Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombination of hepatitis B virus DNA in patients with HIV

Introduction Hepatitis B is a major cause of death in patients with HIV who usually receive drugs active against hepatitis B virus (HBV). The variability of HBV DNA over time has been little studied. Recombination between different HBV genotypes has been described in many cross-sectional studies, but the frequency of intergenotypic and intragenotypic recombinations in individual patients is unknown. Methods 32 HIV-positive and 11 HIV-negative patients who remained HBV viraemic despite antiviral therapy for at least 1 year were studied. Genotyping was based on line probe assays and genotype-specific PCR. The variability of HBV DNA over time was examined with restriction length and single-strand conformational polymorphism (RFLP-SSCP). HBV DNA sequences obtained by cloning a 2800 bp PCR fragment were analysed for phylogenetic parameters (diversity and selection pressure) and recombination was detected with RDP3 software. Results Large fragments of HBV DNA could be amplified at two different time points in 33 patients. Marked quasi-species modifications occurred in 14 patients. In seven of these patients and in one patient with no change detectable by RFLP-SSCP, the 2800 bp fragment was cloned at two time points at least. In four (57%) of these seven patients, various intergenotypic or intragenotypic recombination events were detected between subvariants present in the initial quasi-species. Recombinant fragments mostly harboured antiviral resistance determinants and reflected a large increase in diversity and in positive selection pressure on the entire HBV quasi-species. Conclusions In coinfected patients, HBV DNA recombination events are frequent during antiviral therapy, corresponding to increased positive selection pressure on the HBV quasi-species and to conservation of antiviral resistance mutations. In this population and at the individual level, recombination is a significant source of HBV genetic variability.
Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage*

The minichromosome maintenance complex (MCM) proteins are required for processive DNA replication and are a target of S-phase checkpoints. The eukaryotic MCM complex consists of six proteins (MCM2–7) that form a heterohexameric ring with DNA helicase activity, which is loaded on chromatin to form the pre-replication complex. Upon entry in S phase, the helicase is activated and opens the DNA duplex to recruit DNA polymerases at the replication fork. The MCM complex thus plays a crucial role during DNA replication, but recent work suggests that MCM proteins could also be involved in DNA repair. Here, we employed a combination of stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics with immunoprecipitation of green fluorescent protein-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. Interestingly, the MCM complex showed very dynamic changes in interaction with proteins such as Importin7, the histone chaperone ASF1, and the Chromodomain helicase DNA binding protein 3 (CHD3) following DNA damage. These changes in interactions were accompanied by an increase in phosphorylation and ubiquitination on specific sites on the MCM proteins and an increase in the co-localization of the MCM complex with γ-H2AX, confirming the recruitment of these proteins to sites of DNA damage. In summary, our data indicate that the MCM proteins is involved in chromatin remodeling in response to DNA damage.
Climate policy support under political consensus: exploring the varying effect of partisanship and party cues

ABSTRACT By creating attitudinal rifts among partisan voters, political polarization is expected to negatively affect chances of effectively mitigating climate change. While such expectations generally have found support, less attention has been paid to the opposite claim that political consensus should eliminate the partisan dimension in climate change politics. This study tests this claim by studying how party identification, and party cues specifically, affects public policy attitudes in a context defined by political consensus. Using data from a large online access panel in Sweden, party identification and party cues are shown to matter for policy attitudes even in a consensus context. This effect is not limited to certain issues but is found across a wide range of policies, and the effect of party cues, for a given issue, varies across parties. The implications of this study and areas for future work are discussed.
Idiopathic Chronic Sleep Onset Insomnia in Attention‐Deficit/Hyperactivity Disorder: A Circadian Rhythm Sleep Disorder

