Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of 12 strategies for obtaining second opinions to improve interpretation of breast histopathology: simulation study

Objective To evaluate the potential effect of second opinions on improving the accuracy of diagnostic interpretation of breast histopathology. Design Simulation study. Setting 12 different strategies for acquiring independent second opinions. Participants Interpretations of 240 breast biopsy specimens by 115 pathologists, one slide for each case, compared with reference diagnoses derived by expert consensus. Main outcome measures Misclassification rates for individual pathologists and for 12 simulated strategies for second opinions. Simulations compared accuracy of diagnoses from single pathologists with that of diagnoses based on pairing interpretations from first and second independent pathologists, where resolution of disagreements was by an independent third pathologist. 12 strategies were evaluated in which acquisition of second opinions depended on initial diagnoses, assessment of case difficulty or borderline characteristics, pathologists’ clinical volumes, or whether a second opinion was required by policy or desired by the pathologists. The 240 cases included benign without atypia (10% non-proliferative, 20% proliferative without atypia), atypia (30%), ductal carcinoma in situ (DCIS, 30%), and invasive cancer (10%). Overall misclassification rates and agreement statistics depended on the composition of the test set, which included a higher prevalence of difficult cases than in typical practice. Results Misclassification rates significantly decreased (P<0.001) with all second opinion strategies except for the strategy limiting second opinions only to cases of invasive cancer. The overall misclassification rate decreased from 24.7% to 18.1% when all cases received second opinions (P<0.001). Obtaining both first and second opinions from pathologists with a high volume (≥10 breast biopsy specimens weekly) resulted in the lowest misclassification rate in this test set (14.3%, 95% confidence interval 10.9% to 18.0%). Obtaining second opinions only for cases with initial interpretations of atypia, DCIS, or invasive cancer decreased the over-interpretation of benign cases without atypia from 12.9% to 6.0%. Atypia cases had the highest misclassification rate after single interpretation (52.2%), remaining at more than 34% in all second opinion scenarios. Conclusion Second opinions can statistically significantly improve diagnostic agreement for pathologists’ interpretations of breast biopsy specimens; however, variability in diagnosis will not be completely eliminated, especially for breast specimens with atypia.
Three-Dimensional Growth of Flexural Slip Fault-Bend and Fault-Propagation Folds and Their Geomorphic Expression

The three-dimensional growth of fault-related folds is known to be an important process during the development of compressive mountain belts. However, comparatively little is known concerning the manner in which fold growth is expressed in topographic relief and local drainage networks. Here we report results from a coupled kinematic and surface process model of fault-related folding. We consider flexural slip fault-bend and fault-propagation folds that grow in both the transport and strike directions, linked to a surface process model that includes bedrock channel development and hillslope diffusion. We investigate various modes of fold growth under identical surface process conditions and critically analyse their geomorphic expression. Fold growth results in the development of steep forelimbs and gentler, wider backlimbs resulting in asymmetric drainage basin development (smaller basins on forelimbs, larger basins on backlimbs). However, topographies developed above fault-propagation folds are more symmetric than those developed above fault-bend folds as a result of their different forelimb kinematics. In addition, the surface expression of fault-bend and fault-propagation folds depends both on the slip distribution along the fault and on the style of fold growth. When along-strike plunge is a result of slip events with gently decreasing slip towards the fault tips (with or without lateral propagation), large plunge-panel drainage networks are developed at the expense of backpanel (transport-opposing) and forepanel (transport-facing) drainage basins. In contrast, if the fold grows as a result of slip events with similar displacements along strike, plunge-panel drainage networks are poorly developed (or are transient features of early fold growth) and restricted to lateral fold terminations, particularly when the number of propagation events is small. The absence of large-scale plunge-panel drainage networks in natural examples suggests that the latter mode of fold growth may be more common. The advective component of deformation (implicit in kink-band migration models of fault-bend and fault-propagation folding) exerts a strong control on drainage basin development. In particular, as drainage lengthens with fold growth, more linear, parallel drainage networks are developed as compared to the dendritic patterns developed above simple uplifting structures. Over the 1 Ma of their development the folds modelled here only attain partial topographic equilibrium, as new material is continually being advected through active axial surfaces on both fold limbs and faults are propagating in both the transport and strike directions. We also find that the position of drainage divides at the Earth’s surface has a complex relationship to the underlying fold axial surface locations.
Programmable Scan-Based Logic Built-In Self Test

