bluuebunny/crossref_metadata_2025 huggingface dataset:
‘No cyst, no echinococcosis’: a scoping review update on the diagnosis of cystic echinococcosis after the issue of the WHO-IWGE Expert Consensus and current perspectives
Authors: Siles-Lucas Mar , Uchiumi Leonardo , Tamarozzi Francesca
Published: July 2023

Purpose of review

In 2010, the WHO-Informal Working Group on Echinococcosis (IWGE) published an Expert Consensus on the diagnosis and treatment of echinococcal infections. We provide an update on the diagnosis of cystic echinococcosis through a scoping review of the literature published after the release of the WHO-IWGE document.

Recent findings

Ultrasound accurately and reliably depicts the pathognomonic signs of cystic echinococcosis (CE) stages compared with other imaging techniques. Among these, T2-wighted MRI is to be preferred to computed tomography, which has poor performance for the etiological diagnosis of CE. A negative serology cannot exclude the diagnosis of CE, while a positive serology, applied after the visualization of a CE-compatible lesion, may confirm a CE diagnosis. Serology alone must not be used to define ‘CE’ nor as ‘screening’ tool for infection. Other imaging and laboratory techniques did not show clinically applicable performances.

In the absence of a focal lesion compatible with a CE cyst, no diagnosis of CE should be attempted. There is urgent need to achieve univocal CE case definitions and consensus diagnostic algorithm, as well as standardization of diagnostic methods and issue of a Target Product Profile of CE diagnostics, as advocated by the WHO in the 2021–2030 roadmap for neglected tropical diseases (NTDs).
Mastodon over Mammon: towards publicly owned scholarly knowledge
Authors: Brembs Björn , Lenardic Adrian , Murray-Rust Peter , Chan Leslie , Irawan Dasapta Erwin
Published: July 2023

Twitter is in turmoil and the scholarly community on the platform is once again starting to migrate. As with the early internet, scholarly organizations are at the forefront of developing and implementing a decentralized alternative to Twitter, Mastodon. Both historically and conceptually, this is not a new situation for the scholarly community. Historically, scholars were forced to leave social media platform FriendFeed after it was bought by Facebook in 2006. Conceptually, the problems associated with public scholarly discourse subjected to the whims of corporate owners are not unlike those of scholarly journals owned by monopolistic corporations: in both cases the perils associated with a public good in private hands are palpable. For both short form (Twitter/Mastodon) and longer form (journals) scholarly discourse, decentralized solutions exist, some of which are already enjoying some institutional support. Here we argue that scholarly organizations, in particular learned societies, are now facing a golden opportunity to rethink their hesitations towards such alternatives and support the migration of the scholarly community from Twitter to Mastodon by hosting Mastodon instances. Demonstrating that the scholarly community is capable of creating a truly public square for scholarly discourse, impervious to private takeover, might renew confidence and inspire the community to focus on analogous solutions for the remaining scholarly record—encompassing text, data and code—to safeguard all publicly owned scholarly knowledge.
Does the egg capsule protect against chronic UV-B radiation? A study based on encapsulated and decapsulated embryos of cuttlefish
Sepia officinalis
Authors: MOLINA-CARRILLO Luis , Bassaglia Yann , Schires Gaëtan , BONNAUD-PONTICELLI Laure
Published: July 2023

Although the egg capsule plays a crucial role in the embryonic development of cephalopods, its ability to protect embryos from Ultraviolet (UV) radiation is unknown. Our study evaluated the photoprotection mechanisms of
S. officinalis
to UV-B radiation and estimated the ability of the black capsule to act as a physical shield against it. Embryos with and without capsule and juveniles were exposed to four experimental UVB conditions for 55 days. The effects of different UVB doses were evaluated in terms of morphological abnormalities and differences in gene expression between each group. We observed that the development might be severely impaired in embryos exposed to UVB without capsule protection, and these effects were time- and UVB-dose-dependent. In addition, we found variations in gene expression levels (light-sensitive, stress response and DNA repair) in different tissues as a function of UVB doses. We suggest a relationship between morphological abnormalities and the limit of molecular regulation. These results suggest that the quantitative differences in expression are essential for defining the survivability of the embryo face to UVB. Thus, we demonstrated that the egg capsule could ensure successful embryonic development of the cuttlefish
S. officinalis
even at high doses of UVB.
Evaluating Capabilities of Large Language Models: Performance of GPT4 on Surgical Knowledge Assessments
Authors: Beaulieu-Jones Brendin R , Shah Sahaj , Berrigan Margaret T , Marwaha Jayson S , Lai Shuo-Lun , Brat Gabriel A
Published: July 2023

Background

Artificial intelligence (AI) has the potential to dramatically alter healthcare by enhancing how we diagnosis and treat disease. One promising AI model is ChatGPT, a large general-purpose language model trained by OpenAI. The chat interface has shown robust, human-level performance on several professional and academic benchmarks. We sought to probe its performance and stability over time on surgical case questions.

