Miracle-dz/UniFAR-FTUs huggingface dataset:
Scatter Correction with Combined Single-Scatter Simulation and Monte Carlo Simulation Scaling Improved the Visual Artifacts and Quantification in 3-Dimensional Brain PET/CT Imaging with 15O-Gas Inhalation

In 3-dimensional PET/CT imaging of the brain with 15O-gas inhalation, high radioactivity in the face mask creates cold artifacts and affects the quantitative accuracy when scatter is corrected by conventional methods (e.g., single-scatter simulation [SSS] with tail-fitting scaling [TFS-SSS]). Here we examined the validity of a newly developed scatter-correction method that combines SSS with a scaling factor calculated by Monte Carlo simulation (MCS-SSS). Methods: We performed phantom experiments and patient studies. In the phantom experiments, a plastic bottle simulating a face mask was attached to a cylindric phantom simulating the brain. The cylindric phantom was filled with 18F-FDG solution (3.8–7.0 kBq/mL). The bottle was filled with nonradioactive air or various levels of 18F-FDG (0–170 kBq/mL). Images were corrected either by TFS-SSS or MCS-SSS using the CT data of the bottle filled with nonradioactive air. We compared the image activity concentration in the cylindric phantom with the true activity concentration. We also performed 15O-gas brain PET based on the steady-state method on patients with cerebrovascular disease to obtain quantitative images of cerebral blood flow and oxygen metabolism. Results: In the phantom experiments, a cold artifact was observed immediately next to the bottle on TFS-SSS images, where the image activity concentrations in the cylindric phantom were underestimated by 18%, 36%, and 70% at the bottle radioactivity levels of 2.4, 5.1, and 9.7 kBq/mL, respectively. At higher bottle radioactivity, the image activity concentrations in the cylindric phantom were greater than 98% underestimated. For the MCS-SSS, in contrast, the error was within 5% at each bottle radioactivity level, although the image generated slight high-activity artifacts around the bottle when the bottle contained significantly high radioactivity. In the patient imaging with 15O2 and C15O2 inhalation, cold artifacts were observed on TFS-SSS images, whereas no artifacts were observed on any of the MCS-SSS images. Conclusion: MCS-SSS accurately corrected the scatters in 15O-gas brain PET when the 3-dimensional acquisition mode was used, preventing the generation of cold artifacts, which were observed immediately next to a face mask on TFS-SSS images. The MCS-SSS method will contribute to accurate quantitative assessments.
Pharmacology and phytochemistry of South African plants used as anthelmintics.

Traditional medicine in South Africa is part of the culture of the people and has been in existence for a long-time. Although animal components form part of the ingredients used, plant material constitutes the major component. South Africa is endowed with vast resources of medicinal and aromatic plants which have been employed for treatment against various diseases for decades. A large number of South Africans still depend on traditional medicine for their healthcare needs due to its affordability, accessibility and cultural importance. Helminth infections are among the variety of diseases treated by traditional healers. These infections are regarded as neglected tropical diseases (NTDs) due to their high prevalence among the economically disadvantaged living in rural areas in different regions of the world. For this study, eleven plants from nine families were selected based on their ethnopharmacological uses as anthelmintics. To validate the efficacy of the plants and for possible discovery of bioactive chemicals, it was deemed important to pharmacologically investigate the selected plants. Besides anthelmintic testing, antimicrobial activity and cyclooxygenase (COX) inhibitory activity screening of the plants were also carried out because microbial infections and inflammation are often associated with helminth infections. The plants investigated were also subjected to phytochemical analysis to test for the presence of different secondary metabolites that could be responsible for the biological activities observed. The plant materials were collected in KwaZulu-Natal between February and April 2009. Plant parts used in traditional medicine were collected and for sustainable harvesting of medicinal plants in order to enhance conservation, alternative plant parts (leaves and twigs) of some of the plants were also investigated. Independently, the plant material was extracted using petroleum ether (PE), dichloromethane (DCM), ethanol (EtOH) and water. A total of 80 extracts were prepared from the selected plants which were screened for anthelmintic, antimicrobial and COX inhibitory activities. For the phytochemical analysis, 50% aqueous methanol (MeOH) extracts were used to determine the presence of phenolics and alkaloids, while water
Generation of Structural MR Images from Amyloid PET: Application to MR-Less Quantification

