Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced Deep Convolutional Neural Network for SARS-CoV-2 Variants Classification

High-throughput sequencing techniques and sequence analysis have enabled the taxonomic classification of pathogens present in clinical samples. Sequencing provides an unbiased identification and systematic classification of pathogens and this is generally achieved by comparing novel sequences to pre-existing annotated reference databases. However, this approach is limited by large-scale reference databases which require considerable computational resources and skills to compare against. Alternative robust methods such as machine learning are currently employed in genome sequence analysis and classification, and it can be applied in classifying SARS-CoV-2 variants, whose continued evolution has resulted in the emergence of multiple variants. We developed a deep learning Convolutional Neural Networks-Long Short Term Memory (CNN-LSTM) model to classify dominant SARS-CoV-2 variants (omicron, delta, beta, gamma and alpha) based on gene sequences from the surface glycoprotein (spike gene). We trained and validated the model using > 26,000 SARS-CoV-2 sequences from the GISAID database. The model was evaluated using unseen 3,057 SARS-CoV-2 sequences. The model was compared to existing molecular epidemiology tool, nextclade. Our model achieved an accuracy of 98.55% on training, 99.19% on the validation and 98.41% on the test dataset. Comparing the proposed model to nextclade, the model achieved significant accuracy in classifying SARS-CoV-2 variants from unseen data. Nextclade identified the presence of recombinant strains in the evaluation data, a mechanism that the proposed model did not detect. This study provides an alternative approach to pre-existing methods employed in the classification of SARS-CoV-2 variants. Timely classification will enable effective monitoring and tracking of SARS-CoV-2 variants and inform public health policies in the control and management of the COVID-19 pandemic.
Eyes in the Dark: Using Eye-Tracking Technology to Investigate the Effects of Darkness on Human Cognition and Implications for Cave Archaeology

The ethnographic and archaeological evidence indicates a cross-cultural association of dark zones of caves with supernatural phenomena. In various geographic locations and time periods, human beings have frequented dark zones for ritual purposes. Regarding the unsuitable living conditions of dark zones, the following question arises: what drives humans to choose such places for practicing rituals? The answer to this question lies in the way human beings interact with dark cave environments. In this paper, I suggest that experiencing sensory deprivation, in particular lack of vision in dark zones, precipitates the enhancement of abstract and magical thinking. To verify this hypothesis, I employed the methods of cognitive sciences— namely, experimental research. I conducted an experiment using eye-tracking glasses to record participants’ eye-movement trajectories in darkness. The results indicated that eye-movement patterns during darkness resemble those during activities involving abstract and divergent thinking. Consequently, darkness seems to provoke and facilitate creativity. I thus suggest that in addition to social and cultural incentives, darkness, as an environmental cue, sets the stage for human beings to associate dark zones of caves with supernatural powers and therefore choose to practice rituals in such locations.
Sub-nucleolar trafficking of Hendra virus matrix protein is regulated by ubiquitination and oligomerisation

Hendra virus (HeV) is a highly pathogenic member of the Henipavirus genus (order Mononegavirales), the replication cycle of which occurs primarily in the cytoplasm. The HeV matrix protein (HeV M) plays critical roles in viral assembly and budding at the plasma membrane, but also undergoes nuclear/nucleolar trafficking, to accumulate in nucleoli early in infection and, later, localise predominantly at the plasma membrane. Previously we found that HeV M protein targets specific sub-nucleolar compartments (corresponding to the FC-DFC (fibrillar centre (FC)/dense fibrillar component (DFC)) where it interacts with the nucleolar protein Treacle and modulates rRNA biogenesis by subverting the host nucleolar DNA damage response, indicating the importance of specific sub-nucleolar trafficking to infection. However, the mechanisms underlying targeting and movement between sub-nucleolar compartments by viral or cellular proteins remain poorly defined. Here, we assessed the molecular regulation of HeV M protein nucleolar/sub-nucleolar trafficking, finding that HeV M localizes into Treacle-enriched FC-DFC early after expression, but this localization is progressively depleted through relocalization to the surrounding granular component (GC) of the nucleolus. Analysis using mutated M proteins and pharmacological modulation of ubiquitination indicate that this dynamic localization is regulated by ubiquitination and oligomerisation, with ubiquitination required for retention of HeV M in Treacle-enriched sub-nucleolar compartments, and oligomerisation required for egress. To our knowledge, this study provides the first direct insights into the dynamics and mechanisms of viral protein trafficking between sub-nucleolar compartment, shedding light on the intricate interplay between HeV M and host cell factors during infection.
Comparative proteomics uncovers low asparagine insertion in Plasmodium tRip-KO proteins

tRNAs are not only essential for decoding the genetic code, but their abundance also has a strong impact on the rate of protein production, folding, and on the stability of the translated messenger RNAs. Plasmodium expresses a unique surface protein called tRip, involved in the import of exogenous tRNAs into the parasite. Comparative proteomic analysis of the blood stage of wild-type and tRip-KO variant of P. berghei parasites revealed that down-regulated proteins in the mutant parasite are distinguished by a bias in their asparagine content. Furthermore, the demonstration of the possibility of charging host tRNAs with Plasmodium aminoacyl-tRNA synthetases, led us to propose that, imported host tRNAs participate in parasite protein synthesis. These results also suggest a novel mechanism of translational control in which import of host tRNAs emerge as regulators of gene expression in the Plasmodium developmental cycle and pathogenesis, by enabling the synthesis of asparagine-rich regulatory proteins that efficiently and selectively control the parasite infectivity.
Cell division machinery drives cell-specific gene activation during bacterial differentiation

When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that a unique feature of the sporulation septum, defined by the cell division machinery, drives the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
HIV-Tocky system to visualize proviral expression dynamics

The stably integrated pool of HIV-1 proviruses in the host genome stands against curative strategies. This reservoir is extremely heterogeneous with respect to host cell type, anatomical location, integration site, and replication fitness. During the initial phase of infection, only a few infected cells can resist host immune clearance or cytopathic effect and establish this resistant pool. The mechanisms underlying HIV latency initiation are not fully resolved yet. In the current study, we propose and validate a new reporter model for monitoring HIV-1 provirus silencing and reactivation using Timer of cell kinetics and activity (Tocky). HIV-Tocky system uses a fluorescent Timer protein whose emission spectrum spontaneously shifts from blue to red to reveal HIV-1 provirus dynamics. We dissected provirus transcriptional phases into early, persistent, recently silenced, and latent. To our knowledge, this is the first report to distinguish two latent subsets: a directly non-expressing population and a recently silenced after brief expression. In-depth integration site analysis suggested that the distribution of proviruses in directly latent cells was similar to that in actively transcribing cell population, whereas recently silenced cells tended to harbor proviruses integrated into heterochromatin. Furthermore, we established a library of various single integration clones at which we utilized to demonstrate the efficiency of the block-and-lock strategy by capturing the fast dynamics of silencing that were overlooked in previous models. In summary, we propose HIV-Tocky system to serve as a time-sensitive model that can capture the dynamics of provirus expression, making it a useful tool for HIV latency research. Significance Statement Determinants of HIV-1 latency establishment are yet to be elucidated. This reservoir comprises a rare fraction of infected cells that can survive host and virus-mediated killing. In vitro reporter models so far offered a feasible means to inspect this population, but with limited capabilities to dissect provirus silencing dynamics. Here, we describe a new HIV reporter model (HIV-Tocky) with dual fluorescence spontaneous shifting to reveal provirus silencing and reactivation dynamics. This unique feature allowed; for the first time, identifying two latent populations: a directly latent, and a recently silenced subset, with the latter having integration features suggestive of stable latency. Our proposed model can help address the heterogeneous nature of HIV reservoirs and offers new possibilities for evaluating eradication strategies. Classification Biological Sciences, Microbiology.
Are Perceptions About Government and Social Media Providers Related to Protection Motivation Online?

This study aims to explore the relations between perceptions about government and social media providers, and protection motivation of social media users. A survey was conducted among students at a public university in Slovenia (N=276). The results of PLS-SEM analysis indicate that fear of government intrusions is associated with both perceived threat and privacy concern. This establishes the perceptions about government as important factors related to both privacy concern and threat appraisal according to protection motivation literature. Non-significant relations between trust in internet service provider, and perceived threat and privacy concern indicate that social media users may not consider them as relevant cyberspace actors capable of threatening their privacy on social media. The results also suggest that trust in social media providers moderates the association between privacy concern and protection motivation. Privacy concern appears to be related to protection motivation only if trust in social media provider is high.
VMHdm/cSF-1 neuronal circuits regulate skeletal muscle PGC1-α via the sympathoadrenal drive

