwas used for this study and is made freely available with this manuscript.

Results

Using this script, results are highly consistent between three participating centers. The currently proposed method results in a wider distribution ofwalk-DMCvalues than those previously reported.

Interpretation

Using consistent processing methods, synergy measures are equivalent between centers. The major differences between current and published data are attributed to the use of concatenation of several walking trials.
Multifractality distinguishes reactive from proactive cascades in postural control
Authors: Kelty-Stephen Damian G. , Furmanek Mariusz P. , Mangalam Madhur
Published: October 2020

Intermittency is a flexible control process entailing context-sensitive engagement with task constraints. The present work aims to situate the intermittency of dexterous behavior explicitly in multifractal modeling for non-Gaussian cascade processes. Multiscale probability density function (PDF) analysis of the center of pressure (CoP) fluctuations during quiet upright standing yields non-Gaussianity parameters lambda exhibiting task-sensitive curvilinear relationships with timescale. The present reanalysis aims for a finer-grained accounting of how non-Gaussian cascade processes might align with known, separable postural processes. It uses parallel decomposition of non-Gaussianity lambda-vs.-timescale and CoP. Orthogonal polynomials decompose lambda curvilinearity, and rambling-trembling analysis decomposes CoP into relatively more intentional rambling (displacement to new equilibrium points) and less intentional trembling sway (deviations around new equilibrium points). Modeling orthogonal polynomials of non-Gaussianity’s lambda-vs.-timescale relationship allows us to differentiate linear from quadratic decay, each of which indicates scale-invariant and scale-dependent cascades, respectively. We tested whether scale-dependent and scale-invariant cascades serve different roles, that is, responding to destabilizing task demands and supporting the proactive movement to a new equilibrium point, respectively. We also tested whether these cascades appear more clearly in rambling rather than trembling sway. More generally, we test whether multifractal nonlinear correlations supports this capacity of postural control to this two-step differentiation: both into rambling vs. trembling, then into scale-dependent vs. scale-invariant cascades within rambling sway. The results supported these hypotheses. Thus, the present work aligns specific aspects of task setting with aspects of cascade dynamics and confirms multifractal foundations of the organism-task relationship.
Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections
Authors: Khan Jamshed , Patro Rob
Published: October 2020

Motivation

The construction of the compacted de Bruijn graph from collections of reference genomes is a task of increasing interest in genomic analyses. These graphs are increasingly used as sequence indices for short and long read alignment. Also, as we sequence and assemble a greater diversity of genomes, the colored compacted de Bruijn graph is being used as the basis for efficient methods to perform comparative genomic analyses on these genomes. Therefore, designing time and memory efficient algorithms for the construction of this graph from reference sequences is an important problem.

Results

We introduce a new algorithm, implemented in the toolCuttlefish, to construct the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel approach of modeling de Bruijn graph vertices as finite-state automata; it constrains these automata’s state-space to enable tracking their transitioning states with very low memory usage. Cuttlefish is fast and highly parallelizable. Experimental results demonstrate that it scales much better than existing approaches, especially as the number and the scale of the input references grow. On our test hardware, Cuttlefish constructed the graph for 100 human genomes in under 9 hours, using ~29 GB of memory while no other tested tool completed this task. On 11 diverse conifer genomes, the compacted graph was constructed by Cuttlefish in under 9 hours, using ~84 GB of memory, while the only other tested tool that completed this construction on our hardware took over 16 hours and ~289 GB of memory.

Availability

Cuttlefish is written inC++14, and is available under an open source license athttps://github.com/COMBINE-lab/cuttlefish.

Contact

rob@cs.umd.edu

Supplementary information

Supplementary text are available atBioinformaticsonline.
The Effect of post Chlamydia Trachomatis Infection treatment on Reactive Oxygen Species and Sperm Parameters of Infertile Men
Authors: Azmakan Reza , Yazdi Reza Salman , Farahi Faramarz , Esmaeili Vahid , Bidoki Seyed Kazem , Jafari Saied
Published: October 2020

Background

Chlamydia trachomatis (CT) infection is often mentioned as a silent disease. Reactive oxygen species (ROS) can also cause Sperm apoptosis and have negative impact on Sperm parameters. The objectives of this study were to elucidate the association between Sperm parameters and ROS caused by CT infections resulting in male Infertility as well as evaluating the role of antibiotic therapy.

Materials and methods

A total of 848 infertile males having normal and abnormal Sperm parameters were included. After Semen sampling, the CT IgA were measured by Elisa and confirmed by Nested PCR. ROS was determined by Chemiluminescence. After treatment under the direct supervision of the private urologists. Then, the second Semen samples were taken and subjected to tests on Sperm parameters and ROS levels as assessed again.

