bluuebunny/crossref_metadata_2025 huggingface dataset:
Current Practices and Preferences of Fellows and Program Directors on Taking the Certifying Examination During Subspecialty Fellowships
Authors: Gupta Ankita , Meriwether Kate , Martin Alexandra , Pierson Rebecca C.
Published: June 2021

Objective

Fellows in obstetrics and gynecology subspecialties often take their oral specialty certifying examination (referred to here as generalist certifying examination [GCE]) during fellowship. We sought to compare the opinions of current fellows and program directors (PDs) regarding their program’s handling of GCE during fellowship.

Methods

In this online, survey-based study, fellows and PDs currently affiliated with an accredited fellowship in maternal-fetal medicine, reproductive endocrinology and infertility, female pelvic medicine and reconstructive surgery, or gynecologic oncology (GO) received the link to an unvalidated survey. This survey was open for 8 weeks, between April and June 2020; eligible participants were contacted through their programs, society Listserv, and social media and received 3 reminder e-mails.

Results

Final analysis included 408 (408/834; response rate, 49%) fellows and 163 (163/223; response rate, 73%) PDs across the 4 subspecialties. There were significant differences in whether fellows responded that they were required or encouraged to take the GCE (52% maternal-fetal medicine, 65% reproductive endocrinology and infertility, 39% female pelvic medicine and reconstructive surgery, 8% GO; P < 0.01) during fellowship. Fewer GO fellows noted that they were permitted to use educational funds for GCE when compared with the other subspecialties (P < 0.01). Most fellows responded that the inability to take GCE during fellowship would decrease their satisfaction with fellowship, and this was significantly higher than PD estimates (78% vs 39%, P < 0.01).

Conclusions

There are significant differences in reported ability to take GCE during fellowship across different obstetrics and gynecology subspecialty fellowships. Program directors significantly underestimate fellow dissatisfaction with inability to take GCE during fellowship.
Forced Gazing: A Stimulus-bound Behavior
Authors: Funayama Michitaka , Takata Taketo
Published: June 2021

We studied four patients with acquired brain injury who were compelled to gaze at a moving object or the face of an individual who came into their sight, especially the person’s eyes. The patients continued to gaze at the object or person until it disappeared from their sight. This behavior, referred to as forced gazing, is related to visual groping (part of the instinctive grasp reaction), and, together with a similar sign of visual grasping, constitutes a spectrum of visual stimulus-bound behaviors. In addition to forced gazing, the patients exhibited a primitive reflex such as a grasp or sucking reflex. Each of the patients had lesions in the bilateral frontal lobes of the brain. We considered forced gazing to be a stimulus-bound behavior, in which patients become extremely dependent on a specific external stimulus. As gaze-related communication is considered one of the bases of an infant’s social development, forced gazing may have its basis in innate human behavior that might manifest itself under specific pathological circumstances such as bilateral frontal-lobe damage.
Increasing the Clinical Utility of the Paced Auditory Serial Addition Test: Normative Data for Standard, Dyad, and Cognitive Fatigability Scoring
Authors: Berard Jason A. , Walker Lisa A.S.
Published: June 2021

Background:

No normative data currently exist that would allow clinicians to decide whether the degree of cognitive fatigability (CF) experienced in individuals with neurologic disease is greater than expected when compared with a healthy population.

Objective:

To establish discrete and regression-based normative data for CF as defined by an objective decrement in performance over the course of a cognitive task; namely, the Paced Auditory Serial Addition Test (PASAT). In addition, to develop discrete and regression-based normative data for PASAT performance scores—dyad and percent dyad—for which data do not currently exist.

Method:

One hundred and seventy-eight healthy individuals completed the PASAT as part of a larger neuropsychological battery. PASAT performance scores including total correct responses, total dyads, and percent dyad were calculated. CF scores were calculated by comparing the individuals’ performance on the first half (or third) of the test to their performance on the last half (or third) in order to capture any within-task performance decrements over time.

Results:

Both age- and education-based discrete normative data and demographically adjusted (sex, age, and education) regression-based formulas were established for the PASAT performance scores and the CF scores.

Conclusion:

The development of these normative data will allow for greater interpretation of an individual’s performance on the PASAT, beyond just the total correct score, through the use of dyad and percent dyad scores. With respect to CF, these data will allow clinicians to objectively quantify decrements in cognitive performance over time better in individuals with neurologic diseases.
Cognitive–motor Interference in Individuals With a Neurologic Disorder: A Systematic Review of Neural Correlates
Authors: Veldkamp Renee , Goetschalckx Mieke , Hulst Hanneke E. , Nieuwboer Alice , Grieten Kathleen , Baert Ilse , Leone Carmela , Moumdjian Lousin , Feys Peter
Published: June 2021

Background:

Performing a cognitive task and a motor task simultaneously is an everyday act that can lead to decreased performance on both tasks.

Objective:

To provide insight into the neural correlates associated with cognitive–motor dual tasking in individuals with a neurologic disorder.

