Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional modulation of micro-RNA in human cells differing in radiation sensitivity

Purpose: The molecular basis of gene regulation in cells exposed to ionising radiation is not fully understood. Gene regulation occurs at the transcriptional and post-transcriptional levels. Recent studies have suggested that micro-RNA (miRNA) plays a significant role at the post-transcriptional gene regulation. miRNA are a recently identified class of RNA molecules 18–24 nucleotides in length that have been shown to negatively regulate the stability or translation of target messenger RNA. We hypothesised that ionising radiation induced stress response is controlled in part by miRNA and that a difference in tumour protein 53 (p53) status corresponds with altered expression in miRNA responses to ionising radiation. Materials and methods: To test this hypothesis, we investigated the relative expression of several miRNA by quantitative real-time polymerase chain reaction (QPCR) in human cell lines TK6 and WTK1 that differ in p53 status and radiosensitivity after exposure to high and low doses of X-radiation. Results: The suitability of several endogenous miRNA controls was tested for relative quantification by QPCR. The baseline expression of 21 miRNA targets in TK6 and WTK1 cells indicated a wide range of modulation between the two cell lines without exposure to ionising radiation. Differences in the relative expression of miRNA were observed among the two cell lines after radiation treatment. The expression patterns of many miRNA markedly differed within the same cell line after exposure to either 0.5 Gy or 2 Gy doses of X-rays. The expression of eight miRNA belonging to the lethal-7 (let-7) family, which are negative regulators of the rat sarcoma, RAS oncogene, was upregulated in irradiated TK6 cells but was downregulated in WTK1 cells. Alterations in the myelocytomatosis oncogene, c-MYC induced cluster of miRNA were also observed. The micro RNA, miR-15a and miR-16 were upregulated in 0.5 Gy-irradiated TK6 cells but were downregulated after a 2 Gy dose of X-rays. In contrast miR-15 and miR-16 were repressed in 0.5 Gy-exposed WTK1. The miR-21 was upregulated in 0.5 Gy-treated TK6 cells and its target genes programmed cell death factor 4 (hPDCD4) phosphatase and tensin homolog (hPTEN), and sprouty homolog 2 (hSPRY2) were found to be downregulated in these cells. The miR-21 was downregulated in 2 Gy-irradiated TK6 cells, and all three of its target genes were upregulated in 2 Gy-exposed TK6 cells. Conclusion: Taken together, these results establish the involvement of miRNA in radiation response and may potentially help explain the mechanisms of gene regulation in the cellular response to ionising radiation exposure.
ASIC Integration via Polymer Ultrasonic Bump Bonding to A 64-Channel Penetrating Parylene Multielectrode Array

Using the polymer ultrasonic bump (PUB) bonding technique, we demonstrate functional integration of a digital electrophysiology amplifier application specific integrated circuit (ASIC) with a 64-channel Parylene C penetrating multielectrode array intended for deep brain recordings in rodents. The 89 contacts (72 × 116 µm2, 100 µm pitch) for the bare die ASIC were successfully joined with high yield to the polymer multielectrode array (pMEA) using a tape automated bonding tip on a standard ultrasonic wire bonder tool, resulting in a compact, low profile integrated unit. Recording capability of ASIC-integrated pMEA was comparable to passive pMEAs.
A(H1N1)pdm09 vaccination of healthcare workers: improved immune responses in low responders following revaccination.

