Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time quantitative RT-PCR assay of GADD45 gene expression changes as a biomarker for radiation biodosimetry

Purpose : To assess the efficacy of fluorescent-based quantitative reverse transcription-polymerase chain reaction (QRT-PCR) technology to measure gene expression changes (GEC) for rapid, point-of-care radiation dose assessment. Materials and methods : A real-time QRT-PCR assay based on 5'-fluorogenic nuclease TaqMan TM methodology was developed, which employs both relative and absolute quantification of a candidate mRNA biomarker. Growth arrest and DNA damage gene 45 (GADD45) , a cell-cycle regulation and DNA repair gene, served as the paradigm because of the reported linear dose-response relationship for mRNA induction in the human myeloid tumor cell line (ML-1) over the range of 2-50 cGy. Using an ex vivo whole-blood model, GEC was measured from total blood RNA at 24h and 48 h after 60 Co γ-ray exposures (0-3 Gy; 0.1 Gy/min). Results : A linear and reproducible up-regulation representing a twofold to fourfold change in GADD45 relative and absolute GEC was confirmed in both intra- and inter-assay analyses. Conclusions : Primer and probes to detect GADD45 targets using real-time PCR were developed. This is the first report using realtime QRT-PCR to measure radiation-induced GEC dose response. Real-time QRT-PCR using GEC as biomarkers offers rapidity, sensitivity, and reproducibility as a potential efficient biological dosimetry tool applicable in radiation therapy applications and early-response accident biodosimetry.
Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA‐Seq

Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion‐ and detoxification‐related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c‐album, which is a polyphagous, widely‐distributed butterfly. Urtica dioica and Ribes uva‐crispa are hosts of P. c‐album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life‐history (i.e. 2nd vs. 4th‐instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host‐plant identified genes encoding serine‐type endopeptidases, membrane‐associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.
Post‐Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow

Range expansions and gene flow as micro‐evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographical populations to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples and thus restricted to a single population. Analysis of molecular variance revealed that most of the variation was within populations with no significant genetic structuring on either side of the Atlantic. Demographic analyses indicated that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced a slight trend of increase in population size over time, whereas EC (the English Channel) area experienced expansion beginning approximately 170 000–360 000 BP. The observed complex genetic pattern of C. crispus is consistent with a scenario of multiple unrelated founding events by survival of this species in at least three putative Pleistocene refugia along the European coastline, and subsequent trans‐Atlantic dispersal combined with contiguous northward population expansion predating the LGM and geographically gene flow.
International donor corneas usage in New Zealand in 2013

tions of visual sensations during pars plana vitrectomy under retrobulbar anesthesia. Am J Ophthalmol 2007; 144: 245–51. 4. Kawaguchi N, Inoue M, Sugisaka E, Shinoda K, Tsubota K. Subjective visual sensation during vitrectomy under retrobulbar anesthesia. Am J Ophthalmol 2006; 141: 407–9. 5. Kawamura R, Shinoda K, Inoue M, Noda T, Ohnuma K, Hirakata A. Images of intravitreal objects projected onto posterior surface of model eye. Acta Ophthalmol 2013; [Epub ahead of print]. 91: e561–6. doi: 10.1111/ aos.12042; [2 Aug 2013].
Concomitant aberrant overexpression of RUNX1 and NCAM in regenerating bone marrow of myeloid leukemia of Down's syndrome.

BACKGROUND AND OBJECTIVES Myeloid leukemia of Down's syndrome (ML-DS) has characteristic biological features (e.g. expression of the truncated GATA1s), which are different from those of non-DS childhood acute myeloid leukemias (AML). The objective of this study was to investigate factors predisposing to the development of ML-DS. DESIGN AND METHODS We analyzed 134 bone marrow specimens from 64 children with ML-DS and non-DS AML during chemotherapy and 7 specimens from DS children with- out leukemia,who did not receive any chemotherapy,The specimens were analyzed by multiparameter flow cytometry and quantitative reverse transcriptase polymerase chain reaction for transcription factors involved in hematopoiesis. RESULTS Samples taken from children with ML-DS in complete remission during chemotherapy aberrantly expressed CD56 (NCAM) at the surface of monocytic and granulocytic cells. Compared to non-DS AML cases,children with ML-DS had a statistically significant higher proportion of CD56+ cells in the CD33+ fraction: 71%+/-6% vs. 4%+/-1% (p<0.00001). A significant decrease of the amount of CD33+/CD56+ cells was observed during and after maintenance therapy. An increased number of CD33+/CD56+ cells was also present (>85%) in children with DS who did not receive chemotherapy, but showed a left-shift (due to infection), compared with DS children without left-shift (<10% CD33+/CD56+ cells). Within the CD33+/CD56+ fraction, RUNX1 was overexpressed more than 5-fold (p<0.02) compared to CD33+/CD56- cells, whereas there were no differences regarding GATA1, SPI1, ERG or ETS-2 levels. INTERPRETATION AND CONCLUSIONS The combined overexpression of RUNX1 and NCAM during stress hematopoiesis in children with DS might be a key factor in the development of overt leukemia and/or in the growth advantage of the malignant GATA1s clone in ML- DS.
VinaMPI: Facilitating multiple receptor high‐throughput virtual docking on high‐performance computers

