Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Fusobacterium necrophorum and other upper respiratory tract pathogens isolated from throat swabs

Abstract Fusobacterium necrophorum, an anaerobic, Gram-negative rod, has been identified recently as a significant cause of persistent sore throat syndrome (PSTS). This disease is characterised by chronic, recurrent or persistent sore throat, which is believed to respond poorly to penicillin in vivo. The aim of this study is to examine the prevalence of F. necrophorum in all throat swabs received in our diagnostic microbiology department and to compare the results with those for other recognised respiratory pathogens. All throat swabs received in the laboratory over a four-week period were cultured for β-haemolytic streptococcus groups A, C and G, Corynebacterium diphtheriae, Arcanobacterium haemolyticum and F. necrophorum. Latex agglutination techniques, phenotypic reactions and antibiograms are used to identify these organisms. The age of the patient and the clinical details as stated on the request form were noted. Among a total of 248 samples, 27 were positive for β-haemolytic streptococcus group A, two were positive for β-haemolytic streptococcus group C, five were positive for β-haemolytic streptococcus group G and 24 were positive for F. necrophorum. The most common isolate in the under 20 age group was β-haemolytic streptococcus group A. In the over 20 age group, F. necrophorum was the pathogen most frequently isolated. A clinical diagnosis of ‘sore throat’ was most likely to be positive for β-haemolytic streptococcus group A, a clinical diagnosis of PSTS was most likely to be positive for F. necrophorum and a clinical diagnosis of ‘tonsillitis’ was equally likely to be caused by β-haemolytic streptococcus group A or F. necrophorum. β-haemolytic streptococcus group A was present in 11% of the samples and F. necrophorum was present in 10% of the samples. In total, these two pathogens accounted for 18.5% of throat infections in the sampled group. The results show that F. necrophorum is as significant a cause of throat infection as is β-haemolytic streptococcus group A. Examination of this provisional data suggests that targeting culture towards these two pathogens may be possible in certain cohorts of patients if more precise clinical data are received from medical staff. However, based on the clinical symptoms routinely provided by clinicians requesting microscopy, culture and sensitivity on throat swabs, F. necrophorum culture is required on all throat swabs received in the laboratory.
Intimate Partner Violence Against Women in Northwestern Botswana: The Maun Women’s Study

Factors characterizing intimate partner violence (IPV) against women vary according to setting and must be understood in localized environments if effective interventions are to be identified. This 2009-2010 exploratory study in Maun, Botswana, used semistructured interviews to elicit information from 469 women about their experiences with IPV. Characteristics found to be important included suicide attempts, childhood exposure to familial violence, access to and control over certain tangible assets, number of children, household location and monthly income, controlling behavior by a partner, and alcohol consumption. Controlling behavior by a partner was the single greatest predictor of physical or psychological IPV.
Low Seroprevalence of Neutralizing Antibodies Targeting Two Clade F AAV in Humans.

To assess the therapeutic utility of AAVHSC15 and AAVHSC17, two recently described Clade F adeno-associated viruses, the seroprevalence of neutralizing antibodies to these AAVs was assessed in a representative human population and compared to that of AAV9. Neutralizing antibody levels were measured in 100 unique human sera of different races (34:33:33, Black:Caucasian:Hispanic) and sex (49% Female, 51% Male) collected within the United States. Fifty-six sera were tested in HuH7 cells and 44 sera were tested in 2V6.11 cells with vectors packaged with either a CMV-promoter upstream of LacZ or a CBA-promoter upstream of Firefly Luciferase, respectively. For AAVHSC15, AAVHSC17, and AAV9, 24/100 (24%), 21/100 (21%), and 17/100 (17%), respectively, of all sera tested were seropositive for neutralizing antibodies using 50% inhibition of cellular transduction at a 1/16 dilution of serum as cut-off for seropositivity. Only six percent of positive sera had titers of 1/150 to 1/340 indicating that the majority of positive sera were of low titer. Significant cross-reactivity of neutralizing antibodies across all three AAV serotypes was observed. These data show that approximately 80% of humans evaluated were seronegative for pre-existing neutralizing antibodies to the AAV serotypes tested, suggesting that the vast majority of human subjects would be amenable to therapeutic intervention with Clade F AAVs.
IM2HEIGHT: Height Estimation from Single Monocular Imagery via Fully Residual Convolutional-Deconvolutional Network