This paper presents a programmable approach for performing scan-based logic built-in self test. This approach combines the techniques of reseeding and weighted random patterns testing. Reseeding is used to encode the bias cube and weighted patterns are used to fine tune the weight set. Experimental results show fault coverage comparable to ATPG can be achieved. Most importantly, the scheme fits well in the system test environment and high fault coverage can be obtained with a small number of reconfigurations on the BIST controller.
Supplemental Silicon and Boron Alleviates Aluminum-Induced Oxidative Damage in Soybean Roots

Aluminum (Al) toxicity in acidic soils is a major abiotic stress that negatively impacts plant growth and development. The toxic effects of Al manifest primarily in the root system, leading to inhibited root elongation and functionality, which impairs the above-ground organs of the plant. Recent research has greatly improved our understanding of the applications of small molecule compounds in alleviating Al toxicity. This study aimed to investigate the role of boron (B), silicon (Si), and their combination in alleviating Al toxicity in soybeans. The results revealed that the combined application significantly improved the biomass and length of soybean roots exposed to Al toxicity compared to B and Si treatments alone. Our results also indicated that Al toxicity causes programmed cell death (PCD) in soybean roots, while B, Si, and their combination all alleviated the PCD induced by Al toxicity. The oxidative damage induced by Al toxicity was noticeably alleviated, as evidenced by lower MAD and H2O2 accumulation in the soybean roots treated with the B and Si combination. Moreover, B, Si, and combined B and Si significantly enhanced plant antioxidant systems by up-regulating antioxidant enzymes including CAT, POD, APX, and SOD. Overall, supplementation with B, Si, and their combination was found to alleviate oxidative damage and reduce PCD caused by Al toxicity, which may be one of the mechanisms by which they alleviate root growth inhibition due to Al toxicity. Our results suggest that supplementation with B, Si, and their combination may be an effective strategy to improve soybean growth and productivity against Al toxicity.
Proximity Distribution Kernels for Geometric Context in Category Recognition

We propose using the proximity distribution of vector- quantized local feature descriptors for object and category recognition. To this end, we introduce a novel "proximity distribution kernel" that naturally combines local geometric as well as photometric information from images. It satisfies Mercer's condition and can therefore be readily combined with a support vector machine to perform visual categorization in a way that is insensitive to photometric and geometric variations, while retaining significant discriminative power. In particular, it improves on the results obtained both with geometrically unconstrained "bags of features" approaches, as well as with over-constrained "affine procrustes. " Indeed, we test this approach on several challenging data sets, including Graz-01, Graz-02, and the PASCAL challenge. We registered the average performance at 91.5% on Graz-01, 82.7% on Graz-02, and 74.5% on PASCAL. Our approach is designed to enforce and exploit geometric consistency among objects in the same category; therefore, it does not improve the performance of existing algorithms on datasets where the data is already roughly aligned and scaled. Our method has the potential to be extended to more complex geometric relationships among local features, as we illustrate in the experiments.
Lactic Acid Bacteria as a Cell Factory for the Delivery of Functional Biomolecules and Ingredients in Cereal-Based Beverages: A Review

