Miracle-dz/UniFAR-FTUs huggingface dataset:
Refined Estimates of Net Community Production in the Subarctic Northeast Pacific Derived From ΔO2/Ar Measurements With N2O‐Based Corrections for Vertical Mixing

We present the first field application of a N2O‐based approach to correct for vertical mixing in the estimation of net community production (NCP) from mixed layer O2 measurements. Using new ship‐based observations of N2O and biological oxygen saturation anomalies (ΔO2/Ar) from the Subarctic Northeast Pacific, we provide refined mixed layer NCP estimates across contrasting hydrographic regimes and a comprehensive assessment of the methodological considerations and limitations of the approach. Increased vertical mixing coefficients at the base of the mixed layer, derived using N2O measurements, corresponded with periods of heightened wind speed and coastal upwelling. Corrections were most significant in coastal regions where the vertical supply of low‐O2 water can otherwise falsely imply net heterotrophy from negative ΔO2/Ar measurements. After correcting for the mixing flux, all coastal stations showed autotrophic signatures, with maximum NCP exceeding 100 mmol O2 m−2 d−1 in the spring and summer. Vertical fluxes were lower in off‐shelf waters but often contributed more than 50% to corrected NCP. At some oceanic stations, however, the cooccurrence of N2O minima and O2 maxima resulted in biased (overestimated) N2O corrections. Evaluating vertical fluxes in these regions remains a challenge for ship‐based studies. Nonetheless, our refined NCP estimates show better coherence with surface chlorophyll, temperature, and mixed layer depth than uncorrected values. Potential mixed layer N2O production introduces some uncertainty in the approach, but errors are likely to be small. Ultimately, this work provides rationale for the adoption of the N2O correction to refine NCP estimates, particularly in coastal waters.
An Integrated Software Framework to Support Semantic Modeling and Reasoning of Spatiotemporal Change of Geographical Objects: A Use Case of Land Use and Land Cover Change Study

Evolving Earth observation and change detection techniques enable the automatic identification of Land Use and Land Cover Change (LULCC) over a large extent from massive amounts of remote sensing data. It at the same time poses a major challenge in effective organization, representation and modeling of such information. This study proposes and implements an integrated computational framework to support the modeling, semantic and spatial reasoning of change information with regard to space, time and topology. We first proposed a conceptual model to formally represent the spatiotemporal variation of change data, which is essential knowledge to support various environmental and social studies, such as deforestation and urbanization studies. Then, a spatial ontology was created to encode these semantic spatiotemporal data in a machine-understandable format. Based on the knowledge defined in the ontology and related reasoning rules, a semantic platform was developed to support the semantic query and change trajectory reasoning of areas with LULCC. This semantic platform is innovative, as it integrates semantic and spatial reasoning into a coherent computational and operational software framework to support automated semantic analysis of time series data that can go beyond LULC datasets. In addition, this system scales well as the amount of data increases, validated by a number of experimental results. This work contributes significantly to both the geospatial Semantic Web and GIScience communities in terms of the establishment of the (web-based) semantic platform for collaborative question answering and decision-making.
Weakly Labeled Corpora as Silver Standard for Drug-Drug and Protein-Protein Interaction

Relation extraction is frequently and successfully addressed by machine learning methods. The downside of this approach is the need for annotated training data, typically generated in tedious manual, cost intensive work. Distantly supervised approaches make use of weakly annotated data, which can be derived automatically. Recent work in the biomedical domain has applied distant supervision for protein-protein interaction (PPI) with reasonable results, by employing the IntAct database. Training from distantly labeled corpora is more challenging than from manually curated ones, as such data is inherently noisy. With this paper, we make two corpora publicly available to the community to allow for comparison of different methods that deal with the noise in a uniform setting. The first corpus is addressing protein-protein interaction (PPI), based on named entity recognition and the use of IntAct and KUPS databases, the second is concerned with drug-drug interaction (DDI), making use of the database DrugBank. Both corpora are in addition labeled with 5 state-of-the-art classifiers trained on annotated data, to allow for development of filter methods. Furthermore, we present in short our approach and results for distant supervision on these corpora as a strong baseline for future research.
Towards a scalable social recommender engine for online marketplaces: the case of apache solr

