Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant somatic hypermutation and expression of activation‐induced cytidine deaminase mRNA in mediastinal large B‐cell lymphoma

To determine the possible role of aberrant somatic hypermutation (ASHM) and activation‐induced cytidine deaminase (AID) expression in the pathogenesis of mediastinal large B‐cell lymphoma (MBL), the mutational status of genes affected by ASHM, including c‐MYC, PAX‐5 and RhoH, was analysed, and the expression level of AID mRNA in tumour specimens from six patients with MBL was determined. Mutations in one or more genes and high expression of AID mRNA were detected in all the six cases of MBL. These results suggest that ASHM and AID expression may have a role in the pathogenesis of MBL.
Assisted Ontology Instantiation: a LearningKit perspective

Ontology serves as the blueprint for knowledge dissemination within and across domains and applications. In general, acquisition of ontological knowledge can be automated in many domains. This paper presents a scenario where we semi-automatically instantiate an ontology associated with meta-cognitive skills, with assistance from human experts. We argue why such semi-automatic instantiation of ontologies is a practicable approach to knowledge acquisition.
A complexity aware, variable-bit-depth motion estimation

Demands for using different complexity level algorithms to deliver multimedia content delivery over portable devices are increasing thanks to advanced battery technology. This work describes a novel complexity aware motion estimation for H.264 based on pixel representation of different bit-depth and a simple scene change detection module. The experimental results show that with identical searching complexity, improvement on averaged PSNR is more than 0.2 dB for 4-bit representation and more than 2 dB for 1/2-bit representation as compared to the conventional bit-truncation method.
Pulmonary surfactant proteins and lipids as modulators of inflammation and innate immunity

Objectives: The pulmonary surfactant system of the human lung consists of unique lipids and proteins that contribute to the biophysical and innate immune properties of the organ. Surfactant protein A (SP‐A) is an oligomeric protein consisting of 18 protomers with collagen and lectin–like domains that recognizes glycoconjugates, lipids and protein determinants on both host cells and invading microorganisms. The authors examined the interaction of SP‐A with Mycoplasma pneumoniae and the influence of the protein upon the innate immune response to the bacteria.
Influence of number of backers, goal amount, and project duration on meeting funding goals of crowdfunding projects

Evaluating potential of crowdfunding projects is challenging, and this challenge has multiplied with increasing number of projects in recent years. Using a sample of 74,618 Kickstarter crowdfunding projects and based on linear growth time-trend mixed-effects logit model, with increasing number of crowdfunding projects over time, fewer projects received funding, furthermore, number of backers reduced, higher goal amount increased and shorter duration to meet the funding goal increased the likelihood of achieving the funding goal. The results suggest that over time crowdfunding platforms increase reliance on costlier signals (higher goal amount and shorter duration) and reduce reliance on noisier signals (number of backers).
Evidence for multiple types of Ca2+ channels in acutely isolated hippocampal CA3 neurones of the guinea‐pig.

1. Current through Ca2+ channels was studied in acutely isolated guinea‐pig pyramidal neurones from the CA3 region of the hippocampus. Both the whole‐cell and single‐channel patch‐clamp configuration were used. 2. Both whole‐cell and single‐channel currents displayed holding potential sensitivity indicative of two high‐threshold currents similar to L‐ and N‐type Ca2+ currents. 3. A low‐threshold whole‐cell current, similar to T‐type current seen in dorsal root ganglion (DRG) neurones, activated at ‐60 to ‐50 mV and was blocked by nickel (100 microM) and amiloride (500 microM). Exposure to 50 microM‐cadmium left a fraction of the T‐type current intact but blocked N‐ and L‐type current. This T‐like component needed extremely negative holding potentials to be completely reprimed. 4. Whole‐cell N‐type Ca2+ channel current was blocked by omega‐conotoxin (1 microM). From a holding potential of ‐90 mV, omega‐conotoxin decreased the peak whole‐cell current by 33%. 5. A slowly inactivating high‐threshold Ca2+ current (L‐type) that was present at depolarized holding potentials, displayed dihydropyridine sensitivity. From a holding potential of ‐50 mV, addition of the dihydropyridine Ca2+ channel antagonist nimodipine (2 microM) to the bath decreased whole‐cell peak current by 45%. Interestingly, at negative holding potentials nimodipine worked as an agonist. From a holding potential of ‐90 mV, nimodipine (2 microM) increased peak current at test potentials from ‐50 to ‐20 mV and shifted the peak of the current‐voltage relationship in the hyperpolarizing direction similar to the effect of Ca2+ channel agonist Bay K 8644. Exposure to Bay K 8644 (2 microM) increased peak current and single channel open probability independent of holding potential while shifting the peak of the whole‐cell current‐voltage relationship 11 mV in the hyperpolarizing direction. Our experiments suggest that there are approximately the same number of L‐type as omega‐conotoxin sensitive N‐type Ca2+ channels in CA3 neurones. 6. A high‐voltage‐activated whole‐cell current was still present in cells exposed to both nimodipine and omega‐conotoxin (2 and 1 microM, respectively) suggesting the existence of a fourth type of Ca2+ channel in these neurones or that a population of either L‐type or N‐type Ca2+ channels did not respond to dihydropyridine antagonists or omega‐conotoxin, respectively. (ABSTRACT TRUNCATED AT 400 WORDS)
Emergency department visits for attempted suicide and self harm in the USA: 2006–2013

