bluuebunny/crossref_metadata_2025 huggingface dataset:
Tri-axial accelerometry shows differences in energy expenditure and parental effort throughout the breeding season in long-lived raptors
Authors: López-López Pascual , Perona Arturo M , Egea-Casas Olga , Morant Jon , Urios Vicente
Published: January 2021

Cutting-edge technologies are extremely useful to develop new workflows in studying ecological data, particularly to understand animal behavior and movement trajectories at the individual level. Although parental care is a well-studied phenomenon, most studies have been focused on direct observational or video recording data, as well as experimental manipulation. Therefore, what happens out of our sight still remains unknown. Using high-frequency GPS/GSM dataloggers and tri-axial accelerometers we monitored 25 Bonelli’s eagles Aquila fasciata during the breeding season to understand parental activities from a broader perspective. We used recursive data, measured as number of visits and residence time, to reveal nest attendance patterns of biparental care with role specialization between sexes. Accelerometry data interpreted as the overall dynamic body acceleration, a proxy of energy expenditure, showed strong differences in parental effort throughout the breeding season and between sexes. Thereby, males increased substantially their energetic requirements, due to the increased workload, while females spent most of the time on the nest. Furthermore, during critical phases of the breeding season, a low percentage of suitable hunting spots in eagles’ territories led them to increase their ranging behavior in order to find food, with important consequences in energy consumption and mortality risk. Our results highlight the crucial role of males in raptor species exhibiting biparental care. Finally, we exemplify how biologging technologies are an adequate and objective method to study parental care in raptors as well as to get deeper insight into breeding ecology of birds in general.
Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass
Authors: Altendorf Kayla R , Larson Steven R , DeHaan Lee R , Crain Jared , Neyhart Jeff , Dorn Kevin M , Anderson James A
Published: January 2021

Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here, we introduce an intermediate wheatgrass NAM population developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterized the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM population for understanding the genetic control of flowering time and its potential for application to other traits of interest.
Interaction Between Physical Activity and Polygenic Score on Type 2 Diabetes Mellitus in Older Black and White Participants From the Health and Retirement Study
Authors: Wu Yan Yan , Thompson Mika D , Youkhana Fadi , Pirkle Catherine M
Published: January 2021

This study investigated the association of lifestyle factors and polygenic risk scores (PGS), and their interaction, on type 2 diabetes mellitus (T2D). We examined data from the U.S. Health and Retirement Study, a prospective longitudinal cohort of adults aged 50 years and older, containing nationally representative samples of Black and White Americans with precalculated PGS for T2D (N = 14 001). Predicted prevalence and incidence of T2D were calculated with logistic regression models. We calculated differences in T2D prevalence and incidence by PGS percentiles and for interaction variables using nonparametric bootstrap method. Black participants had approximately twice the prevalence of Whites (26.2% vs 14.2%), with a larger difference between the 90th and 10th PGS percentile from age 50 to 80 years. Significant interaction (pinteraction = .0096) was detected between PGS and physical activity among Whites. Among Whites in the 90th PGS percentile, T2D prevalence for moderate physical activity was 17.0% (95% CI: 14.8, 19.6), 6.8% lower compared to no/some physical activity (23.8%; 95% CI: 20.4, 27.5). T2D prevalence was similar (~10%) for both groups in the 10th PGS percentile. Incident T2D in Whites followed a similar pattern (pinteraction = .0325). No significant interactions with PGS were detected among Black participants. Interaction of different genetic risk profiles with lifestyle factors may inform understanding of varying inventions’ efficacy for different groups of people, potentially improving clinical and prevention interventions.
Correlates of Strength and Balance Training Exercises in Older African American Adults
Authors: Jiakponnah Nwanyieze Ngozi , Unson Christine , Chukwurah Queendaleen Chinenye
Published: January 2021

Background and Objectives

This study investigated the behavioral and psychological correlates of strength and balance training (SBT) participation among older African Americans.

Research Design and Methods

A cross-sectional survey of 90 older African Americans (M = 66.7 ± 8.7 years; 70% female) was conducted to assess correlates of intention to undertake SBT exercises and the number of days that they currently engage in SBT. The Theory of Planned Behavior (TPB) and the threat appraisal of the Protection Motivation Theory (PMT) were used as frameworks for the analyses.

Results

The intention to do SBT exercises was positively associated with favorable attitudes and subjective norm, knowledge about the benefits of SBT, and hours worked per week. The frequency of SBT participation was significantly correlated with behavioral intention, high fear of falling, and a low score on the kinesiophobia scale.

