Miracle-dz/UniFAR-FTUs huggingface dataset:
The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.
Investigation on Measuring Methodology of Rock and Ore Sample Porosity

The authors introduced a method to measure sample porosity based on the Archimedes law of buoyancy.The authors designed a hardware circuit of porosity measuring instrument,presented the technical specificaiton of the instrument,and analyzed experimental results.The instrument consists of weighing sensor,A/D converter integrated amplifiers and filter,single-chip microcontroller,keyboard and a display part.This instrument can not only be used in measuring the porosity of rock and ore samples,but also be used in detecting the multifarious physical parameters,such as weight,volume and density.This invention has many significant advantages,for example,high degree of intelligence,measurement accuracy,simple operation,automatically displaying the value of porosity,communication with computer and low cost and power consumption.The measuring accuracy of porosity less than 0.5% while MSE less than 1%,thus meet the need of porosity measurement.
Students’ Adoption of E-Learning Program during Covid 19: Impact on Students’ Engagement and Effective Teaching Method

The coronavirus (COVID-19) pandemic has forced universities, as well as governments, businesses and other institutions, to rapidly increase their provision of digital services and in doing so accelerated a number of existing trends. Universities have had to rapidly evolve their digital strategies and the digital literacy and skills of their staff in order to respond to the current demands for online delivery and global digital connectivity. This study aims to find the factors that influence student acceptance of e-learning programs during a pandemic using the Technology Acceptance Model (TAM) approach. The study adopts quantitative research methods and data collected from 300 respondents using convenience sampling methodology. The questionnaire was distributed online to 14 universities in Indonesia. The structural equation model PLS (SEM-PLS) was utilized in this study. The results showed that two major problems rendered the online teaching and learning less effective than expected. One problem was arising from the institutional unpreparedness. Both lecturers and students were involved in struggling with this sudden move on global and untested scale. From the practical point of view, this study offers implications for government and universities to provide policies in the process of adopting e-learning regarding on students’ engagement and effective teaching method.
lncRNA H19 Aggravates Brain Injury in Rats following Experimental Intracerebral Hemorrhage via NF-κB Pathway

Objective To explore the effect of long noncoding RNA H19 (lncRNA H19) on brain injury in rats following experimental intracerebral hemorrhage (ICH). Methods Rat ICH model was established with type IV collagenase. The neurological function scores were evaluated, and the water content in brain tissue was measured. The nerve injury indexes, inflammatory factors, and oxidative stress indexes were also measured. Moreover, the expression of lncRNA H19 was determined by qRT-PCR, and Western blot detected NF-κB pathway-related protein expression. Results Compared with the sham group, the neurological function scores, the water content in brain tissue, and levels of injury indicators myelin basic protein (MBP), S-100B, and neuron-specific enolase (NSE) in the ICH rats were significantly increased. Meanwhile, the levels of TNF-α, IL-6, IL-1β, ROS, and MDA were significantly increased, but the levels of SOD were significantly decreased. In addition, the expression of lncRNA H19 in the brain tissue in the ICH group was significantly higher than that in the sham group. After further interference with lncRNA H19 expression (sh-H19 group), the levels of all the above indicators were reversed and the neurological damage was improved. Western blot results showed that the expression of NF-κBp65 and IKKβ was significantly higher, and IκBα expression was lower in the perivascular hematoma tissue in the ICH group compared with the sham group. Compared with the sh-NC group, NF-κBp65 and IKKβ expression were significantly lower and IκBα was significantly higher in the sh-H19 group. Conclusion lncRNA H19 exacerbated brain injury in rats with ICH by promoting neurological impairment, brain edema, and releasing inflammatory responses and oxidative stress. This may be related to the activation of NF-κB signaling pathway.
Resting-state electroencephalographic correlates of cognitive reserve: Moderating the age-related worsening in cognitive function

