Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus

The Kaposi sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi sarcoma (KS), the most common HIV/AIDS-associated tumor worldwide. Involvement of the oral cavity portends a poor prognosis for patients with KS, but the mechanisms for KSHV regulation of the oral tumor microenvironment are largely unknown. Infiltrating fibroblasts are found within KS lesions, and KSHV can establish latent infection within human primary fibroblasts in vitro and in vivo, but contributions for KSHV-infected fibroblasts to the KS microenvironment have not been previously characterized. In the present study, we used Illumina microarray to determine global gene expression changes in KSHV-infected primary human oral fibroblasts (PDLF and HGF). Among significantly altered candidates, we found that a series of interferon-induced genes were strongly up-regulated in these KSHV-infected oral cells. Interestingly, some of these genes in particular ISG15 and ISG20 are required for maintenance of virus latency through regulation of specific KSHV microRNAs. Our data indicate that oral fibroblasts may represent one important host cellular defense component against viral infection, as well as acting as a reservoir for herpesvirus lifelong infection in the oral cavity.
Refactoring Fat Interfaces Using a Genetic Algorithm

Recent studies have shown that the violation of the Interface Segregation Principle (ISP) is critical for maintaining and evolving software systems. Fat interfaces (i.e., interfaces violating the ISP) change more frequently and degrade the quality of the components coupled to them. According to the ISP the interfaces' design should force no client to depend on methods it does not invoke. Fat interfaces should be split into smaller interfaces exposing only the methods invoked by groups of clients. However, applying the ISP is a challenging task when fat interfaces are invoked differently by many clients. In this paper, we formulate the problem of applying the ISP as a multi-objective clustering problem and we propose a genetic algorithm to solve it. We evaluate the capability of the proposed genetic algorithm with 42,318 public Java APIs whose clients' usage has been mined from the Maven repository. The results of this study show that the genetic algorithm outperforms other search based approaches (i.e., random and simulated annealing approaches) in splitting the APIs according to the ISP.
Ieee Transactions on Visualization and Computer Graphics 1 Importance-driven Feature Enhancement in Volume Visualization

— This paper presents importance-driven feature enhancement as a technique for the automatic generation of cutaway and ghosted views out of volumetric data. The presented focus+context approach removes or suppresses less important parts of a scene to reveal more important underlying information. However, less important parts are fully visible in those regions, where important visual information is not lost, i.e., more relevant features are not occluded. Features within the volumetric data are first classified according to a new dimension denoted as object importance. This property determines which structures should be readily discernible and which structures are less important. Next, for each feature various representations (levels of sparseness) from a dense to a sparse depiction are defined. Levels of sparseness define a spectrum of optical properties or rendering styles. The resulting image is generated by ray-casting and combining the intersected features proportional to their importance (importance compositing). The paper includes an extended discussion on several possible schemes for levels of sparseness specification. Furthermore different approaches to importance compositing are treated.
Evaluation of the Effect of Combined Use of Organic and Inorganic Fertilizers on Bulb Onion (Allium Cepa L.) Yields and Forecast Potential Onion Yields Under Climate Change Scenarios in West Ugenya Sub-county, Kenya

Low yields due to declining soil fertility continues to be a major constraint to onion production in Kenya necessitating imports to meet market demand for the increasing population. A field experiment was carried out for two seasons in Ukwala division of West Ugenya Sub-County during the 2015 and 2016 short and long rains seasons, respectively to evaluate the effect of combining organic and inorganic fertilizers on the soil nutrient status and yield of bulb onion (Allium cepa L.). The experiment was a Randomized Complete Block Design (RCBD). Treatments, each replicated three times were: T1 (5 Mega grams ha -1 cattle manure), T2 (46 kg P ha -1 x 26 kg N ha -1 inorganic fertilizers), T3 (unfertilized control), and T4 (half T1 x half T2) were evaluated. Data from T1 and T4 at the end of the two cropping seasons showed significantly (P≤0.05) higher mean yields compared to the control. Highest bulb yield (25.2 Mg ha -1 ) and widest bulb diameter (5.1 cm) were recorded in T4 compared to the other treatments. T4 also had significantly (P≤0.05) higher soil available P and total organic carbon at the end of season II compared to the other treatments in the same season. Seasonal variation in rainfall amount led to considerably lower yields in the short rains (season II), compared to long rains (season I). Observed data concluded that onion yields could be significantly increased by combining organic and inorganic fertilizers at the rates of 2.5 Mgha -1 cattle manure containing 2% N, 0.6% P and 2.3% K, with 23 kg P ha -1 x 13 kg N ha -1 inorganic fertilizers.
Complications of selective laser trabeculoplasty: a review

