Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplex Real-Time PCR Diagnostic of Relapsing Fevers in Africa

Background In Africa, relapsing fever borreliae are neglected arthropod-borne pathogens causing mild to deadly septicemia and miscarriage. The closely related Borrelia crocidurae, Borrelia duttonii, Borrelia recurrentis and Borrelia hispanica are rarely diagnosed at the species level, hampering refined epidemiological and clinical knowledge of the relapsing fevers. It would be hugely beneficial to have simultaneous detection and identification of Borrelia to species level directly from clinical samples. Methodology/Principal Findings We designed a multiplex real-time PCR protocol targeting the 16S rRNA gene detecting all four Borrelia, the glpQ gene specifically detecting B. crocidurae, the recN gene specifically detecting B. duttonii/B. recurrentis and the recC gene specifically detecting B. hispanica. Compared to combined 16S rRNA gene and flaB gene sequencing as the gold standard, multiplex real-time PCR analyses of 171 Borrelia-positive and 101 Borrelia-negative control blood specimens yielded 100% sensitivity and specificity for B. duttonii/B. recurrentis and B. hispanica and 99% sensitivity and specificity for B. crocidurae. Conclusions/Significance The multiplex real-time PCR developed in this study is a rapid technique for both molecular detection and speciation of relapsing fever borreliae from blood in Africa. It could be incorporated in point-of-care laboratory to confirm diagnosis and provide evidence of the burden of infection attributed to different species of known or potentially novel relapsing fever borreliae.
Comparison of the risks of cancer incidence and mortality following radiation therapy for benign and malignant disease with the cancer risks observed in the Japanese A-bomb survivors

Purposes : To compare the radiation-associated relative risks of cancer incidence and mortality in groups exposed to ionizing radiation in the course of treatment for a variety of malignant and non-malignant conditions with those in the Japanese A-bomb survivor cancer incidence and mortality data. Materials and methods : Comparison of the excess relative risk coefficients derived from published information for each study with the excess relative risk coefficient in comparable (age at exposure, time since exposure, sex) matched subsets of the Japanese A-bomb survivor cancer incidence and mortality data. Results : Sixty-five studies of persons who have received appreciable doses of ionizing radiation in the course of treatment and for whom there is adequate ascertainment of cancer incidence or mortality are identified, from which 116 cancer-site-specific estimates of excess relative risk are derived. Relative risks tend to be lower in the medical series than in the Japanese A-bomb survivors. The most marked discrepancies between the relative risks in the medical series and in the A-bomb survivors are for leukaemia, where 12 of the 17 medical studies have significantly lower relative risks than those observed in the Japanese data. However, the ratio between the relative risks in the medical studies and in the Japanese data tends to diminish with increasing average or maximal therapy dose. This is observed for all cancer sites and is particularly marked for leukaemia. After taking account of cell sterilization and dose fractionation the apparent differences between the relative risks for leukaemia in the Japanese A-bomb survivors and in the medical series largely disappear. This suggests that cell sterilization largely accounts for the discrepancy between the relative risks in the Japanese data and the medical studies. Other factors, such as the differences in underlying cancer risks between the Japanese A-bomb survivors and the medical series, and dose-fractionation effects, may also contribute. Conclusions : The relative risks of cancer in studies of persons exposed to appreciable doses of ionizing radiation in the course of treatment for a variety of malignant and non-malignant conditions are generally less than those in comparable subsets of the Japanese A-bomb survivor cancer incidence and mortality data. Cell sterilization effects can largely explain the discrepancy between the Japanese and the medical series.
Optimal Virtualized Resource Slicing for Device-to-Device Communications

