bluuebunny/crossref_metadata_2025 huggingface dataset:
INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
Authors: Wu Qianxin , Suo Chenqu , Brown Tom , Wang Tengyao , Teichmann Sarah A. , Bassett Andrew R.
Published: June 2020

We present INSIGHT (Isothermal NASBA-Sequencing-based hIGH-througput Test): a two-stage COVID-19 testing strategy, using a barcoded isothermal NASBA reaction that combines point-of-care diagnosis with next generation sequencing, aiming to achieve population-scale COVID-19 testing. INSIGHT combines the advantages of near-patient with centralised testing. Stage 1 allows a quick decentralised readout for early isolation of pre-symptomatic or asymptomatic patients. The same reaction products can then be used in a highly multiplexed sequencing-based assay in Stage 2, confirming the near-patient testing results and facilitating centralised data collection. Based on experiments using commercially acquired human saliva with spiked-in viral RNA as input, the INSIGHT platform gives Stage 1 results within one to two hours, using either fluorescence detection or a lateral flow (dipstick) readout, whilst simultaneously incorporating sample-specific barcodes into the amplification product. INSIGHT Stage 2 can be performed by directly pooling and sequencing all post-amplification barcoded Stage 1 products from hundreds of thousands of samples with minimal sample preparation steps. The 95% limit of detection (LoD-95) for INSIGHT is estimated to be below 50 copies of viral RNA per 20 μl of reaction. Our two-stage testing strategy is suitable for further development into a rapid home-based and point-of-care assay, and is potentially scalable to the population level.
Fluorogenic DNase Sensor Reveals Ubiquitous DNase Activity in Podosomes and Invadopodia
Authors: Pal Kaushik , Zhao Yuanchang , Wang Yongliang , Wang Xuefeng
Published: June 2020

Podosomes and invadopodia, collectively termed invadosomes, are important adhesive and degradative units formed in macrophages, osteoclasts, dendritic cells, cancer cells, and many other cell types. Invadosomes are well known for recruiting proteases that degrade matrix proteins and facilitate cell invasion. In contrast to the extensively studied proteases, another important class of degradative enzymes, DNase, remains uninvestigated and in fact, unknown in invadosomes. Using surface nuclease sensor (SNS), which reports deoxyribonuclease (DNase) activity on the cell membrane by fluorescence signal, we revealed that invadosomes, regardless of cell types or species, universally recruit DNase and readily degrade extracellular double-stranded DNA (dsDNA). We identified the recruited DNase as GPI-anchored membrane protein DNase X which functions locally at the cell-substrate interface and is co-localized with the actin cores of the invadosomes. DNase recruitment is highly consistent and rapid in invadosomes. Co-imaging of F-actin and DNase activity shows that 46-86% invadosomes (dependent on cell types) have associated DNase activities. Time series imaging shows that DNase becomes active within a minute after the actin nucleation, functioning concomitantly with protease activity in podosomes but preceding it in invadopodia. Overall, this discovery suggests a richer arsenal of degradative enzymes in invadosomes at the cell-substrate interface. This work would likely prompt more studies to investigate DNase in invadosomes, in particular, to understand the physiological role of invadosome-associated membrane DNase in cell functions such as immune response, cell migration, matrix remodeling, etc.
Strategic and non-strategic semantic expectations hierarchically modulate neural processing
Authors: Vidal-Gran Consuelo , Sokoliuk Rodika , Bowman Howard , Cruse Damian
Published: June 2020

Perception is facilitated by a hierarchy of expectations generated from context and prior knowledge. In auditory processing, violations of local (within-trial) expectations elicit a mismatch negativity, while violations of global (across-trial) expectations elicit a later positive component (P300). This result is taken as evidence of prediction errors ascending through the expectation hierarchy. However, in language comprehension, there is no evidence that violations of semantic expectations across local-global levels similarly elicit a sequence of hierarchical error signals – thus drawing into question the putative link between event-related potentials and prediction errors. We investigated the neural basis of such hierarchical expectations of semantics in a word-pair priming paradigm. By manipulating the overall proportion of related or unrelated word-pairs across the task, we created two global contexts that differentially encouraged strategic use of primes. Across two experiments, we replicated behavioural evidence of greater priming in the high validity context, reflecting strategic expectations of upcoming targets based on ‘global’ context. In our pre-registered EEG analyses, we observed a ‘local’ prediction error ERP effect (i.e. semantic priming) approximately 250ms post-target, which, in exploratory analyses, was followed 100ms later by a signal that interacted with the global context. However, the later effect behaved in an apredictive manner - i.e. was most extreme for fulfilled expectations, rather than violations. Our results are consistent with interpretations of early ERPs as reflections of prediction error and later ERPs as processes related to conscious access and in support of task demands.

