Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural determinants of Trk receptor specificities using BNDF‐based neurotrophin chimeras

Neurotrophins play very important roles in the development and maintenance of the vertebrate nervous system. In mammals, there are four members of the family: NGF, BDNF, NT‐3, and NT‐4/5. Members of the neurotrophin family activate different receptors that belong to a class of receptor tyrosine kinases known as “Trks. ” For example, NGF is the specific ligand of TrkA, while BDNF activates TrkB. To elucidate which regions of the two neurotrophins determine the receptor specificities, chimeric neurotrophins were constructed using BDNF as the backbone, with various regions being substituted by the corresponding regions of NGF. The activity of the chimeras on the Trk receptors was assayed in transfected fibroblasts ectopically expressing the Trk receptors. Our findings revealed that, although BDNF is absolutely conserved in mammals, substitution of several small variable regions from NGF into the BDNF backbone did not lead to significant loss in TrkB activity or gain in TrkA activity. Moreover, important determinants of TrkB activation might be located in the carboxy‐terminal half of BDNF. On the other hand, critical elements for TrkA activation might be located within the amino‐terminal half of the mature NGF molecule. © 1996 Wiley‐Liss, Inc.
Estimating Building Age with 3D GIS

Building datasets (e.g. footprints in OpenStreetMap and 3D city models) are becoming increasingly available worldwide. However, the thematic (attribute) aspect is not always given attention, as many of such datasets are lacking in completeness of attributes. A prominent attribute of buildings is the year of construction, which is useful for some applications, but its availability may be scarce. This paper explores the potential of estimating the year of construction (or age) of buildings from other attributes using random forest regression. The developed method has a two-fold benefit: enriching datasets and quality control (verification of existing attributes). Experiments are carried out on a semantically rich LOD1 dataset of Rotterdam in the Netherlands using 9 attributes. The results are mixed: the accuracy in the estimation of building age depends on the available information used in the regression model. In the best scenario we have achieved predictions with an RMSE of 11 years, but in more realistic situations with limited knowledge about buildings the error is much larger (RMSE = 26 years). Hence the main conclusion of the paper is that inferring building age with 3D city models is possible to a certain extent because it reveals the approximate period of construction, but precise estimations remain a difficult task.
High‐throughput parallel proteogenomics: A bacterial case study

In recent years, a new paradigm for genome annotation has emerged, termed "proteogenomics," that leverages peptide MS to annotate a genome. This is achieved by mapping peptides to a six‐frame translation of a genome, including available splice databases, which may suggest refinements to gene models. Using this approach, it is possible to refine gene regions such as exon boundaries, novel genes, gene boundaries, frame shifts, reverse strands, translated UTRs, and novel splice junctions. One of the challenges of proteogenomics is how best to (1) tackle assigning confidence to any resulting annotation and (2) apply these gene model refinements, either through manual annotation or through an automated process via training gene prediction tools. This is not a straightforward process, as many gene prediction tools have their defined suitability for niche genomes (either eukaryotic or prokaryotic) trained on and refined with model organisms such as Arabidopsis thaliana and Escherichia coli, and varying degrees of features that can leverage the use of external evidence. In this study, we outline a suitable approach toward preprocessing mass spectra and optimizing the MS/MS search for a given dataset. We also discuss future challenges, which continue to pose a problem in the field of proteogenomics, and better strategies to successfully tackle them with, using existing tools. We use Bradyrhizobium diazoefficiens (Nitrogen‐fixing bacteria), with a 9.1 Mb genome as a case study, utilizing the latest in second‐generation proteogenomics tools with multiple gene models for cross‐validation of proteogenomics annotations.
Data Science Vis-à-Vis efficient healthcare and medical systems: A techno-managerial perspective