Recent research has unveiled the importance of online social networks for improving the quality of recommenders in several domains, what has encouraged the research community to investigate ways to better exploit the social information for recommendations. However, there is a lack of work that offers details of frameworks that allow an easy integration of social data with traditional recommendation algorithms in order to yield a straight-forward and scalable implementation of new and existing systems. Furthermore, it is rare to find details of performance evaluations of recommender systems such as hardware and software specifications or benchmarking results of server loading tests. In this paper we intend to bridge this gap by presenting the details of a social recommender engine for online marketplaces built upon the well-known search engine Apache Solr. We describe our architecture and also share implementation details to facilitate the re-use of our approach by people implementing recommender systems. In addition, we evaluate our framework from two perspectives: (a) recommendation algorithms and data sources, and (b) system performance under server stress tests. Using a dataset from the SecondLife virtual world that has both trading and social interactions, we contribute to research in social recommenders by showing how certain social features allow to improve recommendations in online marketplaces. On the platform implementation side, our evaluation results can serve as a baseline to people searching for performance references in terms of scalability, model training and testing trade-offs, real-time server performance and the impact of model updates in a production system.
Reduced 10-Year Risk of Coronary Heart Disease in Patients Who Participated in a Community-Based Diabetes Prevention Program

OBJECTIVE—We evaluated whether participation in a community-based group diabetes prevention program might lead to relative changes in composite 10-year coronary heart disease (CHD) risk for overweight adults with abnormal glucose metabolism. RESEARCH DESIGN AND METHODS—We used the UK Prospective Diabetes Study engine to estimate CHD risk for group-lifestyle and brief counseling (control) groups. Between-group risk changes after 4 and 12 months were compared using ANCOVA. RESULTS—Baseline 10-year risk was similar between treatment groups (P = 0.667). At 4 and 12 months, the intervention group experienced significant decreases in 10-year risk from baseline (−3.28%, P < 0.001; and −2.23%, P = 0.037) compared with control subjects (−0.78%, P = 0.339; and +1.88%, P = 0.073). Between-group differences were statistically significant and increased from the 4- to 12-month visits. CONCLUSIONS—Community-based delivery of the Diabetes Prevention Program lifestyle intervention could be a promising strategy to prevent both CHD and type 2 diabetes in adults with pre-diabetes.
Two-hit inactivation of FHIT by loss of heterozygosity and hypermethylation in breast cancer.

PURPOSE The FHIT gene, which spans the FRA3B fragile site at chromosome 3p14.2, is a candidate tumor suppressor gene in breast carcinomas. In this study, we would like to delineate more precisely its role in breast tumorigenesis. EXPERIMENTAL DESIGN To confirm the tumorigenic role of FHIT, 46 sporadic invasive ductal carcinomas of the breast were tested for the "two hits" required to inactivate this gene. Microsatellite loss of heterozygosity (LOH) was considered as the first hit. To examine the possibility that hypermethylation serves as the second hit for FHIT inactivation, methylation of 5'-CpG islands of FHIT was analyzed by methylation-specific PCR. RESULTS LOH was detected in 8 of 40 informative tumors, and hypermethylation was observed in 22 of 46 (48%) cases. Aberrant FHIT protein expression was found in 31 of 46 (67%) cases examined. All seven tumors showing both LOH and hypermethylation showed complete loss of Fhit protein expression. In addition, a significant positive association was found between the existence of LOH and 5'-CpG island hypermethylation (P = 0.04), which was consistent with the two-hit model. CONCLUSIONS To our knowledge, this study provides the first evidence that biallelic inactivation of FHIT by LOH and hypermethylation leads to the complete inactivation of FHIT gene in patients with breast cancer. Silencing of the FHIT gene by promoter hypermethylation occurs in primary breast carcinomas, especially those with LOH. These findings support a role for this tumor suppressor gene in sporadic breast tumorigenesis.
Feature Extraction From Talking Mouths for Video-Based Bi-Modal Speaker Verification

