Miracle-dz/UniFAR-FTUs huggingface dataset:
Making Nonwoven Fibrous Poly(ε-caprolactone) Constructs for Antimicrobial and Tissue Engineering Applications by Pressurized Melt Gyration

A pressurized melt gyration process has been used for the first time to generate poly(e-caprolactone) (PCL) fibers. Gyration speed, working pressure, and melt temperature are varied and these parameters influence the fiber diameter and the temperature enabled changing the surface morphology of the fibers. Two types of nonwoven PCL fiber constructs are prepared. First, Ag-doped PCL is studied for antibacterial activity using Gram-negative Escherichia coli and Pseudomonas aeruginosa microorganisms. The melt temperature used to make these constructs significantly influences antibacterial activity. Neat PCL nonwoven scaffolds are also prepared and their potential for application in muscular tissue engineering is studied with myoblast cells. Results show significant cell attachment, growth, and proliferation of cells on the scaffolds.
Measuring epigenetics as the mediator of gene/environment interactions in DOHaD

Analysis of DNA methylation data in epigenome-wide association studies provides many bioinformatics and statistical challenges. Not least of these, are the non-independence of individual DNA methylation marks from each other, from genotype and from technical sources of variation. In this review we discuss DNA methylation data from the Infinium450K array and processing methodologies to reduce technical variation. We describe recent approaches to harness the concordance of neighbouring DNA methylation values to improve power in association studies. We also describe how the non-independence of genotype and DNA methylation has been used to infer causality (in the case of Mendelian randomization approaches); suggest the mediating effect of DNA methylation in linking intergenic single nucleotide polymorphisms, identified in genome-wide association studies, to phenotype; and to uncover the widespread influence of gene and environment interactions on methylation levels.
Theory and techniques of electrostatic charging of melt-blown nonwoven webs

Nonwoven webs are widely used as filters, and their use is rapidly increasing every year. Charging the fibers in the nonwoven webs can greatly improve their filtration efficiency by increasing the capture of small particles traveling at low velocity. This paper describes the mechanisms of corona charging of nonwoven webs. Different charging techniques for producing melt-blown electrets are also discussed. Application : describes useful electrode configurations for imparting electret properties to melt-blown webs.
Preparation, optimization, and in vitro simulated inhalation delivery of carvedilol nanoparticles loaded on a coarse carrier intended for pulmonary administration

Carvedilol (CAR) is a potent antihypertensive drug but has poor oral bioavailability (24%). A nanosuspension suitable for pulmonary delivery to enhance bioavailability and bypass first-pass metabolism of CAR could be advantageous. Accordingly, the aim of this work was to prepare CAR nanosuspensions and to use artificial neural networks associated with genetic algorithm to model and optimize the formulations. The optimized nanosuspension was lyophilized to obtain dry powder suitable for inhalation. However, respirable particles must have a diameter of 1–5 µm in order to deposit in the lungs. Hence, mannitol was used during lyophilization for cryoprotection and to act as a coarse carrier for nanoparticles in order to deliver them into their desired destination. The bottom-up technique was adopted for nanosuspension formulation using Pluronic stabilizers (F127, F68, and P123) combined with sodium deoxycholate at 1:1 weight ratio, at three levels with two drug loads and two aqueous to organic phase volume ratios. The drug crystallinity was studied using differential scanning calorimetry and powder X-ray diffractometry. The in vitro emitted doses of CAR were evaluated using a dry powder inhaler sampling apparatus and the aerodynamic characteristics were evaluated using an Andersen MKII cascade impactor. The artificial neural networks results showed that Pluronic F127 was the optimum stabilizer based on the desired particle size, polydispersity index, and zeta potential. Results of differential scanning calorimetry combined with powder X-ray diffractometry showed that CAR crystallinity was observed in the lyophilized nanosuspension. The aerodynamic characteristics of the optimized lyophilized nanosuspension demonstrated significantly higher percentage of total emitted dose (89.70%) and smaller mass median aerodynamic diameter (2.80 µm) compared with coarse drug powder (73.60% and 4.20 µm, respectively). In summary, the above strategy confirmed the applicability of formulating CAR in the form of nanoparticles loaded on a coarse carrier suitable for inhalation delivery.
Glyoxylate reductase activity in blood mononuclear cells and the diagnosis of primary hyperoxaluria type 2.