A large number of structured or unstructured data is the core of big data which organizations and institutions have the potentially for the analysis of business as well as other requirements. In big data platform data or information basically comes from different sources and importantly collected outcome of scientific experiments is used in the internet of things. In Big Data systems, Data may be treated as a source of intelligent systems mechanism by the use of separate software tools before analytics. It is an important fact that technology is rising everyday e.g. social media, in which the creation of information is just takes few seconds from the users. Data Science program is another terminology for Big Data. The Data Science is also referred as Business Analytics or simply Analytics domain. There are several applications of Big Data found in different sectors which include the Healthcare, Banking and Finance, Information Foundations as well as Corporate sectors. There is currently a shortage of data scientists and other analysts who have experience working with big data. Medical service is an emerging area in which applications of cloud based service are highly noticed in these days. Moreover analyzing in Big Data Management System helps in managing information in multiple scales in Health Care Service that include a particular disease to detailed of DNA, proteins and metabolites to cells, tissues, organs, organisms and ecosystems. This is a conceptual and also a kind of policy paper in which several in general aspects of big data with focused on medical systems have been illustrated. Paper is also explores potentialities of creating manpower for medical informatics or similar professionals having adequate knowledge of big data and analytics technologies.
Consistent with hypothesis iii , some studies reported tall trees to be more vulnerable to drought than smaller trees (

Amazonian tree communities have already been seriously impacted by extreme natural droughts, and intense droughts are predicted to increase in frequency. However, our current knowledge of Amazonian tree species’ responses to water stress remains limited, as plant trait databases include few drought tolerance traits, impeding the application and predictive power of models. Here we explored how leaf water potential at turgor loss point (πtlp), a determinant of leaf drought tolerance, varies with species life history, season, tree size and irradiance within a forest in French Guiana. First, we provided a further direct validation of a rapid method of πtlp determination based on osmometer measurements of leaf osmotic potential at full hydration for five Amazonian tree species. Next, we analysed a dataset of 131 πtlp values for a range of species, seasons, size (including saplings), and leaf exposure. We found that early-successional species had less drought-tolerant leaves than late-successional species. Species identity was the major driver of πtlp variation, whereas season, canopy tree size and leaf exposure explained little variation. Shifts in πtlp from saplings to canopy trees varied across species, and sapling leaf drought tolerance was a moderate predictor of canopy tree leaf drought tolerance. Given its low within-species variability, we propose that πtlp is a robust trait, and is useful as one index of species’ drought tolerance. We also suggest that measuring this trait would considerably advance our knowledge on leaf drought tolerance in hyperdiverse communities and would thus likely shed light on the resilience of such vulnerable species-rich ecosystem.
A reconfigurable integrated transmission line ΣΔ modulator for the UWB/WLAN receiver

This paper presents a receiver structure for supporting ultra-wide-band (UWB) and wireless local area network (WLAN) standards using integrated transmission-line sigma delta modulators (ITLSDMs) as the baseband (BB) block. The operational transconductance amplifiers (OTAs) and the integrated transmission lines (ITLs) of the ITLSDM act as the variable gain amplifiers (VGAs) for the on-off keying (OOK) impulse radio UWB. They are reconfigured as high quality factor bandpass filters in the closed loop form for the WLAN standard. The simulation results approve the feasibility and achieving acceptable signal to noise ratio (SNR) at the output of the receiver for both schemes.
Defect evaluation using the phase information of an EC-GMR sensor

Phase information is employed to enhance evaluating defects in the metals by eddy current testing using the conventional probes. But for an EC-GMR sensor, the output phase is not used. In this paper, GMR-based eddy current defect detection is studied, in which the phase of the GMR sensor output is taken into account. Based on Biot-Savart law, amplitude and phase for the EC-GMR sensor's output are studied. This paper shows that defect can be better located through the phase analysis of the GMR sensor's output.
Highly sensitive assay of okadaic acid using protein phosphatase and paranitrophenyl phosphate.

