Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice.

YAP1 is a transcriptional coactivator regulated by the Hippo signaling pathway, including NF2. Meningiomas are the most common primary brain tumors; a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 copy, implicating oncogenic YAP activity in these tumors. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2 wild-type meningiomas. Here, we show that human YAP1-MAML2-positive meningiomas resemble NF2 mutant meningiomas by global and YAP-related gene expression signatures. We then show that expression of YAP1-MAML2 in mice induces tumors that resemble human YAP1 fusion-positive and NF2 mutant meningiomas by gene expression. We demonstrate that YAP1-MAML2 primarily functions by exerting TEAD-dependent YAP activity that is resistant to Hippo signaling. Treatment with YAP-TEAD inhibitors is sufficient to inhibit the viability of YAP1-MAML2-driven mouse tumors ex vivo. Finally, we show that expression of constitutively active YAP1 (S127/397A-YAP1) is sufficient to induce similar tumors, suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a causal oncogenic driver and highlight TEAD-dependent YAP activity as an oncogenic driver in YAP1-MAML2 fusion meningioma as well as NF2 mutant meningioma in general.

Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge.

Understanding immune mechanisms that mediate malaria protection is critical for improving vaccine development. Vaccination with radiation-attenuated Plasmodium falciparum sporozoites (PfRAS) induces high level of sterilizing immunity against malaria and serves as a valuable tool for the study of protective mechanisms. To identify vaccine-induced and protection-associated responses during malarial infection, we performed transcriptome profiling of whole blood and in-depth cellular profiling of PBMCs from volunteers who received either PfRAS or noninfectious mosquito bites, followed by controlled human malaria infection (CHMI) challenge. In-depth single-cell profiling of cell subsets that respond to CHMI in mock-vaccinated individuals showed a predominantly inflammatory transcriptome response. Whole blood transcriptome analysis revealed that gene sets associated with type I and II interferon and NK cell responses were increased in prior to CHMI while T and B cell signatures were decreased as early as one day following CHMI in protected vaccinees. In contrast, non-protected vaccinees and mock-vaccinated individuals exhibited shared transcriptome changes after CHMI characterized by decreased innate cell signatures and inflammatory responses. Additionally, immunophenotyping data showed different induction profiles of vδ2+ γδ T cells, CD56+ CD8+ T effector memory (Tem) cells, and non-classical monocytes between protected vaccinees and individuals developing blood-stage parasitemia, following treatment and resolution of infection. Our data provide key insights in understanding immune mechanistic pathways of PfRAS-induced protection and infective CHMI. We demonstrate that vaccine-induced immune response is heterogenous between protected and non-protected vaccinees and that inducted-malaria protection by PfRAS is associated with early and rapid changes in interferon, NK cell and adaptive immune responses. Trial Registration: ClinicalTrials.gov NCT01994525.

Barriers to Community-Based Eradication of Helicobacter pylori Infection.

Helicobacter pylori (HP) is a causative agent in gastric cancer (GC).1 In the United States, HP is more prevalent in racial and ethnic minorities, including African Americans, Asian Americans, Latinos, and immigrants, the same groups that are more likely to develop and die from GC.2 Although screening for HP is not presently performed in the United States, there are plausible benefits to doing so, because HP is considered a group 1 carcinogen by the World Health Organization, and its link to GC parallels that of human papilloma virus and cervical cancer.1 HP eradication as a means of preventing GC also fulfils the Wilson and Jungner criteria for a successful screening program, and literature has consistently demonstrated that HP eradication reduces GC risk and death from GC.3 In fact, in countries with a high burden of GC, HP eradication is considered primary prevention for GC. As such, targeted HP testing in the United States may reduce GC burden in high-risk groups.4 We evaluate the results of community-based HP testing in an at-risk, underserved population.

Complement-mediated thrombotic microangiopathy treated with anticomplement protein 5 therapy, a retrospective study.