Structural MR images concomitantly acquired with PET images can provide crucial anatomic information for precise quantitative analysis. However, in the clinical setting, not all the subjects have corresponding MR images. Here, we developed a model to generate structural MR images from amyloid PET using deep generative networks. We applied our model to quantification of cortical amyloid load without structural MR. Methods: We used florbetapir PET and structural MR data from the Alzheimer Disease Neuroimaging Initiative database. The generative network was trained to generate realistic structural MR images from florbetapir PET images. After the training, the model was applied to the quantification of cortical amyloid load. PET images were spatially normalized to the template space using the generated MR, and then SUV ratio (SUVR) of the target regions was measured by predefined regions of interest. A real MR-based quantification was used as the gold standard to measure the accuracy of our approach. Other MR-less methods—a normal PET template–based, a multiatlas PET template–based, and a PET segmentation–based normalization/quantification—were also tested. We compared the performance of quantification methods using generated MR with that of MR-based and MR-less quantification methods. Results: Generated MR images from florbetapir PET showed signal patterns that were visually similar to the real MR. The structural similarity index between real and generated MR was 0.91 ± 0.04. The mean absolute error of SUVR of cortical composite regions estimated by the generated MR-based method was 0.04 ± 0.03, which was significantly smaller than other MR-less methods (0.29 ± 0.12 for the normal PET template, 0.12 ± 0.07 for the multiatlas PET template, and 0.08 ± 0.06 for the PET segmentation–based methods). Bland–Altman plots revealed that the generated MR-based SUVR quantification was the closest to the SUVRs estimated by the real MR-based method. Conclusion: Structural MR images were successfully generated from amyloid PET images using deep generative networks. Generated MR images could be used as templates for accurate and precise amyloid quantification. This generative method might be used to generate multimodal images of various organs for further quantitative analyses.
Recombinant human hemoglobin does not affect renal function in humans: analysis of safety and pharmacokinetics.

BACKGROUND Recombinant human hemoglobin (OptroD; rHb1.1) is a genetically engineered protein produced in Escherichia coli. The two alpha-globin polypeptides are genetically joined, resulting in a stable tetramer that does not dissociate into dimers or monomers. Historically, infusion in humans of acellular hemoglobin preparations has resulted in renal toxicity. This study was performed to evaluate the safety and pharmacokinetics of rHb1.1 when infused in humans. METHODS After giving informed consent, 48 healthy male volunteers were randomly assigned to receive either 0.015-0.32 g/kg 5% rHb1.1 (n = 34) or an equivalent amount of 5% human serum albumin (HSA; n = 14) infused intravenously over 0.8-1.9 h. Serum creatinine, creatinine clearance, urine N-acetyl-beta-glucosaminidase, and serum rHb1.1 concentrations were measured before and at timed intervals after infusion. RESULTS Postinfusion urine N-acetyl-beta-glucosaminidase activity did not exceed preinfusion values at any interval in either group. Serum creatinine did not differ from preinfusion values at 1 day, 2-3 days, or 7 days after infusion for either group. Creatinine clearance increased significantly for the HSA group 12 h after infusion (138 +/- 16 ml/min, means +/- SE) and in the rHb1.1 group 1 day after infusion (112 +/- 5 ml/min; P < 0.05). Values for creatinine clearance did not differ from preinfusion values for either group at any other postinfusion interval; serum creatinine and creatinine clearance did not differ between groups at any time. The amount of hemoglobin excreted in the urine did not exceed approximately 0.04% of the administered rHb1.1 dose in any volunteer. Plasma clearance of rHb1.1 decreased and half-life increased as a function of increasing plasma concentration (e.g., the half-life was 2.8 h at a plasma concentration of 0.5 mg/ml and 12 h at 5 mg/ml). The incidence of gastrointestinal symptoms, fever, and chills was greater after infusion of rHb1.1 than after HSA (P < 0.05). CONCLUSIONS No evidence for rHb1.1-mediated nephrotoxicity was observed in volunteers given doses of rHb1.1 as large as 0.32 g/kg. Because the clearance of rHb1.1 varies inversely with its concentration, additional studies with larger doses are necessary to determine the half-life expected in clinical use. Administration of rHb1.1 to conscious humans is associated with some side effects, such as gastrointestinal upset, fever, chills, headache, and backache.
Heterogeneity of Muscle Energetics in Human Muscle Fiber Type Using 31P Nuclear Magnetic Resonance

