Fold Type Research Articles

Comparison of filtration efficiency and respiratory resistance of COVID-19 protective masks by multi-national standards

BackgroundFace masks from worldwide satisfy different standards during the COVID-19 pandemic, which led to the public misunderstanding of the concepts.MethodsWe systematically evaluated the quality of face masks provided by different companies according to multi-national standards, including EN 149-2001+A1: 2009, GB 2626-2019 and NIOSH 42 CFR Part 84-2019, focusing particularly on the particulate filtration efficiency (PFE) and respiratory resistance performance.ResultsThree types of masks (planar, folding and cup type masks) were measured based on different standard protocols. The results indicated that the PFE of the mask decreased in sequence of folding mask ≈ cup type mask > planar mask. The respiratory resistance of the masks ranked as follows: cup type mask > folding mask> planar mask. Overall, when PFE was used as the quality indicator, all the masks have a higher chance of meeting criteria of the EN149-2001+A1:2009, followed by the stricter standard set by the GB2626-2019 and NIOSH 42 CFR Part84-2019. Conversely, the respiratory resistance of the masks fulfilled the highest requirement of the EN149-2001+A1:2009 standard, while it is easier to satisfied the standard of GB 2626-2019 and NIOSH 42 CFR Part 84-2019.ConclusionsWe believe that our study provides effective guidance for customers worldwide to choose proper face masks under different epidemic situations.

An exotic microstructured globular state formed by a single multiblock copolymer chain.

In this work, we studied the equilibrium structures formed by a single (AB)k multiblock copolymer chain. Within our model, the interactions between the A-type beads were repulsive and the B-type beads could form pairwise reversible bonds with each other (BB-bonds). Our goal was to investigate how the formation of pairwise reversible bonds between the A-type beads and the B-type beads (AB-bonds) affected the structure of the chain. We observed the formation of well-studied intramolecular micelles when the AB-bonds were absent; however, the chain folding changed dramatically when the formation of the AB-bonds was introduced. In this case, the multiblock copolymer formed a globule, which had a unique heterogeneous checkerboard-like distribution of the contact density. We discovered that contacts of beads of different types (i.e., AB-contacts) occurred much more frequently than contacts of beads of the same type (i.e., AA- and BB-contacts) in these structures. This effect can be explained by a simple model of chemical equilibrium in a two-component fluid of reversibly interacting particles, which can be solved exactly. This novel type of folding can serve as a basic model for any (AB)k multiblock copolymer chain with a non-vanishing attraction between A and B blocks.

Investigation of the conformational space of hydrophobic-polar heteropolymers by gyration tensor based parameters

• Different folding types such as two-state folding, folding through intermediates, as well as metastability, are presented with an effective order parameter for polymers. • Gyration tensor-based analysis does not need any reference state before the simulation as that is the need for the other order parameters which are chosen in other studies in the same content. • Our paper presents the use of very useful parameters to detect conformational phase transitions in polymer chains. In the earlier works related to this aspect presents another order parameter that needs a reference conformation. Multicanonical simulations of hydrophobic-polar heteropolymers were performed with a simple and effective coarse-grained off-lattice model to identify the folding pathways and the topology of the energy landscape with gyration tensor-based parameters. We examined six exemplified sequences of heteropolymers and illustrated three of them which present definitely different folding types such as two-state folding, folding through intermediates, as well as metastability. The major advantage of this study is our chosen ”order” parameter, namely gyration tensor-based analysis, does not require any reference state before the simulation as that is the need for the other order parameters which are chosen in other studies in the same context. Our paper presents the use of very useful parameters to detect conformational phase transitions in polymer chains. Another order parameter that requires a reference conformation is presented in earlier works related to this aspect. This extends the simulation into two steps. With our analysis, there is no need for a global minimum conformation so-called reference state and our simulation will be completed in one step. Furthermore, there is no relative evaluation according to the reference state.

Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase

DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops’ flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pKa of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7–8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure–function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications.

Caustics of Lagrangian homotopy spheres with stably trivial Gauss map

For each positive integer $n$, we give a geometric description of the stably trivial elements of the group $\pi_n U_n/O_n$. In particular, we show that all such elements admit representatives whose tangencies with respect to a fixed Lagrangian plane consist only of folds. By the h-principle for the simplification of caustics, this has the following consequence: if a Lagrangian distribution is stably trivial from the viewpoint of a Lagrangian homotopy sphere, then by an ambient Hamiltonian isotopy one may deform the Lagrangian homotopy sphere so that its tangencies with respect to the Lagrangian distribution are only of fold type. Thus the stable triviality of the Lagrangian distribution, which is a necessary condition for the simplification of caustics to be possible, is also sufficient. We give applications of this result to the arborealization program and to the study of nearby Lagrangian homotopy spheres.

