Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring whole proteome to contrive multi-epitope-based vaccine for NeoCoV: An immunoinformtics and in-silico approach

Neo-Coronavirus (NeoCoV) is a novel Betacoronavirus (β-CoVs or Beta-CoVs) discovered in bat specimens in South Africa during 2011. The viral sequence is highly similar to Middle East Respiratory Syndrome, particularly that of structural proteins. Thus, scientists have emphasized the threat posed by NeoCoV associated with human angiotensin-converting enzyme 2 (ACE2) usage, which could lead to a high death rate and faster transmission rate in humans. The development of a NeoCoV vaccine could provide a promising option for the future control of the virus in case of human infection. In silico predictions can decrease the number of experiments required, making the immunoinformatics approaches cost-effective and convenient. Herein, with the aid of immunoinformatics and reverse vaccinology, we aimed to formulate a multi-epitope vaccine that may be used to prevent and treat NeoCoV infection. Based on the NeoCoV proteins, B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes were shortlisted. Four vaccines (Neo-1–4) were devised by fusing shortlisted epitopes with appropriate adjuvants and linkers. The secondary and three-dimensional structures of final vaccines were then predicted. The binding interactions of these potential vaccines with toll-like immune receptors (TLR-2, TLR-3, and TLR-4) and major histocompatibility complex molecules (MHC-I and II) reveal that they properly fit into the receptors’ binding domains. Besides, Neo-1 and Neo-4 vaccines exhibited better docking energies of -101.08 kcal/mol and -114.47 kcal/mol, respectively, with TLR-3 as compared to other vaccine constructs. The constructed vaccines are highly antigenic, non-allergenic, soluble, non-toxic, and topologically assessable with good physiochemical characteristics. Codon optimization and in-silico cloning confirmed efficient expression of the designed vaccines in Escherichia coli strain K12. In-silico immune simulation indicated that Neo-1 and Neo-4 vaccines could induce a strong immune response against NeoCoV. Lastly, the binding stability and strong binding affinity of Neo-1 and Neo-4 with TLR-3 receptor were validated using molecular dynamics simulations and free energy calculations (Molecular Mechanics/Generalized Born Surface Area method). The final vaccines require experimental validation to establish their safety and effectiveness in preventing NeoCoV infections.
Efficacy of radiofrequency ablation for metastatic papillary thyroid cancer with and without initial biochemical complete status

Objective The application of radiofrequency ablation (RFA) for recurrent thyroid cancer has been demonstrated to effectively manage lesions at critical locations, such as abutting the trachea, with limited complications. Comprehensive investigation of both biochemical (B) and structural (S) change after RFA remains limited. We herein present the first single-center experience of RFA for the treatment of locoregional recurrent thyroid cancer in Taiwan. Design 23 patients were enrolled, and the treatment responses after RFA were divided into four groups (E, S(+), B(+), and SB(+)), and then compared. The RFA technique, follow-up strategy, changes in pre-and post-operative status, and complications are presented. The volume reduction rate at 1, 3, and 6 months, and the differing responses between lesions abutting/not abutting the trachea are also discussed. Results In patients with pre-RFA structural and biochemical incomplete (SB(+)) status, presenting with lesion with an initial maximum diameter of >3.2cm, a higher rate of structural incomplete status at the 6-month follow-up was noted in ROC analysis, with a sensitivity of 57% and specificity of 91%. Favorable structural remission after RFA was noted, and 60.9% of patients achieved biochemical complete status. No significant correlation was noted between the trachea-abutted lesion number and complete remission (p= 0.474). No significant difference in RFA efficacy was noted between the lesions abutting/not abutting the trachea. Conclusions This retrospective study reveals that RFA can achieve both structural and biochemical improvements for locoregionally recurrent thyroid cancer, with a low complication rate. Nearly half of the patients achieved an excellent response after RFA, while a favorable treatment response can be achieved despite the lesion abutting the trachea, with a mean VRR of 84.74%.
Brain-machine interface-based training for improving upper extremity function after stroke: A meta-analysis of randomized controlled trials

