Localization of lattice dynamics in low-angle twisted bilayer graphene.

Twisted bilayer graphene is created by slightly rotating the two crystal networks in bilayer graphene with respect to each other. For small twist angles, the material undergoes a self-organized lattice reconstruction, leading to the formation of a periodically repeated domain1-3. The resulting superlattice modulates the vibrational3,4 and electronic5,6 structures within the material, leading to changes in the behaviour of electron-phonon coupling7,8 and to the observation of strong correlations and superconductivity9. However, accessing these modulations and understanding the related effects are challenging, because the modulations are too small for experimental techniques to accurately resolve the relevant energy levels and too large for theoretical models to properly describe the localized effects. Here we report hyperspectral optical images, generated by a nano-Raman spectroscope10, of the crystal superlattice in reconstructed (low-angle) twisted bilayer graphene. Observations of the crystallographic structure with visible light are made possible by the nano-Raman technique, which reveals the localization of lattice dynamics, with the presence of strain solitons and topological points1 causing detectable spectral variations. The results are rationalized by an atomistic model that enables evaluation of the local density of the electronic and vibrational states of the superlattice. This evaluation highlights the relevance of solitons and topological points for the vibrational and electronic properties of the structures, particularly for small twist angles. Our results are an important step towards understanding phonon-related effects at atomic and nanometric scales, such as Jahn-Teller effects11 and electronic Cooper pairing12-14, and may help to improve device characterization15 in the context of the rapidly developing field of twistronics16.

Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses.

Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. In this study, we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analyses. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.

Improvements in precision and accuracy of complex- relative to real-domain linear combination model spectral fitting not necessarily recovered by zero filling.

Although the information obtained from in vivo proton magnetic resonance spectroscopy (1H MRS) presents a complex-valued spectrum, spectral quantification generally employs linear combination model (LCM) fitting using the real spectrum alone. There is currently no known investigation comparing fit results obtained from LCM fitting over the full complex data versus the real data and how these results might be affected by common spectral preprocessing procedure zero filling. Here, we employ linear combination modeling of simulated and measured spectral data to examine two major ideas: first, whether use of the full complex rather than real-only data can provide improvements in quantification by linear combination modeling and, second, to what extent zero filling might influence these improvements. We examine these questions by evaluating the errors of linear combination model fits in the complex versus real domains against three classes of synthetic data: simulated Lorentzian singlets, simulated metabolite spectra excluding the baseline, and simulated metabolite spectra including measured in vivo baselines. We observed that complex fitting provides consistent improvements in fit accuracy and precision across all three data types. While zero filling obviates the accuracy and precision benefit of complex fitting for Lorentzian singlets and metabolite spectra lacking baselines, it does not necessarily do so for complex spectra including measured in vivo baselines. Overall, performing linear combination modeling in the complex domain can improve metabolite quantification accuracy relative to real fits alone. While this benefit can be similarly achieved via zero filling for some spectra with flat baselines, this is not invariably the case for all baseline types exhibited by measured in vivo data.

Medial prefrontal cortex neurotransmitter abnormalities in posttraumatic stress disorder with and without comorbidity to major depression.