Selective laser trabeculoplasty is a laser treatment to treat glaucoma. It was initially indicated for open-angle glaucoma but has been proven to be efficacious for various types of glaucoma. This review article summarizes the few rare complications that can be seen with selective laser trabeculoplasty. It also makes recommendations on how to avoid these problems and how to treat patients when these rare complications arise.
Complexity Analysis of Joint Subcarrier and Power Allocation for the Cellular Downlink OFDMA System

Consider the cellular downlink orthogonal frequency division multiple access (OFDMA) system where a single transmitter transmits signals to multiple receivers on multiple discrete subcarriers. To adapt fast channel fluctuations, the transmitter should be able to dynamically allocate subcarrier and power resources. Assuming perfect channel knowledge, we formulate the joint subcarrier and power allocation problem as two optimization problems: the first is the one of minimizing the total transmission power subject to quality of service constraints, and the second is the one of maximizing a system utility function subject to power budget constraints. In this letter, we show that both the aforementioned formulations of the joint subcarrier and power allocation problem are generally NP-hard. We also identify several subclasses of the problems, which are polynomial time solvable.
Comparison of Glibenclamide and Insulin on Neonatal Outcomes in Pregnant Women with Gestational Diabetes

Background: Untreated or poorly controlled gestational diabetes can cause serious complications for mother and newborn. Glibenclamide is rarely used in treating mothers with this disease. This study aimed at comparing the effect of glibenclamide and insulin on neonatal outcomes in women with gestational diabetes mellitus. Methods: In this randomized controlled clinical trial, 249 pregnant women aged 18–45 years within the 11th–33rd weeks of gestation with gestational diabetes, single fetus pregnancy, and in need of hyperglycemia treatment were entered and grouped randomly as either glibenclamide or insulin. In the insulin group (n = 129), insulin was administered with an initial dose of 0.2 IU/kg subcutaneously twice per day, whereas in the glibenclamide group (n = 120), 1.25 mg oral glibenclamide was administered once daily and increased if needed. Results: The results showed no significant difference in means age, gestational age, and body mass index between women in the two groups. In addition, there were no significant differences in the frequency of neonatal hypoglycemia, anomaly, hyperbilirubinemia, admission in Neonatal Intensive Care Unit (NICU), and neonatal respiratory distress between two groups. Macrosomia was lower in the glibenclamide group than the insulin group (3.3% vs. 13.2%, respectively, P = 0.005). Regression logistics model results showed that the type of treatment (odds ratio [OR]: 4.62; confidence interval [CI]: 1.45–14.02; P = 0.01) and gestational age at delivery (OR: 1.41; CI: 1.04–1.74; P = 0.01) were as predictor factors of macrosomia. Conclusions: The results of this study revealed that glibenclamide is able to reduce the risk of fetal macrosomia without increasing neonatal anomalies, jaundice, hypocalcemia, infant respiratory distress, and NICU admission.
Amnestic Mild Cognitive Impairment: Structural MR Imaging Findings Predictive of Conversion to Alzheimer Disease

