Miracle-dz/UniFAR-FTUs huggingface dataset:
Maxwell's Demons, Protein Molecular Machines, and Information Processing in Biophysics

In the intention of its creator, Maxwell's demon was thought to be an intelligent being able to perform work at the expense of the entropy reduction of a closed operating system. The perplexing notion of the demon's intelligence was formalized in terms of the information processing by Szilard, who pointed out that, in order for the system to be consistent with the second law of thermodynamics, the entropy reduction should be compensated for by, at least, the same entropy increase related to the demon's information on the operating system state. A mechanical (non-informational) formulation of the problem was proposed by Smoluchowski and popularized by Feynman as the ratchet and pawl machine, which can operate only in agreement with the second law. A. F. Huxley and followers adopted this way of thinking to propose numerous thermal ratchet mechanisms of the biological molecular machines action. Here we show that, because of the necessary energy dissipation, both for the thermal ratchet and the concurrent power stroke models, no entropy reduction takes place. It is possible only for protein machine models with a number of conformational states organized in a network of transitions that allow the performance of work in a variety of ways. For such models, no information processing is necessary for the generalized fluctuation theorem to be satisfied. A computer realization is investigated of the conformational network, displaying, like networks of the systems biology, a transition from the fractal organization on a small length-scale to the small-world organization on the large length-scale. This model is able to explain a surprising observation to Yanagida and co-workers that the myosin II head can take several steps along the actin filament per ATP molecule hydrolysed. From a broader perspective, of especial importance could be the supposition that the mechanism of the action of small G-proteins, having a common ancestor with the myosin II, is, after a malignant transformation, similar. Presumably, also transcription factors look actively and not passively for their target on the genome.
Azimuthal rotation in the axisymmetric meridional flow due to an electric-current source

The steady laminar flow driven by the meridional electromagnetic force due to an electric-current point source on a plane is considered. The previous studies of the problem (Shercliff 1970; Shilova & Shcherbinin 1971) lead to a self-similar solution of the full Navier–Stokes equations analogous to the classic Landau jet. The solution breaks down when a critical electric-current magnitude is exceeded (Sozou 1971). In the present paper the converging meridional flow is shown to be unstable to an axisymmetric azimuthal perturbation when the corresponding critical Reynolds number is exceeded. The flow solution breakdown is eliminated for the coupled converging and rotating flow. The physical process is suggested by the draining-vortex formation. The fluid-flow equations are solved by the Galerkin method, using expansions in Gegenbauer functions. The mechanism sustaining the rotation is examined; the increased angular momentum in the fluid region is maintained by the balance of viscous diffusion upstream and convection to the axis of symmetry. The experimental evidence for vortex formation is considered.
Kinetics and ability of binding antibody and surrogate virus neutralization tests to predict neutralizing antibodies against the SARS-CoV-2 Omicron variant following BNT162b2 booster administration

Abstract Objectives To assess the long-term humoral immunity induced by booster administration, as well as the ability of binding antibody and surrogate virus neutralization tests (sVNT) to predict neutralizing antibodies (NAbs) against the SARS-CoV-2 Omicron variant. Methods A total of 269 sera samples were analyzed from 64 healthcare workers who had received a homologous booster dose of BNT162b2. Neutralizing antibodies assessed by sVNT and anti-RBD IgG measured with the sCOVG assay (Siemens Healthineers®) were analyzed at five timepoints; before and up to 6 months following the booster. Antibody titers were correlated with neutralizing antibodies against the Omicron BA.1 variant obtained by pseudovirus neutralization test (pVNT) as a reference method. Results While Wild-type sVNT percentage of inhibition (POI) remained above 98.6% throughout the follow-up period after booster administration, anti-RBD IgG and NAbs assessed by Omicron BA.1 pVNT showed respectively a 3.4-fold and 13.3-fold decrease after 6 months compared to the peak reached at day 14. NAbs assessed by Omicron sVNT followed a steady decline until reaching a POI of 53.4%. Anti-RBD IgG and Omicron sVNT assays were strongly correlated (r=0.90) and performed similarly to predict the presence of neutralizing antibodies with Omicron pVNT (area under the ROC: 0.82 for both assays). In addition, new adapted cut-off values of anti-RBD IgG (>1,276 BAU/mL) and Omicron sVNT (POI>46.6%) were found to be better predictors of neutralizing activity. Conclusions This study showed a significant drop in humoral immunity 6 months after booster administration. Anti-RBD IgG and Omicron sVNT assays were highly correlated and could predict neutralizing activity with moderate performance.
The Life Cycle and Internal Structure of a Mesoscale Convective Complex

