Miracle-dz/UniFAR-FTUs huggingface dataset:
OAI-PMH Harvested Collections and User Engagement

ABSTRACT Discovery tools are used in libraries to bring together books, articles, and other resources. Research has focused on user and librarian evaluation of these tools, but there are few evaluations of non-book and non-article sources. Discovery tools can also include metadata for local collections harvested through the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). Creating these harvests can be time consuming for staff, so it is important for libraries to understand if and how patrons use these records. The University of Nebraska-Lincoln Libraries (UNL Libraries) harvests metadata from local collections into the Encore discovery tool. A study was conducted to analyze patron use of OAI-harvested records. This study analyzed usage data for harvested collections obtained from different discovery sources and referrals through Encore. Google Analytics was used to evaluate searcher behavior differences between content referred through Encore and other referrals. Although discovery through Encore did not result in high numbers of traffic, there is evidence that patrons who discover records through Encore take more time looking through records than patrons using other discovery methods. This increase in time is a measure of engagement and may be reason enough for libraries to consider adding OAI-harvested collections to their discovery tool.
Generalized Parking Occupancy Analysis Based on Dilated Convolutional Neural Network †

The importance of vacant parking space detection systems is increasing dramatically as the avoidance of traffic congestion and the time-consuming process of searching an empty parking space is a crucial problem for drivers in urban centers. However, the existing parking space occupancy detection systems are either hardware expensive or not well-generalized for varying images captured from different camera views. As a solution, we take advantage of an affordable visual detection method that is made possible by the fact that camera monitoring is already available in the majority of parking areas. However, the current problem is a challenging vision task because of outdoor lighting variation, perspective distortion, occlusions, different camera viewpoints, and the changes due to the various seasons of the year. To overcome these obstacles, we propose an approach based on Dilated Convolutional Neural Network specifically designed for detecting parking space occupancy in a parking lot, given only an image of a single parking spot as input. To evaluate our method and allow its comparison with previous strategies, we trained and tested it on well-known publicly available datasets, PKLot and CNRPark + EXT. In these datasets, the parking lot images are already labeled, and therefore, we did not need to label them manually. The proposed method shows more reliability than prior works especially when we test it on a completely different subset of images. Considering that in previous studies the performance of the methods was compared with well-known architecture—AlexNet, which shows a highly promising achievement, we also assessed our model in comparison with AlexNet. Our investigations showed that, in comparison with previous approaches, for the task of classifying given parking spaces as vacant or occupied, the proposed approach is more robust, stable, and well-generalized for unseen images captured from completely different camera viewpoints, which has strong indications that it would generalize effectively to other parking lots.
The Use of Droplet Digital PCR to Quantify HIV-1 Replication in the Colorectal Explant Model.

Ex vivo explant models are used to characterize in vitro efficacy of preexposure prophylaxis (PrEP) agents. Tissue is challenged with virus in culture and HIV-1 p24 levels are quantified with enzyme-linked immunosorbent assay (ELISA) on supernatants collected throughout a 14-21-day incubation. Due to the narrow dynamic range of HIV-1 p24 kits, we evaluated whether droplet digital PCR (ddPCR) provides an alternative method to quantify HIV-1 replication in supernatant samples. We used samples from the MWRI-01 study, which evaluated the pharmacokinetic/pharmacodynamic profile of long-acting rilpivirine using the explant model (McGowan et al. Lancet HIV 2016). HIV-1 pol RNA was measured with ddPCR, either directly with a one-step method or reverse transcribed to cDNA before ddPCR (two-step method) on supernatants from the MWRI-01 study. Previously analyzed HIV-1 p24 antigen levels (Alliance; Perkin-Elmer) were available for comparison purposes. Both ddPCR methods strongly correlated with HIV-1 p24 and displayed similar patterns of HIV-1 suppression before and after rilpivirine. Compared to the p24 ELISA, two-step and one-step ddPCR reduced the amount of hands-on time by approximately one-half and two-thirds, respectively. ddPCR also required less sample and based on p24 versus ddPCR correlation, could potentially reduce the explant culture time from 14 to 10 days (r2 = 0.78, p < .001) due to the increased sensitivity of ddPCR. We demonstrate that ddPCR is a suitable alternative to HIV-1 p24 ELISA to quantify HIV-1 infection in the explant model and has the potential to decrease explant culture time.
Ecological restoration of eroded karst utilizing pioneer moss and vascular plant species with selection based on vegetation diversity and underlying soil chemistry

