Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution

To what extent are evolutionary outcomes determined by a population's recent environment, and to what extent do they depend on historical contingency and random chance? Here we apply a unique experimental system to investigate evolutionary reproducibility and path dependence at the protein level. We combined phage-assisted continuous evolution with high-throughput sequencing to analyze evolving protein populations as they adapted to divergent and then convergent selection pressures over hundreds of generations. Independent populations of T7 RNA polymerase genes were subjected to one of two selection histories (“pathways”) demanding recognition of distinct intermediate promoters followed by a common final promoter. We observed distinct classes of solutions with unequal phenotypic activity and evolutionary potential evolve from the two pathways, as well as from replicate populations exposed to identical selection conditions. Mutational analysis revealed specific epistatic interactions that explained the observed path dependence and irreproducibility. Our results reveal in molecular detail how protein adaptation to different environments, as well as stochasticity among populations evolved in the same environment, can both generate evolutionary outcomes that preclude subsequent convergence.
Increasing the probability of timely and correct message delivery in road side unit based vehicular communication

Intelligent transport systems provide a multitude of possibilities when it comes to increasing traffic safety on our roads. Many of the proactive traffic safety applications under development today demand timely and reliable treatment of deadline dependent data traffic. Unfortunately it is not possible to provide any timing guarantees when using the current IEEE 802.11p standard for wireless access in vehicular environments. Additionally, a difficult wireless channel environment makes successful data transmissions very challenging. We suggest adding a real-time layer, comprising a deterministic medium access control protocol and transport layer retransmissions, on top of IEEE 802.11p in order to enable guaranteed real-time behaviour and to improve reliability. In a simulation study we show that the packet error rate can be decreased by several orders of magnitude while being able to guarantee timely treatment of both ordinary transmissions and retransmissions by the help of a real-time schedulability analysis.
Multiple supermassive black holes in galactic bulges

We study the number and interaction rates of supermassive black holes in galactic bulges as predicted by hierarchical models of galaxy formation in which the spheroidal components of galaxies are formed by mergers. In bright ellipticals, the number of events that can eject a central supermassive binary black hole is large. Central binaries must therefore merge in less than a Hubble time - otherwise there will be too much scatter in the M_-σ * relation and too many off-centre galactic nuclei. We propose that binary black holes are able to merge during the major gas accretion events that trigger QSO activity in galaxies. If this is the case, less than 10 per cent of faint ellipticals and 40 per cent of bright ellipticals are predicted to harbour binary black holes with near equal masses at their centres. This binary may be ejected away from the centre of the galaxy or even into intergalactic space in up to 20 per cent of the most luminous ellipticals. The number of low-mass black holes that can interact with the central object is predicted to be a strong function of galaxy luminosity. In most faint ellipticals, no black holes fall into the centre of the galaxy after the last major gas accretion event, but in the most luminous ellipticals, an average of 10 low-mass black holes interact with the central supermassive object after this time. It is expected that stars will be ejected from galaxy cores as these low mass ratio binaries harden. Multiple black holes in galactic bulges thus provide a natural explanation for the strong systematic trends in the observed central density profiles of ellipticals as a function of luminosity.
Coordination Structures in Dependency Treebanks

Paratactic syntactic structures are notoriously difficult to represent in dependency formalisms. This has painful consequences such as high frequency of parsing errors related to coordination. In other words, coordination is a pending problem in dependency analysis of natural languages. This paper tries to shed some light on this area by bringing a systematizing view of various formal means developed for encoding coordination structures. We introduce a novel taxonomy of such approaches and apply it to treebanks across a typologically diverse range of 26 languages. In addition, empirical observations on convertibility between selected styles of representations are shown too.
JMatch: Java plus Pattern Matching

