Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analysis of miRNA-mRNA Interaction Network in Breast Cancer with Brain Metastasis.

BACKGROUND MicroRNAs (miRNAs) have been linked to a number of cancer types including breast cancer. The rate of brain metastases is 10-30% in patients with advanced breast cancer which is associated with poor prognosis. The potential application of miRNAs in the diagnostics and therapeutics of breast cancer with brain metastasis is an area of intense interest. In an initial effort to systematically address the differential expression of miRNAs and mRNAs in primary breast cancer which may provide clues for early detection of brain metastasis, we analyzed the consequent changes in global patterns of gene expression in Gene Expression Omnibus (GEO) data set obtained by microarray from patients with in situ carcinoma and patients with brain metastasis. MATERIALS AND METHODS The miRNA-pathway regulatory network and miRNA-mRNA regulatory network were investigated in breast cancer specimens from patients with brain metastasis to screen for significantly dysregulated miRNAs followed by prediction of their target genes and pathways by Gene Ontology (GO) analysis. RESULTS Functional coordination of the changes of gene expression can be modulated by individual miRNAs. Two miRNAs, hsa-miR-17-5p and hsa-miR-16-5p, were identified as having the highest associations with targeted mRNAs [such as B-cell lymphoma 2 (BCL2), small body size/mothers against decapentaplegic 3 (SMAD3) and suppressor of cytokine signaling 1 (SOCS1)] and pathways associated with epithelial-mesenchymal transitions and other processes linked with cancer metastasis (including cell cycle, adherence junctions and extracellular matrix-receptor interaction). mRNAs for two genes [HECT, UBA and WWE domain containing 1 (HUWE1) and BCL2] were found to have the highest associations with miRNAs, which were down-regulated in brain metastasis specimens of breast cancer. The change of 11 selected miRNAs was verified in The Cancer Genome Atlas (TCGA) breast cancer dataset. Up-regulation of hsa-miR-17-5p was detected in triple-negative breast cancer tissues in TCGA. Furthermore, a negative correlation of hsa-miR-17-5p with overall survival and phosphatase and tensin homolog (PTEN) and BCL2 target genes was found in TCGA breast cancer specimens. CONCLUSION Our findings provide a functionally coordinated expression pattern of different families of miRNAs that may have potential to provide clinicians with a strategy to treat breast cancer with brain metastasis from a systems-rather than a single-gene perspective.
Sialidase inhibition to increase platelet counts: A new treatment option for thrombocytopenia

Finally, we did not detect a specific gene expression signature for GATA2 mutated vs. non-mutated cases. Overall, CR was achieved in 113 patients (88%), of whom 36 relapsed (estimated CIR at 3 and 5 years, 39%). Neither age nor karyotype or gene mutations (including NPM1, FLT3, of GATA2 and type CEBPA mutation) significantly influenced CIR in multivariate analysis. Five-year OS was estimated at 58% in the whole cohort, with longer OS in cases with normal karyotype (P5 0.05) and CEBPA biallelic mutations (dm vs. sm, P5 0.03). In multivariate analysis, younger age (P5 0.020) and normal karyotype (P5 0.029) remained the only factors significantly associated with better overall survival. Of note, CEBPA bi-allelic mutations occur more frequently in younger patients. More specifically, the presence of GATA2 mutations did not affect OS in CEBPA mutated AML in general and not within CEBPA dm mutated AML neither. In conclusion, we confirmed a strong association of GATA2 mutations with CEPBA biallelic-mutations, which was not exclusive. However, we confirmed no prognostic impact of GATA2 mutations (n5 25) compared to wild-type (n5 62) in our cohort of CEBPA dm AML [8,9] (22 vs. 58 and 10 vs. 16) with a trend similar of better outcome in CEBPA dm with GATA2 mutations compared to wild-type [5,6] (18 vs. 62). Furthermore, our study provided first evidence that homozygous CEPBA mutations have a similar gene expression signature as CEPBA dm and thus may be considered as equivalent. Acknowledgments. Authors acknowledge the contribution of Nicolas Duployez PharmD, Olivier Nibourel PharmD PhD, Nathalie Helevaut, C eline Rodriguez, Karine Celli-Lebras, C eline Berthon MD PhD, Guy Leverger MD, Nicolas Boissel MD PhD, Christine Terr e PharmD, Xavier Thomas MD, and Aline Renneville PharmD PhD.
A Six Months Follow-Up on Children Less Than 6 Years Old in Contact With Smear Positive Tuberculosis Patients, Varamin City, Tehran, Iran