Results

The levels of ROS and morphology were improved following the treatments (P<0.05). Antibiotic therapy due to CT infection, could reduce ROS, improve normal morphology and recover some of Semen parameters.

Conclusions

Our findings indicate that CT infection and Sperm parameters were associated with the rate of ROS in infertile men. However, after treatment, ROS value dropped allowing the recovery of certain Sperm parameters. Antibiotic therapy can improve some Semen quality parameters and treat the male Infertility.

Reza Azmakan,rezaazmakan@yahoo.com, Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,https://orcid.org/0000-0001-6718-3348.
Clinical correlations of SARS-CoV-2 antibody responses in patients with COVID-19 infection
Authors: DeSimone Mia , Simmons Daimon P , Tolan Nicole , Melanson Stacy , Petrides Athena , Tanasijevic Milenko , Schur Peter
Published: October 2020

Coronavirus disease 19 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the clinical correlations of antibodies produced by infected individuals will be critical for incorporating antibody results into clinical management. This study was an observational cohort study to evaluate antibody responses in individuals with PCR-confirmed COVID-19, including 48 hospitalized patients diagnosed with COVID-19 by real-time polymerase chain reaction (RT-PCR) at a large tertiary care medical center. Serum samples were obtained from patients at various time points during the disease course and tested for IgM and IgG antibodies against SARS-CoV-2. Medical records were reviewed, and antibody levels were compared with clinical and laboratory findings. Patients did not have high levels of antibodies within one week of symptoms, but most had detectable IgM and IgG antibodies between 8 and 29 days after onset of symptoms. Some individuals did not develop measurable levels of IgM or IgG antibodies. IgM antibodies were associated with elevated ALT, but there were no other significant associations. We did not observe significant associations of SARS-CoV-2 antibodies with clinical outcomes, including intubation and death. SARS-CoV-2 IgM and IgG antibodies were unlikely to be detected in the first week of infection or in severely immunocompromised individuals. Although we did not observe associations with clinical outcomes, IgM antibodies were associated with higher ALT levels. Antibody production reflects the virus-specific immune response, which is important for immunity but also drives pathology, and antibody levels may be important for guiding treatment of individuals with COVID-19.
COVID-19 among patients with hepatitis B or hepatitis C: A systematic review
Authors: Mirzaie Hossein , Vahidi Mohammad , Shokoohi Mostafa , Darvishian Maryam , Sharifi Hamid , Sharafi Heidar , Karamouzian Mohammad
Published: October 2020

Background & aims

Hepatic manifestations of coronavirus disease 2019 (COVID-19) are common among people infected with hepatitis B virus (HBV) and hepatitis C virus (HCV). This systematic review aimed to summarize the evidence on COVID-19 patients with HBV or HCV co-infections.

Methods

We searched multiple electronic databases and preprint servers from December 1, 2019 to August 9, 2020. Studies were included if they reported quantitative empirical data on COVID-19 patients with HBV or HCV co-infections. Descriptive analyses were reported and data were narratively synthesized. Quality assessments was completed using the Joanna Briggs Institute critical appraisal tools.

Results

Out of the 941 identified records, 28 studies were included. Of the eligible studies, 235 patients with COVID-19 were infected with HBV and 22 patients with HCV. Most patients were male and mean age was 49.8 and 62.8 in patients with HBV and HCV, respectively. Death proportion was 6% among COVID-19-HBV and 13% among COVID-19-HCV co-infected patients. Among COVID-19 patients, 34.1% and 76.2% reported at least one comorbidity besides HBV and HCV infections, mainly hypertension and diabetes mellites type 2. The most common COVID-19-related symptoms in both HBV and HCV groups were fever, cough and dyspnea. ICU admission was reported in 14.1% and 21.4% of individuals with HBV and HCV, respectively.

Conclusions

Our findings suggest a considerable risk of morbidity and mortality among COVID-19 patients with HBV and HCV. Careful assessment of hepatic manifestations upon admission of patients could help improve health outcomes among COVID-19 patients with HBV or HCV co-infections.

Key Points

Hepatic manifestations of COVID-19 are common among people infected with HBV and HCV.

Among COVID-19 patients, 34.1% and 76.2% reported at least one comorbidity besides HBV and HCV infections.

The most common COVID-19-related symptoms in both HBV and HCV groups were fever, cough and dyspnea.

