bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium tuberculosis Infection Drives Mitochondria-Biased Dysregulation of Host Transfer RNA–Derived Fragments
Authors: Looney Monika M , Lu Yin , Karakousis Petros C , Halushka Marc K 
Published: September 2020

Abstract

Background
Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis, causes 10 million infections and 1.5 million deaths per year worldwide. The success of Mtb as a human pathogen is directly related to its ability to suppress host responses, which are critical for clearing intracellular pathogens. Emerging evidence suggests that key response pathways may be regulated by a novel class of small noncoding RNA, called transfer RNA (tRNA)–derived fragments (tRFs). tRFs can complex with Argonaute proteins to target and degrade messenger RNA targets, similarly to micro RNAs, but have thus far been overlooked in the context of bacterial infections.

Methods
We generated a novel miRge2.0-based tRF-analysis tool, tRFcluster, and used it to analyze independently generated and publicly available RNA-sequencing datasets to assess tRF dysregulation in host cells following infection with Mtb and other intracellular bacterial pathogens.

Results
We found that Mtb and Listeria monocytogenes drive dramatic tRF dysregulation, whereas other bacterial pathogens do not. Interestingly, Mtb infection uniquely increased the expression of mitochondria-derived tRFs rather than genomic-derived tRFs, suggesting an association with mitochondrial damage in Mtb infection.

Conclusions
tRFs are dysregulated in some, but not all, bacterial infections. Biased dysregulation of mitochondria-derived tRFs in Mtb infection suggests a link between mitochondrial distress and tRF production.
AMR-Intervene: a social–ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective
Authors: Léger Anaïs , Lambraki Irene , Graells Tiscar , Cousins Melanie , Henriksson Patrik J G , Harbarth Stephan , Carson Carolee , Majowicz Shannon , Troell Max , Parmley E Jane , Jørgensen Peter S , Wernli Didier 
Published: September 2020

AbstractThe global threat of antimicrobial resistance (AMR) requires coordinated actions by and across different sectors. Increasing attention at the global and national levels has led to different strategies to tackle the challenge. The diversity of possible actions to address AMR is currently not well understood from a One Health perspective. AMR-Intervene, an interdisciplinary social–ecological framework, describes interventions to tackle AMR in terms of six components: (i) core information about the publication; (ii) social system; (iii) bio-ecological system; (iv) triggers and goals; (v) implementation and governance; and (vi) assessment. AMR-Intervene provides a broadly applicable framework, which can inform the design, implementation, assessment and reporting of interventions to tackle AMR and, in turn, enable faster uptake of successful interventions to build societal resilience to AMR.
Resistance/fitness trade-off is a barrier to the evolution of MarR inactivation mutants in Escherichia coli
Authors: Praski Alzrigat Lisa , Huseby Douglas L , Brandis Gerrit , Hughes Diarmaid 
Published: September 2020

Abstract

Background
Mutations that inactivate MarR reduce susceptibility to ciprofloxacin and competitive growth fitness in Escherichia coli. Both phenotypes are caused by overexpression of the MarA regulon, which includes the AcrAB-TolC drug efflux pump.

Objectives
We asked whether compensatory evolution could reduce the fitness cost of MarR-inactivating mutations without affecting resistance to ciprofloxacin.

Methods
The cost of overexpressing the AcrAB-TolC efflux pump was measured independently of MarA overexpression. Experimental evolution of MarR-inactive strains was used to select mutants with increased fitness. The acquired mutations were identified and their effects on drug susceptibility were measured.

Results
Overexpression of the AcrAB-TolC efflux pump was found not to contribute to the fitness cost of MarA regulon overexpression. Fitness-compensatory mutations were selected in marA and lon. The mutations reduced the level of MarA protein thus reducing expression of the MarA regulon. They restored growth fitness but also reduced resistance to ciprofloxacin.

Conclusions
The fitness cost caused by overexpression of the MarA regulon has multiple contributing factors. Experimental evolution did not identify any single pump-independent cost factor. Instead, efficient fitness compensation occurred only by mechanisms that reduce MarA concentration, which simultaneously reduce the drug resistance phenotype. This resistance/fitness trade-off is a barrier to the successful spread of MarR inactivation mutations in clinical isolates where growth fitness is essential.
Laboratory Perspective on Racial Disparities in Sexually Transmitted Infections
Authors: Lieberman Joshua A , Cannon Chase A , Bourassa Lori A 
Published: September 2020