Significance statement

Semantic expectations have been associated with the ERP N400 component, which is modulated by semantic prediction errors across levels of the hierarchy. However, there is no evidence of a two-stage profile that reflects violations of semantic expectations at a single level of the hierarchy, such as the MMN and P3b observed in the local-global paradigm, which are elicited by violations of local and global expectations, respectively. In the present study, we provided evidence of an early ERP effect that reflects violations of local semantic expectations, followed by an apredictive signal that interacted with the global context. Thus, these results support the notion of early ERPs as prediction errors and later ERPs reflecting conscious access and strategic use of context.
Latent effects of winter warming on Olympia oyster reproduction and larval viability
Authors: Spencer Laura H , Horkan Erin , Crim Ryan , Roberts Steven B
Published: June 2020

For ectothermic marine invertebrates living in temperate regions, impacts of ocean warming will vary considerably by season. In many species, reproductive and metabolic processes are tightly linked to the seasonal change from winter to spring, yet we know little about how these processes will shift as winters become milder. This study examined latent effects of winter warming on spring reproduction in the Olympia oyster,Ostrea lurida. Adults were collected in autumn from central Puget Sound, WA, USA, and exposed to two winter temperatures (7°C, 10°C) in the presence of food limited (5k algal cells/mL) and food abundant (50k algal cells/mL) environments. Following treatments, adults exposed to elevated winter temperature contained larger oocytes regardless of feeding regime, and those also fed abundant food contained more developed sperm. Adults then spawned in common conditions, and larvae were reared through settlement to assess carryover effects of winter conditions on larval viability. Adults previously exposed to elevated winter temperature (10°C) produced larger larvae, particularly if they were also fed high food levels. More developed gametes and larger larvae suggest that gametogenesis occurred at low levels throughout the winter, possibly resulting in increased maternal provisioning to influence larval size. Interestingly, winter temperature did not impact larval survival, or the timing or magnitude of larval production. In the wild, more developed gametes and larger larvae following milder winters could greatly impact recruitment patterns, possibly benefittingO. luridapopulations. In the hatchery setting, larval production and survival is not contingent upon winter conditions, and larval survival does not correlate with oocyte and larval size. Our results suggest thatO. luridareproduction is resilient to winter warming. Furthermore, as global temperature continues to rise, winter conditions should not be overlooked when examining reproductive cycles ofO. luridaand other temperate marine invertebrates with similar reproductive cycles.

Highlights of the manuscript

Elevated winter temperature resulted in more developedO. luridasperm, larger oocytes, and larger larvae.

In experimental settings,O. luridaoocyte and larval size upon release did not predict larval survival, but in the wild where rearing conditions are more challenging, winter warming could benefit wild populations by increasing recruitment.

Winter temperature did not affect larval production timing or magnitude, indicating thatO. luridareproductive capacity is relatively resilient to increasing winter temperatures.
The Autonomic Nervous System Differentiates Between Levels of Motor Intent and Hand Dominance
Authors: Ryu Jihye , Torres Elizabeth
Published: June 2020

While attempting to bridge motor control and cognitive science, the nascent field of embodied cognition has primarily addressed intended, goal-oriented actions. Less explored however, have been unintended motions. Such movements tend to occur largely beneath awareness, while contributing to the spontaneous control of redundant degrees of freedom across the body in motion. We posit that the consequences of such unintended actions implicitly contribute to our autonomous sense of action ownership and agency. We question whether biorhythmic activities from these motions are separable from those which intentionally occur. Here we find that fluctuations in the biorhythmic activities of the nervous systems can unambiguously differentiate across levels of intent. More important yet, this differentiation is remarkable when we examine the fluctuations in biorhythmic activity from the autonomic nervous systems. We find that when the action is intended, the heart signal leads the body kinematics signals; but when the action segment spontaneously occurs without instructions, the heart signal lags the bodily kinematics signals. We posit that such differentiation within the nervous system, may be necessary to acquire the sense of action ownership, which in turn, contributes to the sense of agency. We discuss our results while considering their potential translational value.
Modeling the long-term dynamics of tropical forests: from leaf traits to whole-tree growth patterns
Authors: Petter Gunnar , Kreft Holger , Ong Yongzhi , Zotz Gerhard , Cabral Juliano Sarmento
Published: June 2020