There is a considerable risk of mortality among COVID-19 patients with HBV and HCV.
Object-Attribute Biclustering for Elimination of Missing Genotypes in Ischemic Stroke Genome-Wide Data
Authors: Ignatov Dmitry I. , Khvorykh Gennady V. , Khrunin Andrey V. , Nikolić Stefan , Shaban Makhmud , Petrova Elizaveta A. , Koltsova Evgeniya A. , Takelait Fouzi , Egurnov Dmitrii
Published: October 2020

Missing genotypes can affect the efficacy of machine learning approaches to identify the risk genetic variants of common diseases and traits. The problem occurs when genotypic data are collected from different experiments with different DNA microarrays, each being characterised by its pattern of uncalled (missing) genotypes. This can prevent the machine learning classifier from assigning the classes correctly. To tackle this issue, we used well-developed notions of object-attribute biclusters and formal concepts that correspond to dense subrelations in the binary relationpatients×SNPs. The paper contains experimental results on applying a biclustering algorithm to a large real-world dataset collected for studying the genetic bases of ischemic stroke. The algorithm could identify large dense biclusters in the genotypic matrix for further processing, which in return significantly improved the quality of machine learning classifiers. The proposed algorithm was also able to generate biclusters for the whole dataset without size constraints in comparison to the In-Close4 algorithm for generation of formal concepts.
Fragile X Premutation rCGG Repeats Impairs Synaptic Growth and Synaptic Transmission atDrosophilalarval Neuromuscular Junction
Authors: Bhat Sajad Ahmad , Yousuf Adil , Mushtaq Zeeshan , Kumar Vimlesh , Qurashi Abrar
Published: October 2020

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a progressive neurodegenerative disease manifesting in the premutation (PM) carriers of theFMR1gene with alleles bearing 55-200 CGG repeats. The discovery of a broad spectrum of clinical and cell developmental abnormalities among PM carriers with or without FXTAS, and in model systems suggests that neurodegeneration seen in FXTAS could be the inevitable end-result of pathophysiological processes set during early development. Hence, it is imperative to trace early pathological abnormalities. Our previous studies have shown that transgenicDrosophilacarrying human-derived fragile X premutation-length CGG repeats are sufficient to cause neurodegeneration. Here, we used the same transgenicDrosophilamodel to understand the effects of fragile X premutation-length CGG repeats on the structure and function of the developing nervous system. We show that presynaptic expression of the premutation length CGG repeats restricts synaptic growth, reduces the number of synaptic boutons, leads to aberrant presynaptic varicosities, and impairs synaptic transmission at the larval neuromuscular junctions (NMJs). The postsynaptic analysis shows both glutamate receptor and subsynaptic reticulum proteins are normal. However, a high percentage of boutons show the reduced density of Bruchpilot protein, a key component of presynaptic active zones required for vesicle release. The electrophysiological analysis shows a significant reduction in the quantal content, a measure of total synaptic vesicles released per excitation potential. Together these findings endorse that synapse perturbation caused by rCGG repeats mediate presynaptically during larval NMJ development.
Benchmarking small variant detection with ONT reveals high performance in challenging regions
Authors: Møller Peter L. , Holley Guillaume , Beyter Doruk , Nyegaard Mette , Halldórsson Bjarni V.
Published: October 2020

Background

The development of long read sequencing (LRS) has led to greater access to the human genome. LRS produces long read lengths at the cost of high error rates and has shown to be more useful in calling structural variants than short read sequencing (SRS) data. In this paper we evaluate how to use LRS data from Oxford Nanopore Technologies (ONT) to call small variants in regions in- and outside the reach of SRS.

Results

Calling single nucleotide polymorphisms (SNPs) with ONT data has comparable accuracy to Illumina when evaluating against the Genome in a Bottle truth set v4.2. In the major histocompatibility complex (MHC) and regions where mapping short reads is difficult, the F-measure of ONT calls exceeds those of short reads by 2-4% when sequence coverage is 20X or greater.

We develop recommendations for how to perform small variant calling with LRS data and improve current approaches to the difficult regions by re-genotyping variants to increase the F-measure from 97.24% to 98.78%. Furthermore, we show how LRS can call variants in genomic regions inaccessible to SRS, including medically relevant genes such asSTRCandCFC1B.

Conclusions

Although small variant calling in LRS data is still immature, current methods are clearly useful in difficult and inaccessible regions of the genome, enabling variant calling in medically relevant genes not accessible to SRS.
Tolerogenic Dendritic Cells Shape a Transmissible Gut Microbiota that Protects from Metabolic Diseases
Authors: Lécuyer Emelyne , Roy Tiphaine Le , Gestin Aurélie , Lacombe Amélie , Philippe Catherine , Ponnaiah Maharajah , Huré Jean-Baptiste , Fradet Magali , Ichou Farid , Boudebbouze Samira , Huby Thierry , Gautier Emmanuel , Rhimi Moez , Maguin Emmanuelle , Kapel Nathalie , Gérard Philippe , Venteclef Nicolas , Garlatti Michèle , Chassaing Benoit , Lesnik Philippe
Published: October 2020

Excess of chronic contact between microbial motifs and intestinal immune cells are known to trigger a low-grade inflammation involved in many pathologies such as obesity and diabetes.

