Miracle-dz/UniFAR-FTUs huggingface dataset:
How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit TRAP Suggests a General Mechanism

Background Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated. Methodology/Principal Findings We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data. Conclusions/Significance The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states.
2-D Simulation of Cathode-Directed Streamer in SF6/N2 Gas Mixtures

SF6 has been widely used in the power industry as an arc quenching and insulation medium due to its excellent physical and chemical properties since 1960. However, experience shows that SF6 gas medium has many disadvantages under certain conditions: gas may encounter liquefaction when installed in cold areas; SF6 is still expensive; dielectric strength is sensitive to electric field, and require higher equipment design and manufacturing processes; SF6 is a greenhouse gas, and is used under limitations since the Kyoto Protocol was signed in 1997[. Unfortunately, its difficult to find no environment hazards and to replace SF6 completely at present. In view that the greenhouse impact of SF6 is still very little (it is estimated less than 0.01%) in the atmosphere recently and it does not damage the ozone layer, it becomes a focus to find gas mixtures containing SF6 to replace pure SF6 gas to reduce the emissions and environmental impact of SF6. Scientists from all countries and international major GIS manufacturers, electric power sector are working together to develop new gas mixture of SF6-insulated electrical equipment [2].
DisMatch results for OAEI 2016

DisMatch is an experimental ontology matching system based on the use of corpus based distributional measure for approximating semantic relatedness. Through the use of a domain-related corpus, the measure can be applied to a problem focused on the domain of the corpus, here being the Disease and Phenotype track. In this paper, we aim to briefly present the proposed approach and the results obtained in the evaluation, as well as some early conclusions regarding the performance of DisMatch.
Representations of the Renormalization Group as Matrix Lie Algebra

Renormalization is cast in the form of a Lie algebra of infinite triangular matrices. By exponentiation, these matrices generate counterterms for Feynman diagrams with subdivergences. As representations of an insertion operator, the matrices are related to the Connes-Kreimer Lie algebra. In fact, the right-symmetric nonassociative algebra of the Connes-Kreimer insertion product is equivalent to an "Ihara bracket" in the matrix Lie algebra. We check our results in a three-loop example in scalar field theory. Apart from possible applications in high-precision phenomenology, we give a few ideas about possible applications in noncommutative geometry and functional integration.
Sentiment Mining for Natural Language Documents

The wide variety of possible applications for sentiment mining has made it the focus of considerable research in recent years. High accuracy classification has been achieved by using a variety of techniques, most of which are heavily reliant on machine learning. At its core, sentiment mining involves correct interpretation of natural language, and all the complexities and challenges involved in such a task. Despite this, the published work on the topic shows a surprising lack of work on the application of natural language based techniques to the problem. This report details an attempt to apply Natural Language Processing (NLP) techniques to the problem of accurately classifying the sentiment a document contains relating to a certain subject. Common NLP methods that are implemented in pursuit this goal include part of speech tagging, grammatical structure parsing, and coreference resolution. Combining these NLP approaches gave classification accuracy of 83% on the test corpus, and suggest with improved coreference resolution handling this could be improved
Face detection in a compressed domain

We focus on the Viola-Jones face detector in the Discrete Cosine Transform (DCT). In order to avoid typical pitfalls due to features in the DCT domain we propose to merge the integral image stage with the decompression process, thus saving time for both operations. The proposed method saves 128 additions and 224 multiplications on an 8×8 block for a simple integral image. We propose a similar method for fast feature contrast adjustment by computing the squared integral image using DCT and simple integral image coefficients. These methods are faster and more transmission error resilient than classical methods.
Positive regulation of the Escherichia coli glycine cleavage enzyme system

A new mutation in Escherichia coli, designated gcvA1, that results in noninducible expression of both gcv and a gcvT-lacZ gene fusion was isolated. A plasmid carrying the wild-type gcvA gene complemented the mutation and restored glycine-inducible gcv and gcvT-lacZ gene expression. These results suggest that gcvA encodes a positive-acting regulatory protein that acts in trans to increase expression of gcv.
The origins and implications of using innovation systems perspectives in the design and implementation of agricultural research projects: Some personal observations

