Miracle-dz/UniFAR-FTUs huggingface dataset:
Sleep-promoting action of the endogenous melatonin in schizophrenia compared to healthy controls

Abstract Objective. The aim of this study was to compare the endogenous melatonin sleep-promoting effect in schizophrenic patients to a sample of healthy controls. Methods. Thirty-four schizophrenia outpatients (SP) and 34 healthy subjects (HS) participated in this study. Wrist-actigraphy recordings and a sleep diary were used for sleep–wake cycle assessment. The quality and patterns of sleep were measured with the Pittsburgh Sleep Quality Index (PSQI) and the Positive and Negative Syndrome Scale (PANSS) was used for psychopathology assessment. To quantify and assess nocturnal melatonin profiles, saliva samples were collected for one night under dim light conditions (<50 lux) hourly from 20:00 h to 23:00 h. Results. Scores on PSQI were significantly higher in SP as compared to HS, indicating a worse quality of sleep. Patients sleep more at night, but have poorer sleep efficiency, than HS. Sleep latency and nighttime awakenings were significant higher in SP. Melatonin levels were negatively correlated with sleep latency, total sleep time and positively correlated with sleep efficiency in HS but not in SP. Conclusion. The results of the present study indicate that endogenous melatonin sleep-promoting action seems to be compromised in schizophrenia.
Differential display analysis of Porphyromonas gingivalis gene activation response to heat and oxidative stress.

BACKGROUND/AIMS The etiologic relationship between periodontitis and Porphyromonas gingivalis is attributed to the ability of the organism to express a variety of virulence factors, many of which are cell surface components including lipopolysaccharide and arginine-specific cysteine proteases (Arg-gingipains, RgpA, and RgpB). P. gingivalis responds to the stress of rapid elevation in temperature by activating a set of genes to produce heat shock proteins that mediate the effects of sudden changes in environmental temperatures by repairing or eliminating cellular proteins denatured by that stress. METHODS We used restriction fragment differential display (RFDD) to identify and measure the genes expressed by surrogates of environmental stresses, heat and oxidative stress. The results were then confirmed using quantitative reverse-transcription polymerase chain reaction. RESULTS We selected 16 genes differentially induced from over 800 total expression fragments on the RFDD gels for further characterization. With primers designed from those fragments we found that a + 5 degrees C heat shock caused a statistically significant increase in expression compared 12 of 18 untreated genes tested. The exposure of P. gingivalis to atmospheric oxygen resulted in statistically significant increases in five of the target genes. These genes are likely involved in transport and synthesis of components of the lipopolysaccharide biosynthetic pathway important in anchoring the Arg-gingipains required for virulence-related activities. CONCLUSION These results emphasize the need for studies to measure the coordinated responses of bacteria like P. gingivalis which use a multitude of interrelated metabolic activities to survive the environmental hazards of the infection process.
The Smallest List for the Arbitrarily Varying Channel

The capacity of the discrete memoryless arbitrarily varying channel (AVC) is investigated for deterministic list codes with fixed list size L. For every AVC with positive random code capacity C/sub r/, a nonnegative integer M called the symmetrizability is defined. For the average probability of error criterion, it is shown that the list capacity is given by C(L)=C/sub r/ for L>M and C(L)=0 otherwise. Bounds are given which relate C/sub r/ and M. Also, explicit formulas for C(L) are given for a family of noiseless, additive AVCs.
Mucin gene expression in bile of patients with and without gallstone disease, collected by endoscopic retrograde cholangiography.

