Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Livestock Grazing and Climate on Pinyon Pine (Pinus edulis) Dynamics

Abstract Over the last century there has been marked expansion and infilling of pinyon (Pinus spp.)–juniper (Juniperus spp.) woodlands into grassland and shrubland ecosystems across the western United States. Although range expansions in pinyon-juniper populations have been documented with changing climate throughout the Holocene, over the last century, local scale impacts such as livestock grazing, changes in fire regimes, and increasing atmospheric CO2 concentrations are thought to be more recent drivers of pinyon-juniper woodland distribution. Our objective was to examine the role of historical livestock grazing relative to past climate in regulating pinyon (Pinus edulis Engelm.) recruitment and growth over the last century in a persistent pinyon-juniper woodland. We compared pinyon dynamics on a remote mesa site, minimally grazed by domestic livestock, to a nearby historically grazed site in southeastern Utah. The presence of a significant number of old trees (> 200 yr) at both sites suggests that these populations were well established prior to the 20th century. No differences in pinyon density or basal area were observed between grazed and ungrazed sites. Stand age structure data showed that pinyon recruitment across these sites was highly synchronous, with a large recruitment event occurring during the early 1900s; 17% of the pinyons on both sites dated to the 1920s. Climatic conditions during this decade were consistently cool and wet—conditions known to support enhanced recruitment and growth in pinyon pines. Pinyon growth was also strongly synchronous across sites (r = 0.96). Pinyon growth was significantly correlated with winter/spring precipitation and negatively correlated with June temperature. Taken together, our results suggest that past climate may be more important in structuring pinyon populations than historical land use in these persistent pinyon-juniper woodlands. Given future climate projections of increasing temperature and more extended drought periods, regeneration of pinyon populations following the recent regional-scale dieback may be slow. Moreover, prolonged drought combined with potentially slow regeneration times for pinyon under future climate scenarios could result in substantial declines in pinyon populations across the region, a result that land managers should consider when planning for future restoration treatments in persistent pinyon-juniper woodlands.
Body Posture Modulates Action Perception

Recent studies have highlighted cognitive and neural similarities between planning and perceiving actions. Given that action planning involves a simulation of potential action plans that depends on the actor's body posture, we reasoned that perceiving actions may also be influenced by one's body posture. Here, we test whether and how this influence occurs by measuring behavioral and cerebral (fMRI) responses in human participants predicting goals of observed actions, while manipulating postural congruency between their own body posture and postures of the observed agents. Behaviorally, predicting action goals is facilitated when the body posture of the observer matches the posture achieved by the observed agent at the end of his action (action's goal posture). Cerebrally, this perceptual postural congruency effect modulates activity in a portion of the left intraparietal sulcus that has previously been shown to be involved in updating neural representations of one's own limb posture during action planning. This intraparietal area showed stronger responses when the goal posture of the observed action did not match the current body posture of the observer. These results add two novel elements to the notion that perceiving actions relies on the same predictive mechanism as planning actions. First, the predictions implemented by this mechanism are based on the current physical configuration of the body. Second, during both action planning and action observation, these predictions pertain to the goal state of the action.
In-Place Matrix Transposition on GPUs

Matrix transposition is an important algorithmic building block for many numeric algorithms such as FFT. With more and more algebra libraries offloading to GPUs, a high performance in-place transposition becomes necessary. Intuitively, in-place transposition should be a good fit for GPU architectures due to limited available on-board memory capacity and high throughput. However, direct application of CPU in-place transposition algorithms lacks the amount of parallelism and locality required by GPU to achieve good performance. In this paper we present our in-place matrix transposition approach for GPUs that is performed using elementary tile-wise transpositions. We propose low-level optimizations for the elementary transpositions, and find the best performing configurations for them. Then, we compare all sequences of transpositions that achieve full transposition, and detect which is the most favorable for each matrix. We present an heuristic to guide the selection of tile sizes, and compare them to brute-force search. We diagnose the drawback of our approach, and propose a solution using minimal padding. With fast padding and unpadding kernels, the overall throughput is significantly increased. Finally, we compare our method to another recent implementation.
Title Decreased electrophysiological activity represents the conscious state ofemptiness in meditation

