Miracle-dz/UniFAR-FTUs huggingface dataset:
Stimulus-induced narrowband gamma oscillations are test-retest reliable in healthy elderly in human EEG

Visual stimulus-induced narrowband gamma oscillations in electroencephalogram (EEG) recordings have been recently shown to be compromised in subjects with Mild Cognitive Impairment or Alzheimer’s Disease (AD), suggesting that gamma could be an inexpensive and easily accessible biomarker for early diagnosis of AD. However, to use gamma as a biomarker, its characteristics should remain consistent across multiple recordings, even when separated over long intervals. Previous magnetoencephalography studies in young subjects have reported that gamma power remains consistent over recordings separated by a few weeks to months. Here, we assessed the consistency of slow (20-35 Hz) and fast gamma (36-66 Hz) oscillations induced by static full-field gratings in male (N=20) and female (N=20) elderly subjects (>49 years) in EEG recordings separated by more than a year, and tested the consistency in the magnitude of gamma power, its temporal evolution and spectral profile. Gamma oscillations had distinct spectral and temporal characteristics across subjects, which remained consistent across recordings (average intraclass correlation, ICC of ∼0.7). Alpha oscillations (8-12 Hz) and steady-state-visually-evoked-potentials (SSVEPs) were also found to be reliable. We further tested how EEG features can be used to identify two recordings as belonging to the same versus different subjects and found high classifier performance (area under ROC curve of ∼0.89), with the temporal evolution of slow gamma and spectral profile emerging as the most informative features. These results suggest that EEG gamma oscillations are reliable across recordings and can be used as a clinical biomarker as well as a potential tool for subject identification. Significance statement We demonstrate the reliability of stimulus-induced gamma oscillations in elderly humans for the first time in EEG. Since gamma has recently been shown to be compromised in patients with Mild Cognitive Impairment or early Alzheimer’s Disease (AD), together these results mark the first steps towards an EEG based clinical biomarker for early diagnosis of AD. We observed high reliability in the power spectrum, gamma power and its temporal characteristics, within the test-retest period of one year. Alpha and steady-state-visually-evoked potential power were also found to be reliable. These spectral and temporal features could also be used to identify EEG recordings as belonging to the same versus different subjects with high performance, suggesting a potentially key role in subject identification also.
Pseudomonas syringae effector AvrE associates with plant membrane nanodomains and binds phosphatidylinositides in vitro

Bacterial phytopathogens deliver effector proteins into host cells as key virulence weapons to cause disease. Extensive studies revealed diverse functions and biochemical properties of different effector proteins from pathogens. In this study, we show that the Pseudomonas syringae effector AvrE, the founding member of a broadly conserved and pathologically important bacterial effector family, binds to phosphatidylinositides (PIPs) in vitro and shares some properties with eukaryotic PROPPINs (β-propellers that bind polyphosphoinositides). In planta pull down experiments with transgenic Arabidopsis plants expressing AvrE revealed that AvrE is associated with several plant proteins including plasma membrane lipid-raft proteins. These results shed new light on the properties of a bacterial effector that is crucial for bacterial virulence in plants.
A cell-sorting-based nano-scale pipeline for cell-type specific proteomics in plants

Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the characteristics of each type of cells will reveal specific cell functions and enhance understanding of how an organism organizes and works. Due to the lack of a method to enrich the particular type of cells and the limited sensitivity and capability of mass spectrometry-based technologies, comprehensive analyses of the proteome in a single plant cell are still impossible. Here we report a high-sensitive and efficient cell-type-specific proteomic pipeline, combining simplified flow cytometry-based fluorescent cell-sorting for fluorescent protoplasts and an optimized nano-scale proteomics method, which allows us to identify more than 1,000 unique proteins from 500 guard cell protoplasts. By this method, we performed an in-depth, quantitative comparison between the proteomics of guard cells and mesophyll cells, and revealed that the enrichment of signal transduction-related proteins enables guard cells to respond to various environmental stimuli quickly. This method was also applied to profile the proteome of different cells in root tips of Arabidopsis and rice seedlings. Thus, this pipeline is applicable to various types of cells in plant or non-plant systems to acquire systemic knowledge of how cells work specifically and in highly organized multiple cell organisms.
Efficient gradient boosting for prognostic biomarker discovery

