Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty Quantification Driven Predictive Multi-Scale Model for Synthesis of Mycotoxins

Many toxic molds synthesize and release an array of poisons, termed mycotoxins that have an enormous impact on human health, agriculture and economy (1). These molds contaminate our buildings, indoor air and crops, cause life threatening human and animal diseases and reduce agricultural output (2). In order to design appropriate approaches to minimize the detrimental effects of these fungi, it is essential to develop diagnostic methodologies that can rapidly and accurately determine based on fungal strains and their growth patterns, the extent of mycotoxin mediated damage caused to the environment.Here we developed a novel multi-scale predictive mathematical model that could reliably estimate aflatoxin synthesis from growth features extracted from Aspergillusparasiticus, a well-characterized model for studying mycotoxin biosynthesis. We conducted acoustic imaging experiments to observe and extract the growth features from the biomass profiles of the growing Aspergillus colony growing on an aflatoxin-inducing solid growth medium. We employed the probability-based representation of uncertainty and used Bayes' theorem to infer the uncertain parameters in our mathematical model using biomass observations of the colony at 24h (aflatoxin is not synthesized yet at this time-point) and 48 hours (aflatoxin synthesis occurs at peak levels). We demonstrate that our model could successfully predict with quantified uncertainties the levels of aflatoxin secreted to the environment by the fungus.
A remark on copy number variation detection methods

Copy number variations (CNVs) are gain and loss of DNA sequence of a genome. High throughput platforms such as microarrays and next generation sequencing technologies (NGS) have been applied for genome wide copy number losses. Although progress has been made in both approaches, the accuracy and consistency of CNV calling from the two platforms remain in dispute. In this study, we perform a deep analysis on copy number losses on 254 human DNA samples, which have both SNP microarray data and NGS data publicly available from Hapmap Project and 1000 Genomes Project respectively. We show that the copy number losses reported from Hapmap Project and 1000 Genome Project only have < 30% overlap, while these reports are required to have cross-platform (e.g. PCR, microarray and high-throughput sequencing) experimental supporting by their corresponding projects, even though state-of-art calling methods were employed. On the other hand, copy number losses are found directly from HapMap microarray data by an accurate algorithm, i.e. CNVhac, almost all of which have lower read mapping depth in NGS data; furthermore, 88% of which can be supported by the sequences with breakpoint in NGS data. Our results suggest the ability of microarray calling CNVs and the possible introduction of false negatives from the unessential requirement of the additional cross-platform supporting. The inconsistency of CNV reports from Hapmap Project and 1000 Genomes Project might result from the inadequate information containing in microarray data, the inconsistent detection criteria, or the filtration effect of cross-platform supporting. The statistical test on CNVs called from CNVhac show that the microarray data can offer reliable CNV reports, and majority of CNV candidates can be confirmed by raw sequences. Therefore, the CNV candidates given by a good caller could be highly reliable without cross-platform supporting, so additional experimental information should be applied in need instead of necessarily.
Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes

Nanocarbon allotropes (NCAs), including zero-dimensional carbon dots (CDs), one-dimensional carbon nanotubes (CNTs) and two-dimensional graphene, exhibit exceptional material properties, such as unique electrical/thermal conductivity, biocompatibility and high quenching efficiency, that make them well suited for both electrical/electrochemical and optical sensors/biosensors alike. In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer (FRET). This review analyzes current advances in sensors and biosensors that utilize graphene, CNTs or CDs as the platform in optical sensors and biosensors. Widely utilized synthesis/fabrication techniques, intrinsic material properties and current research examples of such nanocarbon, FRET-based sensors/biosensors are illustrated. The future outlook and challenges for the research field are also detailed.
Association between ALDH 2 487 G / A polymorphism and hepatocellular carcinoma

Background: Although many studies have investigated the association of ALDH2 487G/A polymorphism with the risk of hepatocellular carcinoma (HCC), their conclusions are controversial. So a meta-analysis was carried out to further determine the correlation between the two sides. Methods: The eligible studies were searched in PubMed, ELSEVIER, and Chinese National Knowledge Infrastructure (CNKI) databases. Finally, 10 studies including 1,495 cases and 2,048 controls were incorporated in this meta-analysis. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated by the random or fixed effects model to evaluate the association between ALDH2 487G/A polymorphism and risk of HCC. The heterogeneity among studies was analyzed by Q-test and the publication bias was checked with the Begg’s funnel plot and Egger’s linear regression analysis. Results: The overall result showed that no significant association between ALDH2 487G/A polymorphism and risk of HCC was found under five genetic models including *2*2 vs. *1*1 (OR=1.06, 95% CI=0.80-1.40), *2*2 + *1*2 vs. *1*1 (OR=0.92, 95% CI=0.69-1.23, *2*2 vs. *1*2 + *1*1 (OR=1.22, 95% CI=0.83-1.79), *2 vs. *1 (OR=0.93, 95% CI=0.73-1.19) and *1*2 vs. *1*1 (OR=0.95, 95% CI=0.72-1.24). In subgroup analysis of control source, ALDH2 487G/A polymorphism was also not related to risk of HCC. Conclusion: The study demonstrated ALDH2 487G/A polymorphism may not be a risk factor for HCC. Further well-designed studies with larger sample sizes are needed to verify this result.
The evaluation of minimum detectable phantom thickness change using a scanning liquid filled ion chamber EPID dose response

