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The relationship between the light absorption coefficient of flame-formed soot and its hydrogen content was investigated by coupling UV-Visible spectroscopy with elemental analysis and FT-IR quantification of hydrogen tethered to soot sampled along the axis of a premixed ethylene flame. Just after soot inception, the preferential depletion of aliphatic hydrogen was observed moving from 0.2 to 0.1 hydrogen mole fraction and in correspondence of a relatively slight increase of the absorption coefficient. Soot formation rate decreased just after the disappearance of aliphatic hydrogen due to the consequent decrease of active sites on soot particles necessary for further carbon addition and growth. Crossing the threshold hydrogen mole fraction value of about 0.1, aromatic hydrogen resulted to survive to dehydrogenation producing a highly light-absorbing carbon. Thus, the high absorption coefficient appeared to be due to coagulation and thermal annealing marking the end of the soot formation process. [ABSTRACT FROM PUBLISHER]

A method of UV-visible spectra analysis was developed for investigating the relationship between the optical properties and the complex composition/structure of carbonaceous species formed in a sooting premixed ethylene flame. The UV-visible spectra were measured on carbonaceous species, caught on quartz plates inserted along the flame and recovered by solvent treatment. The contribution and the structure of components in a very wide molecular weight range, from 200 to 1E11 u, were evaluated by size exclusion chromatography coupled with on-line UV-visible spectroscopy of the dichloromethane-soluble and dry soot fractions. The optical band gap and the UV peak position of each MW-segregated fraction were evaluated by means of a spectral deconvolution procedure, to get details on the carbon network structure in terms of sp2 and sp3 sites and size and stacking of the aromatic units. The species included in the 1E8-1E11 u range underwent graphitization/growth reactions during the formation process of carbonaceous species. Large polycyclic aroamtic hydrocarbon (PAH) molecules and clusters of PAH, included in the 200-1E8 u range, did not exhibit molecular growth and internal structure transformation, suggesting that they merely aggregate/coagulate participating to the formation of carbon particles. [ABSTRACT FROM AUTHOR]

Pneumatosis intestinalis is a condition characterized by the presence of gas or air pockets within the walls of the intestines. It can occur in any section of the gastrointestinal tract but it is most commonly found in the colon. Etiology and pathogenesis of PI are not yet fully understood, but several potential factors have been suggested to play a pivotal role in the development of this pathologic condition. Pneumatosis intestinalis seems to arise from a complex interplay between various factors, such as the integrity of the intestinal lining, pressure within the portal vein, the composition of the microbiological flora in the gut. Pneumatosis intestinalis can be caused by a variety of underlying conditions, such as bowel obstruction, intestinal ischemia, infection, inflammatory bowel disease, or certain medications. Symptoms may include abdominal pain, bloating, diarrhea, vomiting, and bloody stools. We present a case report of a 63-year-old male patient who underwent laparoscopic cholecystectomy for symptomatic cholelithiasis with recurrent cholecystitis. Following the surgery, the patient experienced a rapid drop in hemoglobin levels, necessitating an urgency regimen laparoscopic abdominal exploration which revealed Meckel's diverticulitis with active bleeding leading to diverticulectomy. The next day, the patient developed a radiological condition characterized by the co-presence of intermittent pneumatosis intestinalis, Portal pneumatosis and intermittent small bowel obstruction., (© 2023 The Authors. Published by Elsevier Inc. on behalf of University of Washington.)

Assembling peptides allow the creation of structurally complex materials, where amino acid selection influences resulting properties. We present a synergistic approach of experiments and simulations for examining the influence of natural and non-natural amino acid substitutions via incorporation of charged residues and a reactive handle on the thermal stability and assembly of multifunctional collagen mimetic peptides (CMPs). Experimentally, we observed inclusion of charged residues significantly decreased the melting temperature of CMP triple helices with further destabilization upon inclusion of the reactive handle. Atomistic simulations of a single CMP triple helix in explicit water showed increased residue-level and helical structural fluctuations caused by the inclusion of the reactive handle; however, these atomistic simulations cannot be used to predict changes in CMP melting transition. Coarse-grained (CG) simulations of CMPs at experimentally relevant solution conditions, showed, qualitatively, the same trends as experiments in CMP melting transition temperature with CMP design. These simulations show that when charged residues are included electrostatic repulsions significantly destabilize the CMP triple helix and that an additional inclusion of a reactive handle does not significantly change the melting transition. Based on findings from both experiments and simulations, the sequence design was refined for increased CMP triple helix thermal stability, and the reactive handle was utilized for the incorporation of the assembled CMPs within covalently crosslinked hydrogels. Overall, a unique approach was established for predicting stability of CMP triple helices for various sequences prior to synthesis, providing molecular insights for sequence design towards the creation of bulk nanostructured soft biomaterials.

Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The Cambridge Structural Database (CSD) is the world's largest and most comprehensive collection of organic, organometallic, and metal-organic crystal structure information. Analyses using the data have wide impact across the chemical sciences in allowing understanding of structural preferences. In this short review, we illustrate the more common methods by which CSD data influence molecular design. We show how more data could lead to more refined insights into the future using a simple example of trifluoromethylphenyl fragments, highlighting how with sufficient data one can build a reasonable model of geometric change in a chemical fragment with torsional rotation, and show some recent examples where the CSD has been used in conjunction with other methods to provide design ideas and more computationally tractable workflows for derivation of useful insights into structural design.

Activation of inositol-requiring enzyme (IRE1α) is an indispensable step in remedying the cellular stress associated with lipid perturbation in the endoplasmic reticulum (ER) membrane. IRE1α is a single-spanning ER transmembrane protein possessing both kinase and endonuclease functions, and its activation can be fully achieved through the dimerization and/or oligomerization process. How IRE1α senses membrane lipid saturation remains largely unresolved. Using both computational and experimental tools, we systematically investigated the dimerization process of the transmembrane domain (TMD) of IRE1α and found that, with help of the serine 450 residue, the conserved tryptophan 457 residue buttresses the core dimerization interface of IRE1α-TMD. BiFC (bimolecular fluorescence complementation) experiments revealed that mutation on these residues abolished the saturated fatty acid-induced dimerization in the ER membrane and subsequently inactivated IRE1α activity in vivo. Therefore, our results suggest that the structural elements of IRE1α-TMD serve as a key sensor that detects membrane aberrancy., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)

The post-treatment of biomass from phytoremediation is not yet a well-established practice due to the risk induced by the presence of Potentially Toxic Elements (PTEs). Pyrolysis is a thermochemical treatment that reduces the volume and weight of contaminated matter producing a combustible vapor phase and a solid residue (char). A key factor enhancing the economic and the environmental sustainability of biomass valorization through pyrolysis is the production of a market value char. A proper choice of the pyrolysis operating conditions should take into account the effect of final temperature on PTEs release, on the char physicochemical properties as well as on the mobility of retained PTEs. In particular, in this work the influence of both the temperature and the plant parts is discussed (branches and leaves of Populus Nigra L. and rhizomes and culms of Arundo donax L.) on the release of Cd, Pb, Cu, and Zn in the temperature range 653-873 K under steam assisted slow pyrolysis conditions. The mobility of the heavy metals retained in the chars was also studied as well as the product yields, the gas composition and char porosity. The results suggested that in presence of Cd it is necessary to operate at low-temperature (lower than 703 K) to obtain a heavy metals free vapor phase fuel, whereas in presence of one or more metals among Pb, Cu, and Zn, it is possible to conduct a pyrolytic treatment at higher temperatures, thus obtaining a char with high BET surface area and lower metals mobility., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Biomasses to be used in the phytoremediation process are generally selected to match agronomic parameters and heavy metals uptake ability. A proper selection can be made greatly effective if knowledge of the properties of the residual char from pyrolysis is available to identify possible valorization routes. In this study a comparative analysis of the yields and characteristics of char obtained from slow pyrolysis of five uncontaminated biomasses (Populus nigra, Salix alba, Fraxinus oxyphylla, Eucalyptus occidentalis and Arundo donax) was carried out under steam atmosphere to better develop char porosity. Moreover, the dependence of the properties of solid residue on the process final temperature was studied for E. occidentalis in the temperature range of 688-967K. The results demonstrate that, among the studied biomasses, chars from P. nigra and E. occidentalis have to be preferred for applications regulated by surface phenomena given their highest surface area (270-300m 2 /g), whereas char from E. occidentalis is the best choice when the goal is to maximize energy recovery., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells.

We propose the design for a nanoparticle carrier that combines three existing motifs into a single construct: a liposome is stabilized by anchoring it to an enclosed solid core via extended polymeric tethers that are chemically grafted to the core and physisorb into the surrounding lipid membrane. Such a design would exhibit several enticing properties, among them: (i) the anchoring stabilizes the liposome against a variety of external stresses, while preserving an aqueous compartment between core and membrane; (ii) the interplay of design parameters such as polymer length or grafting density enforces strong constraints on nanoparticle size and hence ensures a high degree of uniformity; and (iii) the physical and chemical characteristics of the individual constituents equip the construct with numerous functionalities that can be exploited in many ways. However, navigating the large parameter space requires a sound prior understanding for how various design features work together, and how this impacts potential pathways for synthesizing and assembling these nanoparticles. In this paper, we examine these connections in detail, using both soft matter theory and computer simulations at all levels of resolution. We thereby derive strong constraints on the experimentally relevant parameter space, and also propose potential equilibrium and nonequilibrium pathways for nanoparticle assembly.