Motivation Gradient boosting decision tree (GBDT) is a powerful ensemble machine learning method that has the potential to accelerate biomarker discovery from high-dimensional molecular data. Recent algorithmic advances, such as Extreme Gradient Boosting (XGB) and Light Gradient Boosting (LGB), have rendered the GBDT training more efficient, scalable and accurate. These modern techniques, however, have not yet been widely adopted in biomarkers discovery based on patient survival data, which are key clinical outcomes or endpoints in cancer studies. Results In this paper, we present a new R package Xsurv as an integrated solution which applies two modern GBDT training framework namely, XGB and LGB, for the modeling of censored survival outcomes. Based on a comprehensive set of simulations, we benchmark the new approaches against traditional methods including the stepwise Cox regression model and the original gradient boosting function implemented in the package gbm. We also demonstrate the application of Xsurv in analyzing a melanoma methylation dataset. Together, these results suggest that Xsurv is a useful and computationally viable tool for screening a large number of prognostic candidate biomarkers, which may facilitate cancer translational and clinical research. Availability Xsurv is freely available as an R package at: https://github.com/topycyao/Xsurv Contact xuefeng.wang@moffitt.org Supplementary information Supplementary data are available at Bioinformatics online.
Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes

Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on ~1,550 genes previously described as tumor suppressors, oncogenes, ageing genes in addition to a novel Build of the CellAge database of cell-senescence genes (version 2), herein presented for the first time. Specifically, we analyzed dN/dS rates, positive selection, gene expression (RNA-seq) and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan and body mass we identified 67 genes that in primates co-evolved with those traits. Further, we identified 6 genes, important for immunity, neurodevelopment and telomere maintenance (including TERF2), under positive selection in the great ape ancestor. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that ~8% of the longevity genes are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel “ape-specific” enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus (SVAs). In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.
Role of Cloud Point of the Capping Agent (Nonionic Surfactant, Triton X-100) on the Synthesis of Silver Nanoparticles

The solution behavior of the nonionic surfactants below and above the cloud point (CP) is quite different. Below CP, a single phase of molecular or micellar solution exists, whereas above the CP, the solution separates into two phases: the first one is denser and smaller phase and contains most of the surfactant and the other one is relatively a voluminous aqueous phase and has surfactant concentration close to the critical micelle concentration (cmc). There are many reports available where nonionic surfactant is used as capping agent. But, to the best of our knowledge, there is no report on the CP's role on the synthesis of nanoparticles (NPs). Therefore, it is very important to understand the role of the CP on the synthesis of NPs. In the present work, we report the role of the clouding of the nonionic surfactant Triton X-100 (using as capping agent) on the synthesis of AgNPs below and above the CP. The morphology of AgNPs was studied by transmission electron microscopy (TEM), dynamic light scattering (DLS), UV–Vis absorption, etc., techniques. Below the CP, spherical polydisperse particles of 12 ± 5 nm mean diameter were found, whereas above the CP, the aggregated particles with higher diameter were found. GRAPHICAL ABSTRACT
The Evolution of Safe and Effective Coaguligands for Vascular Targeting and Precision Thrombosis of Solid Tumors and Vascular Malformations

