Strategies for managing corn crop residue in the context of greenhouse gas emissions.

Food production is one of the most important sources of greenhouse gas (GHG) emissions, both in primary production and in processing and the logistics chain. The most problematic and risky is the optimization of environmental effects in the stage of primary production. This is due to the significant influence of factors related to climate and soil that are difficult to predict.

High throughput mutational scanning of a protein via alchemistry on a high-performance computing resource.

Antibiotic resistance presents a significant challenge to public health, as bacteria can develop resistance to antibiotics through random mutations during their life cycles, making the drugs ineffective. Understanding how these mutations contribute to drug resistance at the molecular level is crucial for designing new treatment approaches. Recent advancements in molecular biology tools have made it possible to conduct comprehensive analyses of protein mutations.

Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance.

Efflux-mediated β-lactam resistance is a major public health concern, reducing the effectiveness of β-lactam antibiotics against many bacteria. Structural analyses show the efflux protein TolC in Gram-negative bacteria acts as a channel for antibiotics, impacting bacterial susceptibility and virulence. This study examines β-lactam drug efflux mediated by TolC using experimental and computational methods.

Deciphering GB1's Single Mutational Landscape: Insights from MuMi Analysis.

Mutational changes that affect the binding of the C2 fragment of Streptococcal protein G (GB1) to the Fc domain of human IgG (IgG-Fc) have been extensively studied using deep mutational scanning (DMS), and the binding affinity of all single mutations has been measured experimentally in the literature. To investigate the underlying molecular basis, we perform in silico mutational scanning for all possible single mutations, along with 2 μs-long molecular dynamics (WT-MD) of the wild-type (WT) GB1 in both unbound and IgG-Fc bound forms. We compute the hydrogen bonds between GB1 and IgG-Fc in WT-MD to identify the dominant hydrogen bonds for binding, which we then assess in conformations produced by Mutation and Minimization (MuMi) to explain the fitness landscape of GB1 and IgG-Fc binding.

A stochastic programming approach to the antibiotics time machine problem.

Antibiotics Time Machine is an important problem to understand antibiotic resistance and how it can be reversed. Mathematically, it can be modeled as follows: Consider a set of genotypes, each of which contain a set of mutated and unmutated genes. Suppose that a set of growth rate measurements of each genotype under a set of antibiotics is given.

UV photodetectors based on W-doped ZnO thin films.

W-doped ZnO thin films deposited on Si substrates with (100) orientation by sol-gel spin coating method at temperature 500 °C. W/Zn atomic ratio varies from 0% to 4%. Then, the UV detection performance analysis ofheterojunction UV photodetectors based on W-doped ZnO/Si is analyzed.

Which is the best diet to reduce cardiometabolic risk: dietary counseling or home-delivered diet?

Background: Non-compliance with medical nutrition therapy can lead to an increase in cardiometabolic risk factors, resulting in an increase in the frequency of morbidity and mortality.

Objective: This study aims to compare the effectiveness of two different medical nutrition therapies designed to reduce cardiometabolic risk factors.

Design: The study was conducted on voluntary overweight and obese women who sought services at a specialized Nutrition and Dietary Counseling Clinic.

Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in DHFR.

Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR's crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4'-deoxy methyl trimethoprim (4'-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP).

The prognostic significance of tumor budding and the expression of focal adhesion kinase and survivin in lung adenocarcinoma.

Objectives: Adenocarcinoma is the tumor group with the highest incidence among lung cancers with poor prognosis. Tumor budding (TB) is the migration of single tumor cells or small clusters of cells from the neoplastic epithelium to the invasive front of the tumor. Focal adhesion kinase (FAK) and survivin are considered as poor prognostic factors in several tumors.

The expression of programmed death-ligand 1 and programmed death-ligand 2 in endometrial carcinosarcoma: Correlation with mismatch repair protein expression status, tumor-infiltrating lymphocyte infiltration, and clinical outcomes.

Background: Endometrial carcinosarcomas have high malignant potential with a high recurrence rate and poor prognosis. Immunotherapy may be a promising treatment option. The aim of this study is to evaluate the expression of PD-L1/PD-L2 and its relationship to mismatch repair (MMR) protein status and tumor-infiltrating lymphocyte (TIL) density.

Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations.

This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment.

A longitudinal study of cortical auditory maturation and implications of the short inter-implant delay in children with bilateral sequential cochlear implants.

Objective: This longitudinal study aimed to investigate the maturational development of P1 latency and the effects of a short inter-implant delay in children who received bilateral sequential cochlear implants.

Materials And Methods: Fourteen children (first CI mean age: 1.4 ± 0.

DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies.

Antibiotic resistance is a global health problem in which mutations occurring in functional proteins render drugs ineffective. The working mechanisms of the arising mutants are seldom apparent; a methodology to decipher these mechanisms systematically would render devising therapies to control the arising mutational pathways possible. Here we utilize C-C bond vector relaxations obtained from moderate length MD trajectories to determine conduits for functionality of the resistance conferring mutants of dihydrofolate reductase.

Microsatellite Instability Status and the Expression of p16 and Cyclin D1 Proteins in Uterine Adenosarcoma and Their Clinicopathological Significance.

