bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictions for COVID-19 Outbreak in India using epidemiological models
Authors: Ranjan Rajesh
Published: April 2020

Abstract

COVID-19 data from India is compared against several countries as well as key states in the US with a major outbreak, and it is found that the basic reproduction number R0 for India is in the expected range of 1.4-3.9. Further, the rate of growth of infections in India is very close to that in Washington and California. Exponential and classic susceptible-infected-recovered (SIR) models based on available data are used to make short and long-term predictions on a daily basis. Based on the SIR model, it is estimated that India will enter equilibrium by the end of May 2020 with the final epidemic size of approximately 13,000. However, this estimation will be invalid if India enters the stage of community transmission. The impact of social distancing, again with the assumption of no community transmission, is also assessed by comparing data from different geographical locations.
A novel cohort analysis approach to determining the case fatality rate of COVID-19 and other infectious diseases
Authors: Narayanan Charit Samyak
Published: April 2020

As the Coronavirus contagion develops, it is increasingly important to understand the dynamics of the disease. Its severity is best described by two parameters: its ability to spread and its lethality. Here, we combine a mathematical model with a cohort analysis approach to determine the range of case fatality rates (CFR). We use a logistical function to describe the exponential growth and subsequent flattening of COVID-19 CFR that depends on three parameters: the final CFR (L), the CFR growth rate (k), and the onset-to-death interval (t0). Using the logistic model with specific parameters (L, k and t0), we calculate the number of deaths each day for each cohort. We build an objective function that minimizes the root mean square error between the actual and predicted values of cumulative deaths and run multiple simulations by altering the three parameters. Using all of these values, we find out which set of parameters returns the lowest error when compared to the number of actual deaths. We were able to predict the CFR much closer to reality at all stages of the viral outbreak compared to traditional methods. This model can be used far more effectively than current models to estimate the CFR during an outbreak, allowing for better planning. The model can also help us better understand the impact of individual interventions on the CFR. With much better data collection and labeling, we should be able to improve our predictive power even further.
Common Fronto-temporal Effective Connectivity in Humans and Monkeys
Authors: Rocchi Francesca , Oya Hiroyuki , Balezeau Fabien , Billig Alexander J. , Kocsis Zsuzsanna , Jenison Rick , Nourski Kirill V. , Kovach Christopher K. , Steinschneider Mitchell , Kikuchi Yukiko , Rhone Ariane E. , Dlouhy Brian J. , Kawasaki Hiroto , Adolphs Ralph , Greenlee Jeremy D.W. , Griffiths Timothy D. , Howard Matthew A. , Petkov Christopher I.
Published: April 2020

Cognitive pathways supporting human language and declarative memory are thought to have uniquely evolutionarily differentiated in our species. However, cross-species comparisons are missing on site-specific effective connectivity between regions important for cognition. We harnessed a new approach using functional imaging to visualize the impact of direct electrical brain stimulation in human neurosurgery patients. Applying the same approach with macaque monkeys, we found remarkably comparable patterns of effective connectivity between auditory cortex and ventro-lateral prefrontal cortex (vlPFC) and parahippocampal cortex in both species. Moreover, in humans electrical tractography revealed rapid evoked potentials in vlPFC from stimulating auditory cortex and speech sounds drove vlPFC, consistent with prior evidence in monkeys of direct projections from auditory cortex to vocalization responsive regions in vlPFC. The results identify a common effective connectivity signature that from auditory cortex is equally direct to vlPFC and indirect to the hippocampus (via parahippocampal cortex) in human and nonhuman primates.

Highlights

Privileged human auditory to inferior frontal connectivity, linked to monkeys

Common auditory to parahippocampal effective connectivity in both species

Greater lateralization in human effective connectivity, more symmetrical in monkeys

Human fronto-temporal network function rooted in evolutionarily conserved signature

eTOC short summary

Functional connectivity between regions crucial for language and declarative memory is thought to have substantially differentiated in humans. Using a new technique to similarly visualize directional effective connectivity in humans and monkeys, we found remarkably comparable connectivity patterns in both species between fronto-temporal regions crucial for cognition.
Spike timing in the attention network predicts behavioral outcome prior to target selection
Authors: Fiebelkorn Ian C. , Kastner Sabine
Published: April 2020

