Miracle-dz/UniFAR-FTUs huggingface dataset:
ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

MOTIVATION Boolean network models are suitable to simulate GRNs in the absence of detailed kinetic information. However, reducing the biological reality implies making assumptions on how genes interact (interaction rules) and how their state is updated during the simulation (update scheme). The exact choice of the assumptions largely determines the outcome of the simulations. In most cases, however, the biologically correct assumptions are unknown. An ideal simulation thus implies testing different rules and schemes to determine those that best capture an observed biological phenomenon. This is not trivial because most current methods to simulate Boolean network models of GRNs and to compute their attractors impose specific assumptions that cannot be easily altered, as they are built into the system. RESULTS To allow for a more flexible simulation framework, we developed ASP-G. We show the correctness of ASP-G in simulating Boolean network models and obtaining attractors under different assumptions by successfully recapitulating the detection of attractors of previously published studies. We also provide an example of how performing simulation of network models under different settings help determine the assumptions under which a certain conclusion holds. The main added value of ASP-G is in its modularity and declarativity, making it more flexible and less error-prone than traditional approaches. The declarative nature of ASP-G comes at the expense of being slower than the more dedicated systems but still achieves a good efficiency with respect to computational time. AVAILABILITY AND IMPLEMENTATION The source code of ASP-G is available at http://bioinformatics.intec. ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip.
The Psychodynamics of Gender and Gender Role

Few aspects of psychoanalytic theory are as misunderstood as psychoanalytic models of gender and gender role. The theory has evolved considerably since Freud's time, and contemporary object-relations and self-psychology perspectives contrast sharply with earlier work in this area. Chapters in this text review cutting-edge empirical research on psychoanalytic theories of child development, defence and coping, unconscious mental processing, normal personality functioning, and psychopathology. The essays seek to summarize a tremendous amount of research on this topic, and set the stage for a reinvigorated psychoanalytic understanding of gender and gender roles during the 21st century.
Influence of APOE polymorphism on cognitive and behavioural outcome in moderate and severe traumatic brain injury

Aim: To analyse the influence of apolipoprotein (APOE) ε4 status on the cognitive and behavioural functions usually impaired after moderate and severe traumatic brain injury (TBI). Methods: In all, 77 patients with TBI selected from 140 consecutive admissions were genotyped for APOE. Each patient was subjected to neuropsychological and neurobehavioural assessment at least 6 months after injury. Results: Performance of participants carrying the ε4 allele was notably worse on verbal memory (Auditory Verbal Learning Test), motor speed, fine motor coordination, visual scanning, attention and mental flexibility (Grooved Pegboard, Symbol Digit Modalities Test and part B of the Trail Making Test) and showed considerably more neurobehavioural disturbances (Neurobehavioral Rating Scale—Revised) than the group without the ε4 allele. Conclusions: In particular, performance on neuropsychological tasks that are presumed to be related to temporal lobe, frontal lobe and white matter integrity is worse in patients with the APOE ε4 allele than in those without it. More neurobehavioural disturbances are observed in APOE ε4 carriers than in APOE ε2 and ε3 carriers.
The toxicity of inhaled methanol vapors.

Methanol could become a major automotive fuel in the U.S., and its use may result in increased exposure of the public to methanol vapor. Nearly all of the available information on methanol toxicity in humans relates to the consequences of acute, rather than chronic, exposures. Acute methanol toxicity evolves in a well-understood pattern and consists of an uncompensated metabolic acidosis with superimposed toxicity to the visual system. The toxic properties of methanol are rooted in the factors that govern both the conversion of methanol to formic acid and the subsequent metabolism of formate to carbon dioxide in the folate pathway. In short, the toxic syndrome sets in if formate generation continues at a rate that exceeds its rate of metabolism. Current evidence indicates that formate accumulation will not challenge the metabolic capacity of the folate pathway at the anticipated levels of exposure to automotive methanol vapor.
Enhanced Psychosocial Support for Caregiver Burden for Patients With Chronic Kidney Failure Choosing Not to Be Treated by Dialysis or Transplantation: A Pilot Randomized Controlled Trial.

