Miracle-dz/UniFAR-FTUs huggingface dataset:
Two New Ypt GTPases Are Required for Exit From the Yeast trans-Golgi Compartment

Small GTPases of the Ypt/rab family are involved in the regulation of vesicular transport. These GTPases apparently function during the targeting of vesicles to the acceptor compartment. Two members of the Ypt/rab family, Ypt1p and Sec4p, have been shown to regulate early and late steps of the yeast exocytic pathway, respectively. Here we tested the role of two newly identified GTPases, Ypt31p and Ypt32p. These two proteins share 81% identity and 90% similarity, and belong to the same protein subfamily as Ypt1p and Sec4p. Yeast cells can tolerate deletion of either the YPT31 or the YPT32 gene, but not both. These observations suggest that Ypt31p and Ypt32p perform identical or overlapping functions. Cells deleted for the YPT31 gene and carrying a conditional ypt32 mutation exhibit protein transport defects in the late exocytic pathway, but not in vacuolar protein sorting. The ypt31/ 32 mutant secretory defect is clearly downstream from that displayed by a ypt1 mutant and is similar to that of sec4 mutant cells. However, electron microscopy revealed that while sec4 mutant cells accumulate secretory vesicles, ypt31/32 mutant cells accumulate aberrant Golgi structures. The ypt31/32 phenotype is epistatic to that of a sec1 mutant, which accumulates secretory vesicles. Together, these results indicate that the Ypt31/32p GTPases are required for a step that occurs in the transGolgi compartment, between the reactions regulated by Ypt1p and Sec4p. This step might involve budding of vesicles from the trans-Golgi. Alternatively, Ypt31/ 32p might promote secretion indirectly, by allowing fusion of recycling vesicles with the trans-Golgi compartment.
Phase Transition of Single-Layer Molybdenum Disulfide Nanosheets under Mechanical Loading Based on Molecular Dynamics Simulations

The single-layer molybdenum disulfide (SLMoS2) nanosheets have been experimentally discovered to exist in two different polymorphs, which exhibit different electrical properties, metallic or semiconducting. Herein, molecular dynamics (MD) simulations of nanoindentation and uniaxial compression were conducted to investigate the phase transition of SLMoS2 nanosheets. Typical load–deflection curves, stress–strain curves, and local atomic structures were obtained. The loading force decreases sharply and then increases again at a critical deflection under the nanoindentation, which is inferred to the phase transition. In addition to the layer thickness, some related bond lengths and bond angles were also found to suddenly change as the phase transition occurs. A bell-like hollow, so-called residual deformation, was found to form, mainly due to the lattice distortion around the waist of the bell. The effect of indenter size on the residual hollow was also analyzed. Under the uniaxial compression along the armchair direction, a different phase transition, a uniformly quadrilateral structure, was observed when the strain is greater than 27.7%. The quadrilateral structure was found to be stable and exhibit metallic conductivity in view of the first-principle calculation.
Validation of Class of Applications Using Progressive Failure And Discrete Cohesive Zone Model for Line And Surface Cracks

