Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of rare copy number variation in absence epilepsies

Objective: To identify shared genes and pathways between common absence epilepsy (AE) subtypes (childhood absence epilepsy [CAE], juvenile absence epilepsy [JAE], and unclassified absence epilepsy [UAE]) that may indicate common mechanisms for absence seizure generation and potentially a diagnostic continuum. Methods: We used high-density single-nucleotide polymorphism arrays to analyze genome-wide rare copy number variation (CNV) in a cohort of 144 children with AEs (95 CAE, 26 UAE, and 23 JAE). Results: We identified CNVs that are known risk factors for AE in 4 patients, including 3x 15q11.2 deletion. We also expanded the phenotype at 4 regions more commonly identified in other neurodevelopmental disorders: 1p36.33 duplication, 1q21.1 deletion, 22q11.2 duplication, and Xp22.31 deletion and duplication. Fifteen patients (10.5%) were found to carry rare CNVs that disrupt genes associated with neuronal development and function (8 CAE, 2 JAE, and 5 UAE). Four categories of protein are each disrupted by several CNVs: (1) synaptic vesicle membrane or vesicle endocytosis, (2) synaptic cell adhesion, (3) synapse organization and motility via actin, and (4) gap junctions. CNVs within these categories are shared across the AE subtypes. Conclusions: Our results have reinforced the complex and heterogeneous nature of the AEs and their potential for shared genetic mechanisms and have highlighted several pathways that may be important in epileptogenesis of absence seizures.
Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: A potential mechanism for position-effect variegation

Methylation of lysine-79 (K79) within the globular domain of histone H3 by Dot1 methylase is important for transcriptional silencing and for association of the Sir silencing proteins in yeast. Here, we show that the level of H3-K79 methylation is low at all Sir-dependent silenced loci but not at other transcriptionally repressed regions. Hypomethylation of H3-K79 at the telomeric and silent mating-type loci, but not the ribosomal DNA, requires the Sir proteins. Overexpression of Sir3 concomitantly extends the domain of Sir protein association and H3-K79 hypomethylation at telomeres. In mammalian cells, H3-K79 methylation is found at loci that are active for V(D)J recombination, but not at recombinationally inactive loci that are heterochromatic. These results suggest that H3-K79 methylation is an evolutionarily conserved marker of active chromatin regions, and that silencing proteins block the ability of Dot1 to methylate histone H3. Further, they suggest that Sir proteins preferentially bind chromatin with hypomethylated H3-K79 and then block H3-K79 methylation. This positive feedback loop, and the reverse loop in which H3-K79 methylation weakens Sir protein association and leads to further methylation, suggests a model for position-effect variegation.
Infinitesimal Perturbation Analysis of Stochastic Flow Models with Delays: Application to Multi-Intersection Traffic Light Control

We extend Stochastic Flow Models (SFMs), which are used for a large class of hybrid systems, by including the delays which typically arise in flow movement. We apply this framework to the multi-intersection traffic light control problem by including transit delays for vehicles moving from one intersection to the next. Using Infinitesimal Perturbation Analysis (IPA) for this SFM with delays, we derive new on-line gradient estimates of several congestion cost metrics with respect to the controllable green and red cycle lengths. The IPA estimators are used to iteratively adjust light cycle lengths to improve performance and, in conjunction with a standard gradient-based algorithm, to obtain optimal values which adapt to changing traffic conditions. We introduce two new cost metrics to better capture congestion and show that the inclusion of delays in our analysis leads to improved performance relative to models that ignore delays.
Serious Suicide Attempts: Systematic Review of Psychological Risk Factors