To investigate whether ADHD‐related sleep‐onset insomnia (SOI) is a circadian rhythm disorder, we compared actigraphic sleep estimates, the circadian rest‐activity rhythm, and dim light melatonin onset (DLMO) in ADHD children having chronic idiopathic SOI with that in ADHD children without sleep problems. Participants were 87 psychotropic-medication-naïve children, aged 6 to 12 yrs, with rigorously diagnosed ADHD and SOI (ADHD‐SOI) and 33 children with ADHD without SOI (ADHD‐noSOI) referred from community mental health institutions and pediatric departments of non‐academic hospitals in The Netherlands. Measurements were 1 wk, 24 h actigraphy recordings and salivary DLMO. The mean (±SD) sleep onset time was 21:38±0:54 h in ADHD‐SOI, which was significantly (p<0.001) later than that of 20:49±0:49 h in ADHD‐noSOI. DLMO was significantly later in ADHD‐SOI (20:32±0:55 h), compared with ADHD‐noSOI (19:47±0:49 h; p<0.001). Wake‐up time in ADHD‐SOI was later than in ADHD‐noSOI (p=0.002). There were no significant between‐group differences in sleep maintenance, as estimated by number of wake bouts and activity level in the least active 5 h period, or inter‐ and intradaily rhythm variability. We conclude that children with ADHD and chronic idiopathic sleep‐onset insomnia show a delayed sleep phase and delayed DLMO, compared with ADHD children without SOI.
CONSTRUCTING A NETWORK EVALUATION FRAMEWORK FOR IMPROVING THE FINANCIAL ECOSYSTEM IN SMALL-MEDIUM SIZE FIRMS

This study presents an evaluation framework to measure the various operations to acquire the optimal core operation (CO) when financier provides the supply chain finance (SCF) services in smartphone industry supply chain (SC). The proposed model applies the modify Delphi method and analytic network process (ANP). First, the evaluation model establishes a network with three criteria, eleven sub-criteria and four operations. Next, the ANP is utilized to the framework to obtain the relative weights of the criteria. Finally, the application of the multi-criteria decision making process will list the optimal CO on the basis of their rankings in the framework.The proposed model and the relevant research results can provide academic support to the decision-makers on finance sector with a valuable objective guide for assessing the CO of smartphone industry SC programs to determine the optimal solution in their actual administration of SCF service practices.
Agreement Between HEDIS Performance Assessments in the VA and Medicare Advantage

Medicare Advantage (MA) plans and the Veterans Affairs (VA) health care system assess quality of care using standardized Healthcare Effectiveness Data and Information Set (HEDIS) performance measures. Little is known, however, about the relative accuracy of quality indicators for persons receiving care in more than one health care system. Among Veterans dually enrolled in an MA plan, we examined the agreement between MA and VA HEDIS assessments. Our study tested the hypothesis that private health plans underreport quality of care relative to a fully integrated delivery system utilizing a comprehensive electronic health record. Despite assessing the same individuals using identical measure specifications, reported VA performance was significantly better than reported MA performance for all 12 HEDIS measures. The VA’s performance advantage ranged from 9.8% (glycosylated hemoglobin [HbA1c] < 7.0% in diabetes) to 54.7% (blood pressure < 140/90 mm Hg in diabetes). The overall agreement between VA and MA HEDIS assessments ranged from 38.5% to 62.6%. Performance rates derived from VA and MA aggregate data were 1.6% to 14.3% higher than those reported by VA alone. This analysis suggests that neither MA plans nor the VA fully capture quality of care information for dually enrolled persons. However, the VA’s system-wide electronic health record may allow for more complete capture of quality information across multiple providers and settings.
Relevance of Assessment of Cognitions during Panic Attacks in the Treatment of Panic Disorder

Background: In this paper the effects of cognitive therapy on the belief in causal catastrophical misinterpretations (CCMs) of bodily sensations in panic disorder patients were studied. Methods: CCMs were formulated at the start of treatment and assessed at every treatment session for credibility during panic attacks and during that session. The relation between the belief in CCMs and other measures of panic was also studied. Sixty-six patients rated their belief in 1–3 CCMs during treatment with cognitive therapy. They also filled in questionnaires (ACQ and BSQ) at the start and end of treatment and kept a panic diary. Results: The belief in CCMs diminished significantly in the course of treatment. A significant correlation between panic frequency and belief in CCMs during panic attacks, but not during treatment sessions, was found. Relations between improvement in panic frequency, ACQ- and BSQ-scores on the one hand and belief in CCMs on the other, also revealed significant correlations with belief ratings during panic attacks only. Conclusions: Especially ratings of belief during panic attacks are important in assessing the outcome of cognitive therapy in panic disorder. This measure can be considered as a severity measure. Belief in CCMs during treatment sessions seems to have little clinical significance.
Building creative self-efficacy via learning goal orientation, creativity job requirement, and team learning behavior: The key to employee creativity

