Miracle-dz/UniFAR-FTUs huggingface dataset:
Methicillin-Resistant Staphylococcus aureus Nasal Carriage among Injection Drug Users: Six Years Later

ABSTRACT A survey in 2000 to detect methicillin-resistant Staphylococcus aureus (MRSA) colonization in Vancouver downtown east side injection drug users (IDUs) revealed an MRSA nasal colonization incidence of 7.4%. This is a follow-up study to determine the current prevalence of MRSA colonization and to further characterize the isolates and risk factors for colonization. In this point prevalence study of MRSA nasal carriage among IDUs, nasal swabs were cultured to detect S. aureus. Isolates were studied for their antimicrobial susceptibility patterns and the presence of mecA and Panton-Valentine leukocidin (PVL) genes and by pulsed-field gel electrophoresis (PFGE). S. aureus was isolated from 119 of 301 (39.5%) samples; three (2.5%) participants had both methicillin-sensitive S. aureus (MSSA) and MRSA, resulting in 122 isolates. Of these, 54.1% were MSSA and 45.9% were MRSA, with an overall MRSA rate of 18.6%. USA-300 (CMRSA-10) accounted for 75% of all MRSA isolates; 25% were USA-500 (CMRSA-5). None of the USA-500 isolates were positive for PVL; 41 (97.6%) USA-300 isolates contained PVL. One MSSA isolate, from an individual also carrying USA-300, was positive for PVL. The PFGE pattern of this MSSA isolate was related to that of the MRSA strain. The antibiograms of USA-300 compared to USA-500 isolates showed 100% versus 7.1% susceptibility to trimethoprim-sulfamethoxazole (TMP-SMX) and 54.8% versus 7.1% susceptibility to clindamycin. MRSA nasal colonization in this population has increased significantly within the last 6 years, with USA-300 replacing the previous strain. Most of these strains are PVL positive, and all are susceptible to TMP-SMX.
Data Quality Tags and Decision-making: A Cognitive Process Tracing Study

It has been suggested that metadata describing data quality (DQ), termed DQ tags, be made available in situations where decision-makers are unfamiliar with the data context, for example, in data warehouses. However, there have been conflicting reports as to the impact of such DQ tags on decision-making. Recent studies have not found evidence that DQ tags changed decision choice or confidence, but have reported that decision time can be negatively impacted in certain circumstances. This paper reports on a cognitive process tracing study intended to help us understand why it takes decision-makers longer to make a decision even when they are apparently ignoring the DQ tag information. Protocol analysis, which involves participants verbalizing thoughts while making a decision, is used to collect information on decision-makers' cognitive process. Results suggest that DQ tags are associated with increased cognitive processing in the earlier phases of decision-making.
Performance comparison of blind source separation algorithms using spatial time-frequency distributions

Three blind source separation techniques using time-frequency distributions are examined in terms of achievable performance and computational complexity. The schemes considered involve joint diagonalization and off-diagonalization of a set of spatial time-frequency distribution matrices. These matrices must be constructed at particular time-frequency points for separation to be successful. Robustness to correct choice of the time-frequency points is also examined in this work.
Computer-aided detection of peripheral lung cancers missed at CT: ROC analyses without and with localization.

PURPOSE To retrospectively evaluate whether a difference-image computer-aided detection (CAD) scheme can help radiologists detect peripheral lung cancers missed at low-dose computed tomography (CT). MATERIALS AND METHODS Institutional review board approval and informed patient and observer consent were obtained. Seventeen patients (eight men and nine women; mean age, 60 years) with a missed peripheral lung cancer and 10 control subjects (five men and five women; mean age, 63 years) without cancer at low-dose CT were included in an observer study. Fourteen radiologists were divided into two groups on the basis of different image display formats: Six radiologists (group 1) reviewed CT scans with a multiformat display, and eight radiologists (group 2) reviewed images with a "stacked" cine-mode display. The radiologists, first without and then with the CAD scheme, indicated their confidence level regarding the presence (or absence) of cancer and the most likely position of a lesion on each CT scan. Receiver operating characteristic (ROC) curves were calculated without and with localization to evaluate the observers' performance. RESULTS With the CAD scheme, the average area under the ROC curve improved from 0.763 to 0.854 for all radiologists (P = .002), from 0.757 to 0.862 for group 1 (P = .04), and from 0.768 to 0.848 for group 2 (P = .01). The average sensitivity in the detection of 17 cancers improved from 52% (124 of 238 observations) to 68% (163 of 238 observations) for all radiologists (P < .001), from 49% (50 of 102 observations) to 71% (72 of 102 observations) for group 1 (P = .02), and from 54% (74 of 136 observations) to 67% (91 of 136 observations) for group 2 (P = .006). The localization ROC curve also improved. CONCLUSION Lung cancers missed at low-dose CT were very difficult to detect, even in an observer study. The use of CAD, however, can improve radiologists' performance in the detection of these subtle cancers.
A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

