Miracle-dz/UniFAR-FTUs huggingface dataset:
X-ray absorption spectroscopy of bacterial sulfur globules.

Sulfur K-edge X-ray absorption spectroscopy is a powerful in situ probe of sulfur biochemistry in intact cells and tissues. Under favorable circumstances the technique can provide quantitative information on the chemical identify of the sulfur species that are present in a sample. Prange et al. have recently reported an X-ray absorption spectroscopic study of bacterial sulfur storage globules. Unfortunately there are substantial problems with the experimental technique employed that, they contend, lead to completely erroneous conclusions. In the more recent of their two papers Prange et al. employed a curve-fitting method similar to that used by us (for more than 10 years). In essence, the method employs simply fitting a linear combination of the spectra of standard compounds to that of the unknown, in this case cultures of bacterial cells. This type of analysis can provide quantitative estimates of the individual sulfur types in the sample, but is critically dependent upon the choice of reference spectra. Prange et al. deduce substantial differences between the chemical forms of sulfur stored in the globules of different organisms; they conclude that the globules of Beggiatoa alba and Thiomargarita namibiensis contain cyclo-octasulfur (S{sub 8}), while those of other organisms contain polythionates (Acidithiobacillus ferrooxidans) andmore » polymeric sulfur (e.g. Allochromatium vinosum). This is in contradiction with an earlier study, in which they found that sulfur in all globule species examined resembled that expected for various sized spherical particles of S{sub 8}. The discrepancy is due to an experimental artefact in the work of Prange et al. arising from their choice of transmittance detection, which is also discussed. « less
Standoff Raman spectroscopy detection of trace explosives

During the 2003-present Iraq war, Improvised Explosive Devices (IEDs) are being used extensively by the terrorists against the coalition forces and these IEDs were responsible for 40% of coalition force casualties, by the end of 2007. As these IEDs are not based on standard production formulae, their tracking and detection becomes extremely complicated. Laser Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy are among the many techniques that have shown promise in detection of explosive compounds. However, the performance of these systems is dependent on the concentration of explosives and ambient noise. The research presented in this thesis applies signal processing techniques to Raman spectra of a sample to detect the presence of explosives in trace quantities, at a standoff distance. Partial least squares-Discriminant analysis (PLS-DA) was used to identify peaks in the Raman spectra of the sample, which could better differentiate explosive and non-explosive samples. Since peak strengths are vulnerable to noise, our algorithm uses peak energies instead, by fitting Lorentzian or Gaussian curves about the peak locations. An automatic peak detection and fitting algorithm was developed for this purpose. Also, a wavelet based signal denoising algorithm was implemented to remove noise from the Raman Spectra. Further, a multi-sensor fusion algorithm was developed to combine the results from Laser Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy to generate more accurate detection results. The multi-sensor fusion algorithm gave more accurate detection results, a higher probability of detection and lower probability of false alarms, as compared to the results obtained from individual spectroscopic techniques, i.e. Raman Spectroscopy and Laser Induced Breakdown Spectroscopy alone.
A clinical review of recent findings in the epidemiology of inflammatory bowel disease

Inflammatory bowel diseases (IBD), including both Crohn’s disease and ulcerative colitis, are disorders of chronic inflammation of the gastrointestinal tract marked by episodes of relapse and remission. Over the past several decades, advances have been made in understanding the epidemiology of IBD. The incidence and prevalence of both Crohn’s disease and ulcerative colitis have been increasing worldwide across pediatric and adult populations. As IBD is thought to be related to a combination of individual genetic susceptibility, environmental triggers, and alterations in the gut microbiome that stimulate an inflammatory response, understanding the potentially modifiable environmental risk factors associated with the development or the course of IBD could impact disease rates or management in the future. Current hypotheses as to the development of IBD are reviewed, as are a host of environmental cofactors that have been investigated as both protective and inciting factors for IBD onset. Such environmental factors include breast feeding, gastrointestinal infections, urban versus rural lifestyle, medication exposures, stress, smoking, and diet. The role of these factors in disease course is also reviewed. Looking forward, there is still much to be learned about the etiology of IBD and how specific environmental exposures intimately impact the development of disease and also the potential for relapse.
Comparative evaluation of automated chemiluminescence tests and RIBA assay used in HCV diagnosis

