Identification of genes related to hydrolysis and assimilation of Agave fructans in Candida apicola NRRL Y-50540 and Torulaspora delbrueckii NRRL Y-50541 by denovo transcriptome analysis.

Fructans are the main sugar in agave pine used by yeasts during mezcal fermentation processes, from which Candida apicola NRRL Y-50540 and Torulaspora delbrueckii NRRL Y-50541 were isolated. De novo transcriptome analysis was carried out to identify genes involved in the hydrolysis and assimilation of Agave fructans (AF). We identified a transcript annotated as SUC2, which is related to ß-fructofuranosidase activity, and several differential expressed genes involved in the transcriptional regulation of SUC2 such as: MIG1, MTH1, SNF1, SNF5, REG1, SSN6, SIP1, SIP2, SIP5, GPR1, RAS2, and PKA. Some of these genes were specifically expressed in some of the yeasts according to their fructans assimilation metabolism. Different hexose transporters that could be related to the assimilation of fructose and glucose were found in both the transcriptomes. Our findings provide a better understanding of AF assimilation in these yeasts and provide resources for further metabolic engineering and biotechnology applications.

Generalization of the Tavis-Cummings model for multi-level anharmonic systems: Insights on the second excitation manifold.

Confined electromagnetic modes strongly couple to collective excitations in ensembles of quantum emitters, producing light-matter hybrid states known as polaritons. Under such conditions, the discrete multilevel spectrum of molecular systems offers an appealing playground for exploring multiphoton processes. This work contrasts predictions from the Tavis-Cummings model in which the material is a collection of two-level systems, with the implications of considering additional energy levels with harmonic and anharmonic structures. We discuss the exact eigenspectrum, up to the second excitation manifold, of an arbitrary number N of oscillators collectively coupled to a single cavity mode in the rotating-wave approximation. Elaborating on our group-theoretic approach [New J. Phys. 23, 063081 (2021)], we simplify the brute-force diagonalization of N2 × N2 Hamiltonians to the eigendecomposition of, at most, 4 × 4 matrices for arbitrary N. We thoroughly discuss the eigenstates and the consequences of weak and strong anharmonicities. Furthermore, we find resonant conditions between bipolaritons and anharmonic transitions where two-photon absorption can be enhanced. Finally, we conclude that energy shifts in the polaritonic states induced by anharmonicities become negligible for large N. Thus, calculations with a single or few quantum emitters qualitatively fail to represent the nonlinear optical response of the collective strong coupling regime. Our work highlights the rich physics of multilevel anharmonic systems coupled to cavities absent in standard models of quantum optics. We also provide concise tabulated expressions for eigenfrequencies and transition amplitudes, which should serve as a reference for future spectroscopic studies of molecular polaritons.

Nonequilibrium effects of cavity leakage and vibrational dissipation in thermally activated polariton chemistry.

In vibrational strong coupling (VSC), molecular vibrations strongly interact with the modes of an optical cavity to form hybrid light-matter states known as vibrational polaritons. Experiments show that the kinetics of thermally activated chemical reactions can be modified by VSC. Transition-state theory, which assumes that internal thermalization is fast compared to reactive transitions, has been unable to explain the observed findings. Here, we carry out kinetic simulations to understand how dissipative processes, namely, those introduced by VSC to the chemical system, affect reactions where internal thermalization and reactive transitions occur on similar timescales. Using the Marcus-Levich-Jortner type of electron transfer as a model reaction, we show that such dissipation can change reactivity by accelerating internal thermalization, thereby suppressing nonequilibrium effects that occur in the reaction outside the cavity. This phenomenon is attributed mainly to cavity decay (i.e., photon leakage), but a supporting role is played by the relaxation between polaritons and dark states. When nonequilibrium effects are already suppressed in the bare reaction (the reactive species are essentially at internal thermal equilibrium throughout the reaction), we find that reactivity does not change significantly under VSC. Connections are made between our results and experimental observations.

Polaritonic normal modes in transition state theory.

