bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of self-propelled particles passing a bottleneck
Authors: Mohammadi Mahdieh , Harth Kirsten , Puzyrev Dmitry , Hanselka Tina , Trittel Torsten , Stannarius Ralf
Published: November 2020

We study the passage of active and passive granular particles through a bottleneck under gravitational bias. The grains are pharmaceutical capsules with spherocylindrical shapes on a vibrating table. The vibrating ground plate is slightly tilted in order to break the in-plane symmetry and to give particles a motivation to move in a preferential direction. The passage through a narrow gate with openings comparable to the grain length is studied using video imaging. Particle positions and velocities are extracted from the recorded frames. We find striking differences between the behaviour of asymmetric, active capsules and symmetric, passive ones. The active grains show an astonishingly strong dependence of the passage rates on the gate width, while for passive grains, this dependence is linear as expected. The cumulative distributions of delays between subsequent particles passing the outlet, a key parameter in egress studies, also differ substantially between active and passive grains. Tilt angle and excitation parameters have only little influence on the observed dynamic features, they merely rescale time.
Evaluation of windowing techniques for intramuscular EMG-based diagnostic, rehabilitative and assistive devices
Authors: Ashraf Hassan , Waris Asim , Gilani Syed Omer , Kashif Amer Sohail , Jamil Mohsin , Jochumsen Mads , Niazi Imran Khan
Published: November 2020

Objective. Intramuscular electromyography (iEMG) signals, invasively recorded, directly from the muscles are used to diagnose various neuromuscular disorders/diseases and to control rehabilitative and assistive robotic devices. iEMG signals are potentially being used in neurology, kinesiology, rehabilitation and ergonomics, to detect/diagnose various diseases/disorders. Electromyography-based classification and analysis systems are being designed and tested for the classification of various neuromuscular disorders and to control rehabilitative and assistive robotic devices. Many studies have explored parameters such as the pre-processing, feature extraction and selection of classifiers that can affect the performance and efficacy of iEMG-based classification systems. The pre-processing stage includes the removal of any unwanted noise from the original signal and windowing of the signal. Approach. This study investigated and presented the optimum windowing configurations for robust control and better performance results of an iEMG-based analysis system based on the stationarity rate (SR) and classification accuracy. Both disjoint and overlap, windowing techniques with varying window and overlap sizes have been investigated using a machine learning-based classification algorithm called linear discriminant analysis. Main results. The optimum window size ranges are from 200–300 ms for the disjoint and 225–300 ms for the overlap windowing technique, respectively. The inferred results show that for the overlap windowing technique the optimum range of overlap size is from 10%–30% of the length of window size. The mean classification accuracy (MCA) and mean stationarity rate (MSR) were found to be lower in the disjoint windowing technique compared to overlap windowing at all investigated overlap sizes. Statistical analysis (two-way analysis of variance test) showed that the MSR and MCA of the overlap windowing technique was significantly different at overlap sizes of 10%–30% (p-values < 0.05). Significance. The presented results can be used to achieve the best possible classification results and SR for any iEMG-based real-time diagnosis, detection and control system, which can enhance the performance of the system significantly.
About a plausible explanation of ϒ(10860)
Authors: Bruschini R
Published: November 2020

The experimental resonance ϒ(10860) presents some typical properties of conventional bottomonium states as well as apparently unconventional features. In this talk it is shown that some of the properties of ϒ(10860), namely its mass, dilepton decay width and ππϒ production rates, can be explained from its interpretation as ϒ(5s) bottomonium state, given that one has a consistent description of

b

b
¯

hybrid states. It is also pointed out that other puzzling properties (e.g. the dipion transition rate to hb
) can be understood under the assumption that ϒ(10860) is a mixing of the ϒ(5s) with the ground

b

b
¯

hybrid state.
Hadronic transitions in quarkonium
Authors: Castellá Jaume Tarrús
Published: November 2020

We report on a new approach to compute quarkonium hadronic transitions which does not rely on the standard twist expansion of the intermediate octet propagator. The latter cannot be justified for the energy release of hadronic transitions between heavy quarkonium states with different principal quantum numbers. Instead, we use that the octet state spectrum corresponds to the hybrid quarkonium one which can be obtained from nonrelativistic effective field theories (EFT) of QCD and lattice computations of the heavy-quark-antiquark static energies.
TGenBase - universal database for FAIR experiments
Authors: Lavrik E.
Published: November 2020

TGenBase is a ROOT-based virtual database which allows to communicate and store data in different underlying database management systems such as PostgreSQL, MySQL, SQLite, based on the configuration. It is primarily used for physics analysis parameter storage. However, it is universally applicable for any data storage task. There are several key features of the TGenBase for the user applications. It is a versioned insert only database, meaning that there is no need to update single entries and the whole history of the entries is available. The historical versions of the data can be queried with for a certain date. Being written as extension of the ROOT framework, it supports saving the ROOT objects such as graphs or histograms as well.

