Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual stator dynamics in the Shewanella oneidensis MR‐1 flagellar motor

The bacterial flagellar motor is an intricate nanomachine which converts ion gradients into rotational movement. Torque is created by ion‐dependent stator complexes which surround the rotor in a ring. Shewanella oneidensis MR‐1 expresses two distinct types of stator units: the Na+‐dependent PomA4B2 and the H+‐dependent MotA4B2. Here, we have explored the stator unit dynamics in the MR‐1 flagellar system by using mCherry‐labeled PomAB and MotAB units. We observed a total of between 7 and 11 stator units in each flagellar motor. Both types of stator units exchanged between motors and a pool of stator complexes in the membrane, and the exchange rate of MotAB, but not of PomAB, units was dependent on the environmental Na+‐levels. In 200 mM Na+, the numbers of PomAB and MotAB units in wild‐type motors was determined to be about 7:2 (PomAB:MotAB), shifting to about 6:5 without Na+. Significantly, the average swimming speed of MR‐1 cells at low Na+ conditions was increased in the presence of MotAB. These data strongly indicate that the S. oneidensis flagellar motors simultaneously use H+ and Na+ driven stators in a configuration governed by MotAB incorporation efficiency in response to environmental Na+ levels.
Trigger Analysis - understanding broken tasks

Why do things happen when they happen? Trigger analysis exposes the triggers that prompt subtasks to occur in the right order at the right time, and assess whether tasks are robust to interruptions, delays, and shared responsibility. Trigger analysis starts with task decomposition via any suitable method, proceeding to uncover what trigger prompts each subtask. The obvious answer: “because the previous subtask is complete” is often the precondition, not the actual trigger. Previous analysis has uncovered certain primary triggers and potential failure points. The complete analysis produces an ecologically richer picture, with tasks interacting with and prompted by their environment.
ACCURATE RITZ WAVELENGTHS OF PARITY-FORBIDDEN [Co ii] AND [V ii] LINES OF ASTROPHYSICAL INTEREST

We report a comprehensive list of accurate Ritz wavelengths for parity-forbidden [Co ii] and [V ii] lines obtained from the analysis of energy levels measured in the laboratory with Fourier transform emission spectroscopy. Such lines, particularly those in the infrared, are in demand for the analysis of low-density astrophysical plasmas in and around objects such as planetary nebulae, star-forming regions, and active galactic nuclei. Transitions between all known metastable levels of Co ii and V ii are included in our analysis, producing wavelengths for 1477 [V ii] lines and 782 [Co ii] lines. Of these, 170 [V ii] lines and 171 [Co ii] lines arise from transitions with calculated transition probabilities greater than 1 × 10−2 s−1 and upper level excitations of less than 5 eV, and thus are likely to be observed in astrophysical spectra.
Phenotypic switching in gene regulatory networks

Significance Phenotypes of an isogenic cell population are determined by states of low and high gene expression. These are often associated with multiple steady states predicted by deterministic models of gene regulatory networks. Gene expression is, however, regulated via stochastic molecular interactions at transcriptional and translational levels. Here, we show that intrinsic noise can induce multimodality in a wide class of regulatory networks whose corresponding deterministic description lacks multistability, thus offering a plausible alternative mechanism for phenotypic switching without the need for ultrasensitivity or highly cooperative interactions. We derive a general analytical framework for quantifying this phenomenon, thereby elucidating how cells encode decisions, and how they retain memory of transient environmental signals, using common gene regulatory motifs. Noise in gene expression can lead to reversible phenotypic switching. Several experimental studies have shown that the abundance distributions of proteins in a population of isogenic cells may display multiple distinct maxima. Each of these maxima may be associated with a subpopulation of a particular phenotype, the quantification of which is important for understanding cellular decision-making. Here, we devise a methodology which allows us to quantify multimodal gene expression distributions and single-cell power spectra in gene regulatory networks. Extending the commonly used linear noise approximation, we rigorously show that, in the limit of slow promoter dynamics, these distributions can be systematically approximated as a mixture of Gaussian components in a wide class of networks. The resulting closed-form approximation provides a practical tool for studying complex nonlinear gene regulatory networks that have thus far been amenable only to stochastic simulation. We demonstrate the applicability of our approach in a number of genetic networks, uncovering previously unidentified dynamical characteristics associated with phenotypic switching. Specifically, we elucidate how the interplay of transcriptional and translational regulation can be exploited to control the multimodality of gene expression distributions in two-promoter networks. We demonstrate how phenotypic switching leads to birhythmical expression in a genetic oscillator, and to hysteresis in phenotypic induction, thus highlighting the ability of regulatory networks to retain memory.
Physical health-related quality of life among older adults with personality disorders

