Miracle-dz/UniFAR-FTUs huggingface dataset:
OPTIMIZATION OF HYPERELASTIC MODEL PARAMETERS OF SOFT TISSUE BASED ON GENETIC ALGORITHM UTILIZING EXPERIMENTAL MECHANICAL DATASE

Original Research Paper Received 04 May 2015 Accepted 06 July 2015 Available Online 15 August 2015 Soft tissue’s cancers are related to major variations in the mechanical properties of the tissue. In recent years, number of developing techniques have been introduced for early detection of soft tissue’s cancers. The major advantage of these methods over the common available techniques is that, while being noninvasive to the body, the accuracy of detection is noticeably increased. This article intends to analyze mechanical behavior of the breast tissue by considering Mooney-Rivlin hyperelastic model. Coefficients of the model are defined by using series of experimental mechanical datasets. For this purpose, mechanical device is designed and fabricated based on new non-invasive method named Artificial Tactile Sensing (ATS). The device is examined on patients in the age range of 20 to 50 years referred to as “Jahad Daneshgahi Breast Diseases Clinic” while considering Helsinki agreement’s protocols. Due to wide anatomical variations of the breast tissue in individuals, 40 speci ied regions ar examined on the tissues of all attended cases. Experimental stress versus strain datasets are collected for 40 test points. To achieve reliable and optimized model, genetic algorithm (GA) is used for calculating Mooney-Rivlin’s coefficients. Results confirmed that an accurate model can be afforded to estimate the soft tissue’s mechanical behavior with the least error. The model is suitable for disease diagnosis and follow-up procedure.
Invasive Fungal Infections in Patients with Hematological Malignancies: Emergence of Resistant Pathogens and New Antifungal Therapies

Invasive fungal infections caused by drug-resistant organisms are an emerging threat to heavily immunosuppressed patients with hematological malignancies. Modern early antifungal treatment strategies, such as prophylaxis and empirical and preemptive therapy, result in long-term exposure to antifungal agents, which is a major driving force for the development of resistance. The extended use of central venous catheters, the nonlinear pharmacokinetics of certain antifungal agents, neutropenia, other forms of intense immunosuppression, and drug toxicities are other contributing factors. The widespread use of agricultural and industrial fungicides with similar chemical structures and mechanisms of action has resulted in the development of environmental reservoirs for some drug-resistant fungi, especially azole-resistant Aspergillus species, which have been reported from four continents. The majority of resistant strains have the mutation TR34/L98H, a finding suggesting that the source of resistance is the environment. The global emergence of new fungal pathogens with inherent resistance, such as Candida auris, is a new public health threat. The most common mechanism of antifungal drug resistance is the induction of efflux pumps, which decrease intracellular drug concentrations. Overexpression, depletion, and alteration of the drug target are other mechanisms of resistance. Mutations in the ERG11 gene alter the protein structure of C-demethylase, reducing the efficacy of antifungal triazoles. Candida species become echinocandin-resistant by mutations in FKS genes. A shift in the epidemiology of Candida towards resistant non-albicans Candida spp. has emerged among patients with hematological malignancies. There is no definite association between antifungal resistance, as defined by elevated minimum inhibitory concentrations, and clinical outcomes in this population. Detection of genes or mutations conferring resistance with the use of molecular methods may offer better predictive values in certain cases. Treatment options for resistant fungal infections are limited and new drugs with novel mechanisms of actions are needed. Prevention of resistance through antifungal stewardship programs is of paramount importance.
Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World

Background Discussion surrounding the settlement of the New World has recently gained momentum with advances in molecular biology, archaeology and bioanthropology. Recent evidence from these diverse fields is found to support different colonization scenarios. The currently available genetic evidence suggests a “single migration” model, in which both early and later Native American groups derive from one expansion event into the continent. In contrast, the pronounced anatomical differences between early and late Native American populations have led others to propose more complex scenarios, involving separate colonization events of the New World and a distinct origin for these groups. Methodology/Principal Findings Using large samples of Early American crania, we: 1) calculated the rate of morphological differentiation between Early and Late American samples under three different time divergence assumptions, and compared our findings to the predicted morphological differentiation under neutral conditions in each case; and 2) further tested three dispersal scenarios for the colonization of the New World by comparing the morphological distances among early and late Amerindians, East Asians, Australo-Melanesians and early modern humans from Asia to geographical distances associated with each dispersion model. Results indicate that the assumption of a last shared common ancestor outside the continent better explains the observed morphological differences between early and late American groups. This result is corroborated by our finding that a model comprising two Asian waves of migration coming through Bering into the Americas fits the cranial anatomical evidence best, especially when the effects of diversifying selection to climate are taken into account. Conclusions We conclude that the morphological diversity documented through time in the New World is best accounted for by a model postulating two waves of human expansion into the continent originating in East Asia and entering through Beringia.
Binding of Cyclic Di-AMP to the Staphylococcus aureus Sensor Kinase KdpD Occurs via the Universal Stress Protein Domain and Downregulates the Expression of the Kdp Potassium Transporter

