Miracle-dz/UniFAR-FTUs huggingface dataset:
Apparent Free Space of Plant Roots.

Although it is now generally recognized that solutes may permeate some appreciable fraction of the volume of certain plant organs by free diffusion (4, 6, 10, 19), the magnitude and physiological significance of free space remain highly debatable. Free space measurements have been questioned more with regard to the adequacy of removal of superficial solution than for any other reason. The retention of a very thin film, especially on fine roots after blotting or centrifuging may falsely magnify the free space value (20). To obviate this difficulty, the authors have developed a technique for tagging the external medium with a colloid which does not penetrate free space. India ink particles (Higgins American India Ink No. 4415, Waterproof Black, Higgins Ink Company, Brooklyn, N. Y.) are not adsorbed to or repelled from root surfaces under any of the experimental conditions described. This was confirmed by microscopic examination of roots mounted in India ink following a variety of pretreatments including leaching in distilled water and/or equilibration with NaCl solutions. By measuring the amount of India ink carried over on the surface of the root, the volume of root medium superficially retained by the root is determined. The quantity of test solute present in this volume of medium is subtracted from the total quantity of test solute carried over with the root to give the amount of solute in the free space of the root. Using this technique, the apparent free space values were measured for roots of a number of plant species for which data are available in the literature. In the course of these preliminary studies, variable free space values were found for pea and bean roots depending on experimental conditions. These conditions (duration of washing of roots in distilled water, nature of test solute, and duration of equilibration with solute) were therefore examined critically so that a reasonable explanation of the observed effects could be given. The term "apparent free space" (AFS) includes a built-in apology: The user concedes that AFS describes a hypothetical partial volume which is a true measure of the free space only if the test solute con-
Interleukin-4 Protects against a Genetically Linked Lupus-like Autoimmune Syndrome

Interleukin-4 (IL-4) provides support for humoral immune responses through upregulation of T helper (Th) type 2 cell differentiation, but it is not known whether IL-4 promotes antibodymediated autoimmune diseases such as systemic lupus erythematosus (SLE). Here, we show that the constitutive expression of an IL-4 transgene by B cells completely prevents the development of lethal lupus-like glomerulonephritis in the (NZW × C57BL/6.Yaa)F1 murine model of SLE. This was associated with marked changes in the serum levels of IgG subclasses, rather than in the total levels of anti-DNA antibodies, with a lack of IgG3, a decrease of IgG2a, and an increase in IgG1 subclasses, and by a strong reduction in the serum levels of gp70-antigp70 immune complexes. This effect of the transgene appears to result from a modulation of the Th1 versus Th2 autoimmune response, since the protected mice displayed comparably modified IgG2a and IgG3 antibody response against exogenous T cell–dependent antigen, but not against T cell–independent antigens. Thus, IL-4 prevents the development of this lupuslike autoimmune disease, most likely by downregulating the appearance of Th1-mediated IgG subclasses of autoantibodies such as the IgG3 autoantibodies which have been shown to be especially nephritogenic.
Type I Interferon: Potential Therapeutic Target for Psoriasis?

Background Psoriasis is an immune-mediated disease characterized by aberrant epidermal differentiation, surface scale formation, and marked cutaneous inflammation. To better understand the pathogenesis of this disease and identify potential mediators, we used whole genome array analysis to profile paired lesional and nonlesional psoriatic skin and skin from healthy donors. Methodology/Principal Findings We observed robust overexpression of type I interferon (IFN)–inducible genes and genomic signatures that indicate T cell and dendritic cell infiltration in lesional skin. Up-regulation of mRNAs for IFN-α subtypes was observed in lesional skin compared with nonlesional skin. Enrichment of mature dendritic cells and 2 type I IFN–inducible proteins, STAT1 and ISG15, were observed in the majority of lesional skin biopsies. Concordant overexpression of IFN-γ and TNF-α–inducible gene signatures occurred at the same disease sites. Conclusions/Significance Up-regulation of TNF-α and elevation of the TNF-α–inducible gene signature in lesional skin underscore the importance of this cytokine in psoriasis; these data describe a molecular basis for the therapeutic activity of anti–TNF-α agents. Furthermore, these findings implicate type I IFNs in the pathogenesis of psoriasis. Consistent and significant up-regulation of type I IFNs and their associated gene signatures in psoriatic skin suggest that type I IFNs may be potential therapeutic targets in psoriasis treatment.
Modern computational perspectives on executive mental processes and cognitive control: Where to from here?

