Miracle-dz/UniFAR-FTUs huggingface dataset:
Data‐based model and parameter evaluation in dynamic transcriptional regulatory networks

Finding the causality and strength of connectivity in transcriptional regulatory networks from time‐series data will provide a powerful tool for the analysis of cellular states. Presented here is the design of tools for the evaluation of the network's model structure and parameters. The most effective tools are found to be based on evolution strategies. We evaluate models of increasing complexity, from lumped, algebraic phenomenological models to Hill functions and thermodynamically derived functions. These last functions provide the free energies of binding of transcription factors to their operators, as well as cooperativity energies. Optimization results based on published experimental data from a synthetic network in Escherichia coli are presented. The free energies of binding and cooperativity found by our tools are in the same physiological ranges as those experimentally derived in the bacteriophage lambda system. We also use time‐series data from high‐density oligonucleotide microarrays of yeast meiotic expression patterns. The algorithm appropriately finds the parameters of pairs of regulated regulatory yeast genes, showing that for related genes an overall reasonable computation effort is sufficient to find the strength and causality of the connectivity of large numbers of them. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Cocaine induced inflammatory response in human neuronal progenitor cells

We have employed a genomic approach in homogenous cell culture to investigate the fundamental transcriptional responses which occur in neurons over time as a consequence of a single 30‐min exposure to cocaine. Data from 24 Affymetrix microarrays, representing eight treatment groups, were analyzed by GeneChip Operating Software and then further mined by hierarchical clustering, anova, and Ingenuity Pathway Analysis software to examine known molecular pathways impacted by the observed transcriptional changes. For each time point under investigation, the data sets of genes exhibiting altered expression in treated cells compared with control were interrogated with a specific focus on differential expression of genes involved in immunomodulation and inflammation. The existing literature on the effects of cocaine in a diverse array of experimental paradigms demonstrates a significant modulation of inflammation and immune mechanisms, but these have typically been studies of chronic exposure in immune‐competent cells. Our data show a time‐dependent up‐regulation of genes associated with pro‐inflammatory and immune responses, peaking at 24 h as confirmed by all methods of analysis, suggesting a specific neuronal immunomodulatory response to acute cocaine exposure.
New spiral bacterium in gastric mucosa.

A new spiral bacterium, distinct from Campylobacter pylori, was found in the gastric mucosa of six patients with gastrointestinal symptoms. All patients had chronic active type B gastritis and four had oesophagitis. Culture and microscopy for C pylori infection was negative. These unculturable spiral organisms were probably an incidental finding in patients presenting for upper gastrointestinal endoscopy, but it is not possible to say from this small series whether these organisms cause chronic active gastritis. The organism is helical, 3.5-7.5 microns long and 0.9 micron in diameter with truncated ends flattened at the tips, and up to 12 sheathed flagella 28 nm in diameter at each pole. It is proposed that this spiral bacterium should be called "Gastrospirillum hominis Gen.nov., Sp.nov."
Preclinical evaluation of DISC‐GMCSF for the treatment of breast carcinoma

DISC‐hGMCSF is a gH‐deleted HSV‐2 based vector expressing human GM‐CSF that has entered clinical trials for the therapy of metastatic melanoma. To determine whether this product also has potential to treat breast carcinoma, a series of in vitro and in vivo studies were made.
Analysis of the Upper Thoracic Curve in Surgically Treated Idiopathic Scoliosis: A New Concept of the Double Thoracic Curve Pattern

The authors reviewed 246 idiopathic scoliosis patients with the upper thoracic curve of more than 20$$. Group I (138 patients) had positive T1 tilt and a Spiral fusion which was extended over both the upper and lower thoracic curve with the diagnosis of double thoracic curve. Group II (43 patients) had positive T1 tilt, but the fusion was limited to the lower thoracic curve. Group III (65 patients) had negative or neutral T1 tilt and the fusion was limited to the lower thoracic curve. The average age at operation was 15.9 years (range, 11,2–35 years) and the average length of follow-up was 4.8 years (range, 2–29.5 years). Positive T1 tilt did not correlate well with left shoulder elevation contrary to previous reports, The upper thoracic curve was more rigid than the lower curve in all groups and the lumbar curve was significantly more flexible than the upper and lower thoracic curves in all groups (P< 0.05). No significant difference in the flexibility of the upper thoracic curve was found between the groups regardless of the direction of T1 tilt, When only the lower curve was fused (groups II and III), progression of the upper thoracic curve was less than 5$$ and spontaneous correction of the unfused upper curve occurred in the majority of the cases following the supine bending study. Correction and fusion on the lower curve (groups II and III aggravated shoulder imbalance of all patients with left shoulder elevation. Based on the findings of this study, the authors proposed that the diagnosis of idiopathic double thoracic patterns should be limited to those patterns which require fusion of bath the upper and lower curves. This pattern of idiopathic scoliosis includes double thoracic curves with left shoulder elevation and/or a rigid upper thoracic curve.
Implementation of a fourth-generation 1.8-GHz dual-core SPARC V9 microprocessor