A colorimetric phosphatase-inhibition bioassay was developed for the quantitative measurement of okadaic acid (OA) the main diarrhetic toxin responsible for diarrhetic shellfish poisoning. The assay used an artificial substrate, paranitrophenylphosphate, and a semi-purified protein phosphatase PP2Ac containing extract prepared from rabbit muscle. Calibration dose-inhibition curves were constructed using standard OA and they permitted easy determination of the enzyme concentration Et in their linear portion. In the range of linearity, the slope increased when Et decreased, thus giving a detecting limit of 0.04 pmol in the reaction mixture (1 ml). The lowest assayable concentration of OA was 4 ng/ml in aqueous solutions and 40 ng/ml (i.e., 100 ng of OA per g of mussel tissue) in crude methanol mussels extracts. The intra and interassay coefficients of variation in the measurement of OA for the toxin spiked aqueous samples averaged, respectively, 7.7% and 3.7%, and interexperiments coefficients of variation for the toxin spiked mussel extracts averaged 4.6%. The presence of OA was ascertained by a method in which one assay was performed at two or three different levels of enzyme concentration. The rapidity, accuracy, reproducibility, specificity, and simplicity of the procedure provides a simple way to assay okadaic acid in buffered or complex solutions.
Mycorrhizal abundance affects the expression of plant resistance traits and herbivore performance

The effects of mutualistic interactions on partner phenotype and fitness can vary with many factors, including the abundance of interacting partners. Partner abundance may determine the relative costs and benefits associated with the interaction. Although arbuscular mycorrhizal fungi (AMF) can strongly influence plant phenotype and community interactions, the effects of AMF abundance on plant resistance traits and multitrophic interactions are not well understood. We tested the hypothesis that increasing AMF abundance in soil will increase mycorrhizal colonization and affect plant biomass, foliar phosphorus concentration, the expression of plant resistance and herbivore performance. We inoculated Asclepias syriaca seedlings with Glomus etunicatum, Scutellospora fulgida and a mix of the two species in 11 AMF abundance treatments. We quantified plant phosphorus (P), growth and resistance phenotype and the performance of a specialist herbivore, Danaus plexippus on plants associated with varying amounts of fungi. Increasing abundance of S. fulgida or G. etunicatum in soil increased the proportion of plant root colonized by AMF, but root colonization by a mix of the fungi was not related to inoculum density. The abundance of S. fulgida, but not G. etunicatum, increased per cent foliar P and trichome density, but decreased latex exudation. Abundance of all AMF treatments tended to decrease specific leaf mass (SLM), and the two single‐species treatments unimodally affected the expression of total foliar cardenolides. Increasing abundance of the mix of AMF species also increased above‐ground biomass, foliar P and trichome density, but had little effect on other traits. The presence of AMF, species identity and the AMF abundance all explained significant variation in the expression of plant traits, although their relative contribution varied depending on the trait examined. Mycorrhizal abundance strongly increased caterpillar growth rate, which was associated with a decline in SLM. Synthesis. Variation in mycorrhizal abundance can profoundly influence the expression of plant resistance and subsequent herbivore performance. AMF abundance may be a key, but overlooked factor in determining the outcome of mycorrhizal mutualisms.
Integrated Method for Text Detection in Natural Scene Images

In this paper, we present a novel image operator to extract textual information in natural scene images. First, a powerful refiner called the Stroke Color Extension, which extends the widely used Stroke Width Transform by incorporating color information of strokes, is proposed to achieve significantly enhanced performance on intra-character connection and non-character removal. Second, a character classifier is trained by using gradient features. The classifier not only eliminates non-character components but also remains a large number of characters. Third, an effective extractor called the Character Color Transform combines color information of characters and geometry features. It is used to extract potential characters which are not correctly extracted in previous steps. Fourth, a Convolutional Neural Network model is used to verify text candidates, improving the performance of text detection. The proposed technique is tested on two public datasets, i.e., ICDAR2011 dataset and ICDAR2013 dataset. The experimental results show that our approach achieves state-of-the-art performance.
Hepatic Surgery for Colorectal Cancer Metastasis — Possibilities and Prerequisites

