Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal Sequence Alignment and Its Relationship with Phylogeny

The main motivation for predicting functions of hundreds of thousands of genes and proteins found across genomes and proteomes is variations within a family of related nucleic acid or protein sequences that provide an unreliable source of information for evolutionary biology. Protein molecules are more diverse in structure and function than any other kind of molecule. Then if nucleic acid sequences undergo mutations, insertions, crossing-over and some another changes, these variations have a direct effect on the coded protein molecules (Fitch, 1970; Pearson et al., 1997). If a protein sequence is present in many different organisms or be conserved along evolution, it is predicted that it might have a similar function in all the organisms. Two molecules of related function usually have similar sequences reciprocally two molecules of similar sequence usually have related functions (Dardel, 2006). The objective of bioinformatics is to detect such similarities, using computer methods to draw biological conclusions. Collecting available wealth of sequence information, help to track ancient genes and back trough the tree of life then to discover new organisms based on their sequences (Fitch, 1966). Searching diverse genes may show different evolutionary histories that reflecting transfers of genetic material between species. If we recognize the function and/or structure of a member of an evolutionary family then we can predict the function of all the other members and even identify the important functional groups. For this, we need to identify which proteins are belonging to the same family and then distinguish proteins that are evolved from the same ancestor after a set of accepted mutation events. Such proteins have amino acid sequences that are likely to be more similar than expected for unrelated protein sequences. When two or more than two sequences share a common evolutionary ancestor they called homologous (Fitch, 1970). There is no homology degree, sequences are either homologues or not (Reeck et al., 1987; Tautz, 1998). These types of proteins almost always share a significantly related treedimentional structure. An example for very similar structures which is determined by x-ray crystallography is RBP and β-lactoglobulin (Fig. 1). Once the homology between some related sequences is inferred, identity and similarity are the quantities for describing the relatedness of sequences. In one type of homology, two sequences may be homologous but without sharing statistically significant identity. In general, three dimensional structures differ much more slowly than amino acid identity between two proteins (Chothia & Lesk,
Within-Family Analysis of Interpregnancy Interval and Adverse Birth Outcomes.

OBJECTIVE To examine associations among interpregnancy interval, the duration from the preceding birth to the conception of the next-born index child, and adverse birth outcomes using designs that adjust for measured and unmeasured factors. METHODS In this prospective cohort study, we used population-based Swedish registries from 1973 to 2009 to estimate the associations between interpregnancy interval (referent 18-23 months) and adverse birth outcomes (ie, preterm birth [less than 37 weeks of gestation], low birth weight [LBW; less than 2,500 g], small for gestational age [SGA; greater than 2 SDs below average weight for gestational age]). Analyses included cousin and sibling comparisons and postbirth intervals (ie, the interval between secondborn and thirdborn offspring predicting secondborn outcomes) to address unmeasured familial confounding. RESULTS Traditional cohort-wide analyses showed higher odds of preterm birth (adjusted odds ratio [OR] 1.51, 99% CI 1.39-1.63, 5.99% preterm births]) and LBW (adjusted OR 1.25, 99% CI 1.13-1.39, 3.32% LBW) after a short interpregnancy interval (0-5 months) compared with offspring born after an interpregnancy interval of 18-23 months (3.21% preterm births, 1.92% LBW). Except for preterm birth (adjusted OR 1.72, 99% CI 1.26-2.35), associations were attenuated in cousin comparisons. A small association between a short interpregnancy interval and preterm birth remained in sibling comparisons (adjusted OR 1.22, 99% CI 1.11-1.35), but associations with LBW (adjusted OR 0.83, 99% CI 0.74-0.94) and SGA (adjusted OR 0.74, 99% CI 0.64-0.85) reversed direction. For pregnancy intervals of 60 months or more, odds of preterm birth (adjusted OR 1.51, 99% CI 1.43-1.60, 5.07% preterm births), LBW (adjusted OR 1.61, 99% CI 1.50-1.73, 3.43% low-birth-weight births), and SGA (adjusted OR 1.54, 99% CI 1.42-1.66, 2.49% SGA births) were also higher when compared with the reference interval (1.53% SGA). Associations between long interpregnancy interval and adverse birth outcomes remained through cousin and sibling comparisons. Postbirth interval analyses showed familial confounding is present for short interpregnancy intervals, but supported independent associations for long interpregnancy intervals. CONCLUSION Familial confounding explains most of the association between a short interpregnancy interval and adverse birth outcomes, whereas associations with long interpregnancy intervals were independent of measured and unmeasured factors.
The C. elegans PRMT-3 possesses a type III protein arginine methyltransferase activity

