Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of multispectral data for rapid assessment of wheat straw residue cover

Crop residues influence near surface soil organic carbon (SOC) content, impact our ability to remotely assess soil properties, and play a role in global carbon budgets. Methods that measure crop residues are laborious, and largely inappropriate for field-scale to regional estimates. The objective of this study was to evaluate high spectral resolution remote sensing (RS) data for rapid quantification of residue cover. In March 2000 and April 2001, residue plots (15 by 15 m) were established in the Coastal Plain and Appalachian Plateau physiographic regions of Alabama. Treatments consisted of five wheat (Triticum aestivum L.) straw cover rates (0, 10, 20, 50, and 80%) replicated three times. Spectral measurements were acquired monthly via a handheld spectroradiometer (350-1050 nm) and per availability via the Airborne Terrestrial Applications Sensor (ATLAS) (400-12 500 nm). Overall, treatment separation was influenced by soil water content and percentage of total organic carbon (TOC) of the residue (degree of decomposition). Results showed that atmospherically corrected visible and near-infrared ATLAS data can differentiate between residue coverages. Similar results were obtained with the handheld spectroradiometer, although treatment differentiation was less consistent. Thermal infrared ATLAS imagery best discriminated among residue treatments due to differing heat capacities between soil and residue. Results from our study suggest airborne thermal infrared (TIR) imagery can be used for crop residue variability assessment within the southeastern USA.
Integrative Structural Brain Network Analysis in Diffusion Tensor Imaging

In diffusion tensor imaging, structural connectivity between brain regions is often measured by the number of white matter fiber tracts connecting them. Other features such as the length of tracts or fractional anisotropy (FA) are also used in measuring the strength of connectivity. In this study, we investigated the effects of incorporating the number of tracts, the tract length and FA-values into the connectivity model. Using various node-degree based graph theory features, the three connectivity models are compared. The methods are applied in characterizing structural networks between normal controls and maltreated children, who experienced maltreatment while living in post-institutional settings before being adopted by families in the US.
Simultaneous Multiple MS Binding Assays Addressing D1 and D2 Dopamine Receptors

MS Binding Assays are a label‐free alternative to radioligand binding assays. They provide basically the same capabilities as the latter, but use a non‐labeled reporter ligand instead of a radioligand. In contrast to radioligand binding assays, MS Binding Assays offer—owing to the selectivity of mass spectrometric detection—the opportunity to monitor the binding of different reporter ligands at different targets simultaneously. The present study shows a proof of concept for this strategy as exemplified for MS Binding Assays selectively addressing D1 and D2 dopamine receptors in a single binding experiment. A highly sensitive, rapid and robust LC–ESI‐MS/MS quantification method capable of quantifying both SCH23390 and raclopride, selectively addressing D1 and D2 receptors, respectively, was established and validated for this purpose. Based thereon, simultaneous saturation and competition experiments with SCH23390 and raclopride in the presence of both D1 and D2 receptors were performed and analyzed by LC–MS/MS within a single chromatographic cycle. The present study thus demonstrates the feasibility of this strategy and the high versatility of MS Binding Assays that appears to surpass that common for conventional radioligand binding assays.
The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant

Cut homeodomain transcription factor CUX2 plays an important role in dendrite branching, spine development, and synapse formation in layer II to III neurons of the cerebral cortex. We identify a recurrent de novo CUX2 p.Glu590Lys as a novel genetic cause for developmental and epileptic encephalopathy (DEE).
Workforce characteristics and interventions associated with high-quality care and support to older people with cancer: a systematic review

Objectives To provide an overview of the evidence base on the effectiveness of workforce interventions for improving the outcomes for older people with cancer, as well as analysing key features of the workforce associated with those improvements. Design Systematic review. Methods Relevant databases were searched for primary research, published in English, reporting on older people and cancer and the outcomes of interventions to improve workforce knowledge, attitudes or skills; involving a change in workforce composition and/or skill mix; and/or requiring significant workforce reconfiguration or new roles. Studies were also sought on associations between the composition and characteristics of the cancer care workforce and older people's outcomes. A narrative synthesis was conducted and supported by tabulation of key study data. Results Studies (n=24) included 4555 patients aged 60+ from targeted cancer screening to end of life care. Interventions were diverse and two-thirds of the studies were assessed as low quality. Only two studies directly targeted workforce knowledge and skills and only two studies addressed the nature of workforce features related to improved outcomes. Interventions focused on discrete groups of older people with specific needs offering guidance or psychological support were more effective than those broadly targeting survival outcomes. Advanced Practice Nursing roles, voluntary support roles and the involvement of geriatric teams provided some evidence of effectiveness. Conclusions An array of workforce interventions focus on improving outcomes for older people with cancer but these are diverse and thinly spread across the cancer journey. Higher quality and larger scale research that focuses on workforce features is now needed to guide developments in this field, and review findings indicate that interventions targeted at specific subgroups of older people with complex needs, and that involve input from advanced practice nurses, geriatric teams and trained volunteers appear most promising.
Deformation field interaction in sequential circular indentation of a strain hardening material

