bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast
Authors: Alvarez-Ponce David , Aguilar-Rodríguez José , Fares Mario A
Published: July 2019

Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone–protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding non-client proteins when controlling for their number of protein–protein interactions. We also find that genes encoding client proteins have accumulated more intraspecific genetic diversity than those encoding non-client proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype–phenotype maps, have a considerable accelerating effect on protein evolution.
Monitoring of immunoglobulin N- and O-glycosylation in health and disease
Authors: de Haan Noortje , Falck David , Wuhrer Manfred
Published: July 2019

Protein N- and O-glycosylation are well known co- and post-translational modifications of immunoglobulins. Antibody glycosylation on the Fab and Fc portion is known to influence antigen binding and effector functions, respectively. To study associations between antibody glycosylation profiles and (patho) physiological states as well as antibody functionality, advanced technologies and methods are required. In-depth structural characterization of antibody glycosylation usually relies on the separation and tandem mass spectrometric (MS) analysis of released glycans. Protein- and site-specific information, on the other hand, may be obtained by the MS analysis of glycopeptides. With the development of high-resolution mass spectrometers, antibody glycosylation analysis at the intact or middle-up level has gained more interest, providing an integrated view of different post-translational modifications (including glycosylation). Alongside the in-depth methods, there is also great interest in robust, high-throughput techniques for routine glycosylation profiling in biopharma and clinical laboratories. With an emphasis on IgG Fc glycosylation, several highly robust separation-based techniques are employed for this purpose. In this review, we describe recent advances in MS methods, separation techniques and orthogonal approaches for the characterization of immunoglobulin glycosylation in different settings. We put emphasis on the current status and expected developments of antibody glycosylation analysis in biomedical, biopharmaceutical and clinical research.
Treatment-Specific Composition of the Gut Microbiota Is Associated With Disease Remission in a Pediatric Crohn’s Disease Cohort
Authors: Sprockett Daniel , Fischer Natalie , Boneh Rotem Sigall , Turner Dan , Kierkus Jarek , Sladek Malgorzata , Escher Johanna C , Wine Eytan , Yerushalmi Baruch , Dias Jorge Amil , Shaoul Ron , Kori Michal , Snapper Scott B , Holmes Susan , Bousvaros Athos , Levine Arie , Relman David A
Published: July 2019

Background

The beneficial effects of antibiotics in Crohn’s disease (CD) depend in part on the gut microbiota but are inadequately understood. We investigated the impact of metronidazole (MET) and metronidazole plus azithromycin (MET+AZ) on the microbiota in pediatric CD and the use of microbiota features as classifiers or predictors of disease remission.

Methods

16S rRNA-based microbiota profiling was performed on stool samples from 67 patients in a multinational, randomized, controlled, longitudinal, 12-week trial of MET vs MET+AZ in children with mild to moderate CD. Profiles were analyzed together with disease activity, and then used to construct random forest models to classify remission or predict treatment response.

Results

Both MET and MET+AZ significantly decreased diversity of the microbiota and caused large treatment-specific shifts in microbiota structure at week 4. Disease remission was associated with a treatment-specific microbiota configuration. Random forest models constructed from microbiota profiles before and during antibiotic treatment with metronidazole accurately classified disease remission in this treatment group (area under the curve [AUC], 0.879; 95% confidence interval, 0.683–0.9877; sensitivity, 0.7778; specificity, 1.000; P < 0.001). A random forest model trained on pre-antibiotic microbiota profiles predicted disease remission at week 4 with modest accuracy (AUC, 0.8; P = 0.24).

Conclusions

MET and MET+AZ antibiotic regimens in pediatric CD lead to distinct gut microbiota structures at remission. It may be possible to classify and predict remission based in part on microbiota profiles, but larger cohorts will be needed to realize this goal.
The ecology of infrastructure decommissioning in the North Sea: what we need to know and how to achieve it
Authors: Fowler A M , Jørgensen A -M , Coolen J W P , Jones D O B , Svendsen J C , Brabant R , Rumes B , Degraer S
Published: July 2019