In this review, we aim to describe the mechanisms by which LAB can fulfil the novel role of efficient cell factory for the production of functional biomolecules and food ingredients to enhance the quality of cereal-based beverages. LAB fermentation is a safe, economical, and traditional method of food preservation foremost, as well as having the additional benefits of flavor, texture, and nutrition amelioration. Additionally, LAB fermentation in known to render cereal-based foods and beverages safe, in a chemical-free, consumer-friendly manner, from an antinutrient and toxigenic perspective. Huge market opportunities and potential exist for food manufacturers who can provide the ideal functional beverage fulfilling consumer needs. Newly developed fermented cereal-based beverages must address markets globally including, high-nutrition markets (developing countries), lifestyle choice consumers (vegetarian, vegan, low-fat, low-salt, low-calorie), food-related non-communicable disease sufferers (cardiovascular disease, diabetes), and green label consumers (Western countries). To fulfil these recommendations, a suitable LAB starter culture and cereal-based raw materials must be developed. These strains would be suitable for the biopreservation of cereal beverages and, ideally, would be highly antifungal, anti-mycotoxigenic, mycotoxin-binding and proteolytic (neutralize toxic peptides and release flavor-contributing amino acids) with an ability to ferment cereals, whilst synthesizing oligosaccharides, thus presenting a major opportunity for the development of safe cereal-based prebiotic functional beverages to compete with and replace the existing dairy versions.
VCE-PSO: Virtual Cloud Embedding through a Meta-heuristic Approach

Resource allocation, an integral and continuously evolving part of cloud computing, has been attracting a lot of researchers in recent years. However, most of current cloud systems consider resource allocation only as placement of independent virtual machines, ignoring the performance of a virtual machine is also depending on other cooperating virtual machines and also the net links utilization, which result in a poor efficient resource utilization. In this paper, we propose a novel model Virtual Cloud Embedding (VCE) to formulate the cloud resource allocation problem. VCE regards each resource request as an integral unit rather than independent virtual machines including their link constraints. To address the VCE problem, we develop a meta-heuristic algorithm VCE-PSO, which is based on particle swarm optimization algorithm, to allocate multiple resources as a unit considering the heterogeneity of cloud infrastructure and variety of resource requirements. We exploit specific knowledge like the locations of virtual machines, inter-link distance, etc., to measure the fitness of different resource assignments, and utilize them to define the assignment update operation corresponding to the operations and steps of particle swarm optimization algorithm. Experiment results demonstrate that VCE-PSO can find an optimal resource assignment with 12% reduction of average link-mapped-path length than existing greedy algorithms.
Quantitative evaluation of HIV-1 coreceptor use in the GHOST3 cell assay.

The utility of the GHOST(3) cell assay has been evaluated for testing coreceptor use of primary human immunodeficiency virus type 1 (HIV-1) isolates. GHOST(3) cells were derived from the human osteosarcoma cell line, HOS, and have been engineered to stably express CD4 and one or another of the chemokine receptors CCR3, CCR5, CXCR4, Bonzo, or the orphan receptor BOB. The indicator cell line carries the HIV-2 long terminal repeat-driven green fluorescence protein (GFP) gene, which becomes activated upon infection with HIV or simian immunodeficiency virus. Viral entry is followed by Tat activation of transcription and GFP becomes expressed. Infected cells can be detected 2 or 3 days after infection by simple fluorescence microscopic observation. This simplicity is the main advantage of the GHOST(3) cell system and makes it particularly suitable for screening of a large number of isolates. In addition, the efficiency of coreceptor use can be accurately quantitated with flow cytometric analysis. Here, we evaluated the coreceptor use of 59 primary HIV-1 isolates of different subtypes.
The lbgAB Gene Cluster of Haemophilus ducreyi Encodes a β-1,4-Galactosyltransferase and an α-1,6-dd-Heptosyltransferase Involved in Lipooligosaccharide Biosynthesis