We provide the data description interface-a web-based application which allows the end-user to define what and in which form they want the data to be stored and define the relations between different entities. Based on this definition the database schemas, server and client side code is generated from templates and easily deployed. Another feature of this approach is that we are able to generate the full-fledged content management systems with user roles for read and write access. Data query, visualization and modification are available in C++, Python, Web and LabVIEW thin clients.
Strangeness production measured with HADES
Authors: Spies Simon
Published: November 2020

HADES is a multi-purpose, charged-particle detector operated at the SIS18 synchrotron located at the GSI Helmholtz Center for Heavy Ion Research in Darmstadt, Germany. The provided ion beam energies of 1-2 A GeV are among the lowest of all currently running heavy-ion experiments and result in the highest baryon net-densities at freeze-out in case of Au+Au collisions. At a beam energy of 1.23 A GeV, particles containing strangeness are produced below the quasi-free NN threshold energy. Since the missing energy has to be provided by the collision system, the investigation of the production of strangeness at such energies is a very promising probe of the created medium. The data sample measured with HADES includes multi-differential analysis of charged and neutral kaons, ϕ mesons and Λ hyperons. We present the analysis method and the results.
Detection of delay in post-monsoon agricultural burning across Punjab, India: potential drivers and consequences for air quality
Authors: Liu Tianjia , Mickley Loretta J , Gautam Ritesh , Singh Manoj K , DeFries Ruth S , Marlier Miriam E
Published: November 2020

Since the Green Revolution in the mid-1960s, a widespread transition to a rice–wheat rotation in the Indian state of Punjab has led to steady increases in crop yield and production. After harvest of the summer monsoon rice crop, the burning of excess crop residue in Punjab from October to November allows for rapid preparation of fields for sowing of the winter wheat crop. Here we use daily satellite remote sensing data to show that the timing of peak post-monsoon fire activity in Punjab and regional aerosol optical depth (AOD) has shifted later by approximately two weeks in Punjab from 2003 to 2016. This shift is consistent with delays of 11–15 d in the timing of maximum greenness of the monsoon crop and smaller delays of 4–6 d in the timing of minimum greenness during the monsoon-to-winter crop transition period. The resulting compression of the harvest-to-sowing period coincides with a 42% increase in total burning and 55% increase in regional AOD. Potential drivers of these trends include agricultural intensification and a recent groundwater policy that delays sowing of the monsoon crop. The delay and amplification of burning into the late post-monsoon season suggest greater air quality degradation and public health consequences across the densely populated Indo-Gangetic Plain.
Empirical anomaly measure for finite-variance processes
Authors: Maraj Katarzyna , Szarek Dawid , Sikora Grzegorz , Wyłomańska Agnieszka
Published: November 2020

Anomalous diffusion phenomena are observed in many areas of interest. They manifest themselves in deviations from the laws of Brownian motion (BM), e.g. in the non-linear growth (mostly power-law) in time of the ensemble average mean squared displacement (MSD). When we analyze the real-life data in the context of anomalous diffusion, the primary problem is the proper identification of the type of the anomaly. In this paper, we introduce a new statistic, called empirical anomaly measure (EAM), that can be useful for this purpose. This statistic is the sum of the off-diagonal elements of the sample autocovariance matrix for the increments process. On the other hand, it can be represented as the convolution of the empirical autocovariance function with time lags. The idea of the EAM is intuitive. It measures dependence between the ensemble-averaged MSD of a given process from the ensemble-averaged MSD of the classical BM. Thus, it can be used to measure the distance between the anomalous diffusion process and normal diffusion. In this article, we prove the main probabilistic characteristics of the EAM statistic and construct the formal test for the recognition of the anomaly type. The advantage of the EAM is the fact that it can be applied to any data trajectories without the model specification. The only assumption is the stationarity of the increments process. The complementary summary of the paper constitutes of Monte Carlo simulations illustrating the effectiveness of the proposed test and properties of EAM for selected processes.
The role of nanostructure morphology of nickel-infused alumina on solar-thermal energy conversion
Authors: Wang Xuanjie , Hsieh Mei-Li , Bur James A , Lin Shawn-Yu , Narayanan Shankar
Published: November 2020

Solar-thermal energy conversion can be useful in many applications, including water desalination, and thermal energy storage. In this regard, using spectrally-selective solar absorbers is vital due to their high solar absorptance and low thermal emittance. While selective absorbers can be created using a wide range of nanomaterials, the underlying geometry may control the overall performance of solar-thermal energy conversion. With different geometries, it is possible to obtain a wide range of optical responses ranging from broadband to selective absorption of light. In this study, we focus on the role of nanostructure morphology of nickel-infused alumina (Ni/NPA) based spectrally-selective solar absorbers. This study demonstrates the use of the design of experiments to analyze the effect of various geometric factors on the resulting optical response of Ni/NPA in the context of solar-thermal energy conversion. We show how this approach can provide a unique insight into the role of various geometric factors on the solar absorptance and thermal emittance of Ni/NPA-based absorbers, and demonstrate how it can guide the development of spectrally-selective materials. We believe a similar approach can be useful in the development of other optical materials for different applications.
Repeatable room-temperature self-healing memory device based on gelatin films
Authors: Chang Yu-Chi , Jian Jia-Cheng , Hsu Ya Lan , Huang Wei-Yun , Chen Zhao-Cheng , Liu Kuan-Miao
Published: November 2020

