Reverse Alignment Research Articles

Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction

Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.

Reverse Alignment “Mirror Image” Visualization as a Laparoscopic Training Tool Improves Task Performance

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Learning curve of assistants in laparoscopic colorectal surgery: overcoming mirror imaging

Laparoscopic colorectal resection is widely used because of its safety and effectiveness compared with conventional surgery; however, surgical assistants find it difficult to perform this surgery in mirror image. This study aimed to evaluate assistants' learning curves in laparoscopic colorectal surgery. The subjects were three fellows who began their surgical fellowship training at the Center for Colorectal Cancer of the National Cancer Center, Korea, during 2008. We analyzed the data from 145 laparoscopic colorectal surgeries in which these assistants participated. A learning curve was generated for each assistant using the moving average method to assess the execution time and the error rate for grasping tissue. Assistants A, B, and C participated in 50, 45, and 50 laparoscopic colorectal surgeries, respectively. Learning curves indicated that the execution time reached a steady state after 38 cases for Assistant A, 29 cases for Assistant B, and 24 cases for Assistant C. Based on a decline in the error rate, the steady state was reached after approximately 44 cases for Assistant A, 32 cases for Assistant B, and 41 cases for Assistant C. Analysis of the assistants' learning curves suggests that under reverse alignment conditions, assistants require participation in 30-40 cases before gaining surgical competence. These results have implications for training assistants for laparoscopic colorectal surgery.

No so HoT - heads or tails is not able to reliably compare multiple sequence alignments.

Most phylogenetic-tree building applications use multiple sequence alignments as a starting point. A recent meta-level methodology, called Heads or Tails, aims to reveal the quality of multiple sequence alignments by comparing alignments taken in the forward direction with the alignments of the same sequences when the sequences are reversed. Through an examination of a special case for multiple sequence alignment - pair-wise alignments, where an optimal algorithm exists - and the use of a modified global-alignment application, it is shown that the forward and reverse alignments, even when they are the same, do not capture all the possible variations in the alignments and when the forward and reverse alignments differ there may be other alignments that remain unaccounted for. The implication is that comparing just the forward and (biologically irrelevant) reverse alignments is not sufficient to capture the variability in multiple sequence alignments, and the Heads or Tails methodology is therefore not suitable as a method for investigating multiple sequence alignment accuracy. Part of the reason is the inability of individual multiple sequence alignment applications to adequately sample the space of possible alignments. A further implication is that the Hall [Hall, B.G., 2008. Mol. Biol. Evol. 25, 1576-1580] methodology may create optimal synthetic multiple sequence alignments that extant aligners will be unable to completely recover ab initio due to alternative alignments being possible at particular sites. In general, it is shown that more divergent sequences will give rise to an increased number of alternative alignments, so sequence sets with a higher degree of similarity are preferable to sets with lower similarity as the starting point for phylogenetic tree building. © The Willi Hennig Society 2009.

GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events

Homologous genomic sequences between species usually contain different rearrangement events. Whether some specific patterns existed in the breakpoint regions that caused such events to occur is still unclear. To resolve this question, it is necessary to determine the location of breakpoints at the nucleotide level. The availability of sequences near breakpoints would further facilitate the related studies. We thus need a tool that can identify breakpoints and align the neighboring sequences. Although local alignment tools can detect rearrangement events, they only report a set of discontinuous alignments, where the detailed alignments in the breakpoint regions are usually missing. Global alignment tools are even less appropriate for these tasks since most of them are designed to align the conserved regions between sequences in a consistent order, i.e. they do not consider rearrangement events. We propose an effective and efficient pairwise sequence alignment algorithm, called GR-Aligner (Genomic Rearrangement Aligner), which can find breakpoints of rearrangement events by integrating the forward and reverse alignments of the breakpoint regions flanked by homologously rearranged sequences. In addition, GR-Aligner also provides an option to view the alignments of sequences extended to the breakpoints. These outputs provide materials for studying possible evolutionary mechanisms and biological functionalities of the rearrangement.