Combination of multi-scale and multi-physics Progressive Failure Analysis (PFA) methodology and linear elastic fracture mechanics is introduced. The approach combined approach detects crack-path or multi-site crack path and predicts the complete load-displacement curve correctly. Though more accurate, LEFM based methodologies of Discrete Cohesive Zone Modeling (DCZM) and Virtual Crack Closure Technique (VCCT) alone seem to be test duplication methodologies rather than test prediction for several complex problems. This is primarily because the structural finite element (FE) models need pre-defined crack path information from the test, in addition, to fracture toughness and cohesive material properties. This seriously limits the capability of both DCZM and VCCT approaches. The proposed approach in this paper focuses mainly to use DCZM and VCCT approach as test prediction methods rather than test duplication methodology. The methodology works in two stages: first, analyzing an FE model with the strength-/strain-based PFA; second, performing crack propagation analysis with either DCZM or VCCT approach. The approach is designed as a test prediction/reduction strategy for analyzing crack initiation and propagation problems. The first step of simulating a problem with PFA helps determine the expected crack-path initiation and propagation information that both DCZM and VCCT methodologies require solely based on material stiffness and strength properties. The second step helps improve the simulation results and overcome the stress singularity issues predominate in crack propagation fracture analysis problems (associated with removal of elements in FE simulations). The methodology was validated by simulating the delamination process (initiation and propagation) in composite structural components such as joints and z-pinned reinforced composite beam structures. The two step strategy has been applied to a skin/stringer structural joint debonding analysis subjected to a tension and a threepoint bending load. The FE models are a three dimensional surface crack problem analyzed using PFA and DCZM approach consisting predominantly of Mode II (tension) and Modes I and II (3 point bending) failure. All simulation results are in close agreement with the test data. It is noted that strength-based PFA approach alone gave results which are in good agreement with the test data and was able to show secondary failure mechanisms not visible when DCZM alone was used to analyze the joint. On the other hand, the usefulness of the DCZM methodology is apparent for simulating the crack propagation in z-pinned unidirectional composite double cantilever beam (here crack path is well defined). The results are within reasonable agreement with the test data.
Across-subjects classification of stimulus modality from human MEG high frequency activity

Single-trial analyses have the potential to uncover meaningful brain dynamics that are obscured when averaging across trials. However, low signal-to-noise ratio (SNR) can impede the use of single-trial analyses and decoding methods. In this study, we investigate the applicability of a single-trial approach to decode stimulus modality from magnetoencephalography (MEG) high frequency activity. In order to classify the auditory versus visual presentation of words, we combine beamformer source reconstruction with the random forest classification method. To enable group level inference, the classification is embedded in an across-subjects framework. We show that single-trial gamma SNR allows for good classification performance (accuracy across subjects: 66.44 %). This implies that the characteristics of high frequency activity have a high consistency across trials and subjects. The random forest classifier assigned informational value to activity in both auditory and visual cortex with high spatial specificity. Across time, gamma power was most informative during stimulus presentation. Among all frequency bands, the 75-95 Hz band was the most informative frequency band in visual as well as in auditory areas. Especially in visual areas, a broad range of gamma frequencies (55-125 Hz) contributed to the successful classification. Thus, we demonstrate the feasibility of single-trial approaches for decoding the stimulus modality across subjects from high frequency activity and describe the discriminative gamma activity in time, frequency, and space. Author Summary Averaging brain activity across trials is a powerful way to increase signal-to-noise ratio in MEG data. This approach, however, potentially obscures meaningful brain dynamics that unfold on the single-trial level. Single-trial analyses have been successfully applied to time domain or low frequency oscillatory activity; its application to MEG high frequency activity is hindered by the low amplitude of these signals. In the present study, we show that stimulus modality (visual versus auditory presentation of words) can successfully be decoded from single-trial MEG high frequency activity by combining source reconstruction with a random forest classification algorithm. This approach reveals patterns of activity above 75 Hz in both visual and auditory cortex, highlighting the importance of high frequency activity for the processing of domain-specific stimuli. Thereby, our results extend prior findings by revealing high-frequency activity in auditory cortex related to auditory word stimuli in MEG data. The adopted across-subjects framework furthermore suggests a high inter-individual consistency in the high frequency activity patterns.
Using quantum-behaved particle swarm optimization algorithm to solve non-linear programming problems

In this paper, we focus on solving non-linear programming (NLP) problems using quantum-behaved particle swarm optimization (QPSO). After a brief introduction to the original particle swarm optimization (PSO), we describe the origin and development of QPSO, and the penalty function method for constrained NLP problems. The performance of QPSO is tested on some unconstrained and constrained benchmark functions and compared with PSO with inertia weight (PSO-In) and PSO with constriction factor (PSO-Co). The experimental results show that QPSO outperforms the traditional PSOs and is a promising optimization algorithm.
An empirical approach to the relationship between emotion and music production quality