Flexible gelatin resistive memory device exhibits a high ON/OFF ratio of over 106. Moreover, the bended gelatin resistive memory device can efficiently heal at room temperature without any external stimulus. This self-healing behavior of gelatin resistive memory device was demonstrated based on the metal chelating ligand. Al ions migrating from the top radio frequency Al electrode contributed to the construction of the metal chelating ligand. The carboxylates of gelatin can form multi-dentate coordination compounds with Al ions, which can restore the memory properties of the gelatin resistive memory device. Thus, Al ion migration from the top Al electrodes plays an important role in self-healing capability. The effect of Al ions on the self-healing mechanism was investigated by using secondary ion mass spectrometry, which is useful for the characterization of Al migration from the top electrode. This capability for restoring the electrical properties of gelatin memory device is desirable for flexible electronics and represents a major step toward self-healable bioelectronics.
Canard resonance: on noise-induced ordering of trajectories in heterogeneous networks of slow-fast systems
Authors: D’Huys Otti , Veltz Romain , Dolcemascolo Axel , Marino Francesco , Barland Stéphane
Published: November 2020

We analyse the dynamics of a network of semiconductor lasers coupled via their mean intensity through a non-linear optoelectronic feedback loop. We establish experimentally the excitable character of a single node, which stems from the slow-fast nature of the system, adequately described by a set of rate equations with three well separated time scales. Beyond the excitable regime, the system undergoes relaxation oscillations where the nodes display canard dynamics. We show numerically that, without noise, the coupled system follows an intricate canard trajectory, with the nodes switching on one by one. While incorporating noise leads to a better correspondence between numerical simulations and experimental data, it also has an unexpected ordering effect on the canard orbit, causing the nodes to switch on closer together in time. We find that the dispersion of the trajectories of the network nodes in phase space is minimized for a non-zero noise strength, and call this phenomenon canard resonance.
Spain’s LGBT Movement
Authors: Calvo Kerman , Pichardo J. Ignacio
Published: November 2020

The LGBT movement has been successful in improving the legal and social standing of sexual minorities in Spain; this includes the recognition of same-sex marriages, joint adoption, and the right to change identification in public registers. The movement has also contributed to a wider acceptance of LGBT diversity at the societal level. LGBT mobilizations in Spain started in the 1970s, with the transition toward democracy. The first political generation of activists believed in gay liberation, supported revolutionary ideas, and defended street protesting. This did not prevent activists from seeking collaboration with the state, as urgent legal action was required to end the criminalization of homosexual relations. After a decade of demobilization, a new generation of activists revamped LGBT activism in Spain during the 1990s, again with a well-defined political agenda: reacting to the devastation caused by AIDS, and also to the changes taking place in the international stage, the new “proud” generation demanded not only individual rights, but also family rights. The legalization of same-sex marriage (and joint adoption) in 2005 was the outcome of a vibrant cycle of mobilization. Contrary to some expectations, the Spanish LGBT movement has not become the victim of its own success. By shifting its attention toward the goal of substantive equality and by reaching out to new communities, the movement remains influential and vigilant against threats posed by the consolidation of new forms of conservative countermobilization.
Positive Leadership in Organizations
Authors: Monzani Lucas , Van Dick Rolf
Published: November 2020

Positive leadership is a major domain of positive organizational scholarship. The adjective “positive” applies to any leader behavioral pattern (style) that creates the conditions by which organizational members can self-actualize, grow, and flourish at work. Some examples of style are authentic, transformational, servant, ethical, leader–member exchange, identity leadership, and the leader character model. Despite the myriad constructive outcomes that relate to said positive leadership styles, positive leadership it is not without its critics. The three main criticisms are that (a) the field is fragmented and might suffer from conceptual redundancy, (b) extant research focuses on the individual level of analysis and neglects reciprocal and cross-level effects, and (c) positive leadership is naïve and not useful for managing organizations.

Our multilevel model of positive leadership in organizations proposes that leaders rely on internalization and integration to incorporate meaningful life experiences and functional social norms into their core self. Further, through self-awareness and introspection, leaders discover and exercise their latent character strengths. In turn, positive leaders influence followers through exemplary role modeling and in turn followers validate leaders by adopting their attributes and self-determined behaviors. At the team level of analysis, positive team leaders elevate workgroups into teams by four mechanisms that shape a shared “sense of we,” and workgroup members legitimize positive leaders by granting them a leader role identity and assuming follower role identities. Finally, at the organizational level, organizational leaders can shape a virtuous culture by anchoring it on universal virtues and through corporate social responsibility actions improve their context. Alternatively, organizations can shape a virtuous culture through organizational learning.
Community-Based Participatory Research
Authors: Duke Michael
Published: November 2020