In cardiovascular and cerebrovascular biology, control of thrombosis and the coagulation cascade in ischemic stroke, myocardial infarction, and other coagulopathies is the focus of significant research around the world. Ischemic stroke remains one of the largest causes of death and disability in developed countries. Preventing thrombosis and protecting vessel patency is the primary goal. However, utilization of the body’s natural coagulation cascades as an approach for targeted destruction of abnormal, disease-associated vessels and tissues has been increasing over the last 30 years. This vascular targeting approach, often termed “vascular infarction”, describes the deliberate, targeted delivery of a thrombogenic effector to diseased blood vessels with the aim to induce localized activation of the coagulation cascade and stable thrombus formation, leading to vessel occlusion and ablation. As systemic delivery of pro-thrombotic agents may cause consternation amongst traditional stroke researchers, proponents of the approach must suitably establish both efficacy and safety to take this field forward. In this review, we describe the evolution of this field and, with a focus on thrombogenic effectors, summarize the current literature with respect to emerging trends in “coaguligand” development, in targeted tumor vessel destruction, and in expansion of the approach to the treatment of brain vascular malformations.
Oviposition behavior of Helicoverpa armigera in soybean Comportamento de oviposição de Helicoverpa armigera em soja

Arq. Inst. Biol., v.87, 1-7, e1252018, 2020 RESUMO: O objetivo deste trabalho foi avaliar o comportamento de oviposição de Helicoverpa armigera confinadas em diferentes densidades de casais e estádios fenológicos de plantas de soja, e a resistência de genótipos de soja na categoria não preferência para oviposição para H. armigera. Para o comportamento de oviposição de H. armigera, foram avaliadas as densidades de um, dois e quatro casais por planta, e os estádios fenológicos vegetativo, de florescimento e reprodutivo de plantas de soja do cultivar BR 16. Para o teste de não preferência para oviposição, oito genótipos de soja foram utilizados e um índice de preferência para oviposição foi calculado. A densidade de tricomas nos folíolos foi quantificada para ser correlacionada com a oviposição de H. armigera. A densidade de um casal e plantas de soja em estádio reprodutivo proporcionaram os melhores resultados quanto à preferência para oviposição de H. armigera em soja. Os genótipos M8230 RR e W711 RR apresentaram características de resistência, enquanto o PI 227687 foi o mais preferido para oviposição. A quantidade de tricomas influenciou positivamente no comportamento de oviposição das fêmeas.
InvestigatingDomain Transfer andView- point in the Context of Person Re-Id

Deep learning has significantly improved Re-Id performance but it requires a large amount of data, however, obtaining data is expensive from both time and money perspective. Inspired by ImageNet pretrained models and synthetic data generation techniques, this paper investigates to utilise real-world and synthetic Re-Id datasets to augment task performance. Firstly, we propose two methods to apply external Re-Id data, NDTL (Neighbour-Domain Transfer Learning) and NDDS (Neighbour-Domain Data Stitching). Secondly, we quantitatively illustrate that both real-world and synthetic data could mitigate Re-Id data shortage problems, using Re-Id dataset to pre-train models is better than using ImageNet, we achieve up to 28.2% mAP improvement on DukeMTMC and 5.2% on Market-1501. Moreover, we find out that viewpoint, one of Re-Id relevant factors, has the an influence on the system performance due to viewpoint-wise non-alignment and unbalance of the original dataset, it also assists the performance if train set is augmented balanced. Our research strongly illustrates both real-world and synthetic Re-Id dataset can effectively augment Re-Id task, viewpoint is an essential factor and based on which, train-test distribution dramatically influences Re-Id performance, and balancing train classes are also helpful to improve the performance.
Probing the Energetic Metabolism of Resting Cysts under Different Conditions from Molecular and Physiological Perspectives in the Harmful Algal Blooms-Forming Dinoflagellate Scrippsiella trochoidea