Objective To create a multilingual gold-standard corpus for biomedical concept recognition. Materials and methods We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. Results The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. Discussion The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. Conclusion To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated.
Prediction of Heart Failure Decompensation Events by Trend Analysis of Telemonitoring Data

This paper aims to assess the predictive value of physiological data daily collected in a telemonitoring study in the early detection of heart failure (HF) decompensation events. The main hypothesis is that physiological time series with similar progression (trends) may have prognostic value in future clinical states (decompensation or normal condition). The strategy is composed of two main steps: a trend similarity analysis and a predictive procedure. The similarity scheme combines the Haar wavelet decomposition, in which signals are represented as linear combinations of a set of orthogonal bases, with the Karhunen-Loève transform, that allows the selection of the reduced set of bases that capture the fundamental behavior of the time series. The prediction process assumes that future evolution of current condition can be inferred from the progression of past physiological time series. Therefore, founded on the trend similarity measure, a set of time series presenting a progression similar to the current condition is identified in the historical dataset, which is then employed, through a nearest neighbor approach, in the current prediction. The strategy is evaluated using physiological data resulting from the myHeart telemonitoring study, namely blood pressure, respiration rate, heart rate, and body weight collected from 41 patients (15 decompensation events and 26 normal conditions). The obtained results suggest, in general, that the physiological data have predictive value, and in particular, that the proposed scheme is particularly appropriate to address the early detection of HF decompensation.
Towards a lightweight model driven method for developing SOA systems using existing assets

Developing SOA based systems and migrating legacy systems to SOA are difficult and error prone tasks, where approaches, methods and tools play a fundamental role. For this reason, several proposals have been brought forward in literature to help SOA developers. This paper sketches a novel method for the development of systems based on services, i.e., adhering to the SOA paradigm, which follows the model driven paradigm. Our method is based on a “meet-in-the-middle” approach that allows the reuse of existing assets (e.g., legacy systems). The starting point of this method is a UML model representing the target business process and the final result is a detailed design model of the SOA system. The method, explained in this paper using a simple running example, has been applied successfully within an industrial project.
ETAR: Efficient Traffic Light Aware Routing Protocol for Vehicular Networks

Routing in Vehicular Ad hoc Networks (VANETs) is an important factor to ensure a reliable and efficient delivery of data packets. In urban environments, routing protocols must efficiently handle the constantly changing network topology and frequent disconnections due to the high mobility and direction changes of vehicles. The challenge is greater when there are traffic lights fixed along intersections which affect directly the mobility and therefore can greatly impact routing in urban areas. In our previous work [1] we have proposed IRTIV (Intelligent Routing protocol using real time Traffic Information in urban Vehicular environment) that takes into account the real time traffic variation without any use of pre-installed infrastructures or additional messages. However, IRTIV does not take into consideration the traffic lights impact. In this paper, we propose ETAR (Efficient Traffic Light Aware Routing Protocol for Vehicular Networks). This protocol's objective is to find the most stable path for delivering data packets based on traffic lights and traffic density of vehicles using the periodical exchange of Hello messages. We present simulation-based performance results, which show that the proposed protocol increases the packet delivery ratio and reduces the end-to-end delay.
Channel tracking for massive MIMO systems with spatial-temporal basis expansion model

In this paper, we propose a new channel tracking method for massive multiple-input multiple-output (MIMO) systems under both the time-varying and spatial-varying circumstance. With spatial-temporal basis expansion model (ST-BEM), the channel information is decomposed into the spatial information and gain information, where the former is determined by the central angle as well as the angular spread of the incoming signal. We first blindly track the central angle by the extended Kalman filter (EKF) and obtain the angular spread through Taylor series expansion of the steering vector. Then, the channel gain information can be estimated with only a few pilot symbols. Various numerical results are provided to demonstrate the effectiveness of the proposed method.
Pathway Analysis of Skin from Psoriasis Patients after Adalimumab Treatment Reveals New Early Events in the Anti-Inflammatory Mechanism of Anti-TNF-α