ABSTRACT Objectives: Personality Disorders (PDs) are associated with a multitude of negative consequences. The negative PD effects on health can be even more burdensome for older adults given the physical and social functioning changes that occur with age; however, the majority of research examining the influence of PDs focuses on younger adults. The present study seeks to investigate the relationship between PDs and physical health-related quality of life (PHRQoL) in adults over the age of 50. Methods: Data for 16,884 adults ages 50 and older from the 2001–2002 National Epidemiological Survey on Alcohol and Related Conditions (NESARC) were analyzed. Multiple linear regression models were analyzed to investigate the relationships of seven PDs and participants’ PHRQoL. Results: All PDs except histrionic and avoidant PD had statistically significant negative associations with PHRQoL scores, indicating that respondents diagnosed with PDs were expected to have lower PHRQoL than those without PDs, after controlling for sociodemographic characteristics. When psychosocial covariates were added to the model, only dependent, obsessive-compulsive and paranoid PDs were significantly related to PHRQoL score. Conclusions: For adults ages 50 and older, a diagnosis of PD was weakly associated with lower PHRQoL scores for three PDs, however this is unlikely to be a causal association. The strength of the relationship between PDs and PHRQoL varies by type of PD. Given the higher rates of functional and social changes that occur with age, future research should focus on potential causes of worse physical health among older adults with PDs.
Overcoming The Limitations of Phase Transition by Higher Order Analysis of Regularization Techniques

We study the problem of estimating $\beta \in \mathbb{R}^p$ from its noisy linear observations $y= X\beta+ w$, where $w \sim N(0, \sigma_w^2 I_{n\times n})$, under the following high-dimensional asymptotic regime: given a fixed number $\delta$, $p \rightarrow \infty$, while $n/p \rightarrow \delta$. We consider the popular class of $\ell_q$-regularized least squares (LQLS) estimators, a.k. a. bridge, given by the optimization problem: \begin{equation*} \hat{\beta} (\lambda, q ) \in \arg\min_\beta \frac{1}{2} \|y-X\beta\|_2^2+ \lambda \|\beta\|_q^q, \end{equation*} and characterize the almost sure limit of $\frac{1}{p} \|\hat{\beta} (\lambda, q )- \beta\|_2^2$. The expression we derive for this limit does not have explicit forms and hence are not useful in comparing different algorithms, or providing information in evaluating the effect of $\delta$ or sparsity level of $\beta$. To simplify the expressions, researchers have considered the ideal "no-noise" regime and have characterized the values of $\delta$ for which the almost sure limit is zero. This is known as the phase transition analysis. In this paper, we first perform the phase transition analysis of LQLS. Our results reveal some of the limitations and misleading features of the phase transition analysis. To overcome these limitations, we propose the study of these algorithms under the low noise regime. Our new analysis framework not only sheds light on the results of the phase transition analysis, but also makes an accurate comparison of different regularizers possible.
On Visual Hallmarks of Robustness to Adversarial Malware

A central challenge of adversarial learning is to interpret the resulting hardened model. In this contribution, we ask how robust generalization can be visually discerned and whether a concise view of the interactions between a hardened decision map and input samples is possible. We first provide a means of visually comparing a hardened model's loss behavior with respect to the adversarial variants generated during training versus loss behavior with respect to adversarial variants generated from other sources. This allows us to confirm that the association of observed flatness of a loss landscape with generalization that is seen with naturally trained models extends to adversarially hardened models and robust generalization. To complement these means of interpreting model parameter robustness we also use self-organizing maps to provide a visual means of superimposing adversarial and natural variants on a model's decision space, thus allowing the model's global robustness to be comprehensively examined.
Musical and verbal short‐term memory: insights from neurodevelopmental and neurological disorders