Future research on cognitive control must precisely characterize the supervisory functions of executive mental processes. The achievement of this objective will be facilitated by formal concepts and algorithms from contemporary computer operating systems. In particular, operating-system fundamentals can help to advance work with the Executive-Process Interactive Control (EPIC) architecture, a theoretical framework for computational modeling of human multiple-task performance. EPIC models that incorporate general executive processes like those of operating systems provide insights about how people schedule tasks, allocate perceptual-motor resources, and coordinate task processes during multiple-task performance under both laboratory and real-world conditions. Such insights may lead to discoveries about the acquisition of procedural task knowledge and efficient multitasking skills. _________________________________ * This document is a preprint of a chapter to be published in S. Monsell and J. Driver (Eds.), Control of Cognitive Processes: Attention and Performance XVIII, Cambridge, MA, M.I. T. Press. The subsequent text cites companion chapters by other authors as appearing in "this volume". Support for the research reported herein was provided by grant N00014-92-J-1173 from the Cognitive Sciences Program of the Office of Naval Research to the University of Michigan. We thank members of the Brain, Cognition, and Action Laboratory (David Fencsik, Darren Gergle, Jennifer Glass, Leon Gmeindl, Cerita Jones, Shane Mueller, Eric Schumacher, Mollie Schweppe, and Travis Seymour) for helpful assistance. Comments by Leon Gmeindl, Stephen Monsell, Travis Seymour, and two anonymous reviewers on drafts of this chapter are greatly appreciated. Correspondence about this chapter should be addressed to: David E. Kieras (kieras@eecs. umich.edu), Artificial Intelligence Laboratory, Electrical Engineering and Computer Science Department, Advanced Technology Laboratory Building, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110, USA; David E. Meyer (demeyer@umich.edu), Department of Psychology, University of Michigan, 525 E. University, Ann Arbor, Michigan, MI 48109-1109, USA. Computation and Control Kieras, Meyer, Ballas, & Lauber
Galaxy luminosity evolution: How much is due to model choice?

The cluster and field luminosity functions (LFs) determined on large homogeneous samples (N > 2200 galaxics each) are almost indistinguishable, down to M* + 4 in the r and i filters, suggesting that the effect of the cluster environment on the galaxy properties does not affect the galaxy luminosity function in red bands. The similarity of the red band LFs in different environments suggests that the galaxy mass function is preserved during the galaxy infall in the cluster. By analyzing a large sample of galaxies in clusters, ideal from many points of view (multicolor data, large size, many clusters, metric magnitudes) we found that luminosity evolution is required by the data but its flavour cannot be unambiguously derived if a differential 1uminosity evolution between bright and faint galaxies is allowed. We show that the LF parameters (slope, characteristic magnitude and their evolution) and errors depend on assumptions in a way seldom recognized in the literature. We also point out logical inconsistencies between hypotheses assumed in deriving literature LF and presented results, suggesting caution in interpreting similar published results.
Idempotent Vector Design for Standard Assembly of Biobricks

