Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental comparison of memory management policies for NUMA multiprocessors

Non-uniformity of memory access is an almost inevitable feature of memory architecture in shared memory multiprocessor designs that can scale to large numbers of processors. One implication of NUMA architectures is that the placement and movement of code and data become crucial to performance. As memory architectures become more complex and the nonuniformity becomes less well hidden, systems software must assume a larger role in providing memory management support for the programmer. This paper investigates the role of the operating system. We take an experimental approach to evaluating a wide-range of memory management policies. The target NUMA environment is BBN''s GP-1000 multiprocessor. Extensive local modifications have been made to the memory management subsystem of BBN''s nX operating system to support multiple policy implementations. Policy comparisons are based on the measured performance of real parallel applications. Our results show that there are memory management policies implemented in our system that can improve the performance of programs written using the simpler uniform memory access (UMA) programming model. While achieving the level of performance of a highly tuned NUMA program is still a difficult problem, some examples come close. There appears to be no single policy that can be considered the best over our set of test applications. Investigations into the contributions made by individual policy features toward overall behavior of the workload provide some insight into the design of a set of effective policies.
Fish Consumption and Risk of Stroke: The Zutphen Study

Background and Purpose A low-to-moderate average daily fish consumption has been reported to convey protection against coronary heart disease incidence and mortality. Currently there is no information about its effect on stroke risk. Methods In 1960, 1965, and 1970 cross-check dietary histories were obtained in 552 men aged 50 to 69 years in 1970 in the town of Zutphen, The Netherlands. The association between fish consumption and stroke incidence in the period 1970 to 1985 was assessed by Cox proportional hazards models. Adjustments were made for confounding by age, systolic blood pressure, cigarette smoking, serum total cholesterol, energy intake, alcohol consumption, and prescribed diet. Results The mean fish consumption in 1970 was 17.9 g/d. Men who consumed more than 20 g of fish per day in 1970 had a reduced risk of stroke compared with those who consumed less fish. The hazard ratio (HR) amounted to 0.49 (95% confidence interval [C1], 0.24 to 0.99), and did not change after adjustment for potential confounders. Fewer strokes occurred among the 301 men who always reported fish consumption between 1960 and 1970 than among the men who changed fish consumption habits between 1960 and 1970 or did not consume fish at all (HR, 0.63; 95% CI, 0.34 to 1.16). Conclusions These results suggest that consumption of at least one portion of fish per week may be associated with a reduced stroke incidence. (Stroke. 1994;5 328-332.)
Lithium chloride attenuates root resorption during orthodontic tooth movement in rats

Root resorption is a common side effect of orthodontic treatment. In the current study, lithium chloride (LiCl), a Wnt signaling activator, was examined to determine its effect on root resorption. In total, 10 Sprague Dawley rats were randomly allocated into the experimental group (EG) and control group (CG). Each group consisted of five subjects. By using closed nickel-titanium coil springs, a 50-g force was applied between the upper incisors and the maxillary right first molars in order to mimic orthodontic biomechanics in the EG and CG for 14 days. During the 14 days, the EG rats were gavage-fed 200 mg/kg LiCl every 48 h. Next, digital radiographs were captured using a micro-computational tomography scanner. The movement of the maxillary first molars and the root resorption area ratio were measured electronically on the digital radiographs. The outcomes were analyzed using ANOVA. Following 14 days of experimental force application, all rats had spaces of varying sizes between the first and second right maxillary molars. The average distance measured in the CG was slightly higher than in the EG, however, the difference was not found to be statistically significant (P=0.224). Root resorption craters were observed in the groups following the experiment. Rough cementum areas were observed on the mesial surface of the distobuccal and distopalatal roots. The mean root resorption area ratio of CG was significantly greater than EG (P<0.05). Results of the present study indicate that LiCl can attenuate orthodontically induce root resorption during orthodontic tooth movement. The effect of LiCl on tooth movement is insignificant.
Motion Primitives for Human-to-Humanoid Skill Transfer under Balance Constraint