The program VinaMPI has been developed to enable massively large virtual drug screens on leadership‐class computing resources, using a large number of cores to decrease the time‐to‐completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed‐up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high‐throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information. © 2013 Wiley Periodicals, Inc.
Inflation Expectations and the Stabilization of Inflation: Alternative Hypotheses

This paper examines two candidate hypotheses explaining the stabilization of U.S. inflation since the 1970s and 1980s. The first explanation credits the stabilization of inflation expectations, and assumes those expectations have a strong positive causal effect on actual subsequent inflation, while the second explanation credits the disappearance of such a strong positive causal effect. The paper reports statistical tests favorable to both a stabilization of inflation expectations and a marked decline in the effect of the general public’s inflation expectations on subsequent inflation.
Optical remote sensing for long-term changes of surface sediments on tidal flats: Preliminary results in the West Coast of Korea

The main objective of this study is long-term monitoring of surface sediment on tidal flats using optical remote sensing. Tidal flat reflectance is sensitive to conditions that constantly change and cause variation of interstitial water contents along with exposure time, remnant water, etc. It is difficult to retrieve sediment grain size from optical reflectance alone without correcting the tidal condition effects. In this study, the tidal flat surface reflectance model according to grain size is proposed by two-step PCA transformation to remove tidal effects. The proposed method showed a potential to classify sediment by grain size regardless of exposure time and tidal conditions. We applied the method to nine scenes of LANDSAT TM images acquired between 1988 and 2009. The preliminary results well demonstrated that the proposed approach is effective to monitor changes of grain size distribution at a large scale independent of tidal conditions. However, this method has a limitation particularly over the vegetated areas and sand shoals mainly because of strong reflection in the NIR channels compared with other areas. For the validation, this study requires further field survey to obtain more in-situ data.
Deletion of Irf3 and Irf7 Genes in Mice Results in Altered Interferon Pathway Activation and Granulocyte-Dominated Inflammatory Responses to Influenza A Infection

The interferon (IFN) pathway plays an essential role in the innate immune response following viral infections and subsequent shaping of adaptive immunity. Infections with influenza A viruses (IAV) activate the IFN pathway after the recognition of pathogen-specific molecular patterns by respective pattern recognition receptors. The IFN regulatory factors IRF3 and IRF7 are key players in the regulation of type I and III IFN genes. In this study, we analyzed the role of IRF3 and IRF7 for the host response to IAV infections in Irf3-/-, Irf7-/-, and Irf3-/-Irf7-/- knockout mice. While the absence of IRF3 had only a moderate impact on IFN expression, deletion of IRF7 completely abolished IFNα production after infection. In contrast, lack of both IRF3 and IRF7 resulted in the absence of both IFNα and IFNβ after IAV infection. In addition, IAV infection of double knockout mice resulted in a strong increase of mortality associated with a massive influx of granulocytes in the lung and reduced activation of the adaptive immune response.
Inosine Mediates the Protective Effect of Adenosine in Rat Astrocyte Cultures Subjected to Combined Glucose‐Oxygen Deprivation

