Miracle-dz/UniFAR-FTUs huggingface dataset:
White matter microstructure deteriorates across cognitive stages in Parkinson disease

Objectives: To characterize different stages of Parkinson disease (PD)-related cognitive decline using diffusion tensor imaging (DTI) and investigate potential relationships between cognition and microstructural integrity of primary white matter tracts. Methods: Movement Disorder Society criteria were used to classify 109 patients with PD as having normal cognition (PD-N, n = 63), mild cognitive impairment (PD-MCI, n = 28), or dementia (PD-D, n = 18), and were compared with 32 matched controls. DTI indices were assessed across groups using tract-based spatial statistics, and multiple regression was used to assess association with cognitive and clinical measures. Results: Relative to controls, PD-N showed some increased mean diffusivity (MD) in corpus callosum, but no significantly decreased fractional anisotropy (FA). Decreased FA and increased MD were identified in PD-MCI and PD-D relative to controls. Only small areas of difference were observed in PD-MCI and PD-D compared with PD-N, while DTI metrics did not differ significantly between PD-MCI and PD-D. Executive function, attention, memory, and a composite measure of global cognition were associated with MD, primarily in anterior white matter tracts; only attention was associated with FA. These differences were independent of white matter hyperintensity load, which was also associated with cognition in PD. Conclusions: PD is associated with spatially restricted loss of microstructural white matter integrity in patients with relatively normal cognition, and these alterations increase with cognitive dysfunction. Functional impairment in executive function, attention, and learning and memory appears associated with microstructural changes, suggesting that tract-based spatial statistics provides an early marker for clinically relevant cognitive impairment in PD.
Optimizing Scientific Workflows in the Cloud: A Montage Example

As scientific workflows are increasingly deployed in clouds, a myriad of studies have been conducted-including the development of workflow execution systems and scheduling/resource-management algorithms-for optimizing the execution of these workflows. However, the efficacy of most, if not all, of these previous works is limited by the original design and structure of workflow, i.e., Sequential code and few bottleneck tasks. In this paper, we address the optimization of scientific workflow execution in clouds by exploiting multi-core systems with the parallelization of bottleneck tasks. To this end, we develop a workflow visualization toolkit to synthetize resource consumption and data transfer patterns, as well as to identify the bottleneck, of the workflow being studied. Parallelization techniques are then applied to the module that is identified as the bottleneck in order to take full advantage of the underlying multicore computing environment. Testing results with a 6.0-degree Montage example on Amazon EC2 with various configurations show that our optimization of workflows (bottleneck tasks in particular) reduces completion time (or make span) by 21% to 43% depending on the instance type being used to run the workflow, without any impact on the cost.
“But I Am Not One to Judge Her Actions”: Thematic and Discursive Approaches to University Students’ Responses to Women Who Smoke While Pregnant

Qualitative methodologies offer various approaches to interpreting qualitative data. Here we consider how different approaches to interpreting the same data can be useful in learning about the scope and utility of qualitative methods and in exploring the role of reflexivity in analytic decision making and interpretation. We apply both thematic and discourse analyses to university students’ responses to an open-ended question about women who smoke while pregnant. We show how our interpretations differ when analytic attention is paid to the content (thematic analysis) versus the rhetorical function (discourse analysis) of participants’ responses. We also show how reflexivity, compatible with our discursive analysis, allowed us to identify the local discursive context in which the data were produced and therefore how participants oriented to this context. We use our learning experience as a way of showcasing the value of dynamic and reflexive approaches to qualitative data.
Developing Thinking; Developing Learning

It is now recognised that thinking skills, such as problem-solving, analysis, synthesis, creativity and evaluation, can be nurtured and developed, and education professionals can play a significant role in shaping the way that children learn and think. As a result, schools are being encouraged to make greater use of thinking skills in lessons and the general emphasis on cognition has developed considerably. This book offers a comprehensive introduction to thinking skills in education and provides detailed guidance on how teachers can support cognitive development in their classrooms.
More Practical Bounded-Skew Clock Routing 1