Right © 2014 Hinterberger, Schmidt, Kamei and Walach. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. NAOSITE: Nagasaki University's Academic Output SITE
BET Inhibition Silences Expression of MYCN and BCL2 and Induces Cytotoxicity in Neuroblastoma Tumor Models

BET family proteins are epigenetic regulators known to control expression of genes involved in cell growth and oncogenesis. Selective inhibitors of BET proteins exhibit potent anti-proliferative activity in a number of hematologic cancer models, in part through suppression of the MYC oncogene and downstream Myc-driven pathways. However, little is currently known about the activity of BET inhibitors in solid tumor models, and whether down-regulation of MYC family genes contributes to sensitivity. Here we provide evidence for potent BET inhibitor activity in neuroblastoma, a pediatric solid tumor associated with a high frequency of MYCN amplifications. We treated a panel of neuroblastoma cell lines with a novel small molecule inhibitor of BET proteins, GSK1324726A (I-BET726), and observed potent growth inhibition and cytotoxicity in most cell lines irrespective of MYCN copy number or expression level. Gene expression analyses in neuroblastoma cell lines suggest a role of BET inhibition in apoptosis, signaling, and N-Myc-driven pathways, including the direct suppression of BCL2 and MYCN. Reversal of MYCN or BCL2 suppression reduces the potency of I-BET726-induced cytotoxicity in a cell line-specific manner; however, neither factor fully accounts for I-BET726 sensitivity. Oral administration of I-BET726 to mouse xenograft models of human neuroblastoma results in tumor growth inhibition and down-regulation MYCN and BCL2 expression, suggesting a potential role for these genes in tumor growth. Taken together, our data highlight the potential of BET inhibitors as novel therapeutics for neuroblastoma, and suggest that sensitivity is driven by pleiotropic effects on cell growth and apoptotic pathways in a context-specific manner.
BRAF vs RAS oncogenes: are mutations of the same pathway equal? differential signalling and therapeutic implications

As the increased knowledge of tumour heterogeneity and genetic alterations progresses, it exemplifies the need for further personalized medicine in modern cancer management. Here, the similarities but also the differential effects of RAS and BRAF oncogenic signalling are examined and further implications in personalized cancer diagnosis and therapy are discussed. Redundant mechanisms mediated by the two oncogenes as well as differential regulation of signalling pathways and gene expression by RAS as compared to BRAF are addressed. The implications of RAS vs BRAF differential functions, in relevant tumour types including colorectal cancer, melanoma, lung cancer are discussed. Current therapeutic findings and future viewpoints concerning the exploitation of RAS-BRAF-pathway alterations for the development of novel therapeutics and efficient rational combinations, as well as companion tests for relevant markers of response will be evaluated. The concept that drug-resistant cells may also display drug dependency, such that altered dosing may prevent the emergence of lethal drug resistance posed a major therapy hindrance.
Enhancing Breast Cancer Recurrence Algorithms Through Selective Use of Medical Record Data.