Protein arginine methylation is a common post-translational modification in eukaryotes that is catalyzed by a family of the protein arginine methyltransferases (PRMTs). PRMTs are classified into three types: type I and type II add asymmetrically and symmetrically dimethyl groups to arginine, respectively, while type III adds solely monomethyl group to arginine. However, although the enzymatic activity of type I and type II PRMTs have been reported, the substrate specificity and the methylation activity of type III PRMTs still remains unknown. Here, we report the characterization of Caenorhabditis elegans PRMT-2 and PRMT-3, both of which are highly homologous to human PRMT7. We find that these two PRMTs can bind to S-adenosyl methionine (SAM), but only PRMT-3 has methyltransferase activity for histone H2A depending on its SAM-binding domain. Importantly, thin-layer chromatographic analysis demonstrates that PRMT-3 catalyzes the formation of monomethylated, but not dimethylated arginine. Our study thus identifies the first type III PRMT in C. elegans and provides a means to elucidate the physiological significance of arginine monomethylation in multicellular organisms.
Developing New Media Credibility Scale: A Multidimensional Perspective

The main purposes of this study are to develop a scale that reflects emerging theoretical understandings of new media credibility, based on the evolution of credibility studies in western researches, identification of the determinants of credibility in the media and its components by comparing traditional and new media credibility scales and building accumulative scale to test new media credibility. This approach was built on western researches using conceptualizations of media credibility, which focuses on four principal components: Source (journalist), message (article), medium (newspaper, radio, TV, web, etc.), and organization (owner of the medium), and adding user and cultural context as key components to assess new media credibility in particular. This study’s value lies in its contribution to the conceptualization and development of new media credibility through the creation of a theoretical measurement tool. Future studies should explore this scale to test new media credibility, which represents a promising new approach in the efforts to define and measure credibility of all media types. Keywords—Credibility scale, media credibility components, new media credibility scale, scale development.
The Reciprocal Relationship Between Alliance and Symptom Improvement Across the Treatment of Childhood Anxiety

This study examined changes in the therapeutic alliance and in self-reported anxiety over the course of 16 weeks of manual-based family treatment for child anxiety disorders. Eighty-six children (51.3% female; aged 7.15–14.44; 86.2% Caucasian, 14.8% minority) with a principal diagnosis of separation anxiety disorder, generalized anxiety disorder, and/or social phobia, and their parents, received family treatment for anxiety disorders in youth. Child, therapist, and parent ratings of therapeutic alliance and child ratings of state anxiety were measured each session. Latent difference score growth modeling investigated the interacting relationship. Therapeutic alliance change, as rated by the mother and by the therapist, was a significant predictor (medium effect) of latter change in child anxiety (with greater therapeutic alliance leading to later reduction in anxiety). However, changes in child-reported anxiety also predicted latter change in father- and therapist-reported alliance (small-to-medium effect). Prospective relationships between child-reported therapeutic alliance and child-reported symptom improvement were not significant. Results provide partial support for a reciprocal model in which therapeutic alliance improves outcome, and anxiety reduction improves therapeutic alliance.
Off-the-Record Secure Chat Room

Group Off-the-Record (GOTR) (Bian et al., 2007) was proposed to address the privacy protection concerns in online chat room systems. It extended the original two-party OTR protocol to support more users while preserving the same security properties. A literature survey of different Diffie-Hellman (D-H) conference key implementations will be given to justify that in an application like a chat room, the virtual server approach is truly the most efficient way to establish a private communication environment among a group of people. However, GOTR’s virtual server approach raises a trustworthiness concern of the chosen chair member. Since the chair member has full control over all encryption keys, there is no constraint to prevent him / her from altering the messages while relaying them. In this paper, we present a study of the GOTR protocol and a solution to the virtual server’s trustworthiness problem via employing an additional MD5 integrity check mechanism. Having such an algorithm, makes the GOTR protocol more secure, in that, it gives the other chat members an opportunity to be aware of any potential changes made by the chair member.
Optical detection in microfluidic systems

Optical detection schemes continue to be favoured for measurements in microfluidic systems. A selection of the latest progress mainly within the last two years is critically reviewed. Emphasis is on integrated solutions, such as planar waveguides, coupling schemes to the outside world, evanescent‐wave based detectors and the field of optofluidics. The perspectives and limitations of the different solutions are discussed in terms of analytical performance and fabrication costs. There has been an increased focus on cheap solutions in polymer materials that are amenable for mass production in order to ease commercialisation of the devices. This work will hopefully result in more commercial products that benefit from integrated optics, because the impact on commercial devices so far has been modest.
Dynamic Simulation of Virtual Objects for Augmented Reality Applications. Development of an Augmented Reality Chess

