Joining Of Segments Research Articles

Geometric mean of probability measures and geodesics of Fisher information metric

AbstractThe space of all probability measures having positive density function on a connected compact smooth manifold M, denoted by , carries the Fisher information metric G. We define the geometric mean of probability measures by the aid of which we investigate information geometry of , equipped with G. We show that a geodesic segment joining arbitrary probability measures μ1 and μ2 is expressed by using the normalized geometric mean of its endpoints. As an application, we show that any two points of can be joined by a unique geodesic. Moreover, we prove that the function ℓ defined by , , , gives the Riemannian distance function on . It is shown that geodesics are all minimal.

Morphological characteristic of malaria vector Anopheles aconitus (Family: Culicidae) revealed by advanced light and scanning electron microscope

Abstract. Supriyomo, Soviana S, Novianto D, Musyaffa MF, Tan S, Hadi UK. 2022. Morphological characteristic of malaria vector Anopheles aconitus (Family: Culicidae) revealed by advanced light and scanning electron microscope. Biodiversitas 23: 3546-3552. Anopheles aconitus (An. aconitus) is one of the primary vectors for malaria in several areas in Indonesia, especially in Java Island. Scanning electron microscope (SEM) is a powerful tool that can differentiate Anopheles spp. Morphology that is difficult to identify by using a light microscope only. The adult of An. aconitus used in this study have been reared in the laboratory. This research is conducted to better understand the Anopheles aconitus' external morphology, such as the head, proboscis, wings, thorax and legs, using advanced light and SEM. Results from an advanced light microscope showed that An. aconitus has palpus with the same length as proboscis with one narrow basal end and two broad distal ends; meanwhile, the apical half of proboscis is pale. Anopheles aconitus has wings with four pale spots on the costa side. Legs are uniformly dark with only very narrow, rather faint pale bands at the joining of segments. Using SEM, we found several types of sensilla trichodea: short-sharp tipped, short-blunt tipped, and long-shaped tipped in antenna, apical proboscis, maxillary palps, abdomen, and legs. Antenna is also covered with microtrichia and sensilla. This research is important for basic necessity in fully understanding and determining of mosquito bionomic due to the development of effective and efficient mosquito vector control strategies.

The role of chromatin loop extrusion in antibody diversification.

Cohesin mediates chromatin loop formation across the genome by extruding chromatin between convergently oriented CTCF-binding elements. Recent studies indicate that cohesin-mediated loop extrusion in developing B cells presents immunoglobulin heavy chain (Igh) variable (V), diversity (D) and joining (J) gene segments to RAG endonuclease through a process referred to as RAG chromatin scanning. RAG initiates V(D)J recombinational joining of these gene segments to generate the large number of different Igh variable region exons that are required for immune responses to diverse pathogens. Antigen-activated mature B cells also use chromatin loop extrusion to mediate the synapsis, breakage and end joining of switch regions flanking Igh constant region exons during class-switch recombination, which allows for the expression of different antibody constant region isotypes that optimize the functions of antigen-specific antibodies to eliminate pathogens. Here, we review recent advances in our understanding of chromatin loop extrusion during V(D)J recombination and class-switch recombination at the Igh locus.

Автоматизированное выявление зарастания сельскохозяйственных угодий по спутниковым данным WorldView и Sentinel-2

The author considers the possibility of areas overgrowing automated determination in agricultural territory to reduce the time required to perform tasks of identifying disturbed lands and decrease the human factor influencing the result. The methodology is based on a system of converting the initial remote sensing data into a segmented image. The purpose is to achieve the highest reliability of percentage at further uncontrolled classification. The initial data is that of space survey with high and medium spatial resolution, geometric and atmospheric correction and vector boundaries of agricultural fields. The author applies the watershed method to the original images to increase the reliability of the final result. The Sobel operator is used as preprocessing method to create a gradient image. Further joining of adjacent homogeneous segments together is carried out using the Full Lambda Schedule method. The segmented image is classified through the k-means clustering technique. Materials from WorldView-3 and Sentinel-2 satellites agricultural territories in the Republic of Kalmykia and Kaluga oblast were used. The classification result is analyzed and on its basis an overgrowth vector mask of agricultural fields is created.

