The transcription factor titration effect dictates level of gene expression.

Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment.

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

NaCl, MgCl2, and AlCl3 Surface Coverages on Fused Silica and Adsorption Free Energies at pH 4 from Nonlinear Optics.

We employ amplitude- and phase-resolved second harmonic generation experiments to probe interactions of fused silica:aqueous interfaces with Al3+, Mg2+, and Na+ cations at pH 4 and as a function of metal cation concentration. We quantify the second-order nonlinear susceptibility and the total interfacial potential in the presence and absence of a 10 mM screening electrolyte to understand the influence of charge screening on cation adsorption. Strong cation:surface interactions are observed in the absence of the screening electrolyte. The total potential is then employed to estimate the total number of absorbed cations cm-2. The contributions to the total potential from the bound and mobile charges were separated using Gouy-Chapman-Stern model estimates. All three cations bind fully reversibly, indicating physisorption as the mode of interaction. Of the isotherm models tested, the Kd adsorption model fits the data with binding constants of 3-30 and ∼300 mol-1 for the low (<0.1 mM) and high (0.1-3 mM) concentration regimes, corresponding to adsorption free energies of -13 to -18 and -24 kJ mol-1 at room temperature, respectively. The maximum surface coverages are around 1013 cations cm-2, matching the number of deprotonated silanol groups on silica at pH 4. Clear signs of decoupled Stern and diffuse layer nonlinear optical responses are observed and found to be cation-specific.

Predictors for Long COVID and Differences in Long COVID Symptoms, Findings on Chest Imaging and Pulmonary Function between Hospitalized COVID-19 Patients with versus without Intensive Care Unit Admission.

INTRODUCTION: Many COVID-19 survivors suffer from persisting sequelae after acute disease. This is referred to as long COVID. The objectives of this study were to assess factors associated with long COVID and to analyze differences in persistent symptoms, findings on chest imaging, and pulmonary function between intensive care unit (ICU) and non-ICU hospitalized patients. METHODS: We conducted a retrospective study including patients hospitalized with COVID-19. Patients were stratified into ICU patients and non-ICU patients. We analyzed the outcomes of patients who were in clinical follow-up 6 months after discharge with persistent symptoms, radiological and/or functional abnormalities. Logistic regression was used to examine the association between long COVID and patient characteristics. RESULTS: A total of 549 patients were included. Eighty-one ICU patients (66%) and 146 (34%) non-ICU patients had persistent symptoms or abnormalities on chest imaging or lung function test minimally 6 months after discharge. Significantly more ICU patients had residual fibrotic abnormalities on chest CT and functional impairment. Female gender, myocardial infarction, OSAS, low PCO2 at admission, and longer hospital stay were associated with a higher risk of developing long COVID. Diabetes and treatment with tocilizumab were associated with a lower risk of developing long COVID. CONCLUSION: Of the patients hospitalized for COVID-19, 34-66% suffered from persistent symptoms, residual abnormalities on chest imaging, or reduced lung function at around 6 months after discharge. While persistent sequelae were more frequent in ICU patients, admission to the ICU was not found to be an independent risk factor for developing long COVID.

Large Gas-Phase Source of Esters and Other Accretion Products in the Atmosphere.

Dimeric accretion products have been observed both in atmospheric aerosol particles and in the gas phase. With their low volatilities, they are key contributors to the formation of new aerosol particles, acting as seeds for more volatile organic vapors to partition onto. Many particle-phase accretion products have been identified as esters. Various gas- and particle-phase formation pathways have been suggested for them, yet evidence remains inconclusive. In contrast, peroxide accretion products have been shown to form via gas-phase peroxy radical (RO2) cross reactions. Here, we show that these reactions can also be a major source of esters and other types of accretion products. We studied α-pinene ozonolysis using state-of-the-art chemical ionization mass spectrometry together with different isotopic labeling approaches and quantum chemical calculations, finding strong evidence for fast radical isomerization before accretion. Specifically, this isomerization seems to happen within the intermediate complex of two alkoxy (RO) radicals, which generally determines the branching of all RO2-RO2 reactions. Accretion products are formed when the radicals in the complex recombine. We found that RO with suitable structures can undergo extremely rapid C-C ß scissions before recombination, often resulting in ester products. We also found evidence of this previously overlooked RO2-RO2 reaction pathway forming alkyl accretion products and speculate that some earlier peroxide identifications may in fact be hemiacetals or ethers. Our findings help answer several outstanding questions on the sources of accretion products in organic aerosol and bridge our knowledge of the gas phase formation and particle phase detection of accretion products. As esters are inherently more stable than peroxides, this also impacts their further reactivity in the aerosol.

