Miracle-dz/UniFAR-FTUs huggingface dataset:
PCR based identification and discrimination of agents of mucormycosis and aspergillosis in paraffin wax embedded tissue

Background: Invasive fungal infections are often diagnosed by histopathology without identification of the causative fungi, which show significantly different antifungal susceptibilities. Aims: To establish and evaluate a system of two seminested polymerase chain reaction (PCR) assays to identify and discriminate between agents of aspergillosis and mucormycosis in paraffin wax embedded tissue samples. Methods: DNA of 52 blinded samples from five different centres was extracted and used as a template in two PCR assays targeting the mitochondrial aspergillosis DNA and the 18S ribosomal DNA of zygomycetes. Results: Specific fungal DNA was identified in 27 of 44 samples in accordance with a histopathological diagnosis of zygomycosis or aspergillosis, respectively. Aspergillus fumigatus DNA was amplified from one specimen of zygomycosis (diagnosed by histopathology). In four of 16 PCR negative samples no human DNA was amplified, possibly as a result of the destruction of DNA before paraffin wax embedding. In addition, eight samples from clinically suspected fungal infections (without histopathological proof) were examined. The two PCR assays detected a concomitant infection with Absidia corymbifera and A fumigatus in one, and infections with Rhizopus arrhizus and A fumigatus in another two cases. Conclusions: The two seminested PCR assays described here can support a histopathological diagnosis of mucormycosis or aspergillosis, and can identify the infective agent, thereby optimising antifungal treatment.
The Rise and Fall of Modern Medicine

James Le Fanu ! [][1] Little Brown, £20, pp 490 ISBN 0 316 64836 1 Rating: ! [Graphic][2] ! [Graphic][3] ! [Graphic][4] James Le Fanu tells us that medicine today is dull, which, from his perspective in general practice, it may have become. Whether medicine has lost the excitement that accompanied the explosion in treatments in the past 50 years, as he contends, medicine has certainly changed beyond recognition. He leads us instructively through these years of medical change. In the first of four “paradoxes” with which he introduces and later closes his book, Le Fanu writes: “Medicine is, sadly, no longer as satisfying as in the past. Many of the most interesting diseases that tested the doctor's clinical acumen have simply disappeared, and the family doctor is lucky to see a patient with a serious acute medical problem from one week to the next. ” As a result of past success in prevention and treatment, the primary care doctor is left with the symptomatic care of patients suffering from chronic illnesses and of counselling the “worried well. ” Serious illness, acute as well as chronic, has increasingly become the province of hospital based physicians and surgeons. In his second paradox Le Fanu writes: “It is most peculiar that as medicine has become more successful, the proportion of the public who apparently are ‘worried well’ about their health has increased. ” As a consequence of epidemiological evidence that an individual's life style can affect his or her health, “an excessive concern about ‘health’ can … [1]: /embed/graphic-1.gif [2]: /embed/inline-graphic-1.gif [3]: /embed/inline-graphic-2.gif [4]: /embed/inline-graphic-3.gif
Automatic Registration of Color and Infrared Videos Using Trajectories Obtained from a Multiple Object Tracking Algorithm

The registration of images from multiple types of sensors (particularly infrared sensors and color sensors) is the first step to achieving multi-sensor fusion. This is the subject of this paper. Registration is performed by using the trajectories of the moving objects obtained by a novel multiple object tracking algorithm. The trajectories are matched using a RANSAC-based algorithm. The registration criteria used in this algorithm is based on the number of pixels in intersection after overlapping the two images. Results show registration accuracy close to the ground-truth after about 30 frames. The influence of the tracking method used to obtain the trajectories is also investigated.
A Theoretical Analysis of the Selection of Differentially Expressed Genes