ABSTRACT All Haemophilus ducreyi strains examined contain a lipooligosaccharide (LOS) consisting of a single but variable branch oligosaccharide that emanates off the first heptose (Hep-I) of a conserved Hep3-phosphorylated 3-deoxy-d-manno-octulosonic acid-lipid A core. In a previous report, identification of tandem genes, lbgA and lbgB, that are involved in LOS biosynthesis was described (Stevens et al., Infect. Immun. 65:651-660, 1997). In a separate study, the same gene cluster was identified and the lbgB (losB) gene was found to be required for transfer of the second sugar, d-glycero-d-manno-heptose (dd-Hep), of the major branch structure (Gibson et al., J. Bacteriol. 179:5062-5071, 1997). In this study, we identified the function of the neighboring upstream gene, lbgA, and found that it is necessary for addition of the third sugar in the dominant oligosaccharide branch, a galactose-linked β1→4, to the dd-Hep. LOS from an lbgA mutant and an lbgAB double mutant were isolated and were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, carbohydrate analysis, mass spectrometry, and nuclear magnetic resonance spectroscopy. The results showed that the mutant strains synthesize truncated LOS glycoforms that terminate after addition of the first glucose (lbgAB) or the disaccharide dd-Hepα1→6Glcβ1 (lbgA) that is attached to the heptose core. Both mutants show a significant reduction in the ability to adhere to human keratinocytes. Although minor differences were observed after two-dimensional gel electrophoresis of total proteins from the wild-type and mutant strains, the expression levels of the vast majority of proteins were unchanged, suggesting that the differences in adherence and invasion are due to differences in LOS. These studies add to the mounting evidence for a role of full-length LOS structures in the pathophysiology of H. ducreyi infection.
Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms*

Poly(C)-binding proteins (PCBPs) are important regulatory proteins that contain three KH (hnRNP K homology) domains. Binding poly(C) D/RNA sequences via KH domains is essential for multiple PCBP functions. To reveal the basis for PCBP-D/RNA interactions and function, we determined the structure of a construct containing the first two domains (KH1-KH2) of human PCBP2 by NMR. KH1 and KH2 form an intramolecular pseudodimer. The large hydrophobic dimerization surface of each KH domain is on the side opposite the D/RNA binding interface. Chemical shift mapping indicates both domains bind poly(C) DNA motifs without disrupting the KH1-KH2 interaction. Spectral comparison of KH1-KH2, KH3, and full-length PCBP2 constructs suggests that the KH1-KH2 pseudodimer forms, but KH3 does not interact with other parts of the protein. From NMR studies and modeling, we propose possible modes of cooperative binding tandem poly(C) motifs by the KH domains. D/RNA binding may induce pseudodimer dissociation or stabilize dissociated KH1 and KH2, making protein interaction surfaces available to PCBP-binding partners. This conformational change may represent a regulatory mechanism linking D/RNA binding to PCBP functions.
Emission of VOC and GHG by Bioremediation of Soil Contaminated with Diesel

Bioremediation processes have been credited for reducing high levels of organic contaminants from soils. However, during bioremediation of diesel contaminated soils, for instance, diesel is converted to volatile organic compounds (VOC) and greenhouse gases (GHG), which means that such remediation technique contributes to the greenhouse effect. The ongoing construction of a large petrochemical industrial region in Rio de Janeiro Metropolitan Area (COMPERJ) and the transportation of large volumes of oil byproducts (mainly diesel), have raised deep concerns regarding accidents that may result in soil and air contamination. When the problem comes, remediation techniques shall be applied. The objective of this study was to characterize the emission of GHG and VOC during bioremediation of soils contaminated with diesel oil in pilot scale. Soil samples contaminated with 0.5, 2.0 and 4.0 w/w% diesel oil were kept during 3 months in glass rectors (2 L internal volume) kept under anaerobic/anoxic conditions. The soil moisture was controlled at 80% of field capacity. Bioremediation processes were investigated with nutrient’s adjustment (biostimulation), no adjustment (natural attenuation) and sterilized soil (abiotic process). The gases emitted from different reactors were collected in activated carbon cartridges and the GHG were collected in Tedlar bags. The chemical analyzes were performed using a gas chromatograph (Agilent 7690) with multi-detection using FID for CH 4 , ECD for N 2 O and TCD for CO 2 . VOC were analyzed using a mass spectrometry detector (Varian 450GC MS220). The results indicated that gaseous samples contained high concentrations of CO 2 but low concentrations of CH 4 and N 2 O. The differences in composition of the gas emitted from the reactors regarding CO 2 were statistically not significant. Preliminarily, regarding VOC emissions, such as alkanes and alkenes (both branched), cycloalkanes, and aromatic substituted (such as ethyl benzene), the compounds with higher emissions were cycloalkanes and branched alkanes.
Plasma homocysteine as a risk factor for vascular disease. The European Concerted Action Project.