This exploratory study aimed to investigate the resting-state electroencephalographic (rsEEG) correlates of the cognitive reserve from a life span perspective. Current source density (CSD) and lagged-linear connectivity (LLC) measures were assessed to this aim. We firstly explored the relationship between rsEEG measures for the different frequency bands and a socio-behavioral proxy of cognitive reserve, the Cognitive Reserve Index (CRI). Secondly, we applied moderation analyses to assess whether any of the correlated rsEEG measures showed a moderating role in the relationship between age and cognitive function. Moderate negative correlations were found between the CRI and occipital CSD of delta and beta 2. Moreover, inter- and intrahemispheric LLC measures were correlated with the CRI, showing a negative association with delta and positive associations with alpha 1, beta 1, and beta 2. Among those correlated measures, just two rsEEG variables were significant moderators of the relationship between age and cognition: occipital delta CSD and right hemispheric beta 2 LLC between occipital and limbic regions. The effect of age on cognitive performance was stronger for higher values of both measures. Therefore, lower values of occipital delta CSD and lower beta 2 LLC between right occipital and limbic regions might protect or compensate for the effects of age on cognition. Results of this exploratory study might be helpful to allocate more preventive efforts to curb the progression of cognitive decline in adults with less CR, possibly characterized by these rsEEG parameters at a neural level. However, given the exploratory nature of this study, more conclusive work on these rsEEG measures is needed to firmly establish their role in the cognition–age relationship, for example, verifying if these measures moderate the relationship between brain structure and cognition.
Aggregation of high‐frequency RBD mutations of SARS‐CoV‐2 with three VOCs did not cause significant antigenic drift

Variants of SARS‐CoV‐2 continue to emerge, posing great challenges in outbreak prevention and control. It is important to understand in advance the impact of possible variants of concern (VOCs) on infectivity and antigenicity. Here, we constructed one or more of the 15 high‐frequency naturally occurring amino acid changes in the receptor‐binding domain (RBD) of Alpha, Beta, and Gamma variants. A single mutant of A520S, V367F, and S494P in the above three VOCs enhanced infectivity in ACE2‐overexpressing 293T cells of different species, LLC‐MK2 and Vero cells. Aggregation of multiple RBD mutations significantly reduces the infectivity of the possible three VOCs. Regarding neutralization, it is noteworthy that E484K, N501Y, K417N, and N439K predispose to monoclonal antibodies (mAbs) protection failure in the 15 high‐frequency mutations. Most importantly, almost all possible VOCs (single RBD mutation or aggregation of multiple mutations) showed no more than a fourfold decrease in neutralizing activity with convalescent sera, vaccine sera, and immune sera of guinea pigs with different immunogens, and no significant antigenic drift was formed. In conclusion, our pseudovirus results could reduce the concern that the aggregation of multiple high‐frequency mutations in the RBD of the spike protein of the three VOCs would lead to severe antigenic drift, and this would provide value for vaccine development strategies.
In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets

Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites are not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an in vitro Kinase-to-Phosphosite database (iKiP-DB). We show that iKiP-DB can accurately predict changes in kinase activity in published phosphoproteomic datasets for both well-studied and poorly characterized kinases. We apply iKiP-DB to a newly generated phosphoproteomic analysis of SARS-CoV-2 infected human lung epithelial cells and provide evidence for coronavirus-induced changes in host cell kinase activity. In summary, we show that iKiP-DB is widely applicable to facilitate the functional analysis of phosphoproteomic datasets.
The C-terminal domain of SEC-10 is fundamental for exocyst function, Spitzenkörper organization and cell morphogenesis in Neurospora crassa

The exocyst is a conserved multimeric complex that participates in the final steps of the secretion of vesicles. In the filamentous fungus Neurospora crassa, the exocyst is crucial for polar growth, morphology, and the organization of the Spitzenkörper (Spk), the apical body where secretory vesicles accumulate before being delivered to the plasma membrane. In the highly polarized cells of N. crassa, the exocyst subunits SEC-3, SEC-5, SEC-6, SEC-8, and SEC-15 were previously found localized at the plasma membrane of the cells’ apices, while EXO-70 and EXO-84 occupied the frontal outer layer of the Spk, occupied by vesicles. The localization of SEC-10 had remained so far elusive. In this work, SEC-10 was tagged with the green fluorescent protein (GFP) either at its N- or C-terminus and found localized at the plasma membrane of growing hyphal tips, similar to what was previously observed for some exocyst subunits. While expression of an N-terminally tagged version of SEC-10 at its native locus was fully viable, expression of a C-terminally tagged version at its native locus resulted in severe hyphal growth and polarity defects. Additionally, a sec-10 knockout mutant in a heterokaryotic state (with genetically different nuclei) was viable but showed a strongly aberrant phenotype, confirming that this subunit is essential to maintain hyphal morphogenesis. Transmission electron microscopy analysis revealed the lack of a Spk in the SEC-10-GFP strain, suggesting a critical role of the exocyst in the vesicular organization at the Spk. Mass spectrometry analysis revealed fewer peptides of exocyst subunits interacting with SEC-10-GFP than with GFP-SEC-10, suggesting an essential role of the C-terminus of SEC-10 in exocyst assembly and/or stability. Altogether, our data suggest that an unobstructed C-terminus of SEC-10 is indispensable for the exocyst complex function and that a GFP tag could be blocking important subunit-subunit interactions.
Pressurized intraperitoneal aerosol chemotherapy (PIPAC) in treatment of advanced ovarian cancer. A review of the literature