Abstract : The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly reaction to be both an experimental tool for addressing the current research topic, and an experiment in and of itself. One of our goals is to replace this ad hoc experimental design with a set of standard and reliable engineering mechanisms to remove much of the tedium and surprise during assembly of genetic components into larger systems. William Sellers, in a speech "On a Uniform System of Screw Threads" at the Franklin Institute in Philadelphia on April 21, 1864, remarked that "In this country, no organized attempt has as yet been made to establish any system, each manufacturer having adopted whatever his judgement may have dictated as best, or as most convenient for himself" (Surowiecki 02). He argued forcefully and successfully for the standardization of pitch, diameter, and form of screw threads, providing the infrastructure which allowed the industrial revolution to take off. The machinists of the Franklin Institute built the lathes, drills, taps, and dies necessary to make the standard a success. We anticipate advantages similar to those which accompany the standardization of screw threads in mechanical design -- the widespread ability to interchange parts, to assemble sub-components, to outsource assembly to others, and to rely extensively on previously manufactured components. Here, we present a simple sequence and assembly standard as part of an experiment to see how far this idea of standardized interface technology can be applied. The key notion in the design of our strategy is that the transformations performed on component parts during the assembly reactions are idempotent in a structural sense. That is, each reaction leaves the key structural elements of the component the same. The output of any such transformation, therefore, is a component which can be used as the input to any subsequent manipulation.
Towards Bidirectional Hierarchical Representations for Attention-based Neural Machine Translation

This paper proposes a hierarchical attentional neural translation model which focuses on enhancing source-side hierarchical representations by covering both local and global semantic information using a bidirectional tree-based encoder. To maximize the predictive likelihood of target words, a weighted variant of an attention mechanism is used to balance the attentive information between lexical and phrase vectors. Using a tree-based rare word encoding, the proposed model is extended to sub-word level to alleviate the out-of-vocabulary (OOV) problem. Empirical results reveal that the proposed model significantly outperforms sequence-to-sequence attention-based and tree-based neural translation models in English-Chinese translation tasks.
complexity of natural scenes by exploiting multiple views of the same scene

Intrinsic video decomposition refers to the fundamentally ambiguous task of separating a video stream into its constituent layers, in particular reflectance and shading layers. Such a decomposition is the basis for a variety of video manipulation applications, such as realistic recoloring or retexturing of objects. We present a novel variational approach to tackle this underconstrained inverse problem at real-time frame rates, which enables on-line processing of live video footage. The problem of finding the intrinsic decomposition is formulated as a mixed variational `2–`p-optimization problem based on an objective function that is specifically tailored for fast optimization. To this end, we propose a novel combination of sophisticated local spatial and global spatio-temporal priors resulting in temporally coherent decompositions at real-time frame rates without the need for explicit correspondence search. We tackle the resulting high-dimensional, non-convex optimization problem via a novel data-parallel iteratively reweighted least squares solver that runs on commodity graphics hardware. Real-time performance is obtained by combining a localglobal solution strategy with hierarchical coarse-to-fine optimization. Compelling real-time augmented reality applications, such as recoloring, material editing and retexturing, are demonstrated in a live setup. Our qualitative and quantitative evaluation shows that we obtain high-quality real-time decompositions even for challenging sequences. Our method is able to outperform state-of-the-art approaches in terms of runtime and result quality – even without user guidance such as scribbles.
Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication

The role of long noncoding RNAs (lncRNAs) in viral infection is poorly studied. We have identified hepatitis C virus (HCV)‐Stimulated lncRNAs (CSRs) by transcriptome analysis. Interestingly, two of these CSRs (PVT1 and UCA1) play relevant roles in tumorigenesis, providing a novel link between HCV infection and development of liver tumors. Expression of some CSRs seems induced directly by HCV, while others are upregulated by the antiviral response against the virus. In fact, activation of pathogen sensors induces the expression of CSR32/EGOT. RIG‐I and the RNA‐activated kinase PKR sense HCV RNA, activate NF‐κB and upregulate EGOT. EGOT is increased in the liver of patients infected with HCV and after infection with influenza or Semliki Forest virus (SFV). Genome‐wide guilt‐by‐association studies predict that EGOT may function as a negative regulator of the antiviral pathway. Accordingly, EGOT depletion increases the expression of several interferon‐stimulated genes and leads to decreased replication of HCV and SFV. Our results suggest that EGOT is a lncRNA induced after infection that increases viral replication by antagonizing the antiviral response.
Persist/Dropout Differences In Pre-matriculation Attitudes Of Freshman Towards College Attrition: A Longitudinal Multiple Group Structural Equations Model