As decommissioning of oil and gas (O&G) installations intensifies in the North Sea, and worldwide, debate rages regarding the fate of these novel habitats and their associated biota—a debate that has important implications for future decommissioning of offshore wind farms (OWFs). Calls to relax complete removal requirements in some circumstances and allow part of an O&G installation to be left in the marine environment are increasing. Yet knowledge regarding the biological communities that develop on these structures and their ecological role in the North Sea is currently insufficient to inform such decommissioning decisions. To focus debate regarding decommissioning policy and guide ecological research, we review environmental policy objectives in the region, summarize existing knowledge regarding ecological aspects of decommissioning for both O&G and OWF installations, and identify approaches to address knowledge gaps through science–industry collaboration. We find that in some cases complete removal will conflict with other policies regarding protection and restoration of reefs, as well as the conservation of species within the region. Key ecological considerations that are rarely considered during decommissioning decisions are: (i) provision of reef habitat, (ii) productivity of offshore ecosystems, (iii) enhancement of biodiversity, (iv) protection of the seabed from trawling, and (v) enhancement of connectivity. Knowledge gaps within these areas will best be addressed using industry infrastructure and vessels for scientific investigations, re-analysis of historical data held by industry, scientific training of industry personnel, joint research funding opportunities, and trial decommissioning projects.
Contact Dual Pairs
Authors: Monica Blaga Adara , Amelia Salazar Maria , Giuseppe Tortorella Alfonso , Vizman Cornelia
Published: July 2019

We introduce and study the notion of contact dual pair adopting a line bundle approach to contact and Jacobi geometry. A contact dual pair is a pair of Jacobi morphisms defined on the same contact manifold and satisfying a certain orthogonality condition. Contact groupoids and contact reduction are the main sources of examples. Among other properties, we prove the characteristic leaf correspondence theorem for contact dual pairs that parallels the analogous result of Weinstein for symplectic dual pairs.
Does capsular closure influence patient-reported outcomes in hip arthroscopy for femoroacetabular impingement and labral tear?
Authors: Atzmon Ran , Sharfman Zachary T , Haviv Barak , Frankl Michal , Rotem Gilad , Amar Eyal , Drexler Michael , Rath Ehud
Published: July 2019

Capsulotomy is necessary to facilitate instrument manoeuvrability within the joint capsule in many arthroscopic hip surgical procedures. In cases where a clear indication for capsular closure does not exist, surgeon’s preference and experience often determines capsular management. The purpose of this study was to assess the influence of capsular closure on clinical outcome scores and satisfaction in patients who underwent hip arthroscopy surgery for femoroacetabular impingement (FAI) and labral tear. Data were prospectively collected and retrospectively analysed for hip arthroscopy surgeries with a minimum 2 years follow-up. Patients with developmental dysplasia of the hip, previous back or hip surgeries, and degenerative changes to this hip and secondary gains were excluded. Demographic data, intraoperative findings and patient-reported outcome scores were recorded, including the Modified Harris Hip Score (MHHS) and Hip Outcome Score (HOS). A total of 29 and 35 patients were included in the non-closure and closure groups, respectively. The mean follow-up time was over 3 years for both groups. The mean pre-operative and post-operative HOS scores and MHHS scores did not significantly differ between groups (pre-operative HOS: 65.6 and 66.3, P = 0.898; post-operative HOS: 85.4 and 87.2, P = 0.718; pre-operative MHHS: 63.2 and 58.4, P = 0.223; post-operative MHHS: 85.7 and 88.7, P = 0.510). Overall patient satisfaction did not differ significantly between groups (non-closure 86.3%, closure group 88.6%; P = 0.672). Capsular closure did not significantly influence satisfaction or clinical outcome scores in patients who underwent arthroscopic hip surgery for FAI or labral tear.
Psychopathology and Truth: A Defense of Realism
Authors: Eronen Markus I
Published: July 2019

Recently Kenneth Kendler and Peter Zachar have raised doubts about the correspondence theory of truth and scientific realism in psychopathology. They argue that coherentist or pragmatist approaches to truth are better suited for understanding the reality of psychiatric disorders. In this article, I show that rejecting realism based on the correspondence theory is deeply problematic: It makes psychopathology categorically different from other sciences, and results in an implausible view of scientific discovery and progress. As an alternative, I suggest a robustness-based approach that can accommodate the significance of coherence and pragmatic factors without rejecting scientific realism and the correspondence theory of truth.
Semiclassical perturbation Stark shifts of singly charged argon spectral lines
Authors: Hamdi Rafik , Ben Nessib Nabil , Sahal-Bréchot Sylvie , Dimitrijević Milan S
Published: July 2019

Using semiclassical perturbation approach in impact approximation, Stark shifts for singly charged argon (Ar ii) spectral lines have been calculated. Energy levels and oscillator strengths needed for this calculation were determined using Hartree–Fock method with relativistic correction (HFR). We compare our results with experimental values for 100 spectral lines. We also present results as a function of temperature for 161 spectral lines for collisions with electrons, protons, singly charged helium and singly charged argon. This work extends our previous one.
ExoMol line list – XXXIV. A rovibrational line list for phosphinidene (PH) in its $X\, {}^3\Sigma ^-$ and $a\, {}^1\Delta$ electronic states
Authors: Langleben Jonathan , Tennyson Jonathan , Yurchenko Sergei N , Bernath Peter
Published: July 2019

