Miracle-dz/UniFAR-FTUs huggingface dataset:
Atrazine measurements using surface transverse wave devices

We have developed a new kind of chemical sensor based on the surface transverse have device. The sensor resembles a surface acoustic have sensor with the addition of a metal grating between the transducers and a different crystal orientation. Unlike surface acoustic wave and flexural plate wave devices, no fluid compression is associated with the wave motion. This sensor operates at 250 MHz and is ideally suited to measurements of surface-attached mass under fluid immersion. By immobility atrazine to the surface of the sensor device, we demonstrated the detection of atrazine in the range of 0.06 ppb to 10 ppm. The sensor surface was refreshed by dissociating the antibody, and 100 repeated measurements were made. The measurement can be made rapidly (<3 min), in near real time and without the use of labeled reagents
Inverse regulation of Vibrio cholerae biofilm dispersal by polyamine signals

The global pathogen Vibrio cholerae undergoes cycles of biofilm formation and dispersal in the environment and the human host. Little is understood about biofilm dispersal. Here, we show that MbaA, a periplasmic polyamine sensor, and PotD1, a polyamine importer, regulate V. cholerae biofilm dispersal. Spermidine, a commonly produced polyamine, drives V. cholerae dispersal, whereas norspermidine, an uncommon polyamine produced by vibrios, inhibits dispersal. Spermidine and norspermidine differ by one methylene group. Both polyamines function to control dispersal via periplasmic detection by MbaA and subsequent signal relay. Biofilm dispersal fails in the absence of PotD1 because reuptake of endogenously produced norspermidine does not occur, so it accumulates in the periplasm where it stimulates MbaA. These results suggest that V. cholerae uses MbaA to monitor environmental polyamines, blends of which potentially provide information about numbers of ‘self’ and ‘other’. This information is used to dictate whether or not to disperse from biofilms.
An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development

Accurate standards and extensive development datasets are the foundation of technical progress. To facilitate benchmarking and development, we sequence 9 samples, covering the Genome in a Bottle truth sets on multiple instruments (NovaSeq, HiSeqX, HiSeq4000, PacBio Sequel II System) and sample preparations (PCR-Free, PCR-Positive) for both whole genome and multiple exome kits. We benchmark pipelines, quantifying strengths and limitations for sequencing and analysis methods. We identify variability within and between instruments, preparation methods, and analytical pipelines, across various sequencing depths. We discuss the relevance of this variability to downstream analyses, and strategies to reduce variability.
Drosophila neural stem cells show a unique dynamic pattern of gene expression that is influenced by environmental factors

With the aim of developing a sensor for chromosome loss in vivo, we used the well-established GAL4/GAL80 system combined with a visual GFP marker in Drosophila. We show a low frequency of green cells in most Drosophila tissues, suggesting low aneuploidy levels. Unexpectedly, in the brain, GFP positive cells are more frequent, but in this case, they do not represent chromosome loss. Using genetic manipulations, RNA FISH and time-lapse microscopy, we uncovered a dynamic and reversible silencing of GAL80 that occurs in Drosophila neural stem cells. Further, we showed that this novel gene expression regulation is influenced by environmental changes such as temperature variations or food composition. These results have important implications for the Drosophila community, namely the possible interpretation of false positive cells in clonal experiments. Additionally, they also highlight a level of mosaicism and plasticity in the brain, consistent with possible epigenetic regulation of fly chromosomes, which is different from other organs and tissues.
Basal G-protein-gated inwardly rectifying potassium (Kir3/GirK) channels activity governs synaptic plasticity that supports dorsal hippocampus-dependent cognitive functions

