bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of non-analytical corrections on the phononic thermal transport in InX (X = S, Se, Te) monolayers
Authors: Shafique Aamir , Shin Young-Han
Published: January 2020

We investigate the effect of non-analytical corrections on the phonon thermal transport properties in two-dimensional indium chalcogenide compounds. The longitudinal optical (LO) and transverse optical (TO) branches in the phonon dispersion are split near the Γ-point. The lattice thermal conductivity of monolayer InS is increased by 30.2% under non-analytical corrections because of the large LO-TO splitting at Γ-point. The predicted lattice thermal conductivities with non-analytical corrections at room temperature are 57.1 W/mK, 44.4 W/mK and 33.1 W/mK for the monolayer InS, InSe and InTe, respectively. The lattice thermal conductivity can be effectively reduced by nanostructures because the representative mean free paths are found very large in these monolayers. By quantifying the relative contribution of the phonon modes to the lattice thermal conductivity, we predict that the longitudinal acoustic branch is the main contributor to the lattice thermal conductivity. Due to the low lattice thermalconductivities of these monolayers, they can be useful in the nanoscale thermoelectric devices.
Ovarian mitochondrial dynamics and cell fate regulation in an androgen-induced rat model of polycystic ovarian syndrome
Authors: Salehi Reza , Mazier Hannah L. , Nivet Anne-Laure , Reunov Arkadiy A. , Lima Patricia , Wang Qi , Fiocco Arianna , Isidoro Ciro , Tsang Benjamin K.
Published: January 2020

In this study, we investigated in an androgenized rat model the involvement of autophagy and mitochondrial dynamics in granulosa cells in the pathogenesis of polycystic ovarian syndrome (PCOS) and its modulation by exogenous gonadotropin (eCG). We found 5α-dihydrotestosterone (DHT) treatment reduces ovarian length and weight with predominantly late antral and/or preovulatory stage follicles and no corpora lutea. DHT increased the population of large lysosomes (>50 micron) and macroautophagy, an event associated with granulosa cell apoptosis. Increased granulosa cell Dynamin Related Protein 1 (Drp1) content in the DHT group was accompanied by increased circular and constricted, but reduced rod-shaped, mitochondria. eCG eliminated all atypical follicles and increased the number of late antral and preovulatory follicles with less granulosa cell apoptosis. eCG-treated rats had a higher proportion of connected mitochondria, and in combination with DHT had a lower proportion of circular and constricted mitochondria than rats treated with DHT alone, suggesting that eCG induces mitochondrial fusion and attenuates fission in granulosa cells. In summary, we observed that DHT-induced up-regulation of Drp1 is associated with excessive mitochondrial fission, macroautophagy and apoptosis in granulosa cells at the antral stage of development in an androgenized rat model for PCOS, a response partially attenuated by exogenous gonadotropin.
Consciousness & Brain Functional Complexity in Propofol Anaesthesia
Authors: Varley Thomas F. , Luppi Andrea I. , Pappas Ioannis , Naci Lorina , Adapa Ram , Owen Adrian M. , Menon David K. , Stamatakis Emmanuel A.
Published: January 2020

The brain is possibly the most complex system known to mankind, and its complexity has been called upon to explain the emergence of consciousness. However, complexity has been defined in many ways by multiple different fields: here, we investigate measures of algorithmic and process complexity in both the temporal and topological domains, testing them on functional MRI BOLD signal data obtained from individuals undergoing various levels of sedation with the anaesthetic agent propofol, replicating our results in two separate datasets. We demonstrate that the various measures are differently able to discriminate between levels of sedation, with temporal measures showing higher sensitivity. Further, we show that all measures are strongly related to a single underlying construct explaining most of the variance, as assessed by Principal Component Analysis, which we interpret as a measure of “overall complexity” of our data. This overall complexity was also able to discriminate between levels of sedation and serum concentrations of propofol, supporting the hypothesis that consciousness is related to complexity - independent of how the latter is measured.
Potential effect of non-thermal plasma for the inhibition of scar formation: a preliminary report
Authors: Wang Xiao-Feng , Fang Qing-Qing , Jia Bing , Hu Yan-Yan , Wang Zheng-Cai , Yan Ke-ping , Yin Sheng-Yong , Liu Zhen , Tan Wei-Qiang
Published: January 2020

Non-thermal plasma (NTP) is a promising biomedical tool for application to wound healing. However, there is limited scientific evidence that confirms its efficacy to inhibit scar formation. This study aims to investigate the role of non-thermal plasma in scar formation. Two full-thickness dorsal cutaneous wounds of rats were treated with either a non-thermal helium plasma jet or helium. It was determined that the non-thermal plasma jet accelerated the wound healing process from 5 days after surgery (day 5: 41.27% ± 2.351 vs 54.7% ± 5.314, p < 0.05; day 7: 56.05% ± 1.881 vs 75.28% ± 3.914, p < 0.01; day 14: 89.85% ± 2.991 vs 98.07% ± 0.839, p < 0.05). The width of the scars for the NTP group was narrower than those of control group (4.607 ± 0.416 mm vs 3.260 ± 0.333 mm, p < 0.05). In addition, a lower level of TGF-β1, p-Smad2 and p-Smad3 were detected in the NTP treated wounds (p < 0.05, p < 0.01 and p < 0.01). As expected, α-SMA was also significantly decreased in the NTP treatment group (p < 0.01). Moreover, the expression of type I collagen and the proportion of type I to III collagen were lower in the NTP group (p < 0.05). The results of the study suggest that NTP may play a potential role in scar formation by inhibiting the TGF β1 signal pathway and reducing the levels of α-SMA and type I collagen, and may have clinical utility in the future.
Imbalance in B cell and T Follicular Helper Cell Subsets in Pulmonary Sarcoidosis
Authors: Kudryavtsev I. , Serebriakova M. , Starshinova A. , Zinchenko Y. , Basantsova N. , Malkova A. , Soprun L. , Churilov L. P. , Toubi E. , Yablonskiy P. , Shoenfeld Y.
Published: January 2020