Introduction: Hepatitis C, caused by hepatitis C virus (HCV) can be a mild illness lasting a few weeks or can cause lifelong liver cirrhosis and cancer. Today although the sensitivity of diagnostic tests is increasing; it has often been associated with decreased specificity so the rate of false-positive test results is increasing. The aim of this study was to compare the false-positive rates of anti-HCV results. Methods: During the period of 18.07. 2011 to 18.12. 2013; blood samples of patients admitted to Konya Numune Hospital were screened for anti-HCV using chemiluminescence immunoassay (CIA). After 2012; the new version of same anti-HCV test was used. Borderline and reactive results were retested and tests which were reactive in repeated CIA were confirmed by a recombinant immunoblot-assay (RIBA). Subjects with a positive RIBA test were considered to have been as true positive anti-HCV. Results: A total of 54178 sera were tested for anti-HCV during the period of 18.07. 2011 to 18.12. 2013 and 649 sera were positive with chemiluminescence method. 374 of reactive cases were confirmed by RIBA. The RIBA results showed 171 (45.7 %) negative, 163 (43.5 %) positive, and 40 (10.7 %) indeterminate results. By using the new version of the test; the rate of false positive and indeterminate anti-HCV test results decreased from 75.1% to 35.5 %. Conclusions: In this study it was observed that lower false positive rates of newly developed test. Lowering the false positive rate of ELISA tests will provide more confidence to use these tests in the diagnosis of HCV. There is a need for further studies on this issue.
Enhancing Student Teachers’ Teaching Skills Through a Blended Learning Approach

This study investigated the effect of a blended learning program on student teachers’ teaching skills in an undergraduate microteaching course. The blended learning program lasted for nine weeks. This program aimed at integrating social network tasks and face-to-face teaching activities. Pre-and post-tests were administered to assess student teachers’ micro-teaching performance. Data analysis revealed that blended learning has a significant effect on the participants’ teaching skills. Relevant interpretations and recommendations were offered
Study of the electrical and thermal properties of a silicone elastomer filled with silica for high temperature power device encapsulation

In order to take the full advantage of the high-temperature SiC and GaN operating power devices, package materials able to withstand high-temperature storage and large thermal cycles are required. However, a survey of the commercially available silicone gels mostly used for power module encapsulation, highlights that this type of materials exhibits a maximum temperature limit for continuous operation of about 260 °C. A slight extension of this temperature range might be obtained by using silicone elastomers with hardness still remaining measurable on the Shore A scale. The aim of this paper is to study a silicone elastomer poly(dimethyl)siloxane (PDMS) with silica fillers, with a specified maximum operating temperature of 275 °C, in order to evaluate its ability for high temperature power device encapsulation. First, the nature and size of the filler microparticles were determined using scanning electron microscopy (SEM) observations coupled with energy dispersive X-ray spectroscopy (EDX) analysis. Second.
Fabrication methods and applications of microstructured gallium based liquid metal alloys

This review contains a comparative study of reported fabrication techniques of gallium based liquid metal alloys embedded in elastomers such as polydimethylsiloxane or other rubbers as well as the primary challenges associated with their use. The eutectic gallium–indium binary alloy (EGaIn) and gallium–indium–tin ternary alloy (galinstan) are the most common non-toxic liquid metals in use today. Due to their deformability, non-toxicity and superior electrical conductivity, these alloys have become very popular among researchers for flexible and reconfigurable electronics applications. All the available manufacturing techniques have been grouped into four major classes. Among them, casting by needle injection is the most widely used technique as it is capable of producing features as small as 150 nm width by high-pressure infiltration. One particular fabrication challenge with gallium based liquid metals is that an oxide skin is rapidly formed on the entire exposed surface. This oxide skin increases wettability on many surfaces, which is excellent for keeping patterned metal in position, but is a drawback in applications like reconfigurable circuits, where the position of liquid metal needs to be altered and controlled accurately. The major challenges involved in many applications of liquid metal alloys have also been discussed thoroughly in this article.
Rapid quantification and isotopic analysis of dissolved sulfur species.