In music production, the role of the mix engineer is to take recorded music and convey the expressed emotions as professionally sounding as possible. We investigated the relationship between music production quality and musically induced and perceived emotions. A listening test was performed where 10 critical listeners and 10 non-critical listeners evaluated 10 songs. There were two mixes of each song, the low quality mix and the high quality mix. Each participant's subjective experience was measured directly through questionnaire and indirectly by examining peripheral physiological changes, change in facial expressions and the number of head nods and shakes they made as they listened to each mix. We showed that music production quality had more of an emotional impact on critical listeners. Also, critical listeners had significantly different emotional responses to non-critical listeners for the high quality mixes and to a lesser extent the low quality mixes. The findings suggest that having a high level of skill in mix engineering only seems to matter in an emotional context to a subset of music listeners.
Electric current distribution of carbon fiber reinforced polymer beam: analysis and experimental measurements

The authors have previously proposed an effective method for analyzing the electric current density of carbon fiber-reinforced polymer (CFRP) composites using an anisotropic electric potential function. The method is based on the assumption that CFRP laminates are homogeneous orthotropic materials. Actual CFRP laminates are, however, heterogeneous materials, having resin-rich layers and carbon fiber layers. In the present study, the electric conductance is calculated on the assumption that CFRP laminates are homogeneous using electrical resistance data measured by a four-probe method, and used for electric current analysis. A new specimen design is proposed to allow the electric current distribution of CFRP laminates to be investigated experimentally. The results obtained confirm that our analysis method is accurate for determining the electric current density of actual CFRP laminates. Thus, the assumption that CFRP laminates may be considered homogeneous orthotropic materials for electric current analysis is experimentally verified.
ANG II-related myocardial damage: role of cardiac sympathetic catecholamines and β-receptor regulation.

The objectives of this study were 1) to determine whether ANG II-induced myocardial damage (ANG Dam) is mediated via the β1-adrenergic receptor, 2) to elucidate whether adrenal medulla or cardiac sympathetic neuron catecholamines are responsible for ANG Dam, and 3) to determine whether the lack of damage after 3 days of elevated ANG II levels is due to β1-receptor downregulation. To this end, ANG II was administered to rats 1) that were treated with a β-receptor blocker, 2) after adrenal medullectomy and/or cardiac sympathectomy, and 3) for 3 or 8 days. ANG II caused both myocyte necrosis and coronary vascular damage after adrenal medullectomy but not after cardiac sympathectomy. There was a 38 and 55% decrease in β-receptor density after 3 and 8 days, respectively, of ANG II infusion, and an upregulation to control levels 5 days after a 3-day ANG II infusion was stopped. We conclude that cardiac sympathetic neuron catecholamines are responsible for ANG Dam and that the acute nature of this damage is associated with a downregulation of β1-adrenergic receptors.
A magic state’s fidelity can be superior to the operations that created it

The leading approach to fault tolerant quantum computing requires a continual supply of magic states. When a new magic state is first encoded, its initial fidelity will be too poor for use in the computation. This necessitates a resource-intensive distillation process that occupies the majority of the computer’s hardware; creating magic states with a high initial fidelity minimizes this cost and is therefore crucial for practical quantum computing. Here we present the surprising and encouraging result that raw magic states can have a fidelity significantly better than that of the two-qubit gate operations used to construct them. Our protocol exploits post-selection without significantly slowing the rate of generation and tolerates finite error rates in initializations, measurements and single-qubit gates. This approach may dramatically reduce the size of the hardware needed for a given quantum computing task.
Characterization of Individual Human Antibodies That Bind Pertussis Toxin Stimulated by Acellular Immunization

