bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially distributed representation of taste quality in the gustatory insular cortex of awake behaving mice
Authors: Chen Ke , Kogan Joshua F. , Fontanini Alfredo 
Published: July 2020

SUMMARYVisual, auditory and somatosensory cortices are topographically organized, with neurons responding to similar sensory features clustering in adjacent portions of the cortex. Such topography has not been observed in the piriform cortex, whose responses to odorants are sparsely distributed across the cortex. The spatial organization of taste responses in the gustatory insular cortex (GC) is currently debated, with conflicting evidence from anesthetized rodents pointing to alternative and mutually exclusive models. Here, we rely on calcium imaging to determine how taste and task-related variables are represented in the superficial layers of GC of alert, licking mice. Our data show that the various stimuli evoke sparse responses from a combination of broadly and narrowly tuned neurons. Analysis of the distribution of responses over multiple spatial scales demonstrates that taste representations are distributed across the cortex, with no sign of spatial clustering or topography. Altogether, data presented here support the idea that the representation of taste qualities in GC of alert mice is sparse and distributed, analogous to the representation of odorants in piriform cortex.
Stitching together a nm thick peptide-based semiconductor sheet using UV light
Authors: Alvarez Alain Bolaño , Pino Marcelo , Petersen Steffen B. , Fidelio Gerardo Daniel 
Published: July 2020

AbstractLangmuir monolayer allows for two-dimensional nano-scale organisation of amphiphilic molecules. We here report that two retro-isomers peptides carefully designed to form stable monolayers showed semiconductor-like behaviour. Both exhibit the same hydrophobicity and surface stability but differ in the lateral conductivity and current-voltage due to the asymmetric peptide bond backbone orientation at the interface. The two peptides contain several tyrosines that allow for UVB-induced lateral crosslinking of tyrosines in neighboring peptide molecules. UVB-light induces changes in the lateral conductivity and currentvoltage behaviour as well as monolayer heterogeneity monitored by Brewster angle microscopy that depends on the peptide bond backbone orientation and crosslinking of tyrosines. Our results indicate that one may design extended nano-sheets with particular electric properties, reminiscent of semiconductors. We propose to exploit such properties for biosensing and neural interfaces.
An Antibody to RGMa Promotes Regeneration of Cochlear Synapses after Noise Exposure
Authors: Nevoux Jerome , Alexandru Mihaela , Bellocq Thomas , Tanaka Lei , Hayashi Yushi , Watabe Takahisa , Lahlou Hanae , Tani Kohsuke , Edge Albert S.B. 
Published: July 2020

SUMMARYAuditory neuropathy is caused by the loss of afferent input to the brainstem via the components of the neural pathway comprising inner hair cells and the first order neurons of the spiral ganglion. Recent work has identified the synapse between cochlear primary afferent neurons and sensory hair cells as a particularly vulnerable component of this pathway. Loss of these synapses due to noise exposure or aging results in the pathology identified as hidden hearing loss, an initial stage of cochlear dysfunction that goes undetected in standard hearing tests. We show here that repulsive axonal guidance molecule a (RGMa) acts to prevent regrowth and synaptogenesis of peripheral auditory nerve fibers with inner hair cells. Treatment of noise-exposed animals with an anti-RGMa blocking antibody regenerated inner hair cell synapses and resulted in recovery of wave-I amplitude of the auditory brainstem response, indicating effective reversal of synaptopathy.
High-performance brain-to-text communication via imagined handwriting
Authors: Willett Francis R. , Avansino Donald T. , Hochberg Leigh R. , Henderson Jaimie M. , Shenoy Krishna V. 
Published: July 2020

SummaryBrain-computer interfaces (BCIs) can restore communication to people who have lost the ability to move or speak. To date, a major focus of BCI research has been on restoring gross motor skills, such as reaching and grasping1–5or point-and-click typing with a 2D computer cursor6,7. However, rapid sequences of highly dexterous behaviors, such as handwriting or touch typing, might enable faster communication rates. Here, we demonstrate an intracortical BCI that can decode imagined handwriting movements from neural activity in motor cortex and translate it to text in real-time, using a novel recurrent neural network decoding approach. With this BCI, our study participant (whose hand was paralyzed) achieved typing speeds that exceed those of any other BCI yet reported: 90 characters per minute at >99% accuracy with a general-purpose autocorrect. These speeds are comparable to able-bodied smartphone typing speeds in our participant’s age group (115 characters per minute)8and significantly close the gap between BCI-enabled typing and able-bodied typing rates. Finally, new theoretical considerations explain why temporally complex movements, such as handwriting, may be fundamentally easier to decode than point-to-point movements. Our results open a new approach for BCIs and demonstrate the feasibility of accurately decoding rapid, dexterous movements years after paralysis.
Molecular characterization of a flatworm Girardia isolate from Guanajuato, Mexico
Authors: Duncan Elizabeth M. , Nowotarski Stephanie H. , Guerrero-Hernández Carlos , Ross Eric J. , D’Orazio Julia A. ,   Clubes de Ciencia México Workshop for Developmental Biology, McKinney Sean , McHargue Mark C. , Guo Longhua , McClain Melainia , Alvarado Alejandro Sánchez 
Published: July 2020

