Miracle-dz/UniFAR-FTUs huggingface dataset:
Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium.

BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
Rapid diagnostic tests for malaria at sites of varying transmission intensity in Uganda.

BACKGROUND In Africa, fever is often treated presumptively as malaria, resulting in misdiagnosis and the overuse of antimalarial drugs. Rapid diagnostic tests (RDTs) for malaria may allow improved fever management. METHODS We compared RDTs based on histidine-rich protein 2 (HRP2) and RDTs based on Plasmodium lactate dehydrogenase (pLDH) with expert microscopy and PCR-corrected microscopy for 7000 patients at sites of varying malaria transmission intensity across Uganda. RESULTS When all sites were considered, the sensitivity of the HRP2-based test was 97% when compared with microscopy and 98% when corrected by PCR; the sensitivity of the pLDH-based test was 88% when compared with microscopy and 77% when corrected by PCR. The specificity of the HRP2-based test was 71% when compared with microscopy and 88% when corrected by PCR; the specificity of the pLDH-based test was 92% when compared with microscopy and >98% when corrected by PCR. Based on Plasmodium falciparum PCR-corrected microscopy, the positive predictive value (PPV) of the HRP2-based test was high (93%) at all but the site with the lowest transmission rate; the pLDH-based test and expert microscopy offered excellent PPVs (98%) for all sites. The negative predictive value (NPV) of the HRP2-based test was consistently high (>97%); in contrast, the NPV for the pLDH-based test dropped significantly (from 98% to 66%) as transmission intensity increased, and the NPV for expert microscopy decreased significantly (99% to 54%) because of increasing failure to detect subpatent parasitemia. CONCLUSIONS Based on the high PPV and NPV, HRP2-based RDTs are likely to be the best diagnostic choice for areas with medium-to-high malaria transmission rates in Africa.
Spectropolarimetry of the Type II Supernovae 1997ds, 1998A, and 1999gi

We present single‐epoch spectropolarimetry of the Type II supernovae (SNe II) 1997ds, 1998A, and 1999gi. SN 1997ds and SN 1998A were both observed during the early photospheric phase, less than 50 days after explosion, while spectropolarimetry of SN 1999gi was obtained near the start of the transition to the nebular phase, about 110 days after explosion. Uncorrected for interstellar polarization (ISP), SN 1997ds is characterized by pV = 0.85% ± 0.02%, SN 1998A has pV = 0.24% ± 0.05%, and SN 1999gi is polarized at pV = 5.72% ± 0.01%. SN 1997ds and SN 1999gi exhibit distinct polarization modulations (up to Δptot = 1.6% in SN 1997ds and Δptot = 1.0% in SN 1999gi) at the wavelengths of the strongest spectral line features. While no spectral polarization features were observed in SN 1998A, the data are insensitive to polarization features at the levels confirmed in the other two objects. The low continuum polarization inferred for SN 1997ds and SN 1998A and the amplitude of (or limits on) the polarization modulations are consistent with those measured at similar epochs for SN 1987A and the Type II plateau SN 1999em and supports the growing consensus that core‐collapse events with hydrogen envelopes substantially intact at the time of explosion are not significantly aspherical during the early photospheric phase. The spectral shape of the high continuum polarization of SN 1999gi closely resembles a “Serkowski” ISP curve (characterized by pmax = 5.8%, θ = 154°, and λmax = 5300 Å) and is inconsistent with the wavelength‐independent nature of electron scattering expected for an aspherical SN atmosphere. Since Galactic reddening is minimal along this line of sight, the majority of the observed polarization in SN 1999gi is believed to be due to ISP of the host galaxy, although significant (up to p ≈ 2%) intrinsic polarization cannot be ruled out. The potential power of SN spectropolarimetry to study the properties of interstellar dust in external galaxies is described and applied to the SN 1999gi data, where it is shown that if the polarization is indeed predominantly interstellar in origin, then RV = 3.0 ± 0.2 for the dust along this line of sight in NGC 3184.
Urothelial Bladder Cancer Urinary Biomarkers