Background Upper extremity dysfunction after stroke is an urgent clinical problem that greatly affects patients' daily life and reduces their quality of life. As an emerging rehabilitation method, brain-machine interface (BMI)-based training can extract brain signals and provide feedback to form a closed-loop rehabilitation, which is currently being studied for functional restoration after stroke. However, there is no reliable medical evidence to support the effect of BMI-based training on upper extremity function after stroke. This review aimed to evaluate the efficacy and safety of BMI-based training for improving upper extremity function after stroke, as well as potential differences in efficacy of different external devices. Methods English-language literature published before April 1, 2022, was searched in five electronic databases using search terms including “brain-computer/machine interface”, “stroke” and “upper extremity. ” The identified articles were screened, data were extracted, and the methodological quality of the included trials was assessed. Meta-analysis was performed using RevMan 5.4. 1 software. The GRADE method was used to assess the quality of the evidence. Results A total of 17 studies with 410 post-stroke patients were included. Meta-analysis showed that BMI-based training significantly improved upper extremity motor function [standardized mean difference (SMD) = 0.62; 95% confidence interval (CI) (0.34, 0.90); I2 = 38%; p < 0.0001; n = 385; random-effects model; moderate-quality evidence]. Subgroup meta-analysis indicated that BMI-based training significantly improves upper extremity motor function in both chronic [SMD = 0.68; 95% CI (0.32, 1.03), I2 = 46%; p = 0.0002, random-effects model] and subacute [SMD = 1.11; 95%CI (0.22, 1.99); I2 = 76%; p = 0.01; random-effects model] stroke patients compared with control interventions, and using functional electrical stimulation (FES) [SMD = 1.11; 95% CI (0.67, 1.54); I2 = 11%; p < 0.00001; random-effects model]or visual feedback [SMD = 0.66; 95% CI (0.2, 1.12); I2 = 4%; p = 0.005; random-effects model;] as the feedback devices in BMI training was more effective than using robot. In addition, BMI-based training was more effective in improving patients' activities of daily living (ADL) than control interventions [SMD = 1.12; 95% CI (0.65, 1.60); I2 = 0%; p < 0.00001; n = 80; random-effects model]. There was no statistical difference in the dropout rate and adverse effects between the BMI-based training group and the control group. Conclusion BMI-based training improved upper limb motor function and ADL in post-stroke patients. BMI combined with FES or visual feedback may be a better combination for functional recovery than robot. BMI-based trainings are well-tolerated and associated with mild adverse effects.
Complex instruction set computing architecture for performing accurate quantum $Z$ rotations with less magic

We present quantum protocols for executing arbitrarily accurate $\pi/2^k$ rotations of a qubit about its $Z$ axis. Reduced instruction set computing (\textsc{risc}) architectures typically restrict the instruction set to stabilizer operations and a single non-stabilizer operation, such as preparation of a "magic" state from which $T = Z(\pi/4)$ gates can be teleported. Although the overhead required to distill high-fidelity copies of this magic state is high, the subsequent quantum compiling overhead to realize $Z$ rotations in a \textsc{risc} architecture can be much greater. We develop a complex instruction set computing (\textsc{cisc}) architecture whose instruction set includes stabilizer operations and preparation of magic states from which $Z(\pi/2^k)$ gates can be teleported, for $2 \leq k \leq k_{\text{max}}$. This results in a substantial overall reduction in the number of gates required to achieve a desired gate accuracy for $Z$ rotations. The key to our construction is a family of shortened quantum Reed-Muller codes of length $2^{k+2}-1$, whose magic-state distillation threshold shrinks with $k$ but is greater than 0.85% for $k \leq 6$.
Personalized practice dosages may improve motor learning in older adults compared to “standard of care” practice dosages: A randomized controlled trial