Academic clock routing research results has often had limited impact on industry practice, since such practical considerations as hierarchical buffering, rise-time and overshoot constraints, obstacleand legal location-checking, varying layer parasitics and congestion, and even the underlying design flow are often ignored. This paper explores directions in which traditional formulations can be extended so that the resulting algorithms are more useful in production design environments. Specifically, the following issues are addressed: (i) clock routing for varying layer parasitics with nonzero via parasitics; (ii) obstacle-avoidance clock routing; (iii) a new topology design rule for prescribed-delay clock routing; and (iv) predictive modeling of the clock routing itself. We develop new theoretical analyses and heuristics, and present experimental results that validate our new approaches.
Milgram and the Prevalence of Anthropocentrism

This paper seeks an explanation for the overwhelming prevalence of anthropocentrism in the thinking of Western moral philosophers. It has been thought that such philosophers have been anthropocentric on the basis of reasons for which a rational defense may be given. When this view has been challenged, it has been challenged only by arguing that human interests stand in for rationally defensible reasons. This paper challenges the view that the only explanations of the prevalence of anthropocentrism are rationally defensible reasons or human interests by advancing a competing explanation located in human psychology. The psychological experiments of Stanley Milgram and other empirical work by psychologists provide evidence of a psychological mechanism that supplies this competing explanation.
Discourse or reality?: “Work‐life balance”, flexible working policies and the gendered organization

Purpose – The purpose of this paper is to examine the impact of flexible working arrangements (FWAs) and particularly reduced hours working arrangements on a Dual Agenda of gender equity and workplace effectiveness, in a case study organization employing a relatively high proportion of women scientists.Design/methodology/approach – In‐depth interviews based on the initial stages of collaborative interactive action research (CIAR) are used within a case‐study approach. The interviews explored working practices, the assumptions underpinning them and their un/intended consequences.Findings – The main form of FWA used in the organization, four days a week, is double edged and complex in its effects. It supports mothers, but at a cost because of gendered assumptions. Despite a commitment to flexibility and “work‐life balance”, the gendered construction of the ideal worker and ideas of competence conflated with hegemonic masculinity, remain powerful. This, together with a prevalent “good mother” ideology, under.
Genetic Variation in the NOC Gene Is Associated with Body Mass Index in Chinese Subjects

Circadian clock genes are critical regulators of energy homeostasis and metabolism. However, whether variation in the circadian genes is associated with metabolic phenotypes in humans remains to be explored. In this study, we systemically genotyped 20 tag single nucleotide polymorphisms (SNPs) in 8 candidate genes involved in circadian clock, including CLOCK, BMAL1(ARNTL), PER1, PER2, CRY1, CRY2, CSNK1E,, and NOC(CCRN4L) in 1,510 non-diabetic Chinese subjects in Taipei and Yunlin populations in Taiwan. Their associations with metabolic phenotypes were analyzed. We found that genetic variation in the NOC gene, rs9684900 was associated with body mass index (BMI) (P = 0.0016, Bonferroni corrected P = 0.032). Another variant, rs135764 in the CSNK1E gene was associated with fasting glucose (P = 0.0023, Bonferroni corrected P = 0.046). These associations were consistent in both Taipei and Yunlin populations. Significant epistatic and joint effects between SNPs on BMI and related phenotypes were observed. Furthermore, NOC mRNA levels in human abdominal adipose tissue were significantly increased in obese subjects compared to non-obese controls. Conclusion Genetic variation in the NOC gene is associated with BMI in Chinese subjects.
A closer look into the employee influence