RATIONALE Dissolved sulfur species are of significant interest, both as important substrates for microbial activities and as key intermediaries in biogeochemical cycles. Species of intermediate oxidation state such as sulfite, thiosulfate, and thiols are of particular interest but are notoriously difficult to analyze, because of low concentrations and rapid oxidation during storage and analysis. METHODS Dissolved sulfur species are reacted with monobromobimane which yields a fluorescent bimane derivative that is stable to oxidation. Separation by Ultra-Performance Liquid Chromatography (UPLC) on a C18 column yields baseline resolution of analytes in under 5 min. Fluorescence detection (380 nm excitation, 480 nm emission) provides highly selective and sensitive quantitation, and Time-of-Flight Mass Spectrometry (TOF-MS) is used to quantify isotopic abundance, providing the ability to detect stable isotope tracers (either 33 S or 34 S). RESULTS Sulfite, thiosulfate, methanethiol, and bisulfide were quantified with on-column detection limits of picomoles (μM concentrations). Other sulfur species with unshared electrons are also amenable to analysis. TOF-MS detection of 34 S enrichment was accurate and precise to within 0.6% (relative) when sample and standard had similar isotope ratios, and was able to detect enrichments as small as 0.01 atom%. Accuracy was validated by comparison to isotope-ratio mass spectrometry. Four example applications are provided to demonstrate the utility of this method. CONCLUSIONS Derivatization of aqueous sulfur species with bromobimane is easily accomplished in the field, and protects analytes from oxidation during storage. UPLC separation with fluorescence detection provides low-μM detection limits. Using high-resolution TOF-MS, accurate detection of as little as 0.01% 34 S label incorporation into multiple species is feasible. This provides a useful new analytical window into microbial sulfur cycling. Copyright © 2017 John Wiley & Sons, Ltd.
SYNTHESIS OF FRUCTOOLIGOSACCHARIDES FROM Aspergillus niger COMMERCIAL INULINASE IMMOBILIZED IN POLYURETHANE FOAM AND PRE-TREATED IN PRESSURIZED LGP

Commercial inulinase from Aspergillus niger were immobilized in polyurethane foam and then treated in pressurized in liquefied petroleum gas (LPG). Firstly, the effects of system pressure, exposure time and depressurization rate, using liquefied petroleum gas (LPG), on the enzymatic activity were evaluated through central composite designs (CCD) 2 3 . Residual activities of 145.1% were observed for LPG (30 bar, 6 hours and depressurization rate of 20 bar/min). The catalysts treated at these conditions were then used for the production of fructooligosaccharides using sucrose as substrates, in aqueous systems. The main objective of this step was to evaluate the yield and productivity in fructooligosaccharides, using alternatives for enhance the enzyme activity by means of pressurized fluids and also using low cost supports for enzyme immobilization, aiming at obtaining a stable biocatalyst to be used for synthesis reactions. Yields of 32% were achieved, with 5.42 % of kestose (GF2); 22.27% of nystose (GF3) and 3.52% of fructosylnystose (GF4), which shows the potential of this procedure.
Weight management and physical activity throughout the cancer care continuum

Mounting evidence suggests that weight management and physical activity (PA) improve overall health and well being, and reduce the risk of morbidity and mortality among cancer survivors. Although many opportunities exist to include weight management and PA in routine cancer care, several barriers remain. This review summarizes key topics addressed in a recent National Academies of Science, Engineering, and Medicine workshop entitled, “Incorporating Weight Management and Physical Activity Throughout the Cancer Care Continuum. ” Discussions related to body weight and PA among cancer survivors included: 1) current knowledge and gaps related to health outcomes; 2) effective intervention approaches; 3) addressing the needs of diverse populations of cancer survivors; 4) opportunities and challenges of workforce, care coordination, and technologies for program implementation; 5) models of care; and 6) program coverage. While more discoveries are still needed for the provision of optimal weight‐management and PA programs for cancer survivors, obesity and inactivity currently jeopardize their overall health and quality of life. Actionable future directions are presented for research; practice and policy changes required to assure the availability of effective, affordable, and feasible weight management; and PA services for all cancer survivors as a part of their routine cancer care. CA Cancer J Clin 2018;68:64‐89. © 2017 American Cancer Society.
Post‐translational incorporation of 3,4‐dihydroxyphenylalanine into the C terminus of α‐tubulin in living cells