AbstractTo evaluate the association between muscular phosphate metabolites or intracellular pH at rest and muscle fiber composition of musculus vastus lateralis in human, we measured phosphorus nuclear magnetic resonance (31P NMR) spectra and performed muscle biopsy in 30 subjects. The intracellular pH tended to be higher in cases with a higher percentage of fast-twitch fibers (% FT fibers). On the other hand, no relationship was observed between phosphocreatine (PCr)/inorganic phosphate (Pi) and percent FT fibers. This is inconsistent with previously reported results of 31P NMR studies in animals. These results suggest that PCr concentration is the same for the two major fiber types (FT and slow-twitch [ST] fibers) of human skeletal muscle. Knowledge of which relationship between muscle fiber composition and intracellular pH accounts for our results awaits further investigation.
Prediction of inverse kinematics of a 5-DOF pioneer robotic arm having 6-DOF end-effector using ANFIS

In this paper, a method for forward and inverse kinematics analysis of a 5-DOF pioneer robotic arm PArm having 6-DOF end-effector is proposed. Obtaining the trajectory and computing the required joint angles for a higher DOF robot manipulator is one of the important concerns in robot kinematics and control. The difficulties in solving the inverse kinematics equations of higher DOF robot manipulator arises due to the presence of uncertain, time varying and nonlinear nature of equations having transcendental functions. In this paper, the ability of adaptive neuro-fuzzy inference system ANFIS is used to the generated data for solving inverse kinematics problem. The proposed hybrid neuro-fuzzy system combines the learning capabilities of neural networks with fuzzy inference system for nonlinear function approximation. A single-output Sugeno-type fuzzy inference system FIS using grid partitioning has been modelled in this work. The Denavit-Hartenberg D-H representation is used to model robot links and solve the transformation matrices of each joint. The forward kinematics and inverse kinematics for a 5-DOF manipulator are analysed systemically.
In Vitro Modulation of Human Laryngeal Papilloma Cell Differentiation by Retinoic Acid

Researchers at the Long Island Jewish Medical Center, New York, NY, have recently developed an in vitro model to study the growth of human laryngeal papilloma cells at an air-liquid interface and for determining the effects of various agents. The model permits growth of human laryngeal papilloma cells sustained on a collagen matrix in tissue culture to form stratified squamous epithelium when exposed to an air-liquid interface. In their work reported at the annual meeting of the American Academy of Otolaryngology—Head and Neck Surgery in Kansas City, Mo, Angelo Reppucci, MD, Teresa Dilorenzo, MA, Alan Abramson, MD, and Bettie Steinberg, PhD, presented the effects of retinoic acid in this system. At low concentrations of retinoic acid (10 −9 mol/L and 10 −8 mol/L), the cells formed a stratified squamous epithelium with a differentiation-specific protein stain Section Editor. — Darrell Hunsaker, MD, San Diego, Calif ing pattern identical to that found
Raman Spectroscopy in Graphene-Based Systems: Prototypes for Nanoscience and Nanometrology

Raman spectroscopy is a powerful tool to characterize the different types of sp2 carbon nanostructures, including two-dimensional graphene, one-dimensional nanotubes, and the effect of disorder in their structures. This work discusses why sp2 nanocarbons can be considered as prototype materials for the development of nanoscience and nanometrology. The sp2 nanocarbon structures are quickly introduced, followed by a discussion on how this field evolved in the past decades. In sequence, their rather rich Raman spectra composed of many peaks induced by single- and multiple-resonance effects are introduced. The properties of the main Raman peaks are then described, including their dependence on both materials structure and external factors, like temperature, pressure, doping, and environmental effects. Recent applications that are pushing the technique limits, such as multitechnique approach and in situ nanomanipulation, are highlighted, ending with some challenges for new developments in this field.
The extremely slow‐exchanging core and acid‐denatured state of green fluorescent protein

