bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genomic Origins of Small Mitochondrial RNAs: Are They Transcribed by the Mitochondrial DNA or by Mitochondrial Pseudogenes within the Nucleus (NUMTs)?
Authors: Pozzi Andrea , Dowling Damian K 
Published: June 2019

AbstractSeveral studies have linked mitochondrial genetic variation to phenotypic modifications; albeit the identity of the mitochondrial polymorphisms involved remains elusive. The search for these polymorphisms led to the discovery of small noncoding RNAs, which appear to be transcribed by the mitochondrial DNA (“small mitochondrial RNAs”). This contention is, however, controversial because the nuclear genome of most animals harbors mitochondrial pseudogenes (NUMTs) of identical sequence to regions of mtDNA, which could alternatively represent the source of these RNAs. To discern the likely contributions of the mitochondrial and nuclear genome to transcribing these small mitochondrial RNAs, we leverage data from six vertebrate species exhibiting markedly different levels of NUMT sequence. We explore whether abundances of small mitochondrial RNAs are associated with levels of NUMT sequence across species, or differences in tissue-specific mtDNA content within species. Evidence for the former would support the hypothesis these RNAs are primarily transcribed by NUMT sequence, whereas evidence for the latter would provide strong evidence for the counter hypothesis that these RNAs are transcribed directly by the mtDNA. No association exists between the abundance of small mitochondrial RNAs and NUMT levels across species. Moreover, a sizable proportion of transcripts map exclusively to the mtDNA sequence, even in species with highest NUMT levels. Conversely, tissue-specific abundances of small mitochondrial RNAs are strongly associated with the mtDNA content. These results support the hypothesis that small mitochondrial RNAs are primarily transcribed by the mitochondrial genome and that this capacity is conserved across Amniota and, most likely, across most metazoan lineages.
When Will My Patient Fall? Sensor-Based In-Home Walking Speed Identifies Future Falls in Older Adults
Authors: Piau Antoine , Mattek Nora , Crissey Rachel , Beattie Zachary , Dodge Hiroko , Kaye Jeffrey 
Published: June 2019

Abstract

Background
Although there are known clinical measures that may be associated with risk of future falls in older adults, we are still unable to predict when the fall will happen. Our objective was to determine whether unobtrusive in-home assessment of walking speed can detect a future fall.

Method
In both ISAAC and ORCATECH Living Laboratory studies, a sensor-based monitoring system has been deployed in the homes of older adults. Longitudinal mixed-effects regression models were used to explore trajectories of sensor-based walking speed metrics in those destined to fall versus controls over time. Falls were captured during a 3-year period.

Results
We observed no major differences between those destined to fall (n = 55) and controls (n = 70) at baseline in clinical functional tests. There was a longitudinal decline in median daily walking speed over the 3 months before a fall in those destined to fall when compared with controls, p &lt; .01 (ie, mean walking speed declined 0.1 cm s−1 per week). We also found prefall differences in sensor-based walking speed metrics in individuals who experienced a fall: walking speed variability was lower the month and the week just before the fall compared with 3 months before the fall, both p &lt; .01.

Conclusions
While basic clinical tests were not able to differentiate who will prospectively fall, we found that significant variations in walking speed metrics before a fall were measurable. These results provide evidence of a potential sensor-based risk biomarker of prospective falls in community living older adults.
Functionalization of the TMEM175 p.M393T variant as a risk factor for Parkinson disease
Authors: Jinn Sarah , Blauwendraat Cornelis , Toolan Dawn , Gretzula Cheryl A , Drolet Robert E , Smith Sean , Nalls Mike A , Marcus Jacob , Singleton Andrew B , Stone David J 
Published: June 2019