Posttraumatic stress disorder (PTSD) is a chronic psychiatric condition that follows exposure to a traumatic stressor. Though previous in vivo proton (1H) MRS) research conducted at 4 T or lower has identified alterations in glutamate metabolism associated with PTSD predisposition and/or progression, no prior investigations have been conducted at higher field strength. In addition, earlier studies have not extensively addressed the impact of psychiatric comorbidities such as major depressive disorder (MDD) on PTSD-associated 1H-MRS-visible brain metabolite abnormalities. Here we employ 7 T 1H MRS to examine concentrations of glutamate, glutamine, GABA, and glutathione in the medial prefrontal cortex (mPFC) of PTSD patients with MDD (PTSD+MDD+; N = 6) or without MDD (PTSD+MDD-; N = 5), as well as trauma-unmatched controls without PTSD but with MDD (PTSD-MDD+; N = 9) or without MDD (PTSD-MDD-; N = 18). Participants with PTSD demonstrated decreased ratios of GABA to glutamine relative to healthy PTSD-MDD- controls but no single-metabolite abnormalities. When comorbid MDD was considered, however, MDD but not PTSD diagnosis was significantly associated with increased mPFC glutamine concentration and decreased glutamate:glutamine ratio. In addition, all participants with PTSD and/or MDD collectively demonstrated decreased glutathione relative to healthy PTSD-MDD- controls. Despite limited findings in single metabolites, patterns of abnormality in prefrontal metabolite concentrations among individuals with PTSD and/or MDD enabled supervised classification to separate them from healthy controls with 80+% sensitivity and specificity, with glutathione, glutamine, and myoinositol consistently among the most informative metabolites for this classification. Our findings indicate that MDD can be an important factor in mPFC glutamate metabolism abnormalities observed using 1H MRS in cohorts with PTSD.

Spatially Coherent Tip-Enhanced Raman Spectroscopy Measurements of Electron-Phonon Interaction in a Graphene Device.

Coherence length (Lc) of the Raman scattering process in graphene as a function of Fermi energy is obtained with spatially coherent tip-enhanced Raman spectroscopy. Lc decreases when the Fermi energy is moved into the neutrality point, consistent with the concept of the Kohn anomaly within a ballistic transport regime. Since the Raman scattering involves electrons and phonons, the observed results can be rationalized either as due to unusually large variation of the longitudinal optical phonon group velocity vg, reaching twice the value for the longitudinal acoustic phonon, or due to changes in the electron energy uncertainty, both properties being important for optical and transport phenomena that might not be observable by any other technique.

Coaxial Placement of Balloon-Expandable and Self-Expanding Stents: Impact on Crush Resistance and Luminal Recovery in a Benchtop Model.

During endovascular interventions, coaxial deployment of stents may be required to preserve luminal gain. This study characterized in vitro the effect on crush resistance and postcompression recovery when 316L stainless steel balloon-expandable (BE) and laser-cut nitinol self-expanding (SE) venous stents were deployed coaxially. Various stent configurations were parallel-plate compressed from a fully expanded state to 50% diameter reduction (Criterion, Model 42; MTS, Eden Prairie, Minnesota) in a 37 °C ± 1 water bath. Coaxial deployments of SE stent inside BE stent and BE stent inside SE stent demonstrated higher crush resistances compared with each stent individually or their mathematical summation (analysis of variance P < .0001; pairwise comparison P < .01). The configuration of SE stent inside BE stent showed higher postcompression luminal recovery at 48.7% compared with that of BE stent inside SE stent at 27.5% (P = .0001). Coaxial deployment of SE stent inside BE stent may improve crush resistance and luminal recovery after compression in the appropriate clinical context.

Double-Barrel Nitinol Stent Placement for Iliocaval Reconstruction: The Effect of Deployment Sequence and Direction on Final Configuration.

Double-barrel stent placement across the iliocaval confluence is commonly used for the treatment of chronic bilateral iliocaval occlusion. The difference in the deployment outcomes of synchronous parallel stent deployment versus asynchronous or antiparallel deployment and the underlying stent interactions are poorly understood. In this study, 3 strategies of double-barrel nitinol self-expanding stent deployment across the iliocaval confluence (synchronous parallel, asynchronous parallel, and synchronous antiparallel) were contrasted in vivo in 3 swine followed by assessment of the explanted stent construct. Synchronous parallel stent deployment achieved a desired double-barrel configuration. The asynchronous parallel and antiparallel deployment strategies both resulted in a crushed stent despite subsequent simultaneous balloon angioplasty. These animal model results suggested that in patients who undergo double-barrel iliocaval reconstruction, synchronous parallel stent deployment may provide the desired stent conformation and increase the chance for clinical success.