Standard dosages of motor practice in clinical physical rehabilitation are insufficient to optimize motor learning, particularly for older patients who often learn at a slower rate than younger patients. Personalized practice dosing (i.e., practicing a task to or beyond one's plateau in performance) may provide a clinically feasible method for determining a dose of practice that is both standardized and individualized, and may improve motor learning. The purpose of this study was to investigate whether personalized practice dosages [practice to plateau (PtP) and overpractice (OVP)] improve retention and transfer of a motor task, compared to low dose [LD] practice that mimics standard clinical dosages. In this pilot randomized controlled trial (NCT02898701, ClinicalTrials.gov), community-dwelling older adults (n = 41, 25 female, mean age 68.9 years) with a range of balance ability performed a standing serial reaction time task in which they stepped to specific targets. Presented stimuli included random sequences and a blinded repeating sequence. Participants were randomly assigned to one of three groups: LD (n = 15, 6 practice trials equaling 144 steps), PtP (n = 14, practice until reaching an estimated personal plateau in performance), or OVP (n = 12, practice 100% more trials after reaching an estimated plateau in performance). Measures of task-specific learning (i.e., faster speed on retention tests) and transfer of learning were performed after 2–4 days of no practice. Learning of the random sequence was greater for the OVP group compared to the LD group (p = 0.020). The OVP (p = 0.004) and PtP (p = 0.010) groups learned the repeated sequence more than the LD group, although the number of practice trials across groups more strongly predicted learning (p = 0.020) than did group assignment (OVP vs. PtP, p = 0.270). No group effect was observed for transfer, although significant transfer was observed in this study as a whole (p < 0.001). Overall, high and personalized dosages of postural training were well-tolerated by older adults, suggesting that this approach is clinically feasible. Practicing well-beyond standard dosages also improved motor learning. Further research should determine the clinical benefit of this personalized approach, and if one of the personalized approaches (PtP vs. OVP) is more beneficial than the other for older patients.
Altered cerebral blood flow patterns in ankylosing spondylitis: A three-dimensional pseudo-continuous arterial spin labeling study

Objective This study aimed to detect the cerebral blood flow (CBF) values changes in patients with ankylosing spondylitis (AS) and to evaluate the correlation between the CBF values and the specific clinical characteristics. Materials and methods Forty-eight patients with AS (43 male and 5 female) and 42 healthy controls (HCs) (38 male and 4 female) were recruited. Three-dimensional pseudo-continuous arterial spin labeling (3D-pCASL) was performed on a 3.0T magnetic resonance imaging (MRI). CBF values were obtained on the Philips post-processing workstation based on arterial spin labeling (ASL) data. The two-sample t-test was used to compare CBF differences. The correlation between CBF values and specific clinical characteristics of AS was evaluated. Results The AS group showed increased CBF values in the right precentral gyrus, the left inferior frontal gyrus, and the left temporal pole compared with HCs the AS group also showed decreased CBF values in the left precuneus and the left superior occipital gyrus compared with HCs. There were no significant correlations between the CBF values and the clinical characteristics including total back pain (TBP), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). Conclusion Patients with AS displayed CBF changes compared with HCs using 3D-PCASL. These results may enhance our understanding of the neural substrates of AS and provide evidence of AS-related neurological impairment.
Enactive and simondonian reflections on mental disorders

As an alternative to linear and unidimensional perspectives focused mainly on either organic or psychological processes, the enactive approach to life and mind—a branch of 4-E (embodied, embedded, enactive, extended) cognitive theories—offers an integrative framework to study mental disorders that encompasses and articulates organic, sensorimotor, and intersubjective dimensions of embodiment. These three domains are deeply entangled in a non-trivial manner. A question remains on how this systemic and multi-dimensional approach may be applied to our understanding of mental disorders and symptomatic behavior. Drawing on Gilbert Simondon’s philosophy of individuation (focusing particularly on the concepts of tension, metastability, and preindividual), we provide some enactive conceptual tools to better understand the dynamic, interactive, and multi-dimensional nature of human bodies in mental disorders and psychopathological symptoms. One of such tools cursiva is sense-making, a key notion that captures the relational process of generating meaning by interacting with the sociomaterial environment. The article analyzes five aspects related to sense-making: temporality, adaptivity, the multiplicity of normativities it involves, the fundamental role of tension, and its participatory character. On this basis, we draw certain implications for our understanding of mental disorders and diverse symptoms, and suggest their interpretation in terms of difficulties to transform tensions and perform individuation processes, which result in a reduction of the field of potentialities for self-individuation and sense-making.
E3 ligase RNF5 inhibits type I interferon response in herpes simplex virus keratitis through the STING/IRF3 signaling pathway