ABSTRACT Nucleotide signaling molecules are important intracellular messengers that regulate a wide range of biological functions. The human pathogen Staphylococcus aureus produces the signaling nucleotide cyclic di-AMP (c-di-AMP). This molecule is common among Gram-positive bacteria and in many organisms is essential for survival under standard laboratory growth conditions. In this study, we investigated the interaction of c-di-AMP with the S. aureus KdpD protein. The sensor kinase KdpD forms a two-component signaling system with the response regulator KdpE and regulates the expression of the kdpDE genes and the kdpFABC operon coding for the Kdp potassium transporter components. Here we show that the S. aureus KdpD protein binds c-di-AMP specifically and with an affinity in the micromolar range through its universal stress protein (USP) domain. This domain is located within the N-terminal cytoplasmic region of KdpD, and amino acids of a conserved SXS-X20-FTAXY motif are important for this binding. We further show that KdpD2, a second KdpD protein found in some S. aureus strains, also binds c-di-AMP, and our bioinformatics analysis indicates that a subclass of KdpD proteins in c-di-AMP-producing bacteria has evolved to bind this signaling nucleotide. Finally, we show that c-di-AMP binding to KdpD inhibits the upregulation of the kdpFABC operon under salt stress, thus indicating that c-di-AMP is a negative regulator of potassium uptake in S. aureus. IMPORTANCE Staphylococcus aureus is an important human pathogen and a major cause of food poisoning in Western countries. A common method for food preservation is the use of salt to drive dehydration. This study sheds light on the regulation of potassium uptake in Staphylococcus aureus, an important aspect of this bacterium's ability to tolerate high levels of salt. We show that the signaling nucleotide c-di-AMP binds to a regulatory component of the Kdp potassium uptake system and that this binding has an inhibitory effect on the expression of the kdp genes encoding a potassium transporter. c-di-AMP binds to the USP domain of KdpD, thus providing for the first time evidence for the ability of such a domain to bind a cyclic dinucleotide.
Efficient MW-Assisted Synthesis, Spectroscopic Characterization, X-ray and Antioxidant Properties of Indazole Derivatives

A small series of tetrahydroindazoles was prepared, starting from 2-acetylcyclohexanone and different hydrazines using reflux and a focused microwave reactor. Microwave irradiation (MW) favored the formation of the desired products with improved yields and shortened reaction times. This is a simple and green method for the synthesis of substituted tetrahydroindazole derivatives. The in vitro antioxidant activity was evaluated using the DPPH and ABTS methods. In these assays, 2-(4-fluorophenyl)-3-methyl-4,5,6,7-tetrahydro-2H-indazole (3f) showed moderate DPPH decoloring activity, while 3-methyl-4,5,6,7-tetrahydro-1H-indazole (3a), 3-methyl-2-phenyl-4,5,6,7-tetrahydro-2H-indazole (3b) and 2-(4-fluorophenyl)-3-methyl-4,5,6,7-tetrahydro-2H-indazole (3f) were the most active in the ABTS assay. All compounds were well characterized by IR, 1H-, 13C-NMR and GC-MS spectroscopy and physical data, while the structure of 4-(3-methyl-4,5,6,7-tetrahydro-2H-indazol-2-yl)benzoic acid (3e) was also determined by single crystal X-ray analysis.
Cam impingement causes osteoarthritis of the hip: a nationwide prospective cohort study (CHECK)

Objective To determine the association between cam impingement, which is hip incongruity by a non-spherical femoral head and development of osteoarthritis. Methods A nationwide prospective cohort study of 1002 early symptomatic osteoarthritis patients (CHECK), of which standardised anteroposterior pelvic radiographs were obtained at baseline and at 2 and 5 years follow-up. Asphericity of the femoral head was measured by the α angle. Clinically, decreased internal hip rotation (≤20°) is suggestive of cam impingement. The strength of association between those parameters at baseline and development of incident osteoarthritis (K&L grade 2) or end-stage osteoarthritis (K&L grades 3, 4, or total hip replacement) within 5 years was expressed in OR using generalised estimating equations. Results At baseline, 76% of the included hips had no radiographic signs of osteoarthritis and 24% doubtful osteoarthritis. Within 5 years, 2.76% developed end-stage osteoarthritis. A moderate (α angle >60°) and severe (α angle >83°) cam-type deformity resulted in adjusted OR of 3.67 (95% CI 1.68 to 8.01) and 9.66 (95% CI 4.72 to 19.78), respectively, for end-stage osteoarthritis. The combination of severe cam-type deformity and decreased internal rotation at baseline resulted in an even more pronounced adjusted OR, and in a positive predictive value of 52.6% for end-stage osteoarthritis. For incident osteoarthritis, only a moderate cam-type deformity was predictive OR=2.42 (95% CI 1.15 to 5.06). Conclusions Individuals with both severe cam-type deformity and reduced internal rotation are strongly predisposed to fast progression to end-stage osteoarthritis. As cam impingement might be a modifiable risk factor, early recognition of this condition is important.
Zoonotic bacteria and parasites found in raw meat-based diets for cats and dogs