Objectives: Current international guidelines recommend 6-9 months of Isoniazid (INH) preventive chemotherapy to prevent the development of active tuberculosis in children exposed to smear positive tuberculosis (TB) patients. The aim of the present study was to evaluate the adherence to a six-month of supervised INH prophylaxis program and outcome in children with household exposure to an adult pulmonary tuberculosis index case in Varamin city, Tehran, Iran. Methods: This cross sectional study was conducted among household contacts in Varamin city, between 1997- 1998. All children <6 years old with a household contact with an adult pulmonary tuberculosis index case were screened for tuberculosis and given supervised INH preventive chemotherapy once active tuberculosis was excluded as planned. Adherence and outcome were monitored. Results: In total, 31 index cases and 128 household contact cases were identified; 23 (18%) children <6 years old experienced household exposure, who were fully evaluated. two children were treated for active tuberculosis and 15 (12%) children received preventive chemotherapy. All children completed 6 months of supervised INH prophylaxis with normal clinical examination in 3 and 6 months after beginning INH prophylaxis. No side effects (peripheral neuropathy or liver damage) were reported or observed within this study. Conclusions: Strategy of six months of supervised INH chemoprophylaxis is successful, particularly in children who are at a high risk to progress to disease following exposure.
Technical advancement and the stimulation of companies innovation activity by business support organisations in developed regions

Motivation: Currently, an increasing role in achieving the competitive advantage is attributed to knowledge and its conversion to new products and services. For this reason, institutions have been set up, which are designed to stimulate the innovation activity in the economy. Their development was initiated in developed countries, and then moved to the developing countries. Aim: The article presented the influence of business support institution, which most frequently occur in the Polish reality, i.e., technological parks, technological incubators, academic business incubators, technology transfer centers, business angel networks, local or regional loan funds, credit guarantee funds and training-advisory centers for the innovation activity of industrial companies with consideration of the manufacturing techniques used by them in the developed regions of Poland, i.e., from the Lower Silesia, Silesia and Greater Poland. Results: Innovation attributes were distinguished according to the standards of studying the innovation activity contained in the Oslo methodology. For the conduct of analyses the probit modeling was used. The hypothesis of the article is the statement that the innovation of companies will grow after establishing cooperation with business support institutions, while its level will be bigger when the level of manufacturing technique used by the companies is bigger.
Use of Habitats as Surrogates of Biodiversity for Efficient Coral Reef Conservation Planning in Pacific Ocean Islands

Abstract: Marine protected areas (MPAs) have been highlighted as a means toward effective conservation of coral reefs. New strategies are required to more effectively select MPA locations and increase the pace of their implementation. Many criteria exist to design MPA networks, but generally, it is recommended that networks conserve a diversity of species selected for, among other attributes, their representativeness, rarity, or endemicity. Because knowledge of species’ spatial distribution remains scarce, efficient surrogates are urgently needed. We used five different levels of habitat maps and six spatial scales of analysis to identify under which circumstances habitat data used to design MPA networks for Wallis Island provided better representation of species than random choice alone. Protected‐area site selections were derived from a rarity–complementarity algorithm. Habitat surrogacy was tested for commercial fish species, all fish species, commercially harvested invertebrates, corals, and algae species. Efficiency of habitat surrogacy varied by species group, type of habitat map, and spatial scale of analysis. Maps with the highest habitat thematic complexity provided better surrogates than simpler maps and were more robust to changes in spatial scales. Surrogates were most efficient for commercial fishes, corals, and algae but not for commercial invertebrates. Conversely, other measurements of species‐habitat associations, such as richness congruence and composition similarities provided weak results. We provide, in part, a habitat‐mapping methodology for designation of MPAs for Pacific Ocean islands that are characterized by habitat zonations similar to Wallis. Given the increasing availability and affordability of space‐borne imagery to map habitats, our approach could appreciably facilitate and improve current approaches to coral reef conservation and enhance MPA implementation.
Efficient subchannel allocation based on clustered interference alignment in ultra-dense femtocell networks