Stimuli-responsive biomaterials are used to facilitate drug and gene delivery by shielding the drug/gene during circulation times and selectively releasing the cargo at the desired target. Within stimuli-responsive materials, pH-responsive materials are exploited for delivery to specific organs, intracellular compartments, cancer cells, site of inflammation or infection as those sites are characterized by pH that is different from the blood pH. In this paper we use molecular dynamics (MD) simulations to design such pH-responsive biomaterials where the balance between the various intermolecular interactions (e.g., electrostatics, van der Waals) within the biomaterials allow biofunctional molecules to be reversibly shielded and exposed to the environment with change in pH. In our model the shielding aspect is imparted by a polyethylene glycol (PEG) brush and the pH-responsive component is a PEG-tethered oligopeptide that undergoes changes in conformations via protonation of residues upon changes in pH. Starting with a PEG-tethered peptide in a monodisperse short PEG brush, we first vary the composition and sequence of histidine (H), lysine (K), and glutamate (E) along the oligopeptide sequence to find the design parameters that maximize the shielding and exposure of the oligopeptide at pH ∼ 7.0 and pH < 7.0, respectively. Then, we probe the effect of the PEG brush on the conformations of the oligopeptides by simulating PEG-tethered peptide in a bimodal PEG brush containing short PEG and long PEG chains. We characterize the intermolecular interactions involving the PEG, peptide, and solvent that influence the shielded and exposed conformations of the oligopeptides at the two different pHs. In a short monodisperse PEG brush, with a longer PEG-tethered peptide containing large blocks of histidines that undergo change in protonation state as a response to pH change, placed between a protonated lysine and deprotonated glutamate, the PEG brush exhibits maximum shielding and exposure with pH change. This change from shielded to exposed state is driven by electrostatic repulsion upon H protonation. The presence of long PEG chains in a bimodal PEG brush leads to dominating PEG-peptide attractive interactions that reduces the contrast in shielded and exposed conformations of the PEG-tethered peptide upon protonation of histidines.

Gastro-intestinal disorders in older patients is a medical emergency that requires immediate medical care. Chances of recovery improve with an early diagnosis and treatment. It might be caused by a number of different diseases, including perforations by foreign bodies, colon cancer, diverticulitis, ischemia. CT is often the initial modality used to assess patients with acute abdomen, the radiologist may be the first to suggest such a diagnosis. Computed tomography allows to identify the site of gastrointestinal perforations, of ischemia and to determine the most predictive signs in this diagnosis. The purpose of this study was to assess the diagnostic performance of CT gastrointestinal emergency of elderly patients with nontraumatic acute abdominal pain. The cases of 126 consecutively registered patients 65 years old or older presenting to the emergency department with acute abdominal pain and who underwent CT were retrospectively reviewed by two radiologists. Diagnostic accuracy was calculated according to the level of correctly classified cases in both the entire cohort and a surgical subgroup and was compared between readings. Agreement between each reading and the reference diagnosis and interobserver agreement were assessed with kappa statistics. In both the entire cohort (87.5% vs 85.3%, p = 0.07) and the surgical group (94% vs 91%, p = 0.15), there was no significant difference in CT accuracy between diagnoses made by the radiologist. Agreement between the CT diagnosis and the final diagnosis was excellent. In the care of elderly patients, CT is accurate for diagnosing the cause of acute abdominal pain, particularly when it is of gastrointestinal surgical origin. Thus CT interpretation should not be delayed until complete clinicobiologic data are available, and the images should be quickly transmitted to the emergency physician so that appropriate therapy can be begun., (Copyright © 2014 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.)

Authors evaluated the effects of selective adrenergic blockade by means of doxazosin on blood pressure in 48 patients operated on for pheochromocytoma by a multicenter retrospective study. Age, tumor size, surgical approach, and operative time were analyzed as predictive factors of intraoperative hypertensive crises. Forty-eight patients underwent adrenalectomy--four open surgery and 44 laparoscopic surgery--for pheochromocytoma of adrenal glands from 1998 to 2008 after preoperative administration of doxazosin. Perioperative cardiovascular status modifications and surgical medium- and long-term outcomes were analyzed. There was no mortality, conversion rate was 4.5 per cent, and morbidity rate was 8.3 per cent. Intraoperative hypertensive crises (180/90 mmHg or higher) were observed in 14.5 per cent (seven of 48) of patients and were treated pharmacologically with no aftermath. None of the examined variables influenced the occurrence of intraoperative hypertensive episodes. Postoperative hypotension (lower than 90/60 mmHg) was observed in four of 48 patients (8.3%) and was treated by crystalloids and hydrocortisone. In the surgical treatment of pheochromocytoma, the preoperative adrenergic blockade by doxazosin does not prevent intraoperative hypertensive crises. Nevertheless, in our series, they were of short duration and were not associated with major cardiovascular complications. Perioperative hemodynamic instability was managed by preoperative pharmacological treatment, allowing low morbidity.