Auditory short‐term memory (STM) is a fundamental ability to make sense of auditory information as it unfolds over time. Whether separate STM systems exist for different types of auditory information (music and speech, in particular) is a matter of debate. The present paper reviews studies that have investigated both musical and verbal STM in healthy individuals and in participants with neurodevelopmental and neurological disorders. Overall, the results are in favor of only partly shared networks for musical and verbal STM. Evidence for a distinction in STM for the two materials stems from (1) behavioral studies in healthy participants, in particular from the comparison between nonmusicians and musicians; (2) behavioral studies in congenital amusia, where a selective pitch STM deficit is observed; and (3) studies in brain‐damaged patients with cases of double dissociation. In this review we highlight the need for future studies comparing STM for the same perceptual dimension (e.g., pitch) in different materials (e.g., music and speech), as well as for studies aiming at a more insightful characterization of shared and distinct mechanisms for speech and music in the different components of STM, namely encoding, retention, and retrieval.
GaN-HEMT-based three level T-type NPC inverter using reverse-conducting mode in rectifying

The paper presents a design method of a gallium-nitride high-electron-mobility-transistor (GaN-HEMT) based three level T-type neutral-point-clamped (NPC) inverter using a reverse-conducting mode of the GaN-HEMT. The GaN-HEMT provides high-frequency switching speed and the T-type inverter supports such switching by decreasing conduction loss and heat dissipation. The GaN-HEMT has two operation mode, an enhancement mode and the reverse-conducting mode. In the enhancement mode, resistance on the GaN-HEMT is controlled by gate-source voltage. The reverse-conducting mode appears when gate-source voltage is less than zero. This characteristic provides advantage on design of the T-type NPC inverter. Then, the paper shows that a normally-off inverter is easily attained by using the reverse-conducting mode. Verification of the designed-circuit is conducted by some validation.
Controlling epidemics with transmissible vaccines

As the density of human and domestic animal populations increases, the threat of localized epidemics and global pandemics grows. Although effective vaccines have been developed for a number of threatening pathogens, manufacturing and disseminating vaccines in the face of a rapidly spreading epidemic or pandemic remains a formidable challenge. One potentially powerful solution to this problem is the use of transmissible vaccines. Transmissible vaccines are capable of spreading from one individual to another and are currently being developed for a range of infectious diseases. Here we develop and analyze mathematical models that allow us to quantify the benefits of vaccine transmission in the face of an imminent or ongoing epidemic. Our results demonstrate that even a small amount of vaccine transmission can greatly increase the rate at which a naïve host population can be protected against an anticipated epidemic and substantially reduce the size of unanticipated epidemics if vaccination is initiated shortly after pathogen detection. In addition, our results identify key biological properties and implementation practices that maximize the impact of vaccine transmission on infectious disease.
Short-Term Effect of Reduction in Forced Vital Capacity After Diving Exposure

To discuss whether there is relationship between short-term and long-time attenuation effects of ventilation caused by diving activity. The ventilation observed before and after hyperbaric exposure for 20min by case-control experiments. Participants of the experimental group (EG) stayed for 20min under 12-m underwater and the control group (CG) stayed in hyperbaric chamber under pressure of 2.2ATA. Immediate effects of pulmonary ventilation detected by the Spirometer and compared by paired T test to reveal the different caused by environmental pressure. The Vital Capacity (VC) rises while the Minute Ventilation (MV), Maximal Voluntary Ventilation (MVV) decreases after the exposure for 20min in both groups. The Forced Vital Capacity (FVC) is detected decreased significantly in EG (t=1.21, P =0.25) while it slightly increased in CG (t=-0.42, P =0.68). The ratio of Forced Expiratory Volume in one second to VC (FEV1.0/VC %) increase in EG (t=-0.73, P=0.48) while decrease in CG (t=0.42, P=0.17). The Ratio of FEV1.0 to FVC (FEV1.0 %) values increase obviously in EG (t=-1.48, P =0.16) and a bit in CG (t=-0.23, P =0.82). High pressure is the common factor in both groups that leads the changes in the same trend in VC, MV and MVV. Extra factors as immersion effect, loading of diving equipment and low temperature underwater, would encounter EG participants. Instant reduced effects of FVC under diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which illustrated even small depth of short-range diving exercise have definite influences on ventilation.
Metabolic responses of meniscal explants to injury and inflammation ex vivo