Objective: The majority of advanced ovarian cancer (OC) patients do not fully respond to systemic chemotherapy, thus complete cytoreduction can not be achieved in such cases. Pressurized intraperitoneal aerosol chemotherapy (PIPAC) has been suggested as an alternative approach for these women. Our study aimed to review the literature regarding the application of pressurized intraperitoneal aerosol chemotherapy (PIPAC) in OC patients with peritoneal carcinomatosis (PC). Data source: Articles in the English language were searched in PubMed. Search terms included “PIPAC” and “ovarian cancer”. Methods of study selection: The authors evaluated all studies presenting an application of pressurised intraperitoneal aerosol chemotherapy (PIPAC) on ovarian cancer patients. The published guidelines for Systematic Reviews and Meta-analyses (PRISMA) were followed in the present systematic review which was performed based on the authors’ predetermined inclusion criteria. Tabulation: Table 1 presents the main characteristics and outcomes of the OC patients undergoing PIPAC. Integration: Study selection and data extraction were independently undertaken by two reviewers. Results: 235 patients from 15 studies retrieved from PubMed were included. Conclusions: Our results indicate that PIPAC is efficient and safe in selected OC patients with PC not responding to systemic chemotherapy. The toxicity is manageable and the quality of life sustained. Further, randomised controlled trials are warranted to confirm our findings.
The role of LHCBM1 in non-photochemical quenching in Chlamydomonas reinhardtii

Non-photochemical quenching (NPQ) is the process that protects photosynthetic organisms from photodamage by dissipating the energy absorbed in excess as heat. In the model green alga Chlamydomonas reinhardtii, NPQ was abolished in the knock-out mutants of the pigment-protein complexes LHCSR3 and LHCBM1. However, while LHCSR3 was shown to be a pH sensor and switching to a quenched conformation at low pH, the role of LHCBM1 in NPQ has not been elucidated yet. In this work, we combine biochemical and physiological measurements to study short-term high light acclimation of npq5, the mutant lacking LHCBM1. We show that while in low light in the absence of this complex, the antenna size of PSII is smaller than in its presence, this effect is marginal in high light, implying that a reduction of the antenna is not responsible for the low NPQ. We also show that the mutant expresses LHCSR3 at the WT level in high light, indicating that the absence of this complex is also not the reason. Finally, NPQ remains low in the mutant even when the pH is artificially lowered to values that can switch LHCSR3 to the quenched conformation. It is concluded that both LHCSR3 and LHCBM1 need to be present for the induction of NPQ and that LHCBM1 is the interacting partner of LHCSR3. This interaction can either enhance the quenching capacity of LHCSR3 or connect this complex with the PSII supercomplex.
Virtual Reality Technology and Speech Analysis for People Who Stutter

Virtual reality (VR) technology provides an interactive computer-generated experience that artificially simulates real-life situations by creating a virtual environment that looks real and stimulates the user’s feelings. During the past few years, the use of VR technology in clinical interventions for assessment, rehabilitation and treatment have received increased attention. Accordingly, many clinical studies and applications have been proposed in the field of mental health, including anxiety disorders. Stuttering is a speech disorder in which affected individuals have a problem with the flow of speech. This can manifest in the repetition and prolongation of words or phrases, as well as in involuntary silent pauses or blocks during which the individual is unable to produce sounds. Stuttering is often accompanied by a social anxiety disorder as a secondary symptom, which requires separate treatment. In this study, we evaluated the effectiveness of using a VR environment as a medium for presenting speech training tasks. In addition, we evaluated the accuracy of a speech analyzer module in detecting stuttering events.
Structural and thermodynamic analyses of the β-to-α transformation in RfaH reveal principles of fold-switching proteins