Organic synthesis in the study of terpene-derived oxidation products in the atmosphere.

Covering: 1997 up to 2022Volatile biogenic terpenes involved in the formation of secondary organic aerosol (SOA) particles participate in rich atmospheric chemistry that impacts numerous aspects of the earth's complex climate system. Despite the importance of these species, understanding their fate in the atmosphere and determining their atmospherically-relevant properties has been limited by the availability of authentic standards and probe molecules. Advances in synthetic organic chemistry directly aimed at answering these questions have, however, led to exciting discoveries at the interface of chemistry and atmospheric science. Herein we provide a review of the literature regarding the synthesis of commercially unavailable authentic standards used to analyze the composition, properties, and mechanisms of SOA particles in the atmosphere.

Quantification of Stern Layer Water Molecules, Total Potentials, and Energy Densities at Fused Silica:Water Interfaces for Adsorbed Alkali Chlorides, CTAB, PFOA, and PFAS.

We have employed amplitude- and phase-resolved second-harmonic generation spectroscopy to investigate ion-specific effects of monovalent cations at the fused silica:water interface maintained under acidic, neutral, and alkaline conditions. We find a negligible dependence of the total potential (as negative as -400 mV at pH 14), the second-order nonlinear susceptibility (as large as 1.5 × 10-21 m2 V-1 at pH 14), the number of Stern layer water molecules (1 × 1015 cm-2 at pH 5.8), and the energy associated with water alignment upon going from neutral to high pH (ca. -24 kJ mol-1 to -48 kJ mol-1 at pH 13 and 14, close to the cohesive energy of liquid water but smaller than that of ice) on chlorides of the alkali series (M+ = Li+, Na+, K+, Rb+, and Cs+). Attempts are presented to provide estimates for the molecular hyperpolarizability of the cations and anions in the Stern layer at high pH, which arrive at ca. 20-fold larger values for αtotal ions(2) = αM+(2) + αOH-(2) + αCl-(2) when compared to water's molecular hyperpolarizability estimate from theory and point to a sizable contribution of deprotonated silanol groups at high pH. In contrast to the alkali series, a pronounced dependence of the total potential and the second-order nonlinear susceptibility on monovalent cationic (cetrimonium bromide, CTAB) and anionic (perfluorooctanoic and perfluorooctanesulfonic acid, PFOA and PFOS) surfactants was quantifiable. Our findings are consistent with a low surface coverage of the alkali cations and a high surface coverage of the surfactants. Moreover, they underscore the important contribution of Stern layer water molecules to the total potential and second-order nonlinear susceptibility. Finally, they demonstrate the applicability of heterodyne-detected second-harmonic generation spectroscopy for identifying perfluorinated acids at mineral:water interfaces.

Preoperative BChE serves as a prognostic marker in patients with resectable AEG after neoadjuvant chemotherapy.

BACKGROUND: Diminished systemic serum butyrylcholinesterase (BChE), a biomarker for chronic inflammation, cachexia, and advanced tumor stage, has shown to play a prognostic role in various malignancies. The aim of this study was to investigate the prognostic value of pretherapeutic BChE levels in patients with resectable adenocarcinoma of the gastroesophageal junction (AEG), treated with or without neoadjuvant therapy. METHODS: Data of a consecutive series of patients with resectable AEG at the Department for General Surgery, Medical University of Vienna, were analyzed. Preoperative serum BChE levels were correlated to clinic-pathological parameters as well as treatment response. The prognostic impact of serum BChE levels on disease-free (DFS) and overall survival (OS) was evaluated by univariate and multivariate cox regression analysis, and Kaplan-Meier curves used for illustration. RESULTS: A total of 319 patients were included in this study, with an overall mean (standard deviation, SD) pretreatment serum BChE level of 6.22 (± 1.91) IU/L. In univariate models, diminished preoperative serum BChE levels were significantly associated with shorter overall (OS, p < 0.003) and disease-free survival (DFS, p < 0.001) in patients who received neoadjuvant treatment and/or primary resection. In multivariated analysis, decreased BChE was significantly associated with shorter DFS (HR: 0.92, 95% CI: 0.84-1.00, p 0.049) and OS (HR: 0.92, 95% CI: 0.85-1.00, p < 0.49) in patients receiving neoadjuvant therapy. Backward regression identified the interaction between preoperative BChE and neoadjuvant chemotherapy as a predictive factor for DFS and OS. CONCLUSION: Diminished serum BChE serves as a strong, independent, and cost-effective prognostic biomarker for worse outcome in patients with resectable AEG who had received neoadjuvant chemotherapy.