BACKGROUND AND PURPOSE: Mild cognitive impairment (MCI) is considered by many to be a prodromal phase of Alzheimer disease (AD). We used voxel-based morphometry (VBM) to find out whether structural differences on MR imaging could offer insight into the development of clinical AD in patients with amnestic MCI at 3-year follow-up. MATERIALS AND METHODS: Twenty-four amnestic patients with MCI were included. After 3 years, 46% had progressed to AD (n = 11; age, 72.7 ± 4.8 years; women/men, 8/3). For 13 patients (age, 72.4 ± 8.6 years; women/men, 10/3), the diagnosis remained MCI. Baseline MR imaging at 1.5T included a coronal heavily T1-weighted 3D gradient-echo sequence. Localized gray matter differences were assessed with VBM. RESULTS: The converters had less gray matter volume in medial (including the hippocampus) and lateral temporal lobe, parietal lobe, and lateral temporal lobe structures. After correction for age, sex, total gray matter volume, and neuropsychological evaluation, left-sided atrophy remained statistically significant. Specifically, converters had more left parietal atrophy (angular gyrus and inferior parietal lobule) and left lateral temporal lobe atrophy (superior and middle temporal gyrus) than stable patients with MCI. CONCLUSION: By studying 2 MCI populations, converters versus nonconverters, we found atrophy beyond the medial temporal lobe to be characteristic of patients with MCI who will progress to dementia. Atrophy of structures such as the left lateral temporal lobe and left parietal cortex may independently predict conversion.
A non-local cost aggregation method for stereo matching

Matching cost aggregation is one of the oldest and still popular methods for stereo correspondence. While effective and efficient, cost aggregation methods typically aggregate the matching cost by summing/averaging over a user-specified, local support region. This is obviously only locally-optimal, and the computational complexity of the full-kernel implementation usually depends on the region size. In this paper, the cost aggregation problem is re-examined and a non-local solution is proposed. The matching cost values are aggregated adaptively based on pixel similarity on a tree structure derived from the stereo image pair to preserve depth edges. The nodes of this tree are all the image pixels, and the edges are all the edges between the nearest neighboring pixels. The similarity between any two pixels is decided by their shortest distance on the tree. The proposed method is non-local as every node receives supports from all other nodes on the tree. As can be expected, the proposed non-local solution outperforms all local cost aggregation methods on the standard (Middlebury) benchmark. Besides, it has great advantage in extremely low computational complexity: only a total of 2 addition/subtraction operations and 3 multiplication operations are required for each pixel at each disparity level. It is very close to the complexity of unnormalized box filtering using integral image which requires 6 addition/subtraction operations. Unnormalized box filter is the fastest local cost aggregation method but blurs across depth edges. The proposed method was tested on a MacBook Air laptop computer with a 1.8 GHz Intel Core i7 CPU and 4 GB memory. The average runtime on the Middlebury data sets is about 90 milliseconds, and is only about 1.25× slower than unnormalized box filter. A non-local disparity refinement method is also proposed based on the non-local cost aggregation method.
Reward Systems and Incentives in a Project Based Organisation Identification of Reward Systems and Incentives influencing Construction Site Managers

Aim – This study sets out to identify and investigate how rewards, reward systems and organisational incentives influence construction site managers in a project based organisation. Method – The research was designed as a case study within one district in Skanska Sweden AB. The main data source in was approximately 10 semi-structured interviews conducted with managers at Skanska. Questions aimed to identify rewards related to the organisational context of the construction site managers. Findings – Construction site manager rewards were identified to stem from the project environment, the company, social relationships, the job position and the individual personal values. Moreover a number of incentives and reward systems affecting the provision of site manager rewards were identified, among which the manager were identified to have the largest impact. Furthermore, results are discussed and related to common problems related in project based organisations. Conclusions – The paper provides insights in how construction site managers perceive their work context from a reward perspective.
Plasma clearance of hemoglobin and haptoglobin in mice and effect of CD163 gene targeting disruption.

