Miracle-dz/UniFAR-FTUs huggingface dataset:
Oats and CVD risk markers: a systematic literature review

High consumption of whole-grain food such as oats is associated with a reduced risk of CVD and type 2 diabetes. The present study aimed to systematically review the literature describing long-term intervention studies that investigated the effects of oats or oat bran on CVD risk factors. The literature search was conducted using Embase, Medline and the Cochrane library, which identified 654 potential articles. Seventy-six articles describing sixty-nine studies met the inclusion criteria. Most studies lacked statistical power to detect a significant effect of oats on any of the risk factors considered: 59 % of studies had less than thirty subjects in the oat intervention group. Out of sixty-four studies that assessed systemic lipid markers, thirty-seven (58 %) and thirty-four (49 %) showed a significant reduction in total cholesterol (2–19 % reduction) and LDL-cholesterol (4–23 % reduction) respectively, mostly in hypercholesterolaemic subjects. Few studies (three and five, respectively) described significant effects on HDL-cholesterol and TAG concentrations. Only three out of twenty-five studies found a reduction in blood pressure after oat consumption. None of the few studies that measured markers of insulin sensitivity and inflammation found any effect after long-term oat consumption. Long-term dietary intake of oats or oat bran has a beneficial effect on blood cholesterol. However, there is no evidence that it favourably modulates insulin sensitivity. It is still unclear whether increased oat consumption significantly affects other risk markers for CVD risk, and comprehensive, adequately powered and controlled intervention trials are required to address this question.
Poly(amidoxime) from Polymer-Grafted Khaya Cellulose : An Excellent Medium for the Removal of Transition Metal Cations from Aqueous Solution

A free radical chain initiation reaction was exploited to prepare poly(acrylonitrile)-grafted Khaya cellulose. The synthesis of the poly(amidoxime) ligand was also performed using oximation reactions. Transition metal cations formed some complexes with the polymeric ligand. The pH of the solution played an important role in the optical detection of Cu2+ ions. The highest absorbance (approximately 94%) of the [Cu-ligand]n+ complex was at pH 6. The sorption quantity increased with increasing Cu2+ ion concentration, which was reflected by a broad peak at 600 nm that was attributed to the charge transfer (- transition) process. The equilibrium sorption capacity of 282 mg/g, with faster adsorption rates (t1/2 = 8 min), suggested that copper possessed excellent adsorption capacity compared with the other cations (Fe3+, Co3+, Cr3+, Ni2+, and Zn2+). The sorption data for all of the cations followed the Freundlich isotherm model, with a high coefficient of determination, reflecting a heterogeneous sorption process by the cellulose-based, poly(amidoxime) adsorbent. The feasibility for recycling of adsorbent was evaluated by the sorption/ desorption study, and the results suggest that a new type adsorbent can be reused in seven cycles without any significant loss in its original sensing and removal performances.
Small Molecule-Assisted PET: Approaches to Imaging of Conformational Diseases of the Brain

PET (positron emission tomography) in vivo imaging of cerebral conformational diseases is essentially based on non-peptide small molecule ligands used to detect early alterations in peptide secondary structures and subsequent accumulation of aberrant oligomers and protein deposits involved in progressive neurodegeneration, cognitive and movement disorders. In this article, an overview is given about tracers currently available and lead structures of potential PET probes for detection of β-amyloid (Aβ), tau protein, α-synuclein, constitutive (PrPc) and infectious isoforms (PrPsc) of prions (proteinaceous infectious particles) as imaging targets. Whereas the styrylpyridine derivative florbetapir, approved for clinical applications, the stilbene derivative florbetaben and the benzoxazole derivative BF227 show high affinity binding to Aβ, preclinical investigations promise improved pharmacokinetics for benzoimidazothiazoles, aryloxazoles and benzofuran derivatives. Tau protein imaging based clinically, presently, on the pyridine-pyridoindole T807 has got new incentives following identification of a series of pyrrolopyridine quinolines and pharmacokinetic improvements of fluoropropoxy quinolines including for instance THK-5351. The pyridine isoquinoline MK6240 is involved now in clinical trials. Most forward-looking efforts apply to small molecule ligands of α-synuclein, which are expected to permit a breakthrough in differential diagnostics of Parkinson-related dementia and Lewy body diseases. However, at the moment the proposed lead structures are in affinity and blood brain barrier delivery properties below the possibilities of Aβ and tau protein ligands. This is the case also for potential tracers of prion proteins.
Object-Oriented Bayesian Networks for Condition Monitoring, Root Cause Analysis and Decision Support on Operation of Complex Continuous Processes: Methodology & Applications