BACKGROUND The utility of data-based algorithms in research has been questioned because of errors in identification of cancer recurrences. We adapted previously published breast cancer recurrence algorithms, selectively using medical record (MR) data to improve classification. METHODS We evaluated second breast cancer event (SBCE) and recurrence-specific algorithms previously published by Chubak and colleagues in 1535 women from the Life After Cancer Epidemiology (LACE) and 225 women from the Women's Health Initiative cohorts and compared classification statistics to published values. We also sought to improve classification with minimal MR examination. We selected pairs of algorithms-one with high sensitivity/high positive predictive value (PPV) and another with high specificity/high PPV-using MR information to resolve discrepancies between algorithms, properly classifying events based on review; we called this "triangulation. " Finally, in LACE, we compared associations between breast cancer survival risk factors and recurrence using MR data, single Chubak algorithms, and triangulation. RESULTS The SBCE algorithms performed well in identifying SBCE and recurrences. Recurrence-specific algorithms performed more poorly than published except for the high-specificity/high-PPV algorithm, which performed well. The triangulation method (sensitivity = 81.3%, specificity = 99.7%, PPV = 98.1%, NPV = 96.5%) improved recurrence classification over two single algorithms (sensitivity = 57.1%, specificity = 95.5%, PPV = 71.3%, NPV = 91.9%; and sensitivity = 74.6%, specificity = 97.3%, PPV = 84.7%, NPV = 95.1%), with 10.6% MR review. Triangulation performed well in survival risk factor analyses vs analyses using MR-identified recurrences. CONCLUSIONS Use of multiple recurrence algorithms in administrative data, in combination with selective examination of MR data, may improve recurrence data quality and reduce research costs.
Exploring Jasmonates in the Hormonal Network of Drought and Salinity Responses

Present and future food security is a critical issue compounded by the consequences of climate change on agriculture. Stress perception and signal transduction in plants causes changes in gene or protein expression which lead to metabolic and physiological responses. Phytohormones play a central role in the integration of different upstream signals into different adaptive outputs such as changes in the activity of ion-channels, protein modifications, protein degradation, and gene expression. Phytohormone biosynthesis and signaling, and recently also phytohormone crosstalk have been investigated intensively, but the function of jasmonates under abiotic stress is still only partially understood. Although most aspects of jasmonate biosynthesis, crosstalk and signal transduction appear to be similar for biotic and abiotic stress, novel aspects have emerged that seem to be unique for the abiotic stress response. Here, we review the knowledge on the role of jasmonates under drought and salinity. The crosstalk of jasmonate biosynthesis and signal transduction pathways with those of abscisic acid (ABA) is particularly taken into account due to the well-established, central role of ABA under abiotic stress. Likewise, the accumulating evidence of crosstalk of jasmonate signaling with other phytohormones is considered as important element of an integrated phytohormonal response. Finally, protein post-translational modification, which can also occur without de novo transcription, is treated with respect to its implications for phytohormone biosynthesis, signaling and crosstalk. To breed climate-resilient crop varieties, integrated understanding of the molecular processes is required to modulate and tailor particular nodes of the network to positively affect stress tolerance.
In Vitro-in Vivo Correlation of Mucoadhesion Studies on Buccal Mucosa.

BACKGROUND For the development of novel buccoadhesive formulations, their physicochemical properties, strength of the interfacial joint, and residence time on the buccal mucosa are considered as a measure for their in vivo mucoadhesive properties. Focusing on these parameters, the predictive power of established in vitro systems was assessed for mucoadhesive properties in humans using discs as the model solid dosage form. METHODS Compressed into discs, hydroxyethyl cellulose, carboxymethyl cellulose, carbopol, polycarbophil, alginate, and xanthan gum were used as model polymers. Mucosal residence time, maximum detachment force (MDF), and total work of adhesion (TWA) were determined ex vivo on the porcine buccal mucosa and in vivo on healthy volunteers. The impact of detachment velocity, humidification, and experimental set-up employed for tensile studies was examined and correlated to in vivo studies. RESULTS Ex vivo results for mucosal residence time showed a very high correlation ( r = 0.997) with data obtained in vivo. For tensile studies, a set-up optimized for moistening the interface, speed, and alignment of the tensile force provided ex vivo results with very high correlation to in vivo experiments with r = 0.983 obtained for MDF and r = 0.973 for TWA, respectively. CONCLUSIONS Experimental set-ups for the determination of mucosal residence time and tensile studies could be identified as valid methods for the development of intraoral solid dosage forms.
Measuring Career Anchors and Investigating the Role of Career Anchor Congruence.