A rovibronic line list for the ground (X 3Σ−) and first excited (a 1Δ) states of phosphinidene, 31PH, is computed. The line list is designed for studies of exoplanetary and cool stellar atmospheres with temperatures up to 4000 K. A combination of empirical and ab initio data is used to produce the line list: potential energy curves (PECs) are fitted using experimental transition frequencies; these transitions are reproduced with a root mean square error of 0.01 cm−1. The nuclear Schrödinger equation is solved using these PECs plus Born–Oppenheimer and spin splitting correction terms. Line intensities and Einstein   A coefficients are computed using ab initio dipole moment curves for X–X and a–a transitions. The resulting LaTY line list, which contains 65 055 transitions for 2528 rovibronic states up to 24 500 cm −1 and J = 80, is used to simulate spectra in emission and absorption for a range of temperatures. The line list is made available in electronic form at the CDS and ExoMol data bases.
Misdiagnosis of Lyme Disease With Unnecessary Antimicrobial Treatment Characterizes Patients Referred to an Academic Infectious Diseases Clinic
Authors: Kobayashi Takaaki , Higgins Yvonne , Samuels Roger , Moaven Aurasch , Sanyal Abanti , Yenokyan Gayane , Lantos Paul M , Melia Michael T , Auwaerter Paul G
Published: July 2019

Background

Although Lyme disease is the most common vector-borne infection in the United States, diagnostic accuracy within community settings is not well characterized.

Methods

A retrospective observational cohort study of patients referred to an academic center with a presumed diagnosis or concern for Lyme disease between 2000 and 2013 was performed to analyze diagnoses and treatments. Characteristics of those with Lyme disease and those misdiagnosed as having Lyme disease were compared.

Results

Of 1261 patients, 911 (72.2%) did not have Lyme disease, 184 (14.6%) had active or recent Lyme disease, 150 (11.9%) had a remote history of Lyme disease, and 16 (1.3%) were identified as having possible Lyme disease. Patients without current Lyme disease were more likely to be female (odds ratio [OR], 1.56; 95% confidence interval [CI], 1.08–2.45), to have had symptoms for >3 months (OR, 8.78; 95% CI, 5.87–13.1), to have higher symptom counts (OR per additional symptom, 1.08; 95% CI, 1.02–1.13), to have had more Lyme-related laboratory testing (OR per additional laboratory test, 1.17; 95% CI, 1.03–1.32), and to have been diagnosed with what were regarded as coinfections (OR, 3.13; 95% CI, 1.14–8.57). Of the 911 patients without Lyme disease, 764 (83.9%) had received antimicrobials to treat Lyme disease or their coinfections. The percentage of patients established to have Lyme disease was lower than in earlier studies of referred populations.

Conclusions

Among patients referred to an academic Infectious Diseases practice for Lyme disease, incorrect diagnoses and unnecessary antibiotic treatment were common, both for Lyme disease and for coinfections.
Efficacy of Superior Hypogastric Plexus Neurolysis for the Treatment of Cancer-Related Pelvic Pain
Authors: Hou Saiyun , Novy Diane , Felice Francis , Koyyalagunta Dhanalakshmi
Published: July 2019

Objective

Cancer-related abdominal and pelvic pain syndromes can be debilitating and difficult to treat. The objective of this study was to evaluate the efficacy of superior hypogastric plexus blockade or neurolysis (SHPN) for the treatment of cancer-related pelvic pain.

Design

Retrospective study.

Setting

MD Anderson Cancer Center, Houston, Texas.

Methods

We enrolled 46 patients with cancer-related pelvic pain who underwent SHPN. A numeric rating scale (NRS) was used for pain intensity, and symptom burden was evaluated using the Edmonton Symptom Assessment System at baseline, visit 1 (within one month), and visit 2 (within one to six months).

Results

Forty-six patients who received SHPN showed a significant reduction in pain score from 6.9 to 5.6 at visit 1 (P = 0.01). Thirty of the 46 patients continued to complete visit 2 follow-up, and the NRS score was consistently lower at 4.5 at visit 2 (P < 0.0001), with anxiety and appetite improved significantly. There was no significant change in the morphine equivalent dose at visits 1 and 2. The efficacy of the block was not influenced by patients’ age, gender, type of cancer, cancer stage, regimen of chemotherapy and/or radiation therapy, diagnostic block, approach or laterality of procedure, or type or amount of neurolytic agent. Nonsmokers with high baseline pain scores were more likely to have improved treatment outcomes from SHPN at short-term follow-up. Adverse effects with SHPN were mild and well tolerated.