Community-based participatory research (CBPR) refers to a methodological and epistemological approach to applied community projects in which researchers and community members collaborate as equals in the research process. Also known as participatory action research (PAR), CBPR has gained considerable acceptance both as a set of methods for identifying and addressing local issues of concern and as a vehicle for applying the principles of equity, cultural humility, mutual learning, and social justice to the relationships between researchers and communities. Although somewhat distinct from applied anthropology, CBPR shares with ethnography in particular an attentiveness to rapport building and community engagement and an overall validation of local knowledge. There is little consensus regarding the threshold of community participation necessary for a given research project to be considered CBPR. However, at a minimum the approach requires that community members define the problems to be assessed, provide consultation on the cultural and social dimensions of the study population, and serve in an advisory capacity over the entire project. The history of CBPR and its antecedents reflects its twin values as a pragmatic approach to researching and addressing local problems and as an emancipatory social justice project that seeks to diminish the hierarchical relationship between researchers and community members. Specifically, the pragmatic perspective was developed in the United States by social psychologist Kurt Lewin in the 1930s (and subsequently by the anthropologists Laura Thompson and Sol Tax), while the emancipatory approach derives from the work of educational theorist Paulo Freire in Brazil in the 1970s. Community Advisory Boards (CABs) play an outsized role in the success of CBPR projects, since they typically represent the community in these studies, and thus maintain oversight over all aspects of the research process, including the study design, sampling and recruitment protocols, and the dissemination of findings. Accordingly, nurturing and maintaining trust between researchers, the CAB, and the community constitutes a foundational practice for any CBPR study.
Consumption of dietary nuts in midlife and risk of cognitive impairment in late-life: the Singapore Chinese Health Study
Authors: Jiang Yi-Wen , Sheng Li-Ting , Feng Lei , Pan An , Koh Woon-Puay
Published: November 2020

Background

evidence from prospective studies investigating the association between consumption of nuts in midlife and risk of cognitive impairment in late life is limited.

Methods

this study analysed data from 16,737 participants in a population-based cohort, the Singapore Chinese Health Study. Intake of nuts was assessed using a validated food-frequency questionnaire at baseline (1993–1998), when participants were 45–74 years old (mean age = 53.5 years). Cognitive function was tested using the Singapore modified Mini-Mental State Examination during the third follow-up visit (2014–2016), when participants were 61–96 years old (mean age = 73.2 years). Cognitive impairment was defined using education-specific cut-off points. Logistic regression models were used to estimate the odds ratio (OR) and the 95% confidence interval (CI) for the association between intake and risk of cognitive impairment.

Results

cognitive impairment was identified in 2,397 (14.3%) participants. Compared with those who consumed <1 serving/month of nuts, participants who consumed 1–3 servings/month, 1 serving/week and ≥2 servings/week had 12% (95% CI 2–20%), 19% (95% CI 4–31%) and 21% (2–36%) lower risk of cognitive impairment, respectively (P-trend = 0.01). Further adjustment for intake of unsaturated fatty acids attenuated the association to non-significance. Mediation analysis showed that the 50.8% of the association between nuts and risk of cognitive impairment was mediated by the intake of total unsaturated fatty acids (P < 0.001).

Conclusion

higher intake of nuts in midlife was related to a lower risk of cognitive impairment in late life, which was partly mediated by unsaturated fatty acids.
Prevalence of atrial fibrillation and outcomes in older long-term care residents: a systematic review
Authors: Ritchie Leona A , Oke Oluwakayode B , Harrison Stephanie L , Rodgers Sarah E , Lip Gregory Y H , Lane Deirdre A
Published: November 2020

Background

anticoagulation is integral to stroke prevention for atrial fibrillation (AF), but there is evidence of under-treatment in older people in long-term care (LTC).

Objective

to synthesise evidence on the prevalence and outcomes (stroke, mortality or bleeding) of AF in LTC and the factors associated with the prescription of anticoagulation.

Methods

studies were identified from Medline, CINAHL, PsycINFO, Scopus and Web of Science from inception to 31 October 2019. Two reviewers independently applied the selection criteria and assessed the quality of studies using the Newcastle Ottawa Scale.

Results

twenty-nine studies were included. Prevalence of AF was reported in 21 studies, ranging from 7 to 38%. Two studies reported on outcomes based on the prescription of anticoagulation or not; one reported a reduction in the ischaemic stroke event rate associated with anticoagulant (AC) prescription (2.84 per 100 person years, 95% confidence interval [CI]: 1.98–7.25 versus 3.95, 95% CI: 2.85–10.08) and a non-significant increase in intracranial haemorrhage rate (0.71 per 100 person years, 95% CI: 0.29–2.15 versus 0.65, 95% CI: 0.29–1.93). The second study reported a 76% lower chance of ischaemic stroke with AC prescription and a low incidence of bleeding (n = 4 events). Older age, dementia/cognitive impairment and falls/falls risk were independently associated with the non-prescription of anticoagulation. Conversely, previous stroke/transient ischaemic attack and thromboembolism were independently associated with an increased prescription of anticoagulation.

