Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity begets diversity under microbial niche construction

Microbial interactions are expected to modulate microbial diversity, but whether they inhibit or stimulate further diversity in complex microbial communities, and how, remains poorly understood. By assembling microbial communities in multiple identical habitats with a single limiting nutrient, here we provide direct evidence for the role of microbial niche construction and cross-feeding in driving a positive relationship between community diversity and focal lineage diversity in microbial communities. Combining these experiments with simulations, we show that this positive relationship is not inevitable but depends on the underlying metabolic structure of by-product secretions and uptake between different taxonomic levels.
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

Severe COVID-19 patients present a clinical and laboratory overlap with other hyperinflammatory conditions such as hemophagocytic lymphohistiocytosis (HLH). However, the underlying mechanisms of these conditions remain to be explored. Here, we investigated the transcriptome of 1596 individuals, including patients with COVID-19 in comparison to healthy controls, other acute inflammatory states (HLH, multisystem inflammatory syndrome in children [MIS-C], Kawasaky disease [KD]), and different respiratory infections (seasonal coronavirus, influenza, bacterial pneumonia). We observed that COVID-19 and HLH share immunological pathways (cytokine/chemokine signaling and neutrophil-mediated immune responses), including gene signatures that stratify COVID-19 patients admitted to the intensive care unit (ICU) and COVID-19_nonICU patients. Of note, among the common differentially expressed genes (DEG), there is a cluster of neutrophil-associated genes that reflects a generalized hyperinflamatory state since it is also dysregulated in patients with KD and bacterial pneumonia. These genes are dysregulated at protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins that point to neutrophil hyperactivation in COVID-19 patients admitted to the intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.
Self-assembly of pericentriolar material in interphase cells lacking centrioles

The major microtubule-organizing center (MTOC) in animal cells, the centrosome, comprises a pair of centrioles surrounded by pericentriolar material (PCM), which nucleates and anchors microtubules. Centrosome assembly depends on PCM binding to centrioles, PCM self-association and dyneinmediated PCM transport, but the self-assembly properties of PCM in interphase cells are poorly understood. Here, we used experiments and modeling to study centriole-independent features of interphase PCM assembly. We showed that when centrioles are lost due to PLK4 depletion or inhibition, dynein-based PCM transport and PCM self-clustering are sufficient to form a single compact MTOC, which generates a dense radial microtubule array. Interphase PCM self-assembly depends on γ-tubulin, pericentrin, CDK5RAP2 and ninein, but not NEDD1, CEP152 or CEP192. Formation of a compact acentriolar MTOC is inhibited by AKAP450-dependent PCM recruitment to the Golgi or by randomly organized CAMSAP2-stabilized microtubules, which keep PCM mobile and prevent its coalescence. Linking of CAMSAP2 to a minus-end-directed motor leads to the formation of an MTOC, but MTOC compaction requires cooperation with pericentrin-containing self-clustering PCM. Our data reveal that interphase PCM contains a set of components that can self-assemble into a compact structure and organize microtubules, but PCM self-organization is sensitive to motor-and microtubule-based rearrangement.
Possible Cross Reactivity of Feline and White-tailed Deer Antibodies Against the SARS-CoV-2 Receptor Binding Domain

In late 2019, a novel coronavirus began circulating within humans in central China. It was designated SARS-CoV-2 because of its genetic similarities to the 2003 SARS coronavirus (SARS-CoV). Now that SARS-CoV-2 has spread worldwide, there is a risk of it establishing new animal reservoirs and recombination with native circulating coronaviruses. To screen local animal populations in the United States for exposure to SARS-like coronaviruses, we developed a serological assay using the receptor binding domain (RBD) from SARS-CoV-2. SARS-CoV-2’s RBD is antigenically distinct from common human and animal coronaviruses allowing us to identify animals previously infected with SARS-CoV or SARS-CoV-2. Using an indirect ELISA for SARS-CoV-2’s RBD, we screened serum from wild and domestic animals for the presence of antibodies against SARS-CoV-2’s RBD. Surprisingly pre-pandemic feline serum samples submitted to the University of Tennessee Veterinary Hospital were ∼50% positive for anti-SARS RBD antibodies. Some of these samples were serologically negative for feline coronavirus (FCoV), raising the question of the etiological agent generating anti-SARS-CoV-2 RBD cross-reactivity. We also identified several white-tailed deer from South Carolina with anti-SARS-CoV-2 antibodies. These results are intriguing as cross-reactive antibodies towards SARS-CoV-2 RBD have not been reported to date. The etiological agent responsible for seropositivity was not readily apparent, but finding seropositive cats prior to the current SARS-CoV-2 pandemic highlights our lack of information about circulating coronaviruses in other species. Importance We report cross-reactive antibodies from pre-pandemic cats and post-pandemic South Carolina white-tailed deer that are specific for that SARS-CoV RBD. There are several potential explanations for this cross-reactivity, each with important implications to coronavirus disease surveillance. Perhaps the most intriguing possibility is the existence and transmission of an etiological agent (such as another coronavirus) with similarity to SARS-CoV-2’s RBD region. However, we lack conclusive evidence of pre-pandemic transmission of a SARS-like virus. Our findings provide impetus for the adoption of a One Health Initiative focusing on infectious disease surveillance of multiple animal species to predict the next zoonotic transmission to humans and future pandemics.
High Resolution and Multidimensional Protein Condensate Phase Diagrams with a Combinatorial Microdroplet Platform