TO THE EDITOR—I read with great interest the article by Pathirana et al [1], which demonstrated that a 2-dose vaccination regimen with ASO3 adjuvant is needed to improve immune responses against 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) infection in low responders. The authors, in their discussion, suggested that the rapid induction of antibodies in the responders may have been due to a recall response to prior infection/vaccination. Indeed, that seems to be the case, although they did not elaborate on this in the results section. According to Figure 2A in their article [1], at the time of vaccination at least 10 of 25 subjects in the control (ie, responder) group had detectable and significant hemagglutination inhibition (HI) titers against A(H1N1)pdm09, which ranged from 8–64, while only 2 of 15 low responders had HI titers (8 in one low responder and 32 in the other). It would be interesting if the data from these 10 subjects were analyzed and shown separately, to allow assessment of
Localization of components involved in protein transport and processing through the yeast Golgi apparatus

Saccharomyces cerevisiae sec7 mutants exhibit pleiotropic deficiencies in the transit of proteins through the Golgi apparatus, and elaborate an array of Golgi apparatus-like cisternae at a restrictive growth temperature (37 degrees C). The SEC7 gene encodes an essential high- molecular weight protein (227 kD) that is phosphorylated in vivo. In cell lysates, Sec7 protein (Sec7p) is recovered in both sedimentable and soluble fractions. A punctate immunofluorescent pattern of Sec7p- associated structures seen in SEC cells coalesces in sec14 mutant yeast that accumulate exaggerated Golgi cisternae at 37 degrees C. Sec7p may function as a peripheral membrane protein that cycles between a soluble, cytosolic pool and a sedimentable, membrane-associated complex for its essential role in vesicular traffic through the Golgi apparatus. The transmembrane Kex2 protease, which processes precursors of secreted peptides within the yeast secretory pathway, is also localized by indirect immunofluorescence to multiple structures in the yeast cell (Redding, K., and R. Fuller, manuscript submitted for publication). In double-immunofluorescence labeling experiments, significant colocalization of Sec7 and Kex2 proteins was found. Colocalization of the two antigens, one implicated in protein transport through the Golgi apparatus and the other in processing within a late Golgi compartment, supports the conclusion that we have visualized the yeast Golgi apparatus.
Body mass index, urinary incontinence, and female sexual dysfunction: how they affect female postmenopausal health

Objective: The aim of this study was to evaluate the relationship between body mass index (BMI) and female sexual dysfunction (FSD) among perimenopausal and postmenopausal women with urinary incontinence (UI). Methods: From 2005 to 2008, we enrolled 208 consecutive women affected by UI; all underwent a comprehensive history including two validated questionnaires, physical examination, and urodynamic evaluation. Based on BMI, participants were grouped into normal weight, overweight, and obese. Results: A total of 158 participants completed both questionnaires (76% response rate); 41 (26%) were normal weight, 73 (46%) were overweight, and 44 (28%) were obese. The increasing Urogenital Distress Inventory score had a direct correlation with age (P < 0.01), year of menopause onset (P < 0.05), and BMI (P < 0.01). FSD was diagnosed in 97 women (61%): 31 (32%) with hypoactive sexual desire, 20 (21%) with sexual arousal disorder, 7 (7%) with orgasmic deficiency, and 39 (40%) with sexual pain disorder. BMI greater than 30 kg/m2 was independently associated with an increased risk of FSD (odds ratio [OR], 2.02) and UI (OR, 2.03). With adjustment for BMI, the OR for FSD was 1.22 for overweight women and 1.56 for obese women, with respect to healthy participants. The total Female Sexual Function Index score correlated with BMI (r = −0.82, P = 0.0001); in particular, arousal (r = −0.82), orgasm (r = −0.72), lubrication (r = −0.61), and satisfaction (r = −0.63, all P < 0.001) showed an inverse correlation with BMI, whereas desire and pain did not. Conclusions: Increased BMI early in menopause represents a risk both for UI and for sexual dysfunction. Weight control has an essential role in postmenopause and should be considered early in perimenopause to safeguard female quality of life as well as to prevent or improve UI and female sexual dysfunction symptoms.
Adding confidentiality to application-level multicast by leveraging the multicast overlay