Aims. To characterise and identify nationwide trends in suicide-related emergency department (ED) visits in the USA from 2006 to 2013. Methods. We used data from the Nationwide Emergency Department Sample (NEDS) from 2006 to 2013. E-codes were used to identify ED visits related to suicide attempts and self-inflicted injury. Visits were characterised by factors such as age, sex, US census region, calendar month, as well as injury severity and mechanism. Injury severity and mechanism were compared between age groups and sex by chi-square tests and Wilcoxon rank-sum tests. Population-based rates were computed using US Census data. Results. Between 2006 and 2013, a total of 3 567 084 suicide attempt-related ED visits were reported. The total number of visits was stable between 2006 and 2013, with a population-based rate ranging from 163.1 to 173.8 per 100 000 annually. The frequency of these visits peaks during ages 15–19 and plateaus during ages 35–45, with a mean age at presentation of 33.2 years. More visits were by females (57.4%) than by males (42.6%); however, the age patterns for males and females were similar. Visits peaked in late spring (8.9% of all visits occurred in May), with a smaller peak in the fall. The most common mechanism of injury was poisoning (66.5%), followed by cutting and piercing (22.1%). Males were 1.6 times more likely than females to use violent methods to attempt suicide (OR = 1.64; 95% CI = 1.60–1.68; p < 0.001). The vast majority of patients (82.7%) had a concurrent mental disorder. Mood disorders were the most common (42.1%), followed by substance-related disorders (12.1%), alcohol-related disorders (8.9%) and anxiety disorders (6.4%). Conclusions. The annual incidence of ED visits for attempted suicide and self-inflicted injury in the NEDS is comparable with figures previously reported from other national databases. We highlighted the value of the NEDS in allowing us to look in depth at age, sex, seasonal and mechanism patterns. Furthermore, using this large national database, we confirmed results from previous smaller studies, including a higher incidence of suicide attempts among women and individuals aged 15–19 years, a large seasonal peak in suicide attempts in the spring, a predominance of poisoning as the mechanism of injury for suicide attempts and a greater use of violent mechanisms in men, suggesting possible avenues for further research into strategies for prevention.
Short‐term exposure to constant light promotes strong circadian phase‐resetting responses to nonphotic stimuli in Syrian hamsters

