Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for clonal expansion after antibiotic selection pressure: pneumococcal multilocus sequence types before and after mass azithromycin treatments.

BACKGROUND A clinical trial of mass azithromycin distributions for trachoma created a convenient experiment to test the hypothesis that antibiotic use selects for clonal expansion of preexisting resistant bacterial strains. METHODS Twelve communities in Ethiopia received mass azithromycin distributions every 3 months for 1 year. A random sample of 10 children aged 0-9 years from each community was monitored by means of nasopharyngeal swab sampling before mass azithromycin distribution and after 4 mass treatments. Swab specimens were tested for Streptococcus pneumoniae, and isolates underwent multilocus sequence typing. RESULTS Of 82 pneumococcal isolates identified before treatment, 4 (5%) exhibited azithromycin resistance, representing 3 different sequence types (STs): 177, 6449, and 6494. The proportion of isolates that were classified as one of these 3 STs and were resistant to azithromycin increased after 4 mass azithromycin treatments (14 of 96 isolates [15%]; P = .04). Using a classification index, we found evidence for a relationship between ST and macrolide resistance after mass treatments (P < .0001). The diversity of STs-as calculated by the unbiased Simpson index-decreased significantly after mass azithromycin treatment (P = .045). CONCLUSIONS Resistant clones present before mass azithromycin treatments increased in frequency after treatment, consistent with the theory that antibiotic selection pressure results in clonal expansion of existing resistant strains.
Travel-time prediction with support vector regression

Travel time is a fundamental measure in transportation. Accurate travel-time prediction also is crucial to the development of intelligent transportation systems and advanced traveler information systems. We apply support vector regression (SVR) for travel-time prediction and compare its results to other baseline travel-time prediction methods using real highway traffic data. Since support vector machines have greater generalization ability and guarantee global minima for given training data, it is believed that SVR will perform well for time series analysis. Compared to other baseline predictors, our results show that the SVR predictor can significantly reduce both relative mean errors and root-mean-squared errors of predicted travel times. We demonstrate the feasibility of applying SVR in travel-time prediction and prove that SVR is applicable and performs well for traffic data analysis.
Elucidating the Hemodynamic Origin of Ballistocardiographic Forces: Toward Improved Monitoring of Cardiovascular Health at Home

The ballistocardiogram (BCG), a signal describing the reaction forces of the body to cardiac ejection of blood, has recently gained interest in the research community as a potential tool for monitoring the mechanical aspects of cardiovascular health for patients at home and during normal activities of daily living. An important limitation in the field of BCG research is that while the BCG signal measures the forces of the body, the information desired (and understood) by clinicians and caregivers, regarding mechanical health of the cardiovascular system, is typically expressed as blood pressure or flow. This paper aims to explore, using system identification tools, the mathematical relationship between the BCG signal and the better-understood impedance cardiography (ICG) and arterial blood pressure (ABP) waveforms, with a series of human subject studies designed to asynchronously modulate cardiac output and blood pressure and with different magnitudes. With this approach, we demonstrate for 19 healthy subjects that the BCG waveform more closely maps to the ICG (flow) waveform as compared with the finger-cuff-based ABP (pressure) waveform, and that the BCG can provide a more accurate estimate of stroke volume (r=0.73, p <; 0.05) as compared with pulse pressure changes (r = 0.26). We also examined, as a feasibility study, for one subject, the ability to calibrate the BCG measurement tool with an ICG measurement on the first day, and then track changes in stroke volume on subsequent days. Accordingly, we conclude that the BCG is a signal more closely related to blood flow than pressures, and that a key health parameter for titrating care-stroke volume-can potentially be accurately measured with BCG signals at home using unobtrusive and inexpensive hardware, such as a modified weighing scale, as compared with the state-of-the-art ICG and ABP devices, which are expensive and obtrusive for use at home.
Is pre-operative imaging essential prior to ureteric stone surgery?