AIM To investigate the pattern of mucin expression and concentration in bile obtained during endoscopic retrograde cholangiography (ERC) in relation to gallstone disease. METHODS Bile samples obtained at ERC from 29 consecutive patients, 17 with and 12 without gallstone disease were evaluated for mucin content by gel filtration on a Sepharose CL-4B column. Dot blot analysis for bile mucin apoproteins was performed with antibodies to Mucin 1 (MUC1), MUC2, MUC3, MUC5AC, MUC5B and MUC6. Staining intensity score (0-3) was used as a measure of antigen expression. RESULTS MUC1, MUC2, MUC3, MUC5AC, MUC5B and MUC6 were demonstrated in 34.4%, 34.4%, 51.7%, 51.7%, 55.1% and 27.5% of bile samples, respectively. The staining intensity scores were 0.62 +/- 0.94, 0.58 +/- 0.90, 0.79 +/- 0.97, 1.06 +/- 1.22, 1.20 +/- 1.26 and 0.41 +/- 0.73, respectively. Mean mucin concentration measured in bile by the Sepharose CL-4B method was 22.8 +/- 24.0 mg/mL (range 3.4-89.0 mg/mL). Mean protein concentration was 8.1 +/- 4.8 mg/mL (range 1.7-23.2 mg/mL). CONCLUSION High levels of MUC3, MUC5AC and MUC5B are expressed in bile aspirated during ERC examination. A specific pattern of mucin gene expression or change in mucin concentration was not found in gallstone disease.
Motion retargeting to preserve spatial relationship between skinned characters

Applying motion capture data for multi-person interaction to virtual characters is challenging because one needs to preserve interaction semantics in addition to satisfying the general requirements for motion retargeting, such as preventing penetration and preserving naturalness. An efficient method for representing the scene semantics of interaction motions is to define the spatial relationships between body parts of characters. However, existing methods of this kind consider only character skeleton, and thus may require post-processing to refine the interaction motions and remove artifacts from the viewpoint of skin meshes. This paper proposes a novel method for retargeting interaction motions with respect to character skins. To this end, we introduce the aura mesh surrounding a character's skin in order to represent skin-level spatial relationships between body parts. Using the aura mesh, we can retarget interaction motions while preserving skin-level spatial relationships and reducing skin inter-penetrations.
Large-Scale Zygosity Testing Using Single Nucleotide Polymorphisms

Abstract A requirement for performing robust genetic and statistical analyses on twins is correctly assigned zygosities. In order to increase the power to detect small risk factors of disease, zygosity testing should also be amenable for high throughput screening. In this study we validate and implement the use of a panel of 50 single nucleotide polymorphisms (SNPs) for reliable high throughput zygosity testing and compare it to a panel of 16 short tandem repeats (STRs). We genotyped both genomic (gDNA) and whole genome amplified DNA (WGA DNA), ending up with 47 SNP and 11 STR markers fulfilling our quality criteria. Out of 99 studied twin pairs, 2 were assigned a different zygosity using SNP and STR data as compared to self reported zygosity in a questionnaire. We also performed a sensitivity analysis based on simulated data where we evaluated the effects of genotyping error, shifts in allele frequencies and missing data on the qualitative zygosity assignments. The frequency of false positives was less than 0.01 when assuming a 1% genotyping error, a decrease of 10% of the observed minor allele frequency compared to the actual values and up to 10 missing markers. The SNP markers were also successfully genotyped on both gDNA and WGA DNA from whole blood, saliva and filter paper. In conclusion, we validate a robust panel of 47 highly multiplexed SNPs that provide reliable and high quality data on a range of different DNA templates.
Peer effects in risk aversion Balsa

Using data on Uruguayan adolescents, we estimate peer effects in risk attitudes. Relative risk aversion is elicited in an experimental setting. Identification is based on parents not being able to choose the class within the school of their choice. After controlling for school-grade fixed effect and addressing endogeneity due to simultaneity, we find a significant and quantitative large impact of peers on individuals risk aversion. An increase in one standard deviation of the group risk aversion produces an increase in 44-64% on an individual risk aversion. These findings enhance the importance of multiplicative effects related to risk behavior.
Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR

PCR was used to detect Pseudomonas aeruginosa from water samples by amplifying a 396-bp region of the exotoxin A (ETA) structural gene sequence. The identify of the amplified 396-bp fragment was confirmed by digesting it with PvuI restriction endonuclease, which produced the predicted 246- and 150-bp fragments. Specific primers amplified ETA-positive P. aeruginosa DNA, whereas other species of Pseudomonas and GC-rich bacteria did not yield any 396-bp fragment. The specificity and sensitivity of the assay were 100 and 96%, respectively, which confirms the assay's reliability for diagnostic and epidemiological studies. The assay can detect as few as 5 to 10 cells in a 10-ml water sample or 0.1 pg of P. aeruginosa DNA per reaction mixture (5 microliters) by ethidium bromide staining of an agarose gel. Ten-times-lower concentrations were detected by hybridization with a digoxigenin-labeled oligonucleotide probe internal to the PCR product. With this PCR method, ETA-positive P. aeruginosa was detected in animal cage water samples at a level of 40 cells per ml. This method is rapid and less cumbersome than other diagnostic methods for the identification of P. aeruginosa strains. The method described can be used to detect a low level of P. aeruginosa from environmental and clinical samples without the use of selective media or additional biochemical tests.
Circular DNA's from HeLa cell nuclei and mitochondria.

An electron microscopic observation was made on the DNA's extracted from purified HeLa cell nuclei, mitochondria, and the whole cell, and fractionated by ethidium bromide-cesium chloride density gradient method or sucrose density gradient method. Nuclear DNA presents mainly long linear DNA derived from fragmented chromosomal DNA. In addition to this, the existence of small circular DNA molecules measuring 0.32 -1.78 μ, was confirmed. Mitochondrial DNA was mainly circular DNA, which measured 4.87 μ in the mean value of the contour lengths in the highest frequency group, and small circular DNA molecules, measuring 0.3-1.01 μ in contour length, were also found in an extremely low frequency.
Histopathology of gastritis in Helicobacter pylori-infected children from populations at high and low gastric cancer risk.

Infection with Helicobacter pylori has been recognized as a cause of gastric carcinoma. Although the neoplasia is always detected in adults, the infection starts in childhood. It has been reported that early age at first infection is a determinant of gastric cancer risk. In this study, we examined the histopathology of the gastric mucosa in infected children from a population at high risk for gastric cancer (Pasto, Colombia) and compared it with that of a lower-risk population (New Orleans, LA). Gastric biopsies obtained from antrum and corpus were stained with hematoxylin and eosin and Steiner's silver method. Immunohistochemical stains were used to identify B lymphocytes (CD20), T lymphocytes (CD3 and CD8), macrophages (CD68), and polymorphonuclear neutrophil myeloperoxidase. Morphometric techniques were used to evaluate the immunohistochemical stains. In both populations, the inflammatory lesions were seen predominantly in the antrum. Compared with children from the lower-risk populations, children from the higher-risk population exhibited more severe polymorphonuclear neutrophil infiltration, stromal and intraepithelial lymphocyte infiltration, mucus depletion, and H. pylori colonization density. Regenerative activity was significantly more marked in the lower-risk population. Morphometric analysis of immunohistochemical stains showed increased representation of T lymphocytes and macrophages in the higher-risk population. Most T lymphocytes stained positive for CD8, a marker of suppressor/cytotoxic cells. B lymphocytes were relatively more abundant in the lower-risk population. The possibility that the aforementioned characteristics of H. pylori infection in children are related to cancer risk in adults is discussed.
Modeling and experiment of pneumatic position system with spring-and-diaphragm actuator

In this paper a nonlinear and continuous model of pulse width modulation (PWM)-based pneumatic position system with diaphragm-and-spring actuator is presented via theoretical analysis; against experimental data, the unknown parameters are identified by particle swarm optimization (PSO). Using open-loop tests, the experimental data are obtained by controlling the on/off valves with three different duty ratios: 50, 80, and 100% over a period of 100 ms. The analytical-experimental comparisons show the validity of the model. The modeling is useful for intelligent valve positioner algorithm design, control valve optimization design and actuators fault diagnosis.
Coherent swarming from local interaction by exploiting molecular dynamics and stokesian dynamics methods