The C‐terminal tyrosine (Tyr) of the α‐tubulin chain is subjected to post‐translational removal and readdition in a process termed the “detyrosination/tyrosination cycle”. We showed in previous studies using soluble rat brain extracts that l‐3,4‐dihydroxyphenylalanine (l‐Dopa) is incorporated into the same site as Tyr. We now demonstrate that l‐Dopa incorporation into tubulin also occurs in living cells. We detected such incorporation by determining the “tyrosination state” of tubulin before and after incubation of cells in the presence of l‐Dopa. The presence of a tubulin isospecies following l‐Dopa incubation that was not recognized by antibodies specific to Tyr‐ and deTyr‐tubulin was presumed to reflect formation of Dopa‐tubulin. l‐Dopa was identified by HPLC as the C‐terminal compound bound to α‐tubulin. l‐Dopa incorporation into tubulin was observed in Neuro 2A cells and several other cell lines, and was not due to de novo protein biosynthesis. Dopa‐tubulin had microtubule‐forming capability similar to that of Tyr‐ and deTyr‐tubulin. l‐Dopa incorporation into tubulin did not notably alter cell viability, morphology, or proliferation rate. CAD cells (a neuron‐like cell line derived from mouse brain) are easily cultured under differentiating and nondifferentiating conditions, and can be treated with l‐Dopa. Treatment of CAD cells with l‐Dopa and consequent increase in l‐Dopa‐tubulin resulted in reduction of microtubule dynamics in neurite‐like processes.
Detection and Quantiflcation of Corrosion Damage Using Ground Penetrating Radar (GPR)

This research aims to detect the damage due to corrosion of reinforcing steel in concrete structures using ground penetrating radar (GPR) and conventional method, half-cell potential (HCP). A method to accelerate corrosion of steel rebar in concrete samples to difierent degrees is applied, the method consists of introducing a direct current (DC) power supply and 5% sodium chloride (NaCl) solution as an electrolyte to the rebar to induce signiflcant corrosion within a short period of time. The 2GHz GPR is used to detect the corrosion in the reinforced concrete slabs after 28 days of standard moist preservation. The results are compared with those obtained using the HCP method. Both of the GPR and the HCP show good performance in determining the degree of corrosion.
Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis

Lignin is a polymer present in the secondary cell walls of all vascular plants. It is a known barrier to pulping and the extraction of high-energy sugars from cellulosic biomass. The challenge faced with predicting outcomes of transgenic plants with reduced lignin is due in part to the presence of unique protein-protein interactions that influence the regulation and metabolic flux in the pathway. Yet, it is unclear why certain plants have evolved to create these protein complexes. In this study, we use mathematical models to investigate the role that the protein complex, formed specifically between Ptr4CL3 and Ptr4CL5 enzymes, have on the monolignol biosynthesis pathway. The role of this Ptr4CL3-Ptr4CL5 enzyme complex on the steady state flux distribution was quantified by performing Monte Carlo simulations. The effect of this complex on the robustness and the homeostatic properties of the pathway were identified by performing sensitivity and stability analyses, respectively. Results from these robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex. Specifically, the presence of Ptr4CL3-Ptr4CL5 complex increased the stability of the pathway by 22%. The robustness in the pathway is maintained due to the presence of multiple enzyme isoforms as well as the presence of alternative pathways resulting from the presence of the Ptr4CL3-Ptr4CL5 complex.
Transferable low-attenuation scaffold based on transparent conductive oxide nanoparticles for nanoplasmonics and optical metamaterials