The important skewing of intestinal adaptive immunity in the context of diet-induced obesity (DIO) is well described but how dendritic cells (DCs) participate to these changes is still poorly documented. To address this question, transgenic mice with enhanced DCs lifespan and immunogenicity (DChBcl-2mice), are challenged with a high fat diet.

Those mice display resistance to DIO and metabolic alterations. The DIO resistant phenotype is associated with healthier parameters of intestinal barrier function and lower intestinal inflammation. DChBcl-2DIO-resistant mice demonstrate a particular increase in tolerogenic DC numbers and function which is associated with strong intestinal IgA, Th17 and T regulatory immune responses.

Microbiota composition and function analyses reveal that the DChBcl-2mice microbiota is characterized by a lower immunogenicity and an enhanced butyrate production. Cohousing experiments and fecal microbial transplantations are sufficient to transfer the DIO resistance status to WT mice demonstrating that maintenance of DCs tolerogenic ability sustains a microbiota able to drive DIO resistance. DCs tolerogenic function is revealed as a new potent target in metabolic diseases management.
Dynamics of central remyelination and treatment evolution in a model of Multiple Sclerosis with Optic Coherence Tomography
Authors: Benítez-Fernández Rocío , Melero-Jerez Carolina , Gil Carmen , de la Rosa Enrique , Martínez Ana , de Castro Fernando
Published: October 2020

The need for remyelinating drugs is essential for healing important diseases such as multiple sclerosis (MS). One of the reasons for the lack of this class of therapies is the impossibility to follow remyelinationin vivo, which is of utmost importance to perform good clinical trials. Here, we show how the optical coherence tomography (OCT), a cheap and non-invasive technique commonly used in ophthalmology, may be used to follow remyelinationin vivoin MS patients. Our pioneer study validates the study of myelin/remyelination in the optic nerve using OCT and reflects what is occurring in non accessible CNS structures, like the spinal cord. For this study we used the oral bioavailable small molecule VP3.15, confirming its therapeutical potential as neuroprotective, antinflammatory and remyelinating drug for MS. Altogether, our present results confirm the usefulness of OCT to monitor the effectivity of remyelinating therapiesin vivoand underscore the relevance of VP3.15 as potential disease modifying drug for MS therapy.
Biogenesis of NDUFS3-less complex I indicates TMEM126A/OPA7 as an assembly factor of the ND4-module
Authors: D’Angelo Luigi , Astro Elisa , De Luise Monica , Kurelac Ivana , Umesh-Ganesh Nikkitha , Ding Shujing , Fearnley Ian M. , Zeviani Massimo , Gasparre Giuseppe , Porcelli Anna Maria , Fernandez-Vizarra Erika , Iommarini Luisa
Published: October 2020

Complex I (CI) is the largest enzyme of the mitochondrial respiratory chain and its defects are the main cause of mitochondrial disease. To understand the mechanisms regulating the extremely intricate biogenesis of this fundamental bioenergetic machine, we analyzed the structural and functional consequences of the ablation of NDUFS3, a non-catalytic core subunit. We prove that in diverse mammalian cell types a small amount of functional CI can still be detected in the complete absence of NDUFS3. In addition, we have determined the dynamics of CI disassembly when the amount of NDUFS3 is gradually decreased. The process of degradation of the complex occurs in a hierarchical and modular fashion where the ND4-module remains stable and bound to TMEM126A. We have thus, uncovered the function of TMEM126A, the product of a disease gene causing recessive optic atrophy, as a factor necessary for the correct assembly and function of CI.
Graph–based integration of histone modifications profiles: haematopoietic cell differentiation as a case study
Authors: Baccini Federica , Bianchini Monica , Geraci Filippo
Published: October 2020