Abstract
Multiple genome-wide association studies (GWAS) in Parkinson disease (PD) have identified a signal at chromosome 4p16.3; however, the causal variant has not been established for this locus. Deep investigation of the region resulted in one identified variant, the rs34311866 missense SNP (p.M393T) in TMEM175, which is 20 orders of magnitude more significant than any other SNP in the region. Because TMEM175 is a lysosomal gene that has been shown to influence α-synuclein phosphorylation and autophagy, the p.M393T variant is an attractive candidate, and we have examined its effect on TMEM175 protein and PD-related biology. After knocking down each of the genes located under the GWAS peak via multiple shRNAs, only TMEM175 was found to consistently influence accumulation of phosphorylated α-synuclein (p-α-syn). Examination of the p.M393T variant showed effects on TMEM175 function that were intermediate between the wild-type (WT) and knockout phenotypes, with reduced regulation of lysosomal pH in response to starvation and minor changes in clearance of autophagy substrates, reduced lysosomal localization, and increased accumulation of p-α-syn. Finally, overexpression of WT TMEM175 protein reduced p-α-syn, while overexpression of the p.M393T variant resulted in no change in α-synuclein phosphorylation. These results suggest that the main signal in the chromosome 4p16.3 PD risk locus is driven by the TMEM175 p.M393T variant. Modulation of TMEM175 may impact α-synuclein biology and therefore may be a rational therapeutic strategy for PD.
Developmental Stage Affects the Consequences of Transient Salinity Exposure in Toad Tadpoles
Authors: Welch Allison M , Bralley Jordan P , Reining Ashlyn Q , Infante Allison M 
Published: June 2019

AbstractDevelopment can play a critical role in how organisms respond to changes in the environment. Tolerance to environmental challenges can vary during ontogeny, with individual- and population-level impacts that are associated with the timing of exposure relative to the timing of vulnerability. In addition, the life history consequences of different stressors can vary with the timing of exposure to stress. Salinization of freshwater ecosystems is an emerging environmental concern, and habitat salinity can change rapidly due, for example, to storm surge, runoff of road deicing salts, and rainfall. Elevated salinity can increase the demands of osmoregulation in freshwater organisms, and amphibians are particularly at risk due to their permeable skin and, in many species, semi-aquatic life cycle. In three experiments, we manipulated timing and duration of exposure to elevated salinity during larval development of southern toad (Anaxyrus terrestris) tadpoles and examined effects on survival, larval growth, and timing of and size at metamorphosis. Survival was reduced only for tadpoles exposed to elevated salinity early in development, suggesting an increase in tolerance as development proceeds; however, we found no evidence of acclimation to elevated salinity. Two forms of developmental plasticity may help to ameliorate costs of transient salinity exposure. With early salinity exposure, the return to freshwater was accompanied by a period of rapid compensatory growth, and metamorphosis ultimately occurred at a similar age and size as freshwater controls. By contrast, salinity exposure later in development led to earlier metamorphosis at reduced size, indicating an acceleration of metamorphosis as a mechanism to escape salinity stress. Thus, the consequences of transient salinity exposure were complex and were mediated by developmental state. Salinity stress experienced early in development resulted in acute costs but little long-lasting effect on survivors, while exposures later in development resulted in sublethal effects that could influence success in subsequent life stages. Overall, our results suggest that elevated salinity is more likely to affect southern toad larvae when experienced early during larval development, but even brief sublethal exposure later in development can alter life history in ways that may impact fitness.
A Geometric Model for the Module Category of a Gentle Algebra
Authors: Baur Karin , Coelho Simões Raquel 
Published: June 2019

AbstractIn this article, gentle algebras are realised as tiling algebras, which are associated to partial triangulations of unpunctured surfaces with marked points on the boundary. This notion of tiling algebras generalise the notion of Jacobian algebras of triangulations of surfaces and the notion of surface algebras. We use this description to give a geometric model of the module category of any gentle algebra.
The Traveller’s Risk Perception (TRiP) questionnaire: pre-travel assessment and post-travel changes
Authors: Tardivo S , Zenere A , Moretti F , Marchiori F , Berti D , Migliorini M , Tomasi A , Ferrari S , Tognon F , Napoletano G , Rossanese A 
Published: June 2019

Abstract

Background
Travellers’ risk perception is a key component of travel risk assessment because it influences the adequate implementation of safety precautions. The aims of this study are to validate a tool to analyse travellers’ risk perception to identify which factors can influence it and how it changes upon return.

Methods
The Traveller’s Risk Perception (TRiP) questionnaire was developed and administered to outpatients before and after travel in three travel clinics. A principal component analysis (PCA) was performed to validate the questionnaire and multivariate regression analysis was used to evaluate the effect of travellers’ characteristics on the risk scores.