Although Electronic Portal imagingDevices (EPIDs) have originally developed forpositioning verification, they can also be used fordosimetric purposes. In the current work, the doseresponse of minimum detectable thickness of aScanning Liquid filled Ion Chamber EPID, SLIC-EPID,and the variation of transmitted dose with the shift ofinhomogeneity inside of phantom were investigated.
Using data mining technique to improve billing system performance in semiconductor industry

The new billing approaches are manly to apply the integrated concept of data warehouse with relevant billing data; in addition, use the methods of mining association rule to sort out the Billing Quantities Pattern and then figure out the billing quantities. Moreover, employ the Decision Tree algorithm of data mining to find out the unit billing price. As a result, the new billing approach is made of the methods of data warehouse and date mining. This study is mainly focused on improving the operation of current billing system to establish the new functionality of the Billing quantities and Billing price. As for the benefit of these two new functions, it is not only able to lead into clients' billing systems, but it is also capable of upgrading the efficiency in rapid setup; especially for the enterprises that already possessed billing system internally but not yet implemented. In addition, it can also reduce the difference in revenue, shorten the process of issuing invoice, speed up the export operation, increase the export efficiency and provide the revenue data for integrating into the Executive Data System (EIS), Decision Support System (DSS) and Business Intelligent System (BIS) to allow enterprises making the right decisions promptly.
ESTIMATING SELECTION ON QUANTITATIVE TRAITS USING CAPTURE‐RECAPTURE DATA

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Cortical oxygen consumption in mental arithmetic as a function of task difficulty: a near-infrared spectroscopy approach

The present study investigated changes in cortical oxygenation during mental arithmetic using near-infrared spectroscopy (NIRS). Twenty-nine male volunteers were examined using a 52-channel continuous wave system for analyzing activity in prefrontal areas. With the help of a probabilistic mapping method, three regions of interest (ROIs) on each hemisphere were defined: The inferior frontal gyri (IFG), the middle frontal gyri (MFG), and the superior frontal gyri (SFG). Oxygenation as an indicator of functional brain activation was compared over the three ROI and two levels of arithmetic task difficulty (simple and complex additions). In contrast to most previous studies using fMRI or NIRS, in the present study arithmetic tasks were presented verbally in analogue to many daily life situations. With respect to task difficulty, more complex addition tasks led to higher oxygenation in all defined ROI except in the left IFG compared to simple addition tasks. When compared to the channel positions covering different gyri of the temporal lobe, the observed sensitivity to task complexity was found to be restricted to the specified ROIs. As to the comparison of ROIs, the highest oxygenation was found in the IFG, while MFG and SFG showed significantly less activation compared to IFG. The present cognitive-neuroscience approach demonstrated that NIRS is a suitable and highly feasible research tool for investigating and quantifying neural effects of increasing arithmetic task difficulty.
The Centenary of the Omori Formula for a Decay Law of Aftershock Activity

The Omori formula n(t)=K(t+c)-1 and its modified form n(t)=K(t+c)-P have been successfully applied to many aftershock sequences since the former was proposed just 100 years ago. This paper summarizes studies using these formulae. The problems of fitting these formulae and related point process models to observational data are discussed mainly. Studies published during the last 1/3 century confirmed that the modified Omori formula generally provides an appropriate representation of the temporal variation of aftershock activity. Although no systematic dependence of the index p has been found on the magnitude of the main shock and on the lowest limit of magnitude above which aftershocks are counted, this index (usually p = 0.9-1.5) differs from sequence to. sequence. This variability may be related to the tectonic condition of the region such as structural heterogeneity, stress, and temperature, but it is not clear which factor is most significant in controlling the p value. The constant c is a controversial quantity. It is strongly influenced by incomplete detection of small aftershocks in the early stage of sequence. Careful analyses indicate that c is positive at least for some sequences. Point process models for the temporal pattern of shallow seismicity must include the existence of aftershocks, most suitably expressed by the modified Omori law. Among such models, the ETAS model seems to best represent the main features of seismicity with only five parameters. An anomalous decrease in aftershock activity below the level predicted by the modified Omori formula sometimes precedes a large aftershock. An anomalous decrease in seismic activity of a region below the level predicted by the ETAS model is sometimes followed by a large earthquake in the same or in a neighboring region.
Contribution IN VIVO MULTIPARAMETRIC ULTRASOUND IMAGING OF STRUCTURAL AND FUNCTIONALTUMOR MODIFICATIONS DURING THERAPY