A series of experiments demonstrates that strong light-matter coupling between vibrational excitations in isotropic solutions of molecules and resonant infrared optical microcavity modes leads to modified thermally activated kinetics. However, Galego et al. [Phys. Rev. X 9, 021057 (2019)] recently demonstrated that, within transition state theory, effects of strong light-matter coupling with reactive modes are mostly electrostatic and essentially independent of light-matter resonance or even of the formation of vibrational polaritons. To analyze this puzzling theoretical result in further detail, we revisit it under a new light, invoking a normal mode analysis of the transition state and reactant configurations for an ensemble of an arbitrary number of molecules in a cavity, obtaining simple analytical expressions that produce similar conclusions as Feist. While these effects become relevant in optical microcavities if the molecular dipoles are anisotropically aligned, or in cavities with extreme confinement of the photon modes, they become negligible for isotropic solutions in microcavities. It is concluded that further studies are necessary to track the origin of the experimentally observed kinetics.

Computational method for highly constrained molecular dynamics of rigid bodies: Coarse-grained simulation of auxetic two-dimensional protein crystals.

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on Molecular Dynamics (MD) that addresses the geometric degrees of freedom of an auxetic two-dimensional protein crystal. This model consists of a network of impenetrable rigid squares linked through massless rigid rods. Our MD methodology extends the well-known protocols SHAKE and RATTLE to include highly non-linear holonomic and non-holonomic constraints, with an emphasis on collision detection and response between anisotropic rigid bodies. The presented method enables the simulation of long-time dynamics with reasonably large time steps. The data extracted from the simulations allow the characterization of the dynamical correlations featured by the protein subunits, which show a persistent motional interdependence across the array. On the other hand, non-holonomic constraints (collisions between subunits) increase the number of inhomogeneous deformations of the network, thus driving it away from an isotropic response. Our work provides the first long-timescale simulation of the dynamics of protein crystals and offers insights into promising mechanical properties afforded by these materials.

Hemangioma with dabskoid features: a rare histopathologic variant of acquired hemangioma.

Dabska tumor, also known as papillary intralymphatic angioendothelioma (PILA), is a locally aggressive hemangiendothelioma characterized by intravascular papillary proliferations of atypical endothelial cells. Besides PILA, papillary tufts lined by hobnail endothelial cells have been rarely described in vascular proliferations. We report two cases of acquired hemangiomas, which focally showed this finding. We present a 15-year-old male and a 7-year-old girl with erythematous nodules. Both lesions were composed of capillary lobules intermingled with large sinusoidal spaces lined with a single layer of flat endothelial cells, which focally developed intravascular papillary proliferations lined by plump hyperchromatic endothelial cells and a central connective tissue core. Both types of cells were positive with CD31 and ERG and negative for Lyve-1, Prox-1 and podoplanin. Wilm's tumor 1 marker was strongly positive in the capillary hemangioma areas while negative in the intravascular tufts. Both lesions recurred after the first excision but we did not observe further recurrence or evidence of metastasis in the follow-up. In summary, our cases expand the histopathologic findings that may be seen in conventional acquired capillary hemangiomas. The focal presence of dabskoid tufts within an otherwise conventional capillary hemangioma should be not misinterpreted as evidence of malignancy.

In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back.

Computational chemistry is an indispensable tool for understanding molecules and predicting chemical properties. However, traditional computational methods face significant challenges due to the difficulty of solving the Schrödinger equations and the increasing computational cost with the size of the molecular system. In response, there has been a surge of interest in leveraging artificial intelligence (AI) and machine learning (ML) techniques to in silico experiments. Integrating AI and ML into computational chemistry increases the scalability and speed of the exploration of chemical space. However, challenges remain, particularly regarding the reproducibility and transferability of ML models. This review highlights the evolution of ML in learning from, complementing, or replacing traditional computational chemistry for energy and property predictions. Starting from models trained entirely on numerical data, a journey set forth toward the ideal model incorporating or learning the physical laws of quantum mechanics. This paper also reviews existing computational methods and ML models and their intertwining, outlines a roadmap for future research, and identifies areas for improvement and innovation. Ultimately, the goal is to develop AI architectures capable of predicting accurate and transferable solutions to the Schrödinger equation, thereby revolutionizing in silico experiments within chemistry and materials science.

Giant benign lymphangioendothelioma.

Benign lymphangioendothelioma is a rare locally infiltrative vascular neoplasm, presenting as a slow-growing, asymptomatic, reddish-violaceous plaque. Histopathologically, it is characterized by irregular and thin-walled vascular spaces, lined by a single and discontinuous layer of flat endothelial cells, dissecting dermal collagen bundles. We present the case of a 75-year-old man with a giant benign lymphangioendothelioma, to our knowledge, the largest example described in the literature. The immunohistochemical expression of Wilms tumor 1 gene is useful in vascular lesions to differentiate malformations from proliferative endothelial lesions. In our case, the positivity for WT1 supports the neoplastic nature of this lesion.

