Miracle-dz/UniFAR-FTUs huggingface dataset:
Reactions of BglI and Other Type II Restriction Endonucleases with Discontinuous Recognition Sites*

Type II restriction enzymes generally recognize continuous sequences of 4–8 consecutive base pairs on DNA, but some recognize discontinuous sites where the specified sequence is interrupted by a defined length of nonspecific DNA. To date, a mechanism has been established for only one type II endonuclease with a discontinuous site, SfiI at GGCCNNNNNGGCC (where N is any base). In contrast to orthodox enzymes such as EcoRV, dimeric proteins that act at a single site, SfiI is a tetramer that interacts with two sites before cleaving DNA.BglI has a similar recognition sequence (GCCNNNNNGGC) to SfiI but a crystal structure like EcoRV.BglI and several other endonucleases with discontinuous sites were examined to see if they need two sites for their DNA cleavage reactions. The enzymes included some with sites containing lengthy segments of nonspecific DNA, such as XcmI (CCANNNNNNNNNTGG). In all cases, they acted at individual sites. Elongated recognition sites do not necessitate unusual reaction mechanisms. Other experiments on BglI showed that it bound to and cleaved DNA in the same manner as EcoRV, thus further delineating a distinct group of restriction enzymes with similar structures and a common reaction mechanism.
Systems and Software Verification, Model-Checking Techniques and Tools

Model checking is a powerful approach for the formal verification of software. It automatically provides complete proofs of correctness, or explains, via counter-examples, why a system is not correct. Here, the author provides a well written and basic introduction to the new technique. The first part describes in simple terms the theoretical basis of model checking: transition systems as a formal model of systems, temporal logic as a formal language for behavioral properties, and model-checking algorithms. The second part explains how to write rich and structured temporal logic specifications in practice, while the third part surveys some of the major model checkers available.
Weakly-Supervised Cross-lingual Predicate Cluster Acquisition to Improve Bilingual Event Extraction

In this paper we present two approaches to automatically extract cross-lingual predicate clusters, based on bilingual parallel corpora and cross-lingual information extraction. We demonstrate how these clusters can be used to improve the NIST Automatic Content Extraction (ACE) event extraction task. We propose a new inductive learning framework to automatically augment background data for lowconfidence events and then conduct global inference. Without using any additional data or accessing the baseline algorithms this approach obtained significant improvement over a state-of-the-art bilingual (English and Chinese) event extraction system.
PD-1, but Not PD-L1, Expressed by Islet-Reactive CD4+ T Cells Suppresses Infiltration of the Pancreas During Type 1 Diabetes

The inhibitory receptor programmed death-1 (PD-1) constrains type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse. However, how PD-1 influences diabetogenic CD4+ T cells during natural diabetes is not fully understood. To address this question, we developed a novel model to investigate antigen-specific CD4+ T cells under physiological conditions in vivo. We transferred a low number of naïve CD4+ T cells from the BDC2.5 mouse into prediabetic NOD mice to mimic a physiological precursor frequency and allowed the cells to become primed by endogenous autoantigen. Transferred BDC2.5 T cells became activated, differentiated into T-bet+ IFN-γ–producing cells, and infiltrated the pancreas. In this model, loss of PD-1, but not programmed death ligand-1 (PD-L1), on the antigen-specific CD4+ T cell resulted in increased cell numbers in the spleen, pancreas-draining lymph node, and pancreas. PD-1 deficiency also increased expression of the chemokine receptor CXCR3. Lastly, histological data showed that a loss of PD-1 caused BDC2.5 cells to penetrate deep into the islet core, resulting in conversion from peri-insulitis to destructive insulitis. These data support a model by which PD-1 regulates islet-reactive CD4+ T cells in a cell intrinsic manner by suppressing proliferation, inhibiting infiltration of the pancreas, and limiting diabetes.
Evaluation of dynamic communities in large-scale vehicular networks

The topology of vehicular ad hoc networks (VANETs) is highly dynamic due to the mobility of the vehicles and changing traffic conditions in time and space. The development of any efficient service in such networks is challenging and requires thorough understanding of the characteristics and dynamics of the underlying communication topology. This work analyses the connectivity and the potential for creating communities in large-scale and realistic VANETs. In addition, the performance of a state-of-the-art decentralised community detection algorithm is studied in terms of how communities form and evolve when considering real-world vehicular mobility.
Bootstrapping Path-Based Pronoun Resolution

We present an approach to pronoun resolution based on syntactic paths. Through a simple bootstrapping procedure, we learn the likelihood of coreference between a pronoun and a candidate noun based on the path in the parse tree between the two entities. This path information enables us to handle previously challenging resolution instances, and also robustly addresses traditional syntactic coreference constraints. Highly coreferent paths also allow mining of precise probabilistic gender/number information. We combine statistical knowledge with well known features in a Support Vector Machine pronoun resolution classifier. Significant gains in performance are observed on several datasets.
Detection and Quantification of Plectosphaerella cucumerina, a Potential Biological Control Agent of Potato Cyst Nematodes, by Using Conventional PCR, Real-Time PCR, Selective Media, and Baiting