Sarcoidosis is a systemic granulomatous disease that develops due to the Th1, Th17 and Treg lymphocytes disturbance. There is an assumption, that B cells and follicular T-helper (Tfh) cells may play an important role in this disorder, as well as in several other autoimmune diseases. The aim of this study was to determine CD19+ B cells subset distribution in the peripheral blood and to define disturbance in the circulating Tfh cells subsets in patients with sarcoidosis. The prospective comparative study was performed in 2016–2018, where peripheral blood B cell subsets and circulating Tfh cell subsets were analyzed in 37 patients with primarily diagnosed sarcoidosis and 35 healthy donors using multicolor flow cytometry. In the results of our study we found the altered distribution of peripheral B cell subsets with a predominance of “naïve” (IgD + CD27−) and activated B cell (Bm2 and Bm2′) subsets and a decreased frequency of memory cell (IgD+ CD27+ and IgD− CD27+) in peripheral blood of sarcoidosis patients was demonstrated. Moreover, we found that in sarcoidosis patients there are increased levels of B cell subsets, which were previously shown to display regulatory capacities (CD24+++ CD38+++ and CD5 + CD27−). Next, a significantly higher proportion of CXCR5-expressing CD45RA − CCR7+ Th cells in patients with sarcoidosis in comparison to the healthy controls was revealed, that represents the expansion of this memory Th cell subset in the disease. This is the first study to demonstrate the association between the development of sarcoidosis and imbalance of circulating Tfh cells, especially CCR4− and CXCR3-expressing Tfh subsets. Finally, based on our data we can assume that B cells and Tfh2- and Tfh17-like cells – most effective cell type in supporting B-cell activity, particularly in antibody production – may be involved in the occurrence and development of sarcoidosis and in several other autoimmune conditions. Therefore, we can consider these results as a new evidence of the autoimmune mechanisms in the sarcoidosis development.
p53 functional states are associated with distinct aldehyde dehydrogenase transcriptomic signatures
Authors: Gui Shanying , Xie Xiujie , O’Neill Wendi Q. , Chatfield-Reed Kate , Yu Jun-Ge , Teknos Theodoros N. , Pan Quintin
Published: January 2020

p53 and aldehyde dehydrogenase (ALDH) have been implicated in key tumorigenesis processes including cancer initiating cell (CIC) maintenance; however, the relationship between these two mediators remains poorly defined. In this study, ALDH isoform expression diversity was revealed in CICs with disparate p53 functional states: gain of function, high risk p53 mutation (p53HRmut) and wildtype p53 (p53WT) inactivated by the human papillomavirus 16 (HPV16) E6 oncogene. Interrogation of head and neck squamous cell carcinoma (HNSCC) cell lines and patient tumors showed that HPV16+/p53WT cases have higher ALDH variance score (AVS), a measure of tumor ALDH isoform expression diversity, compared to HPV−/p53HRmut cases (p = 0.03). AVS and several individual ALDH isoforms were associated with prognosis in HPV16+/p53WT HNSCC but not in HPV−/p53HRmut HNSCC. Knockdown of the dominant ALDH isoform in high AVS HNSCC depleted the CIC pool in vitro and in vivo. Our results demonstrate that p53 functional states are associated with distinct ALDH isoform transcriptomic signatures. Moreover, tumor ALDH profiling may provide insight on which ALDH isoform to target in high AVS HNSCC tumors to deplete the CIC population.
Design and implementation of magnetically–tunable quad–band filter utilizing split–ring resonators at microwave frequencies
Authors: Asci Cihan , Sadeqi Aydin , Wang Wei , Rezaei Nejad Hojatollah , Sonkusale Sameer
Published: January 2020

In this article, we present a magnetically–tunable quad–band filter with high tunability in the frequency range of 2.1–3.9 GHz. A multi–band filter with four stop–bands comprises of a microstrip line coupled to four frequency–selective split–ring resonators (SRRs). We achieve tuning of individual frequency bands using magnetic reed switches connected in between the capacitive gaps of each split–ring resonator. Application of magnetic field tunes this capacitance affecting its resonance frequency. The measured reflection spectrum of the proposed device matches well with the simulation results. The results show more than 25% tunability for each of the four bands with bandwidth values in the range of 30–70 MHz with over 100% overall tunability in the 2.1–3.9 GHz frequency spectrum.
Nocturnal heart rate variability may be useful for determining the efficacy of mandibular advancement devices for obstructive sleep apnea
Authors: Kim Jeong-Whun , Kwon Sung Ok , Lee Woo Hyun
Published: January 2020