Conclusion

estimates of AF prevalence and factors associated with AC prescription varied extensively. Limited data on outcomes prevent the drawing of definitive conclusions. We recommend panel data collection and systems for linkage to create longitudinal cohorts to provide more robust evidence.
Clinical and Financial Implications of Second-Opinion Surgical Pathology Review
Authors: Johnson Steven M , Samulski Teresa D , O’Connor Siobhan M , Smith Scott V , Funkhouser William K , Broaddus Russell R , Calhoun Benjamin C
Published: November 2020

Objectives

Second-opinion pathology review identifies clinically significant diagnostic discrepancies for some patients. Discrepancy rates and laboratory-specific costs in a single health care system for patients referred from regional affiliates to a comprehensive cancer center (“main campus”) have not been reported.

Methods

Main campus second-opinion pathology cases for 740 patients from eight affiliated hospitals during 2016 to 2018 were reviewed. Chart review was performed to identify changes in care due to pathology review. To assess costs of pathology interpretation, reimbursement rates for consultation Current Procedural Terminology billing codes were compared with codes that would have been used had the cases originated at the main campus.

Results

Diagnostic discrepancies were identified in 104 (14.1%) patients, 30 (4.1%) of which resulted in a change in care. In aggregate, reimbursement for affiliate cases was 65.6% of the reimbursement for the same cases had they originated at the main campus. High-volume organ systems with low relative consultation reimbursement included gynecologic, breast, and thoracic.

Conclusions

Preventable diagnostic errors are reduced by pathology review for patients referred within a single health care system. Although the resulting changes in care potentially lead to overall cost savings, the financial value of referral pathology review could be improved.
A deep learning approach for filtering structural variants in short read sequencing data
Authors: Liu Yongzhuang , Huang Yalin , Wang Guohua , Wang Yadong
Published: November 2020

Short read whole genome sequencing has become widely used to detect structural variants in human genetic studies and clinical practices. However, accurate detection of structural variants is a challenging task. Especially existing structural variant detection approaches produce a large proportion of incorrect calls, so effective structural variant filtering approaches are urgently needed. In this study, we propose a novel deep learning-based approach, DeepSVFilter, for filtering structural variants in short read whole genome sequencing data. DeepSVFilter encodes structural variant signals in the read alignments as images and adopts the transfer learning with pre-trained convolutional neural networks as the classification models, which are trained on the well-characterized samples with known high confidence structural variants. We use two well-characterized samples to demonstrate DeepSVFilter’s performance and its filtering effect coupled with commonly used structural variant detection approaches. The software DeepSVFilter is implemented using Python and freely available from the website at https://github.com/yongzhuang/DeepSVFilter.
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
Authors: Ahlmann-Eltze Constantin , Huber Wolfgang
Published: November 2020

Motivation

The Gamma-Poisson distribution is a theoretically and empirically motivated model for the sampling variability of single cell RNA-sequencing counts and an essential building block for analysis approaches including differential expression analysis, principal component analysis and factor analysis. Existing implementations for inferring its parameters from data often struggle with the size of single cell datasets, which can comprise millions of cells; at the same time, they do not take full advantage of the fact that zero and other small numbers are frequent in the data. These limitations have hampered uptake of the model, leaving room for statistically inferior approaches such as logarithm(-like) transformation.

Results

We present a new R package for fitting the Gamma-Poisson distribution to data with the characteristics of modern single cell datasets more quickly and more accurately than existing methods. The software can work with data on disk without having to load them into RAM simultaneously.

Availabilityand implementation

The package glmGamPoi is available from Bioconductor for Windows, macOS and Linux, and source code is available on github.com/const-ae/glmGamPoi under a GPL-3 license. The scripts to reproduce the results of this paper are available on github.com/const-ae/glmGamPoi-Paper.

Supplementary information

Supplementary data are available at Bioinformatics online.
Food Insecurity and T-cell Dysregulation in Women Living With Human Immunodeficiency Virus on Antiretroviral Therapy
Authors: Peters Brandilyn A , Sheira Lila A , Hanna David B , Qi Qibin , Sharma Anjali , Adedimeji Adebola , Wilson Tracey , Merenstein Daniel , Tien Phyllis C , Cohen Mardge , Wentz Eryka L , Kinslow Jennifer , Landay Alan L , Weiser Sheri D
Published: November 2020

Background

Food insecurity is associated with increased morbidity and mortality in people with human immunodeficiency virus (HIV) on antiretroviral therapy, but its relationship with immune dysregulation, a hallmark of HIV infection and comorbidity, is unknown.

Methods

In 241 women participating in the Women’s Interagency HIV Study, peripheral blood mononuclear cells were characterized by flow cytometry to identify cell subsets, comprising surface markers of activation (%CD38+HLADR+), senescence (%CD57+CD28−), exhaustion (%PD-1+), and co-stimulation (%CD57− CD28+) on CD4+ and CD8+ T cells. Mixed-effects linear regression models were used to assess the relationships of food insecurity with immune outcomes, accounting for repeated measures at ≤3 study visits and adjusting for sociodemographic and clinical factors.

Results

At the baseline study visit, 71% of participants identified as non-Hispanic Black, 75% were virally suppressed, and 43% experienced food insecurity. Food insecurity was associated with increased activation of CD4+ and CD8+ T cells, increased senescence of CD8+ T cells, and decreased co-stimulation of CD4+ and CD8+ T cells (all P < .05), adjusting for age, race/ethnicity, income, education, substance use, smoking, HIV viral load, and CD4 count. In stratified analyses, the association of food insecurity with CD4+ T-cell activation was more pronounced in women with uncontrolled HIV (viral load >40 copies/mL and CD4 <500 cells/mm3) but remained statistically significant in those with controlled HIV.