AIM In humans, plasma haptoglobin (Hp) and the macrophage receptor CD163 promote a fast scavenging of hemoglobin (Hb). In the present study, we have compared the mouse and human CD163-mediated binding and uptake of Hb and HpHb complex in vitro and characterized the CD163-mediated plasma clearance of Hb in CD163 gene knockout mice and controls. RESULTS Contrary to human Hp, mouse Hp did not promote high-affinity binding to CD163. This difference between mouse and man was evident both by analysis of the binding of purified proteins and by ligand uptake studies in CD163-transfected cells. Plasma clearance studies in mice showed a fast clearance (half-life few minutes) of fluorescently labeled mouse Hb with the highest uptake in the kidney and liver. HPLC analysis of serum showed that the clearance curve exhibited a two-phase decay with a faster clearance of Hb than plasma-formed HpHb. In CD163-deficient mice, the overall clearance of Hb was slightly slower and followed a one-phase decay. INNOVATION AND CONCLUSION In conclusion, mouse Hp does not promote high-affinity binding of mouse Hb to CD163, and noncomplexed mouse Hb has a higher CD163 affinity than human Hb has. Moreover, CD163-mediated uptake in mice seems to only account for a part of the Hb clearance. The new data further underscore the fact that the Hp system in man seems to have a broader and more sophisticated role. This has major implications in the translation of data on Hb metabolism from mouse to man.
Enrofloxacin and Toltrazuril Are Able to Reduce Toxoplasma gondii Growth in Human BeWo Trophoblastic Cells and Villous Explants from Human Third Trimester Pregnancy

Classical treatment for congenital toxoplasmosis is based on combination of sulfadiazine and pyrimethamine plus folinic acid. Due to teratogenic effects and bone marrow suppression caused by pyrimethamine, the establishment of new therapeutic strategies is indispensable to minimize the side effects and improve the control of infection. Previous studies demonstrated that enrofloxacin and toltrazuril reduced the incidence of Neospora caninum and Toxoplasma gondii infection. The aim of the present study was to evaluate the efficacy of enrofloxacin and toltrazuril in the control of T. gondii infection in human trophoblast cells (BeWo line) and in human villous explants from the third trimester. BeWo cells and villous were treated with several concentrations of enrofloxacin, toltrazuril, sulfadiazine, pyrimethamine, or combination of sulfadiazine+pyrimethamine, and the cellular or tissue viability was verified. Next, BeWo cells were infected by T. gondii (2F1 clone or the ME49 strain), whereas villous samples were only infected by the 2F1 clone. Then, infected cells and villous were treated with all antibiotics and the T. gondii intracellular proliferation as well as the cytokine production were analyzed. Finally, we evaluated the direct effect of enrofloxacin and toltrazuril in tachyzoites to verify possible changes in parasite structure. Enrofloxacin and toltrazuril did not decrease the viability of cells and villous in lower concentrations. Both drugs were able to significantly reduce the parasite intracellular proliferation in BeWo cells and villous explants when compared to untreated conditions. Regardless of the T. gondii strain, BeWo cells infected and treated with enrofloxacin or toltrazuril induced high levels of IL-6 and MIF. In villous explants, enrofloxacin induced high MIF production. Finally, the drugs increased the number of unviable parasites and triggered damage to tachyzoite structure. Taken together, it can be concluded that enrofloxacin and toltrazuril are able to control T. gondii infection in BeWo cells and villous explants, probably by a direct action on the host cells and parasites, which leads to modifications of cytokine release and tachyzoite structure.
Social Support, Stress, and Blood Pressure in Black Adults

Psychosocial factors arising from socioeconomic disadvantage and discrimination may contribute to the excess risk of elevated blood pressure in African‐Americans. The purpose of this study was to assess the association of social support and stress with blood pressure in a community‐based sample of 25‐ to 50‐year‐old black adults in Pitt County, NC. A stratified random sample of dwellings was selected in 1988, and 1,784 black adults (80% of those eligible) were interviewed. Analyses were sex specific and adjusted for age, obesity, and waist/hip ratio. In separate analyses of emotional support, instrumental support, and stress with blood pressure, all associations were in the predicted direction (inverse for support, direct for stress) but were stronger for systolic than for diastolic blood pressure. Differences in systolic blood pressure associated with low support or high stress ranged from 5.2 to 3.6 mmHg in women and 3.5 to 2.5 mmHg in men. In simultaneous regression analyses of support and stress, each of the separate effects was reduced for women, but a sizable aggregate effect of low support and high stress remained [+7.2 mmHg (95% confidence limits = +1.3, +13.1) for systolic blood pressure and +4.0 mmHg (95% confidence limits = +0.1, +7.9) for diastolic blood pressure].
Carotid Plaque Morphology Improves Stroke Risk Prediction: Usefulness of a New Ultrasonographic Score