Method:

We searched the PubMed and Web of Science databases for studies that had been published up to January 16th, 2019. Studies investigating the neural correlates of cognitive–motor dual task performance in individuals with a variety of neurologic disorders were included, independently from whether the study included healthy controls. Clinical and imaging data were abstracted for the comparison between single tasks and a dual task in the individuals with a neurologic disorder and for the comparison between the healthy controls and the individuals with a neurologic disorder.

Results:

Eighteen studies met the inclusion criteria. Study populations included individuals with Parkinson disease, multiple sclerosis, mild cognitive impairment, Alzheimer disease, traumatic brain injury, and stroke. Neuroimaging types used to study the neural correlates of cognitive–motor dual tasking during upper limb or gait tasks included fMRI, functional near-infrared spectroscopy, EEG, and PET.

Conclusion:

Despite large heterogeneity in study methodologies, some recurrent patterns were noted. Particularly, in neurologic patients, an already higher brain activation during single tasks was seen compared with healthy controls, perhaps compromising the patients’ ability to further adapt brain activation with increasing load during dual tasking and resulting in reduced behavioral dual task performance.
A comparative study on phosphate removal from water using
Phragmites australis
biochars loaded with different metal oxides
Authors: Wang Pengfei , Zhi Mengmeng , Cui Guannan , Chu Zhaosheng , Wang Shuhang
Published: June 2021

Metal oxide-loaded biochars are a promising material to remove phosphate from polluted water to ultra-low concentrations. To facilitate preparing the metal oxide-loaded biochar with the best phosphate adsorption performance, five biochars loaded with Al, Ca, Fe, La and Mg oxides, respectively (Al-BC, Ca-BC, Fe-BC, La-BC and Mg-BC) were produced using
Phragmites australis
pretreated with 0.1 mol AlCl
3
, CaCl
2
, FeCl
3
, LaCl
3
and MgCl
2
, respectively, characterized, and phosphate adsorption kinetics and isotherms of the biochars were determined. The maximum phosphate adsorption capacities (

Q
m

) of the biochars ranked as Al-BC (219.87 mg g
−1
) > Mg-BC (112.45 mg g
−1
) > Ca-BC (81.46 mg g
−1
) > Fe-BC (46.61 mg g
−1
) > La-BC (38.93 mg g
−1
). The time to reach the adsorption equilibrium ranked as La-BC (1 h) < Ca-BC (12 h) < Mg-BC (24 h) = Fe-BC (24 h) <Al-BC (greater than 72 h).

Q
m

of Ca-BC, Fe-BC, La-BC and Mg-BC depend on the molar content of metals in the biochars. The small phosphate adsorption rate of Al-BC is due to the slow intra-particle diffusion of phosphate attributed to the undeveloped porosity and dispersed distribution of AlOOH crystals on the Al-BC surface. Mg-BC is suggested for phosphate removal from water considering adsorption rate and capacity. Al-BC is applicable when a long contact time is allowed, e.g. as a capping material to immobilize phosphate in lake sediments.
The constraints between amino acids influence the unequal distribution of codons and protein sequence evolution
Authors: Qian Yi , Zhang Rui , Jiang Xinglu , Wu Guoqiu
Published: June 2021

Four nucleotides (A, U, C and G) constitute 64 codons at free combination but 64 codons are unequally assigned to 21 items (20 amino acids plus one stop). About 500 amino acids are known but only 20 are selected to make up the proteins. However, the relationships between amino acid and codon and between 20 amino acids have been unclear. In this paper, we studied the relationships between 20 amino acids in 33 species and found there were three constraints between 20 amino acids, such as the relatively stable mean carbon and hydrogen (C : H) ratios (0.50), similarity interactions between the constituent ratios of amino acids, and the frequency of amino acids according with Poisson distribution under certain conditions. We demonstrated that the unequal distribution of 64 codons and the choice of amino acids in molecular evolution would be constrained to remain stable C : H ratios. The constituent ratios and frequency of 20 amino acids in a species or a protein are two determinants of protein sequence evolution, so this finding showed the constraints between 20 amino acids played an important role in protein sequence evolution.
The roles of environmental variation and parasite survival in virulence–transmission relationships
Authors: Turner Wendy C. , Kamath Pauline L. , van Heerden Henriette , Huang Yen-Hua , Barandongo Zoe R. , Bruce Spencer A. , Kausrud Kyrre
Published: June 2021

Disease outbreaks are a consequence of interactions among the three components of a host–parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host–parasite coevolution. Here, we review research on how environmental context alters virulence–transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related ‘approaches’ that have dominated the study of the evolution of virulence and transmission for different host–parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence–transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence–transmission relationships across a diversity of host–parasite systems that have eluded experimental study of parasite life history.
In-phase and in-antiphase connectivity in EEG
Authors: O’Reilly Christian , Lewis John D. , Theilmann Rebecca J. , Elsabbagh Mayada , Townsend Jeanne
Published: June 2021