This study examined the antecedents of an individual’s creative self-efficacy (CSE) using a sample of 41 semiconductor design teams. Drawing from social cognitive theory, we expected that a dynamic interaction of an individual’s learning goal orientation, creativity as a job requirement, and team learning behavior would build CSE. In addition, employing the combinational perspective, we conjectured that consistency among the three antecedents would enhance CSE, and subsequently, creative performance. As predicted, results showed that effects of learning goal orientation and job requirement on CSE were subject to other members’ learning behavior. A significant three-way interaction supported the position that individual–contextual congruence facilitates the development of CSE, while incongruence of these factors impedes such development. Implications for theory and human resource practices are discussed in light of these findings. JEL Classification: M54, O32
Analysis and simulation of power system stability 500 kv Java Bali using methods of Runge Kutta lower order and higher order

This paper presents the comparatives analysis and simulations of power system stability 500 KV Java Bali using methods of Runge Kutta between lower order and higher order. The stability of a system refers to the ability of a system to return back to its steady state when subjected to a disturbance. As mentioned before, power is generated by synchronous generators that operate in synchronism with the rest of the system. The main purpose of this comparatives is to analyze the oscillation load angle and frequency so that it would improve the stability of electric power. Simulation results show that the proposed method of Runge Kutta higher order is very effective for improving electromechanical oscillation of the power system. With step-size of 0.1, and 0.01 the results are practically identical. When the time step is increased to 0.5 s, errors become noticeable.
Sister Mary Joseph's nodule as presenting sign of a desmoplastic small round cell tumor

Umbilical metastases, also named Sister Mary Joseph's nodules, are well documented in the adult population and most often represent an underlying intra‐abdominal malignancy, usually a carcinoma of gastrointestinal or gynecologic origin. They are indicative of widespread abdominal disease and are associated with a poor prognosis. An extensive review of the literature reveals only two such presentations in the pediatric population. A 14‐year‐old male presented with an umbilical mass, which was found to be a metastatic lesion of a desmoplastic small round cell tumor (DSRCT) of the abdomen. The diagnosis of an intra‐abdominal malignancy, most commonly a DSRCT, should be considered in the presence of an umbilical mass in a child. Pediatr Blood Cancer 2008;50:388–390. © 2006 Wiley‐Liss, Inc.
Managing the competitiveness in CIS countries and Ukraine: the goal and conditions

The study is focused on the analysis of conditions for business development and the industrial enterprises’ competitiveness formation in Commonwealth of Independent States (CIS). The study is based on several concepts – sustainable development, macroeconomic stability, “green economy”, and competitiveness. The article analyses the level of macroeconomic instability in a sample of CIS countries and Ukraine following the statistical approach and using the variation coefficient. The authors suggest calculating the indicators of stable development (SD-indicator) and business simplicity (SB-indicator) based on the international analytical reports data. Several CIS countries are visualized in SD and SB coordinates. The study defines the countries where the conditions for business competitiveness are to be improved due to the comparatively higher level of macroeconomic instability. The article will be interesting to scientists whose subject of research is the competitiveness of enterprises or the economic instability phenomena.
Perforating folliculitis of hemodialysis

ABSTRACTThree patients developed perforating skin lesions on the legs shortly after beginning hemodialysis for chronic renal failure. All had long-standing insulin-dependent diabetes mellitus and all three were white. The skin disease was refractory to all attempts at management. In one patient, however, the eruption cleared completely when hemodialysis was stopped in favor of a renal allograft transplanted from a cadaver. Clinically and histologically, some of the lesions showed evidence of prurigo nodularis, a consequence of vigorous rubbing of a discrete focus.
Immersive Interactive SAR Image Representation Using Non-negative Matrix Factorization