BACKGROUND Primary hyperoxaluria type 2 (PH2) is a rare monogenic disorder characterized by an elevated urinary excretion of oxalate. Increased oxalate excretion in PH2 patients can cause nephrolithiasis and nephrocalcinosis, and can, in some cases, result in renal failure and systemic oxalate deposition. The disease is due to a deficiency of glyoxylate reductase/hydroxypyruvate reductase (GRHPR) activity. A definitive diagnosis of PH2 is currently made by the analysis of GR activity in a liver biopsy. GRHPR is expressed in virtually every tissue in the body, suggesting that utilization of more readily available cells could be used to determine GRHPR deficiency. In this study, we have evaluated the potential of determining GR and d-glycerate dehydrogenase (DGDH) activity in blood mononuclear cells (BMC) as a diagnostic indicator of PH2. METHODS Blood samples were obtained from 10 male and 10 female normal subjects, median age 31, range 21-63, at the Wake Forest University Medical Center and from primary hyperoxaluria patients at the Mayo Clinic. The BMC were isolated and GR and DGDH activities measured in cell lysates. RESULTS An assay of 20 normal individuals indicated that BMC contained a DGDH and GR activity of 0.97+/-0.20 (range 0.62-1.45), and 10.6+/-3.3 (range 8.3-16.6) nmol/min/mg protein, respectively. The intra-assay coefficient of variation for DGDH and GR activity was 8.2 and 11.5%, respectively. The BMC lysates from normal adult subjects and patients with PH1 showed similar GR and DGDH activities. This was confirmed by the presence of immunoreactive GRHPR protein by western blot analysis. In contrast, PH2 BMC lysates did not exhibit DGDH or GR activity, and showed no immunoreactive GRHPR by western blot analysis. CONCLUSION These results suggest that the assay of DGDH or GR activity in BMC could be used as a minimally invasive diagnostic test for PH2.
Effect of Section Thickness On The Microstructure And Hardness Of Gray Cast Iron (A Simulation Study)

Cast iron being a material very sensitive to section has been a choice of automotive industries because of its versatile properties. This study was aimed to examine the effect of section thickness on microstructure of grey cast iron. Grey cast iron micro-structure consists of flakes of graphite with a matrix of pearlite or ferrite. It was found in this study that size of the graphite flake changes with the change in cooling rate. Flake size affects the properties like hardness, UTS and damping capacity of grey iron. It was observed that small section thickness contains small graphite flakes, whereas thick sections consist of larger graphite flakes. Hardness of thin section was also found greater than thick section. The hardness results obtained from Pro-cast simulation were validated and it was found that simulation results are in quite agreement with experimental results. This paper also provides the heat transfer model of Pro-cast and its sequential steps to follow for simulation of grey iron solidification.
Complex Chemistry in Star-forming Regions: An Expanded Gas-Grain Warm-up Chemical Model

Gas-phase processes were long thought to be the key formation mechanisms for complex organic molecules in star-forming regions. However, recent experimental and theoretical evidence has cast doubt on the efficiency of such processes. Grain-surface chemistry is frequently invoked as a solution, but until now there have been no quantitative models taking into account both the high degree of chemical complexity and the evolving physical conditions of star-forming regions. Here, we introduce a new gas-grain chemical network, wherein a wide array of complex species may be formed by reactions involving radicals. The radicals we consider (H, OH, CO, HCO, CH3, CH3O, CH2OH, NH, and NH2) are produced primarily by cosmic ray-induced photodissociation of the granular ices formed during the colder, earlier stages of evolution. The gradual warm up of the hot core is crucial to the formation of complex molecules, allowing the more strongly bound radicals to become mobile on grain surfaces. This type of chemistry is capable of reproducing the high degree of complexity seen in Sgr B2(N), and can explain the observed abundances and temperatures of a variety of previously detected complex organic molecules, including structural isomers. Many other complex species are predicted by this model, and several of these species may be detectable in hot cores. Differences in the chemistry of high- and low-mass star formation are also addressed; greater chemical complexity is expected where evolution timescales are longer.
Diagnosis of Barmah Forest Virus Infection by a Nested Real-Time SYBR Green RT-PCR Assay