Water Structure in the Electrical Double Layer and the Contributions to the Total Interfacial Potential at Different Surface Charge Densities.

The electric double layer governs the processes of all charged surfaces in aqueous solutions; however, elucidating the structure of the water molecules is challenging for even the most advanced spectroscopic techniques. Here, we present the individual Stern layer and diffuse layer OH stretching spectra at the silica/water interface in the presence of NaCl over a wide pH range using a combination of vibrational sum frequency generation spectroscopy, heterodyned second harmonic generation, and streaming potential measurements. We find that the Stern layer water molecules and diffuse layer water molecules respond differently to pH changes: unlike the diffuse layer, whose water molecules remain net-oriented in one direction, water molecules in the Stern layer flip their net orientation as the solution pH is reduced from basic to acidic. We obtain an experimental estimate of the non-Gouy-Chapman (Stern) potential contribution to the total potential drop across the insulator/electrolyte interface and discuss it in the context of dipolar, quadrupolar, and higher order potential contributions that vary with the observed changes in the net orientation of water in the Stern layer. Our findings show that a purely Gouy-Chapman (Stern) view is insufficient to accurately describe the electrical double layer of aqueous interfaces.

High-Temperature Majorana Zero Modes.

We employ analytical and numerical approaches to show that unpaired Majorana zero modes can occur in cores of Abrikosov vortices at the interface between a three-dimensional topological insulator, such as Bi_{2}Se_{3}, and a twisted bilayer of high-T_{c} cuprate superconductor, such as Bi_{2}Sr_{2}CaCu_{2}O_{8+δ}. When the twist angle is close to 45° the latter has been predicted to form a fully gapped topological superconductor up to temperatures approaching its native T_{c}≃90 K. Majorana zero modes in these structures will persist up to unprecedented high temperatures and, depending on the quality of the interface, may be protected by gaps with larger magnitudes than other candidate systems.

Severe Dysphagia is Rare After Magnetic Sphincter Augmentation.

BACKGROUND: Dysphagia remains the most significant concern after anti-reflux surgery, including magnetic sphincter augmentation (MSA). The aim of this study was to evaluate postoperative dysphagia rates, its risk factors, and management after MSA. METHODS: From a prospectively collected database of all 357 patients that underwent MSA at our institution, a total of 268 patients were included in our retrospective study. Postoperative dysphagia score, gastrointestinal symptoms, proton pump inhibitor intake, GERD-HRQL, Alimentary Satisfaction, and serial contrast swallow imaging were evaluated within standardized follow-up appointments. To determine patients' characteristics and surgical factors associated with postoperative dysphagia, a multivariable logistic regression analysis was performed. RESULTS: At a median follow-up of 23 months, none of the patients presented with severe dysphagia, defined as the inability to swallow solids or/and liquids. 1% of the patients underwent endoscopic dilatation, and 1% had been treated conservatively for dysphagia. 2% of the patients needed re-operation, most commonly due to recurrent hiatal hernia. Two patients underwent device removal due to unspecific discomfort and pain. No migration of the device or erosion by the device was seen. The LINX® device size ≤ 13 was found to be the only factor associated with postoperative dysphagia (OR 5.90 (95% CI 1.4-24.8)). The postoperative total GERD-HRQL score was significantly lower than preoperative total score (2 vs. 19; p = 0.001), and daily heartburn, regurgitations, and respiratory complains improved in 228/241 (95%), 131/138 (95%) and 92/97 (95%) of patients, respectively. CONCLUSIONS: Dysphagia requiring endoscopic or surgical intervention was rare after MSA in a large case series. LINX® devices with a size < 13 were shown to be an independent risk factor for developing postoperative dysphagia.