The JMatch language extends Java with iterable abstract pattern matching, pattern matching that is compatible with the data abstraction features of Java and makes iteration abstractions convenient. JMatch has ML-style deep pattern matching, but patterns can be abstract; they are not tied to algebraic data constructors. A single JMatch method may be used in several modes; modes may share a single implementation as a boolean formula. Modal abstraction simplifies specification and implementation of abstract data types. This paper describes the JMatch language and its implementation.
Opinion Graphs for Polarity and Discourse Classification

This work shows how to construct discourse-level opinion graphs to perform a joint interpretation of opinions and discourse relations. Specifically, our opinion graphs enable us to factor in discourse information for polarity classification, and polarity information for discourse-link classification. This inter-dependent framework can be used to augment and improve the performance of local polarity and discourse-link classifiers.
Reducing Major Depression in Children at High Risk: Opportunities for Prevention

Objective: The profound negative impact of a parent's Major Depressive Disorder (MDD) on his or her children is of increasing concern to public health and mental health professionals. Children of a depressed parent have a markedly elevated risk for psychiatric illness, including a fourfold increased risk for MDD. The objective is to examine the scientific literature for ways to reduce this high risk to the offspring. First, we consider the relation between effective treatment of a parent's depression and reduced risk to the offspring, and review the effectiveness of treatments for adult MDD. We then review emerging evidence that risk for psychopathology can be reduced in children of depressed parents by preventive intervention, including targeting two pathways hypothesized as links between parental MDD and offspring psychopathology: parenting skills and child coping. Data Sources: Three 5-year PubMed searches, and a Cochrane Database search, and one Medline and two PsycLit searches (to 1970) were completed (search words in combinations included: depression, prevention, treatments, depression in families, family interaction, adolescents). Study Selection: Randomized controlled studies are included, and review studies and meta-analyses are highlighted to provide a critical overview of the considerable scientific literatures for specific steps that can be taken to reduce the high risk of depression to the offspring of parents with MDD. Results: A deliberate clinical focus on better treatment of MDD in parents is clearly needed and has the potential additional benefit of reducing psychopathology in their children. Altering clinical treatment to address MDD “co-occurring” in both parent and child is supported by the scientific literature. There is also good evidence that preventive intervention with high-risk adolescents reduces the incidence of MDD. Targeting parenting skills and teaching children how to better cope with a parent's illness that they cannot control, appears to reduce MDD in the offspring.
Inflammatory markers and cardiometabolic diseases

Abstract Objectives: A growing body of evidence emerges that obesity, metabolic syndrome, type 2 diabetes and cardiovascular disease are intimately related to chronic inflammation. Methods: A narrative review summarizing the most recent data of the literature describing the pathological implications of inflammation in obese patients with cardiometabolic disorders. Results: Besides high-sensitive C-reactive protein, various circulating or in situ inflammatory markers have been identified, presumably reflecting the presence of inflammation in various key-organs (visceral adipose tissue, skeletal muscle, pancreatic islets, liver, intestine, arterial wall). Available data support the concept that targeting inflammation, not only reduces systemic inflammatory markers, but also improves insulin sensitivity and ameliorates glucose control in insulin-resistant patients, thus potentially reducing the risk of cardiovascular complications. Conclusion: These observations confirm the role of inflammation in cardiometabolic diseases and support the development of pharmacological strategies that aim at reducing inflammation, especially in patients with type 2 diabetes.
An area-efficient BCH codec with echelon scheduling for NAND flash applications

This paper presents an area-efficient BCH codec with echelon scheduling for NAND flash memory systems. In our proposed design, instead of the common inversionless Berlekamp-Massey algorithm, the BM algorithm using a low-complexity 2-stage composite field divider is applied in the key equation solver. Moreover, by making use of the fact that the degree of error locator polynomial increases at most by 1 in each iteration, an echelon scheduling architecture with 6 finite field multipliers is presented. After implemented in UMC 1P9M 90 nm process, the proposed codec can achieve 385 MHz and 3.08 Gbit/s throughput with 147.8K gate-count from post-layout simulation results.
Bonding in hydrogenated diamond-like carbon by Raman spectroscopy