Conclusions

SHPN was an effective and relatively safe procedure for pain associated with pelvic malignancies. There is a need for larger prospective trials.
Association of gout medications and risk of cataract: a population-based case–control study
Authors: Li Y-J , Perng W-T , Tseng K-Y , Wang Y-H , Wei J C-C
Published: July 2019

Background

The relationship between gout medication use and cataract development is controversial. Moreover, limited clinical studies have evaluated this relationship.

Aim

To assess the effects of colchicine, allopurinol and benzbromarone on the risk of cataract in patients with gout.

Design

Population-based nested case–control study.

Methods

We enrolled 7900 patients who had received a new diagnosis of cataract >3 years after gout diagnosis into the study group and 33 475 patients who did not receive a diagnosis of cataract into the control group by matching for age, sex and the year of gout diagnosis at a ratio of 1:1. We used World Health Organization’s defined daily dose (DDD) as a measure to assess the dosage of colchicine, allopurinol and benzbromarone exposure. Logistic regression was used to estimate crude and adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of cataract.

Results

The risk of cataract significantly increased in patients who received colchicine at a cumulative DDD of ≥66.5 (OR = 1.17, 95% CI = 1.01–1.36, P = 0.041). In the age-stratified analysis, patients with gout aged >60 years had a higher risk of cataract (OR = 1.27, 95% CI = 1.06–1.53, P = 0.011) than did patients aged <60 years. Allopurinol and benzbromarone had no association with cataract.

Conclusions

In this population-based nested case–control study, we observed that colchicine use increased the risk of cataract in patients with gout, especially in those aged >60 years who received colchicine at a cumulative DDD of >66.5.
Different factors underlie recurrent and de novo organ involvement in immunoglobulin G4–related disease
Authors: Mizushima Ichiro , Tsuge Syunsuke , Fujisawa Yuhei , Hara Satoshi , Suzuki Fae , Ito Kiyoaki , Fujii Hiroshi , Yamada Kazunori , Kawano Mitsuhiro
Published: July 2019

Objectives

In IgG4-related disease (IgG4-RD), relapse including recurrent organ involvement (ROI) and de novo organ involvement (DNOI) occurs frequently during the clinical course. This study aimed to clarify the differences between the risk factors underlying ROI and DNOI in IgG4-RD.

Methods

We retrospectively investigated factors related to ROI and DNOI in 86 IgG4-RD patients. For assessment of factors related to ROI and DNOI, we performed uni- and multivariate Cox regression analyses. On stepwise multivariate analysis, we applied the variables with P < 0.1 in the univariate analysis and the predictors of relapse suggested in past reports.

Results

During the mean follow-up period of 63.1 months, ROI was detected at 1.0–120 months after diagnosis in 20 patients, 4 of whom were not receiving glucocorticoid (GC) at the time of ROI. In contrast, DNOI was detected at 5.0–120 months after diagnosis in 15 patients, 8 of whom were not receiving GC at the time of DNOI. In the multivariate analysis, blood eosinophil counts at diagnosis [per 100/μl; hazard ratio (HR) 1.072 (95% CI 1.018, 1.129)] and continuation of GC [vs discontinuation or observation without GC; HR 0.245 (95% CI 0.076, 0.793)] had a significant impact on the time to DNOI, whereas age [HR 0.942 (95% CI 0.899, 0.986)] and ANA positivity [vs negativity; HR 6.632 (95% CI 1.892, 23.255)] had a significant impact on the time to ROI.

Conclusion

The present study suggests that the risk factors of ROI and DNOI are different in IgG4-RD, highlighting the need for different preventative strategies.
Is Routine Monitoring for Hypoglycemia Required in Intramural Asymptomatic Infant of Diabetic Mother? An Audit in a Tertiary Care Hospital
Authors: Khandare Jayant , DS Madhusudhan , Ananthan Anitha , Nanavati Ruchi
Published: July 2019

Aims

This retrospective audit aimed to analyze whether routine frequent monitoring for hypoglycemia is required in asymptomatic infant of diabetic mother born in tertiary care hospital.

Methods

The study analyzed the blood sugar level of 196 infants of diabetic mothers.