Results
A total of 1020 travellers completed the questionnaire. PCA identified two latent factors: ‘generic-disseminated risks’ and ‘specific-circumstantial risks’. Cronbach’s α was acceptable (0.76 and 0.70, respectively). The ‘generic-disseminated risks’ dimension scored higher than the ‘specific-circumstantial risks’ (p&lt;0.001). The items with the highest scores were insect bites, gastrointestinal disorders and malaria. The mean scores were significantly lower after the travel for all items but one.

Conclusions
The TRiP questionnaire is a valid and reliable tool for rating travellers’ perceptions. Staff in travel clinics should be trained to systematically assess travellers’ risk perception in order to tailor the consultation according to specific information needs.
Unambivalent alignment: Japan’s China strategy, the US alliance, and the ‘hedging’ fallacy
Authors: Liff Adam P 
Published: June 2019

AbstractThis article examines whether the Asia-Pacific region’s geopolitical vicissitudes are causing Japan to ‘hedge’ against deepening uncertainty and risk through major strategic realignments or diversification of security and economic ties, as the original hedging literature would expect. It examines trends since 2009 in three domains fundamental to identifying whether shifts are underway in Japan’s strategic orientation vis-à-vis China: security policy (primary), trade/investment, and public opinion. Despite deepening uncertainty (and volatility), especially in ‘the Trump era’, this study finds negligible evidence of hedging behavior: e.g., realigning toward Beijing or adopting a ‘middle position’, much less developing any meaningful security ties with China. Rather, contemporary trends point in the opposite direction: Japan’s China strategy primarily centers on strengthening indigenous deterrence capabilities, bolstering the US–Japan alliance, and diversifying regional security ties beyond Beijing. Even the latter, somewhat paradoxically, aims to deepen ties with Washington and to keep it actively engaged in regional affairs.
Pre-treatment and acquired HIV drug resistance in Dar es Salaam, Tanzania in the era of tenofovir and routine viral load monitoring
Authors: Barabona Godfrey , Mahiti Macdonald , Masoud Salim , Mbelele Peter , Mgunya Amina Shaban , Minja Lilian , Sunguya Bruno , Shigemi Urara , Matsuda Masakazu , Hachiya Atsuko , Iwatani Yasumasa , Lyamuya Eligius , Ueno Takamasa 
Published: June 2019

AbstractObjectivesWe investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations (DRMs) in Tanzania as a ‘treat all’ strategy, virological monitoring and the progressive increase in usage of tenofovir are being implemented in HIV treatment programmes.MethodsViral RNA was isolated from plasma of 60 ART-naive and 166 treated-but-viraemic (>400 copies/mL) HIV-1-infected adults attending a care and treatment clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania, between June and October 2017. Viral genes encoding protease and reverse transcriptase were amplified by PCR and directly sequenced.ResultsViral genotyping of successfully amplified samples revealed pre-treatment DRMs in 14/47 (29.8%) ART-naive subjects. Of these, 7/47 (14.9%) harboured mutations that confer high-level resistance to at least one drug of the default first-line regimen. In treated-but-viraemic subjects, DRMs were found in 100/111 (90%), where DRMs against NNRTI, NRTI and PI were observed in 95/100 (95%), 92/100 (92%) and 13/100 (13%), respectively. Tenofovir-resistance mutations K65R and K70G/E or ≥3 thymidine analogue resistance mutations including M41L and L210W were found in 18/36 (50%) subjects on a tenofovir-containing regimen at failure. Four patients harboured multiple DRMs, which can confer resistance to all available ART regimens in Tanzania.ConclusionsTaken together, pre-treatment and acquired DRMs were highly prevalent, which represents a major risk for the efficacy of ART programmes in Tanzania. Availability of a newer generation of antiretroviral drugs with a higher genetic barrier to resistance and robust treatment monitoring is warranted for effective and sustainable HIV treatment.
Activity of cefepime/zidebactam (WCK 5222) against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii endemic to New York City medical centres
Authors: Khan Zeb , Iregui Alejandro , Landman David , Quale John 
Published: June 2019

Abstract

Background
The combination of cefepime and zidebactam (WCK5222), a novel β-lactam enhancer, has demonstrated activity against a wide variety of Gram-negative pathogens and is currently under clinical evaluation.

Objectives
To examine the activity of cefepime/zidebactam against: (i) a contemporary collection of Gram-negative isolates from New York City; (ii) a collection of carbapenem-resistant clinical isolates; and (iii) a collection of isolates with characterized resistance mechanisms.