The increasing complexity of large-scale industrial processes and the struggle for cost reduction and higher profitability implies automated systems for processes diagnosis in plant operation and maintenance are required. We have developed a methodology to address this issue and have designed a prototype system on which this methodology has been applied. The methodology integrates decision-theoretic troubleshooting with risk assessment for industrial process control. It is applied to a pulp operation and screening process. The process is modeled using object-oriented Bayesian networks (OOBNs). Most abnormalities are derived from the context- adaptive signal classifications with their enable and action events. The system performs reasoning under uncertainty based on multi- sensor information extraction and presents to users corrective actions, with explanations of the root causes. It records users' actions with associated cases and the OOBN models are prepared to perform sequential learning to increase its performance in diagnostics and advice. The system allows modeling during the design phase of a new plant, can provide guidance already in the start up phase and allows adaptation to process changes during plant operation.
Distributed Convex Optimization with Many Convex Constraints

We address the problem of solving convex optimization problems with many convex constraints in a distributed setting. Our approach is based on an extension of the alternating direction method of multipliers (ADMM) that recently gained a lot of attention in the Big Data context. Although it has been invented decades ago, ADMM so far can be applied only to unconstrained problems and problems with linear equality or inequality constraints. Our extension can handle arbitrary inequality constraints directly. It combines the ability of ADMM to solve convex optimization problems in a distributed setting with the ability of the Augmented Lagrangian method to solve constrained optimization problems, and as we show, it inherits the convergence guarantees of ADMM and the Augmented Lagrangian method.
Markov Model and Data Mining Approach for PCB Component Defect

Currently the various electronic components which are manufactured use surface mount technology (SMT). This technology is a higher end assembly technique which produces printed circuit boards with very tiny electronic components. Due to the device area issues, the demand of PCBs is increasing. In order to cater this issue, high-volume production is demanded. Key challenge with PCB manufacturers is to maintain the quality of PCB with zero defects and assured quality. But due to the changing technologies in PCB fabrication, component placements and soldering of surface mount technology, defects are increasing in terms of the number and the type of defect. Various approaches have been proposed in this field of defect detection, based on the image processing techniques and data mining technique. To overcome these issues of PCB defects, we propose a new approach for the defect detection in the printed circuit boards for surface mount device inspection. According to the proposed approach defective points are extracted by detecting highlighted areas and then invalid areas are recognized and removed. To achieve this we utilize color features for the three channels, whereas invalid areas are recognized and removed by comparing the features of target and reference objects. Color feature extraction is carried out by applying proposed color distribution model. After extracting the features, classification technique is applied to classify the given the database into two classes: (a) defect detected and (b) no defect. In order to perform classification, Markov model is utilized which considers image features (i.e. color features). Proposed approach is implemented using MATLAB tool by combining image processing and data mining approach. Experimental study shows the efficiency of the proposed approach in terms of defect detection.
Efficient Generation of Recombinant Influenza A Viruses Employing a New Approach to Overcome the Genetic Instability of HA Segments