The Device-to-Device (D2D) communication principle is envisaged to become the key enabler of direct localized communication between mobile nodes that will propel a plethora of novel location-based services. On parallel efforts, virtualization of the Radio Access Network (RAN) is rising as a primal technology for emerging and future wireless networks in which multiple mobile network providers can dynamically share underlying radio resources based on the physical infrastructure. In essence, this work shortens the gap between these two important areas by proposing a set of optimization problem formulations to extend previous works on RAN virtualization and explicitly provide resource slicing for D2D communications. To this end, we aim to yield upper bounds on network performance by devising optimal D2D resource slicing via mathematical programming formulations. In addition, sub-optimal low complexity algorithms, amenable to practical (real-time) implementation, are detailed. Via a wide set of numerical investigations, we show that the proposed solution achieves significant gains in terms of system throughput compared to previous related resource slicing techniques which are D2D oblivious.
Effect of Mix Constituents and Curing Conditions on Compressive Strength of Sustainable Self-Consolidating Concrete

The production of cement requires significant energy and is responsible for more than 5% of global CO2 emissions; therefore it is imperative to reduce the production and use of ordinary portland cement (OPC). This paper examines the compressive strength development of low water-to-binder (w/b) ratio self-consolidating concrete (SCC) in which 90% of the cement is replaced with industrial by-products including ground granulated blast furnace slag (GGBS), fly ash, and silica fume. The emphasis in this paper is on replacing a large volume of cement with GGBS, which represented 10% to 77.5% of the cement replaced. Fresh properties at w/b ratio of 0.27 were examined by estimating the visual stability index (VSI) and t50 time. The compressive strength was determined after 3, 7, 28, and 56 days of curing. The control mix made with 100% OPC developed compressive strength ranging from 55 MPa after three days of curing to 76.75 MPa after 56 days of curing. On average, sustainable SCC containing 10% OPC developed strength ranging from 31 MPa after three days of curing to 56.4 MPa after 56 days of curing. However, the relative percentages of fly ash, silica fume, and GGBS in the 90% binder affect the strength developed as well. In addition, this paper reports the effect of the curing method on the 28 day compressive strength of environmentally friendly SCC in which 90% of the cement is replaced by GGBS, silica fume, and fly ash. The highest compressive strength was achieved in samples that were cured for three days under water, then left to air-dry for 25 days, compared to samples cured using chemical compounds or samples continuously cured under water for 28 days. The study confirms that SCC with 10% OPC and 90% supplementary cementitious composites (GGBS, silica fume, fly ash) can achieve compressive strength sufficient for many practical applications by incorporating high amounts of GGBS. In addition, air-curing of samples in a relatively high temperature (after three days of water curing) produce a higher 28 day compressive strength compared to water curing for 28 days, or membrane curing.
Robust information-theoretic clustering

How do we find a natural clustering of a real world point set, which contains an unknown number of clusters with different shapes, and which may be contaminated by noise? Most clustering algorithms were designed with certain assumptions (Gaussianity), they often require the user to give input parameters, and they are sensitive to noise. In this paper, we propose a robust framework for determining a natural clustering of a given data set, based on the minimum description length (MDL) principle. The proposed framework, Robust Information-theoretic Clustering (RIC), is orthogonal to any known clustering algorithm: given a preliminary clustering, RIC purifies these clusters from noise, and adjusts the clusterings such that it simultaneously determines the most natural amount and shape (subspace) of the clusters. Our RIC method can be combined with any clustering technique ranging from K-means and K-medoids to advanced methods such as spectral clustering. In fact, RIC is even able to purify and improve an initial coarse clustering, even if we start with very simple methods such as grid-based space partitioning. Moreover, RIC scales well with the data set size. Extensive experiments on synthetic and real world data sets validate the proposed RIC framework.
New Strategy for Rapid Diagnosis and Characterization of Fungal Infections: The Example of Corneal Scrapings

