bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gamma oscillations in primate primary visual cortex are severely attenuated by small stimulus discontinuities
Authors: Shirhatti Vinay , Ravishankar Poojya , Ray Supratim 
Published: July 2020

SummaryGamma oscillations have been hypothesized to play an important role in feature binding, based on the observation that continuous long bars induce stronger gamma in the visual cortex than bars with a small gap. Recently, many studies have shown that natural images, that have discontinuities in several low-level features, do not induce strong gamma oscillations, questioning their role in feature binding. However, the effect of different discontinuities on gamma has not been well studied. To address this, we recorded spikes and local field potential from two monkeys while they were shown gratings with discontinuities in space, orientation, phase or contrast. Gamma, but not spiking activity, drastically reduced with small discontinuities in all cases, suggesting that gamma could be a resonant phenomenon. An excitatory-inhibitory population model with stimulus-tuned recurrent inputs showed such resonant properties. Therefore, gamma could be a signature of excitation-inhibition balance, which gets disrupted due to discontinuities.
Genomic GC content drifts slowly downward in most bacterial genomes
Authors: Ely Bert 
Published: July 2020

AbstractIn every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is slowly declining in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing at a slow rate. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of twoCaulobactergenomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genome content as well.
Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
Authors: Polydorides S. , Archontis G. 
Published: July 2020

ABSTRACTThe coronavirus SARS-CoV-2, that is responsible for the COVID-19 pandemic, and the closely related SARS-CoV coronavirus enter cells by binding at the human angiotensin converting enzyme 2 (hACE2). The stronger hACE2 affinity of SARS-CoV-2 has been connected with its higher infectivity. In this work, we study hACE2 complexes with the receptor binding domains (RBDs) of the human SARS-CoV-2 and human SARS-CoV viruses, using all-atom molecular dynamics (MD) simulations and Computational Protein Design (CPD) with a physics-based energy function. The MD simulations identify charge-modifying substitutions between the CoV-2 and CoV RBDs, which either increase or decrease the hACE2 affinity of the SARS-CoV-2 RBD. The combined effect of these mutations is small, and the relative affinity is mainly determined by substitutions at residues in contact with hACE2. Many of these findings are in line and interpret recent experiments. Our CPD calculations redesign positions 455, 493, 494 and 501 of the SARS-CoV-2 RBM, which contact hACE2 in the complex and are important for ACE2 recognition. Sampling is enhanced by an adaptive importance sampling Monte Carlo method. Sequences with increased affinity replace CoV-2 glutamine by a negative residue at position 493, and serine by nonpolar, aromatic or a threonine at position 494. Substitutions at positions positions 455 and 501 have a smaller effect on affinity. Substitutions suggested by our design are seen in viral sequences encountered in other species, including bat and pangolin. Our results might be used to identify potential virus strains with higher human infectivity and assist in the design of peptide-based or peptidomimetic compounds with the potential to inhibit SARS-CoV-2 binding at hACE2.SIGNIFICANCEThe coronavirus SARS-CoV-2 is responsible for the current COVID-19 pandemic. SARS-CoV-2 and the earlier, closely related SARS-CoV virus bind at the human angiotensin converting enzyme 2 (hACE2) receptor at the cell surface. The higher human infectivity of SARS-CoV-2 may be linked to its stronger affinity for hACE2. Here, we study by computational methods complexes of hACE2 with the receptor binding domains (RBDs) of viruses SARS-CoV-2 and SARS-CoV. We identify residues affecting the affinities of the two domains for hACE2. We also propose mutations at key SARS-CoV-2 positions, which might enhance hACE2 affinity. Such mutations may appear in viral strains with increased human infectivity and might assist the design of peptide-based compounds that inhibit infection of human cells by SARS-CoV-2.
Punctuated equilibrium as the default mode of evolution of large populations on fitness landscapes dominated by saddle points in the weak-mutation limit
Authors: Bakhtin Yuri , Katsnelson Mikhail I. , Wolf Yuri I. , Koonin Eugene V. 
Published: July 2020

