Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of the structure and mechanism of a PQQ biosynthetic pathway component, PqqC, and a bioinformatics analysis of potential PQQ producing organisms

PQQ is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenase reaction. It has also been proposed to play a role as a bacterial vitamin. The following work has defined 144 bacteria species that contain the machinery to form PQQ. PQQ formation is based on a conserved operon, pqqABCDEF, in Klebsiella pneumoniae. The last enzymatic step in the PQQ biogenesis pathway is catalyzed by PqqC and involves a ring closure and eight electron oxidation of the substrate AHQQ. Wild type (WT) PqqC and various active site mutants have been studied. The asparagine and alanine mutations at the histidine 84 position have supported the published mechanism and shown a new role for H84 as an active site acid. This was shown by anaerobic reactions, where H84A was capable of proceeding to a quinol intermediate anaerobically, but the more conservative H84N mutation was not. Aerobically, both mutations were able to form PQQ. Recent X-ray investigations of PqqC variants Y175F (with PQQ bound), H154S (with PQQ bound) and a R179S/Y175S double mutant (with AHQQ bound) show that the enzyme is alternately in a closed, open and open conformation, respectively. Though R179S/Y175S does not form the characteristic closed conformation seen in the WT-PQQ structure, it is still able to inititate a ring closure with AHQQ. Using apo-glucose dehydrogenase to assay for PQQ production, none of the mutants are capable of product formation. Spectrophotometric assays give insight into the incomplete reactions being catalyzed by the mutants. Active site variants Y175F, H154N and R179S form a quinoid intermediate anaerobically. Y175S is capable of reaction further and forms a quinol intermediate anaerobically after forming a quinoid. Y175F, H154N and R179S require O2 to proceed to the quinol intermediate. None of the mutants preclude substrate/product binding. Indicating that in all cases, oxidative chemistry is impeded because no mutants can react fully to form quinone even in the presence of O2. The residues targeted are proposed to form a proteinaceous core O2 binding structure that also contributes to O2 activation.
Tracking People and Activities in Video Recordings of Classroom Presentations

This paper presents an intelligent system for video recording of classroom presentations. The system includes a tracking algorithm to track the speaker, recognizes six speaker’s activities and records the presentation in video. The tracking algorithm considerably supports different indoor illumination conditions, tracks the speaker in both frontal and side views, and adapts to body scale. Speaker’s face and hand regions are obtained by tracking skin regions and torso vertical boundaries are given by the median edge points. The activity classiﬁers achieved recall rates from 10 to 86.67%.
Container Network Topology Modeling Extended

Distributed applications are heavily inﬂuenced by the properties of the underlying network, i.e. , bandwidth, link latency, packet loss rate and jitter. Nevertheless, researchers, practitioners and engineers should be able to assess the impact of those properties on the system’s performance and correctness. Those network properties have direct observable and measurable eﬀects on the application, while the internal behavior of the underlying network elements, such as switches and routers, is harder to capture from an application perspective. This observation leads us to explore designs that only emulate the macro behavior of complex topologies rather than its internal details. We present Need , a decentralized network topology emulator that explores this idea. It emulates a network topology beneath unmodiﬁed containerized applications, it is agnostic of the application language or transport protocol and can scale to thousands of containers by adding more nodes to a cluster of commodity machines. Our evaluation shows that Need emulation accuracy is on-par with state-of-the-art systems that emulate the full state of the network. We show that it can be used not only to reproduce previous results from the literature but also to assess the behavior of geo-distributed systems as if they were deployed on a WAN testbed or production network.
The Interplay Between Sexually Transmitted Infections and Human Immunodeficiency Virus An Evolving Story