Behavioral (nonphotic) stimuli can shift circadian rhythms by serotonin (5‐HT) and/or neuropeptide Y (NPY) inputs to the suprachiasmatic nucleus (SCN) circadian clock. Based on the idea that behavioral phase resetting is modulated by endogenous changes in postsynaptic sensitivity to such transmitters, hamsters were exposed to constant light (LL; ∼ 250 lx) for 1–3 days, which suppresses locomotor activity and eliminates the daily rhythm of SCN 5‐HT release measured by microdialysis. Groups subjected to brief LL or maintained under a light/dark cycle (LD) received phase‐resetting treatments with the 5‐HT1A,7 agonist (±)‐2‐dipropyl‐amino‐8‐hydroxyl‐1,2,3,4‐tetrahydronapthalene (8‐OH‐DPAT) or sleep deprivation (SD). Animals were released to constant darkness at the start of the treatments. Phase advances to 8‐OH‐DPAT and SD during the day were 11 and 3 h for LL vs. 2 and 1 h for LD, respectively. Phase delays during the night were −12 and −5 h for LL vs. no responses for LD, respectively. Phase‐transition curves for both LL treatments had slopes approximating 0, indicative of Type 0 phase resetting. For all treatments, the degree of locomotor suppression by LL was not correlated with the phase shift magnitude. Re‐establishing locomotor activity by overnight food deprivation did not prevent potentiated shifting to SD. However, re‐establishing peak extracellular 5‐HT levels by intra‐SCN 5‐HT reverse microdialysis perfusion in LL did significantly reduce potentiated 8‐OH‐DPAT phase advances. Constant light also enhanced intra‐SCN NPY‐induced phase advances during the day (6 vs. 2 h for LD). These results suggest that LL promotes Type 0 phase resetting by supersensitizing 5‐HT and/or NPY postsynaptic responses and possibly by attenuating the amplitude of the circadian pacemaker, thus enhancing circadian clock resetting nonspecifically.
Hybrid FDTD/UTD Indoor Channel Modeling. Application to Wifi Transmission Systems

Classical theories such as the uniform theory of diffraction (UTD) use analytical expressions for diffraction coefficients. These methods are convenient for canonical problems and objects much greater than the wavelength and enable to rise in frequency. For more complex and smaller scattering structures, rigorous methods like the finite difference time domain method (FDTD) is more adapted. In this paper, we present an original approach, combining the advantages of these two methods. This hybrid channel modelling is finally used to evaluate the BER in a Wifi transmission.
The growing burden of foodborne outbreaks due to contaminated fresh produce: risks and opportunities

SUMMARY Foodborne outbreaks from contaminated fresh produce have been increasingly recognized in many parts of the world. This reflects a convergence of increasing consumption of fresh produce, changes in production and distribution, and a growing awareness of the problem on the part of public health officials. The complex biology of pathogen contamination and survival on plant materials is beginning to be explained. Adhesion of pathogens to surfaces and internalization of pathogens limits the usefulness of conventional processing and chemical sanitizing methods in preventing transmission from contaminated produce. Better methods of preventing contamination on the farm, or during packing or processing, or use of a terminal control such as irradiation could reduce the burden of disease transmission from fresh produce. Outbreak investigations represent important opportunities to evaluate contamination at the farm level and along the farm-to-fork continuum. More complete and timely environmental assessments of these events and more research into the biology and ecology of pathogen-produce interactions are needed to identify better prevention strategies.
Intensification and Intra-Household Decisions: Fertilizer Adoption on Collective and Individual Fields in Burkina Faso

We contribute to the understanding of technology adoption decisions by complex farm households in the Sudano-Sahelian region of West Africa, where production is organized collectively under the leadership of a senior head who also allocates individual fields to members. Farm families span generations and encompass several nuclear households. We examine the nature of the linkage between fertilizer use decisions on collective and individual plots based on a conceptual model of intra-household bargaining that enables us to draw inferences about efficiency of input allocation. Although the share of individual maize plots receiving fertilizer is lower, use rates on maize tend to be higher than on collective fields. Adoption of fertilizer on a collective plot contributes to a 0.32 rise in adoption probability on an individual plot, but the converse is not true. The marginal effect of application rates on collective plots is positively associated with intensity of use on individual plots but of a magnitude consistent with inefficiency of resource allocation. Determinants of adoption differ between individual and collective fields, and between the decision to use fertilizer and the intensity of use. Findings have implications for the design of extension programs and policies to support agricultural intensification in the region.
A comparison of two different program complexity measures

In recent years, a number of program complexity metrics have been developed to measure various characteristics of computer programs [1, 3]. Included among these metrics are Zolnowski's composite measure of program complexity [4, 5] and McCade's cyclomatic measure of program complexity [2]. The present paper examines these two metrics and attempts to measure their correlation with a third metric assigned by the program's author. This metric has been called the psychological complexity or the intuitive complexity of a program.
Molecular dynamics simulation and molecular docking studies of 1,4-Dihydropyridines as P-glycoprotein’s allosteric inhibitors