This thesis empirically examines the career orientations inventory (COI) as a measure of career anchors and then, using this measure, it goes on to investigate the relationship between career anchor congruence and work related outcomes, specifically job satisfaction and organisational commitment. The psychometric properties of the 40 item COI (presented by Igbaria and Baroudi, 1993) were explored by the administration of the measure to a sample of 658 individuals from 27 organisations in the UK. Through factor analysis an eight factor structure was demonstrated in line with that proposed by Schein (1993). The factor structure was replicated with a second sample. The COI demonstrated good levels of internal consistency (.59-.83) and test retest reliability (.68-.90). Similarly it was deemed to have acceptable levels of face validity and construct validity when compared to Mantech’s (1983) Work Values Questionnaire (WVQ). An analysis of the prevalence of career anchors and the demographic differences within the current sample was undertaken. This analysis provided evidence to suggest that certain career anchors may be increasing in prevalence while others are decreasing. These findings are in line with current research on the way in which workplace changes are impacting upon careers (Baruch, 2004). Evidence was found that indicated gender differences in scores on the COI subscales. Specifically women were found to score higher on the lifestyle anchor and men to score higher on the general management anchor. Differences were also found between the age groups considered in this study in the general management, creativity, pure challenge and lifestyle anchors. Interaction effects for age and gender were found for the general management and sense of service anchors. The COI was then used to develop a commensurate measure of job career anchors. This job career anchor measure discriminated between jobs within one police organisation. The measure was then used to explore the relationship between career anchors, career anchor congruence (congruence between individual and job career anchors), job satisfaction and organisational commitment. Evidence was found to suggest that career anchors and career anchor congruence have a direct effect on job satisfaction (predicting 10% and 4% of the variance respectively). The analysis also showed support for the role of career anchor congruence as a moderator to the relationship between career anchors and job satisfaction. This thesis makes full consideration of the academic contributions and practical implications of the research presented whilst also considering its limitations. A number of suggestions for the direction of future research have been made.
Phase II study of imatinib mesylate plus hydroxyurea in adults with recurrent glioblastoma multiforme.

PURPOSE We performed a phase II study to evaluate the combination of imatinib mesylate, an adenosine triphosphate mimetic, tyrosine kinase inhibitor, plus hydroxyurea, a ribonucleotide reductase inhibitor, in patients with recurrent glioblastoma multiforme (GBM). PATIENTS AND METHODS Patients with GBM at any recurrence received imatinib mesylate plus hydroxyurea (500 mg twice a day) orally on a continuous, daily schedule. The imatinib mesylate dose was 500 mg twice a day for patients on enzyme-inducing antiepileptic drugs (EIAEDs) and 400 mg once a day for those not on EIAEDs. Assessments were performed every 28 days. The primary end point was 6-month progression-free survival (PFS). RESULTS Thirty-three patients enrolled with progressive disease after prior radiotherapy and at least temozolomide-based chemotherapy. With a median follow-up of 58 weeks, 27% of patients were progression-free at 6 months, and the median PFS was 14.4 weeks. Three patients (9%) achieved radiographic response, and 14 (42%) achieved stable disease. Cox regression analysis identified concurrent EIAED use and no more than one prior progression as independent positive prognostic factors of PFS. The most common toxicities included grade 3 neutropenia (16%), thrombocytopenia (6%), and edema (6%). There were no grade 4 or 5 events. Concurrent EIAED use lowered imatinib mesylate exposure. Imatinib mesylate clearance was decreased at day 28 compared with day 1 in all patients, suggesting an effect of hydroxyurea. CONCLUSION Imatinib mesylate plus hydroxyurea is well tolerated and associated with durable antitumor activity in some patients with recurrent GBM.
Multi-Gigabit Communication : the ADC Bottleneck