CONTEXT Elevated plasma homocysteine is a known risk factor for atherosclerotic vascular disease, but the strength of the relationship and the interaction of plasma homocysteine with other risk factors are unclear. OBJECTIVE To establish the magnitude of the vascular disease risk associated with an increased plasma homocysteine level and to examine interaction effects between elevated plasma homocysteine level and conventional risk factors. DESIGN Case-control study. SETTING Nineteen centers in 9 European countries. PATIENTS A total of 750 cases of atherosclerotic vascular disease (cardiac, cerebral, and peripheral) and 800 controls of both sexes younger than 60 years. MEASUREMENTS Plasma total homocysteine was measured while subjects were fasting and after a standardized methionine-loading test, which involves the administration of 100 mg of methionine per kilogram and stresses the metabolic pathway responsible for the irreversible degradation of homocysteine. Plasma cobalamin, pyridoxal 5'-phosphate, red blood cell folate, serum cholesterol, smoking, and blood pressure were also measured. RESULTS The relative risk for vascular disease in the top fifth compared with the bottom four fifths of the control fasting total homocysteine distribution was 2.2 (95% confidence interval, 1.6-2.9). Methionine loading identified an additional 27% of at-risk cases. A dose-response effect was noted between total homocysteine level and risk. The risk was similar to and independent of that of other risk factors, but interaction effects were noted between homocysteine and these risk factors; for both sexes combined, an increased fasting homocysteine level showed a more than multiplicative effect on risk in smokers and in hypertensive subjects. Red blood cell folate, cobalamin, and pyridoxal phosphate, all of which modulate homocysteine metabolism, were inversely related to total homocysteine levels. Compared with nonusers of vitamin supplements, the small number of subjects taking such vitamins appeared to have a substantially lower risk of vascular disease, a proportion of which was attributable to lower plasma homocysteine levels. CONCLUSIONS An increased plasma total homocysteine level confers an independent risk of vascular disease similar to that of smoking or hyperlipidemia. It powerfully increases the risk associated with smoking and hypertension. It is time to undertake randomized controlled trials of the effect of vitamins that reduce plasma homocysteine levels on vascular disease risk.
Multimodal Fusion of Muscle and Brain Signals for a Hybrid-BCI

Practical Brain-Computer Interfaces (BCIs) for disabled people should allow them to use all their remaining functionalities as control possibilities. Sometimes these people have residual activity of their muscles, most likely in the morning when they are not exhausted. In this work we fuse electromyographic (EMG) with electroencephalographic (EEG) activity in the framework of a so called “Hybrid-BCI” (hBCI) approach. Thereby, subjects could achieve a good control of their hBCI independently of their level of muscular fatigue. Furthermore, although EMG alone yields good performance, it is outperformed by the hybrid fusing of EEG and EMG. Two different fusion techniques are explored showing graceful performance degradation in the case of signal attenuation. Such a system allows a very reliable control and a smooth handover if the subjects get exhausted or fatigued during the day.
Digital model of automated unmanned aerial vehicle with edge computing application for railway reconnaissance

In the last decade, unmanned aerial vehicles have been widely used in various civil and military field operations. Most modern drones are manually controlled by an operator and require decision making, which requires experience gained through training, which is time consuming and expensive, and even with experienced operators, the human factor can never be excluded. In this paper, an algorithm for an automatic flight mode of unmanned aerial vehicles without an operator’s participation has been developed. The proposed algorithm has been considered in the military reconnaissance of railways using edge computing and computer vision approaches to recognise railroads and moving trains for simulated and real cases as well as send report data to the web platform. As a result, the head of the operation received information about the number of carriages and Global Positioning System coordinates of the recognised train to make the necessary decisions.