BACKGROUND: Complement-mediated thrombotic microangiopathy (CM-TMA), also called atypical hemolytic uremic syndrome (aHUS), is a difficult-to-diagnose rare disease that carries severe morbidity and mortality. Anti-C5 monoclonal antibodies (aC5-mab) are standard treatments, but large studies and long-term data are scarce. Here, we report our single institution experience to augment the knowledge of CM-TMA treated with aC5-mab therapy. METHODS: We aimed to assess the short and long-term effects of aC5-mab in patients diagnosed with CM-TMA treated outside of a clinical trial. This was a retrospective study. We included all patients diagnosed with CM-TMA and treated with aC5-mab at our institution. There were no exclusion criteria. Endpoints included complete TMA response (CR) defined as normalization of hematological parameters and ≥25% improvement in serum creatinine (Cr) from baseline in patients with renal disease, relapse defined as losing the previously achieved CR, morbidity, adverse events, and survival. RESULTS: We found 28 patients with CM-TMA treated with aC5-mab. The median age was 50 years. Baseline laboratories: platelet counts 93 × 109 /L, hemoglobin 8.6 g/dL, lactate dehydrogenase 1326 U/L, serum Cr 4.7 mg/dL, and estimated glomerular filtration rate 19 mL/min. One individual was on renal replacement therapy (RRT) and 10 initiated RRT within 5 days of the first dose of aC5-mab. Genetic variants associated with CM-TMA included mutations in C3, CFB, CFH, CFHR1/3, CFI, and MCP. The mean duration of hospitalization was 24 days. The median time to initiation of aC5-mab was 10 days. Sixteen subjects received RRT. At the time of hospital discharge, 27 were alive, 14 remained on RRT, and 4 had a CR. At 6 months, 23 patients were alive, 18 continued aC5-mab, 8 remained on RRT, and 9 had a CR. At the last follow-up visit past 6 months, 20 were alive, 14 continued aC5-mab, 5 remained on RRT, 12 had a CR, and 1 was lost to follow-up. CONCLUSIONS: Our study provides real-world experience and insight into the long-term outcomes of CM-TMA treated with aC5-mab. Our findings validate that CM-TMA is an aggressive disease with significant morbidity and mortality, and confirm that aC5-mab is a relatively effective therapy for CM-TMA. Our study adds practical, real-world experience to the literature, but future research remains imperative.

Modeling the electroluminescence of atomic wires from quantum dynamics simulations.

Static and time-dependent quantum-mechanical approaches have been employed in the literature to characterize the physics of light-emitting molecules and nanostructures. However, the electromagnetic emission induced by an input current has remained beyond the realm of molecular simulations. This is the challenge addressed here with the help of an equation of motion for the density matrix coupled to a photon bath based on a Redfield formulation. This equation is evolved within the framework of the driven-Liouville von Neumann approach, which incorporates open boundaries by introducing an applied bias and a circulating current. The dissipated electromagnetic power can be computed in this context from the time derivative of the energy. This scheme is applied in combination with a self-consistent tight-binding Hamiltonian to investigate the effects of bias and molecular size on the electroluminescence of metallic and semiconducting chains. For the latter, a complex interplay between bias and molecular length is observed: there is an optimal number of atoms that maximizes the emitted power at high voltages but not at low ones. This unanticipated behavior can be understood in terms of the band bending produced along the semiconducting chain, a phenomenon that is captured by the self-consistency of the method. A simple analytical model is proposed that explains the main features revealed by the simulations. The methodology, applied here at a self-consistent tight-binding level but extendable to more sophisticated Hamiltonians such as density functional tight binding and time dependent density functional theory, promises to be helpful for quantifying the power and quantum efficiency of nanoscale electroluminescent devices.

Robust and prototypical immune responses toward influenza vaccines in the high-risk group of Indigenous Australians.