Tropical forests are the most diverse terrestrial ecosystems and home to numerous tree species with diverse ecological strategies competing for resources in space and time. Functional traits influence the ecophysiological performance of tree species, yet the relationship between traits and emergent long-term growth pattern is poorly understood. Here, we present a novel 3D forest stand model in which growth patterns of individual trees and forest stands are emergent properties of leaf traits. Individual trees are simulated as 3D functional-structural tree models (FSTMs), considering branches up to the second order and leaf dynamics at a resolution of one m3. Each species is characterized by a set of leaf traits that corresponds to a specific position on the leaf economic spectrum and determines light-driven carbon assimilation, respiration and mortality rates. Applying principles of the pipe model theory, these leaf scale-processes are coupled with within-tree carbon allocation, i.e., 3D tree growth emerges from low-level processes. By integrating these FSTMs into a dynamic forest stand model, we go beyond modern stand models to integrate structurally-detailed internal physiological processes with interspecific competition, and interactions with the environment in diverse tree communities. For model calibration and validation, we simultaneously compared a large number of emergent patterns at both the tree and forest levels in a pattern-oriented modeling framework. At the tree level, varying specific leaf area and correlated leaf traits determined the maximum height and age of a tree, as well as its size-dependent growth rate and shade tolerance. Trait variations along the leaf economic spectrum led to a continuous transition from fast-growing, short-lived and shade-intolerant to slow-growing, long-lived and shade-tolerant trees. These emerging patterns resembled well-known functional tree types, indicating a fundamental impact of leaf traits on long-term growth patterns. At the forest level, a large number of patterns taken from lowland Neotropical forests were reproduced, indicating that our forest model simulates structurally realistic forests over long time spans. Our ecophysiological approach improves the understanding of how leaf level processes scale up to the tree and the stand level, and facilitates the development of next-generation forest models for species-rich forests in which tree performance emerges directly from functional traits.
Muscle fiber type differences in nitrate and nitrite storage and nitric oxide signaling in rats
Authors: Long Gary M. , Gray Derrick A. , Troutman Ashley D. , Fisher Amanda , Brown Mary Beth , Coggan Andrew R.
Published: June 2020

Recent studies have emphasized the importance of the nitric oxide synthase (NOS)-independent, nitrate (NO3−) → nitrite (NO2−) → nitric oxide (NO) pathway in skeletal muscle. In particular, it has been hypothesized that this pathway is especially active in type II, or fast-twitch, muscle fibers, necessitating greater NO3−and NO2−storage. We therefore measured NO3−and NO2−concentrations in the predominantly fast-twitch vastus lateralis and predominantly slow-twitch soleus muscles of rats. Contrary to the above hypothesis, we found that NO3−and NO2−concentrations were 3.4-fold and 1.8-fold higher, respectively, in the soleus. On the other hand, NO signaling (i.e., cyclic guanosine monophosphate (cGMP) level) was comparable in the two muscles. Although the physiological significance of these observations remains to be determined, we speculate that NO production via the NO3−→ NO2−→ NO pathway is normally higher in slow-twitch muscles, thus helping compensate for their inherently lower NOS activity.
A domestic cat whole exome sequencing resource for trait discovery
Authors: Rodney Alana R. , Buckley Reuben M. , Fulton Robert S. , Fronick Catrina , Richmond Todd , Helps Christopher R. , Pantke Peter , Trent Dianne J. , Lyons Leslie A. , Warren Wesley C.
Published: June 2020

Over 94 million domestic cats are considered pets, who, as our companions, are also susceptible to cancers, common and rare diseases. Whole exome sequencing (WES) is a cost-effective strategy to study their putative disease-causing variants. Presented is ~35.8 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. WES was conducted on 41 cats from various breeds with known and unknown diseases and traits, including 10 cats with prior whole genome sequence (WGS) data available, to test WES capture probe performance. A WES and WGS comparison was completed to understand variant discovery capability of each platform. At ~80x exome coverage, the percent of on-target base coverage >20x was 96.4% with an average of 10.4% off-target. For variant discovery, greater than 98% of WGS SNPs were also discovered by WES. Platform specific variants were mainly restricted to a small number of sex chromosome and olfactory receptor genes. Within the 41 cats with ~31 diseases and normal traits, 45 previously known disease or trait causal variants were observed, such as Persian progressive retinal degeneration and hydrocephalus. Novel candidate variants for polycystic kidney disease and atrichia in the Peterbald breed were also identified as well as a new cat patient with a known variant for cystinuria. These results show the discovery potential of deep exome sequencing to validate existing disease gene models and identify novel gene candidate alleles for many common and rare diseases in cats.
Dihydroceramide desaturase regulates the compartmentalization of Rac1 for neuronal oxidative stress
Authors: Tzou Fei-Yang , Su Tsu-Yi , Yu Yu-Lian , Yeh Yu-Han , Liu Chung-Chih , Huang Shu-Yi , Chan Chih-Chiang
Published: June 2020

Disruption of sphingolipid homeostasis has been shown to cause neurological disorders. How specific sphingolipid species modulate the pathogenesis remains unknown. The last step of sphingolipidde novosynthesis is the conversion of dihydroceramide to ceramide catalyzed by dihydroceramide desaturase (human DEGS1;DrosophilaIfc). Loss ofifcleads to dihydroceramide accumulation and oxidative stress, resulting in photoreceptors degeneration, whileDEGS1variants were associated with leukodystrophy and neuropathy. Here, we demonstrated thatifcregulates Rac1 compartmentalization in fly photoreceptors and further showed that dihydroceramide alters the association of active Rac1 to membranes mimicking specific organelles. We also revealed that the major source of ROS originated from Rac1 and NADPH oxidase (NOX) in the cytoplasm, as the NOX inhibitor apocynin ameliorated the oxidative stress and functional defects in both flyifc-KO photoreceptors and human neuronal cells with disease-associated variantDEGS1H132R. Therefore,DEGS1/ifcdeficiency causes dihydroceramide accumulation, resulting in Rac1 translocation and NOX-dependent neurodegeneration.