Purpose – The purpose of this study is to elucidate the relationship between perceived employee influence and organizational commitment by applying a multidimensional approach that includes influence perceived to stem from the individual and the team, as well as affective and normative commitment.Design/methodology/approach – A total of 526 out of a population of 732 employees (72 percent reply rate) from four Danish companies in different industries and with different types of teams participated in the questionnaire study.Findings – Results of bootstrapping mediation analyses reveal that a relationship between perceived influence of the team and affective commitment is fully mediated by perceived individual influence. Results of multiple regression analyses show a positive relationship between team and individual influence, and that normative commitment moderated the relationship negatively. The results are to suggest that influence of the team may stimulate employees’ individual influence, and in turn t.
FEN1 Stimulation of DNA Polymerase β Mediates an Excision Step in Mammalian Long Patch Base Excision Repair*

In mammalian cells, single-base lesions, such as uracil and abasic sites, appear to be repaired by at least two base excision repair (BER) subpathways: “single-nucleotide BER” requiring DNA synthesis of just one nucleotide and “long patch BER” requiring multi-nucleotide DNA synthesis. In single-nucleotide BER, DNA polymerase β (β-pol) accounts for both gap filling DNA synthesis and removal of the 5′-deoxyribose phosphate (dRP) of the abasic site, whereas the involvement of various DNA polymerases in long patch BER is less well understood. Recently, we found that β-pol plays a role in mammalian cell extract-mediated long patch BER, in that formation of a key excision product, 5′-dRP-trinucleotide (5′-dRP-N3), is dependent upon β-pol (Dianov, G. L., Prasad, R., Wilson, S. H., and Bohr, V.A. (1999)J. Biol. Chem. 274, 13741–13743). The structure-specific endonuclease flap endonuclease 1 (FEN1) has also been suggested to be involved in long patch BER excision. Here, we demonstrate by immunodepletion experiments that 5′-dRP-N3excision in long patch BER of uracil-DNA in a human lymphoid cell extract is, indeed, dependent upon FEN1. Next, we reconstituted the excision step of long patch BER using purified human proteins and an oligonucleotide substrate with 5′-dRP at the margin of a one-nucleotide gap. Formation of the excision product 5′-dRP-N3 was dependent upon both strand displacement DNA synthesis by β-pol and FEN1 excision. FEN1 stimulated strand displacement DNA synthesis of β-pol. FEN1 acting either alone, or without DNA synthesis by β-pol, produced a two-nucleotide excision product, 5′-dRP-N1, but not 5′-dRP-N3. These results demonstrate that human FEN1 and β-pol can cooperate in long patch BER excision and specify the predominant excision product seen with a cell extract.
Loss of E-cadherin independently predicts the lymph node status in colorectal cancer

Background: The identification of biomarkers that improve risk stratification in patients with colorectal cancer (CRC) is still a challenge. The objective of our study was to identify independent protein markers as predictors of lymph node (N) stage in CRC. Methods: Tumour specimens from 221 CRC patients were mounted onto a multiple-punch tissue microarray and evaluated for 21 tumour related factors and one host related factor involved in CRC carcinogenesis, namely β-catenin, E-cadherin, EGFR, pERK, RHAMM, pAKT, pSMAD2, p21, p16, Bcl-2, Ki-67, APAF-1, MST1, RKIP, VEGF, EphB2, MMP7, Laminin5γ2, MUC1, CDX2, caspase-3 as well as intra-tumoural and stromal CD8+ tumour infiltrating lymphocytes (iTILs and sTILs). Results: Node positive cancers showed significant losses for p21 (p = 0.026), Bcl-2 (p = 0.027), APAF-1 (p = 0.033), EphB2 (p = 0.006), E-cadherin (p < 0.001), RKIP (p = 0.019), CD8+ iTILs and sTILs (p < 0.001 and p = 0.008, respectively) and cytoplasmic MST1 (p = 0.014). Based on the area under the receiver operating characteristic curve (AUC) EphB2, E-cadherin, iTILs and sTILs were identified as potential predictors of N stage (AUC values >0.6), but only loss of E-cadherin was an independent predictor in multivariate analysis. Conclusions: E-cadherin appears to be a strong predictor of N stage in CRC and should be considered in pre-operative and post-operative management of colon and rectal cancer patients.
Strategies for Scaling and Pivoting for Sparse Symmetric Indefinite Problems