In this paper, we show that quantifying histone modifications by counting the number of high– resolution peaks in each gene allows to build profiles of these epigenetic marks, associating them to a phenotype. The significance of this approach is verified by applying graph–cut techniques for assessing the differentiation between myeloid and lymphoid cells in haematopoiesis, i.e. the process through which all the different types of blood cells originate starting from a unique cell type. The experiments are conducted on a population of samples from 24 cell types involved in haematopoiesis. Six profiles are constructed for each cell type, based on a different histone modification signal. Following the experimentally verified idea that the peak number distribution per gene behaves similarly to gene expression, the profile computation employs standard differential analysis tools to find genes whose epigenetic modifications are related to a given phenotype. Next, six similarity networks of cell types are constructed, based on each histone modification, and then combined into a unique one through similarity network fusion. Finally, the similarity networks are transformed into dissimilarity graphs, to which two different cuts are applied and compared to evaluate the classic differentiation between myeloid and lymphoid cells. The results show that all histone modifications contribute almost equally to the myeloid/lymphoid differentiation, and this is also confirmed by the analysis of the fused network. However, they also suggest that histone modifications may not be the only mechanism for regulating the differentiation of hematopoietic cells.
Lymphatic PD-L1 expression restricts tumor-specific CD8+ T cell responses
Authors: Cousin Nikola , Cap Stefan , Dihr Manuel , Tacconi Carlotta , Detmar Michael , Dieterich Lothar C.
Published: October 2020

Lymph node (LN)-resident lymphatic endothelial cells (LECs) mediate peripheral tolerance by self-antigen presentation on MHC-I and constitutive expression of T cell inhibitory molecules, including PD-L1. Tumor-associated LECs also upregulate PD-L1 but the specific role of lymphatic PD-L1 in tumor immunity is not well understood. We generated a mouse model lacking lymphatic PD-L1 expression and challenged these mice with two orthotopic tumor models, B16F10 melanoma and MC38 colorectal carcinoma. Lymphatic PD-L1 deficiency resulted in a consistent expansion of tumor-specific CD8+ T cells in tumor-draining LNs in both tumor models, reduced primary tumor growth in the MC38 model, and increased the efficacy of adoptive T cell therapy in the B16F10 model. Strikingly, lymphatic PD-L1 primarily acted via apoptosis induction in tumor-specific CD8+ central memory T cells. Our findings demonstrate that LECs restrain tumor-specific immunity via PD-L1 and may explain why some cancer patients without PD-L1 expression in the tumor microenvironment still respond to PD-L1 / PD-1 targeting immunotherapy.
Systematic characterization and genetic interaction analysis of adhesins inCandida albicansvirulence
Authors: Rosiana Sierra , Zhang Liyang , Kim Grace H. , Revtovich Alexey V. , Sukumaran Arjun , Geddes-McAlister Jennifer , Kirienko Natalia V. , Shapiro Rebecca S.
Published: October 2020

Candida albicansis a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role inC. albicans’ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of the role and relationships between these adhesins has not been explored. We previously established a CRISPR-based platform for efficient generation of single- and double-gene deletions inC. albicans, which was used to construct a library of 144 mutants, comprising 12 unique adhesin genes deleted singly, or in every possible combination of double deletions. Here, we exploit this adhesin mutant library to explore the role of adhesin proteins inC. albicansvirulence. We perform a comprehensive, high-throughput screen of this library, usingCaenorhabditis elegansas a simplified model host system, which identified mutants critical for virulence and significant genetic interactions. We perform follow-up analysis to assess the ability of high- and low-virulence strains to undergo cellular morphogenesis and form biofilmsin vitro, as well as to colonize theC. eleganshost. We further perform genetic interaction analysis to identify novel significant negative genetic interactions between adhesin mutants, whereby combinatorial perturbation of these genes significantly impairs virulence, more than expected based on virulence of the single mutant constituent strains. Together, this yields important new insight into the role of adhesins, singly and in combinations, in mediating diverse facets of virulence of this critical fungal pathogen.

Candida albicansis a human fungal pathogen and cause of life-threatening systemic infections. Cell surface-associated adhesins play a central role in this pathogen’s ability to establish infection. Here, we provide a comprehensive analysis of adhesin factors, and their role in fungal virulence. Exploiting a high-throughput workflow, we screened an adhesin mutant library usingC. elegansas a simple model host, and identified mutants and genetic interactions involved in virulence. We found that adhesin mutants are impaired inin vitropathogenicity, irrespective of their virulence. Together, this work provides new insight into the role of adhesin factors in mediating fungal virulence.
Mechanistic picture for chemo-mechanical couplings in a bacterial proton-coupled oligopeptide transporter from Streptococcus thermophilus
Authors: Immadisetty Kalyan , Moradi Mahmoud
Published: October 2020

Proton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemo-mechanical couplings involved in substrate/proton transport and protein structural changes is missing. We therefore performed microsecond-level molecular dynamics (MD) simulations of bacterial POT transporter PepTSt, which shares ~80% sequence identity with the human POT, PepT1, in the substrate binding region. Three different conformational states of PepTStwere simulated including, (i) occluded,apo, (ii) inward-facing,apo, and (iii) inward-facingoccluded, Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward-to outward-facing state) in the substrate transport. Additionally, E299 and E400 should disengage from interacting with the substrate either through protonation or through co-ordination with a cation for the substrate to get transported.
Resonance Raman spectra for the in-situ identification of bacteria strains and their inactivation mechanism
Authors: Dhankhar Dinesh , Nagpal Anushka , Li Runze , Chen Jie , Cesario Thomas C. , Rentzepis Peter M.
Published: October 2020