Graphical Abstract

ADEGS1/ifcconverts dihydroceramide to ceramide in neuronal cells, and the endolysosomal NOX complex is not activated.

BDihydroceramide accumulates without functionalDEGS1/ifcand causes alterations in membrane microdomains and recruits active Rac1 to endolysosomes. The activation of endolysosomal Rac1-NOX complex elevates cytosolic ROS levels, causing neurodegeneration.

In Brief (eTOC blurb)

Deficiency in dihydroceramide desaturase causes oxidative stress-mediated neurological disorders. Tzou and Su et al. show that increased dihydroceramide causes the relocalization of active Rac1, whilst inhibition of the Rac1-NOX ameliorates the oxidative stress and neuronal defects. NOX inhibitor apocynin may provide new direction of treatments for patients withDEGS1variants.

Highlights

Deficiency in dihydroceramide (dhCer) desaturase induces cytoplasmic ROS elevation

dhCer alters the binding of active Rac1 to reconstituted organelle membranes

Active Rac1 is enriched in endolysosomes inifc-KO neurons for ROS genesis

Rac1-NADPH oxidase elicits ROS, degenerating leukodystrophy-related neuronal cells
A humanTSC1mutation screening platform in GABAergic cortical interneurons for Genotype to Phenotype assessments
Authors: Wundrach Dean , Martinetti Luis E , Stafford April M , Bilinovich Stephanie M , Angara Kartik , Crandall Shane R , Vogt Daniel
Published: June 2020

Tuberous Sclerosis Complex is a complex syndrome that affects multiple organs and is caused by dysfunction of either theTSC1orTSC2genes. One of the least understood features of TSC is the impact ofTSC1&2variants on brain phenotypes, including elevated rates of autism spectrum disorder and seizures. Moreover, while a great deal of work has uncovered how loss of either gene can alter various neural cell types, the impact of many variants in TSC and on these cell types is poorly understood. In particular, missense variants that cause minor changes in the proteins are expected to cause functional changes that differ from a complete loss of the protein. Herein, we examined how some missense variants inTSC1impacted the development of cortical inhibitory interneurons, a cell type whose molecular, cellular and physiological properties are known to be altered after loss of mouseTsc1. Importantly, we found that most missense variants complemented phenotypes caused by loss ofTsc1and resulting in elevated MTOR activity as well as several cell intrinsic physiological properties. However, distinct variants showed deficits in complementing an increase in parvalbumin levels, which is observed after loss ofTsc1and demonstrated smaller amplitudes of after hyperpolarizations. These data suggest subtle but sensitive phenotypes can be detected by someTSC1missense variants and provide anin vivosystem in which to better assess TSC variants.
Limbal Niche Cells in Three-Dimensional Matrigel Induced Dedifferentiation of Mature Corneal Epithelial Cells toward a Progenitor State
Authors: Zhu Hui , Wang Wei , Xu Lingjuan , Jiang Menglin , Tan Yongyao , Wang Yunming , Meir Yaa-Jyuhn James , Li Guigang
Published: June 2020

Purpose

To investigate the possibility and the key factors of stably committed mature corneal epithelial cells dedifferentiate into corneal epithelial stem cellsin vitro.

Methods

Mature cornea epithelia cell (MCEC) sheets or limbal epithelial progenitor cell (LEPC) sheets were isolated from central corneas or limbal segments by Dispase II and further digested with 0.25% trypsin/1 mM EDTA (T/E) to yield single cells. Limbal niche cells (LNC) were isolated from the limbal stroma by collagenase A and expanded on 5% Matrigel coated plastic. Single MCECs were seeded on 50% Matrigel with or without LNC culturing for 10 days, regarding as three-dimensional MCEC (3D-MCEC) group or three-dimensional MCEC+LNC (3D-MCEC+LNC) group. Expression of CK12, p63α, PCK, Vimentin were analyzed with immunofluorescence staining.

Results

The expression of mature cornea epithelial marker (CK12) in MCEC was higher than that in LEPC (P=0.020) but epithelial stem cell marker (p63α) was lower than that in LEPC (P=0.000). When seeded in 3D Matrigel, single MCEC cells could form spheres within 72 hours, and the expression of CK12 reduced (P=0.005) and the expression of p63α also reduced to zero (P=0.000) compared to MCEC. Serial passages of LNC which were expanded in coated Matrigel could form spheres in 3D Matrigel. After mixing MCECs with LNC, rounder spheres emerged within 24 hours which consisted of both epithelia cells (PCK+/Vim-) and LNC (PCK-/Vim+). Moreover, epithelia cells in 3D-MCEC+LNC group expressed less CK12 and more p63α than those in MCEC group (P=0.043, 0.000). Besides, the diameter of spheres in 3D-MCEC+LNC group were larger than that in 3D-MCEC group (P=0.000).