Method for Segmentation and Hybrid Joining of Additive Manufactured Segments in Prototyping Using the Example of Trim Parts

Rapid prototyping has become increasingly popular over the past years. However, its application is heavily confined to a part size that fits the small build volume of additive machines. This paper presents a universal design method to overcome this limitation while preserving the economic advantages of rapid prototyping over conventional processes. It segments large, thin-walled parts and joins the segments. The method aims to produce an assembly with minimal loss to the performance and characteristics of a solid part. Based on a set of requirements, a universal segmentation approach and a novel hybrid joint design combining adhesive bonding and press fitting are developed. This design allows for the force transmission, positioning, and assembly of the segments adaptive to their individual geometry. The method is tailored to fused deposition modeling (FDM) by minimizing the need for support structures and actively compensating for manufacturing tolerances. While a universal application cannot be guaranteed, the adaptive design was proven for a variety of complex geometries. Using automotive trim parts as an example, the usability, benefits, and novelty of the design method is presented. The method itself shows a high potential to overcome the build volume limitation for thin-walled parts in an economic manner.

Vectorial crystallization problems and collective behavior.

We propose and analyze a class of vectorial crystallization problems, with applications to crystallization of anisotropic molecules and collective behavior such as birds flocking and fish schooling. We focus on two-dimensional systems of "oriented" particles: Admissible configurations are represented by vectorial empirical measures with density in [Formula: see text]. We endow such configurations with a graph structure, where the bonds represent the "convenient" interactions between particles, and the proposed variational principle consists in maximizing their number. The class of bonds is determined by hard sphere type pairwise potentials, depending both on the distance between the particles and on the angles between the segment joining two particles and their orientations, through threshold criteria. Different ground states emerge by tuning the angular dependence in the potential, mimicking ducklings swimming in a row formation and predicting as well, for some specific values of the angular parameter, the so-called diamond formation in fish schooling.

Shape Accuracy and Surface Quality of Additively Manufactured, Optimized, Patient-Specific Bone Plates

Abstract Powder-based additive manufacturing technologies such as powder bed fusion (PBF) using a laser beam (PBF-LB) and PBF using an electron beam (PBF-EB) allow the manufacturing of complex, patient-specific implants from titanium alloys at appropriate manufacturing expenses and thus production cost. To meet medical quality requirements, mechanical post-treatment (e.g., grinding and polishing) is often required. However, different medical applications require specific quality characteristics. It is therefore necessary to assess the fulfillment of the requirements for each case individually with regard to the manufacturing technologies. This study investigated the potential of the two mentioned additive manufacturing technologies for manufacturing patient-specific, topology-optimized bone plates that are used for osteosynthesis (the joining of bone segments) in the reconstruction of the mandible (lower jaw). Identical individualized implants were manufactured and subsequently treated with established industrial processes and examined according to medical quality requirements. Crucial quality requirements for this medical application are the shape accuracy (for exact bone positioning and even load transmission) as well as the surface quality (to enhance fatigue strength and prevent bone ingrowth in view of the subsequent easy removal of the plates). The machining of the implants is shown in comparison to distinguish the two manufacturing processes from established procedures.

An Enhanced Planar Linked Segment Model for Predicting Lumbar Spine Loads during Symmetric Lifting Tasks

The present technical note aimed at enriching the planar linked segment model originally proposed by Chaffin with the prediction of the moment arm and of the orientation of the line of action of the back extensor muscles during symmetric lifting tasks. The prediction equations proposed by van Dieen and de Looze for their single equivalent muscle model were used for such a purpose. Their prediction was based on the thorax-to-pelvis flexion angle as computed from 3D video-based motion capture. In order to make these prediction equations compliant with a two-dimensional analysis, the planar angle formed by the segment joining L5/S1 to the shoulder with the longitudinal axis of the pelvis was introduced. This newly computed planar trunk flexion angle was used to feed van Dieen and de Looze’s equations, comparing the results with the original model. A full-body Plug-in-Gait model relative to 10 subjects performing manual lifting activities using a stoop and a squat technique was used for model validation. A strong association was found between the proposed planar trunk flexion angle and that used by van Dieen and de Looze (r = 0.970). A strong association and a high level of agreement were found between the back extensor muscle moment arm (r = 0.965; bias < 0.001 m; upper limit of agreement (LOA) = 0.002 m; lower LOA < 0.001 m) and the orientation of the line of action (r = 0.970; bias = 2.8°; upper LOA = 5.3°; lower LOA = 0.2°) as computed using the two methods. For both the considered variables, the prediction error fell within the model sensitivity.