While scalability, routing and performance are core issues for application-level multicast (ALM) protocols, an important but less studied problem is security. In particular, confidentiality (i.e. data secrecy, achieved through data encryption) in ALM protocols is needed. Key management schemes must be simple, scalable, and must not degrade the performance of the ALM protocol. We explore three key management schemes that leverage the underlying overlay to distribute the key(s) and secure ALM. We evaluate their impact on three well-known ALM protocols: ESM, ALMI and NICE. Through analysis and simulations, we show that utilizing the ALM overlay to distribute key(s) is feasible. For a given ALM protocol, choice of the best key management scheme depends on the application needs: minimizing rekeying latency or minimizing data multicasting latency.
Language variety identification in Spanish tweets

We study the problem of language variant identification, approximated by the problem of labeling tweets from Spanish speaking countries by the country from which they were posted. While this task is closely related to “pure” language identification, it comes with additional complications. We build a balanced collection of tweets and apply techniques from language modeling. A simplified version of the task is also solved by human test subjects, who are outperformed by the automatic classification. Our best automatic system achieves an overall F-score of 67.7% on 5-class classification.
CRêPE: A System for Enforcing Fine-Grained Context-Related Policies on Android

Current smartphone systems allow the user to use only marginally contextual information to specify the behavior of the applications: this hinders the wide adoption of this technology to its full potential. In this paper, we fill this gap by proposing CRêPE, a fine-grained Context-Related Policy Enforcement System for Android. While the concept of context-related access control is not new, this is the first work that brings this concept into the smartphone environment. In particular, in our work, a context can be defined by: the status of variables sensed by physical (low level) sensors, like time and location; additional processing on these data via software (high level) sensors; or particular interactions with the users or third parties. CRêPE allows context-related policies to be set (even at runtime) by both the user and authorized third parties locally (via an application) or remotely (via SMS, MMS, Bluetooth, and QR-code). A thorough set of experiments shows that our full implementation of CRêPE has a negligible overhead in terms of energy consumption, time, and storage, making our system ready for a production environment.
Structural and magnetic characterisation of Heusler alloy thin films under optimised growth condition for spintronic devices

Spintronic devices have been playing an important role in magnetic storage and memory applications for the last 20 years. For such a trend to continue, it is critical to develop new magnetic materials, in particular, in the context of antiferromagnetic spintronics, materials with high Curie temperatures, large spin polarisations, and low saturation magnetisations. In this study, three Heusler alloys, Mn2VSi, Mn3Ga and Mn3Ge have been investigated and experimental results have been carried out. 80 nm thick polycrystalline Mn2VSi films have been deposited on silicon substrates with an 18 nm silver seed layer and a 3 nm aluminium capping layer using a sputtering system. The best quality film is obtained for 723 K growth. The Mn2VSi thin film is verified to be antiferromagnetic, where an exchange bias is found when a 3 nm ferromagnetic CoFe layer has been deposited on the top of the Mn2VSi layer. The exchange bias is measured to be 34 Oe at 100 K. The blocking and thermal activation temperature of Mn2VSi is estimated to be below 100 K and within a range between 100 K and 448 K, respectively. Polycrystalline Mn3Ga layers with thickness in the range from 3-20 nm were deposited at room temperature. To investigate the onset of exchange-bias, a ferromagnetic Co0.6Fe0. 4 layer (3.3-9 nm thick) capped with 5 nm Ta, were subsequently deposited. X-ray diffraction measurements confirm the presence of Mn3Ga (0002) and (0004) peaks characteristic of the D019 antiferromagnetic structure. The 6 nm thick Mn3Ga film shows the largest exchange bias of 430 Oe at 120 K with a blocking temperature of 225 K. The blocking temperature is found to decrease with increasing Mn3Ga thickness. These results in combination with X-ray reflectivity measurements confirm that the quality of the Mn3Ga/Co0.6Fe0. 4 interface controls the exchange bias, with the sharp interface with the 6-nm-thick Mn3Ga inducing the largest exchange bias. The magneto-crystalline anisotropy for 6 nm thick Mn3Ga thin film sample is calculated to be Polycrystalline Mn3Ge samples with same stack layer structure as Mn3Ga films were also studied. A growth temperature of 773 K promotes the crystallisation of the 100 nm thick Mn3Ge layer showing a D019 antiferromagnetic structure. The exchange bias cannot be observed due to the potential interlayer diffusion during high temperature sputtering.
THERMAL ANALYSIS AND MICROSTRUCTURAL STUDY OF POROUS β-TiNb INCORPORATED WITH TiH2 POWDER VIA LOW-COST PROCESSING ROUTE

