Miracle-dz/UniFAR-FTUs huggingface dataset:
An efficient programming model for memory-intensive recursive algorithms using parallel disks

In order to keep up with the demand for solutions to problems with ever-increasing data sets, both academia and industry have embraced commodity computer clusters with locally attached disks or SANs as an inexpensive alternative to supercomputers. With the advent of tools for parallel disks programming, such as MapReduce, STXXL and Roomy --- that allow the developer to focus on higher-level algorithms --- the programmer productivity for memory-intensive programs has increased many-fold. However, such parallel tools were primarily targeted at iterative programs. We propose a programming model for migrating recursive RAM-based legacy algorithms to parallel disks. Many memory-intensive symbolic algebra algorithms are most easily expressed as recursive algorithms. In this case, the programming challenge is multiplied, since the developer must re-structure such an algorithm with two criteria in mind: converting a naturally recursive algorithm into an iterative algorithm, while simultaneously exposing any potential data parallelism (as needed for parallel disks). This model alleviates the large effort going into the design phase of an external memory algorithm. Research in this area over the past 10 years has focused on per-problem solutions, without providing much insight into the connection between legacy algorithms and out-of-core algorithms. Our method shows how legacy algorithms employing recursion and non-streaming memory access can be more easily translated into efficient parallel disk-based algorithms. We demonstrate the ideas on a largest computation of its kind: the determinization via subset construction and minimization of very large nondeterministic finite set automata (NFA). To our knowledge, this is the largest subset construction reported in the literature. Determinization for large NFA has long been a large computational hurdle in the study of permutation classes defined by token passing networks. The programming model was used to design and implement an efficient NFA determinization algorithm that solves the next stage in analyzing token passing networks representing two stacks in series.
A Tool for Participatory Negotiation: LINKing-UP Participatory Design and Design Knowledge Reuse

We describe a web-based prototype that enhances participatory design by providing participatory negotiation mechanisms between designers and potential end-users of a proposed system. As a module of LINK-UP, a repository for reusable design knowledge, our tool compliments scenario-based design processes, helping designers and potential end-users improve consensus. Negotiation spans a whole design cycle, but our initial focus is on requirements analysis. We report promising results from a pilot evaluation and suggest directions that will further improve the synthesis of participatory design, reuse of design knowledge, and development of design-support tools.
Relationships between College Characteristics and Student Achievement1

As greater numbers of young people continue on to college, it becomes of increasing concern to know which institutional characteristics are associated with how much a student learns during his four years in college. Such information is important not only to the theorist who is attempting to understand how and to what extent college characteristics influence student behavior, but to the college administrator who requires such information for decisions concerning the optimum allocation of limited funds among many competing educational programs and processes. In addition, the recent increase in student population has been accompanied by an ever increasing flow of both public and private funds into the college system, resulting in an increasing need to evaluate the potential payoff of differential funding policies. Many of the differences among colleges with respect to their resources have been documented by Astin and Holland (1962), Cartter (1964), and the College Data Bank of Columbia's Bureau of Applied Social Research (1966). However, little additional light has been shed on whether or not these differences are associated with differential student achievement. Certainly any study of the impact of various
Chronic dietary intake of quercetin alleviates hepatic fat accumulation associated with consumption of a Western-style diet in C57/BL6J mice.

SCOPE To determine the effect of consumption of a quercetin-rich diet on obesity and dysregulated hepatic gene expression. METHODS AND RESULTS C56BL/6J mice were fed for 20 wk on AIN93G (control) or a Western diet high in fat, cholesterol and sucrose, both with or without 0.05% quercetin. Triglyceride levels in plasma, thiobarbituric acid-reactive substances (oxidative stress marker) and glutathione levels and peroxisome proliferator-activated receptor α expression in livers of mice fed with the Western diet were all improved after 8 wk feeding with quercetin. After 20 wk, further reductions of visceral and liver fat accumulation and improved hyperglycemia, hyperinsulinemia, dyslipidemia and plasma adiponectin and TNFα levels in these mice fed with quercetin were observed. The expression of hepatic genes related to steatosis, such as peroxisome proliferator-activated receptor γ and sterol regulatory element-binding protein-1c was also normalized by quercetin. In mice fed with the control diet, quercetin did not affect body weight but reduces the plasma TNFα and hepatic thiobarbituric acid-reactive substance levels. CONCLUSION In mice fed with a Western diet, chronic dietary intake of quercetin reduces liver fat accumulation and improves systemic parameters related to metabolic syndrome, probably mainly through decreasing oxidative stress and reducing PPARα expression, and the subsequent reduced expression in the liver of genes related to steatosis.
The Role of the Conserved Residues His-246, His-199, and Tyr-255 in the Catalysis of Catechol 2,3-Dioxygenase from Pseudomonas stutzeri OX1*