SLAAM: Simultaneous Localization and Additive Manufacturing

This article presents a viable approach to mobile 3-D printing in which a large object is printed in segments. The printer's motion between printing each segment is localized precisely using the novel procedure of simultaneous localization and additive manufacturing (SLAAM), enabling the joining of subsequent segments while also maintaining overall geometric compliance of the printed part. SLAAM achieves sub-mm accuracy on objects over 400 mm long. SLAAM demonstrates the importance of fusing local (3-D scanner), and global (total-station range finder) sensing, and of maintaining, and updating estimates of the printed part geometry in a global frame. A six-parameter representation for a printed object's planar surfaces, consisting of the plane's normal vector, and a 3-D point on the planar patch itself, demonstrates good performance even in the presence of high odometry error.

Dynamics of heavy chain junctional length biases in antibody repertoires

Antibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 and junctional segment length distributions are biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naive and antigen experienced B cell compartments but not in nonproductive recombination products, indicating B cell selection as a major driver of these biases. Our findings reveal biases in the antibody CDR H3 diversity landscape shaped by VH, VL, and JH germline segment use during naive and antigen-experienced repertoire selection.

Robotinė pieloplastika: klinikinio atvejo analizė

[straipsnis ir santrauka lietuvių kalba; santrauka anglų kalba]
 Dėl geresnių operacinių ir pooperacinių rezultatų urologai vis dažniau atlieka minimaliai invazyvias operacijas. Robotinė pieloplastika – vienas iš metodų, kuris palengvina pielourterinio segmento susiuvimą. Ši operacija mažiau vargina operuojantį gydytoją, trumpėja operacijos ir hospitalizacijos laikas.
 2019 m. sausio 4 d. Klaipėdos universitetinėje ligoninėje atlikta pirmoji robotinė (Senhance Transenterixsistema) pieloplastika. Operuota 61 m. pacientė, turėjusi sunkių gretutinių ligų. Operacinis ir pooperacinis periodai praėjo be komplikacijų, ketvirtą parą pacientė išrašyta į namus. Po dviejų mėnesių pacientė kliniškai nusiskundimų neturėjo, atlikus KT tyrimą, nustatyta regresuojanti hydronefrozė po robotinės pieloplastikos.
 Įvertinus gautus rezultatus, galima teigti, kad robotinė pieloplastika yra minimaliai invazyvus, saugus ir efektyvus chirurginis metodas, išsiskiriantis labai greita paciento reabilitacija.

Intracellular pairing of TCRα and TCRβ mRNA at the single-cell level using DNA Origami

Abstract T cell receptors (TCRαβ) are heterodimeric proteins that recognize MHC:peptide ligands. Coding sequences of TCRαβ is determined by semi-random and imprecise joining of variable, diversity, and joining gene segments. Complementarity determining region 3 (CDR3) spans the joint between these segments and typically makes the most contact with peptide during TCR recognition, largely determining specificity. A problem in identifying TCR from cells for clinical applications has been development of high-throughput methods for obtaining CDR3 sequence information from TCRαβ pairs from individual cells. We developed novel DNA origami nanostructures to simultaneously capture TCRαβ mRNA from single cells. T cells are transfected with the origami, and TCRαβ mRNA are co-captured onto bowtie-integral probes. Individual TCR sequences are then reverse transcribed and appended to origami-specific unique bowtie oligonucleotide barcodes that can be matched in downstream next-generation high-throughput sequencing. We have validated this approach using P14 TCR transgenic T cells, expressing known TCRαβ sequences. Following the synthesis of DNA origami with TCRα and TCRβ capture probes, transfection of P14 CD8+ T cells with the scaffold resulted in the specific capture and amplification of TCR sequences. Validation using Sanger sequencing confirmed capture of barcoded TCRα and TCRβ CDR3 sequences. We have developed an approach to single cell analysis of multiple mRNA species. Using a custom bowtie dual-barcoding system, we captured and re-isolated barcoded TCR sequences from individual cells. Although our focus is on the TCR repertoire, this technology is highly adaptable and can capture sequence information of any two genes of interest.

