bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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

AbstractA 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

AbstractCanine 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

AbstractMycobacterium 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

AbstractRegional 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

AbstractInvasive 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

AbstractRabies 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

AbstractMachine 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

AbstractIn 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

AbstractThis 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

AbstractControlled 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

AbstractThe 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

AbstractIsogenic 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

AbstractSingle 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

AbstractOver 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

AbstractAntibiotic 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.