Results

The overall incidence of hypoglycemia from 196 study participants was 9.18% (N = 18). The incidence of hypoglycemia at 2 h of life was maximum (83.33%) and it was significant when compared to 3, 6, 9 and 12 h (p < 0.0001). Blood glucose levels were significantly more at 6 (p = 0.0002)), 9 (p = 0.0001) and 12 h (p = 0.0001) when compared to glucose level at 2 h except at 3 h of life (p = 0.062). Similarly blood glucose at 9 (p = 0.0001) and 12 h of life (p = 0.0002) were significantly more than at 3 h of life. Blood glucose at 9 h was significantly more than at 6 h of life (0.032) and at 12 hours of life (p = 0.0237) was significantly higher than at 6 h of life.

Conclusion

The frequent blood glucose monitoring for hypoglycemia in infant of diabetic mother as per American Academy of Pediatrics may be reduced as per the findings in our study. However, this needs to be confirmed by a properly designed observational study/adequately powered randomized controlled trial.
Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis
Authors: Benítez-Burraco Antonio , Chekalin Evgeny , Bruskin Sergey , Morozova Irina
Published: July 2019

Human evolution resulted from changes in our biology, behavior, and culture. One source of these changes has been hypothesized to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. In this paper we compare whole-genome data between Late Neolithic/Bronze Age individuals and modern Europeans and show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. We hypothesize how these changes might account for the increased features of self-domestication in modern humans and ultimately, for subtle recent changes in human cognition and behavior, including language.
Deep learning detects virus presence in cancer histology
Authors: Kather Jakob Nikolas , Schulte Jefree , Grabsch Heike I. , Loeffler Chiara , Muti Hannah , Dolezal James , Srisuwananukorn Andrew , Agrawal Nishant , Kochanny Sara , Stillfried Saskia von , Boor Peter , Yoshikawa Takaki , Jaeger Dirk , Trautwein Christian , Bankhead Peter , Cipriani Nicole A. , Luedde Tom , Pearson Alexander T.
Published: July 2019

Oncogenic viruses like human papilloma virus (HPV) or Epstein Barr virus (EBV) are a major cause of human cancer. Viral oncogenesis has a direct impact on treatment decisions because virus-associated tumors can demand a lower intensity of chemotherapy and radiation or can be more susceptible to immune check-point inhibition. However, molecular tests for HPV and EBV are not ubiquitously available.

We hypothesized that the histopathological features of virus-driven and non-virus driven cancers are sufficiently different to be detectable by artificial intelligence (AI) through deep learning-based analysis of images from routine hematoxylin and eosin (HE) stained slides. We show that deep transfer learning can predict presence of HPV in head and neck cancer with a patient-level 3-fold cross validated area-under-the-curve (AUC) of 0.89 [0.82; 0.94]. The same workflow was used for Epstein-Barr virus (EBV) driven gastric cancer achieving a cross-validated AUC of 0.80 [0.70; 0.92] and a similar performance in external validation sets. Reverse-engineering our deep neural networks, we show that the key morphological features can be made understandable to humans.

This workflow could enable a fast and low-cost method to identify virus-induced cancer in clinical trials or clinical routine. At the same time, our approach for feature visualization allows pathologists to look into the black box of deep learning, enabling them to check the plausibility of computer-based image classification.
Female-specific and dosage selections restore genes through transpositions onto the degenerated songbird W chromosomes
Authors: Xu Luohao , Zhou Qi
Published: July 2019

Sex chromosomes are usually suppressed for homologous recombination, which leads to the loss of functional genes on the Y or W chromosomes. It remains unclear how species like birds with a ZW sex system cope with the consequential gene expression imbalance, usually in the absence of global dosage compensation mechanism. Here we tackle this conundrum by reporting 14 genes recently transposed from the Z to the W chromosomes of three songbird lineages, after analyzing a total of 12 songbird species’ genomes. These transpositions are estimated to have occurred within 9 million years. Besides the expected signatures of functional degeneration in some genes on the non-recombining W chromosomes, the other retained genes after transposition are enriched for haploinsufficient genes or housekeeping genes. Several genes show biased expression in ovaries of birds or lizard, or function in female germ cells. These results, together with the reported X-to-Y transpositions provide direct evidence that sex-specific and dosage selections may have recurrently driven the restoration of genes on the Y or W chromosomes, and suggest their evolutionary processes are more dynamic than simply becoming completely degenerated.
Integrative Analysis of Axolotl Gene Expression Data From Regenerative and Wound Healing Limb Tissues
Authors: Sibai Mustafa , Parlayan Cüneyd , Tuğlu Pelin , Öztürk Gürkan , Demircan Turan
Published: July 2019

Axolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and full restoration of amputated limbs. Several regenerative cues of the axolotl limb were successfully unraveled due to the advent of high-throughput technologies and their employment in tackling research questions on several OMICS levels. The field of regenerative biology and medicine has therefore utilized the axolotl as a major and powerful experimental model. Studies which have previously unraveled differentially expressed (DE) genes en masse in different phases of the axolotl limb regeneration have primarily used microarrays and RNA-Seq technologies. However, as different labs are conducting such experiments, sufficient consistency may be lacking due to statistical limitations arising from limited number of sample replicates as well as possible differences in study designs. This study, therefore, aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs. Three biological groups were conceived for the analysis; homeostatic tissues (control group), from amputation/injury timepoint up to around 50 hours post amputation (wound healing group), and from 50 hours to 28 days post amputation/injury (regenerative group). Integrative analysis was separately carried out on the selected microarray and RNA-Seq data from axolotl limb samples using the “merging” method. Differential expression analysis was separately implemented on the processed data from both technologies using the R/Bioconductor “limma” package. A total of 1254 genes (adjusted P < 0.01) were found DE in regenerative samples compared to the control, out of which 351 showed magnitudes of Log Fold Changes (LogFC) > 1 and were identified as the top DE genes from data of both technologies. Downstream analyses illustrated consistent correlations of the logFCs of DE genes distributed among the biological comparisons, within and between both technologies. Gene ontology annotations demonstrated concordance with the literature on the biological process involved in the axolotl limb regeneration. qPCR analysis validated the observed gene expression level differences between regenerative and control samples for a set of five genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.
Perceived direction of deformation flow
Authors: Kawabe Takahiro
Published: July 2019

In everyday circumstances, human observers can easily discriminate the direction of transparent liquid flow. However, the mechanism of direction discrimination is not so straightforward. The present study focused on the flow of image deformation, which is closely related to the flow of transparent liquid in the natural world. To determine what image information is important in discriminating the direction of deformation flow, a natural image in a stimulus clip was deformed by using a deformation vector map that translated leftward or rightward. The task of the observers was to judge whether the transparent liquid in the clip flowed leftward or rightward. Manipulating the amplitude of deformation, we found that the discrimination performance improved with the amplitude. Interestingly, the observers’ performance was high overall only when shearing deformation was applied to the stimuli, while the observers reported an opposite-motion direction when only compressive deformation was applied. We computationally analyzed motion statistics of stimuli and found that the combination of mean and skewness of horizontal motion vectors reliably predicted the performance. The results indicate that human observers use global motion directions in order to determine the direction of deformation flow.
Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family
Authors: Rajarammohan Sivasubramanian , Paritosh Kumar , Pental Deepak , Kaur Jagreet
Published: July 2019

Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. Additionally, we sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.
Model order reduction for left ventricular mechanics via congruency training
Authors: Di Achille Paolo , Parikh Jaimit , Khamzin Svyatoslav , Solovyova Olga , Kozloski James , Gurev Viatcheslav
Published: July 2019

Computational models of the cardiovascular system and heart function are currently being investigated as analytic tools to assist medical practice and clinical trials. Recent technological advances allow for finite element models of heart ventricles and atria to be customized to medical images and to assimilate electrical and hemodynamic measurements. Optimizing model parameters to physiological data is, however, challenging due to the computational complexity of finite element models. Metaheuristic algorithms and other optimization strategies typically require sampling hundreds of points in the model parameter space before converging to optimal solutions. Similarly, resolving uncertainty of model outputs to input assumptions is difficult for finite element models due to their computational cost. In this paper, we present a novel, multifidelity strategy for model order reduction of 3-D finite element models of ventricular mechanics. Our approach is centered around well established findings on the similarity between contraction of an isolated muscle and the whole ventricle. Specifically, we demonstrate that simple linear transformations between sarcomere strain (tension) and ventricular volume (pressure) are sufficient to reproduce global pressure-volume outputs of 3-D finite element models even by a reduced model with just a single myocyte unit. We further develop a procedure for congruency training of a surrogate low-order model from multi-scale finite elements, and we construct an example of parameter optimization based on medical images. We discuss how the presented approach might be employed to process large datasets of medical images as well as databases of echocardiographic reports, paving the way towards application of heart mechanics models in the clinical practice.
Tail Vein Injections of Recombinant Human Thioredoxin Prevents High Fat-induced Endothelial Dysfunction in Mice
Authors: Hilgers Rob H.P.
Published: July 2019

Background

Obesity is a serious risk factor for cardiovascular diseases. A high fat diet results in cellular oxidative stress and endothelial dysfunction in resistance-sized arteries, characterized by reduced nitric oxide (NO) and endothelium-dependent hyperpolarizing (EDH) responses. Thioredoxin-1, a sulfo-oxidoreductase protein that cleaves disulfide bridges between two adjacent cysteine residues in oxidized proteins, has been shown to lower blood pressure and improve endothelium-dependent relaxing responses in aged C57Bl6/J mice.

