Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomics in serum and culture medium reveal shared and differential gene regulation in pathogenic and commensal Streptococcus suis

Streptococcus suis colonizes the upper respiratory tract of healthy pigs at high abundance but can also cause opportunistic respiratory and systemic disease. Disease-associated S. suis reference strains are well studied, but less is known about commensal lineages. It is not known what mechanisms enable some S. suis lineages to cause disease while others persist as commensal colonizers, or to what extent gene expression in disease-associated and commensal lineages diverge. In this study we compared the transcriptomes of 21 S. suis strains grown in active porcine serum and Todd-Hewitt yeast broth. These strains included both commensal and pathogenic strains, including several strains of sequence type (ST) 1, which is responsible for most cases of human disease and considered the most pathogenic S. suis lineage. We sampled the strains during their exponential growth phase and mapped RNA-sequencing reads to the corresponding strain genomes. We found that the transcriptomes of pathogenic and commensal strains with large genomic divergence were unexpectedly conserved when grown in active porcine serum, but that regulation and expression of key pathways varied. Notably, we observed strong variation of expression across media of genes involved in capsule production in pathogens, and of the agmatine deiminase system in commensals. ST1 strains displayed large differences in gene expression between the two media compared to strains from other clades. Their capacity to regulate gene expression across different environmental conditions may be key to their success as zoonotic pathogens.
Seemingly Counter-Intuitive Features of Good-to-Great Companies Actually Make Perfect Sense: Possible Algorithmics-Based Explanations

In the late 1990s, researchers analyzed what distinguishes great companies from simply good ones. They found several features that are typical for great companies. Interestingly, most of these features seem counter-intuitive. In this paper, we show, on the qualitative level, that from the algorithmic viewpoint, many of these features make perfect sense. Some of the resulting explanations are simple and straightforward, other explanations rely on complex not-well-publicized results from theoretical computer science.
Effective and Efficient Heuristic Approaches for Solving the Capacitated P-Median Clustering Problem

The Capacitated Clustering Problem (CCP) involves the definition of capacity-constrained weighted individuals’ sets such that the maximum similarity with respect to the cluster center value is granted among points belonging to the same cluster. The individuals’ weights are represented by their demand, all the demands belonging to the same cluster have to be covered. This work concerns the application of the CCP problem where the center of a given cluster is a particular individual of the cluster. We focused on the Capacitated p-Median (CpMP) variant of the problem proposed by Mulvay and Beck, where the number of clusters is given. Specifically, we propose its mathematical programming formulation and, being this problem NP hard, a two-phase polynomial heuristic algorithm: the first phase consists in generating the desired number of clusters without any constraint on their capacity (different variations are provided); the second one aims to capacitate the former clusters to respect capacity limits.
A Review on the Technological Advances and Future Perspectives of Axon Guidance and Regeneration in Peripheral Nerve Repair

Despite a significant advance in the pathophysiological understanding of peripheral nerve damage, the successful treatment of large nerve defects remains an unmet medical need. In this article, axon growth guidance for peripheral nerve regeneration was systematically reviewed and discussed mainly from the engineering perspective. In addition, the common approaches to surgery, bioengineering approaches to emerging technologies such as optogenetic stimulation and magnetic stimulation for functional recovery were discussed, along with their pros and cons. Additionally, clear future perspectives of axon guidance and nerve regeneration were addressed.
Identification of the common differentially expressed genes and pathogenesis between neuropathic pain and aging

Background Neuropathic pain is a debilitating disease caused by damage or diseases of the somatosensory nervous system. Previous research has indicated potential associations between neuropathic pain and aging. However, the mechanisms by which they are interconnected remain unclear. In this study, we aim to identify the common differentially expressed genes (co-DEGs) between neuropathic pain and aging through integrated bioinformatics methods and further explore the underlying molecular mechanisms. Methods The microarray datasets GSE24982, GSE63442, and GSE63651 were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and co-DEGs were first identified. Functional enrichment analyses, protein-protein Interaction (PPI) network, module construction and hub genes identification were performed. Immune infiltration analysis was conducted. Targeted transcription factors (TFs), microRNAs (miRNAs) and potential effective drug compounds for hub genes were also predicted. Results A total of 563 and 1,250 DEGs of neuropathic pain and aging were screened, respectively. 16 genes were further identified as co-DEGs. The functional analysis emphasizes the vital roles of the humoral immune response and complement and coagulation cascades in these two diseases. Cxcl14, Fblim1, RT1-Da, Serping1, Cfd, and Fcgr2b were identified as hub genes. Activated B cell, mast cell, activated dendritic cell, CD56 bright natural killer cell, effector memory CD8 + T cell, and type 2 T helper cell were significantly up-regulated in the pain and aging condition. Importantly, hub genes were found to correlate with the activated B cell, activated dendritic cell, Gamma delta T cell, central memory CD4 + T cell and mast cell in pain and aging diseases. Finally, Spic, miR-883-5p, and miR-363-5p et al. were predicted as the potential vital regulators for hub genes. Aldesleukin, Valziflocept, MGD-010, Cinryze, and Rhucin were the potential effective drugs in neuropathic pain and aging. Conclusion This study identified co-DEGs, revealed molecular mechanisms, demonstrated the immune microenvironment, and predicted the possible TFs, miRNAs regulation networks and new drug targets for neuropathic pain and aging, providing novel insights into further research.
How does COVID-19 pandemic affect entrepreneur anxiety? The role of threat perception and performance pressure