Carotid thickening and plaque detected by B-mode imaging ultrasound are useful to improve the ischemic risk evaluation in asymptomatic subjects over and beyond the traditional cardiovascular risk factors. Some plaque’s echographic parameters help describing the vascular risk. We hypothesized that the stenosis degree, plaque surface irregularity, echolucency and texture, compounded in a Total Plaque Risk Score (TPRS), are predictors of the ischemic events in the San Daniele study, a general population-based study of 1,348 subjects followed for 12 years in average. In the 171 subjects with at least one plaque at baseline, high TPRS was the most powerful independent predictor of cerebrovascular events, which occurred in 115 subjects. Addition of plaque characteristics significantly increased the area under the ROC curve (0.90 vs. 0.88, p = 0.04) versus the Framingham risk score alone. The TPRS is a potential new tool to improve the stroke risk prediction.
Utility and diagnostic accuracy of ureteroscopic biopsy in upper tract urothelial carcinoma.

CONTEXT Ureteroscopic biopsy is the gold standard for the histopathologic diagnosis of urothelial carcinoma of the upper urinary tract. OBJECTIVE To assess the accuracy of endoscopically obtained biopsy samples in diagnosing, grading, and staging urothelial carcinoma and correlate diagnostic findings to biopsy sample size. DESIGN We retrospectively reviewed endoscopic biopsies of the ureter, renal pelvis, and ureteropelvic junction from 2008 to 2011. Biopsy diagnoses that were discordant with follow-up pathology and/or ureteroscopic impression were re-reviewed and samples were immunohistochemically analyzed. RESULTS Endoscopic biopsies (n = 118) yielded a sensitivity of 85.4% for the ureter (n = 79), 77.8% for the renal pelvis (n = 37), and 100% for the ureteropelvic junction (n = 2). A specificity of 100% for all locations and a diagnostic accuracy of 98.3% were identified. The median sample size was 0.3 cm for true positives, 0.3 cm for true negatives, and 0.2 cm for false negatives with no statistical significance. We found that 87.1% of tumors diagnosed on biopsy had concordant grade and 60.0% had concordant pT stage with follow-up surgical resections (n = 43) and biopsies (n = 24). Biopsy samples with concordant tumor grades (mean = 0.6 cm) compared with follow-up resection were larger than biopsy samples with discordant grades (mean = 0.3 cm) (P = .04). CONCLUSIONS Though highly specific, endoscopic biopsy does provide a significant false-negative rate owing to both sampling and diagnostic errors when assessing the upper urinary tract for urothelial carcinoma. Tumor grading is accurate, particularly with larger tissue samples, but tumor staging is unreliable.
Immunoglobulin G in 1·6 Million-year-old Fossil Bones from Venta Micena (Granada, Spain)

Abstract We studied the presence of immunoglobulin G (IgG) in equid fossil bones from Venta Micena (Granada, Spain), dated at 1·6 Myr old, and from Atapuerca (Burgos, Spain) (0·12 Myr), and in ostensibly hominid fossils VM1960 and VM3691 (1·6 Myr) from Venta Micena and CV1 and CV2 (1·4 Myr) from Cueva Victoria (Murcia, Spain). Samples taken from the specimens were crushed to a fine powder and their mineral structure was dissolved in an ethylenediaminetetracetic acid (EDTA) solution. Fossil extracts were tested with antibodies against human IgG and against horse IgG with two independent immunological methods: dot-blotting (DB) and a modification of this latter method: quantitative dot-blotting (QDB). IgG was detected by DB and was quantifiable by QDB in some of the fossils tested. Equid fossils from Atapuerca and Venta Micena gave stronger reactions with the antibodies against horse IgG than with the antibodies against human IgG. Fossils VM3691 and VM1960 reacted more strongly with the antibodies against human IgG than with antibodies against horse IgG, whereas no IgG was detected in fossils CV1 and CV2. These findings show that species-specific IgG can be detected in fossils as old as 1·6 Myr. The immunological analysis of fossil proteins may help to solve palaeontological controversies.