bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drop, Swap, and Generate: A Self-Supervised Approach for Generating Neural Activity
Authors: Liu Ran , Azabou Mehdi , Dabagia Max , Lin Chi-Heng , Azar Mohammad Gheshlaghi , Hengen Keith B. , Valko Michal , Dyer Eva L. 
Published: July 2021

AbstractMeaningful and simplified representations of neural activity can yield insights into how and what information is being processed within a neural circuit. However, without labels, finding representations that reveal the link between the brain and behavior can be challenging. Here, we introduce a novel unsupervised approach for learning disentangled representations of neural activity called Swap-VAE. Our approach combines a generative modeling framework with an instance-specific alignment loss that tries to maximize the representational similarity between transformed views of the input (brain state). These transformed (or augmented) views are created by dropping out neurons and jittering samples in time, which intuitively should lead the network to a representation that maintains both temporal consistency and invariance to the specific neurons used to represent the neural state. Through evaluations on both synthetic data and neural recordings from hundreds of neurons in different primate brains, we show that it is possible to build representations that disentangle neural datasets along relevant latent dimensions linked tso behavior.
Discriminative and affective touch converge: Somatosensory cortex represents Aß input in a CT-like manner
Authors: Schirmer Annett , Lai Oscar , McGlone Francis , Cham Clare , Lau Darwin 
Published: July 2021

AbstractCurrent theory divides the human mechanical sense into discriminative and affective systems. A discriminative system supports tactile exploration and manipulation via fast Aß signaling, whereas an affective system supports the pleasure of friendly interpersonal touch via slow CT signaling. To probe this system segregation, we recorded the electroencephalogram from participants being stroked and reporting stroke pleasantness. We observed a somatosensory negativity that was maximal for CT optimal as compared with sub-optimal velocities, that predicted subjective pleasantness, and showed only for stroking of hairy skin known to be CT innervated. Importantly, the latency of this negativity preceded C fiber input to the brain by several hundred milliseconds and is best explained by interactions between CT and Aß processes in the spinal cord. Our data challenge the divide between discriminative and affective touch implying instead that both fast Aß and slow CT signaling play an important role in tactile pleasure.
High-throughput Mutational Surveillance of the SARS-CoV-2 Spike Gene
Authors: Özkan Ezgi , Strobl Marcus Martin , Novatchkova Maria , Yelagandula Ramesh , Albanese Tanino Guiseppe , Triska Petr , Endler Lukas , Penz Thomas , Patocka Timothej , Felsenstein Vera , Vogt Alexander , Tamir Ido , Seitz Tamara , Födinger Manuela , Herwig Ralf , Indra Alexander , Schmid Daniela , Bock Christoph , Bergthaler Andreas , Stark Alexander , Allerberger Franz , Elling Ulrich , Cochella Luisa 
Published: July 2021

AbstractSARS-CoV-2 has evolved rapidly towards higher infectivity and partial immune escape over the course of the pandemic. This evolution is driven by the enormous virus population, that has infected close to 200 million people by now. Therefore, cost effective and scalable methods are needed to monitor viral evolution globally. Mutation-specific PCR approaches have become inadequate to distinguish the variety of circulating SARS-CoV-2 variants and are unable to detect novel ones. Conversely, whole genome sequencing protocols remain too labor- and cost-intensive to monitor SARS-CoV-2 at the required density. By adapting SARSeq we present a simple, fast, and scalable S-gene tiling pipeline for focused sequencing of the S-gene encoding for the spike protein. This method reports on all sequence positions with known importance for infectivity and immunity, yet scales to >20K samples per run. S-gene tiling is used for nationwide surveillance of SARS-CoV-2 at a density of 10% to 50% of all cases of infection in Austria. SARSeq S-tiling uncovered several infection clusters with variants of concern such as the biggest known cluster of Beta/B.1.351 outside Africa and successfully informed public health measures in a timely manner, allowing their successful implementation. Our close monitoring of mutations further highlighted evolutionary constraints and freedom of the spike protein ectodomain and sheds light on foreseeable evolutionary trajectories.
The human vestibular cortex: functional anatomy, connectivity and the effect of vestibular disease
Authors: Ibitoye Richard T. , Mallas Emma-Jane , Bourke Niall J. , Kaski Diego , Bronstein Adolfo M. , Sharp David J. 
Published: July 2021