This paper discusses a fully decentralized algorithm able to create a coherent swarm of autonomous mobile robots from the viewpoint of "computational physics". To this end, we particularly focus on the "molecular dynamics method" and the "stokesian dynamics method", both of which are widely used to investigate multi-body systems. To verify the feasibility of our approach, this idea has been implemented to a swarm of 2D radio-connected autonomous mobile robots as a practical example. Simulation results indicate that the proposed algorithm can control the shape of the swarm appropriately according to the current situation without losing the coherence of the swarm nor exchanging any global information among the modules. Furthermore, we have found that the local interaction that is used to exploit stokesian dynamics plays an essential role in order to maintain the coherence of the swarm particularly under an unstructured environment.
A multi-scale code for flexible hybrid simulations

Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale computations using the Atomistic Simulation Environment (ASE). This implementation can mix classical codes like LAMMPS and the Density Functional Theory-based GPAW. Any combination of codes linked via the ASE interface however can be mixed. We also introduce a framework to easily add classical force fields calculators for ASE using LAMMPS, which also allows harnessing the full performance of classical-only molecular dynamics. Our work makes it possible to combine different simulation codes, quantum mechanical or classical, with great ease and minimal coding effort.
Smart Web Visibility of Organizations

Smart Web Visibility, in this paper, is the study of measure techniques used to retrieval information aboutwords, expressions or terms (for example, acronyms) on the web. The visibility has straight relation with presentation order of information retrieved. We consider the Smart Web Visibility as a subfield of the Webometrics, the same as Web Visibility is its subfield too. Our approach is based on different rankings from different search engines to evaluate the Smart Web Visibility by processing the homonymous problem before scoring. We begin with original results of search engines output, to emphasise after with methods to adding semantics to the queries. Finally, to demonstrate the viability of our ideas we employed acronyms of Brazilian universities to evaluate the smart visibility and compare with the actual situation of Brazil universities published by Webometrics Ranking. The main contribution of this work is a new way to evaluate the Web Visibility, named Smart Web Visibility, which shows how the universities are ranked by multiple
Evaluating Ungulate Mortality Associated With Helicopter Net-Gun Captures in the Northern Great Plains

Abstract Ungulate mortality from capture-related injuries is a recurring concern for researchers and game managers throughout North America and elsewhere. We evaluated effects of 7 variables to determine whether ungulate mortality could be reduced by modifying capture and handling procedures during helicopter net-gunning. During winter 2001–2006, we captured 208 white-tailed deer (Odocoileus virginianus) and 281 pronghorn (Antilocapra americana) by helicopter net-gunning throughout the Northern Great Plains. Of 281 pronghorn, 25 (8.9%) died from capture-related injuries; 12 were from direct injuries during capture, and 13 occurred postrelease. Of 208 deer, 3 (1.4%) died from injuries sustained during helicopter captures, with no mortalities documented postrelease. We used logistic regression to evaluate the probability that ungulates would die of injuries associated with helicopter net-gun captures by analyzing effects of snow depth, transport distance, ambient and rectal temperatures, pursuit and handling times, and whether individuals were transported to processing sites. The probability of capture-related mortality postrelease decreased 58% when transport distance was reduced from 14.5 km to 0 km and by 69% when pursuit time decreased from 9 minutes to <1 minute. Wildlife managers and researchers using helicopter capture services in landscapes of the Midwest should limit pursuit time and eliminate animal transport during pronghorn and white-tailed deer capture operations to minimize mortality rates postrelease.
Comparison of Digital Signature Algorithm and Authentication Schemes for H.264 Compressed Video

In this paper we present the advantages of the elliptic curve cryptography for the implementations of the electronic signature algorithms “elliptic curve digital signature algorithm, ECDSA”, compared with “the digital signature algorithm, DSA”, for the signing and authentication of H.264 compressed videos. Also, we compared the strength and add-time of these algorithms on a database containing several videos sequences.
JUVENILE OFFENDERS