In this paper we tackle a very novel problem, namely height estimation from a single monocular remote sensing image, which is inherently ambiguous, and a technically ill-posed problem, with a large source of uncertainty coming from the overall scale. We propose a fully convolutional-deconvolutional network architecture being trained end-to-end, encompassing residual learning, to model the ambiguous mapping between monocular remote sensing images and height maps. Specifically, it is composed of two parts, i.e., convolutional sub-network and deconvolutional sub-network. The former corresponds to feature extractor that transforms the input remote sensing image to high-level multidimensional feature representation, whereas the latter plays the role of a height generator that produces height map from the feature extracted from the convolutional sub-network. Moreover, to preserve fine edge details of estimated height maps, we introduce a skip connection to the network, which is able to shuttle low-level visual information, e.g., object boundaries and edges, directly across the network. To demonstrate the usefulness of single-view height prediction, we show a practical example of instance segmentation of buildings using estimated height map. This paper, for the first time in the remote sensing community, attempts to estimate height from monocular vision. The proposed network is validated using a large-scale high resolution aerial image data set covered an area of Berlin. Both visual and quantitative analysis of the experimental results demonstrate the effectiveness of our approach.
Autophagy regulates TGF-β2-induced epithelial-mesenchymal transition in human retinal pigment epithelium cells

Transforming growth factor (TGF)-β2-induced epithelial-mesenchymal transition (EMT) in human retinal pigment epithelium (RPE) cells has an important role in the pathophysiology of intraocular fibrotic disorders, which may cause vision impairment and blindness. Autophagy, an intracellular homeostatic pathway, contributes to the physiological and pathological processes of RPE. Furthermore, autophagy has previously been reported to function in the EMT process in numerous tissue and cell types. However, the association between autophagy and the EMT process in RPE cells has not yet been fully determined. The present study demonstrated that TGF-β2-treated human RPE cells (ARPE-19 cell line) exhibited a significantly increased autophagic flux compared with control cells, as determined by western blot analysis of the protein levels of microtubule-associated protein 1 light chain 3-II and p62 (also termed sequestosome 1). Furthermore, it was demonstrated that autophagy activation enhanced the TGF-β2-induced EMT process in ARPE-19 cells, and inhibition of autophagy by chloroquine administration attenuated TGF-β2-induced EMT, which was determined by analyzing the expression of mesenchymal and epithelial markers by reverse transcription-quantitative polymerase chain reaction and/or western blotting. A transwell migration and invasion assays was also performed that demonstrated that autophagy activation by rapamycin enhanced TGF-β2-stimulated RPE cell migration and invasion, and inhibition of autophagy reduced TGF-β2-stimulated RPE cell migration and invasion. These results also demonstrated that autophagy activation enhanced the TGF-β2-induced EMT process in ARPE-19 cells, and inhibition of autophagy attenuated TGF-β2-induced EMT. Overall, the results of the present study demonstrated that TGF-β2-induced EMT may be regulated by autophagy, thus indicating that autophagy may serve as a potential therapeutic target for the attenuation of EMT in intraocular fibrotic disorders.
Blood analytes of oceanic-juvenile loggerhead sea turtles (Caretta caretta) from Azorean waters: reference intervals, size-relevant correlations and comparisons to neritic loggerheads from western Atlantic coastal waters

This study reports reference intervals and correlations of blood analytes of oceanic-juvenile loggerhead sea turtles from Azorean waters with body size and comparison of data to neritic loggerheads from the US Atlantic coast. The observed findings highlight conservation-relevant biological (e.g. diet, somatic growth) and habitat differences among both populations.
Efficacy and pharmacokinetic activity of frovatriptan compared to rizatriptan in patients with moderate-to-severe migraine

Background Migraine is a painful neurological disorder that affects over 10% of the general population. Frovatriptan and rizatriptan are antimigraine agents belonging to the triptan class. Although previous studies have independently compared the efficacy of these agents, contemporaneous data examining both pharmacokinetic (PK) properties and efficacy in parallel have not previously been available. Materials and methods In this single-center double-blind study, 18 subjects (ten female) were treated for a single migraine attack with frovatriptan 2.5 mg or rizatriptan 10 mg. Plasma concentrations were measured predose and at 2, 4, 6, 12, 24, 48, and 72 hours after drug administration. The primary end point of this study was to evaluate the association between PK parameters and efficacy measures and recurrence rate. Secondary end points were pain-free and pain-relief episodes at 2 and 4 hours, recurrent episodes within 48 hours, and cumulative hazard of recurrence within 72 hours. Results At baseline, approximately 17% of patients had mild migraine, while 83% had moderate–severe migraine. Although the time to maximum concentration was similar for both drugs (2.7 versus 2.3 hours), the terminal half-life for frovatriptan was longer than rizatriptan (29.3 versus 3.2 hours, P<0.0001). The proportion of patients who were pain-free at 4 hours without rescue medication was higher in the frovatriptan-treated group, (38.9 versus 5.6%, P=0.045). The cumulative hazard of recurrence over 72 h was reduced by frovatriptan compared to rizatriptan-treated patients (log-rank test, P=0.04). Pain-free and pain-relief episodes for the study period were positively correlated with the concentration:maximum concentration (Cmax) ratio for frovatriptan (r=0.52, P=0.028), but not rizatriptan. Recurrence rate was negatively correlated with the concentration:Cmax ratio for both frovatriptan (r=−0.96, P=0.0024) and rizatriptan (r=−0.98, P=0.0004). Fewer adverse events were observed for frovatriptan compared to rizatriptan (one versus eight, P=0.021). Conclusion This pilot study indicates that a similar extent of initial pain relief is afforded by both triptans in migraine treatment. The longer duration of action of frovatriptan parallels and correlates with its PK profile.
Determinants of non-adherence to disease-modifying therapies in multiple sclerosis: A cross-Canada prospective study