I t is recognized that persons with sexually transmitted infections (STIs) are at increased risk for acquisition of human immunodeficiency virus (HIV). Early studies primarily linked this association to high-risk sexual behaviors that placed persons at risk for both STIs and HIV. However, continuing research has elegantly revealed that independent of behavioral factors, the presence of an STI, especially ulcerative types (eg, herpes simplex virus 2 [HSV-2], primary syphilis), seems to be associated with a higher risk for subsequent HIV acquisition. The mechanisms for this heightened risk include the disruption of the mucosal epithelial lining of the genital tract together with the local recruitment and influx of immature dendritic and CD4 cells as part of the local inflammatory process. These cells contain the CCR5 receptor, the primary target for the entry of HIV into the body. Although the initial findings of increased acquisition focused on ulcerative STIs, recent evidence has demonstrated the importance of nonulcerative STIs (eg, gonorrhea, Chlamydia), as reviewed by Naresh et al. In addition to these traditional nonulcerative STIs, data just released indicate that human papillomavirus (HPV) infections are also a risk factor for HIV acquisition among both heterosexual men and men who have sex with men as described in studies done in South Africa and the United States, respectively. Of note, multiple and Bhigh-risk[ HPV types seem to convey the highest risk. In addition to the heightened risk for HIV acquisition, the presence of an STI may increase the transmission of HIV from infected persons to their partners because of the higher plasma HIV viral load and via disruption of the normal mucosal barriers, with elevated genital HIV viral load shedding at the site of the coexisting infection. Collectively, these data suggest that STIs have had a dramatic worldwide impact on the HIV epidemic through the interplay between STIs and the increased risk of HIV acquisition and transmission. What should we do with these findings? Intuitively, it would seem that STI prevention and treatment programs should be implemented where needed and reinforced where ongoing in an effort to reduce the number of incident HIV infections. Several community-based studiesVlargely within AfricaVhave examined the impact of STI treatment on reducing the incidence of HIV infections. As described by Naresh et al (Table 3), to date, many of these studies have revealed surprisingly little to no benefit from such interventions. Potential reasons for the lack of efficacy are explored by Naresh et al including that STIs may play a smaller role in a more advanced HIV epidemic, that the antibiotic used in some studies had a suboptimal effect against many of the prevalent STIs in the community, and of course, the possibility that control of bacterial STIs may not be an effective means of preventing HIV-1 infection. EDITORIAL COMMENT
DeepData: Web application for Azores deep sea

Azores’ deep sea is the habitat of several living beings. Knowing the relationships that these living beings establish with their habitats is essential for the development of appropriate measures for protecting marine ecosystems. The species distribution models (SDM), which associate environmental conditions with the occurrence of species, are an effective way to predict the relationships between living beings and the environment. This paper describes the web application DeepData, which integrates several data sources that store marine data, stores the data in a relational database and enables the application of predictive models of species distribution to the marine region of the Azores. In this paper, we also present the validation of the application DeepData. The validation results highlight the ease of use of the application DeepData and its usefulness for the calculation of SDM. However, some features need to be adjusted to allow for greater user interaction with statistical models.
Predicting Economic Releases using Genetic Support Vector Machines

—This work’s goal is ﬁnancial markets forecasting. More speciﬁcally, it aims at predicting exchange rate market behaviour during isolated periods: the period after the release of macroeconomic indicators. Soft computing techniques (Support Vector Machines and Genetic Algorithms as a hybrid model) are used to predict Foreign Exchange market returns. The innovation lies not only in the used hybrid model, but also in a combination of predictive factors (including fundamental, technical and emotional) and the focus on proximity to real world practices rather than a theoretically-leaned overview. The model includes variables to increase the ability to trade under different scenarios, including unpredictable and unstable times. The Genetic Algorithm is used to pinpoint three different goals: Support Vector Machine hyperparameter tuning; ﬁnding the optimal periodicity of the technical indicators used and selecting the back-testing variables. The model was also tested under different conditions, namely trading a different instrument (future contract of the Standard & Poor’s 500 index) and without period isolation (trading continuously). The results were positive and consistently beat the corresponding benchmarks in the analyzed periods, in and out-of-sample. The success is veriﬁed not only in the macroeconomic release isolation but also (and with even better performance across all the used metrics) when applied to different conditions.
Early Invasive Adenocarcinoma of the Uterine Cervix

In an attempt to determine the natural history of early invasive adenocarcinoma of the cervix, defined as depth of invasion of 5 mm or less, an extensive review of the literature was undertaken, together with recent unpublished material of the author. Many of the cases had to be extracted from series dealing with microinvasive squamous cell carcinoma. The pons asinoruma for the pathologist is the differentiation between adenocarcinoma in situ and early invasion. The criteria for microinvasion are: 1. ) obvious invasion to 5 mm or less; 2. ) usually complete obliteration of the normal endocervical crypts; 3. ) extension beyond the normal glandular field; and 4. ) a stromal response characteristic of invasive carcinoma. Not all of these criteria are present in every case. In all 436 cases were collected. Allowing for vagueness of reports, 126 patients were treated by radical hysterectomy, and none had parametrial involvement. No cases of adnexal tumors were found in the 155 patients in whom one or both ovaries were removed. Of the 219 patients with pelvic lymph node dissection, five (2%) had metastasis. There were 15 recurrences and six tumor-related deaths in the 436 patients. Only 21 patients had conization as the only treatment, and none has suffered a recurrence. It appears that early invasive adenocarcinoma behaves in the same way as its squamous counterpart. Cold knife conization is acceptable treatment only when the cone biopsy has been adequately sampled and the margins are free, especially when preservation of fertility is an issue. Loop excision procedures obscure depth of invasion and margins and are not acceptable either for diagnosis or therapy. Multicentricity does not appear to require cylindrical cones. If hysterectomy is contemplated, removal of the adnexa, per se, is unnecessary.
Panton-Valentine LeukocidinYPositive Methicillin-Resistant Staphylococcus aureus Necrotizing Pneumonia Presenting as Fever of Unknown Origin