ABSTRACT An experimental study was made to characterise and model the deformation field in sequential circular indentation of a model strain hardening material. Digital image correlation was used to measure the evolving subsurface deformation field in terms of displacement, strain rate and strain as a function of indentation spacing and depth. These measurements were used to validate a finite element model for complementary simulations. The results identify relationships between sequential indentation parameters and overlap of subsurface strain distributions, maximum subsurface strains and indentation loads. Maximum strain and the degree of strain field overlap in the deformed subsurface were maximised when the ratio of indentation spacing (S) to projected indentation contact length (L) was approximately S/L = [1.1, 1.2]. Also discussed are the implications for understanding process-scale considerations for indentation-based mechanical surface treatments, including energy dissipation and relationship of surface coverage measures to subsurface strain overlap. Relative differences in energy expended were found for conditions that produce similar levels of subsurface plastic strain and strain field overlap. Finally, the role of sequential indentation parameters on strain path changes and path reversals in the deformed subsurface is investigated and discussed in the context of heterogeneous mechanics and corresponding effects on subsurface microstructure evolution.
Do they belong to the same class: active learning by querying pairwise label homogeneity

Traditional active learning methods request experts to provide ground truths to the queried instances, which can be expensive in practice. An alternative solution is to ask nonexpert labelers to do such labeling work, which can not tell the definite class labels. In this paper, we propose a new active learning paradigm, in which a nonexpert labeler is only asked "whether a pair of instances belong to the same class". To instantiate the proposed paradigm, we adopt the MinCut algorithm as the base classifier. We first construct a graph based on the pairwise distance of all the labeled and unlabeled instances and then repeatedly update the unlabeled edge weights on the max-flow paths in the graph. Finally, we select an unlabeled subset of nodes with the highest prediction confidence as the labeled data, which are included into the labeled data set to learn a new classifier for the next round of active learning. The experimental results and comparisons, with state-of-the-art methods, demonstrate that our active learning paradigm can result in good performance with nonexpert labelers.
Evaluating UK National Guidance for Screening of Children for Tuberculosis. A Prospective Multicenter Study

Rationale: To identify infected contacts of tuberculosis (TB) cases, the UK National Institute for Health and Care Excellence (NICE) recommended the addition of IFN‐&ggr; release assays (IGRA) to the tuberculin skin test (TST) in its 2006 TB guidelines. Treatment for TB infection was no longer recommended for children who screened TST‐positive but IGRA‐negative. Objectives: We performed a cohort study to evaluate the risk of TB disease in this group. Methods: Children exposed to an infectious case of TB in their household were recruited from 11 pediatric TB clinics. TST and IGRA were performed at baseline, with IGRA repeated at 8 weeks and TST repeated if initially negative. Children were treated according to 2006 NICE guidelines and followed for 24 months. Measurements and Main Results: Of 431 recruited children, 392 completed the study. We diagnosed 48 (12.2%) cases of prevalent TB disease, 105 (26.8%) with TB infection, and 239 (60.9%) without TB infection or disease. Eighteen children aged 2 years and above had a positive TST but persistently negative IGRA. None received TB infection treatment and none developed TB disease. Ninety (26.1%) children qualified for TB infection treatment according to 2006 NICE guidelines. In contrast, 147 (42.7%) children would have qualified under revised NICE guidance, issued in 2016. Conclusions: In this low‐prevalence setting we saw no incident cases of TB disease in children who were TST‐positive but IGRA‐negative and did not receive treatment for TB infection. Following the latest NICE guidance, significantly more children will require medication.
Monitoring the Early Signs of Cognitive Decline in Elderly by Computer Games: An MRI Study

Background It is anticipated that current and future preventive therapies will likely be more effective in the early stages of dementia, when everyday functioning is not affected. Accordingly the early identification of people at risk is particularly important. In most cases, when subjects visit an expert and are examined using neuropsychological tests, the disease has already been developed. Contrary to this cognitive games are played by healthy, well functioning elderly people, subjects who should be monitored for early signs. Further advantages of cognitive games are their accessibility and their cost-effectiveness. Purpose The aim of the investigation was to show that computer games can help to identify those who are at risk. In order to validate games analysis was completed which measured the correlations between results of the 'Find the Pairs' memory game and the volumes of the temporal brain regions previously found to be good predictors of later cognitive decline. Participants and Methods 34 healthy elderly subjects were enrolled in the study. The volume of the cerebral structures was measured by MRI. Cortical reconstruction and volumetric segmentation were performed by Freesurfer. Results There was a correlation between the number of attempts and the time required to complete the memory game and the volume of the entorhinal cortex, the temporal pole, and the hippocampus. There was also a correlation between the results of the Paired Associates Learning (PAL) test and the memory game. Conclusions The results gathered support the initial hypothesis that healthy elderly subjects achieving lower scores in the memory game have increased level of atrophy in the temporal brain structures and showed a decreased performance in the PAL test. Based on these results it can be concluded that memory games may be useful in early screening for cognitive decline.
Folic Acid Supplementation during Pregnancy Induces Sex-Specific Changes in Methylation and Expression of Placental 11β-Hydroxysteroid Dehydrogenase 2 in Rats