Catechol 2,3-dioxygenase (C2,3O) from Pseudomonas stutzeri OX1, which is able to grow on various aromatic substrates as the sole source of carbon and energy, has been expressed in Escherichia coli, purified, characterized, and found to be very similar to other dioxygenases from Pseudomonas species. Interestingly, the activity of the protein shows a rather unusual pH dependence when assayed on catechol. A model of the catalytic mechanism was developed that is able to reproduce the catalytic behavior of the protein as a function of the pH. The model includes multiple equilibria and four productive intermediates with different ionization states of the enzyme-substrate complex. The fitting of the theoretical curve to the experimental data suggests that a tyrosine and two histidine residues are involved in catalysis. Mutants (H246N)-, (H246A)-, (H199N)- and (Y255F)-C2,3O were produced to investigate the role of highly conserved His-199, His-246, and Tyr-255. The strongly reduced activity of the mutants suggests a primary catalytic role for each of these residues. Moreover, mutants at positions 199 and 246 display pH profiles different from that of the wild-type protein, thus indicating that residues His-246 and His-199 play a role in determining the unusual pH dependence of the enzyme. In addition, electron-withdrawing groups on catechol, which increase the acidity of the phenolic hydroxyl group, are able to counterbalance the effect of the mutation H246N in reducing catalytic activity but cause a further reduction of the activity of (H199N)-C2,3O. This finding suggests that His-246 is involved in the initial catechol deprotonation, whereas His-199 promotes the reaction between oxygen and the aromatic ring.
A Single-File Version of Linear Hashing with Partial Expansions

Linear hashing with partial expansions is a file organization intended for dynamic files. In this paper an improved version of the method is presented. Instead of having a separate overflow area, the storage area for overflow records is incorporated into the main file. Hence, all the records are stored in one file which grows and shrinks according to the number of records stored. By using several overflow chains per page, the retrieval performance is further improved. The expected performance of the new scheme is studied by means of a few examples.
Trend in DRAM soft errors

Summary form only given. The quality of electrical tests during irradiation of components has also improved a lot. Test patterns have been modified and characteristics of recent DRAMs have had to be taken into account. We can also observe a trend in the results of soft error tests. In the beginning, we mostly got single-bit events and did not ask for more. The trend is now moving toward a complete listing of error rates for any number of fail-bits per event in combination with the fail-bit addresses. Soft errors with fail-counts up to several thousand per event have to be handled by the tests
Heat storage regulation in exercise during thermal transients.

Rate of heat storage (S) was measured by using direct and indirect calorimetry simultaneously in 11 subjects during rest and exercise at three ambient temperatures (Ta of 20, 25, and 30 degrees C), and at two work intensities (40 and 90 W). At rest, the mean value of S was -64.9 W at 20 degrees C, -26.1 W at 25 degrees C, and +9.9 W at 30 degrees C. After 50 min of exercise at 40 or 90 W, S tended toward zero at the three ambient temperatures. This indicates that thermal equilibrium was reached. In addition, at the end of the exercise periods total heat losses (R + C + E) measured at a Ta of 20, 25, and 30 degrees C were similar, i.e., independent of Ta. During the thermal transients and the steady state of exercise, the calorimetric method allows immediate measurement of S to be made, since all the physical terms of the body heat balance equation are determined. The changes in mean body temperature (delta Tb) measured by thermometry showed a delay of 5-10 min when compared with delta Tb measured by calorimetry. Thus, determination of delta Tb by thermometry is not directly applicable during thermal transients, unless the observed delay is taken into account. Our results also support the concept that Tb may be the regulated variable of the thermoregulatory system, since we obtained a very significant and uniform correlation between Esk and delta Tb at the three Ta and the two work intensities which were studied.
Tree-Rings Mirror Management Legacy: Dramatic Response of Standard Oaks to Past Coppicing in Central Europe