Abstract This paper describes the life cycle and precipitation structure of a Mesoscale Convective Complex (MCC) that passed through the data-collecting network of the Texas portion of the High Plains Cooperative Program (HIPLEX) on 8 June 1980. The MCC was the third in a sequence of five mesoscale convective systems that formed in association with a low-level frontal zone, short-wave perturbations in the 500 mb flow, outflow from previous convection, and upslope forcing. Quantitative radar data, together with surface, upper-air and satellite data, were used to determine the three-dimensional structure of the MCC. Isolated echoes formed over the Davis Mountains of far western Texas and merged as they moved eastward to form a mesoscale convective system with a lifetime of ∼24 h and a low-level precipitation pattern ∼500 km across. The leading edge of the low-level precipitation pattern was a north-south line of intense convective cells possessing the echo structure and low-level kinematic and thermodynamic.
The Transformation of Tropical Storm Agnes into an Extratropical Cyclone. Part II: Moisture, Vorticity and Kinetic Energy Budgets

Abstract Moisture, vorticity and kinetic energy budgets are constructed to diagnose the transformation of tropical storm Agnes (June 1972) into an extratropical cyclone in this second of two papers on Agnes. The vertical motions and divergent wind components used in the computations are taken from the solution of the nonlinear balance model described in Part I [DiMego and Bosart (1982)]. The budget equations are formulated in a quasi-Lagrangian reference frame centered with respect to the moving surface cyclone for several storm volumes. The results are displayed spatially as well as in time-section format. Synoptic-scale transport and moisture convergence dominate the moisture budget and all terms together define well the areas of observed precipitation. Both budget and model-computed precipitation, particularly the latter, underestimate the observed precipitation. The discrepancy is attributed to the sub-grid scale convective processes and model underestimation of the divergent wind components. Advectio.
Design of Compact Double-Layer Microwave Absorber for X-Ku Bands Using Genetic Algorithm

In this paper, an efficient lightweight double-layer microwave absorber with impedance- matching structure at X-Ku bands was designed, optimized and implemented. First, genetic algorithm (GA) was considered to optimize the thicknesses and material properties for better absorption of the incident electromagnetic wave and reduction of radar cross section (RCS). Next, with the aid of the obtained dielectric and magnetic properties, the microwave absorber was fabricated from magneto- dielectric composite materials besides a natural rubber. Finally, the analytical and numerical results were compared with the measurements to check the validity of the design. Experiments showed that the reflection coefficient for each layer backed with a metallic sheet was insufficient; however, for the double layer absorber, the reflectivity measurement values reached up to −28 dB in the case of normal incidence and −17 dB for oblique incidence.
The effects of government subsidies according to the financial status of start-ups: Focusing on Moral Hazard of Smart Technology Entrepreneurs in the edible insect industry

ABSTRACT The purpose of this study is to investigate the efficiency of smart farm facilities of insect business entities. A questionnaire was conducted to investigate the actual conditions of smart farm edible insect business entities. A survey of 500 edible insect farms, all of which raised insects within 7 years of establishment, was conducted, and all of them raised insects in smart farm facilities. First, after dividing the smart farm into three levels, efficiency was measured. In particular, efficiency was analysed by distinguishing cases of possessing capital and those of receiving support from the government. The results confirmed that receiving government subsidies is more efficient than using own capital. The most significant finding is that if a business entity has a large amount of its own capital and receives government subsidies, efficiency decreases. In other words, when allocating government subsidies, the efficiency of those subsidies can be improved by first identifying the status of existing capital.
LSD microdosing attenuates the impact of temporal priors in time perception