ABSTRACTPlanarian flatworms are best known for their impressive regenerative capacity, yet this trait varies across species. In addition, planarians have other features that share morphology and function with the tissues of many other animals, including an outer mucociliary epithelium that drives planarian locomotion and is very similar to the epithelial linings of the human lung and oviduct. Planarians occupy a broad range of ecological habitats and are known to be sensitive to changes in their environment. Yet, despite their potential to provide valuable insight to many different fields, very few planarian species have been developed as laboratory models for mechanism-based research.Here we describe a previously undocumented planarian isolate,Girardia sp. (Guanajuato). After collecting this isolate from a freshwater habitat in central Mexico, we characterized it at the morphological, cellular, and molecular level. We show thatGirardia sp. (Guanajuato) shares features with animals in theGirardiagenus but also possesses traits that appear unique to this isolate. By thoroughly characterizing this new planarian isolate, our work facilitates future comparisons to other flatworms and further molecular dissection of the unique and physiologically-relevant traits observed in thisGirardia sp. (Guanajuato) isolate.
Gastric metabolomics analysis supportsH. pylori’s catabolism of organic and amino acids in both the corpus and antrum
Authors: Keilberg Daniela , Steele Nina , Fan Sili , Yang Christina , Zavros Yana , Ottemann Karen M. 
Published: July 2020

AbstractHelicobacter pyloriis a chronic bacterial pathogen that thrives in several regions of the stomach, causing inflammation that can vary by site and result in distinct disease outcomes. It is not known, however, whether the host-derived metabolites differ between the two main regions, the corpus and antrum. We thus characterized the metabolomes of mouse gastric corpus and antrum organoids and tissue. The secreted organoid metabolites differed significantly between the corpus and antrum in only seven metabolites: lactic acid, malic acid, phosphoethanolamine, alanine, uridine, glycerol, and isoleucine, with only lactic acid and phosphoethanolamine exceeding two-fold differences. Multiple chemicals were depleted uponH. pyloriinfection including urea, cholesterol, glutamine, fumaric acid, lactic acid, citric acid, malic acid, and multiple non-essential amino acids. Many are knownH. pylorinutrients and did not differ between the two regions. When tissue was examined, there was little overlap with the organoid metabolites. The two tissue regions were distinct, however, including in antrum-elevated 5-methoxytryptamine, lactic acid, and caprylic acid, and corpus-elevated phospholipid products. Over an 8 month infection time course, the corpus and antrum remained distinct. The antrum displayed no significant changes, in contrast to the corpus which exhibited metabolite changes indicating stress, tissue damage, and depletion of key nutrients such as glutamine and fructose-6-phosphate. Overall, our results suggest theH. pyloripreferentially uses carboxylic acids and amino acids in complex environments, and these are found in both the corpus and antrum.
Disentangling the relative roles of vertical transmission, subsequent colonizations and diet on cockroach microbiome assembly
Authors: Germer Kristjan , Renelies-Hamilton Justinn , Sillam-Dussès David , Bodawatta Kasun H. , Poulsen Michael 
Published: July 2020

AbstractA multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach vs. termite gut provisioned), and varying diets (matched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroachShelfordella lateralisusing 16S rDNA amplicon sequencing. We show that the presence of a pre-existing bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a stronghold and which stabilize the microbiome. However, the subsequent inoculation sources more strongly affect ultimate community composition, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets that consequently strongly impact community functions predicted using PICRUSt2. In conclusion, our findings suggest that inoculations drive communities towards different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.Contribution to the fieldWhen host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers through interactions with potential colonizers that may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale, but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.
Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing
Authors: Harbourt David E. , Haddow Andrew D. , Piper Ashley E. , Bloomfield Holly , Kearney Brian J. , Fetterer David , Gibson Kathleen , Minogue Timothy 
Published: July 2020

