Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Infection Associated Metabolic Markers in Human African Trypanosomiasis

Human African trypanosomiasis (HAT) remains a major neglected tropical disease in Sub-Saharan Africa. As clinical symptoms are usually non-specific, new diagnostic and prognostic markers are urgently needed to enhance the number of identified cases and optimise treatment. This is particularly important for disease caused by Trypanosoma brucei rhodesiense, where indirect immunodiagnostic approaches have to date been unsuccessful. We have conducted global metabolic profiling of plasma from T.b. rhodesiense HAT patients and endemic controls, using 1H nuclear magnetic resonance (NMR) spectroscopy and ultra-performance liquid chromatography, coupled with mass spectrometry (UPLC-MS) and identified differences in the lipid, amino acid and metabolite profiles. Altogether 16 significantly disease discriminatory metabolite markers were found using NMR, and a further 37 lipid markers via UPLC-MS. These included significantly higher levels of phenylalanine, formate, creatinine, N-acetylated glycoprotein and triglycerides in patients relative to controls. HAT patients also displayed lower concentrations of histidine, sphingomyelins, lysophosphatidylcholines, and several polyunsaturated phosphatidylcholines. While the disease metabolite profile was partially consistent with previous data published in experimental rodent infection, we also found unique lipid and amino acid profile markers highlighting subtle but important differences between the host response to trypanosome infections between animal models and natural human infections. Our results demonstrate the potential of metabolic profiling in the identification of novel diagnostic biomarkers and the elucidation of pathogenetic mechanisms in this disease.
Ion recombination correction factors (Pion) for Varian TrueBeam high‐dose‐rate therapy beams

Ion recombination is approximately corrected for in the Task Group 51 protocol by Pion, which is calculated by a two‐voltage measurement. This measurement approach may be a poor estimate of the true recombination, particularly if Pion is large (greater than 1.05). Concern exists that Pion in high‐dose‐per‐pulse beams, such as flattening filter free (FFF) beams, may be unacceptably high, rendering the two‐voltage measurement technique inappropriate. Therefore, Pion was measured for flattened beams of 6, 10, 15, and 18 MV and for FFF beams of 6 and 10 MV. The values for the FFF beams were verified with 1/V versus 1/Q curves (Jaffé plots). Pion was also measured for electron beams of 6, 12, 16, 18, and 20 MeV on a traditional accelerator, as well as on the high‐dose‐rate Varian TrueBeam accelerator. The measurements were made at a range of depths and with PTW, NEL, and Exradin Farmer‐type chambers. Consistent with the increased dose per pulse, Pion was higher for FFF beams than for flattening filter beams. However, for all beams, measurement locations, and chambers examined, Pion never exceeded 1.018. Additionally, Pion was always within 0.3% of the recombination calculated from the Jaffé plots. We conclude that ion recombination can be adequately accounted for in high‐dose‐rate FFF beams using Pion determined with the standard two‐voltage technique. PACS numbers: 87.56. ‐v, 87.56. Da
A Closed-Loop Mode-Localized Accelerometer

This paper reports a closed-loop mode-localized accelerometer for the first time. The accelerometer utilizes weakly coupled single-tine resonators as the sensing element to decrease the number of vibration modes. Based on a proposed closed-loop readout technique, the transient responses of the mode-localized accelerometer can be measured directly in the time domain. The test results show that the measured amplitude ratio noise and the resolution under closed-loop circumstances are <inline-formula> <tex-math notation="LaTeX">$1.409 \times 10^{-5}/\surd $ </tex-math></inline-formula>Hz and <inline-formula> <tex-math notation="LaTeX">$7.608~\mu \text{g}/\surd $ </tex-math></inline-formula>Hz, respectively, which are largely improved compared with those (<inline-formula> <tex-math notation="LaTeX">$9.883 \times 10^{-4}/\surd $ </tex-math></inline-formula>Hz and 0.744 mg/<inline-formula> <tex-math notation="LaTeX">$\surd $ </tex-math></inline-formula>Hz) under the open-loop measurement. The sensitivity based on the amplitude ratio readout is ~124 times higher than that of the frequency with the acceleration input of [−1g, +1g], which indicates that the high sensitivity of the mode-localized sensors can be also obtained utilizing closed-loop control. [2017–0148]
A Systematic Review and Meta-Analysis of the In Vivo Haemodynamic Effects of Δ9-Tetrahydrocannabinol