Methods and Results

Young (∼ 3 month-old) male C57Bl6/J mice were fed a high fat diet (42% kcal from fat; obese) or a normal chow (lean) for 3 months. Mice were administered recombinant human thioredoxin-1 (rhTrx; 25 mg/kg) or saline (0.9% NaCl) via tail vein injection at the start, after one month, and after two months. Body weight (BW) was comparable between lean/rhTrx1 and lean/saline at the time of euthanasia (32 ±1 g versus 32 ± 1 g). The high fat regimen resulted in a comparable BW between obese/saline and obese/rhTrx mice (47 ± 1 g versus 45 ± 2 g, respectively). Small (second-order branches) mesenteric arteries (MA2), coronary and femoral arteries were isolated and mounted on the wire-myograph. MA2 and femoral arteries from obese/saline had blunted acetylcholine (10−9 – 10−5 M)-mediated relaxations compared to lean/saline mice, but not to the NO donor sodium nitroprusside. NO and EDH-mediated relaxing responses were blunted in MA2 from obese/lean mice compared to the three other groups.

Conclusion

Tail vein injections with rhTrx prevented endothelial dysfunction in obese mice by improving NO and EDH relaxing responses in MA2.
Numerical study of boundary layer transition using intermittency model
Authors: Tatar Massoud , Tahani Mojtaba , Masdari Mehran
Published: July 2019

Purpose

In this paper, the applicability of shear stress transport k-ω model along with the intermittency concept has been investigated over pitching airfoils to capture the laminar separation bubble (LSB) position and the boundary layer transition movement. The effect of reduced frequency of oscillations on boundary layer response is also examined.

Design/methodology/approach

A two-dimensional computational fluid dynamic code was developed to compute the effects of unsteadiness on LSB formation, transition point movement, pressure distribution and lift force over an oscillating airfoil using transport equation of intermittency accompanied by the k-ω model.

Findings

The results indicate that increasing the angle of attack over the stationary airfoil causes the LSB size to shorten, leading to a rise in wall shear stress and pressure suction peak. In unsteady cases, both three- and four-equation models are capable of capturing the experimentally measured transition point well. The transition is delayed for an unsteady boundary layer in comparison with that for a static airfoil at the same angle of attack. Increasing the unsteadiness of flow, i.e. reduced frequency, moves the transition point toward the trailing edge of the airfoil. This increment also results in lower static pressure suction peak and hence lower lift produced by the airfoil. It was also found that the fully turbulent k-ω shear–stress transport (SST) model cannot capture the so-called figure-of-eight region in lift coefficient and the employment of intermittency transport equation is essential.

Practical implications

Boundary layer transition and unsteady flow characteristics owing to airfoil motion are both important for many engineering applications including micro air vehicles as well as helicopter blade, wind turbine and aircraft maneuvers. In this paper, the accuracy of transition modeling based on intermittency transport concept and the response of boundary layer to unsteadiness are investigated.

Originality/value

As a conclusion, the contribution of this paper is to assess the ability of intermittency transport models to predict LSB and transition point movements, static pressure distribution and aerodynamic lift variations and boundary layer flow pattern over dynamic pitching airfoils with regard to oscillation frequency effects for engineering problems.
Information-based quality management in reverse logistics supply chain
Authors: Jayasinghe Ruchini Senarath , Chileshe Nicholas , Rameezdeen Raufdeen
Published: July 2019

Purpose

The purpose of this paper is to explore the synergies among reverse logistics supply chain (RLSC), quality management (QM) and information management (IM) concepts to enhance the effectiveness of demolition waste management (DWM) practices.

Design/methodology/approach

A systematic literature review was conducted using 70 articles published between the years of 2006 and 2017, which were subjected to descriptive and thematic analysis.

Findings

The descriptive analysis established that the RLSC concept was dealt within the majority of the publications (61 per cent), followed by concepts related to quality in RLSC (24 per cent). Only 14 per cent of the articles were based on IM concepts related to RLSC. Quality and information are interrelated in the effective implementation of RLSC. The thematic analysis demonstrated that there is a need for using quality parameters in a regulatory environment in an information-based environment. Based on the findings, future research directions were developed.

Research limitations/implications

The study encourages researchers to identify novel directions by combining these three concepts. The study developed a future research agenda regarding use of building information modelling (BIM) for existing buildings under novel technologies; analysis of secondary market demand and supply; and assessment of cost and safety management with quality in a BIM-enabled environment.