A great deal of recent research has focused on the challenging task of selecting differentially expressed genes from microarray data ("gene selection"). Numerous gene selection algorithms have been proposed in the literature, but it is often unclear exactly how these algorithms respond to conditions like small sample sizes or differing variances. Choosing an appropriate algorithm can therefore be difficult in many cases. In this paper we propose a theoretical analysis of gene selection, in which the probability of successfully selecting differentially expressed genes, using a given ranking function, is explicitly calculated in terms of population parameters. The theory developed is applicable to any ranking function which has a known sampling distribution, or one which can be approximated analytically. In contrast to methods based on simulation, the approach presented here is computationally efficient and can be used to examine the behavior of gene selection algorithms under a wide variety of conditions, even when the number of genes involved runs into the tens of thousands. The utility of our approach is illustrated by comparing three widely-used gene selection methods.
The Membrane Transport System of the Guard Cell and Its Integration for Stomatal Dynamics1[CC-BY]

While guard cells have come to represent the premier model for ion transport, the coordination of transport in driving stomatal movements continues to challenge an intuitive understanding. Stomatal guard cells are widely recognized as the premier plant cell model for membrane transport, signaling, and homeostasis. This recognition is rooted in half a century of research into ion transport across the plasma and vacuolar membranes of guard cells that drive stomatal movements and the signaling mechanisms that regulate them. Stomatal guard cells surround pores in the epidermis of plant leaves, controlling the aperture of the pore to balance CO2 entry into the leaf for photosynthesis with water loss via transpiration. The position of guard cells in the epidermis is ideally suited for cellular and subcellular research, and their sensitivity to endogenous signals and environmental stimuli makes them a primary target for physiological studies. Stomata underpin the challenges of water availability and crop production that are expected to unfold over the next 20 to 30 years. A quantitative understanding of how ion transport is integrated and controlled is key to meeting these challenges and to engineering guard cells for improved water use efficiency and agricultural yields.
Collaborative Multi-Camera Surveillance with Automated Person Detection

This paper presents the groundwork for a distributed network of collaborating, intelligent surveillance cameras, implemented with low-cost embedded microprocessor camera modules. Each camera trains a person detection classifier using the Winnow algorithm for unsupervised, online learning. Training examples are automatically extracted and labelled, and the classifier is then used to locate person instances. To improve detection performance, multiple cameras with overlapping fields of view collaborate to confirm results. We present a novel, unsupervised calibration technique that allows each camera module to represent its spatial relationship with the rest. During runtime, cameras apply the learned spatial correlations to confirm each other’s detections. This technique implicitly handles non-overlapping regions that cannot be confirmed. Its computational efficiency is well-suited to real-time processing on our hardware.
Construction of a Generalized DFT Codebook Using Channel-Adaptive Parameters

Discrete Fourier transform (DFT)-based codebooks are known to work efficiently for spatially correlated channels produced by uniform linear arrays. Although the long-term codebooks are selected to suit to channel correlation characteristics, such selections may not be optimal for the given channel of the target user equipment (UE), due to the specific structure and constraints of the codebook in use. In this letter, we propose a generalized DFT-based codebook structure employing variable parameters to provide enhanced resolution of codevectors and adjustable spacing among them. The proposal includes the Release 10 codebook of LTE-advanced as a special case, with added flexibility via parameter configurations. When tested over the 3GPP spatial channel model, the new codebook exhibits significant gains over existing ones, outperforming the LTE-advanced codebook in entire UE locations within the sector.
Anomaly detection in wireless sensor networks via support vector data description with mahalanobis kernels and discriminative adjustment

In the past few years, wireless sensor networks (WSNs) have been increasingly gaining impact in the real world with with various applications such as healthcare, condition monitoring, control networks, etc. Anomaly detection in WSNs is an important aspect of data analysis in order to identify data items which does not conform to an expected pattern or other items in a dataset. This paper describes a anomaly detection method using support vector data description (SVDD) kernelized by Mahalanobis distance with adjusted discriminant threshold. The efficiency of this method is studied over a real data set. Numerical result demonstrates that the proposed approach achieved a high-level of detection accuracy and a low percentage of false alarm rate owing to wise choices of discriminant threshold.
Controlled Porosity Alumina Structures for Ultra‐Precision Hydrostatic Journal Bearings