As the low-cost video transmission becomes popular, video-based bi-modal (audio and visual) authentication has great potential in various applications that require access control over handheld terminals. In this paper, we propose to use the averaged mouth image (AMI) for speaker verification. The AMI is computed by averaging properly aligned mouth images over the whole video sequence. Despite its simplicity, the AMI not only contains appearance information but also describes stylistic articulation gestures of individual speakers. The AMI is found to be fairly invariant against the spoken content. The experimental results show that the AMI based features are very effective in discriminating speaking persons. Explicit and precise extraction of lip contours or other feature points are not required. For bi-modal verification, the proposed video features are found to be highly complementary to the audio features
Tumor cytotoxicity and endothelial Rac inhibition induced by TNP-470 in anaplastic thyroid cancer

Anaplastic thyroid carcinoma is an aggressive form of cancer with no treatment. Angiogenesis inhibitors, such as TNP-470, a synthetic derivative of fumagillin, have been shown to reduce tumor size and increase survival in heterotopic animal models of thyroid cancer. Our goals were to determine the effect of TNP-470 on anaplastic thyroid cancer using an orthotopic murine model, to identify the molecular pathways of TNP-470 actions on endothelial cells, and to determine the non-endothelial tumor effects of TNP-470. We injected human anaplastic thyroid carcinoma cells (DRO′90) into the thyroid glands of nude mice. Mice received TNP-470 (30 mg/kg) s.c. for 6 weeks. TNP-470 prolonged survival and reduced liver metastases. TNP-470 had direct cytotoxic effects on anaplastic thyroid carcinoma cells in vitro and in vivo. Paradoxically, TNP-470 increased vascular endothelial growth factor secretion from tumor cells in vitro and in vivo. However, there was no associated increase in tumor microvessel density. In endothelial cells, TNP-470 prevented vascular endothelial growth factor–induced endothelial permeability, intercellular gap formation, and ruffle formation by preventing Rac1 activation. [Mol Cancer Ther 2007;6(4):1329–37]
Early experience with a commercial hardware transactional memory implementation

We report on our experience with the hardware transactional memory (HTM) feature of two pre-production revisions of a new commercial multicore processor. Our experience includes a number of promising results using HTM to improve performance in a variety of contexts, and also identifies some ways in which the feature could be improved to make it even better. We give detailed accounts of our experiences, sharing techniques we used to achieve the results we have, as well as describing challenges we faced in doing so.
A Positive Feedback Between Sediment Deposition and Tidal Prism May Affect the Morphodynamic Evolution of Tidal Deltas

Tidal deltas are fragile systems whose morphology can be easily impacted by variations in water and sediment fluxes caused by natural and human processes. Here we explore the relation between tidal prism and sediment dynamics in tidal deltas using the recent evolution of the Yangtze River estuary, China, as an example. Using the numerical model Delft3D, we examine how changes in delta morphology can trigger variations in tidal signal, suspended and bed load transport, and how these could ultimately cause additional morphological changes. Our results show that a positive feedback between sediment deposition and tidal prism dominates the morphodynamic evolution of the delta. Accretion of the shoals in the delta front increases the dissipation of tides and decreases the tidal prism leading to weaker tidal flows. This reduction in tidal currents lowers the sediment flushing capacity of the system, promoting deposition on the shoals and tidal dissipation. This positive feedback potentially traps more sediment in the delta topset and possibly offsets the decrease in sediment load triggered by the construction of upstream dams, often present in tidal deltas.
COLA: A cloud-based system for online aggregation