AbstractPunctuated equilibrium is a mode of evolution in which phenetic change occurs in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but no major phenotypic change occurs. Punctuated equilibrium has been originally proposed within the framework of paleobiology, to explain the lack of transitional forms that is typical of the fossil record. Theoretically, punctuated equilibrium has been linked to self-organized criticality (SOC), a model in which the size of ‘avalanches’ in an evolving system is power-law distributed, resulting in increasing rarity of major events. We show here that, under the weak-mutation limit, a large population would spend most of the time in stasis in the vicinity of saddle points in the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNetime (Ne, effective population size), when a new beneficial mutation is fixed in the evolving population, which moves to a different saddle, or on much rarer occasions, from a saddle to a local peak. Thus, punctuated equilibrium is the default mode of evolution under a simple model that does not involve SOC or other special conditions.SignificanceThe gradual character of evolution is a key feature of the Darwinian worldview. However, macroevolutionary events are often thought to occur in a non-gradualist manner, in a regime known as punctuated equilibrium, whereby extended periods of evolutionary stasis are punctuated by rapid transitions between states. Here we analyze a mathematical model of population evolution on fitness landscapes and show that, for a large population in the weak-mutation limit, the process of adaptive evolution consists of extended periods of stasis, which the population spends around saddle points on the landscape, interrupted by rapid transitions to new saddle points when a beneficial mutation is fixed. Thus, punctuated equilibrium appears to be the default regime of biological evolution.
In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh
Authors: Shishir Tushar Ahmed , Naser Iftekhar Bin , Faruque Shah M. 
Published: July 2020

AbstractThe COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh.
Vesicle Navigation of Microtubule Ends Distinguished by A Single Rate-Constant Model
Authors: Gramlich M.W. , Gómez S. Balseiro , Tabei S. M. Ali , Parkes M. , Yogev S. 
Published: July 2020

AbstractAxonal motor driven cargo utilizes the microtubule cytoskeleton in order to direct cargo, such as presynaptic vesicle precursors, to where they are needed. This transport requires vesicles to travel up to microns in distance. It has recently been observed that finite microtubule lengths can act as roadblocks inhibiting vesicles and increasing the time required for transport. Vesicles reach the end of a microtubule and pause until they can navigate to a neighboring microtubule in order to continue transport. The mechanism by which axonal vesicles navigate the end of a microtubule in order to continue mobility is unknown. In this manuscript we model experimentally observed vesicle pausing at microtubule ends inC. elegans. We show that a single rate-constant model reproduces the time vesicles pause at MT-ends. This model is based on the time a vesicle must detach from its current microtubule and re-attach to a neighboring microtubule. We show that vesicle pause times are different for anterograde and retrograde motion, suggesting that vesicles utilize different proteins at plus and minus end sites. Last, we show that vesicles do not likely utilize a tug-of-war like mechanism and reverse direction in order to navigate microtubule ends.
Reentry guidance by accelerated fractional-order particle swarm optimization method
Authors: Sana Khurram Shahzad , Hu Weiduo 
Published: July 2020

Purpose
The aim of this study is to design a guidance method to generate a smoother and feasible gliding reentry trajectory, a highly constrained problem by formalizing the control variables profile.

Design/methodology/approach
A novel accelerated fractional-order particle swarm optimization (FAPSO) method is proposed for velocity updates to design the guidance method for gliding reentry flight vehicles with fixed final energy.

Findings
By using the common aero vehicle as a test case for the simulation purpose, it is found that during the initial phase of the longitudinal guidance, there are oscillations in the state parameters which cause to violate the path constraints. For the glide phase of the longitudinal guidance, the path constraints have higher values because of the increase in the atmosphere density.

Research limitations/implications
The violation in the path constraints may compromise the flight vehicle safety, whereas the enforcement assures the flight safety by flying it within the reentry corridor.

Originality/value
An oscillation suppression scheme is proposed by using the FAPSO method during the initial phase of the reentry flight, which smooths the trajectory and enforces the path constraints partially. To enforce the path constraints strictly in the glide phase, ultimately, another scheme by using the FAPSO method is proposed. The simulation results show that the proposed algorithm is efficient to achieve better convergence and accuracy for nominal as well as dispersed conditions.
Changes in industrial network logics: the case of the Japanese retail industry
Authors: Hara Yoritoshi 
Published: July 2020