Barmah Forest virus (BFV) is a mosquito borne (+) ssRNA alphavirus found only in Australia. It causes rash, myalgia and arthralgia in humans and is usually diagnosed serologically. We developed a real-time PCR assay to detect BFV in an effort to improve diagnosis early in the course of infection. The limit of detection was 16 genome equivalents with a specificity of 100%. Fifty five serum samples from BFV-infected patients were tested by the PCR. 52 of 53 antibody-positive samples were PCR negative. Two culture-positive (neutralizing antibody negative) samples were positive on first round PCR, while one sample (IgM and neutralizing antibody strongly positive, IgG negative) was positive on second round PCR, suggesting that viral RNA is detectable and transiently present in early infection. PCR can provide results faster than culture, is capable of high throughput and by sequencing the PCR product strain variants can be characterized.
Urinary semaphorin 3A as an early biomarker to predict contrast-induced acute kidney injury in patients undergoing percutaneous coronary intervention

Contrast-induced acute kidney injury (CI-AKI) is a serious complication of diagnostic coronary angiograph and percutaneous coronary intervention (PCI). However, the exact pathophysiological mechanisms underlying CI-AKI development are largely unknown. The present study examined whether urinary semaphorin 3A levels predict the development of CI-AKI in patients undergoing PCI. This study enrolled 168 patients with stable angina undergoing elective PCI. Serial urine samples, obtained at baseline and 2, 6, 12, 24, 36, and 48 h post-PCI were analyzed by semaphorin 3A and neutrophil gelatinase-associated lipocalin (NGAL) ELISA kit. AKI was defined as an increase in serum creatinine beyond 50% according to the RIFLE classification system. Receiver operator characteristic (ROC) curve analyses identified optimal semaphorin 3A and NGAL values for diagnosing CI-AKI. CI-AKI occurred in 20 of 168 patients. There were no significant differences in the baseline clinical characteristics and angiographic findings between non-AKI patients group and AKI patients group. Both urinary semaphorin 3A and NGAL levels significantly increased at 2 and 6 h post-PCI. ROC analysis showed that the cut-off value of 389.5 pg/mg semaphorin 3A at 2 h post-PCI corresponds to 94% sensitivity and 75% specificity and the cut-off value of 94.4 ng/mg NGAL at 2 h post-PCI corresponds to 74% sensitivity and 82% specificity. Logistic regression showed that semaphorin 3A levels at 2 and 6 h post-PCI were the significant predictors of AKI in our cohort. Urinary semaphorin 3A may be a promising early biomarker for predicting CI-AKI in patients undergoing PCI.
Kernel-based anatomical image-guided optical tomographic reconstruction

Author(s): Baikejiang, Reheman | Advisor(s): Li, Changqing | Abstract: Optical tomography, specically, diffuse optical tomography (DOT) and fluorescent molecular tomography (FMT) are promising functional imaging modalities with a high sensitivity and specicity. However, the inverse problem of DOT and FMT are ill-posed and ill-conditioned due to strong optical scattering in deep tissues, which results in poor spatial resolution for deep target imaging. It is well known that DOT and FMT image quality can be improved substantially by applying the structural guidance in the reconstruction algorithm.In this dissertation, First, I conducted a feasibility study of computed tomography (CT) guided DOT system for breast cancer imaging. I built a noncontact projection style prototype DOT which consists of a laser at the wavelength of 650 nm and an electron multiplying charge coupled device (EMCCD) camera. We have validated the CT-guided DOT reconstruction algorithms with numerical simulations and phantom experiments, in which different imaging setup parameters, such as projection number of measurements and width of measurement patch, have been investigated.Secondly, inspired by the kernel methods in machine learning, I introduced a kernel-based image reconstruction algorithm into anatomical image-guided DOT. Compared with conventional Laplacian approaches that include structural priors by regularization matrix, the developed method applied in this research incorporates a kernel matrix with the projection model into the objective function and does not require image segmentation. The optical absorption coefficient at each nite element node is represented as a function of a set of features obtained fromanatomical images such as computed tomography (CT) images. The proposed kernel method is validated with numerical simulations and agar phantom experiments. The proposed method utilized a CT volume data set without segmentation from a clinical breast CT system in the DOT.Lastly, I implemented kernel-based anatomical guidance into the FMT image reconstruction. In FMT, the fluorophore concentration at each node is dened as a function of a set of feature vectors, which is directly extracted from the voxel intensities of the corresponding anatomical 3D images. This research studied the effects of voxel size and a number of nearest neighbors in the kernel method on the quality of reconstructed FMT images. The results indicate that the spatial resolution and the accuracy of the reconstructed FMT images have been improved substantially after applying the anatomical guidance with the proposed kernel method. The proposed method utilized magnetic resonance imaging (MRI) rat brain image in FMT simulation, which further proved that we do not need to segment the anatomical image for the kernel method. The proposed kernel method was found to be robust to the false positive guidance in the anatomical image.As future work, the DOT prototype system will be integrated with a dedicated CT system, and clinical trials will be conducted using kernel-based image reconstruction algorithm.
Classification of inter-subject fMRI data based on graph kernels