BACKGROUND Family caregivers of patients with chronic kidney failure have increased burden, as reflected by their high frequency of physical and mental disturbances. The impact of enhanced psychosocial support to caregivers of patients with chronic kidney failure remains unclear. STUDY DESIGN Open-label randomized controlled trial. SETTING & PARTICIPANTS All new patients referred to the renal palliative clinic were screened. Caregivers of patients who met the following criteria were recruited: (1) chronic kidney failure as defined by creatinine clearance < 15 mL/min, (2) opted for conservative management by nephrology team or patient, (3) never treated with dialysis or transplantation, and (4) able to provide informed consent. INTERVENTIONS Random assignment to treatment with enhanced psychosocial support or standard renal care (control). Enhanced psychosocial support included counseling and psychosocial interventions by an on-site palliative care nurse and designated social worker. Each caregiver was followed up at 2- to 4-week intervals for up to 6 months. OUTCOMES Zarit Burden Inventory (ZBI) and Hospital Anxiety and Depression Scale (HADS) in caregivers and McGill Quality of Life scores in patients of both groups were compared. RESULTS 29 pairs of family caregivers/patients with chronic kidney failure were randomly assigned (intervention, n=14; control, n=15). Mean ages of patients and caregivers were 81.6 ± 5.1 and 59.8 ± 14.2 (SD) years, respectively. The intervention group showed significantly lower ZBI scores than the control group at 1 and 3 months (22.0 ± 5.3 vs 31.6 ± 9.5 and 21.3 ± 6.6 vs 33.4 ± 7.2; P=0.006 and P=0.009, respectively). HADS anxiety scores of caregivers who received the intervention were significantly lower than those of controls at 1 and 3 months (7.1 ± 3.2 vs 10.1 ± 2.2 and 6.5 ± 4.5 vs 11.0 ± 3.1; P=0.01 and P=0.03, respectively). Insignificant reductions in ZBI and HADS scores were found at 6 months. 19 patients died (intervention, n=10; control, n=9) during the study period. LIMITATIONS The study is limited by a relatively small sample size and short duration. CONCLUSIONS Enhanced psychosocial support program in patients with chronic kidney failure and caregivers resulted in an early significant reduction in caregiver burden and anxiety.
Inorganic arsenite inhibits IgE receptor‐mediated degranulation of mast cells

Millions of people worldwide are exposed to arsenic (As), a toxicant which increases the risk of various cancers, cardiovascular disease and several other health problems. Arsenic is a potent endocrine disruptor, including of the estrogen receptor. It was recently shown that environmental estrogen‐receptor disruptors can affect the signaling of mast cells, which are important players in parasite defense, asthma and allergy. Antigen (Ag) or allergen crosslinking of IgE‐bound receptors on mast cells leads to signaling, culminating in degranulation, the release of histamine and other mediators. Because As is an endocrine disruptor and because endocrine disruptors have been found to affect degranulation, here we have tested whether sodium arsenite affects degranulation. Using the rat basophilic leukemia (RBL) mast cell model, we have measured degranulation in a fluorescence assay. Arsenic alone had no effect on basal levels of degranulation. However, As strongly inhibited Ag‐stimulated degranulation at environmentally relevant concentrations, in a manner that is very dependent on concentrations of both As and Ag. The concentrations of As effective at inhibiting degranulation were not cytotoxic. This inhibition may be a mechanism underlying the traditional Chinese medicinal use of As to treat asthma. These data indicate that As may inhibit the ability of humans to fight off parasitic disease. Copyright © 2010 John Wiley & Sons, Ltd.
Comparative Efficacy of Handwashing Agents against Cytomegalovirus