The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet(UV) radiation dose have been used to differentiate between live and dead bacteria. The enhanced resonance Raman spectra of color-pigmented bacteria were recorded after excitation with visible light diode lasers. In addition, the resonance enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations (~108cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in-situ was designed, constructed and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses and plants, in-situ, and detect infections within a very short period of time.
Beyond integration: modeling every pixel to obtain better structure factors from stills
Authors: Mendez Derek , Bolotovsky Robert , Bhowmick Asmit , Brewster Aaron S. , Kern Jan , Yano Junko , Holton James M. , Sauter Nicholas K.
Published: October 2020

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (104−106) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb3+L-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.
X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA
Authors: Shimekake Yuya , Hirato Yuki , Funabashi Rikako , Okazaki Sayoko , Goto Masaru , Furuichi Takehiro , Suzuki Hideyuki , Kera Yoshio , Takahashi Shouji
Published: October 2020

D-Amino-acid oxidases (DAAOs) catalyze the oxidative deamination of neutral and basic D-amino acids. The DAAO from the thermophilic fungus Rasamsonia emersonii strain YA (ReDAAO) has a high thermal stability and a unique broad substrate specificity that includes the acidic D-amino acid D-Glu as well as various neutral and basic D-amino acids. In this study, ReDAAO was crystallized by the hanging-drop vapor-diffusion method and its crystal structure was determined at a resolution of 2.00 Å. The crystal structure of the enzyme revealed that unlike other DAAOs, ReDAAO forms a homotetramer and contains an intramolecular disulfide bond (Cys230–Cys285), suggesting that this disulfide bond is involved in the higher thermal stability of ReDAAO. Moreover, the structure of the active site and its vicinity in ReDAAO indicates that Arg97, Lys99, Lys114 and Ser231 are candidates for recognizing the side chain of D-Glu.
Embedding parallelohedra into primitive cubic networks and structural automata description
Authors: Bouniaev Mikhail M. , Krivovichev Sergey V.
Published: October 2020

The main goal of the paper is to contribute to the agenda of developing an algorithmic model for crystallization and measuring the complexity of crystals by constructing embeddings of 3D parallelohedra into a primitive cubic network (pcu net). It is proved that any parallelohedron P as well as tiling by P, except the rhombic dodecahedron, can be embedded into the 3D pcu net. It is proved that for the rhombic dodecahedron embedding into the 3D pcu net does not exist; however, embedding into the 4D pcu net exists. The question of how many ways the embedding of a parallelohedron can be constructed is answered. For each parallelohedron, the deterministic finite automaton is developed which models the growth of the crystalline structure with the same combinatorial type as the given parallelohedron.
A systematic literature review on the usage of eye-tracking in understanding process models
Authors: Batista Duarte Rafael , Silva da Silveira Denis , de Albuquerque Brito Vinícius , Lopes Charlie Silva
Published: October 2020

Purpose

Business process modeling can involve multiple stakeholders, so it is natural that problems may occur during the designing and understanding processes. One way to perceive these problems is to evaluate the comprehension of business process models through the collection of data related to the readers' eye movement via an eye-tracking device. The purpose of this paper is to provide a comprehensive overview of the use of eye-trackers in understanding process models and to offer a research roadmap to challenge the community to address the identified limitations and open issues that require further investigation.

Design/methodology/approach

To achieve this goal, Systematic Literature Review (SLR) was performed following good practices from the Evidence-Based Software Engineering's (EBSE) field.

Findings

This study resulted in 10 primary studies selected for analysis and data extraction, from the 1,482 initially retrieved. The major findings indicate that the business process community still benefits little from the use of eye-tracking, e.g. not offering sufficient support for inexperienced designers and not having an explicit standardization in its use. These and other findings are synthesized in a research roadmap which results would benefit researchers and practitioners.

Originality/value

In the studies found, the methods used to explore eyes' movement in process models' comprehension analysis were presented as an advantage of the current study. Additionally, another aspect presented in this SRL as an originality is presenting a set of open questions, suggesting valuable topics for future research through a research script (research roadmap).
Can joint-contract functions promote PPP project sustainability performance? A moderated mediation model
Authors: Cheng Mengyuan , Liu Guoliang , Xu Yongshun
Published: October 2020

Purpose

The role of conventional contracts in achieving sustainability goals in public–private partnership (PPP) projects has been questioned. From the multifunctional perspective of contract theory, joint-contract functions that combine contractual control, coordination and adaptation may be a potential approach for improving PPP project sustainability performance. This research intends to investigate the link between the joint-contract functions and PPP project sustainability performance, and their underlying mechanism, by analyzing the mediating role of relationship quality and moderating roles of environmental uncertainty and behavioral uncertainty.