In the placenta, 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2) limits fetal glucocorticoid exposure and its inhibition has been associated to low birth weight. Its expression, encoded by the HSD11B2 gene is regulated by DNA methylation. We hypothesized that maternal diets supplemented with folic acid (FA) during pregnancy modify the expression of placental HSD11B2 through gene methylation. Wistar rats were fed with high (8 mg/kg) or normal low (1mg/kg, control) levels of FA during pregnancy. Concentrations of mRNA and protein in placentas were determined by qRT-PCR and Western blot respectively. Methylation in five CpG sites of the placental HSD11B2 promoter (−378 to −275) was analyzed by bacterial cloning and subsequent sequencing. In the FA-supplemented group, mRNA and protein levels of 11β-HSD2 decreased by 58% and increased by 89%, respectively, only in placentas attached to males. In controls, most CpG sites were not methylated except for the CpG2 site which was 80% methylated. CpG2 methylation level increased under the FA treatment; however, only in placentas attached to females was this increase significant (113%). This change was not related to HSD11B2 expression. Fetal weight of females from FA- supplemented mothers was 6% higher than females from control mothers. In conclusion, this is the first study reporting that FA over supplementation during pregnancy modifies the placental HSD11B2 gene expression and methylation in a sex-dependent manner, suggesting that maternal diets with high content of FA can induce early sex-specific responses, which may lead to long-term consequences for the offspring.
Automated Segmentation of Epithelial Tissue Using Cycle-Consistent Generative Adversarial Networks

A central problem in biomedical imaging is the automated segmentation of images for further quantitative analysis. Recently, fully convolutional neural networks, such as the U-Net, were applied successfully in a variety of segmentation tasks. A downside of this approach is the requirement for a large amount of well-prepared training samples, consisting of image - ground truth mask pairs. Since training data must be created by hand for each experiment, this task can be very costly and time-consuming. Here, we present a segmentation method based on cycle consistent generative adversarial networks, which can be trained even in absence of prepared image - mask pairs. We show that it successfully performs image segmentation tasks on samples with substantial defects and even generalizes well to different tissue types.
An examination of the perceived impact of a continuing interprofessional education experience on opiate prescribing practices

ABSTRACT Chronic pain is increasingly recognized as a public health problem. We assessed the effectiveness of a multi-modal, interprofessional educational approach aimed at empowering healthcare professionals to make deliberative changes, especially in opiate prescribing practices. Education activities included enduring webcasts, regional interprofessional roundtable events, and state-level conference presentations within targeted Kentucky and West Virginia regions of the United States. Over 1,000 participants accessed the various activities. For the live events, the largest groups reached included nurses (38.1%), nurse practitioners (31.2%), and physicians (22.1%). In addition to our reach, higher levels of educational effectiveness were measured, specifically, learner’s intentions to change practice patterns, confidence in meeting patient’s needs, and knowledge of pain management guidelines. The majority of the conference (58%) and roundtable (69%) participants stated they intend to make a practice change in one or more areas of chronic pain patient management in post-event evaluation. Differences in pre- and post-activity responses on the measures of confidence and knowledge, with additional comparison to a control population who were not in attendance, were analyzed using non-parametric tests of significance. While neither activity produced significant changes in confidence from pre-activity, participants were more confident post-activity than their control group peers. There were significant changes in knowledge for both live event and webcast participants. Impactful chronic pain continuing the education that emphasizes collaborative care is greatly needed; these results show that the approaches taken here can impact learner’s knowledge and confidence, and hold potential for creating change in how opioid prescribing is managed.
Non-Negative Spherical Deconvolution for Fiber Orientation Distribution Estimation