P-glycoprotein (P-gp) is a main factor contributing to multidrug resistance. The effect of this transporter protein on limiting the effectiveness of chemotherapy has been shown by various studies. In a previous report, we synthesized some 14-dihydropyridine (DHP) derivatives as inhibitors of human P-gp. In the present study, a computational approach has been exploited to reveal the main interactions between DHPs and P-gp. In order to do this, homology modeling was performed to obtain a model of the protein. Then, molecular dynamics simulation was used to refine the constructed model of P-gp in the presence of the lipids bilayer. Model validation was performed with several tools. Finally, molecular docking followed by MD simulation of ligand–protein complex was employed to elucidate the binding mode and the dynamical changes of protein with/without DHPs bound. The results emphasized that interaction of the residues Gln912, Ser909, Arg905, Ser474, Val472 with DHPs play a crucial role in the inhibitory of these ligands and this was in a relatively good accordance with the results reported in the experimental studies.
A new PANI biosensor based on catalase for cyanide determination

Cyanide is one of the most widespread of compounds measured in environmental analysis due to their toxic effects on environment and health. We report a highly sensitive, reliable, selective amperometric sensor for determination of cyanide, using a polyaniline conductive polymer. The enzyme catalase was immobilized by electropolymerization. The steps during the immobilization were controlled by electrochemical impedance spectroscopy. Optimum pH, temperature, aniline concentration, enzyme concentration, and the number of scans obtained during electropolymerization, were investigated. In addition, the cyanide present in artificial waste water samples was determined. In the characterization studies of the biosensor, some parameters such as reproducibility and storage stability, were analyzed.
Genetic differences between paediatric and adult Burkitt lymphomas

Dysregulation of MYC is the genetic hallmark of Burkitt lymphoma (BL) but it is encountered in other aggressive mature B‐cell lymphomas. MYC dysregulation needs other cooperating events for BL development. We aimed to characterize these events and assess the differences between adult and paediatric BLs that may explain the different outcomes in these two populations. We analysed patterns of genetic aberrations in a series of 24 BLs: 11 adults and 13 children. We looked for genomic imbalances (copy number variations), copy‐neutral loss of heterozygosity (CN‐LOH) and mutations in TP53, CDKN2A, ID3 (exon 1), TCF3 (exon17) and CCND3 (exon 6). Young patients displayed more frequent 13q31.3q32. 1 amplification, 7q32q36 gain and 5q23.3 CN‐LOH, while 17p13 and 18q21.3 CN‐LOH were only detected in adult BLs. ID3 mutations were present in all adult samples, but only in 42% of childhood cases. CCND3 and ID3 double‐hit mutations, as well as 18q21 CN‐LOH, seemed to be associated with poorer outcome. For the first time, we report different genetic anomalies between adult and paediatric BLs, suggesting age‐related heterogeneity in Burkitt lymphomagenesis. This may explain the poorer prognosis of adult BLs. Additional studies are needed to confirm these results in the setting of clinical trials.
Overexpression of hypoxia‐inducible factor‐1α predicts an unfavorable outcome in urothelial carcinoma of the upper urinary tract

Objectives: Hypoxia‐inducible factor‐1 (HIF‐1) is a transcription factor that plays an important role in cell hypoxia adaptation. Overexpression of HIF‐1α subunit has been reported to be involved in the carcinogenesis, progression and metastasis of many human cancers. We evaluated the clinical significance of HIF‐1α expression in urothelial carcinoma (UC) of the upper urinary tract.
Utilizing self‐prepared ELISA plates for a cross‐population study of different anti‐HBe IgG subclass profiles