Purpose The prognosis of people infected with Fungi especially immunocompromised depends on rapid and accurate diagnosis to capitalize on time administration of specific treatments. However, cultures produce false negative results and nucleic-acid amplification techniques require complex post-amplification procedures to differentiate relevant fungal types. The objective of this work was to develop a new diagnostic strategy based on real-time polymerase-chain reaction high-resolution melting analysis (PCR-HRM) that a) detects yeasts and filamentous Fungi, b) differentiates yeasts from filamentous Fungi, and c) discriminates among relevant species of yeasts. Methods PCR-HRM detection limits and specificity were assessed with a) isolated strains; b) human blood samples experimentally infected with Fungi; c) blood experimentally infected with other infectious agents; d) corneal scrapings from patients with suspected fungal keratitis (culture positive and negative) and e) scrapings from patients with suspected bacterial, viral or Acanthamoeba infections. The DNAs were extracted and mixed with primers diluted in the MeltDoctor® HRM Master Mix in 2 tubes, the first for yeasts, containing the forward primer CandUn (5'CATGCCTGTTTGAGCGTC) and the reverse primer FungUn (5'TCCTCCGCTT ATTGATATGCT) and the second for filamentous Fungi, containing the forward primer FilamUn (5'TGCCTGTCCGAGCGTCAT) and FungUn. Molecular probes were not necessary. The yields of DNA extraction and the PCR inhibitors were systematically monitored. Results PCR-HRM detected 0.1 Colony Forming Units (CFU)/µl of yeasts and filamentous Fungi, differentiated filamentous Fungi from yeasts and discriminated among relevant species of yeasts. PCR-HRM performances were higher than haemoculture and sensitivity and specificity was 100% for culture positive samples, detecting and characterizing Fungi in 7 out 10 culture negative suspected fungal keratitis. Conclusions PCR-HRM appears as a new, sensitive, specific and inexpensive test that detects Fungi and differentiates filamentous Fungi from yeasts. It allows direct fungal detection from clinical samples and experimentally infected blood in less than 2.30 h after DNA extraction.
Combining Gold Nanoparticles with Real-Time Immuno-PCR for Analysis of HIV p24 Antigens

We have improved real-time immuno-PCR (IPCR) with nanoparticle based amplification. Gold magnetic particles were functionalized with antibodies against the HIV capsid protein p24 and gold nanoparticles were functionalized with both oligonucleotide barcodes and antibodies against a non- overlapping region of the cognate p24. In the presence of p24, the gold magnetic particles and the gold nanoparticles form sandwiched structures that are magnetically separated from mixture. After dehybridization of the barcode DNA on the gold nanoparticle, the released barcodes are quickly identified by realtime PCR. The limit of detection was 100 copies of p24 antigens. Results show that the real-time IPCR through nanoparticle based barcode amplification offers an disruptive approach to p24 detection and quantification, thus may potentially shorten the window of HIV-1 diagnosis, and might be valuable to monitor the response to anti-retroviral treatment when RNA copy number is very below.
Metaphorical Sentences Are More Emotionally Engaging than Their Literal Counterparts

Why do people so often use metaphorical expressions when literal paraphrases are readily available? This study focuses on a comparison of metaphorical statements involving the source domain of taste (e.g., “She looked at him sweetly”) and their literal paraphrases (e.g., “She looked at him kindly”). Metaphorical and literal sentences differed only in one word and were normed for length, familiarity, imageability, emotional valence, and arousal. Our findings indicate that conventional metaphorical expressions are more emotionally evocative than literal expressions, as the amygdala and the anterior portion of the hippocampus were more active in the metaphorical sentences. They also support the idea that even conventional metaphors can be grounded in sensorimotor and perceptual representations in that primary and secondary gustatory areas (lateral OFC, frontal operculum, anterior insula) were more active as well. A comparison of the individual words that distinguished the metaphorical and literal sentences revealed greater activation in the lateral OFC and the frontal operculum for the taste-related words, supporting the claim that these areas are relevant to taste.
Long Term Research Project # 20197 – PageSpace Report A : Redesigning theWeb : From Passive Pages to Coordinated Agents in PageSpaces

