AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses.

AlphaFold2 (AF2) has emerged in recent years as a groundbreaking innovation that has revolutionized several scientific fields, in particular structural biology, drug design, and the elucidation of disease mechanisms. Many scientists now use AF2 on a daily basis, including non-specialist users. This chapter is aimed at the latter. Tips and tricks for getting the most out of AF2 to produce a high-quality biological model are discussed here. We suggest to non-specialist users how to maintain a critical perspective when working with AF2 models and provide guidelines on how to properly evaluate them. After showing how to perform our own structure prediction using ColabFold, we list several ways to improve AF2 models by adding information that is missing from the original AF2 model. By using software such as AlphaFill to add cofactors and ligands to the models, or MODELLER to add disulfide bridges between cysteines, we guide users to build a high-quality biological model suitable for applications such as drug design, protein interaction, or molecular dynamics studies.

Superior Medial-Based Breast Reduction with Inverted T Incision: A Precise Description of Our Refined Preoperative Marking and Operative Technique.

The purpose of this paper was to compile a thoroughly elaborated step-by-step guide for the preoperative marking and operative technique for superior medial pedicle inverted T breast reduction based on our long experience and technical refinements. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Homology Modeling of Transporter Proteins.

Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological importance. Several presently used therapeutic compounds elucidate their effects by targeting membrane transporter proteins, including anti-arrhythmic, anesthetic, antidepressant, anxiolytic and diuretic drugs. The lack of three-dimensional structures of human transporters hampers experimental studies and drug discovery. In this chapter, the use of homology modeling for generating structural models of membrane transporter proteins is reviewed. The increasing number of atomic resolution structures available as templates, together with improvements in methods and algorithms for sequence alignments, secondary structure predictions, and model generation, in addition to the increase in computational power have increased the applicability of homology modeling for generating structural models of transporter proteins. Different pitfalls and hints for template selection, multiple-sequence alignments, generation and optimization, validation of the models, and the use of transporter homology models for structure-based virtual ligand screening are discussed.

A Novel Detection Refinement Technique for Accurate Identification of Nephrops norvegicus Burrows in Underwater Imagery.

With the evolution of the convolutional neural network (CNN), object detection in the underwater environment has gained a lot of attention. However, due to the complex nature of the underwater environment, generic CNN-based object detectors still face challenges in underwater object detection. These challenges include image blurring, texture distortion, color shift, and scale variation, which result in low precision and recall rates. To tackle this challenge, we propose a detection refinement algorithm based on spatial-temporal analysis to improve the performance of generic detectors by suppressing the false positives and recovering the missed detections in underwater videos. In the proposed work, we use state-of-the-art deep neural networks such as Inception, ResNet50, and ResNet101 to automatically classify and detect the Norway lobster Nephrops norvegicus burrows from underwater videos. Nephrops is one of the most important commercial species in Northeast Atlantic waters, and it lives in burrow systems that it builds itself on muddy bottoms. To evaluate the performance of proposed framework, we collected the data from the Gulf of Cadiz. From experiment results, we demonstrate that the proposed framework effectively suppresses false positives and recovers missed detections obtained from generic detectors. The mean average precision (mAP) gained a 10% increase with the proposed refinement technique.

Tuneable Phase, Morphology, and Performance of Bismuth Oxyhalide Photocatalysts via Microwave-Assisted Synthesis.