Extensive modelling and quantum chemical study of sterol C-22 desaturase mechanism: A commercially important cytochrome P450 family

CYP450s, first wave biocatalysts and nature’s tool used for catalysing complex reactions like C-H bond hydroxylation, N-dealkylation, N-hydroxylation, O-dealkylation, etc. Engineered CYP450s catalyse new-to-nature carbene and nitrene transfer some of which have no precedent using chemical methods. Due to broad substrate range and immense biocatalytic scope, CYP450s are extensively used in synthesising of active pharmaceutical ingredients (APIs) and drugs. CYP450 desaturase adds double bonds to form mono and poly desaturated sterols. The addition of a double bond at a specific position is conserved within a particular structural fold type of CYP450. Minimal information is currently available on the mechanism of enzyme action of CYP450 desaturase, especially no information is available concerning experimental details on C-22 desaturase. Here, for the first time, we report the structure-function of desaturase and the detailed mechanism of the enzyme using quantum chemical (QC) calculations. The study provides atomistic details from precise near attack conformations of different sterols in the active site of CYP450 desaturase to the active site residues that define substrate specificity. A novel finding on second hydrogen abstraction; QC studies revealed transition states involving hydrogen abstractions. The second hydrogen abstraction takes place in a relay mode moving from carbon to carbon and then to electronegative oxygen attached to haem. Sterol diffusion path was predicted, and its plasticity was studied using extended molecular dynamic simulation experiments. This report is also a source of information for N-terminal modification and its effect on heterologous expression and the role of reductase binding for electron transfer. The results presented here will be valuable for guiding the experimental work to further improve the biocatalytic applicability of CYP450 desaturase enzymes.

Mechanism of folding a strip into isotetrahedra or rectangle dihedra

Any net of an isotetrahedron I (a tetrahedron with all congruent four faces) and a rectangle dihedra RD satisfies the Conway criterion. Does the converse proposition hold? If so, are there practical algorithms for it? The difficult part of the proof of it comes down to the following problem [5], [6]: Find the practical algorithm for folding a parallelogramic strip into I or RD. The process of how to cover a thin rectangular board by a long tape without making gaps or overlaps has been known as a folklore among natives in various places globally [1]. By generalizing the known folklore foldings, this paper gives the practical algorithms to obtain all isotetrahedra and rectangle dihedra into which a strip can be folded. As a result of it, it is also proved that there is no other way to fold a given strip into rectangle dihedra other than the known two types of folklore foldings.

Formation Mechanism and Control Strategy of Edge Seam Defects for Hot Rolling Interstitial‐Free Steel

During the process of hot rolling, seam defects often appear on the edges of the interstitial‐free (IF) steel, which seriously affects product quality and yield. To this end, the macro‐ and micromorphology of edge seam defects are analyzed, their specific characteristics are summarized, and the defect cast slab rolling experiment is conducted. The experiment shows that the pore, crack, and slag inclusion are not the causes of the seam defects. Then, through a combination of theoretical analysis, actual parameters’ detection, and experiments, the formation mechanisms of the seam defects are evidently side folding of the intermediate slab and flipping of the corner metal. The mechanisms of the two types of folds are also described in detail. Finally, in view of the mechanisms, the advantages and disadvantages of control measures are analyzed, and the concave anvil of the slab sizing press is selected at last. To determine the effectiveness of the scheme, a pass experiment is conducted on a slab sizing press at the production site. Results show that the steel coils without slab sizing press generally have seam defects, whereas the coils with a concave anvil slab sizing press do not. The defects are almost totally eliminated.