We consider ways of implementing preordering and scaling for symmetric systems and show the effect of using this technique with a multifrontal code for sparse symmetric indefinite systems. After having presented a new method for scaling, we propose a way of using an approximation to a symmetric weighted matching to predefine $1 \times 1$ and $2 \times 2$ pivots prior to the ordering and analysis phase. We also present new classes of orderings called "(relaxed) constrained orderings" that mix structural and numerical criteria.
Retroviruses Pseudotyped with the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Efficiently Infect Cells Expressing Angiotensin-Converting Enzyme 2

ABSTRACT Infection of receptor-bearing cells by coronaviruses is mediated by their spike (S) proteins. The coronavirus (SARS-CoV) that causes severe acute respiratory syndrome (SARS) infects cells expressing the receptor angiotensin-converting enzyme 2 (ACE2). Here we show that codon optimization of the SARS-CoV S-protein gene substantially enhanced S-protein expression. We also found that two retroviruses, simian immunodeficiency virus (SIV) and murine leukemia virus, both expressing green fluorescent protein and pseudotyped with SARS-CoV S protein or S-protein variants, efficiently infected HEK293T cells stably expressing ACE2. Infection mediated by an S-protein variant whose cytoplasmic domain had been truncated and altered to include a fragment of the cytoplasmic tail of the human immunodeficiency virus type 1 envelope glycoprotein was, in both cases, substantially more efficient than that mediated by wild-type S protein. Using S-protein-pseudotyped SIV, we found that the enzymatic activity of ACE2 made no contribution to S-protein-mediated infection. Finally, we show that a soluble and catalytically inactive form of ACE2 potently blocked infection by S-protein-pseudotyped retrovirus and by SARS-CoV. These results permit studies of SARS-CoV entry inhibitors without the use of live virus and suggest a candidate therapy for SARS.
Runtime Distribution-Aware Dynamic Voltage Scaling

We propose a new intra-task dynamic voltage scaling (DVS) method to capture an important fact of 'software runtime distribution' and integrate it into DVS effectively. Specifically, the proposed method finds performance levels, for a given software runtime distribution, i.e. statistical profiling of execution cycles (neither the execution cycle of worst-case execution path nor the worst-case execution cycles of basic blocks), which leads to a minimal energy consumption while satisfying the given deadline constraints. Experimental results report that the proposed method gives 19.2%~33.3% further energy reduction compared with the best-known methods for two industrial multimedia software programs, H.264 decoder andMPEG4 decoder
A Speech/Music/Silence/Garbage/ Classifier for Searching and Indexing Broadcast News Material

An audio classifier that can distinguish between speech, music, silence and garbage has been developed. The classifier was trained and tested on broadcast news material provided by VRT (Flemish Radio and Television Network). Several feature sets and machine learning algorithms have been tested, providing choices of speed and performance for a target system. The audio classifier is part of a greater system that together with visual data can retrieve information from news broadcasts: speech can be converted to text and the speaker can be recognized. Music can be further used for genre classification, jingle recognition or copyright infringement detection. Silence is recognized and used to provide cues on topic changes or speaker turns. At this point everything that is not classified as speech, music or silence is labeled garbage. Garbage classes can be further used for background categorization giving information on the environment where someone speaks (an anchor in the studio or a reporter in the street).
Privacy-Preserving Lawful Contact Chaining: [Preliminary Report]

How can government agencies acquire actionable, useful information about legitimate targets, while preserving the privacy of innocent parties and holding government agencies accountable? Towards understanding this crucial issue, we present the first privacy-preserving protocol for contact chaining, an operation that law-enforcement and intelligence agencies have used effectively. Our experiments suggest that a three-hop, privacy-preserving graph traversal producing 27,000 ciphertexts can be done in under two minutes.
Mechanical Stress Stimulates the Osteo/Odontoblastic Differentiation of Human Stem Cells from Apical Papilla via ERK 1/2 and JNK MAPK Pathways