Feeding raw meat-based diets (RMBDs) to companion animals has become increasingly popular. Since these diets may be contaminated with bacteria and parasites, they may pose a risk to both animal and human health. The purpose of this study was to test for the presence of zoonotic bacterial and parasitic pathogens in Dutch commercial RMBDs. We analysed 35 commercial frozen RMBDs from eight different brands. Escherichia coli serotype O157:H7 was isolated from eight products (23 per cent) and extended-spectrum beta-lactamases-producing E coli was found in 28 products (80 per cent). Listeria monocytogenes was present in 19 products (54 per cent), other Listeria species in 15 products (43 per cent) and Salmonella species in seven products (20 per cent). Concerning parasites, four products (11 per cent) contained Sarcocystis cruzi and another four (11 per cent) S tenella. In two products (6 per cent) Toxoplasma gondii was found. The results of this study demonstrate the presence of potential zoonotic pathogens in frozen RMBDs that may be a possible source of bacterial infections in pet animals and if transmitted pose a risk for human beings. If non-frozen meat is fed, parasitic infections are also possible. Pet owners should therefore be informed about the risks associated with feeding their animals RMBDs.
The Rheological Properties of Redcurrant and Highbush Blueberry Berries

Abstract The load values corresponding to the compressive strength of high-bush blueberry and redcurrant fruits during the compression test between two rigid plates were measured. The changes of coefficient of elasticity and coefficient of viscosity values during the creep and the relaxation tests were studied in the selected interval of time, also direction of load application in relation to the longitudinal axis of fruit was considered. The creep and relaxation tests were carried out with the load of 40% of determined compressive strength of berries. To describe behavior of testing the material rheological standard, Maxwell and Kelvin models as well as experimental models were used. Comparatively small changes of parameter values of assumed empirical models were reported in the course of tests. It may be recognized as characteristic for the investigated material.
Carving Metacognition at Its Joints: Protracted Development of Component Processes.

Two experiments investigated the development of metacognitive monitoring and control, and conditions under which children engage these processes. In Experiment 1, 5-year-olds (N = 30) and 7-year-olds (N = 30), unlike adults (N = 30), showed little evidence of either monitoring or control. In Experiment 2, 5-year-olds (N = 90) were given performance feedback (aimed at improving monitoring), instruction to follow a particular strategy (aimed at improving control), or both. Across conditions, feedback improved children's monitoring, and instruction improved both monitoring and control. Thus, children's poor metacognitive performance likely reflects a difficulty engaging the component processes spontaneously rather than a lack of metacognitive ability. These findings also suggest that the component processes are distinct, with both undergoing protracted development.
In vivo and protease-activated receptor-1-mediated platelet activation but not response to antiplatelet therapy predict two-year outcomes after peripheral angioplasty with stent implantation

Summary Data linking the response to antiplatelet therapy with clinical outcomes after angioplasty and stenting for lower extremity artery disease (LEAD) are scarce. Moreover, associations of in vivo and thrombin-inducible platelet activation with the occurrence of adverse events have not been investigated in these patients, so far. We therefore assessed clinical outcomes and on-treatment platelet reactivity by four test systems in 108 patients receiving dual antiplatelet therapy after infrainguinal angioplasty and stenting for LEAD. Further, in vivo and thrombin receptor-activating peptide (TRAP)-6-inducible glycoprotein (GP) IIb/IIIa activation and P-selectin expression were measured as sensitive parameters of platelet activation. The primary endpoint was defined as the composite of atherothrombotic events and target vessel restenosis or reocclusion. Residual platelet reactivity to adenosine diphosphate and arachidonic acid was similar between patients without and with adverse outcomes within two-year follow-up (all p>0.05). Further, the occurrence of clinical endpoints did not differ significantly between patients without and with high on-treatment residual platelet reactivity by all test systems (all p>0.05). In contrast, in vivo and TRAP-6-inducible platelet activation were significantly more pronounced in patients with subsequent adverse events (all p<0.05), and high levels of platelet activation were independent predictors of the primary endpoint (adjusted hazard ratios: 3.5 for high in vivo activated GPIIb/IIIa, 2.9 for high TRAP-6-inducible activated GPIIb/IIIa, 2.3 for high in vivo P-selectin, and 3 for high TRAP-6-inducible P-selectin; all p<0.05). In conclusion, in vivo and protease-activated receptor-1-mediated platelet activation predict two-year clinical outcomes in stable patients undergoing angioplasty and stenting for LEAD.
List-coloring embedded graphs