In this study, a facile microwave-assisted synthesis approach was used to produce a series of bismuth oxyhalide photocatalysts, with systematic changes in synthesis pH between 1 and 14 allowing control over a broad range of material properties and characteristics. Detailed structural and morphological investigations with powder X-ray diffraction (PXRD), Rietveld refinements, pair distribution function (PDF) analysis, and scanning electron microscopy (SEM) show that thin particles of BiOCl, BiOBr, Bi24O31Cl10, and Bi24O31Br10 were selectively produced, with progressive changes in morphology, facet dominance, and phase as a function of pH. The impact of these changes on photocatalytic performance was evaluated by studying the aerobic oxidation of benzylamine to N-benzylidenebenzylamine, with all materials exhibiting photocatalytic abilities under UV or blue light. While a combination of material properties and characteristics influenced the photocatalytic performance, certain factors such as surface area, facet dominance, amorphous content, and band gap were found to have a larger impact on the photocatalytic yield. Overall, this study demonstrates the possibilities of phase, morphology, and performance of bismuth oxyhalide photocatalysts over the entire pH range, produced using a fast and facile microwave-assisted synthesis technique as an alternative to the more widely applied hydrothermal synthesis approach. Additionally, the detailed structural and morphological investigations of the materials contribute to a greater understanding of bismuth oxyhalide photocatalysts in general, while also highlighting some of the most desirable properties for improved photocatalytic performance of these materials.

GluN3A NMDA receptor subunits: more enigmatic than ever?

Non-conventional N-methyl-d-aspartate receptors (NMDARs) containing GluN3A subunits have unique biophysical, signalling and localization properties within the NMDAR family, and are typically thought to counterbalance functions of classical NMDARs made up of GluN1/2 subunits. Beyond their recognized roles in synapse refinement during postnatal development, recent evidence is building a wider perspective for GluN3A functions. Here we draw particular attention to the latest developments for this multifaceted and unusual subunit: from finely timed expression patterns that correlate with plasticity windows in developing brains or functional hierarchies in the mature brain to new insight onto presynaptic GluN3A-NMDARs, excitatory glycine receptors and behavioural impacts, alongside further connections to a range of brain disorders.

Refining Procedures within Regulatory Toxicology Studies: Improving Animal Welfare and Data.

During the development of potential new medicines or agrochemicals, an assessment of the safety profile to humans and environmental species is conducted using a range of different in silico and in vitro techniques in conjunction with metabolism and toxicity studies using animals. The required studies are outlined within international regulatory guidelines which acknowledge and support the application of the 3Rs to reduce the number of animals used or to refine the procedures performed when these studies are deemed to be necessary. The continued development of new technologies and adoption of best-practice approaches to laboratory animal housing and study procedures has generated a series of refinements that can be incorporated into animal studies throughout the package. These refinements benefit the welfare of fish, mice, rats, rabbits, dogs, minipigs, and non-human primates (NHPs) whilst maintaining or improving data quality within general toxicology, metabolism, and other studies and can also bring efficiencies to processes that benefit study costs and timings. Examples are shared which cover the following topics: social housing of dogs and NHPs, surgical refinements in the rat bile duct cannulation model for collection of data for metabolism studies, whether fasting is really required prior to clinical pathology sampling, and the use of microsampling for toxicokinetics.

Effects of Nanodomains on Local and Long-Range Phase Transitions in Perovskite-Type Eu0.8Ca0.2TiO3-δ.

The determination of reversible phase transitions in the perovskite-type thermoelectric oxide Eu0.8Ca0.2TiO3-δ is fundamental, since structural changes largely affect the thermal and electrical transport properties. The phase transitions were characterized by heat capacity measurements, Rietveld refinements, and pair distribution function (PDF) analysis of the diffraction data to achieve information on the phase transition temperatures and order as well as structural changes on the local level and the long range. On the long-range scale, Eu0.8Ca0.2TiO3-δ showed a phase transition sequence during heating from cubic at 100 < T < 592 K to tetragonal and finally back to cubic at T > 846 K. The phase transition at T = 592 K (diffraction)/606 K (thermal analysis) was reversible with a very small thermal hysteresis of about 2 K. The local structure at 100 K was composed of a complex nanodomain arrangement of Amm2- and Pbnm-like local structures with different coherence lengths. Since in Eu0.8Ca0.2TiO3-δ the amount of Pbnm domains was too small to percolate, the competition of ferroelectrically distorted octahedra (Amm2 as in BaTiO3) and rigid, tilted octahedra (Pbnm as in CaTiO3) resulted in a cubic long-range structure at low temperatures.