Background One of the main obstacles in studying suicide risk factors is the difference between cases in which the individual died by suicide and those in which the individual engaged in suicidal behavior. A promising strategy that overcomes this obstacle is the study of survivors of serious suicide attempt (SSA), i.e., an attempt that would have been lethal had it not been for the provision of rapid and effective emergency treatment. Serious suicide attempters are epidemiologically very much like those who died by suicide, and thus may serve as valid proxies for studying suicides. This paper aims to define the specific risk factors for SSAs by conducting a qualitative data synthesis of existing studies. Methods Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, we conducted a systematic search of the literature in PubMed, ProQuest, and Psychlit electronic research-literature databases. Search terms were “serious” “OR” “near lethal,” combined with the Boolean “AND” operator with “suicide*. ” In addition, we performed a manual search on Google Scholar for further studies not yet identified. Results The preliminary search identified 683 citations. A total of 39 research reports that met the predefined criteria were analyzed. Mental pain, communication difficulties, decision-making impulsivity, and aggression, as well as several demographic variables, were found to be major risk factors for SSAs. Limitations We found a variability of definitions for SSA that hamper the ability to draw a model for the risk factors and processes that facilitate it. Moreover, the role of suicide intent and planning in SSA is still unclear. Further studies should aim to clarify and refine the concepts and measures of SSA, thereby enabling more specific and concrete modeling of the psychological element in its formation. Conclusion SSA is a distinguishable phenomenon that needs to be addressed specifically within the scope of suicidal behavior. Interpersonal problems, as well as impulsivity and aggression, seem to facilitate SSA when mental pain serves as a secondary factor. Healthcare professionals should be aware of SSA, and familiar with its specific risk factors. Moreover, psychological and suicidal risk assessment should include a designated evaluation of these risk factors as part of intervention and prevention models for SSA.
On Acting Together

Joint action by a team does not consist merely of simultaneous and coordinated individual actions; to act together, a team must be aware of and care about the status of the group effort as a whole. We present a formal definition of what it could mean for a group to jointly commit to a common goal, and explore how these joint commitments relate to the individual commitments of the team members. We then consider the case of joint intention, where the goal in question involves the team performing some action. In both cases, the theory is formulated in a logical language of belief, action, and time previously used to characterize individual commitment and intention. An important consequence of the theory is the types of communication among the team members that it predicts will often be necessary.
Improvement of Geomechanical Properties of Bio-remediated Aeolian Sand

ABSTRACT Aeolian sand is widely distributed in the desert. It is susceptible to wind erosion because it consists of fine particles that lack cohesion between them. Wind erosion of Aeolian sand, dune migration, and dust storms in deserts affect the environment and infrastructure severely. Conventional chemical methods for lessening the effect of wind erosion are environmentally unfriendly. This paper examines Aeolian sand bio-remediated by microbially induced calcite precipitations (MICPs). The geomechanical properties of the Aeolian sand remediated by MICP were tested to explore its behavior as a desert bio-crust. The results indicated that a bio-crust of Aeolian sand with suitable strength required 7 days for formation. The remediated Aeolian sand had an average unconfined compression strength of 0.66 MPa and an average inner friction angle of 36° at a bacterial concentration in the OD600 range of 0.5–0.8. These findings indicate that formation of bio-crust could serve as protection against desert erosion. The particle characteristics and the porosity of Aeolian sand play an important role in the formation of the bio-crust. Crust from bio-remediated well-graded, high-porosity soil is stronger than crust from bio-remediated, poorly graded, low-porosity soil, given that both soils have the same bacteria concentration.
Minimizing the trace length of a rod endpoint in the presence of polygonal obstacles is NP-hard

We continue, and in a sense complete, our study the motion of a rod (line segment) in the plane in the presence of polygonal obstacles, under an optimality criterion based on minimizing the trace length of a fixed but arbitrary point (called the focus) on the rod. In an earlier paper, we showed that this problem is NP-hard when the focus is in the relative interior of the rod. Our proof did not cover the case where the focus lies at one of the rod endpoints. Indeed, considerable evidence suggested that this special case might admit a polynomial time solution. In this paper we settle this open problem by proving, by means of a non-trivial adaptation of our earlier construction, that this remaining case is also NP-hard.
Who Eats Whom in a Pool? A Comparative Study of Prey Selectivity by Predatory Aquatic Insects