Introduction: In diffusion MRI, Spherical Deconvolution (SD) was proposed to estimate the fiber Orientation Distribution Function (fODF) based on spherical deconvolution using a single-fiber response function [1,2]. The peaks or the shape of fODFs can be used to infer local fiber directions. Constrained Spherical Deconvolution (CSD) [1], which takes into consideration the non-negative of the fODF, is the most widely used method among SD variants. Although CSD is capable of accurately determining fiber directions, it is susceptible to false positive peaks especially in the regions with lowanisotropy. This is a common drawback of all existing SD-based methods. Moreover, in practice the fODF estimated using CSD still has significant negative values. We propose a method called Non-Negative Spherical Deconvolution (NNSD) to solve the above two problems. Based on a Riemannian framework of ODFs [3] and Square Root Parameterized Estimation for non-negative definite Ensemble Average Propagator [4], NNSD is formulated such that the non-negativity of the fODF is guaranteed with largely reduced false positive peaks.
In vitro activity of a combination of bacteriophages and antimicrobial plant extracts

The continuing threat of antimicrobial resistance presents a considerable challenge to researchers to develop novel strategies ensuring that bacterial infections remain treatable. Many plant extracts have been shown to have antibacterial properties and could potentially be combined with other antibacterial agents to create more effective formulations. In this study, the antibacterial activity of three plant extracts and virulent bacteriophages have been assessed as individual components and in combination. When assessed with a modified suspension test, these plant extracts also exhibit antiviral activity at bacterial inhibitory concentrations. Hence, to investigate any potential additive effects between the extracts and virulent phages, the extracts were tested at subantiviral concentrations. Phages alone and in combination with plant extracts significantly reduced (P < 0·05) the bacterial concentration compared to untreated and extract treated controls up to 6 h (2–3log10), but this reduction did not extend to 24 h. In most cases, the phage and extract combinations did not significantly reduce bacterial content compared to phages alone. Additionally, there was little impact on the ability of the phages to reproduce within their bacterial hosts. To our knowledge, this study represents the first of its kind, in which antimicrobial plant extracts have been combined with virulent phages and has highlighted the necessity for plant extracts to be functionally characterized prior to the design of combinatorial therapies.
Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh in Bacillus subtilis

Utilization of energy-rich carbon sources such as glucose is fundamental to the evolutionary success of bacteria. Glucose can be catabolized via glycolysis for feeding the intermediary metabolism. The methylglyoxal synthase MgsA produces methylglyoxal from the glycolytic intermediate dihydroxyacetone phosphate. Methylglyoxal is toxic, requiring stringent regulation of MgsA activity. In the Gram-positive bacterium Bacillus subtilis, an interaction with the phosphoprotein Crh controls MgsA activity. In the absence of preferred carbon sources, Crh is present in the nonphosphorylated state and binds to and thereby inhibits MgsA. To better understand the mechanism of regulation of MgsA, here we performed biochemical and structural analyses of B. subtilis MgsA and of its interaction with Crh. Our results indicated that MgsA forms a hexamer (i.e. a trimer of dimers) in the crystal structure, whereas it seems to exist in an equilibrium between a dimer and hexamer in solution. In the hexamer, two alternative dimers could be distinguished, but only one appeared to prevail in solution. Further analysis strongly suggested that the hexamer is the biologically active form. In vitro cross-linking studies revealed that Crh interacts with the N-terminal helices of MgsA and that the Crh–MgsA binding inactivates MgsA by distorting and thereby blocking its active site. In summary, our results indicate that dimeric and hexameric MgsA species exist in an equilibrium in solution, that the hexameric species is the active form, and that binding to Crh deforms and blocks the active site in MgsA.
The Max Clinic: Medical Care Designed to Engage the Hardest‐to‐Reach Persons Living with HIV in Seattle and King County, Washington

Abstract The Max Clinic in Seattle, Washington is designed to engage patients who have extensive barriers to HIV care. In this article, we describe the clinic’s evolution and outcomes of patients enrolled in the first 2 years. The clinic is a high‐intensity, low‐threshold, incentivized care model that includes walk‐in access to primary care in a Sexually Transmitted Disease Clinic. Patients who have failed to engage in care and achieve viral suppression with lower intensity support are referred by clinicians, case managers, and the health department Data to Care program. The clinic offers food vouchers, cash incentives, no‐cost bus passes, and cell phones, as well as intensive case management with cross‐agency coordinated care. The primary evaluation outcome was the percentage of patients who achieved viral suppression (HIV RNA <200 copies/mL) at least once after enrollment. Secondary outcomes were continuous viral suppression (≥2 suppressed results in a row ≥60 days apart) and engagement in care (≥2 completed medical visits ≥60 days apart). During January 2015‐December 2016, 263 patients were referred; 170 (65%) were eligible, and 95 (56% of eligible) were enrolled. Most patients used illicit drugs or hazardous levels of alcohol (86%) and had diagnosed psychiatric illness (72%) and unstable housing (65%). During the year after enrollment, 90 (95%) patients engaged in care. As of the end of 2016, 76 (80%) had achieved viral suppression, and 54% had continuous viral suppression. The Max Clinic successfully treated HIV in high‐need patients and, to date, has been sustainable through a combination of federal, state, and local funding.