ABSTRACT Potato cyst nematodes (PCN) are serious pests in commercial potato production, causing yield losses valued at approximately $300 million in the European Community. The nematophagous fungus Plectosphaerella cucumerina has demonstrated its potential as a biological control agent against PCN populations by reducing field populations by up to 60% in trials. The use of biological control agents in the field requires the development of specific techniques to monitor the release, population size, spread or decline, and pathogenicity against its host. A range of methods have therefore been developed to monitor P. cucumerina. A species-specific PCR primer set (PcCF1-PcCR1) was designed that was able to detect the presence of P. cucumerina in soil, root, and nematode samples. PCR was combined with a bait method to identify P. cucumerina from infected nematode eggs, confirming the parasitic ability of the fungus. A selective medium was adapted to isolate the fungus from root and soil samples and was used to quantify the fungus from field sites. A second P. cucumerina-specific primer set (PcRTF1-PcRTR1) and a Taqman probe (PcRTP1) were designed for real-time PCR quantification of the fungus and provided a very sensitive means of detecting the fungus from soil. PCR, bait, and culture methods were combined to investigate the presence and abundance of P. cucumerina from two field sites in the United Kingdom where PCN populations were naturally declining. All methods enabled differences in the activity of P. cucumerina to be detected, and the results demonstrated the importance of using a combination of methods to investigate population size and activity of fungi.
Process for the recovery of precious metals

The invention relates to a method for detaching precious metal layers from a correspondingly coated material by dissolving the precious metals in a salt-containing alkali cyanide solution containing oxidizing agents. According to the invention the alkali cyanide solution continuously flows around the material positioned in a dissolution unit (22), preferably contains at least an alkali sulfate, an alkali metaborate and/or a nitroaromatic compound and for obtaining and/or regenerating the oxidizing agent is electrolytically oxidized in a closed circuit in an electrolytic cell (10). The method provided for by the invention there requires minimal quantities of chemicals, which results in correspondingly low recycling costs. If a nitroaromatic compound is used the oxidized solution is stable to such a degree that the dissolution process in the dissolution unit (22) and the oxidizing process in the electrolytic cell (10) can be carried out independently of each other. The precious metals dissolved in the alkali cyanide solution, such as gold, silver, palladium or such like, and/or impurities are preferably separated out electrolytically in the cathode compartment (28) of a further electrolytic cell (26) which chamber is separated from the corresponding anode compartment (30), which is filled with a powerful electrolyte, for example a 10 % potassium hydroxide solution, by a cation exchange membrane (32). Said membrane is preferably coated with a precious metal, notably gold, since this permits extremely high degrees of purity of up to 99 % during separation.
Participation patterns of children with acquired brain injury

Objective: To describe the participation patterns of children and youth with Acquired Brain Injury (ABI) and to compare these patterns with typically-developing peers. Methods: One hundred and thirty-five children with ABI completed the Children Assessment of Participation and Enjoyment (CAPE) to measure their participation diversity and intensity in outside-of-school activities (i.e. recreational, physical, social, self-improvement and skill-based activities). Results were compared to 354 typically-developing peers. ANOVA analyses were performed while controlling for age and gender. Results: Similar to typically-developing children, individuals with ABI proportionally participated mostly in social and recreational activities and were less likely to engage in skill-based activities. However, level of intensity and diversity within each activity type was different between the two groups. Children with ABI participated in fewer activities and were less frequently involved in all the CAPE's activity types except for intensity in social activities. These differences, characterized by small-to-medium effect sizes, were not dependent on the child's age and gender. Conclusions: Participation of children with ABI is restricted in comparison to their typically-developing peers even in a sample where minor injury is predominant. Future studies might address additional factors that potentially affect participation, e.g. child's preferences and family function.
DeNet: An explicit distance ensemble model for person re-identification

In this paper, we address the problem of person reidentification (re-id), which remains to be challenging due to view point changes, pose variations, different camera settings, etc. Different from common methods that concatenate descriptors extracted from different support regions and feature channels directly as a long vector, we encode the importance of different feature channels and support regions explicitly and propose a two-layer distance ensemble model called DeNet to measure the similarity between two images. The first layer of DeNet combines distances of different support regions while the second layer weights different feature channels. Weight parameters of DeNet are learnt under the large margin framework with the goal of maximizing the difference between distances of positive and negative matching pairs. Our method achieves very competitive results on the widely used VIPeR and PRID 450S datasets.
Measuring Security Investment Benefit for Off the Shelf Software Systems - A Stakeholder Value Driven Approach