INTRODUCTION The aim of this study was to identify patients not requiring ureteric stone surgery based on pre-operative imaging (within 24 hours) prior to embarking on semirigid ureteroscopy (R-URS) for urolithiasis. METHODS The imaging of all consecutive patients on whom R-URS for urolithiasis was performed over a 12-month period was reviewed. All patients had undergone a plain x-ray of the kidney, ureters and bladder (KUB), abdominal non-contrast computed tomography (NCCT-KUB) or both on the day of surgery. RESULTS A total of 96 patients were identified for the study. Stone sizes ranged from 3mm to 20mm. Thirteen patients (14%) were cancelled as no stone(s) were identified on pre-operative imaging. Of the patients cancelled, 8 (62%) required NCCT-KUB to confirm spontaneous stone passage. CONCLUSIONS One in seven patients were stone free on the day of surgery. This negates the need for unnecessary anaesthetic and instrumentation of the urinary tract, with the associated morbidity. Up-to-date imaging prior to embarking on elective ureteric stone surgery is highly recommended.
Microbiological Screening Is Necessary to Distinguish Carriers of Plasmid-Mediated AmpC Beta-Lactamase-Producing Enterobacteriaceae and Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacteriaceae because of Clinical Similarity

Objectives Plasmid-mediated AmpC beta-lactamase-producing (pAmpC) Enterobacteriaceae are increasing worldwide, difficult to identify and often confounded with extended-spectrum beta-lactamase (ESBL) producers. The low prevalence precludes routine universal admission screening. Therefore, we evaluated potential risk factors for carriage of pAmpC-producing Enterobacteriaceae that would allow targeted screening to improve yield and reduce cost. Patients and methods We performed a case control study at a tertiary care center from 1/2006 to 12/2010. Cases were adult patients in whom pAmpC-producing Enterobacteriaceae were isolated; controls were chosen among carriers of ESBL-producing Enterobacteriaceae. Both infected and colonized patients were included. Results Over five years, we identified 40 pAmpC producers in 39 patients among 16,247 screened consecutive isolates of Enterobacteriaceae. The pAmpC prevalence was low (0.25%), but more than 30% of pAmpC carriers received incorrect empirical antibiotic treatment. When compared with 39 ESBL controls, pAmpC carriage was associated with clinically confirmed infections in 74% (versus 51%) (p=0.035), mainly of the urinary tract, previous antibiotic exposure in 63% (versus 36%) (p=0.035) and carriage of a nasogastric tube in 23% (versus 0%) (p=0.002). In the multivariate regression analysis only clinically confirmed infections remained significantly associated with pAmpC carriage (OR 1.44 (95%CI 1.15-2.57)). No other clinical and blood test-associated risk factor allowed discrimination of pAmpC-carrying patients from ESBL controls. The type of acquisition – nosocomial versus community-acquired – was also non-informative for resistance type, as 46% of pAmpC- and 44% of ESBL-producing Enterobacteriaceae were community-acquired. Conclusions This study could not identify a clinical profile that would allow targeted screening for pAmpC-producing Enterobacteriaceae when compared to ESBL carriers. Because empiric antimicrobial therapy was inappropriate in more than 30%, rapid identification of pAmpC carriers is needed. New microbiological methods are therefore required to simplify rapid and reliable detection of pAmpC carriers.
Learning similarity measures in non-orthogonal space

Many machine learning and data mining algorithms crucially rely on the similarity metrics. The Cosine similarity, which calculates the inner product of two normalized feature vectors, is one of the most commonly used similarity measures. However, in many practical tasks such as text categorization and document clustering, the Cosine similarity is calculated under the assumption that the input space is an orthogonal space which usually could not be satisfied due to <i>synonymy</i> and <i>polysemy</i>. Various algorithms such as Latent Semantic Indexing (LSI) were used to solve this problem by projecting the original data into an orthogonal space. However LSI also suffered from the high computational cost and data sparseness. These shortcomings led to increases in computation time and storage requirements for large scale realistic data. In this paper, we propose a novel and effective similarity metric in the non-orthogonal input space. The basic idea of our proposed metric is that the similarity of features should affect the similarity of objects, and vice versa. A novel iterative algorithm for computing non-orthogonal space similarity measures is then proposed. Experimental results on a synthetic data set, a real MSN search click-thru logs, and 20NG dataset show that our algorithm outperforms the traditional Cosine similarity and is superior to LSI.
BpaB and EbfC DNA-Binding Proteins Regulate Production of the Lyme Disease Spirochete's Infection-Associated Erp Surface Proteins