Recent theoretical work embedded within the predictive processing framework has proposed that the neurocognitive and therapeutic effects of psychedelics are driven by the modulation of priors (Carhart-Harris & Friston, 2019). We conducted pre-registered re-analyses of previous research (Yanakieva et al., 2019) to examine whether microdoses of lysergic acid diethylamide (LSD) alleviate the temporal reproduction bias introduced by priors, as predicted by this theoretical framework. In a between-groups design, participants were randomly assigned to one of four groups receiving LSD (5, 10, or 20 μg) or placebo (0 μg) and completed a visual temporal reproduction task spanning subsecond to suprasecond intervals (0.8 to 4 sec). Using mixed-effects modelling, we evaluated the impact of the treatment group, and of the overall history of stimulus intervals (global priors) and the local stimulus history (local priors), weighted by their respective precision weights (inverse of variance), on temporal reproduction. Our principal finding was that the precision-weighted local priors and their precision weights reduced the under-reproduction bias observed under LSD in the original research. Furthermore, controlling for the precision- weighted local prior eliminated the reduced temporal reproduction bias under LSD, indicating that LSD microdosing mitigated the temporal under-reproduction by reducing the relative weighting of priors. These results suggest that LSD microdosing alters human time perception by decreasing the influence of local temporal priors.
Genome-resolved transcriptomics reveals novel organohalide-respiring bacteria from Aarhus Bay sediments

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from PCE-respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 high quality bins with over 75 % completeness and less than 5 % contamination. Sixteen bins harbored RDase genes, and were affiliated taxonomically to the class of Bacilli, and phyla of Bacteroidota, Synergistota, and Spirochaetota, that have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically closely related to the genus Vulcanibacillus, contained an unprecedented 97 RDase genes. Of these, 84 RDase genes of bin.26 were transcribed during PCE dechlorination in addition to RDase genes from members of Synergistales (bin.15 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested the RDase genes were likely under the regulation of transcriptional regulators not previously associated with OHR, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to provide evidence towards the diversity, activity and regulation of reductive dehalogenases.
Nucleus accumbens and dorsal medial striatal dopamine and neural activity are essential for action sequence performance

Separable striatal circuits have unique functions in Pavlovian and instrumental behaviors but how these roles relate to performance of sequences of actions with and without associated cues is less clear. Here we tested whether dopamine release and neural activity more generally in three striatal subdomains are necessary for performance of an action chain leading to reward delivery. Male and female Long-Evans rats were trained to press a series of three spatially-distinct levers to receive reward. We assessed the contribution of neural activity or dopamine release within each striatal subdomain when progression through the action sequence was explicitly cued and in the absence of cues. Behavior in both task variations was substantially impacted following microinfusion of the dopamine antagonist, flupenthixol, into nucleus accumbens core (NAc) or dorsomedial striatum (DMS), with impairments in sequence timing and a strong impact on motivation after NAc flupenthixol. In contrast, after pharmacological inactivation to suppress overall activity, there was minimal impact on motivation, except within the uncued task after DMS inactivation. Inactivation of both NAc and DMS impaired sequence timing and led to sequence errors in the uncued, but not cued task. There was virtually no impact of dopamine antagonism or reversible inactivation of dorsolateral striatum on either cued or uncued action sequence completion. These results highlight an essential contribution of NAc and DMS dopamine systems in motivational and performance aspects of chains of actions, whether cued or internally generated, as well as the impact of intact NAc and DMS function for correct sequence performance.
EGFR+ lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth

The limited efficacy of currently approved immunotherapies in EGFR-mutant lung adenocarcinoma (LUAD) underscores the need to better understand mechanisms governing local immunosuppression. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophages (TA-AM) to proliferate and support tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF—PPARγ signaling and inhibition of airway GM-CSF or PPARγ in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPARγ in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases T cell effector functions. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how such cancer cells can metabolically co-opt TA-AMs through GM-CSF—PPARγ signaling to provide nutrients that promote oncogenic signaling and growth.
Driving and suppressing the human language network using large language models

Transformer models such as GPT generate human-like language and are highly predictive of human brain responses to language. Here, using fMRI-measured brain responses to 1,000 diverse sentences, we first show that a GPT-based encoding model can predict the magnitude of brain response associated with each sentence. Then, we use the model to identify new sentences that are predicted to drive or suppress responses in the human language network. We show that these model-selected novel sentences indeed strongly drive and suppress activity of human language areas in new individuals. A systematic analysis of the model-selected sentences reveals that surprisal and well-formedness of linguistic input are key determinants of response strength in the language network. These results establish the ability of neural network models to not only mimic human language but also noninvasively control neural activity in higher-level cortical areas, like the language network.
Analysis of the Internal Gravity Wave Occurrence of 19 April 1970 in the Midwest

Abstract An analysis is made of high frequency, fluctuations of surface pressure and wind with a period of 3–4 h observed in the midwestern United States in the early morning hours of 19 April 1470. The phenomenon is shown to be of subsynoptic scale and clear interrelationships are established between the surface pressure, wind, and cloudiness variations. Solutions from a simple model of atmospheric dynamics for a compressible and hydrostatic flow are compared with the observations. It is shown that the fluctuations in the atmosphere correspond well to simple gravity wave concepts and in particular to internal gravity waves propagating to the northeast with an approximate speed of 50 m/s and an average wavelength of 500 km.
Raman study of electric-field-induced first-order metal-insulator transition in VO2-based devices

An abrupt first-order metal-insulator transition (MIT) as a current jump has been observed by applying a dc electric field to Mott insulator VO2-based two-terminal devices. The size of the jumps was measured to be asymmetrical depending on the direction of the applied voltage due to heating effects. The structure of VO2 is investigated by micro-Raman scattering experiments. An analysis of the Raman-active Ag modes at 195 and 222cm−1, explained by pairing and tilting of V cations, and 622cm−1, shows that the modes below a low compliance (restricted) current do not change when the MIT occurs, whereas a structural phase transition above the low compliance current is found to occur secondarily, due to heating effects in the device induced by the MIT. The MIT has applications in the development of high-speed and high-gain switching devices.
PTEN knockout using retrogradely transported AAVs restores locomotor abilities in both acute and chronic spinal cord injury

Restoring function in chronic stages of spinal cord injury (SCI) has often been met with failure or reduced efficacy when regenerative strategies are delayed past the acute or sub-acute stages of injury. Restoring function in the chronically injured spinal cord remains a critical challenge. We found that a single injection of retrogradely transported adeno-associated viruses (AAVrg) to knockout the phosphatase and tensin homolog protein (PTEN) in chronic SCI can effectively target both damaged and spared axons and restore locomotor functions in near-complete injury models. AAVrg’s were injected to deliver cre recombinase and/or a red fluorescent protein (RFP) under the human Synapsin 1 promoter (hSyn1) into the spinal cords of C57BL/6 PTENFloxΔ/Δ mice to knockout PTEN (PTEN-KO) in a severe thoracic SCI crush model at both acute and chronic time points. PTEN-KO improved locomotor abilities in both acute and chronic SCI conditions over a 9-week period. Regardless of whether treatment was initiated at the time of injury (acute), or three months after SCI (chronic), mice with limited hindlimb joint movement gained hindlimb weight support after treatment. Interestingly, functional improvements were not sustained beyond 9 weeks coincident with a loss of RFP reporter-gene expression and a near-complete loss of treatment-associated functional recovery by 6 months post-treatment. Treatment effects were also specific to severely injured mice; animals with weight support at the time of treatment lost function over a 6-month period. Retrograde tracing with Fluorogold revealed viable neurons throughout the motor cortex despite a loss of RFP expression at 9 weeks post-PTEN-KO. However, few Fluorogold labeled neurons were detected within the motor cortex at 6 months post-treatment. BDA labeling from the motor cortex revealed a dense corticospinal tract (CST) bundle in all groups except chronically treated PTEN-KO mice indicating a potential long-term toxic effect of PTEN-KO to neurons in the motor cortex. PTEN-KO mice had significantly more β-tubulin III labeled axons within the lesion when treatment was delivered acutely, but not chronically post-SCI. In conclusion, we have found that using AAVrg’s to knockout PTEN is an effective manipulation capable of restoring motor functions in chronic SCI and can enhance axon growth of currently unidentified axon populations when delivered acutely after injury. However, the long-term consequences of PTEN-KO may exert neurotoxic effects.
Staying in control: characterising the mechanisms underlying cognitive control in high and low arousal states

Throughout the day, humans show natural fluctuations in arousal that impact cognitive function. To study the behavioural dynamics of cognitive control during high and low arousal states, healthy participants performed an auditory conflict task during high-intensity physical exercise (N = 39) or drowsiness (N = 33). In line with the pre-registered hypothesis, conflict and conflict adaptation effects were preserved during both altered arousal states. Overall task performance was markedly poorer during low arousal, but not for high arousal. Modelling behavioural dynamics with drift-diffusion analyses revealed evidence accumulation and non-decision time decelerated, and decisional boundaries became wider during low arousal, whereas high arousal was unexpectedly associated with a decrease in the interference of task-irrelevant information processing. These findings show how arousal differentially modulates cognitive control at both sides of normal alertness, and further validates drowsiness and physical exercise as key experimental models to disentangle the interaction between physiological fluctuations on cognitive dynamics.