The Web in its current state does not support distributed applications well. Existing approaches are oriented towards centralized applications at servers, or local programs within clients. To overcome this deficit, a framework for distributed, coordinated agents within the Web is designed with PageSpace. We take a specific approach to coordinate agents in PageSpace applications, namely variants of coordination language Linda that support rules and services to guide their cooperation. This technology is integratedwith the standardWeb technology and the programming language Java. Several kinds of agents life in the PageSpace: User interface agents, personal homeagents, the agents that implement applications, and the kernel agents of the platform. Within the architecture it is possible to support fault-tolerance and mobile agents as well.
On the impact of fading and inter-piconet interference on Bluetooth performance

In this paper we propose a simple method to evaluate the impact of fading and inter-piconet interference on Bluetooth performance. We consider in detail the joint effect, on packet error statistics, of interference produced by adjacent Bluetooth piconets and fading. Hence, we illustrate the proposed method by investigating the potential performance tradeoff among the different radio packet formats supplied by Bluetooth, as a function of the radio channel conditions and interference levels.
Learning Large-Scale Conditional Random Fields

Conditional Random Fields (CRFs) [Lafferty et al., 2001] can offer computational and statistical advantages over generative models, yet traditional CRF parameter and structure learning methods are often too expensive to scale up to large problems. This thesis develops methods capable of learning CRFs for much larger problems. We do so by decomposing learning problems into smaller, simpler subproblems. These decompositions allow us to trade off sample complexity, computational complexity, and potential for parallelization, and we can often optimize these trade-offs in model- or data-specific ways. The resulting methods are theoretically motivated, are often accompanied by strong guarantees, and are effective and highly scalable in practice. In the first part of our work, we develop core methods for CRF parameter and structure learning. For parameter learning, we analyze several methods and produce PAC learnability results for certain classes of CRFs. Structured composite likelihood estimation proves particularly successful in both theory and practice, and our results offer guidance for optimizing estimator structure. For structure learning, we develop a maximum-weight spanning tree-based method which outperforms other methods for recovering tree CRFs. In the second part of our work, we take advantage of the growing availability of parallel platforms to speed up regression, a key component of our CRF learning methods. Our Shotgun algorithm for parallel regression can achieve near-linear speedups, and extensive experiments show it to be one of the fastest methods for sparse regression.
Person trip data browser, analyzer and space-time visualizer

Understanding human mobility from a spatial perspective is important to urban transport planners, human geographers, social scientists and other geospatial information users in order to improve public transport planning, sustainable urban planning and socio-economic planning by acquiring information about transportation mode by age, gender, occupation, purposes, etc. This PTS Person Trip Survey data was converted as one minute synthesized dataset by applying OD Origin and Destination route identification process and stored in csv files. However, handling of these large amounts PTS data requires high-speed computational power, complex database management systems and considerable period of time to extract, manipulate and analyse the data for end users. In this paper we discuss about handling of large scale PTS data with Web-GIS in order to use in scientific and research communities in time and cost effective way.
Robot Team Exploration with Communication Restrictions

In the event of an earthquake or fire, search and rescue efforts may be delayed until it is safe for a human team to enter the area. A team of robots could enter in advance to provide maps, images and locations of interest to the human team, allowing them to prepare their approach when they can enter. In a disaster area, communication may also be limited. We have developed a set of distributed algorithms that make use of a small number of robots to fully explore an unknown environment even with restrictions on communication, team size, and available sensors. We show, through proofs and experiments, that the algorithm will allow the team of robots to fully explore the environment and maintain the necessary communication to return the information to the search and rescue team waiting outside.
Self-Perception of Swallowing-Related Problems in Laryngopharyngeal Reflux Patients Diagnosed with 24-Hour Oropharyngeal pH Monitoring