Abstract Urothelial bladder cancer is the fourth most prevalent male malignancy in the United States and also one of the ten most lethal. Superficial or non-muscle-invasive bladder cancer has a high rate of recurrence and can progress to muscle invasive disease. Conventional surveillance requires regular cystoscopy and is used often with urinary cytology. Unfortunately, the cystoscopy procedure is invasive for patients and costly for health care providers. Urinary biomarkers have the potential to improve bladder cancer diagnosis, the efficiency and also the cost-effectiveness of follow up. It may also be possible for urinary biomarkers to help prognosticate particularly for patients with high-grade bladder cancer who may want enhanced assessment of their risk of disease progression. In this review the important historical urinary biomarkers and the newly emerging biomarkers are discussed. As will be presented, although many of the tests have good performance characteristics, unfortunately no single test can fulfill all the roles currently provided by cystoscopy and cytology. It is likely that in the future, urinary biomarker testing will be used selectively in a personalized manner to try and improve prognostication or reduce the necessity for invasive cystoscopy in patients understanding the limits of the test.
Response to Industrial Wind Action Group Critiques

On November 20, 2009, the Industrial Wind Action Group (IWAG) posted an editorial that, in part, lists a number of concerns about Berkeley Lab’s efforts to investigate the presence of residential property value impacts associated with U.S. wind power facilities. 1 That editorial follows from more-extensive review comments provided on September 11, 2009 by the Industrial Wind Action Group. 2 The more extensive comments were provided during the external review of the draft Berkeley Lab report, and were one of roughly 20 sets of external review comments received by stakeholders and experts at that time. All of these comments were considered during revisions to the draft report, culminating in the final analysis and report issued on December 2, 2009.
Intelligent Sensor Network Simulation for Battlefield Resources Management

This paper presents a study of a battlefield simulation platform with consideration of sensor network and optimal resources management. This development is mainly based on two public ally available software - GECCO and REPAST. The platform allows integration with a user developed optimization engine for optimal battlefield management. A simulation example was presented to show the application to a wireless sensor network composed of unattended ground sensors and unmanned aerial vehicles for target detection, classification and localization in the battlefield.
Observations of the Crab nebula with HESS

Context. The Crab nebula was observed with the HESS stereoscopic Cherenkov-telescope array between October 2003 and January 2005 for a total of 22.9 h (after data quality selection). This period of time partly overlapped with the commissioning phase of the experiment; observations were made with three operational telescopes in late 2003 and with the complete 4 telescope array in January–February 2004 and October 2004–January 2005. Aims. Observations of the Crab nebula are discussed and used as an example to detail the flux and spectral analysis procedures of HESS. The results are used to evaluate the systematic uncertainties in HESS flux measurements. Methods. The Crab nebula data are analysed using standard HESS analysis procedures, which are described in detail. The flux and spectrum of γ-rays from the source are calculated on run-by-run and monthly time-scales, and a correction is applied for long-term variations in the detector sensitivity. Comparisons of the measured flux and spectrum over the observation period, along with the results from a number of different analysis procedures are used to estimate systematic uncertainties in the measurements. Results. The data, taken at a range of zenith angles between 45◦ and 65◦, show a clear signal with over 7500 excess events. The energy spectrum is found to follow a power law with an exponential cutoff, with photon index Γ = 2.39 ± 0.03stat and cutoff energy Ec = (14.3 ± 2.1stat) TeV between 440 GeV and 40 TeV. The observed integral flux above 1 TeV is (2.26 ± 0.08stat) × 10−11 cm−2 s−1. The estimated systematic error on the flux measurement is estimated to be 20%, while the estimated systematic error on the spectral slope is 0.1.
Optimal space subdivision for parallel approximate nearest neighbour determination

Many computer vision tasks rely on correspondence between features. SIFT and related descriptors represent features as high-dimensional vectors, which are used to compute a distance between features for matching. Calculating these distances is expensive in large datasets, so approximate nearest neighbour (ANN) approaches are used. ANN schemes that can be efficiently parallelised have been proposed, some of which divide up high-dimensional vectors into lower-dimensional subspaces. However, the feature descriptors computed by SIFT and similar methods are not computed in a homogeneous manner. There are clear statistical patterns within and between the components of feature vectors, and in this work we show that these patterns can have a strong effect on approximate nearest neighbor searching algorithms that are based on space subdivision.
Space-Time-Frequency Transmit Diversity in Broadband Wireless OFDM Systems

We consider space-time -frequency transmit diversity with orthogonal designs in a broadband OFDM system. Based on capacity considerations for Gaussian as well as real world signal constellations, we show that the concatenation of an outer error control code, a bit interleaver and orthogonal spatial transmit diversity provides an attractive MIMO scheme which is simple and fairly robust to channel imperfections such as spatial correlation or keyhole effects. Particularly, we discuss orthogonal transmit diversity versus spatial multiplexing and space-timefrequency codes which have been discussed in literature recently. Furthermore, we propose a simple and pragmatic application of orthogonal designs for space-time-frequency transmit diversity and give design criteria which allow to use a simple combiner at the receiver also in time-varying and severly frequency-selective channels.
Robust Active Learning Using Crowdsourced Annotations for Activity Recognition