PurposeThis study aims to examine changes in “network logics” that refer to cognitive views socially accepted by actors about the network. These logics provide organizations with templates on how to act in business networks. This study investigates the causes and processes of network logic changes and the phases in the changes.Design/methodology/approachThis study relies on content analysis using text data from newspaper articles on global retailers entering the Japanese retail industry. Three different logics were found to describe the actions of the retailers. Two of the logics are related to institutional and strategic logics including network logics, while the third is associated with institutional works that mean actions to create, maintain and disrupt institutions.FindingsWith regard to transitions in network logics in the Japanese retail industry, the analysis identified four phases: politicization, reflection, establishment and evaluation. Changes in regulative and normative logics were resulted from institutional works of the global retailers into the Japanese market. The findings also include empirical description about how network changes progress through interactions among business actors. Additionally, compared to the regulative and normative logics, it would be difficult to influence the cultural-cognitive logics.Originality/valueBusiness networks often transform with changes in network logics. This study contributes to the literature on industrial network changes by exploring the interactions between macro-level structural states and micro-level events in network logic transitions.
Dermoscopic clues of palmoplantar hyperkeratotic eczema and palmoplantar psoriasis: A prospective, comparative study of 90 patients
Authors: Çetinarslan Tubanur , Türel Ermertcan Aylin , Temiz Peyker 
Published: July 2020

AbstractDiagnosis can be difficult in isolated palmar and plantar lesions in patients with psoriasis and eczema. The purpose of our study is to compare the dermoscopic findings in patients with palmoplantar psoriasis and palmoplantar hyperkeratotic eczema. This prospective, comparative study included 90 patients histopathologically diagnosed with eczema or psoriasis (35 psoriasis and 55 eczema). The age range was 18–75 years. The most common vessel type was dot vessel in psoriasis. Red globular ring vessels were seen in five patients with psoriasis, but not in any with eczema (P = 0.007). The most common vascular distribution pattern was regular in psoriasis (40%). Patchy vascular pattern was significant in eczema. The most common background color was light red in psoriasis (48.6%) (P < 0.001). Brownish‐orange globules were observed in 25.7% of patients with eczema and 5.7% in patients with psoriasis (P = 0.02). There is only one study in the published work about dermoscopy of palmoplantar psoriasis and eczema. In our study, yellow crusts, patchy scale distribution, patchy vascular pattern, yellow scale color, dull red background color and brownish‐orange globules were significant in patients with palmoplantar eczema. On the other hand, patients with psoriasis had light red background color, regular vascular distribution pattern and white scale color. We observed globule structures with a pale center and dark peripheral rim only in patients with eczema, which was not identified in previous studies. This globule structure may be a new finding in eczema.
Resveratrol ameliorates thymus senescence changes in D‐galactose induced mice
Authors: Wei Ting‐ting , Li Meng‐jie , Guo Li , Xie Yan‐dong , Chen Wen‐hui , Sun Yun , Liu Guo‐hong , Ding Yi , Chai Yu‐rong 
Published: July 2020

AbstractThe thymic microenvironment plays an important role in the development of T cells. A decrease of thymic epithelial cells is the main cause of age‐related thymic atrophy or degeneration. Resveratrol (RSV), a phytoalexin produced from plants, has been shown to inhibit the adverse effects of dietary obesity on the structure and function of the thymus. D‐Galactose (D‐gal) can induce accelerated aging in mice. In the present study, young mice (2 months old) were injected with D‐gal (120 mg/kg/day) for 8 consecutive weeks to construct an accelerated aging model. Compared with normal control mice, the thymus epithelium of the D‐gal treated mice had structural changes, the number of senescent cells increased, the number of CD4+ T cells decreased, and CD8+ T cells increased. After RSV administration by gavage for 6 weeks, it was found that RSV improved the surface phenotypes of D‐gal treated mice, and recovered thymus function by maintaining the ratio of CD4+ to CD8+ cells. It also indicated that RSV enhanced the cell proliferation and inhibited cell senescence. Increased autoimmune regulator (Aire) expression was present in the RSV treated mice. The lymphotoxin‐beta receptor (LTβR) expression also increased. These findings suggested that RSV intake could restore the alterations caused by D‐gal treatment in the thymus via stimulation of Aire expression.
Alteration in miRNAs expression in paediatric acute lymphocyticleukaemia: Insight into patients' therapeutic response
Authors: El‐maadawy Eman A. , Bakry Rania M. , Moussa Mohamed M. , El‐Naby SobhyHasab , Talaat Roba M. 
Published: July 2020