The entrepreneurial firms may be more vulnerable to the COVID-19 pandemic, and the entrepreneurs of entrepreneurial firms are also threatened by the revenues decline and business failure, which vehemently affect their well-being. The mental health of the entrepreneur decides whether the entrepreneurial firms can make the right decision, which is related to the healthy development of the entrepreneurial firms. Based on the event system theory and the cognitive appraisal theory, this paper aims to explore the effect of COVID-19 pandemic on the entrepreneur anxiety, and the threat perception and performance pressure are introduced to investigate the mediating mechanism and boundary of this effect. Using the simple random sampling to obtain questionnaire survey data, 168 entrepreneurs of entrepreneurial firms have participated in the empirical study, and the research results are as follows. First, the COVID-19 pandemic significantly positively affects entrepreneur anxiety. Second, the entrepreneur threat perception plays a mediating role between the COVID-19 pandemic and the entrepreneur anxiety, which means the COVID-19 pandemic can enhance the external threat perception of entrepreneurs, and then affect the entrepreneur anxiety. Third, the positive effect of the COVID-19 pandemic on the entrepreneur anxiety is strengthened by the entrepreneur performance pressure, while the positive effect of entrepreneur threat perception on entrepreneur anxiety is weakened by the entrepreneur performance pressure. The above findings are helpful to explore the mechanism of the COVID-19 pandemic and other critical crisis events on entrepreneurs’ mental health from the new perspective of cognitive appraisal theory and event system theory, filling the research gaps between the COVID-19 pandemic and entrepreneur anxiety. Besides, this study broadens the applied range of the cognitive appraisal theory and the event system theory in the fields of crisis situations and entrepreneur research, and enriches the research outputs. Furthermore, this study will help provide a new theoretical analysis insight for the related research on how the COVID-19 pandemic affects entrepreneurs’ psychology, and further deepen researchers to understand the mechanism of entrepreneur anxiety under the COVID-19 pandemic, providing theoretical inspirations for reducing entrepreneur anxiety. What’s more, this study finds that individual pressure can affect their cognitive appraisal, which means that future research should take the pressure influential mechanism into consideration in the process of exploring “external stimulus--cognitive appraisal--emotional response,” further expanding the theoretical model of cognitive appraisal proposed from the perspective of pressure.
Establishment of a model for predicting delayed post-polypectomy bleeding: A real-world retrospective study

Background Delayed post-polypectomy bleeding (DPPB) is the most common complication which occurs within 30 days after polypectomy, it has become rather common with the widespread of colorectal cancer screening. It is important to clarified predictors of DPPB and identify patients at high risk. Materials and methods This was a real-world retrospective study based on medical records from The First Affiliated Hospital of Nanjing Medical University. Cases of patients who underwent colonoscopic polypectomy between January 2016 and December 2020 were reviewed to identify risk factors of DPPB. We use the LASSO-Logistic regression analysis model to identify independent predictors and create a predictive model. The model finally got visualized by developing a nomogram. Results Colonoscopic polypectomy was done on 16,925 patients in our study. DPPB occurred in 125 (0.74%) of these instances. In multivariate analysis, age, sex, hypertension, polyp location, polyp size, and operative modality were found to be independent risk factors and were integrated for the construction of a nomogram. The model’s C-index is 0.801 (95%CI: 0.761–0.846). We also found polyps located at the right semicolon and polyp ≥ 1 cm associated with active bleeding under the therapeutic colonoscopy. Conclusion Young age, male, hypertension, polyp ≥ 1 cm, proximal colon location and operative modality were finally identified as significant predictors of DPPB. We developed and validated a nomogram which performs well in predicting the incidence of DPPB, the model we established can be used as a valuable screening tool to identify patients who are at high risk of bleeding.
Are environmental regulation tools effective? An analysis based on financial investment of entity enterprises