The two-domain protein RfaH, a paralog of the universally conserved NusG/Spt5 transcription factors, is regulated by autoinhibition coupled to the reversible conformational switch of its 60-residue C-terminal KOW domain between an α-hairpin and a β-barrel. In contrast, NusG/Spt5-KOW domains only occur in the β-barrel state. To understand the principles underlying the drastic fold switch in RfaH, we elucidated the thermodynamic stability and the structural dynamics of two RfaH- and four NusG/Spt5-KOW domains by combining biophysical and structural biology methods. We find that the RfaH-KOW β-barrel is thermodynamically less stable than that of most NusG/Spt5-KOWs and we show that it is in equilibrium with a globally unfolded species, which, strikingly, contains two helical regions that prime the transition towards the α-hairpin. Our results suggest that transiently structured elements in the unfolded conformation might drive the global folding transition in metamorphic proteins in general.
Probabilistic Risk Assessment – The Keystone for the Future of Toxicology

Safety sciences must cope with uncertainty of models and results as well as information gaps. Acknowledging this uncertainty necessitates embracing probabilities and accepting the remaining risk. Every toxicological tool delivers only probable results. Traditionally, this is taken into account by using uncertainty / assessment factors and worst-case / precautionary approaches and thresholds. Probabilistic methods and Bayesian approaches seek to characterize these uncertainties and promise to support better risk assessment and, thereby, improve risk management decisions. Actual assessments of uncertainty can be more realistic than worst-case scenarios and may allow less conservative safety margins. Most importantly, as soon as we agree on uncertainty, this defines room for improvement and allows a transition from traditional to new approach methods as an engineering exercise. The objective nature of these mathematical tools allows to assign each methodology its fair place in evidence integration, whether in the context of risk assessment, systematic reviews, or in the definition of an integrated testing strategy (ITS) / defined approach (DA) / integrated approach to testing and assessment (IATA). This article gives an overview of methods for probabilistic risk assessment and their application for exposure assessment, physiologically-based kinetic modelling, probability of hazard assessment (based on quantitative and read-across based structure-activity relationships, and mechanistic alerts from in vitro studies), individual susceptibility assessment, and evidence integration. Additional aspects are opportunities for uncertainty analysis of adverse outcome pathways and their relation to thresholds of toxicological concern. In conclusion, probabilistic risk assessment will be key for constructing a new toxicology paradigm – probably!
Using intracerebral microdialysis to probe the efficacy of repurposed drugs in Alzheimer’s disease pathology

All disease-targeting drug trials completed to date have fallen short of meeting the clinical endpoint of significantly slowing cognitive decline in Alzheimer’s disease patients. Even the recently approved drug Aducanumab, has proven effective in removing amyloid-β, but does not reduce cognitive decline. This emphasizes the urgent need for novel therapeutic approaches that could reduce several AD neuropathologies simultaneously, eventually leading to improved cognitive performance. To validate whether our mouse model replicates AD neuropathology as observed in patients, we characterized the 3xTg AD mouse model to avoid premature translation of successful results. In this study we have repurposed two FDA-approved drugs, Fasudil and Lonafarnib, targeting the Wnt signaling and endosomal-lysosomal pathway respectively, to test their potential to attenuate AD pathology. Using intracerebral microdialysis, we simultaneously infused these disease-targeting drugs between 1-2 weeks, separately and also in combination, while collecting cerebrospinal fluid. We found that Fasudil reduces intracellular amyloid-β in young, and amyloid plaques in old animals, and overall cerebrospinal fluid amyloid-β. Lonafarnib reduces tau neuropathology and cerebrospinal fluid tau biomarkers in young and old animals. Co-infusion of both drugs was more effective in reducing intracellular amyloid-β than either drug alone, and appeared to improve contextual memory performance. However, an unexpected finding was that Lonafarnib treatment increased amyloid plaque size, suggesting that activating the endosomal-lysosomal system may inadvertently increase amyloid-β pathology if administered too late in the AD continuum. Taken together, these findings lend support to the application of repurposed drugs to attenuate AD neuropathology at various therapeutic time windows. One Sentence Summary Here we circumvented the blood-brain barrier for drug delivery aimed at attenuating AD neuropathology.
A Heterogeneous Multi-criteria Hierarchical Evaluation Model For Web site Services

Nowadays, there are a lot of websites related to the same topic that oﬀer similar services in Internet and try to attract as many people as possible. The quality of the web services has become a critical factor in the success of these web sites. Diﬀerent evaluation approaches for diﬀerent types of web sites have been developed in which the users provide their opinions in a predeﬁned numerical scale to evaluate their services. Nevertheless, the criteria used in these evaluations are related to human perceptions and not all the criteria have the same nature, therefore, the evaluation process is deﬁned in an heterogeneous context. In this contribution, we shall propose a heterogeneous multi-criteria hierarchical evaluation model that is able to deal with aspects assessed in diﬀerent domains.