Zero-lag synchrony is generally discarded from functional connectivity studies to eliminate the confounding effect of volume conduction. Demonstrating genuine and significant unlagged synchronization between distant brain regions would indicate that most electroencephalography (EEG) connectivity studies neglect an important mechanism for neuronal communication. We previously demonstrated that local field potentials recorded intracranially tend to synchronize with no lag between homotopic brain regions. This synchrony occurs most frequently in antiphase, potentially supporting corpus callosal inhibition and interhemispheric rivalry. We are now extending our investigation to EEG. By comparing the coherency in a recorded and a surrogate dataset, we confirm the presence of a significant proportion of genuine zero-lag synchrony unlikely to be due to volume conduction or to recording reference artifacts. These results stress the necessity for integrating zero-lag synchrony in our understanding of neural communication and for disentangling volume conduction and zero-lag synchrony when estimating EEG sources and their functional connectivity.
Is my cough a cold or covid? A qualitative study of COVID-19 symptom recognition and attitudes towards testing in the UK
Authors: Mowbray Fiona , Woodland Lisa , Smith Louise E , Amlôt Richard , Rubin G James
Published: June 2021

Objective

Key to reducing the spread of COVID-19 in the UK is increased use of the NHS Test and Trace (NHSTT) system. This study explored one of the main issues that determine whether people engage with NHSTT, how people understand symptoms that may indicate the presence of COVID-19 and that should trigger a request for a test.

Methods

In this qualitative study, a series of semi-structured telephone interviews were conducted with 40 people (21 members of the general population, 19 students). There was nearly an equal split between male and female participants in both populations. Data were collected between 30 November and 11 December 2020 and explored using thematic analysis. There was substantial similarity in responses for both populations so we combined our results and highlighted where differences were present.

Results

Participants generally had good knowledge of the main symptoms of COVID-19 (high temperature, new, persistent cough, anosmia) but had low confidence in their ability to differentiate them from symptoms of other illnesses. Attribution of symptoms to COVID-19 was most likely where the symptoms were severe, many symptoms were present, symptoms had lasted for some time and when perceived risk of exposure to infection was high due to previous contact with others. Participants felt encouraged to engage in testing where symptoms were present and had persisted for several days, though many had concerns about the safety of testing centres and the accuracy of test results. Students had mixed feelings about mass asymptomatic testing, seeing it as a way to access a more normal student experience, but also a potential waste of resources.

Conclusions

This study offers novel insights into how people attribute symptoms to COVID-19 and barriers and facilitators to engaging with testing. Participants had positive views of testing, but there is a need to improve not just recognition of each main symptom, but also understanding that even single, mild symptoms may necessitate a test rather than a “wait and see” approach, and to address concerns around test accuracy to increase testing uptake.
Malaria treatment-seeking behaviour and its associated factors: A cross-sectional study in rural East Nusa Tenggara Province, Indonesia
Authors: Guntur Robertus Dole , Kingsley Jonathan , Islam Fakir M. Amirul
Published: June 2021

Introduction

The World Health Organization recommends seeking medical treatment within 24 hours after transmission of malaria to reduce the risk of severe complications and its onwards spread. However, in some parts of Indonesia, including East Nusa Tenggara Province (ENTP), this adherence is not achieved for a range of reasons including delays in visiting health centres. This study aims to determine factors related to the poor understanding of appropriate malaria treatment-seeking behaviour (AMTSB) of rural adults in ENTP. AMTSB was defined as seeking treatment at professional health facilities within 24 hours of the onset of malaria symptoms.

Methods

A cross-sectional study was conducted in the East Sumba, Belu, and East Manggarai district of ENTP between October and December 2019. A multi-stage cluster sampling procedure was applied to enrol 1495 participants aged between 18 and 89 years old. Data were collected through face-to-face interview. Multivariable logistic regression analyses were used to assess significant factors associated with the poor understanding of AMTSB.

Results

86% of participants were found to be familiar with the term malaria. However, poor understanding level of AMTSB in rural adults of ENTP achieved 60.4% with a 95% confidence interval (CI): 56.9 – 63.8. The most important factors associated with the poor understanding were lower levels of education, low socio-economic status (SES), occupation, and distance to the nearest health facilities. The poor understanding of AMTSB was significantly higher for adults with no education (adjusted odds ratio (AOR) 3.42, 95% CI: 1.81, 6.48); having low SES (AOR: 1.87, 95% CI: 1.19, 2.96); residing three km away from the nearest health facilities (AOR: 1.73, 95% CI: 1.2, 2.5); and working as housewife (AOR: 1.63, 95%CI: 1.01 – 2.63). Ethnicity, and family size were not associated with the poor understanding of AMTSB.