Practical implications

The practical implications include the application of sustainable management principles based on stakeholders and the regulatory environment.

Originality/value

Integration of the three concepts is an emerging area. This integration developed a robust approach to achieve QM in RLSC operations under a sound information flow enabling the optimisation of DWM.
Evaluation of the usability of the Canay’s equivalent circuit diagrams for the calculation of subsynchronous resonances
Authors: Gołębiowski Marek , Göbel Carsten
Published: July 2019

Purpose

In the shaft and end windings of large turbogenerators, unacceptably high mechanical stresses can occur as a result of subsynchronous resonances (SSRs) in the system network-generator-shaft. These stresses can cause severe damages. Subsynchronous resonances are characterized by the occurrence of currents and electromagnetic torques in the air gap of the generator with frequencies that are significantly below the synchronous frequency. When simulating the balancing processes in multi-machine networks, the generators are represented by Canay’s equivalent circuit diagrams. The parameters used here are determined from geometric dimensions of the generator, taking into account material properties, and verified by means of surge short-circuit tests in which the 50 and 100 Hz components are dominant. This paper aims to examine whether the parameters of the equivalent circuit diagram determined in this way reproduce correctly the dynamic behavior of a synchronous machine, even if the SSR occur.

Design/methodology/approach

The simulation program NETOMAC is used to simulate the SSRs for different parameters. The results of these simulations are then compared with those obtained by the finite difference (FD) method calculations.

Findings

The comparison of the waveforms calculated with NETOMAC and FELMEC for an SSR shows that the original equivalent circuit diagram parameters provide satisfactory results. An extension of Canay’s equivalent circuit diagram is not necessary. Optimization of the discussed parameters leads to a significant improvement in comparison to the calculation with the parameters from the generator data sheet.

Originality/value

The unresolved doubt has been proven, that the Parka generator model with the manufacturer’s parameters can also be used for subsynchronous studies of electromechanical resonances of systems. However, it was advisable to improve the simulation results by optimizing the generator parameters used in the calculations. By optimizing the parameters for the SSRs, the calculation of the occurring torques has been significantly improved.
Modelling and co-simulation of a permanent magnet synchronous generator
Authors: Quintal-Palomo Roberto Eduardo , Gwozdziewicz Maciej , Dybkowski Mateusz
Published: July 2019

Purpose

The purpose of this paper is to obtain an accurate methodology for modelling and analysis of the permanent magnet synchronous generator connected to power electronic components.

Design/methodology/approach

This paper presents the methodology of the co-simulation of a permanent magnet synchronous generator. It combines Simulink, Maxwell and Simplorer software to demonstrate the electrical machine behaviour connected with the power electronics’ circuit. The finite element analysis performed on the designed machine exhibit a more accurate behaviour over simplified Simulink models. Results between both simulation and co-simulation are compared to measurements.

Findings

The co-simulation approach offers a more accurate depiction of the machine behaviour and its interaction with the non-linear circuits.

Research limitations/implications

This paper focuses on the interior permanent magnet type of PMSG and its interaction with a passive rectifier (nonlinear circuit).

Practical implications

The advanced capabilities of the co-simulation method allow to analyse more variations (geometry, materials, etc.), and its interaction with non-linear circuits, than previous simulation techniques.

Originality/value

The co-simulation as a tool for analysis and design of systems interconnected with unconventional and conventional electrical machines and prototypes, and the comparison of the obtained results with classical analysis and design methods, against measurements obtained from the prototype.
Simultaneous effects of multiple cues in restaurant reviews
Authors: Kim Esther L. , Tanford Sarah
Published: July 2019

Purpose

The purpose of this paper is to evaluate how consumers simultaneously process multiple cues for different dining occasions when making a restaurant decision.

Design/methodology/approach

This paper investigates the influence of priming (review prototype), effort (distance) and involvement (occasion) on restaurant evaluations, willingness to drive and willingness to pay for a restaurant meal. A 2 (prototype: negative, positive) × 2 (distance: close, far) × 2 (occasion: casual, special) between-subjects factorial design was used.

Findings

The paper finds that each variable influences a different outcome, whereby people rely on a review prototype for restaurant evaluation and choice, a distance cue for willingness to drive and a dining occasion for willingness to pay.

Practical implications

This paper suggests that restaurant marketers can highlight exemplary service through online reviews, increase profitability by promoting special occasions and geographically expand their market by attracting people to drive for a special dinner.

Originality/value

This paper evaluates the simultaneous interactive effects of multiple cues in service settings. It demonstrates that situational cues moderate the effect of primary cues in online reviews.