Psoriasis is a chronic cutaneous inflammatory disease. The immunopathogenesis is a complex interplay between T cells, dendritic cells and the epidermis in which T cells and dendritic cells maintain skin inflammation. Anti-tumour necrosis factor (anti-TNF)-α agents have been approved for therapeutic use across a range of inflammatory disorders including psoriasis, but the anti-inflammatory mechanisms of anti-TNF-α in lesional psoriatic skin are not fully understood. We investigated early events in skin from psoriasis patients after treatment with anti-TNF-α antibodies by use of bioinformatics tools. We used the Human Gene 1.0 ST Array to analyse gene expression in punch biopsies taken from psoriatic patients before and also 4 and 14 days after initiation of treatment with the anti-TNF-α agent adalimumab. The gene expression was analysed by gene set enrichment analysis using the Functional Annotation Tool from DAVID Bioinformatics Resources. The most enriched pathway was visualised by the Pathview Package on Kyoto Encyclopedia of Genes and Genomes (KEGG) graphs. The analysis revealed new very early events in psoriasis after adalimumab treatment. Some of these events have been described after longer periods of anti-TNF-α treatment when clinical and histological changes appear, suggesting that effects of anti-TNF-α treatment on gene expression appear very early before clinical and histological changes. Combining microarray data on biopsies from psoriasis patients with pathway analysis allowed us to integrate in vitro findings into the identification of mechanisms that may be important in vivo. Furthermore, these results may reflect primary effect of anti-TNF-α treatment in contrast to studies of gene expression changes following clinical and histological changes, which may reflect secondary changes correlated to the healing of the skin.
A population‐based registry on paraproteinaemia in the Netherlands

Patients with monoclonal gammopathies comprise a heterogenous group. The few studies on incidence and follow‐up are single‐centre‐based and may reflect referral bias. To avoid this, all patients (n = 1275) in mid‐western Netherlands with a newly discovered paraproteinaemia in 1991, 1992 and 1993 were included in a population‐based registry and divided into four major diagnostic groups: multiple myeloma and plasmacytoma (n = 230, 18%), other haematological diseases (n = 141, 11%), paraprotein‐related internal diseases (n = 191, 15%) and monoclonal gammopathy of undetermined significance (MGUS, n = 713, 56%). To avoid a possibly erroneous diagnosis, patients who were classified as having MGUS but who did not undergo confirmatory bone marrow examination were included in a separate group ‘provisional MGUS’ (n = 524, 41%), whereas patients who did were classified as having ‘definite MGUS’ (n = 189, 15%). The ‘provisional MGUS’ patients were relatively older and had more often a poor performance status, but differences between this and the ‘definite MGUS’ group were otherwise small. Patients complaining of general malaise more often had a full work‐up of their paraproteinaemia. Bone pain, hypercalcaemia, high total protein, and high ESR occurred predominantly in the myeloma group, whereas fever or infection was less often seen in these patients. This registry of patients with paraproteinaemias provided valuable data related to all different diseases associated with paraproteinaemia.
Direct and Indirect Effects of Parenting on the Academic Functioning of Young Homeless Children

Research Findings: Effects of parenting quality on the academic functioning of young homeless children were examined using data from 58 children ages 4 to 7 and their parents during their stay at an emergency homeless shelter. Parenting quality, child executive function, child intellectual functioning, and risk status were assessed in the shelter, and teacher reports of academic functioning were obtained when the children began kindergarten or 1st grade. As hypothesized, parenting quality was associated with children's academic success, and this effect was mediated by executive function skills in the child. Parenting quality also had a moderating effect on risk, consistent with a protective role of high-quality parenting among children with higher risk levels. Concomitantly, children with higher risk and lower parenting quality appeared to be more vulnerable to academic problems. Practice or Policy: In homeless families, parenting may play an especially important role in academic success through multiple pathways, including the development of executive function skills in their children. Policies and practices to support parents and foster the executive function skills of young children in homeless families may be important strategies to promote child academic success. Implications for intervention efforts with homeless parents and children are discussed.
Urban growth and agricultural change: England and the Continent in the early modern period

An examination of the relationship between economic growth and urban growth in England and the rest of Europe in the early modern period is presented. In particular the author attempts to determine what additional insights into differential economic development in Europe result from a separation of population growth into rural and urban components. The importance of the rapid growth of urban population in England is stressed. (ANNOTATION)
Consuming the Planet to Excess

This article examines some major changes relating to the contemporary conditions of life upon Earth. It deals especially with emergent contradictions that stem from shifts within capitalism in the rich North over the course of the last century or so. These shifts involve moving from low-carbon to high-carbon economies/societies, from societies of discipline to societies of control, and more recently from specialized and differentiated zones of consumption to mobile, de-differentiated consumptions of excess. Societies become centres of conspicuous, wasteful consumption. The implications of such forms of ‘excess’ consumption are examined for clues as to the nature and characteristics of various futures. Special attention is paid to the interdependent system effects of climate change, the peaking of oil and exceptional growth of urban populations. It is argued that the 20th century has left a bleak legacy for the new century, with a very limited range of possible future scenarios which are briefly described.
A brain slice bath for physiology and compound microscopy, with dual‐sided perifusion