Herpes simplex keratitis (HSK), caused by the herpes simplex virus 1 (HSV-1), is a major blinding disease in developed countries. HSV-1 can remain latent in the host for life and cannot be eradicated. The infection causes the secretion of various cytokines and aggregation of inflammatory cells. In the early stage of inflammation, mainly neutrophils infiltrate the cornea, and CD4+ T cells mediate the immunopathological changes in herpetic stromal keratitis in the subsequent progression. The STING/IRF3-mediated type I interferon (IFN) response can effectively inhibit viral replication and control infection, but the activity of STING is affected by various ubiquitination modifications. In this study, we found that the expression of RNF5 was elevated in corneal tissues and corneal epithelial cells after infection with HSV-1. Immunofluorescence staining confirmed that RNF5 was mainly expressed in the corneal epithelial layer. We silenced and overexpressed RNF5 expression in corneal epithelial cells and then inoculated them with HSV-1. We found that the expressions of STING, p-IRF3, p-TBK1, and IFN-β mRNA increased after RNF5 silencing. The opposite results were obtained after RNF5 overexpression. We also used siRNA to silence RNF5 in the mouse cornea and then established the HSK model. Compared with the siRNA-control group, the siRNA-RNF5 group showed significantly improved corneal inflammation, reduced clinical scores and tear virus titers, and significantly increased corneal IFN-β expression. In addition, the expressions of the proinflammatory cytokines IL-6 and TNF-α in the corneal tissue were significantly decreased, indicating that RNF5 silencing could effectively promote IFN-I expression, inhibit virus replication, alleviate inflammation, and reduce corneal inflammatory damage. In summary, our results suggest that RNF5 limits the type I IFN antiviral response in HSV corneal epithelitis by inhibiting STING/IRF3 signaling.
The effect of customer trust and commitment on customer sustainable purchasing in e-marketplace, the antecedents of customer learning value and customer purchasing value

The e-marketplace is a platform used by vendors to conduct transactions and shopping. The success of implementing an e-marketplace depends on customers’ sustainable purchasing. This study integrates customer learning (formative construct) and purchasing (reflective construct) values to measure the level of customer trust and commitment in the e-marketplace to examine their effects on sustainable customer purchases. A total of 428 valid respondents were processed using SmartPLS 3. The results show that the six proposed hypotheses have positive values and significant effects. Customer learning and purchasing values have positive values and significant effects on customer trust and loyalty and have indirect positive values and significant effects on sustainable customer purchases. In other words, customer trust and loyalty have positive values and significant effects on sustainable customer purchases. Thus, the findings of this study have implications for other researchers and practitioners conducting studies on e-marketplaces.
Editorial: Cross-cultural occupational health psychology challenges for the 21st century

COPYRIGHT © 2022 Sarfraz, Ivascu, Shah and Farid. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Cross-cultural occupational health psychology challenges for the 21st century
Specific quantitative detection of Streptococcus suis and Actinobacillus pleuropneumoniae in co-infection and mixed biofilms