The assembly of intracellular proteins into biomolecular condensates through phase separation is a fundamental process underlying organisation of the intracellular space and regulation of many central cellular processes. Elucidating the physico-chemical parameters that modulate phase separation is crucial in order to understand its effects in health and disease, as well as to develop therapeutic strategies that target biomolecular condensate systems. Phase behaviour is described by the phase diagram that defines conditions at which distinct phases exist, as well as the boundaries between these phases. Phase diagrams are typically built up from numerous individual measurements sampling different parts of the phase space. For biomolecular condensates, this process is slow, low throughput and associated with significant sample consumption even when performed in microwell format. Due to the rapidly increasing number of biologically and disease-relevant condensate systems, experimental techniques that enable high-throughput analysis of protein phase behaviour are required. To address this challenge, we present here a combinatorial droplet microfluidic platform, termed PhaseScan, for the rapid and high-resolution acquisition of protein phase diagrams in multiple chemical and physical dimensions. Using this platform, we characterise the phase behaviour of a wide range of protein systems under a variety of conditions and show that this platform can be used to characterise quantitatively the effect of small molecules on biomolecular phase transitions.
Effect of Leader-Member Exchange on Perceived Organizational Support

Human Resources are the most important assets of any organizations. Further, to achieve competitive advantages through human resources, leadership can be named as the most effective factors in this concern. Furthermore, leaders’ style, action, motivation, ethics, etc. can determine whether leadership is effective or not. The relationships between Leaders and subordinates shape LMX theory which states that leaders establish different relationships with different followers. These relationships will have many outcomes both for employees and organizations. In this study, the authors investigate the relationship between LMX and Perceived Organizational Support. 1500 employees of Iran Insurance Organization in Tehran, capital of Iran, have been selected as statistical population of this study. Based on Krejcie & Morgan (1970) table, the minimum number of sample size was determined as 306 people. After distributing 350 questionnaires among respondent, 310 usable questionnaires were returned. The results of the current study show that the selected organizations enjoy an appropriate level of LMX which has a significant positive effect on employees’ perception about organizational support.
Electronic Cigarette Vaping Did Not Enhance the Neural Process of Working Memory for Regular Cigarette Smokers

Background Electronic cigarettes (e-cigs) as substitute devices for regular tobacco cigarettes (r-cigs) have been increasing in recent times. We investigated neuronal substrates of vaping e-cigs and smoking r-cigs from r-cig smokers. Methods Twenty-two r-cig smokers made two visits following overnight smoking cessation. Functional magnetic resonance imaging (fMRI) data were acquired while participants watched smoking images. Participants were then allowed to smoke either an e-cig or r-cig until satiated and fMRI data were acquired. Their craving levels and performance on the Montreal Imaging Stress Task and a 3-back alphabet/digit recognition task were obtained and analyzed using two-way repeated-measures analysis of variance. Regions-of-interest (ROIs) were identified by comparing the abstained and satiated conditions. Neuronal activation within ROIs was regressed on the craving and behavioral data separately. Results Craving was more substantially reduced by smoking r-cigs than by vaping e-cigs. The response time (RT) for the 3-back task was significantly shorter following smoking r-cigs than following vaping e-cigs (interaction: F (1, 17) = 5.3, p = 0.035). Neuronal activations of the right vermis (r = 0.43, p = 0.037, CI = [-0.05, 0.74]), right caudate (r = 0.51, p = 0.015, CI = [0.05, 0.79]), and right superior frontal gyrus (r = −0.70, p = 0.001, CI = [−0.88, −0.34]) were significantly correlated with the RT for the 3-back task only for smoking r-cigs. Conclusion Our findings suggest that insufficient satiety from vaping e-cigs for r-cigs smokers may be insignificant effect on working memory function.
Spray-Dried Porcine Plasma Promotes the Association Between Metabolic and Immunological Processes at Transcriptional Level in Gilthead Sea Bream (Sparus aurata) Gut