Fourteen serum samples obtained from hepatitis B virus (HBV) chronic carriers and patients recovered from hepatitis B infection were used with four sodium dodecyl sulfate‐treated enzyme‐linked immunosorbent assay (ELISA) plates available commercially, and one self‐prepared HBcAg analog for evaluation of anti‐HBe subclass pattern absorbance. The self‐prepared plates had the best performance and were thus used for samples obtained from 104 (60 male and 44 female) HBV chronic carriers and 439 (247 male and 192 female) recovered individuals. Tests for aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were also carried out in 21 of the subjects (>25 IU/ml). Statistical comparison of these patients with elevated ALT/AST levels with other ALT/AST‐normal chronic carriers revealed no significant differences in the anti‐HBe OD, although the mean optical density (OD) of patients with elevated ALT/AST levels was higher. The results suggest that the anti‐HBe IgG subclass profiles in the chronic carriers did not change with inflammation of the liver, and were independent of sex and age. In contrast to previous anti‐HBc findings, the distribution pattern of anti‐HBe subclasses in HBV chronic carriers was IgG1 > IgG4 > IgG3 while in the recovered individuals it was IgG1 > IgG3 > IgG4, for both males and females. Subclasses IgG1 and IgG2 were the most and least prevalent isotypes, respectively, in both study groups. The results of the study suggest that induction of IgG1 and/or IgG3 antibodies is important for effective virus neutralization, while IgG2 antibodies are of limited importance. Significantly higher OD values for anti‐HBe IgG4 were observed when comparing samples from the chronic carriers and recovered individuals, which may reflect the effects of persistence. Further, in contrast to previous anti‐HBs results, the concentrations of total IgG and IgG1 were higher in the samples from chronic carriers relative to those from recovered individuals. J. Med. Virol. 79:495–502, 2007. © 2007 Wiley‐Liss, Inc.
Service discovery based on tree structure

Since more and more services are published on the open web, service discovery is becoming a critical technology for service applications. In order to discover services it is important to calculate the similarity between services. Current approaches, such as ontology concept-based techniques, and information retrieval-based techniques only consider service's input/output as a simple datatype for service similarity calculation. However real-world services published on the web always have input/output parameters with complex datatype. Therefore it is significantly important to discover services considering complex datatype. In this paper, we propose an algorithm considering complex datatype of service's input/output by mapping services to tree structures for service discovery. And we calculate service similarity using the tree structure. First, we propose a method to mapping services to tree structure considering complex datatype. Second, we use the combination of depth among the trees to calculate the similarity between two service trees. Finally, an experiment is done and our evaluation shows our approach for service discovery based on tree structure has a better performance comparing with approaches which are only considering simple datatype.
The Change of Emerging Technology Application Domains Based on Patent Assignee

Obtaining the rule of emerging technologies evoluting in different domains can significantly contribute to fully tap the potential of technologies and promote their maximum economical efficiency.Research in this field,however,is quite limited.Firstly,it defines the technology application domain and its change.Secondly,it discusses the limitations of the methodology in previous research.Meanwhile,it puts forward the idea of detecting the change of technology application domain by tracing the change of the assignee number and the industry the assignee belongs to.Finally,it makes an empirical analysis on fuel cell and solar cell industry to verify the feasibility of the idea.
Challenges in Special Populations: HIV/HCV Coinfection, Liver Transplantation and Patients with End-Stage Renal Disease

Until recently, the combination of PEG-interferon and ribavirin (RBV) was the main treatment for all genotypes of chronic hepatitis C virus (HCV) infection. Sustained virological response (SVR) rates varied signiﬁcantly across patient subgroups and the concept of ‘special populations' emerged. Now, in the era of direct acting antivirals, with a better safety profile and higher efficacy rates, those patients with comorbidities or conditions that limited IFN-based antiviral treatment but with unmet medical needs have been considered for therapy again. With the currently approved all-oral antivirals, patients coinfected with human immunodeficiency virus and HCV have SVR rates similar to patients with HCV monoinfection. However, drug-drug interactions (DDIs) with antiretroviral drugs are still challenging. In the setting of liver transplantation, with an accelerated course of hepatitis C, previous IFN-RBV treatments were poorly tolerated and attained low SVR rates. Today, all-oral therapies have proven to be efficacious and safe in this population. Nevertheless, questions such as the optimal treatment duration or the need for RBV still remain opened. In this population as well, DDIs are an issue, as some regimens require adjustments and monitoring of immunosuppressive drugs during therapy. Finally, preliminary data show promising results in terms of efficacy and safety in patients with end-stage renal disease. However, there is clear need for more clinical studies since treatment options are still very limited.