Recognizing human activities from wearable sensor data is an important problem, particularly for health and eldercare applications. However, collecting sufficient labeled training data is challenging, especially since interpreting IMU traces is difficult for human annotators. Recently, crowdsourcing through services such as Amazon's Mechanical Turk has emerged as a promising alternative for annotating such data, with active learning (Cohn, Ghahramani, and Jordan 1996) serving as a natural method for affordably selecting an appropriate subset of instances to label. Unfortunately, since most active learning strategies are greedy methods that select the most uncertain sample, they are very sensitive to annotation errors (which corrupt a significant fraction of crowdsourced labels). This paper proposes methods for robust active learning under these conditions. Specifically, we make three contributions: 1) we obtain better initial labels by asking labelers to solve a related task; 2) we propose a new principled method for selecting instances in active learning that is more robust to annotation noise; 3) we estimate confidence scores for labels acquired from MTurk and ask workers to relabel samples that receive low scores under this metric. The proposed method is shown to significantly outperform existing techniques both under controlled noise conditions and in real active learning scenarios. The resulting method trains classifiers that are close in accuracy to those trained using ground-truth data.
Neurorehabilitation and Neural Repair

DOI: 10.1177/1545968308326636 2009; 23; 97 Neurorehabil Neural Repair Teo, Nicholas Ward and Steven Wolf Greenwood, David Howard, Masud Husain, Malcolm Macleod, Randolph Nudo, John Rothwell, Anthony Rudd, James Cumberland Consensus Working Group, Binith Cheeran, Leonardo Cohen, Bruce Dobkin, Gary Ford, Richard Basic Science to Rehabilitation of People After Stroke The Future of Restorative Neurosciences in Stroke: Driving the Translational Research Pipeline From
Whither or wither the AI of AIED?

This position paper explores the relationship between the his- toric roots of AIED and the challenges of restricting our vision to EdTech that has AI. It argues that the founders of AIED had a broad vi- sion of the field, primarily driven by the goals of creating advanced technology for personalised learning. They were not wedded to a tech- no-centric view, demanding use of particular techniques that are now thought of as "AI". The paper argues that we have accepted work with no AI, notably in Open Learner Modelling. We discourage, either di- rectly or just because of our name, work that is true to the AIED found- ers' vision. In doing so, we miss many exciting and promising ways to create better technology for education.
Usability experiments for determining document-related awareness in real-time cooperative editing

Distributed, collaborative editing of documents in a synchronous manner is increasingly becoming a very common and highly necessary task. It is, therefore, crucial to produce extremely easy-to-use editors facilitating this document-centered task. Providing awareness is a vital feature enhancing the usability of real-time cooperative document editing systems. Document-related awareness provides users with sufficient knowledge about the status of a document itself and all activities other users perform upon the document. This research develops a conceptual framework for workspace awareness in real-time cooperative document editing. This research exploits an intergrated approach—a “top-down” approach merged with a “bottom-up” approach—in determining highly suitable candidates for documentrelated awareness support mechanisms. This more relevant and complete approach has been ignored in other research. This research has found some new documentrelated awareness mechanisms, for instance, a dynamic users’ task list and toggle multi-user scrollbars. These are types of mechanism not revealed from the solely “bottom-up” approaches used in other research.
Parameter Estimation and Application of Time-varying FARIMA Model

The prediction model of network traffic has been a hot research spot. In this paper, a time-varying FARIMA model is proposed based on the traditional FARIMA model, in which the parameter d is changed into time-varying parameter d(t) and the time-varying parameters are estimated combined with time-varying ARMA model. The new model overcomes the fractal information loss caused by the global average and improves the accuracy of parameter estimation. Finally, the model's application in the anomaly detection of network traffic is analyzed.
Anchor-supported multi-modality hashing embedding for person re-identification

Person re-identification is a challenging problem in multi-camera surveillance systems. Most existing methods focus on metric learning which aims to match images from different cameras in a common metric space. Boosted hashing projection provides a new way of identifying instances based on pairwise similarity. However, both of these approaches ignore the underlying fact that images captured by two cameras should be seen as in different modalities. To address this drawback, we formulate person re-identification as an Anchor-supported Multi-Modality Hashing Embedding (AMMHE) problem, in which different projections are used to map data from different cameras into a common Hamming space. The data are projected to binary bits by using boosted hash projections, making the weighted Hamming distance of intra-class data pairs minimized and simultaneously those of inter-class data pairs maximized. We also introduce an anchor-supported dimension reduction method to avoid the computational burden of high feature dimensionality. Our approach obtains competitive performance compared with state-of-the-art methods on publicly available benchmarks.
Software verification at Bell Labs: One line of development