In recent years the there has been an increasing recognition of the potential of the innovation systems concept to provide new ways of making more effective use of agricultural research and improve its impact on socially desirable outcomes. This paper documents the experiences of a group of researchers in India who experimented with this framework and tried to operationalise its principles in project design. The paper comments on some of the implications of using this approach and the challenges it presents for implementers of agricultural research projects in developing countries.
A High Temperature Cyclic Oxidation Data Base for Selected Materials Tested at NASA Glenn Research Center

The cyclic oxidation test results for some 1000 high temperature commercial and experimental alloys have been collected in an EXCEL database. This database represents over thirty years of research at NASA Glenn Research Center in Cleveland, Ohio. The data is in the form of a series of runs of specific weight change versus time values for a set of samples tested at a given temperature, cycle time, and exposure time. Included on each run is a set of embedded plots of the critical data. The nature of the data is discussed along with analysis of the cyclic oxidation process. In addition examples are given as to how a set of results can be analyzed. The data is assembled on a read-only compact disk which is available on request from Materials Durability Branch, NASA Glenn Research Center, Cleveland, Ohio.
DEEP MEAN FIELD THEORY: LAYERWISE VARIANCE

A recent line of work has studied the statistical properties of neural networks to great success from a mean field theory perspective, making and verifying very precise predictions of neural network behavior and test time performance. In this paper, we build upon these works to explore two methods for taming the behaviors of random residual networks (with only fully connected layers and no batchnorm). The first method is width variation (WV), i.e. varying the widths of layers as a function of depth. We show that width decay reduces gradient explosion without affecting the mean forward dynamics of the random network. The second method is variance variation (VV), i.e. changing the initialization variances of weights and biases over depth. We show VV, used appropriately, can reduce gradient explosion of tanh and ReLU resnets from exp(Θ( √ L)) and exp(Θ(L)) respectively to constant Θ(1). A complete phase-diagram is derived for how variance decay affects different dynamics, such as those of gradient and activation norms. In particular, we show the existence of many phase transitions where these dynamics switch between exponential, polynomial, logarithmic, and even constant behaviors. Using the obtained mean field theory, we are able to track surprisingly well how VV at initialization time affects training and test time performance on MNIST after a set number of epochs: the level sets of test/train set accuracies coincide with the level sets of the expectations of certain gradient norms or of metric expressivity (as defined in Yang and Schoenholz (2017)), a measure of expansion in a random neural network. Based on insights from past works in deep mean field theory and information geometry, we also provide a new perspective on the gradient explosion/vanishing problems: they lead to ill-conditioning of the Fisher information matrix, causing optimization troubles.
Urethral substitution with ileum in traumatic bladder neck-vagina fistula

A five-year-old girl presented with post traumatic urinary incontinence secondary to rupture of the bladder neck into the vagina. Operative repair included a midline exposure with resection of the symphysis pubis, separation of the bladder neck from the vagina, repair of the torn bladder neck and urethral substitution with ileum. Normal continence and voiding was achieved.
Climate Change and Tropical Andean Glacier Recession: Evaluating Hydrologic Changes and Livelihood Vulnerability in the Cordillera Blanca, Peru

Climate change is forcing dramatic glacier mass loss in the Cordillera Blanca, Peru, resulting in hydrologic transformations across the Rio Santa watershed and increasing human vulnerability. This article presents results from two years of transdisciplinary collaborative research evaluating the complex relationships between coupled environmental and social change in the region. First, hydrologic results suggest there has been an average increase of 1.6 (± 1.1) percent in the specific discharge of the more glacier-covered catchments (>20 percent glacier area) as a function of changes in stable isotopes of water (δ18O and δ2H) from 2004 to 2006. Second, there is a large (mean 60 percent) component of groundwater in dry season discharge based on results from the hydrochemical basin characterization method. Third, findings from extensive key interviews and seventy-two randomly sampled household interviews within communities located in two case study watersheds demonstrate that a large majority of households perceive that glacier recession is proceeding very rapidly and that climate change–related impacts are affecting human vulnerability across multiple shifting vectors including access to water resources, agro-pastoral production, and weather variability.
Model-based compensation of the additive noise for continuous speech recognition. experiments using the Aurora II database and tasks