This paper presents the Threat Modeling method based on Attacking Path Analysis (T-MAP) which quantifies security threats by calculating the total severity weights of relevant attacking paths for Commercial Off The Shelf (COTS) based systems. Compared to existing approaches, T-MAP is sensitive to an organization’s business value priorities and IT environment. It distills the technical details of thousands of relevant software vulnerabilities into management-friendly numbers at a high-level, and systematically establishes the traceability and consistency from management-level organizational value propositions to technical-level security threats and corresponding mitigation strategies. In its initial usage in a large IT organization, T-MAP has demonstrated promising strength in prioritizing and estimating security investment effectiveness, as well as in evaluating the security performance of COTS systems. In the case study, we demonstrate the steps of using T-MAP to analyze the cost-effectiveness of how system patching, user account control and firewall can improve security. In addition, we introduce a software tool that automates the T-MAP.
Interconnection system with software able to interconnect 4.0 generation machines with the whole enterprise system

An important application of the industrial vision consists in the quality control and the verification, in particular, of the completeness of the assembled products (presence/absence of parts, type, position, orientation, etc.). In fact, in Europe there are around 3,000 small and medium-sized enterprises which operate in the field of artificial vision. They provide services and products to another 300,000 SMEs engaged in the construction of machinery and automation. Around 80% of the industrial vision systems applications are related to quality control, such as 2D and 3D analysis, surface inspection and completeness inspection. The completeness inspection or completeness check is one of the basic applications of the artificial vision. It is about identifying the object, verifying the presence of parts of this object, identifying faulty components and sometimes estimating the position and features of a component. On the market there are several available products that try to solve this problem using 2D technologies. However, these 2D completeness inspection systems suffer from serious shortcomings that limit their performance and robustness. This project aims to develop efficient 3D systems for completeness checking that are similar to current 2D inspection systems in terms of speed, ease of use and integration, while offering more features. The developed project analyzes and devises a system of interconnection within the Italgom Company, in which a series of experimental and research actions have been activated 3110 Pagani Antonio et al. in order to connect a series of new 4.0 machines to the company system. The project therefore witnessed the development of a series of code writing actions, configurations and tests to define the control system that is completely interconnected with the company.
Perspectives on Performance : The Performance Prism Professor

The same confusion and uncertainty exists in many organisations when it comes to performance. A few years ago one of the authors spent some time working with the senior management team of a manufacturing company that produced door and window frames. The aim of the project was to establish whether people at different levels of the organisation’s hierarchy had the same understanding of performance. Two interactions in particular stand out. The first involved the managing director explaining how he felt the business won orders.
Design Principles for Pluripotent Stem Cell-Derived Organoid Engineering

Human morphogenesis is a complex process involving distinct microenvironmental and physical signals that are manipulated in space and time to give rise to complex tissues and organs. Advances in pluripotent stem cell (PSC) technology have promoted the in vitro recreation of processes involved in human morphogenesis. The development of organoids from human PSCs represents one reliable source for modeling a large spectrum of human disorders, as well as a promising approach for drug screening and toxicological tests. Based on the “self-organization” capacity of stem cells, different PSC-derived organoids have been created; however, considerable differences between in vitro-generated PSC-derived organoids and their in vivo counterparts have been reported. Advances in the bioengineering field have allowed the manipulation of different components, including cellular and noncellular factors, to better mimic the in vivo microenvironment. In this review, we focus on different examples of bioengineering approaches used to promote the self-organization of stem cells, including assembly, patterning, and morphogenesis in vitro, contributing to tissue-like structure formation.
Developing a comprehensive and comparative questionnaire for measuring personality in chimpanzees using a simultaneous top‐down/bottom‐up design

One effective method for measuring personality in primates is to use personality trait ratings to distill the experience of people familiar with the individual animals. Previous rating instruments were created using either top‐down or bottom‐up approaches. Top‐down approaches, which essentially adapt instruments originally designed for use with another species, can unfortunately lead to the inclusion of traits irrelevant to chimpanzees or fail to include all relevant aspects of chimpanzee personality. Conversely, because bottom‐up approaches derive traits specifically for chimpanzees, their unique items may impede comparisons with findings in other studies and other species. To address the limitations of each approach, we developed a new personality rating scale using a combined top‐down/bottom‐up design. Seventeen raters rated 99 chimpanzees on the new 41‐item scale, with all but one item being rated reliably. Principal components analysis, using both varimax and direct oblimin rotations, identified six broad factors. Strong evidence was found for five of the factors (Reactivity/Undependability, Dominance, Openness, Extraversion, and Agreeableness). A sixth factor (Methodical) was offered provisionally until more data are collected. We validated the factors against behavioral data collected independently on the chimpanzees. The five factors demonstrated good evidence for convergent and predictive validity, thereby underscoring the robustness of the factors. Our combined top‐down/bottom‐up approach provides the most extensive data to date to support the universal existence of these five personality factors in chimpanzees. This framework, which facilitates cross‐species comparisons, can also play a vital role in understanding the evolution of personality and can assist with husbandry and welfare efforts. Am. J. Primatol. 75:1042–1053, 2013. © 2013 Wiley Periodicals, Inc.
Tactile interface for stimulation of fingertip via lateral traction.