Bottleneck Effect Explained by Le Bail Refinements: Structure Transformation of Mg-CUK-1 by Confining H2O Molecules.

The structure transformation of Mg-CUK-1 due to the confinement of H2O molecules was investigated. Powder X-ray diffraction (PXRD) patterns were collected at different H2O loadings and the cell parameters of the H2O-loaded Mg-CUK-1 material were determined by the Le Bail strategy refinements. A bottleneck effect was observed when one hydrogen-bonded H2O molecule per unit cell (18% relative humidity (RH)) was confined within Mg-CUK-1, confirming the increase in the CO2 capture for Mg-CUK-1.

Effects of Sb Deviation from Its Stoichiometric Ratio on the Micro- and Electronic Structures and Thermoelectric Properties of Cu12Sb4S13.

Thermoelectric material tetrahedrite Cu12Sb4S13 has attracted much attention because of its intrinsic low lattice thermal conductivity, excellent electrical transport property, and environment-friendly constituents. However, its thermoelectric figure merit, ZT, is limited because of the low Seebeck coefficient (S) and power factor (PF). Hence, it is indispensable to enhance its S and PF to increase its ZT. Here, we show that when Sb deviation from its stoichiometric ratio in the Cu12Sb4S13 band structure is modulated, it gives rise to increased density of states and enhancement of the Seebeck coefficient. Moreover, carrier concentration is tuned by changing sulfur and copper vacancies through controlling the Cu3SbS4 phase with an atomic ratio of Sb, leading to increased electrical conductivity. In addition, as large as ∼60% reduction of lattice thermal conductivity is obtained by intensified phonon scattering using an impurity phase/element and vacancy-like defects induced by different Sb contents. As a result, a high ZT = 0.86 is achieved at 723 K for the Cu12Sb4+δS13 sample with δ = 0.2, which is ∼50% larger than that of stoichiometric Cu12Sb4S13 studied here, indicating that ZT of Cu12Sb4S13 can be improved through simple modulation of the Sb stoichiometric ratio.

Solvent saturation transfer to proteins (SSTP) for structural and functional characterization of proteins.

Protein structure determination using NMR is dependent on experimentally acquired distance restraints. Often, however, an insufficient number of these restraints are available for determining a protein's correct fold, much less its detailed three-dimensional structure. In consideration of this problem, we propose a simple means to acquire supplemental structural restraints from protein surface accessibilities using solvent saturation transfer to proteins (SSTP), based on the principles of paramagnetic chemical-exchange saturation transfer. Here, we demonstrate the utility of SSTP in structure calculations of two proteins, TSG101 and ubiquitin. The observed SSTP was found to be directly proportional to solvent accessibility. Since SSTP does not involve the direct excitation of water, which compromises the analysis of protein protons entangled in the breadth of the water resonance, it has an advantage over conventional water-based magnetization transfers. Inclusion of structural restraints derived from SSTP improved both the precision and accuracy of the final protein structures in comparison to those determined by traditional approaches, when using minimal amounts of additional structural data. Furthermore, we show that SSTP can detect weak protein-protein interactions which are unobservable by chemical shift perturbations.

Photochemical reactivity of apical oxygen in KSr(2)Nb(5)O(15) materials for environmental remediation under UV irradiation.