Green fluorescent protein (GFP) is a large protein with a complex eleven‐stranded β‐barrel structure. Previous studies have shown that it has a complex energy landscape for folding on which there are several intermediate states and a denatured state with significant residual structure. Here, we use two different types of H/D exchange measurement and nuclear magnetic resonance (NMR) techniques to probe the energy landscape for folding of GFP in further detail. H/D exchange experiments were performed over a wide range of conditions including different concentrations of denaturant. Results show that the penetration model dominates the exchange mechanism, consistent with the known stability and slow unfolding kinetics of GFP. H/D exchange experiments at high pH establish that there is an extremely slow‐exchanging superstable core of amide protons in GFP that are clustered and located in β‐strands 1, 2, 4, 5, and 6. These residues form part of a mini‐β‐sheet which we propose constitutes a folding nucleus. Using a pulsed‐labeling strategy, the acid‐denatured state has been investigated and the residual structure observed in earlier studies shown to locate to β‐strands 1 and 3. There is some evidence that this residual structure is stabilized by a localized hydrophobic collapse of the polypeptide chain.
Factors associated with multi-drug resistant tuberculosis in Kenya

Multi-drug resistant tuberculosis (MDR-TB) and weak health systems threaten global tuberculosis control. Kenya is ranked 13th among the 22 high TB burden countries worldwide,and currently has an estimated 2,300 MDR-TB patients. A case-controlstudy to determine factors associated with MDR-TB in Kenya was conducted toinform policy in designing public health interventions that are best suited to thecountry’s needs.This was an unmatched case control study conducted in 41 health facilities in 20 districts across the eight provinces in Kenya from September 2009 to January 2010.Cases were confirmed MDR-TB (resistance to at least rifampicin and isoniazid)patients while controls were sputum- smear positive TB patients with clinicalresponse and negative sputum smear at the fifth month of treatment with first-lineanti-tuberculosis drugs. Study approval was sought and obtained from relevantinstitutions. Using the health facility TB register as the sampling frame, MDR-TBpatients and two randomly selected unmatched controls per case were enrolled. Apretested structured interviewer administered questionnaire was used for patientinterviews and to abstract information from records. Data on socio-demographic,behavioural, and clinical exposure history were obtained. Data were entered andanalyzed using Epi-info and Stata versions 3.5 and 9.0 software respectively.A total of 81cases {mean age: 32 years (SD: 10), 62% males} and 162 controls{mean age: 35 years (SD: 13), 59% males} there was no statistically significantdifference with respect to baseline socio-demographic characteristics. Six (7.4%) ofthe MDR-TB cases having no previous history of TB, reported living in the samehouse with a known MDR-TB patient. Cases were more likely to have history ofprevious exposure to first line anti-Tuberculosis drugs (OR= 85, 95% CI=29.7-243.3; P<0.0001) and be non Kenyan (OR=5.5, 95% CI=1.4-21.8; P=0.007). Casepatientswith positive HIV status (OR=0.34, 95% CI= 0.1-0.9;P=0.025) and thosewho had received TB treatment under the Directly Observed Therapy program(DOT) (OR=0.23, 95% CI= 0.1-0.6; P=0.002) were less likely to have MDR-TB.The study established that MDR-TB was associated with previous TB treatment, andbeing non Kenyan while use of DOT was protective. MDR-TB could be transmittedto otherwise healthy individuals. The protective association with HIV positive serostatusmay reflect selective survival of HIV negative MDR-TB and thus need to beinvestigated.We recommend strengthening of MDR-TB surveillance among previously treated TBcases and refugees and active MDR-TB case finding among HIV infected TBpatients. More rapid MDR-TB diagnostic tests should be used among the HIVinfected patients. Access to TB care services by all population groups includingimmigrants, implementation of DOT, MDR-TB contact tracing and screening andinfection prevention should be strengthened in Kenya.
Efficacy of primary PCI: the microvessel perspective