ALEXANDRE DIZEUX,* THOMAS PAYEN,* DELPHINE LE GUILLOU-BUFFELLO,* EVA COMPERAT,y JEAN-LUC GENNISSON,z MICKAEL TANTER,z MICHAEL OELZE,x and S. LORI BRIDAL* *Sorbonne Universit es, UPMCUniv Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biom edicale, Paris, France; yAcademic Department of Pathology, Pitie-Salpetriere Hospital, AP-HP, UPMC Univ Paris 06, Paris, France; z Institut Langevin—Ondes et Images, ESPCI ParisTech, PSL Research University, CNRS UMR7587, INSERM U979, Paris, France; and xBioacoustics Research Laboratory, Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois, USA
A genetically inducible porcine model of intestinal cancer

Transgenic porcine cancer models bring novel possibilities for research. Their physical similarities with humans enable the use of surgical procedures and treatment approaches used for patients, which facilitates clinical translation. Here, we aimed to develop an inducible oncopig model of intestinal cancer. Transgenic (TG) minipigs were generated using somatic cell nuclear transfer by handmade cloning. The pigs encode two TG cassettes: (a) an Flp recombinase‐inducible oncogene cassette containing KRAS‐G12D, cMYC, SV40LT – which inhibits p53 – and pRB and (b) a 4‐hydroxytamoxifen (4‐OHT)‐inducible Flp recombinase activator cassette controlled by the intestinal epithelium‐specific villin promoter. Thirteen viable transgenic minipigs were born. The ability of 4‐OHT to activate the oncogene cassette was confirmed in vitro in TG colonic organoids and ex vivo in tissue biopsies obtained by colonoscopy. In order to provide proof of principle that the oncogene cassette could also successfully be activated in vivo, three pigs were perorally treated with 400 mg tamoxifen for 2 × 5 days. After two months, one pig developed a duodenal neuroendocrine carcinoma with a lymph node metastasis. Molecular analysis of the carcinoma and metastasis confirmed activation of the oncogene cassette. No tumor formation was observed in untreated TG pigs or in the remaining two treated pigs. The latter indicates that tamoxifen delivery can probably be improved. In summary, we have generated a novel inducible oncopig model of intestinal cancer, which has the ability to form metastatic disease already two months after induction. The model may be helpful in bridging the gap between basic research and clinical usage. It opens new venues for longitudinal studies of tumor development and evolution, for preclinical assessment of new anticancer regimens, for pharmacology and toxicology assessments, as well as for studies into biological mechanisms of tumor formation and metastasis.
Association between polypharmacy and dementia – A systematic review and metaanalysis

Abstract Objective: The association between polypharmacy and dementia is controversial. This systematic review and meta-analysis aims to summarize existing literature concerning the association between polypharmacy and dementia. Methods: A systematic literature review was performed by searching the EMBASE, PubMed, Scopus and International Pharmaceutical Abstract databases using terms related to polypharmacy and dementia. A meta-analysis was performed using random effect models. Results: Seven studies were included in this meta-analysis. The included studies were of medium to high quality with a potential for publication bias. A strong association between polypharmacy and dementia was found (pooled adjusted risk ratio (aRR) = 1.30 (95% CI: 1.16–1.46), I2 = 68%). Excessive polypharmacy was also strongly associated with dementia (pooled aRR = 1.52 (95% CI: 1.39–1.67), I2 = 24%). Conclusion: Pooled risk estimates from this meta-analysis showed that polypharmacy was associated with dementia. Although the causality of the relationship cannot be concluded from this analysis, the finding encourages the use of multidimensional assessment tools for dementia that includes the number of medications as a component.
Diversity-Guided Dynamic Step Firefly Algorithm

Firefly Algorithm is a nature-inspired optimization method, which has been shown to implement well on numerous optimization problems. But it can easily fall into the local optima and low precision. Therefore, it is very important to overcome these defects. In this paper, we use a dynamic strategy for step setting, which takes into account the population diversity of fireflies. The experiments show that the proposed algorithm improves the performance of original firefly algorithm.
Miniature fibre optic probe for minimally invasive photoacoustic sensing