A mandibular advancement device (MAD) is recommended as an alternative therapy for obstructive sleep apnea (OSA), which effectively reduces the collapsibility of the upper airway during sleep by advancing the mandible. However, the effects of MAD therapy on cardiac autonomic modulation remain unclear. We evaluated the effects of MAD on nocturnal heart rate variability (HRV) in OSA. Anthropometric data, questionnaire results, and HRV parameters (evaluated using time domain and frequency domain methods) of 58 adult patients with OSA treated with MAD therapy were retrospectively reviewed. All patients underwent polysomnography at baseline and 3-month follow-up. The average normal-to-normal (NN) interval, standard deviation of the NN interval, low-frequency power in normalized units (LFnu), and high-frequency power in normalized units (HFnu) showed significant changes with MAD therapy. Based on the criteria for success (decrease in the apnea-hypopnea index by >50% and value <20/h), 34 and 24 patients were classified into the response and nonresponse groups, respectively. No differences in baseline characteristics were detected between groups, except for higher body mass index and lower minimal oxygen saturation in the nonresponse group. A subgroup analysis indicated that the average NN interval and HFnu significantly increased, and that Total power (TP), very low frequency, low frequency(LF), low frequency/high frequency and LFnu significantly decreased compared to baseline in the response group; however, no HRV changes were found in the nonresponse group. After adjusting for age, sex, and body mass index, the response group showed significant changes from baseline in TP and LF compared to the nonresponse group. Therefore, HRV may be useful for determining the efficacy of MAD therapy in OSA.
Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort
Authors: Rodriguez-Campos S. , Rostaher A. , Zwickl L. , Fischer N. , Brodard I. , Vidal S. , Brandt B. W. , Favrot C. , Perreten V.
Published: January 2020

Canine atopic dermatitis (CAD) is a prevalent inflammatory skin disease of dogs worldwide. Certain breeds such as the West Highland White Terriers (WHWT) are predisposed to suffer from CAD. Microbial dysbiosis is known to play a significant role in the pathogenesis of the disease, which is similar to its human counterpart, atopic dermatitis (AD). To date, no large cohort-study has been conducted in a predisposed dog breed to study the impact of the early-life microbiota on the development of CAD, as well as the possible implication of factors such as hygiene and access to the outdoors. In this study skin samples of 143 WHWT, including 109 puppies up to three weeks old and 34 parent dogs, from 17 breeders, were subjected to 16S rRNA gene and ITS2 amplicon sequencing to disclose the bacterial and fungal oral and skin microbiota, respectively. The oral samples served as a control group to confirm differences between haired and mucosal surfaces. The cutaneous microbiota differed between sample sites and age of the dogs. The season of sampling, geographical origin as well as hygiene status of the household and the access to the outdoors shaped the skin microbiota of the puppies significantly. However, we found that the individual early-life microbiota did not predispose for the later development of CAD.
Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure
Authors: Matern William M. , Jenquin Robert L. , Bader Joel S. , Karakousis Petros C.
Published: January 2020

Mycobacterium avium subsp. hominissuis (MAH) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying lung impairment. Disease due to MAH is particularly difficult to treat, often requiring years of antibiotic therapy. Identification of genes essential for MAH growth may lead to novel strategies for improving curative therapy. Here we have generated saturating genome-wide transposon mutant pools in a strain of MAH (MAC109) and developed a novel computational technique for classifying annotated genomic features based on the in vitro effect of transposon mutagenesis. Our findings may help guide future genetic and biochemical studies of MAH pathogenesis and aid in the identification of new drugs to improve the treatment of these serious infections.
Characterization of the woody biomass feedstock potential resulting from California’s drought
Authors: Tubbesing Carmen L. , Lara José Daniel , Battles John J. , Tittmann Peter W. , Kammen Daniel M.
Published: January 2020

Regional tree die-off events generate large quantities of standing dead wood, raising concern over catastrophic wildfire and other hazards. Governmental responses to tree die-off have often focused on incentivizing biomass energy production that utilizes standing dead trees removed for safety concerns. However, the full distribution of potential woody bioenergy feedstock after tree die-off has not been evaluated due to the complexities of surveying and precisely measuring large forested areas. In this paper, we present a novel method for estimating standing dead biomass at a fine spatial resolution that combines aerial survey data with forest structure maps. Using this method, we quantify biomass generated by the unprecedented tree die-off that occurred in California following a 4-year drought and widespread pest outbreaks. The results are used to estimate feasibly recoverable feedstock for energy production. We find that approximately 95.1 million bone-dry tons (BDT) of dead biomass resulted from 2012–2017 mortality, with a lower bound of 26.2 million BDT. In other words, of the aboveground live tree biomass in 2012, ~1.3–4.8% died by 2017. Of the standing dead biomass, 29% meets minimum constraints for potential cost-effective bioenergy feedstock. This proportion drops to as low as 15% in the most affected areas due to terrain slope, wilderness status, and other factors, highlighting the need to complement disposal via biomass energy with other strategies to mitigate the risks of the tree mortality crisis, which is likely to only become more severe over time due to climate change.
In silico Design of a Multivalent Vaccine Against Candida albicans
Authors: Tarang Shikha , Kesherwani Varun , LaTendresse Blake , Lindgren Laramie , Rocha-Sanchez Sonia M. , Weston Michael D.
Published: January 2020