In order to properly function in real-world environments, the gait of a humanoid robot must be able to adapt to new situations as well as to deal with unexpected perturbations. A promising research direction is the modular generation of movements that results from the combination of a set of basic primitives. Humans seem to be able to adapt their motion in an effortless way and efficient way. In this work we present a methodology to extract a single demonstration signal from a human teacher that can be used in a biped robot to walk in an efficient way and quickly adapt to new situations. Instead of using a normal human gait, the demonstrator walks on a gait we called "robot-like". It is our belief that the retargeting task will be more efficient and easier by using this methodology. The acquired signal is then used to train a set of Dynamic Movement Primitives (DMP) that directly retrieves the trajectories of the end effector in the Cartesian space. In previous works we have used this methodology with efficiency in several tasks, e.g., walking over irregularities, overcoming an obstacle. Now, by combining rhythmic DMP with discrete DMP, we show that the adaptability performance to new situations that require precise foot placement is increased.
Measuring the Formaldehyde Protein–DNA Cross-Link Reversal Rate

Protein–DNA binding interactions play critical roles in important cellular processes such as gene expression, cell division, and chromosomal organization. Techniques to identify and characterize these interactions often utilize formaldehyde cross-linking for stabilization of the complexes. Advantages of formaldehyde as a cross-linking reagent include cell permeability, relatively fast cross-linking kinetics, and short cross-linker length. In addition, formaldehyde cross-links are reversible, which has the advantage of allowing complexes to be dissociated if desired but may also present a problem if undesired dissociation occurs in the course of an experiment. While the kinetics of formaldehyde cross-link formation have been well-established in numerous studies, there have been no reports of the rate of cross-link dissociation, even though it is clearly a critical variable when developing a biochemical protocol involving formaldehyde cross-linking. We present here a method for measurement of the rate of formaldehyde cross-link reversal based upon the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) procedure and use it to determine the rate of cross-link reversal for cross-linked protein–DNA complexes from yeast cell lysate. The half-life of the protein–DNA cross-links varies from 179 h at 4 °C to 11.3 h at 47 °C, with a rate that increases exponentially with temperature and is independent of salt concentration.
Efficient Selection and Sorting Schemes for Processing Large Distributed Files in de Bruijn Networks and Hypercubes

In this paper we show the power of sampling techniques in designing efficient distributed algorithms. In particular, we show that using sampling techniques, on the hypercube and de Bruijn network, the selection can be done in such a way that the message complexity is less sensitive to the cardinality of the set (file). Our selection schemes outperform the existing approaches in terms of both message complexity and communication delay. The property that the number of messages needed and the communication delay are less sensititive to the size of the file makes our distributed selection schemes extremely attractive in such domains as very large database systems. Making use of our selection algorithms, we also show that both quicksort-based sorting scheme and enumeration sorting scheme can be developed for sorting large distributed files on the hypercube and de Bruijn networks.
Clustering Large and Sparse Co-occurrence Data

A novel approach to clustering co-occurrence data poses it as an optimization problem in information theory — in this framework, an optimal clustering is one which minimizes the loss in mutual information. Recently a divisive clustering algorithm was proposed that monotonically reduces this loss function. In this paper we show that sparse high-dimensional data presents special challenges which can result in the algorithm getting stuck at poor local minima. We propose two solutions to this problem: (a) a prior to overcome infinite relative entropy values as in the supervised Naive Bayes algorithm, and (b) local search to escape local minima. Finally, we combine these solutions to get a powerful algorithm that is computationally efficient. We present detailed experimental results to show that the proposed method is highly effective in clustering document collections and outperforms previous approaches.
Land Use-Land-Cover Changes in Saiwa Swamp Watershed, Western Kenya

Land use activities have altered a large proportion of the planet's land surface. Although land use practices vary greatly across the world, their ultimate outcome is the way they alter the structure and functioning of ecosystems. Due to the significance of such changes on the biosphere, monitoring changes in land use-land cover is a high priority area for research (De Fries et al., 2007). Quantifying land transformation is essential in understanding and modelling of complex interactions and impacts between the natural and human environments, from local, regional to global scales. Multi-temporal analyses of land use-land cover changes provide important insights into long term trends which serve to identify the drivers and determinants of these changes (De Fries et al., 2007). The most significant changes in land use are related to agricultural expansion resulting in decrease in natural vegetation formations such as forests, bush lands, grasslands and wetlands (Githui et al., 2009). These changes are a result of the increasing human population and increased demand for ecosystem goods and services. While these significant changes in land use-land cover have allowed sustained human population growth and economic development in the past, it raises concerns regarding local and regional environmental impacts and their consequences on human well-being and environmental quality.
Charge at the lidocaine binding site residue Phe‐1759 affects permeation in human cardiac voltage‐gated sodium channels