The spray-dried porcine plasma (SDPP) is an abattoir by-product used in animal nutrition with beneficial effects reported in livestock and commercial aquatic species. Previous results have found that the dietary inclusion of SDPP in gilthead sea bream (Sparus aurata) increased the density of intestinal goblet cells, and it did not result in significant changes in the autochthonous microbiota. However, there is no comprehensive data on the mechanisms that could take place on the intestine of gilthead sea bream fed with an SDPP-supplemented diet. For this reason, this study aimed to unveil the biological mechanisms modulated in response to the dietary administration of SDPP in the gilthead sea bream gut. To achieve this goal, we made a microarrays-based transcriptomic approach in gut samples from gilthead sea bream fed with an SDPP-supplemented diet for 95 days. As control diet, we used a protein-rich commercial feed (51% crude protein, 17% crude fat, and 20.6 MJ/kg gross energy) which was supplemented with 3% SDPP at the expense of LT70 fishmeal. The microarray analyses showed a total of 803 (468 up- and 335 down-regulated) differential expressed genes (DEGs). The functional network analysis revealed that dietary inclusion of SDPP induced sustained changes in 120 biological processes, grouped in 12-clusters. Among them, the metabolic-related process (cellular catabolic process, organic substance catabolic process, protein metabolism process), protein transport, and leukocyte mediated immunity interacted in the leading interactome network. This evidence confirms the previous evidence of the enhancement of the mucosal health status in response to the dietary administration of SDPP and provides further understanding of the mode of action of this ingredient in aquafeeds.
P2 Manifests Subjective Evaluation of Reward Processing Under Social Comparison

Several recent studies have found that when the other’s gain is greater, even subjects’ reward may seem like a loss and lead to a negative experience. These studies indicate the complexity of reward evaluation in the context of social comparison. The satisfaction rating of reward outcome not only depends on objective social comparison but also on subjective evaluation. However, less is known about the neural time course of subjective evaluation. Therefore, we employed a 2 (subjective evaluation: advantageous vs. disadvantageous) × 2 (comparison direction: upward vs. downward) within-subjects factorial design, in which we manipulated the reward distribution for the subjects. Electroencephalography (EEG) responses were recorded, while two subjects concurrently but independently performed a simple dot-estimation task that entailed monetary rewards. Behavioral results showed that the subjects were more satisfied with the advantageous distribution, regardless of upward or downward comparison. The analysis of event-related potentials (ERPs) revealed that disadvantageous distribution elicited a larger P2 than advantageous distribution, and this effect was not modulated by comparison direction. In contrast, the late positive potential (LPP) showed an effect of comparison direction independent of subjective evaluation. The data suggest that subjective evaluation acts upon the early stage of reward processing and manifests in the P2 component, whereas social comparison plays a role in the later appraisal process.
Consistent Biofilm Formation by Streptococcus pyogenes emm 1 Isolated From Patients With Necrotizing Soft Tissue Infections

Objectives Biofilm formation has been demonstrated in muscle and soft tissue samples from patients with necrotizing soft tissue infection (NSTI) caused by Streptococcus pyogenes, but the clinical importance of this observation is not clear. Although M-protein has been shown to be important for in vitro biofilm formation in S. pyogenes, the evidence for an association between emm type and biofilm forming capacity is conflicting. Here we characterize the biofilm forming capacity in a collection of S. pyogenes isolates causing NSTI, and relate this to emm type of the isolates and clinical characteristics of the patients. Methods Bacterial isolates and clinical data were obtained from NSTI patients enrolled in a multicenter prospective observational study. Biofilm forming capacity was determined using a microtiter plate assay. Results Among 57 cases, the three most frequently encountered emm types were emm1 (n = 22), emm3 (n = 13), and emm28 (n = 7). The distribution of biofilm forming capacity in emm1 was qualitatively (narrow-ranged normal distribution) and quantitatively (21/22 isolates in the intermediate range) different from other emm types (wide ranged, multimodal distribution with 5/35 isolates in the same range as emm1). There were no significant associations between biofilm forming capacity and clinical characteristics of the patients. Conclusions The biofilm forming capacity of emm1 isolates was uniform and differed significantly from other emm types. The impact of biofilm formation in NSTI caused by S. pyogenes on clinical outcomes remains uncertain.
Changes in the Proportion of Gastrointestinal Emergency Endoscopy and Peptic Ulcer Disease During the COVID-19 Pandemic: A Local Retrospective Observational Study From Vietnam