Abstract Conscientious handwashing is often recommended as an important method for limiting transmission of cytomegalovirus (CMV) from infected individuals to health, education, and child care professionals. To assess the efficacy of handwashing, fingertips of radiation-sterilized latex gloves were inoculated with 0.2 mL of ten different CMV strains. Virus in each inoculum was quantitated by plaque assay. After five minutes, viral inocula were allowed to remain (control), or were washed away by dropwise application of 10 mL of distilled water (DI), 5 mL of 0.08% soap followed by 5 mL of DI, 5 mL of 0.01% Chlorhexidine gluconate followed by 5 mL of DI, or 5 mL of 0.025% povidone-iodine solution followed by 5 mL of DI. Separate glove fingertips were sampled 5, 15, 30, 60, 120 and 240 minutes after washing and cultured in duplicate for CMV. Similar studies were performed using human cadaver skin. Ordinary soap was as effective at preventing CMV recovery as other more expensive agents. For inocula with <5 log10 pfu CMV/mL, washing with water alone was as effective as other agents. This was confirmed in similar studies with human hands using five CMV stains. Handwashing is probably an effective method for removing CMV from contaminated hands.
Parallel hardware objects for dynamically partial reconfiguration

Many of todaypsilas software-to-hardware compiler projects try to find dataflow parallelism in a sequential program description and use it to generate parallel running hardware components. In this paper we present a new possibility to do a parallel description based on the combination of object-oriented programming and dynamically partial reconfiguration. Our compiler translates software objects directly to hardware objects, which are running in parallel and can be instantiated and removed dynamically. Furthermore, we focus on parallel inter object communication which allows the hardware objects to communicate in parallel.
Analysis and reduction of capacitive coupling noise in high-speed VLSI circuits

Scaling the minimum feature size of VLSI circuits to sub-quarter micron and its clock frequency to 2 GHz has caused crosstalk noise to become a serious problem, that degrades the performance and reliability of high speed integrated circuits. This paper presents an efficient method for computing the capacitive crosstalk in sub-quarter micron VLSI circuits. In particular, we provide closed-form expressions for the peak amplitude, the pulse width, and the time-domain waveform of the crosstalk noise. Experiments show that our analytical predictions are at least two times better than the previous models in terms of the prediction accuracy. More precisely, experimental results show that the maximum error of our predictions is less than 10% while the average error is only 4%. Finally, based on the proposed analytical models, we discuss the effects of transistor sizing and buffering on crosstalk noise reduction in VLSI circuits.
Difficulty of Processing Japanese and Korean Center-embedding Constructions

This research investigates the effects of syntactic, semantic, and morphophonemic similarity in the processing of center-embedding constructions in Japanese and Korean. Six Japanese experiments study the effects of syntactic and semantic similarity, while one Korean experiment deals with the effects of syntactic and morphophonemic similarity. The results from these experiments support the view that the difficulty of processing center-embeddings is in part explained by similarity-based interference in working memory.
Management of Oil Revenues: Has That of Azerbaijan Been Prudent?

To help explain the common failure of oil or other natural resource exporting countries to diversify into industry, it has been common to trace this failure to real exchange rate appreciation. This has also been done in Azerbaijan. However, because Azerbaijan has devoted so much of its oil revenues to government investment, Azerbaijan provides a suitable case for examining an alternative link through government investment. This study applies the ARDL cointegration method to quarterly time series data on oil prices, government capital formation, non-oil exports and non-oil GDP to estimate the long run relationships linking oil prices to government investment expenditures and further to generation of non-oil GDP. The results show that despite the massive government investment expenditures, extremely little non-oil production of the tradable type has been generated, calling attention to the need for policy reform.
Q69 (an E. faecalis-Infecting Bacteriophage) As a Biocontrol Agent for Reducing Tyramine in Dairy Products

Biogenic amines (BAs) are low molecular weight nitrogenous compounds with biological activity, formed from amino acids by decarboxylation. BAs are naturally present in all living organisms playing essential roles. However, their accumulation in food through the metabolic activity of certain microorganisms constitutes a toxicological hazard. Among foods, cheeses accumulate some of the highest concentrations of BAs since they provide an ideal environment for their accumulation. Most of the methods proposed for reducing BAs in cheese, such as milk pasteurization, have not only failed to completely solve the problem, they also affect non-BA producing lactic acid bacteria, i.e., the bacteria that participate in the development of the organoleptic characteristics of cheese. Novel technologies specifically targeted against BA producers are therefore needed to control BA accumulation. Bacteriophages have been proposed as agents for specifically controlling the presence of foodborne pathogens in food. Due to its specificity, they could be used as a biotechnological tool targeted to reduce the population of BA-producing bacteria. The present work reports the isolation, from cheese, and the characterization of bacteriophage Q69, which infects specifically Enterococcus faecalis, the species mainly responsible of the accumulation of the BA tyramine in foods. Furthermore, its capacity to reduce the accumulation of tyramine in different conditions –including a model cheese- was proven. The obtained results open up the possibility of use bacteriophages to prevent BA accumulation in fermented foods.
Alterations in murine host defense functions by adriamycin or liposome-encapsulated adriamycin.