Colorectal cancer is among the most frequent malignant tumours. Liver metastases develop in 70–75% of patients affected by colorectal carcinoma. Nowadays, surgical treatment can significantly improve the 5-year survival ranging 40–58% of the patients undergoing liver surgery. The operation extent ranges from nonanatomic minor resection to major hepatectomy. Recently, liver transplantation has been performed for metastatic colorectal cancer. Laparoscopic approach and robotic surgery can be used by experienced specialists. The prerequisites for successful surgical treatment include exact radiologic diagnostics to determine the number and size of metastases and their association with anatomic structures; individual anatomic peculiarities and remnant liver volume, ranging 20–40% in respect to functional liver status. Magnetic resonance imaging is the most sensitive method that has marked advantages in the diagnostics of lesions smaller than 1 cm and metastases on the background of liver steatosis. Computed tomography is an acceptable alternative that benefits from high spatial resolution and optimal reconstructions to evaluate the anatomy. Additional information can be obtained from tumour markers, including traditional, e.g., carcinoembryonic antigen (CEA) and novel, e.g., microRNAs. To ensure that each colorectal cancer patient receives the best care, the medical society should be well informed about the possibilities in the treatment of liver metastases of colorectal cancer regarding the methods, indications and limits.
Establishing human prostate cancer cell xenografts in bone: Induction of osteoblastic reaction by prostate‐specific antigen‐producing tumors in athymic and SCID/bg mice using LNCaP and lineage‐derived metastatic sublines

LNCaP lineage‐derived human prostate cancer cell lines C4‐2 and C4‐2B4 acquire androgen independence and osseous metastatic potential in vivo. Using C4‐2 and C4‐2B4 the goals of the current investigation were 1) to establish an ideal bone xenograft model for prostate cancer cells in intact athymic or SCID/bg mice using an intraosseous route of tumor cell administration and 2) to compare prostate cancer metastasis by administering cells either through intravenous (i.v.) or intracardiac administration in athymic or SCID/bg mice. Subsequent to tumor cell administration, prostate cancer growth in the skeleton was assessed by radiographic bone density, serum prostate‐specific antigen (PSA) levels, presence of hematogenous prostate cancer cells and histopathologic evaluation of tumor specimens in the lymph node and skeleton. Our results show that whereas LNCaP cells injected intracardially failed to develop metastasis, C4‐2 cells injected similarly had the highest metastatic capability in SCID/bg mice. Retroperitoneal and mediastinal lymph node metastases were noted in 3/7 animals, whereas 2/7 animals developed osteoblastic spine metastases. Intracardiac injection of C4‐2 in athymic hosts produced spinal metastases in 1/5 animals at 8–12 weeks post‐injection; PC‐3 injected intracardially also metastasized to the bone but yielded osteolytic responses. Intravenous injection of either LNCaP or C4‐2 failed to establish tumor colonies. Intrailiac injection of C4‐2 but not LNCaP nor C4‐2B4 cells in athymic mice established rapidly growing tumors in 4/8 animals at 2–7 weeks after inoculation. Intrafemoral injection of C4‐2 (9/16) and C4‐2B4 (5/18) but not LNCaP (0/13) cells resulted in the development of osteoblastic bone lesions in athymic mice (mean: 6 weeks, range: 3–12 weeks). In SCID/bg mice, intrafemoral injection of LNCaP (6/8), C4‐2 (8/8) and C4‐2B4 (8/8) cells formed PSA‐producing, osteoblastic tumors in the bone marrow space within 3–5 weeks after tumor cell inoculation. A stepwise increase of serum PSA was detected in all animals. Reverse transcription‐polymerase chain reaction (RT‐PCR) to detect hematogenously disseminated prostate cancer cells could not be correlated to either serum PSA level or histological evidence of tumor cells in the marrow space. We have thus established a PSA‐producing and osteoblastic human prostate cancer xenograft model in mice. Int. J. Cancer 77:887–894, 1998. © 1998 Wiley‐Liss, Inc.
Anticoagulant use in cancer patients