AbstractBackgroundRates of sexually transmitted infections (STI) have risen steadily in recent years, and racial and ethnic minorities have borne the disproportionate burden of STI increases in the United States. Historical inequities and social determinants of health are significant contributors to observed disparities and affect access to diagnostic testing for STI.ContentPublic health systems rely heavily on laboratory medicine professionals for diagnosis and reporting of STI. Therefore, it is imperative that clinicians and laboratory professionals be familiar with issues underlying disparities in STI incidence and barriers to reliable diagnostic testing. In this mini-review, we will summarize contributors to racial/ethnic disparity in STI, highlight current epidemiologic trends for gonorrhea, chlamydia, and syphilis, discuss policy issues that affect laboratory and public health funding, and identify specific analytic challenges for diagnostic laboratories.SummaryRacial and ethnic disparities in STI in the US are striking and are due to complex interactions of myriad social determinants of health. Budgetary cuts for laboratory and public health services and competition for resources during the COVID-19 pandemic are major challenges. Laboratory professionals must be aware of these underlying issues and work to maximize efforts to ensure equitable access to diagnostic STI testing for all persons, particularly those most disproportionately burdened by STI.
A Comprehensive Multi-Analyte Method for Hair Analysis: Substance-Specific Quantification Ranges and Tool for Task-Oriented Data Evaluation
Authors: Scholz C , Cabalzar J , Kraemer T , Baumgartner M R 
Published: September 2020

Abstract
The aim of the present study was to quantify a large number of analytes including opioids, stimulants, benzodiazepines, z-drugs, antidepressants and neuroleptics within a single sample workup followed by a single analytical measurement. Expected drug concentrations in hair are strongly substance dependent. Therefore, three different calibration ranges were implemented: 0.5 to 600 pg/mg (group 1), 10 to 12,000 pg/mg (group 2) and 50 to 60,000 pg/mg (group 3). In order to avoid saturation effects, different strategies were applied for selected transitions including the use of parent mass ions containing one or two 13C-isotopes and detuning of the declustering potential and/or collision energy. Drugs were extracted from pulverized hair by a two-step extraction protocol and measured by liquid chromatrography--tandem mass spectrometry (LC--MS-MS) using Scheduled MRM™ Algorithm Pro. In total, 275 MRM transitions including 43 deuterated standards were measured. The method has been fully validated according to international guidelines. A MultiQuant™ software based tool for task-oriented data evaluation was established, which allows extracting selected information from the measured data sets. The matrix effects and recoveries were within the allowed ranges for the majority of the analytes. The lower limits of quantification (LLOQs) were for ∼72% of the analytes in the low-pg/mg range (0.5–5 pg/mg) and for ∼24% of the analytes between 10 and 50 pg/mg. These LLOQs considered cut-offs by the Society of Hair Testing (SoHT), if recommended. The herein established multi-analyte approach meets the specific requirements of forensic hair testing and can be used for the rapid and robust measurement of a wide range of psychoactive substances. The analyte-specific wide concentration ranges open up a wide field of applications.
COVID-19 and Canadian Gastroenterology Trainees
Authors: Khan Rishad , Tandon Parul , Scaffidi Michael A , Bishay Kirles , Pawlak Katarzyna M , Kral Jan , Amin Sunil , Bilal Mohammad , Lui Rashid N , Sandhu Dalbir S , Hashim Almoutaz , Bollipo Steven , Charabaty Aline , de-Madaria Enrique , Rodríguez-Parra Andrés F , Sánchez-Luna Sergio A , Żorniak Michał , Siau Keith , Walsh Catharine M , Grover Samir C 
Published: September 2020

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic has impacted endoscopy services and education worldwide. This study aimed to characterize the impact of COVID-19 on gastroenterology trainees in Canada.

Methods
An analysis of Canadian respondents from the international EndoTrain survey, open from April 11 to May 2 2020 and distributed by program directors, trainees, and national and international gastroenterology societies’ representatives, was completed. The survey included questions on monthly endoscopy volume, personal protective equipment availability, trainee well-being and educational resources. The primary outcome was change in procedural volume during the COVID-19 pandemic. Secondary outcomes included trainee’s professional and personal concerns, anxiety and burnout.

Results
Thirty-four Canadian trainees completed the survey. Per month, participants completed a median of 30 esophagogastroduodenoscopies (interquartile range 16 to 50) prior to the pandemic compared to 2 (0 to 10) during the pandemic, 20 (8 to 30) compared to 2 (0 to 5) colonoscopies and 3 (1 to 10) compared to 0 (0 to 3) upper gastrointestinal bleeding procedures. There was a significant decrease in procedural volumes between the pre-COVID-19 and COVID-19 time periods for all procedures (P &lt; 0.001). Thirty (88%) trainees were concerned about personal COVID-19 exposure, 32 (94%) were concerned about achieving and/or maintaining clinical competence and 24 (71%) were concerned about prolongation of training time due to the pandemic. Twenty-six (79%) respondents experienced some degree of anxiety, and 10 (31%) experienced some degree of burnout.