INTRODUCTION T h e problem This paper deals with a group of girls aged 12 to 17, whose behaviour brought them into conflict with the Law, and who were referred by Juvenile Courts for a psychiatric assessment. It is obvious that this group represents only a small fraction of delinquent girls dealt with by Juvenile Courts. The great majority of them are disposed of by the Courts without being referred for a psychiatric opinion. All these girls were remanded in a Training School, which also served as a Remand Home. In Northern Ireland there is no equivalent to the English institution of a ‘Classifying School’, where the young offenders are examined and assessed, and from where they can be sent to an appropriate school, such as a School for Maladjusted Children, or a Training Scool, or an Approved School, or a Borstal School, etc.
ANTI-WINDUP PROPORTIONAL INTEGRAL STRATEGY FOR SHUNT ACTIVE POWER FILTER INTERFACED BY PHOTOVOLTAIC SYSTEM USING TECHNIQUE OF DIRECT POWER CONTROL

This paper focuses on power quality improvement in the distribution network using three phase shunt active power filter, where this later is connected to photovoltaic system. In the present work, a new control method has been presented to eliminate harmonic currents that is caused by nonlinear loads, and to compensate reactive power. This control method has a good accuracy and high efficiency, it bases on direct control of power, rather than conventional one (p-q theory) that relies on current harmonic identification and current control loops. This work proposes to combine a photovoltaic generator with the Dc side of the inverter via boost converter, hence this solution allows to inject the maximum of active power produced by photovoltaic system into the grid in addition to power quality enhancement. The proposed system has been verified by using MATLAB/Simulink and power system. Simulation results demonstrate the effectiveness of the system, where the THD of the source current is reduced to 2.2 %.
Molecular-genetic profiling and high-throughput in vitro drug screening in NUT midline carcinoma—an aggressive and fatal disease

NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair. A high-throughput drug screen confirmed that microtubule inhibitors, topoisomerase inhibitors and anthracyclines are highly cytotoxic in the majority of NMC lines, and that cell lines expressing the BRD4-NUTM1 (exon11:exon2) variant are an order of magnitude more responsive to bromodomain inhibitors (iBETs) on average than those with other BRD4-NUTM1 translocation variants. We also identified a highly significant correlation between iBET and aurora kinase inhibitor efficacy in this study. Integration of exome sequencing, transcriptome, and drug sensitivity profiles suggested that aberrant activity of the nuclear receptor co-activator NCOA3 may correlate with poor response to iBETs. In conclusion, our data emphasize the heterogeneity of NMC and highlights genetic aberrations that could be explored to improve therapeutic strategies. The novel finding of a recurring RECQL5 mutation, together with recent reports of chromoplexy in this disease, suggests that DNA-repair pathways are likely to play a central role in NMC tumorigenesis.
MicroRNA-351 regulates TMEM 59 (DCF1) expression and mediates neural stem cell morphogenesis

MicroRNAs (miRNA) are small noncoding RNAs that play important roles in cell development, differentiation and apoptosis. Recent studies showed that transmembrane protein 59 (TMEM59) affects neural stem cell (NSC) differentiation and β-amyloid precursor protein (APP) glycosylation. In this study, we predicted that microRNA-351 (miR-351) could target TMEM59 and demonstrated that miR-351 negatively regulates TMEM59 expression in different cell types. Moreover, we found that miR-351 overexpression could lead to morphological change in the mouse NSC cell line C17.2, indicating an important role of miR-351 in the regulation of differentiation. Our investigations focused on the functions of miR-351 in the nervous system and the posttranscriptional regulation of TMEM59 by microRNA. These original findings provide promising grounds for future in-depth research into the functions of miR-351 and TMEM59 in nervous system development.
Large-scale timing-driven rectilinear steiner tree construction in presence of obstacles

In the paper, we provide a timing-driven rectilinear routing tree algorithm which applies top-down partitioning followed by the bottom-up routing tree construction in the presence of the obstacles. The objective is to simultaneously minimize the source-to-terminal delay and the total wirelength. First, a top-down partitioning method is used to divide the chip into four sub-regions according to the position of the source. Then, the terminals in each sub-region are connected by a fast sequential routing tree algorithm. The major steps of the routing algorithm include minimal spanning tree constructing, invalid edges pushing and routing. It shows experimentally that the maximum source-to-terminal delay of the routing tree is improved by 74%. Compared to previous results, total wirelength is significantly reduced by 34.7%.