Conclusion

The proportion of rural adults having a poor understanding of AMTSB was high leading to ineffective implementation of artemisinin-based combination therapies as the method to treat malaria in ENTP. Improving awareness of AMTSB for rural adults having low-level education, low SES, working as a housewife, and living three km from the nearest health facilities is critical to support the efficacy of malaria treatment in ENTP, as well as to advance the Indonesian government’s objective to achieve malaria elimination by 2030.
Virucidal activity of a proprietary blend of plant-based oils (Viruxal) against SARS-CoV-2 and influenza viruses – an in vitro study
Authors: Kristjánsson Jón Magnús , Rolfsson Óttar
Published: June 2021

Background

The emergence of a novel coronavirus known as SARS-CoV-2 resulting in a global pandemic COVID-19 has led to a dramatic loss of life worldwide and presented an unprecedented challenge to public health. Viruxal is a medical device in a form of a nasal and oral spay containing a a proprietary blend of plant-based oils which acts against enveloped viruses. The aim of this study was to evaluate the virus deactivation activity of Viruxal against SARS-CoV-2 and Influenza A(H1N1) viruses.

Methods

An assay to detect virucidal activity was performed with four concentrations of Viruxal on two virus suspensions. Assessments were made based on log reduction values measured from the assay.

Results

Viruxal exhibited virucidal activity by reducing virus titer more than 90% for the enveloped viruses SARS-CoV-2 and influenza A(H1N1) after 30 minutes contact.

Conclusions

Viruxal was validated for its potential usefulness as a medical device for treatment and prevention of enveloped respiratory viruses.
LRRC23 is a conserved component of the radial spoke that is necessary for sperm motility and male fertility in mice
Authors: Zhang Xin , Sun Jiang , Lu Yonggang , Zhang Jintao , Shimada Keisuke , Noda Taichi , Zhao Shuqin , Koyano Takayuki , Matsuyama Makoto , Zhou Shushu , Wu Jiayan , Ikawa Masahito , Liu Mingxi
Published: June 2021

Cilia and flagella are ancient structures that achieve controlled motor functions through the coordinated interaction of structures including dynein arms, radial spokes (RSs), microtubules, and the dynein regulatory complex (DRC). RSs facilitate the beating motion of these organelles by mediating signal transduction between dyneins and a central pair (CP) of singlet microtubules. RS complex isolation from Chlamydomonas axonemes enabled the detection of 23 different proteins (RSP1-23), with the roles of RSP13, RSP15, RSP18, RSP19, and RSP21 remained poorly understood. Herein, we show that Lrrc23 is an evolutionarily conserved testis-enriched gene encoding an RSP15 homolog in mice. Through immunoelectron microscopy, we demonstrate that LRRC23 localizes to the RS complex within murine sperm flagella. We further found that LRRC23 was able to interact with RSHP9 and RSPH3A/B. The knockout of Lrrc23 resulted in RS disorganization and impaired motility in murine spermatozoa, whereas the ciliary beating was unaffected by the loss of this protein. Spermatozoa lacking LRRC23 were unable to efficiently pass through the uterotubal junction and exhibited defective zona penetration. Together these data indicate that LRRC23 is a key regulator underpinning the integrity of RS complex within the flagella of mammalian spermatozoa, whereas it is dispensable in cilia.

Author summary
Distinct phosphorylation signals drive acceptor versus self-ubiquitination selection by Parkin
Authors: Dunkerley Karen M. , Rintala-Dempsey Anne C. , Salzano Guilia , Tadayon Roya , Hadi Dania , Barber Kathryn R. , Walden Helen , Shaw Gary S.
Published: June 2021

The RBR E3 ligase parkin is recruited to the outer mitochondrial membrane (OMM) during oxidative stress where it becomes activated and ubiquitinates numerous proteins. Parkin activation involves binding of a phosphorylated ubiquitin (pUb), followed by phosphorylation of parkin itself, both mediated by the OMM kinase, PINK1. However, targeted mitochondrial proteins have little structural or sequence similarity, with the commonality between substrates being proximity to the OMM. Here, we demonstrate that parkin efficiently ubiquitinates a mitochondrial acceptor pre-ligated to pUb and phosphorylation of parkin triggers autoubiquitination activity. Mitochondrial target proteins, Miro1 or CISD1, tethered to pUb are ubiquitinated by parkin more efficiently than if alone or Ub-tethered and ubiquitin molecules are ligated to acceptor protein lysines and not pUb. Parkin phosphorylation is not required for acceptor-pUb ubiquitination. In fact, only phospho-parkin induced self-ubiquitination and deletion of Ubl or mutation at K211N inhibited self-ubiquitination. We propose divergent parkin mechanisms whereby parkin-mediated ubiquitination of acceptor proteins is driven by binding to pre-existing pUb and subsequent parkin phosphorylation triggers autoubiquitination. This finding is critical for understanding parkin’s role in mitochondrial homeostasis and has implications on targets for therapeutics.
Label-free imaging for quality control of cardiomyocyte differentiation
Authors: Qian Tongcheng , Heaster Tiffany M. , Houghtaling Angela R. , Sun Kexin , Samimi Kayvan , Skala Melissa C.
Published: June 2021