Energetic metabolism is essential in maintaining the viability of all organisms. Resting cysts play important roles in the ecology of dinoflagellates, particularly for harmful algal blooms (HABs)-causative species. However, the energetic metabolism underlying the germination potency maintenance of resting cysts of dinoflagellate have been extremely scarce in studies from physiological and, particularly, molecular perspectives. Therefore, we used the cosmopolitan Scrippsiella trochoidea as a representative of HABs-forming and cyst-producing dinoflagellates in this work to obtain novel insights into the molecular mechanisms, regulating the energetic metabolism in dinoflagellate resting cysts, under different physical condition. As the starting step, we established a cDNA subtractive library via suppression subtractive hybridization (SSH) technology, from which we screened an incomplete sequence for the β subunit of ATP synthase gene (β-F1-ATPase), a key indicator for the status of cell’s energetic metabolism. The full-length cDNA of β-F1-ATPase gene from S.trochoidea (Stβ-F1-ATPase) was then obtained via rapid amplification of cDNA ends (RACE) (Accession: MZ343333). Our real-time qPCR detections, in vegetative cells and resting cysts treated with different physical conditions, revealed that (1) the expression of Stβ-F1-ATPase in resting cysts was generally much lower than that in vegetative cells, and (2) the Stβ-F1-ATPase expressions in the resting cysts under darkness, lowered temperature, and anoxia, and during an extended duration of dormancy, were significantly lower than that in cysts under the condition normally used for culture-maintaining (a 12 h light:12 h dark cycle, 21 °C, aerobic, and newly harvested). Our detections of the viability (via Neutral Red staining) and cellular ATP content of resting cysts, at the conditions corresponding to the abovementioned treatments, showed that both the viability and ATP content decreased rapidly within 12 h and then maintained at low levels within the 4-day experimentation under all the three conditions applied (4 °C, darkness, and anoxia), which are well in accordance with the measurements of the transcription of Stβ-F1-ATPase. These results demonstrated that the energy consumption of resting cysts reaches a low, but somehow stable, level within a short time period and is lower at low temperature, darkness, and anoxia than that at ambient temperature. Our work provides an important basis for explaining that resting cysts survive long-term darkness and low temperature in marine sediments from molecular and physiological levels.
The Syndromes of Thrombotic Microangiopathy: A Critical Appraisal on Complement Dysregulation

Thrombotic microangiopathy (TMA) is a rare and potentially life-threatening condition that can be caused by a heterogeneous group of diseases, often affecting the brain and kidneys. TMAs should be classified according to etiology to indicate targets for treatment. Complement dysregulation is an important cause of TMA that defines cases not related to coexisting conditions, that is, primary atypical hemolytic uremic syndrome (HUS). Ever since the approval of therapeutic complement inhibition, the approach of TMA has focused on the recognition of primary atypical HUS. Recent advances, however, demonstrated the pivotal role of complement dysregulation in specific subtypes of patients considered to have secondary atypical HUS. This is particularly the case in patients presenting with coexisting hypertensive emergency, pregnancy, and kidney transplantation, shifting the paradigm of disease. In contrast, complement dysregulation is uncommon in patients with other coexisting conditions, such as bacterial infection, drug use, cancer, and autoimmunity, among other disorders. In this review, we performed a critical appraisal on complement dysregulation and the use of therapeutic complement inhibition in TMAs associated with coexisting conditions and outline a pragmatic approach to diagnosis and treatment. For future studies, we advocate the term complement-mediated TMA as opposed to the traditional atypical HUS-type classification.
Willingness to Receive the COVID-19 and Seasonal Influenza Vaccines among the Saudi Population and Vaccine Uptake during the Initial Stage of the National Vaccination Campaign: A Cross-Sectional Survey

This study aimed to assess the willingness to receive the coronavirus disease 2019 (COVID-19) and seasonal influenza vaccines and vaccine uptake during the early stage of the national vaccination campaign in Saudi Arabia. A cross-sectional online survey was conducted among adult Saudis between 20 January and 20 March 2021. The questionnaire addressed vaccine hesitancy, perceived risk, willingness, and vaccine uptake. Approximately 39% of the participants expressed vaccine hesitancy, and 29.8% and 24% felt highly vulnerable to contracting COVID-19 and seasonal influenza, respectively. The majority (59.5%) were willing to receive the COVID-19 vaccine, although only 31.7% were willing to receive the flu vaccine. Adjusted analysis showed that vaccine hesitancy (OR 0.34, 95% CI 0.27–0.43) and the perception of being at high risk (OR 2.78, 95% CI 1.68–4.60) independently affected the intention to be vaccinated. Vaccine hesitancy was similar among those who were willing to be vaccinated (29.8%) and those who had already been vaccinated (33.1%). The perceived risk was significantly higher among those who had been vaccinated (48.1%) than among those who were willing to be vaccinated but had not yet been vaccinated (29.1%). In conclusion, the acceptance of the COVID-19 vaccine in Saudi Arabia is high. Saudis who received the vaccine had a similar level of vaccine hesitancy and a higher level of perceived risk.
S000305541900042X 1029..1044