Earth observation (EO) images clustering is a challenging problem in data mining, where each image is represented by a high-dimensional feature vector. However, the feature vectors might not be appropriate to express the semantic content of images, which eventually lead to poor results in clustering and classification. To tackle this problem, we propose an interactive approach to generate compact and informative features from images content. To this end, we utilize a 3-D interactive application to support user-images interactions. These interactions are used in the context of two novel nonnegative matrix factorization (NMF) algorithms to generate new features. We assess the quality of new features by applying k-means clustering on the generated features and compare the obtained clustering results with those achieved by original features. We perform experiments on a synthetic aperture radar (SAR) image dataset represented by different state-of-the-art features and demonstrate the effectiveness of the proposed method. Moreover, we propose a divide-and-conquer approach to cluster a massive amount of images using a small subset of interactions.
Reduction of steroid-induced intraocular pressure elevation in sheep by tissue plasminogen activator.

PURPOSE To investigate whether tissue plasminogen activator (tPA) can prevent and/or reverse steroid-induced IOP elevation in an ovine model. METHODS Three animal groups were subjected to bilateral steroid-induced IOP elevation using thrice daily topical ocular prednisolone administration. In the first group (N = 8), one eye each of two sheep was injected intravitreally with 100 μg, 200 μg, 500 μg, or 1 mg human recombinant tPA, while contralateral eyes received vehicle. In the second group (N = 2), one eye was injected intravitreally with tPA (100 μg), while contralateral eyes received vehicle containing L-arginine. In the third group (N = 4), each animal received intravitreal tPA in one eye concurrently with initiation of bilateral steroid administration. IOP was monitored for the duration of the experiment. Tissues from eyes of the third group were used to determine relative gene expression. RESULTS In the first and second groups, IOP decreased by 9.7 (±2.8) and 9.7 (±1.6) mm Hg, respectively, 24 hours after tPA administration. In the third group, tPA-treated eyes did not develop IOP elevation with ΔIOP of 11.8 (±1.3) mm Hg 8 days later. In all tPA-treated eyes, IOP remained low until the end of the study. mRNA levels in the trabecular meshwork were decreased for plasminogen activator tissue (PLAT), increased for matrix-metalloproteinase 1 (MMP-1), and stable for plasminogen activator inhibitor 1 (PAI-1), MMP-2, MMP-9, and MMP-13 in tPA-treated eyes compared with contralateral controls. PAI-1 mRNA levels in ciliary processes also remained similar. CONCLUSIONS Recombinant human tPA is effective in both preventing and reversing steroid-induced IOP elevation in sheep. Tissue plasminogen activator may be useful as a therapeutic agent in steroid-induced glaucoma.
Differential Expression of Biphenyl Synthase Gene Family Members in Fire-Blight-Infected Apple ‘Holsteiner Cox’ 1[W][OA]

Fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple (Malus × domestica). The phytoalexins of apple are biphenyls and dibenzofurans, whose carbon skeleton is formed by biphenyl synthase (BIS), a type III polyketide synthase. In the recently published genome sequence of apple ‘Golden Delicious’, nine BIS genes and four BIS gene fragments were detected. The nine genes fall into four subfamilies, referred to as MdBIS1 to MdBIS4. In a phylogenetic tree, the BIS amino acid sequences from apple and Sorbus aucuparia formed an individual cluster within the clade of the functionally diverse type III polyketide synthases. cDNAs encoding MdBIS1 to MdBIS4 were cloned from fire-blight-infected shoots of apple ‘Holsteiner Cox,’ heterologously expressed in Escherichia coli, and functionally analyzed. Benzoyl-coenzyme A and salicoyl-coenzyme A were the preferred starter substrates. In response to inoculation with E. amylovora, the BIS3 gene was expressed in stems of cv Holsteiner Cox, with highest transcript levels in the transition zone between necrotic and healthy tissues. The transition zone was the accumulation site of biphenyl and dibenzofuran phytoalexins. Leaves contained transcripts for BIS2 but failed to form immunodetectable amounts of BIS protein. In cell cultures of apple ‘Cox Orange,’ expression of the BIS1 to BIS3 genes was observed after the addition of an autoclaved E. amylovora suspension. Using immunofluorescence localization under a confocal laser-scanning microscope, the BIS3 protein in the transition zone of stems was detected in the parenchyma of the bark. Dot-shaped immunofluorescence was confined to the junctions between neighboring cortical parenchyma cells.
Melatonin protects from ischemia/reperfusion‐induced renal injury in rats: this effect is not mediated by proinflammatory cytokines