Predatory aquatic insects are a diverse group comprising top predators in small fishless water bodies. Knowledge of their diet composition is fragmentary, which hinders the understanding of mechanisms maintaining their high local diversity and of their impacts on local food web structure and dynamics. We conducted multiple-choice predation experiments using nine common species of predatory aquatic insects, including adult and larval Coleoptera, adult Heteroptera and larval Odonata, and complemented them with literature survey of similar experiments. All predators in our experiments fed selectively on the seven prey species offered, and vulnerability to predation varied strongly between the prey. The predators most often preferred dipteran larvae; previous studies further reported preferences for cladocerans. Diet overlaps between all predator pairs and predator overlaps between all prey pairs were non-zero. Modularity analysis separated all primarily nectonic predator and prey species from two groups of large and small benthic predators and their prey. These results, together with limited evidence from the literature, suggest a highly interconnected food web with several modules, in which similarly sized predators from the same microhabitat are likely to compete strongly for resources in the field (observed Pianka’s diet overlap indices >0.85). Our experiments further imply that ontogenetic diet shifts are common in predatory aquatic insects, although we observed higher diet overlaps than previously reported. Hence, individuals may or may not shift between food web modules during ontogeny.
Clinical Outcome of Cardiac Surgery in Octogenarians

The purpose of this study was to investigate the operative results and the clinical outcomes for octogenarians who underwent cardiac surgery. Twenty consecutive octogenarians who had cardiac operations at Samsung Medical Center from October 1994 through December 2004 were included in the study. The medical records were retrospectively reviewed and the follow-up results were obtained by the interview. The patients were 15 men and 5 women, and their mean age was 83.1 yr (range: 80-89 yr). The surgical priority was urgent for 5 patients and it was elective for 15 patients. Coronary artery bypass grafting (CABG) was performed in 14 patients, valve surgery was performed in 4 patients and CABG plus valve surgery was performed in 2 patients. There was one hospital death on day one after urgent CABG in an 80-yr-old man who had left main coronary artery occlusion. There were three deaths during the follow-up. Sudden death occurred in one patient at 2 months after valve surgery, and there were two non-cardiac deaths at 12 and 14 months, respectively, after CABG. Non-fatal postoperative complications occurred in 2 of 5 urgent patients and in 3 of 15 electives. The survival rate for the 19 hospital survivors at 24 months after surgery was 80% and the mean follow-up period was 22.5 months (range: 1-58 months). In conclusion, cardiac surgery could be performed within acceptable limits of the risk and its long-term results could be expected to be favorable for the octogenarians.
Implementation of an Automated ECG-based Diagnosis Algorithm for a Wireless Body Sensor Plataform

Wireless Body Sensor Networks (WBSN) are poised to become a key enabling technology of personal systems for pervasive healthcare. Recent results have however shown that the conventional approach to their design, which consists in continuous wireless streaming of the sensed data to a central data collector, is unsustainable in terms of network lifetime and autonomy. Furthermore, it was established that wireless data communication is responsible for most of the energy consumption. To address the energy inefficiency of conventional WBSNs, we advocate an advanced WBSN concept where sensor nodes exploit their available, yet limited processing and storage resources to deploy advanced embedded intelligence and processing, to reduce the amount of wireless data communication and consequently energy consumption. More specifically, this paper addresses the design and optimization of an automated real-time electrocardiogram (ECG) signal analysis and cardiovascular arrhythmia diagnosis application for a prototype sensor node called Wireless 25 EEG/ECG system. The satifactory accuracy of this on-line automated ECG-based analysis and diagnosis system is assessed and compared to the salient off-line automated ECG analysis algorithms. More importantly, our results show an energy consumption reduction of 80% to 100% with respect to conventional WBSNs, when our analysis and diagnosis algorithm is used to process the sensed ECG data to extract its relevant features, which are then wirelessly reported to the WBSN central data collector, after the node can automatically determine the potential cardiovascular pathology without human monitoring.
Effects of macamides on endurance capacity and anti-fatigue property in prolonged swimming mice