Doethnic riots affect prosocial behavior? A common view among scholars of ethnic violence is that riots increase cooperation within the warring groups, while cooperation across groups is reduced. We revisit this hypothesis by studying the aftermath of the 2010Osh riot inKyrgyzstan, which saw Kyrgyz from outside the city kill over 400 Uzbeks. We implement a representative survey, which includes unobtrusive experimental measures of prosocial behavior. Our causal identification strategy exploits variation in the distance of neighborhoods to armored military vehicles, which were instrumental in orchestrating the riot. We find that victimized neighborhoods show substantially lower levels of prosocial behavior. Importantly, we demonstrate that the reduction is similarly stark both within and across groups. Using qualitative interviews, we parse out two mechanisms that help explain the surprising reduction in ingroup prosociality: Victimized Uzbeks felt abandoned by their coethnics, and variation in victimization created a feeling of suspicion.
Biotechnological Insights on the Expression and Production of Antimicrobial Peptides in Plants

The emergence of drug-resistant pathogens poses a serious critical threat to global public health and requires immediate action. Antimicrobial peptides (AMPs) are a class of short peptides ubiquitously found in all living forms, including plants, insects, mammals, microorganisms and play a significant role in host innate immune system. These peptides are considered as promising candidates to treat microbial infections due to its distinct advantages over conventional antibiotics. Given their potent broad spectrum of antimicrobial action, several AMPs are currently being evaluated in preclinical/clinical trials. However, large quantities of highly purified AMPs are vital for basic research and clinical settings which is still a major bottleneck hindering its application. This can be overcome by genetic engineering approaches to produce sufficient amount of diverse peptides in heterologous host systems. Recently plants are considered as potential alternatives to conventional protein production systems such as microbial and mammalian platforms due to their unique advantages such as rapidity, scalability and safety. In addition, AMPs can also be utilized for development of novel approaches for plant protection thereby increasing the crop yield. Hence, in order to provide a spotlight for the expression of AMP in plants for both clinical or agricultural use, the present review presents the importance of AMPs and efforts aimed at producing recombinant AMPs in plants for molecular farming and plant protection so far.
Running title: FAST SPREADING OF Ovachlamys fulgens IN BRAZIL Academy Section: CELLULAR AND MOLECULAR BIOLOGY

The Japanese invasive jumping snail Ovachlamys fulgens is a pest of ornamental plants and an intermediate host of a nematode that causes eosinophilic meningitis. We expand its distribution to eight municipalities from Rio de Janeiro State, and one locality from the Paraná State, and generated for the first time partial sequences of the cytochrome c oxidase subunit I (COI) gene for Brazilian populations. External morphology, reproductive system, shell, radula, and jaw were also analyzed and described. Twenty-one lots were collected from Rio de Janeiro, Niterói, Magé, Miguel Pereira, Petrópolis, Teresópolis, Nova Friburgo, Bom Jardim and Paraty, in Rio de Janeiro State, and from Foz do Iguaçu, Paraná State. External morphology, shell and reproductive system were typical of O. fulgens, with some peculiarities found in the shell and radula. A single haplotype was found, which was 100% similar to sequences of COI available in GenBank for specimens from Japan and Argentina. The species seems to be adapted to many habitats and be rapidly expanding its distribution in Southeastern and Southern Brazil, and other South America countries. We highlight the importance of monitoring O. fulgens, considering its potential to compete with native mollusks, attack several plants, and be a transmitter of diseases.