G-protein-gated inwardly rectifying potassium (Kir3/GirK) channel is the effector of many G-protein-coupled receptors. Its dysfunction has been linked to the pathophysiology of Down syndrome, Alzheimer’s and Parkinson’s diseases, psychiatric disorders, epilepsy, drug addiction, or alcoholism. GirK channels are constitutively activated in the dorsal hippocampus contributing to resting membrane potential, and their synaptic activation compensates any excitation excess. Here, in order to elucidate the role of GirK channels activity in the maintenance of dorsal hippocampus-dependent cognitive functions, their involvement in controlling neuronal excitability at different levels of complexity was examined. For that purpose, basal GirK activity was pharmacologically modulated by two specific drugs: ML297, a GirK channel opener, and Tertiapin-Q, a GirK channel blocker. Ex vivo, using dorsal hippocampal slices, we studied pharmacological GirK modulation effect on synaptic plasticity processes induced in CA1 by Schaffer collateral stimulation. In vivo, we performed acute intracerebroventricular injections of both GirK modulators to study their contribution to CA3–CA1 synapse electrophysiological properties, synaptic plasticity, and learning and memory capabilities during hippocampal dependent tasks. We found that pharmacological disruption of basal GirK activity in dorsal hippocampus, causing either function gain or loss, induced learning and memory deficits by a mechanism involving neural excitability impairments and alterations in induction and maintenance of long-term synaptic plasticity processes. These results support the contention that an accurate control of GirK activity must take place in the hippocampus to sustain cognitive functions. Significance Statement The dorsal hippocampus mostly performs cognitive functions related to contextual/spatial associations. These functions rely on synaptic plasticity processes that are critically ruled by a finely tuned neural excitability. Being the downstream physiological effectors of a variety of G-coupled receptors, activation of G protein-gated inwardly rectifying K+ (GirK) channels induces neurons to hyperpolarize, contributing to neural excitability throughout the control of excitatory excess. Here, we demonstrate that modulation of basal GirK channels activity, causing either function gain or loss, transforms HFS-induced LTP into LTD, inducing deficits in dorsal hippocampus-dependent learning and memory. Together, our data show a crucial GirK activity-mediated mechanism that governs synaptic plasticity direction and modulates subsequent hippocampal-dependent cognitive functions.
Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America

We report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.
The Tomato brown rugose fruit virus movement protein overcomes Tm-22 resistance while attenuating viral transport

Tomato brown rugose fruit virus (ToBRFV) is a new virus of the Tobamovirus genus, causing substantial damage to tomato crops in the Middle East. Reports of recent ToBRFV outbreaks from around the world indicate an emerging global epidemic. ToBRFV overcomes all tobamovirus resistances in tomato, including the durable Tm-22 resistance gene. Here, we show that the ToBRFV movement protein (MPToBRFV) is the cause for overcoming Tm-22 resistance. Transient expression of MPToBRFV failed to activate the Tm-22 resistance response. Replacement of the original MP sequences of Tomato mosaic virus (ToMV) with MPToBRFV enabled this recombinant virus to overcome Tm-22 resistance. Hybrid protein analysis revealed that the resistance-breaking elements are located between MPToBRFV amino acids 1 and 216, and not the C terminus as previously assumed. Interestingly, replacement of Tobacco mosaic virus (TMV) and ToMV MPs with MPToBRFV caused an attenuation of systemic infection of both viruses. Cell-to-cell movement analysis revealed that MPToBRFV moves less effectively compared to the TMV MP (MPTMV). These findings suggest that overcoming Tm-22 is associated with attenuated MP function. This viral fitness cost may explain the high durability of Tm-22 resistance, which had remained unbroken for over 60 years.
Swallowing‐related neural oscillation: an intracranial EEG study

Swallowing is a unique movement due to the indispensable orchestration of voluntary and involuntary movement. The transition from voluntary to involuntary swallowing is executed on the order of milliseconds. We hypothesized that its neural mechanism is revealed by high frequency cortical activities. Eight epileptic participants fitted with intracranial electrodes over the orofacial cortex were asked to swallow a water bolus, and cortical oscillatory changes, including high γ band (75–150 Hz) and β band (13–30 Hz) were investigated at the time of mouth-opening, water-injection, and swallowing. High γ power increases associated with mouth-opening were observed in the ventrolateral prefrontal cortex with water-injection in the lateral central sulcus and with swallowing in the region along the Sylvian fissure. Mouth-opening induced a β power decrease, which continued until the completion of swallowing. The high γ burst activity was focal and specific to swallowing, however, the β activities were extensive and not specific to swallowing. At the boundary time between voluntary and involuntary swallowing, swallowing-related high γ power achieved the peak, and subsequently, the power decreased. We demonstrated three distinct activities related to mouth-opening, water-injection, and swallowing induced at different timings, using high γ activities. The peak of high γ power related to swallowing suggests that during voluntary swallowing phases, the cortex is the main driving force for swallowing rather than the brain stem.
Evolution-inspired dissection of caspase activities enables the redesign of caspase-4 into an LPS sensing interleukin-1 converting enzyme