Methods
Susceptibility tests were performed using broth microdilution for cefepime, zidebactam and cefepime/zidebactam (1:1).

Results
More than 99% of a contemporary collection of Escherichia coli, Klebsiella pneumoniae and Enterobacter spp. had cefepime/zidebactam MICs ≤2 mg/L, the susceptibility breakpoint for cefepime. For K. pneumoniae, the acquisition of blaKPC resulted in increased MICs, although MICs remained ≤2 mg/L for 90% of KPC-possessing isolates. Overall for Pseudomonas aeruginosa, 98% of isolates had MICs ≤8 mg/L and MICs were affected by increased expression of ampC. For carbapenem-resistant P. aeruginosa, 78% of isolates had cefepime/zidebactam MICs ≤8 mg/L. The activity of cefepime/zidebactam against Acinetobacter baumannii was lower, with 85% of all isolates and 34% of carbapenem-resistant isolates with MICs ≤8 mg/L (cefepime interpretative criteria).

Conclusions
Cefepime/zidebactam demonstrated excellent activity against Enterobacteriaceae and P. aeruginosa, although activity was reduced in carbapenem-non-susceptible isolates. The activity against A. baumannii was reduced and studies examining the therapeutic efficacy in strains with high cefepime/zidebactam MICs are warranted.
Tolerance of Immature Black Soldier Flies (Diptera: Stratiomyidae) to Cold Temperatures Above and Below Freezing Point
Authors: Villazana Joshua , Alyokhin Andrei 
Published: June 2019

Abstract
Black soldier flies, Hermetia illucens (L.), consume decaying organic materials at the larval stage and can be used for recycling a variety of biogenic wastes into value-added products. Black soldier flies are normally found in subtropical and warm temperate regions. Cold temperatures may prevent their establishment in colder areas, thus alleviating a concern of their becoming an invasive species. Potentially, cold temperatures can also be used to manipulate the rate of black soldier fly development, which may be needed for timing certain life stages for mass-production needs. In the present study, immature black soldier flies were highly susceptible to freezing. Their survivorship decreased as time spent at −12°C increased from 10 to 60 min. Only ca. 2% of eggs, &lt;1% of larvae, and no pupae survived after 60 min of exposure. Chilling at 4°C also had a significant negative effect that became more pronounced as duration of exposure increased from 24 to 72 h. Only ca. 2% of eggs and second instars and ca. 23% of pupae survived after 72 h. In the same time, &gt;80% of third instars and &gt;90% of fifth instars were still alive following 72 h of exposure. Chilling fifth instars resulted in smaller adults but freezing them for 48 h resulted in bigger adults. Based on these results, black soldier fly is unlikely to establish in areas with long periods of subfreezing winter temperatures. Low temperatures may be used to manipulate development of the late instars, but at a cost of higher mortality.
Virulence of Some Entomopathogenic Fungi Isolates of Beauveria bassiana (Hypocreales: Cordycipitaceae) and Metarhizium anisopliae (Hypocreales: Clavicipitaceae) to Aulacaspis tubercularis (Hemiptera: Diaspididae)and Icerya seychellarum (Hemiptera: Monophlebidae) on Mango Crop
Authors: Sayed Atef M M , Dunlap Christopher A 
Published: June 2019