There has been little evidence linking changes in spiking activity that occur prior to a spatially predictable target (i.e., prior to target selection) to behavioral outcomes, despite such preparatory changes being widely assumed to enhance the sensitivity of sensory processing. We simultaneously recorded from frontal and parietal nodes of the attention network, while macaques performed a spatial-cueing task. When anticipating a spatially predictable target, different patterns of coupling between spike timing and oscillatory phase in local field potentials—but not changes in spike rate—were predictive of different behavioral outcomes. These behaviorally relevant differences in local and between-region synchronization occurred among specific cell types that were defined based on their sensory and motor properties, providing insight into the mechanisms underlying enhanced sensory processing prior to target selection. We propose that these changes in neural synchronization reflect differential, anticipatory engagement of the network nodes and functional units that shape attention-related sampling.
ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming
Authors: Li Fei , Yuan Qiuyue , Di Wei , Xia Xinyi , Liu Zhuang , Mao Ninghui , Li Lin , Li Chunfeng , He Juan , Li Yunguang , Guo Wangxin , Zhang Xiaoyu , Zhu Yiqin , Aji Rebiguli , Wang Shangqian , Chi Ping , Carver Brett , Wang Yong , Chen Yu , Gao Dong
Published: April 2020

While cancer is commonly perceived as a disease of dedifferentiation, the hallmark of early stage prostate cancer is paradoxically the loss of more plastic basal cells and the abnormal proliferation of more differentiated secretory luminal cells. However, the mechanism of prostate cancer pro-luminal differentiation is largely unknown. Through integrating analysis of the transcription factors (TFs) from 806 human prostate cancers, we have identified that ERG highly correlated with prostate cancer luminal subtyping. ERG overexpression in luminal epithelial cells inhibits its normal plasticity to transdifferentiate into basal lineage and ERG supersedes PTEN-loss which favors basal differentiation. ERG knock-out disrupted prostate cell luminal differentiation, whereas AR knock-out had no such effects. Trp63 is a known master regulator of prostate basal lineage. Through analysis of 3D chromatin architecture, we found that ERG binds and inhibits the enhancer activity and chromatin looping of a Trp63 distal enhancer, thereby silencing its gene expression. Specific deletion of the distal ERG binding site resulted in the loss of ERG-mediated inhibition of basal differentiation. Thus, ERG orchestrates chromatin interactions and regulates prostate cell lineage toward pro-luminal program, as its fundamental role on lineage differentiation in prostate cancer initiation.
Bats are key hosts in the radiation of mammal-associated Bartonella bacteria
Authors: McKee Clifton D. , Bai Ying , Webb Colleen T. , Kosoy Michael Y.
Published: April 2020

Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized lineages and 121 new cultured strains from bats, and used these data to perform the most comprehensive phylogenetic analysis of Bartonella to date. This analysis included estimation of divergence dates using a molecular clock and ancestral reconstruction of host associations and geography. We estimate that Bartonella began infecting mammals 62 million years ago near the Cretaceous-Paleogene boundary. Additionally, the radiation of particular Bartonella clades correlate strongly to the timing of diversification and biogeography of mammalian hosts. Bats were inferred to be the ancestral hosts of all mammal-associated Bartonella and appear to be responsible for the early geographic expansion of the genus. We conclude that bats have had a deep influence on the evolutionary radiation of Bartonella bacteria and their spread to other mammalian orders. These results support a ‘bat seeding’ hypothesis that could explain similar evolutionary patterns in other mammalian parasite taxa. Application of such phylogenetic tools as we have used to other taxa may reveal the general importance of bats in the ancient diversification of mammalian parasites.

Significance statement

Discovering the evolutionary history of infectious agents in animals is important for understanding the process of host adaptation and the origins of human diseases. To clarify the evolution of the Bartonella genus, which contains important human pathogens, we performed phylogenetic analysis on a broad diversity of Bartonella strains, including novel strains from bats. Our results indicate that Bartonella clades diversified along with their mammal hosts over millions of years. Bats appear to be especially important in the early radiation and geographic dispersal of Bartonella lineages. These patterns are consistent with research indicating a chiropteran origin of important human viruses and eukaryotic parasites, suggesting that bats may play a unique role as historical sources of infections to other hosts.
Genetic basis of a spontaneous mutation’s expressivity
Authors: Schell Rachel , Hale Joseph J. , Mullis Martin N. , Matsui Takeshi , Foree Ryan , Ehrenreich Ian M.
Published: April 2020

Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal geneMRP20. Initial results suggested that a single large effect locus influences the mutation’s expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutation’s expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.
Comparative genomics identified a genetic locus in plant-associatedPseudomonasspp. that is necessary for induced systemic susceptibility
Authors: Beskrovnaya Polina , Melnyk Ryan A. , Liu Zhexian , Liu Yang , Higgins Melanie A. , Song Yi , Ryan Katherine , Haney Cara H.
Published: April 2020

The author has withdrawn this manuscript as it is a revision of a previously posted manuscript 517870. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two European cohort studies
Authors: Carmeli Cristian , Kutalik Zoltán , Mishra Pashupati P. , Porcu Eleonora , Delpierre Cyrille , Delaneau Olivier , Kelly-Irving Michelle , Bochud Murielle , Dhayat Nasser A. , Ponte Belen , Pruijm Menno , Ehret Georg , Kähönen Mika , Lehtimäki Terho , Raitakari Olli T. , Vineis Paolo , Kivimäki Mika , Chadeau-Hyam Marc , Dermitzakis Emmanouil , Vuilleumier Nicolas , Stringhini Silvia
Published: April 2020