∆9-Tetrahydrocannabinol (THC) has complex effects on the cardiovascular system. We aimed to systematically review studies of THC and haemodynamic alterations. PubMed, Medline, and EMBASE were searched for relevant studies. Changes in blood pressure (BP), heart rate (HR), and blood flow (BF) were analysed using the Cochrane Review Manager Software. Thirty-one studies met the eligibility criteria. Fourteen publications assessed BP (number, n = 541), 22 HR (n = 567), and 3 BF (n = 45). Acute THC dosing reduced BP and HR in anaesthetised animals (BP, mean difference (MD) −19.7 mmHg, p < 0.00001; HR, MD −53.49 bpm, p < 0.00001), conscious animals (BP, MD −12.3 mmHg, p = 0.0007; HR, MD −30.05 bpm, p < 0.00001), and animal models of stress or hypertension (BP, MD −61.37 mmHg, p = 0.03) and increased cerebral BF in murine stroke models (MD 32.35%, p < 0.00001). Chronic dosing increased BF in large arteries in anaesthetised animals (MD 21.95 mL/min, p = 0.05) and reduced BP in models of stress or hypertension (MD −22.09 mmHg, p < 0.00001). In humans, acute administration increased HR (MD 8.16 bpm, p < 0.00001). THC acts differently according to species and experimental conditions, causing bradycardia, hypotension and increased BF in animals; and causing increased HR in humans. Data is limited, and further studies assessing THC-induced haemodynamic changes in humans should be considered.
Aryl hydrocarbon receptor inhibits inflammation in DSS-induced colitis via the MK2/p-MK2/TTP pathway

The pathogenesis of inflammatory bowel disease (IBD) is believed to be associated with the abnormal expression of inflammatory factors. The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor, which can suppress the inflammatory response and attenuate experimental colitis. However, the detailed mechanism underlying the effects of AhR remains unclear. The present study investigated the role of AhR in the pathogenesis of IBD. Colitis was induced in mice by administration of 3% dextran sulphate sodium (DSS) for 7 days. The mice were also administered injections of the AhR agonist, 6-formylindolo(3,2-b)carbazole (FICZ), starting 2 days after the first administration of DSS. Furthermore, LoVo cells were treated with lipopolysaccharide (LPS) in the presence or absence of FICZ for 8 h. The protein expression levels of AhR, cytochrome P450 1A1 (CYP1A1) and tristetraprolin (TTP) were assessed by western blotting and immunofluorescence, whereas mRNA expression levels were assessed by reverse transcription-quantitative polymerase chain reaction. The results indicated that injection of mice with FICZ significantly attenuated DSS-induced colitis; in addition, the expression levels of inflammatory cytokines were markedly downregulated. Conversely, the expression levels of AhR and TTP were upregulated. In addition, mice in the AhR-knockout + DSS group exhibited elevated inflammatory cytokine production and developed more severe colitis. In LoVo cells, incubation with FICZ decreased the expression levels of inflammatory cytokines, whereas AhR and TTP expression was increased. In addition, the levels of phosphorylated-mitogen-activated protein kinase-activated protein kinase 2 (p-MK2) were decreased. These results suggested that AhR deficiency resulted in increased susceptibility to colitis, whereas activation of AhR by FICZ could ameliorate DSS-induced colitis via the MK2/p-MK2/TTP pathway.
Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa

Significance Helicoverpa armigera is a major agricultural and horticultural pest that recently spread from its historical distribution throughout much of the Old World to the Americas, where it is already causing hundreds of millions of dollars in damage every year. The species is notoriously quick to generate and disseminate pesticide resistance throughout its range and has a wider host range than the native Helicoverpa zea. Hybridization between the two species increases the opportunity for novel, agriculturally problematic ecotypes to emerge and spread through the Americas. Within the mega-pest lineage of heliothine moths are a number of polyphagous, highly mobile species for which the exchange of adaptive traits through hybridization would affect their properties as pests. The recent invasion of South America by one of the most significant agricultural pests, Helicoverpa armigera, raises concerns for the formation of novel combinations of adaptive genes following hybridization with the closely related Helicoverpa zea. To investigate the propensity for hybridization within the genus Helicoverpa, we carried out whole-genome resequencing of samples from six species, focusing in particular upon H. armigera population structure and its relationship with H. zea. We show that both H. armigera subspecies have greater genetic diversity and effective population sizes than do the other species. We find no signals for gene flow among the six species, other than between H. armigera and H. zea, with nine Brazilian individuals proving to be hybrids of those two species. Eight had largely H. armigera genomes with some introgressed DNA from H. zea scattered throughout. The ninth resembled an F1 hybrid but with stretches of homozygosity for each parental species that reflect previous hybridization. Regions homozygous for H. armigera-derived DNA in this individual included one containing a gustatory receptor and esterase genes previously associated with host range, while another encoded a cytochrome P450 that confers insecticide resistance. Our data point toward the emergence of novel hybrid ecotypes and highlight the importance of monitoring H. armigera genotypes as they spread through the Americas.
AutoLock: a semiautomated system for radiotherapy treatment plan quality control

A semiautomated system for radiotherapy treatment plan quality control (QC), named AutoLock, is presented. AutoLock is designed to augment treatment plan QC by automatically checking aspects of treatment plans that are well suited to computational evaluation, whilst summarizing more subjective aspects in the form of a checklist. The treatment plan must pass all automated checks and all checklist items must be acknowledged by the planner as correct before the plan is finalized. Thus AutoLock uniquely integrates automated treatment plan QC, an electronic checklist, and plan finalization. In addition to reducing the potential for the propagation of errors, the integration of AutoLock into the plan finalization workflow has improved efficiency at our center. Detailed audit data are presented, demonstrating that the treatment plan QC rejection rate fell by around a third following the clinical introduction of AutoLock. PACS number: 87.55. Qr
RNN-SM: Fast Steganalysis of VoIP Streams Using Recurrent Neural Network

Quantization index modulation (QIM) steganography makes it possible to hide secret information in voice-over IP (VoIP) streams, which could be utilized by unauthorized entities to set up covert channels for malicious purposes. Detecting short QIM steganography samples, as is required by real circumstances, remains an unsolved challenge. In this paper, we propose an effective online steganalysis method to detect QIM steganography. We find four strong codeword correlation patterns in VoIP streams, which will be distorted after embedding with hidden data. To extract those correlation features, we propose the codeword correlation model, which is based on recurrent neural network (RNN). Furthermore, we propose the feature classification model to classify those correlation features into cover speech and stego speech categories. The whole RNN-based steganalysis model (RNN-SM) is trained in a supervised learning framework. Experiments show that on full embedding rate samples, RNN-SM is of high detection accuracy, which remains over 90% even when the sample is as short as 0.1 s, and is significantly higher than other state-of-the-art methods. For the challenging task of conducting steganalysis towards low embedding rate samples, RNN-SM also achieves a high accuracy. The average testing time for each sample is below 0.15% of sample length. These clues show that RNN-SM meets the short sample detection demand and is a state-of-the-art algorithm for online VoIP steganalysis.
Predicting cancer outcomes from histology and genomics using convolutional networks