Conclusion

Human LNC and three-dimensional Matrigel could induce the dedifferentiation of mature corneal epithelial cells into corneal epithelial stem cells.
Partitiviruses infectingDrosophila melanogasterandAedes aegyptiexhibit efficient biparental vertical transmission
Authors: Cross Shaun T. , Maertens Bernadette L. , Dunham Tillie J. , Rodgers Case P. , Brehm Ali L. , Miller Megan R. , Williams Alissa M. , Foy Brian D. , Stenglein Mark D.
Published: June 2020

Partitiviruses are segmented, multipartite dsRNA viruses that until recently were only known to infect fungi, plants, and protozoans. Metagenomic surveys have revealed that partitivirus-like sequences are also commonly associated with arthropods. One arthropod-associated partitivirus, galbut virus, is extraordinarily common in wild populations ofDrosophila melanogasterfruit flies. To begin to understand the processes that underlie this virus’s high global prevalence, we established colonies of wild-caught infected flies. Infection remained at stably high levels over three years, with between 63-100% of individual flies infected. Galbut virus infects fly cells and replicates in tissues throughout infected adults, including reproductive tissues and the gut epithelium. We detected no evidence of horizontal transmission via ingestion but vertical transmission from either infected females or infected males was ~100% efficient. Vertical transmission of a related partitivirus, verdadero virus, that we discovered in a laboratory colony ofAedes aegyptimosquitoes was similarly efficient. This suggests that efficient biparental vertical transmission may be a feature of at least a subset of insect-infecting partitiviruses. To study the impact of galbut virus infection free from the confounding effect of other viruses, we generated an inbred line of flies with galbut virus as the only detectable virus infection. We were able to transmit infection experimentally via microinjection of homogenate from these galbut-only flies. This sets the stage for experiments to understand the biological impact and possible utility of partitiviruses infecting important model organisms and disease vectors.

Importance

Galbut virus is a recently discovered partitivirus that is extraordinarly common in wild populations of the model organismDrosophila melanogaster. Like most viruses discovered through metagenomics, most of the basic biological questions about this virus remain unanswered. We found that galbut virus, along with a closely related partitivirus found inAedes aegyptimosquitoes, is transmitted from infected females or males to offspring with ~100% efficiency and can be maintained in laboratory colonies over years. This represents one of the most efficient means of virus transmission described, and likely underlies the successful spread of these viruses through insect populations. We createdDrosophilalines that contained galbut virus as the only virus infection and showed that these flies can be used as a source for experimental infections. This provides insight into how arthropod-infecting partitiviruses may be maintained in nature and sets the stage for exploration of their biology and potential utility.
Collecting data on HIV-related mortality during household surveys: a randomized validation study in Malawi
Authors: Amoah Abena , Brumfield Sarah , Crampin Amelia C. , Dube Albert N. , Helleringer Stéphane , McLean Estelle , Reniers Georges
Published: June 2020

Background

In many African countries, there are limited representative data on HIV/AIDS mortality. We tested whether such data could be collected during household surveys periodically conducted in most African countries.

Methods

We added HIV questions to the module on adult and maternal mortality used in Demographic and Health Surveys. We conducted a validation study of the data generated by these questions in northern Malawi. We randomly assigned men and women aged 15–59 years old to a face-to-face interview or audio computer-assisted self-interviewing (ACASI). We compared survey reports of adult deaths to prospective data on mortality and HIV collected by the Karonga Health and Demographic Surveillance Site. We calculated the sensitivity and specificity of survey data in recording the HIV status of deceased siblings of respondents. We adjusted for partial verification bias using multiple imputations.

Results

We interviewed 535 participants, who reported 885 deaths at ages 15 and older. The added HIV questions yielded largely complete data on the HIV status of respondents’ deceased siblings, particularly those who died recently. The adjusted sensitivity of survey data on HIV status of the deceased was high in both study groups (0.78–0.82). There were few false positive reports of the HIV status of deceased siblings (specificity = 0.96–0.98). ACASI did not improve the accuracy of survey data, but it required more time to collect mortality reports. Asking the HIV questions only took 0.4 minute (≈25 seconds) per deceased sibling in face-to-face interviews.

Conclusions

Adding HIV questions to mortality questionnaires used in household surveys yields accurate data on the HIV status of deceased adults. These new data could aid in tracking progress towards global HIV elimination targets.