DNA solution based on sequence alignment to the Minimum Spanning Tree problem

Sequence alignment reveals the relations between the characters in different sequences, and there are the reverse complement relations between the characters in DNA double strand. We introduce sequence alignment to the field of DNA computing, propose the definitions of complement alignment and reverse complement alignment, give a method of computing the scores of complement alignment and reverse complement alignment, and devise a DNA encoding method and the corresponding DNA algorithm for the Minimum Spanning Tree (MST) problem by means of reverse complement alignments. Our work enriches the theory of DNA computing and extends the range of DNA computing to solve optimisation problems.

Reverse-alignment surgical skills assessment

During the course of certain laparoscopic procedures, a surgeon may encounter circumstances where the camera and working instruments are not aligned along the same axis. When the alignment is off by 180 degrees, the laparoscope is pointed directly at the surgeon and a mirror image of the operative field is created. Under reverse alignment conditions, surgeons often become disoriented and task performance may be degraded. The aim of this study is to measure the degree to which reverse alignment conditions impair the performance of operators of varying laparoscopic surgical skill and experience. Nineteen general surgery residents and 3 attending surgeons were tested in a video trainer. A task designed to simulate tack placement during laparoscopic ventral hernia repair was created. Time required to successfully complete this task in both forward and reverse alignment conditions was measured for all participants. For this study, the impact of visual-spatial discordances of angles other than 180 degrees on task performance was not assessed. Data regarding prior laparoscopic case volume and MISTELS scores were collected for each resident. Significant and strong correlations were observed between resident experience and individual MISTELS scores. No significant correlation was found between reverse image times and any other surrogate measure of experience or skill for the residents. All study participants required a significantly longer period of time to complete the simulated tack task in reverse alignment compared to forward alignment conditions. Attendings required 65% more time and resident times increased by 470%. Attendings completed the task significantly faster than residents in reverse alignment conditions. Reverse-alignment surgical skills can be improved with experience, but may require a volume of cases exceeding that encountered in residency training. Reverse image skills are not derivative from surgical skills developed in a video trainer with forward orientation.

Radius Requirements for Trucks on Three-Dimensional Reverse Horizontal Curves with Intermediate Tangents

Minimum radius requirements for reverse horizontal curves are currently based on the design of each arc as a separate simple horizontal curve on flat terrain, with the effects of reverse horizontal curvature and vertical alignment being ignored. This paper establishes minimum radius requirements for trucks on three-dimensional (3-D) reverse horizontal curves with intermediate tangents on the basis of vehicle stability. With vehicle simulation software, vehicle dynamics were recorded for the base case of two-dimensional simple curves and for reverse curves superimposed with different vertical alignments (upgrade, downgrade, crest curve, and sag curve). The simulation was run for two maximum superelevation rates, three design vehicles, and different vertical grades. Two mathematical models were developed for flat and 3-D reverse curves. The models provided the minimum radius of the sharper arc of the reverse curve as a function of design speed, maximum superelevation, ratio of flatter to sharper curve radius, design vehicle, and intermediate tangent length. The results showed that an increase in the minimum radius of existing design guides (ranging from 5% to 27%) was required to compensate for the effects of reverse curvature and vertical alignment. The required increase can be reduced by using longer intermediate tangents. Design requirements for the spiral length of reverse curves are also presented.

Photoinduced anisotropy of second-harmonic generation from azobenzene-modified alkylsiloxane monolayers

Noncontact alignment of liquid crystal displays offers the advantage of reduced contamination and minimal surface charging. This approach also provides a means of reversible alignment after a device has been assembled. With this objective we have synthesized self-assembled monolayers based on dimethylaminoazobenzene units covalently attached to a glass surface by means of a short alkylsiloxane anchor, a derivatized version of methyl red (d-MR). The resulting architecture favors an orientation in which the axis of the azobenzene group should be nearly parallel to the surface with an isotropic azimuthal distribution. Under illumination with polarized light the trans–cis isomerization and subsequent relaxation serves to wiggle the molecule into an orientation perpendicular to the treatment polarization. We have tested this scenario using optical second harmonic generation and supporting optical techniques. We are able to identify a surface order parameter that characterizes the photoalignment of the azobenzene group, and have shown that the treatment illumination promotes the formation of H aggregates of the azobenzene species. We have also demonstrated that the treated d-MR layer successfully aligns a nematic liquid crystal.