Background Coppicing was one of the most important forest management systems in Europe documented in prehistory as well as in the Middle Ages. However, coppicing was gradually abandoned by the mid-20th century, which has altered the ecosystem structure, diversity and function of coppice woods. Methodology/Principal Findings Our aim was to disentangle factors shaping the historical growth dynamics of oak standards (i.e. mature trees growing through several coppice cycles) in a former coppice-with-standards in Central Europe. Specifically, we tried to detect historical coppicing events from tree-rings of oak standards, to link coppicing events with the recruitment of mature oaks, and to determine the effects of neighbouring trees on the stem increment of oak standards. Large peaks in radial growth found for the periods 1895–1899 and 1935–1939 matched with historical records of coppice harvests. After coppicing, the number of newly recruited oak standards markedly grew in comparison with the preceding or following periods. The last significant recruitment of oak standards was after the 1930s following the last regular coppicing event. The diameter increment of oak standards from 1953 to 2003 was negatively correlated with competition indices, suggesting that neighbouring trees (mainly resprouting coppiced Tilia platyphyllos) partly suppressed the growth of oak standards. Our results showed that improved light conditions following historical coppicing events caused significant increase in pulses of radial growth and most probably maintained oak recruitment. Conclusions/Significance Our historical perspective carries important implications for oak management in Central Europe and elsewhere. Relatively intense cutting creating open canopy woodlands, either as in the coppicing system or in the form of selective cutting, is needed to achieve significant radial growth in mature oaks. It is also critical for the successful regeneration and long-term maintenance of oak populations.
A Review of Islet of Langerhans Degeneration in Rodent Models of Type 2 Diabetes

Type 2 diabetes mellitus (TTDM) is characterized by progressive loss of glucose control through multifactorial mechanisms. The search for an understanding of TTDM has relied on animal models since the realization of the importance of the pancreas in controlling plasma glucose concentration. Rodent models of TTDM are developed to express hyperglycemia and not islet degeneration per se. Degeneration of the islets of Langerhans with β-cell loss is secondary to insulin resistance and is regarded as the more important lesion. Despite this, differences between models are seen in the development and progression of islet degeneration. Assessing the differences between the models is important to appreciate the various aspects of TTDM and understand their advantages as well as their deficiencies. Relevant animal models of TTDM provide opportunities to investigate important physiological and cell biological processes that may ultimately lead to development of targeted therapies. This article reviews the importance, advantages, and limitations of rodent models of TTDM in relation to the histopathological changes that characterize islet degeneration. Pathophysiological mechanisms that contribute to islet degeneration are also discussed and are placed into the context of changes in islet histological appearances.
Awareness: A Personal Memoir on the Declining Quality of Life in Alzheimer’s

I am 61 years old, a retired professor; I live alone. At the University of California Santa Barbara I used to teach a course called ‘The Social Psychology of Affliction’. One of its inspirations was the book Suffering by radical Christian theologian Dorothee Soelle (1975). Compassion means understanding and overcoming the tendency to blame or ignore the victim and refusing to worship a false God who abets this. It means healing interventions on a personal and societal level, and when nothing concrete can be done, to be in solidarity with the afflicted person and help him bear his burden. In 1997 what seemed to be a progressive attention-deficit disorder led me to a neurologist. The initial MRI suggested frontotemporal dementia, but in August 1998 a PET scan at UCLA led to a diagnosis of Alzheimer’s. Since then my clinical presentation has become more characteristic of AD, with impairment of visual processing and slowness of thought, but without marked frontal symptomatology. I have pioneered the application of brain-injury rehabilitation concepts to dementia, presented my studies at conferences, and recorded my journey in essays (see my website: http://members.aol.com/MorrisFF). Recently, I have been experiencing decline; vital active living feels more remote, as does the past when I used to be ‘normal’. It increasingly takes all my mental energy to do a creative writing project like this article and otherwise just get through the day. I evaluate myself as having decreased quality of life (QOL). I ask myself: is it worthwhile to monitor my QOL, or does awareness have an unreasonable cost? If it is indeed worthwhile, how can I assess and monitor my QOL, both as a basis for improving it and for making ultimate decisions? It is an attempt to address some of these issues that consumes the remainder of this personal account. de men tia
Lesions of lateral or central amygdala abolish aversive Pavlovian-to-instrumental transfer in rats

Aversive Pavlovian conditioned stimuli (CSs) elicit defensive reactions (e.g., freezing) and motivate instrumental actions like active avoidance (AA). Pavlovian reactions require connections between the lateral (LA) and central (CeA) nuclei of the amygdala, whereas AA depends on LA and basal amygdala (BA). Thus, the neural circuits mediating conditioned reactions and motivation appear to diverge in the amygdala. However, AA is not ideal for studying conditioned motivation, because Pavlovian and instrumental learning are intermixed. Pavlovian-to-instrumental transfer (PIT) allows for the study of conditioned motivation in isolation. PIT refers to the ability of a Pavlovian CS to modulate a separately-trained instrumental action. The role of the amygdala in aversive PIT is unknown. We designed an aversive PIT procedure in rats and tested the effects of LA, BA, and CeA lesions. Rats received Pavlovian tone-shock pairings followed by Sidman shock-avoidance training. PIT was assessed by comparing shuttling rates in the presence and absence of the tone. Tone presentations facilitated instrumental responding. Aversive PIT was abolished by lesions of LA or CeA, but was unaffected by lesions of BA. These results suggest that LA and CeA are essential for aversive conditioned motivation. More specifically, the results are consistent with a model of amygdala processing in which the CS is encoded in the LA and then, via connections to CeA, the motivation to perform the aversive task is enhanced. These findings have implications for understanding the contribution of amygdala circuits to aversive instrumental motivation, but also for the relation of aversive and appetitive behavioral control.
Elemental carbon in snow at Changbai Mountain, northeastern China: concentrations, scavenging ratios, and dry deposition velocities