MEIRU – LSHTM – JHU Partnership for improving adult mortality data1,2
Evaluation of symptomatic patient saliva as a sample type for the Abbott ID NOW COVID-19 assay
Authors: SoRelle Jeffrey A. , Mahimainathan Lenin , McCormick-Baw Clare , Cavuoti Dominick , Lee Francesca , Bararia Anjali , Thomas Abey , Sarode Ravi , Clark Andrew E. , Muthukumar Alagarraju
Published: June 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has presented significant challenges for laboratories including supply chain limitations with restricted access to reagents and sample collection materials (i.e. swabs, viral transport media (VTM)) for patients testing. Therefore, saliva has been evaluated as an alternative specimen for COVID-19 diagnosis. comparable performance between dry nasal swabs (NS) and nasopharyngeal swabs (NPS) collected in VTM has been observed with the ID NOW for SARS-CoV-2; the majority of false-negative results occur with higher cycle number (CN) or cycle threshold (Ct) values suggesting low viral load in these specimens. We performed clinical validation of saliva specimens on the ID NOW molecular platform to detect SARS-CoV-2. Saliva was compared to nasopharyngeal swabs tested on the ID NOW and the Cepheid molecular assay. We also performed stability studies of saliva samples over 5 days. A total of 96 saliva samples and 64 paired NPS were analyzed. We observed 78% (18/23) positive percent agreement (PPA) and 100% (44/44) negative percent agreement (NPA) between matched saliva and nasopharyngeal specimens performed on ID NOW. We found 83% (19/23) PPA and 100% NPA (25/25) between saliva run on the ID NOW and Cepheid assay. Six saliva specimens positive for SARS-CoV-2 were continuously positive for five days when stored at room temperature. Therefore, we propose further investigation of saliva as an alternative sample type for testing symptomatic patients with ID NOW as a promising method to address COVID-19 testing.
CD39+PD-1+CD8+T cells mediate metastatic dormancy in breast cancer
Authors: de Lara Paulino Tallón , Castañón Héctor , Vermeer Marijne , Núñez Nicolás , Silina Karina , Sobottka Bettina , Urdinez Joaquín , Cecconi Virginia , Yagita Hideo , Attar Farkhondeh Movahedian , Hiltbrunner Stefanie , Glarner Isabelle , Moch Holger , Tugues Sònia , Becher Burkhard , van den Broek Maries
Published: June 2020

Some breast tumors metastasize aggressively whereas others remain in a state of metastatic dormancy for months or even years. The mechanism governing such metastatic dormancy remains largely unknown. Through high-parametric single-cell mapping in mice, we identified a discrete population of CD39+PD-1+CD8+T cells present both in primary tumors and in dormant metastasis, which was hardly found in aggressively metastasizing tumors. Using blocking antibodies, we found that dormancy depended on TNFαand IFNγ. Of note, immunotherapy reduced the number of dormant cancer cells in the lungs. Adoptive transfer of purified CD39+PD-1+CD8+T cells prevented metastatic outgrowth. In human breast cancer, the frequency of CD39+PD-1+CD8+but not of total CD8+T cells correlated with delayed metastatic relapse after resection (disease-free survival), thus underlining the biological relevance of CD39+PD-1+CD8+T cells for controlling experimental and human breast cancer. Furthermore, density of CD39+PD-1+CD8+T cells may serve as a novel biomarker and may serve as a potential immunotherapy target. Thus, we discovered that a primary breast tumor primes a systemic, CD39+PD-1+CD8+T cell response that is essential for metastatic dormancy in the lungs.
Getting stuck in a rut as an emergent feature of a dynamic decision-making system
Authors: Warburton Matthew , Brookes Jack , Hasan Mohamed , Leonetti Matteo , Dogar Mehmet , Wang He , Cohn Anthony G. , Mushtaq Faisal , Mon-Williams Mark A.
Published: June 2020

Human sensorimotor decision-making has a tendency to get ‘stuck in a rut’, being biased towards selecting a previously implemented action structure (‘hysteresis’). Existing explanations cannot provide a principled account of when hysteresis will occur. We propose that hysteresis is an emergent property of a dynamical system learning from the consequences of its actions. To examine this, 152 participants moved a cursor to a target on a tablet device whilst avoiding an obstacle. Hysteresis was observed when the obstacle moved sequentially across the screen between trials, but not with random obstacle placement. Two further experiments (n = 20) showed an attenuation when time and resource constraints were eased. We created a simple computational model capturing dynamic probabilistic estimate updating that showed the same patterns of results. This provides the first computational demonstration of how sensorimotor decision-making can get ‘stuck in a rut’ through the dynamic updating of its probability estimates.

Significance Statement

Humans show a bias to select the organisational structure of a recently carried out action, even when an alternative option is available with lower costs. This ‘hysteresis’ is said to be more efficient than creating a new plan and it has been interpreted as a ‘design feature’ within decision-making systems. We suggest such teleological arguments are redundant, with hysteresis being a naturally emergent property of a dynamic control system that evolved to operate effectively in an uncertain and partially observable world. Empirical experimentation and simulations from a ‘first principle’ computational model of decision-making were consistent with our hypothesis. The identification of such a mechanism can inform robotics research, suggesting how robotic agents can show human-like flexibility in complex dynamic environments.
Tracking Adoptive T Cell Therapy Using Magnetic Particle Imaging
Authors: Rivera-Rodriguez Angelie , Hoang-Minh Lan B. , Chiu-Lam Andreina , Sarna Nicole , Marrero-Morales Leyda , Mitchell Duane A. , Rinaldi Carlos
Published: June 2020