A series of fine-grade alumina powders has been used in combination with maize starch granules to produce porous structures for porous hydrostatic journal-bearing applications. A comprehensive series of tests was conducted to characterize porosity in terms of density, pore size, and permeability. Successful processing of quality journal-bearing components has been demonstrated for preferred combinations of alumina size and starch content, using fixed-processing parameters. The new porous ceramic bearings showed consistent and reproducible properties and are suitable for a wide range of higher precision engineering applications. The porous ceramic-bearing processing route has also proved to be low cost and environmentally sound.
Slow cortical potential neurofeedback and self-management training in outpatient care for children with ADHD: study protocol and first preliminary results of a randomized controlled trial

Background: Treatment for children with attention deficit/hyperactivity disorder (ADHD) today is predominantly pharmacological. While it is the most common treatment, it might not always be the most appropriate one. Moreover, long term effects remain unclear. Behavior therapy (BT) and non-pharmacological treatments such as neurofeedback (NF) are promising alternatives, though there are no routine outpatient care/effectiveness studies yet that have included children with medication or changes in medication. Methods/design: This paper presents the protocol of a randomized controlled trial to compare the effectiveness of a Slow Cortical Potential (SCP) NF protocol with self-management (SM) in a high frequent outpatient care setting. Both groups (NF/SM) receive a total of 30 high frequent therapy sessions. Additionally, 6 sessions are reserved for comorbid problems. The primary outcome measure is the reduction of ADHD core symptoms according to parent and teacher ratings. Preliminary Results: Untill now 58 children were included in the study (48 males), with a mean age of 8.42 (1.34) years, and a mean IQ of 110 (13.37). Conners-3 parent and teacher ratings were used to estimate core symptom change. Since the study is still ongoing, and children are in different study stages, pre-post and follow-up results are not yet available for all children included. Preliminary results suggest overall good pre-post effects, though. For parent and teacher ratings an ANOVA with repeated measures yielded overall satisfying pre-post effects (η2 0.175–0.513). Differences between groups (NF vs. SM) could not yet be established (p = 0.81). Discussion: This is the first randomized controlled trial to test the effectiveness of a NF protocol in a high frequent outpatient care setting that does not exclude children on or with changes in medication. First preliminary results show positive effects. The rationale for the trial, the design, and the strengths and limitations of the study are discussed. Trial registration: This trial is registered in www.clinicaltrials. gov as NCT01879644.
Extended Dependency Tree-HMM for Non-Rectangular Sub-Images Modeling

This work is motivated by the need of evaluating the likelihood probability on sub-images of not necessarily rectangular shape in some frameworks. For this purpose, we propose an alternative of Dependency TreeHMM that allows the four traditional interactions between neighboring pixels instead of just two. To demonstrate the accuracy of the proposed model, we provide some classification results performed on high resolution aerial images.
Are You Smarter Than a Sixth Grader? Textbook Question Answering for Multimodal Machine Comprehension

We introduce the task of Multi-Modal Machine Comprehension (M3C), which aims at answering multimodal questions given a context of text, diagrams and images. We present the Textbook Question Answering (TQA) dataset that includes 1,076 lessons and 26,260 multi-modal questions, taken from middle school science curricula. Our analysis shows that a significant portion of questions require complex parsing of the text and the diagrams and reasoning, indicating that our dataset is more complex compared to previous machine comprehension and visual question answering datasets. We extend state-of-the-art methods for textual machine comprehension and visual question answering to the TQA dataset. Our experiments show that these models do not perform well on TQA. The presented dataset opens new challenges for research in question answering and reasoning across multiple modalities.
A low complexity soft-output data detection scheme based on Jacobi method for massive MIMO uplink transmission