A miniature (175 μm) all-optical photoacoustic probe has been developed for minimally invasive sensing and imaging applications. The probe comprises a single optical fibre which delivers the excitation light and a broadband 50 MHz Fabry-Pérot (F-P) ultrasound sensor at the distal end for detecting the photoacoustic waves. A graded index lens proximal to the F-P sensor is used to reduce beam walk-off and thus increase sensitivity as well as confine the excitation beam in order to increase lateral spatial resolution. The probe was evaluated in non-scattering media and found to provide lateral and axial resolutions of < 100 μm and < 150 μm respectively for distances up to 1 cm from the tip of the probe. The ability of the probe to detect a blood vessel mimicking phantom at distances up to 7 mm from the tip was demonstrated in order to illustrate its potential suitability for needle guidance applications.
Soluble antigens from the neurotropic pathogen Angiostrongylus cantonensis directly induce thymus atrophy in a mouse model

The nematode Angiostrongylus cantonensis (A.C.) is a neurotropic pathogen; stage-III larva invade the human (non-permissive host) central nervous system (CNS) to cause eosinophilic meningitis or meningoencephalitis accompanied by immunosuppression. In an A.C. -infectedmouse (another non-permissive host) model, CNS damage-associated T cell immune deficiency and severe inflammation were proposed to result from activation of the hypothalamic-pituitary-adrenal (HPA) axis. However, glucocorticoids are anti-inflammatory agents. Additionally, while defects in thymic stromal/epithelial cells (TECs) are the major reason for thymic atrophy, TECs do not express the glucocorticoid receptor. Therefore, activation of the HPA axis cannot fully explain the thymic atrophy and inflammation. Using an A.C. -infected mouse model, we found that A.C. -infected mice developed severe thymic atrophy with dramatic impairments in thymocytes and TECs, particularly cortical TECs, which harbor CD4+CD8+ double-positive thymocytes. The impairments resulted from soluble antigens (sAgs) from A.C. in the thymuses of infected mice, as intrathymic injection of these sAgs into live mice and the addition of these sAgs to thymic cell culture resulted in thymic atrophy and cellular apoptosis, respectively. Therefore, in addition to an indirect effect on thymocytes through the HPA axis, our study reveals a novel mechanism by which A.C. infection in non-permissive hosts directly induces defects in both thymocytes and TECs via soluble antigens.
Sub-national health care financing reforms in Indonesia

Indonesia has seen an emergence of local health care financing schemes over the last decade, implemented and operated by district governments. Often motivated by the local political context and characterized by a large degree of heterogeneity in scope and design, the common objective of the district schemes is to address the coverage gaps for the informal sector left by national social health insurance programs. This paper investigates the effect of these local health care financing schemes on access to health care and financial protection. Using data from a unique survey among District Health Offices, combined with data from the annual National Socioeconomic Surveys, the study is based on a fixed effects analysis for a panel of 262 districts over the period 2004–10, exploiting variation in local health financing reforms across districts in terms of type of reform and timing of implementation. Although the schemes had a modest impact on average, they do seem to have provided some contribution to closing the coverage gap, by increasing outpatient utilization for households in the middle quintiles that tend to fall just outside the target population of the national subsidized programs. However, there seems to be little effect on hospitalization or financial protection, indicating the limitations of local health care financing policies. In addition, we see effect heterogeneity across districts due to differences in design features.
Bioremediation of Thiocyanate from Coke-Oven Wastewater Using a Novel Cyanobacterial Strain and Synthesis of Biomolecules

In the present study bioremediation of thiocyanate from coke-oven wastewater using a cyanobacterial strain Leptolyngbya foveolauram was done. Kinetic study for the bioremediation of thiocyanate was done by varying the initial concentration of thiocyanate from 10 to 250 mg/L while other parameters were kept constant as inoculum size of 10% and pH 10. Concentrations of biomolecules viz., carbohydrate, protein and lipid in the cyanobacterial strain are also measured during remediation of thiocyanate. Results revealed that 100% and 78.20% of thiocyanate has been remediated in synthetic wastewater with initial thiocyanate concentration of 10 and 50 mg/L respectively. Fatty Acid Methyl Ester (FAME) analysis was studied and compared with native strain and thiocyanate treated one.
Association of Vascular Endothelial Growth Factor Expression with Tumor Angiogenesis and with Early Relapse in Primary Breast Cancer

Angiogenesis is an independent prognostic indicator in breast cancer. In this report, the relationship between expression of vascular endothclial growth factor (VEGF; a selective mitogen for endothelial cells) and the microvessel density was examined in 103 primary breast cancers. The expression of VEGF was evaluated by immunocytochemical staining using anti‐VEGF antibody. The microvessel density, which was determined by immunostaining for factor VIII antigen, in VEGF‐rich tumors was clearly higher than that in VEGF‐poor tumors (P<0.01). There was a good correlation between VEGF expression and the increment of microvessel density. Furthermore, postoperative survey demonstrated that the relapse‐free survival rate of VEGF‐rich tumors was significantly worse than that of VEGF‐poor tumors. It was suggested that the expression of VEGF is closely associated with the promotion of angiogenesis and with early relapse in primary breast cancer.