Morbidity and mortality rates from seasonal and pandemic influenza occur disproportionately in high-risk groups, including Indigenous people globally. Although vaccination against influenza is recommended for those most at risk, studies on immune responses elicited by seasonal vaccines in Indigenous populations are largely missing, with no data available for Indigenous Australians and only one report published on antibody responses in Indigenous Canadians. We recruited 78 Indigenous and 84 non-Indigenous Australians vaccinated with the quadrivalent influenza vaccine into the Looking into InFluenza T cell immunity - Vaccination cohort study and collected blood to define baseline, early (day 7), and memory (day 28) immune responses. We performed in-depth analyses of T and B cell activation, formation of memory B cells, and antibody profiles and investigated host factors that could contribute to vaccine responses. We found activation profiles of circulating T follicular helper type-1 cells at the early stage correlated strongly with the total change in antibody titers induced by vaccination. Formation of influenza-specific hemagglutinin-binding memory B cells was significantly higher in seroconverters compared with nonseroconverters. In-depth antibody characterization revealed a reduction in immunoglobulin G3 before and after vaccination in the Indigenous Australian population, potentially linked to the increased frequency of the G3m21* allotype. Overall, our data provide evidence that Indigenous populations elicit robust, broad, and prototypical immune responses following immunization with seasonal inactivated influenza vaccines. Our work strongly supports the recommendation of influenza vaccination to protect Indigenous populations from severe seasonal influenza virus infections and their subsequent complications.

Nanobubble Stability and Formation on Solid-Liquid Interfaces in Open Environments.

Are surface nanobubbles transient or thermodynamically stable structures? This question remained controversial until recently, when the stability of gas nanobubbles at solid-liquid interfaces was demonstrated from thermodynamic arguments in closed systems, establishing that bubbles with radii of hundreds of nanometers can be stable at modest supersaturations if the gas amount is finite. Here we develop a grand-canonical description of bubble formation that predicts that nanobubbles can nucleate and remain thermodynamically stable in open boundaries at high supersaturations when pinned to hydrophobic supports as small as a few nanometers. While larger bubbles can also be stable at lower supersaturations, the corresponding barriers are orders of magnitude above kT, meaning that their formation cannot proceed via heterogeneous nucleation on a uniform solid interface but must follow some alternative path. Moreover, we conclude that a source of growth-limiting mechanism, such as pinning or gas availability, is necessary for the thermodynamic stabilization of surface bubbles.

Fluorescence in quantum dynamics: Accurate spectra require post-mean-field approaches.

Real time modeling of fluorescence with vibronic resolution entails the representation of the light-matter interaction coupled to a quantum-mechanical description of the phonons and is therefore a challenging problem. In this work, taking advantage of the difference in timescales characterizing internal conversion and radiative relaxation-which allows us to decouple these two phenomena by sequentially modeling one after the other-we simulate the electron dynamics of fluorescence through a master equation derived from the Redfield formalism. Moreover, we explore the use of a recent semiclassical dissipative equation of motion [C. M. Bustamante et al., Phys. Rev. Lett. 126, 087401 (2021)], termed coherent electron electric-field dynamics (CEED), to describe the radiative stage. By comparing the results with those from the full quantum-electrodynamics treatment, we find that the semiclassical model does not reproduce the right amplitudes in the emission spectra when the radiative process involves the de-excitation to a manifold of closely lying states. We argue that this flaw is inherent to any mean-field approach and is the case with CEED. This effect is critical for the study of light-matter interaction, and this work is, to our knowledge, the first one to report this problem. We note that CEED reproduces the correct frequencies in agreement with quantum electrodynamics. This is a major asset of the semiclassical model, since the emission peak positions will be predicted correctly without any prior assumption about the nature of the molecular Hamiltonian. This is not so for the quantum electrodynamics approach, where access to the spectral information relies on knowledge of the Hamiltonian eigenvalues.

Molecular dynamics study of the mechanical properties of drug loaded model systems: A comparison of a polymersome with a bilayer.