The photocatalytic activity of a series of novel KSr2Nb5O15 materials was studied using the photooxidation of methylene blue as model reaction. The influence of the calcination time upon the crystalline structure and photoactivity was verified. Characterization was performed by XRD, SEM, FTIR, UV-Vis/DR, Helium picnometry, and N2 and CO2 adsorption-desorption isotherms. The diffraction line profile and the refinement of the structural parameters of KSr2Nb5O15 were obtained from the XRD patterns by the Rietveld method. Data showed that samples were photoactive under UV irradiation, regardless the synthesis conditions. However, the calcination time had a clear influence upon the photocatalytic activity of the samples, being more efficient towards the degradation of the dye those obtained at a lower calcination time. Indeed, the sample calcined for 4h showed up to 4 times higher photocatalytic activity than commercial TiO2. Additionally, a correlation between the photocatalytic activity and the displacement of the Nb ion from the central position in the [NbO6] octahedron was found. It is suggested that this fact causes an important polarization of the niobate structure. The apical oxygen in these samples is very reactive and can lead to the formation of superoxoradical anions (O2-) showing that KSr2Nb5O15 can be potentially used in photocatalytic reactions under UV irradiation.

Two cubic phases in kimzeyite garnet from the type locality Magnet Cove, Arkansas.

The crystal structure of an optically anisotropic kimzeyite garnet from Magnet Cove, Arkansas, USA, where it was first discovered, was refined with the Rietveld method, cubic space group, Ia\overline 3 d, and monochromatic [λ = 0.41422 (2) Å] synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. The Rietveld refinement reduced χ2 and overall R(F2) values are 1.840 and 0.0647, respectively. The sample, with the general garnet formula [8]X3[6]Y2[4]Z3[4]O12, contains an intergrowth of two cubic phases that occur initially as oscillatory growth zoning, and patchy intergrowths arise later from fluid-enhanced dissolution and re-precipitation. The two compositions obtained with electron-probe microanalyses (EPMA) are Ca3.00(Zr1.31Ti4+0.46Fe3+0.22Mn3+0.01)∑2[Al0.76Fe3+1.01Si1.23]∑3O12 for phase 1a and Ca2.99(Zr1.48Ti4+0.37Fe3+0.15)∑2[Al0.87Fe3+0.98Si1.15]∑3O12 for phase 1b. The weight percentage, unit-cell parameter (Å), distances (Å), and site occupancy factors (s.o.f.s) for phase 1a are as follows: 42.6 (2)%, a = 12.46553 (3) Å, average 〈X-O〉 = 2.482, Y-O = 2.059 (2), Z-O = 1.761 (2) Å, Ca (X s.o.f.) = 0.960 (4), Zr (Y s.o.f.) = 0.809 (3), and Fe (Z s.o.f.) = 0.623 (2). The corresponding values for phase 1b are 57.4 (2)%, a = 12.47691 (2) Å, average 〈X-O〉 = 2.482, Y-O = 2.062 (1), Z-O = 1.762 (1) Å, Ca (X s.o.f.) = 0.957 (3), Zr (Y s.o.f.) = 0.828 (2) and Fe (Z s.o.f.) = 0.617 (2). The main structural differences between the two phases are in the unit-cell parameter, Δa = 0.01138 Å, Y(s.o.f.), and Y-O distance. Structural mismatch between the two cubic phases in a crystal gives rise to strain-induced optical anisotropy.

Laparoscopic management of recurrent inguinal hernia in childhood.

BACKGROUND: Open repair of recurrent inguinal hernias [RIH] in infancy and childhood is difficult and there is definite risk of damaging the vas deferens and testicular vessels. Laparoscopic repair of RIH has the benefit of avoiding the previous operative site. The aim of this study is to present our experience with laparoscopic repair of RIH either after open or laparoscopic hernia repair with stress on technical refinements to prevent recurrence. PATIENTS AND METHODS: This is a retrospective study of laparoscopic repair of RIH. Records of 38 patients with 42 recurrent hernial defects that have been subjected to laparoscopic inguinal hernia repair [LIHR] for RIH were reviewed and evaluated. The primary outcome measurements of this study include; operative time and recurrence rate. The secondary outcomes include intraoperative and postoperative complications, hydrocele formation and testicular atrophy. RESULTS: In this study 38 children with 42 recurrent hernial defects [4 patients had bilateral recurrent hernia] were operated upon laparoscopically. They were 34 males and 4 females with a mean age of 2.54±1.989years (range=0.58-10.00years). In 35 hernial defects the recurrence developed after open herniotomy, while in 7 hernial defects it occurred after laparoscopic repair. All procedures were completed laparoscopically without any conversion and there were no intraoperative or postoperative complications during this study. Mean operating time was 15±2.3minutes for unilateral and 20±1.7minutes for bilateral inguinal hernia. All patients achieved full recovery and were discharged on the same day of admission. Two patients developed hydroceles that responded well to conservative management. At mean follow-up of 12.7±2months (range=8-38.4months), there was no recurrence, no testicular atrophy. CONCLUSION: Laparoscopic repair of RIH in infancy and childhood is an attractive option that avoids the difficulties of redo surgery in scarred operative field with delicate structures liable to injury even with expert operator.