AbstractSix fungal isolates of Beauveria bassiana (Balsamo) Vuillemin and one isolate of Metarhizium anisopliae (Metschnikoff) Sorokin were isolated and evaluated for their pathogenicity to Icerya seychellarum (Westwood) and Aulacaspis tubercularis Newstead. There is a positive correlation between the concentration of the fungal blastospore concentrations and the percentage of mortality. Bio-efficacy increased significantly after inoculation with increasing concentration of blastospores and elapsed time up to 12 d after inoculation. The mortality of nymphs exposed to fungal isolates at various concentrations varied between 2.5 and 88.8%. Probit analysis of data at 95% confidence limits of LC50 and LT50s showed significant differences in the susceptibility of nymphs of I. seychellarum and A. tubercularis to the tested fungal isolates. The fungal isolates of Egy-6 and Egy-9 were the most effective against I. seychellarum and A. tubercularis, respectively. They had the lowest LC50 (4.20 × 105 and 5.71 × 103 blastospore ml−1) and LT50 (ranged from 4.61 to 9.79 and 4.84 to 8.71 d), respectively. The current study showed that all the fungal isolates yielded moderate mortality rates of nymphs and adult female populations of both the tested insect pests. To our knowledge, this is the first report of bio-efficacy of Beauveria and Metarhizium isolates against members of the Diaspidadae and Monophlebidae family insects. These results establish that the use of these native entomopathogenic fungi isolates of B. bassiana (Egy-3, Egy-4, Egy-6, Egy-7, Egy-9, and Egy-10) and M. anisopliae (Egy-5) could be considered for further development as microbial control agents of the mealybug and scale insects as a potential biological agent for use in an IPM program.
CJEU excludes retroactive application of reformed language of Article 7(1)(e)(iii) of the EU Trade Mark Regulation and does (not) clarify what ‘another characteristic’ means
Authors: Rosati Eleonora 
Published: June 2019

Abstract
CJEU, Textilis Ltd and Ozgur Keskin v Svenskt Tenn Aktiebolag, C-21/18, EU:C:2019:199, 14 March 2019
Multiple lines of evidence reveal a composite of species in the plateau mouse, Peromyscus melanophrys (Rodentia, Cricetidae)
Authors: López-González Celia , García-Mendoza Diego F , López-Vidal Juan Carlos , Elizalde-Arellano Cynthia 
Published: June 2019

AbstractPeromyscus melanophrys is a Mexican endemic distributed in seasonal tropical forests and semiarid lands. Molecular work based on mitochondrial and nuclear markers proposed the existence of four haplogroups within P. melanophrys. Peromyscus mekisturus (Puebla deer mouse) was included in one of these haplogroups. We tested the consistency between this hypothesis and external morphology, quantitative and qualitative cranial attributes, and ecological data for a sample of 1,155 specimens spanning the species distribution. We found ecological and morphological consistency with the phylogenetic pattern for P. melanophrys but not for P. mekisturus. We reassessed the taxonomic and nomenclatural status of the populations and type specimens formerly included in P. melanophrys. We concluded that these populations constitute four species: P. zamorae (Zamora deer mouse), distributed in the Mexican Plateau at elevations > 1,500 m; P. micropus (small-footed deer mouse), from lowland tropical deciduous forests of the San Pedro-Mezquital and Lerma-Santiago basins in western Mexico; P. melanophrys (black-eyed deer mouse) from lowland tropical deciduous forests of southeastern Mexico as far as eastern Oaxaca; and P. leucurus (Tehuantepec deer mouse), partially sympatric with P. melanophrys but reaching as far as Chiapas. Data on P. mekisturus were contradictory, and thus was kept as a valid species.Peromyscus melanophrys es un roedor endémico de México, distribuido en bosques tropicales caducifolios y regiones semiáridas. Datos moleculares usando marcadores mitocondriales y nucleares indicaron la existencia de cuatro haplogrupos dentro de P. melanophrys. Peromyscus mekisturus (ratón de Puebla) se incluyó dentro de uno de éstos. Con base en una muestra de 1,155 ejemplares de toda la distribución de la especie, se examinó si esta hipótesis era consistente con datos de morfología externa y craneal, morfometría e información ecológica. Se encontró coincidencia para P. melanophrys pero no para P. mekisturus. Estos resultados hicieron necesaria la reevaluación del estado taxonómico y nomenclatural de las poblaciones incluidas en P. melanophrys. Se concluye que existen cuatro especies dentro de lo que se conocía como P. melanophrys: P. zamorae (ratón de Zamora) distribuido en el Altiplano Mexicano a elevaciones ≥ 1,500 m; P. micropus (ratón de pata pequeña) distribuido en los bosques tropicales caducifolios de las cuencas San Pedro-Mezquital y Lerma-Santiago en el occidente de México; P. melanophrys (ratón de ojo oscuro) de los bosques y matorrales tropicales caducifolios del sureste de México, al menos hasta el este de Oaxaca, y P. leucurus (ratón de Tehuantepec) parcialmente simpátrico con P. melanophrys pero llegando hasta el estado de Chiapas. La información disponible no permitió asignar a P. mekisturus a ninguno de los grupos y por tanto se sigue considerando como especie válida.