In this work we implement a new methodology to study structural and mechanical properties of systems having spherical and planar symmetries throughout Molecular Dynamics simulations. This methodology is applied here to a drug delivery system based in polymersomes, as an example. The chosen model drug was the local anesthetic prilocaine due to previous parameterization within the used coarse grain scheme. In our approach, mass density profiles (MDPs) are used to obtain key structural parameters of the systems, and pressure profiles are used to estimate the curvature elastic parameters. The calculation of pressure profiles and radial MPDs required the development of specific methods, which were implemented in an in-house built version of the GROMACS 2018 code. The methodology presented in this work is applied to characterize poly(ethylene oxide)-poly(butadiene) polymersomes and bilayers loaded with the model drug prilocaine. Our results show that structural properties of the polymersome membrane could be obtained from bilayer simulations, with significantly lower computational cost compared to whole polymersome simulations, but the bilayer simulations are insufficient to get insights on their mechanical aspects, since the elastic parameters are canceled out for the complete bilayer (as consequence of the symmetry). The simulations of entire polymersomes, although more complex, offer a complementary approach to get insights on the mechanical behavior of the systems.

Impact of Normal and Overweight Pregnancy in GLUT4 and Glucose-Dependent Vascular Contractility.

INTRODUCTION: Obesity during pregnancy can contribute to hypertensive complications through changes in glucose utilization. We investigated the impact of vascular glucose uptake, GLUT4 density, and endothelium on agonist-induced vasoconstriction in the aortas of overweight pregnant rats. METHODS: Isolated aortic rings with or without endothelium from pregnant or nonpregnant rats fed a standard (SD) or hypercaloric diet (HD) were contracted with phenylephrine or serotonin (10-9 to 10-4M) using standard (11 mm) or without (0 mm) glucose Krebs solution. GLUT4 density in the aortas was measured using the en face method. RESULTS: Aortas from overweight pregnant animals (PHD) showed increased Phe-induced vasoconstriction (p < 0.05 vs. pregnant standard diet [PSD]), which was endothelium-independent. The contraction decreased significantly in the absence of glucose. In contrast, vessels from pregnant SD rats maintained their contraction in glucose-free Krebs solution. 5-HT increases PHD aortic contraction only in the absence of glucose. The fetal aortas from PHD mothers showed blunted vasoconstriction. Overweight significantly reduced GLUT4 expression in maternal and fetal aortas (p < 0.05 vs. PSD). CONCLUSIONS: Aortic contractility is independent of glucose uptake during healthy pregnancy. In contrast, overweight pregnancy increases contractility. This increase depends directly on smooth muscle glucose uptake and inversely on GLUT-4 density. The increased contraction observed in the vasculature of overweight mothers was inverted in the fetal aortas.

Color and translucency of enamel in vital maxillary central incisors.

STATEMENT OF PROBLEM: Limited data, especially in vivo data, exist regarding translucency parameter (TP) values for vital anterior nonrestored dentition. Additionally, published information on the CIELab values of vital enamel at a theoretical infinite thickness is lacking. Obtaining TP and CIELab values in a population that varies in terms of ethnicity, age, and sex would be useful to inform the development and placement of esthetic dental restorations that more accurately capture the complex optical qualities of enamel. PURPOSE: The purpose of this clinical study was to investigate in vivo the TP and CIELab values of vital anterior incisor enamel at a theoretical infinite thickness in a diverse pool of participants who varied in age, ethnicity, and sex. MATERIAL AND METHODS: Spectral reflectance measurements (380 to 780 nm at 2-nm intervals) of the mid-incisal region of vital, unrestored maxillary anterior teeth were made in 120 participants, equally divided into 2 sexes, 4 racial or ethnic groups, and 5 age ranges. Instruments were oriented to achieve 0-degree observation and 45-degree illumination, and spectral measurements were made with white and black silicone backgrounds. Reflectance spectra of the incisal enamel from both the black and white silicone backing were used to fit to the Kubelka-Munk (K-M) reflectance theory. The CIEDE2000 color difference formula was used to determine TP, and data were compared among participant demographics. CIELab color coordinate values for enamel at an infinite thickness were calculated by using a D65 illumination and CIE standard human (2-degree) observer. To determine value ranges and significant differences among participant groups, CIELab values were analyzed with a 4-way ANOVA, and TP values were analyzed with a generalized linear mixed model. Pairwise comparisons of interest were evaluated with Bonferroni-corrected Student t tests. RESULTS: For maxillary central incisor enamel, the average TP was 10.1 ±3.6, and the average CIELab color coordinates were L∗=73.5 ±7.6, a∗=2.2 ±1.8, b∗=11.9 ±8.4. TP values of incisal enamel significantly differed among specific age and ethnic groups, with general significant interactions of age and sex (P=.009), as well as ethnicity and age (P=.042). CIE color coordinates of enamel at an infinite thickness were found in the L∗ coordinate among different age groups with the same sex and ethnicity, specifically when comparing CIELab direction with the population characteristics of age (P=.011) and the interaction between age, sex, and ethnicity (P=.035). CONCLUSIONS: In vivo L∗ values and TP values of incisal enamel differed significantly among groups determined by ethnicity, age, and sex.