Abstract Soil erosion in karst areas not only destroys the natural environment but also accelerates the decline in land productivity together with the associated increase in poverty for local communities. There are no simple or straightforward answers to controlling soil erosion on karst. Such erosion has become a serious problem in China. This study addresses both the diversity of vegetation (mosses, herbs, shrubs and trees) on karst and the underlying soil chemical characteristics, in order to provide a scientific basis by which suitable plant species can be selected for recovery and restoration of karst degraded by soil erosion. Vegetation diversity and soil chemistry were assessed in areas with five different grades of soil erosion in Guiyang Karst Park, Guizhou, China. Mosses are more tolerant than vascular plants of soil erosion and associated environmental degradation of karst and the order of species diversity was: mosses > herbs > shrubs > trees. Mosses were found to play a major role in ecological restoration of microhabitats on karst. Soil microbial biomass carbon was found to be significantly higher in soil under mosses than in bare soil associated with other plant categories. Mosses were more effective in converting unavailable potassium to available potassium. Vascular plants were found to have a positive effect on total nitrogen fixation and the availability of phosphorus in the soil. Increasing soil degradation was associated with lower levels of total Nitrogen in soil underlying mosses than in soil underlying vascular plants. Thus, based on their different but complementary contributions to soil chemistry, mosses and vascular plants in combination can provide the most practical outcome for the repair and restoration of areas of karst affected by soil erosion. The combination of the moss species, Homomallium plagiangium, Cyrto-hypnum pygmaeuman and Brachythecium perminusculum, the herbs Veronica arvensis and Youngia japonica, and the tree Prunus salicina, are recommended as suitable pioneer plant species to cultivate for use in restoration of regions of karstic soil erosion.
Novel Immune Features of the Systemic Inflammation Associated with Primary Hypercholesterolemia: Changes in Cytokine/Chemokine Profile, Increased Platelet and Leukocyte Activation

Primary hypercholesterolemia (PH) is associated with a low grade systemic inflammation that is likely the main driver of premature atherosclerosis. Accordingly, we characterized the immune cell behaviour in PH and its potential consequences. Whole blood from 22 PH patients and 21 age-matched controls was analysed by flow cytometry to determine the percentage of leukocyte immunophenotypes, activation, and platelet-leukocyte aggregates. Plasma markers were determined by Enzyme-Linked ImmunoSorbent Assay (ELISA). The adhesion of platelet-leukocyte aggregates to tumor necrosis factor-α (TNFα)-stimulated arterial endothelium was investigated using the dynamic model of the parallel-plate flow chamber. PH patients presented greater percentage of Mon 3 monocytes, Th2 and Th17 lymphocytes, activated platelets, and leukocytes than controls. The higher percentages of circulating platelet-neutrophil, monocyte and lymphocyte aggregates in patients caused increased platelet-leukocyte adhesion to dysfunctional arterial endothelium. Circulating CXCL8, CCL2, CX₃CL1, and IL-6 levels positively correlated with key lipid features of PH, whereas negative correlations were found for IL-4 and IL-10. We provide the first evidence that increased platelet and leukocyte activation leads to elevated platelet-leukocyte aggregates in PH and augmented arterial leukocyte adhesiveness, a key event in atherogenesis. Accordingly, modulation of immune system behavior might be a powerful target in the control of further cardiovascular disease in PH.
Patterns of decline in naming and semantic knowledge in primary progressive aphasia

ABSTRACT Background: Individuals with primary progressive aphasia (PPA) and their caregivers want to know what to expect so that they can plan support appropriately. The ability to predict decline in naming and semantic knowledge, and advise individuals with PPA and their caregivers regarding future planning, would be invaluable clinically. Aims: The aims of this study were to investigate patterns of decline in naming and semantic knowledge in each of the clinical variants of PPA (logopenic variant PPA, lvPPA; nonfluent agrammatic PPA, nfaPPA; and semantic variant PPA, svPPA) and to examine the effects of other variables on rate of decline. We hypothesized that speech-language rehabilitation, higher education, and higher baseline test scores would be associated with slower decline, and older age with faster decline. Methods and Procedures: A total of 94 participants with PPA underwent language testing, including 36 participants with lvPPA, 31 participants with nfaPPA, and 27 participants with svPPA. All participant groups were similar in age and education. We focused on decline on three tests: the short form of the Boston Naming Test (BNT), the Hopkins Assessment of Naming Actions (HANA), and the short form of the Pyramids and Palm Trees Test (PPTT). Outcome and Results: Across language tests, the most precipitous rates of decline (loss of points per month) occurred in nfaPPA, followed by svPPA, then lvPPA. Female sex, longer symptom duration, higher baseline test score, and speech-language rehabilitation were associated with slower decline. Conclusions: PPA variants were distinguishable by rapidity of decline, with nfaPPA having the most precipitous decline. As hypothesized, higher baseline test scores and speech-language rehabilitation were associated with slower decline. Surprisingly, age and education were not important prognostically for individuals in this study. Further study of prognostically-relevant variables in PPA is indicated in this population.
Is the Compression of Morbidity a Universal Phenomenon