Adoptive cellular therapy (ACT) is a potent strategy to boost the immune response against cancer. ACT is an effective treatment for blood cancers, such as leukemias and lymphomas, but faces challenges treating solid tumors and cancers in locations like the brain. A critical step for success of ACT immunotherapy is achieving efficient trafficking of T cells to solid tumors, and the non-invasive and quantitative tracking of adoptively transferred T cell biodistribution would accelerate its development. Here, we demonstrate the use of Magnetic Particle Imaging (MPI) to non-invasively track ACT T cellsin vivo. Labeling T cells with the superparamagnetic iron oxide nanoparticle tracer ferucarbotran did not affect T cell viability, phenotype, or cytotoxic functionin vitro. Following ACT, ferucarbotran-labeled T cells were detected and quantified using MPIex vivoandin vivo, in a mouse model of invasive brain cancer. Proof-of-principlein vivoMPI demonstrated its capacity to detect labeled T cells in lungs and liver after intravenous administration and to monitor T cell localization in the brain after intraventricular administration.Ex vivoimaging using MPI and optical imaging suggests accumulation of systemically administered ferucarbotran-labeled T cells in the brain, where MPI signal from ferucarbotran tracers and fluorescently tagged T cells were observed.Ex vivoimaging also suggest differential accumulation of nanoparticles and viable T cells in other organs like the spleen and liver. These results support the use of MPI to track adoptively transferred T cells and accelerate the development of ACT treatments for brain tumors and other cancers.
Neuronal activity in sensory cortex predicts the specificity of learning
Authors: Wood Katherine C. , Angeloni Christopher F. , Oxman Karmi , Clopath Claudia , Geffen Maria N.
Published: June 2020

Learning to avoid dangerous signals while preserving normal responses to safe stimuli is essential for everyday behavior and survival. Fear learning has a high level of inter-subject variability. Following identical experiences, subjects exhibit fear specificities ranging from high (specializing fear to only the dangerous stimulus) to low (generalizing fear to safe stimuli). Pathological fear generalization underlies emotional disorders, such as post-traumatic stress disorder. The neuronal basis of fear specificity remains unknown. Here, we identified the neuronal code that underlies inter-subject variability in fear specificity using longitudinal imaging of neuronal activity before and after differential fear conditioning in the auditory cortex of mice. Neuronal activity prior to, but not after learning predicted the level of specificity following fear conditioning across subjects. Stimulus representation in auditory cortex was reorganized following conditioning. However, the reorganized neuronal activity did not relate to the specificity of learning. These results present a novel neuronal code that determines individual patterns in learning.
Presynaptic precursor vesicles originate from thetrans-Golgi network, promoted by the small GTPase RAB2
Authors: Götz Torsten W. B. , Puchkov Dmytro , Lützkendorf Janine , Nikonenko Alexander G. , Quentin Christine , Lehmann Martin , Sigrist Stephan J. , Petzoldt Astrid G.
Published: June 2020

Reliable delivery of presynaptic material, including active zone and synaptic vesicle proteins from neuronal somata to synaptic terminals is prerequisite for faithful synaptogenesis and neurotransmission. However, molecular mechanisms controlling the somatic assembly of presynaptic precursors remain insufficiently understood. Here we show that in mutants of the small GTPase RAB2 active zone and synaptic vesicle proteins accumulated in the neuronal somata at thetrans-Golgi network and were consequently depleted at synaptic terminals, provoking neurotransmission deficits. The ectopic presynaptic material accumulations consisted of heterogeneous vesicles and short tubules of 40×60 nm and segregated in subfractions either positive for active zone proteins or co-positive for synaptic vesicle proteins and LAMP1, a lysosomal membrane protein. Genetically,rab2behaved epistatic overarl8, a lysosomal adaptor controlling axonal export of precursors. Collectively, we here identified a Golgi-associated assembly sequence in presynaptic precursor vesicle biogenesis controlled by RAB2 dependent membrane remodelling and protein sorting at thetrans-Golgi.
FIRM: Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets
Authors: Ming Jingsi , Lin Zhixiang , Zhao Jia , Wan Xiang , Yang Can , Wu Angela Ruohao
Published: June 2020