We study the 514 and 244 nm Raman spectra of a wide variety of hydrogenated amorphous carbons (a-C:H). The hydrogen content can be estimated from the slope of the photoluminescence background (PL) of the spectra measured at 514.5 nm. Generally, the evolution of the sp and sp phases is not independent for as-deposited a-C:H samples. This, in principle, allows us to derive their structural and optical properties just by studying the visible Raman spectra. For highly hydrogenated samples, the PL background overshadows the visible Raman spectra, and UV excitation is the only way to measure a Raman spectrum. D 2005 Elsevier B.V. All rights reserved.
Study of near-surface layers of Omerelu area using low velocity layer ( LVL ) method

It is important that we have good knowledge of the soil type so as to appreciate the enormous resources we are stepping on. It is more compelling for oil explorationists to know more as this will go a long way to determine the success or failure of search for minerals. Seismic methods give a good overview of a wide area though they involve greater logistics and operational requirements than some other geophysical methods. The purpose of present study is to determine the depth of the weathered layer and velocities of near-surface layers over the investigated area. Twelve sample points were picked with a grid system spread over a perimeter of approximately 4km x 4km. The inhouse UpSphere computer program was utilised to analyse and display result in a way that makes final interpretation very easy. This program actually removed the burden of plotting the graphs and the contour maps manually. The depth of weathered layer in the study area varies between 12m and 13m. The velocities of the weathered layer and the consolidated layer vary between 500 m/s – 550 m/s and 1790 m/s – 1875 m/s respectively. Also the dip is in the north east – south west direction.
Environment-Detection-and-Mapping Algorithm for Autonomous Driving in Rural or Off-Road Environment

This paper presents an environment-detection-and-mapping algorithm for autonomous driving that is provided in real time and for both rural and off-road environments. Environment-detection-and-mapping algorithms have been designed to consist of two parts: (1) lane, pedestrian-crossing, and speed-bump detection algorithms using cameras and (2) obstacle detection algorithm using LIDARs. The lane detection algorithm returns lane positions using one camera and the vision module “VisLab Embedded Lane Detector (VELD),” and the pedestrian-crossing and speed-bump detection algorithms return the position of pedestrian crossings and speed bumps. The obstacle detection algorithm organizes data from LIDARs and generates a local obstacle position map. The designed algorithms have been implemented on a passenger car using six LIDARs, three cameras, and real-time devices, including personal computers (PCs). Vehicle tests have been conducted, and test results have shown that the vehicle can reach the desired goal with the proposed algorithm.
Mechanism of Beneficial Effects of Physical Activity on Athersclerosis and Coronary Heart Disease Thrombosis , physical activity , and acute coronary syndromes

Kumar A, Kar S, Fay WP. Thrombosis, physical activity, and acute coronary syndromes. J Appl Physiol 111: 599–605, 2011. First published May 19, 2011; doi:10.1152/japplphysiol.00017. 2011. —Acute coronary syndromes (ACS) are common, life-threatening cardiac disorders that typically are triggered by rupture or erosion of an atherosclerotic plaque. Platelet deposition and activation of the blood coagulation cascade in response to plaque disruption lead to the formation of a platelet-fibrin thrombus, which can grow rapidly, obstruct coronary blood flow, and cause myocardial ischemia and/or infarction. Several clinical studies have examined the relationship between physical activity and ACS, and numerous preclinical and clinical studies have examined specific effects of sustained physical training and acute physical activity on atherosclerotic plaque rupture, platelet function, and formation and clearance of intravascular fibrin. This article reviews the available literature regarding the role of physical activity in determining the incidence of atherosclerotic plaque rupture and the pace and extent of thrombus formation after plaque rupture.
Effect of a Selective Mas Receptor Agonist in Cerebral Ischemia In Vitro and In Vivo

Functional modulation of the non-AT1R arm of the renin-angiotensin system, such as via AT2R activation, is known to improve stroke outcome. However, the relevance of the Mas receptor, which along with the AT2R forms the protective arm of the renin-angiotensin system, as a target in stroke is unclear. Here we tested the efficacy of a selective MasR agonist, AVE0991, in in vitro and in vivo models of ischemic stroke. Primary cortical neurons were cultured from E15-17 mouse embryos for 7–9 d, subjected to glucose deprivation for 24 h alone or with test drugs, and percentage cell death was determined using trypan blue exclusion assay. Additionally, adult male mice were subjected to 1 h middle cerebral artery occlusion and were administered either vehicle or AVE0991 (20 mg/kg i.p.) at the commencement of 23 h reperfusion. Some animals were also treated with the MasR antagonist, A779 (80 mg/kg i.p.) 1 h prior to surgery. Twenty-four h after MCAo, neurological deficits, locomotor activity and motor coordination were assessed in vivo, and infarct and edema volumes estimated from brain sections. Following glucose deprivation, application of AVE0991 (10−8 M to 10−6 M) reduced neuronal cell death by ~60% (P<0.05), an effect prevented by the MasR antagonist. By contrast, AVE0991 administration in vivo had no effect on functional or histological outcomes at 24 h following stroke. These findings indicate that the classical MasR agonist, AVE0991, can directly protect neurons from injury following glucose-deprivation. However, this effect does not translate into an improved outcome in vivo when administered systemically following stroke.
Insights into ALS pathomechanisms: from flies to humans

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease causing the death of motor neurons with consequent muscle atrophy and paralysis. Several neurodegenerative diseases have been modeled in Drosophila and genetic studies on this model organism led to the elucidation of crucial aspects of disease mechanisms. ALS, however, has lagged somewhat behind possibly because of the lack of a suitable genetic model. We were the first to develop a fly model for ALS and over the last few years, we have implemented and used this model for a large scale, unbiased modifier screen. We also report an extensive bioinformatic analysis of the genetic modifiers and we show that most of them are associated in a network of interacting genes controlling known as well as novel cellular processes involved in ALS pathogenesis. A similar analysis for the human homologues of the Drosophila modifiers and the validation of a subset of them in human tissues confirm and expand the significance of the data for the human disease. Finally, we analyze a possible application of the model in the process of therapeutic discovery in ALS and we discuss the importance of novel “non-obvious” models for the disease.
Multi-Dimensional Comparative Visualization for Patent Landscaping

Patent landscaping is a significant activity for modern businesses. Understanding and taking action on information gleaned from analyses of intellectual property (IP) in specific product or technology domains is necessary for many business decisions. Examples include decisions about future product development, about how to guard against litigation threats from competitors, about how to set R&D priorities, about how to value IP for sale or licensing, and about how to target companies for mergers and acquisitions. This paper proposes a novel method for visualizing patent landscapes that supports the complex hierarchical, multi-dimensional, multi-typed data found in this domain. Our solution directly addresses the problem of how to provide high-level overviews of such a complex domain while at the same time providing enough detail to draw attention to the most significant areas of difference for further drill-down leading to actionable intelligence. 2015 BusinessVis15, IEEE VIS Workshop, Chicago, IL, October 24, 2015. This work may not be copied or reproduced in whole or in part for any commercial purpose. Permission to copy in whole or in part without payment of fee is granted for nonprofit educational and research purposes provided that all such whole or partial copies include the following: a notice that such copying is by permission of Mitsubishi Electric Research Laboratories, Inc.; an acknowledgment of the authors and individual contributions to the work; and all applicable portions of the copyright notice. Copying, reproduction, or republishing for any other purpose shall require a license with payment of fee to Mitsubishi Electric Research Laboratories, Inc. All rights reserved. Copyright c © Mitsubishi Electric Research Laboratories, Inc., 2015 201 Broadway, Cambridge, Massachusetts 02139 Multi-Dimensional Comparative Visualization for Patent Landscaping Kent Wittenburg, Senior Member, IEEE, and Georgiy Pekhteryev Abstract—Patent landscaping is a significant activity for modern businesses. Understanding and taking action on informationPatent landscaping is a significant activity for modern businesses. Understanding and taking action on information gleaned from analyses of intellectual property (IP) in specific product or technology domains is necessary for many business decisions. Examples include decisions about future product development, about how to guard against litigation threats from competitors, about how to set R&D priorities, about how to value IP for sale or licensing, and about how to target companies for mergers and acquisitions. This paper proposes a novel method for visualizing patent landscapes that supports the complex hierarchical, multi-dimensional, multi-typed data found in this domain. Our solution directly addresses the problem of how to provide high-level overviews of such a complex domain while at the same time providing enough detail to draw attention to the most significant areas of difference for further drill-down leading to actionable intelligence.
Back Education Efficacy in Elementary Schoolchildren: A 1-Year Follow-Up Study