Heterojunction of Zinc Blende/Wurtzite in Zn1-xCdxS Solid Solution for Efficient Solar Hydrogen Generation: X-ray Absorption/Diffraction Approaches.

In the past decade, inorganic semiconductors have been successfully demonstrated as light absorbers in efficient solar water splitting to generate chemical fuels. Pseudobinary semiconductors Zn1-xCdxS (0≤x≤1) have exhibited a superior photocatalytic reactivity of H2 production from splitting of water by artificial solar irradiation without any metal catalysts. However, most studies had revealed that the extremely high efficiency with an optimal content of Zn1-xCdxS solid solution was determined as a result of elevating the conduction band minimum (CBM) and the width of bandgap. In addition to corresponding band structure and bandgap, the local crystal structure should be taken into account as well to determine its photocatalytic performance. Herein, we demonstrated the correlations between the photocatalytic activity and structural properties that were first studied through synchrotron X-ray diffraction and X-ray absorption spectroscopy. The crystal structure transformed from zinc blende to coexisted phases of major zinc blende and minor wurtzite phases at a critical point. The heterojunction formed by coexistence of zinc blende and wurtzite phases in the Zn1-xCdxS solid solution can significantly improve the separation and migration of photoinduced electron-hole pairs. Besides, X-ray absorption spectra and UV-vis spectra revealed that the bandgap of the Zn0.45Cd0.55S sample extended into the region of visible light because of the incorporation of Cd element in the sample. These results provided a significant progress toward the realization of the photoelectrochemical mechanism in heterojunction between zinc blende and wurtzite phases, which can effectively separate the charge-carriers and further suppress their recombination to enhance the photocatalytic reactivity.

High temperature and composition induced phase transitions in LiZnV1-xAsxO4 phenacites: Crystal structure and Raman spectroscopy studies.

In this work, using techniques of X-ray diffraction and Raman spectroscopy, we report the composition and high-temperature induced phase transition in the system LiZnV1-xAsxO4 (0⩽x⩽1). Both techniques showed that the increase of arsenic amount induced a structural transition from R-3 LiZnVO4 type to LiZnAsO4 type belonging to R3 space group, the transition occurring between x=0.7 and x=0.8. Furthermore, increasing temperature for the compositions (0.8⩽x⩽1) manifests a transition from the LiZnAsO4 structural type with R3 space group to the R-3 LiZnVO4 structural type. For this series, the transition from the space group R3 to the centro-symmetric space group R-3 shows considerable changes in the compositional and temperature dependencies of the bands: spectral positions of all the observed Raman bands exhibit shifts linearly proportional to the temperature increase, with points of shift-rate changes revealing a symmetry change. The Raman-spectra based temperature-composition phase diagram confirms the results obtained using the method of Rietveld refinements, thus showing the R-3 to R3 transition occurring between x=0.7 and 0.8.

Refinements and secondary surgery after flap reconstruction of the traumatized hand.

The traumatized hand often has soft tissue loss requiring flap reconstruction. Before proceeding with flap selection, the need for future refinement and secondary surgery should be taken into consideration. Although muscle flaps may offer better contour, fasciocutaneous flaps allow easier secondary flap elevation. After the initial flap reconstruction, indications for secondary procedures may be managed according to tissue type: bone, joint, tendon, nerve, and soft tissue.