In the development of Ti-based alloy bio-implant material, Titanium Hydride (TiH 2 ) which is commonly used as a pore former agent has become one of the new approaches of starting material via powder metallurgy processing route with the aim of low-cost production in the fabrication of Beta-typed Titanium Niobium (β-TiNb) alloy. However, the thermal behaviour of TiNb alloy by TiH 2 substitution is still not well understood. Thus, in the present work the compacted of Ti and Nb mixture was subjected to thermal analysis via differential thermal analysis (DTA) and dilatometry to evaluate thermal events existed during sintering process. It was found that the overall reaction had undergone four-step processes; the first two steps were subjected to the dehydrogenation process whereas the last two steps corresponded to the formation of TiNb alloy. In addition, the β phase of TiNb exhibited better appearance at 1200°C sintered temperature which was supported by X-ray Diffraction (XRD) analysis.
Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
A Novel Methodology for Automatically Measuring Psychological Dimensions in Textual Data

The processing of textual data to obtain psychological measures is becoming prevalent. However, the problemisthatinmostcases,taggedcorporaareunavailableandthereforeconventionalclassiﬁcation methods cannot be easily applied. We present a novel solution for measuring psychological dimensions in textual data. The solution is based on (i) the construction of patterns from validated psychological questionnaires measuring the target dimension and (ii) similarity measurements of some of the text’s sentences to the pre-deﬁned patterns. Our proposed methodology was tested on (i) the identiﬁ-cation of the ﬁve personality dimensions in a gold standard corpus, (ii) the measurement of depression and (iii) the screening of civilian mass murderers, gaining preliminary support for its validity.
Spliceosome Database: a tool for tracking components of the spliceosome

The spliceosome is the extremely complex macromolecular machine responsible for pre-mRNA splicing. It assembles from five U-rich small nuclear RNAs (snRNAs) and over 200 proteins in a highly dynamic fashion. One important challenge to studying the spliceosome is simply keeping track of all these proteins, a situation further complicated by the variety of names and identifiers that exist in the literature for them. To facilitate studies of the spliceosome and its components, we created a database of spliceosome-associated proteins and snRNAs, which is available at http://spliceosomedb.ucsc. edu and can be queried through a simple browser interface. In the database, we cataloged the various names, orthologs and gene identifiers of spliceosome proteins to navigate the complex nomenclature of spliceosome proteins. We also provide links to gene and protein records for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, we created tools to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. Together, the information in the database provides an easy reference for spliceosome components and will support future modeling of spliceosome structure and dynamics.
CD36‐dependent signaling mediates fatty acid‐induced gut release of secretin and cholecystokinin