Background and Objectives. Swallowing difficulty is considered one of the nonspecific symptoms that many patients with laryngopharyngeal reflux complain of. However, the relationship between laryngopharyngeal reflux and swallowing problems is not clear. The purpose of this work is to explore correlation between swallowing-related problems and laryngopharyngeal reflux (LPR) in a group of patients diagnosed with oropharyngeal pH monitoring and to study the effect of laryngopharyngeal reflux on the patients' self-perception of swallowing problems. Methods. 44 patients complaining of reflux-related problems were included in the study. Patients underwent 24-hour oropharyngeal pH monitoring and were divided into positive and negative LPR groups based on the pH monitoring results. All patient filled out the Dysphagia Handicap Index (DHI) and Reflux Symptom Index (RSI) questionnaires. Comparison was made between the positive and negative LPR groups regarding the results of the DHI and RSI ratings. Also, correlation between DHI scores, RSI scores, and pH monitoring results was studied. Results. Significant difference was reported between positive and negative LPR groups regarding DHI scores, RSI scores, and overall rating of swallowing difficulty. There was significant correlation demonstrated between DHI scores, RSI scores, and 24-hour oropharyngeal pH results. Conclusion. Laryngopharyngeal reflux appears to have a significant impact on patients' self-perception of swallowing problems as measured by DHI.
List-coloring apex-minor-free graphs

A graph H is t-apex if H-X is planar for some subset X of V(H) of size t. For any integer t>=0 and a fixed t-apex graph H, we give a polynomial-time algorithm to decide whether a (t+3)-connected H-minor-free graph is colorable from a given assignment of lists of size t+4. The connectivity requirement is the best possible in the sense that for every t>=1, there exists a t-apex graph H such that testing (t+4)-colorability of (t+2)-connected H-minor-free graphs is NP-complete. Similarly, the size of the lists cannot be decreased (unless P=NP), since for every t>=1, testing (t+3)-list-colorability of (t+3)-connected K_{t+4}-minor-free graphs is NP-complete.
RAD9 and RAD24 define two additive, interacting branches of the DNA damage checkpoint pathway in budding yeast normally required for Rad53 modification and activation

In budding yeast, RAD9 and RAD24/RAD17/MEC3 are believed to function upstream of MEC1 and RAD53 in signalling the presence of DNA damage. Deletion of any one of these genes reduces the normal G1/S and G2/M checkpoint delays after UV irradiation, whereas in rad9Δ–rad24Δ cells the G1/S checkpoint is undetectable, although there is a residual G2/M checkpoint. We have shown previously that RAD9 also controls the transcriptional induction of a DNA damage regulon (DDR). We now report that efficient DDR induction requires all the above‐mentioned checkpoint genes. Residual induction of the DDR after UV irradiation observed in all single mutants is not detectable in rad9Δ–rad24Δ. We have examined the G2/M checkpoint and UV sensitivity of single mutants after overexpression of the checkpoint proteins. This analysis indicates that RAD9 and the RAD24 epistasis group can be placed onto two separate, additive branches that converge on MEC1 and RAD53. Furthermore, MEC3 appears to function downstream of RAD24/RAD17. The transcriptional response to DNA damage revealed unexpected and specific antagonism between RAD9 and RAD24. Further support for genetic interaction between RAD9 and RAD24 comes from study of the modification and activation of Rad53 after damage. Evidence for bypass of RAD53 function under some conditions is also presented.
Protein aggregation : A perspective from amyloid and inclusion-body formation

Over the past few decades, an overwhelmingly vast amount of research has been dedicated to understanding protein aggregation. This review summarizes the current understanding of protein aggregation from the viewpoint of its two important manifestations: formation of amyloid fibrils and inclusion bodies. The article summarizes the structure, mechanism of formation, predisposing factors and measures of overcoming inclusion body and amyloid formation. The protective role played by molecular evolution in curbing aggregation and results from recent studies on the prediction of aggregation rates based on primary structure have also been discussed.