In massive multiple-input multiple-output (MIMO) systems, linear minimum mean-square error (MMSE) detection can achieve near-optimal performance. However, it suffers from high computational complexity due to the involvement of matrix inversion. This issue becomes severer when user number (U) and receive antenna number (S) increase. Existing approaches such as Neumann series expansion method, Gauss-Seidel and Jacobi methods, can partly address this issue by approaching the matrix inversion with matrix multiplications or solving linear equations with iterative methods, respectively. However, matrix multiplications and the initialization for iterative methods are still costly. In this paper, we propose a further improved Jacobi method based soft-output massive MIMO detection scheme. The contributions include the use of matrix-vector product and a new approach to compute the log likelihood ratio (LLR). By using the matrix-vector product, the overall computational complexity is reduced from O (B × U2) to O(B × U). The new approach uses the noise-plus-interference (NPI) from the MMSE estimation, instead of using that from the first iteration. We then propose an approximation method to obtain the covariance of the NPI from MMSE estimation. Finally, we demonstrate through numerical simulations that the proposed scheme outperforms the existing schemes in terms of computational complexity and system bit error rate performance.
An Unsuspected Metabolic Role for Atrial Natriuretic Peptides: The Control of Lipolysis, Lipid Mobilization, and Systemic Nonesterified Fatty Acids Levels in Humans

In normal and obese humans, lipid mobilization and systemic nonesterified fatty acid levels are thought to be acutely controlled by catecholamines (ie, epinephrine and norepinephrine) and insulin. Natriuretic peptides (NPs) are known to play a key role in the regulation of salt and water balance and blood pressure homeostasis. They are involved in the pathophysiology of hypertension and heart failure. NPs have recently been found to exert potent lipolytic effects (ie, activating the breakdown of stored triacylglycerols) in isolated human fat cells and to promote lipid mobilization in vivo. Atrial natriuretic peptide increases the intracellular 3′, 5′-cyclic guanosine monophosphate (cGMP) concentration which activates cGMP-dependent protein kinase leading to perilipin and hormone-sensitive lipase phosphorylation and lipolysis. NPs promote lipid mobilization when administered intravenously. NPs are also responsible for the residual lipid-mobilizing action observed under oral β-blockade in subjects performing physical exercise. NPs are therefore novel factors which may open promising research pathways to explain the control of lipid mobilization in physiological and pathological conditions. The metabolic impact of altered production and circulation of NPs remains to be established. The potential influence of NPs on the development of lipid disorders, obesity-related cardiovascular events, and cardiac cachexia will be discussed in this review.
Enzymic, Phylogenetic, and Structural Characterization of the Unusual Papain-like Protease Domain of Plasmodium falciparum SERA5*

Serine repeat antigen 5 (SERA5) is an abundant antigen of the human malaria parasite Plasmodium falciparum and is the most strongly expressed member of the nine-gene SERA family. It appears to be essential for the maintenance of the erythrocytic cycle, unlike a number of other members of this family, and has been implicated in parasite egress and/or erythrocyte invasion. All SERA proteins possess a central domain that has homology to papain except in the case of SERA5 (and some other SERAs), where the active site cysteine has been replaced with a serine. To investigate if this domain retains catalytic activity, we expressed, purified, and refolded a recombinant form of the SERA5 enzyme domain. This protein possessed chymotrypsin-like proteolytic activity as it processed substrates downstream of aromatic residues, and its activity was reversed by the serine protease inhibitor 3,4-diisocoumarin. Although all Plasmodium SERA enzyme domain sequences share considerable homology, phylogenetic studies revealed two distinct clusters across the genus, separated according to whether they possess an active site serine or cysteine. All Plasmodia appear to have at least one member of each group. Consistent with separate biological roles for members of these two clusters, molecular modeling studies revealed that SERA5 and SERA6 enzyme domains have dramatically different surface properties, although both have a characteristic papain-like fold, catalytic cleft, and an appropriately positioned catalytic triad. This study provides impetus for the examination of SERA5 as a target for antimalarial drug design.
Synergistic Effects of the Lactobacillus acidophilus Surface Layer and Nisin on Bacterial Growth