Online aggregation is a promising solution to achieving fast early responses for interactive ad-hoc queries that compute aggregates on massive data. To process large datasets on large-scale computing clusters, MapReduce has been introduced as a popular paradigm into many data analysis applications. However, typical MapReduce implementations are not well-suited to analytic tasks, since they are geared towards batch processing. With the increasing popularity of ad-hoc analytic query processing over enormous datasets, processing aggregate queries using MapReduce in an online fashion is therefore an emerging important application need. We present a MapReduce-based online aggregation system called COLA, which provides progressive approximate aggregate answers for both single table and multiple joined tables. COLA provides an online aggregation execution engine with novel sampling techniques to support incremental and continuous computing of aggregation, and minimize the waiting time before an acceptably precise estimate is available. In addition, user-friendly SQL queries are supported in COLA. Furthermore, COLA can implicitly convert non-OLA jobs into online version so that users don't have to write any special-purpose code to make estimates.
Biological Monitoring of Fuel Stations Workers Occupationally Exposed to Petroleum Products

The increased use of petroleum products in automobiles and industry has led to the deterioration in air quality and human health. Petrol (or gasoline) is a volatile and inflammable petroleum derived liquid mixture primarily used for internal combustion of engines. Occupational exposure to gasoline and air pollutant from vehicular sources are relatively unexplored. The main purpose of this study was conducting biological monitoring for petrol workers occupationally exposed to petroleum product and air pollutants. The study was conducted on fifty male workers employed in petrol filler stations and fifty subjects were recruited as a control group matched for age, sex and socio-economic status. Results revealed that presence of high significant association in the levels of liver enzymes and some haematological changes among exposed workers. In addition to the significant decline in the lung function. Also significant increase in urinary phenol as a biomarker of benzene exposure was found. Sulphur dioxide nitrogen dioxide, carbon dioxide and carbon monoxide did not exceed the standards indoor air quality guidelines. However, particulate matter exceeded the limits as indoor air quality guidelines. This study demonstrated that it is possible to detect human health risks at an early stage using sensitive techniques. It is concluded that petrol pump workers should be carefully monitored and should take adequate protective measures to prevent long term effects.
Towards a Continuous Biometric System Based on ECG Signals Acquired on the Steering Wheel

Electrocardiogram signals acquired through a steering wheel could be the key to seamless, highly comfortable, and continuous human recognition in driving settings. This paper focuses on the enhancement of the unprecedented lesser quality of such signals, through the combination of Savitzky-Golay and moving average filters, followed by outlier detection and removal based on normalised cross-correlation and clustering, which was able to render ensemble heartbeats of significantly higher quality. Discrete Cosine Transform (DCT) and Haar transform features were extracted and fed to decision methods based on Support Vector Machines (SVM), k-Nearest Neighbours (kNN), Multilayer Perceptrons (MLP), and Gaussian Mixture Models - Universal Background Models (GMM-UBM) classifiers, for both identification and authentication tasks. Additional techniques of user-tuned authentication and past score weighting were also studied. The method’s performance was comparable to some of the best recent state-of-the-art methods (94.9% identification rate (IDR) and 2.66% authentication equal error rate (EER)), despite lesser results with scarce train data (70.9% IDR and 11.8% EER). It was concluded that the method was suitable for biometric recognition with driving electrocardiogram signals, and could, with future developments, be used on a continuous system in seamless and highly noisy settings.
Functional Characterization of Permuted Enhanced Green Fluorescent Proteins Comprising Varying Linker Peptides¶

Abstract New variants of green fluorescent protein (GFP) can be engineered by circular permutation of their amino acid sequence. We characterized a series of permuted enhanced GFP (PEGFP) with new termini introduced at N144-Y145 and linkers of 1, 3, 5 and 6 residues inserted between G232 and M1, as well as a variant with an extended 7-residues linker between K238 and M1. A minimum linker length of 3 residues was necessary for a functional chromophore to be formed, and linkers exceeding 4 residues yielded almost the same fluorescence quantum yield as enhanced GFP (EGFP). PEGFP exhibited dual-wavelength absorption and fluorescence excitation with peaks at 395 and 490 nm but single-wavelength emission at 512 nm. Fluorescence emission increased with increasing pH for all excitation wavelengths with a pKa of 7.7. Between the pH values of 6 and 8 optical absorption showed an isobestic point at 445 nm. PEGFP rapidly denatured in urea between 50 and 60°C. Renaturation proceeded with a short (∼29 s) and a longer (>150 s) time constant. Transient transfection of HEK293 and HeLa cells revealed the expression dynamics of PEGFP to be similar to that of EGFP. Laser-scanning microscopy of HeLa cells demonstrated that the PEGFP are particularly well suited as fluorescent indicators in two-photon imaging.
Effects of Lipoic Acid on Immune Function, the Antioxidant Defense System, and Inflammation-Related Genes Expression of Broiler Chickens Fed Aflatoxin Contaminated Diets