This study was designed to characterize metabolic responses of meniscal tissue explants to injury and inflammation. We hypothesized that impact injury and interleukin (IL‐1β) stimulation of meniscal explants would result in significant increases in matrix metalloproteinase (MMP) activity and relevant cytokine production compared to controls. Mature canine meniscal explants (n = 9/group) were randomly assigned to: (i) IL‐1β (0.1 ng/ml) treated (IL); (ii) 25% strain (25); (iii) 75% strain (75); (iv) 25% + IL‐1β (25IL); (v) 75% + IL‐1β (75IL); or (vi) 0% + no IL‐1β control (NC). Explants were impacted at 100 mm/s to 0%, 25%, or 75% strain and then cultured for 12 days with or without 0.1 ng/ml rcIL‐1β. Media were refreshed every 3 days and analyzed for MMP activity, ADAMTS‐4 activity, MMP‐1, MMP‐2, MMP‐3, GAG, NO, PGE2, IL‐6, IL‐8, MCP‐1, and KC concentrations. Treatment with IL‐1β alone significantly increased NO, PGE2, general MMP activity, IL‐6, IL‐8, KC, and MCP‐1 media concentrations compared to negative controls. Impact at 75% significantly increased PGE2, IL‐6, IL‐8, and KC media concentrations compared to negative controls. The combination of IL‐1β and 75% strain significantly increased production of PGE2 compared to IL‐1β or 75% strain alone. Impact injury to meniscal explants ex vivo is associated with increased production of pro‐inflammatory mediators and degradative enzyme activity, which are exacerbated by stimulation with IL‐1β. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2657–2663, 2018.
DECISION-MAKING IN A COACHING ENVIRONMENT: HOW A COACH MAKES DECISIONS WHEN COACHING A MATHEMATICS TEACHER ON STUDENT/TEACHER DISCOURSE

The purpose of this study was to determine how a mathematics coach made decisions when coaching a middle school mathematics teacher on using classroom discourse in a reform mathematics classroom. This was a researcher participant qualitative study using design experiment methodology in which the coaching process was studied in an environment that is typical of an educational coaching setting. The teacher and coach/researcher made conjectures on what was happening in the classroom based on observations; the conjectures provided the basis for the development of the interventions. The teacher modified her pedagogy using the interventions; the results of the pedagogical changes were discussed as the teacher and coach engaged in discourse in the coaching sessions. The process was repeated four times over an eight-month period. In this study, the researcher found that the coach’s decisions were based on the teacher’s current beliefs and practice, the relationship between the coach and the teacher, and current educational research
The Fungal Gene Avr9 and the Oomycete Gene inf1 Confer Avirulence to Potato Virus X on Tobacco

The AVR9 peptide of the fungal pathogen Cladosporium fulvum and the INF1 protein of the oomycete pathogen Phytophthora infestans elicit the hypersensitive response (HR) on Cf9 tomato or Cf-9 transgenic tobacco and on all cultivars of tobacco, respectively. Expression of either the functional Avr9 or inf1 genes from engineered potato virus X (PVX) genomes resulted in localized HR lesions on tobacco plants responsive to the elicitors and inhibited spread of the recombinant virus. In contrast, PVX derivatives producing mutant forms of AVR9 and INF1 with reduced elicitor activity caused systemic necrotic and/or mosaic symptoms, and were unable to inhibit PVX spread. These results demonstrate that HR is a highly versatile defense mechanism active against unrelated pathogens irrespective of the HR-inducing agent, and that resistance to recombinant PVX in tobacco is correlated with the strength of the transgene-encoded elicitor.
Sensitizing potential of enzymatically cross-linked peanut proteins in a mouse model of peanut allergy.