Discussion and Implications

This study demonstrated the utility of the TPB and PMT’s threat appraisal construct in modeling intention and number of days of SBT participation among African American older adults. The study affirmed the link between intention and behavior and between knowledge of the benefits of SBT and intention. Fear of falling’s positive association with days of SBT suggests that respondents’ saw SBT’s efficacy in reducing falls. The unique contributions of this study are the inclusions of kinesiophobia as a correlate and multiple threat appraisals in the PMT. Health promotion interventions should consider the interrelationship among these constructs.
Economic evaluation of a hybrid renewable energy system (HRES) using hybrid optimization model for electric renewable (HOMER) software—a case study of rural India
Authors: Sharma Kamal Kant , Gupta Akhil , Kumar Raman , Chohan Jasgurpreet Singh , Sharma Shubham , Singh J , Khalilpoor Nima , Issakhov Alibek , Chattopadhyaya Somnath , Dwivedi Shashi Prakash
Published: January 2021

This paper unveils a sustainable energy plan for optimal utilization of available electrical energy resources for an energy-deficient village. The chosen village is Nangal, near Barnala, Punjab, India. Primarily, the requirements of electric energy are recorded and elaborated for around 450 households. Aiming this, the potential to harness electric power and its effective utilization has been identified from the available resources of energy: biomass, agriculture waste and solar photovoltaic (PV) technology. In order to achieve this, a hybrid renewable energy system (HRES) model is proposed whose performance is evaluated by implementing it in hybrid optimization model for electric renewable (HOMER) software. HOMER software provides optimal solution for a commercial biogas plant for catering cooking gas demand. Also, a coordinated solution for solar PV-operated water pumps used for irrigation, village water supply and solar PV street lights is presented and analyzed. In this way, the accurateness of proposed model is investigated by estimating the optimal electric power demand and its economic benefits. It has been revealed that the computed cost of energy and total net present cost are $0.032/KWh and $76,837, respectively, by the parametric assessment of proposed HRES system. It is envisaged that the proposed model can be a road map for future research engineers in designing an effective energy utilization for villages.
Pericyte migration and proliferation are tightly synchronized to endothelial cell sprouting dynamics
Authors: Payne Laura Beth , Darden Jordan , Suarez-Martinez Ariana D , Zhao Huaning , Hendricks Alissa , Hartland Caitlin , Chong Diana , Kushner Erich J , Murfee Walter L , Chappell John C
Published: January 2021

Pericytes are critical for microvascular stability and maintenance, among other important physiological functions, yet their involvement in vessel formation processes remains poorly understood. To gain insight into pericyte behaviors during vascular remodeling, we developed two complementary tissue explant models utilizing ‘double reporter’ animals with fluorescently-labeled pericytes and endothelial cells (via Ng2:DsRed and Flk-1:eGFP genes, respectively). Time-lapse confocal imaging of active vessel remodeling within adult connective tissues and embryonic skin revealed a subset of pericytes detaching and migrating away from the vessel wall. Vessel-associated pericytes displayed rapid filopodial sampling near sprouting endothelial cells that emerged from parent vessels to form nascent branches. Pericytes near angiogenic sprouts were also more migratory, initiating persistent and directional movement along newly forming vessels. Pericyte cell divisions coincided more frequently with elongating endothelial sprouts, rather than sprout initiation sites, an observation confirmed with in vivo data from the developing mouse brain. Taken together, these data suggest that (i) pericyte detachment from the vessel wall may represent an important physiological process to enhance endothelial cell plasticity during vascular remodeling, and (ii) pericyte migration and proliferation are highly synchronized with endothelial cell behaviors during the coordinated expansion of a vascular network.
Crayfish Eating in Snakes: Testing How Anatomy and Behavior Affect Prey Size and Feeding Performance
Authors: Gripshover N D , Jayne B C
Published: January 2021

Synopsis

Quantifying the performance of animals is a powerful methodology for determining the functional consequences of morphological variation. For example, snakes consume prey whole, and variation in the anatomy of their trophic apparatus directly affects gape and limits maximal prey size. However, for the foraging ecology of snakes and other systems, scant data exist regarding how often maximal capacities are taxed in nature. Hence, we quantified: (1) maximal gape, (2) the size of prey relative to maximal gape, and (3) how the type and relative size of prey affected behavior and prey handling times (HTs) for two species of natricine snakes that primarily eat soft- (Regina septemvittata) or hard-shelled (Liodytes alleni) crayfish. Liodytes alleni had significantly larger maximal gape than R. septemvittata with equal snout–vent length. The percentages of large prey (>60% maximal gape area) consumed in the field were low in both R. septemvittata (22%) and L. alleni (2%). However, R. septemvittata, especially juveniles, ate relatively larger prey than L. alleni. Strategies for dealing with the seasonal scarcity of small crayfish differed as juvenile R. septemvittata commonly removed and ate only chelipeds from crayfish too large to swallow whole, whereas juvenile L. alleni ate many small odonate nymphs. During laboratory trials, unlike R. septemvittata, L. alleni usually used its body to restrain prey with behaviors that depended on relative prey size and prey hardness. Liodytes alleni consumed soft-shelled crayfish significantly faster than R. septemvittata and significantly faster than hard-shelled crayfish. Several of the differences in gape, prey size, and prey HTs and behavior between the crayfish-eating snakes resemble those between two phylogenetically distant species of homalopsid snakes that consume either hard- or soft-shelled crabs. In both groups of crustacean-eating snakes, the decreased capture success in captivity and the rare consumption of relatively large hard-shelled crustaceans in the field suggest that the ability to capture this type of prey constrains prey size more commonly than maximal gape. Based on data integrating snake size and gape with the relative mass of intact prey, the predicted potential feeding performance R. septemvittata consuming intact prey exceeded that of the other three species.
COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
Authors: Wang Jingqi , Abu-el-Rub Noor , Gray Josh , Pham Huy Anh , Zhou Yujia , Manion Frank J. , Liu Mei , Song Xing , Xu Hua , Rouhizadeh Masoud , Zhang Yaoyun
Published: January 2021