Individuals growing up during childhood in a socioeconomically disadvantaged family experience a higher rate of inflammation-related diseases later in life. Little is known about the mechanisms linking early life experiences to the functioning of the immune system decades later. Here we explore the relationship across social-to-biological layers of early life social exposures on levels of adulthood inflammation (C-reactive protein) and the mediating role of gene regulatory mechanisms, epigenetic and transcriptomic profiling from blood, in 2,329 individuals from two European cohort studies. Consistently across both studies, we find transcriptional activity explains a substantive proportion (up to 78%) of the estimated effect of early life disadvantaged social exposures on levels of adulthood inflammation. Furthermore, we show that mechanisms other than DNA methylation potentially regulate those transcriptional fingerprints. These results further our understanding of social-to-biological transitions by pinpointing the role of pro-inflammatory genes regulation that cannot fully be explained by differential DNA methylation.
Separate Fever Clinics Prevent the Spread of COVID-19 and Offload Emergency Resources: Analysis from a large tertiary hospital in China
Authors: Wang Jiangshan , Zong Liang , Zhang Jinghong , Sun Han , Walline Joseph Harold , Sun Pengxia , Xu Shengyong , Li Yan , Wang Chunting , Liu Jihai , Li Fan , Xu Jun , Li Yi , Yu Xuezhong , Zhu Huadong
Published: April 2020

Objectives

COVID-19 began spreading widely in China in January 2020. Outpatient “Fever Clinics” (FCs), instituted during the SARS epidemic in 2003 were upgraded to provide COVID-19 screening and prevention attached to large tertiary hospitals. We sought to analyze the effect of upgraded FCs to detecting COVID-19 at our institution.

Design

A population-based cross-sectional study.

Participants

A total of 6,365 patients were screened in the FC.

Methods

The FC of Peking Union Medical College Hospital (PUMCH) was upgraded on January 20, 2020. We performed a retrospective study of patients presenting to the FC between December 12, 2019 to February 29, 2020, covering a period of 40 days before and after upgrading the FC. All necessary data, including baseline patient information, diagnoses, follow-up conditions for critical patients, transfer information between the FC and emergency department (ED) were collected and analyzed.

Results

6,365 patients were screened in the FC, among whom 2,192 patients were screened before January 21, 2020, while 3,453 were screened afterwards. Screening results showed that upper respiratory infection was the major disease associated with fever. Compared to before the outbreak, patients transferred from the FC to ED decreased significantly [39.21% vs 15.75%, p<0.001] and tended to spend more time in the FC [55 vs 203mins, p<0.001]. For critically-ill patients waiting for a screening result, the total length of stay in the FC was 22mins before the outbreak, compared to 442mins after the outbreak (p< 0.001). The number of in-hospital deaths of critical-care patients seen first in the FC was 9 of 29 patients before the outbreak and 21 of 38 after (p<0.050). Nineteen COVID-19 cases were confirmed in the FC, but no other patients or medical care providers were cross-infected.

Conclusion

The work-load of the FC increased after the COVID-19 outbreak and effectively prevented COVID-19 from spreading in the hospital,as well as offload ED resources.
Pressure-Regulated Ventilator Splitting (PReVentS) – A COVID-19 Response Paradigm from Yale University
Authors: Brickman Raredon Micha Sam , Fisher Clark , Heerdt Paul , Deshpande Ranjit , Nivison Steven , Fajardo Elaine , Akhtar Shamsuddin , Raredon Thomas , Niklason Laura
Published: April 2020

In the current COVID-19 crisis, the US and many countries in the world are suffering acute shortages of modern ventilators to care for desperately ill patients. Since modern ICU ventilators are powerful devices that can deliver very high gas flow rates and pressures, multiple physicians have attempted to ventilate more than one patient on a single ventilator – so-called “vent splitting”. Early applications of this approach have utilized simple concatenations of ventilator tubing and T-pieces, to provide flow to more than one patient. Additional approaches using custom flow splitters – sometimes made using 3D printing technologies – have also advanced into the clinic with FDA approval. However, heretofore there has been less progress made on controlling individual ventilatory pressures for patients with severe lung disease. Given the inherent variability and instability of lung compliance amongst patients with COVID-19, there remains an important need to provide a means of extending ventilator usefulness to more than one patient, but in a way that provides more tailored pressures that can be titrated over time. In this descriptive report, we provide the basis for a ventilator circuit that can support two patients with individualized peak inspiratory and end-expiratory pressures. The circuit is comprised of exclusively “off the shelf” materials and is inexpensive to produce. The circuit can be used with typical ICU ventilators, and with anesthesia ventilators used in operating rooms. Inspiratory and end-expiratory pressures for each patient can be titrated over time, without changes for one patient affecting the ventilation parameters of the other patient. Using in-line spirometry, individual tidal volumes can be measured for each patient. This Pressure-Regulated Ventilator Splitting (PReVentS) Yale University protocol operates under a pressure-control ventilatory mode, and may function optimally when patients are not triggering breaths from the ventilator.

This method has been tested thus far only in the laboratory with mock lungs, and has not yet been deployed in animals or in patients. However, given the novelty and potential utility of this approach, we deemed it appropriate to provide this information to the broader critical care community at the present time. In coming days and weeks, we will continue to characterize and refine this approach, using large animal models and proof-of-principle human studies.
Peripheral Zone Enlargement: a newly described entity on MRI
Authors: Wasserman Neil F. , Murguan Paari , Spilseth Ben , Metzger Gregory J. , Sanghvi Tina
Published: April 2020

Purpose

A retrospective study was performed to describe and characterize a previously unreported finding on T2-weighted magnetic resonance imaging (MRI) of peripheral zone enlargement (PZE) associated with total prostatic enlargement without necessary association with benign prostatic hyperplasia (BPH) or lower urinary tract symptoms.

Methods

T2-weighted MRI were reviewed from 2012-2018. Patients were referred for elevated serum prostatic specific antigen (PSA) levels, prostatic enlargement, or abnormal digital rectal examination (DRE) suggestive of adenocarcinoma. Enlargement of the thickness of the peripheral zone (PZ) was defined as a measurement of postero-lateral thickness (PLPZ) of ≥ 15.8 mm in the maximal transaxial plane. Endorectal coils were used in 2 patients. Microscopic pathology was described in 3 patients.

Results

There were 22 patients who met the criteria out of 2871 subjects (<1%). Mean age was 63 years, Mean PLPZ was 17.7 mm (CI=0.45, range, 15.8-21.3). mean total prostatic volume was 55.1 cc (range, 19.9-127.2 cc), mean transition zone volume was 20.6 cc (range, 2.7-71.9 cc), mean transition zone index (TZI) was 0.34 (range, 0.31-0.68), mean prostatic specific antigen (PSA) was 13.9 ng/mL (range, 0.28-144.7), mean body mass index was 28.9 (range 23.0-36.3).. Enlargement was described in 14 of 20 (70%). Pathological findings showed marked glandular distention and atrophy with interstitial edema and chronic inflammatory cells. Significance of these results is discussed.
Maternal Continuous Oral Oxycodone Self-Administration Alters Pup Affective/Social Communication but not Spatial Learning or Sensory-Motor Function
Authors: Zanni Giulia , Robinson-Drummer Patrese A. , Dougher Ashlee A. , Deutsch Hannah M. , DeSalle Matthew J. , Teplitsky David , Vemulapalli Aishwarya , Sullivan Regina M. , Eisch Amelia J. , Barr Gordon A.
Published: April 2020

The broad use and misuse of prescription opioids during pregnancy has resulted in a surge of infants diagnosed with Neonatal Opioid Withdrawal Syndrome (NOWS). Short-term irritability and neurological complications are hallmarks of NOWS, but the long-term consequences are unknown. Our newly-developed preclinical model of oxycodone self-administration enables adult female rats to readily drink oxycodone (0.06-0.12 mg/ml, ∼10/mg/kg/day) continuously before and during pregnancy and after delivery, to achieve similar liquid intake in oxycodone moms relative to water-only controls. Oxycodone levels were detected in the serum of mothers and pups. Growth parameters in dams and pups, and litter mass and size were similar to controls. Maternal behavior at postnatal day 1 (PN1) was unchanged by perinatal oxycodone consumption. Regarding the plantar thermal response, there were no differences in paw retraction latency between oxycodone and control pups at PN2 or PN14. Oxycodone and control pups had similar motor coordination, cliff avoidance, righting time, pivoting, and olfactory spatial learning from PN3 through PN13. Separation-induced ultrasonic vocalizations at PN8 revealed higher call frequency in oxycodone pups relative to controls. Finally, during naltrexone precipitated withdrawal at PN9, oxycodone males vocalized more than control pups, consistent with a previously-published withdrawal phenotype. Thus, our rat model of continuous oral oxycodone self-administration in pregnancy shows exacerbated affect/social communication in pups in a sex-dependent manner but spared cognition and locomotion. Our preclinical, high face validity NOWS model reproduces key aspects of human opioid use during pregnancy, enabling longitudinal analysis of how maternal oxycodone changes emotional behavior in the offspring.

HIGHLIGHTS

Female rats self-administered oxycodone at clinically relevant doses before and during pregnancy and for the first two weeks after parturition.

Both dams and pups, for the14 day postnatal experimental period, had detectable levels of oxycodone in their blood

Dams drinking oxycodone only or water only did not differ in weight gain, water intake, or the number of pups born and their pups did not differ in weight throughout.