Department of Electrical and Computer Engineering Electrical and Computer Engineering by Marios-Fotios Bikos In order to enhance immersion in augmented reality systems, solutions must not only present a realistic visual rendering of the virtual objects, but also allow natural hand interactions. The main goal of this project was to utilize and introduce advanced techniques for the superimposition and manipulation of virtual objects over the view of the real world for mixed reality simulations. In this work, a board of markers was used for computing the camera pose seamlessly and a pinch gesture detection algorithm was implemented, employing users thumb and forefinger to interact with the virtual content, using an RGB-D camera. Ultimately, a Mixed Reality Chess was developed, focused on providing an immersive experience to users, so that they are able to manipulate virtual chess pieces in front of a real table and play against a chess engine.
A Continuous Culture System for Assessing Microbial Activities in the Piezosphere

ABSTRACT Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere.
Modeling of Transmission Distortion for Multi-View Video in Packet Lossy Networks

In this paper, a mathematical model is proposed to estimate the distortion caused by random packet losses for multi-view video transmission. Based on the study of multi-view video coding, the proposed model takes into account the disparity/motion compensation which relates the channel-induced distortion in the current frame with that in the previous frame or the adjacent view, and allows for any motion-compensated and disparity-compensated concealment method at the decoder. Comparative studies between the modeled and simulated distortion results demonstrates that the proposed model is able to estimate the transmission distortion of multi-view video with high accuracy.
Study & Analysis of Dynamic Routing Protocols in real time for Optimal Resource Utilization

Optimal selection of a Dynamic Routing Protocol plays a significant role in impacting the performance and resource utilization of a networking device. The suitability of the protocol is highly dependent in-terms of bandwidth usage and ability to manage increasing number of entries in the routing table. In this paper, three well-known dynamic routing protocols such as i)Routing Information Protocol (RIPv2), ii) Enhanced Interior Gateway Routing Protocol (EIGRP) and iii) Open shortest Path First protocol (OSPFv2) are studied and analyzed based on the bandwidth used during convergence, using real-time networking devices. In addition to that, testing their unequal-cost, load balancing capability in order to address the issue of choosing the optimal routing protocol based on the network specifications/requirements is also carried out.
Efficient partitioning of parameterized 45-degree polygons with mixed ILP

Partitioning parameterized polygons is an essential process in a proposed layout-aware analog integrated circuit design flow. To deal with constraints associated with parameterized polygons, constraint programming (CP) technologies have been used in a previous partitioning algorithm. Although CP solvers are capable of coping with complex constraints, CP-based partitioning processes can be very time-consuming. In this paper, we propose the use of mixed integer linear programming (MILP) solvers in the partitioning of parameterized 45-degree polygons. Experimental results show that more than 150X speedup can be achieved for partitioning parameterized polygons containing very complex constraints.
Direct Positioning with Channel Database Assistance

When we have knowledge of the positions of nearby walls and buildings, estimating the source location becomes a very efficient way of characterizing and estimating a radio channel. We consider localization performance with and without this wall knowledge. We treat the multipath channel as a set of 'virtual receivers' whose positions can be pre-stored in a channel database. Using wall knowledge, we develop a direct positioning MUSIC algorithm that treats the wall reflection parameter as a nuisance variable. We compare this to a classic MVDR direct positioning algorithm that lacks wall knowledge. In a simple scenario, we find that lack of wall knowledge can increase location error by 7-100x, depending on the number of antennas, SNR, and true reflection parameter. Interestingly, as the number of antennas increases, the value of wall knowledge decreases.
Skill Level Evaluation of Motion Curved Surface Character

The skill teaching/succession method is not quantitative but qualitative, which is abstract oral or gesture expression. Quantitative teaching is difficult for teacher/instructor. In previous research, Expert and beginner perform the sports and entertainment motion, and the character of the motion curved surface is analysed using Microsoft Kinect (RGBD camera). The character is the maximum curvature and surface area. However, the usage of characters is uncertain. In this research, we investigate the correlation of maximum curvature and surface area from motion curved surface in before and after training. Therefore, we visualize the different correlation of experts and beginners from the characters and the transition of the skill training.
AUTOIMMUNE, CHOLESTATIC AND BILIARY DISEASE Loss of Tolerance in C57BL/6 Mice to the Autoantigen E2 Subunit of Pyruvate Dehydrogenase by a Xenobiotic with Ensuing Biliary Ductular Disease