AbstractArea OP2 in the posterior peri-sylvian cortex has been proposed to be the core human vestibular cortex. We defined the functional anatomy of OP2 using spatially constrained independent component analysis of functional MRI data from the Human Connectome Project. Ten distinct subregions were identified. Most subregions showed significant connectivity to other areas with vestibular function: the parietal opercula, the primary somatosensory cortex, the supracalcarine cortex, the left inferior parietal lobule and the anterior cingulate cortex. OP2 responses to vestibular and visual-motion were analysed in 17 controls and 17 right-sided unilateral vestibular lesion patients (vestibular neuritis) who had previously undergone caloric and optokinetic stimulation during functional MRI. In controls, a posterior part of right OP2 showed: (a) direction-selective responses to visual motion; and (b) activation during caloric stimulation that correlated positively with perceived self-motion, and negatively with visual dependence. Patients showed abnormal OP2 activity, with an absence of visual or caloric activation of the healthy ear and no correlations with dizziness or visual dependence – despite normal brainstem responses to caloric stimulation (slow-phase nystagmus velocity). A lateral part of right OP2 showed activity that correlated with chronic dizziness (situational vertigo) in patients. Our results define the functional anatomy of OP2 in health and disease. A posterior subregion of right OP2 shows strong functional connectivity to other vestibular regions and a visuo-vestibular profile that becomes profoundly disrupted after vestibular disease. In vestibular patients, a lateral subregion of right OP2 shows responses linked to the challenging long-term symptoms which define poorer clinical outcomes.Significance statementThe human cortical vestibular network is critical to higher vestibular functions such as the perception of self-motion, judgements about verticality (‘which way is up’), and adaptation following peripheral vestibular disease (e.g. vestibular neuritis). The functional organisation of this network has remained poorly understood. In this study, we define the functional anatomy of area OP2 - a core region within the human cortical vestibular network. We identify subregions of OP2 with strong connectivity to other cortical vestibular areas. We show specific subregions of right OP2 process vestibular and visual motion information in health and that such processing is disrupted following peripheral vestibular disease. Abnormal signal processing within OP2 may underpin chronic dizziness following peripheral vestibular disease.
Blood bacterial DNA, intestinal adenoma and colorectal cancer
Authors: Mutignani Massimiliano , Penagini Roberto , Gargari Giorgio , Guglielmetti Simone , Cintolo Marcello , Airoldi Aldo , Leone Pierfrancesco , Carnevali Pietro , Ciafardini Clorinda , Petrocelli Giulio , Mascaretti Federica , Oreggia Barbara , Dioscoridi Lorenzo , Cavalcoli Federica , Primignani Massimo , Pugliese Francesco , Bertuccio Paola , Soru Pietro , Magistro Carmelo , Ferrari Giovanni , Speciani Michela , Bonato Giulia , Bini Marta , Cantù Paolo , Caprioli Flavio , Vangeli Marcello , Forti Edoardo , Mazza Stefano , Tosetti Giulia , Bonzi Rossella , Vecchi Maurizio , Vecchia Carlo La , Rossi Marta 
Published: July 2021