Invasive candidiasis (IC) is the most common nosocomial infection and a leading cause of mycoses-related deaths. High-systemic toxicity and emergence of antifungal-resistant species warrant the development of newer preventive approaches against IC. Here, we have adopted an immunotherapeutic peptide vaccine-based approach, to enhance the body’s immune response against invasive candida infections. Using computational tools, we screened the entire candida proteome (6030 proteins) and identified the most immunodominant HLA class I, HLA class II and B- cell epitopes. By further immunoinformatic analyses for enhanced vaccine efficacy, we selected the 18- most promising epitopes, which were joined together using molecular linkers to create a multivalent recombinant protein against Candida albicans (mvPC). To increase mvPC’s immunogenicity, we added a synthetic adjuvant (RS09) to the mvPC design. The selected mvPC epitopes are homologous against all currently available annotated reference sequences of 22 C. albicans strains, thus offering a higher coverage and greater protective response. A major advantage of the current vaccine approach is mvPC’s multivalent nature (recognizing multiple-epitopes), which is likely to provide enhanced protection against complex candida antigens. Here, we describe the computational analyses leading to mvPC design.
Quantifying the risk of rabies in biting dogs in Haiti
Authors: Ma Xiaoyue , Blanton Jesse D. , Millien Max Francois , Medley Alexandra M. , Etheart Melissa D. , Fénelon Natael , Wallace Ryan M.
Published: January 2020

Rabies is a fatal viral disease typically transmitted through the bite of rabid animal. Domestic dogs cause over 99% of human rabies deaths. Over half of the world’s population lives in a country where the canine rabies virus variant is endemic and dog bites are common. An estimated 29 million people worldwide receive post-bite vaccination after being exposed to animals suspected of rabies. Accurate and timely risk assessment of rabies in biting dogs is critical to ensure that rabies PEP is administered to all persons with a suspected rabies exposure, while avoiding PEP administration in situations where rabies can be definitively ruled out. In this study, a logistic regression model was developed to quantify the risk of rabies in biting dogs, using data from Haiti’s animal rabies surveillance program. Significant risk factors identified in the model were used to quantify the probability of rabies in biting dogs. The risk of rabies in a biting dog as assessed through Haiti’s rabies surveillance program was highly elevated when the dog displayed hypersalivation (OR = 34.6, 95% CI 11.3–106.5) or paralysis (OR = 19.0, 95% CI 4.8–74.8) and when the dog was dead at the time of the assessment (OR = 20.7, 95% CI 6.7–63.7). Lack of prior rabies vaccination, biting 2 or more people, and if the dog was a puppy also increased the probability that a biting dog would have rabies. The model showed high sensitivity (100%) and specificity (97%) when examined using validation data. This model enables us to project the risk of rabies in biting dogs in Haiti shortly after the bite event and make provisional PEP recommendations prior to laboratory testing or dog quarantine results. Application of this model may improve adherence to PEP for bite victims who can be educated on the quantitative risk of the exposure event. This model can also be used to reduce unnecessary PEP costs when the risk of rabies is determined as sufficiently low and the animal is available for observation.
Likelihood contrasts: a machine learning algorithm for binary classification of longitudinal data
Authors: Klén Riku , Karhunen Markku , Elo Laura L.
Published: January 2020

Machine learning methods have gained increased popularity in biomedical research during the recent years. However, very few of them support the analysis of longitudinal data, where several samples are collected from an individual over time. Additionally, most of the available longitudinal machine learning methods assume that the measurements are aligned in time, which is often not the case in real data. Here, we introduce a robust longitudinal machine learning method, named likelihood contrasts (LC), which supports study designs with unaligned time points. Our LC method is a binary classifier, which uses linear mixed models for modelling and log-likelihood for decision making. To demonstrate the benefits of our approach, we compared it with existing methods in four simulated and three real data sets. In each simulated data set, LC was the most accurate method, while the real data sets further supported the robust performance of the method. LC is also computationally efficient and easy to use.
Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria
Authors: Capt Charlotte , Bouvet Karim , Guerra Davide , Robicheau Brent M. , Stewart Donald T. , Pante Eric , Breton Sophie
Published: January 2020

In animals, strictly maternal inheritance (SMI) of mitochondria is the rule, but one exception (doubly uniparental inheritance or DUI), marked by the transmission of sex-specific mitogenomes, has been reported in bivalves. Associated with DUI is a frequent modification of the mitochondrialcox2gene, as well as additional sex-specific mitochondrial genes not involved in oxidative phosphorylation. With the exception of freshwater mussels (for 3 families of the order Unionida), these DUI-associated features have only been shown in few species [within Mytilidae (order Mytilida) and Veneridae (order Venerida)] because of the few complete sex-specific mitogenomes published for these orders. Here, we present the complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida,Scrobicularia plana(Semelidae) andLimecola balthica(Tellinidae). These species display the largest differences in genome size between sex-specific mitotypes in DUI species (>10 kb), as well as the highest mtDNA divergences (sometimes reaching >50%). An important in-frame insertion (>3.5 kb) in the malecox2gene is partly responsible for the differences in genome size. TheS. plana cox2gene is the largest reported so far in the Kingdom Animalia. The mitogenomes may be carrying sex-specific genes, indicating that general mitochondrial features are shared among DUI species.
The morphology of an intercalated Au layer with its effect on the Dirac point of graphene
Authors: Bayani Amirhossein , Larsson Karin
Published: January 2020