Innate immune signaling pathways comprise multiple proteins that promote inflammation. This multistep means of information transfer suggests that complexity is a prerequisite for pathway design. Herein, we examined this possibility by studying caspases that regulate inflammasome-dependent inflammation. Several caspases differ in their ability to recognize bacterial LPS and cleave interleukin-1β (IL-1β). No caspase is known to contain both activities, yet distinct caspases with complementary activities bookend an LPS-induced pathway to IL-1β cleavage. Using unique caspases present in carnivorans as a guide, we identified molecular determinants of IL-1β cleavage specificity within caspase-1. This knowledge enabled the redesign of human caspase-4 to operate as a one-protein signaling pathway, which intrinsically links LPS detection to IL-1β cleavage and release, independent of inflammasomes. Strikingly, cat caspase-4 displays the activities of redesigned human caspase-4. These findings illustrate natural signaling pathway diversity and highlight how multistep innate immune pathways can be condensed into a single protein.
A new Petri Net Model of Working Memory to Predict the Root Causes of Attention Deficit Disorder Symptoms

Working memory is a system that helps us to store, retrieve, and manipulate information for a short period. The improper function of working memory is highly reported in people with attention deficit disorder. Attention deficit disorder is one of the most common disruptive behavioral disorders in children. Finding the actual reasons that may lead to inattentive symptoms is still an enigma for scientists. In this study, a model was proposed to show the flow of information through sensory, long-term, and working memory based on the Petri net approach. A new “selective updating” mechanism is also suggested. It is speculated that the central executive part of working memory uses this mechanism for updating the less important content with new incoming essential inputs. The analysis of the proposed model shows how an abnormality in the time setting or unexpected delays in information transmission may lead to some symptoms of inattention. These predictions about the possible causes of inattentive symptoms would be valuable for psychologists to find new possible treatments. This study also illustrates the great potential of Petri net approach for modeling and analysis of biological systems.
Analysis of Lexical Semantic Changes in Corpora with the Diachronic Engine

English. With the growing availability of digitized diachronic corpora, the need for tools capable of taking into account the di-achronic component of corpora becomes ever more pressing. Recent works on di-achronic embeddings show that computational approaches to the diachronic analysis of language seem to be promising, but they are not user friendly for people without a technical background. This paper presents the Diachronic Engine , a sys-tem for the diachronic analysis of corpora lexical features. Diachronic Engine computes word frequency, concordances and collocations taking into account the temporal dimension. It is also able to compute temporal word embeddings and time-series that can be exploited for lexical semantic change detection.
Odd–even effect on viscoelastic properties of twin-dimer nematic liquid crystals

By using a combination of dynamic light scattering and capacitance measurements, we investigate the viscoelastic properties of nematic liquid crystalline α,ω-bis(4-cyanobiphenyl-4′-yloxy)alkane (BCBO-m) dimers and the corresponding 6OCB monomer. The results show that the K11 and K33 elastic constants are larger for the even-m dimers than for the odd-m dimers. K11 and K33 are twice as large for the odd-m dimers than for the 6OCB monomer, and the ratios K33/K11 ~ 2 are similar to that of 6OCB over the entire range of temperature investigated. The even-m dimers are characterised by large K11 and K33, which are respectively 3 and 10 times larger than the corresponding values for 6OCB at T/TNI = 0.980. Furthermore, K33/K11 = 6 upon decreasing T/TNI to 0.943. In contrast, the viscosities ηsplay and ηbend are not characteristic of dimers. The viscosity ηsplay increases with increasing molecular mass and ηbend is comparable to the corresponding value for 6OCB.
Irrelevant speech disrupts memory more 2 when spoken by a familiar talker