Respiratory infections seriously affect the swine industry worldwide. Co-infections of two vital pathogenic bacteria Streptococcus suis (S. suis) and Actinobacillus pleuropneumoniae (A. pleuropneumoniae), colonizing the respiratory tract often occurs in veterinary clinical practice. Moreover, our previous research found that S. suis and A. pleuropneumoniae can form biofilm in vitro. The formation of a mixed biofilm not only causes persistent infections, but also increases the multiple drug resistance of bacteria, which brings difficulties to disease prevention and control. However, the methods for detecting S. suis and A. pleuropneumoniae in co-infection and biofilm are immature. Therefore, in this study, primers and probes were designed based on the conservative sequence of S. suis gdh gene and A. pleuropneumoniae apxIVA gene. Then, a TaqMan duplex real-time PCR method for simultaneous detection of S. suis and A. pleuropneumoniae was successfully established via optimizing the reaction system and conditions. The specificity analysis results showed that this TaqMan real-time PCR method had strong specificity and high reliability. The sensitivity test results showed that the minimum detection concentration of S. suis and A. pleuropneumoniae recombinant plasmid was 10 copies/μL, which is 100 times more sensitive than conventional PCR methods. The amplification efficiencies of S. suis and A. pleuropneumoniae were 95.9% and 104.4% with R2 value greater than 0.995, respectively. The slopes of the calibration curves of absolute cell abundance of S. suis and A. pleuropneumoniae were 1.02 and 1.09, respectively. The assays were applied to cultivated mixed biofilms and approximately 108 CFUs per biofilm were quantified when 108 CFUs planktonic bacteria of either S. suis or A. pleuropneumoniae were added to biofilms. In summary, this study developed a TaqMan real-time PCR assay for specific, accurate quantification of S. suis or A. pleuropneumoniae in mixed biofilms, which may help for the detection, prevention and control of diseases caused by a bacterial mixed infection involving S. suis and A. pleuropneumoniae.
Beyond the Individual -A Scoping Review and Bibliometric Mapping of Ecological Determinants of Eating Behavior in Older Adults

Objectives: The objective of this scoping review was to summarize and provide a visual overview of the present-day knowledge on ecological determinants of eating behavior in community-dwelling elderly persons in relation with nutrition communication, considering the evolution of the field. The second objective was to integrate results in recommendations for the development of nutrition communication strategies. Methods: A literature review was performed on Medline, PubMed and Google Scholar, according with the PRISMA protocol for scoping reviews. An a-priori analysis was executed by categorizing determinants from the literature according with the different levels represented in the ecological framework and an a-posteriori analysis by using VosViewer for a chronological bibliometric mapping analysis. Results: Of 4029 articles retrieved, 77 were selected for analysis. Initial publications focused more on individual determinants of eating behavior. Over time, there was a shift towards a holistic view of eating behavior considering the “food environment”, including social networks, physical settings and public policy. Conclusion: Beyond the individual, all ecological levels are relevant when targeting eating behavior in the elderly. Nutrition communication strategies should be structured considering these influences.
Torção de Reidemeister das formas espaciais esféricas

In this work, we study the action of the generalized quaternionic groups Q4t on the spheres to compute the Reidemeister torsion of the quotient spaces, which are called Quaternionic Spherical Space Forms. Using the base of the homology defined by Ray and Singer in [27] we compute also the Ray-Singer torsion of the spheres, lens spaces and the cone over the spheres. This last one provides the disc as a particular case. For the closed manifolds we obtain the analytic torsion using the Cheeger-Muller Theorem [7, 22] and for the disc using a formula proved by Bruning and Ma in [5].
Fault tolerant deterministic secure quantum communication using logical Bell states against collective noise

This study proposes two novel fault tolerant deterministic secure quantum communication (DSQC) schemes resistant to collective noise using logical Bell states. Either DSQC scheme is constructed based on a new coding function, which is designed by exploiting the property of the corresponding logical Bell states immune to collective-dephasing noise and collective-rotation noise, respectively. The secret message can be encoded by two simple unitary operations and decoded by merely performing Bell measurements, which can make the proposed scheme more convenient in practical applications. Moreover, the strategy of one-step quanta transmission, together with the technique of decoy logical qubits checking not only reduces the influence of other noise existing in a quantum channel, but also guarantees the security of the communication between two legitimate users. The final analysis shows that the proposed schemes are feasible and robust against various well-known attacks over the collective noise channel.