Protein-Mediated Electroporation in a Cardiac Voltage-Sensing Domain Due to an nsPEF Stimulus.

This study takes a step in understanding the physiological implications of the nanosecond pulsed electric field (nsPEF) by integrating molecular dynamics simulations and machine learning techniques. nsPEF, a state-of-the-art technology, uses high-voltage electric field pulses with a nanosecond duration to modulate cellular activity. This investigation reveals a relatively new and underexplored phenomenon: protein-mediated electroporation. Our research focused on the voltage-sensing domain (VSD) of the NaV1.5 sodium cardiac channel in response to nsPEF stimulation. We scrutinized the VSD structures that form pores and thereby contribute to the physical chemistry that governs the defibrillation effect of nsPEF. To do so, we conducted a comprehensive analysis involving the clustering of 142 replicas simulated for 50 ns under nsPEF stimuli. We subsequently pinpointed the representative structures of each cluster and computed the free energy between them. We find that the selected VSD of NaV1.5 forms pores under nsPEF stimulation, but in a way that significant differs from the traditional VSD opening. This study not only extends our understanding of nsPEF and its interaction with protein channels but also adds a new effect to further study.

Targeted Nanoparticles with High Heating Efficiency for the Treatment of Endometriosis with Systemically Delivered Magnetic Hyperthermia.

Endometriosis is a devastating disease in which endometrial-like tissue forms lesions outside the uterus. It causes infertility and severe pelvic pain in ≈176 million women worldwide, and there is currently no cure for this disease. Magnetic hyperthermia could potentially eliminate widespread endometriotic lesions but has not previously been considered for treatment because conventional magnetic nanoparticles have relatively low heating efficiency and can only provide ablation temperatures (>46 °C) following direct intralesional injection. This study is the first to describe nanoparticles that enable systemically delivered magnetic hyperthermia for endometriosis treatment. When subjected to an alternating magnetic field (AMF), these hexagonal iron-oxide nanoparticles exhibit extraordinary heating efficiency that is 6.4× greater than their spherical counterparts. Modifying nanoparticles with a peptide targeted to vascular endothelial growth factor receptor 2 (VEGFR-2) enhances their endometriosis specificity. Studies in mice bearing transplants of macaque endometriotic tissue reveal that, following intravenous injection at a low dose (3 mg per kg), these nanoparticles efficiently accumulate in endometriotic lesions, selectively elevate intralesional temperature above 50 °C upon exposure to external AMF, and completely eradicate them with a single treatment. These nanoparticles also demonstrate promising potential as magnetic resonance imaging (MRI) contrast agents for precise detection of endometriotic tissue before AMF application.

The Pivotal Role of NF-kB in the Pathogenesis and Therapeutics of Alzheimer's Disease.

Alzheimer's Disease (AD) is the most common neurodegenerative disease worldwide, with a high prevalence that is expected to double every 20 years. Besides the formation of Aß plaques and neurofibrillary tangles, neuroinflammation is one the major phenotypes that worsens AD progression. Indeed, the nuclear factor-κB (NF-κB) is a well-established inflammatory transcription factor that fuels neurodegeneration. Thus, in this review, we provide an overview of the NF-κB role in the pathogenesis of AD, including its interaction with various molecular factors in AD mice models, neurons, and glial cells. Some of these cell types and molecules include reactive microglia and astrocytes, ß-secretase, APOE, glutamate, miRNA, and tau protein, among others. Due to the multifactorial nature of AD development and the failure of many drugs designed to dampen AD progression, the pursuit of novel targets for AD therapeutics, including the NF-κB signaling pathway, is rising. Herein, we provide a synopsis of the drug development landscape for AD treatment, offering the perspective that NF-κB inhibitors may generate widespread interest in AD research in the future. Ultimately, the additional investigation of compounds and small molecules that target NF-κB signaling and the complete understanding of NF-κB mechanistic activation in different cell types will broaden and provide more therapeutic options for AD patients.