This is a theoretical investigation where Density Functional Theory (DFT) has been used in studying the phenomenon of Au intercalation within the 4H-SiC/graphene interface. The electronic structure of some carefully chosen morphologies of the Au layer has then been of special interest to study. One of these specific Au morphologies is of a more hypothetical nature, whilst the others are, from an experimental point of view, realistic ones. The latter ones were also found to be energetically stable. Band structure calculations showed that intercalated Au layers with morphologies different from a planar Au layer will induce a band gap at the Dirac point of graphene (with up to 174 meV for the morphologies studied in the present work). It should here be mentioned that this bandgap size is four times larger than the energy of thermal motion at room temperature (26 meV). These findings reveal that a wide bandgap at the Dirac point of graphene comes from an inhomogeneous staggered potential on the Au layer, which non-uniformly breaks the sublattice symmetry. The presence of spin-orbit (SO) interactions have also been included in the present study, with the purpose to find out if SO will create a bandgap and/or band splitting of graphene.
Adjuvant-free immunization with infective filarial larvae as lymphatic homing antigen carriers
Authors: Card Catherine , Wilson David S. , Hirosue Sachiko , Rincon-Restrepo Marcela , de Titta Alexandre , Güç Esra , Martin Coralie , Bain Odile , Swartz Melody A. , Kilarski Witold W.
Published: January 2020

Controlled infection with intestinal nematodes has therapeutic potential for preventing the symptoms of allergic and autoimmune diseases. Here, we engineered larvae of the filarial nematodeLitomosoides sigmodontisas a vaccine strategy to induce adaptive immunity against a foreign, crosslinked protein, chicken egg ovalbumin (OVA), in the absence of an external adjuvant. The acylation of filarial proteins with fluorescent probes or biotin was not immediately detrimental to larval movement and survival, which died 3 to 5 days later. At least some of the labeled and skin-inoculated filariae migrated through lymphatic vessels to draining lymph nodes. The immunization potential of OVA-biotin-filariae was compared to that of an OVA-bound nanoparticulate carrier co-delivered with a CpG adjuvant in a typical vaccination scheme. Production of IFNγ and TNFα by restimulated CD4+ cells but not CD8+ confirmed the specific ability of filariae to stimulate CD4+T cells. This alternative method of immunization exploits the intrinsic adjuvancy of the attenuated nematode carrier and has the potential to shift the vaccination immune response towards cellular immunity.
Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9
Authors: Sakurai Takayuki , Kamiyoshi Akiko , Kawate Hisaka , Watanabe Satoshi , Sato Masahiro , Shindo Takayuki
Published: January 2020

The CRISPR/Cas9 system is widely used to generate gene-edited animals. Here, we developed an efficient system for generating genetically modified mice using maternal Cas9 from Cas9 transgenic mice. Using this system, we achieved lower mosaicism and higher rates of knock-in success, gene-editing, and birth compared to the similar parameters obtained using exogenously administered Cas9 (mRNA/protein) system. Furthermore, we successfully induced simultaneous mutations at multiple loci (a maximum of nine). Our novel gene-editing system based on maternal Cas9 could potentially facilitate the generation of mice with single and multiple gene modifications.
The PoV mycovirus affects extracellular enzyme expression and fruiting body yield in the oyster mushroom, Pleurotus ostreatus
Authors: Song Ha-Yeon , Kim Nayeon , Kim Dae-Hyuk , Kim Jung-Mi
Published: January 2020

Isogenic virus-cured and virus-infected fungal strains were previously obtained and compared to investigate mycoviral diseases and, specifically, the influence of viral infection on the vegetative growth of Pleurotus ostreatus. The present study demonstrated that infection with mycovirus PoV-ASI2792 (PoV) caused phenotypic and physiological changes in fungal cells and mycelia. The microscopically determined growth rate of the virus-infected strain was lower than that of the virus-cured strain, due to the conglomerate phenomenon during the mycelial growth process. An exploration of the viral effects of PoV on fruiting bodies yield showed significantly lower than that on virus-cured P. ostreatus. A colorimetric assay of polyphenol oxidase activity in the strains showed very weak activity in the virus-infected strain. To estimate the activity levels of enzymes related to the growth and fruiting body formation, the relative expression levels of genes encoding various extracellular enzymes such as Carbohydrate-Active Enzymes (CAZymes) were measured by quantitative RT-PCR. The expression levels of the assayed genes were significantly lower in virus-infected than in virus-cured P. ostreatus. Together, these results indicate that PoV infection affects the spawn growth and fruiting body formation of P. ostreatus via decreased expression and activity of some extracellular enzymes including lignocellulolytic enzymes.
Reference Jitter Values for Concentric Needle Electrode of Orbicularis Oculi and Frontalis Muscles Using Voluntary Activation Method in Sudanese Population
Authors: Musa Afraa M. M. , Ahmed Ammar E. M.
Published: January 2020