Light-absorbing aerosol - particularly elemental carbon (EC) - while mixed with snow and ice is an important climate driver from the enhanced absorption of solar radiation. Currently, considerable efforts are being made to estimate its radiative forcing on a global scale, but several uncertainties remain, particularly those regarding its deposition processes. In this study, concurrent measurements of EC in air and snow are performed for three years (2009-2012) at Changbai station, northeastern China. The scavenging ratio and the wet-and dry-deposition fluxes of EC over the snow surface are estimated. The mean EC concentration in the surface snow is 1000 +/- 1500 ng g(-1), ranging from 7 to 7640 ng g(-1). The mean value of the scavenging ratio of EC by snow is 140 +/- 100, with a median value of 150, which is smaller than that reported in Arctic areas. A non-rimed snow process is a significant factor in interpreting differences with Arctic areas. Wet-deposition fluxes of EC are estimated to be 0.47 +/- 0.37 mu g cm(-2) month(-1) on average over the three snow seasons studied. Dry deposition is more than five times higher, with an average of 2.65 +/- 1.93 mu g cm(-2) month(-1); however, only winter period estimation is possible (December-February). During winter in Changbai, 87% of EC in snow is estimated to be due to dry deposition, with a mean dry deposition velocity of 6.44 x 10(-3) ms(-1) and median of 8.14 x 10(-3) ms(-1). Finally, the calculation of the radiative effect shows that 500 ng g(-1) of dry-deposited EC to a snow surface absorbs three times more incoming solar energy than the same mass mixed in the snow through wet deposition. Deposition processes of an EC-containing snow surface are, therefore, crucial to estimate its radiative forcing better, particularly in northeastern China, where local emission strongly influences the level and gradient of EC in the snowpack, and snow-covered areas are cold and dry due to the atmospheric general circulation. Furthermore, this study builds on the knowledge to characterize the conditions in the snow-laden Chinese rural areas better as well as to constrain transport of EC to the Arctic better.
Pathways Implicated in Tadalafil Amelioration of Duchenne Muscular Dystrophy

Numerous therapeutic approaches for Duchenne and Becker Muscular Dystrophy (DMD and BMD), the most common X‐linked muscle degenerative disease, have been proposed. So far, the only one showing a clear beneficial effect is the use of corticosteroids. Recent evidence indicates an improvement of dystrophic cardiac and skeletal muscles in the presence of sustained cGMP levels secondary to a blocking of their degradation by phosphodiesterase five (PDE5). Due to these data, we performed a study to investigate the effect of the specific PDE5 inhibitor, tadalafil, on dystrophic skeletal muscle function. Chronic pharmacological treatment with tadalafil has been carried out in mdx mice. Behavioral and physiological tests, as well as histological and biochemical analyses, confirmed the efficacy of the therapy. We then performed a microarray‐based genomic analysis to assess the pattern of gene expression in muscle samples obtained from the different cohorts of animals treated with tadalafil. This scrutiny allowed us to identify several classes of modulated genes. Our results show that PDE5 inhibition can ameliorate dystrophy by acting at different levels. Tadalafil can lead to (1) increased lipid metabolism; (2) a switch towards slow oxidative fibers driven by the up‐regulation of PGC‐1α; (3) an increased protein synthesis efficiency; (4) a better actin network organization at Z‐disk. J. Cell. Physiol. 230: 224–232, 2016. © 2015 Wiley Periodicals, Inc.
Parametric design of rocket engine turbopumps with genetic algorithms

In a rocket engine, the main turbopump parameters must be estimated considering that the power output of the turbine essentially has to equal the power demand of the pump. Considering the properties of the turbine drive gas (specific heat, temperature and other features), the strength limits of the turbine materials, and the likely pressure drop, it is possible to determine the basic dimensions of the blades like pitch line velocity, turbine nozzle outlet velocity, number of rows of blades, turbine type or turbine efficiency. The particular arrangement or geometry of the major turbopump components is related to their selection process. Most propellant pumps have a single-stage main impeller. Usually some design limit is reached which requires one or more iterations, each with a new changed approach or parameter. The present work considers the development of a software tool based on genetic algorithms to assist the determination of the excellent parameters of configuration of turbopumps in engines for liquid propellant rockets. We present results for alcohol/LOX propellant mixture, some discussion on its applications on rocket engines.