Nanosecond Pulsed Electric Field (nsPEF): Opening the Biotechnological Pandora's Box.

Nanosecond Pulsed Electric Field (nsPEF) is an electrostimulation technique first developed in 1995; nsPEF requires the delivery of a series of pulses of high electric fields in the order of nanoseconds into biological tissues or cells. They primary effects in cells is the formation of membrane nanopores and the activation of ionic channels, leading to an incremental increase in cytoplasmic Ca2+ concentration, which triggers a signaling cascade producing a variety of effects: from apoptosis up to cell differentiation and proliferation. Further, nsPEF may affect organelles, making nsPEF a unique tool to manipulate and study cells. This technique is exploited in a broad spectrum of applications, such as: sterilization in the food industry, seed germination, anti-parasitic effects, wound healing, increased immune response, activation of neurons and myocites, cell proliferation, cellular phenotype manipulation, modulation of gene expression, and as a novel cancer treatment. This review thoroughly explores both nsPEF's history and applications, with emphasis on the cellular effects from a biophysics perspective, highlighting the role of ionic channels as a mechanistic driver of the increase in cytoplasmic Ca2+ concentration.

DNA repair-related genes and adipogenesis: Lessons from congenital lipodystrophies.

Classical and progeroid congenital lipodystrophies are a collection of rare diseases displaying a large genetic heterogeneity. They occur due to pathogenic variants in genes associated with adipogenesis, DNA repair pathways, and genome stability. Subjects with lipodystrophy exhibit an impairment in the homeostasis of subcutaneous white adipose tissue (sWAT), resulting in low leptin and adiponectin levels, insulin resistance (IR), diabetes, dyslipidemia, ectopic fat deposition, inflammation, mitochondrial and endoplasmic reticulum commitments, among others. However, how pathogenic variants in adipogenesis-related genes modulate DNA repair in some classical congenital lipodystrophies has not been elucidated. In the same way, no data is clarifying how pathogenic variants in DNA repair genes result in sWAT loss in different types of progeroid lipodystrophies. This review will concentrate on the main molecular findings to understand the link between DNA damage/repair and adipogenesis in human and animal models of congenital lipodystrophies. We will focus on classical and progeroid congenital lipodystrophies directly or indirectly related to DNA repair pathways, highlighting the role of DNA repair-related proteins in maintaining sWAT homeostasis.

Local photodoping in monolayer MoS2.

Inducing electrostatic doping in 2D materials by laser exposure (photodoping effect) is an exciting route to tune optoelectronic phenomena. However, there is a lack of investigation concerning in what respect the action of photodoping in optoelectronic devices is local. Here, we employ scanning photocurrent microscopy (SPCM) techniques to investigate how a permanent photodoping modulates the photocurrent generation in MoS2 transistors locally. We claim that the photodoping fills the electronic states in MoS2 conduction band, preventing the photon-absorption and the photocurrent generation by the MoS2 sheet. Moreover, by comparing the persistent photocurrent (PPC) generation of MoS2 on top of different substrates, we elucidate that the interface between the material used for the gate and the insulator (gate-insulator interface) is essential for the photodoping generation. Our work gives a step forward to the understanding of the photodoping effect in MoS2 transistors and the implementation of such an effect in integrated devices.

Anisotropic Flow Control and Gate Modulation of Hybrid Phonon-Polaritons.