Conclusion
The COVID-19 pandemic has substantially impacted gastroenterology trainees in Canada. As the pandemic eases, it important for gastrointestinal programs to adapt to maximize resident learning, maintain effective clinical care and ensure development of endoscopic competence.
Numerical study on combined thermal radiation and magnetic field effects on entropy generation in unsteady fluid flow past an inclined cylinder
Authors: Mburu Zachariah Mbugua , Mondal Sabyasachi , Sibanda Precious 
Published: September 2020

Abstract
This study reports on combined thermal radiation, chemical reaction, and magnetic field effects on entropy generation in an unsteady nanofluid flow past an inclined cylinder using the Buongiorno model. We consider the impact of viscous dissipation, velocity slip conditions, thermal slip conditions, and the Brownian motion. The transport equations governing the flow are solved using an overlapping grid spectral collocation method. The results indicate that entropy generation is suppressed significantly by thermal radiation and chemical reaction parameters but enhanced with the magnetic field, viscous dissipation, the Brinkman number, and the Reynolds number. Also, fluid flow variables are affected by the thermophoresis parameter, the angle of cylinder inclination, and the Richardson number. We present the findings of the skin friction coefficient, the Nusselt number, and the Sherwood number. The model is applicable in fields such as the petroleum industry, building industries, and medicine.
Second primary cancers and recurrence in patients after resection of colorectal cancer: An integrated analysis of trials by Japan Clinical Oncology Group: JCOG1702A
Authors: Tanaka Kiyo , Ogawa Gakuto , Mizusawa Junki , Kadota Tomohiro , Nakamura Kenichi , Shimada Yasuhiro , Hamaguchi Tetsuya , Fujita Shin , Kitano Seigo , Inomata Masafumi , Kanemitsu Yukihide , Fukuda Haruhiko ,   Colorectal Cancer Study Group of Japan Clinical Oncology Group (JCOG)
Published: September 2020

Abstract

Background
Improvements in early detection and treatment have resulted in an increasing number of long-term survivors of colorectal cancer (CRC). For the survivors, second primary cancer and recurrence are important issues; however, evidence for an appropriate surveillance strategy remains limited.
This study aimed to investigate the frequency and timing of second primary cancer in patients after surgery for exploring an appropriate surveillance strategy by using an integrated analysis of three large-scale randomized controlled trials in Japan.

Methods
The eligibility criteria of three trials included histologically confirmed CRC and having received surgery. The timing, site and frequency of second primary cancers and recurrence were investigated. Risk factors associated with second primary cancers were also examined. The standardized incidence ratio (SIR) of second primary cancers compared with the national database of the Japan Cancer Registry was estimated.

Results
A total of 2824 patients were included in this study. The cumulative incidence of second primary cancer increased over time. The SIR of any second primary cancer was 1.07 (95% CI: 0.94–1.21). The SIR for second primary cancers of colon was 1.09 (95% CI: 0.79–1.47). The cumulative incidence of recurrence almost reached plateau at 3 years.

Conclusions
A common surveillance strategy for the general population can be applied even for curatively resected CRC patients, as the risk of second primary cancers was almost the same as that of the general population.
Fragmentation does not affect gene flow in forest populations of the dusky pipistrelle bat on the eastern seaboard of South Africa
Authors: Moir Monika , Richards Leigh R , Rambau Ramugondo V , Wannenburgh Andrew , Cherry Michael I 
Published: September 2020

AbstractThe Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.
Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture
Authors: Nisler Jaroslav , Kopečný David , Pěkná Zuzana , Končitíková Radka , Koprna Radoslav , Murvanidze Nino , Werbrouck Stefaan P O , Havlíček Libor , De Diego Nuria , Kopečná Martina , Wimmer Zdeněk , Briozzo Pierre , Moréra Solange , Zalabák David , Spíchal Lukáš , Strnad Miroslav 
Published: September 2020

Abstract
Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10–8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.
‘Beauty is Truth, Truth Beauty’: A Novel Account of Beauty, Bildung, and Truth in Hegel and Thomas Mann
Authors: Casewell Deborah 
Published: September 2020