Objective: Uterine adenosarcoma has low malignant potential, except in cases with sarcomatous overgrowth (SOG) and a high-grade morphology. We here point out the prognostic clinicopathological and immunohistochemical features as well as the microsatellite instability (MSI) status of high- and low-grade adenosarcomas.

Material And Method: In this study, DNA mismatch repair proteins, p16, cyclin D1, ER, PR, and CD10 were examined in uterine adenosarcoma cases using immunohistochemistry.

A Catalytically Accessible Polyoxometalate in a Porous Fiber for Degradation of a Mustard Gas Simulant.

Polyoxometalates (POMs) are versatile materials for chemical catalysis due to their tunable acidity and rich redox properties. While POMs have attracted significant attention in homogeneous catalysis, challenges regarding aggregation and instability in solvents often prevent the wide implementation of POMs as heterogeneous catalysts. Therefore, the successful incorporation of a POM into a solid support, such as a polymer, is desirable for practical applications where unique functionalities of the POM combine with the advantages of the polymer.

Catalytic Degradation of Polyethylene Terephthalate Using a Phase-Transitional Zirconium-Based Metal-Organic Framework.

Polyethylene terephthalate (PET) is utilized as one of the most popular consumer plastics worldwide, but difficulties associated with recycling PET have generated a severe environmental crisis with most PET ending its lifecycle in landfills. We report that zirconium-based metal-organic framework (Zr-MOF) UiO-66 deconstructs waste PET into the building blocks terephthalic acid (TA) and mono-methyl terephthalate (MMT) within 24 hours at 260 °C (total yield of 98 % under 1 atm H and 81 % under 1 atm Ar). Extensive structural characterization studies reveal that during the degradation process, UiO-66 undergoes an intriguing transformation into MIL-140A, which is another Zr-MOF that shows good catalytic activity toward PET degradation under similar reaction conditions.

BODIPY-Based Polymers of Intrinsic Microporosity for the Photocatalytic Detoxification of a Chemical Threat.

Effective heterogeneous photocatalysts capable of detoxifying chemical threats in practical settings must exhibit outstanding device integrity. We report a copolymerization that yields robust, porous, processible, chromophoric BODIPY (BDP; boron-dipyrromethene)-containing polymers of intrinsic microporosity (BDP-PIMs). Installation of a pentafluorophenyl at the meso position of a BDP produced reactive monomer that when combined with 5,5,6,6-tetrahydroxy-3,3,3,3-tetramethyl-1,1-spirobisindane (TTSBI) and tetrafluoroterephthalonitrile (TFTPN) yields .

Computational strategies for protein conformational ensemble detection.

Protein function is constrained by the three-dimensional structure but is delineated by its dynamics. This framework must satisfy specificity of function along with adaptability to changing environments and evolvability under external constraints. The accessibility of the available regions of the energy landscape for a set of conditions and shifts in the populations upon their modulation have effects propagating across scales, from biomolecular interactions, to organisms, to populations.

A trimethoprim derivative impedes antibiotic resistance evolution.

The antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4'-desmethyltrimethoprim (4'-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments.

Spectral resolution and speech perception after cochlear implantation using the round window versus cochleostomy technique.

Objective: To evaluate the spectral resolution achieved with a cochlear implant in users who were implanted using round window route electrode insertion versus a traditional cochleostomy technique.

Methods: Twenty-six patients were classified into two groups according to the surgical approach: one group (n = 13) underwent cochlear implantation via the round window technique and the other group (n = 13) underwent surgery via cochleostomy.

Results: A statistically significant difference was found in spectral ripple discrimination scores between the round window and cochleostomy groups.

The effect of intratesticular dexpanthenol on experimentally-induced testicular ischaemia/reperfusion injury.

Introduction: Testis torsion is a urological emergency and a serious situation that may cause testis atrophy, testicular dysfunction and infertility due to ischaemia/reperfusion(I/R) injury even with early intervention.

Objective: To assess the protective effect of dexpanthenol administered intratesticular after detorsion against testis I/R injury.

Study Design: Twenty-seven rats were randomly divided into 3 groups containing 9 rats each.

Effects of spatial separation with better- ear listening on N1-P2 complex.

Objective: The purpose of this study was to determine better- ear listening effect on spatial separation with the N1-P2 complex.

Methods: Twenty individuals with normal hearing participated in this study. The speech stimulus /ba/ was presented in front of the participant (0°).

Dynamic Community Composition Unravels Allosteric Communication in PDZ3.

The third domain of PSD-95 (PDZ3) is a model for investigating allosteric communication in protein and ligand interactions. While motifs contributing to its binding specificity have been scrutinized, a conformational dynamical basis is yet to be established. Despite the miniscule structural changes due to point mutants, the observed significant binding affinity differences have previously been assessed with a focus on two α-helices located at the binding groove (α) and the C-terminus (α).

N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding.

PDZ domains constitute common models to study single-domain allostery without significant structural changes. The third PDZ domain of PSD-95 (PDZ3) is known to have selective structural features that confer unique modulatory roles to this unit. In this model system, two residues, H372 directly connected to the binding site and G330 holding an off-binding-site position, were designated to assess the effect of mutations on binding selectivity.