ABSTRACTObjectiveWe aimed to investigate the relation of blood bacterial DNA load and profiling with intestinal adenoma (IA) and colorectal cancer (CRC) patients.DesignWe performed 16S rRNA gene analysis of blood from 100 incident histologically confirmed CRC cases, 100 IA and 100 healthy subjects, matched to cases by centre, sex and age. Bacterial load was analysed using multiple conditional logistic regression. Differences in terms of abundance of bacteria between groups were estimated through analysis based on negative binomial distribution normalization. Random Forest was applied to predict the group assignment.ResultsWe found an overrepresentation of blood 16S rRNA gene copies in colon cancer as compared to tumor-free controls (IA and healthy subjects). The odds ratio of colon cancer for the highest versus the lowest three quintiles of gene copies was 2.62. (95% confidence interval=1.22-5.65). No difference was found for rectal cancer and IA. For high 16S rRNA, community diversity was higher in colon cancers than controls. CRC cases had an enrichment of Peptostreptococcaceae and Acetobacteriaceae and a reduced abundance of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae. Identified variables predicted CRC from control and IA patients with an accuracy of 0.70.ConclusionColon cancer patients had a higher DNA bacterial load and a different bacterial profiling as compared to healthy subjects, IA and rectal cancers, indicating a higher passage of bacteria from gastrointestinal tract to bloodstream. Further studies are needed to confirm this result and exploit it to conceive new non-invasive techniques for an early diagnosis of CRC.
Baseline psychological traits contribute to Lake Louise Acute Mountain Sickness score at high altitude
Authors: Talks Benjamin James , Campbell Catherine , Larcombe Stephanie J , Marlow Lucy , Finnegan Sarah L , Lewis Christopher T , Lucas Samuel J E , Harrison Olivia K , Pattinson Kyle TS 
Published: July 2021

AbstractBackgroundInteroception refers to an individual’s ability to sense their internal bodily sensations. Acute mountain sickness (AMS) is a common feature of ascent to high altitude that is only partially explained by measures of peripheral physiology. We hypothesised that interoceptive ability may explain the disconnect between measures of physiology and symptom experience in AMS.Methods and MaterialTwo groups of 18 participants were recruited to complete a respiratory interoceptive task three times at two-week intervals. The control group remained in Birmingham (140m altitude) for all three tests. The altitude group completed test 1 in Birmingham, test 2 the day after arrival at 2624m, and test 3 at 2728m after an 11-day trek at high altitude (up to 4800m).ResultsBy measuring changes to metacognitive performance, we showed that acute ascent to altitude neither presented an interoceptive challenge, nor acted as interoceptive training. However, AMS symptom burden throughout the trek was found to relate to sea-level measures of anxiety, agoraphobia, and neuroticism.ConclusionsThis suggests that the Lake Louise AMS score is not solely a reflection of physiological changes on ascent to high altitude, despite often being used as such by researchers and commercial trekking companies alike.
Dissection of brain-wide spontaneous and functional somatosensory circuits by fMRI with optogenetic silencing
Authors: Jung Won Beom , Jiang Haiyan , Lee Soohyun , Kim Seong-Gi 
Published: July 2021

AbstractTo further advance functional magnetic resonance imaging (fMRI)-based brain science, it is critical to dissect fMRI activity at the circuit level. To achieve this goal, we combined brain-wide fMRI with neuronal silencing in well-defined regions. Since focal inactivation suppresses excitatory output to downstream pathways, intact input and suppressed output circuits can be separated. Highly specific cerebral blood volume-weighted fMRI was performed with optogenetic simulation of local GABAergic neurons in mouse somatosensory regions. Brain-wide spontaneous somatosensory networks were found mostly in ipsilateral cortical and subcortical areas, which differed from the bilateral homotopic connections commonly observed in resting-state fMRI data. The evoked fMRI responses to somatosensory stimulation in regions of the somatosensory network were successfully dissected, allowing the relative contributions of spinothalamic (ST), thalamocortical (TC), corticothalamic (CT), corticocortical (CC) inputs and local intracortical circuits to be determined. The ventral posterior thalamic nucleus (VPL) receives ST inputs, while the posterior medial thalamic nucleus (POm) receives CT inputs from the primary somatosensory cortex (S1) with TC inputs. The secondary somatosensory cortex (S2) receives mostly direct CC inputs from S1 and a few TC inputs from the VPL. The TC and CC input layers in cortical regions were identified by laminar-specific fMRI responses with a full width at half-maximum of <150 µm. Long-range synaptic inputs in cortical areas were amplified approximately 2-fold by local intracortical circuits, which is consistent with electrophysiological recordings. Overall, whole-brain fMRI with optogenetic inactivation revealed brain-wide, population-based long-range circuits, which could complement data typically collected in conventional microscopic functional circuit studies.
High-throughput production of functional prototissues capable of producing NO for vasodilation
Authors: Zhang Xiangxiang , Li Chao , Liu Fukai , Mu Wei , Ren Yongshuo , Yang Boyu , Han Xiaojun 
Published: July 2021