ABSTRACT Despite high vaccination rates, the incidence of whooping cough has steadily been increasing in developing countries for several decades. The current acellular pertussis (aP) vaccines all include the major protective antigen pertussis toxin (PTx) and are safer, but they appear to be less protective than infection or older, whole-cell vaccines. To better understand the attributes of individual antibodies stimulated by aP, we isolated plasmablast clones recognizing PTx after booster immunization of two donors. Five unique antibody sequences recognizing native PTx were recovered and expressed as recombinant human IgG1 antibodies. The antibodies all bind different epitopes on the PTx S1 subunit, B oligomer, or S1-B subunit interface, and just one clone neutralized PTx in an in vitro assay. To better understand the epitopes bound by the nonneutralizing S1-subunit antibodies, comprehensive mutagenesis with yeast display provided a detailed map of the epitope recognized by antibodies A8 and E12. Residue R76 is required for antibody A8 binding and is present on the S1 surface but is only partially exposed in the holotoxin, providing a structural explanation for A8's inability to neutralize holotoxin. The B-subunit-specific antibody D8 inhibited PTx binding to a model receptor and neutralized PTx in vitro as well as in an in vivo leukocytosis assay. This is the first study, to our knowledge, to identify individual human antibodies stimulated by the acellular pertussis vaccine and demonstrates the feasibility of using these approaches to address outstanding issues in pertussis vaccinology, including mechanisms of accelerated waning of protective immunity despite repeated aP immunization.
Allometry of Constitutive Defense: A Model and a Comparative Test with Tree Bark and Fire Regime

In a simulation model, the relative advantage of negative versus positive allometry of defense, that is, early versus delayed defensive investment, depends on the forms of the relationships between body size and growth, body size and mortality deterrence, and defense size and mortality deterrence. Positive allometry is favored by strongly sigmoidal growth, a strongly convex body‐size/deterrence relationship, and a concave defense‐size/deterrence relationship. Rapid early growth, a weakly convex body‐size/deterrence relationship, and a convex defense‐size/deterrence relationship favor negative allometry. The model is tested by comparing, among Pinus and Quercus species, measured intraspecific bark allometry with a predicted ranking of bark allometry along the negative‐positive continuum. The ranking is based on the forms of body‐size/deterrence and defense‐size/deterrence relationships expected in each species' typical habitat given the fire regime and canopy type. This predicted ranking of bark allometry is significantly correlated with measured bark allometry. Negative bark allometry and thick sapling bark are associated with habitats characterized by frequent low‐intensity fire and relatively open canopies. Fire‐resilient Pinus spp. and species of infrequently burned, closed‐canopy forests tend to have positive bark allometry and thin sapling bark.
ATP is involved in myocardial and vascular effects of exogenous bradykinin in ejecting guinea pig heart.

It has recently been reported that bradykinin induces selective left ventricular (LV) relaxation in isolated guinea pig hearts via the release of nitric oxide. Exogenous bradykinin also induces vasodilation, which is only partly due to nitric oxide release. In the present study we investigated the role of adenyl purines on these bradykinin-induced effects. Isolated ejecting guinea pig hearts were studied. LV pressure was monitored by a 2-Fr micromanometer-tipped catheter. ATP concentrations were measured using a luciferin-luciferase assay. Bradykinin (1 and 100 nM) caused a progressive acceleration of LV relaxation together with a transient increase in coronary flow. These effects were inhibited by the nonselective P2 purinoceptor antagonist suramin (1 μM, n = 6) but were unaffected by the selective P2x purinoceptor antagonist pyridoxal phosphate 6-azophenyl-2',4'-disulfonic acid (1 μM, n = 6). These myocardial and vascular effects of bradykinin were associated with increased ATP levels in coronary effluent. These data suggest that the selective enhancement of LV relaxation and rise in coronary flow induced by exogenous bradykinin involve endogenous ATP and the subsequent stimulation of P2 purinoceptors.
Feedback Leads to Better Exercise Quality in Adolescents with Patellofemoral Pain