Genetic variants in the fatty acid (FA) translocase FAT/CD36 associate with abnormal postprandial lipids and influence risk for the metabolic syndrome. CD36 is abundant on apical enterocyte membranes in the proximal small intestine, where it facilitates FA uptake and FA‐initiated signaling. We explored whether CD36 signaling influences FA‐mediated secretion of cholecystokinin (CCK) and secretin, peptides released by enteroendocrine cells (EECs) in the duodenum/jejunum, which regulate events important for fat digestion and homeostasis. CD36 was immunodetected on apical membranes of secretin‐ and CCK‐positive EECs and colocalized with cytosolic granules. Intragastric lipid administration to CD36–/– mice released less secretin (–60%) and CCK (–50%) compared with wild‐type mice. Likewise, diminished secretin and CCK responses to FA were observed with CD36–/– intestinal segments in vitro, arguing against influence of alterations in fat absorption. Signaling mechanisms underlying peptide release were examined in STC‐1 cells stably expressing human CD36 or a signaling‐impaired mutant (CD36K/A). FA stimulation of cells expressing CD36 (vs. vector or CD36K/A) released more secretin (3.5‐ to 4‐fold) and CCK (2‐ to 3‐fold), generated more cAMP (2‐ to 2.5‐fold), and enhanced protein kinase A activation. Protein kinase A inhibition (H‐89) blunted secretin (80%) but not CCK release, which was reduced (50%) by blocking of calmodulin kinase II (KN‐62). Coculture of STC‐1 cells with Caco‐2 cells stably expressing CD36 did not alter secretin or CCK release, consistent with a minimal effect of adjacent enterocytes. In summary, CD36 is a major mediator of FA‐induced release of CCK and secretin. These peptides contribute to the role of CD36 in fat absorption and to its pleiotropic metabolic effects. —Sundaresan, S. , Shahid, R. , Riehl, T. E. , Chandra, R. , Nassir, F. , Stenson, W. F. , Liddle, R. A. , Abumrad, N. A. CD36‐dependent signaling mediates fatty acid‐induced gut release of secretin and cholecystokinin. FASEB J. 27, 1191–1202 (2013). www.fasebj. org
Constructing Human Brain-Function Association Models from fMRI Literature

Toward the goal of understanding the human brain function, we have developed a web-based human brain functional mapping knowledge base (HBFMKB) system to mining human brain-function association model from vast Medline abstracts. Since nomenclature and relationships among cognitive functions have no consensus yet, we use rule-based natural language processing methods to extract behavioral task and cognitive function and do n-gram approximate concept mapping by the unified medical language system (UMLS) knowledge source. The HBFMKB system has an automatic PubMed MEDLINE download and import system, name entity extraction system and interactive visualization system. In summary, the HBFMKB system helps scientists to get digest knowledge before design experiments and compare their results with current literature.
Modeling quality of life in patients with rheumatic diseases: the role of pain catastrophizing, fear-avoidance beliefs, physical disability, and depression

Abstract Purpose: To examine factors in the fear-avoidance model, such as pain, pain catastrophizing, fear-avoidance beliefs, physical disability, and depression and their relationships with physical and psychological quality of life in patients with rheumatic diseases. Materials and methods: The data were obtained from 360 patients with rheumatic diseases who completed self-report measures assessing study variables. Structural equation modeling was used to examine the hypothesized relationships among factors specified in the fear-avoidance model predicting physical and psychological quality of life. Results: Final models fit the data well, explaining 96% and 82% of the variance in physical and psychological quality of life, respectively. Higher pain catastrophizing was related to stronger fear-avoidance beliefs that had a direct negative association with physical disability and depression, which, in turn, negatively affected physical quality of life. Pain severity was also directly related to physical disability. Physical disability also affected physical quality of life indirectly through depression. The hypothesized relationships specified in the model were also confirmed for psychological quality of life. However, physical disability had an indirect association with psychological quality of life via depression. Conclusion: The current results underscore the significant role of cognitive, affective, and behavioral factors in perceived physical disability and their mediated detrimental effect on physical and psychological quality of life in patients with rheumatic diseases. Implications for rehabilitation The fear-avoidance model is applicable to the prediction of quality of life in patients with rheumatic diseases. As pain-catastrophizing and fear-avoidance beliefs are important factors linked to physical disability and depression, intervening these cognitive factors is necessary to improve physical function and depression in patients with rheumatic diseases. Considering the strong association between depression and physical and psychological quality of life, the assessment and treatment of the former should be included in the rehabilitation of patients with rheumatic diseases. Interventions targeting physical function and depression are likely to be effective in terms of improving physical and psychological quality of life in patients with rheumatic diseases.