Methods

We evaluated the performance of ChatGPT-4 on two surgical knowledge assessments: the Surgical Council on Resident Education (SCORE) and a second commonly used knowledge assessment, referred to as Data-B. Questions were entered in two formats: open-ended and multiple choice. ChatGPT output were assessed for accuracy and insights by surgeon evaluators. We categorized reasons for model errors and the stability of performance on repeat encounters.

Results

A total of 167 SCORE and 112 Data-B questions were presented to the ChatGPT interface. ChatGPT correctly answered 71% and 68% of multiple-choice SCORE and Data-B questions, respectively. For both open-ended and multiple-choice questions, approximately two-thirds of ChatGPT responses contained non-obvious insights. Common reasons for inaccurate responses included: inaccurate information in a complex question (n=16, 36.4%); inaccurate information in fact-based question (n=11, 25.0%); and accurate information with circumstantial discrepancy (n=6, 13.6%). Upon repeat query, the answer selected by ChatGPT varied for 36.4% of inaccurate questions; the response accuracy changed for 6/16 questions.

Conclusion

Consistent with prior findings, we demonstrate robust near or above human-level performance of ChatGPT within the surgical domain. Unique to this study, we demonstrate a substantial inconsistency in ChatGPT responses with repeat query. This finding warrants future consideration and presents an opportunity to further train these models to provide safe and consistent responses. Without mental and/or conceptual models, it is unclear whether language models such as ChatGPT would be able to safely assist clinicians in providing care.
Marker and readout genes for priming in the Arabidopsis –Pseudomonas cannabinapv. alisalensis interaction
Authors: Sistenich Andrea J. , Fürtauer Lisa , Scheele Franziska , Conrath Uwe
Published: July 2023

After a local infection, the entire plant foliage becomes primed for the superinduction of defense responses after rechallenge. The identity of genes expressed during priming (priming-marker genes) or with hyperexpression in primed plants after rechallenge (priming-readout genes) remained largely unknown. We show inArabidopsis thalianathat genesAT1G76960(with unknown function),AT3G51860(encoding vacuolar Ca2+/H+antiporter CAX3), andAT3G45860(cysteine-rich receptor-like protein kinase CRK4) are strongly expressed duringPseudomonas cannabinapv. alisalensis-induced priming but not, or much less, in uninfected or challenged plants, or in primed plants after rechallenge. Expression of these genes thus solely marks the primed state for enhanced defense. In contrast to these genes, expression ofAT2G14610(pathogenesis-related protein PR1),AT2G32680(receptor-like protein RLP23),AT3G25010(RLP41) and some less expressed loci are activated, about equally, in primed plants before and after rechallenge. They may also serve as marker genes for priming. In further contrast, genesAT2G39530(encoding Casparian strip domain-like protein 4D1),AT2G19190(flg22-induced receptor-like kinase FRK1),AT3G28510(P loop-containing nucleoside triphosphate hydrolases superfamily protein) and some less strongly expressed genes are not, or only faintly activated in uninfected plants, during priming and upon challenge. However, their expression is very strong in primed plants after rechallenge. They are, therefore, specific readout genes for the primed state. Remarkably, mutation in solely priming-readout geneAT5G36970(encoding NDR1/HIN1-like protein 25) impaired both infection-induced defense priming and systemic acquired resistance suggesting a previously unknown critical role of this gene in the systemic plant immune response.
A Template for Translational Bioinformatics: Facilitating Multimodal Data Analyses in Preclinical Models of Neurological Injury
Authors: Gaudio Hunter A. , Padmanabhan Viveknarayanan , Landis William P. , Silva Luiz E. V. , Slovis Julia , Starr Jonathan , Weeks M. Katie , Widmann Nicholas J. , Forti Rodrigo M. , Laurent Gerard H. , Ranieri Nicolina R. , Mi Frank , Degani Rinat E. , Hallowell Thomas , Delso Nile , Calkins Hannah , Dobrzynski Christiana , Haddad Sophie , Kao Shih-Han , Hwang Misun , Shi Lingyun , Baker Wesley B. , Tsui Fuchiang , Morgan Ryan W. , Kilbaugh Todd J. , Ko Tiffany S.
Published: July 2023

Background

Pediatric neurological injury and disease is a critical public health issue due to increasing rates of survival from primary injuries (e.g., cardiac arrest, traumatic brain injury) and a lack of monitoring technologies and therapeutics for the treatment of secondary neurological injury. Translational, preclinical research facilitates the development of solutions to address this growing issue but is hindered by a lack of available data frameworks and standards for the management, processing, and analysis of multimodal data sets.

Methods

Here, we present a generalizable data framework that was implemented for large animal research at the Children’s Hospital of Philadelphia to address this technological gap. The presented framework culminates in an interactive dashboard for exploratory analysis and filtered data set download.