Human pluripotent stem cell (hPSC)-derived cardiomyocytes provide a promising regenerative cell therapy for cardiovascular patients and an important model system to accelerate drug discovery. However, cost-effective and time-efficient platforms must be developed to evaluate the quality of hPSC-derived cardiomyocytes during biomanufacturing. Here, we developed a non-invasive label-free live cell imaging platform to predict the efficiency of hPSC differentiation into cardiomyocytes. Autofluorescence imaging of metabolic co-enzymes was performed under varying differentiation conditions (cell density, concentration of Wnt signaling activator) across three hPSC lines. Live cell autofluorescence imaging and multivariate classification models provided high accuracy to separate low (< 50%) and high (≥ 50%) differentiation efficiency groups (quantified by cTnT expression on day 12) within 1 day after initiating differentiation (area under the receiver operating characteristic curve, 0.98). This non-invasive and label-free method could be used to avoid batch-to-batch and line-to-line variability in cell manufacturing from hPSCs.
Detection of Alzheimer’s associated microRNAs using a DNA-based smart
reagent
Authors: Chandrasekaran Arun Richard , Halvorsen Ken
Published: June 2021

Alzheimer’s disease (AD) is the most common neurodegenerative disorder, with
significant research efforts devoted to identifying new biomarkers for clinical
diagnosis and treatment. MicroRNAs have emerged as likely disease regulators and
biomarkers for AD, now implicated as having roles in several biological
processes related to progression of the disease. In this work, we use the
miRacles assay
(microRNA
activated conditional
looping of engineered
switches) for single-step detection of AD-related
microRNAs. The technology is based on conformationally responsive DNA
nanoswitches that loop upon recognition of a target microRNA and report their
on/off status through an electrophoretic readout. Unlike many other methods, our
approach directly detects native microRNAs without amplification or labeling,
eliminating the need for expensive enzymes, reagents, and equipment. We used
this assay to screen for AD-related microRNAs, demonstrate specificity within a
microRNA family, sensitivity of ∼ 8 fM, and multiplexing capability to
simultaneously detect four microRNA targets. Toward clinical use, we provide
proof-of-concept detection and quantifiable dysregulation of specific microRNAs
from total RNA extracts derived from healthy and AD brain samples. In the
context of AD, this “smart reagent” could facilitate biomarker discovery,
accelerate efforts to understand the role of microRNAs in AD, and have clinical
potential as a diagnostic or monitoring tool for validated biomarkers.
Structural mechanism of GTPase-powered ribosome-tRNA movement
Authors: Petrychenko Valentyn , Peng Bee-Zen , Schwarzer Ana C. de A. P. , Peske Frank , Rodnina Marina V. , Fischer Niels
Published: June 2021

GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP–Pi form stabilizes ribosomal subunit rotation and induces twisting of the sarcin-ricin loop of the 23S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a cascade of rearrangements and a large-scale rotation of EF-G that exerts force on the ribosome and ultimately drives tRNA movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.
Learning to represent continuous variables in heterogeneous neural networks
Authors: Darshan Ran , Rivkind Alexander
Published: June 2021

Animals must monitor continuous variables such as position or head direction. Manifold attractor networks—which enable a continuum of persistent neuronal states—provide a key framework to explain this monitoring ability. Neural networks with symmetric synaptic connectivity dominate this framework, but are inconsistent with the diverse synaptic connectivity and neuronal representations observed in experiments. Here, we developed a theory for manifold attractors in trained neural networks, which approximate a continuum of persistent states, without assuming unrealistic symmetry. We exploit the theory to predict how asymmetries in the representation and heterogeneity in the connectivity affect the formation of the manifold via training, shape network response to stimulus, and govern mechanisms that possibly lead to destabilization of the manifold. Our work suggests that the functional properties of manifold attractors in the brain can be inferred from the overlooked asymmetries in connectivity and in the low-dimensional representation of the encoded variable.
Male age andWolbachiadynamics: Investigating how fast and why bacterial densities and cytoplasmic incompatibility strengths vary
Authors: Shropshire J. Dylan , Hamant Emily , Cooper Brandon S.
Published: June 2021

Endosymbionts can influence host reproduction and fitness to favor their maternal transmission. For example, endosymbioticWolbachiabacteria often cause cytoplasmic incompatibility (CI) that kills uninfected embryos fertilized byWolbachia-modified sperm. Infected females can rescue CI, providing them a relative fitness advantage.Wolbachia-induced CI strength varies widely and tends to decrease as host males age. Since strong CI drivesWolbachiato high equilibrium frequencies, understanding how fast and why CI strength declines with male age is crucial to explaining age-dependent CI’s influence onWolbachiaprevalence. Here, we investigate ifWolbachiadensities and/or CI gene (cif) expression covary with CI-strength variation and explore covariates of age-dependentWolbachia-density variation in two classic CI systems.wRi CI strength decreases slowly withDrosophila simulansmale age (6%/ day), butwMel CI strength decreases very rapidly (19%/ day), yielding statistically insignificant CI after only three days ofD. melanogasteremergence.Wolbachiadensities andcifexpression in testes decrease aswRi-infected males age, but both surprisingly increase aswMel-infected males age, and CI strength declines. We then tested if phage lysis, Octomom copy number (which impactswMel density), or host immune expression covary with age-dependentwMel densities—only host immune expression correlated with density. Together, our results identify how fast CI strength declines with male age in two model systems and reveal unique relationships between male age,Wolbachiadensities,cifexpression, and host immunity. We discuss new hypotheses about the basis of age-dependent CI strength and its contributions toWolbachiaprevalence.