Background: Poor adherence to the disease-modifying therapies (DMTs) for multiple sclerosis (MS) may attenuate clinical benefit. A better understanding of characteristics associated with non-adherence could improve outcomes. Objective: To evaluate characteristics associated with non-adherence to injectable DMTs. Methods: Consecutive patients from four Canadian MS Clinics were assessed at three time points over two years. Clinical and demographic information included self-reported DMT use, missed doses in the previous 30 days, health behaviors, and comorbidities. Non-adherence was defined as <80% of expected doses taken. We employed generalized estimating equations to examine characteristics associated with non-adherence at all time points with findings reported as adjusted odds ratios (OR). Results: In all, 485 participants reported use of an injectable DMT, of whom 107 (22.1%) were non-adherent over the study period. Non-adherence was associated with a lower Expanded Disability Status Scale score (0–2.5 vs 3.0–5.5, OR: 1.80; 95% confidence interval (CI): 1.06–3.04), disease duration (⩽5 vs <5 years, OR: 2.23; 95% CI: 1.10–4.52), alcohol dependence (OR: 2.14; 95% CI: 1.23–3.75), and self-reported cognitive difficulties, measured by the Health Utilities Index-3 (OR: 1.55; 95% CI: 1.08–2.22). Conclusions: Nearly one-quarter of participants were non-adherent during the study. Alcohol dependence, perceived cognitive difficulties, longer disease duration, and mild disability status were associated with non-adherence. These characteristics may help healthcare professionals identify patients at greatest risk of poor adherence.
Abel-Jacobi map, integral Hodge classes and decomposition of the diagonal

Given a smooth projective 3-fold Y, with $H^{3,0}(Y)=0$, the Abel-Jacobi map induces a morphism from each smooth variety parameterizing 1-cycles in Y to the intermediate Jacobian J(Y). We study in this paper the existence of families of 1-cycles in Y for which this induced morphism is surjective with rationally connected general fiber, and various applications of this property. When Y itself is rationally connected, we relate this property to the existence of an integral homological decomposition of the diagonal. We also study this property for cubic threefolds, completing the work of Iliev-Markoushevich. We then conclude that the Hodge conjecture holds for degree 4 integral Hodge classes on fibrations into cubic threefolds over curves, with restriction on singular fibers.
Soft Somatosensitive Actuators via Embedded 3D Printing

Humans possess manual dexterity, motor skills, and other physical abilities that rely on feedback provided by the somatosensory system. Herein, a method is reported for creating soft somatosensitive actuators (SSAs) via embedded 3D printing, which are innervated with multiple conductive features that simultaneously enable haptic, proprioceptive, and thermoceptive sensing. This novel manufacturing approach enables the seamless integration of multiple ionically conductive and fluidic features within elastomeric matrices to produce SSAs with the desired bioinspired sensing and actuation capabilities. Each printed sensor is composed of an ionically conductive gel that exhibits both long‐term stability and hysteresis‐free performance. As an exemplar, multiple SSAs are combined into a soft robotic gripper that provides proprioceptive and haptic feedback via embedded curvature, inflation, and contact sensors, including deep and fine touch contact sensors. The multimaterial manufacturing platform enables complex sensing motifs to be easily integrated into soft actuating systems, which is a necessary step toward closed‐loop feedback control of soft robots, machines, and haptic devices.
Functional Genomics Approach Identifies Novel Signaling Regulators of TGFα Ectodomain Shedding