Single fibre electromyography is the most sensitive neurophysiological test for the diagnosis of neuromuscular junction disorders, particularly myasthenia gravis. The study aimed at establishing concentric needle (CN) normal jitter values for voluntarily activated orbicularis-oculi (V-OOc) & Frontalis (V-FRO) muscles in Sudanese population. 57 healthy volunteers (20 males & 37 females) were included in the study (mean Age 43.6 ± 14.2 years, range 18–70 years). V-OOc and V-FRO were tested in the same individual using CN. Jitter values were expressed as the mean consecutive difference (MCD) of 30 potential pairs in microseconds. The mean jitter, mean individual fibre pairs jitter & mean outliers jitter values with (upper 95% Confidence Limit-CL) for [OOc] were [26.9 ± 3.3 (31.97), 26.1 ± 8.9 (41.8) & 38.5 ± 5.7 (49.0) µs] & for [FRO] were [27.1 ± 3.0 (31.32), 26.4 ± 9.4 (42.9) & 39.9 ± 5 (49.2) µs] respectively. The suggested practical upper limits for mean jitter & for outliers were (32, 49 µs) for OOc & (31, 49 µs) for FRO. Our CN-jitter values were within the range of the few published studies. The study was unique in that it established and compared between CN reference jitter values of two voluntarily activated facial muscles (V-OOc & V-FRO) in the same individual in large number of healthy subjects.
Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits
Authors: Shikov Anton E. , Skitchenko Rostislav K. , Predeus Alexander V. , Barbitoff Yury A.
Published: January 2020

Over the recent decades, genome-wide association studies (GWAS) have dramatically changed the understanding of human genetics. A recent genetic data release by UK Biobank (UKB) has allowed many researchers worldwide to have comprehensive look into the genetic architecture of thousands of human phenotypes. In this study, we used GWAS summary statistics derived from the UKB cohort to investigate functional mechanisms of pleiotropic effects across the human phenome. We find that highly pleiotropic variants often correspond to broadly expressed genes with ubiquitous functions, such as matrisome components and cell growth regulators; and tend to colocalize with tissue-shared eQTLs. At the same time, signaling pathway components are more prevalent among highly pleiotropic genes compared to regulatory proteins such as transcription factors. Our results suggest that protein-level pleiotropy mediated by ubiquitously expressed genes is the most prevalent mechanism of pleiotropic genetic effects across the human phenome.
Lipid oligonucleotides as a new strategy for tackling the antibiotic resistance
Authors: Kauss Tina , Arpin Corinne , Bientz Léa , Vinh Nguyen Phouc , Vialet Brune , Benizri Sebastien , Barthélémy Philippe
Published: January 2020

Antibiotic resistance has become a major issue in public health especially for one of the most used antibiotics; the third-generation cephalosporins. One of the main resistance mechanisms in Enterobacteriaceae, is the production of Extended-Spectrum β-lactamases. Here, we demonstrated that the oligonucleotide therapy is an efficient approach to reduce the resistance of bacteria to antibiotic treatment. Lipid oligonucleotides (LONs) were proved to be efficient strategies in both delivering the oligonucleotide sequences in the prokaryotic cells and decreasing the Minimum Inhibitory Concentration of resistant bacteria to a third generation cephalosporin, the ceftriaxone. Accordingly, we demonstrated the strong antimicrobial potential of this LON strategy targeting the ß-lactamase activity on both clinical and laboratory strains. Our results support the concept that the self-delivery of oligonucleotide sequences via lipid conjugation may be extended to other antimicrobial drugs, which opens novel ways to struggle against the antibiotic resistance.
Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking
Authors: Ando Jun , Shima Tomohiro , Kanazawa Riko , Shimo-Kon Rieko , Nakamura Akihiko , Yamamoto Mayuko , Kon Takahide , Iino Ryota
Published: January 2020

Cytoplasmic dynein is a dimeric motor protein which processively moves along microtubule. Its motor domain (head) hydrolyzes ATP and induces conformational changes of linker, stalk, and microtubule binding domain (MTBD) to trigger stepping motion. Here we applied scattering imaging of gold nanoparticle (AuNP) to visualize load-free stepping motion of processive dynein. We observed artificially-dimerized chimeric dynein, which has the head, linker, and stalk from Dictyostelium discoideum cytoplasmic dynein and the MTBD from human axonemal dynein, whose structure has been well-studied by cryo-electron microscopy. One head of a dimer was labeled with 30 nm AuNP, and stepping motions were observed with 100 μs time resolution and sub-nanometer localization precision at physiologically-relevant 1 mM ATP. We found 8 nm forward and backward steps and 5 nm side steps, consistent with on- and off-axes pitches of binding cleft between αβ-tubulin dimers on the microtubule. Probability of the forward step was 1.8 times higher than that of the backward step, and similar to those of the side steps. One-head bound states were not clearly observed, and the steps were limited by a single rate constant. Our results indicate dynein mainly moves with biased small stepping motion in which only backward steps are slightly suppressed.
First annulus formation in the European anchovy; a two-stage approach for robust validation
Authors: Basilone Gualtiero , Barra Marco , Ferreri Rosalia , Mangano Salvatore , Pulizzi Maurizio , Giacalone Giovanni , Fontana Ignazio , Aronica Salvatore , Gargano Antonella , Rumolo Paola , Genovese Simona , Bonanno Angelo
Published: January 2020