ABSTRACT Vector-borne pathogens regulate their protein expression profiles, producing factors during host infection that differ from those produced during vector colonization. The Lyme disease agent, Borrelia burgdorferi, produces Erp surface proteins throughout mammalian infection and represses their synthesis during colonization of vector ticks. Known functions of Erp proteins include binding of host laminin, plasmin(ogen), and regulators of complement activation. A DNA region immediately 5′ of erp operons, the erp operator, is required for transcriptional regulation. The B. burgdorferi BpaB and EbfC proteins exhibit high in vitro affinities for erp operator DNA. In the present studies, chromatin immunoprecipitation (ChIP) demonstrated that both proteins bind erp operator DNA in vivo. Additionally, a combination of in vivo and in vitro methods demonstrated that BpaB functions as a repressor of erp transcription, while EbfC functions as an antirepressor.
The predicament of generation 1.5 English language learners: Three disjunctures and a possible way forward

This article reports key findings from a project that focused on the academic literacy development of children who are born and/or begin their formal schooling in Canada but are raised in homes where the societally dominant language is not the primary idiom. Analyses involved characterizing students’ home ecological environments; assessing the nature of students’ challenges in relation to schoolbased literacy demands; and documenting collaborations with professional educators in generating cognitively and pedagogically differentiated instructional approaches. Findings are interpreted as three disjunctive conditions that impede the development of academic literacy competencies and, thus, schooling success of G1.5 linguistic minority students.
The Differential of the Exponential Map, Jacobi Fields and Exact Principal Geodesic Analysis

In fields ranging from computer vision to signal processing and statistics, increasing computational power allows a move from classical linear models to models that incorporate non-linear phenomena. This shift has created interest in computational aspects of differential geometry, and solving optimization problems that incorporate non-linear geometry constitutes an important computational task. In this paper, we develop methods for numerically solving optimization problems over spaces of geodesics using numerical integration of Jacobi fields and second order derivatives of geodesic families. As an important application of this optimization strategy, we compute exact Principal Geodesic Analysis (PGA), a non-linear version of the PCA dimensionality reduction procedure. By applying the exact PGA algorithm to synthetic data, we exemplify the differences between the linearized and exact algorithms caused by the non-linear geometry. In addition, we use the numerically integrated Jacobi fields to determine sectional curvatures and provide upper bounds for injectivity radii.
Managing Relational Legacies: Lessons from British Columbia, Canada

Issues related to company-community relations and the social license to operate have emerged as strategic business issues. This paper aims to contribute to the growing body of research on long-term company-community relations. An analysis of the relationship between Alcan (Aluminum of Canada, Montreal, Canada part of Rio Tinto since 2007) with the Cheslatta Carrier First Nation in the Kemano-Kitimat area of northern British Columbia, Canada, provides three contributions. The first is related to the notion of relational legacy, which refers to the sedimentation of unresolved issues that have the potential to impede the realization of corporate activities and the reproduction of low levels of social license to operate. The second concerns stakeholder management. While the literature suggests that stakeholders should be managed by companies according to the degree of salience, this analysis suggests that researchers and managers should consider the evolution of the environmental context in their analyses. Third, the analysis suggests that small or marginalized groups, depicted by the stakeholder management literature as dormant stakeholders, should not be underestimated.
Understanding metacognitive awareness among teachers in the school system: issues and benefits