Water Self-Dissociation is Insensitive to Nanoscale Environments.

Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from experiments and simulations in a few specific cases, leading to dissimilar conclusions. Here, with the use of carefully designed ab initio simulations, we demonstrate that the energetics of bulk water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. The reason is that most of the free-energy involved in water autoionization comes from breaking the O-H covalent bond, which has a comparable barrier in the bulk liquid, in a small droplet of nanometer size, or in a nanopore in the absence of strong interfacial interactions. Thus, dissociation free-energy profiles in nanoscopic aggregates or in 2D slabs of 1 nm width reproduce the behavior corresponding to the bulk liquid, regardless of whether the corresponding nanophase is delimited by a solid or a gas interface. The present work provides a definite and fundamental description of the mechanism and thermodynamics of water dissociation at different scales with broader implications on reactivity and self-ionization at the air-liquid interface.

Posterior Leg Pain: Understanding Soleus Muscle Injuries.

Soleus muscle injuries are frequently unrecognized, representing a common cause of sports inactivity. This is mainly because little is known about the anatomy of the soleus muscle and the clinical manifestations of injury. Unlike other muscles, the soleus muscle has a complex myoconnective structure with three intramuscular tendons, which makes the interpretation of muscle pathologic conditions challenging. Soleus muscle injuries can be acute or chronic and are usually considered to be a minor discomfort by both the patient and the sports medicine physician, leading to a relatively quick return to sporting activity with a high risk for reinjury. The authors review the soleus muscle anatomy and the importance of being familiar with the most frequent locations of injuries, which are fundamental aspects that every radiologist should understand to avoid underdiagnosis. The role of imaging, the clinical manifestations of injuries, and the differential diagnoses are key aspects to know when evaluating posterior leg pain. The online slide presentation from the RSNA Annual Meeting is available for this article. ©RSNA, 2022.

Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower.

Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin. In leaves, an intragenic loop is formed, blocking HaWRKY6 transcription. While in cotyledons (Cots), formation of an alternative loop, encompassing the whole HaWRKY6 gene, enhances transcription of the gene. The formation of this loop changes the promoter directionality, reducing IR transcription, and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machineries.

Laparoscopic Single-Port versus Mini-Laparoscopic Hysterectomy: An International Study.