The outcome of patients with acute myocardial infarction (AMI) is critically dependent on adequate reperfusion at the tissue level. Primary percutaneous coronary intervention (PCI) achieves full patency of the infarct-related vessel in >90% of the patients with AMI. Despite the restoration of large-vessel flow, tissue perfusion in area at risk frequently continues to be compromised. To optimize microvascular reperfusion and clinical outcomes, additional measures are needed. Thus far, mechanical approaches to improve distal perfusion, such as the use of distal protection devices, have not been shown beneficial. Among the pharmacological approaches, high-dose adenosine infusion holds promise but has to be proved by further clinical studies. Glycoprotein IIb/IIIa receptor blockade with abciximab has a documented efficacy in improving microvascular flow, contractile recovery, and patient survival after primary PCI in AMI. In addition to the inhibition of platelet aggregation, prevention of pro-inflammatory heterotypic platelet interactions may contribute to the beneficial effect of this drug.
Exploiting multi-layered vector spaces for signal peptide detection

Analysing and classifying sequences based on similarities and differences is a mathematical problem of escalating relevance and importance in many scientific disciplines. One of the primary challenges in applying machine learning algorithms to sequential data, such as biological sequences, is the extraction and representation of significant features from the data. To address this problem, we have recently developed a representation, entitled Multi-Layered Vector Spaces (MLVS), which is a simple mathematical model that maps sequences into a set of MLVS. We demonstrate the usefulness of the model by applying it to the problem of identifying signal peptides. MLVS feature vectors are generated from a collection of protein sequences and the resulting vectors are used to create support vector machine classifiers. Experiments show that the MLVS-based classifiers are able to outperform or perform on par with several existing methods that are specifically designed for the purpose of identifying signal peptides.
Brain–specific proteins in Multiple Sclerosis

Brain–specific proteins (BSP) are each relatively specific for particular cell–types within the nervous system. The BSP studied were glial fibrillary acidic protein (GFAP) and S100B for the astrocyte, ferritin for microglia and neurofilaments (Nf) for the axon. BSP are released into the extracellular fluid (ECF) following cellular destruction and during phases of high cellular activity such as astrocytic or microglial activation. ECF BSP equilibrate with those in the cerebrospinal fluid (CSF). This allows us to quantify BSP from the CSF and estimate the overall average of axonal damage (CSF Nf), astrocytic and microglia activation (respectively CSF S100B, CSF ferritin) and astrogliosis (CSF GFAP). New enzyme linked immunoabsorbant assays (ELISA) have been developed for measuring Nf and GFAP in the CSF. Previously established ELISAs have been used to measure S100B and ferritin. It has been shown that spinal cord atrophy in a mouse model of autoimmune encephalomyelitis (EAE) was paralleled by a decrease of Nf indicating loss of axons, and an increase in GFAP indicating astrogliosis. These findings have been confirmed and extended in a human post–mortem study where BSP levels were quantified in multiple sclerosis (MS) lesions of different age and activity. S100B and Nf were associated with acute lesions, ferritin was elevated in all lesion types, while GFAP was increased in both acute and chronic lesions. CSF BSP levels were then quantified in a cross–sectional study of MS patients with the aim of distinguishing clinical subgroups, such as relapsing remitting (RR), primary progressive (PP) and secondary progressive (SP) disease. In addition an attempt was made to relate CSF BSP levels to grades of disability using clinical scales including Kurtzke’s EDSS, an ambulation index (AI) and the 9–hole PEG test (9HPT). It was shown that CSF S100B was higher in RR MS while CSF ferritin was elevated in PP MS patients. The S100B:ferritin ratio emphasised the distinction between the MS subtypes. CSF GFAP was higher in poorly ambulating (AI) and severely disabled (EDSS) patients. CSF GFAP correlated with the EDSS in SP MS patients. This suggests that gliosis is an important feature in SP MS. CSF Nf levels were quantified in a longitudinal study at baseline and at 3–year follow–up. It was shown that more SP/PP than RR MS patients experienced an increase in CSF Nf levels over this time, suggesting cumulative axonal damage in this subgroup. RR MS patients who had elevated CSF Nf levels at baseline had a worse clinical course, suggesting that initial high CSF Nf levels in RR MS patients are a poor prognostic sign. CSF Nf levels at follow–up correlated with the EDSS, AI and 9HPT suggesting that axonal pathology in MS is a dynamic process possibly balancing features of de- and regenerative activities.