ABSTRACT We have previously described a murein hydrolase activity for the surface layer (S-layer) of Lactobacillus acidophilus ATCC 4356. Here we show that, in combination with nisin, this S-layer acts synergistically to inhibit the growth of pathogenic Gram-negative Salmonella enterica and potential pathogenic Gram-positive bacteria, Staphylococcus aureus and Bacillus cereus. In addition, bacteriolytic effects were observed for the Gram-positive species tested. We postulate that the S-layer enhances the access of nisin into the cell membrane by enabling it to cross the cell wall, while nisin provides the sudden ion-nonspecific dissipation of the proton motive force required to enhance the S-layer murein hydrolase activity.
Predicting the likelihood of carrying a BRCA1 or BRCA2 mutation: validation of BOADICEA, BRCAPRO, IBIS, Myriad and the Manchester scoring system using data from UK genetics clinics

Objectives: Genetic testing for the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2 has important implications for the clinical management of people found to carry a mutation. However, genetic testing is expensive and may be associated with adverse psychosocial effects. To provide a cost-efficient and clinically appropriate genetic counselling service, genetic testing should be targeted at those individuals most likely to carry pathogenic mutations. Several algorithms that predict the likelihood of carrying a BRCA1 or a BRCA2 mutation are currently used in clinical practice to identify such individuals. Design: We evaluated the performance of the carrier prediction algorithms BOADICEA, BRCAPRO, IBIS, the Manchester scoring system and Myriad tables, using 1934 families seen in cancer genetics clinics in the UK in whom an index patient had been screened for BRCA1 and/or BRCA2 mutations. The models were evaluated for calibration, discrimination and accuracy of the predictions. Results: Of the five algorithms, only BOADICEA predicted the overall observed number of mutations detected accurately (ie, was well calibrated). BOADICEA also provided the best discrimination, being significantly better (p<0.05) than all models except BRCAPRO (area under the receiver operating characteristic curve statistics: BOADICEA = 0.77, BRCAPRO = 0.76, IBIS = 0.74, Manchester = 0.75, Myriad = 0.72). All models underpredicted the number of BRCA1 and BRCA2 mutations in the low estimated risk category. Conclusions: Carrier prediction algorithms provide a rational basis for counselling individuals likely to carry BRCA1 or BRCA2 mutations. Their widespread use would improve equity of access and the cost-effectiveness of genetic testing.
Maps of Computer Science

We describe a practical approach for visual exploration of research papers. Specifically, we use the titles of papers from the DBLP database to create what we call maps of computer science (MoCS). Words and phrases from the paper titles are the cities in the map, and countries are created based on word and phrase similarity, calculated using co-occurence. With the help of heatmaps, we can visualize the profile of a particular conference or journal over the base map. Similarly, heatmap profiles can be made of individual researchers or groups such as a department. The visualization system also makes it possible to change the data used to generate the base map. For example, a specific journal or conference can be used to generate the base map and then the heatmap overlays can be used to show the evolution of research topics in the field over the years. As before, individual researchers or research group profiles can be visualized using heatmap overlays over a specific journal or conference base map. We outline a modular and extensible system for term extraction using natural language processing techniques, and show the applicability of methods of information retrieval to calculation of term similarity and creation of a topic map. The system is available at mocs.cs. arizona.edu.
In-Place versus Re-Build versus Re-Merge: Index Maintenance Strategies for Text Retrieval Systems

Indexes are the key technology underpinning efficient text search. A range of algorithms have been developed for fast query evaluation and for index creation, but update algorithms for high-performance indexes have not been evaluated or even fully described. In this paper, we explore the three main alternative strategies for index update: in-place update, index merging, and complete re-build. Our experiments with large volumes of web data show that re-merge is for large numbers of updates the fastest approach, but in-place update is suitable when the rate of update is low or buffer size is limited.