Results

Compared with existing clinical and preclinical data management solutions, the presented framework accommodates heterogeneous data types (single measure, repeated measures, time series, and imaging), integrates data sets across various experimental models, and facilitates dynamic visualization of integrated data sets. We present a use case of this framework for predictive model development for intra-arrest prediction of cardiopulmonary resuscitation outcome.

Conclusions

The described preclinical data framework may serve as a template to aid in data management efforts in other translational research labs that generate heterogeneous data sets and require a dynamic platform that can easily evolve alongside their research.
Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source toolmrQA
Authors: Sinha Harsh , Raamana Pradeep Reddy
Published: July 2023

Abstract

Pooling data across diverse sources acquired by multisite consortia requires compliance with a predefined reference protocoli.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Traditionally, this has been an arduous and manual process due to difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance. Moreover, issues of protocol compliance is often overlooked for lack of realization that parameter values are routinely improvised/modified locally at various sites. The inconsistencies in acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether. An open-source tool, mrQA was developed to automatically assess protocol compliance on standard dataset formats such as DICOM and BIDS, and to study the patterns of non-compliance in over 20 open neuroimaging datasets, including the large ABCD study. The results demonstrate that the lack of compliance is rather pervasive. The frequent sources of non-compliance include but are not limited to deviations in Repetition Time, Echo Time, Flip Angle, and Phase Encoding Direction. It was also observed that GE and Philips scanners exhibited higher rates of non-compliance relative to the Siemens scanners in the ABCD dataset. Continuous monitoring for protocol compliance is strongly recommended before any pre/post-processing, ideally right after the acquisition, to avoid the silent propagation of severe/subtle issues. Although, this study focuses on neuroimaging datasets, the proposed tool mrQA can work with any DICOM-based datasets.
An individual’s skin stiffness predicts their tactile acuity
Authors: Li Bingxu , Gerling Gregory J.
Published: July 2023

Individual differences in tactile acuity have been correlated with age, gender, and finger size, while the role of the skin’s stiffness has been underexplored. Using an approach to image the 3- D deformation of the skin surface while in contact with transparent elastic objects, we evaluate a cohort of 40 young participants, who present a diverse range of finger size, skin stiffness, and fingerprint ridge breadth. The results indicate that skin stiffness generally correlates with finger size, although individuals with relatively softer skin can better discriminate compliant objects. Analysis of contact at the skin surface reveals that softer skin generates more prominent patterns of deformation, in particular greater rates of change in contact area, which correlate with higher rates of perceptual discrimination, regardless of finger size. Moreover, upon applying hyaluronic acid to soften individuals’ skin, we observe immediate, marked and systematic changes in skin deformation and consequent improvements in perceptual acuity. Together, the combination of 3- D imaging of the skin surface, biomechanics measurements, multivariate regression and clustering, and psychophysical experiments show that subtle distinctions in skin stiffness modulate the mechanical signaling of touch and shape individual differences in perceptual acuity.

Key points described in the manuscript

While declines in tactile acuity with aging are a function of multiple factors, for younger people the current working hypothesis has been that smaller fingers are better at informing perceptual discrimination due to a higher density of neural afferents.

To decouple relative impacts on tactile acuity of skin properties of finger size, skin stiffness, and fingerprint ridge breadth, we combined 3D imaging of skin surface deformation, biomechanical measurements, multivariate regression and clustering, and psychophysics.

The results indicate skin stiffness generally correlates with finger size, although more robustly correlates with and predicts an individual’s perceptual acuity.

In particular, more elastic skin generates higher rates of deformation, which correlate with perceptual discrimination, shown most dramatically by softening each participant’s skin with hyaluronic acid.

In refining the current working hypothesis, we show the skin’s stiffness strongly shapes the signaling of touch and modulates individual differences in perceptual acuity.
DNA methylation sites in early adulthood characterised by pubertal timing and development: A twin study
Authors: Sehovic Emir , Zellers Stephanie M. , Youssef Markus K. , Heikkinen Aino , Kaprio Jaakko , Ollikainen Miina
Published: July 2023

Background

Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic characterisation of pubertal timing and development could lead to important insights. Blood DNA methylation, reacting to both genotype and environment, has been associated with puberty; however, such studies are relatively scarce. We investigated peripheral blood DNA methylation profiles (using Illumina 450K and EPIC platforms) of 1539 young adult Finnish twins associated with pubertal development scale (PDS) and pubertal age (PA).

Results

Fixed effect meta-analysis of the two platforms on 347521 CpGs in common identified 58 CpG sites associated (p < 1 x 10-5) with either PDS or PA. All four CpGs associated with PA and 45 CpGs associated with PDS were sex specific. Thirteen CpGs had a high heritability (h2: 0.51-0.98), while one CpG site (mapped toGET4) had a high shared environmental component accounting for 68% of the overall variance in methylation at the site. Utilising twin discordance analysis, we found 6 CpG sites (5 associated with PDS and 1 with PA) that had an environmentally driven association with puberty. Furthermore, genes with PDS- or PA-associated CpGs were linked to various developmental processes and diseases, such as breast, prostate and ovarian cancer, while methylation quantitative trait loci (meQTLs) of associated CpG sites were enriched in immune pathways developing during puberty.