Objective To adapt to metabolically challenging environments, the central nervous system (CNS) orchestrates metabolism of peripheral organs including skeletal muscle. The organ-communication between the CNS and skeletal muscle has been investigated, yet our understanding of the neuronal pathway from the CNS to skeletal muscle is still limited. Neurons in the dorsomedial and central parts of the ventromedial hypothalamic nucleus (VMHdm/c) expressing steroidogenic factor-1 (VMHdm/cSF-1 neurons) are key for metabolic adaptations to exercise, including increased basal metabolic rate and skeletal muscle mass in mice. However, the mechanisms by which VMHdm/cSF-1 neurons regulate skeletal muscle function remain unclear. Here, we show that VMHdm/cSF-1 neurons increase the sympathoadrenal activity and regulate skeletal muscle peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α) in mice via multiple downstream nodes. Methods Optogenetics was used to specifically manipulate VMHdm/cSF-1 neurons combined with genetically-engineered mice and surgical manipulation of the sympathoadrenal activity. Results Optogenetic activation of VMHdm/cSF-1 neurons dramatically elevates mRNA levels of skeletal muscle Pgc-1α, which regulates a spectrum of skeletal muscle function including protein synthesis and metabolism. Mechanistically, the sympathoadrenal drive coupled with β2 adrenergic receptor (β2AdR) is essential for VMHdm/cSF-1 neurons-mediated increases in skeletal muscle PGC1-α. Specifically, both adrenalectomy and β2AdR knockout block augmented skeletal muscle PGC1-α by VMHdm/cSF-1 neuronal activation. Optogenetic functional mapping reveals that downstream nodes of VMHdm/cSF-1 neurons are functionally redundant to increase circulating epinephrine and skeletal muscle PGC1-α. Conclusions Collectively, we propose that VMHdm/cSF-1 neurons-skeletal muscle pathway, VMHdm/cSF-1 neurons→multiple downstream nodes→the adrenal gland→skeletal muscle β2AdR, underlies augmented skeletal muscle function for metabolic adaptations.
Growth of Vistula sea trout [Salmo trutta m. trutta L.] based on adults caught in the Vistula River prior to the construction of the dam in Wloclawek

The growth of winter and summer Vistula sea trout was compared using archival material from 1961-1968 before the construction of the dam near W3oc3awek. The average value of fish body growth during their first year in the sea was back calculated. The second growth measure was the fish size from the same year class (A.B+) during its occurrence in the river both in summer and winter. Growth variability, resulting from sex structure, smolt age and various calendar years, was eliminated by the proper choice of materials. The average body growth in the first year the fish were in the sea was greater in winter sea trout than in summer sea trout, and the differences that were evaluated with t-Student tests were statistically significant. No statistically significant differences were observed for the average lengths and masses of summer and winter sea trout or that the summer sea trout was larger than the winter one. Thus, its longer stay in feeding grounds before its spawning migration compensates for the lower rate of summer sea trout body growth.
Assessing the impact of climate change on the frequency of floods in the Red River basin

The impact of climate change on the frequency distribution of spring floods in the Red River basin is investigated. Several major floods in the last couple of decades have caused major damages and inconvenience to people living in the Red River flood plain south of Winnipeg, and have raised the question of whether climate change is at least partly responsible for what appears to be more frequent occurrences of high spring runoff. To investigate whether this is the case, a regression model is used to associate spring peak flow at the US–Canada border with predictor variables that include antecedent precipitation in the previous fall (used as a proxy for soil moisture at freeze-up), winter snow accumulation and spring precipitation. Data from the Coupled Model Intercomparison Project – Phase 5 (CMIP5) are used to derive information about possible changes to the predictor variables in the future, and this information is then used to derive flood distributions for future climate conditions. While mean monthly precipitation during the winter months is expected to increase, winters are expected to be shorter in warmer climates and evaporation losses are expected to be higher, resulting in a net reduction in average snow pack accumulations. On the other hand, precipitation during the active snowmelt period is expected to increase. The average of future flood distributions obtained from an ensemble of 16 climate models is close to the distribution fitted to observed data, but there is considerable uncertainty surrounding the average, highlighting the difficulty in assessing changes in the frequency of extreme events.
A Novel Fast Sparse Bayesian Learning STAP Algorithm for Conformal Array Radar

: Space-time adaptive processing (STAP) is an important method of clu tt er suppression that requires adequate training samples. For an airborne conformal array radar, conventional STAP methods do not have enough training samples to acquire good performance due to the range dependent clu tt er caused by geometry and the problem of polarization. Sparse-recovery-based STAP (SR-STAP) methods have garnered signi ﬁ cant a tt ention in the past few decades because they only require a small number of training samples. Sparse Bayesian Learning (SBL) methods have seen increasing amounts of development due to its robust, self-regularizing nature and because it is not sensitive to user parameters, but it converges slowly. In this paper, a novel fast SBL (NFSBL) method is put forward to increase the rate of convergence. To minimize the SBL penalty function, the proposed method introduces the conjugate function to construct a surrogate function. Additional solu-tion sparsity will be achieved through iteratively minimizing the surrogate function. Then, from the proposed method, we could obtain a more accurate clu tt er plus noise covariance matrix. Numerical simulation results express that this method could acquire be tt er performance of STAP and improvement in convergence and computational complexity for a conformal array.
Adapting to Intermittent Faults in Multicore Systems Appears in 13 th International Conference on Architectural Support for Programming Languages and Operating Systems ( ASPLOS-XIII )