Molecular dynamics (MD) simulations were used to gain insight on the molecular interactions in a model biological membrane comprised of a bilayer with DPPC (dipalmitoylphosphotidylcholine) and antimicrobial dendritic amphiphile molecules [RCONHC(CH(2)CH(2)COOH)(3), where R is the saturated hydrocarbon tail (R = n-C(n)H(2n+1)), to be abbreviated as 3CAmn]. This study analyzes different biophysical properties of the equilibrated mixed bilayers, at 300 and 325 K, to determine how the presence of the 3CAmn, in varying concentrations and tail lengths, affects the lipid bilayer. Lipid tail order parameter data, bilayer thickness trends, and qualitative lipid tail tilt observations suggest that a molar ratio of 0.2 3CAm19/DPPC is sufficient to induce a phase transition in the bilayer from gel to liquid crystalline at 300 K. These results also imply that the phase transition temperature of the mixed bilayer decreases upon incorporation of higher concentrations of 3CAm19. Hydrogen bonding takes place between the 3CAmn and DPPC at specific sites, as evidenced by the radial distribution function. Increased hydrogen bonding and the smaller headgroup size of the 3CAmn molecule result in a decrease in the total lateral area with higher concentrations of 3CAm19. Diffusion constants of 3CAmn varied with concentration and tail length; diffusion constants of DPPC and 3CAm19 increased with increasing 3CAm19 concentration at 300 K and shorter 3CAmn tails had higher diffusion constants at both temperatures. These computational studies provide a comprehensive understanding of the biophysical changes to model biological membranes by the association of 3CAmn.

Metanephric adenoma (MA) is a rare benign tumor, diagnosis of which is often carried out after surgical treatment. In case of peripheral lesions, a partial nephrectomy (PN)--either open or laparoscopic may be preferred--and, furthermore, a radiofrequency (RF)-assisted procedure may facilitate adequate hemostasis. In November 2010, the authors performed a RF-assisted PN, according to Habib's technique, using a 4-needle bipolar device, on a woman affected by a small exophytic MA of the right kidney. Fibrin glue was applied on the cut surface. Postoperative course was uneventful, and discharge was on postoperative day 4. MA is an extremely rare benign tumor with a favorable prognosis. In case of a preoperative cytological diagnosis, a careful follow-up has to be considered. PN represents the standard of care for small exophytic MA, and RF-assisted procedures allow an excellent hemostasis and a rapid conservative resection, with very low morbidity.

Human prion diseases are neurodegenerative disorders associated to the misfolding of the prion protein (PrP). Common features of prion disorders are the fibrillar amyloid deposits and the formation of prefibrillar oligomeric species also suggested as the origin of cytotoxicity associated with diseases. Although the process of PrP misfolding has been extensively investigated, many crucial aspects of this process remain unclear. We have here carried out a molecular dynamics study to evaluate the intrinsic dynamics of PrP β-sheet, a region that is believed to play a crucial role in prion aggregation. Moreover, as this region mediates protein association in dimeric assemblies frequently observed in prion crystallographic investigations, we also analyzed the dynamics of these intermolecular interactions. The extensive sampling of replica exchange shows that the native antiparallel β-structure of the prion is endowed with a remarkable stability. Therefore, upon unfolding, the persistence of a structured β-region may seed molecular association and influence the subsequent phases of the aggregation process. The analysis of the four-stranded β-sheet detected in the dimeric assemblies of PrP shows a tendency of this region to form dynamical structured states. The impact on the β-sheet structure and dynamics of disease associated point mutations has also been evaluated.

Splenic abscess is an uncommon but potentially life-threatening disease that generally occurs in patients with neoplasia, immunodeficiency, hemoglobinopathies, trauma, metastatic infection, splenic infarction and diabetes. Splenic abscess should be considered in a patient with fever, left upper abdominal pain, and leukocytosis. Splenectomy has been the gold standard treatment for splenic abscess, however, burdened by high morbidity rate related clinical conditions of the patient. With the recent development of minimally invasive techniques and percutaneous US- or CT-guided procedures, the placement of a drainage has achieved excellent results with resolution of the disease in a high percentage of cases with low morbidity and negligible mortality. Percutaneous drainage is indicated for uniloculated or biloculated abscesses and for high risk surgical patients. It is a reliable technique with a high rate of therapeutical success and low costs compared to surgery. Other advantages include avoiding risks of intra-abdominal spillage and perioperative complications and saving time, along with a better patient compliance and an easier nursing care. The authors describe a case of splenic abscess treated by percutaneous US-guided drainage. Our results suggest that ultrasound-guided percutaneous drainage is a safe and feasible alternative to surgery in the treatment of splenic abscesses. In addition, it allows spleen preservation.