Our homology molecular model of the open/inactivated state of the Na+ channel pore predicts, based on extensive mutagenesis data, that the local anaesthetic lidocaine docks eccentrically below the selectivity filter, such that physical occlusion is incomplete. Electrostatic field calculations suggest that the drug's positively charged amine produces an electrostatic barrier to permeation. To test the effect of charge at this pore level on permeation in hNaV1.5 we replaced Phe‐1759 of domain IVS6, the putative binding site for lidocaine's alkylamino end, with positively and negatively charged residues as well as the neutral cysteine and alanine. These mutations eliminated use‐dependent lidocaine block with no effect on tonic/rested state block. Mutant whole cell currents were kinetically similar to wild type (WT). Single channel conductance (γ) was reduced from WT in both F1759K (by 38%) and F1759R (by 18%). The negatively charged mutant F1759E increased γ by 14%, as expected if the charge effect were electrostatic, although F1759D was like WT. None of the charged mutations affected Na+/K+ selectivity. Calculation of difference electrostatic fields in the pore model predicted that lidocaine produced the largest positive electrostatic barrier, followed by lysine and arginine, respectively. Negatively charged glutamate and aspartate both lowered the barrier, with glutamate being more effective. Experimental data were in rank order agreement with the predicted changes in the energy profile. These results demonstrate that permeation rate is sensitive to the inner pore electrostatic field, and they are consistent with creation of an electrostatic barrier to ion permeation by lidocaine's charge.
Chloride/bicarbonate exchange in human erythrocytes.

1. The exchange of chloride and bicarbonate across the human erythrocyte membrane has been followed by measuring the changes in extracellular pH which occur when chloride‐rich erythrocytes are added to chloride‐free media containing varying concentrations of bicarbonate and carbonic anhydrase. 2. The dependence of the rate of chloride/bicarbonate exchange on the extracellular concentration of bicarbonate was consistent with the existence of a saturable membrane anion transporter exhibiting Michaelis‐‐Menten kinetics. In a medium containing sodium gluconate buffered to pH 7.0 with imidazole‐‐malate the Km for bicarbonate activation of transport was 0.39 (+/‐ 0.03) mM and the Vmax was 2033 (+/‐ 80 m‐mole anions exchanged/3 X 10(13) cells. min, at 10 degrees C. 3. Chloride/bicarbonate exchange was temperature‐dependent with an Arrhenius activation energy of 19.4 kcal/mole in the temperature range 2‐‐10 degrees C. 4. Exchange of intracellular chloride for extracellular bicarbonate was inhibited by the presence of extracellular halides. Inhibition by chloride, bromide and fluoride was competitive and the affinity of the transport system decreased in the order HCO‐3 greater than Cl‐ greater than Br‐ greater than F‐. The kinetics of inhibition by iodide were complex, but inhibitory effects of low concentrations of iodide were less than those of chloride and bromide.
Pharmacological concentrations of recombinant factor VIIa restore hemostasis independent of tissue factor in antibody‐induced hemophilia mice

Essentials The role of tissue factor (TF) in recombinant factor VIIa (rFVIIa) therapy in hemophilia is unclear. An acquired mouse hemophilia model with very low or normal levels of human TF was used in the study. rFVIIa is equally effective in correcting the bleeding in mice expressing low or normal levels of TF. Pharmacological doses of rFVIIa restore hemostasis in hemophilia independent of TF.
Implicit structured sequence learning: an fMRI study of the structural mere-exposure effect

In this event-related fMRI study we investigated the effect of 5 days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL) paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the fMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45) and the medial prefrontal regions (centered on BA 8/32). Importantly, and central to this study, the inclusion of a naive preference fMRI baseline measurement allowed us to conclude that these fMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax) in unsupervised AGL paradigms with proper learning designs.
Single versus sequential culture medium: which is better at improving ongoing pregnancy rates? A systematic review and meta-analysis