Importance

Wolbachiaare the most common animal-associated endosymbionts due in large part to their manipulation of host reproduction. ManyWolbachiacause cytoplasmic incompatibility (CI) that kills uninfected host eggs. Infected eggs are protected from CI, favoringWolbachiaspread in natural systems and in transinfected mosquito populations where vector-control groups use strong CI to maintain pathogen-blockingWolbachiaat high frequencies for biocontrol of arboviruses. CI strength varies considerably in nature and declines as males age for unknown reasons. Here, we determine that CI strength weakens at different rates with age in two model symbioses.Wolbachiadensity and CI gene expression covary withwRi-induced CI strength inDrosophila simulans, but neither explain rapidly decliningwMel-induced CI in agingD. melanogastermales. Patterns of host immune gene expression suggest a candidate mechanism behind age-dependentwMel densities. These findings inform how age-dependent CI may contribute toWolbachiaprevalence in natural systems and potentially in transinfected systems.
Effects of the COVID-19 pandemic on publication landscape in chimeric antigen receptor-modified immune cell research
Authors: Yilmaz Ahmet , Yu Jianhua
Published: June 2021

Chimeric antigen receptors (CARs) are artificial receptors introduced mainly into T cells. CAR-induced immune cell (CARi) products have achieved impressive success rates in treating some difficult-to-treat hematological malignancies. Here, we describe effects of the global COVID-19 pandemic on CARi publication landscape. Due to the pandemic, the total number of publications decreased in 2020 compared to 2019 in all fields of cancer immunotherapy except CARi. Nearly exponential increases in the number of CARi publications slowed-down in 2020 for the first time in the past 11 years. There were more CARi than coronavirus publications until 2020 when coronavirus publications increased over 5,000% compared to 2019 (575 publications in 2019 vs. 30,390 in 2020). Unlike cancer immunotherapy where the majority of the publications consist of conference abstracts and review articles, majority of the coronavirus publications are original research articles. There are more coronavirus publications in Pubmed than Embase. The opposite is true for CARi publications. Our analysis of the data from the FDA Adverse Event Reporting System (FAERS) show significantly higher death rate in patients treated with Kymirah than Yescarta (28.14% vs. 16.02%). Kymirah and Yescarta are the two main CAR T cell products for treatment of DLBCL and/or B-ALL. However, despite being highly significant, this result is not easily interpretable due to multiple confounding variables in the FAERS data. Our analysis additionally suggest that the significant effects of co-stimulatory domains (4-1BB vs. CD28) consistently reported in preclinical studies do not translate into clinical results. Our manual curation of the CARi publications in PubMed shows that only 5.2% of the publications report results from CARi clinical trials, although we found 663 clinical trials listed on ClinicalTrials.gov database. In conclusion, publication landscape in CARi as well as other fields of cancer immunotherapy has changed due to the global COVID-19 pandemic. This trend will likely continue in the near future. CARi research is now in need of increased measures by publishers to reduce repetitive and/or duplicate publications and more stringent criteria for data entry into public databases including PubMed, Embase, ClinicalTrials.gov, and FAERS to advance this important field of medical research.
A three-sodium-to-glycine stoichiometry shapes the structural relationships of ATB0,+ with GlyT2 and GlyT1 in the SLC6 family
Authors: Le Guellec Bastien , Rousseau France , Bied Marion , Supplisson Stéphane
Published: June 2021

ATB0,+ (SLC6A14) absorbs all neutral and cationic amino acids in the distal colon and lung epithelia, and is part of the amino acid transporter branch I of the SLC6 family with GlyT1 (SLC6A9) and GlyT2 (SLC6A5), two glycine-specific transporters coupled to 2:1 and 3:1 Na+:Cl−, respectively. However, ATB0,+ stoichiometry that specifies its driving force and electrogenicity remains unsettled. Using the reversal potential slope method, here we demonstrate that ATB0,+-mediated glycine transport is coupled to 3 Na+ and 1 Cl− and has a charge coupling of 2.1 e/glycine. ATB0,+ behaves as a unidirectional transporter with limited efflux and exchange capabilities. Analysis and computational modeling of the pre-steady-state charge movement reveal higher sodium affinity of the apo-ATB0,+, and a locking trap preventing Na+ loss at depolarized potentials. A 3 Na+/ 1 Cl− stoichiometry substantiates ATB0,+ concentrative-uptake and trophic role in cancers and rationalizes its structural proximity with GlyT2 despite their divergent substrate specificity.
In Situ Visualization of the pKM101-Encoded Type IV Secretion System Reveals a Highly Symmetric ATPase Energy Center at the Channel Entrance
Authors: Khara Pratick , Christie Peter J. , Hu Bo
Published: June 2021