AbstractA new coronavirus (SARS-CoV-2) emerged in the winter of 2019 in Wuhan, China, and rapidly spread around the world. The extent and efficiency of SARS-CoV-2 pandemic is far greater than previous coronaviruses that emerged in the 21st Century. Here, we modeled stability of SARS-CoV-2 on skin, paper currency, and clothing to determine if these surfaces may factor in the fomite transmission dynamics of SARS-CoV-2. Skin, currency, and clothing samples were exposed to SARS-CoV-2 under laboratory conditions and incubated at three different temperatures (4°C± 2°C, 22°C± 2°C, and 37°C ± 2°C). Stability was evaluated at 0 hours (h), 4 h, 8 h, 24 h, 72 h, 96 h, 7 days, and 14 days post-exposure. SARS-CoV-2 was shown to be stable on skin through the duration of the experiment at 4°C (14 days). Virus remained stable on skin for at least 96 h at 22°C and for at least 8h at 37°C. There were minimal differences between the tested currency samples. The virus remained stable on the $1 U.S.A. Bank Note for at least 96 h at 4°C while viable virus was not detected on the $20 U.S.A. Bank Note samples beyond 72 h. The virus remained stable on both Bank Notes for at least 8 h at 22°C and 4 h at 37°C. Clothing samples were similar in stability to the currency with the virus being detected for at least 96 h at 4°C and at least 4 h at 22°C. No viable virus was detected on clothing samples at 37°C after initial exposure. This study confirms the inverse relationship between virus stability and temperature. Furthermore, virus stability on skin demonstrates the need for continued hand hygiene practices to minimize fomite transmission both in the general population as well as workplaces where close contact is common.
Low plasma 25(OH) vitamin D level is associated with increased risk of COVID-19 infection: an Israeli population-based study
Authors: Merzon Eugene , Tworowski Dmitry , Gorohovski Alessandro , Vinker Shlomo , Cohen Avivit Golan , Green Ilan , Morgenstern Milana Frenkel 
Published: July 2020

ABSTRACTAimTo evaluate associations of plasma 25(OH)D status with the likelihood of coronavirus disease (COVID-19) infection and hospitalization.MethodsThe study population included the 14,000 members of Leumit Health Services who were tested for COVID-19 infection from February 1stto April 30th2020, and who had at least one previous blood test for plasma 25(OH)D level. “Suboptimal” or “low” plasma 25(OH)D level was defined as plasma 25-hydroxyvitamin D, or 25(OH)D, concentration below 30 ng/mL.ResultsOf 7,807 individuals, 782 (10.1%) were COVID-19-positive, and 7,025 (89.9%) COVID-19-negative. The mean plasma vitamin D level was significantly lower among those who tested positive than negative for COVID-19 [19.00 ng/mL (95% confidence interval [CI] 18.41-19.59)vs. 20.55 (95% CI 20.32-20.78)]. Univariate analysis demonstrated an association between low plasma 25(OH)D level and increased likelihood of COVID-19 infection [crude odds ratio (OR) of 1.58 (95% CI 1.24-2.01, p<0.001)], and of hospitalization due to the SARS-CoV-2 virus [crude OR of 2.09 (95% CI 1.01-4.30, p<0.05)]. In multivariate analyses that controlled for demographic variables, and psychiatric and somatic disorders, the adjusted OR of COVID-19 infection [1.45 (95% CI 1.08-1.95, p<0.001)], and of hospitalization due to the SARS-CoV-2 virus [1.95 (95% CI 0.98-4.845, p=0.061)] were preserved. In the multivariate analyses, age over 50 years, male gender and low-medium socioeconomic status were also positively associated with the risk of COVID-19 infection; age over 50 years was positively associated with the likelihood of hospitalization due to COVID-19.ConclusionLow plasma 25(OH)D level appears to be an independent risk factor for COVID-19 infection and hospitalization.
Recombination of repeat elements generates somatic complexity in human genomes
Authors: Pascarella G. , Hashimoto K. , Busch A. , Luginbühl J. , Parr C. , Hon C. C. , Yip W. H. , Abe K. , Kratz A. , Bonetti A. , Agostini F. , Severin J. , Murayama S. , Suzuki Y. , Gustincich S. , Frith M. , Carninci P. 
Published: July 2020

SummaryMillions of Alu and L1 copies in our genomes contribute to evolution and genetic disorders via non-allelic homologous recombination, but the somatic extent of these rearrangements has not been systematically investigated. Here we combine short and long DNA reads sequencing of repeat elements with a new bioinformatic pipeline to show that somatic recombination of Alu and L1 elements is common in human genomes. We report new tissue-specific recombination hallmarks, and show that retroelements acting as recombination hotspots are enriched in centromeres and cancer genes. We compare recombination profiles in human induced pluripotent stem cells and differentiated neurons and show that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Finally, we find that somatic recombination profiles are altered in Parkinson’s and Alzheimer’s disease, indicating a link between retroelements recombination and genomic instability in neurodegeneration. This work shows that somatic recombination of repeat elements contributes massively to genomic diversity in health and disease.
Chromosome Compartments on the Inactive X Guide TAD Formation Independently of Transcription during X-Reactivation
Authors: Bauer Moritz , Vidal Enrique , Zorita Eduard , Pinter Stefan F. , Filion Guillaume J. , Payer Bernhard 
Published: July 2020