AbstractBottom-up synthesis of prototissues helps us to understand the internal cellular communications in the natural tissues and their functions, as well as to improve or repair the damaged tissues. The existed prototissues are rarely used to improve the function of living tissues. We demonstrated a methodology to produce spatially programmable prototissues based on the magneto-Archimedes effect in a high-throughput manner. More than 2000 prototissues are produced once within 2 hours. Two-component and three-component spatial coded prototissues are fabricated by varying the addition giant unilamellar vesicles (GUVs) order/number, and the magnetic field distributions. Two-step and three-step signal communications in the prototissues are realized using cascade enzyme reactions. More importantly, the two-component prototissues capable of producing nitric oxide (NO) cause vasodilation of rat blood vessels in the presence of glucose and hydroxyurea. The tension force decreases 2.59 g, meanwhile the blood vessel relaxation is of 31.2%. Our works pave the path to fabricate complicated programmable prototissues, and hold great potential in tissue transplantation in the biomedical field.
Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease
Authors: Assante Gabriella , Chandrasekaran Sriram , Ng Stanley , Tourna Aikaterini , Chung Carolina H. , Isse Kowsar A. , Filippi Celine , Dhawan Anil , Liu Mo , Rozen Steven G. , Hoare Matthew , Campbell Peter , Ballard J. William. O. , Turner Nigel , Morris Margaret J. , Chokshi Shilpa , Youngson Neil A 
Published: July 2021

AbstractThe rate of nonalcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically-driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis. Genome-wide histone acetylation is increased in steatotic livers of rodents fed high fructose or high fat diet. In vitro, steatosis relaxes chromatin and increases DNA damage marker γH2AX, which is reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX are enriched at gene clusters in telomere-proximal regions which contain HCC tumor suppressors in hepatocytes and human fatty livers. Regions of metabolically-driven epigenetic change also have increased levels of DNA mutation in non-cancerous tissue from NAFLD patients. Finally, genome-scale network modelling indicates that redox balance is a key contributor to this mechanism. Thus abnormal histone hyperacetylation is a potential initiating event in HCC carcinogenesis.
A competitive advantage through fast dead matter elimination in confined cellular aggregates
Authors: Pollack Yoav G. , Bittihn Philip , Golestanian Ramin 
Published: July 2021

AbstractCompetition of different species or cell types for limited space is relevant in a variety of biological processes such as biofilm development, tissue morphogenesis and tumor growth. Predicting the outcome for non-adversarial competition of such growing active matter is non-trivial, as it depends on how processes like growth, proliferation and the degradation of cellular matter are regulated in confinement; regulation that happens even in the absence of competition to achieve the dynamic steady state known as homeostasis. Here, we show that passive by-products of the processes maintaining homeostasis can significantly alter fitness. Even for purely pressure-regulated growth and exclusively mechanical interactions, this enables cell types with lower homeostatic pressure to outcompete those with higher homeostatic pressure. We reveal that interfaces play a critical role in the competition: There, growing matter with a higher proportion of active cells can better exploit local growth opportunities that continuously arise as the active processes keep the system out of mechanical equilibrium. We elucidate this effect in a theoretical toy model and test it in an agent-based computational model that includes finite-time mechanical persistence of dead cells and thereby decouples the density of growing cells from the homeostatic pressure. Our results suggest that self-organization of cellular aggregates into active and passive matter can be decisive for competition outcomes and that optimizing the proportion of growing (active) cells can be as important to survival as sensitivity to mechanical cues.
Assessing anatomical changes in male reproductive organs in response to larval crowding using micro-computed tomography imaging
Authors: Morimoto Juliano , Barcellos Renan , Schoborg Todd A. , Nogueira Liebert Parreiras , Colaço Marcos Vinicius 
Published: July 2021