The age determination in fast-growing short-living species, such as European anchovy (Engraulis encrasicolus), has been widely recognized as a difficult task and bias introduced by readers leads to bias in reconstructing the population age structure. In this context, it is worth to note that age structure of fish population represents key information in fishery ecology and for stock assessment models. The uncertainty in estimating the age of the European anchovy by otolith reading is linked to the number of false-growth increments (checks) laid down before the annulus formation. While direct validation methods (e.g. mark-recapture, rearing, radiochemical dating) are difficult to implement specially for this short living species, the use of different indirect methods, supported by a coherent statistical approach, represents a robust and easier validation tool. A statistical modeling approach has been here adopted to assess the coherence of two well-known methods, namely Edge Analysis and Marginal Increment Analysis, in order to validate the first annulus formation in European anchovy. Both methodologies in two different yearly cycles converged toward the same result, thus confirming the annulus identification for the first year class. In addition, the completion dates of the checks and the first annulus were computed in order to gain a better insight into otolith growth dynamic. According to the species spawning period, the completion date of the first annulus falls in the summer period, while the first and second checks completion dates were mostly found in summer and winter respectively. General additive models using marginal increments as dependent variable showed a significant effect of the month, highlighting the presence of only one clear minimum in July/August, as well as specific relationships with condition factor and gonadosomatic index. Modeling the otolith edge morphology, the probability to find a hyaline band displayed in both years a similar shape, characterized by a minimum in July/August and higher values between November and January. The obtained results evidenced temporally coherent patterns providing a better insight in the otolith growth dynamic as well as a more robust validation of the first annulus formation in the European anchovy.
Static intra-access pressure ratio and cardiovascular events in patients undergoing haemodialysis
Authors: Jeon Hee Jung , Oh Jieun , Lee Young-Ki , Cho Ajin , Yoon Jong Woo , Kim Hyunsuk , Shin Dong Ho
Published: January 2020

Static intra-access pressure ratio (SIAPR) measurement, using haemodialysis machine transducers, is the vascular access surveillance method in patients undergoing haemodialysis. However, little is known about the relationship between the SIAPR and arterial stiffness, and the clinical usefulness of the SIAPR in predicting cardiovascular events. A total of 209 patients undergoing maintenance haemodialysis were evaluated. The SIAPRs ranged from 0.01 to 0.52 (median: 0.23). When the patients were divided into two groups according to their median of SIAPR, the incidence of previous cardiovascular disease, E/E′ ratio, and brachial-ankle pulse wave velocity were significantly higher in the patients with SIAPRs of ≤0.23 than in those with SIAPRs of >0.23. Conversely, patients with worse comorbid status had a lower SIAPR than patients without it. In the Kaplan-Meier analysis, the cumulative incidence of cardiovascular events was significantly higher in the patients with SIAPRs of ≤0.23 than in those with SIAPRs of >0.23 (P < 0.001). In the multiple Cox regression analysis, an increase in the SIAPR was associated with a reduced risk for cardiovascular events [hazard ratio: 0.36, 95% confidence interval: 0.21–0.60, P = 0.001]. Therefore, a low SIAPR related with arterial stiffness was a predictor for cardiovascular events.
Identifying unreliable predictions in clinical risk models
Authors: Myers Paul D. , Ng Kenney , Severson Kristen , Kartoun Uri , Dai Wangzhi , Huang Wei , Anderson Frederick A. , Stultz Collin M.
Published: January 2020

The ability to identify patients who are likely to have an adverse outcome is an essential component of good clinical care. Therefore, predictive risk stratification models play an important role in clinical decision making. Determining whether a given predictive model is suitable for clinical use usually involves evaluating the model’s performance on large patient datasets using standard statistical measures of success (e.g., accuracy, discriminatory ability). However, as these metrics correspond to averages over patients who have a range of different characteristics, it is difficult to discern whether an individual prediction on a given patient should be trusted using these measures alone. In this paper, we introduce a new method for identifying patient subgroups where a predictive model is expected to be poor, thereby highlighting when a given prediction is misleading and should not be trusted. The resulting “unreliability score” can be computed for any clinical risk model and is suitable in the setting of large class imbalance, a situation often encountered in healthcare settings. Using data from more than 40,000 patients in the Global Registry of Acute Coronary Events (GRACE), we demonstrate that patients with high unreliability scores form a subgroup in which the predictive model has both decreased accuracy and decreased discriminatory ability.
Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice
Authors: Ali Zahir , Shami Ashwag , Sedeek Khalid , Kamel Radwa , Alhabsi Abdulrahman , Tehseen Muhammad , Hassan Norhan , Butt Haroon , Kababji Ahad , Hamdan Samir M. , Mahfouz Magdy M.
Published: January 2020

Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.
Sub-molecular structural relaxation at a physisorbed interface with monolayer organic single-crystal semiconductors
Authors: Yamamura Akifumi , Fujii Hiromasa , Ogasawara Hirohito , Nordlund Dennis , Takahashi Osamu , Kishi Yuutaro , Ishii Hiroyuki , Kobayashi Nobuhiko , Niitsu Naoyuki , Blülle Balthasar , Okamoto Toshihiro , Wakabayashi Yusuke , Watanabe Shun , Takeya Jun
Published: January 2020

Arranging molecules into highly symmetric, topological crystal structures has been recognized as the best approach to functionalize electronic properties in molecular crystals, where the constituent molecules have been assumed to be rigid in shape. Here, in striking contrast, we demonstrate that the molecules in a monolayer organic crystal can undergo a significant deformation in proximity to the substrate, which is reflected by an asymmetry in the electron density profile. X-ray reflectivity and X-ray absorption spectroscopies in conjunction with density-functional theory calculations reveal that the highly planarized π-core are deformed into a bent shape, while the bulk lattice parameters are maintained. The molecular shape change is found to be perfectly suppressed in a bilayer single crystal, which leads to a 40% increase in mobility in the bilayer crystal. Our finding of a unique, sub-molecular scale shape change in monolayer single crystals can offer possibilities for functionalizing electrical properties via nano-scale physisorption.
Automated sample preparation and GC-API-MS/MS as a powerful tool for analysis of legacy POPs in human serum and plasma
Authors: Huber Sandra , Averina Maria , Brox Jan
Published: January 2020