Sensory and motor function in the pups was not altered, nor was hippocampal dependent spatial learning.

Oxycodone exposed pups were physically dependent and displayed increased withdrawal behaviors with or without the opioid antagonist naltrexone.

Pups expressed more negative affect, expressed by increased ultrasonic vocalizations, following naltrexone precipitated withdrawal or when separated from their mother.
ZNF423patient variants, truncations, and in-frame deletions in mice define an allele-dependent range of midline brain abnormalities
Authors: Deshpande Ojas , Lara Raquel Z. , Zhang Oliver R. , Concepcion Dorothy , Hamilton Bruce A.
Published: April 2020

Interpreting rare variants remains a challenge in personal genomics, especially for disorders with several causal genes and for genes that cause multiple disorders.ZNF423encodes a transcriptional regulatory protein that intersects several developmental pathways.ZNF423has been implicated in rare neurodevelopmental disorders, consistent with midline brain defects inZfp423-mutant mice, but pathogenic potential of most patient variants remains uncertain. We engineered ~50 patient-derived and small deletion variants into the highly-conserved mouse ortholog and examined neuroanatomical measures for 791 littermate pairs. Three substitutions previously asserted pathogenic appeared benign, while a fourth was effectively null. Heterozygous premature termination codon (PTC) variants showed mild haploabnormality, consistent with loss-of-function intolerance inferred from human population data. In-frame deletions of specific zinc fingers showed mild to moderate abnormalities, as did low-expression variants. These results affirm the need for functional validation of rare variants in biological context and demonstrate cost-effective modeling of neuroanatomical abnormalities in mice.

AUTHOR SUMMARY

Gene identification in rare disorders is typically supported by finding different mutations of the same gene in multiple families with the same disorder. However, causal evidence for any specific mutation found in one or a few related individuals is weaker, especially if the disorder can be caused by any of several genes and the functional effect of the mutation is not certain. Experimental models can be helpful in testing causal effects, but only to the extent that the model is validated to recapitulate one or more aspects of the disorder. We used CRISPR/Cas9-based genome engineering to create a wide range of mutations in mouseZfp423, whose human cognate is implicated in neurodevelopmental disorders, especially cerebellar vermis hypoplasia and Joubert syndrome. This large collection of animal models shows that both reducedZfp423expression, including heterozygosity for loss-of-function mutations, and normally-expressed domain deletions, including specific zinc finger domains, produce measureable abnormalities in midline development. Despite this high level of validation, most patient-derived amino acid substitution variants tested do not produce measureable effects. The single exception is a substitution, H1277Y, that destroys a structural element in the last zinc finger domain and results in dramatic loss of steady-state Zfp423 protein level.
Behavioral thermal tolerance predicts distribution pattern but not habitat use in sympatric Neotropical frogs
Authors: Diaz-Ricaurte Juan C. , Serrano Filipe C. , Guevara-Molina Estefany Caroline , Araujo Cybele , Martins Marcio
Published: April 2020

Environmental temperatures are a major constraint on ectotherm abundance and diversity, influencing their distribution and natural history. Comparing thermal tolerances with environmental temperatures is a simple way to estimate thermal constraints on species distributions. We investigate the potential effects of thermal tolerance on anuran local (habitat) and global distribution patterns and associated behavioral responses. We tested for differences in Voluntary Thermal Maximum of two sympatric frog species of the genusPhysalaemusin the Cerrado ecoregion. For each species, we constructed models to assess the effects of period of day, duration of experiment, initial body mass, initial body temperature and heating rate on the VTMax. We mapped the difference between VTMaxand maximum daily temperature (VTMax- ETMax) for each occurrence point.Physalaemus nattererihad a significantly higher VTMaxthanP. cuvieri. ForP. nattereri, the model including only period of day was chosen as the best to explain variation in the VTMax. ForP. cuvieri, no model was selected as best to predict VTMax. The VTMax- ETMaxvalues were significantly different between species, withP. nattererimostly found in localities that attain maximum temperatures lower than its VTMaxandP. cuvierishowing the reverse pattern. Regarding habitat use, we foundP. cuvierito be slightly more abundant in open habitats than in non-open habitats, whereasP. nattererishows the reverse pattern. The difference in VTMaxvalues between these two species might be related to their different body sizes, but additionally might reflect their natural history, especially the way they use their habitats, and phylogenetic constraints (the species studied are in different clades withinPhysalaemus). Our study indicates that differences in behavioral thermal tolerance may be important in shaping local and regional distribution patterns. Furthermore, small-scale habitat use might reveal a link between behavioral thermal tolerance and natural history strategies.
A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins
Authors: Zuzic Lorena , Marzinek Jan K , Warwicker Jim , Bond Peter J
Published: April 2020