Conclusions

Food insecurity may contribute to the persistent immune activation and senescence in women with HIV on antiretroviral therapy, independently of HIV control. Reducing food insecurity may be important for decreasing non–AIDS-related disease risk in this population.
The Mediterranean mussel Mytilus galloprovincialis: responses to climate change scenarios as a function of the original habitat
Authors: Lassoued Jihene , Padín X A , Comeau Luc A , Bejaoui Nejla , Pérez Fiz F , Babarro Jose M F
Published: November 2020

The impact of simulated seawater acidification and warming conditions on specimens of the mussel Mytilus galloprovincialis locally adapted to very distinct, widely separated sites in the Mediterranean Sea (Tunisia) and Atlantic Sea (Galicia, NW Spain) was evaluated in relation to key behavioural and eco-physiological parameters. Over the 2-month exposure to the experimental conditions, mussels were fed optimally to ensure that there are no synergistic interactions between climate change drivers and energetic status of the individuals. In general, regardless of origin (Atlantic or Mediterranean), the mussels were rather resilient to acidification for most of the parameters considered and they were able to grow in strongly acidified seawater through an increased feeding activity. However, shell strength decreased (40%) consistently in both mussel populations held in moderately and highly acidified seawater. The observed reduction in shell strength was not explained by slight alterations in organic matter, shell thickness or aragonite:calcite ratio. The combined effects of high acidification and warming on the key response of byssus strength caused a strong decline in mussel performance, although only in Galician mussels, in which the valve opening time decreased sharply as well as condition index (soft tissue state) and shell growth. By contrast, the observed negative effect of highly acidified scenario on the strength of Tunisian mussel shells was (partly but not totally) counterbalanced by the higher seawater temperature. Eco-physiological and behavioural interactions in mussels in relation to climate change are complex, and future scenarios for the ecology of the species and also the feasibility of cultivating them in Atlantic and Mediterranean zones are discussed.
Using claws to compare reproduction, stress and diet of female bearded and ringed seals in the Bering and Chukchi seas, Alaska, between 1953–1968 and 1998–2014
Authors: Crain Danielle D , Karpovich Shawna A , Quakenbush Lori , Polasek Lori
Published: November 2020

Rapid climate warming is decreasing sea ice thickness, extent and duration. Marine mammals such as bearded (Erignathus barbatus) and ringed (Pusa hispida) seals, which use sea ice for pupping, molting and resting, may be negatively affected. Claws from bearded and ringed seals store up to 14 and 12 years of sequential analyte data, respectively. These data can be used to compare reproduction, stress and diet across decades. In this study, we compare progesterone, cortisol and carbon and nitrogen stable isotopes in female bearded and ringed seals during 1953–1968 (pre-1968, a period prior to sea ice decline) to 1998–2014 (post-1998, a period during sea ice decline). When comparing these periods, bearded seals had statistically higher cortisol concentrations post-1998, and for both species δ13C was more negative post-1998, while progesterone and δ15N did not change. There was a positive relationship between progesterone and cortisol Z-scores for both species, except for ringed seals post-1998. There was a negative relationship between cortisol Z-scores and δ13C for bearded seals evident in post-1998 indicating that higher cortisol Z-scores are associated with more negative δ13C in bearded seals in recent years. This negative relationship between cortisol and δ13C in bearded seals suggests a shift to higher prey diversity, possibly due to changes in sea ice in the Pacific Arctic evident post 1998. Progesterone Z-scores corresponded to expected differences among non-pregnant, unimplanted, implanted and post-partum individuals. Using these data, pregnancy history was determined for reproductive years for each individual female sampled, which could allow for yearly pregnancy rates to be calculated given a large enough representative sample of the population. These results combine decades of observational studies with hormones and stable isotopes to infer changes in reproduction, stress and diet, as well as the connection between these life history parameters.
Transcriptional profiling of theL. monocytogenesPrfA regulon identifies six novel putative PrfA-regulated genes
Authors: Henderson L O , Gaballa A , Orsi R H , Boor K J , Wiedmann M , Guariglia-Oropeza V
Published: November 2020

The transcriptional activator Positive Regulatory Factor A (PrfA) regulates expression of genes essential for virulence in Listeria monocytogenes. To define the PrfA regulon, the 10403S wildtype (WT) strain, a constitutively active prfA* mutant, and an isogenic ∆prfA mutant were grown under PrfA-inducing conditions in a medium containing glucose-1-phosphate and pre-treated with 0.2% activated charcoal. RNA-seq-generated transcript levels were compared as follows: (i) prfA* and WT; (ii) WT and ∆prfA and (iii) prfA* and ∆prfA. Significantly higher transcript levels in the induced WT or constitutively active PrfA* were identified for 18 genes and 2 ncRNAs in at least one of the three comparisons. These genes included: (i) 10/12 of the genes previously identified as directly PrfA-regulated; (ii) 2 genes previously identified as PrfA-regulated, albeit likely indirectly; and (iii) 6 genes newly identified as PrfA-regulated, including one (LMRG_0 2046) with a σA-dependent promoter and PrfA box located within an upstream open reading frame. LMRG_0 2046, which encodes a putative cyanate permease, is reported to be downregulated by a σB-dependent anti-sense RNA. This newly identified overlap between the σB and PrfA regulons highlights the complexity of regulatory networks important for fine-tuning bacterial gene expression in response to the rapidly changing environmental conditions associated with infection.
Effect of capsaicin on the protozoan parasite Trypanosoma cruzi
Authors: Valera-Vera Edward A , Reigada Chantal , Sayé Melisa , Digirolamo Fabio A , Galceran Facundo , Miranda Mariana R , Pereira Claudio A
Published: November 2020

Trypanosoma cruzi is the causative agent of Chagas disease. There are only two approved treatments, both of them unsuitable for the chronic phase, therefore the development of new drugs is a priority. Trypanosoma cruzi arginine kinase (TcAK) is a promising drug target since it is absent in humans and it is involved in cellular stress responses. In a previous study, possible TcAK inhibitors were identified through computer simulations resulting the best compounds capsaicin and cyanidin derivatives. Here, we evaluate the effect of capsaicin on TcAK activity and its trypanocidal effect. Although capsaicin produced a weak enzyme inhibition, it had a strong trypanocidal effect on epimastigotes and trypomastigotes (IC50 = 6.26 µM and 0.26 µM, respectively) being 20-fold more active on trypomastigotes than mammalian cells. Capsaicin was also active on the intracellular cycle reducing by half the burst of trypomastigotes at approximately 2 µM. Considering the difference between the concentrations at which parasite death and TcAK inhibition occur, other possible targets were predicted.

Capsaicin is a selective trypanocidal agent active in nanomolar concentrations, with an IC50 57-fold lower than benznidazole, the drug currently used for treating Chagas disease.
GrimAge Outperforms Other Epigenetic Clocks in the Prediction of Age-Related Clinical Phenotypes and All-Cause Mortality
Authors: McCrory Cathal , Fiorito Giovanni , Hernandez Belinda , Polidoro Silvia , O’Halloran Aisling M , Hever Ann , Ni Cheallaigh Cliona , Lu Ake T , Horvath Steve , Vineis Paolo , Kenny Rose Anne
Published: November 2020

The aging process is characterized by the presence of high interindividual variation between individuals of the same chronical age prompting a search for biomarkers that capture this heterogeneity. Epigenetic clocks measure changes in DNA methylation levels at specific CpG sites that are highly correlated with calendar age. The discrepancy resulting from the regression of DNA methylation age on calendar age is hypothesized to represent a measure of biological aging with a positive/negative residual signifying age acceleration (AA)/deceleration, respectively. The present study examines the associations of 4 epigenetic clocks—Horvath, Hannum, PhenoAge, GrimAge—with a wide range of clinical phenotypes (walking speed, grip strength, Fried frailty, polypharmacy, Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MOCA), Sustained Attention Reaction Time, 2-choice reaction time), and with all-cause mortality at up to 10-year follow-up, in a sample of 490 participants in the Irish Longitudinal Study on Ageing (TILDA). HorvathAA and HannumAA were not predictive of health; PhenoAgeAA was associated with 4/9 outcomes (walking speed, frailty MOCA, MMSE) in minimally adjusted models, but not when adjusted for other social and lifestyle factors. GrimAgeAA by contrast was associated with 8/9 outcomes (all except grip strength) in minimally adjusted models, and remained a significant predictor of walking speed, .polypharmacy, frailty, and mortality in fully adjusted models. Results indicate that the GrimAge clock represents a step-improvement in the predictive utility of the epigenetic clocks for identifying age-related decline in an array of clinical phenotypes promising to advance precision medicine.
Why IACUCs Need Ethicists
Authors: Nobis Nathan
Published: November 2020

Some animal research is arguably morally wrong, and some animal research is morally bad but could be improved. Who is most likely to be able to identify wrong or bad animal research and advocate for improvements? I argue that philosophical ethicists have the expertise that makes them the likely best candidates for these tasks. I review the skills, knowledge, and perspectives that philosophical ethicists tend to have that makes them ethical experts. I argue that, insofar as Institutional Animal Care and Use Committees are expected to ensure that research is ethical, they must have philosophical ethicists as members.
An R848-Conjugated Influenza Virus Vaccine Elicits Robust Immunoglobulin G to Hemagglutinin Stem in a Newborn Nonhuman Primate Model
Authors: Clemens Elene A , Holbrook Beth C , Kanekiyo Masaru , Yewdell Jonathan W , Graham Barney S , Alexander-Miller Martha A
Published: November 2020

Eliciting broadly protective antibodies is a critical goal for the development of more effective vaccines against influenza. Optimizing protection is of particular importance in newborns, who are highly vulnerable to severe disease following infection. An effective vaccination strategy for this population must surmount the challenges associated with the neonatal immune system as well as mitigate the inherent immune subdominance of conserved influenza virus epitopes, responses to which can provide broader protection. Here, we show that prime-boost vaccination with a TLR7/8 agonist (R848)-conjugated influenza A virus vaccine elicits antibody responses to the highly conserved hemagglutinin stem and promotes rapid induction of virus neutralizing stem-specific antibodies following viral challenge. These findings support the efficacy of R848 as an effective adjuvant for newborns and demonstrate its ability to enhance antibody responses to subdominant antigenic sites in this at-risk population.
Investigation of a Large Diphtheria Outbreak and Cocirculation of Corynebacterium pseudodiphtheriticum Among Forcibly Displaced Myanmar Nationals, 2017–2019
Authors: Weil Lauren M , Williams Margaret M , Shirin Tahmina , Lawrence Marlon , Habib Zakir H , Aneke Janessa S , Tondella Maria L , Zaki Quazi , Cassiday Pamela K , Lonsway David , Farrque Mirza , Hossen Tanvir , Feldstein Leora R , Cook Nicholas , Maldonado-Quiles Gladys , Alam Ahmed N , Muraduzzaman A K M , Akram Arifa , Conklin Laura , Doan Stephanie , Friedman Michael , Acosta Anna M , Hariri Susan , Fox LeAnne M , Tiwari Tejpratap S P , Flora Meerjady S
Published: November 2020

Background

Diphtheria, a life-threatening respiratory disease, is caused mainly by toxin-producing strains of Corynebacterium diphtheriae, while nontoxigenic corynebacteria (eg, Corynebacterium pseudodiphtheriticum) rarely causes diphtheria-like illness. Recently, global diphtheria outbreaks have resulted from breakdown of health care infrastructures, particularly in countries experiencing political conflict. This report summarizes a laboratory and epidemiological investigation of a diphtheria outbreak among forcibly displaced Myanmar nationals in Bangladesh.

Methods

Specimens and clinical information were collected from patients presenting at diphtheria treatment centers. Swabs were tested for toxin gene (tox)-bearing C. diphtheriae by real-time polymerase chain reaction (RT-PCR) and culture. The isolation of another Corynebacterium species prompted further laboratory investigation.

Results

Among 382 patients, 153 (40%) tested tox positive for C. diphtheriae by RT-PCR; 31 (20%) PCR-positive swabs were culture confirmed. RT-PCR revealed 78% (298/382) of patients tested positive for C. pseudodiphtheriticum. Of patients positive for only C. diphtheriae, 63% (17/27) had severe disease compared to 55% (69/126) positive for both Corynebacterium species, and 38% (66/172) for only C. pseudodiphtheriticum.

Conclusions

We report confirmation of a diphtheria outbreak and identification of a cocirculating Corynebacterium species. The high proportion of C. pseudodiphtheriticum codetection may explain why many suspected patients testing negative for C. diphtheriae presented with diphtheria-like symptoms.
Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) β-lactamase enzymes inAcinetobacter baumannii
Authors: Takebayashi Yuiko , Findlay Jacqueline , Heesom Kate J , Warburton Philip J , Avison Matthew B , Evans Benjamin A
Published: November 2020

Objectives

To measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterize the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC–MS/MS.

Methods

Antimicrobial susceptibility tests were performed on 10 clinical Acinetobacter baumannii isolates. Carbapenem MICs were evaluated for all oxaAb variants cloned into A. baumannii CIP70.10 and BM4547, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC–MS/MS.

Results

Only the OxaAb variants with I129L and L167V substitutions, OxaAb(82), OxaAb(83), OxaAb(107) and OxaAb(110) increased carbapenem MICs when expressed in susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC–MS/MS analysis on the original clinical isolates confirmed overexpression of the four I129L and L167V variants. No other differences in expression levels of proteins commonly associated with carbapenem resistance were detected.

Conclusions

Elevated carbapenem MICs were observed by expression of OxaAb variants carrying clinically prevalent substitutions I129L and L167V. To drive carbapenem resistance, these variants required overexpression by their upstream ISAba1 promoter. This study clearly demonstrates that a combination of IS-driven overexpression of oxaAb and the presence of particular amino acid substitutions in the active site to improve carbapenem capture is key in conferring carbapenem resistance in A. baumannii and other mechanisms are not required.
Navigating treatment approaches for presumed ESBL-producing infections
Authors: Tamma Pranita D , Mathers Amy J
Published: November 2020

ESBL-producing Enterobacterales (ESBL-E) remain a significant global threat. In several regions of the world, ESBLs are produced by over half of Escherichia coli or Klebsiella pneumoniae infections, contributing to significant morbidity and mortality. Though it is accepted that carbapenems are effective for the treatment of invasive ESBL-E infections, controversy remains as to whether carbapenem alternatives can be considered in select cases. Indiscriminate carbapenem use for the treatment of ESBL-E infections will likely further the international antimicrobial resistance crisis, underscoring the importance of investigating the role of non-carbapenem options. In this issue of JAC-Antimicrobial Resistance, we present a PRO/CON debate exploring whether carbapenems are necessary for all infections caused by ceftriaxone-resistant Enterobacterales.