Purpose Adolescents with patellofemoral pain (PFP) do not comply with their exercise prescription, performing too few and too fast repetitions, compromising recovery. We investigated if real-time feedback on contraction time would improve the ability of adolescents with PFP to perform exercises as prescribed. Methods A randomized, controlled, participant-blinded, superiority trial with a 6-wk intervention of three weekly sessions of three elastic band exercises was undertaken. Forty 15- to 19-yr-old adolescents with PFP were randomized to real-time BandCizer™-iPad feedback on contraction time or not by a physiotherapist. The primary outcome was the mean deviation from the prescribed contraction time of 8 s per repetition. Secondary outcomes included isometric hip and knee strength, Kujala Patellofemoral Scale, and Global Rating of Change. Results The mean deviation from prescribed 8 s per repetition contraction time was 1.5 ± 0.5 s for the feedback group, compared with 4.3 ± 1.0 s for the control group (mean difference: 2.7 s (95% confidence interval = 2.2–3.2, P < 0.001). On the basis of total contraction time during the intervention, the feedback group received 35.4% of the prescribed exercise dose whereas the control group received 20.3%. Isometric hip and knee strength increased significantly more in the feedback group compared with controls (mean difference = 1.35 N·kg−1, 95% confidence interval = 0.02–2.68, P = 0.047). There were no significant differences in Kujala Patellofemoral Scale and Global Rating of Change between groups, but the study was not powered for this. Conclusion Real-time feedback on contraction time resulted in the ability to perform exercises closer to the prescribed dose and also induced larger strength gains.
How jet lag impairs Major League Baseball performance

Significance Although circadian clocks have been studied extensively in controlled laboratory settings, examining the function and misalignment of these biological clocks in natural settings has been more challenging. Here, we examined data from Major League Baseball (MLB) where players frequently travel long distances in the east–west direction. By using 20 years of MLB data, we found the effect of jet lag to be context dependent and remarkably specific. Overall, our findings demonstrate how circadian misalignment can impact specific features of human performance in natural settings. Laboratory studies have demonstrated that circadian clocks align physiology and behavior to 24-h environmental cycles. Examination of athletic performance has been used to discern the functions of these clocks in humans outside of controlled settings. Here, we examined the effects of jet lag, that is, travel that shifts the alignment of 24-h environmental cycles relative to the endogenous circadian clock, on specific performance metrics in Major League Baseball. Accounting for potential differences in home and away performance, travel direction, and team confounding variables, we observed that jet-lag effects were largely evident after eastward travel with very limited effects after westward travel, consistent with the >24-h period length of the human circadian clock. Surprisingly, we found that jet lag impaired major parameters of home-team offensive performance, for example, slugging percentage, but did not similarly affect away-team offensive performance. On the other hand, jet lag impacted both home and away defensive performance. Remarkably, the vast majority of these effects for both home and away teams could be explained by a single measure, home runs allowed. Rather than uniform effects, these results reveal surprisingly specific effects of circadian misalignment on athletic performance under natural conditions.
Proteomic profiling identifies the SIM‐associated complex of KSHV‐encoded LANA

The Kaposi's sarcoma‐associated herpesvirus (KSHV) encoded latent nuclear antigen latency‐associated nuclear antigen (LANA) plays an essential role in viral episome maintenance. LANA also contributes to DNA replication and tumorigenesis during latency. Recent studies suggested that LANA was involved in regulation of SUMOylation, which results in chromatin silencing. To examine the pleiotropic effects of LANA protein on host cell gene expression, we utilized MS analysis to identify cellular proteins associated with the small ubiquitin related modifier (SUMO) interacting motif of LANA (LANASIM). In addition to the six bands identified as substantially associated with LANASIM, 151 proteins were positively identified by MS/MS analysis. Compared with previous proteomic analysis of the N‐ and C‐truncated mutants of LANA (LANANC), our results revealed that a complex of specific proteins with relatively high SUMOylation and SIM motifs is associated with LANASIM. Intriguingly, consistent with our previous report that identified KAP1 as a key component, the in vitro SUMO‐2‐modified isoform has a substantially higher affinity with LANASIM than the SUMO‐1‐modified isoform. Moreover, via cluster and pathway analysis, we proposed a hypothetical model for the LANASIM regulatory circuit involving aberrant SUMOylation of cell cycle (particular mitotic), DNA unwinding and replication, and pre‐mRNA/mRNA processing related proteins. This study provides a SUMOylated and non‐SUMOylated proteome profile of LANASIM‐associated complex and facilitates our understanding that viral‐mediated gene regulation through SUMOylation is important for Kaposi's sarcoma‐associated herpesvirus persistence and pathogenesis.