Peritoneal exudate cells (PEC) from C57BL/6 mice were collected on different days following an i.p. injection of Adriamycin (10 mg/kg) as free drug (ADM) or encapsulated in multilamellar liposomes (ADM/Lip). Macrophages harvested from mice at various times (Days 4-14) after either drug treatment were responsive to in vitro lipopolysaccharide induction of tumoricidal activity, maximum response being seen on Day 7. In addition, 18 days after treatment, significant macrophage tumoricidal activity was observed only in the ADM/Lip-treated group. When supernatants from cultures of PEC obtained 7 days after treatment were assayed for interleukin 1 following lipopolysaccharide stimulation, activity was found with both ADM- and ADM/Lip-treated cells. Without lipopolysaccharide stimulation, only PEC from ADM-treated mice elaborated factor(s) with interleukin 1-like activity. Both ADM and ADM/Lip induced significant PEC-natural killer (PEC-NK) activity by Day 4, while the ADM/Lip treatment sustained PEC-NK activity more effectively than free drug at later time points (7 or 11 days posttreatment). Drug-induced PEC-NK activity (Day 7) was (a) ablated by treatment in vitro with anti-asialo GM1 antibody and complement, and (b) associated with a population of PEC nonadherent to plastic. A transient suppression of splenic NK activity was seen 4 days following either ADM or ADM/Lip administration with recovery to control level by Day 7. These data demonstrate that following ADM or ADM/Lip administration some of the changes necessary for macrophage tumoricidal activation must have occurred in vivo. Liposome encapsulation of ADM extended the duration of ADM-induced augmentation of certain host defenses.
Partition of portal-drained visceral net flux in beef steers

1. Blood from chronic indwelling catheters in the caudal aorta and anterior mesenteric, gastrosplenic and hepatic portal veins was used to measure blood flow and net flux of oxygen, glucose and nitrogenous compounds across hepatic portal-drained viscera (PDV), post-stomach (anterior mesenteric-drained viscera (MDV)) and stomach tissues of two beef steers (390 kg mean live weight). 2. Steers were fed in sequence on (1) chopped lucerne (Medicago sativa) hay (twelve meals/d), (2) chopped lucerne hay (two meals/d) and (3) a pelleted concentrate diet containing 780 g ground maize/kg (two meals/d). The lucerne hay and concentrate contained 26.5 and 16.8 g nitrogen/kg respectively. 3. Five measurements of net flux (blood flow multiplied by venous-arterial concentration differences (VA)) were obtained hourly on 2 d for each dietary regimen, beginning 0.5 h before feeding at 08.00 hours. Blood flow was measured by downstream dilution of p-aminohippurate (PAH). 4. Blood flow across MDV averaged 42% of PDV blood flow (665 litres/h). 5. Net use of O2 across MDV accounted for 51 % of net PDV use of O2 (920 mmol/h). This disproportionate use of O2 in relation to blood flow was due to greater VA for O2 across MDV than across stomach tissues. Dietary regimen had no effect on the proportions of PDV blood flow and net O2 consumption attributable to MDV or stomach tissues. 6. When lucerne was given, net glucose use across MDV represented 69% of PDV use (35 mmol/h). When concentrate was given, MDV glucose use switched to net absorption (29 mmol/h), reducing net PDV glucose use to I mmol/h. 7. When concentrate was given, net MDV absorption of α-amino-N (AAN) increased from 98 to 190 mmol/h, yet net PDV absorption (101 mmol/h) was not affected. Net stomach AAN flux increased from -7 to -69 mmol/h when concentrate was given, negating the increase in net MDV absorption. 8. Net absorption of ammonia-N across MDV represented 28 and 52% of net PDV absorption when lucerne and concentrate were given respectively. Net NH3-N absorption across PDV was lower when lucerne was given than when concentrate was given (295 v. 154 mmol/h), reflecting lower dietary N intake (153 v. 83 g/d). Net MDV absorption of NH3-N was not affected by diet. Net removal of blood urea-N (BUN) across PDV (101 mmol/h) was not affected by diet. Across MDV, BUN removal was lower when concentrate was given than when lucerne was given (32 v. 77 mmol/h). In beef steers, MDV tissues account for substantial portions of net flux of non-protein-N across PDV and are responsible for essentially all PDV absorption of AAN.
Robust Decentralized Coordinated Control of a Multimotor Web-Winding System