Molecular dynamics (MD) simulations in combination with small organic probes present in the solvent have previously been used as a method to reveal cryptic pockets that may not have been identified in experimental structures. We report such a method implemented within the CHARMM forcefield to effectively explore cryptic pockets on the surfaces of membrane-embedded proteins using benzene as a probe molecule. This relies on modified non-bonded parameters in addition to repulsive potentials between membrane lipids and benzene molecules. The method was tested on part of the outer shell of the dengue virus (DENV), for which research into a safe and effective neutralizing antibody or drug molecule is still ongoing. In particular, the envelope (E) protein, associated with the membrane (M) protein, is a lipid membrane-embedded complex which forms a dimer in the mature viral envelope. Solvent mapping was performed for the full, membrane-embedded EM protein complex and compared with similar calculations performed for the isolated, soluble E protein ectodomain dimer in solvent. Ectodomain-only simulations with benzene exhibited unfolding effects not observed in the more physiologically relevant membrane-associated systems. A cryptic pocket which has been experimentally shown to bindn-octyl-β-D-glucoside detergent was consistently revealed in all benzene-containing simulations. The addition of benzene also enhanced the flexibility and hydrophobic exposure of cryptic pockets at a key, functional interface in the E protein, and revealed a novel, potentially druggable pocket that may be targeted to prevent conformational changes associated with viral entry into the cell.

GRAPHICAL ABSTRACT
OptiFlex: video-based animal pose estimation using deep learning enhanced by optical flow
Authors: Liu XiaoLe , Yu Si-yang , Flierman Nico , Loyola Sebastian , Kamermans Maarten , Hoogland Tycho M. , De Zeeuw Chris I.
Published: April 2020

Deep learning based animal pose estimation tools have greatly improved animal behaviour quantification. However, those tools all make predictions on individual video frames and do not account for variability of animal body shape in their model designs. Here, we introduce the first video-based animal pose estimation architecture, referred to as OptiFlex, which integrates a flexible base model to account for variability in animal body shape with an optical flow model to incorporate temporal context from nearby video frames. This approach can be combined with multi-view information, generating prediction enhancement using all four dimensions (3D space and time). To evaluate OptiFlex, we adopted datasets of four different lab animal species (mouse, fruit fly, zebrafish, and monkey) and proposed a more intuitive evaluation metric - percentage of correct key points (aPCK). Our evaluations show that OptiFlex provides the best prediction accuracy amongst current deep learning based tools, and that it can be readily applied to analyse a wide range of behaviours.
Glycogen synthase kinase 3 alpha/beta deletion induces precocious growth plate remodeling and cell loss in mice
Authors: Bali Supinder Kour , Bryce Dawn , Prein Carina , Woodgett James R. , Beier Frank
Published: April 2020

Glycogen synthase kinase (GSK) 3 acts to negatively regulate multiple signaling pathways, including canonical Wnt signaling. The two mammalian GSK3 proteins (alpha and beta) are at least partially redundant. WhileGsk3aKO mice are viable and display a metabolic phenotype, abnormal neuronal development and accelerated aging,Gsk3bKO animals die late in embryogenesis or at birth. SelectiveGsk3bKO in bone delayed development of some bones, whereas cartilage-specificGsk3bKO mice are normal except for elevated levels of GSK3alpha protein. However, the collective role of these two GSK3 proteins in cartilage was not evaluated. To address this, we generated tamoxifen-inducible, cartilage-specificGsk3a/Gsk3bKO in juvenile mice and investigated their skeletal phenotypes. We found that cartilage-specificGsk3a/Gsk3bdeletion in young, skeletally immature mice causes precocious growth plate remodeling, culminating in shorter long bones and hence, growth retardation. These mice exhibit inefficient breathing patterns at later stages and fail to survive. The disrupted growth plates in KO mice showed progressive loss of cellular and proteoglycan components and Sox9 positive cells, with increased staining for osteocalcin and type II collagen. In addition, an increase in osteoclast recruitment and cell apoptosis was observed in growth plates. Surprisingly, changes in articular cartilage ofGsk3a/Gsk3bKO mice were mild compared to growth plates, signifying differential regulation of articular cartilage vs growth plate tissues. Taken together, these findings emphasize a crucial role of two GSK3 proteins in skeletal development, in particular in the maintenance and function of growth plates.

Significance

Growth plate cartilage dynamics determine the rate of endochondral bone growth and thus, our final height. These processes are disturbed in many genetic and acquired diseases, but the intracellular mechanisms responsible for normal growth plate function, as well as the cessation of growth plate activity in puberty, are poorly understood. Here, we demonstrate that specific removal of both GSK3 genes (Gsk3aandGsk3b) in postnatal cartilage of mice leads to a severe reduction of endochondral bone growth, premature remodelling of the growth plate, and early death. In contrast, articular cartilage is only mildly affected by deletion of both genes. These studies identify GSK3 signaling as a key regulator of growth plate dynamics and endochondral bone growth.
Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Authors: Auslander Noam , Gussow Ayal B. , Benler Sean , Wolf Yuri I. , Koonin Eugene V.
Published: April 2020

Advances in metagenomics enable massive discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. The existing methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct bacteriophage families. We present Seeker, a deep-learning tool for reference-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and clean differentiation of phage sequences from bacterial ones, even for phages with little sequence similarity to established phage families. We comprehensively validate Seeker’s ability to identify unknown phages and employ Seeker to detect unknown phages, some of which are highly divergent from known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly python package (https://github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.
Molecular characterization of selectively vulnerable neurons in Alzheimer’s Disease
Authors: Leng Kun , Li Emmy , Eser Rana , Piergies Antonia , Sit Rene , Tan Michelle , Neff Norma , Li Song Hua , Rodriguez Roberta Diehl , Suemoto Claudia Kimie , Paraizo Leite Renata Elaine , Pasqualucci Carlos A. , Seeley William W. , Spina Salvatore , Heinsen Helmut , Grinberg Lea T. , Kampmann Martin
Published: April 2020

Alzheimer’s disease (AD) is characterized by the selective vulnerability of specific neuronal populations, the molecular signatures of which are largely unknown. To identify and characterize selectively vulnerable neuronal populations, we used single-nucleus RNA sequencing to profile the caudal entorhinal cortex and the superior frontal gyrus – brain regions where neurofibrillary inclusions and neuronal loss occur early and late in AD, respectively – from postmortem brains spanning the progression of AD-type tau neurofibrillary pathology. We identified RORB as a marker of selectively vulnerable excitatory neurons in the entorhinal cortex, and subsequently validated their depletion and selective susceptibility to neurofibrillary inclusions during disease progression using quantitative neuropathological methods. We also discovered an astrocyte subpopulation, likely representing reactive astrocytes, characterized by decreased expression of genes involved in homeostatic functions. Our characterization of selectively vulnerable neurons in AD paves the way for future mechanistic studies of selective vulnerability and potential therapeutic strategies for enhancing neuronal resilience.
Antibiotics shift the temperature response curve ofEscherichia coligrowth
Authors: Cruz-Loya Mauricio , Tekin Elif , Kang Tina Manzhu , Rodriguez-Verdugo Alejandra , Savage Van M. , Yeh Pamela J.
Published: April 2020

Temperature variation—through time and across climatic gradients—affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here we quantify two key features—optimal temperature and temperature breadth—to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth ofEscherichia coliunder single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes.
Signaling mechanism of phytochromes in solution
Authors: Isaksson Linnéa , Gustavsson Emil , Persson Cecilia , Brath Ulrika , Vrhovac Lidija , Karlsson Göran , Orekhov Vladislav , Westenhoff Sebastian
Published: April 2020

Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. The proteins change their structure in response to light, thereby altering their biochemical activity. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the helical spine and a figure-of-eight knot, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module fromD. radiodurans(DrBphP). Photoswitching between the resting and active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The new pathway underpins functional studies of plant phytochromes and may explain photo-sensing by phytochromes under biological conditions.
Quantifying relative virulence: When μmaxfails and AUC alone just isn’t enough
Authors: Ceballos Ruben Michael , Stacy Carson Len
Published: April 2020

Abstract

One of the more challenging aspects in quantitative virology is quantifying relative virulence between two (or more) viruses that have different replication dynamics in a given susceptible host. Host growth curve analysis is often used to detail virus-host interactions and to determine the impact of viral infection on a host. Quantifying relative virulence using canonical parameters such as maximum specific growth rate (μmax) can fail to provide accurate information regarding experimental infection, especially for non-lytic viruses. Although area-under-the-curve (AUC) can be more robust by through calculation of a percent inhibition (PIAUC), this metric can be sensitive to limit selection. In this study, using empirical and extrapolated data from Sulfolobus Spindle-shaped Virus (SSV) infections, we introduce a novel, simple metric that is proven to be more robust and less sensitive than traditional measures for determining relative virulence. This metric (ISC) more accurately aligns biological phenomena with quantified metrics from growth curve analysis to determine trends in relative virulence. It also addresses a major gap in virology by allowing comparisons between non-lytic single-virus/single-host (SVSH) infections and between non-lytic versus lytic virus infection on a given host. HowISCmay be applied to polymicrobial infection – both coinfection of a host culture and superinfection of a single cell with more than one virus (or other pathogen type) is a topic of ongoing investigation.
Detection of Static, Dynamic, and No Tactile Friction Based on Non-linear dynamics of EEG Signals: A Preliminary Study
Authors: Baghdadi Golnaz , Amiri Mahmood
Published: April 2020

Touching an object leads to a frictional interaction between the skin and the object. There are two kinds of friction: the first contact that leads to static friction and the dragging phase that leads to dynamic friction. No study has been performed to show the effect of friction type on EEG signals. The main goal of the current study is to investigate the effect of tactile friction on non-linear features of EEG signals.

Participants performed a tactile task that each of its trials had three states: the sensation of 1) static friction, 2) dynamic friction, and 3) no friction. During the experiment, EEG signals were recorded, and different linear and non-linear EEG indices were extracted and analyzed to find the effect of the tactile friction on EEG signals.

Linear features such as spectral features were not a good choice to distinguish between the states. However, non-linear features such as Lyapunov exponent, Higuchi’s dimension, and Hurst exponent had the potential to separate the mentioned states. Results also showed signs of predictability (negative Lyapunov exponent) in the signals recorded during dynamic friction and the existence of long-range dependency (memory) in EEG signals recorded during all states. The complexity of the tactile system in Theta band was also higher than the Delta band. The results of this research not only increase our knowledge about brain non-linear dynamics in response to tactile friction but also lead to a design of a preliminary system that can automatically detect friction between the skin and surfaces.
Neural computation underlying rapid learning and dynamic memory recall for sensori-motor control in insects
Authors: Rapp Hannes , Nawrot Martin Paul
Published: April 2020

Foraging is a vital behavioral task for living organisms. Behavioral strategies and abstract mathematical models thereof have been described in detail for various species. To explore the link between underlying nervous systems and abstract computational principles we present how a biologically detailed neural circuit model of the insect mushroom body implements sensory processing, learning and motor control. We focus on cast & surge strategies employed by flying insects when foraging within turbulent odor plumes. Using a synaptic plasticity rule the model rapidly learns to associate individual olfactory sensory cues paired with food in a classical conditioning paradigm. Without retraining, the system dynamically recalls memories to detect relevant cues in complex sensory scenes. Accumulation of this sensory evidence on short timescales generates cast & surge motor commands. Our systems approach is generic and predicts that population sparseness facilitates learning, while temporal sparseness is required for dynamic memory recall and precise behavioral control.
Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle
Authors: Chakraborty Anindita , Ko Chunkyu , Henning Christin , Lucko Aaron , Zhuang Xiaodong , Wettengel Jochen M. , Protzer Ulrike , McKeating Jane A
Published: April 2020

Hepatitis B virus (HBV) is an enveloped DNA virus that contains a partially double-stranded relaxed circular (rc) DNA. Upon infection, rcDNA is delivered to the nucleus where it is repaired to covalently closed circular (ccc) DNA that serves as the transcription template for all viral RNAs. Our understanding of HBV particle entry dynamics and host pathways regulating intracellular virus trafficking and cccDNA formation is limited. The discovery of sodium taurocholate co-transporting peptide (NTCP) as the primary receptor allows studies on these early steps in viral life cycle. We employed a synchronized infection protocol to quantify HBV entry kinetics. HBV attachment to cells at 4°C is independent of NTCP, however, subsequent particle uptake is NTCP-dependent and reaches saturation at 12h post-infection. HBV uptake is clathrin- and dynamin dependent with actin and tubulin playing a role in the first 6h of infection. Cellular fractionation studies demonstrate HBV DNA in the nucleus within 6h of infection and cccDNA was first detected at 24h post-infection. Our studies show the majority (83%) of cell bound particles enter HepG2-NTCP cells, however, only a minority (<1%) of intracellular rcDNA was converted to cccDNA, highlighting this as a rate-limiting in establishing infectionin vitro. This knowledge highlights the deficiencies in ourin vitrocell culture systems and will inform the design and evaluation of physiologically relevant models that support efficient HBV replication.
APenicillium rubensplatform strain for secondary metabolite production
Authors: Pohl Carsten , Polli Fabiola , Schütze Tabea , Viggiano Annarita , Mózsik László , Jung Sascha , de Vries Maaike , Bovenberg Roel A.L. , Meyer Vera , Driessen Arnold J.M.
Published: April 2020

We present aPenicillium rubensstrain with an industrial background in which the four highly expressed biosynthetic gene clusters (BGC) required to produce penicillin, roquefortine, chrysogine and fungisporin were removed. This resulted in a minimal secondary metabolite background. Amino acid pools under steady-state growth conditions showed reduced levels of methionine and increased intracellular aromatic amino acids. Expression profiling of remaining BGC core genes and untargeted mass spectrometry did not identify products from uncharacterized BGCs. This platform strain was repurposed for expression of the recently identified polyketide calbistrin gene cluster and achieved high yields of decumbenone A, B and C. The penicillin BGC could be restored throughin vivoassembly with eight DNA segments with short overlaps. Our study paves the way for fast combinatorial assembly and expression of biosynthetic pathways in a fungal strain with low endogenous secondary metabolite burden.