SummaryA hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments and into topologically associating domains (TADs). Both structures were regarded absent from the inactive X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC-reprogramming system and high-resolution Hi-C to produce the first time-course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we uncover A/B-like compartments on the inactive X harboring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, coinciding with acquisition of naive pluripotency, leading to downregulation ofXist. Importantly, we find that TAD formation precedes transcription, suggesting them to be causally independent. Instead, TADs form first within Xist-poor compartments, establishing Xist as common denominator, opposing both gene reactivation and TAD formation through separate mechanisms.Graphical Summary
Mobbing-like response to secondary predator cues is not a form of teaching in meerkats
Authors: Driscoll Isabel , Manser Marta , Thornton Alex 
Published: July 2020

AbstractAcross many taxa, individuals learn how to detect, recognise and respond to predators via social learning. Learning to recognise and interpret predator cues is essential in the accurate assessment of risk. Cues can come directly from a predator’s presence (visual, acoustic) or from secondary predator cues (SPCs, such as hair/feathers, urine or faeces) left in the environment. Animals show various responses to encountering SPCs, which are thought to act in reducing risk to the individual. Meerkats, Suricata suricatta, show a response to SPCs not described in any other species: they display a mobbing-like behaviour. The function of this behaviour is unclear as unlike mobbing, the response it so closely resembles, it cannot serve to drive predators away. We used experiments to investigate whether adults may use this mobbing-like response to teach naïve young how to recognise and respond to predators. Meerkats are known to teach pups hunting skills, but there is as yet no evidence that any species other than humans teaches across multiple contexts. We used experimental presentations of SPCs to test whether wild adult meerkats respond more intensely to SPCs in the presence of naïve pups, as would be expected if the behaviour serves to promote learning. Contrary to this prediction, response intensity was lower when pups were present than when they were absent, and declined as the number of pups in the group increased, possibly due to costs associated with foraging with dependent young. Response intensity instead increased with increasing group size, number of group members interacting with the cue, and varied with predator cue type. These results suggest that the mobbing-like response to SPCs is not a form of teaching in meerkats. Instead, this behaviour may function to increase the recruitment of others to investigate the SPC. Exposing group members to SPCs may better inform them of the nature of the threat, facilitating more effective defensive group responses.
Realistic boundary conditions for perivascular pumping in the mouse brain reconcile theory, simulation, and experiment
Authors: Ladrón-de-Guevara Antonio , Shang Jessica K. , Nedergaard Maiken , Kelley Douglas H. 
Published: July 2020

ABSTRACTCerebrospinal fluid (CSF) flows through the perivascular spaces (PVSs) surrounding cerebral arteries. Revealing the mechanisms driving that flow could bring improved understanding of brain waste transport and insights for disorders including Alzheimer’s disease and stroke. In vivo velocity measurements of CSF in surface PVSs in mice have been used to argue that flow is driven primarily by the pulsatile motion of artery walls — perivascular pumping. However, fluid dynamics theory and simulation have predicted that perivascular pumping produces flows differing from in vivo observations starkly, particularly in the phase and relative amplitude of flow oscillation. Here we show that coupling theoretical and simulated flows to realistic end boundary conditions, using resistance and compliance values measured in mice, results in velocities that match observations closely in phase, relative amplitude of oscillation, and mean flow speed. This new, quantitative agreement among theory, simulation, and in vivo measurement further supports the idea that perivascular pumping is a primary CSF driver in physiological conditions.
Distinct lipid profile, low-level inflammation and increased antioxidant defense as a signature in HIV-1 elite control status
Authors: Sperk Maike , Mikaeloff Flora , Svensson-Akusjärvi Sara , Ponnan Sivasankaran Munusamy , Nowak Piotr , Sönnerborg Anders , Neogi Ujjwal 
Published: July 2020

AbstractHIV-1 elite controllers (EC) are a rare but heterogeneous group of HIV-1-infected individuals who are able to suppress viral replication in the absence of antiretroviral therapy. The mechanisms of how EC achieve undetectable viral loads remain unclear. This study aimed to investigate host plasma metabolomics and targeted plasma proteomics in a Swedish HIV-1 cohort including EC and treatment-naïve viremic progressors (VP) as well as HIV-negative individuals (HC) to get insights into mechanisms governing EC status. Metabolites belonging to antioxidant defense had higher levels in EC relative to VP while inflammation markers were increased in VP compared to EC. Only four plasma proteins (CCL4, CCL7, CCL20, and NOS3) were increased in EC compared to HC and CCL20/CCR6 axis can play important role. Our study suggests that low-level inflammation and oxidative stress at physiological levels could be important factors contributing to control of viral replication.One Sentence SummaryHIV-1 elite controllers had a distinct lipid profile, reduced inflammation, and increased antioxidant defense that might contribute to elite control status.