In this paper, we exploit clustered interference alignment (IA) for efficient subchannel allocation in ultra-dense orthogonal frequency division multiplexing access (OFDMA) based femtocell networks, which notably improves the spectral efficiency as well as addresses the feasibility issue of IA. Our problem is formulated as a combinatorial optimization problem which is NP-hard. To avoid obtaining its optimal solution by exhaustive search, we propose a two-phases efficient solution with low-complexity. The first phase groups all the femtocell user equipments (FUEs) into disjoint clusters, and the second phase allocates subchannels to the formed clusters where IA is performed. By doing this, the intra-cluster and inter-cluster interferences are mitigated by clustered IA and subchannel allocation in ultra-dense femtocell networks, respectively. Also, low-complexity algorithm is proposed to solve the corresponding sub-problem in each phase. Simulation results demonstrate that the proposed scheme not only outperforms other related schemes, but also provides a close performance to the optimal solution.
The First 3-D-Printed z-Axis Accelerometers With Differential Capacitive Sensing

In this paper, additive manufacturing and wet metallization process are combined to fabricate three prototypes of differential electro-mechanical <inline-formula> <tex-math notation="LaTeX">${z}$ </tex-math></inline-formula>-axis accelerometers. The smart combination of existing fabrication processes makes the proposed fabrication flow unique in the sensors field. The mechanical design of the three proposed devices exploits the three-dimensionality of the 3-D-printing technique and the electrostatic differential readout is allowed thanks to the wet-metallization process of the printed structure. Experimental measurements show a very good agreement with theoretical predictions thus proving a good reliability of the proposed design flow and fabrication process. With their relative small footprints (minimum dimension in the order of hundreds of <inline-formula> <tex-math notation="LaTeX">${\mu }\text{m}$ </tex-math></inline-formula>), good performances (sensitivity >12 fF/g, sub % linearity error up to 11 g of full scale and theoretical noise estimation of few tens of ng/<inline-formula> <tex-math notation="LaTeX">$\surd $ </tex-math></inline-formula>Hz) and high customizability, they represent an important step toward novel application fields of inertial sensors.
Calcium‐binding proteins define interneurons in HVC of the zebra finch (Taeniopygia guttata)

Nucleus HVC of the avian song system is essential to song patterning and is a prime site for auditory–vocal integration important to vocal learning. These processes require precise, high‐frequency action potential activity, which, in other systems, is often correlated with the expression of calcium‐binding proteins. To characterize any such functional specializations in HVC, we retrogradely labeled projection neurons innervating HVC's known targets, namely, area X or nucleus robustus arcopallialis (RA), then stained HVC sections with antibodies to the calcium‐binding proteins parvalbumin, calbindin, and calretinin. Under epifluorescent illumination, neither projection neuron type exhibited detectable levels of calcium‐binding protein immunoreactivity, whereas a third cell type, made up of nonprojection neurons (interneurons), was immunopositive for one, two, or all three of the calcium‐binding proteins. In fact, most of these interneurons were either doubly or triply labeled. To explore the link between the electrical and calcium‐binding protein properties of individual HVC neurons, we used intracellular methods in brain slices to record from identified HVC cell types based on their intrinsic electrical properties. Intracellular neurobiotin combined with immunostaining revealed that fast‐spiking interneurons, but not the slower‐spiking projection neurons, were positive for one or more calcium‐binding proteins. Confocal microscopy confirmed these results and also revealed that RA‐projecting cells might contain very low levels of parvalbumin. These results indicate that HVC interneurons are specialized in their calcium‐binding proteins and suggest how it might be possible to resolve the details of HVC microcircuits underlying song selectivity and auditory–vocal learning. J. Comp. Neurol. 483:76–90, 2005. © 2005 Wiley‐Liss, Inc.
Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass

ABSTRACT Here, we present the genome sequence of the dark septate fungal endophyte Microdochium bolleyi (Ascomycota, Sordariomycetes, Xylariales). The assembled genome size was 38.84 Mbp and consisted of 173 scaffolds and 13,177 predicted genes.
Minute Pulsed Electromagnetic Neurostimulation for Mixed Trauma Syndromes