This study aimed to evaluate if single medium is better than sequential medium at improving ongoing pregnancy rates in patients undergoing assisted reproductive technology (ART) procedures. The data featured in this meta-analysis were extracted from four randomized controlled trials yielded from a systematic search carried out on electronic databases. The primary endpoint was ongoing pregnancy rate. Secondary endpoints included clinical pregnancy and miscarriage rates. The endpoints for ongoing pregnancy rate were also analyzed based on the time at which the embryo transfers were performed: cleavage stage (day 2/3) and/or blastocyst stage (day 5/6). There were no significant differences between single and sequential medium for clinical pregnancy (RR=1.09; 95%CI=0.83-1.44; p=0.53), ongoing pregnancy (RR=1.11; 95%CI=0.87-1.40; p=0.39), or miscarriage rates (RR=0.89; 95%CI=0.44-1.81; p=0.74). No significant difference was found for ongoing pregnancy rate (RR=1.29; 95%CI=0.93-1.78; p=0.12) between single and sequential medium when only trials in which embryos were transferred at the blastocyst stage were included. In conclusion, the choice of embryo culture approach - single or sequential medium - did not affect the ongoing pregnancy rates of patients undergoing ART cycles.
Constraint-Induced Therapy of Chronic Aphasia After Stroke

Patients with chronic aphasia were assigned randomly to a group to receive either conventional aphasia therapy or constraint-induced (CI) aphasia therapy, a new therapeutic technique requiring intense practice over a relatively short period of consecutive days. CI aphasia therapy is realized in a communicative therapeutic environment constraining patients to practice systematically speech acts with which they have difficulty. Patients in both groups received the same amount of treatment (30 to 35 hours) as 10 days of massed-practice language exercises for the CI aphasia therapy group (3 hours per day minimum; 10 patients) or over a longer period of ≈4 weeks for the conventional therapy group (7 patients). CI aphasia therapy led to significant and pronounced improvements on several standard clinical tests, on self-ratings, and on blinded-observer ratings of the patients’ communicative effectiveness in everyday life. Patients who received the control intervention failed to achieve comparable improvements. Data suggest that the language skills of patients with chronic aphasia can be improved in a short period by use of an appropriate massed-practice technique that focuses on the patients’ communicative needs.
Functional abnormalities underlying pathological gambling in Parkinson disease.

BACKGROUND Pathological gambling (PG) may develop in patients with Parkinson disease (PD) during dopamine replacement therapy, but the underlying neural correlates are still unclear. OBJECTIVE To investigate resting state brain perfusion in PD patients with active PG compared with matched PD controls and healthy controls. DESIGN Case-control study. SETTING Outpatient tertiary clinic. PARTICIPANTS Eleven right-handed PD patients with active PG according to Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition, Text Revision) criteria, 40 matched PD controls, and 29 age-matched healthy controls. INTERVENTION All the participants underwent resting state brain perfusion single-photon emission computed tomography using technetium TC 99m ethylcysteinate dimer bicisate. All PD subjects were taking dopaminergic medication. MAIN OUTCOME MEASURE Statistical Parametric Mapping was used for data analysis (P<.005, false discovery rate corrected). RESULTS PD patients with PG showed resting state overactivity in a right hemisphere network that included the orbitofrontal cortex, the hippocampus, the amygdala, the insula, and the ventral pallidum. No areas of perfusion reduction were detected. CONCLUSIONS We found that PD patients with PG have abnormal resting state dysfunction of the mesocorticolimbic network possibly associated with a drug-induced overstimulation of relatively preserved reward-related neuronal systems. These findings support the concept that PG is a "behavioral" addictive disorder.
3D bioprinting: improving in vitro models of metastasis with heterogeneous tumor microenvironments

ABSTRACT Even with many advances in treatment over the past decades, cancer still remains a leading cause of death worldwide. Despite the recognized relationship between metastasis and increased mortality rate, surprisingly little is known about the exact mechanism of metastatic progression. Currently available in vitro models cannot replicate the three-dimensionality and heterogeneity of the tumor microenvironment sufficiently to recapitulate many of the known characteristics of tumors in vivo. Our understanding of metastatic progression would thus be boosted by the development of in vitro models that could more completely capture the salient features of cancer biology. Bioengineering groups have been working for over two decades to create in vitro microenvironments for application in regenerative medicine and tissue engineering. Over this time, advances in 3D printing technology and biomaterials research have jointly led to the creation of 3D bioprinting, which has improved our ability to develop in vitro models with complexity approaching that of the in vivo tumor microenvironment. In this Review, we give an overview of 3D bioprinting methods developed for tissue engineering, which can be directly applied to constructing in vitro models of heterogeneous tumor microenvironments. We discuss considerations and limitations associated with 3D printing and highlight how these advances could be harnessed to better model metastasis and potentially guide the development of anti-cancer strategies. Summary: Here, Albritton and Miller discuss recent 3D bioprinting advances that can be used to produce heterogeneous tumor microenvironments for improved physical modeling of cancer metastasis.