Study Design. A control group–designed 1-year follow-up study involving 9 to 11-year-old schoolchildren who followed back education. Objectives. To evaluate the efficacy of a back education program, consisting of six sessions of 1 hour each, in elementary school. Summary of Background Data. In surveys among children and teenagers during the past few years, as many as half of all children in a community report a history of low back pain. Although several authors advocate the implementation of back education in elementary school, no guidelines exist and little is known about the efficacy of such a program. Methods. A total of 198 children (subjected to back education) and 165 controls performed a practical test, evaluating the use of back care principles while sitting, taking off shoes, picking up a pen, and handling a load and a book bag. Post-tests were performed within 1 week after the intervention, after 3 months, and after 1 year. The week prevalence of back and neck pain was evaluated at these test moments in extended samples of intervention children (n = 347) and controls (n = 349). To evaluate habit changes, a limited group of intervention pupils (n = 38) and controls (n = 31) was additionally evaluated in a candid camera observation at the last post-test. Results. At all post-tests intervention pupils scored significantly higher (P < 0.001) than controls for all practical test items. Candid camera evaluation scores were higher in the intervention group sample compared with the control group sample for four of the eight evaluated items. Following back education significantly decreased the week prevalence of back and neck pain. Conclusions. Back education in elementary schoolchildren is efficacious up to 1 year. The role of early back education in preventing back pain at the adult age merits further attention.
Characterization of a cellular factor which interacts functionally with Oct-1 in the assembly of a multicomponent transcription complex.

Induction of transcription of the immediate-early (IE) genes of herpes simplex virus involves the assembly of a DNA-binding complex containing the viral protein Vmw65 and the cellular transcription factor Oct-1. We show that Oct-1 is not sufficient for complex formation and that another cellular factor(s) which is absolutely required for complex formation can be separated from Oct-1 under native conditions. We have purified this factor by approximately 100-fold using DNA-cellulose, ion-exchange and size-exclusion chromatographies. The assay used throughout the purification procedure follows the ability of the cellular factor to form a complex when added to purified Oct-1, Vmw65 and an IE specific DNA probe. The complex forming factor (CFF) had a sedimentation coefficient of about 4.4 S (i.e. molecular mass of about 70K, under non-denaturing conditions) and the polypeptide profile of highly purified CFF demonstrated two major species with molecular masses of 80K and 70K. Unequivocal association of either of these two species with CFF activity could not presently be demonstrated due to the sensitivity of CFF to denaturation. CFF, when tested on its own or in the presence of Vmw65, did not bind to the IE-specific consensus motif. We have also used deletion mutants of Oct-1 to show that the POU domain of this protein was sufficient for CFF-dependent complex formation with Vmw65. Deletions of the POU specific region of Oct-1 significantly reduced the complex forming ability, although detectable levels of complex were reconstituted using Vmw65, CFF and just the homeodomain of Oct-1.