Conclusions

By identifying puberty-associated DNA methylation sites and examining the effects of sex, environment and genetics, we shed light on the intricate interplay between environment and genetics in the context of puberty. Through our comprehensive analysis, we not only deepen the understanding of the significance of both genetic and environmental factors in the complex processes of puberty and its timing but also gain insights into potential links with disease risks.
Predicting cell morphological responses to perturbations using generative modeling
Authors: Palma Alessandro , Theis Fabian J. , Lotfollahi Mohammad
Published: July 2023

Advancements in high-throughput screening have enabled the exploration of rich phenotypic readouts like high-content microscopy, expediting drug target identification and mode of action studies. However, scaling these experiments to the vast space of drug or genetic manipulations poses challenges, as only a small subset of compounds show activity in screenings. Despite being widely used in various applications, machine learning methods have not shown a reliable ability to extrapolate predictions to scenarios involving unseen phenomena, specifically transforming an unseen control cell image into a desired perturbation. We present a generative model, the IMage Perturbation Autoencoder (IMPA), which predicts cellular morphological effects of chemical and genetic perturbations using untreated cells as input. IMPA learns perturbation-specific styles from generalized embeddings and generates counterfactual treatment response predictions in control cells. We demonstrate IMPA can predict morphological changes caused by small molecule perturbations on breast cancer cells. Additionally, we test IMPA on the unseen drug effect prediction task, showing improved performance over state-of-the-art generative models when compounds are structurally related to the training set. Finally, generalizability and capability to predict more subtle effects are showcased through its application to large microscopy datasets with hundreds of genetic perturbations on U2OS cells. We envision IMPA to become a valuable tool in computational microscopy for aiding phenotypic drug discovery, facilitating navigation of the perturbation space, and rational experimental design.
Attractor neural networks with double well synapses
Authors: Feng Yu , Brunel Nicolas
Published: July 2023

It is widely believed that memory storage depends on activity-dependent synaptic modifications. Classical studies of learning and memory in neural networks describe synaptic efficacy either as continuous [1, 2] or discrete [2–4]. However, recent results suggest an intermediate scenario in which synaptic efficacy can be described by a continuous variable, but whose distribution is peaked around a small set of discrete values [5, 6]. Motivated by these results, we explored a model in which each synapse is described by a continuous variable that evolves in a potential with multiple minima. External inputs to the network can switch synapses from one potential well to another. Our analytical and numerical results show that this model can interpolate between models with discrete synapses which correspond to the deep potential limit [7], and models in which synapses evolve in a single quadratic potential [8]. We find that the storage capacity of the network with double-well synapses exhibits a power law dependence on the network size, rather than the logarithmic dependence observed in models with single well synapses [9]. In addition, synapses with deeper potential wells lead to more robust information storage in the presence of noise. When memories are sparsely encoded, the scaling of the capacity with network size is similar to previously studied network models in the sparse coding limit [2, 10–13].
Measuring Connectivity in Linear Multivariate Processes with Penalized Regression Techniques
Authors: Antonacci Y. , Toppi J. , Pietrabissa A. , Anzolin A. , Astolfi L.
Published: July 2023

The evaluation of time and frequency domain measures of coupling and causality relies on the parametric representation of linear multivariate processes. The study of temporal dependencies among time series is based on the identification of a Vector Autoregressive model. This procedure is pursued through the definition of a regression problem solved by means of Ordinary Least Squares (OLS) estimator. However, its accuracy is strongly influenced by the lack of data points and a stable solution is not always guaranteed. To overcome this issue, it is possible to use penalized regression techniques. The aim of this work is to compare the behavior of OLS with different penalized regression methods used for a connectivity analysis in different experimental conditions. Bias, accuracy in the reconstruction of network structure and computational time were used for this purpose. Different penalized regressions were tested by means of simulated data implementing different ground-truth networks under different amounts of data samples available. Then, the approaches were applied to real electroencephalographic signals (EEG) recorded from a healthy volunteer performing a motor imagery task. Penalized regressions outperform OLS in simulation settings when few data samples are available. The application on real EEG data showed how it is possible to use features extracted from brain networks for discriminating between two tasks even in conditions of data paucity. Penalized regression techniques can be used for brain connectivity estimation and can be exploited for the computation of all the connectivity estimators based on linearity assumption overcoming the limitations imposed by the classical OLS.
Click-train evoked steady state harmonic response as a novel pharmacodynamic biomarker of cortical oscillatory synchrony
Authors: Gautam Deepshila , Raza Muhammad Ummear , Miyakoshi M , Molina JL , Joshi YB , Clayson PE , Light GA , Swerdlow NR , Sivarao Digavalli V.
Published: July 2023