OBJECTIVES: Laparoendoscopic single-site surgery (LESS) and mini-laparoscopic surgery (Mini-LPS) have been performed with comparable results to conventional laparoscopy. However, there are few data on the comparison between them. Our main objective was to compare LESS and Mini-LPS in terms of surgical time, postoperative pain, and hospital stay in patients who underwent hysterectomy for benign pathology. DESIGN: It is a retrospective international multicentric study carried out in 5 centers including 2 Spanish and 3 Italian. METHODS: Data from patients who underwent hysterectomy for benign pathology between January 1, 2010, and December 31, 2015, were reviewed. We collected the clinical-pathological characteristics of the patients and the perioperative results. The main variables of the study were surgical time, the switch to oral analgesia, and the hospital stay. The two comparison groups in the study included patients undergoing hysterectomy for benign pathology by LESS or by Mini-LPS. The decision to perform the type of procedure was left to the discretion of the surgeon, based primarily on the surgical skills and experience of the center. All data were collected retrospectively by an online encrypted platform. RESULTS: 161 patients were included in the study. 104 (64.6%) patients underwent LESS hysterectomy and 57 (35.4%) Mini-LPS. Median surgical time was significantly longer in the LESS group when compared to the Mini-LPS group (120 vs. 75 min, respectively; p < 0.001). Moreover, longer median hospital stay was observed in the LESS group compared to Mini-LPS (48 vs. 36 h, respectively; p < 0.001). Conversion of the technique to conventional LPS was performed in 4 (2.5%) patients, all of them in the Mini-LPS group (p = 0.015). LIMITATIONS: It is a retrospective study with the biases that this implies. Furthermore, some variables have been incompletely registered in the database, which implies loss of information. This is a nonrandomized study since the decision to intervene with one or another technique was made by the surgeon, which generated 2 nonhomogeneous groups in terms of the number of patients. On the other hand, all the patients who underwent Mini-LPS hysterectomy belonged to the same center, which may have made these results center dependent. CONCLUSIONS: Significant shorter surgical time and shorter hospital stay were observed in patients undergoing Mini-LPS hysterectomy compared to LESS technique; however, intraoperative complications related to instrumentation flaws were higher in the mini-LPS group that required conversion to standard laparoscopy in all cases. Both ultra-minimally invasive techniques seem safe to perform hysterectomies for benign pathology and emphasize the importance in surgical training to adapt them to our current practice.

Implementation of QbD Approach to the Development of Chromatographic Methods for the Determination of Complete Impurity Profile of Substance on the Preclinical and Clinical Step of Drug Discovery Studies.

The purpose of this work was to demonstrate the use of the AQbD with the DOE approach to the methodical step-by-step development of a UHPLC method for the quantitative determination of the impurity profile of new CPL409116 substance (JAK/ROCK inhibitor) on the preclinical and clinical step of drug discovery studies. The critical method parameters (CMPs) have been tested extensively: the kind of stationary phase (8 different columns), pH of the aqueous mobile phase (2.6, 3.2, 4.0, 6.8), and start (20-25%) and stop (85-90%) percentage of organic mobile phase (ACN). The critical method attributes (CMAs) are the resolution between the peaks (≥2.0) and peak symmetry of analytes (≥0.8 and ≤1.8). In the screening step, the effects of different levels of CMPs on the CMAs were evaluated based on a full fractional design 22. The robustness tests were established from the knowledge space of the screening step and performed by application fractional factorial design 2(4-1). Method operable design region (MODR) was generated. The probability of meeting the specifications for the CMAs was calculated by Monte-Carlo simulations. In relation to literature such a complete AQbD approach including screening, optimization, and validation steps for the development of a new method for the quantitative determination of the full profile of nine impurities of an innovative pharmaceutical substance with the structure-based pre-development pointed out the novelty of our work. The final working conditions were as follows: column Zorbax Eclipse Plus C18, aqueous mobile phase 10 mM ± 1 mM aqueous solution of HCOOH, pH 2.6, 20% ± 1% of ACN at the start and 85% ± 1% of ACN at the end of the gradient, and column temperature 30 °C ± 2 °C. The method was validated in compliance with ICH guideline Q2(R1). The optimized method is specified, linear, precise, and robust. LOQ is on the reporting threshold level of 0.05% and LOD at 0.02% for all impurities.

FindICI: Using machine learning to detect linguistic inconsistencies between code and natural language descriptions in infrastructure-as-code.

Linguistic anti-patterns are recurring poor practices concerning inconsistencies in the naming, documentation, and implementation of an entity. They impede the readability, understandability, and maintainability of source code. This paper attempts to detect linguistic anti-patterns in Infrastructure-as-Code (IaC) scripts used to provision and manage computing environments. In particular, we consider inconsistencies between the logic/body of IaC code units and their short text names. To this end, we propose FindICI a novel automated approach that employs word embedding and classification algorithms. We build and use the abstract syntax tree of IaC code units to create code embeddings used by machine learning techniques to detect inconsistent IaC code units. We evaluated our approach with two experiments on Ansible tasks systematically extracted from open source repositories for various word embedding models and classification algorithms. Classical machine learning models and novel deep learning models with different word embedding methods showed comparable and satisfactory results in detecting inconsistent Ansible tasks related to the top-10 used Ansible modules.