There have been important advances in defining effector mechanisms for several human autoimmune diseases. However, for most human autoimmune diseases, the induction stage is less well defined and there are very few clues on etiology. Our laboratory has focused on defining the molecular basis of autoantibody recognition and epitope modification in primary biliary cirrhosis (PBC). Our work has demonstrated that antibodies to mitochondria, the hallmark of disease, are directed against a very conserved site of pyruvate dehydrogenase, the E2 subunit of pyruvate dehydrogenase (PDC-E2). We have also demonstrated that several chemical xenobiotics, chosen based on quantitative structural activity relationship analysis and rigorous epitope analysis, when coupled to the lysine residue that normally binds the lipoic acid cofactor of PDC-E2, reacts as well or better to PBC sera than native autoantigen. In the present studies, we immunized C57BL/6 mice with one such xenobiotic, 2-octynoic acid, coupled to bovine serum albumin and we followed the mice for 24 weeks. Animals were studied for appearance of histologic lesions as well as appearance of antibodies to PDC-E2, serum levels of tumor necrosis factor– and interferon, and splenic and liver lymphoid phenotyping by flow cytometry. Mice immunized with 2-octynoic acid manifest autoimmune cholangitis, typical mitochondrial autoantibodies, increased liver lymphoid cell numbers, an increase in CD8 liver infiltrating cells, particularly CD8 T cells that coexpress CD44, and finally an elevation of serum tumor necrosis factor– and interferon. Conclusion: these data provide a persuasive argument in favor of an environmental origin for human PBC. (HEPATOLOGY 2008;48:531-540.)
Evaluating Pressure Ulcer Development in Wheelchair-Bound Population Using Sitting Posture Identification

Pressure ulcers are a common complication among wheelchair-bound population. They are resulted from prolonged exposure to high pressure, which restricts blood flow and leads to tissue necrosis. In this work, a continuous pressure monitoring system is developed for pressure ulcer prevention. The system consists of 64 pressure sensors on a 40×50 cm2 sheet. Real time pressure data and corresponding maps are displayed on a computer simultaneously. Furthermore, a posture detection procedure is proposed for sitting posture identification. Having information about the patient’s postural history, caregivers are capable of a better decision about repositioning and treating the patient.
Postnatal Growth of the Lung

SUMMARY A quantitative study of postnatal lung growth has been made and shows that the number of alveoli increases over tenfold between birth andadult life. Thisincrease occurs mainlyin the firsteight years. After this age, increase in lung volume takes place by increase in linear dimen-sions of existing alveoli. The mean number of generations of airways increases from 21 to 23, from 3 months to 8 years of age. This increasetakes place in the most distal respiratory airways.There is a linear relationship between the surfacearea of the air-tissue interface and the bodysurface area during the period of growth. It issuggested that information of this type maywellbe useful in assessing such conditions as pul-monary hypoplasia, respiratory syndrome of thenewborn, and the lung in prematurity. I am grateful to Miss Nancy Purdum for technicalassistance and to Drs. Andre Cournand, D. M.Gomez, and Dickinson W. Richards for much encouragement and advice. The medical examiners of New York City and Dr. M.
Test transformation to improve compaction by statistical encoding

In test compression/decompression schemes the objective is to achieve the highest compression without sacrificing fault coverage. In this paper, we propose a method to transform a test set in order to achieve higher compression without sacrificing fault coverage, while using statistical encoding techniques. The compression ratio of a test set depends on the entropy of the test set, and hence our test transformation method decreases the entropy of the test set without losing the fault coverage. Experimental results show that the proposed method transforms given test sets into highly compressible ones.
WLS-dependent secretion of WNT3A requires Ser209 acylation and vacuolar acidification

Wnt proteins are secreted post-translationally modified proteins that signal locally to regulate development and proliferation. The production of bioactive Wnts requires a number of dedicated factors in the secreting cell whose coordinated functions are not fully understood. A screen for small molecules identified inhibitors of vacuolar acidification as potent inhibitors of Wnt secretion. Inhibition of the V-ATPase or disruption of vacuolar pH gradients by diverse drugs potently inhibited Wnt/β-catenin signaling both in cultured human cells and in vivo, and impaired Wnt-regulated convergent extension movements in Xenopus embryos. WNT secretion requires its binding to the carrier protein wntless (WLS); we find that WLS is ER-resident in human cells and WNT3A binding to WLS requires PORCN-dependent lipid modification of WNT3A at serine 209. Inhibition of vacuolar acidification results in accumulation of the WNT3A–WLS complex both in cells and at the plasma membrane. Modeling predictions suggest that WLS has a lipid-binding β-barrel that is similar to the lipocalin-family fold. We propose that WLS binds Wnts in part through a lipid-binding domain, and that vacuolar acidification is required to release palmitoylated WNT3A from WLS in secretory vesicles, possibly to facilitate transfer of WNT3A to a soluble carrier protein.