Ectodomain shedding of cell-surface precursor proteins by metalloproteases generates important cellular signaling molecules. Of importance for disease is the release of ligands that activate the EGFR, such as TGFα, which is mostly carried out by ADAM17 [a member of the A-disintegrin and metalloprotease (ADAM) domain family]. EGFR ligand shedding has been linked to many diseases, in particular cancer development, growth and metastasis, as well as resistance to cancer therapeutics. Excessive EGFR ligand release can outcompete therapeutic EGFR inhibition or the inhibition of other growth factor pathways by providing bypass signaling via EGFR activation. Drugging metalloproteases directly have failed clinically because it indiscriminately affected shedding of numerous substrates. It is therefore essential to identify regulators for EGFR ligand cleavage. Here, integration of a functional shRNA genomic screen, computational network analysis, and dedicated validation tests succeeded in identifying several key signaling pathways as novel regulators of TGFα shedding in cancer cells. Most notably, a cluster of genes with NFκB pathway regulatory functions was found to strongly influence TGFα release, albeit independent of their NFκB regulatory functions. Inflammatory regulators thus also govern cancer cell growth–promoting ectodomain cleavage, lending mechanistic understanding to the well-known connection between inflammation and cancer. Implications: Using genomic screens and network analysis, this study defines targets that regulate ectodomain shedding and suggests new treatment opportunities for EGFR-driven cancers. Mol Cancer Res; 16(1); 147–61. ©2017 AACR.
Estimation of diagnostic accuracy of a combination of continuous biomarkers allowing for conditional dependence between the biomarkers and the imperfect reference‐test

Estimating biomarker‐index accuracy when only imperfect reference‐test information is available is usually performed under the assumption of conditional independence between the biomarker and imperfect reference‐test values. We propose to define a latent normally‐distributed tolerance‐variable underlying the observed dichotomous imperfect reference‐test results. Subsequently, we construct a Bayesian latent‐class model based on the joint multivariate normal distribution of the latent tolerance and biomarker values, conditional on latent true disease status, which allows accounting for conditional dependence. The accuracy of the continuous biomarker‐index is quantified by the AUC of the optimal linear biomarker‐combination. Model performance is evaluated by using a simulation study and two sets of data of Alzheimer's disease patients (one from the memory‐clinic‐based Amsterdam Dementia Cohort and one from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database). Simulation results indicate adequate model performance and bias in estimates of the diagnostic‐accuracy measures when the assumption of conditional independence is used when, in fact, it is incorrect. In the considered case studies, conditional dependence between some of the biomarkers and the imperfect reference‐test is detected. However, making the conditional independence assumption does not lead to any marked differences in the estimates of diagnostic accuracy.
Inverse estimation of soil hydraulic and solute transport parameters from transient field experiments: Heterogeneous soil

While inverse parameter estimation techniques for determining key parameters affecting water flow and solute transport are becoming increasingly common in saturated and unsaturated zone studies, their application to practical problems, such as irrigation, have received relatively little attention. In this article, we used the Levenberg–Marquardt optimization algorithm in combination with the HYDRUS–2D numerical code to estimate soil hydraulic and solute transport parameters of several soil horizons below experimental furrows. Three experiments were carried out, each of the same duration but with different amounts of water and solutes resulting from 6, 10, and 14 cm water depths in the furrows. Two more experiments were performed with the same amounts of applied water and solute and, consequently, for different durations, on furrows with depths of 6 and 10 cm of water. We first used a scaling method to characterize spatial variability in the soil hydraulic properties, and then simultaneously estimated the saturated hydraulic conductivity (Ks) and the longitudinal dispersivity (DL) for the different horizons. Model predictions showed only minor improvements over those previously obtained assuming homogeneous soil profiles. In an effort to improve the predictions, we also carried out a two–step, sequential optimization in which we first estimated the soil hydraulic parameters followed by estimation of the solute transport parameters. This approach allowed us to include additional parameters in the optimization process. A sensitivity analysis was performed to determine the most sensitive hydraulic and solute transport parameters. Soil water contents were found to be most sensitive to the n parameter in van Genuchten’s soil hydraulic model, followed by the saturated water content (.s), while solute concentrations were most affected by . s and DL. For these reasons, we estimated . s and n for the various soil horizons of the sequential optimization process during the first step, and only DL during the second step. Sequential estimation somewhat improved predictions of the cumulative infiltration rates during the first irrigation event. It also significantly improved descriptions of the soil water content, particularly of the upper horizons, as compared to those obtained using simultaneous estimation, whereas deep percolation rates of water did not improve. Solute concentrations in the soil profiles were predicted equally well with both optimization approaches.
Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway.

Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.