Sensory networks naturally entrain to rhythmic stimuli like a click train delivered at a particular frequency. Such synchronization is integral to information processing, can be measured by electroencephalography (EEG) and is an accessible index of neural network function. Click trains evoke neural entrainment not only at the driving frequency (F), referred to as the auditory steady state response (ASSR), but also at its higher multiples called the steady state harmonic response (SSHR). Since harmonics play an important and non-redundant role in acoustic information processing, we hypothesized that SSHR may differ from ASSR in presentation and pharmacological sensitivity. In female SD rats, a 2 s-long train stimulus was used to evoke ASSR at 20 Hz and its SSHR at 40, 60 and 80 Hz. Narrow band evoked responses were evident at all frequencies; signal power was strongest at 20 Hz while phase synchrony was strongest at 80 Hz. SSHR at 40 Hz took the longest time (∼180 ms from stimulus onset) to establish synchrony. The NMDA antagonist MK801 (0.025-0.1 mg/kg) did not consistently affect 20 Hz ASSR phase synchrony but robustly and dose-dependently attenuated synchrony of all SSHR. Evoked power was attenuated by MK801 at 20 Hz ASSR and 40 Hz SSHR only. Thus, presentation as well as pharmacological sensitivity distinguished SSHR from ASSR, making them non-redundant markers of cortical network function. SSHR is a novel and promising translational biomarker of cortical oscillatory dynamics that may have important applications in CNS drug development and personalized medicine.
Mapping and targeting ofC1ql1-expressing cells in the mouse
Authors: Moghimyfiroozabad Shayan , Paul Maëla A. , Sigoillot Séverine M. , Selimi Fekrije
Published: July 2023

The C1Q complement protein C1QL1 is highly conserved in mammals where it is expressed in various tissues including the brain. This secreted protein interacts with Brain-specific Angiogenesis Inhibitor 3, BAI3/ADGRB3, and controls synapse formation and maintenance.C1ql1is expressed in the inferior olivary neurons that send projections to cerebellar Purkinje cells, but its expression in the rest of the brain is less documented. To mapC1ql1expression and enable the specific targeting ofC1ql1-expressing cells, we characterized a knockin mouse model expressing the Cre recombinase under the control ofC1ql1regulatory sequences. We characterized the capacity for Cre-driven recombination in the brain and mapped Cre expression in various neuron types using reporter mouse lines. Using an intersectional strategy with viral particle injections, we show that this mouse line can be used to target specific afferents of Purkinje cells. AsC1ql1is also expressed in other regions of the brain, as well as in other tissues such as adrenal glands, placenta, colon and testis, our mouse model is a useful tool to targetC1ql1-expressing cells in a broad variety of tissues.
Annual dynamics and distribution ofXylella fastidiosain infected almond trees
Authors: Zecharia Noa , Miri Vanunu , Dror Orit , Hatib Kamel , Holland Doron , Dani Shtienberg , Bahar Ofir
Published: July 2023

This research focused on studying the dynamics of the bacterial pathogenXylella fastidiosain almond trees at different developmental stages and in various tree parts. The objective was to understand the annual distribution and concentration ofX. fastidiosawithin almond trees. Different tree parts, including leaf petioles, annual and perennial shoots, fruit parts, flowers, and roots, from tenX. fastidiosa-infected almond trees were sampled over two years. The distribution and concentration ofX. fastidiosawere determined using qPCR and serial dilution plating. Throughout the study,X. fastidiosawas never found in the fruit, flowers, and roots of almond trees, but it was present in leaves and annual and perennial shoots. We show that the inability ofX. fastidiosato colonize roots is likely due to incompatibility with the GF677 rootstock. The presence ofX. fastidiosain shoots remained consistent throughout the year, while in leaf petioles it varied across developmental stages, with lower detection during early and late stages of the season. Similarly, viableX. fastidiosacells could be isolated from shoots at all developmental stages, while in leaf petioles no successful isolations were achieved during the vegetative and nut growth stage. Examining the development of almond leaf scorch symptoms over time in trees with preliminary infections revealed that once symptoms have appeared on a single branch, other asymptomatic limbs were likely already colonized by the bacterium, hence, selective pruning of symptomatic branches is unlikely to cure the tree. Overall, this study enhances our understanding ofX. fastidiosadynamics in almonds and may have practical applications for its detection and control in almond orchards.
A natural disaster exacerbates and redistributes disease risk across free-ranging macaques by altering social structure
Authors: Motes-Rodrigo Alba , Albery Gregory F. , Negron-Del Valle Josue E. , Philips Daniel ,   Cayo Biobank Research Unit, Platt Michael L. , Brent Lauren J.N. , Testard Camille
Published: July 2023