Contemporary in vitro brain slice studies can employ compound microscopes to identify individual neurons or their processes for physiological recording or imaging. This requires that the bath used to maintain the tissue fits within the working distances of a water‐dipping objective and microscope condenser. A common means of achieving this is to maintain thin tissue slices on the glass floor of a recording bath, exposing only one surface of the tissue to oxygenated bathing medium. Emerging evidence suggests that physiology can be compromised by this approach. Flowing medium past both sides of submerged brain slices is optimal, but recording baths utilizing this principle are not readily available for use on compound microscopes. This paper describes a tissue bath designed specifically for microscopy and physiological recording, in which temperature‐controlled medium flows past both sides of the slices. A particular feature of this design is the use of concentric mesh rings to support and transport the live tissue without mechanical disturbance. The design is also easily adapted for use with thin acute slices, cultured slices, and acutely dispersed or cultured cells maintained either on cover slips or placed directly on the floor of the bath. The low profile of the bath provides a low angle of approach for electrodes, and allows use of standard condensers, nosepieces and water‐dipping objective lenses. If visualization of individual neurons is not required, the bath can be mounted on a simple stand and used with a dissecting microscope. Heating is integral to the bath, and any temperature controller capable of driving a resistive load can be used. The bath is robust, readily constructed and requires minimal maintenance. Full construction and operation details are given.
The Impact of Labour Turnover: Theory and Evidence from UK Micro-Data

We analyse the impact of labour turnover on profits. We extend the efficiency wage model of Salop (1979) by separating incumbent and newly hired workers in the production function. We show that an exogenous increase in the turnover rate can increase profits, but only where firms do not choose the wage. This effect of turnover varies across firms as it depends on turnover costs, the substitutability of incumbents and new hires and other factors. We test our model on UK cross-sectional establishment-level data. We find that our predictions are consistent with the data.
Nucleotide sequences involved in bacteriophage T4 gene 32 translational self-regulation.

We have determined the nucleotide sequence of a cloned segment of the bacteriophage T4D chromosome, which contains the regulatory sequences and the structural gene (gene 32) for the single-stranded DNA binding protein (gp32). The amino acid sequence predicted by translation of the structural gene agrees well with that published for gp32 [Williams, K. R. , Lo-Presti, M. B. , Setoguchi, M. & Konigsberg, W. H. (1980) Proc. Natl. Acad. Sci. USA 77, 4614-4617]. To localize the nucleotide sequence involved in translational self-regulation of gene 32, we have constructed a series of plasmids in which gene 32 is fused to an amino-terminal deletion mutant of the beta-galactosidase gene of Escherichia coli. Expression of a beta-galactosidase fusion protein that contains only the first seven amino acids of gp32 is still repressed by gp32. The ribosomal binding site of gene 32 is flanked by a repetitive A+T-rich sequence. Preferential and cooperative binding of gp32 to this region of its mRNA could inhibit translation initiation and, thus, would account for the autoregulation.
Optimal trajectories for a liquid piston compressor/expander in a Compressed Air Energy Storage system with consideration of heat transfer and friction

For a Compressed Air Energy Storage (CAES) approach to be viable, the air compressor/expander must be sufficiently powerful and efficient. Since efficiency is governed by heat transfer, there is a generally a tradeoff between efficiency and compression/expansion time (or power). In this paper, we determine Pareto optimal compression/expansion profiles for a liquid piston air compressor/expander that maximizes efficiency (power) for a given power (efficiency). Compared to previous works, a numerical optimization approach is proposed that allows for more general heat transfer model, the consideration of the viscous friction, and system limitations in the optimization. The resulting optimal profiles are compared to other trajectories. At compression ratio of 10, the optimal profile results in 10%-40% increase in power density relative to other methods. Optimal geometries that trades off friction and heat transfer improvement can also be determined using this method.
Networks of Collaborating Criminals: Assessing the Structural Vulnerability of Drug Markets

Uncovering the resiliency of ties between individuals involved in criminal enterprise will contribute to our understanding of how illicit markets function. To examine activities along the entire drug market commodity chain, this study extracted information about individuals involved or associated with trafficking (1,998 people) from police intelligence reports generated from 2004 to 2006. Significant differences were found for centrality and cohesion across market niches. Results show that the highest fragmentation potential lies with individuals who are involved with smuggling, supply, and financing, particularly when these individuals are also involved in other niches. Variability in small-world and scale-free properties suggest that interdiction strategies must be tailored to niche characteristics.