An automated high-throughput SPE method for selected persistent organic pollutants comprising 17 organochlorine pesticides, 22 polychlorinated biphenyls, 9 polybrominated diphenylethers and octachlorostyrene in human serum and plasma was developed.
Engineering work function of graphene oxide from p to n type using a low power atmospheric pressure plasma jet
Authors: Dey Avishek , Ghosh Paheli , Bowen James , Braithwaite Nicholas St. J. , Krishnamurthy Satheesh
Published: January 2020

In this work, we demonstrate doping graphene oxide (GO) films using a low power atmospheric pressure plasma jet (APPJ) with subsequent tuning of the work function.
Characterizing microplastic size and morphology of photodegraded polymers placed in simulated moving water conditions
Authors: Hebner Tayler S. , Maurer-Jones Melissa A.
Published: January 2020

Aquatic plastic debris experiences environmental stressors that lead to breakdown into smaller micro-sized plastic particles.
Developmental toxicity of trichloroethylene in zebrafish (Danio rerio)
Authors: Horzmann Katharine A. , Portales Ana M. , Batcho Kathryn G. , Freeman Jennifer L.
Published: January 2020

Embryonic exposure to ecologically relevant concentrations of TCE disrupts development, morphology, heart rate, and behavior in the zebrafish (Danio rerio) model system.
Fibre-based oleogels: effect of the structure of insoluble fibre on its physical properties
Authors: Phoon Pui Yeu , Henry Christiani Jeyakumar
Published: January 2020

Natural, insoluble food fibres were processed to entrap liquid oil in a network, creating an oleogel.
Luminescent MOF crystals embedded in PMMA/PDMS transparent films as effective NO2 gas sensors
Authors: G. Moscoso Francisco , Almeida José , Sousaraei Ahmad , Lopes-Costa Tânia , Silva Ana M. G. , Cabanillas-Gonzalez Juan , Cunha-Silva Luís , Pedrosa José M.
Published: January 2020

Transparent polymeric matrices serve as efficient platforms to immobilize Tb(BTC) crystals whose fluorescence is quenched in the presence of NO2.
Ultrathin sputter-deposited plasmonic silver nanostructures
Authors: Goetz Selina , Bauch Martin , Dimopoulos Theodoros , Trassl Stephan
Published: January 2020

A new fabrication approach allows for an easy-to-produce Ag disk–hole array showing strong plasmonic modes in experiment and simulation.
PEGylation and macroporous carrier adsorption enabled long-term enzymatic transesterification
Authors: Wang Honghai , Duan Baoxuan , Li Hao , Li Shihao , Lu Yifan , Liu Zhiling , Su Weiyi
Published: January 2020

A novel enzyme catalyst with excellent stability and catalytic efficiency expected to be used in the ERD industry was prepared.
Phenolic cross-links: building and de-constructing the plant cell wall
Authors: Mnich Ewelina , Bjarnholt Nanna , Eudes Aymerick , Harholt Jesper , Holland Claire , Jørgensen Bodil , Larsen Flemming Hofmann , Liu Ming , Manat Renil , Meyer Anne S. , Mikkelsen Jørn Dalgaard , Motawia Mohammed Saddik , Muschiol Jan , Møller Birger Lindberg , Møller Svenning Rune , Perzon Alixander , Petersen Bent Larsen , Ravn Jonas Laukkonen , Ulvskov Peter
Published: January 2020

Phenolic cross-links and inter-unit linkages result from the oxidative coupling of hydroxycinnamates leading to lignin assembly and cross-linking with cell wall polysaccharides and extensin proteins.
How metallic are noble-metal clusters? Static screening and polarizability in quantum-sized silver and gold nanoparticles
Authors: Sinha-Roy Rajarshi , García-González Pablo , Weissker Hans-Christian
Published: January 2020

Small noble-metal clusters of about 2 nm are strongly metallic, even one atomic shell screens 96% of external fields, whereas electronic shell-closings and Friedel oscillations modify the classical picture.
Wideband saturable absorption in metal–organic frameworks (MOFs) for mode-locking Er- and Tm-doped fiber lasers
Authors: Zhang Qian , Jiang Xiantao , Zhang Meng , Jin Xinxin , Zhang Han , Zheng Zheng
Published: January 2020

Metal–organic frameworks (MOFs) for mode-locking Er- and Tm-doped fiber laser and as a promising nanomaterial for application in ultrafast photonic.
The encapsulation of MnFe2O4 nanoparticles into the carbon framework with superior rate capability for lithium-ion batteries
Authors: Li Weiqin , An Cuihua , Guo Huinan , Zhang Yan , Chen Kai , Zhang Zeting , Liu Guishu , Liu Yafei , Wang Yijing
Published: January 2020

The mesoporous MnFe2O4@C nanorods has been prepared using self-template method. Benefiting from the synergistic effect of carbon coating and mesoporous feature, MnFe2O4@C displays outstanding electrochemical performances for LIBs.