Graph Coverings for Investigating Non Local Structures in Proteins, Music and Poems

We explore the structural similarities in three different languages, first in the protein language whose primary letters are the amino acids, second in the musical language whose primary letters are the notes, and third in the poetry language whose primary letters are the alphabet. For proteins, the non local (secondary) letters are the types of foldings in space (α-helices, β-sheets, etc.); for music, one is dealing with clear-cut repetition units called musical forms and for poems the structure consists of grammatical forms (names, verbs, etc.). We show in this paper that the mathematics of such secondary structures relies on finitely presented groups fp on r letters, where r counts the number of types of such secondary non local segments. The number of conjugacy classes of a given index (also the number of graph coverings over a base graph) of a group fp is found to be close to the number of conjugacy classes of the same index in the free group Fr−1 on r−1 generators. In a concrete way, we explore the group structure of a variant of the SARS-Cov-2 spike protein and the group structure of apolipoprotein-H, passing from the primary code with amino acids to the secondary structure organizing the foldings. Then, we look at the musical forms employed in the classical and contemporary periods. Finally, we investigate in much detail the group structure of a small poem in prose by Charles Baudelaire and that of the Bateau Ivre by Arthur Rimbaud.

A novel kind of equations linking the quantum dynamics and the classical wave motions based on the catastrophe theory

Considering that the catastrophe theory could describe quantitatively any phase transition process, we adopt the folding and cusp catastrophe types as the potential functions in the Schrödinger equation to attempt to link the quantum dynamics and the classical wave motions. Thus, through the dimensionless analysis a novel kind of partial differential equations is derived out. When the scaling parameter of the novel equation is equal to the Planck's constant, this equation becomes a detailed time-independent Schrödinger equation, from which Bohr correspondence principle can be found. On the other hand, when the scaling parameter tends to zero, this equation could degenerate to the classical Helmholtz equation. Therefore, this novel kind of equations could describe quantitatively the variation process of the wave functions from the macroscopic level to the quantum size.

Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium.

Serine hydroxymethyltransferase (SHMT) is a ubiquitous enzyme belonging to the fold type I or aspartate aminotransferase (AspAT) family of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. Like other PLP-dependent enzymes, SHMT also undergoes the so-called transimination reaction before exhibiting its enzymatic activity. The transimination process constitutes an important pre-step for all PLP-dependent enzymes, where an internal aldimine of the PLP-enzyme complex gets converted to an external aldimine of the substrate-PLP complex at the active site of the enzyme. In case of the transimination reaction involving SHMT, the PLP molecule bound to the active site lysine residue of SHMT (internal aldimine) gets detached from the enzyme by a serine substrate to produce an external aldimine complex, where the PLP is now bound to the serine substrate. In the current study, the free energy surfaces and reaction pathways of different steps of the transimination reaction at the active site of SHMT are investigated by employing hybrid quantum mechanical/molecular mechanical (QM/MM) simulations combined with metadynamics methods of rare event sampling. It is found that the process of transimination involving serine and PLP at the active site of the SHMT enzyme takes place through different elementary steps such as the formation of the first geminal diamine intermediate (GDI1), transfer of a proton from the substrate serine to the phenolic oxygen of PLP, followed by another proton transfer from PLP to the amine nitrogen of lysine with the formation of the second geminal diamine intermediate (GDI2), and finally, detachment of the active site lysine residue from PLP to produce the external aldimine.

N-doped reduced graphene oxide for room-temperature NO gas sensors

In this study, we use nitrogen-doped to improving the gas-sensing properties of reduced graphene oxide. Graphene oxide was prepared according to a modified Hummers’ method and then nitrogen-doped reduced graphene oxide (N-rGO) was synthesized by a hydrothermal method using graphene oxide and NH4OH as precursors. The rGO is flat and smooth with a sheet-like morphology while the N-rGO exhibits folded morphology. This type of folding of the surface morphology can increase the gas sensitivity. The N-rGO and the rGO sensors showed n-type and p-type semiconducting behaviors in ambient conditions, respectively, and were responsive to low concentrations of NO gases (< 1000 ppb) at room temperature. The gas-sensing results showed that the N-rGO sensors could detect NO gas at concentrations as low as 400 ppb. The sensitivity of the N-rGO sensor to 1000 ppb NO (1.7) is much better than that of the rGO sensor (0.012). Compared with pure rGO, N-rGO exhibited a higher sensitivity and excellent reproducibility.