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 SignSym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.
Comparison of Efficacy of Povidone-Iodine, Ethanol, and an Aerosol Formulation of Silver Sulfadiazine in Controlling Microbial Burden on Sutures From Clean Surgeries
Authors: Prezzavento Gustavo E , Mas Carlos R , Achaval Rodríguez Juan , Juárez Calvi Rodrigo N , Piskulic Laura , Angelini Julia , Allasia María B , Smania Andrea M , Moyano Alejandro J
Published: January 2021

In the surgical suture, the implanted thread can be a source of microbial contamination. Implanted materials are frequently described as being substrates prone for biofilm development provoking surgical site infections. Treatment of postsurgical wounds with different topical antimicrobial agents is a current practice applied to every patient. However, to date, there is little evidence on the efficacy of different antiseptic treatments on suture materials in preventing environmental or skin bacterial adhesion and further infection. Here, the authors compared the ability of an aerosol formulation of silver sulfadiazine, vitamin A, and lidocaine (AF-SSD) and of two of the most frequently used topical treatments, povidone-iodine and ethanol, in eradicating or controlling the microbial contamination of suture threads in patients who have undergone clean surgeries. Postsurgical suture threads treated with AF-SSD showed a significantly reduced proportion of contaminated samples containing viable microbial cells compared with those treated with povidone-iodine or ethanol. Furthermore, those samples that were positive for bacterial growth showed a lesser number of viable cells in AF-SSD-treated sutures than those treated with povidone-iodine or ethanol. Confocal laser scanning microscopy showed that AF-SSD-treated postsurgical sutures presented significantly less attached microbial cells than povidone-iodine and ethanol, with scarce observable microbial cells on the surface of the suture. Taken together, the results suggest that treatment with AF-SSD is more effective than the other two antiseptics, and there is a potential for improvement in reducing the microbial burden of implanted materials such as the suture thread.
Completeness of the Gaia-verse – IV. The astrometry spread function of Gaia DR2
Authors: Everall Andrew , Boubert Douglas , Koposov Sergey E , Smith Leigh , Holl Berry
Published: January 2021

Gaia Data Release 2 (DR2) published positions, parallaxes, and proper motions for an unprecedented 1331 909 727 sources, revolutionizing the field of Galactic dynamics. We complement this data with the astrometry spread function (ASF), the expected uncertainty in the measured positions, proper motions, and parallax for a non-accelerating point source. The ASF is a Gaussian function for which we construct the 5D astrometric covariance matrix as a function of position on the sky and apparent magnitude using the Gaia DR2 scanning law and demonstrate excellent agreement with the observed data. This can be used to answer the question ‘What astrometric covariance would Gaia have published if my star was a non-accelerating point source?’. The ASF will enable characterization of binary systems, exoplanet orbits, astrometric microlensing events, and extended sources that add an excess astrometric noise to the expected astrometry uncertainty. By using the ASF to estimate the unit weight error of Gaia DR2 sources, we demonstrate that the ASF indeed provides a direct probe of the excess source noise. We use the ASF to estimate the contribution to the selection function of the Gaia astrometric sample from a cut on astrometric_sigma5d_max showing high completeness for G < 20 dropping to ${\lt} 1{{\ \rm per\ cent}}$ in underscanned regions of the sky for G = 21. We have added an ASF module to the python package scanninglaw (https://github.com/gaiaverse/scanninglaw) through which users can access the ASF.
A thermophysical and dynamical study of the Hildas, (1162) Larissa, and (1911) Schubart
Authors: Chavez Cristian F , Müller T G , Marshall J P , Horner J , Drass H , Carter B
Published: January 2021