Design/methodology/approach

Based on 170 valid survey data collected from the Chinese PPP professionals, partial least squares structural equation modeling (PLS-SEM) was adopted to test the hypothesis.

Findings

The results reveal that joint-contract functions are positively associated with the PPP project sustainability performance. This relationship is strengthened by environmental and behavioral uncertainty. Moreover, the relationship between the joint-contract functions and PPP project sustainability performance is mediated by relationship quality.

Research limitations/implications

This research extends contract governance theory and sustainability research in PPP projects. The research implications are as follows: (1) joint-contract functions are a second-order construct consisting of three first-order dimensions: control, coordination and adaptation and are positively associated with PPP project sustainability performance; (2) joint-contract functions enhance the sustainable benefits of PPP projects during environmental uncertainty and behavioral uncertainty; (3) informal relationships are a critical bridge connecting formal institutions with the sustainability performance of PPP projects.

Practical implications

In general, these findings guide project participants who aim to achieve sustainable outcomes in PPP projects. (1) Project participants should consider the process of contract design and sign contracts that focus on joint-contract functions. (2) Project participants should investigate the degree of uncertainty of a PPP project before designing contracts, and design the contracts with corresponding complexity. (3) Project participants should work to enhance PPP sustainable benefits by improving the relationship between partners, such as encouraging mutual trust and joint problem-solving.

Originality/value

This research verifies the relationship between joint-contract functions and PPP project sustainability performance, and the boundary and intermediary conditions between them.
South Sudanese perceptions of health and illness in South Australia
Authors: Mude William Wingard , Fisher Christopher M. , Gautier Roslyn Le , Wallace Jack , Richmond Jacqueline A.
Published: October 2020

Purpose

South Sudanese people form the largest number of resettled refugees in Australia between 2003 and 2004. This study aims to explore how this community understands and responds to health and illness. No study has specifically examined the concept of health and illness in the broader socio-cultural context of the South Sudanese people in Australia.

Design/methodology/approach

The design was a qualitative study using interviews and focus group discussions with 33 South Sudanese people in Adelaide, South Australia. Participants were asked to reflect on their understanding of health and illness and influences on their access and use of health and other services. Data were electronically audio-recorded, transcribed verbatim and analysed thematically.

Findings

Three main themes emerged from the analysis demonstrating complex and multifaceted views on health and illness. Participants described health as both a lack of disease and wider issues involving social belonging and participation, cultural well-being, living conditions and harmony in the society. They revealed that illnesses are predetermined by God or caused by a curse, breaking a cultural taboo, disharmony with the environment, community and ancestral spirits. Participants deeply tied their beliefs about illness causation and treatment to their historical, social and cultural lived realities, shaping their responses and health-care-seeking decisions.

Originality/value

The current study revealed a complex understanding of health and health-care-seeking practices amongst South Sudanese Australians. The multifaceted views of health and health-care-seeking practices underscore the importance of person-centred care for culturally and linguistically diverse people.
Safeguarding adults and COVID-19: a sector-led improvement response
Authors: Cooper Adi
Published: October 2020

Purpose

This study aims to describe the sector-led response to the COVID-19 pandemic and national lockdown in terms of safeguarding adults.

Design/methodology/approach

This study uses a case study method to examine a sector-led improvement response to COVID-19 and safeguarding adults.

Findings

The study describes how safeguarding issues and concerns were identified and brought together, and then responded to. It reviews this initiative in the context of crisis intervention theory and discusses the achievements of this initiative regarding COVID-19 and safeguarding adults during the period April–July 2020.

Originality/value

The study describes a unique joint initiative between the Local Government Association and the Association of Directors of Adult Social Services, which worked with the Networks of Chairs of Safeguarding Adults Boards, Safeguarding Adults Boards’ managers and Principal Social Workers. This initiative developed resources and shared information and good practice to support a response in unprecedented circumstances.
Political discourse of President Bashar Al-Assad after the Syrian revolution (analytical vision)
Authors: Gaber Shireen
Published: October 2020

Purpose

There is no doubt that the political speech of the Syrian President Bashar Al-Assad is of exceptional importance in understanding the developments of the war in Syria, and clarifies the position of all parties involved in the war, whether local, regional or international. Accordingly, and based on the dismantling of political discourse, the identification of its core, as well as its variables and major themes of this discourse, this study aims to understand the levels of complexity, paths and the fate of the war in Syria that certainly does not come free of charge, the hardest of which is the human cost whether for the victims or the displaced persons.