Epithermal gold-bearing sulfide ore deposit Tulallar: Structure, structural geology and mineralization patterns

In the latest decades, the characteristic of geology and mineralization in Somkhito&ndash;Karabakh island&ndash;arc paleosystem undergoes cardinal rethinking. This article describes epithermal gold-bearing sulfide ore deposit Tulallar in the Lesser Caucasus in Azerbaijan. The deposit adjoins a partly eroded volcano-tectonic depression and localizes in the east&ndash;westward striking Upper Jurassic andesite-dacitic and andesite strata more than 500 m thick. In the center, the Tulallar Fault splits the structure into three blocks &mdash; Western, Central and Eastern, which hold the same-name zone of gold-bearing ore lodes and veins. The main concentrators of finely dispersed and free gold are chalcopyrite and pyrite. The essential tectonic structures which govern distribution of the mineralization are the bordering branches of the Tulallar&ndash;Chiragdar&ndash;Toganaly fault. The test deposit is the volcanic epithermal shallow and medium-depth cluster within the structurally isolated wedge-like junction of the regional northwestern and northeastern faults. Based on the revealed localization patterns of the mineralization, the prognostic estimation procedure is developed for different-scale ore potentials. The direct and indirect signs of a mineralization are identified. The type, spatial location and intensity of these signs are assumed as the estimation criteria. Regarding the lithological criterion, these are the volcano-clastic facies and the same-age sub-volcanic Kimmeridgian bodies. The types of folds are considered as different values of folding structures. The same principle is used to differentiate between two types of faulting (strike-slip faults and thrustfaults). The information content of the criteria was assessed by the relative weights found empirically during filed operations, and by the method of analogy.

Mapping the glycosyltransferase fold landscape using interpretable deep learning

Glycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversification of GTs presents a major challenge in mapping the relationships connecting sequence, structure, fold and function using traditional bioinformatics approaches. Here, we present a convolutional neural network with attention (CNN-attention) based deep learning model that leverages simple secondary structure representations generated from primary sequences to provide GT fold prediction with high accuracy. The model learns distinguishing secondary structure features free of primary sequence alignment constraints and is highly interpretable. It delineates sequence and structural features characteristic of individual fold types, while classifying them into distinct clusters that group evolutionarily divergent families based on shared secondary structural features. We further extend our model to classify GT families of unknown folds and variants of known folds. By identifying families that are likely to adopt novel folds such as GT91, GT96 and GT97, our studies expand the GT fold landscape and prioritize targets for future structural studies.

Endo-xylanases from Cohnella sp. AR92 aimed at xylan and arabinoxylan conversion into value-added products.

The genus Cohnella belongs to a group of Gram-positive endospore-forming bacteria within the Paenibacillaceae family. Although most species were described as xylanolytic bacteria, the literature still lacks some key information regarding their repertoire of xylan-degrading enzymes. The whole genome sequence of an isolated xylan-degrading bacterium Cohnella sp. strain AR92 was found to contain five genes encoding putative endo-1,4-β-xylanases, of which four were cloned, expressed, and characterized to better understand the contribution of the individual endo-xylanases to the overall xylanolytic properties of strain AR92. Three of the enzymes, CoXyn10A, CoXyn10C, and CoXyn11A, were shown to be effective at hydrolyzing xylans-derived from agro-industrial, producing oligosaccharides with substrate conversion values of 32.5%, 24.7%, and 10.6%, respectively, using sugarcane bagasse glucuronoarabinoxylan and of 29.9%, 19.1%, and 8.0%, respectively, using wheat bran-derived arabinoxylan. The main reaction products from GH10 enzymes were xylobiose and xylotriose, whereas CoXyn11A produced mostly xylooligosaccharides (XOS) with 2 to 5 units of xylose, often substituted, resulting in potentially prebiotic arabinoxylooligosaccharides (AXOS). The endo-xylanases assay displayed operational features (temperature optima from 49.9 to 50.4°C and pH optima from 6.01 to 6.31) fitting simultaneous xylan utilization. Homology modeling confirmed the typical folds of the GH10 and GH11 enzymes, substrate docking studies allowed the prediction of subsites (- 2 to + 1 in GH10 and - 3 to + 1 in GH11) and identification of residues involved in ligand interactions, supporting the experimental data. Overall, the Cohnella sp. AR92 endo-xylanases presented significant potential for enzymatic conversion of agro-industrial by-products into high-value products.Key points• Cohnella sp. AR92 genome encoded five potential endo-xylanases.• Cohnella sp. AR92 enzymes produced xylooligosaccharides from xylan, with high yields.• GH10 enzymes from Cohnella sp. AR92 are responsible for the production of X2 and X3 oligosaccharides.• GH11 from Cohnella sp. AR92 contributes to the overall xylan degradation by producing substituted oligosaccharides.