Significance Predicting the expected outcome of patients diagnosed with cancer is a critical step in treatment. Advances in genomic and imaging technologies provide physicians with vast amounts of data, yet prognostication remains largely subjective, leading to suboptimal clinical management. We developed a computational approach based on deep learning to predict the overall survival of patients diagnosed with brain tumors from microscopic images of tissue biopsies and genomic biomarkers. This method uses adaptive feedback to simultaneously learn the visual patterns and molecular biomarkers associated with patient outcomes. Our approach surpasses the prognostic accuracy of human experts using the current clinical standard for classifying brain tumors and presents an innovative approach for objective, accurate, and integrated prediction of patient outcomes. Cancer histology reflects underlying molecular processes and disease progression and contains rich phenotypic information that is predictive of patient outcomes. In this study, we show a computational approach for learning patient outcomes from digital pathology images using deep learning to combine the power of adaptive machine learning algorithms with traditional survival models. We illustrate how these survival convolutional neural networks (SCNNs) can integrate information from both histology images and genomic biomarkers into a single unified framework to predict time-to-event outcomes and show prediction accuracy that surpasses the current clinical paradigm for predicting the overall survival of patients diagnosed with glioma. We use statistical sampling techniques to address challenges in learning survival from histology images, including tumor heterogeneity and the need for large training cohorts. We also provide insights into the prediction mechanisms of SCNNs, using heat map visualization to show that SCNNs recognize important structures, like microvascular proliferation, that are related to prognosis and that are used by pathologists in grading. These results highlight the emerging role of deep learning in precision medicine and suggest an expanding utility for computational analysis of histology in the future practice of pathology.
Association of Histologic Chorioamnionitis With Perinatal Brain Injury and Early Childhood Neurodevelopmental Outcomes Among Preterm Neonates

Importance Understanding the role of chorioamnionitis, a major factor leading to preterm birth, in the pathogenesis of neonatal brain injury and adverse neurodevelopmental outcomes may help in identifying potentially modifiable perinatal variables affecting brain health and outcomes among children born preterm. Objective To evaluate whether histologic chorioamnionitis among neonates born very preterm is associated with intraventricular hemorrhage (IVH) and punctate white matter injury (WMI) or with adverse neurodevelopmental outcomes during early childhood. Design, Setting, and Participants Prospective cohort study conducted across 3 academic centers (from April 2006 to September 2013 in Canada, from March 2007 to March 2013 in the Netherlands, and from January 2004 to August 2011 in the United States). Children who were born preterm (24-32 weeks’ gestation) and who had undergone a placental pathologic evaluation, magnetic resonance imaging as soon as clinically stable, and Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) assessments between 18 and 24 months’ corrected age (CA) were included. Magnetic resonance imaging scans were assessed for grade of IVH and volume of punctate WMI. Data analysis occurred between December 2016 and January 2018. Final multivariable analyses examining the association of chorioamnionitis with motor and cognitive outcomes accounted for academic center and perinatal and postnatal factors. Main Outcomes and Measures Punctate WMI volume and IVH detected on neonatal magnetic resonance imaging scans; motor and cognitive outcomes defined using Bayley-III assessments conducted among these children between 18 and 24 months’ CA. Results Of 350 neonates (182 male) in the final cohort, 145 (41.4%) had histologic chorioamnionitis. Gestational age was significantly lower among those with chorioamnionitis (median, 26.4 weeks; interquartile range [IQR], 25.6-27.7 weeks) than among those without chorioamnionitis (median, 28.0 weeks; IQR, 27.0-29.7 weeks). Chorioamnionitis was not associated with IVH or WMI, nor was it associated with worse motor outcomes in univariable or multivariable analyses (adjusted Bayley-III motor score, −2.2; 95% CI, −5.6 to 1.3). Cognitive scores were marginally yet statistically significantly lower among children with chorioamnionitis (median, 105; IQR, 95-110) than among those without chorioamnionitis (median, 105; IQR, 100-115) in the univariable model. This difference was attenuated in the multivariable model (adjusted Bayley-III cognitive score, −3.0; 95% CI, −6.4 to 0.4). Conclusions and Relevance Histologic chorioamnionitis was not associated with IVH or WMI near birth or with worse cognitive or motor outcomes from 18 to 24 months’ CA after accounting for perinatal factors. Postnatal factors attenuated the association between chorioamnionitis and neurodevelopmental outcomes, highlighting the importance of preventing postnatal illness, such as infection, to promote optimal outcomes among children born preterm.
Analysis of the Effect of Source Capacitance and Inductance on $N$ -Path Mixers and Filters