23 When listening, familiarity with an attended talker’s voice improves speech 24 comprehension. Here, we instead investigated the effect of familiarity with a distracting 25 talker. In an irrelevant-speech task, we assessed listeners’ working memory for the serial 26 order of spoken digits when a task-irrelevant, distracting sentence was produced by either 27 a familiar or an unfamiliar talker. We tested two groups of listeners using the same 28 experimental procedure. The first group were undergraduate psychology students (N=66) 29 who had attended an introductory statistics course. Critically, each student had been 30 taught by one of two course instructors, whose voices served as familiar and unfamiliar 31 task-irrelevant talkers. The students made more errors when the task-irrelevant sentence 32 was produced by the familiar compared to the unfamiliar talker. There was evidence for 33 the absence of this effect in a second group of listeners — that is, family members and 34 friends (N=20) who had known either one of the two talkers for more than ten years. While 35 familiarity with an attended talker benefits speech comprehension, our findings indicate 36 that familiarity with an ignored talker deteriorates working memory for target speech. The 37 absence of this effect for family members and friends suggests that the degree of talker 38 familiarity modulates distraction by irrelevant speech. 39
State estimation of chemical engineering systems tending to multiple solutions

A well-evaluated state covariance matrix avoids error propagation due to divergence issues and, thereby, it is crucial for a successful state estimator design. In this paper we investigate the performance of the state covariance matrices used in three unconstrained Extended Kalman Filter (EKF) formulations and one constrained EKF formulation (CEKF). As benchmark case studies we have chosen: a) a batch chemical reactor with reversible reactions whose system model and measurement are such that multiple states satisfy the equilibrium condition and b) a CSTR with exothermic irreversible reactions and cooling jacket energy balance whose nonlinear behavior includes multiple steady-states and limit cycles. The results have shown that CEKF is in general the best choice of EKF formulations (even if they are constrained with an ad hoc clipping strategy which avoids undesired states) for such case studies. Contrary to a clipped EKF formulation, CEKF incorporates constraints into an optimization problem, which minimizes the noise in a least square sense preventing a bad noise distribution. It is also shown that, although the Moving Horizon Estimation (MHE) provides greater robustness to a poor guess of the initial state, converging in less steps to the actual states, it is not justified for our examples due to the high additional computational effort.
Neuropredictome: a data-driven predictome for cognitive, psychiatric, medical, and lifestyle factors on the brain

Most neuroimaging studies individually provide evidence on a narrow aspect of the human brain function, on distinct data sets that often suffer from small sample sizes. More generally, the high technical and cost demands of neuroimaging studies (combined with the statistical unreliability of neuroimaging pilot studies) may lead to observational bias, discouraging discovery of less obvious associations that nonetheless have important neurological implications. To address these problems, we built a machine-learning based classification framework, NeuroPredictome, optimized for the reliability and robustness of its associations. NeuroPredictome is grounded in a large-scale dataset, UK-Biobank (N=19,831), which includes resting and task functional MRI as well as structural T1-weighted and diffusion tensor imaging. Participants were assessed with respect to a comprehensive set of 5,034 phenotypes, including the physical and lifestyle factors most relevant to general medicine. Results generated by data-driven classifiers were then cross-validated, using deep-learning textual analyses, against 14,371 peer-reviewed research articles, providing an unbiased hypothesis-generator of linkages between diverse phenotypes and the brain. Our results show that neuroimaging reveals as many neurological links to physical and lifestyle factors as to cognitive factors, supporting a more integrative approach to medicine that considers disease interactions between multiple organs and systems.
Extended in vitro inactivation of SARS-CoV-2 by titanium dioxide surface coating

SARS-CoV-2 transmission occurs via airborne droplets and surface contamination. We show tiles coated with TiO2 120 days previously can inactivate SARS-CoV-2 under ambient indoor lighting with 87% reduction in titres at 1h and complete loss by 5h exposure. TiO2 coatings could be an important tool in containing SARS-CoV-2.
The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and a global resource for epigenetics research from the FDA’s Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus was on 5-methylcytosine modifications. Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), one enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC), and single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, BWAMeth, and GemBS), we found overall high concordance between assays (R=0.87-R0.93), differences in efficency of read mapping and CpG capture and coverage, and platform performance. The data provided herein can guide continued used of these reference materials in epigenomics assays, as well as provide best practices for epigenomics research and experimental design in future studies.