On some new length problem for analytic functions

Let $\mathcal{H}$ denote the class of analytic functions in the unit disk $|z|<1$. Let $C(r,f)$ be the closed curve which is the image of the circle $|z|=r<1$ under the mapping $w=f(z)\in\mathcal{H}$, $L(r,f)$ the length of $C(r,f)$ and let $A(r,f)$ be the area enclosed by $C(r,f)$. Let $l(re^{i\theta},f)$ be the length of the image curve of the line segment joining $re^{i\theta}$ and $re^{i(\theta+\pi)}$ under the mapping $w=f(z)$ and let $l(r,f)=\max_{0\leq\theta 2 \pi}l(re^{i\theta},f)$. We find upper bound for $l(r,f)$ for $f(z)$ in some known classes of functions. Moreover, we prove that $l(r,f)=\mathcal{O}\left( \log\frac{1}{1-r} \right)$ and that $L(r,f)=\mathcal{O}\left\{ A(r,f)\log \frac{1}{1-r} \right\}^{1/2}$ as $r\to 1$ under weaker assumptions on $f(z)$ than some previous results of this type.

Modelling of joining route segments of different curvature

The paper presents a new general method of modelling route segments curvature using differential equations. The method enables joining of route segments of different curvature. Transitional curves of linear and nonlinear curvatures have been identified in the case of joining two circular arcs by S-shaped and C-oval transitions. The obtained S-shaped curves have been compared to the cubic C-Bezier curves and to the Pythagorean hodograph quantic Bezier curve using the Lateral Change of Acceleration diagram and the dynamic model. The analysis of dynamic properties has showed an advantage of the obtained transition curve of nonlinear curvature over Bezier curves.

Insecurity is generic in a conformal class of Riemannian metrics

A pair of points x, y in a Riemannian manifold (M,g) is said to be secure if there exists a finite set of points intercepting every geodesic segment joining x to y. Given any conformal equivalence class C of Riemannian metrics on a closed manifold M of dimension at least two and given any pair of points x, y in M, there exists a dense Gδ set C′⊂C such that x and y are not secure for every metric g in C′.

Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia

Immunoglobulins (Ig) are produced by B lymphocytes as secreted antibodies or as part of the B-cell receptor. There is tremendous diversity of potential Ig transcripts (>1 × 10(12)) as a result of hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments into a complete transcript, and the process of somatic hypermutation at individual nucleotides. This recombination and mutation process takes place in the maturing B cell and is responsible for the diversity of potential epitope recognition. Cancers arising from mature B cells are characterized by clonal production of Ig heavy (IGH@) and light chain transcripts, although whether the sequence has undergone somatic hypermutation is dependent on the maturation stage at which the neoplastic clone arose. Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults and arises from a mature B cell with either mutated or unmutated IGH@ transcripts, the latter having worse prognosis and the assessment of which is routinely performed in the clinic. Currently, IGHV mutation status is assessed by Sanger sequencing and comparing the transcript to known germ-line genes. In this paper, we demonstrate that complete IGH@ V-D-J sequences can be computed from unselected RNA-seq reads with results equal or superior to the clinical procedure: in the only discordant case, the clinical transcript was out-of-frame. Therefore, a single RNA-seq assay can simultaneously yield gene expression profile, SNP and mutation information, as well as IGHV mutation status, and may one day be performed as a general test to capture multidimensional clinically relevant data in CLL.

Crystal structure of the V(D)J recombinase RAG1-RAG2.

V(D)J recombination in the vertebrate immune system generates a highly diverse population of immunoglobulins and T-cell receptors by combinatorial joining of segments of coding DNA. The RAG1-RAG2 protein complex initiates this site-specific recombination by cutting DNA at specific sites flanking the coding segments. Here we report the crystal structure of the mouse RAG1-RAG2 complex at 3.2Å resolution. The 230-kilodalton RAG1-RAG2 heterotetramer is 'Y-shaped', with the amino-terminal domains of the two RAG1 chains forming an intertwined stalk. Each RAG1-RAG2 heterodimer composes one arm of the 'Y', with the active site in the middle and RAG2 at its tip. The RAG1-RAG2 structure rationalizes more than 60 mutations identified in immunodeficient patients, as well as a large body of genetic and biochemical data. The architectural similarity between RAG1 and the hairpin-forming transposases Hermes and Tn5 suggests the evolutionary conservation of these DNA rearrangements.