Environmental regulation and economic development are consistent in the long run, but there are certain contradictions in the short term. Examining the characteristics of available environmental regulation tools and using them in a way that will align the interests of local governments and enterprises can improve environmental regulation and enhance green transformation and development. This study considers two general types of environmental regulation tools: negative punishment types and positive incentive types. Applying an intermediary effect model and the two-stage least squares method, a sample of Chinese A-share listed companies from 2007 to 2019 is used to test the impact of these different types of environmental regulation tools on the financial investment levels of entity enterprises. The mechanism through which these macro-environmental regulation tools function and the micro-enterprise heterogeneity factors that influence their impact are systematically studied. The results show that negative punishment type environmental regulation tools have a positive impact on the financial investment levels of entity enterprises, while positive incentive type environmental regulation tools inhibit financial investment levels. This impact is formed through managerial incentive mechanisms referred to as “whipping the fast ox” and “heavy rewards and light punishments. ” Factors such as financing constraints, relocation costs, pollution levels, and enterprise scale have heterogeneous effects on these paths. Policy suggestions are offered based on the findings. This study makes a significant contribution to the literature by clarifying the channel through which environmental regulation influences micro-enterprise decision-making. It provides a theoretical basis and policy reference for local government officials as they address the conflict between economic growth and environmental protection in the short term. Moreover, the results offer long-term development decision-making ideas for shareholders and managers in the process of green transformation and upgrading of enterprises.
A before-after-control-impact study of wildlife fencing along a highway in the Canadian Rocky Mountains

Wildlife exclusion fencing has become a standard component of highway mitigation systems designed to reduce collisions with large mammals. Past work on the effectiveness of exclusion fencing has relied heavily on control–impact (i.e., space-for-time substitutions) and before–after study designs. These designs limit inference and may confound the effectiveness of mitigation with co-occurring process that also changes the rate of collisions. We used a replicated (n = 2 sites monitored for over 1000 km years combined) before-after-control-impact study design to assess fencing effectiveness along the Trans-Canada Highway in the Rocky Mountains of Canada. We found that collisions declined for common ungulates species (elk, mule deer, and white-tailed deer) by up to 96% but not for large carnivores. The weak response of carnivores is likely due to the combination of fence intrusions and low sample sizes. We calculated realized fencing effectiveness by applying the same change in collision rates observed at control (unfenced) sites as the expected change for adjacent fenced sections. Compared with the apparent fencing effectiveness (i.e., the difference in WVCs rates before and after fencing was installed), the realized estimates of fencing effectiveness declined by 6% at one site and increased by 10% at another site. When factoring in the cost of ungulate collisions to society, fencing provided a net economic gain within 1 year of construction. Over a 10-year period, fencing would provide a net economic gain of > $500,000 per km in reduced collisions. Our study highlights the benefits of long-term monitoring of road mitigation projects and provides evidence of fencing effectiveness for reducing wildlife–vehicle collisions involving large mammals.
Exogenous naphthaleneacetic acid alleviated alkalinity-induced morpho-physio-biochemical damages in Cyperus esculentus L. var. sativus Boeck

Cyperus esculentus L. var. sativus Boeck (commonly called Chufa) is a perennial species that produces nutritious underground tubers and contributes to the diet and health of human worldwide. However, it is salt-sensitive and its adaptation to salinity stress remains an enigma. Naphthaleneacetic acid (NAA) plays a vital role in regulating plant salt stress tolerance. Thus, we aimed to investigate the impact of NAA (150 mg/L) application on growth and physio-biochemical response mechanisms of Chufa plants to different levels of salinity stress (0-, 90-, and 180 mM of alkaline stress ([1:1 ratio of Na2CO3 and NaHCO3]). In response to increasing stress levels, shoot-root growth decreased, whereas malondialdehyde (MDA), hydrogen peroxide (H2O2), osmolytes (soluble protein, proline, and soluble sugars), and activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) significantly increased. Alkalinity led to significant increase in Na+ and Cl–, but decrease in Mg2+ concentration in both roots and leaves; however, K+ decreased significantly in leaves under both stresses. Additionally, NO 3 − and. levels, nitrate reductase (NR) activities, and glutamate synthase (GOGAT) decreased significantly. However, glutamine synthetase (GS) increased non-significantly at 90 mM but declined at 180 mM. Foliar NAA application reduced Na+ and Cl-, MDA, and H2O2 but increased photosynthetic pigments, K+ and Mg2+, osmolytes, nitrogen (N) metabolism, and upregulating the enzymatic antioxidant system to reduce oxidative stress under alkaline conditions. Hence, our findings manifest that NAA application is an effective strategy that can be utilized to enhance tolerance of chufa plants to alkaline stress. Future studies should explore whether NAA can positively alter the nutrient composition of chufa tubers at deeper molecular levels, which might offer solutions to nutritious problems in developing countries.
Effects of nitrogen addition and root fungal inoculation on the seedling growth and rhizosphere soil microbial community of Pinus tabulaeformis