Tactile displays are gaining recognition as new human-machine interfaces. This paper present a low-weight, single-axis tactile interface designed to stimulate the fingertip through lateral traction. It operates with two ultrasonic linear motors able to move a small plate in contact with the user’s fingertip. This miniature interface is capable of a wide range of stimulation signals due to its high force output (0.6 N), its long throw (3 mm) and its high speed (13 mm/s). This interface is driven under closed loop control employing a Hall-effect sensor for position measurement. A model and experimental results will be presented.
Regional differences in the developmental trajectory of lateralization of the language network

The timing and developmental factors underlying the establishment of language dominance are poorly understood. We investigated the degree of lateralization of traditional frontotemporal and modulatory prefrontal‐cerebellar regions of the distributed language network in children (n = 57) ages 4 to 12—a critical period for language consolidation. We examined the relationship between the strength of language lateralization and neuropsychological measures and task performance. The fundamental language network is established by four with ongoing maturation of language functions as evidenced by strengthening of lateralization in the traditional frontotemporal language regions; temporal regions were strongly and consistently lateralized by age seven, while frontal regions had greater variability and were less strongly lateralized through age 10. In contrast, the modulatory prefrontal‐cerebellar regions were the least strongly lateralized and degree of lateralization was not associated with age. Stronger core language skills were significantly correlated with greater right lateralization in the cerebellum. Hum Brain Mapp 35:270–284, 2014. © 2012 Wiley Periodicals, Inc.
Robot localization and mapping problem with unknown noise characteristics

In this paper, we examine the H<inf>∞</inf> Filter-based SLAM especially about its convergence properties. In contrast to Kalman Filter approach that considers zero mean gaussian noise, H<inf>∞</inf> Filter is more robust and may provide sufficient solutions for SLAM in an environment with unknown statistical behavior. Due to this advantage, H<inf>∞</inf> Filter is proposed in this paper, to efficiently estimate the robot and landmarks location under worst case situations. H<inf>∞</inf> Filter requires the designer to appropriately choose the noise's covariance with respect to γ to obtain a desired outcome. We show some of the conditions to be satisfy in order to achieve better estimation results than Kalman Filter. From the experimental results, H<inf>∞</inf> Filter performs better than Kalman Filter for a case of bigger robot initial uncertainties. Subsequently, this proved that <inf>∞</inf> Filter can provide another available estimation method for especially in SLAM.
Simultaneous Detection of Six Diarrhea-Causing Bacterial Pathogens with an In-House PCR-Luminex Assay

ABSTRACT Diarrhea can be caused by a range of pathogens, including several bacteria. Conventional diagnostic methods, such as culture, biochemical tests, and enzyme-linked immunosorbent assay (ELISA), are laborious. We developed a 7-plex PCR-Luminex assay to simultaneously screen for several of the major diarrhea-causing bacteria directly in fecal specimens, including pathogenic Aeromonas, Campylobacter jejuni, Campylobacter coli, Salmonella, Shigella, enteroinvasive Escherichia coli (EIEC), Vibrio, and Yersinia. We included an extrinsic control to verify extraction and amplification. The assay was first validated with reference strains or isolates and exhibited a limit of detection of 103 to 105 CFU/g of stool for each pathogen as well as quantitative detection up to 109 CFU/g. A total of 205 clinical fecal specimens from individuals with diarrhea, previously cultured for enteric pathogens and tested for Campylobacter by ELISA, were evaluated. Using these predicate methods as standards, sensitivities and specificities of the PCR-Luminex assay were 89% and 94% for Aeromonas, 89% and 93% for Campylobacter, 96% and 95% for Salmonella, 94% and 94% for Shigella, 92% and 97% for Vibrio, and 100% and 100% for Yersinia, respectively. All discrepant results were further examined by singleplex real-time PCR assays targeting different gene regions, which revealed 89% (55/62 results) concordance with the PCR-Luminex assay. The fluorescent signals obtained with this approach exhibited a statistically significant correlation with the cycle threshold (CT ) values from the cognate real-time PCR assays (P < 0.05). This multiplex PCR-Luminex assay enables sensitive, specific, and quantitative detection of the major bacterial causes of gastroenteritis.