Light-matter interaction in two-dimensional photonic or phononic materials allows for the confinement and manipulation of free-space radiation at sub-wavelength scales. Most notably, the van der Waals heterostructure composed of graphene (G) and hexagonal boron nitride (hBN) provides for gate-tunable hybrid hyperbolic plasmon phonon-polaritons (HP3). Here, we present the anisotropic flow control and gate-voltage modulation of HP3 modes in G-hBN on an air-Au microstructured substrate. Using broadband infrared synchrotron radiation coupled to a scattering-type near-field optical microscope, we launch HP3 waves in both hBN Reststrahlen bands and observe directional propagation across in-plane heterointerfaces created at the air-Au junction. The HP3 hybridization is modulated by varying the gate voltage between graphene and Au. This modifies the coupling of continuum graphene plasmons with the discrete hBN hyperbolic phonon polaritons, which is described by an extended Fano model. This work represents the first demonstration of the control of polariton propagation, introducing a theoretical approach to describe the breaking of the reflection and transmission symmetry for HP3 modes. Our findings augment the degree of control of polaritons in G-hBN and related hyperbolic metamaterial nanostructures, bringing new opportunities for on-chip nano-optics communication and computing.

Anomalous Nonlinear Optical Response of Graphene Near Phonon Resonances.

In this work we probe the third-order nonlinear optical property of graphene and hexagonal boron nitride and their heterostructure by the use of coherent anti-Stokes Raman spectroscopy. When the energy difference of the two input fields matches the phonon energy, the anti-Stokes emission intensity is enhanced in h-BN, as usually expected, while for graphene an anomalous decrease is observed. This behavior can be understood in terms of a coupling between the electronic continuum and a discrete phonon state. We have also measured a graphene/h-BN heterostructure and demonstrate that the anomalous effect in graphene dominates the heterostructure nonlinear optical response.

The evolution of climatic niches in squamate reptiles.

Despite the remarkable diversity found in squamate reptiles, most of their species tend to be found in warm/dry environments, suggesting that climatic requirements played a crucial role in their diversification, yet little is known about the evolution of their climatic niches. In this study, we integrate climatic information associated with the geographical distribution of 1882 squamate species and their phylogenetic relationships to investigate the tempo and mode of climatic niche evolution in squamates, both over time and among lineages. We found that changes in climatic niche dynamics were pronounced over their recent squamate evolutionary history, and we identified extensive evidence for rate heterogeneity in squamate climatic niche evolution. Most rate shifts involved accelerations, particularly over the past 50 Myr. Most squamates occupy similar regions of the climatic niche space, with only a few lineages diversifying into colder and humid climatic conditions. The changes from arid to mesic conditions in some regions of the globe may have provided opportunities for climatic niche evolution, although most lineages tended to remain near their ancestral niche. Variation in rates of climatic niche evolution seems common, particularly in response to the availability of new climatic conditions over evolutionary time.

Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene.

We report on magnetotransport studies of dual-gated, Bernal-stacked trilayer graphene (TLG) encapsulated in boron nitride crystals. We observe a quantum Hall effect staircase which indicates a complete lifting of the 12-fold degeneracy of the zeroth Landau level. As a function of perpendicular electric field, our data exhibit a sequence of phase transitions between all integer quantum Hall states in the filling factor interval -8<ν<0. We develop a theoretical model and argue that, in contrast to monolayer and bilayer graphene, the observed Landau level splittings and quantum Hall phase transitions can be understood within a single-particle picture, but imply the presence of a charge density imbalance between the inner and outer layers of TLG, even at charge neutrality and zero transverse electric field. Our results indicate the importance of a previously unaccounted band structure parameter which, together with a more accurate estimate of the other tight-binding parameters, results in a significantly improved determination of the electronic and Landau level structure of TLG.

Hemophagocytic lymphohistiocytosis and macrophage activation syndrome: two rare sides of the same devastating coin.

Hemophagocytic lymphohistiocytosis (HLH) is a rare genetic hyperinflammatory syndrome that occurs early in life. Macrophage activation syndrome (MAS) usually refers to a secondary form of HLH associated with autoimmunity, although there are other causes of secondary HLH, such as infections and malignancy. In this article, we reviewed the concepts, epidemiology, clinical and laboratory features, diagnosis, differential diagnosis, prognosis, and treatment of HLH and MAS. We also reviewed the presence of MAS in the most common autoimmune diseases that affect children. Both are severe diseases that require prompt diagnosis and treatment to avoid morbidity and mortality.