Due to the strong coupling, model uncertainties, and external perturbations, the multimotor web-winding system presents a great control challenge. In order to deal with these problems, a decentralized coordinated control (DCC) strategy is proposed in this paper. First, the web-winding system is regarded as a synthetic system with several dynamic interval subsystems, and an interval matrix is introduced to cope with the modification of the set point and the change of parameters. Then, a decentralized coordinated controller is designed based on state feedback. By virtue of choosing suitable state variables of neighbor subsystems as coordination variables, the proposed control strategy can improve perturbation rejection performance and reduce the coupling existing between subsystems. Sufficient conditions of asymptotic stabilization of the system are derived based on the Lyapunov stability theory. Controller gain matrices are obtained by solving linear matrix inequalities. Finally, a three-motor web-winding system is considered as an application example, and the effectiveness of the proposed DCC is evaluated by both simulations and experimental tests.
P-element-induced control mutations at the r gene of Drosophila melanogaster

The P-M hybrid dysgenesis system was used to produce five putative regulatory mutations at the rudimentary locus, r. All five mutations were the result of insertions at the 5' end of the gene, upstream of the proposed start of transcription. All of the mutants displayed a leaky wing phenotype, and four of the mutants showed an uncoupling of the wing and female-sterility phenotypes, suggesting that they altered the normal spatial and temporal expression of the r gene. Four of the insertions were P elements. The fifth insertion, which was larger than an intact P element, consisted of a small P element connected to non-P-element DNA. Two of the mutants produced very little r transcript in adult females and were clustered 80 to 150 base pairs upstream of the start of transcription. The other three mutants had higher levels of r transcript in adult females and were clustered 440 to 500 base pairs upstream of the start of transcription. All of the data suggest that the insertions are in a 5' noncoding region of the r gene involved in the control of its spatial and temporal expression.
The Psychophysiology of Novelty Processing: Do Brain Responses to Deviance Predict Recall, Recognition, and Response Time?

Events that violate expectations are biologically significant and accordingly elicit various physiological responses. We investigated the functional relationship between three of these responses: the P300, the Novelty P3 and the pupil dilation response (PDR), with a particular focus on their co-variance with reaction time and measures of subsequent memory. In a modified Novelty P3 oddball paradigm, participants semantically categorized a sequence of stimuli including (1) words of a frequent category, (2) words of an infrequent category (14% of the trials) and (3) pictures of the frequent category (14% of the trials). The Novelty P3 oddball task was followed by a recalland a recognition test. Larger amplitudes of the P300, identified by a spatial principal component analysis (PCA), were associated with enhanced subsequent recall as well as faster reaction times during the recognition test, suggesting a close relationship between the cognitive process indexed by the P300 and memory encoding. The PDR was larger for infrequents (which required a response switch) than both frequents and pictures (which did not require a switch). Furthermore, its latency was correlated with reaction time on the same trial and with reaction time on the immediately following trial. There was only weak evidence for a correlation with subsequent memory, suggesting that the cognitive process associated with the PDR might be a direct link in the stimulus-response stream. Larger Novelty P3 amplitudes were associated with both faster reaction times on the same trial and stronger memory traces, suggesting that its amplitude might index resource allocation. These findings suggest that each of the physiological responses