Influenza A viruses (IAVs) are the most relevant and continual source of severe infectious respiratory complications in humans and different animal species, especially poultry. Therefore, an efficient vaccination that elicits protective and neutralizing antibodies against the viral hemagglutinin (HA) and neuraminidase (NA) is an important strategy to counter annual epidemics or occasional pandemics. With the help of plasmid-based reverse genetics technology, it is possible that IAV vaccine strains (IVVS) are rapidly generated. However, the genetic instability of some cloned HA-cDNAs after transformation into competent bacteria represents a major obstacle. Herein, we report efficient cloning strategies of different genetically volatile HA segments (H5- and H9-subtypes) employing either a newly constructed vector for reverse genetics (pMKPccdB) or by the use of the Escherichia coli strain HB101. Both approaches represent improved and generalizable strategies to establish functional reverse genetics systems preventing genetic changes to the cloned (HA) segments of IAV facilitating more efficient rescue of recombinant IAV for basic research and vaccine development.
Design and modeling of an autonomous multi-link snake robot , capable of 3 D-motion

The paper presents the design of an autonomous, wheeless, mechanical snake robot that was modeled and built at Notre Dame University – Louaize. The robot is also capable of 3D motion with an ability to climb in the z-direction. The snake is made of a series links, each containing one to three high torque DC motors and a gearing system. They are connected to each other through Aluminum hollow rods that can be rotated through a 180° span. This allows the snake to move in various environments including unfriendly and cluttered ones. The front link has a proximity sensor used to map the environment. This mapping is sent to a microcontroller which controls and adapts the motion pattern of the snake. The snake can therefore choose to avoid obstacles, or climb over them if their height is within its range. The presented model is made of five links, but this number can be increased as their role is repetitive. The novel design is meant to overcome previous limitations by allowing 3D motion through electric actuators and low energy consumption.
Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence

The opportunistic fungal pathogen Cryptococcus neoformans is a leading cause of mortality among the human immunodeficiency virus/acquired immunodeficiency syndrome population and is known for frequently causing life-threatening relapses. To investigate the potential contribution of in-host microevolution to persistence and relapse, we have analyzed two serial isolates obtained from a patient with acquired immunodeficiency syndrome who suffered an initial and relapse episode of cryptococcal meningoencephalitis. Despite being identical by multilocus sequence typing, the isolates differ phenotypically, exhibiting changes in key virulence factors, nutrient acquisition, metabolic profiles, and the ability to disseminate in an animal model. Whole-genome sequencing uncovered a clonal relationship, with only a few unique differences. Of these, two key changes are expected to explain the phenotypic differences observed in the relapse isolate: loss of a predicted AT-rich interaction domain protein and changes in copy number of the left and right arms of chromosome 12. Gene deletion of the predicted transcriptional regulator produced changes in melanin, capsule, carbon source use, and dissemination in the host, consistent with the phenotype of the relapse isolate. In addition, the deletion mutant displayed altered virulence in the murine model. The observed differences suggest the relapse isolate evolved subsequent to penetration of the central nervous system and may have gained dominance following the administration of antifungal therapy. These data reveal the first molecular insights into how the Cryptococcus neoformans genome changes during infection of humans and the manner in which microevolution progresses in this deadly fungal pathogen.
TOOL WEAR MEASUREMENT AFTER MILLING OF ALUMINUM ALLOY USING COMBINED ROUGHNESS AND CONTOUR DEVICE

During separation of work surface in machining process and transforming it into chips, tool remains in constant contact with the workpiece. During this contact, there are a series of phenomena leading to the tool wear. Tool wear monitoring, and determination of tool life which is a signal to replace the tool with a new one, is important to ensure the continuity of production process in any company where elements are produced by machining. The article presents the results of tool wear measurement after milling of AlSi10Mg aluminum alloy using combined roughness and contour device.
Nuclear export of misfolded SOD1 mediated by a normally buried NES-like sequence reduces proteotoxicity in the nucleus