This study proposes a structural equations model of college student attrition based on prematriculation freshman attitudes. The study uses a survey administered annually from 1995 to 1999 and tracks persistence and dropout behavior for five years until the last cohort graduated. It discusses seven constructs of pre-matriculation freshman attitudes that resemble the Cabrera, Nora, and Castañeda (1993) model of College Persistence that was based on attitudes of first-to-second year enrolled college students. We applied our survey to a Northeastern sectarian private college. Our model includes external factors such as financial attitude, and endogenous variables such as academic reputation, social integration, institutional commitment, goal commitment, academic performance, and intent to persist. In addition to the variables related to the Cabrera model, we added two measures of social integration, “political interests” and “concern-for the disadvantaged” because these were suitable to the type of college which hosted the study. Results provide a multiple group comparative and predictive model of student attrition for annual use by the Dean of Student Affairs in designing proactive plans and implementing intervention strategies to enhance student retention.
A Matched Case-Control Study on Open and Endovascular Treatment of Popliteal Artery Aneurysms

Objective: To compare early and late results of open and endovascular management of popliteal artery aneurysm in a retrospective single-center matched case-control study Methods: From 1981 to 2015, 309 consecutive interventions for popliteal artery aneurysm were performed in our institution, in 59 cases with endovascular repair and in 250 cases with open repair. Endovascular repair was preferred in older asymptomatic patients, while open repair was offered more frequently to patients with a thrombosed popliteal artery aneurysm and a poor run-off status. A one-to-one coarsened exact matching on the basis of the baseline demographic, clinical, and anatomical covariates significantly different between the two treatment options was performed and two equivalent groups of 56 endovascular repairs and open repairs were generated. The two groups were compared in terms of perioperative results with χ2 test and of follow-up outcomes with the Kaplan–Meier curves and log-rank test. Results: There were no differences between the two groups in terms of perioperative outcomes. Median duration of follow-up was 38 months. Five-year survival rates were 94% in endovascular repair group and 89.5% in open repair group (p = 0.4, log-rank 0.6). Primary patency rates at 1, 3, and 5 years were 81%, 78%, and 72% in endovascular repair group and 82.5%, 80%, and 64% in open repair group (p = 0.8, log-rank 0.01). Freedom from reintervention at 5 years was 65.5% in endovascular repair group and 76% in open repair group (p = 0.2, log-rank 1.2). Secondary patency at 1, 3, and 5 years was 94%, 86%, and 74% in endovascular repair group, and 94%, 89%, and 71% in open repair group, respectively (p = 0.9, log-rank 0.01). The rates of limb preservation at 5 years were 94% in endovascular repair group and 86.4% in open repair group (p = 0.3, log-rank 0.8). Conclusion: Open repair and endovascular repair of popliteal artery aneurysms provided in this retrospective single-center experience similar perioperative and follow-up results in equivalent groups of patients.
Effects of blasting fumes on exposure and short-term lung function changes in tunnel construction workers.

OBJECTIVES This study attempts to determine the effects of exposure to blasting fumes and its influence on the lung function of tunnel workers. METHODS Two groups of tunnel workers, one using ammonium nitrate fuel oil (ANFO) as the explosive and the other using size-sensitized emulsion (SSE), with 24 workers per group, were compared with a reference group (N=34) with low exposure. Spirometry was used to determine lung function. Personal exposure to total and respirable dust, alpha-quartz, volatile organic compounds, oil mist and vapors, formaldehyde, nitrogen dioxide, and carbon monoxide was measured. RESULTS The ANFO workers were more exposed to all the agents than the reference group and more exposed than the SSE workers to all the agents except total dust and carbon monoxide. The SSE workers were significantly more exposed to total dust and alpha-quartz than the reference group. High peak exposures to nitrogen dioxide (up to 20 ppm) occurred for the ANFO workers in contrast to the SSE workers, whose exposure did not exceed 2 ppm. The lung function of the ANFO workers significantly decreased by 3% for forced vital capacity, 7% for forced expiratory volume in 1 second, and 8% for forced expiratory flow rate from 25% to 75% of the forced vital capacity over the 11-day period. The changes were reversible. There were no significant changes among the SSE workers and the outdoor workers. The ANFO workers had a significant decrease in FEV1.0 when compared with both the SSE and outdoor workers. CONCLUSIONS Tunnel workers using ANFO explosive show a temporary reduction in lung function, whereas those using SSE do not. The most likely explanation for the observed changes is peak exposures to nitrogen dioxide.
The effects of yoga on body dissatisfaction, self-objectification, and mindfulness of the body in college women