For any fixed surface Sigma of genus g, we give an algorithm to decide whether a graph G of girth at least five embedded in Sigma is colorable from an assignment of lists of size three in time O(|V(G)|). Furthermore, we can allow a subgraph (of any size) with at most s components to be precolored, at the expense of increasing the time complexity of the algorithm to O(|V(G)|^{K(g+s)+1}) for some absolute constant K; in both cases, the multiplicative constant hidden in the O-notation depends on g and s. This also enables us to find such a coloring when it exists. The idea of the algorithm can be applied to other similar problems, e.g., 5-list-coloring of graphs on surfaces.
Low‐Fire Processing and Properties of Ferrite+Dielectric Ceramic Composite

A low-fire Ni-Cu-Zn ferrite+dielectric ceramic composite and its multilayer integrated laminate, which can be densified at temperatures below 900°C, is prepared. To densify Ni-Cu-Zn ferrite at low temperatures, the dielectric needs to contain an effective sintering flux of Bi 2 O 3 or PbO to the Ni-Cu-Zn ferrite. This enables densification of the resulting ceramic composite or multilayer integrated dielectric/ferrite laminate at temperatures close to those of pure ferrite and dielectric. The dielectric constant decreases but the initial permittivity increases with increasing amount of ferrite existing in the ferrite+dielectric ceramic composite.
COPA: Constrained PARAFAC2 for Sparse & Large Datasets

PARAFAC2 has demonstrated success in modeling irregular tensors, where the tensor dimensions vary across one of the modes. An example scenario is modeling treatments across a set of patients with the varying number of medical encounters over time. Despite recent improvements on unconstrained PARAFAC2, its model factors are usually dense and sensitive to noise which limits their interpretability. As a result, the following open challenges remain: a) various modeling constraints, such as temporal smoothness, sparsity and non-negativity, are needed to be imposed for interpretable temporal modeling and b) a scalable approach is required to support those constraints efficiently for large datasets. To tackle these challenges, we propose a COnstrained PARAFAC2 (COPA) method, which carefully incorporates optimization constraints such as temporal smoothness, sparsity, and non-negativity in the resulting factors. To efficiently support all those constraints, COPA adopts a hybrid optimization framework using alternating optimization and alternating direction method of multiplier (AO-ADMM). As evaluated on large electronic health record (EHR) datasets with hundreds of thousands of patients, COPA achieves significant speedups (up to 36 times faster) over prior PARAFAC2 approaches that only attempt to handle a subset of the constraints that COPA enables. Overall, our method outperforms all the baselines attempting to handle a subset of the constraints in terms of speed, while achieving the same level of accuracy. Through a case study on temporal phenotyping of medically complex children, we demonstrate how the constraints imposed by COPA reveal concise phenotypes and meaningful temporal profiles of patients. The clinical interpretation of both the phenotypes and the temporal profiles was confirmed by a medical expert.
Apitherapeutics and phage-loaded nanofibers as wound dressings with enhanced wound healing and antibacterial activity.

AIM Develop green wound dressings which exhibit enhanced wound-healing ability and potent antibacterial effects. METHODS Honey, polyvinyl alcohol, chitosan nanofibers were electrospun and loaded with bee venom, propolis and/or bacteriophage against the multidrug-resistant Pseudomonas aeruginosa and examined for their antibacterial, wound-healing ability and cytotoxicity. RESULTS Among different formulations of nanofibers, honey, polyvinyl alcohol, chitosan-bee venom/bacteriophage exhibited the most potent antibacterial activity against all tested bacterial strains (Gram-positive and -negative strains) and achieved nearly complete killing of multidrug-resistant P. aeruginosa. In vivo testing revealed enhanced wound-healing results and cytotoxicity testing proved improved biocompatibility. CONCLUSION The developed biocompatible nanofibers represent competitive wound-healing dressings with potent antibacterial and wound-healing activity.
Genetic Population Structure in the Antarctic Benthos: Insights from the Widespread Amphipod, Orchomenella franklini

Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1–10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F ST = 0.086, R ST = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with Nem≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos.