Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Crop Proportion Phenology Index models with machine learning algorithms for estimating winter wheat areas

Monitoring crop areas is a key issue in remote sensing studies. A Crop Proportion Phenology Index (CPPI) model has previously been developed for estimation of winter wheat areas. Here we test the CPPI model in different areas using remote sensing data for varied kernel functions, including linear regression (LR), Artificial Neural Network (ANN), and Support Vector Regression (SVR). The differences of the model performances among different kernel functions were found to be small for areas with simple planting structure. For areas where multiple crop types have similar phenology cycles, the non-linear model of ANN was found to perform the best. This study indicates that the CPPI model can be applied to map winter wheat distribution in areas with complex planting structures, thus it holds promises for estimating fractional areas of winter wheat areas over large geographic areas.
Assembly of hepatitis delta virus particles

Hepatitis delta virus (HDV) is a subviral satellite of hepatitis B virus (HBV). Since the RNA genome of HDV can replicate in cultured cells in the absence of HBV, it has been suggested that the only helper function of HBV is to supply HBV coat proteins in the assembly process of HDV particles. To examine the factors involved in such virion assembly, we transiently cotransfected cells with various hepadnavirus constructs and cDNAs of HDV and analyzed the particles released into the medium. We report that the HDV genomic RNA and the delta antigen can be packaged by coat proteins of either HBV or the related hepadnavirus woodchuck hepatitis virus (WHV). Among the three co-carboxy-terminal coat proteins of WHV, the smallest form was sufficient to package the HDV genome; even in the absence of HDV RNA, the delta antigen could be packaged by this WHV coat protein. Also, of the two co-amino-terminal forms of the delta antigen, only the larger form was essential for packaging.
Detection of air trapping on inspiratory and expiratory phase images obtained by 0.3-second cine CT in the lungs of free-breathing young children.

OBJECTIVE The objective of our study was to evaluate whether 0.3-second cine CT can be used to detect air trapping in the lungs of young children. SUBJECTS AND METHODS In 30 children (mean age, 25 months), 0.3-second cine CT was performed at six levels during 3 seconds of quiet breathing. The study population was divided into an air trapping group (n = 24) and a no-air trapping group (n = 6). Lung density was measured at an abnormal area (with or without air trapping) and an adjacent normal area on inspiratory and expiratory phase images. Lung density differences between inspiration and expiration were calculated and compared in abnormal areas (with or without air trapping) and in normal areas. Their percentages were calculated and compared between the two groups. In addition, lung density differences between abnormal and adjacent normal areas were calculated and compared between the two groups. RESULTS Lung density differences between inspiration and expiration were smaller in areas with air trapping (mean +/- SD, -19 +/- 34 H) than in abnormal areas without air trapping (138 +/- 36 H) (p < 0.001) or in normal areas (111 +/- 49 H) (p < 0.001). Their percentages were smaller in the group with air trapping (-27% +/- 54%) than in the group with no air trapping (120% +/- 87%) (p < 0.001). In the group with air trapping, lung density differences were larger at the expiratory phase (260 +/- 77 H) than at the inspiratory phase (129 +/- 69 H) (p < 0.001), but did not change through the respiratory cycle in the group with no air trapping (p > 0.05). CONCLUSION Air trapping can be accurately detected in the lungs of free-breathing young children using 0.3-second cine CT.
Interactive endothelial phenotype maintenance and osteogenic differentiation of adipose tissue stromal vascular fraction SSEA‐4+‐derived cells

Bone formation relies on complex processes that require well‐orchestrated interactions between several cell types, such as bone‐forming cells (osteoblasts, OBs) and endothelial cells (ECs). Their co‐culture has been proved relevant to mimicking specific features of the bone niche. Here we propose the co‐culture of microvascular‐like ECs and pre‐OBs, both derived from the SSEA‐4+ cell subpopulation from the stromal vascular fraction of human adipose tissue (SSEA‐4+ hASCs), to define the conditions in which cells synergistically communicate to support the full differentiation of pre‐OBs and maintenance of the EC phenotype. Co‐cultures of different ratios of the two cell types were established and maintained for up to 21 days in standard endothelial maintenance (ENDO) and osteogenic differentiation (OST) media, as well as in a mixture of these (MIX). The osteogenic maturation of pre‐OBs (ALP activity, OPN and OCN expression, calcium deposition), the evolution of EC numbers (CD31+ cells) and maintenance of the endothelial phenotype (CD31 and vWF expression, LDL uptake) were assessed throughout the culture time as a function of cell ratio and culture media. The results obtained demonstrate that EC number has a significant effect on the osteogenic differentiation of pre‐OBs, depending on the medium used. While in ENDO medium the osteogenic differentiation was not observed, in the OST and MIX media it was attained at similar levels, except for the co‐culture with a higher number of ECs in MIX medium. These findings demonstrate that the use of SSEA‐4+ hASCs as a single‐cell source is promising to attain 3D bone‐like models with the potential to promote vascularized bone tissue regeneration. Copyright © 2015 John Wiley & Sons, Ltd.
Dogger Bank Itch: Survey of Trawlermen

The critical size-that is, the size beyond which aneurysms suddenly become unstable and likely to rupture-was a maximum external diameter of 4 mm. Aneurysms can probably form or begin at any age and may enlarge and rupture rapidly. In patients with multiple aneurysms the largest aneurysm had ruptured in 88%. When combinations of middle cerebral and internal carotid aneurysms were present on the same side the proximal aneurysm was more often ruptured. Infiltration of the wall of the aneurysm with white blood cells and fibrin was thought to precede enlargement or rupture. This was thought to be due to endothelial damage as a result of pulsation, turbulent flow, or ischaemia resulting from mural thrombosis.
Hepatitis C virus genotype 1: How genetic variability of the core protein affects the response to pegylated‐interferon and ribavirin therapy

Hepatitis C virus subgenotypes 1a and 1b are found worldwide and cause 60% of all hepatitis C cases. It has been reported recently that viral genetic variations have a critical impact on the patient treatment outcome. In particular, polymorphisms of the HCV core protein have been linked to poor treatment response. However, most of these studies were conducted on Asian populations, Japanese in particular who are infected with HCV subgenotype 1b. Hence, we aimed in this study to examine the core protein polymorphisms in Saudi patients who are infected with chronic HCV genotype 1 (1a and 1b subtypes) and its association with treatment outcome. Direct sequencing of full‐length core protein and data mining analyses were utilized. Results have shown that the response to treatment is dependent on subgenotypes. Indeed, HCV‐1b showed different point mutations that are associated with treatment outcome where the point mutations at positions 70 (Arg70Gln) and 75 (Thr75Ala) in HCV‐1b are significantly associated with PEG‐IFN/RBV treatment response. In contrast, HCV‐1a showed no significant association between core protein mutations and response to treatment. In addition, analyses of HCV‐1a core protein sequences revealed a highly conserved region especially in the responder group. This study provides a new insight in the genetic variability of full‐length core protein in HCV genotype 1 in Saudi infected patients. J. Med. Virol. 86:224–234, 2014. © 2013 Wiley Periodicals, Inc.
Endothelin type A and B receptors in the control of afferent and efferent arterioles in mice.

BACKGROUND Endothelin 1 contributes to renal blood flow control and pathogenesis of kidney diseases. The differential effects, however, of endothelin 1 (ET-1) on afferent (AA) and efferent arterioles (EA) remain to be established. METHODS We investigated endothelin type A and B receptor (ETA-R, ETB-R) functions in the control of AA and EA. Arterioles of ETB-R deficient, rescued mice [ETB(-/-)] and wild types [ETB(+/+)] were microperfused. RESULTS ET-1 constricted AA stronger than EA in ETB(-/-) and ETB(+/+) mice. Results in AA: ET-1 induced similar constrictions in ETB(-/-) and ETB(+/+) mice. BQ-123 (ETA-R antagonist) inhibited this response in both groups. ALA-ET-1 and IRL1620 (ETB-R agonists) had no effect on arteriolar diameter. L-NAME did neither affect basal diameters nor ET-1 responses. Results in EA: ET-1 constricted EA stronger in ETB(+/+) compared to ETB(-/-). BQ-123 inhibited the constriction completely only in ETB(-/-). ALA-ET-1 and IRL1620 constricted only arterioles of ETB(+/+) mice. L-NAME decreased basal diameter in ETB(+/+), but not in ETB(-/-) mice and increased the ET-1 response similarly in both groups. The L-NAME actions indicate a contribution of ETB-R in basal nitric oxide (NO) release in EA and suggest dilatory action of ETA-R in EA. CONCLUSIONS ETA-R mediates vasoconstriction in AA and contributes to vasoconstriction in EA in this mouse model. ETB-R has no effect in AA but mediates basal NO release and constriction in EA. The stronger effect of ET-1 on AA supports observations of decreased glomerular filtration rate to ET-1 and indicates a potential contribution of ET-1 to the pathogenesis of kidney diseases.
Contextual Influences and Campaign Awareness Among Young Adults: Evidence from the National truth® Campaign

Mass media campaigns have been found to shape the public's knowledge, attitudes, beliefs, and behavior around tobacco. This study examines the influence of contextual factors with respect to awareness of the national truth® campaign, a mass media, branded tobacco use prevention campaign, among a sample of young adults (n = 2,804) aged 24–34 years old; these respondents were within the age range for both the primary and secondary targets of the campaign during the period (2000–2007) when the campaign was airing television advertising at consistently high levels. Mulitvariable models reveal lower educational attainment and Hispanic ethnicity as significant contextual factors predictive of lower campaign awareness, controlling for media use. In contrast, gender, state tobacco control policy, sensation-seeking, current smoking status, and community-level SES variables were not significantly associated with campaign awareness. Further research is needed to identify the mechanisms through which public education campaigns operate, particularly among disadvantaged communities.
IRL‐1620, a tumor selective vasodilator, augments the uptake and efficacy of chemotherapeutic agents in prostate tumor rats

IRL‐1620, a potent endothelin B receptor agonist, enhanced the efficacy of paclitaxel in a breast tumor model, but its effect in prostate cancer is not known. The present study was conducted to evaluate the effect of IRL‐1620 on tumor perfusion, uptake of [14C]‐doxorubicin in the tumor and efficacy of doxorubicin (DOX), and 5‐flurouracil (5‐FU) in a rat prostate tumor model.
Simultaneous extraction of cellular lipids and water‐soluble metabolites: Evaluation by NMR spectroscopy

A method for simultaneous extraction of lipids and water‐soluble metabolites from a single cell sample was developed and optimized for NMR spectroscopy. Intermediary metabolites in cultured M2R mouse melanoma cells and changes therein in response to challenge with melanotropin were studied by 31P and 13C NMR. Cells were extracted with methanol, chloroform, and water (1:1:1, v/v/v). The contents of the chloroform and methanol‐water phases were separated and quantitatively recovered. The contents of the upper and lower phases compared well with the homologous fractions obtained by perchloric acid and Folch's lipid extraction methods. The pH of the extracts remained within the physiologic range, eliminating potential deleterious effect on cellular metabolites. The water phase contained minimal amounts of salts, making these extracts amenable to subsequent analytical procedures. Obtaining lipid‐ and water‐soluble metabolites from the same sample enables characterization of metabolic pathways that bridge the two cellular components in a quantitative manner.
Epicardial and subcutaneous adipose tissue Fatty acids profiles in diabetic and non-diabetic patients candidate for coronary artery bypass graft.

INTRODUCTION We have recently shown that in high cholesterol-fed rabbits, the sensitivity of epicardial adipose tissue to changes in dietary fat is higher than that of subcutaneous adipose tissue. Although the effects of diabetes on epicardial adipose tissue thickness have been studied, the influence of diabetes on profile of epicardial free fatty acids (FFAs) has not been studied. The aim of this study is to investigate the effect of diabetes on the FFAs composition in serum and in the subcutaneous and epicardial adipose tissues in patients undergoing coronary artery bypass graft (CABG). METHODS Forty non-diabetic and twenty eight diabetic patients candidate for CABG with >75% stenosis participated in this study. Fasting blood sugar (FBS) and lipid profiles were assayed by auto analyzer. Phospholipids and non-estrified FFA of serum and the fatty acids profile of epicardial and subcutaneous adipose tissues were determined using gas chromatography method. RESULTS In the phospholipid fraction of diabetic patients' serum, the percentage of 16:0, 18:3n-9, 18:2n-6 and monounsaturated fatty acids (MUFAs) was lower than the corresponding values of the non-diabetics; whereas, 18:0 value was higher. A 100% increase in the amount of 18:0 and 35% decrease in the level of 18:1n-11 was observed in the diabetic patients' subcutaneous adipose tissue. In epicardial adipose tissue, the increase of 18:0 and conjugated linolenic acid (CLA) and decrease of 18:1n-11, w3 (20:5n-3) and 22:6n-3 were significant; but, the contents of arachidonic acid and its precursor linoleic acid were not affected by diabetes. CONCLUSION The fatty acids' profile of epicardial and subcutaneous adipose tissues is not equally affected by diabetes. The significant decrease of 16:0 and w3 fatty acids and increase of trans and conjugated fatty acids in epicardial adipose tissue in the diabetic patients may worsen the formation of atheroma in the related arteries.
A novel laboratory version management system for tracking complex biological experiments

Ability to keep track of records for various biological experiments allows for future validation of the current experiments and other non-experimental laboratory procedures. With the increasing popularity of publishing biological data in XML format, there arises the need for the control and management of this data, as well as dynamically exporting this data to various formats for reporting purposes. As such data is constantly changing, users want to be able to query previous versions, plotting data across different versions from history, query changes in documents, as well as to retrieve a particular document version efficiently. This paper proposes an XML-based version management system for tracking and analyzing data obtained from any laboratory experiments in an effective and meaningful manner. This includes experiments ranging from genomic, proteomic and protein structural. We also present methods for importing non XML data into the system as well as generating reports in multiple formats dynamically.
CloudML based dynamic deployment configuration for scaling enterprise applications in the cloud

In light of the popularity of cloud computing, it is really important to be free to change cloud providers when needed. However, in most cases, system configuration relies on provider services, such as load balancing or databases and this makes it much harder to change the provider. This thesis describes a CloudML based solution that is capable of deploying complex systems using different cloud providers with minimum changes including embedded load balancers. This feature allows the creation of scalable configurations that are independent from providers' load balancing services and allow any component of the system to be scalable on demand. The proposed solution also has an integrated generic LP (linear programming) model to control system scaling. We conducted a number of experiments to show that the system could be used for deploying complex systems that follow most popular workflows. The results of the experiments show that this system is capable of scaling properly to support incoming workflow regardless of chosen workflow or number of the system components.
A modified Friedman test for randomized complete block designs

Abstract The Friedman test is often used for a randomized complete block design when the normality assumption is not satisfied or the data are ordinal. The Friedman test can be viewed as an extension of the sign test for multiple measurements within each subject or block. We propose a modified Friedman test based on the Wilcoxon sign rank approach. Coincidentally, Tukey proposed a test statistic similar to our proposed test, but blocks are ranked by the minimum difference within each block. In the proposed test, we use the variance of block to rank the blocks, with the least variance being ranked the smallest. In both Tukey test and the modified Friedman test, linear ranks are used for blocks and treatments. The Tukey test belongs to the family of weighted-ranking test from Quade (1979). The modified Friedman test, the Friedman test and the Tukey test are compared under various conditions and the results indicate that the proposed test is generally more powerful than the Friedman test and the Tukey test when the number of groups is small.
Scaling perspective for III-V broken gap nanowire TFETs: An atomistic study using a fast tight-binding mode-space NEGF model

We report an in-depth atomistic study of the scaling potential of III-V GAA nanowire heterojunction TFET using an innovative tight-binding mode space (MS) technique with large speedup (up to 250×) while keeping good accuracy (error < 1%). It is shown that both n- and pTFET performances are best above 20 nm gate length for a cross-section of 5.5 nm in the [111] crystal orientation. At V<inf>dd</inf> = 0.3 V and I<inf>off</inf> = 50 pA/μm, the on-current (Ion) and energy-delay product (ETP) gain over a Si NW GAA MOSFET are 58× and 56× respectively. In a beyond 5 nm node low power ITRS 2.0 horizontal GAA design rule however, where the gate length is restricted to 12 nm, a [100] orientation is best but features up to 3× I<inf>on</inf> and 2.4× ETP degradation vs. the 20 nm TFET GAA design.
Effects of vitamin E and melatonin on serum testosterone level in sleep deprived Wistar rats.