by Sara Elysia Clancy, Ph.D. Washington State University August 2010 Chair: Laurie Dawn McCubbin Previous research on the Objectification Theory suggests that woman may experience self-objectification and body dissatisfaction. Research has demonstrated that yoga is associated with lower self-objectification and lower body dissatisfaction (Daubenmeir, 2005; Impett, Daubenmeir, & Hirschman, 2006) and thus may be a key intervention toward increasing body satisfaction among woman. The purpose of this between and within groups repeated measures experimental study is to determine whether or not a yoga program has positive effects on decreasing body dissatisfaction, increasing body satisfaction, decreasing self-objectification, and increasing mindfulness of the body in college women. Volunteers experiencing dissatisfaction with their bodies and who have zero to limited yoga experience based on their self-report were recruited for the study. Participants were comprised of 32 college students. Participants completed a survey packet consisting of the following measures: (a) A demographics questionnaire (Clancy, unpublished dissertation, 2008); (b) The Self-Objectification Questionnaire (SOQ; Noll & Fredrickson, 1998); (c) The Surveillance subscale of the Objectified Body Consciousness (OBC)
In Vitro Study of the Effects of Angiostrongylus cantonensis Larvae Extracts on Apoptosis and Dysfunction in the Blood-Brain Barrier (BBB)

It has been hypothesized that blood-brain barrier (BBB) dysfunction in Angiostrongylus cantonensis infection might be due to the apoptosis of the hosts' BBB cells. Here, we evaluated this hypothesis through several methods, all based on an in vitro mouse BBB model consisting of primary culture brain microvascular endothelial cells (BMECs) and brain astrocytic cells (BACs). In the present study, a four-hour percolation and HRP permeability experiment showed that A. cantonensis larvae extracts can increase the permeability of the BBB. Apoptosis among BMECs and BACs after exposure to larvae extracts was monitored by TUNEL and annexin-V-FITC/PI double staining. A. cantonensis larvae extracts were found to induce apoptosis in both BMECs and BACs. For this reason, we concluded that the induction of apoptosis might participate in the BBB dysfunction observed during angiostrongyliasis. Improved fundamental understanding of how A. cantonensis induces apoptosis may lead to new approaches to the treatment or prevention of this parasitic disease.
Estimating the number of quit attempts it takes to quit smoking successfully in a longitudinal cohort of smokers

Objectives The number of quit attempts it takes a smoker to quit successfully is a commonly reported figure among smoking cessation programmes, but previous estimates have been based on lifetime recall in cross-sectional samples of successful quitters only. The purpose of this study is to improve the estimate of number of quit attempts prior to quitting successfully. Design We used data from 1277 participants who had made an attempt to quit smoking in the Ontario Tobacco Survey, a longitudinal survey of smokers followed every 6 months for up to 3 years beginning in 2005. We calculated the number of quit attempts prior to quitting successfully under four different sets of assumptions. Our expected best set of assumptions incorporated a life table approach accounting for the declining success rates for subsequent observed quit attempts in the cohort. Results The estimated average number of quit attempts expected before quitting successfully ranged from 6.1 under the assumptions consistent with prior research, 19.6 using a constant rate approach, 29.6 using the method with the expected lowest bias, to 142 using an approach including previous recall history. Conclusions Previous estimates of number of quit attempts required to quit may be underestimating the average number of attempts as these estimates excluded smokers who have greater difficulty quitting and relied on lifetime recall of number of attempts. Understanding that for many smokers it may take 30 or more quit attempts before being successful may assist with clinical expectations.