Driving chemical reactions with polariton condensates.

When molecular transitions strongly couple to photon modes, they form hybrid light-matter modes called polaritons. Collective vibrational strong coupling is a promising avenue for control of chemistry, but this can be deterred by the large number of quasi-degenerate dark modes. The macroscopic occupation of a single polariton mode by excitations, as observed in Bose-Einstein condensation, offers promise for overcoming this issue. Here we theoretically investigate the effect of vibrational polariton condensation on the kinetics of electron transfer processes. Compared with excitation with infrared laser sources, the vibrational polariton condensate changes the reaction yield significantly at room temperature due to additional channels with reduced activation barriers resulting from the large accumulation of energy in the lower polariton, and the many modes available for energy redistribution during the reaction. Our results offer tantalizing opportunities to use condensates for driving chemical reactions, kinetically bypassing usual constraints of fast intramolecular vibrational redistribution in condensed phase.

Clinical performance of provisional screw-retained metal-free acrylic restorations in an immediate loading implant protocol: a 242 consecutive patients' report.

OBJECTIVE: To evaluate the clinical performance of provisional screw-retained metal-free acrylic restorations in an immediate loading implant protocol. MATERIAL AND METHODS: Two hundred and forty-two consecutive patients were selected retrospectively, who received 1011 implants and 311 immediate provisional screw-retained implant restorations (2-4 h after implant surgery). The patients were monitored for a period of 2-3 months, until they were referred for a final restoration. The primary variables recorded include the survival time and the appearance of fractures in the provisional restoration, and the independent variables included age, sex, dental arch, type of restoration, type of attachment and components used, as well as cantilevers and opposing dentition. A survival analysis (Kaplan-Meier) and a Cox regression analysis were performed. RESULTS: Twenty-three restorations in 20 patients (8.26%, 95% CI 4.8-11.7) showed at least one fracture (7.39%). More than half of the new fractures (52%, 12 cases) occurred in the first 4 weeks. The cumulative survival probability observed was greater in mandible (P=0.05) and non-cantilever restorations (P=0.001), and in those opposed by full restorations or natural teeth (P=0.001). With an opposing implant-supported prosthesis, the risk of fracture was multiplied by 4.7, and the use of cantilevers as well as the location of the restoration in the maxilla multiply the risk by 3.4-3.5. CONCLUSIONS: Immediate provisional screw-retained metal-free implant-supported restorations can be considered a reliable restoration (92.6% remain intact) for the healing period of 3 months.

Correction: Polariton chemistry: controlling molecular dynamics with optical cavities.

[This corrects the article DOI: 10.1039/C8SC01043A.].

Primary cutaneous cribriform apocrine carcinoma: a clinicopathologic and immunohistochemical study of 26 cases of an under-recognized cutaneous adnexal neoplasm.

BACKGROUND: Cribriform carcinoma is the histopathologic variant of cutaneous apocrine carcinoma characterized by interconnected solid aggregations of neoplastic cells that are punctuated by small round spaces. OBJECTIVE: To describe the histopathologic and immunohistochemical characteristics of this under-recognized cutaneous adnexal neoplasm. METHODS: Twenty-six cases of primary cutaneous cribriform apocrine carcinoma were clinically, histopathologically, and immunohistochemically studied. RESULTS: Seven neoplasms arose in males and 19 in females. The median age of the patients was 47.8 years. The lower and upper limbs were the most frequent sites. Histopathologically, the neoplasms consisted of well-circumscribed dermal nodules composed of multiple, interconnected, solid aggregations of basophilic epithelial cells that were punctuated by small round spaces. Immunohistochemically, the neoplastic cells expressed immunoreactivity for MNF116, AE1/AE3, Cam 5.2, cytokeratin 7, carcinoembryonic antigen, and epithelial membrane antigen. LIMITATIONS: All specimens came from dermatopathology laboratories, and some inherent selection bias may exist. CONCLUSIONS: Primary cutaneous cribriform apocrine carcinoma is a distinctive but little-known variant of cutaneous apocrine carcinoma.

Plaque-like osteoma cutis with transepidermal elimination.