Nitrogen (N) availability is significant in different ecosystems, but the response of forest plant-microbial symbionts to global N deposition remains largely unexplored. In this study, the effects of different N concentration levels on four types of fungi, Suillus granulatus (Sg), Pisolithus tinctorius (Pt), Pleotrichocladium opacum (Po), and Pseudopyrenochaeta sp. (Ps), isolated from the roots of Pinus tabulaeformis were investigated in vitro. Then, the effects of the fungi on the growth performance, nutrient uptake, and rhizosphere soil microbial community structure of P. tabulaeformis under different N addition conditions (0, 40, and 80 kg hm−2 year−1) were examined. The biomass and phytohormone contents of the Sg, Pt and Po strains increased with increasing N concentration, while those of the Ps strain first increased and then decreased. All four fungal strains could effectively colonize the plant roots and form a strain-dependent symbiosis with P. tabulaeformis. Although the effects depended on the fungal species, the growth and root development of inoculated seedlings were higher than those of uninoculated seedlings under N deficiency and normal N supply conditions. However, these positive effects disappeared and even became negative under high N supply conditions. The inoculation of the four fungal strains also showed significant positive effects on the shoot and root nutrient contents of P. tabulaeformis. Fungal inoculation significantly increased different microbial groups and the total soil microorganisms but decreased the microbial diversity under N deficiency stress. In summary, exogenous symbiotic fungal inoculations could increase the growth performance of P. tabulaeformis under N deficiency and normal N supply conditions, but the effects were negative under excessive N addition.
Daily, self-test rapid antigen test to assess SARS-CoV-2 viability in de-isolation of patients with COVID-19

Background Isolation of COVID-19 patients is a crucial infection control measure to prevent further SARS-CoV-2 transmission, but determining an appropriate timing to end the COVID-19 isolation is a challenging. We evaluated the performance of the self-test rapid antigen test (RAT) as a potential proxy to terminate the isolation of COVID-19 patients. Materials and methods Symptomatic COVID-19 patients were enrolled who were admitted to a regional community treatment center (CTC) in Seoul (South Korea). Self-test RAT and the collection of saliva samples were performed by the patients, on a daily basis, until patient discharge. Cell culture and subgenomic RNA detection were performed on saliva samples. Results A total of 138 pairs of saliva samples and corresponding RAT results were collected from 34 COVID-19 patients. Positivity of RAT and cell culture was 27% (37/138) and 12% (16/138), respectively. Of the 16 culture-positive saliva samples, seven (43.8%) corresponding RAT results were positive. Using cell culture as the reference standard, the overall percent agreement, percent positive agreement, and percent negative agreement of RAT were 71% (95% CI, 63–78), 26% (95% CI, 12–42), and 82% (95% CI, 76–87), respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of the RAT for predicting culture results were 44% (95% CI, 20–70), 75% (95% CI, 66–82), 18% (95% CI, 8–34), and 91% (95% CI, 84–96), respectively. Conclusion About half of the patients who were SARS-CoV-2 positive based upon cell culture results gave negative RAT results. However, the remaining positive culture cases were detected by RAT, and RAT showed relatively high negative predictive value for viable viral shedding.
The role of perireceptor events in flavor perception

The sensory perception of food is a complex phenomenon involving the integration of different stimuli (aroma, taste, trigeminal sensations, texture and visual). Flavor compounds activate odorant, taste and trigeminal chemoreceptors, generating a depolarization of the sensory neurons and then the consciousness of food flavor perception. Recent studies are increasingly highlighting the importance of perireceptor events, which include all the molecular events surrounding the receptors, in the modulation of flavor perception. These events affect the quantity and quality of flavor compounds in the environment of chemoreceptors. They include the metabolization of flavor compounds by enzymes present in biological fluids (saliva and mucus) and the oronasal epithelia and noncovalent interactions with binding proteins. Perireceptor mechanisms have been extensively studied in insects and mammals, demonstrating the importance of the entailed processes in the termination of the chemical signal. In humans, research is in full swing. Here, we reviewed the perireceptor mechanisms recently reported in vitro, in biological fluids and in cells and in vivo in humans. These studies indicate that perireceptor mechanisms likely have an important contribution to flavor perception. This mini-review focuses on recent pioneering studies that are paving the way for this new research area. It also suggests that new approaches taking into account the real conditions of food consumption will be required in the future to accurately address this question.