Retrofitting to Correct Uplift of Curved Girder Bridge Through: Field Testing and Analysis

The Ramp C bridge at the New York State Thruway interchange with I-287 and New York State Route 17 in Rockland County near the New Jersey state line is a continuous four-span bridge with a reverse horizontal curve alignment. It consists of five steel girders with radial abutments and skewed pier supports (61 degrees). During construction immediately after the girders were erected and the counterweights were poured, at low temperatures, an unanticipated girder uplift occurred at one corner of an end span. Physical testing and analysis were undertaken to investigate this occurrence and to estimate the uplift forces. The data were used to design a tie-down system to correct the uplift problem and thus avoid delays in opening the bridge to traffic.

Methods for improving performance under reverse alignment conditions during endoscopic surgery.

There are times during endoscopic procedures when the surgeon has to operate ahead of the camera/telescope assembly. As a result, the image displayed on the monitor will be an inverted mirror image of the operative field (reverse alignment). The present study addresses the extent of these difficulties and suggests some techniques that may be used to overcome the problem. Eight specialist registrars participated in experiments involving the execution of a simulated dissection task under 12 different imaging conditions. These conditions included normal alignment, reverse alignment, total or partial digital correction of reverse alignment (about the horizontal and vertical axes independently and together), and a simple rotation of the camera through 180 degrees. Normal, reverse, and corrected reverse alignment were also tested with optical axes of 45 degrees and 60 degrees. The endpoints were the task execution and the errors rate. A marked deterioration in execution time was observed when the surgeons worked under reverse alignment rather than under normal viewing (p = 0.036). Significant improvement in execution-time errors rate was found when both the horizontal and vertical axes were digitally corrected simultaneously (p = 0.27) and when the camera was rotated 180 degrees with respect to the telescope during reverse alignment (p = 0.28). The effect on performance produced by reverse alignment of the endoscope and instruments can be overcome by means of digital electronic processing, or simply by turning the camera through 180 degrees.

Synthesis of a series of chiral copolymers with azo groups and investigations of reversible liquid crystalline alignment induced by the LB films of these materials

A series of liquid crystalline copolymers, poly{2-hydroxyethyl methacrylate}-co-{6-[4-(S2-methyl-l-butyloxycarbonylphenylazo)phenoxy]hexyl methacrylate} with an azobenzene moiety as photoreactive mesogenic unit, was prepared and investigated by using DSC, polarized optical microscopy and X-ray diffraction. The results show that these polymers exhibit smectic phases. Z-type Langmuir-Blodgett films of these copolymers were successfully deposited onto calcium fluoride and quartz. Reversible homeotropic and planar liquid crystal alignments were induced by using the photochromism of the LB films of one of the copolymers containing 20.6 mol% of the azo unit.

Reversible alignment change of liquid crystals induced by photochromic molecular films: Properties of azobenzene chromophores covalently attached to silica surfaces

Abstract In connection with the mechanism of reversible alignment change of nematic liquid crystals induced by photoisomerizable azobenzene molecules attached to a quartz surface, a static contact angle measurement was carried out for azo-modified plates before and after UV irradiation. The results were not in line with the so-called Friedel-Creagh-Kmetz rule which claims that the alignment is governed by a mutual relationship between a substrate surface energy and surface tension of a liquid crystal. On the other hand, electronic absorption spectra of the plate demonstrated that the ratio of an absorbance at around 340 nm to that at around 240 nm of the azo-chromophore on the surface is reduced by wetting the surface with a UV-transparent nematic liquid crystal. This reflects that the surface azobenzene units are induced to stand approximately perpendicular to the surface upon contact with the liquid crystal. Further discussion is made concerning the photo-induced homogeneous alignment triggered by a rubbed and azo-modified quartz plate determined by polarized absorption spectroscopy.

Reversible alignment change of liquid crystals induced by photochromic molecular films

Abstract The nematic director alignment in the liquid crystal cell was reversibly regulated by the geometrical isomerization of α-hydrazono- β-keto esters chemically linked on the substrate surface. Two methods for the surface modification were employed successfully. Method I was based on direct modification of substrates with α-hydrazono-β-keto ester units having a silylating group. Cells fabricated with these substrates showed altering reversible liquid crystal alignment through a combination of photoirradiation and heating. In method II, ω-acryloyloxyalkyl α-hydrazono-β-keto ester units were introduced through Michael addition to substrates modified with 3-aminopropyltriethoxysilane. The liquid crystal alignment in this case altered reversibly according to the reversible photoisomerization of the α-hydrazono-β-keto units on the substrates. The results strongly support the observation that a change in molecular shape, due to geometrical isomerization, is responsible for regulating the nematic director a...