Energy conversion via metal nanolayers.

Current approaches for electric power generation from nanoscale conducting or semiconducting layers in contact with moving aqueous droplets are promising as they show efficiencies of around 30%, yet even the most successful ones pose challenges regarding fabrication and scaling. Here, we report stable, all-inorganic single-element structures synthesized in a single step that generate electrical current when alternating salinity gradients flow along its surface in a liquid flow cell. Nanolayers of iron, vanadium, or nickel, 10 to 30 nm thin, produce open-circuit potentials of several tens of millivolt and current densities of several microA cm-2 at aqueous flow velocities of just a few cm s-1 The principle of operation is strongly sensitive to charge-carrier motion in the thermal oxide nanooverlayer that forms spontaneously in air and then self-terminates. Indeed, experiments suggest a role for intraoxide electron transfer for Fe, V, and Ni nanolayers, as their thermal oxides contain several metal-oxidation states, whereas controls using Al or Cr nanolayers, which self-terminate with oxides that are redox inactive under the experimental conditions, exhibit dramatically diminished performance. The nanolayers are shown to generate electrical current in various modes of application with moving liquids, including sliding liquid droplets, salinity gradients in a flowing liquid, and in the oscillatory motion of a liquid without a salinity gradient.

Allosteric modulation of ß-cell M3 muscarinic acetylcholine receptors greatly improves glucose homeostasis in lean and obese mice.

Given the global epidemic in type 2 diabetes, novel antidiabetic drugs with increased efficacy and reduced side effects are urgently needed. Previous work has shown that M3 muscarinic acetylcholine (ACh) receptors (M3Rs) expressed by pancreatic ß cells play key roles in stimulating insulin secretion and maintaining physiological blood glucose levels. In the present study, we tested the hypothesis that a positive allosteric modulator (PAM) of M3R function can improve glucose homeostasis in mice by promoting insulin release. One major advantage of this approach is that allosteric agents respect the ACh-dependent spatiotemporal control of M3R activity. In this study, we first demonstrated that VU0119498, a drug known to act as a PAM at M3Rs, significantly augmented ACh-induced insulin release from cultured ß cells and mouse and human pancreatic islets. This stimulatory effect was absent in islets prepared from mice lacking M3Rs, indicative of the involvement of M3Rs. VU0119498 treatment of wild-type mice caused a significant increase in plasma insulin levels, accompanied by a striking improvement in glucose tolerance. These effects were mediated by ß-cell M3Rs, since they were absent in mutant mice selectively lacking M3Rs in ß cells. Moreover, acute VU0119498 treatment of obese, glucose-intolerant mice triggered enhanced insulin release and restored normal glucose tolerance. Interestingly, doses of VU0119498 that led to pronounced improvements in glucose homeostasis did not cause any significant side effects due to activation of M3Rs expressed by other peripheral cell types. Taken together, the data from this proof-of-concept study strongly suggest that M3R PAMs may become clinically useful as novel antidiabetic agents.

Integration of Eukaryotic Energy Metabolism: The Intramitochondrial and Cytosolic Energy States ([ATP]f/[ADP]f[Pi]).

Maintaining a robust, stable source of energy for doing chemical and physical work is essential to all living organisms. In eukaryotes, metabolic energy (ATP) production and consumption occurs in two separate compartments, the mitochondrial matrix and the cytosol. As a result, understanding eukaryotic metabolism requires knowledge of energy metabolism in each compartment and how metabolism in the two compartments is coordinated. Central to energy metabolism is the adenylate energy state ([ATP]/[ADP][Pi]). ATP is synthesized by oxidative phosphorylation (mitochondrial matrix) and glycolysis (cytosol) and each compartment provides the energy to do physical work and to drive energetically unfavorable chemical syntheses. The energy state in the cytoplasmic compartment has been established by analysis of near equilibrium metabolic reactions localized in that compartment. In the present paper, analysis is presented for energy-dependent reactions localized in the mitochondrial matrix using data obtained from both isolated mitochondria and intact tissues. It is concluded that the energy state ([ATP]f/[ADP]f[Pi]) in the mitochondrial matrix, calculated from the free (unbound) concentrations, is not different from the energy state in the cytoplasm. Corollaries are: (1) ADP in both the cytosol and matrix is selectively bound and the free concentrations are much lower than the total measured concentrations; and (2) under physiological conditions, the adenylate energy states in the mitochondrial matrix and cytoplasm are not substantially different.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.

BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Molecular Chirality and Cloud Activation Potentials of Dimeric α-Pinene Oxidation Products.

The surface activity of ten atmospherically relevant α-pinene-derived dimers having varying terminal functional groups and backbone stereochemistry is reported. We find ∼10% differences in surface activity between diastereomers of the same dimer, demonstrating that surface activity depends upon backbone stereochemistry. Octanol-water (KOW) and octanol-ammonium sulfate partitioning coefficient (KOAS) measurements of our standards align well with the surface activity measurements, with the more surface-active dimers exhibiting increased hydrophobicity. Our findings establish a link between molecular chirality and cloud activation potential of secondary organic aerosol particles. Given the diurnal variations in enantiomeric excess of biogenic emissions, possible contributions of such a link to biosphere:atmosphere feedbacks as well as aerosol particle viscosity and phase separation are discussed.

Effects of a time out consultation with the general practitioner on cancer treatment decision-making: a randomised controlled trial: Time out with the general practitioner and cancer treatment decision.

OBJECTIVE: Improving shared decision-making (SDM) enables more tailored cancer treatment decisions. We evaluated a Time Out consultation (TOC) with the general practitioner (GP), between cancer diagnosis and treatment decision, which aims at supporting SDM and improving continuity of primary care. This study aims to evaluate the effects of a TOC on perceived SDM, information provision and self-efficacy. METHODS: This randomised controlled trial included newly diagnosed patients with curable cancer (breast, lung, colorectal, gynaecologic and melanoma) from four Dutch hospitals. Primary outcome is perceived SDM and secondary outcomes are information provision and self-efficacy. RESULTS: One hundred fifty-four patients (control n = 77, intervention n = 77) - female: 75%, mean age: 61 (SD ± 11.9). In the intervention group, 80.5% (n = 62) had a TOC, of which 82.3% (n = 51) took place after treatment decision. Perceived SDM was lower in the intervention group (-8.9 [95% CI: 0.6-17.1]). Among those with a TOC before treatment decision (n = 11), perceived SDM was comparable to the control group (66.5 ± 27.2 vs. 67.9 ± 26.1). CONCLUSION: Even though patients are motivated to have a TOC, implementing a TOC between diagnosis and treatment decision is challenging. Effects of a timely TOC could not be established. Non-timely TOC decreased perceived SDM. Planning of the TOC should be optimised, and future research should establish if adequately timed TOC results in improved SDM in cancer patients.

Pericarditis as a cardiac manifestation of acute leptospirosis.

Leptospirosis is an infectious disease with an increasing incidence worldwide. The clinical presentation is unspecific and ranges from an asymptomatic clinical course to an acute fulminant disease. The current case report describes a 32-year-old male patient who presented with ST segment elevation in the electrocardiogram about 14 days after cross-country running. Pericarditis was diagnosed and linked to an acute leptospirosis that was serologically confirmed.

Divalent Ion Specific Outcomes on Stern Layer Structure and Total Surface Potential at the Silica:Water Interface.

The second-order nonlinear susceptibility, χ(2), in the Stern layer and the total interfacial potential drop, Φ(0)tot, across the oxide:water interface are estimated from SHG amplitude and phase measurements for divalent cations (Mg2+, Ca2+, Sr2+, and Ba2+) at the silica:water interface at pH 5.8 and various ionic strengths. We find that interfacial structure and total potential depend strongly on ion valency. We observe statistically significant differences between the experimentally determined χ(2) value for NaCl and that of the alkali earth series but smaller differences between ions of the same valency in that series. These differences are particularly pronounced at intermediate salt concentrations, which we attribute to the influence of hydration structure in the Stern layer. Furthermore, we corroborate the differences by examining the effects of anion substitution (SO42- for Cl-). Finally, we identify that hysteresis in measuring the reversibility of ion adsorption and desorption at fused silica in forward and reverse titrations manifests itself both in Stern layer structure and in total interfacial potential for some of the salts, most notably for CaCl2 and MgSO4 but less so for BaCl2 and NaCl.