The analysis of human brain connectivity networks has become an increasingly prevalent task in neuroimaging. A few recent studies have shown the possibility of decoding brain states based on brain graph classification. Graph kernels have emerged as a powerful tool for graph comparison that allows the direct use of machine learning classifiers on brain graph collections. They allow classifying graphs with different number of nodes and therefore the inter-subject analysis without any kind of previous alignment of individual subject's data. Using whole-brain fMRI data, in this paper we present a method based on graph kernels that provides above-chance accuracy results for the inter-subject discrimination of two different types of auditory stimuli. We focus our research on determining whether this method is sensitive to the relational information in the data. Indeed, we show that the discriminative information is not only coming from topological features of the graphs like node degree distribution, but also from more complex relational patterns in the neighborhood of each node. Moreover, we investigate the suitability of two different graph representation methods, both based on data-driven parcellation techniques. Finally, we study the influence of noisy connections in our graphs and provide a way to alleviate this problem.
N400 Effects of Semantic Richness Can Be Modulated by Task Demands

Semantic richness is a multidimensional construct that can be defined as the amount of semantic information associated with a concept. Objective: To investigate neurophysiological correlates of semantic richness information associated with words and its interaction with task demands. Method: Two different dimensions of semantic richness (number of associates and number of semantic neighbors) were investigated using event-related potentials (ERPs) in lexical decision (LDT) and semantic categorization tasks (SCT) using the same stimuli in 2 groups of participants (24 in each group). Results: The amplitude of the N400 ERP component, which is associated with semantic processing, was smaller for words with a high number of associates (p = .003 at fronto-centro-parietal sites) or semantic neighbors (p < .03 at centro-parietal sites) than for words with a low number of associates or number of semantic neighbors, in the LDT but not the SCT. Conclusions: These results suggest that the effects of semantic richness vary with task demands and may be used in a top-down manner to accommodate the current context.
Investigation of Drought and Salinity Tolerance Related Genes and their Regulatory Mechanisms in Arabidopsis (Arabidopsis thaliana)

Results: Under drought stress, 2558 gene accessions in root and 3691 in shoot tissues had significantly differential expression with respect to control condition. Likewise, under salinity stress 9078 gene accessions in root and 5785 in shoot tissues were discriminated between stressed and non-stressed conditions. Furthermore, the transcription regulatory activity of differentially expressed genes was mainly due to hormone, light, circadian and stress responsive cis-acting regulatory elements among which ABRE, ERE, P-box, TATC-box, CGTCA-motif, GARE-motif, TGACG-motif, GAG-motif, GA-motif, GATAmotif, TCT-motif, GT1-motif, Box 4, G-Box, I-box, LAMP-element, Sp1, MBS, TC-rich repeats, TCA-element and HSE were the most important elements in the identified up-regulated genes.
Evaluation of Antioxidant, Antimicrobial, and Antiurolithiatic Potential of Different Solvent Extracts of Aerva lanata Linn Flowers