In this paper we apply a model-based compensation method to cancel the effect of the additive noise in Automatic Speech Recognition systems. The method is formulated in a statistical framework in order to perform the optimal compensation of the noise effect given the observed noisy speech, a model describing the statistics of the speech recorded in a clean reference environment and the estimation of the noise in the noisy recognition environment. The noise is estimated using the first frames of the sentence to be recognized and a frame-by-frame noise compensation algorithm is performed, so that the compensation procedure does not constrain real-time speech recognition systems and is compatible with emerging technologies based on distributed speech recognition. We have performed recognition experiments under noise conditions using the AURORA II database for the recognition tasks developed for this database as a standard reference. Experiments have been carried out including both, clean and multicondition training approaches. The experimental results show the improvements in the recognition performance when the proposed model-based compensation method is applied.
Some Aspects of the Transfer of Oxygen Across the Syndesmochorial Placenta of the Sheep *

Since the classical studies of Grosser1" the classification of mammalian placental types has been based upon the number of tissue layers separating the maternal vascular system from the fetal vessels and across which the diffusable materials essential to intrauterine development must move from the maternal to the fetal plasma. Grosser's classification is based on the concepts: (i) that in phylogeny as in ontogeny the simplest or primary stage in placentation is one in which the barrier consists of the following intervening structures-the maternal vascular endothelium, the maternal connective tissue, the maternal epithelium, the cavity of the uterus, the chorionic epithelium, chorionic connective tissue and endothelium; and (ii) that the phylogenetic development of the placenta involved the destruction of the tissue layers separating the maternal blood from the uterine cavity one after another as in implantation during ontogeny. First, the maternal epithelium breaks down either before the application of the chorionic epithelium of the embryo to the uterine wall or after the obliteration of the uterine cavity at the site of implantation, i.e., after the apposition or fusion of the fetal and maternal epithelial layers. Next, the maternal connective tissue is absorbed-the endothelium alone remains and finally this, too, is destroyed and the maternal blood bathes the fetal epithelium. From his studies Grosser concluded that only the maternal tissue layers were destroyed in the ontogenetic development and phylogenetic evolution of the placenta and accordingly he assumed the highest type or final stage in development to be that in which the fetal epithelium was in direct contact with the maternal blood; but the more recent observations of Mossman19 demonstrate that there is yet another stage-one in which the fetal epithelium and connective tissue disintegrate. The maternal and fetal bloods are in this stage separated by but a single layer of cells, the fetal vascular endothelium. The basic phylogenetic pattern of the placenta according to Grosser's scheme-consisting of six layers, three maternal and three fetal, separated by a potential space representing the obliterated uterine cavity-is found in the pig and in the horse. In the ruminants-the sheep, the goat, and the deer-the maternal epithelium is lost to a greater or lesser degree, and in some areas the connective tissue is destroyed. The slit-like cavity of the uter-
The effect of counselling, graded exercise and usual care for people with chronic fatigue in primary care: a randomized trial

Background To evaluate the effectiveness of graded exercise therapy (GET), counselling (COUNS) and usual care plus a cognitive behaviour therapy (CBT) booklet (BUC) for people presenting with chronic fatigue in primary care. Method A randomized controlled trial in general practice. The main outcome measure was the change in the Chalder fatigue score between baseline and 6 months. Secondary outcomes included a measure of global outcome, including anxiety and depression, functional impairment and satisfaction. Results The reduction in mean Chalder fatigue score at 6 months was 8.1 [95% confidence interval (CI) 6.6–10.4] for BUC, 10.1 (95% CI 7.5–12.6) for GET and 8.6 (95% CI 6.5–10.8) for COUNS. There were no significant differences in change scores between the three groups at the 6- or 12-month assessment. Dissatisfaction with care was high. In relation to the BUC group, the odds of dissatisfaction at the 12-month assessment were less for the GET [odds ratio (OR) 0.11, 95% CI 0.02–0.54, p=0.01] and COUNS groups (OR 0.13, 95% CI 0.03–0.53, p=0.004). Conclusions Our evidence suggests that fatigue presented to general practitioners (GPs) tends to remit over 6 months to a greater extent than found previously. Compared to BUC, those treated with graded exercise or counselling therapies were not significantly better with respect to the primary fatigue outcome, although they were less dissatisfied at 1 year. This evidence is generalizable nationally and internationally. We suggest that GPs ask patients to return at 6 months if their fatigue does not remit, when therapy options can be discussed further.
A comprehensive representation of extensive similarity linkage between large numbers of proteins