Collectors often greet the first report of a new type of minting error for commonly circulating coins with enthusiasm. A coin is a rare example of an object that can increase, rather than decrease, in value when it is faulty. In software design we are not so fortunate. Software faults are often intriguing, but they rarely increase the value of a product. Since the early days of computers, programmers have sought effective ways to defend against software bugs. Software verification techniques are meant to help the user locate possible defects in a software product reliably and, preferably, mechanically. In this paper we examine a line of research that has led to one of the most widely used verification systems for distributed software today.
Polo-like kinase 4 controls centriole duplication but does not directly regulate cytokinesis

Polo-like kinase 4 (Plk4) plays an essential role in centriole duplication, but recent work led to the conclusion that Plk4 also directly regulates cytokinesis. The consequence of reduced Plk4 levels in human and mouse cells is studied. It is shown that Plk4 controls centriole duplication but does not directly regulate cytokinesis.
Policy Reforms, Competitiveness and Prospects of Kenya's Manufacturing Industries: 1984-1997

This paper attempts to answer the question whether trade liberalization and other measures of structural adjustment undertaken in Kenya since the mid-1980s have led to increased competitiveness of the manufacturing sector. It uses a method of analysis that consists of the computation of three unit cost indicators, of domestic and international competitiveness, and of comparative advantage, and their break-down according to the main sources. It distinguishes real sources from nominal ones based on price distortions, including those of factor and product prices, exchange rate misalignment, various trade restrictions, interest rate distortions and subsidies. Using data from two manufacturing sector surveys in Kenya, of 1984 and 1997, the study shows that comparative advantage has increased on average, but industry competitiveness has declined during the 13-year period of structural adjustment and policy reforms, due to higher distortion levels, mainly in the financial cost of credit and exchange rate misalignment, but also through deteriorating infrastructure and public services.
Rehabilitation Quality Improvement in an Intensive Care Unit Setting: Implementation of a Quality Improvement Model

Abstract Objective: There are barriers to providing early physical medicine and rehabilitation (PM&R) in the intensive care unit (ICU). We present a specific model for undertaking quality improvement (QI) projects and a case study focused on QI for early PM&R in the ICU. Methods: The QI project was undertaken using a 4-step model: (1) summarizing the evidence, (2) identifying barriers, (3) establishing performance measures, and (4) ensuring patients receive the intervention. To evaluate the application and outcomes of this model, we present data collected during a 4-month QI period versus an immediately preceding 3-month control period. Results: Deep sedation was a major barrier to early PM&R that was addressed in the QI project. Compared to the control period, there was a decrease in medical ICU (MICU) days with any benzodiazepine use (73% vs 96% of days, P = .03) and narcotic use (77% vs 96%, P = .05) and improved delirium status (MICU days without delirium, 53% vs 21%, P = .003). In addition, more QI patients had physical therapy consultations (93% vs 59%, P = .004) and greater number of rehabilitation treatments with higher functional mobility (treatments involving sitting or greater mobility, 78% vs 56%, P = .03). Hospital data for the QI period demonstrated a decrease in average length of stay in the MICU (4.9 vs 7.0 days, P = .02) and hospital (14.1 vs 17.2, P = .03) compared to the prior year. Conclusion: A structured QI model can be applied to implementation of early PM&R in the ICU resulting in markedly improved delirium status, delivery of PM&R, functional mobility, and length of stay.
Gaussian mixture cardinalized PHD filter for ground moving target tracking

The cardinalized probability hypothesis density (CPHD) filter is a recursive Bayesian algorithm for estimating multiple target states with varying target number in clutter. In particular, the Gaussian mixture variant (GMCPHD) for linear, Gaussian systems is a candidate for real time multi target tracking. The present work addresses the following three issues: (i) we show the equivalence between the GMCPHD filter and the standard Multi Hypothesis Tracker (MHT) in the case of single targets; (ii) using a Gaussian sum approach, we extend the GMCPHD filter by employing digital road maps for road constraint targets. The utilization of such external information leads to more precise tracks and faster and more reliable target number estimates; (iii) we model the effect of Doppler blindness by a target state dependent detection probability, leading to more stable target number estimation in the case of low Doppler targets.