Bacterial conjugation systems are members of the type IV secretion system (T4SS) superfamily. T4SSs can be classified as ‘minimized’ or ‘expanded’ based on whether assembly requires only a core set of signature subunits or additional system-specific components. The prototypical ‘minimized’ systems mediating Agrobacterium tumefaciens T-DNA transfer and conjugative transfer of plasmids pKM101 and R388 are built from 12 subunits generically named VirB1-VirB11 and VirD4. In this study, we visualized the pKM101-encoded T4SS in the native context of the bacterial cell envelope by in situ cryoelectron tomography (CryoET). The T4SSpKM101 is composed of an outer membrane core complex (OMCC) connected by a thin stalk to an inner membrane complex (IMC). The OMCC exhibits 14-fold symmetry and resembles that of the T4SSR388, a large substructure of which was previously purified and analyzed by negative-stain electron microscopy (nsEM). The IMC of the in situ T4SSpKM101 machine is highly symmetrical and exhibits 6-fold symmetry, dominated by a hexameric collar in the periplasm and a cytoplasmic complex composed of a hexamer of dimers of the VirB4-like TraB ATPase. The IMC closely resembles equivalent regions of three ‘expanded’ T4SSs previously visualized by in situ CryoET, but strikingly differs from the IMC of the purified T4SSR388 whose cytoplasmic complex instead presents as two side-by-side VirB4 hexamers. Together, our findings support a unified architectural model for all T4SSs assembled in vivo regardless of their classification as ‘minimized’ or ‘expanded’: the signature VirB4-like ATPases invariably are arranged as central hexamers of dimers at the entrances to the T4SS channels.

Significance

Bacterial type IV secretion systems (T4SSs) play central roles in antibiotic resistance spread and virulence. By cryoelectron tomography (CryoET), we solved the structure of the plasmid pKM101-encoded T4SS in the native context of the bacterial cell envelope. The inner membrane complex (IMC) of the in situ T4SS differs remarkably from that of a closely-related T4SS analyzed in vitro by single particle electron microscopy. Our findings underscore the importance of comparative in vitro and in vivo analyses of the T4SS nanomachines, and firmly support a unified model in which the signature VirB4 ATPases of the T4SS superfamily function as a central hexamer of dimers to regulate substrate entry into and passage through T4SS channels.
Hitting more birds with one stone: CD70 as an actionable immunotherapeutic target in recurrent glioblastoma
Authors: Seyfrid M , Maich W , Shaikh MV , Tatari N , Upreti D , Piyasena D , Subapanditha M , Savage N , McKenna D , Kuhlmann L , Khoo A , Salim SK , Bassey-Archibong B , Gwynne W , Chokshi C , Brown K , Murtaza N , Bakhshinyan D , Vora P , Venugopal C , Moffat J , Singh SK
Published: June 2021

Purpose

Glioblastoma (GBM) patients suffer from a dismal prognosis, with standard of care therapy inevitably leading to therapy-resistant recurrent tumors. The presence of brain tumor initiating cells (BTICs) drives the extensive heterogeneity seen in GBM, prompting the need for novel therapies specifically targeting this subset of tumor-driving cells. Here we identify CD70 as a potential therapeutic target for recurrent GBM BTICs.

Experimental Design

In the current study, we identified the relevance and functional influence of CD70 on primary and recurrent GBM cells, and further define its function using established stem cell assays. We utilize CD70 knockdown studies, subsequent RNAseq pathway analysis, andin vivoxenotransplantation to validate CD70’s role in GBM. Next, we developed and tested an anti-CD70 CAR-T therapy, which we validatedin vitroandin vivousing our established preclinical model of human GBM. Lastly, we explored the importance of CD70 in the tumor immune microenvironment (TIME) by assessing the presence of its receptor, CD27, in immune infiltrates derived from freshly resected GBM tumor samples.

Results

CD70 expression is elevated in recurrent GBM and CD70 knockdown reduces tumorigenicity in vitro and in vivo. CD70 CAR-T therapy significantly improves prognosisin vivo. We also found CD27 to be present on the cell surface of multiple relevant GBM TIME cell populations.