The economies of scale in modern communication systems are enabled by architectures that take advantage of Moore’s law to implement most transceiver functionalities in digital signal processing (DSP). The bottleneck in scaling such “mostly digital” architectures to multi-Gigabit rates becomes the analog-to-digital converter (ADC): high-speed, high-precision ADCs are either not available, or are too costly and powerhungry. In this paper, we report on recent results on two approaches towards addressing this bottleneck. The first is to simply use drastically low-precision (1-4 bit) ADCs than current practice. This could be suitable for applications that require limited dynamic range (e.g., line-of-sight communication using small constellations), but there are fundamental and algorithmic questions as to whether all the functions of a communication receiver can be realized with such a significant nonlinearity early in the processing. The second is to use a time-interleaved ADC, where a large number of low-speed, high-precision ADCs are employed in parallel to realize a high-speed, high-precision ADC. This is more generally applicable to applications requiring large dynamic range (e.g., large constellations and/or dispersive channels), but the important question is how to effectively address the mismatch between the component ADCs, which leads to a performance floor if left uncompensated.
Differentiating Types of Verb Particle Constructions

A verb particle construction (VPC) classification scheme gleaned from linguistic sources has been used to assess its usefulness for identifying issues in decomposability. Linguistic sources have also been used to inform the features suitable for use in building an automatic classifier for the scheme with a series of good performance results. The notions of how to define the task of computing phrasal verbs are discussed and new proposals are presented.
Multiple Description Source Coding and Diversity Routing: A Joint Source Channel Coding Approach to Real-Time Services over Dense Networks

We investigate the interaction of the source coding mechanism and the transport mechanism for real time data packet transmission over dense networks. We show that single path routing does not make efficient use of network capacity whereas multi path routing techniques do ( Proposition 1 and 2). We then consider the interaction of single versus multiple description source coding with single versus multi path routing. The most sophisticated scheme (multiple descriptions source coding and multi path routing) performs significantly better that the usual single path and single description scheme. This improvement is more remarkable in the case of low rates and shorter maximum allowed delay (about 18 dB in the best case).
Racial and sex disparities in life expectancy losses among HIV-infected persons in the united states: impact of risk behavior, late initiation, and early discontinuation of antiretroviral therapy.

BACKGROUND Most persons with human immunodeficiency virus (HIV) infection in the United States present to care with advanced disease, and many patients discontinue therapy prematurely. We sought to evaluate sex and racial/ethnic disparities in life-years lost as a result of risk behavior, late presentation, and early discontinuation of HIV care, and we compared these survival losses for HIV-infected persons with losses attributable to high-risk behavior and HIV disease itself. METHODS With use of a state-transition model of HIV disease, we simulated cohorts of HIV-infected persons and compared them with uninfected individuals who had similar demographic characteristics. We estimated non-HIV-related mortality with use of risk-adjusted standardized mortality ratios, as well as years of life lost because of late presentation and early discontinuation of antiretroviral therapy (ART) for HIV infection. Data from the national HIV Research Network, stratified by sex and race/ethnicity, were used for estimating CD4+ cell counts at ART initiation. RESULTS For HIV-uninfected persons in the United States who have risk profiles similar to those of individuals with HIV infection, the projected life expectancy, starting at 33 years of age, was 34.58 years, compared with 42.91 years for the general US population. Those with HIV infection lost an additional 11.92 years of life if they received HIV care concordant with guidelines; late treatment initiation resulted in 2.60 additional years of life lost, whereas premature ART discontinuation led to 0.70 more years of life lost. Losses from late initiation and early discontinuation were greatest for Hispanic individuals (3.90 years). CONCLUSIONS The high-risk profile of HIV-infected persons, HIV infection itself, as well as late initiation and early discontinuation of care, all lead to substantial decreases in life expectancy. Survival disparities resulting from late initiation and early discontinuation of therapy are most pronounced for Hispanic HIV-infected men and women. Interventions focused on risk behaviors, as well as on earlier linkage to and better retention in care, will lead to improved survival for HIV-infected persons in the United States.