Electron densities by the maximum entropy method (MEM) for various types of prior densities: a case study on three amino acids and a tripeptide.

Dynamic model densities according to Mondal et al. [(2012), Acta Cryst. A68, 568-581] are presented for independent atom models (IAM), IAMs after high-order refinements (IAM-HO), invariom (INV) models and multipole (MP) models of α-glycine, DL-serine, L-alanine and Ala-Tyr-Ala at T ≃ 20 K. Each dynamic model density is used as prior in the calculation of electron density according to the maximum entropy method (MEM). We show that at the bond-critical points (BCPs) of covalent C-C and C-N bonds the IAM-HO and INV priors produce reliable MEM density maps, including reliable values for the density and its Laplacian. The agreement between these MEM density maps and dynamic MP density maps is less good for polar C-O bonds, which is explained by the large spread of values of topological descriptors of C-O bonds in static MP densities. The density and Laplacian at BCPs of hydrogen bonds have similar values in MEM density maps obtained with all four kinds of prior densities. This feature is related to the smaller spatial variation of the densities in these regions, as expressed by small magnitudes of the Laplacians and the densities. It is concluded that the use of the IAM-HO prior instead of the IAM prior leads to improved MEM density maps. This observation shows interesting parallels to MP refinements, where the use of the IAM-HO as an initial model is the accepted procedure for solving MP parameters. A deconvolution of thermal motion and static density that is better than the deconvolution of the IAM appears to be necessary in order to arrive at the best MP models as well as at the best MEM densities.

Aesthetical outcome after breast reconstruction using deep inferior epigastric perforator flap: Personal techniques.

BACKGROUND: Now-a-days, deep inferior epigastric perforator (DIEP) flap breast reconstruction is widespread throughout the world. The aesthetical result is very important in breast reconstruction and its improvement is mandatory for plastic surgeons. MATERIALS AND METHODS: The most frequent problems, we have observed in breast reconstruction with DIEP flap are breast asymmetry in terms of volume and shape, the bulkiness of the inferior lateral quadrant of the new breast, the loss of volume of the upper pole and the lack of projection of the inferior pole. We proposed our personal techniques to improve the aesthetical result in DIEP flap breast reconstruction. Our experience consists of more than 220 DIEP flap breast reconstructions. RESULTS: The methods mentioned for improving the aesthetics of the reconstructed breast reported good results in all cases. CONCLUSION: The aim of our work is to describe our personal techniques in order to correct the mentioned problems and improve the final aesthetical outcome in DIEP flap breast reconstruction.

Powder X-Ray Reference Patterns of Sr2RGaCu2O y (R = Pr, Nd, Sm, Eu, Gd, Dy, Ho, Er, Tm, and Y).

X-Ray Rietveld refinements were conducted on a series of eleven lanthanide phases, Sr2RGaCu2O y (2112 phase, R = Pr, Nd, Sm, Eu, Gd, Dy, Ho, Y, Er, Tm, and Yb) that are structurally related to the high T c superconductor Ba2YCu3O7 (213). In the 2112 structure, instead of square planar Cu-O chains, tetrahedral GaO4 chains were found to run in a zig-zag fashion along the diagonal of the basal 213 ab-direction. Reference powder patterns for these compounds were prepared by using the Rietveld decomposition technique. The unit cell volume of these compounds follows the expected trend of the lanthanide contraction. The lattice parameters range from a = 22.9694(3) Å, b = 5.5587(2) Å, and c = 5.44743(7) Å for R = Pr, to a = 22.8059(2) Å, b = 5.46031(5) Å, and c = 5.37773(5) Å for R = Yb. An electon diffraction study of the Sm- and Er-analogs showed characteristic diffuse streaks along the b-axis, suggesting some disorder within the GaO4 chains.