The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme.

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

On Fuzzy Fundamental Groups and Fuzzy Folding of Fuzzy Minkowski Space

In this paper, we studied the relations between new types of fuzzy retractions, fuzzy foldings, and fuzzy deformation retractions, on fuzzy fundamental groups of the fuzzy Minkowski space M ˜ 4 . These geometrical transformations are used to give a combinatorial characterization of the fundamental groups of fuzzy submanifolds on M ˜ 4 . Then, the fuzzy fundamental groups of the fuzzy geodesics and the limit fuzzy foldings of M ˜ 4 are presented and obtained. Finally, we proved a sequence of theorems concerning the isomorphism between the fuzzy fundamental group and the fuzzy identity group.

Influence of skin folding types on the efficiency of feed in Groznensky sheep

Influence of skin folding types on the efficiency of feed in Groznensky sheep

High resolution architecture of neotectonic fault zones and post-8-Ma deformations in western Hungary: Observations and neotectonic characteristics of the fault zone at the Eastern Lake Balaton

Lake Balaton (Hungary), the largest lake in Central Europe, formed by the interplay of tectonic and external forces. Its shallow water and young soft sediments together allow to carry out ultra-high resolution reflection seismic surveys to investigate shallow tectonic structures and near surface stratigraphy at depth of ca. 0–30 m. To document neotectonics of the eastern lake basin and its onshore surroundings to the East, we have integrated new ultra-high-resolution seismic-reflection data with deeper penetrating multichannel lake and land seismic profiles, regional geological, geophysical and seismicity data, and geomorphological observations. Combined use of these different data sets provided an opportunity to understand better, how these different types and scales of structural features are linked. In our study area, late middle to late Miocene formations compose a deepening than shallowing sedimentary cycle from terrestrial clastic through offshore marl and deltaic sequence filling up the basin between ca. 8.6 to 7.5 Ma. The deltaic sequence is unconformably overlain by erosional remnants of late Pleistocene fluvial deposits and a mantle of latest Pleistocene to Holocene lake mud. Post-early Miocene deformation history involved two phases; a latest middle to early late Miocene transtension and a dominantly strike-slip regime with locally transpressional or transtensional character. The latter neotectonic phase reactivated the earlier faults and resulted in the propagation of 4 major fault zones across the complete late Miocene sequence. The resulting young faults show segmented geometry, stepovers, and connecting splays. The deformation also induced the modest but penetrative folding of the highest preserved Miocene deltaic sequence. The change in deformation style could happen during the late-stage of delta formation, at ca. 8 Ma although a slightly younger timing is not excluded. Faults imaged offshore apparently do not offset the Holocene lacustrine mud by discrete fractures, but the improved distribution map of recent seismicity and morphotectonic indices along their onshore continuations suggests that several segments of the fault pattern are still active, and might be capable of generating earthquakes. Integration of these different data provided an opportunity to understand better, how these different types and scales of structural features are linked and evolved one after another. • 4 fault zones and 4 types of folds were mapped below Lake Balaton. • Post-8-Ma neotectonic faults are the reactivation of earlier Miocene structures. • The mapped fault pattern serves as an example for the complexity of segmented fault zone. • Faults below the lake continue onland form a coherent structural pattern. • Recent fault activity is suggested by the new seismicity map.

Influence Depth of the Tensile Capacity of Ground Anchors Folding Type in Cohesive Soils

A ground anchor is used to withstand tensile stresses caused by loading both the natural load of the soil and external pressures, then passing the force into the ground. It is generally used to retain tensile form and lateral power structures in constructing walls, foundations, transmission towers, pile, floating docks, mooring dolphin, and offshore buildings. Various ground anchors have been widely used, such as drag, helical, circular-shaped plates, and squares. Especially for massive plate anchors, installation is complicated because it must be excavated first before installation. A challenge in engineering is especially on cohesive soil conditions (soft soil). With these considerations, it is necessary to develop innovative models that are easier to install but still have a large enough tensile capacity. This research analyzes the tensile capacity by using ground anchor folding type to overcome building problems on cohesive soil. The test was tensile capacity with four leaves and a Variation of depth-the performance of this folding type anchor based on the tensile capacity and the anchor. The results obtained in this study; the greater area of the element occurred a significant increase in tensile capacity.