BACKGROUND Sleep deprivation affects a significant proportion of the global population. It has been reported to induce oxidative stress in the testes and reduce serum testosterone levels. Exogenous anti-oxidants have been known to prevent damages and diseases associated with oxidative stress but there is dearth of knowledge on their effectiveness during sleep deprivation. AIM This study was designed to investigate the effects of two anti-oxidants; melatonin and vitamin E on serum testosterone concentration in sleep deprived male Wistar rats. METHODS Thirty (30) male Wistar rats were used for this study. Animals were divided into six (6) groups (n = 5). Group 1 was the control, group 2 rats were sleep deprived, group 3 received vitamin E (200 mg/ kg bwt) only, group 4 rats received vitamin E and were sleep deprived, group 5 received melatonin only (10 mg/kg bwt), and group 6 rats received melatonin (10 mg/kg bwt) and were sleep deprived. Sleep deprivation was induced using the modified multiple platform technique. Body weights were taken on days 7, 14 and 21. Blood was collected at sacrifice and serum was obtained for analyses of testosterone, corticosterone and melatonin. Testicular malondialdehyde, superoxide dismutase and catalase levels were determined by the methods of Adam-Vizi and Seregi (1982), Misra and Fridovich (1972), and Sinha, (1972) respectively. Data obtained were analyzed using one way ANOVA and p < 0.05 was considered significant. RESULTS Serum testosterone (nmol/l) of the sleep deprived animals (0.6 ± 0.3) reduced significantly (p < 0.05) compared with control group (3.3 ± 0.04), sleep deprived+vitamin E group (2.8 ± 0.5) and sleep deprived+melatonin group (2.0 ± 0.3). Also, melatonin+sleep deprived group had reduced testosterone compared with control. There were no significant changes in the serum corticosterone (nmol/l) and melatonin levels in all the groups compared with the sleep deprived group. However, corticosterone was increased in the sleep deprived+Vitamin E group (51.6 ± 20.5) compared with control (6.3 ± 0.6) Sleep deprived group had increased testicular malondialdehyde (MDA) (1.6 ± 0.1 unit/mg), superoxide dismutase (SOD) (3.2 ± 0.2 unit/mg), and catalasel evels (44.3 ± 1.1 unit/ mg) compared with control (0.9 ± 0.0 μmg). MDA, and catalase were significantly reduced in sleep deprived+vitamin E (1.1 ± 0.2, 2.4 ± 0.3, 39 ± 1.0 unit/ mg) compared with sleep deprived while melatonin alone had increased MDA. level (1.7 ± 0.2unit/mg) compared with control. SOD in the sleep deprived+melatonin group (2.7 ± 0.2 μ/mg) as compared with control increased (p < 0.05) while MDA and catalase levels as compared with control and sleep deprived groups showed no difference. Histological findings showed that the pathology in the testes of sleep deprived rats was ameliorated by vitamin E. CONCLUSION Vitamin E had a more potent effect than melatonin in maintaining testosterone level in sleep deprived Wistar rat.
RGS12 Is Essential for RANKL‐Evoked Signaling for Terminal Differentiation of Osteoclasts In Vitro

How RANKL evokes [Ca2+]i oscillations and leads to osteoclast differentiation is unclear. We identified a new signaling protein, RGS12, and found that RGS12 is essential for [Ca2+]i oscillations and osteoclast differentiation induced by RANKL. RGS12 may play a critical role in the RANKL‐evoked PLCγ–calcium channels–[Ca2+]i oscillation–NFAT2 pathway.
Epistatic Interactions

The term "epistasis" is sometimes used to describe some form of statistical interaction between genetic factors and is alternatively sometimes used to describe instances in which the effect of a particular genetic variant is masked by a variant at another locus. In general statistical tests for interaction are of limited use in detecting "epistasis" in the sense of masking. It is, however, shown that there are relations between empirical data patterns and epistasis that have not been previously noted. These relations can sometimes be exploited to empirically test for "epistatic interactions" in the sense of the masking of the effect of a particular genetic variant by a variant at another locus.
Combined 8‐methoxypsoralen and black light therapy of psoriasis TECHNIQUE AND RESULTS

Seventy‐four patients with psoriasis underwent a combined topical treatment with an 8‐methoxypsoralen solution and black light. In thirty‐four patients the skin lesions healed; in twenty‐three patients they improved considerably. Eleven patients showed only a moderate regression of the lesions, whilst in six patients treatment was for various reasons discontinued during the first phase, The 8‐methoxypsoralen‐black light therapy can be performed in out‐patients and has the advantage over dithranol treatment of being entirely clean. Relapses are not resistant to further similar treatment.