Climate change is intensifying extreme weather events, with severe implications for ecosystem dynamics. A key behavioural mechanism whereby animals may cope with such events is by increasing social cohesion to improve access to scarce resources like refuges, which in turn could exacerbate epidemic risk due to increased close contact. However, how and to what extent natural disasters affect disease risk via changes in sociality remains unexplored in animal populations. By modelling disease spread in free-living rhesus macaque groups (Macaca mulatta) before and after a hurricane, we demonstrate doubled pathogen transmission rates up to five years following the disaster, equivalent to an increase in pathogen infectivity from 10% to 20%. Moreover, the hurricane redistributed the risk of infection across the population, decreasing status-related differences found in pre-hurricane years. These findings demonstrate that natural disasters can exacerbate and homogenise epidemic risk in an animal population via changes in sociality. These observations provide unexpected further mechanisms by which extreme weather events can threaten wildlife health, population viability, and spillover to humans.
Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice
Authors: Ouwendijk Werner J.D. , Roychoudhury Pavitra , Cunningham Anthony L. , Jerome Keith R. , Koelle David M. , Kinchington Paul R. , Mohr Ian , Wilson Angus C. , Verjans Georges M.G.M. , Depledge Daniel P.
Published: July 2023

Most individuals are latently infected with herpes simplex virus type 1 (HSV-1) and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent virus is also present in immune cells recovered from ganglia in a mouse model used for studying latency. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for this conclusion. Unexpectedly, off-target priming in 3’ scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1latency-associated transcript(LAT) intronic RNAs. However,LATreads were near-exclusively detected in a mixed population of cells undergoing cell death. Specific loss of HSV-1LATand neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained by inaccuracies in the data analyses.
Inflammasomes primarily restrict cytosolicSalmonellareplication within human macrophages
Authors: Egan Marisa S. , O’Rourke Emily A. , Mageswaran Shrawan Kumar , Zuo Biao , Martynyuk Inna , Demissie Tabitha , Hunter Emma N. , Bass Antonia R. , Chang Yi-Wei , Brodsky Igor E. , Shin Sunny
Published: July 2023

Salmonella entericaserovar Typhimurium is a facultative intracellular pathogen that utilizes its type III secretion systems (T3SSs) to inject virulence factors into host cells and colonize the host. In turn, a subset of cytosolic immune receptors respond to T3SS ligands by forming multimeric signaling complexes called inflammasomes, which activate caspases that induce interleukin-1 (IL-1) family cytokine release and an inflammatory form of cell death called pyroptosis. Human macrophages mount a multifaceted inflammasome response toSalmonellainfection that ultimately restricts intracellular bacterial replication. However, how inflammasomes restrictSalmonellareplication remains unknown. We find that caspase-1 is essential for mediating inflammasome responses toSalmonellaand restricting bacterial replication within human macrophages, with caspase-4 contributing as well. We also demonstrate that the downstream pore-forming protein gasdermin D (GSDMD) and Ninjurin-1 (NINJ1), a mediator of terminal cell lysis, play a role in controllingSalmonellareplication in human macrophages. Notably, in the absence of inflammasome responses, we observed hyperreplication ofSalmonellawithin the cytosol of infected cells as well as increased bacterial replication within vacuoles, suggesting that inflammasomes controlSalmonellareplication primarily within the cytosol and also within vacuoles. These findings reveal that inflammatory caspases and pyroptotic factors mediate inflammasome responses that restrict the subcellular localization of intracellularSalmonellareplication within human macrophages.
Benchmarking and optimization of cell-free DNA deconvolution
Authors: Hill Tom , Redekar Neelam , Andargie Temesgen E. , Jang Moon K. , Agbor-Enoh Sean
Published: July 2023

Reference methylomes, used in deconvolution algorithms to determine cell-free DNA tissue sources, were based on driver CpGs from either microarray or sequencing platforms. Cross-validation of these algorithms is important to allow interpretation of data across studies, select optimal sequencing depth, and thus reduce costs of cf-DNA deconvolution assays. Towards this end, we assessed the performance of two reference-based deconvolution algorithms: ‘cfDNAme’, sequencing-based methylome signatures, and ‘Meth-Atlas’, a microarray-based methylome signatures using a cfDNA bisulfite sequencing. While both algorithms use NNLS model, cfDNAme uses CpG windows, while Meth-Atlas uses individual CpGs as cell or tissue signatures. We determined the optimal the number of informative CpGs signatures, and the best sequencing depths for precise deconvolution. We found that above 5-fold coverage, much lower coverage than what is frequently used, there is little difference between our two chosen algorithms, both identifying the correct tissue make-up with a high accuracy, suggesting that whole genome bisulfite sequencing for tissue of origin identification can be completed in a much more cost-effective manner than previously thought.
Fitness Tradeoffs of Multidrug Efflux Pumps inEscherichia coliK-12 in Acid or Base, and with Aromatic Phytochemicals
Authors: Liu Yangyang , Van Horn Andrew M. , Pham Minh T. N. , Dinh Bao Ngoc N. , Chen Rachel , Raphael Slaybrina D. R. , Paulino Alejandro , Thaker Kavya , Somadder Aaryan , Menke Chelsea C. , Slimak Zachary C. , Slonczewski Joan L.
Published: July 2023

Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness tradeoffs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH is important as it contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-culturedEscherichia coliK-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with CCCP, or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical’s lipophilicity (logP). MdtEF-TolC and EmrAB-TolC each conferred a fitness cost at pH 5.5, but salicylate and benzoate conferred a net positive fitness contribution for the pump. Expression of pump genes was measured by digital PCR. Between pH 5.5 – 8.0,acrAandemrAwere upregulated in log phase, whereasmdtEexpression was upregulated in transition-to-stationary phase and at pH 5.5 in log phase. Methyl salicylate did not affect pump gene expression, despite selecting against AcrAB-TolC. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without positive section for others.

IMPORTANCE

For drugs that are administered orally, we need to understand how ingested phytochemicals modulate intrinsic drug resistance in our gut microbiome. Intrinsic drug resistance of bacteria is mediated by PMF-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring low-level resistance to antimicrobial agents at first exposure, while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH) which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
EGFR-to-Src family tyrosine kinase switching in proliferating-DTP TNBC cells creates a hyperphosphorylation-dependent vulnerability to EGFR TKI
Authors: Chaudhary Nazia , Choudhary Bhagya Shree , Shivashankar Anusha , Manna Subhakankha , Ved Khyati , Shaikh Shagufa , Khanna Sonal , Barr Jeetnet , Dani Jagruti , Verma Nandini
Published: July 2023

Triple-Negative Breast Cancer (TNBC) is the most aggressive type of breast malignancy, with chemotherapy as the only mainstay treatment. TNBC patients have the worst prognoses as a large fraction of them do not achieve complete pathological response post-treatment and develop drug-resistant residual disease. Molecular mechanisms that trigger proliferation in drug-resistant chemo-residual TNBC cells are poorly understood due to the lack of investigations using clinically relevant cellular models. In this study, we have established TNBC subtype-specific cellular models of proliferating drug-tolerant persister (PDTP) cells using different classes of chemotherapeutic agents that recapitulate clinical residual disease with molecular heterogeneity. Analysis of total phospho-tyrosine signals in TNBC PDTPs showed an enhanced phospho-tyrosine content compared to the parental cells (PC). Interestingly, using mass-spectrometry analysis, we identified a dramatic decrease in epidermal growth factor receptor (EGFR) expression in the PDTPs, while the presence of hyper-activated tyrosine phosphorylation of EGFR compared to PC. Further, we show that EGFR has enhanced lysosomal trafficking in PDTPs with a concomitant increase in N-Myc Downstream Regulated-1 expression that co-localizes with EGFR to mediate receptor degradation. More surprisingly, we found that reduced protein levels of EGFR are coupled with a robust increase in Src family kinases, including Lyn and Fyn kinases, that creates a hyper-phosphorylation state of EGFR-Src tyrosine kinases axis in PDTPs and mediates downstream over-activation of STAT3, AKT and MAP kinases. Moreover, paclitaxel-derived PDTPs show increased sensitivity to EGFR TKI Gefitinib and its combination with paclitaxel selectively induced cell death in PDTP-P TNBC cells and 3D spheroids by strongly downregulating phosphorylation of EGFR-Src with concomitant downregulation of Lyn and Fyn tyrosine kinases. Collectively, this study identifies a unique hyper-phosphorylation cellular state of TNBC PDTPs established by switching of EGFR–Src family tyrosine kinases creating a vulnerability to EGFR TKI.
The SWI/SNF nucleosome remodeler constrains enhancer activity duringDrosophilawing development
Authors: Niederhuber Matthew J. , Leatham-Jensen Mary , McKay Daniel J.
Published: July 2023

Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodeling complexes are known to work together to control access to enhancers, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions that are characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of ATP-dependent nucleosome remodeling complexes in the control of dynamic enhancer activity. We find that theDrosophilaBAP complex, a member of the SWI/SNF family of nucleosome remodelers, is required for repression of a temporally dynamic enhancer,brdisc. Contrary to expectations, we find that the BAP-specific subunit, Osa, is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels ofbrdiscactivity in imaginal wing discs when the enhancer is normally active. Genome-wide profiling reveals that Osa binds directly to thebrdiscenhancer as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. We find that Osa loss of function results in development of ectopic sensory structures that are normally patterned by Notch signaling early in wing development. Moreover, we find that Osa loss of function results in hyperactivation of theDeltagene, which encodes the Notch ligand. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.
Methods for making and observing model lipid droplets
Authors: Gandhi Sonali A. , Parveen Shahnaz , Alduhailan Munirah , Tripathi Ramesh , Junedi Nasser , Saqallah Mohammad , Sanders Matthew A. , Hoffmann Peter M. , Truex Katherine , Granneman James G. , Kelly Christopher V
Published: July 2023