Abstract Recent reviews of national health trends show conflicting results. It is clear today that the various health dimensions follow different trends over time. For instance an expansion of morbidity may accompany a compression of disability. What do we measure when we observe a decline in disability? Is the elderly population intrinsically healthier or are individuals more independent and less helped by children, using more technical devices in a more favorable environment? The recent OECD study, reviewing trends in ADL disability at age 65 and over in 12 OECD countries during the 1990s, demonstrates that there is clear evidence of a decline in disability among elderly people in only five of the 12 countries studied: Denmark, Finland, Italy, the Netherlands and the United States. Three countries (Belgium, Japan and Sweden) report an increasing rate and two countries (Australia and Canada) a stable rate. In France and the United Kingdom, different surveys show different trends in ADL disability (OECD, 2007). These results suggest that a decline in ADL disability may be less universal than expected. More importantly, the OECD study shows that ADL disability at age 65 and over ranges widely from a low 7.1 percent in the Netherlands (HIS) to a high of 18 percent in the United Kingdom (GHS survey). This paper reviews available evidence about the compression of morbidity and the disability decline and discusses the context in which they occur: initial level of disability, initial value of life expectancy and trend in life expectancy.
Perceptions of caring behaviours: A comparison of surgical oncology nurses and patients.

AIMS AND OBJECTIVES The purpose of this article was to compare surgical oncology nurses caring behaviours to perceptions of their surgical oncology inpatients and determine internal consistency of the CAT-Nurse. BACKGROUND Nursing practice at the H. Lee Moffitt Cancer Center & Research Institute in Tampa, FL is guided by Duffy's Quality-Caring Model© . No study using Duffy's model for both oncology nurses and patients has been found. DESIGN A descriptive correlation design was used adhering to the STROBE guidelines. Data were collected using CAT-Nurse and compared to data from a previous study using CAT (version V). METHODS Item responses were compared between nurses and patients using t tests. RESULTS Patients scored higher on perceptions of caring behaviours. Mutual problem solving was an area for improvement. The CAT-Nurse demonstrated internal consistency reliability. CONCLUSION Results from this study can make nurses more aware of the caring perceptions that are not as strong as others, and therefore may have the ability to promote transformation. RELEVANCE TO CLINICAL PRACTICE The results can serve as foundational knowledge for action plans aimed at increasing nurse comfort addressing lower scoring caring behaviours that would then result in improving patient perceptions which could be linked to patient satisfaction and reimbursement.
Altered global brain network topology as a trait marker in patients with anorexia nervosa

Abstract Background Resting state functional magnetic resonance imaging studies have identified functional connectivity patterns associated with acute undernutrition in anorexia nervosa (AN), but few have investigated recovered patients. Thus, a trait connectivity profile characteristic of the disorder remains elusive. Using state-of-the-art graph–theoretic methods in acute AN, the authors previously found abnormal global brain network architecture, possibly driven by local network alterations. To disentangle trait from starvation effects, the present study examines network organization in recovered patients. Methods Graph–theoretic metrics were used to assess resting-state network properties in a large sample of female patients recovered from AN (recAN, n = 55) compared with pairwise age-matched healthy controls (HC, n = 55). Results Indicative of an altered global network structure, recAN showed increased assortativity and reduced global clustering as well as small-worldness compared with HC, while no group differences at an intermediate or local network level were evident. However, using support-vector classifier on local metrics, recAN and HC could be separated with an accuracy of 70.4%. Conclusions This pattern of results suggests that long-term recovered patients have an aberrant global brain network configuration, similar to acutely underweight patients. While the finding of increased assortativity may represent a trait marker of AN, the remaining findings could be seen as a scar following prolonged undernutrition.
Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network

Abstract Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
Assessing Patient Perspectives on Receiving Bad News: A Survey of 1337 Patients With Life-Changing Diagnoses