Over 170 different mutations in the gene encoding SOD1 all cause amyotrophic lateral sclerosis (ALS). Available studies have been primarily focused on the mechanisms underlying mutant SOD1 cytotoxicity. How cells defend against the cytotoxicity remains largely unknown. Here, we show that misfolding of ALS-linked SOD1 mutants and wild-type (wt) SOD1 exposes a normally buried nuclear export signal (NES)-like sequence. The nuclear export carrier protein CRM1 recognizes this NES-like sequence and exports misfolded SOD1 to the cytoplasm. Antibodies against the NES-like sequence recognize misfolded SOD1, but not native wt SOD1 both in vitro and in vivo. Disruption of the NES consensus sequence relocalizes mutant SOD1 to the nucleus, resulting in higher toxicity in cells, and severer impairments in locomotion, egg-laying, and survival in Caenorhabditis elegans. Our data suggest that SOD1 mutants are removed from the nucleus by CRM1 as a defense mechanism against proteotoxicity of misfolded SOD1 in the nucleus. DOI: http://dx.doi. org/10.7554/eLife.23759. 001
Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

The distribution of fitness effects (DFE) encompasses the fraction of deleterious, neutral, and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (α). Inferring DFE and α from patterns of polymorphism, as given through the site frequency spectrum (SFS) and divergence data, has been a longstanding goal of evolutionary genetics. A widespread assumption shared by previous inference methods is that beneficial mutations only contribute negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and α is then predicted by contrasting the SFS with divergence data from an outgroup. We develop a hierarchical probabilistic framework that extends previous methods to infer DFE and α from polymorphism data alone. We use extensive simulations to examine the performance of our method. While an outgroup is still needed to obtain an unfolded SFS, we show that both a DFE, comprising both deleterious and beneficial mutations, and α can be inferred without using divergence data. We also show that not accounting for the contribution of beneficial mutations to polymorphism data leads to substantially biased estimates of the DFE and α. We compare our framework with one of the most widely used inference methods available and apply it on a recently published chimpanzee exome data set.
Composition, Elastic Property and Packing Efficiency Predictions for Bulk Metallic Glasses in Binary, Ternary and Quaternary Systems

The results of database based on the efficiency packed model for metallic glasses. The database contains the atomic radii information as well as elastic properties of the most commonly used alloying elements, permitting composition, packing efficiency and elastic property predictions to be made for binary, ternary and quaternary bulk metallic glasses. Twenty different alloys per system (binary, ternary and quaternary) experimentally reported in the literature were compared with those estimated by the database. Comparison charts and diagrams showed good agreement between the composition predictions and those reported from the experimentally processed metallic glasses. The elastic properties predictions could be used to elaborate Blackman diagrams in order to know, in advance, the intrinsic toughness that the investigated alloys might present. The database is intended for designing bulk metallic glasses. Finally, some quaternary alloys were experimentally produced based on the prediction obtained with the database, showing a glassy phase. The microhardness values obtained experimentally of the Zr57.52Ag10. 62Al10.62Co21. 24, Zr57.19Al10. 7Ni10.7Cu21. 41 and Hf60.22Al9. 95Cu9.95Ni19. 89alloys, are 3.8, 4.0 and 3.6 GPa, respectively. The Young´s modulus calculated using microhardness values (E/Hv = 20) are closed to the values obtained by the "mixing rules".
Regulation of the CRISPR-Associated Genes by Rv2837c (CnpB) via an Orn-Like Activity in Tuberculosis Complex Mycobacteria

ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas) provide bacteria and archaea with adaptive immunity to specific DNA invaders. Mycobacterium tuberculosis encodes a type III CRISPR-Cas system that has not been experimentally explored. In this study, we found that the CRISPR-Cas systems of both M. tuberculosis and Mycobacterium bovis BCG were highly upregulated by deletion of Rv2837c (cnpB), which encodes a multifunctional protein that hydrolyzes cyclic di-AMP (c-di-AMP), cyclic di-GMP (c-di-GMP), and nanoRNAs (short oligonucleotides of 5 or fewer residues). By using genetic and biochemical approaches, we demonstrated that the CnpB-controlled transcriptional regulation of the CRISPR-Cas system is mediated by an Orn-like activity rather than by hydrolyzing the cyclic dinucleotides. Additionally, our results revealed that tuberculosis (TB) complex mycobacteria are functional in processing CRISPR RNAs (crRNAs), which are also more abundant in the ΔcnpB strain than in the parent strain. The elevated crRNA levels in the ΔcnpB strain could be partially reduced by expressing Escherichia coli orn. Our findings provide new insight into transcriptional regulation of bacterial CRISPR-Cas systems. IMPORTANCE Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas) provide adaptive immunity to specific DNA invaders. M. tuberculosis encodes a type III CRISPR-Cas system that has not been experimentally explored. In this study, we first demonstrated that the CRISPR-Cas systems in tuberculosis (TB) complex mycobacteria are functional in processing CRISPR RNAs (crRNAs). We also showed that Rv2837c (CnpB) controls the expression of the CRISPR-Cas systems in TB complex mycobacteria through an oligoribonuclease (Orn)-like activity, which is very likely mediated by nanoRNA. Since little is known about regulation of CRISPR-Cas systems, our findings provide new insight into transcriptional regulation of bacterial CRISPR-Cas systems.
Karyopherin α-3 is a key protein in the pathogenesis of spinocerebellar ataxia type 3 controlling the nuclear localization of ataxin-3

Significance Ataxin-3 is the affected protein in the neurodegenerative disorder spinocerebellar ataxia type 3 (SCA3). Nuclear ataxin-3 has been linked to disease progression and formation of aggregates. Our present findings implicate karyopherin alpha 3 (KPNA3) in the in vitro transport of ataxin-3 and in the SCA3-related phenotypes in Drosophila and mouse models. We have demonstrated that altering transport proteins has an effect on both pathogenic mechanisms (e.g., the intracellular localization and the formation of aggregates) and key features of ataxin-3 toxicity such as anxiety, total activity, and gait abnormalities. A better appreciation of this cellular mechanism can enhance our understanding of polyglutamine diseases and the role of nuclear/cytoplasmic compartments in toxicity and clearance of ataxin-3. Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disorder caused by a CAG expansion in the ATXN3 gene leading to a polyglutamine expansion in the ataxin-3 protein. The nuclear presence and aggregation of expanded ataxin-3 are critical steps in disease pathogenesis. To identify novel therapeutic targets, we investigated the nucleocytoplasmic transport system by screening a collection of importins and exportins that potentially modulate this nuclear localization. Using cell, Drosophila, and mouse models, we focused on three transport proteins, namely, CRM1, IPO13, KPNA3, and their respective Drosophila orthologs Emb, Cdm, and Kap-α3. While overexpression of CRM1/Emb demonstrated positive effects in Drosophila, KPNA3/Kap-α3 emerged as the most promising target, as knockdown via multiple RNAi lines demonstrated its ability to shuttle both truncated and full-length expanded ataxin-3, rescue neurodegeneration, restore photoreceptor formation, and reduce aggregation. Furthermore, KPNA3 knockout in SCA3 mice resulted in an amelioration of molecular and behavioral disturbances such as total activity, anxiety, and gait. Since KPNA3 is known to function as an import protein and recognize nuclear localization signals (NLSs), this work unites ataxin-3 structure to the nuclear pore machinery and provides a link between karyopherins, NLS signals, and polyglutamine disease, as well as demonstrates that KPNA3 is a key player in the pathogenesis of SCA3.
Combining manual haptic path planning of industrial robots with automatic path smoothing

Nowadays, industrial robots are preferably programmed offline, i.e. without interference with the real cell and running production processes. Usually a simulation tool is used to manually define individual locations and to check the created raw path for possible collisions. Within this paper an approach is presented, that combines a haptic input device by means of automated path smoothing. The quality of the generated path can be significantly improved by subsequent automatic filtering. Removing redundant locations or modifying intermediate ones increases the smoothness of the path. The semi-automatic programming paradigm with haptic interaction is expected to lead to an improved workflow for robot offline programming.