The mechanisms by which the lipid droplet (LD) membrane is remodeled in concert with the activation of lipolysis incorporate a complex interplay of proteins, phospholipids, and neutral lipids. Model LDs (mLDs) provide an isolated, purified system for testing the mechanisms by which the droplet composition, size, shape, and tension affects triglyceride metabolism. Described here are methods of making and testing mLDs ranging from 0.1 to 40 µm diameter with known composition. Methods are described for imaging mLDs with high-resolution microscopy during buffer exchanges for the measurement of membrane binding, diffusion, and tension via fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), fluorescence lifetime imaging microscopy (FLIM), atomic force microscopy (AFM), pendant droplet tensiometry, and imaging flow cytometry. These complementary, cross-validating methods of measuring LD membrane behavior reveal the interplay of biophysical processes in triglyceride metabolism.
Partitioning variance in cortical morphometry into genetic, environmental, and subject-specific components
Authors: Smith Diana M. , Parekh Pravesh , Kennedy Joseph , Loughnan Robert , Frei Oleksandr , Nichols Thomas E. , Andreassen Ole A. , Jernigan Terry L. , Dale Anders M.
Published: July 2023

The relative contributions of genetic variation and experience in shaping the morphology of the adolescent brain are not fully understood. Using longitudinal data from 11,665 subjects in the ABCD Study®, we fit vertex-wise variance components including family effects, genetic effects, and subject-level effects using a computationally efficient framework. Variance in cortical thickness and surface area is largely attributable to genetic influence, whereas sulcal depth is primarily explained by subject-level effects. Our results identify areas with heterogeneous distributions of heritability estimates that have not been seen in previous work using data from cortical regions. We discuss the biological importance of subject-specific variance and its implications for environmental influences on cortical development and maturation.
Can food and temperature influence regional connectivity patterns of Bivalvia in fragmented archipelagos? Evidence from biophysical modeling applied to French Polynesia
Authors: Raapoto H. , Monaco C.J. , Van Wynsberge S. , Le Gendre R. , Le Luyer J.
Published: July 2023

Larval dispersal and connectivity are key processes that drive marine metapopulation dynamics, and therefore should be well characterized when designing effective management strategies. While temperature and food availability can structure marine species connectivity patterns, their relative contribution has not been thoroughly investigated in highly fragmented archipelagos. We used biophysical modeling of larval dispersal to explore the connectivity patterns of species with complex life-cycles across French Polynesia (FP), a territory formed by more than a hundred small, geographically isolated islands covering an area as large as Europe. We first simulated ten years of larval dispersal to investigate the spatial and temporal (seasonal and interannual) variability in larval dispersal pathways for different hypothetical species exhibiting a range of Larval Precompetency Period (LPP) values. Then, using the black-lip pearl oyster (Pinctada margaritifera) as a model species, we accounted for variability in the LPP induced by temperature and food availability, as derived from a Dynamic Energy Budget (DEB) model. The model showed that food availability and meso-scale turbulence (eddies) in the Marquesas jointly constrained larval dispersal, reducing its potential connectivity with other archipelagos in FP. However, accounting for food and temperature effects on larval development, barely changed the connectivity pattern at regional scale due to the remoteness of this archipelago. The DEB simulations further revealed seasonal and interannual variability in connectivity driven by environmental conditions. Our results highlight the importance of considering temperature and food in biophysical models to adequately capture dispersal, connectivity and to identify appropriate management units at the regional scale.
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
Authors: Byrne Ashley , Le Daniel , Sereti Kostianna , Menon Hari , Patel Neha , Lund Jessica , Xavier-Magalhaes Ana , Shi Minyi , Sterne-Weiler Timothy , Modrusan Zora , Stephenson William
Published: July 2023

Single-cell RNA sequencing predominantly employs short-read sequencing to characterize cell types, states and dynamics; however, it is inadequate for comprehensive characterization of RNA isoforms. Long-read sequencing technologies enable single-cell RNA isoform detection but are hampered by lower throughput and unintended sequencing of artifacts. Here we developed Single-cell Targeted Isoform Long-Read Sequencing (scTaILoR-seq), a hybridization capture method which targets over a thousand genes of interest, improving the median number of unique transcripts per cell by 29-fold. We used scTaILoR-seq to identify and quantify RNA isoforms from ovarian cancer cell lines and primary tumors, yielding 10,796 single-cell transcriptomes. Using long-read variant calling we revealed associations of expressed single nucleotide variants (SNVs) with alternative transcript structures. In addition, phasing of SNVs across transcripts facilitated measurement of allelic imbalance within distinct cell populations. Overall, scTaILoR-seq is a long-read targeted RNA sequencing method and analytical framework for exploring transcriptional variation at single-cell resolution.