Panton-Valentine leukocidinYproducing strains of Staphylococcus aureus have been linked to rapidly progressive severe necrotizing pneumonia with low survival rates. We describe a previously healthy child who presented in a nontoxic fashion with prolonged fever and a radiographic picture of pulmonary nodules caused by a PantonValentine leukocidinYproducing S. aureus. Complete resolution was achieved after 4 weeks of antimicrobial therapy. (Infect Dis Clin Pract 2009;17: 55Y57) The pulmonary manifestations of Staphylococcus aureus infections have been well described. The community strains of S. aureus that carry the genes lukS-PV and lukF-PV encoding the subunits of the Panton-Valentine leukocidin (PVL), a poreforming toxin, seem to be associated with more severe disease, especially of the lung. The typical course of necrotizing pneumonia described in patients infected with such strains is characterized by a rapidly progressive illness, consisting of Bflulike^ symptoms, hemoptysis, leukopenia, and extensive lung necrosis. We describe an otherwise healthy child with necrotizing pneumonia caused by a PVL-positive methicillin-resistant S. aureus (MRSA) strain, presenting in an indolent fashion with fever for 26 days.
BaZINGA: Whitebox Fuzzing for Detecting Web Application Vulnerabilities

—Despite much research done in web security in the past few years, the security of web applications remains an important concern. The major issue with these applications comes from the source code itself, that is often written in unsafe languages, leading to the existence of vulnerabilities. This paper aims to improve the detection of vulnerabilities in PHP code. For that purpose it presents a whitebox fuzzer called BaZINGA that combines static analysis and concolic testing with fuzzing. We provide experimental results of running BaZINGA with code samples and open source applications.
South African Journal of Industrial Engineering May 2008 Vol 19(1): 17-30 ENTERPRISE RESOURCE PLANNING SOLUTION SELECTION CRITERIA IN MEDIUM- SIZED SOUTH AFRICAN COMPANIES

The purpose of this study is to identify the factors that medium-sized South African companies consider important in the acquisition of an Enterprise Resource Planning (ERP) solution. Through an extensive literature review, fourteen ERP selection criteria were identified. Using these fourteen criteria, a questionnaire was developed to test and rate these criteria on a 10-point scale. Results from the survey show that manufacturing and non-manufacturing companies rate reliability, compatibility, service, and support as the most important criteria when selecting an ERP solution.
Sources of Economic Growth for the period from 2003 to 2014 in Russia: a Structural Decomposition Analysis (SDA)

The last thirty years for the Russian economy have been characterized by a transition from plan to market. During this time, the Russian economy has experienced periods of recession and rapid recovery, the potential of which approached exhaustion at the end of the first decade of the 21st century. Three crises were superimposed on these trends: 1998, 2008 and 2014, accompanied by a decline in production, followed by a rapid (after the crises of 1998 and 2008) or a long (after the crisis of 2014) recovery of economic growth. Despite the fact that, in general, over the period covered, the volume of production in Russia increased slightly, large-scale changes in its structure occurred [Baranov, Bessonov, 2018]. Among such changes, there are large structural changes in the industries, characterized by changes over time of the structure and production volumes of various domestic goods. In the intercrisis decade (1998–2008) and the period from 2009–2014 production of manufacturing industries grew at a fast pace, while production of extractive industries, showed a smoother dynamics. In the period of recession (2008–2009) however, production of extractive industries fell slightly, while the dynamic of the manufacturing industries, showed a more noticeable decline in production. In addition, in the intercrisis decade (1998–2008) and the period from 2009–2014 there was a sharp growth in the services, whereas the mining and manufacturing industries saw a slower growth; we also saw a growth in production and exports, but a sharper growth in products imported. The presented dynamics of indicators can be considered as quite an understandable phenomenon. In Russia, in the epoch of a planned economy, the service sector was not developed, in the process of becoming a market, it only “made up for lost time”. With regard to the dynamics of the manufacturing industry, in a transition economy, to which the Russian economy was in the period under review, “products of the manufacturing sector were characterized by greater mobility
Authentication via User Profiling Extended Abstract

Online authentication using only a username and a textual password has been proven flawed over years. Some solutions have been adopting different types of passwords or adding more authentication factors. Due to sometimes requiring expensive hardware or demanding several actions from the user, some of these solutions are unusable in mobile devices. The solution described in this work is an additional authentication factor that uses the smartphone characteristics and its user configuration in order to create user profiles that will be used to authenticate the user, requiring no actions from the user. This way, the proposed solution provides a fast authentication that does not requires the user to perform any actions. The proposed solution is also as secure as existing solutions. Since mobile devices are subject to changes such as the installed applications, memorized networks and accounts, operating system upgrades among others, profile verification must be made allowing small changes. Therefore, the Authentication Server evaluates whether the freshly received profile is similar enough to the stored profile using defined thresholds. If static attributes are changed, or if a large number of attributes have been changed, then the verification fails immediately, activating the fallback mechanism defined by the third-party application.
The measurement of anterior chamber depth and axial length with the IOLMaster compared with contact ultrasonic axial scan