This study was designed to evaluate the effect of low level of Aflatoxin B1 (AFB1) on oxidative stress, immune reaction and inflammation response and the possible ameliorating effects of dietary alpha-lipoic acid (α-LA) in broilers. Birds were randomly allocated into three groups and assigned to receive different diets: basal diet, diet containing 74 μg/kg AFB1, and 300 mg/kg α-LA supplementation in diet containing 74 μg/kg AFB1 for three weeks. The results showed that the serum levels of malondialdehyde, tumor necrosis factor alpha (TNFα) and interferon gamma (IFNγ) in the AFB1-treated group were significantly increased than the control group. In addition, the increased expressions of interleukin 6 (IL6), TNFα and IFNγ were observed in birds exposed to the AFB1-contaminated diet. These degenerative changes were inhibited by α-LA-supplement. The activities of total superoxide dismutase and glutathione peroxidase, the levels of humoral immunity, and the expressions of nuclear factor-κB p65 and heme oxygenase-1, however, were not affected by AFB1. The results suggest that α-LA alleviates AFB1 induced oxidative stress and immune changes and modulates the inflammatory response at least partly through changes in the expression of proinflammatory cytokines of spleen such as IL6 and TNFα in broiler chickens.
More doctors, but not enough: Australian medical workforce supply 2001–2012

This year, some 2400 young Australians entered our medical schools, and in the coming years their numbers will increase further. The Prime Minister recently announced yet another new medical school and continues to top up medical school places. With these developments one thing is obvious — policy announcement is easy, but policy implementation is not. Already, there is talk that the existing health system might find it difficult to meet the educational needs of increased numbers of students. Already, medical students are voicing concern about the effect of increased student numbers on the quality of their education in the clinical years, especially the high student-to-teacher ratios and projected bottlenecks in future vocational training. And this pressurecooker environment can only worsen. In short, we are heading to a crisis in medical education. There is talk in academic circles of “new ways” — sharing teaching hospitals among medical schools, simulation centres, increased involvement of private hospitals, specialist and general practices, and community health services in teaching. But the realisation of these new ways requires time, as does the development of skilled clinical teachers. Undoubtedly, the issue is complex. Crucial to effective medical education is the capacity of an already stretched public hospital system to sustain both service delivery and quality clinical training. It’s time for the federal and state governments to take stock and ensure that medical education and training are not jeopardised by overburdened, under-resourced and suboptimal clinical environments. Funding for capacity building is necessary, but undoubtedly will fall victim to the federal–state political game of who pays. No matter that both are responsible for the health rights of all Australians. The last thing we want is a future generation of medical students disillusioned through questionable quality of clinical exposure and experience.
Proton Pump Inhibitors Accelerate Endothelial Senescence.

RATIONALE Proton pump inhibitors (PPIs) are popular drugs for gastroesophageal reflux, which are now available for long-term use without medical supervision. Recent reports suggest that PPI use is associated with cardiovascular, renal, and neurological morbidity. OBJECTIVE To study the long-term effect of PPIs on endothelial dysfunction and senescence and investigate the mechanism involved in PPI-induced vascular dysfunction. METHODS AND RESULTS Chronic exposure to PPIs impaired endothelial function and accelerated human endothelial senescence by reducing telomere length. CONCLUSIONS Our data may provide a unifying mechanism for the association of PPI use with increased risk of cardiovascular, renal, and neurological morbidity and mortality.