Case report: two novel PPARG pathogenic variants associated with type 3 familial partial lipodystrophy in Brazil.

INTRODUCTION AND AIM: Type 3 Familial Partial Lipodystrophy (FPLD3) is a rare metabolic disease related to pathogenic PPARG gene variants. FPLD3 is characterized by a loss of fatty tissue in the upper and lower limbs, hips, and face. FPLD3 pathophysiology is usually associated with metabolic comorbidities such as type 2 diabetes, insulin resistance, hypertriglyceridemia, and liver dysfunction. Here, we clinically and molecularly characterized FPLD3 patients harboring novel PPARG pathogenic variants. MATERIALS AND METHODS: Lipodystrophy-suspected patients were recruited by clinicians from an Endocrinology Reference Center. Clinical evaluation was performed, biological samples were collected for biochemical analysis, and DNA sequencing was performed to define the pathogenic variants associated with the lipodystrophic phenotype found in our clinically diagnosed FPLD subjects. Bioinformatics predictions were conducted to characterize the novel mutated PPARγ proteins. RESULTS: We clinically described FPLD patients harboring two novel heterozygous PPARG variants in Brazil. Case 1 had the c.533T > C variant, which promotes the substitution of leucine to proline in position 178 (p.Leu178Pro), and cases 2 and 3 had the c.641 C > T variant, which results in the substitution of proline to leucine in the position 214 (p.Pro214Leu) at the PPARγ2 protein. These variants result in substantial conformational changes in the PPARγ2 protein. CONCLUSION: Two novel PPARG pathogenic variants related to FPLD3 were identified in a Brazilian FPLD cohort. These data will provide new epidemiologic data concerning FPLD3 and help understand the genotype-phenotype relationships related to the PPARG gene.

Sex differences in the biomechanical and biochemical responses of caudal rat intervertebral discs to injury.

Background: Intervertebral disc degeneration (IDD) is a major cause of low back pain (LBP) worldwide. Sexual dimorphism, or sex-based differences, appear to exist in the severity of LBP. However, it is unknown if there are sex-based differences in the inflammatory, biomechanical, biochemical, and histological responses of intervertebral discs (IVDs). Methods: Caudal (Coccygeal/Co) bone-disc-bone motion segments were isolated from multiple spinal levels (Co8 to Co14) of male and female Sprague-Dawley rats. Changes in motion segment biomechanics and extracellular matrix (ECM) biochemistry (glycosaminoglycan [GAG], collagen [COL], water, and DNA content) were evaluated at baseline and in response to chemical insult (lipopolysaccharide [LPS]) or puncture injury ex vivo. We also investigated the contributions of Toll-like receptor (TLR4) signaling on responses to LPS or puncture injury ex vivo, using a small molecule TLR4 inhibitor, TAK-242. Results: Findings indicate that IVD motion segments from female donors had greater nitric oxide (NO) release in LPS groups compared to male donors. HMGB1 release was increased in punctured discs, but not LPS injured discs, with no sex effect. Although both male and female discs exhibited reductions in dynamic moduli in response to LPS and puncture injuries, dynamic moduli from female donors were higher than male donors across all groups. In uninjured (baseline) samples, a significant sex effect was observed in nucleus pulposus (NP) DNA and water content. Female annulus fibrosus (AF) also had higher DNA, GAG, and COL content (normalized by dry weight), but lower water content than male AF. Additional injury- and sex-dependent effects were observed in AF GAG/DNA and COL/DNA content. Finally, TAK-242 improved the dynamic modulus of female but not male punctured discs. Conclusions: Our findings demonstrate that there are differences in rat IVD motion segments based on sex, and that the response to injury in inflammatory, biomechanical, biochemical, and histological outcomes also exhibit sex differences. TLR4 inhibition protected against loss of mechanical integrity of puncture-injured IVD motion segments, with differences responses based on donor sex.