The Hilda asteroids are among the least studied populations in the asteroid belt, despite their potential importance as markers of Jupiter’s migration in the early Solar system. We present new mid-infrared observations of two notable Hildas, (1162) Larissa, and (1911) Schubart, obtained using the Faint Object infraRed CAmera for the SOFIA Telescope (FORCAST), and use these to characterize their thermal inertia and physical properties. For (1162) Larissa, we obtain an effective diameter of 46.5$^{+2.3}_{-1.7}$ km, an albedo of 0.12 ± 0.02, and a thermal inertia of 15$^{+10}_{-8}$ Jm−2 s1/2 K−1. In addition, our Larissa thermal measurements are well matched with an ellipsoidal shape with an axial ratio a/b = 1.2 for the most-likely spin properties. Our modelling of (1911) Schubart is not as refined, but the thermal data point towards a high-obliquity spin-pole, with a best fit a/b = 1.3 ellipsoidal shape. This spin-shape solution is yielding a diameter of 72$^{+3}_{-4}$ km, an albedo of 0.039± 0.02, and a thermal inertia below 30 Jm−2 s1/2 K−1 (or 10$^{+20}_{-5}$ Jm−2 s1/2 K−1). As with (1162) Larissa, our results suggest that (1911) Schubart is aspherical, and likely elongated in shape. Detailed dynamical simulations of the two Hildas reveal that both exhibit strong dynamical stability, behaviour that suggests that they are primordial, rather than captured objects. The differences in their albedos, along with their divergent taxonomical classification, suggests that despite their common origin, the two have experienced markedly different histories.
Selenomethionine ameliorates LPS-induced intestinal immune dysfunction in chicken jejunum
Authors: Cui Yuan , Qu Yingying , Yin Kai , Zhang Xintong , Lin Hongjin
Published: January 2021

Selenomethionine (SeMet) is a widely used food supplement. However, the research on the effect of SeMet on intestinal immune function is not enough. Therefore, in this experiment, SeMet was added to the diet of chickens, and lipopolysaccharide (LPS) was used as harmful stimulation to study the effect of SeMet on intestinal immune function in chickens. We chose chicken jejunum as the research object. The results showed that LPS treatment decreased the expressions of selenoproteins and induced inflammatory reaction, cytokine disorder, decreases of immunoglobulin levels, heat shock protein expression disorder, and decreases of defensin expression levels in jejunum. However, dietary SeMet can effectively alleviate the above injury caused by LPS. Our results showed that SeMet could improve the intestinal immunity in chickens, and feeding SeMet could alleviate the intestinal immune dysfunction caused by LPS. The application range of SeMet in feed can be roughly given through our experiment; i.e. 0.35–0.5 mg/kg SeMet was effective. We speculated that dietary SeMet could effectively alleviate the intestinal immune dysfunction caused by harmful stimulation and help to resist the further damage caused by harmful stimulation.
Infectious Period of Severe Acute Respiratory Syndrome Coronavirus 2 in 17 Nursing Home Residents—Arkansas, June–August 2020
Authors: Surie Diya , Huang Jennifer Y , Brown Allison C , Gable Paige , Biedron Caitlin , Gilbert Sarah E , Garner Kelley , Bollinger Susan , Gulley Trent , Haney Tafarra , Lyons Amanda K , Beshearse Elizabeth , Gregory Christopher J , Sabour Sarah , Clemmons Nakia S , James Allison E , Tamin Azaibi , Reese Natashia , Perry-Dow K Allison , Brown Robin , Harcourt Jennifer L , Campbell Davina , Houston Hollis , Chakravorty Rohan , Paulick Ashley , Whitaker Brett , Murdoch Jordan , Spicer Lori , Stumpf Megan M , Mills Lisa , Coughlin Melissa M , Higdem Pamela , Rasheed Mohammad Ata Ur , Lonsway David , Bhatnagar Amelia , Kothari Atul , Anderson Karen , Thornburg Natalie J , Breaker Erin , Adamczyk Michelle , McAllister Gillian A , Halpin Alison L , Seely Kathryn A , Patil Naveen , McDonald L Clifford , Kutty Preeta K
Published: January 2021

Background

To estimate the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in older adults with underlying conditions, we assessed duration of coronavirus disease 2019 (COVID-19) symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity, and culture positivity among nursing home residents.

Methods

We enrolled residents within 15 days of their first positive SARS-CoV-2 test (diagnosis) at an Arkansas facility from July 7 to 15, 2020 and instead them for 42 days. Every 3 days for 21 days and then weekly, we assessed COVID-19 symptoms, collected specimens (oropharyngeal, anterior nares, and saliva), and reviewed medical charts. Blood for serology was collected on days 0, 6, 12, 21, and 42. Infectivity was defined by positive culture. Duration of culture positivity was compared with duration of COVID-19 symptoms and RT-PCR positivity. Data were summarized using measures of central tendency, frequencies, and proportions.

Results

We enrolled 17 of 39 (44%) eligible residents. Median participant age was 82 years (range, 58–97 years). All had ≥3 underlying conditions. Median duration of RT-PCR positivity was 22 days (interquartile range [IQR], 8–31 days) from diagnosis; median duration of symptoms was 42 days (IQR, 28–49 days). Of 9 (53%) participants with any culture-positive specimens, 1 (11%) severely immunocompromised participant remained culture-positive 19 days from diagnosis; 8 of 9 (89%) were culture-positive ≤8 days from diagnosis. Seroconversion occurred in 12 of 12 (100%) surviving participants with ≥1 blood specimen; all participants were culture-negative before seroconversion.