Objectives The coronavirus disease 2019 (COVID-19) pandemic has disrupted the practice of gastrointestinal (GI) endoscopy units and may increase the risk of digestive disorders. We described the situational changes in GI endoscopy and peptic ulcer disease (PUD) proportion during COVID-19 in Vietnam and examined the associated factors. Methods A retrospective ecological study was conducted on data of Hanoi Medical University Hospital, Vietnam. The number of upper GI endoscopy and the proportion of GI emergency endoscopy and PUD were compared between 2019 and 2020 by month (January to June). Log-binomial regression was used to explore associated factors of GI emergency endoscopy and PUD. Results The number of endoscopies decreased remarkably during the nationwide social distancing in April 2020. Compared to April 2019, the proportion in April 2020 of both GI emergency endoscopy [4.1 vs. 9.8%, proportion ratio (PR) 2.39, 95% CI 2, 2.87], and PUD [13.9 vs. 15.8%; PR, 1.14; 95% CI, 1.01, 1.29] was significantly higher. In log-binomial models, the proportion of GI emergency endoscopy was higher in April 2020 compared to April 2019 (adjusted PR, 2.41; 95% CI, 2.01, 2.88). Male sex and age of ≥50 years were associated with an increased PUD and GI emergency conditions. Conclusion The proportion of both GI emergency endoscopy and PUD was significantly higher during the time of the state of emergency due to the ongoing COVID-19 pandemic in 2020 when compared to 2019 at the same health facility in Vietnam. The findings suggest that healthcare delivery reforms during the era of an emerging pandemic are required to reduce digestive disorders, in particular, and chronic diseases in general.
Antitumor Anesthetic Strategy in the Perioperatory Period of the Oncological Patient: A Review

The stress response triggered by the surgical aggression and the transient immunosuppression produced by anesthetic agents stimulate the inadvertent dispersion of neoplastic cells and, paradoxically, tumor progression during the perioperative period. Anesthetic agents and techniques, in relation to metastatic development, are investigated for their impact on long-term survival. Scientific evidence indicates that inhaled anesthetics and opioids benefit immunosuppression, cell proliferation, and angiogenesis, providing the ideal microenvironment for tumor progression. The likely benefit of reducing their use, or even replacing them as much as possible with anesthetic techniques that protect patients from the metastatic process, is still being investigated. The possibility of using “immunoprotective” or “antitumor” anesthetic techniques would represent a turning point in clinical practice. Through understanding of pharmacological mechanisms of anesthetics and their effects on tumor cells, new perioperative approaches emerge with the aim of halting and controlling metastatic development. Epidural anesthesia and propofol have been shown to maintain immune activity and reduce catecholaminergic and inflammatory responses, considering the protective techniques against tumor spread. The current data generate hypotheses about the influence of anesthesia on metastatic development, although prospective trials that determinate causality are necessary to make changes in clinical practice.
Phonological Training and Word Learning in a Novel Language

In reading Chinese words, learners may process segment and tone either separately or as an integral unit, as evidenced in previous research. The present study compared two ways—Segmental versus Whole-Syllable-Based Training—for improving learners’ phonological and word learning in Chinese as a novel language, while controlling for learners’ musical ability, an important factor that may contribute to phonological learning. Forty-two American college students learned Chinese words represented by Pinyin, a Romanized script which denotes the pronunciation of Chinese characters. Before the training, all participants were introduced to the phonology and Pinyin system. Then, they were trained on the pronunciation and meaning of the Pinyin words with or without an emphasis on separating the tonal from segmental information. All participants’ musical ability was assessed using a musical ability test. Learning outcomes were measured through tasks of same-different phonological judgment, tone identification, and word comprehension. Results showed the equal success of the two training methods, probably due to the consistent involvement of Pinyin and learner’s reliance on segment and tone as an integral unit rather than separate cues in phonological and word learning. Furthermore, musical ability seems to play a role in phonological and word learning among novel learners of Chinese.
Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids

Genetically encoded non-canonical amino acids (ncAAs) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These ncAAs, including a series of alkyl bromide-based ncAAs, mainly target cysteine residues to form protein-protein cross-links. Although some reactivities towards lysine and tyrosine residues have been reported, a comprehensive understanding of their reactivity towards a broad range of nucleophilic amino acids is lacking. Here we used a recently developed OpenUaa search engine to perform an in-depth analysis of mass spec data generated for Thioredoxin and its direct binding proteins cross-linked with an alkyl bromide-based ncAA, BprY. The analysis showed that, besides cysteine residues, BprY also targeted a broad range of nucleophilic amino acids. We validated this broad reactivity of BprY with Affibody/Z protein complex. We then successfully applied BprY to map a binding interface between SUMO2 and SUMO-interacting motifs (SIMs). BprY was further applied to probe SUMO2 interaction partners. We identified 264 SUMO2 binders, including several validated SUMO2 binders and many new binders. Our data demonstrated that BprY can be effectively used to probe protein-protein interaction interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.