Abstract Context: Lepidium meyenii Walp. (Brassicaceae), most commonly known as “maca”, has been used as a food or folk medicine to improve vitality in Peru. Previous research demonstrated that lipid-soluble extract from maca improved swimming endurance capacity. Macamides are considered the typical lipid-soluble markers for maca and proved to have several pharmacological properties, such as improving sexual performance and neuroprotective activies. Objective: The present study investigates the effects of macamides on endurance capacity and anti-fatigue property in prolonged swimming mice. Materials and methods: The Balb/c mice were divided into seven groups: a control group, low-dose groups of N-benzyllinoleamide, N-benzyloleamide, and N-benzylpalmitamide, high-dose groups of these macamides. The macamides groups received the commercial products (12 and 40 mg/kg, ig), while the control group received vehicle for 21 d. On the 14th day, the mice were given the weight-loaded swimming test. On the 21st day, the mice were sacrificed immediately after 90 min swimming, and some biochemical parameters were measured. Results and discussion: Compared with the control group, exhaustive swimming time was significantly prolonged in high-dose group of N-benzyloleamide (p < 0.05); the levels of lactic acid (LD), blood ammonia (BA), and lactate dehydrogenase (LDH) were significantly decreased (p < 0.05), whereas the levels of liver glycogen (LG) and non-esterified fatty acid (NEFA) were significantly increased (p < 0.05) in high-dose group of N-benzyloleamide. The malondialdehyde (MDA) contents in the brain, muscle, and liver were significantly decreased (p < 0.05), whereas superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) activities in the brain, muscle, and liver were significantly increased in high-dose group of N-benzyloleamide (p < 0.05). Conclusion: The results indicate that N-benzyloleamide has pharmaceutical property against exercise-induced fatigue, and this effect can be explained by the modulated energy metabolism and improved antioxidant status.
An Experimental Study on Hydro-Mechanical Characteristics of Compacted Bentonite-Sand Mixtures

Nuclear and hazardous waste disposal issues have become universal issues and problems related to the final disposal of these waste including finding a suitable site, natural and engineered barriers used, construction of the repository, long-term performance assessment have gained increasing attention all over the world. High-level radioactive and hazardous waste are required to be buried in deep geological repositories. In Germany, the ongoing researches have assessed the suitability of salt-stone formation in the country as a host rock candidate for its nuclear waste repository. Bentonite-based materials have been proposed to be used as sealing and buffer elements for the nuclear waste repository. Several hydro-mechanical processes will take place in the field and influence behaviour of the sealing and buffer elements of the repository. In this dissertation, a study on the hydro-mechanical characterisation of bentonite-sand mixtures is presented. Mixtures of a calcium-type bentonite, named Calcigel, and quartz sand were used in the investigation. Series of experiments including basic and physico-chemical characterisation, microstructure and fabric studies, suction and swelling pressure measurements, wetting and drying test, one-dimensional compression-rebound test, one-dimensional cyclic wetting-drying test under constant vertical stress, and saturated permeability test were conducted. The experimental data obtained are analysed and several characteristics of the material are brought out in this dissertation. Conclusions regarding basic behaviour of the materials are drawn based on the results of microstructure and fabric studies. Factors influencing the magnitude of suction and swelling pressure of the materials are outlined and discussed. The suction-induced compression and rebound characteristics of the material are described. The wetting and drying behaviour as influenced by the material boundary conditions are discussed. Permeability characteristics of the materials are examined based on several available permeability models. Several mechanical and hydraulic parameters that can be used in modelling using some available constitutive modelling approaches are derived based on the experimental data. At the end, conclusions regarding the hydro-mechanical characteristics of the materials are drawn and suggestions for future studies are made.
Fatty Acid Binding Protein 4 Deficiency Protects against Oxygen-Induced Retinopathy in Mice