Design/methodology/approach

After a careful study of all the resilient factors in the literature review to categorize the primary data based on Assad’s discourses in the media, through a “qualitative research study” of his “interviews and discourses,” it is found that the Assad’s rhetoric is highly relevant to his tenacious presidency. The research reveals the themes that dominated Assad’s interview responses and speeches and his strategy of framing the revolution as a foreign insurgency against his government. In fact, Assad delegitimizes any semblance of the uprisings as a “pro-democracy movement” or “revolution,” denying the presence of a rebellion against his government.

Findings

By the analysis the study found out that Bashar Al-Assad continued to focus on certain reasons and issues that led to the crisis and the continuation of the war, such as the Muslim Brotherhood’s involvement, considering the Syrian opposition abroad as agents of Western countries, Syria is subject to a regional and international conspiracy, terrorism is a major scourge that must be fought and that the army is essential in resolving the battles taking place there. Likewise, emphasizing the internal dialogue with all stakeholders and involved parties is the way to solve the crisis.The Syrian President’s speeches do not focus much on the accusations against his regime from the opposition or the international parties involved in the conflict.

Originality/value

Assad’s resiliency has made him a distinct leader in the region. This paper analyzes the factors contributing to Assad’s resiliency. The literature review consists of the existing theories on authoritarian persistence and Assad’s power base in particular. The literature review discusses the factors that helped Assad adopts his resiliency strategies to the conflict environment. The research focuses on how Assad used the media as a platform for displaying his own manipulative narrative of the conflict. It concludes that Assad’s use of the media as his propaganda tool legitimized his rule, making it highly relevant to his persistence.
Cross-nationality importance performance analysis of Middle East all-inclusive mass tourism destination image
Authors: Ceylan Demet , Cizel Beykan , Karakas Hatice
Published: October 2020

Purpose

The paper aims to analyze cognitive attributes affecting the overall destination image perception of British, German and Russian tourists toward Antalya, a well-positioned mass tourism destination in the East Mediterranean region dominated by an all-inclusive (AI) system.

Design/methodology/approach

The paper is an empirical study using a structured questionnaire conducted in the summer of 2018 with 274 British, 179 German and 231 Russian tourists departing to their respective source markets from Antalya International Airport. The mean values are used as performance and correlation coefficients of the relationship between each cognitive image dimension and overall image evaluation is used to express importance.

Findings

The paper provides empirical insights that these three nationalities prefer Antalya as an AI holiday destination for different reasons and that each nationality demands attention to different factors of the destination for improvement or preservation.

Research limitations/implications

This study provides specific recommendations for AI destinations such as Antalya for the German, British and Russian source markets. When other source markets or types of destinations are considered, the findings of this study should be re-considered. Utilization of the original and modernized importance performance analysis (IPA) plot interpretations in this research reveals a deeper understanding of current findings and provides a new perspective for further research and guidance for destination managers and marketers.

Practical implications

Utilization of both original and modernized IPA plot interpretation in this research not only reveals a deeper understanding of current findings but also provides a new perspective for future studies and guidance for destination managers and marketers.

Originality/value

Unlike the majority of destination image research, this study of destination image based on individual nationalities enables tailor-made destination image development according to diversified importance and performance of destination attributes affecting the overall destination image for each nationality.
Tacit vs explicit knowledge as antecedents for organizational change
Authors: Gamble Jordan R.
Published: October 2020

Purpose

The aim of this paper is to explore the dichotomous role of knowledge through an examination of tacit and explicit knowledge in organizational change contexts.

Design/methodology/approach

The study's aim is achieved by an analytical review of the seminal and contemporary knowledge management literature.

Findings

The paper contributes to the current body of knowledge management literature by analyzing a wide range of key literature and presenting a contemporary overview that compares the role of tacit and explicit knowledge within organizational change contexts.

Research limitations/implications

The findings contribute toward theoretical development in the knowledge management field by providing researchers with future research directions to build upon previous theoretical understandings and advance our collective knowledge of the research domain.

Practical implications

The paper offers practical and pragmatic insights that will help firm managers to use tacit and/or explicit knowledge to manage organizational change.

Originality/value

This article presents an original comparative table that summarizes and compares the key understandings and insights from across the literature sources on a range of important aspects, and then presents implications for the two knowledge typologies. The paper also presents an original research framework containing a structured database of related calls for research by the latest academic publications. Furthermore, it provides specific and informed managerial recommendations for best practice in the integration of these knowledge typologies into organizational change management.