Conclusions

Duration of infectivity was considerably shorter than duration of symptoms and RT-PCR positivity. Severe immunocompromise may prolong SARS-CoV-2 infectivity. Seroconversion indicated noninfectivity in this cohort.
Checkpoint immunotherapy for NK/T cell lymphoma—Time for a showdown?
Authors: Chan Jason Yongsheng , Lim Jing Quan , Ong Choon Kiat
Published: January 2021

Editor's note

A commentary on “Combination of anti-PD-1 antibody with P-GEMOX as a potentially effective immunochemotherapy for advanced natural killer/T cell lymphoma”.
To stop or not to stop ‘culture’: determining the essential behavior of the government, church and public in fighting against COVID-19
Authors: Cordero Dalmacito A
Published: January 2021

Culture is a way of life. A recent correspondence emphasizes that it is a contributory factor in combatting the COVID-19 pandemic, and this must be considered by each government around the world. However, I argue that various elements in culture do not need to stop or else it will create public outrage. I therefore propose a win–win solution for both parties with the inclusion of the church that can serve as a framework for the sake of public health. It is primarily based on a kind of behavior that is needed to be embodied by the involved groups—‘supportive’ government, ‘creative’ church and an ‘adaptive’ public. These essential behaviors of all groups are possible to embody for a successful implementation of public health.
The evolving view of replay and its functions in wake and sleep
Authors: Findlay Graham , Tononi Giulio , Cirelli Chiara
Published: January 2021

The term hippocampal replay originally referred to the temporally compressed reinstantiation, during rest, of sequential neural activity observed during prior active wake. Since its description in the 1990s, hippocampal replay has often been viewed as the key mechanism by which a memory trace is repeatedly rehearsed at high speeds during sleep and gradually transferred to neocortical circuits. However, the methods used to measure the occurrence of replay remain debated, and it is now clear that the underlying neural events are considerably more complicated than the traditional narratives had suggested. “Replay-like” activity happens during wake, can play out in reverse order, may represent trajectories never taken by the animal, and may have additional functions beyond memory consolidation, from learning values and solving the problem of credit assignment to decision-making and planning. Still, we know little about the role of replay in cognition, and to what extent it differs between wake and sleep. This may soon change, however, because decades-long efforts to explain replay in terms of reinforcement learning (RL) have started to yield testable predictions and possible explanations for a diverse set of observations. Here, we (1) survey the diverse features of replay, focusing especially on the latest findings; (2) discuss recent attempts at unifying disparate experimental results and putatively different cognitive functions under the banner of RL; (3) discuss methodological issues and theoretical biases that impede progress or may warrant a partial revaluation of the current literature, and finally; (4) highlight areas of considerable uncertainty and promising avenues of inquiry.
Aquarium: open-source laboratory software for design, execution and data management
Authors: Vrana Justin , de Lange Orlando , Yang Yaoyu , Newman Garrett , Saleem Ayesha , Miller Abraham , Cordray Cameron , Halabiya Samer , Parks Michelle , Lopez Eriberto , Goldberg Sarah , Keller Benjamin , Strickland Devin , Klavins Eric
Published: January 2021

Automation has been shown to improve the replicability and scalability of biomedical and bioindustrial research. Although the work performed in many labs is repetitive and can be standardized, few academic labs can afford the time and money required to automate their workflows with robotics. We propose that human-in-the-loop automation can fill this critical gap. To this end, we present Aquarium, an open-source, web-based software application that integrates experimental design, inventory management, protocol execution and data capture. We provide a high-level view of how researchers can install Aquarium and use it in their own labs. We discuss the impacts of the Aquarium on working practices, use in biofoundries and opportunities it affords for collaboration and education in life science laboratory research and manufacture.
Anatomical variation of mesophyll conductance due to salt stress inPopulus cathayanafemales and males growing under different inorganic nitrogen sources
Authors: Liu Miao , Liu Xiucheng , Du Xuhua , Korpelainen Helena , Niinemets Ülo , Li Chunyang
Published: January 2021

Synergistic regulation in leaf architecture and photosynthesis is essential for salt tolerance. However, how plant sex and inorganic nitrogen sources alter salt stress-dependent photosynthesis remains unknown. Leaf anatomical characteristics and photosynthesis of Populus cathayana Rehder females and males were investigated under salt stress conditions combined with nitrate NO3− and ammonium NH4+ supplies to clarify the underlying mechanisms. In salt-stressed females, we observed an increased mesophyll spongy cell density, a reduced chloroplast density, a decreased surface area of chloroplasts adjacent to the intercellular air space (Sc/S) and an increased mesophyll cell area per transverse section width (S/W), consequently causing mesophyll conductance (gm) and photosynthesis inhibition, especially under NH4+ supply. Conversely, males with a greater mesophyll palisade tissue thickness and chloroplast density, but a lower spongy cell density had lower S/W and higher Sc/S, and higher gm and photosynthesis. NH4+-fed females had a lower CO2 conductance through cell wall and stromal conductance perpendicular to the cell wall, but a higher chloroplast conductance from the cell wall (gcyt1) than females supplied with NO3−, whereas males had a higher chloroplast conductance and lower CO2 conductance through cell wall when supplied with NO3− instead of NH4+ under salt stress. These findings indicate sex-specific strategies in coping with salt stress related to leaf anatomy and gm under both types of nitrogen supplies, which may contribute to sex-specific CO2 capture and niche segregation.
Imaging in Cystic Lung Diseases: An Update
Authors: Aluja-Jaramillo Felipe , Gutiérrez Fernando , Rossi Santiago
Published: January 2021