We report on functionalized freestanding membrane-based plasmonic structures transferable to various substrates, including curved and flexible surfaces, biological tissues, etc., but also usable as freestanding, self-supported media. The functionalized membranes consist of a supporting layer with a thickness of the order of tens of nanometers, to which additional layers containing doped transparent conductive oxide nanoparticles were deposited. The supporting layer provides mechanical strength to the structure, while the additionally deposited layers impart plasmonic functionality. Carbon nanotubes were utilized for the reinforcement of the supporting layer. Indium tin oxide and aluminum-doped zinc oxide nanoparticles produced by nonaqueous route were utilized as fillers to impart plasmonic functionality, their losses at near infrared being lower than those of usual plasmonic metals. Dip coating and drop coating were chosen as the deposition methods for the functionalized layers. The obtained plasmonic-dielectric-plasmonic multilayer scaffold is a candidate structure for further tailoring, for instance by forming a 2D array of nanoholes in it.
Learning‐based deformable registration for infant MRI by integrating random forest with auto‐context model

Purpose: Accurately analyzing the rapid structural evolution of human brain in the first year of life is a key step in early brain development studies, which requires accurate deformable image registration. However, due to (a) dynamic appearance and (b) large anatomical changes, very few methods in the literature can work well for the registration of two infant brain MR images acquired at two arbitrary development phases, such as birth and one‐year‐old. Methods: To address these challenging issues, we propose a learning‐based registration method, which can handle the anatomical structures and the appearance changes between the two infant brain MR images with possible time gap. Specifically, in the training stage, we employ a multioutput random forest regression and auto‐context model to learn the evolution of anatomical shape and appearance from a training set of longitudinal infant images. To make the learning procedure more robust, we further harness the multimodal MR imaging information. Then, in the testing stage, for registering the two new infant images scanned at two different development phases, the learned model will be used to predict both the deformation field and appearance changes between the images under registration. After that, it becomes much easier to deploy any conventional image registration method to complete the remaining registration since the above‐mentioned challenges for state‐of‐the‐art registration methods have been well addressed. Results: We have applied our proposed registration method to intersubject registration of infant brain MR images acquired at 2‐week‐old, 3‐month‐old, 6‐month‐old, and 9‐month‐old with the images acquired at 12‐month‐old. Promising registration results have been achieved in terms of registration accuracy, compared with the counterpart nonlearning based registration methods. Conclusions: The proposed new learning‐based registration method have tackled the challenging issues in registering infant brain images acquired from the first year of life, by leveraging the multioutput random forest regression with auto‐context model, which can learn the evolution of shape and appearance from a training set of longitudinal infant images. Thus, for the new infant image, its deformation field to the template and also its template‐like appearances can be predicted by the learned models. We have extensively compared our method with state‐of‐the‐art deformable registration methods, as well as multiple variants of our method, which show that our method can achieve higher accuracy even for the difficult cases with large appearance and shape changes between subject and template images.
GRVI Phalanx: A Massively Parallel RISC-V FPGA Accelerator Accelerator

GRVI is an FPGA-efficient RISC-V RV32I soft processor. Phalanx is a parallel processor and accelerator array framework. Groups of processors and accelerators form shared memory clusters. Clusters are interconnected with each other and with extreme bandwidth I/O and memory devices by a Hoplite NOC with 300-bit links. An example Kintex UltraScale 040 system has 400 RISC-V cores, peak throughput of 100,000 MIPS, peak shared memory bandwidth of 600 GB/s, NOC bisection bandwidth of 700 Gb/s, and uses 12-17 W.
High transmissibility of norovirus among infants and school children during the 2016/17 season in Osaka, Japan

The number of person-to-person transmitted norovirus cases (n = 4,712) in school children in Osaka, Japan, during 2016/17 was the largest since 2012/13. Norovirus outbreaks were reported by 101 schools including 53 nursery schools (1,927 cases), 18 kindergartens (1,086 cases) and 30 elementary schools (1,699 cases). The dominant genotype among outbreaks was GII.P16-GII.2 (57.4%; 58/101), followed by GII.P2-GII.2 (8.9%; 9/101) and GII.P7-GII.6 (5.9%; 6/101). GII.4 was not detected despite dominance in previous years.