Single-cell RNA-sequencing (scRNA-seq) is being used extensively to measure the mRNA expression of individual cells from deconstructed tissues, organs, and even entire organisms to generate cell atlas references, leading to discoveries of novel cell types and deeper insight into biological trajectories. These massive datasets are usually collected from many samples using different scRNA-seq technology platforms, including the popular SMART-Seq2 (SS2) and 10X platforms. Inherent heterogeneities between platforms, tissues, and other batch effects makes scRNA-seq data difficult to compare and integrate, especially in large-scale cell atlas efforts; yet, accurate integration is essential for gaining deeper insights into cell biology. Through comprehensive data exploration, we found that accurate integration is often hampered by differences in cell-type compositions. Herein we describe FIRM, an algorithm that addresses this problem and achieves efficient and accurate integration of heterogeneous scRNA-seq datasets across multiple tissue types, platforms, and experimental batches. We applied FIRM to numerous large-scale scRNA-seq datasets from mouse, mouse lemur, and human, comparing its performance in dataset integration with other state-of-the-art methods. FIRM-integrated datasets show accurate mixing of shared cell type identities and superior preservation of original structure without overcorrection, generating robust integrated datasets for downstream exploration and analysis. It is also a facile way to transfer cell type labels and annotations from one dataset to another, making it a reliable and versatile tool for scRNA-seq analysis, especially for cell atlas data integration.
Decoding neural signals and discovering their representations with a compact and interpretable convolutional neural network
Authors: Petrosuan Arthur , Lebedev Mikhail , Ossadtchi Alexei
Published: June 2020

Abstract

Brain-computer interfaces (BCIs) decode information from neural activity and send it to external devices. In recent years, we have seen an emergence of new algorithms for BCI decoding including those based on the deep-learning principles. Here we describe a compact convolutional network-based architecture for adaptive decoding of electrocorticographic (ECoG) data into finger kinematics. We also propose a theoretically justified approach to interpreting the spatial and temporal weights in the architectures that combine adaptation in both space and time, such as the one described here. In these architectures the weights are optimized not only to align with the target sources but also to tune away from the interfering ones, in both the spatial and the frequency domains. The obtained spatial and frequency patterns characterizing the neuronal populations pivotal to the specific decoding task can then be interpreted by fitting appropriate spatial and dynamical models.

We first tested our solution using realistic Monte-Carlo simulations. Then, when applied to the ECoG data from Berlin BCI IV competition dataset, our architecture performed comparably to the competition winners without requiring explicit feature engineering. Moreover, using the proposed approach to the network weights interpretation we could unravel the spatial and the spectral patterns of the neuronal processes underlying the successful decoding of finger kinematics from another ECoG dataset with known sensor positions.

As such, the proposed solution offers a good decoder and a tool for investigating neural mechanisms of motor control.
Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration
Authors: Begley Victoria , Jordán-Pla Antonio , Peñate Xenia , Garrido-Godino Ana I. , Challal Drice , Cuevas-Bermúdez Abel , Mitjavila Adrià , Barucco Mara , Gutiérrez Gabriel , Singh Abhyudai , Alepuz Paula , Navarro Francisco , Libri Domenico , Pérez-Ortín José E. , Chávez Sebastián
Published: June 2020

mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques inSaccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5’ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3’ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favoring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.
Template-based prediction of protein structure with deep learning
Authors: Zhang Haicang , Shen Yufeng
Published: June 2020

Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. However, accurate template-query alignment and template selection are still very challenging, especially for the proteins with only distant homologs available. We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. ThreaderAI formulates the task of aligning query sequence with template as the classical pixel classification problem in computer vision and naturally applies deep residual neural network in prediction. ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residueresidue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix. We evaluated our methods both in generating accurate template-query alignment and protein threading. Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56%, 13%, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. And on CASP13’s TBM-hard data, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 16%, 9% and 8% in terms of TM-score, respectively. These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins.

Availability

https://github.com/ShenLab/ThreaderAI
How citizen science could improve Species Distribution Models and their independent assessment
Authors: Florence Matutini , Jacques Baudry , Guillaume Pain , Morgane Sineau , Joséphine Pithon
Published: June 2020

Abstract

Species distribution models (SDM) have been increasingly developed in recent years but their validity is questioned. Their assessment can be improved by the use of independent data but this can be difficult to obtain and prohibitive to collect. Standardized data from citizen science may be used to establish external evaluation datasets and to improve SDM validation and applicability. We used opportunistic presence-only data along with presence-absence data from a standardized citizen science program to establish and assess habitat suitability maps for 9 species of amphibian in western France. We assessed Generalized Additive and Random Forest Models’ performance by (1) cross-validation using 30% of the opportunistic dataset used to calibrate the model or (2) external validation using different independent data sets derived from citizen science monitoring. We tested the effects of applying different combinations of filters to the citizen data and of complementing it with additional standardized fieldwork. Cross-validation with an internal evaluation dataset resulted in higher AUC (Area Under the receiver operating Curve) than external evaluation causing overestimation of model accuracy and did not select the same models; models integrating sampling effort performed better with external validation. AUC, specificity and sensitivity of models calculated with different filtered external datasets differed for some species. However, for most species, complementary fieldwork was not necessary to obtain coherent results, as long as the citizen science data was strongly filtered. Since external validation methods using independent data are considered more robust, filtering data from citizen sciences may make a valuable contribution to the assessment of SDM. Limited complementary fieldwork with volunteer’s participation to complete ecological gradients may also possibly enhance citizen involvement and lead to better use of SDM in decision processes for nature conservation.