A method is described for the representation of a bird's-eye view of similarity relationships between large numbers of proteins. With the aid of single-linkage clustering, proteins are clustered into groups on the basis of various types of similarity such as sequence similarity estimated between all the protein pairs. Proteins in a group are directly or indirectly connected to all proteins in the same group by similarities higher than a given threshold and show no similarity higher than the threshold to any proteins outside the group. Thus, all the proteins directly or indirectly related to a protein can be selected out of a large number of proteins by the clustering. Recursion of this clustering of proteins in each group leads to further classification of the proteins. The similarity relationships in each group are visually represented by a similarity matrix. This representation has the advantage of easy detection of the existence of multidomain proteins and diverged families as well as closely related proteins. Such as exhaustive approach to similarity relationships of proteins will be useful for revealing functional/structural/evolutionary units in proteins.
Creating Playable Social Experiences through Whole-Body Interaction with Virtual Characters

This paper describes work towards the goal of enabling unscripted interaction with non-player characters in virtual environments. We hypothesize that we can define a layer of social affordances, based on physical and non-verbal signals exchanged between individuals and groups, which can be reused across games. We have implemented a first version of that substrate that employs whole body interaction with virtual characters and generates nuanced, real-time character performance in response. We describe the playable experience produced by the system, the implementation architecture (based on the behavior specification technology used in Façade, the social model employed in Prom Week, and gesture recognition technology), and illustrate the key behaviors and programming idioms that enable character performance. These idioms include orthogonal coding of attitudes and activities, use of relational rules to nominate social behavior, use of volition rules to rank options, and priority based interleaving of character animations.
Real-Time Impedance Characterization Method for RFID-Type Backscatter Communication Devices

This paper presents a radio frequency (RF) measurement method that allows to determine electrical characteristics such as scattering parameters or impedance of contactless passive chips, using common measurement devices such as oscilloscope, personal computer, and directional coupler. The measurements obtained using this method are as accurate as those obtained with vector network analyzer (VNA) measurements, while providing several improvements. First, the method makes it possible to measure a chip’s impedance in activation state, which requires large input power, not compatible with VNA measurements. Second, this method realizes a real-time measurement, which consists in impedance measurement as a function of time. Therefore, this real-time measurement makes it possible to detect and measure the impedance changes of an actual contactless smart card’s integrated circuit during a load modulation communication at different powers. Finally, this real-time impedance measurement gives important information on chips’ electrical characteristics that can be used to optimize near-field communication devices design in order to reduce the power losses within an RF identification tag.
Design and implementation of a cooperative collision warning system

Collision warning systems (CWSs) are becoming an important part of vehicle active safety. Commercial CWSs using radar, lidar, and camera have been available on the market. Another emerging trend in the development of CWS is based on the cooperative driving concept, where either the vehicle or the infrastructure can communicate its location, intention or other information to surrounding vehicles or nearby infrastructure. Since installing a lower-cost Global Positioning System (GPS) unit is becoming a common practice in vehicle applications, its implications in cooperative driving and vehicle safety deserve a closer investigation. This paper explores the feasibility of a cooperative CWS based on the proposed future-trajectory-based design, which estimates and communicates vehicle positions, and predicts and processes future trajectories for collision decision making. An exemplary system has been developed and the feasibility of the proposed design has been demonstrated with experimental data
A mutation in a new gene of Escherichia coli, psu, requires secondary mutations for survival: psu mutants express a pleiotropic suppressor phenotype

A mutation in an apparently new gene of Escherichia coli, psu, maps close to ara (1.3 min). psu mutants express a pleiotropic suppressor phenotype in which several auxotrophic requirements and some deletion mutations are suppressed. psu cloned in pBR322 can be maintained by the transformed cell only in the presence of several secondary mutations which accumulate in cultures of psu mutants and have an apparently compensatory role. The accumulation of secondary mutations is not due to mutator activity. The secondary mutations can each act as a suppressor of an auxotrophic requirement in the absence of psu, while suppression of deletions requires the presence of psu. Thus, the suppressor phenotype of psu mutants is due to both psu and the secondary mutations. The functions of psu and the secondary mutations are not known. However, two observations suggest an association with DNA gyrase and with DNA supercoiling. (i) psu mutants are highly resistant to oxolinic acid, the gyrase A inhibitor, while the secondary mutants vary from being very sensitive to more resistant than the wild-type strain. (ii) Novobiocin, which decreases the level of DNA supercoiling, significantly stimulates suppression of auxotrophy in some secondary mutants.