AbstractEcological conditions shape (adaptive) responses at the molecular, anatomical, and behavioural levels. Understanding these responses is key to predict the outcomes of intra- and inter-specific competitions and the evolutionary trajectory of populations. Recent technological advances have enabled large-scale molecular (e.g., RNAseq) and behavioural (e.g., computer vision) studies, but the study of anatomical responses to ecological conditions has lagged behind. Here, we highlight the role of X-Ray micro-computed tomography (micro-CT) in generatingin vivoandex vivo3D imaging of anatomical structures, which can enable insights into adaptive anatomical responses to ecological environments. To demonstrate the application of this method, we manipulated the larval density ofDrosophila melanogasterflies and applied micro-CT to investigate the anatomical responses of the male reproductive organs to varying intra-specific competition levels during development. Our data is suggestive of two classes of anatomical responses which broadly agree with sexual selection theory: increasing larval density led to testes and ejaculatory duct to be overall larger (in volume), while the volume of accessory glands and, to a lesser extent, ejaculatory duct decreased. These two distinct classes of anatomical responses might reflect shared developmental regulation of the structures of the male reproductive system. Overall, we show that micro-CT can be an important tool to advance the study of anatomical (adaptive) responses to ecological environments.
Beneficial effects of novel strains of Aureobasidium pullulans produced 1,3-1,6 β-glucans on non-esterified fatty acid levels in diabetic KKAy mice
Authors: Ikewaki Nobunao , Onaka Takashi , Ikeue Yasunori , Nagataki Mitsuru , Kurosawa Gene , Dedeepiya Vidyasagar Devaprasad , Rajmohan Mathaiyan , Vaddi Suryaprakash , Senthilkumar Rajappa , Preethy Senthilkumar , Abraham Samuel JK 
Published: July 2021

AbstractObesity, metabolic syndrome, associated lipotoxicity and its cascade of events contribute to the majority of the burden related to non-communicable diseases globally. Preventive lifestyle changes aside, several beneficial effects have been reported in type II diabetes mellitus and dyslipidaemia patients with biological response modifier glucans (BRMG) produced as an exopolysaccharide by Aureobasidium pullulans. In this study, we compared two strains (AFO-202 and N-163) that produce beta glucans in alleviating lipotoxicity. This study was performed in obese diabetic mice model of KK-Ay mice, in four groups with six subjects in each group - Group 1: sacrificed on Day 0 for baseline values; Group 2: control (drinking water); Group 3: AFO-202 beta glucan—200 mg/kg/day; Group 4: N-163 beta glucan—300 mg/kg/day. The animals in groups 2–4 had the test solutions administered by gavage once daily for 28 consecutive days. Biochemical analyses were conducted of blood glucose, triglycerides, total cholesterol, LDL cholesterol, HDL cholesterol and non-esterified fatty acids (NEFA). Group 4 (N-163) had the lowest NEFA levels, as compared to the other groups, and marginally decreased triglyceride levels. The groups had no significant differences in blood glucose, HbA1c, triglycerides, or LDL and HDL cholesterol. N-163 produced by A. pullulans decreased NEFA in a diabetic mice model in 28 days. These results, although modest, warrant further in-depth research into lipotoxicity and associated inflammatory cascades in both healthy and disease affected subjects to develop novel strategies for prevention and management.
Effects of reward history on decision-making and movement vigor
Authors: Sukumar Shruthi , Shadmehr Reza , Ahmed Alaa A. 
Published: July 2021

AbstractDuring foraging, animals explore a site and harvest reward, and then abandon that site and travel to the next opportunity. One aspect of this behavior involves decision-making, while the other involves movement control. We recently proposed that control of decision-making and movements may be linked via a desire to maximize a single normative utility: the sum of all rewards acquired, minus all efforts expended, divided by time. If this is the case, then the history of rewards, and not just its immediate availability, should dictate how long one decides to stay and harvest reward, and how fast one travels to the next opportunity. We tested this theory in a series of experiments in which humans used their hand to harvest tokens at a reward patch, and then used their arm to reach toward a subsequent opportunity. Experiencing a history of poor rewards not only led people to forage longer, but they also reached slower toward the next reward site. Thus, reward history had a consistent effect on both the decision-making process regarding when to abandon a reward site, and the motor control process regarding how fast to move to the next opportunity.