Conclusion

CD70 plays a key role in recurrent GBM cell aggressiveness and maintenance. Immunotherapeutic targeting of CD70 significantly improves survival in animal models and the CD70/CD27 axis may be a viable poly-therapeutic avenue to co-target both GBM and its TIME.
Staring at the naked Goddess. Unraveling structure and reactivity of Artemis endonuclease interacting with a DNA double strand
Authors: Hognon Cécilia , Monari Antonio
Published: June 2021

Artemis is an endonuclease responsible for breaking hairpin DNA strand during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, or the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulation, both classically and at hybrid quantum mechanics/ molecular mechanics level, we evidence the stable interaction modes of Artemis with a model DNA strand. We also analyze the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.
A Functional Menadione Biosynthesis Pathway is Required for Capsule Production by Staphylococcus aureus
Authors: Altwiley Dina , Brignoli Tarcisio , Edwards Andrew , Recker Mario , Lee Jean , Massey Ruth C.
Published: June 2021

Staphylococcus aureus is a major human pathogen that utilises a wide array of pathogenic and immune evasion strategies to cause disease. One immune evasion strategy, common to many bacterial pathogens, is the ability of S. aureus to produce a capsule that protects the bacteria from several aspects of the human immune system. To identify novel regulators of capsule production by S. aureus we applied a genome wide association study (GWAS) to a collection of 300 bacteraemia isolates that represent the two major MRSA clones in UK and Irish hospitals: CC22 and CC30. One of the loci associated with capsule production, the menD gene, encodes an enzyme critical to the biosynthesis of menadione. Mutations in this gene that result in menadione auxotrophy induce the slow growing small-colony variant (SCV) form of S. aureus often associated with chronic infections due to their increased resistance to antibiotics and ability to survive inside phagocytes. Utilising such an SCV we functionally verified this association between menD and capsule production. Although the clinical isolates with polymorphisms in the menD gene in our collections had no apparent growth defects, they were more resistant to gentamicin when compared to those with the wild-type menD gene. Our work suggests that menadione plays a critical role in the production of the S. aureus capsule, and that amongst clinical isolates polymorphisms exist in the menD gene that confer the characteristic increased gentamicin resistance, but not the major growth defect associated with SCV phenotype.
Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations
Authors: Ansell T. Bertie , Curran Luke , Horrell Michael R. , Pipatpolkai Tanadet , Letham Suzanne C. , Song Wanling , Siebold Christian , Stansfeld Phillip J. , Sansom Mark. S. P. , Corey Robin. A.
Published: June 2021

Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-EM densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities by experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in e.g. cryo-EM derived membrane protein structures surrounded by a plethora of ancillary lipid densities.
Amyloid precursor protein localises to ependymal cilia in vertebrates and is required for ciliogenesis and brain development in zebrafish
Authors: Chebli Jasmine , Rahmati Maryam , Lashley Tammaryn , Edeman Birgitta , Oldfors Anders , Zetterberg Henrik , Abramsson Alexandra
Published: June 2021

Amyloid precursor protein (APP) is ubiquitously expressed in human, mice and in zebrafish. In zebrafish, there are two orthologues, Appa and Appb. Interestingly, some cellular processes associated with APP overlap with cilia-mediated functions. Whereas the localization of APP to primary cilia ofin vitro-cultured cells has been reported, we addressed the presence of APP in motile and in non-motile sensory cilia and its potential implication for ciliogenesis using zebrafish, mouse, and human samples. We report that Appa and Appb are expressed by ciliated cells and become localized at the membrane of cilia in the olfactory epithelium, otic vesicle and in the brain ventricles of zebrafish embryos. App in ependymal cilia persisted in adult zebrafish and was also detected in mouse and human brain. Finally, we found morphologically abnormal ependymal cilia and smaller brain ventricles inappa-/-appb-/-mutant zebrafish. Our findings demonstrate an evolutionary conserved localisation of APP to cilia and suggest a role of App in ciliogenesis and cilia-related functions.
An atlas of transcriptionally defined cell populations in the rat ventral tegmental area
Authors: Phillips Robert A. , Tuscher Jennifer J. , Black Samantha L. , Ianov Lara , Day Jeremy J.
Published: June 2021

The ventral tegmental area (VTA) is a complex brain region that is essential for reward function but is also implicated in neuropsychiatric diseases including substance abuse. While decades of research on VTA function have focused on the role of dopaminergic neurons, recent evidence has identified critical roles for VTA GABAergic and glutamatergic neurons in reward processes as well. Interestingly, molecular characterization has revealed that subsets of these neurons express genes involved in the transport, synthesis, and vesicular packaging of multiple neurotransmitters, providing evidence for co-release neurons. However, these studies have largely relied on low-throughput methods, and the molecular architecture of the VTA has not been comprehensively examined. Here, we performed single nucleus RNA-sequencing (snRNA-seq) on 21,600 VTA cells from male and female Sprague-Dawley rats to generate a transcriptional atlas of the rat VTA. We identified 16 transcriptionally distinct cell types within the VTA, including 7 neuronal populations. Further subclustering revealed several VTA neuronal populations expressing markers for more than one neurotransmitter system, with one cluster exhibiting high expression levels of genes involved in the synthesis and transport of GABA, glutamate, and dopamine. Finally, snRNA-seq enabled the de novo identification of thousands of marker genes for each transcriptionally distinct population, revealing cluster-specific enrichment of gene sets implicated in neuropsychiatric and neurodevelopmental disorders, as well as specific phenotypes associated with alcohol and tobacco use. Together, these results highlight the heterogeneity of cellular populations in the VTA and identify novel markers and disease-linked genes enriched in distinct neuronal subtypes.