Reversible alignment change of liquid crystals induced by photochromic molecular films, 15. Convenient methods to prepare “command surfaces” by surface‐selective modification of thin films of poly(vinyl alcohol) with azobenzene units

AbstractA thin film of poly(vinyl alcohol) (PVA of different saponification degree) coated on a glass plate was subjected to a surface‐selective introduction of azobenzene moieties by treatment with a solution of 4‐(4‐hexylphenylazo) phenoxyacetyl chloride/pyridine or 4‐(4‐hexylphenylazo) phenoxybutanal /ptoluenesulfonic acid. Cells were fabricated by sandwiching a nematic liquid‐crystalline material between two surface‐modified glass plates. Alternating exposure to UV and visible light causes a reversible alignment of the liquid crystal molecules. Rubbing of the surface‐modified PVA resulted in an improved optical quality of the cell and enabled us to construct a photoresponsive twisted nematic cell. The advantages of the present method for preparing “command surfaces” are discussed from a practical point of view.

Modulated photoregulation of liquid crystal alignment by azobenzene Langmuir-Blodgett layers: reversible alignment changes of liquid crystals induced by photochromic molecular films, Part 11

In-plane homogeneous alignment controls of a liquid crystal on photochromic azobenzene (Az) Langmuir-Blodgett layers are investigated. A nematic liquid crystal takes the parallel (planar) alignment with the cis-Az surface. In this mode LC molecules are oriented parallel to the dipping direction when the deposition number is more than 3. Under particular conditions a linearly polarized UV light induces subsequent in-plane reorientation of the LC molecules, the reorientation direction being perpendicular to the polarization plane.

Reversible alignment changes of Liquid Crystals Induced by Photochromic Molecular Films. Part 19. Structural effects of LB molecules on the command-surface-type photocontrols of liquid crystal alignment.

Reversible alignment changes of Liquid Crystals Induced by Photochromic Molecular Films. Part 19. Structural effects of LB molecules on the command-surface-type photocontrols of liquid crystal alignment.

Reversible alignment changes of liquid crystals induced by photochromic molecular films. Part 10. Photoregulation of liquid crystal alignment by Langmuir-Blodgett layers of azobenzene polymers.

Reversible alignment changes of liquid crystals induced by photochromic molecular films. Part 10. Photoregulation of liquid crystal alignment by Langmuir-Blodgett layers of azobenzene polymers.

フォトクロミック分子層による可逆的液晶配向制御

A new type of photoresponsive liquid crystalline cells has been developed. The cells were constructed by putting a nematic liquid crystal between two glass plates modified with azobenzene monolayers, the photoisomerization of which induces reversible alignment change between the homeotropic and parallel modes. Detailed studies revealed that the factors affecting the photoregulation of the alignment involve the molecular structure and occupied area of the azobenzene unit and the coexistence of long alkyl chain. Derivatives of stilbene and α-hydrazono-β-ketoester were found to be also effective for the photoregulation. This suggests that the reversible structural alteration between the rodlike and L-shaped photochromic units plays an essential role in the photoregulation. Discussion was made on the mechanism of the regulation, based on the relationship between the regulation efficiency and the surface energy change and on the spectroscopic alteration of photochromic units upon the contact with liquid crystalline molecules.

Reversible alignment change of nematic liquid crystals by photochromic polymer films

AbstractThe alignment of a nematic liquid crystal (LC) was changed reversibly by a photochromic reaction of vinyl‐polymer films bearing azobenzene (Az) chromophores. Photoisomerization of Az in the polymer films proceeded slower than in solution systems with an irreversible nature, due to a limited free volume of polymers and the presence of Az aggregates. Photoregulative Az films were obtained by two procedures: (i) spin‐coating followed by baking processes: and (ii) adsorption from a LC/polymer mixture onto a lecithin‐coated glass surface. Perpendicular alignment, which is achieved both in the surface Az and in the LC layer, allows a parallel interaction between them and enables the photoregulation of the LC alignment.