The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity.

In plants, small RNAs are loaded into ARGONAUTE (AGO) proteins to fulfill their regulatory functions. MicroRNAs (miRNAs), one of the most abundant classes of endogenous small RNAs, are preferentially loaded into AGO1. Such loading, long believed to happen exclusively in the cytoplasm, was recently proposed to also occur in the nucleus. Here, we identified CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9), a nuclear-localized, intrinsically disordered protein, as a factor promoting miRNA activity in Arabidopsis (Arabidopsis thaliana). Mutations in the CARP9-encoding gene led to a mild reduction of miRNAs levels, impaired gene silencing, and characteristic morphological defects, including young leaf serration and altered flowering time. Intriguingly, we found that CARP9 was able to interact with HYPONASTIC LEAVES1 (HYL1), but not with other proteins of the miRNA biogenesis machinery. In the same way, CARP9 appeared to interact with mature miRNA, but not with primary miRNA, positioning it after miRNA processing in the miRNA pathway. CARP9 was also able to interact with AGO1, promoting its interaction with HYL1 to facilitate miRNA loading in AGO1. Plants deficient in CARP9 displayed reduced levels of AGO1-loaded miRNAs, partial retention of miRNA in the nucleus, and reduced levels of AGO1. Collectively, our data suggest that CARP9 might modulate HYL1-AGO1 cross talk, acting as a scaffold for the formation of a nuclear post-primary miRNA-processing complex that includes at least HYL1, AGO1, and HEAT SHOCK PROTEIN 90. In such a complex, CARP9 stabilizes AGO1 and mature miRNAs, allowing the proper loading of miRNAs in the effector complex.

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics.

The dynamical description of the radiative decay of an electronically excited state in realistic many-particle systems is an unresolved challenge. In the present investigation electromagnetic radiation of the charge density is approximated as the power dissipated by a classical dipole, to cast the emission in closed form as a unitary single-electron theory. This results in a formalism of unprecedented efficiency, critical for ab initio modeling, which exhibits at the same time remarkable properties: it quantitatively predicts decay rates, natural broadening, and absorption intensities. Exquisitely accurate excitation lifetimes are obtained from time-dependent DFT simulations for C^{2+}, B^{+}, and Be, of 0.565, 0.831, and 1.97 ns, respectively, in accord with experimental values of 0.57±0.02, 0.86±0.07, and 1.77-2.5 ns. Hence, the present development expands the frontiers of quantum dynamics, bringing within reach first-principles simulations of a wealth of photophysical phenomena, from fluorescence to time-resolved spectroscopies.

Doping and coupling strength in molecular conductors: polyacetylene as a case study.

The doping mechanisms responsible for elevating the currents up to eleven orders of magnitude in semiconducting polymer films are today well characterized. Doping can also improve the performance of nanoscale devices or single molecule conductors, but the mechanism in this case appears to be different, with theoretical studies suggesting that the dopant affects the electronic properties of the junctions. In the present report, multiscale time-dependent DFT transport simulations help clarify the way in which n-type doping can raise the current flowing through a polymer chain connected to a pair of electrodes, with the focus on polyacetylene. In particular, our multiscale methodology offers control over the magnitude of the chemical coupling between the molecule and the electrodes, which allows us to analyze the effect of doping in low and strong coupling regimes. Interestingly, our results establish that the impact of dopants is the highest in weakly coupled devices, while their presence tends to be irrelevant in low-resistance junctions. Our calculations point out that both the equalization of the frontier orbitals with the Fermi level and a small gap between the HOMO and the LUMO must result from doping in order to observe any significant increase of the currents.