Abstract 12625: Mechanical Shear Stress Restores Mitochondrial Cytoarchitecture in Human Endothelial Cells Exposed to Angiotensin II by Modulating Activity of the Fission-Inducing Protein Dynamin Related Protein 1

Background: The mitochondria exist in a state of balance between fission (fragmentation) and fusion (joining of mitochondrial segments). Disease is characterized by excessive fission, leading to an overproduction of mitochondrial reactive oxygen species (ROS) which mediate pathological changes in vascular endothelium. Dynamin-related protein-1 (DRP-1) is the primary mediator of mitochondrial fission. The therapeutic benefit of exercise is largely due to increased endothelial shear; however the effects of shear stress on DRP-1 expression and mitochondrial structure are unknown. Hypothesis: Shear stress reduces mitochondrial fission in cultured human umbilical vein endothelial cells (HUVECs) exposed to the fission-inducing stimulus angiotensin II (ANG II) by reducing DRP-1 expression and activity. Methods: HUVECs were treated with MitoRFP for 24 hours to fluorescently label the mitochondria, then were exposed to ANG II (10 pM; 4 hours), fixed, and 25 random cells/group were imaged with a confocal microscope. Separate groups of cells were sheared (15 dyn/cm2; 24 hours) immediately following ANG II exposure using the Ibidi Pump System. To quantify mitochondrial fission, images were converted to binary color and ImageJ was used to count non-contiguous mitochondrial fragments. This value was divided by the number of pixels in the mitochondrial network and multiplied by 1000 to yield a Mitochondrial Fragmentation Index (MFI). Total DRP-1 expression and phosphorylation of the S616 activator and S637 suppressor sites were analyzed by Western blot. Results: ANG II increased MFI (1.13±0.25 vs. 0.75±0.06), DRP-1 expression (+48%) and phosphorylation of the S616 activator site (+141%; p&lt;0.05 for all) compared to static controls. Conversely, ANG II-treated cells sheared for 24 hours showed reduced mitochondrial fission (MFI = 0.50 vs. 0.75±0.06), DRP-1 expression (-24%) and phosphorylation at S616 (-11%) compared to control. ANG II treated cells exposed to shear also showed a robust increase (+528%) in phosphorylation of the S637 suppressor site of DRP-1. Conclusions: High shear stress restores mitochondrial network integrity in HUVECs exposed to ANG II, suggesting exercise may promote vascular health by modulating mitochondrial fission.

On Locally Gabriel Geometric Graphs

Let \(P\) be a set of \(n\) points in the plane. A geometric graph \(G\) on \(P\) is said to be locally Gabriel if for every edge \((u,v)\) in \(G\), the Euclidean disk with the segment joining \(u\) and \(v\) as diameter does not contain any points of \(P\) that are neighbors of \(u\) or \(v\) in \(G\). A locally Gabriel graph(LGG) is a generalization of Gabriel graph and is motivated by applications in wireless networks. Unlike a Gabriel graph, there is no unique LGG on a given point set since no edge in a LGG is necessarily included or excluded. Thus the edge set of the graph can be customized to optimize certain network parameters depending on the application. The unit distance graph(UDG), introduced by Erdos, is also a LGG. In this paper, we show the following combinatorial bounds on edge complexity and independent sets of LGG: (i) For any \(n\), there exists LGG with \(\Omega (n^{5/4})\) edges. This improves upon the previous best bound of \(\Omega (n^{1+\frac{1}{\log \log n}})\). (ii) For various subclasses of convex point sets, we show tight linear bounds on the maximum edge complexity of LGG. (iii) For any LGG on any \(n\) point set, there exists an independent set of size \(\Omega (\sqrt{n}\log n)\).

DNA origami: single cell analysis of T cell receptors without single cell sorting. (LYM7P.719)

Abstract The immune system must be able to recognize virtually any pathogen (diversity) while maintaining enough cells specific for each pathogen in order to mount an effective response (protection). T cells generate diversity by imprecise joining of gene segments to generate alpha/beta heterodimeric receptors. Linking sequence information for TCRα and TCRβ from individual cells has been problematic due to the cost of single cell sorting and inadequate molecular approaches for linking mRNA encoding these proteins. We have developed novel DNA origami nanostructures to capture and protect both TCRα and TCRβ mRNA from individual cells, which can then be physically linked via a unique dual-primed reverse-transcription and ligation reaction to generate single amplicons containing both TCR from individual cells for use in next generation sequencing. We have demonstrated high efficiency transfection and recovery of DNA origami, optimized methods for purification with bound TCR mRNA, and validated this approach with transgenic T cells expressing a known TCR sequence. Surprisingly, we find that &amp;lt;1% of TCR are shared even between genetically identical individuals, challenging the idea of “public” TCR. This approach is directly amenable to single cell analysis of other immune receptors (or other species) by relatively simple modifications of the origami sequences, and could be applied to virtually any heterogeneous cell population for which sequence information on any two genes is required.