Abstract Background: Guidelines for breaking bad news are largely directed at and validated in oncology patients, based on expert opinion, and neglect those with other diagnoses. We sought to determine whether existing guidelines for breaking bad news, particularly SPIKES, are consistent with patient preferences across patient populations. Methods: Patients from an online community responded to 5 open-ended and 11 Likert-scale questions identifying their preferences in having bad news delivered. Patient participants received a diagnosis of cancer, lupus, amyotrophic lateral sclerosis, multiple sclerosis, HIV/AIDS, or Parkinson’s disease. Additionally, we surveyed all 14 English-curriculum Canadian medical schools regarding resources used to teach breaking bad news. Results: Ten of 12 responding schools used the SPIKES model. Preferences of 1337 patients were consistent with the recommendations of SPIKES. There was one exception: Most patients disagree that empathetic physical touch is important and some described apprehension. Responses were consistent across disease states. Content analysis of 220 open-ended patient responses revealed 16 patient-important themes. Themes were largely addressed by the SPIKES guidelines, but five were not: ensuring timely follow-up is planned; offering informational sheets about the diagnosis; offering contact information of support organizations, with some patients preferring patient support groups while others preferring counselors; and conveying a sense of determination to aid the patient through the diagnosis. The four most patient-important components of SPIKES were physicians conveying empathy, taking their time, explaining the diagnosis and its implications, and asking the patient if they understand. Conclusion: SPIKES is the most commonly taught framework for breaking bad news in Canadian medical schools. This is the first work to demonstrate that the existing guidelines in breaking bad news such as SPIKES largely reflect the perspectives of many patient groups, as assessed by quantitative and qualitative measures. We highlight the most important components of SPIKES to patients and identify five additional suggestions to aid clinicians in breaking bad news.
Association between tamoxifen use and acute myocardial infarction in women with breast cancer

Abstract The relationship between tamoxifen use and acute myocardial infarction in women with breast cancer remains uncertain. The goal of the study was to assess whether tamoxifen use could be associated with acute myocardial infarction in women with breast cancer in Taiwan. A population-based case–control study was conducted to analyze the database of the Taiwan National Health Insurance Program. Totally, 489 women with breast cancer aged 20 to 84 years having the first episode of acute myocardial infarction from 2000 to 2011 were found as the cases. In addition, 1718 women with breast cancer aged 20 to 84 years without any type of ischemic heart disease were selected as the matched controls. Ever use of tamoxifen was classified as the studied women who had at least a prescription for tamoxifen before the index date. Never use of tamoxifen was classified as the studied women who never had a prescription for tamoxifen before the index date. We used the multivariable logistic regression model to estimate the odds ratio (OR) and 95% confidence interval (CI) for acute myocardial infarction associated with tamoxifen use. In a multivariable-adjusted analysis, women with acute myocardial infarction were 1.71 times more likely to be exposed to tamoxifen than those women without acute myocardial infarction (adjusted OR 1.71, 95% CI 1.38–2.13). The odds of tamoxifen use are 1.71 times higher in women with acute myocardial infarction versus those women without acute myocardial infarction in Taiwan.
STAT3‐induced upregulation of lncRNA ABHD11‐AS1 promotes tumour progression in papillary thyroid carcinoma by regulating miR‐1301‐3p/STAT3 axis and PI3K/AKT signalling pathway

Emerging evidences indicated the importance of long non‐coding RNAs (lncRNAs) in the tumorigenesis and deterioration of malignant tumours. To our knowledge, the study about lncRNAs in papillary thyroid carcinoma (PTC) is still inadequate. ABHD11‐AS1 was highly expressed in the PTC samples of The Cancer Genome Atlas database. This study focused on the biological function and mechanism of lncRNA ABHD11‐AS1 in PTC.
Tri-Hydroxy-Triacylglycerol Is Efficiently Produced by Position-Specific Castor Acyltransferases1[OPEN]

Efficient incorporation of hydroxy-fatty acid into triacylglycerol requires multiple castor acyltransferases. Understanding the biochemistry of triacylglycerol (TAG) assembly is critical in tailoring seed oils to produce high-value products. Hydroxy-fatty acid (HFA) is one such valuable modified fatty acid, which can be produced at low levels in Arabidopsis (Arabidopsis thaliana) seed through transgenic expression of the castor (Ricinus communis) hydroxylase. The resulting plants have low seed oil content and poor seedling establishment, indicating that Arabidopsis lacks efficient metabolic networks for biosynthesis and catabolism of hydroxy-containing TAG. To improve utilization of such substrates, we expressed three castor acyltransferase enzymes that incorporate HFA at each stereochemical position during TAG synthesis. This produced abundant tri-HFA TAG and concentrated 44% of seed HFA moieties into this one TAG species. Ricinoleic acid was more abundant than any other fatty acid in these seeds, which had 3-fold more HFA by weight than that in seeds following simple hydroxylase expression, the highest yet measured in a nonnative plant. Efficient utilization of hydroxy-containing lipid substrates increased the rate of TAG synthesis 2-fold, leading to complete relief of the low-oil phenotype. Partition of HFA into specific TAG molecules increased the storage lipid available for mobilization during seedling development, resulting in a 1.9-fold increase in seedling establishment. Expression of a complete acyltransferase pathway to efficiently process HFA establishes a benchmark in the quest to successfully produce modified oils in plants.