Future multicore processors will be more susceptible to a variety of hardware failures. In particular, intermittent faults, caused in part by manufacturing, thermal, and voltage variations, can cause bursts of frequent faults that last from several cycles to several seconds or more. Due to practical limitations of circuit techniques, costeffective reliability will likely require the ability to temporarily suspend execution on a core during periods of intermittent faults. We investigate three of the most obvious techniques for adapting to the dynamically changing resource availability caused by intermittent faults, and demonstrate their different system-level implications. We show that system software reconfiguration has very high overhead, that temporarily pausing execution on a faulty core can lead to cascading livelock, and that using spare cores has high faultfree cost. To remedy these and other drawbacks of the three baseline techniques, we propose using a thin hardware/firmware layer to manage an overcommitted system — one where the OS is configured to use more virtual processors than the number of currently available physical cores. We show that this proposed technique can gracefully degrade performance during intermittent faults of various duration with low overhead, without involving system software, and without requiring spare cores.
Beyond Rhetoric

Many of the serious public health problems affecting U.S. citizens and the global community can be addressed by prevention science and practice. Instructive standards or guidance for prevention work have largely been missing from the professional literature. Despite empirical evidence that prevention works, the epidemiological literature continues to reflect significant disparities in the health status of ethnic minorities and the poor. The Major Contribution by Hage and colleagues addresses this gap in the literature by offering standards for conducting meaningful and effective prevention work. This response highlights the imperatives for prevention work and other themes that deserve attention if prevention's potential impact on health is to be realized. The author discusses the necessity for training in prevention, multidisciplinary collaboration, and understanding and changing the social determinants of health. Prevention scientists must disseminate effective prevention strategies, and prevention practitioners must work with prevention scientists to adapt these strategies to respond to the challenges of conducting prevention work across diverse settings.
Synthetic aperture imaging using dense camera arrays

Synthetic aperture imaging is a technique that projects images of a scene from different views on to a virtual focal surface, enabling us to "see through" occlusions in the scene. Using a 100-camera array we have used synthetic aperture imaging to view objects concealed behind dense foliage and to track a person moving through a crowd. The ability to see through occlusions makes synthetic aperture imaging a potentially powerful tool for surveillance. This work makes two contributions. First, we characterize the image warps required for synthetic aperture imaging using projective geometry. This analysis leads to a robust camera calibration procedure for synthetic aperture imaging. Our analysis also shows the relation between the geometric complexity of the image warps and camera/focal plane configurations. In particular, we show that we can vary the focus through families of frontoparallel and tilted focal planes by simply shifting and adding the camera images. As image shifts are relatively simple to realize in hardware, this leads to a real-time system, which we demonstrate for tracking a person moving through a crowd. Second, we explore methods to achieve sharp focus at every pixel in the synthetic aperture image by reconstructing the 3D surfaces of the occluded objects we wish to see. We compare classical shape from stereo with shape from synthetic aperture focus, and describe variants of stereo that improves image contrast by deleting some of the light rays that are incident on the occluder.
The Energy Benefits of the Pantograph Wing Mechanism in Flapping Flight : Case Study of a Gull Gene

Bird wings generally contain a 4-bar pantograph mechanism in the forearm that enables the wrist joint to be actuated from the elbow joint thus reducing the number of wing muscles and hence reducing the wing inertia and inertial drag. In this paper we develop a theoretical model of inertial power for flapping flight to estimate the advantage of the 4-bar pantograph mechanism by comparing the inertial power required for the case where wrist muscles are present in the forearm with the case where wrist muscles are not present in the forearm. It is difficult to predict how wrist muscles would look when there is no pantograph mechanism. Therefore a lower bound and upper bound case are defined. The lower bound case involves redistributing the elbow muscles with no increase in wing mass. The upper bound case involves replicating the biceps-triceps muscles near the wrist joint. At minimum power speed the model estimates that the 4-bar pantograph mechanism reduces the inertial power for the gull from between 6.1%-12.3% and reduces the overall power by 0.6%-1.2%. When account is taken of the tight margins involved in the design of a flying vehicle, the energy savings produced by the pantograph mechanism are significant. A ring-billed gull was chosen for the case study and an adult specimen was obtained to gather morphometric data. Lessons for the design of flapping micro air vehicles are discussed. Nomenclature b Wing span (m) CL Lift coefficient Cw Wing width (m) I Wing inertia ×10-6 (kgm2) (with 4-bar mechanism) I’LB Wing inertia ×10 -6 (kgm2) (without 4-bar mechanism) LB I’UB Wing inertia ×10 -6 (kgm2) (without 4-bar mechanism) UB f Flapping frequency (Hz) Lw Length wing (m) mb-t mass of biceps-triceps (kg) mw Wing mass ×10 -3 (kg) mw-m mass of wrist muscles (kg) rb-t radius of biceps-triceps (m) rw-m radius of wrist muscle S Single wing area ×10-4 (m2) ωmax Maximum angular velocity (rad/s) ρ Air density (kg/m3)