Abstract: Preliminary evidence suggests adenosine, a neuromodulator, has neuroprotective properties during cerebral ischemia. It is unclear, however, if adenosine has glioprotective effects. We studied the effect of adenosine on cellular injury in astroglial cultures subjected to combined glucose‐oxygen deprivation. Adenosine (100–1,000 µM) dramatically reduced astroglial injury, whereas the adenosine agonists 2‐chloroadenosine (10 nM–100 µM), N6‐cyclopentyladenosine (1 nM–10 µM), 5′‐N‐ethylcarboxamidoadenosine (10 nM–100 µM), and N6‐2‐(4‐aminophenyl)ethyladenosine (10 nM–100 µM) had no effect. Furthermore, the adenosine antagonists 8‐cyclopentyl‐1,3‐dipropylxanthine (1 nM–1 µM), xanthine amine congener (10 nM–10 µM), and 8‐(p‐sulfophenyl)‐theophylline (10–300 µM) failed to reverse the protective effect of 200 µM adenosine. Next, adenosine degradation products were studied. Inosine proved to be glioprotective at concentrations nearly identical to those of adenosine, but hypoxanthine and ribose had no effect. The protective effect of 200 µM inosine was not reversed by 8‐(p‐sulfophenyl)theophylline (10–300 µM). Adenosine deaminase (1 unit/ml) had no effect on protection produced by adenosine, whereas erythro‐9‐(2‐hydroxy‐3‐nonyl)adenine hydrochloride (10 µM) reversed the protective effect of adenosine. Dipyridamole (4 µM) inhibited the protective effect of both adenosine and inosine. We conclude that adenosine dramatically decreases astroglial injury during combined glucose‐oxygen deprivation and that this protective effect appears to be mediated by inosine.
Applicability of common reference intervals for serum creatinine concentrations to the Croatian population

Abstract Background: In accordance with an ongoing activity for worldwide harmonization based on traceability in laboratory methods, the goal of this study was to validate the applicability of recommended “common” reference intervals for serum creatinine concentrations using a specific enzymatic method to the Croatian population. Methods: The reference group consisted of 240 healthy subjects (120 males and 120 females), between 18 and 74 years of age (median 57 years), who were selected in accordance with the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) recommendations. Creatinine in serum was measured using the creatinine enzymatic assay (Olympus OSR61204) that was standardized to the isotopic dilution mass spectrometry (IDMS) method and National Institute of Standards and Technology (NIST) Standard Reference Material (SRM) 967. In addition, creatinine was measured using a kinetic Jaffe method (Olympus OSR6178) standardized to NIST SRM 909b level 2 standard. Results: Method comparison between enzymatic creatinine (x) and the Jaffe kinetic method (y) gave the following P/B equation for the entire group (n=240): y=1.00x+17.00; r=0.968. Reference intervals for serum creatinine (central 95th percentiles) obtained using the enzymatic creatinine method ranged from 54 to 107 μmol/L for males and from 50 to 93 μmol/L for females. The IFCC recommended common reference intervals for global applications are 64–104 μmol/L and 49–90 μmol/L for males and females, respectively. Conclusions: Comparability of obtained results confirmed the applicability of recently recommended “common” reference intervals to the Croatian population for all laboratories measuring serum creatinine concentrations using enzymatic methods traceable to the IDMS method and NIST SRM 967. Clin Chem Lab Med 2010;48:231–5.
First results of clinical application of videokymography

Objectives: Stroboscopy is based on the assumption that the vibration of the vocal folds is stable and regular. Irregular vibrations, which are common in voice pathology, cannot easily be studied and described in a reliable way. Videokymography overcomes most of these drawbacks. Design: The use of the recently invented videokymography for studying vocal fold vibrations in patients is introduced. Method: Videokymography, using a modified CCD‐video camera, works in two modes: standard and high speed. In standard mode the vocal folds are displayed on a video monitor in the usual way, providing 50 images per second (or 60 in the National Television Standards Committee (NTSC) system). This is used for routine laryngoscopic and stroboscopic examination of the larynx. In high‐speed mode (nearly 8000 images per second) only one line from the whole image is selected and displayed on the x‐axis of the monitor; the y‐axis represents the time dimension. Results: All kinds of vocal fold vibrations, including those leading to pathological rough, breathy, hoarse, or diplophonic voice productions can be observed. Videokymography visualizes small left‐right asymmetries, open quotient differences along the glottis, lateral propagation of mucosal waves, and movements of the upper margin and, sometimes in the closing phase, the lower margin of the vocal folds. Conclusion: Videokymography is advantageous for a more accurate diagnosis of voice disorders. Videokymography provides a simple way to study irregular vibrations of the vocal folds. Information is directly available for further processing and allows a first‐time quantification of vibrations registered.
Providing assistive technology in Italy: the perceived delivery process quality as affecting abandonment