Research regarding noninvasive brain stimulation technologies for the treatment of mild traumatic brain injury (mTBI), posttraumatic stress disorder (PTSD), and mixed (mTBI/PTSD) trauma syndromes has been increasing exponentially. Technologies with the greatest potential thus far include repetitive transcranial magnetic stimulation (rTMS), transcranial direct current stimulation (tDCS), and cranial electrotherapy stimulation (CES). The nature and some of the controversies distinguishing mTBI, PTSD, and mTBI/PTSD are reviewed along with evidence for shared underlying mechanisms. An overview of treatment applications for rTMS, tDCS, and CES are also reviewed. A novel variant of a minute pulsed electromagnetic stimulation technology linked to ongoing electroencephalograph monitoring known as the Flexyx Neurotherapy System is introduced with an overview of the technology and technique, as well as a summary of supportive data to date that explores potential applications for amelioration of these syndromes.
Energy management strategy for Diesel hybrid electric vehicle

This paper focuses on hybrid energy management for a Diesel hybrid electric vehicle (HEV). The paper presents an adaptation of the equivalent consumption minimization strategy (ECMS) dedicated to the Diesel HEV control issues. The purpose of this paper is to introduce an additional degree of freedom into the ECMS that allows to modify the optimization tradeoffs from the pure fuel economy case to the pure NOx limitation case. The influence of this weighting parameter is evaluated for several engine configurations. The main contribution of this paper is to provide tools and methods to deal with the Diesel HEV control task. This paper applies a methodology based on SiL and HiL simulations in order to understand the system performance according to the powertrain configurations and also to tune the proposed energy management strategy. The simulation results are confirmed by experiments performed on hybrid-hardware in the loop (Hy-HiL) test bench. These results demonstrate the ability of the proposed strategy to reduce the NOx emissions while maintaining a reasonable fuel consumption. This result is mostly due to the ability of the modified ECMS to operate the Diesel engine within its LTC region where the NOx emissions are very low.
Keratinocytes from patients with atopic dermatitis and psoriasis show a distinct chemokine production profile in response to T cell-derived cytokines.

BACKGROUND Atopic dermatitis (AD) and psoriasis are genetically determined inflammatory skin disorders. Keratinocytes actively participate in cutaneous inflammatory responses by elaborating various chemokines. OBJECTIVE We investigated the capacity of IL-4, IFN-gamma, and TNF-alpha to modulate the expression of CCL and CXCL chemokines in cultured keratinocytes from patients and healthy individuals, as well as chemokine expression in situ. METHODS Keratinocyte cultures were established from normal-looking skin of adult patients with AD or psoriasis vulgaris and from healthy subjects. Monocyte chemoattractant protein 1 (MCP-1)/CCL2, RANTES/CCL5, IL-8/CXCL8, and IFN-gamma-induced protein of 10 kd (IP-10)/CXCL10 production was evaluated at the mRNA and protein levels by using RNase protection assay and ELISA, respectively. The expression of the same chemokines was studied in chronic lesional skin by means of immunohistochemistry or in situ hybridization. RESULTS Only IL-8 mRNA was detected in unstimulated ke-ratinocyte cultures. MCP-1 and IP-10 were potently induced by IFN-gamma, whereas IL-8 and RANTES were preferentially upregulated by TNF-alpha and, to a lesser extent, by IFN-gamma. IL-4 weakly induced IP-10, RANTES, and IL-8 but not MCP-1. Keratinocytes of patients with AD invariably responded with significantly earlier and higher RANTES expression. By contrast, keratinocytes of patients with psoriasis displayed much higher levels of both constitutive and induced IL-8 and a stronger induction of MCP-1 and IP-10. RANTES and MCP-1 mRNA(+) keratinocytes were detected in the basal layer of lesions of patients with AD and psoriasis. IP-10 and IL-8 were consistently upregulated in the epidermis of patients with psoriasis but not in lesions of patients with AD. CONCLUSIONS Keratinocytes of patients with AD and psoriasis show an intrinsically abnormal and different chemokine production profile and may thus favor the recruitment of distinct leukocyte subsets into the skin.
Assessment of myocardial adrenergic innervation with a solid-state dedicated cardiac cadmium-zinc-telluride camera: first clinical experience.