Background Information. Stem cells from apical papilla (SCAPs) are a potent candidate for the apexogenesis/apexification due to their multiple differentiation capacity. During the orthodontic treatment of developing teeth, SCAPs in vivo are usually subjected to the cyclic stress induced by compression forces. However, it remains unclear whether mechanical stress can affect the proliferation and differentiation of human SCAPs. Results. Human SCAPs were isolated and stimulated by 200 g mechanical stimuli for 30 min and their proliferation and differentiation capacity were evaluated in vitro at different time points. MTT and FCM results demonstrated that cell proliferation was enhanced, while TEM findings showed the morphological and ultrastructural changes in stress-treated SCAPs. ALP activity and mineralization capacity of stress-treated SCAPs were upregulated . In the meantime, higher odontogenic and osteogenic differentiation were found in stress-treated SCAPs by real-time RT-PCR and Western blot, as indicated by the expression of related markers at both mRNA and protein levels. Moreover, the protein expressions of pJNK and pERK MAPK pathways were upregulated. Conclusion. Together, these findings suggest that mechanical stress is an important factor affecting the proliferation and differentiation of SCAPs via the activation of ERK and JNK signaling pathway.
Undecidability for arbitrary public announcement logic

Arbitrary public announcement logic (AP AL) is an extension of multi-agent epistemic logic that allows agents' knowledge states to be updated by the public announcement of (possibly arbitrary) epistemic for- mulae. It has been shown to be more expressive than epistemic logic, and a sound and complete axiomatization has been given. Here we address the question of decidability. We present a proof that the satisfiability problem for arbitrary public announcement logic (AP AL) is co-RE complete, via a tiling argument.
Instrumental interaction: an interaction model for designing post-WIMP user interfaces

This article introduces a new interaction model called Instrumental Interaction that extends and generalizes the principles of direct manipulation. It covers existing interaction styles, including traditional WIMP interfaces, as well as new interaction styles such as two-handed input and augmented reality. It defines a design space for new interaction techniques and a set of properties for comparing them. Instrumental Interaction describes graphical user interfaces in terms of domain objects and interaction instruments. Interaction between users and domain objects is mediated by interaction instruments, similar to the tools and instruments we use in the real world to interact with physical objects. The article presents the model, applies it to describe and compare a number of interaction techniques, and shows how it was used to create a new interface for searching and replacing text.
Two-Step Regulation of Ad4BP/SF-1 Gene Transcription during Fetal Adrenal Development: Initiation by a Hox-Pbx1-Prep1 Complex and Maintenance via Autoregulation by Ad4BP/SF-1

ABSTRACT The orphan nuclear receptor Ad4BP/SF-1 (adrenal 4 binding protein/steroidogenic factor 1) is essential for the proper development and function of reproductive and steroidogenic tissues. Although the expression of Ad4BP/SF-1 is specific for those tissues, the mechanisms underlying this tissue-specific expression remain unknown. In this study, we used transgenic mouse assays to examine the regulation of the tissue-specific expression of Ad4BP/SF-1. An investigation of the entire Ad4BP/SF-1 gene locus revealed a fetal adrenal enhancer (FAdE) in intron 4 containing highly conserved binding sites for Pbx-Prep, Pbx-Hox, and Ad4BP/SF-1. Transgenic assays revealed that the Ad4 sites, together with Ad4BP/SF-1, develop an autoregulatory loop and thereby maintain transcription, while the Pbx/Prep and Pbx/Hox sites initiate transcription prior to the establishment of the autoregulatory loop. Indeed, a limited number of Hox family members were found to be expressed in the adrenal primordia. Whether a true fetal-type adrenal cortex is present in mice remained controversial, and this argument was complicated by the postnatal development of the so-called X zone. Using transgenic mice with lacZ driven by the FAdE, we clearly identified a fetal adrenal cortex in mice, and the X zone is the fetal adrenal cells accumulated at the juxtamedullary region after birth.