Abstract Purpose: The study brings together three aspects rarely observed at once in assistive technology (AT) surveys: (i) the assessment of user interaction/satisfaction with AT and service delivery, (ii) the motivational analysis of AT abandonment, and (iii) the management/design evaluation of AT delivery services. Methods: 15 health professionals and 4 AT experts were involved in modelling and assessing four AT Local Health Delivery Service (Centres) in Italy through a SWOT analysis and a Cognitive Walkthrough. In addition 558 users of the same Centres were interviewed in a telephone survey to rate their satisfaction and AT use. Results: The overall AT abandonment was equal to 19.09%. Different Centres' management strategies resulted in different percentages of AT disuse, with a range from 12.61% to 24.26%. A significant difference between the declared abandonment and the Centres' management strategies (p = 0.012) was identified. A strong effect on abandonment was also found due to professionals' procedures (p = 0.005) and follow-up systems (p = 0.002). Conclusions: The user experience of an AT is affected not only by the quality of the interaction with the AT, but also by the perceived quality of the Centres in support and follow-up. Implications for Rehabilitation AT abandonment surveys provide useful information for modelling AT assessment and delivery process. SWOT and Cognitive Walkthrough analyses have shown suitable methods for exploring limits and advantages in AT service delivery systems. The study confirms the relevance of person centredness for a successful AT assessment and delivery process.
Plasma membrane recruitment of dephosphorylated β-catenin upon activation of the Wnt pathway

The standard model of Wnt signaling specifies that after receipt of a Wnt ligand at the membranous receptor complex, downstream mediators inhibit a cytoplasmic destruction complex, allowing β-catenin to accumulate in the cytosol and nucleus and co-activate Wnt target genes. Unexpectedly, shortly after Wnt treatment, we detected the dephosphorylated form of β-catenin at the plasma membrane, where it displayed a discontinuous punctate labeling. This pool of β-catenin could only be detected in E-cadherin–/– cells, because in E-cadherin+/+ cells Wnt-induced, membranous β-catenin was concealed by a constitutive junctional pool. Wnt-signaling-dependent dephosphorylated β-catenin colocalized at the plasma membrane with two members of the destruction complex – APC and axin – and the activated Wnt co-receptor LRP6. β-catenin induced through the Wnt receptor complex was significantly more competent transcriptionally than overexpressed β-catenin, both in cultured cells and in early Xenopus embryos. Our data reveal a new step in the processing of the Wnt signal and suggest regulation of signaling output beyond the level of protein accumulation.
The role of accounting in public governance process

The intensification of the relations between government and society, whether by means of public-private interaction or of the participation of civil society, contributes to the appreciation of accounting in the scope of public administration. Accounting gains a new feature with this configuration. In addition to its basic capacities of registering and interpreting all phenomena, among which are public budgets, accounting may also provide citizens power and perform an active role in the socio-economic development of a country or a community. The main objective of this article is to analyze literature on accounting from the public governance context. Specific objectives are: to comprehend the role of accounting in the process of public governance, present the experiences in Brazil and present challenges of the accounting reform in Brazil. This investigation is characterized as a qualitative, descriptive bibliographic and documental research. In the documental research we analyzed normative instruction, law and the Federal Accounting Council in Brazil, all related to the functionality of accounting in Brazil and its accounting reform. This study demonstrates that accounting presents a potential to perform the role of strengthening democracy, social control, accountability, creating a social power in the dynamic process of public governance. Key words: Public accounting, public governance, accounting reform.
Wavelet method for breath detection in audio signals

An algorithm for automatic detection of breath events in a speech signal is suggested in this paper. The issues of breath events occurrences in recordings are discussed as well as their statistical parameters. Also the role of breath pauses for signalizing punctuation and emotional or physical state of the speaker, in both spontaneous and read speech, is described. Wavelet parameters of energy in frequency subbands are obtained from discrete packet wavelet decomposition with mel-scale as patterns of breaths. In the beginning of the detection procedure, preliminary hypotheses of breath are indicated in the analyzed speech signal using temporal features. Then, discrete wavelet transform parameters are calculated. Dynamic time warping is applied to establish final recognition. The algorithm will be used for automatic speech recognition for measuring similarity between training and test features vectors.