AIMS To investigate the relationships between regional adrenergic innervation heterogeneity, myocardial perfusion, and contractile function obtained by means of a low-dose imaging protocol with a cadmium-zinc-telluride (CZT) dedicated camera. METHODS Twenty-eight patients with or without ischaemic heart disease underwent (123)I-metaiodobenzylguanidine (MIBG) planar scintigraphic and CZT early and delayed evaluations followed by (99m)Tc-tetrofosmin rest gated CZT with a single-day protocol. The heart-to-mediastinum ratio and the washout rate were computed from planar (123)I-MIBG images. The summed (123)I-MIBG defect scores (SS-MIBG) were semi-quantitatively assessed from CZT images. The summed rest score (SRS), summed motion score (SMS), and summed thickening score (STS) were quantitated from (99m)Tc-tetrofosmin images. RESULTS Sixteen patients showed a depressed left ventricular systolic function [ejection fraction (EF)<50%]. They presented higher SRS (P = 0.007), SMS (P < 0.001), STS (P < 0.001), and early SS-MIBG (P = 0.007) values than those with normal contractile function. Interestingly, higher early SS-MIBG values, index of regional sympathetic innervation heterogeneity, clustered with more elevated SRS (P = 0.023), and more impaired measures of regional and global left ventricle systolic function, i.e. SMS (P = 0.046), STS (P = 0.014), and EF (P = 0.027). At multivariate analysis, a higher SRS (P = 0.039) remained the only independent predictor of more elevated early SS-MIBG values. In the 20 of 28 ischaemic patients, the correlations between early SS-MIBG and SMS (P = 0.017) and also STS (P = 0.036) were further confirmed. The effective dose of the investigation was 4.2 ± 0.72 mSv. CONCLUSIONS An altered early SS-MIBG, assessed with a low-dose imaging protocol and a CZT cardiac camera, identifies patients with more impaired myocardial perfusion and contractile function.
Recent progress in polar metabolite quantification in plants using liquid chromatography–mass spectrometry.

Metabolite analysis or metabolomics is an important component of systems biology in the post-genomic era. Although separate liquid chromatography (LC) methods for quantification of the major classes of polar metabolites of plants have been available for decades, a single method that enables simultaneous determination of hundreds of polar metabolites is possible only with gas chromatography–mass spectrometry (GC–MS) techniques. The rapid expansion of new LC stationary phases in the market and the ready access of mass spectrometry in many laboratories provides an excellent opportunity for developing LC–MS based methods for multi-target quantification of polar metabolites. Although various LC–MS methods have been developed over the last 10 years with the aim to quantify one or more classes of polar compounds in different matrices, currently there is no consensus LC–MS method that is widely used in plant metabolomics studies. The most promising methods applicable to plant metabolite analysis will be reviewed in this paper and the major problems encountered highlighted. The aim of this review is to provide plant scientists, with limited to moderate experience in analytical chemistry, with up-to-date and simplified information regarding the current status of polar metabolite analysis using LC–MS techniques.
Tumor risks and genotype–phenotype–proteotype analysis in 358 patients with germline mutations in SDHB and SDHD

Succinate dehydrogenase B (SDHB) and D (SDHD) subunit gene mutations predispose to adrenal and extraadrenal pheochromocytomas, head and neck paragangliomas (HNPGL), and other tumor types. We report tumor risks in 358 patients with SDHB (n=295) and SDHD (n=63) mutations. Risks of HNPGL and pheochromocytoma in SDHB mutation carriers were 29% and 52%, respectively, at age 60 years and 71% and 29%, respectively, in SDHD mutation carriers. Risks of malignant pheochromocytoma and renal tumors (14% at age 70 years) were higher in SDHB mutation carriers; 55 different mutations (including a novel recurrent exon 1 deletion) were identified. No clear genotype–phenotype correlations were detected for SDHB mutations. However, SDHD mutations predicted to result in loss of expression or a truncated or unstable protein were associated with a significantly increased risk of pheochromocytoma compared to missense mutations that were not predicted to impair protein stability (most such cases had the common p.Pro81Leu mutation). Analysis of the largest cohort of SDHB/D mutation carriers has enhanced estimates of penetrance and tumor risk and supports in silicon protein structure prediction analysis for functional assessment of mutations. The differing effect of the SDHD p.Pro81Leu on HNPGL and pheochromocytoma risks suggests differing mechanisms of tumorigenesis in SDH‐associated HNPGL and pheochromocytoma. Hum Mutat 31:41–51, 2010. © 2009 Wiley‐Liss, Inc.