Switch <inline-formula> <tex-math notation="LaTeX">$R-C$ </tex-math></inline-formula> passive <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula>-path mixers and filters enable interference-robust radio receivers with a flexibly programmable center frequency defined by a digital multi-phase clock. The radio frequency (RF) range of these circuits is limited by parasitic shunt capacitances, which introduce signal loss and degrade noise figure. Moreover, the linear periodically time varying nature of switch <inline-formula> <tex-math notation="LaTeX">$R-C$ </tex-math></inline-formula> circuits results in unwanted signal folding which needs to be suppressed by linear time- invariant (LTI) prefiltering by passive LC filters. This paper analyzes the interaction between capacitive or inductive LTI prefiltering and an <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula>-path mixer or filter, leveraging an analysis technique based on the impulse response of the adjoint network. Previously reported results for an inductive source impedance are derived in a simpler fashion, while providing circuit intuition. Moreover, new results for <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula>-path receivers with a shunt capacitor, and a combination of a series inductor and shunt capacitor are derived, as well as design criteria to minimize loss and frequency shifting in the peak response of these circuits.
The Effect of Primary γ' Distribution on Grain Growth Behavior of GH720Li Alloy

In this paper, a series of hot compression tests were carried out under different hot deformation parameters, covering the temperature range of 1000oC to 1170oC, strain rate range of 0.01s -1 to 1s -1 and compression reduction of 30%, 50%, and 70%. After that, all specimens were heat treated under the standard heat treatment schedule of GH720Li to investigate its hot deformation characteristics, especially the grain growth behaviors. The further OM and SEM observations were adopted to investigate the interaction mechanism of the primary γ′ distribution and grain growth for GH720Li alloy. The results show that for GH720Li alloy, when hot deformed below γ′ solvus, the banded or bi-model structure always occurs; while hot deformed near or over γ′ solvus, the uniform grain size distribution can be obtained. Further microstructure analysis shows that the bi-model or banded grain size distribution in GH720Li alloy is mainly due to the nonuniform re-dissolving of primary γ′ during heating process; while the uniformity of primary γ′ phase is determined by the uniformity of elements in this alloy. In other word, the homogenizing process for ingot is the key reason for later grain size control. Introduction GH720Li (UDIMET 720Li) is a high strength nickel-based superalloy being considered for applications for modern gas turbines and aero-engines. The chemical composition of this alloy is related to that of GH720 (UDIMET 720) from which it is derived, but differs from it with respect to the chromium, carbon and boron levels. Till now, a lot of studies [1-6] have been done for GH720Li alloy including the solutioning and precipitating of γ prime phase, the ingot to billet conversion process control, the heat treatment schedule optimizing, the mechanical behavior under service conditions, etc. However, the microstructure of GH720Li consists of primary, secondary and tertiary γ′ due to its special heat treatment schedule. Primary γ′ lies at the γ-grain boundaries and
Sustainable Fly Ash Based Roof Tiles with Waste Polythene Fibre: An Experimental Study

The compressive stress-strain behavior and other characteristics of treated fly ash based roof tiles have been studied by several experimental tests. This paper attempts to presents the results and observations of a study and comparison based on the past reported experimental data. Based on the results and observations of the comprehensive experimental study, five “control points” have been identified. The new sets of experiment have been carried out to investigate whether it might be possible the use of fly ash in fly ash based roof tiles for residential construction. In the present study, treated fly ash (TFA) of C category was used with different materials as a replacement of clay for making treated fly ash stone dust roof tiles (TFASDRT). Treated fly ash stone dust roof tiles (TFASDRT) were studied at varying percentages of cement, coarse sand, and radish stone dust (RSD) along with the constant percentage of waste polythene fibre (WPF). A research program was undertaken to evaluate the suitability of such test for assessing the properties of treated fly ash stone dust roof tiles (TFASDRT). The result of this study recommends that the fly ash based roof tiles provides a sustainable supplement to the traditional clay roof tiles, they increase the efficiency of traditional roof tiles and significantly help to reduce the environmental issues associated with the disposal of these waste materials.