Osteoma cutis is a rare lesion that consists of the presence of bone tissue within the dermis and/or hypodermis. It may be classified as primary osteoma cutis, when bone tissue develops in the skin without any pre-existing lesion and secondary osteoma cutis, which is more frequent and occurs when osseous tissue develops on a pre-existing lesion. We present a case of primary plaque-like osteoma cutis involving the scalp, left forehead and left cheek, which appeared in an adult male. Histopathological study showed several islands of mature osseous tissue involving the full thickness of the dermis. In some areas, there was also transepidermal elimination of bone spicules. We review the literature about previously reported similar cases.

Immediate efficacy of diode laser application in the treatment of dentine hypersensitivity in periodontal maintenance patients: a randomized clinical trial.

BACKGROUND: To evaluate the immediate efficacy in the reduction of dentine hypersensitivity (DH) when applying an 810 nm diode laser (DL), and a 10% potassium nitrate bioadhesive gel (NK10%). MATERIAL AND METHODS: Forty-five consecutive periodontal maintenance patients of both sexes, with a DH >or= 2 on the verbal rating scale (VRS) in one or more teeth, were randomly allocated into three equal groups: 15 patients received DL and placebo gel; 15 patients were tested with a placebo laser and NK10%; and the remaining 15 received a placebo laser and placebo gel. The DH was evaluated at the start of the study, 15 and 30 min. after the laser application, and on days 2, 4, 7, 14, 30 and 60 by a blind examiner. RESULTS: After 15 min., observations showed a reduction in DH after an evaporative stimulus (ES) of 36.9% (0.86), three times greater than that of the control group (0.23) (p=0.008). After 14 days, this effect was even greater [DL 71.7% (1.67)/NK10% 36.3% (1.73)/control 28.1% (0.73); p=0.004], and lasted until day 60 [65.7% (1.53)/30.4% (0.73)/25.8% (0.67); p=0.01]. CONCLUSIONS: The DL and NK10% gel were proven effective in the treatment of DH. A significantly greater immediate response was observed with DL.

Resonant catalysis of thermally activated chemical reactions with vibrational polaritons.

Interaction between light and matter results in new quantum states whose energetics can modify chemical kinetics. In the regime of ensemble vibrational strong coupling (VSC), a macroscopic number [Formula: see text] of molecular transitions couple to each resonant cavity mode, yielding two hybrid light-matter (polariton) modes and a reservoir of [Formula: see text] dark states whose chemical dynamics are essentially those of the bare molecules. This fact is seemingly in opposition to the recently reported modification of thermally activated ground electronic state reactions under VSC. Here we provide a VSC Marcus-Levich-Jortner electron transfer model that potentially addresses this paradox: although entropy favors the transit through dark-state channels, the chemical kinetics can be dictated by a few polaritonic channels with smaller activation energies. The effects of catalytic VSC are maximal at light-matter resonance, in agreement with experimental observations.

Leukemia cutis presenting as localized cutaneous hyperpigmentation.

The usual clinical presentations of leukemia cutis include solitary infiltrated erythematous or violaceous plaques or nodules and multiple localized or generalized papules. On the other hand, cutaneous hyperpigmentation is a frequent finding in patients with malignancies, most of the cases because of chemotherapy or other drugs that the patient is taking. We present a case of cutaneous hyperpigmentation as the presenting sign of leukemia cutis. A 61-year-old male presented with cutaneous hyperpigmentation, which had appeared during the last chemotherapy cycle for treatment for biphenotypic leukemia. Cutaneous lesions consisted of bluish to brownish irregular well-defined discoloration of the skin involving the upper part of the trunk and the temporal regions of the forehead. The patient was asymptomatic and the skin was not infiltrated at all. However, histopathologic study showed nodular infiltrates involving the full-thickness of the dermis and destroying pre-existing adnexa. This infiltrate was composed of atypical basophilic cells with large hyperchromatic nuclei and scant cytoplasm. Immunohistochemical studies showed intense immunoexpression for CD43, CD68, CD45RO and myeloperoxidase within these cells. A diagnosis of biphenotypic leukemia cutis was established. In our review of the literature we have not found any report of cutaneous hyperpigmentation as the presenting manifestation of leukemia cutis.