SCOPE The cross-linking of proteins by enzymes to form high-molecular-weight protein, aggregates can be used to tailor the technological or physiological functionality of food products. Aggregation of dietary proteins by food processing may promote allergic sensitization, but the effects of enzymatic cross-linking of dietary proteins on the allergenic potential of food are not known. In this study, the bioavailability and the sensitizing or tolerizing potential of peanut proteins (PE) cross-linked with microbial tyrosinase from Trichoderma reesei and mushroom tyrosinase from Agaricus bisporus, were investigated. METHODS AND RESULTS The impact of cross-linking of PE on the in vitro bioavailability of fluorescein isothiocyanate-labeled peanut proteins was tested in a Caco-2 cell monolayer and by competitive ELISA. The in vivo allergenicity or capacity to induce oral tolerance in mice were measured by serum levels of PE-specific antibodies and T cell cytokine production after exposure to PE and cross-linked PE. CONCLUSION Enzymatic processing of peanut proteins by the two tyrosinases increased the bioavailability of major peanut allergen Ara h 2, but did not significantly change the allergenic or tolerizing properties of peanut. Enzymatic treatment of peanut proteins yielded cross-linked proteins with preserved molecular and immunological features of peanut allergens.
Effects of AAV2-mediated co-transfection of CTGF and TIMP1 genes on degenerative lumbar intervertebral discs in rhesus monkeys in vivo.

OBJECTIVE This study aims to investigate the effects of co-transfection of the genes for connective tissue growth factor (CTGF) and tissue inhibitor of metalloproteinase-1 (TIMP1) mediated by adeno-associated virus 2 (AAV2) on degenerative lumbar intervertebral discs in a primate model. METHODS Twelve 4-7 year-old rhesus monkeys weighing 4.5-7.0 kg were utilized. CTGF and TIMP1 genes carried by AAV2 were injected into the degenerative lumbar intervertebral discs. Cytokine expression and biological effects were determined using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and 35S-sulfate incorporation assays. A rhesus monkey model of intervertebral disc degeneration was successfully established. RESULTS At post-transfection, CTGF mRNA expression was higher in the transfection group than in the control group (P < 0.05). Furthermore, TIMP1 mRNA expression in the transfection group was several times the levels observed in the control group (P < 0.05). Moreover, type-II collagen mRNA expression was higher in the transfection group than in the control group (P < 0.05). In addition, higher aggrecan mRNA expression and synthesis were observed in the transfection group, compared to that in the control group (P < 0.05). CONCLUSION The stable expression of CTGF and TIMP1 genes in vivo promoted the synthesis of aggrecan and type II collagen in the nucleus pulposus in the rhesus monkey model of intervertebral disc degeneration, which has a potential for intervertebral disc regeneration.
Wisdom in Sum of Parts: Multi-Platform Activity Prediction in Social Collaborative Sites

In this paper, we proposed a novel framework which uses user interests inferred from activities (a.k.a., activity interests) in multiple social collaborative platforms to predict users' platform activities. Included in the framework are two prediction approaches: (i) direct platform activity prediction, which predicts a user's activities in a platform using his or her activity interests from the same platform (e.g., predict if a user answers a given Stack Overflow question using the user's interests inferred from his or her prior answer and favorite activities in Stack Overflow), and (ii) cross-platform activity prediction, which predicts a user's activities in a platform using his or her activity interests from another platform (e.g., predict if a user answers a given Stack Overflow question using the user's interests inferred from his or her fork and watch activities in GitHub). To evaluate our proposed method, we conduct prediction experiments on two widely used social collaborative platforms in the software development community: GitHub and Stack Overflow. Our experiments show that combining both direct and cross platform activity prediction approaches yield the best accuracies for predicting user activities in GitHub (AUC=0.75) and Stack Overflow (AUC=0.89).