Introduction: Aerva lanata (Linn) of family Amaranthaceae is an important and commonly used plant for its medicinal and pharmacological properties and proving the traditional uses of flowers of A. lanata Linn. Objective: All extracts of A. lanata were further evaluated for antioxidant, antimicrobial, and antiurolithiatic potential to scientifically prove the traditional uses. Materials and Methods: In the present investigation, different solvent extracts of flowers were obtained using a Soxhlet extractor. Microorganisms were obtained from IMTECH, Chandigarh. Antiurolithiatic study was carried out in Albino Research and Training Centre, Hyderabad. Results: Regardless of the antioxidant studied, the methanolic extract presented the highest antioxidant activity and the aqueous extracts offered the lowest, following the order: methanolic extract > ethyl acetate > chloroform > aqueous. The results of this antimicrobial study indicate that methanolic extract of A. lanata could be used as antimicrobial agents. Overall, the methanolic flower extract of A. lanata (Linn) was significantly more promising as antiurolithiatic spectrum. This result also suggested the potential usefulness of the methanolic extract as an antiurolithiatic agent. Conclusion: Henceforward, this research can be acknowledged as a prime new report that focuses on the application of A. lanata (Linn) as an antioxidant, antimicrobial, and antiurolithiatic agent. Abbreviations used: IMTECH Chandigarh: Institute of Microbial Technology, Chandigarh; IMMT: Institute of Mineral and Material Technology; CSIR: Council of Scientific & Industrial Research; DPPH: 1,1-diphenyl-2-picrylhydrazyl; MTCC: Microbial Type Culture Collection; BHT: Butylated Hydroxyl Toluene.
Aging as Accelerated Accumulation of Somatic Variants: Whole-Genome Sequencing of Centenarian and Middle-Aged Monozygotic Twin Pairs

It has been postulated that aging is the consequence of an accelerated accumulation of somatic DNA mutations and that subsequent errors in the primary structure of proteins ultimately reach levels sufficient to affect organismal functions. The technical limitations of detecting somatic changes and the lack of insight about the minimum level of erroneous proteins to cause an error catastrophe hampered any firm conclusions on these theories. In this study, we sequenced the whole genome of DNA in whole blood of two pairs of monozygotic (MZ) twins, 40 and 100 years old, by two independent next-generation sequencing (NGS) platforms (Illumina and Complete Genomics). Potentially discordant single-base substitutions supported by both platforms were validated extensively by Sanger, Roche 454, and Ion Torrent sequencing. We demonstrate that the genomes of the two twin pairs are germ-line identical between co-twins, and that the genomes of the 100-year-old MZ twins are discerned by eight confirmed somatic single-base substitutions, five of which are within introns. Putative somatic variation between the 40-year-old twins was not confirmed in the validation phase. We conclude from this systematic effort that by using two independent NGS platforms, somatic single nucleotide substitutions can be detected, and that a century of life did not result in a large number of detectable somatic mutations in blood. The low number of somatic variants observed by using two NGS platforms might provide a framework for detecting disease-related somatic variants in phenotypically discordant MZ twins.
Confronting Uncertainty in Wildlife Management: Performance of Grizzly Bear Management

Scientific management of wildlife requires confronting the complexities of natural and social systems. Uncertainty poses a central problem. Whereas the importance of considering uncertainty has been widely discussed, studies of the effects of unaddressed uncertainty on real management systems have been rare. We examined the effects of outcome uncertainty and components of biological uncertainty on hunt management performance, illustrated with grizzly bears (Ursus arctos horribilis) in British Columbia, Canada. We found that both forms of uncertainty can have serious impacts on management performance. Outcome uncertainty alone – discrepancy between expected and realized mortality levels – led to excess mortality in 19% of cases (population-years) examined. Accounting for uncertainty around estimated biological parameters (i.e., biological uncertainty) revealed that excess mortality might have occurred in up to 70% of cases. We offer a general method for identifying targets for exploited species that incorporates uncertainty and maintains the probability of exceeding mortality limits below specified thresholds. Setting targets in our focal system using this method at thresholds of 25% and 5% probability of overmortality would require average target mortality reductions of 47% and 81%, respectively. Application of our transparent and generalizable framework to this or other systems could improve management performance in the presence of uncertainty.