Cystic lung diseases represent a broad set of disorders with different causes, but all of them are characterized by multiple thin-walled parenchymal lesions. Multidetector CT (MDCT), especially high-resolution CT (HRCT), is the imaging modality of choice for the diagnosis and follow-up of these entities. Cavities and emphysema are the most common alternative diagnoses that must be differentiated from true pulmonary cysts. In this review, we discuss the most common cystic lung diseases, their physiopathology, and the CT imaging appearance, with special emphasis on the key imaging findings that are crucial in their differential diagnosis.
The composition and function ofEnterococcus faecalismembrane vesicles
Authors: Afonina Irina , Tien Brenda , Nair Zeus , Matysik Artur , Lam Ling Ning , Veleba Mark , Koh Augustine , Rashid Rafi , Cazenave-Gassiot Amaury , Wenk Marcus , Wai Sun Nyunt , Kline Kimberly A.
Published: January 2021

Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, host immune evasion, and cross-species communication. MVs are frequently being discharged from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. InEnterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe, and functionally characterize MVs fromE. faecalis. Here we show thatE. faecalisreleases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane, and are enriched in lipoproteins. MVs ofE. faecalisare specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.
Reliance on polyfunctional tissue leads to a reproduction-immunity tradeoff due to inherent constraint
Authors: Gupta Vanika , Frank Ashley M. , Matolka Nick , Lazzaro Brian P.
Published: January 2021

The use of one tissue for multiple purposes can result in constraints, impaired function, and tradeoffs. The insect fat body performs remarkably diverse functions including metabolic control, reproductive provisioning, and systemic immune responses. Immunity and reproduction are observed to trade off in many organisms, although the mechanistic basis for the tradeoff is generally unknown. More generally, how do polyfunctional tissues simultaneously execute multiple distinct physiological functions? Using single-nucleus sequencing, we determined theDrosophila melanogasterfat body executes diverse basal functions with heterogenous cellular subpopulations. However, as an emergency function, the immune response engages the entire tissue. We found that reproductively active females exhibit impaired capacity to produce new protein in response to infection, resulting in the reproduction-immunity tradeoff. We suggest that such inherent internal limitations may provide a general explanation for the wide prevalence of physiological and evolutionary tradeoffs.
A genetic approach to dissect the role of prefoldins inArabidopsis
Authors: Blanco-Touriñán Noel , Esteve-Bruna David , Serrano-Mislata Antonio , María Esquinas Rosa , Resentini Francesca , Forment Javier , Carrasco-López Cristian , Novella-Rausell Claudio , Palacios Alberto , Carrasco Pedro , Salinas Julio , Blázquez Miguel Á. , Alabadí David
Published: January 2021

The prefoldin complex (PFDc) was identified in humans as co-chaperone of the cytosolic chaperonin TRiC/CCT. It is conserved in eukaryotes and is composed of subunits PFD1 to 6. PFDc-TRiC/CCT operates folding actin and tubulins. In addition to this function, PFDs participate in a wide range of cellular processes, both in the cytoplasm and in the nucleus, and their malfunction cause developmental alterations and disease in animals, and altered growth and environmental responses in yeast and plants. Genetic analyses in yeast indicate that not all functions performed by PFDs require the participation of the canonical complex. The lack of systematic genetic analyses in higher eukaryotes makes it difficult to discern whether PFDs participate in a particular process as canonical complex or in alternative configurations,i.e. as individual subunits or in other complexes. To tackle this question, and on the premise that the canonical complex cannot be formed if one subunit is missing, we have prepared anArabidopsismutant deficient in the six prefoldins, and compared various growth and environmental responses with those of the individualpfd. In this way, we demonstrate that the PFDc is required to delay flowering, for seed germination, or to respond to high salt stress, whereas two or more PFDs redundantly attenuate the response to osmotic stress. A coexpression analysis of differentially expressed genes in the sextuple mutant has identified several transcription factors, such as ABI5 or PIF4, acting downstream of PFDs. Furthermore, it has made possible to assign novel roles for PFDs, for instance, in the response to warm temperature.
Spatial organization of transcript elongation and splicing kinetics
Authors: Casill Alyssa D. , Haimowitz Adam J. , Kosmyna Brian , Query Charles C. , Ye Kenny , Gamble Matthew J.
Published: January 2021

The organization of the genome in three-dimensional space has been shown to play an important role in gene expression. Specifically, facets of genomic interaction such as topologically associated domains (TADs) have been shown to regulate transcription by bringing regulatory elements into close proximity1. mRNA production is an intricate process with multiple control points including regulation of Pol II elongation and the removal of non-coding sequences via pre-mRNA splicing2. The connection between genomic compartments and the kinetics of RNA biogenesis and processing has been largely unexplored. Here, we measure Pol II elongation and splicing kinetics genome-wide using a novel technique that couples nascent RNA-seq with a mathematical model of transcription and co-transcriptional RNA processing. We uncovered multiple layers of spatial organization of these rates: the rate of splicing is coordinated across introns within individual genes, and both elongation and splicing rates are coordinated within TADs, as are alternative splicing outcomes. Overall, our work establishes that the kinetics of transcription and splicing are coordinated by the spatial organization of the genome and suggests that TADs are a major platform for coordination of alternative splicing.
A senescence-like cellular response inhibits bovine ephemeral fever virus proliferation
Authors: Zeng Yu-Jing , Hsu Min-Kung , Tsai Chiao-An , Chu Chun-Yen , Wu Hsing-Chieh , Wang Hsian-Yu
Published: January 2021

During industrial scale production of virus for vaccine manufacturing, antiviral response of host cells can dampen maximal viral antigen yield. In addition to interferon responses, many other cellular responses such as the AMPK signaling pathway or senescence-like response may inhibit or slow down virus amplification in the cell culture system. In this study, we first performed a Gene Set Enrichment Analysis of the whole-genome mRNA transcriptome and found a senescence-like cellular response in BHK-21 cells when infected with bovine ephemeral fever virus (BEFV). To demonstrate that this senescence-like state may reduce virus growth, BHK-21 subclones showing varying degrees of senescence-like state were infected with BEFV. Results showed the BHK-21 subclones showing high senescence staining could inhibit BEFV replication while low senescence-staining subclones are permissive to virus replication. Using a different approach, a senescence-like state was induced in BHK-21 using a small molecule, camptothecin (CPT), and BEFV susceptibility was examined. Results showed that indeed CPT-treated BHK-21 is more resistant to virus infection. Overall, these results indicate that a senescence-like response may be at play in BHK-21 upon virus infection. Furthermore, cell clone selection and modulating treatments using small molecules may be tools in countering anti-viral responses.
Hyperpiliation reducesPseudomonas aeruginosapathogenicity by impeding type III secretion
Authors: Kilmury Sara L.N. , Graham Katherine J. , Lamers Ryan P. , MacNeil Lesley T. , Burrows Lori L.
Published: January 2021

Type IVa pili (T4aP) are important virulence factors for many bacterial pathogens. Previous studies suggested that the retraction ATPase, PilT, modulates pathogenicity due to its critical role in pilus dynamics and twitching motility. Here we use aCaenorhabditis elegansslow killing model to show that hyperpiliation, not loss of pilus retraction, reduces virulence ofPseudomonas aeruginosastrains PAK and PA14 by interfering with function of the contact-dependent type III secretion system (T3SS). Hyperactivating point mutations in theP. aeruginosaPilSR two-component system that controls transcription of the major pilin gene,pilA, increased levels of surface pili to the same extent as deletingpilT, without impairing twitching motility. These functionally hyperpiliated PilSR mutants had significant defects in pathogenicity that were rescued by deletingpilAor by increasing the length of T3SS needles via deletion of the needle-length regulator, PscP. HyperpiliatedpilTdeletion orpilOpoint mutants showed similar PilA-dependent impairments in virulence, validating the phenotype. Together, our data support a model where a surfeit of pili prevents effective engagement of contact-dependent virulence factors. These findings suggest that the role of T4aP retraction in virulence should be revised.

SIGNIFICANCE

Pseudomonas aeruginosais a major contributor to hospital-acquired infections and particularly problematic due to its intrinsic resistance to many front-line antibiotics. Strategies to combat this and other important pathogens include development of anti-virulence therapeutics. We show that the pathogenicity ofP. aeruginosais impaired when the amount of type IVa pili (T4aP) expressed on the cell surface increases, independent of the bacteria’s ability to twitch. We propose that having excess T4aP on the cell surface can physically interfere with productive engagement of the contact-dependent type III secretion toxin delivery system. A better understanding of how T4aP modulate interaction of bacteria with target cells will improve the design of therapeutics targeting components involved in regulation of T4aP expression and function, to reduce the clinical burden ofP. aeruginosaand other T4aP-expressing bacteria.
The DEAD-box RNA helicases RhlE2 is a global regulator ofPseudomonas aeruginosalifestyle and pathogenesis
Authors: Hausmann Stéphane , Gonzalez Diego , Geiser Johan , Valentini Martina
Published: January 2021

The RhlE DEAD-box RNA helicase protein family is widespread among Proteobacteria, but it is the least understood due to the lack of a clear biological function. Here, we study the two RhlE homologs present in the opportunistic pathogenPseudomonas aeruginosa. RhlE1 and RhlE2 diverged duringP. aeruginosaevolution; our data indicate that this resulted in a non-redundant biological role, a distinct molecular action and an enzymatic activity differentially stimulated by RNA. Whereas RhlE1 is specifically necessary for bacteria growth in cold, we show that RhlE2 acts as global post-transcriptional regulator, affecting the level of hundreds of cellular transcripts and multiple functionalities indispensable not only forP. aeruginosaenvironmental adaptation, but also for its virulence. The global action of RhlE2 relies on a unique C-terminal extension, which establishes an RNA-dependent interaction with the RNase E endonuclease and the cellular RNA degradation machinery.
3D Visualization of the Podocyte Actin Network using Integrated Membrane Extraction, Electron Microscopy, and Deep Learning
Authors: Qu Chengqing , Roth Robyn , Loitman Charles , Hammad Dina , Genin Guy M. , Miner Jeffrey H. , Suleiman Hani Y.
Published: January 2021

Although actin stress fibers are abundant in cultured cells, little is known about these structuresin vivo.In podocytes of the kidney glomerulus, much evidence suggests that mechanobiological mechanisms underlie injury, with changes to actin stress fiber structures potentially responsible for pathological changes to cell morphology. However, this hypothesis is difficult to rigorously testin vivodue to challenges with visualization. We therefore developed the first visualization technique capable of resolving the three-dimensional (3D) podocyte actin network with unprecedented detail in healthy and injured podocytes, and applied this technique to reveal the changes in the actin network that occur upon podocyte injury. Using isolated glomeruli from healthy mice as well as from three different mouse injury models (Cd2ap-/-, Lamb2-/-and theCol4a3-/-model of Alport syndrome), we applied our novel imaging technique that integrates membrane-extraction, focused ion bean scanning electron microscopy (FIB-SEM), and deep learning image segmentation. In healthy glomeruli, we observed actin cables that link the interdigitating podocyte foot processes to newly described actin structures located at the periphery of the cell body. The actin cables within the foot processes formed a continuous, mesh-like, electron dense sheet that incorporated the slit diaphragms required for kidney filtration. After injury, the actin network was markedly different, having lost its organization and presenting instead as a disorganized assemblage of actin condensates juxtaposed to the glomerular basement membrane. The new visualization method enabled us, for the first time, to observe the detailed 3D organization of actin networks in both healthy and injured podocytes. Shared features of actin condensations across all three injury models further suggested common mechanobiological pathways that govern changes to podocyte morphology after injury.
pUL36 de-ubiquitinase activity augments both the initiation and progression of lytic virus infection in IFN–primed cells
Authors: Mohnke Jonas , Stark Irmgard , Fischer Mara , Grothey Arnhild , O’Hare Peter , Sodeik Beate , Erhard Florian , Dölken Lars , Hennig Thomas
Published: January 2021

The conserved, structural HSV-1 tegument protein pUL36 is essential for both virus entry and assembly. While its N-terminal de-ubiquitinase (DUB) activity is dispensable for infection in cell culture, it is required for efficient virus spreadin vivoby acting as a potent viral immune evasin. Here, we show that the pUL36 DUB activity was required to overcome interferon-(IFN)-mediated suppression of both plaque initiation and progression to productive infection. Immediately upon virus entry, incoming tegument-derived pUL36-DUB activity helped the virus to escape intrinsic antiviral resistance and efficiently initiate lytic virus replication in IFN-primed cells. Subsequently,de novoexpressed pUL36-DUB augmented the efficiency of productive infection and virus yield. Interestingly, removal of IFN shortly after inoculation only resulted in a partial rescue of plaque formation, indicating that an IFN-induced defense mechanism eliminates invading virus particles unless counteracted by pUL36-DUB activity. Taken together, we demonstrated that the pUL36 DUB disarms IFN-induced antiviral responses at two levels, namely, to protect the infectivity of invading virus as well as to augment productive virus replication in IFN-primed cells.

Author Summary

HSV-1 is an ubiquitous human pathogen that is responsible for common cold sores but may also cause life-threatening disease. pUL36 is an essential and conserved protein of infectious herpesvirus virions with a unique de-ubiquitinating (DUB) activity. The pUL36 DUB is dispensable for efficient virus infection in cell culture but represents an important viral immune evasinin vivo. Here, we showed that tegument-derived DUB activity delivered by the invading virus particles is required to overcome IFN-induced host resistance and to initiate efficient lytic infection.De novoexpressed pUL36 DUB subsequently augments productive infection and virus yield. These data indicate that the pUL36 DUB antagonizes the activity of yet unidentified IFN-inducible E3 ligases to facilitate productive infection at multiple levels. Our findings underscore the therapeutic potential of targeting conserved herpesvirus DUBs to prevent or treat herpesvirus disease.