Abstract: The pathophysiologic mechanisms leading to acute ischemic renal failure are not completely understood. Melatonin, a compound with well‐known antioxidant properties, reduces IR‐induced renal injury. The purpose of the present study was to investigate the changes in levels of tumor necrosis factor (TNF)‐α, IL‐β, and IL‐6 in postischemic reperfused renal tissue, and to determine whether the protective effect of melatonin is related the modulation of the production of these inflammatory molecules. Male Wistar albino rats were unilaterally nephrectomized and subjected to 1 hr of renal pedicle occlusion followed by 2 hr or 24 hr of reperfusion. Melatonin (10 mg/kg, i.p.) or vehicle was administrated at 10 min prior to ischemia. After 24 hr of the reperfusion, following decapitation, kidney samples were taken both for histologic examination and for the determination of malondialdehyde (MDA), myeloperoxidase (MPO) activity, total antioxidant capacity (TAC), total oxidative stress (TOS), creatinine, and blood urea nitrogen (BUN). These were measured in serum samples. TNF‐α, IL‐β, and IL‐6 were measured in kidney samples after 2 hr of reperfusion. IR caused a significant increase in renal MDA, MPO, TOS, creatinine, and BUN while decrease TAC without any change in TNF‐α, IL‐β, and IL‐6 levels. Melatonin treatment reduced the biochemical indices without any change in the cytokine levels and ameliorated histopathologic alterations induced by IR. The protective effect of melatonin on IR‐induced renal injury is related to its antioxidant properties but not to proinflammatory cytokines.
Polymorphism of propafenone metabolism and disposition in man: clinical and pharmacokinetic consequences.

The relationship between debrisoquine metabolic phenotype and the pharmacokinetics and pharmacodynamics of propafenone was studied in 28 patients with chronic ventricular arrhythmias (22 extensive metabolizers [EMs] and six poor metabolizers [PMs] of debrisoquine). EMs were characterized by a shorter propafenone elimination half-life (5.5 +/- 2.1 vs 17.2 +/- 8.0, p less than .001), lower average plasma concentration (Cp) (1.1 +/- 0.6 vs 2.5 +/- 0.5 ng/ml/mg daily dosage, p less than .001), and higher oral clearance (1115 +/- 1238 vs 264 +/- 48 ml/min, p less than .001). The active metabolite 5-hydroxypropafenone, assayed in 12 patients, was identified in nine of 10 EMs but in neither of the PMs. A lower incidence of central nervous system side effects was noted in EMs (14% vs 67%, p less than .01). The magnitude of QRS widening at any given propafenone Cp was greater in EMs than PMs. There was no significant difference between EMs and PMs in effective propafenone dose or frequency of antiarrhythmic response. Inhibition of debrisoquine 4-hydroxylation by propafenone was demonstrated both in vivo and in a human liver microsomal system in vitro. We conclude that propafenone is metabolized via the same cytochrome P-450 responsible for debrisoquine's 4-hydroxylation, and that its pharmacokinetics and concentration-response relationships and the incidence of central nervous system side effects are different in patients of different debrisoquine metabolic phenotype.
Model-based Segmentation of 3D Point Clouds for Phenotyping Sunflower Plants

This article presents a model-based segmentation method applied to 3D data acquired on sunflower plants. Our objective is the quantification of the plant growth using observations made automatically from sensors moved around plants. Here, acquisitions are made on isolated plants: a 3D point cloud is computed using Structure from Motion with RGB images acquired all around a plant. Then the proposed method is applied in order to segment and label the plant leaves, i.e. to split up the point cloud in regions corresponding to plant organs: stem, petioles, and leaves. Every leaf is then reconstructed with NURBS and its area is computed from the triangular mesh. Our segmentation method is validated comparing these areas with the ones measured manually using a planimeter: it is shown that differences between automatic and manual measurements are less than 10%. The present results open interesting perspectives in direction of high-throughput sunflower phenotyping.