AIM: To compare the measurement of anterior chamber depth (ACD) and axial length (AL) by IOLMaster and contact ultrasonic (US) axial scan (A-scan). ·METHODS: Measurements of ACD and AL were prospectively obtained in 137 eyes of 121 subjects with the IOLMaster compared with measurements with the US. ·RESULTS: There was an excellent correlation between IOL Master and US measurements for the ACD ( =0.823; < 0.001) and AL ( =0.996; <0.001). The mean values of the parameters measured by IOLMaster and US were, respectively, as follows: ACD, 2.94± 0.49mm, 2.58± 0.51mm; AL, 24.37± 3.04mm, 23.81± 2.83mm. The mean differences of ACD and AL values between IOLMaster and US measurements were 0.36 ± 0.30mm, 0.56 ± 0.34 mm respectively, and they proved to be statistically significant ( < 0.001), with the 95% limits of agreement (LoA) from -0.08mm to +0.38mm for ACD and from -0.09mm to +0.69mm for AL. ·CONCLUSION: As noncontact biometry, IOLMaster provides accurate values. A high degree of agreement between US and IOLMaster was noted. It not only has the advantage of performing noncontact examinations, but also produces various additional data simultaneously and may thus obviate the need for multiple examinations. Further studies are needed to assess the interchangeability of measurements in clinical practice. ·
Pulmonary Infections WithMycobacterium avium-intracellulare in Women With Confirmed or Suspected Malignancy

Background: In the last 2 decades, there has been an increased interest in infections caused by nontuberculous mycobacteria (NTM). Mycobacterium avium complex is the most common PNTM in the United States. Pulmonary disease caused byMAI is often chronic and occurs particularly in the elderly, in women frequently without underlying lung disease. Although NTM infections are reported in patients with malignancy, few studies investigated the epidemiological, clinical, and radiological characteristics of pulmonary MAI infection in women with cancer. Materials andMethods:We retrospectively reviewedmedical and microbiologic records and radiographic findings of all female patients seen at the Moffitt Cancer Center in Tampa, Florida, with positive lung specimen cultures for MAI from January 1987 to January 2011. Microbiologic records included the cultures of expectorated sputum samples, bronchial wash or lavage, and lung biopsies. Radiographic findings obtained by high-resolution computed tomography permitted a classification of the lung MAI disease in 3 forms: cavitary, nodular bronchiectatic, and nodular form. Results: A total of 46 patients met the inclusion criteria during a 24-year period. The median age at the time of diagnoses was 68 years. There were some patients who had an underlying cancer, an underlying chronic lung disease, and a comorbid condition. Cough was the most common pulmonary symptom in most of our patients. The most common radiologic finding was consistent with a single nodule. A few of the female patients were definable as LadyWindermere syndrome. Symptomatic improvement was seen in most of the patients with either a monotherapy or a combination therapy. Conclusions: Physicians need to be aware of the possibility of coexisting pulmonary MAI in elderly women with cancer, principally breast and lung cancer, or chronic lung disease, with a chronic cough and a new nodule on the lung computed tomography scan. Early suspicion can lead to appropriate diagnosis, prompt therapy, and reduction of mortality.
An Efficient Unsupervised AdaptiveAntihub Technique for Outlier Detection in High Dimensional Data

-------------------------------------------------------- ABSTRACT ------------------------------------------------------------ Identification of unsupervised outliers in a high dimensional data becomes an emerging technique in today’s research in the area of data mining. Increase of dimensionality leads to various challenges. Hubness especially Antihubs (points that infrequently occur in k nearest neighbor lists) is the recently known concept for the increase of dimensionality pertaining to nearest neighbors. Outlier detection using AntiHub method is refined as Antihub 2 to reevaluate the outlier scores of a point produced by the AntiHub method. However, it leads to increase the computation time of an algorithm with large number of computations. This paper establishes an approach called AdaptiveAntihub, which embeds an adaptive technique in Antihub 2 for unsupervised outlier detection mainly to reduce the number of computations and computation time of an algorithm and compares the results produced by Antihub 2 with AdaptiveAntihub. The experimental results illustrate that AdaptiveAntihub outperforms well and it also proves that there is a significant reduction in the number of computations and computation time when this proposed technique is applied to detect unsupervised outliers in high dimensional data