AbstractMicroRNAs (miRNAs) revealed themselves as potential tumour markers and play a significant role in the pathogenesis and progression of acute lymphocytic leukaemia (ALL). This work is designed to investigate the expression of miR‐21, miR‐26, miR‐148a, miR‐133b and miR‐24 in paediatric ALL patients in response to treatment. The expression of miRNAs was determined by quantitative reverse transcriptase–polymerase chain reaction (qRT–‐PCR) in 43 paediatric ALL patients (33 treatment responders and 10 non‐responders) compared to 42 healthy controls. miR‐21, miR‐148a, and miR‐24 were found to be significantly (P < .05, P < .01, P < .05; respectively) up‐regulated in ALL patients compared to controls. No statistically significant differences in expression levels of miR‐26a and miR133b were detected in both groups. Concerning treatment, responders are found to have a decreased level of miR‐24 compared to non‐responder patients. A significant increase (P < .01) in miR‐24 expression level in relapsed patients compared to non‐relapsed ones was found. Positive correlations were detected between miR‐148a and miR‐24 (r = .347; P < .05) and between miR‐26a and miR‐24 (r = .353; P < .05) in ALL group. The highest sensitivity (72%) and specificity (81%) among miRNAs were detected in miR‐24 at a cut‐off value of 2.928. Taken together, the up‐regulation of tumour suppressor miRNA(miR‐148a) concur with the up‐regulation of oncomiR (miR‐21) might provide a new era that could help in disease management strategy. The reduction of oncomiR‐24 is one of the promising effects of treatment. A larger prospective study is highly recommended to confirm our findings.
The Heritability of Palatal Rugae Morphology Among Siblings*†
Authors: Chong Jun Ai , Syed Mohamed Alizae Marny Fadzlin , Marizan Nor Murshida , Pau Allan 
Published: July 2020

AbstractAlthough there is clinical applicability of the palatal rugae as an identification tool in forensic odontology, controversy exists whether the palatal rugae patterns are stable or variable. The greater the genetic component, the higher the probability that palatal rugae patterns are stable. The aim of this study was to compare the palatal rugae morphology between full siblings and the proportion of variability due to genetic component. This cross‐sectional study was conducted on digital models of 162 siblings aged 15–30 years old. The palatal rugae patterns were assessed with Thomas and Kotze (1983) classification using Geomagic Studio software (3D Systems, Rock Hill, SC). The palatal rugae morphology between siblings showed significantly similar characteristics for total number of left rugae (p = 0.001), left primary rugae (p = 0.017), secondary rugae for right (p = 0.024) and left sides (p = 0.001), right straight rugae (p = 0.010), and right convergent rugae (p = 0.005) accounting for at least 6.25%‐12.8% of the variability due to heredity. Despite the similarities found, the palatal rugae patterns showed significant differences between siblings of at least 46.9% (p = 0.001). Zero heritability was found in 9 of the 14 rugae patterns. Meanwhile, total number of rugae, primary, backward, and convergent rugae showed moderate heritability (h2 > 0.3) and total number of secondary rugae showed high heritability (h2 > 0.6). In conclusion, despite the individuality characteristics, an appreciable hereditary component is observed with significant similarities found between sibling pairs and the palatal rugae patterns were both environmentally and genetically influenced.
Analysis of insects colonised on human corpses during autopsy in Riyadh, Saudi Arabia
Authors: Mashaly Ashraf , Al‐Khalifa Mohammed , Al‐Qahtni Abdulmani , Alshehri Adel 
Published: July 2020

AbstractIn medicolegal cases, an analysis of the presence of insects on human bodies may have potential legal significance. This study investigates the presence of insects on human bodies during autopsies in legal medicine. It was implemented in Riyadh, Saudi Arabia. Nine cadavers were examined, respectively, from four cases of homicide, two cases of burning, one suicide, one accident and one case of neglect. Insects associated with the human corpses were carefully collected and identified using valid taxonomic keys. Three of the cadavers were of children with ages ranging from seven months to nine years. In seven cases decomposition had occurred outdoors while in two cases it was indoors. Overall, eleven different species of insects were identified. Six of the cases exhibited species from five families within Diptera (Calliphoridae, Muscidae, Ulidiidae, Tachinidae and Sarcophagidae), specifically Chrysomya albiceps (Wiedemann), Musca domestica (Linnaeus), Tachinidae sp. (Bigot), Physiphora alceae (Preyssler) and Sarcophaga dux (Thompson). Six of the cadavers hosted beetles, which were identified as Dermestes maculatus (DeGeer), D. frischii (Kugelann), Necrobia rufipes (Fabricius), Nitidula bipunctata (Linnaeus), Pimelia interjecta (Solier) and Latridiidae sp. (Erichson). Moreover, the suicide corpse was colonised by more fly species than the other corpses, while the beetles colonised the homicide and accident corpses more than the other corpses. Analysis of the diversity of insects on human corpses may lead to advances in the understanding of forensic entomology and more sophisticated estimates of the minimum post‐mortem interval.