Retinopathy of prematurity (ROP) is a leading cause of blindness in children worldwide due to increasing survival rates of premature infants. Initial suppression, followed by increased production of the retinal vascular endothelial growth factor-A (VEGF) expression are key events that trigger the pathological neovascularization in ROP. Fatty acid binding protein 4 (FABP4) is an intracellular lipid chaperone that is induced by VEGF in a subset of endothelial cells. FABP4 exhibits a pro-angiogenic function in cultured endothelial cells and in airway microvasculature, but whether it plays a role in modulation of retinal angiogenesis is not known. We hypothesized that FABP4 deficiency could ameliorate pathological retinal vascularization and investigated this hypothesis using a well-characterized mouse model of oxygen-induced retinopathy (OIR). We found that FABP4 was not expressed in retinal vessels, but was present in resident macrophages/microglial cells and endothelial cells of the hyaloid vasculature in the immature retina. While FABP4 expression was not required for normal development of retinal vessels, FABP4 expression was upregulated and localized to neovascular tufts in OIR. FABP4−/− mice demonstrated a significant decrease in neovessel formation as well as a significant improvement in physiological revascularization of the avascular retinal tissues. These alterations in retinal vasculature were accompanied by reduced endothelial cell proliferation, but no effect on apoptosis or macrophage/microglia recruitment. FABP4−/− OIR samples demonstrated decreased expression of genes involved in angiogenesis, such as Placental Growth Factor, and angiopoietin 2. Collectively, our findings suggest FABP4 as a potential target of pathologic retinal angiogenesis in proliferative retinopathies.
ffect of partial replacement of dietary fish meal 1 and oil by pumpkin kernel cake and rapeseed oil 2 on fatty acid composition and metabolism in Arctic 3 charr ( Salvelinus alpinus ) 4

(2014) Effect of partial replacement of dietary fish meal and oil by pumpkin kernel cake and rapeseed oil on fatty acid composition and metabolism in Arctic charr (Salvelinus alpinus), Aquaculture, 431, pp. 85-91. NOTICE: this is the author's version of a work that was accepted for publication in Aquaculture. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published Aquaculture, [VOL 431 (2014)] DOI: Abstract 15 The aim of this 15-month feeding study was to investigate the effects of more 16 sustainable feeds on specific growth rate, fatty acid composition and 17 metabolism of Arctic charr (Salvelinus alpinus). A control feed, formulated with 18 fish meal and fish oil (F1), was compared with feeds where the marine 19 ingredients were increasingly replaced by pumpkin kernel cake and rapeseed oil 20 (Feeds F2, F3, and F4). Arctic charr were randomly distributed into 12 tanks and 21 fed one of the feeds in triplicate. The biomass of fish fed F1 and F2 diets was 22 significantly higher compared to fish fed diet F4 with highest replacement level. 23 However, the dorsal and ventral muscle tissues had very similar total saturated, 24 monounsaturated, and polyunsaturated fatty acid (PUFA) contents, irrespective 25 of dietary supply. Although diets F3 and F4 contained 6-fold less fish oil than 26 diets F1 and F2, fish fed diets F3 and F4 retained only 2-fold less highly desired 27 omega-3 (n-3) long-chain (LC)-PUFA in their dorsal and ventral muscle tissues. 28 Incubating isolated hepatocytes with 14 C-labeled α-linolenic acid (18:3n-3) 29 provided evidence that Arctic charr can bioconvert this essential dietary PUFA to 30 n-3 LC-PUFA, including docosahexaenoic acid. The results suggested that tissue 31 fatty acid compositions in Arctic charr are dependent, not only on dietary fatty 32 acid supply, but also on their ability for endogenous synthesis of n-3 LC-PUFA. 33 Finally, this long-term feeding study indicated that feeds containing 34 pumpkinseed press cake and rapeseed oil produced fish with largely similar fatty 35 acid composition to fish fed diets containing higher contents of fish meal and 36 fish oil. 37 38