[Evaluation of Gastric Atrophy. Comparison between Sidney and OLGA Systems]. / Evaluación histopatológica de gastritis atrófica. Comparación de los sistemas Sidney y OLGA.

BACKGROUND: histopathologic identification of atrophy and metaplasia is decisive to stop the way of gastritis?carcinoma in patients with chronic gastritis. OBJECTIVE: to compare diagnostic concordance between Sidney system and the operative Link on Gastritis Assessment (OLGA) system. METHODS: 120 consecutive biopsies were analyzed by general pathologists according to the Sidney system. All of them were evaluated by a second pathologist who used OLGA System. We employed kappa index to evaluate diagnostic concordance between the classifications. RESULTS: the clinical picture includes dyspepsia (94 %), abdominal pain (50 %), gastroesophageal reflux (30 %), bleed of the upper digestive system (24 %), and presence of Helicobacter pylori (47.5 %). Four were diagnosed as atrophy by Sidney system and 26 cases with atrophy by OLGA system. The concordance between two classifications systems was too low (p = 0.05). CONCLUSIONS: the atrophy diagnosis, between systems, had low concordance. The description of metaplastic atrophy in the OLGA system represents the only one difference. The non-metaplastic atrophy is the same for both classifications. Therefore, the general pathologist should include this evaluation more consistently using OLGA system.

Polariton chemistry: controlling molecular dynamics with optical cavities.

Molecular polaritons are the optical excitations which emerge when molecular transitions interact strongly with confined electromagnetic fields. Increasing interest in the hybrid molecular-photonic materials that host these excitations stems from recent observations of their novel and tunable chemistry. Some of the remarkable functionalities exhibited by polaritons include the ability to induce long-range excitation energy transfer, enhance charge conductivity, and inhibit or accelerate chemical reactions. In this review, we explain the effective theories of molecular polaritons which form a basis for the interpretation and guidance of experiments at the strong coupling limit. The theoretical discussion is illustrated with the analysis of innovative applications of strongly coupled molecular-photonic systems to chemical phenomena of fundamental importance to future technologies.

Localized panniculitis secondary to subcutaneous glatiramer acetate injections for the treatment of multiple sclerosis: a clinicopathologic and immunohistochemical study.

BACKGROUND: Glatiramer acetate has been shown to be effective in reducing the relapse and improving the disability of patients with multiple sclerosis. The most common adverse effects at the injection sites include pain, inflammation, and induration that spontaneously disappear within hours or a few days. OBJECTIVE: We sought to characterize the histopathologic findings of localized panniculitis induced by glatiramer acetate at the injection sites. METHODS: Seven patients receiving daily glatiramer acetate injections for treatment of multiple sclerosis developed localized panniculitis at the injection sites. The lesions were histopathologically and immunohistochemically studied. RESULTS: The lesions consisted of a mostly lobular panniculitis, with lipophagic granuloma, namely histiocytes engulfing the lipids from necrotic adipocytes. In many areas, scattered neutrophils and eosinophils were seen both in the septa and in the fat lobules. Connective tissue septa showed widening and fibrosis in conjunction with many lymphoid follicles, presenting with germinal center formation. Immunohistochemically, the inflammatory infiltrate of the fat lobule consisted of CD68+ histiocytes and suppressor/cytotoxic T lymphocytes. In contrast, the lymphoid follicles in the septa and at the interface between septum and fat lobule were mainly composed of B lymphocytes. LIMITATIONS: Only one biopsy was performed in each patient and, therefore, it was not possible to study the histopathologic evolution of the panniculitic process. CONCLUSIONS: Localized panniculitis at the sites of subcutaneous injections of glatiramer acetate for treatment of multiple sclerosis seems to be a rare, but characteristic side effect of this therapy. The histopathologic pattern of these lesions consists of a mostly lobular panniculitis, with histiocytes and T lymphocytes in the fat lobule and thickened septa with scattered lymphoid follicles, which are mostly composed of B lymphocytes.

Genome Sequence of Torulaspora delbrueckii NRRL Y-50541, Isolated from Mezcal Fermentation.

Torulaspora delbrueckii presents metabolic features interesting for biotechnological applications (in the dairy and wine industries). Recently, the T. delbrueckii CBS 1146 genome, which has been maintained under laboratory conditions since 1970, was published. Thus, a genome of a new mezcal yeast was sequenced and characterized and showed genetic differences and a higher genome assembly quality, offering a better reference genome.