Abstract
Both Thomas Mann and G.W.F. Hegel accord beauty a particular role in their work: that of revealing truth. However, both differ in its particular stature and effectiveness. For Hegel it is an essential part of Bildung, a step to fuller knowledge of the Absolute Idea, whereas for Mann it is revelatory of the failures of Bildung, of knowledge, and self-control, and doing so it unmasks an existential truth. Drawing on Nietzsche, Schopenhauer, Lukács, and Gadamer, this article explores the way in which Mann’s account of beauty, as detailed in Little Herr Friedemann and Death in Venice, challenges both Hegel’s philosophy and in doing so a particular ideal of Bildung, especially with regards to its relationship to truth.
The intrinsic reddening of the Magellanic Clouds as traced by background galaxies – II. The Small Magellanic Cloud
Authors: Bell Cameron P M , Cioni Maria-Rosa L , Wright A H , Rubele Stefano , Nidever David L , Tatton Ben L , van Loon Jacco Th , Zaritsky Dennis , Choi Yumi , Choudhury Samyaday , Clementini Gisella , de Grijs Richard , Ivanov Valentin D , Majewski Steven R , Marconi Marcella , Martínez-Delgado David , Massana Pol , Muñoz Ricardo R , Niederhofer Florian , Noël Noelia E D , Oliveira Joana M , Olsen Knut , Pennock Clara M , Ripepi V , Subramanian Smitha , Vivas A Katherina 
Published: September 2020

ABSTRACT
We present a map of the total intrinsic reddening across ≃34 deg2 of the Small Magellanic Cloud (SMC) derived using optical (ugriz) and near-infrared (IR; YJKs) spectral energy distributions (SEDs) of background galaxies. The reddening map is created using a subsample of 29 274 galaxies with low levels of intrinsic reddening based on the lephare χ2 minimization SED-fitting routine. We find statistically significant enhanced levels of reddening associated with the main body of the SMC compared with regions in the outskirts [ΔE(B − V) ≃ 0.3 mag]. A comparison with literature reddening maps of the SMC shows that, after correcting for differences in the volume of the SMC sampled, there is good agreement between our results and maps created using young stars. In contrast, we find significant discrepancies between our results and maps created using old stars or based on longer wavelength far-IR dust emission that could stem from biased samples in the former and uncertainties in the far-IR emissivity and the optical properties of the dust grains in the latter. This study represents one of the first large-scale categorizations of extragalactic sources behind the SMC and as such we provide the lephare outputs for our full sample of ∼500 000 sources.
Dynamical modelling of globular clusters: challenges for the robust determination of IMBH candidates
Authors: Aros Francisco I , Sippel Anna C , Mastrobuono-Battisti Alessandra , Askar Abbas , Bianchini Paolo , van de Ven Glenn 
Published: September 2020

ABSTRACTThe presence or absence of intermediate-mass black holes (IMBHs) at the centre of Milky Way globular clusters (GCs) is still an open question. This is due to either observational restrictions or limitations in the dynamical modelling method; in this work, we explore the latter. Using a sample of high-end Monte Carlo simulations of GCs, with and without a central IMBH, we study the limitations of spherically symmetric Jeans models assuming constant velocity anisotropy and mass-to-light ratio. This dynamical method is one of the most widely used modelling approaches to identify a central IMBH in observations.With these models, we are able to robustly identify and recover the mass of the central IMBH in our simulation with a high-mass IMBH ($M_{\rm IMBH}/M_{\rm GC}\sim 4{{\ \rm per\ cent}}$). Simultaneously, we show that it is challenging to confirm the existence of a low-mass IMBH ($M_{\rm IMBH}/M_{\rm GC}\sim 0.3{{\ \rm per\ cent}}$), as both solutions with and without an IMBH are possible within our adopted error bars. For simulations without an IMBH, we do not find any certain false detection of an IMBH. However, we obtain upper limits that still allow for the presence of a central IMBH. We conclude that while our modelling approach is reliable for the high-mass IMBH and does not seem to lead towards a false detection of a central IMBH, it lacks the sensitivity to robustly identify a low-mass IMBH and to definitely rule out the presence of an IMBH when it is not there.
Non-parametric density reconstruction of the Galactic bulge area using red clump stars in the VVV survey
Authors: Paterson Dylan , Coleman Brenna , Gordon Chris 
Published: September 2020

ABSTRACT
Studies of the red clump giant population in the inner Milky Way suggest the Galactic bulge/bar has a boxy/peanut/X-shaped structure as predicted by its formation via a disc buckling instability. We used a non-parametric method of estimating the Galactic bulge morphology that is based on maximum entropy regularization. This enabled us to extract the 3D distribution of the red giant stars in the bulge from deep photometric catalogues of the VISTA Variables in the Via Lactea survey. Our high-resolution reconstruction confirms the well-known boxy/peanut/X-shaped structure of the bulge. We also find spiral arm structures that extend to around 3 kpc in front of and behind the bulge and are on different sides of the bulge major axis. We show that the detection of these structures is robust to the uncertainties in the luminosity function.