This paper deals with the understanding of metacognitive awareness among teachers. The concept of metacognition is operationalized. This is followed by the essence of metacognition and learning. We move further to examine issues and benefits of metacognition in the school system. To make metacognitive strategies an integral part of the school curriculum, the paper proposes: (1) Specific metacognitive strategies in the classroom, and (2) deliberate school training programmes on metacognitive instruction. The study concludes that both pre-service and in-service teachers should be trained on general awareness of metacognition to enhance learners’ academic performance.
Optimizing the performance of Lattice Gauge Theory simulations with Streaming SIMD extensions

Two factors, which affect simulation quality are the amount of computing power and implementation. The Streaming SIMD (single instruction multiple data) extensions (SSE) present a technique for influencing both by exploiting the processor's parallel functionalism. In this paper, we show how SSE improves performance of lattice gauge theory simulations. We identified two significant trends through an analysis of data from various runs. The speed-ups were higher for single precision than double precision floating point numbers. Notably, though the use of SSE significantly improved simulation time, it did not deliver the theoretical maximum. There are a number of reasons for this: architectural constraints imposed by the FSB speed, the spatial and temporal patterns of data retrieval, ratio of computational to non-computational instructions, and the need to interleave miscellaneous instructions with computational instructions. We present a model for analyzing the SSE performance, which could help factor in the bottlenecks or weaknesses in the implementation, the computing architecture, and the mapping of software to the computing substrate while evaluating the improvement in efficiency. The model or framework would be useful in evaluating the use of other computational frameworks, and in predicting the benefits that can be derived from future hardware or architectural improvements.
Note: A Separation Principle for a Class of Assemble-to-Order Systems with Expediting

In an assemble-to-order system, a wide variety of products are rapidly assembled from component inventories in response to customer orders. We assume that orders must be filled within a product-specific target lead time. In the event that some of the components required to fill an order are out of stock, these components must be expedited. The objective is to minimize the expected infinite-horizon discounted cost of primary component production and expediting. Our formulation captures financial holding costs but implicitly assumes that physical holding costs are negligible. The controls are (1) sequencing orders for assembly, (2) primary component production, and (3) component expediting. We prove that the multidimensional assemble-to-order control problem separates into single-item inventory control problems. In particular, under an optimal policy for assembly sequencing, the optimal production and expediting policy for each component is independent of all other components. Hence, the literature on single-item inventory management with expediting or lost sales is directly relevant to the control of assemble-to-order systems.
Early Effects of Radical Position Legality in Chinese: An ERP Study

This study aimed to investigate the timecourse and neural underpinnings of the coding of radical positions in Chinese character reading. To isolate effects of radical positions, four types of pseudocharacters were created in which the constituent radicals appeared in positions varying in probability of occurrence, that is, Unique, Dominant, Subordinate, or Illegal positions. Twenty native Chinese readers performed a character detection task where real characters were identified among pseudocharacters. The event-related potential data demonstrated that Illegal items were reliably distinguished from other pseudocharacter items within 100 ms, with larger P100 amplitudes at left posterior electrodes. At the N170, Illegal items elicited a smaller negativity than Unique items. In these time windows, pseudocharacter conditions in legal radical positions did not differ among themselves. The early timecourse effects suggested that radical position legality was detected at the initial stage of visual processing, which challenged theoretical models that assume primacy of position-general radical representations.
A Novel Representation of Parts for Accurate 3D Object Detection and Tracking in Monocular Images

We present a method that estimates in real-time and under challenging conditions the 3D pose of a known object. Our method relies only on grayscale images since depth cameras fail on metallic objects, it can handle poorly textured objects, and cluttered, changing environments, the pose it predicts degrades gracefully in presence of large occlusions. As a result, by contrast with the state-of-the-art, our method is suitable for practical Augmented Reality applications even in industrial environments. To be robust to occlusions, we first learn to detect some parts of the target object. Our key idea is to then predict the 3D pose of each part in the form of the 2D projections of a few control points. The advantages of this representation is three-fold: We can predict the 3D pose of the object even when only one part is visible, when several parts are visible, we can combine them easily to compute a better pose of the object, the 3D pose we obtain is usually very accurate, even when only few parts are visible.
User ' s Manual