Introduction: The development of venous thromboembolism (VTE) in patients with cancer adversely affects their prognosis. Several autopsy- and population-based studies have clearly shown a negative impact of VTE on patient outcome in cancer patients. Areas covered: An up-to-date review of VTE prophylaxis and treatment in cancer patients is provided with some insights on areas of uncertainty to be answered in the near future. Particular attention is paid to recent cohort studies, randomized clinical trials and consensus guidelines. Expert opinion: Cancer patients at a higher risk for VTE may be identified with five variables easily available before initiation of chemotherapy. Long-term treatment with low-molecular-weight heparin (LMWH) demonstrated a superior efficacy over vitamin K antagonists. The intensity and duration of anticoagulant therapy should be tailored to the risk of VTE recurrences or bleeding in an individual patient.
Identification of N-Acetyltransferase 2 and CYP2C19 Genotypes for Hair, Buccal Cell Swabs, or Fingernails Compared With Blood

Genotyping of polymorphic drug metabolizing enzymes may be useful to estimate the blood concentration, efficacy, and toxicity of drugs before administration. Blood samples are most generally used for genotyping; however, sampling is invasive and complicated by handling and transport. Therefore, the authors developed genotyping methods using nonblood specimens, and then each genotype was compared with that from blood. Healthy Japanese volunteers provided hairs (n = 50), buccal cell swabs (n = 50), and fingernails (n = 30) for N-acetyltransferase 2 and CYP2C19 genotyping. Recovery of genomic DNA from each nonblood specimen was lower than that from 0.5 mL blood. Using a modification of the DNA extraction and polymerase chain reaction amplification method, genotypes were diagnosed without failure, even for those with very low levels of DNA. Both genotypes from these specimens completely matched the genotypes from the blood of the same subject. These nonblood specimens can be convenient, accessible, and economical alternatives to blood as a source of DNA for genotyping.
Limiting Dilution Analysis of Interleukin 2‐Producing Mature T Cells

Evaluation of lymphokine production by individual activated T cells is necessary to characterize their growth requirements. We have studied interleukin 2 (IL‐2) secretion by mature T lymphocytes using a high resolution assay system with the following characteristics: (a) a threshold of IL‐2 detection 25 times lower than classic IL‐2 titration: (b) the ability to discriminate between IL‐2 and IL‐4 activities: (c) absence of ‘in situ’ IL‐2 absorption; (d) IL‐2 production revealed al the single cell level By this method an average of 10% of spleen cells, and 75% of L3T4 cells were detected as producers in a concanavalin A (Con A)‐dependent T cell activation system. Our results also suggest the complete restriction of II ‐2 secretion to cells with this phenotype. Therefore, factors other than IL‐2 must play a major role in Lyt 2+ mitogen‐driven, helper‐independent T cell proliferation.
Isoform‐specific localization of Nogo protein in the optic pathway of mouse embryos

Expression of Nogo protein was investigated in the optic pathway of embryonic mice by using isoform‐specific antibodies Bianca and 11C7, which recognize Nogo‐A/B and Nogo‐A, respectively. Our previous reports from using antibody N18 have shown that Nogo is localized on the radial glia in the retina and at the midline of the ventral diencephalon in mouse embryos during the ingrowth of retinal ganglion cells (RGCs) axons. This glial‐specific localization is markedly different from findings in other studies. This study showed Nogo‐A/B primarily on radial glia in the retina at E13 and then later on retinal ganglion cells and axons at E14 and E15, whereas Nogo‐A was expressed preferentially by RGCs and their axons. In the ventral diencephalon, Nogo‐A/B was expressed strongly on radial glia, particularly in those located in the midline region of the chiasm but also on RGC axons. In Nogo‐A knockout embryos, the isoform Nogo‐B (revealed by Bianca) was observed on radial glia in the ventral diencephalon and on RGCs and their axons. We concluded that Nogo‐A is localized on the ganglion cells and retinal axons, whereas Nogo‐B is expressed by the radial glia in the optic pathway. Nogo‐B may play an important role in guiding axon growth in decisive regions of the visual pathway, which include the optic disc and the optic chiasm. J. Comp. Neurol. 524:2322–2334, 2016. © 2016 Wiley Periodicals, Inc.