GLISP User's Manual Gordon S. Novak Jr. Compute r Science Depar tmen t Stanford Univers i ty Stanford, Cal i fornia 94305 Report No. HPP-82-1, January 1982, 36 pages. GLISP is a high-level, LISP-based language which is compiled into LISP. GLISP provides a powerful abstract datatype facility, allowing description and use of both LISP objects and objects in AI representa t ion languages. GLISP language features include PASCAL-l ike control structures, infix expressions with operators which facilitate list manipulation, and reference to objects in PASCAL-l ike or English-like syntax. English-like definite reference to features of objects which are in the current computational context is allowed; definite references are understood and compiled relative to a knowledge base of object descriptions. Objec t -cen te red programming is supported; GLISP can substantially improve runtime performance of object -centered programs by optimized compilation of references to objects. This manual describes the GLISP language and u s e of GLISP within INTERLISP. How to Solve It w i th PROLOG Helder Coelho, Jose C. Cotta, and Luis M. Pereira Centro de In format ica Laboratorio Nacional de Engenharia Civil 101, Av. do Brasil 1799 Lisboa Codex, PORTUGAL Research Report, 2nd edition, 1980, 215 pages. Our purpose is to present the outstanding features of P R O L O G through a collection of small problems and exercises, divided in general application areas such as deductive reasoning over data bases, natural language, symbolic calculus, etc. Logic Programming Bibliography Helder Coelho Centro de Informatica Laboratorio Nacional de Engenharia Civil 101, Av. do Brasil 1799 Lisboa Codex, PORTUGAL Research Report, 2nd edition, October 1981, 41 pages. This is a provisional version of an evolving bibliography on logic programming and P R O L O G , covering field work carried out in all known groups spread over the whole world. It is the first draft, and consequently incomplete. The purpose behind its construct ion is very simple. Every researcher needs to have available an up-to-date and complete list of references. The motivation to work out this list came from the bibliography for my previous report "H o w to Solve it With P R O L O G , " and from the Hungar ian list delivered during the Logic Programming Workshop at Debrecen, July 11980. A N e w Point of V i e w on Children's Stories
Nocturnal Wakefulness Is Associated With Next-Day Suicidal Ideation in Major Depressive Disorder and Bipolar Disorder.

OBJECTIVE Self-reported sleep disturbances may confer elevated risk for suicidal ideation, suicide attempts, and death. However, limited research has evaluated polysomnographically determined sleep disturbance as an acute physiologic risk factor for suicidal thoughts. This study sought to investigate the relationship between nocturnal wakefulness in association with next-day suicidal ideation using overnight polysomnography assessment from data collected between 2006 and 2013. METHODS Sixty-five participants with DSM-IV-diagnosed major depressive disorder or bipolar depression underwent overnight polysomnography monitoring in a sleep laboratory. The Hamilton Depression Rating Scale (HDRS) was administered the morning after polysomnography recording to assess next-day suicidal ideation, severity of depressive symptoms, and subjective sleep disturbances. RESULTS Using a generalized linear mixed model, a significant time-by-ideation interaction was found indicating greater nocturnal wakefulness at 4:00 am among participants with suicidal ideation (F4,136 = 3.65, P = .007). Increased time awake during the 4:00 am hour (4:00 to 4:59) was significantly associated with elevated suicidal thoughts the next day (standardized β = 0.31, P = .008). This relationship persisted after controlling for age, gender, diagnosis, and severity of depressive symptoms. CONCLUSIONS Greater nocturnal wakefulness, particularly in the early morning hours, was significantly associated with next-day suicidal thoughts. Polysomnographically documented sleep disruption at specific times of night may represent an acute risk factor of suicidal ideation that warrants additional research. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT00024635.