This fourth-generation processor combines two enhanced third-generation cores using an advanced 90-nm dual-Vt, dual-gate-oxide technology. Hardware additions feature expanded caches and inclusion of a 2-MB Level-2 cache and a Level-3 tag. Layout was completely redrawn to optimize the design for manufacturability and performance in the latest technology. Special emphasis was placed on library development to improve automation and assist in custom design. The memory design methodologies were completely updated to make quality design simpler and more robust. The chip operates at 1.8 GHz while dissipating 90 W of power at 1.1 V.
Distinct and Opposite Activities of Human Terminal Deoxynucleotidyltransferase Splice Variants1

Evidence for potential human TdT (hTdT) isoforms derived from hTdT genomic sequences led us to identify the short isoform (hTdTS), as well as mature long transcripts containing exon XII (hTdTL1) and another including exon VII (hTdTL2) in lymphoid cells. Normal B and T lymphocytes express exclusively hTdTS and hTdTL2, whereas hTdTL1 expression appears to be restricted to transformed lymphoid cell lines. In in vitro recombination and primer assays, both long isoforms were shown to have 3′→5′ exonuclease activity. Overexpression of hTdTS or hTdTL2 greatly reduced the efficiency of recombination, which was reverted to normal levels by the simultaneous expression of both enzymes. Therefore, alternative splicing may prevent the adverse effects of unchecked elongation or diminution of coding ends during V(D)J recombination, thus affecting the survival of a B or T cell precursor during receptor gene rearrangements. Finally, the newly discovered hTdT isoforms should be considered in future screening of human leukemias.
Responses to ligation of a coronary artery in conscious rats and the actions of antiarrhythmics.

A method for ligating the left anterior descending coronary artery in conscious rats and measuring the resultant cardiovascular responses, arrhythmias, cardiac tissue loss, electrocardiogram (ECG), and mortality is described. Analyses of such responses identified statistically acceptable measures for which precision and interrelationships were defined. Responses to ligation were a variable function of the amount of ligated myocardial tissue. For example, arrhythmia score was a linear function of the square root of the occluded zone size. To test the ability of the model to detect beneficial drugs, verapamil, lidocaine, disopyramide, and quinidine were given. Low doses of verapamil (0.2 mg/kg i.v. + 0.3 mg X kg-1 X h-1), and of disopyramide (10 mg/kg) had few antiarrhythmic, or other actions, whereas high doses of verapamil (20 mg/kg) and disopyramide (40 mg/kg i.v. repeated) were markedly antiarrhythmic as measured by all indices. Quinidine (20 mg/kg i.v. repeated) was also antiarrhythmic but less so than high dose disopyramide and verapamil. Lidocaine (10 mg/kg i.v. + 5 mg X kg-1 X h-1) reduced the incidence of ventricular flutter and fibrillation. High-dose verapamil and quinidine, but not disopyramide, increased the number of nonarrhythmic deaths and the incidence of atrioventricular conduction defects.
Automated Spacing Support Tools for Interval Management Operations during Continuous Descent Approaches

In this study, pilots were asked to achieve a specific time in trail while flying an arrival into Louisville International airport. Weather shortly before the start of the descent added variability to the initial intervals. A spacing tool calculated airspeeds intended to achieve the desired time in trail at the final approach fix. Pilots were exposed to four experimental conditions which varied how strictly the pilots were told to follow these speeds and whether speeds had to be entered into the autopilot manually. Giving the pilots more discretion had little effect on the final spacing interval. However, pilots required to enter speeds into the autopilot manually did not effectively manage their airplane’s energy resulting in less accurate performance. While these results may not always generalize to alternative spacing implementations, one should not assume pilots manually closing the loop on automated commands can perform as well as a fully automated system.
Secondary hyperparathyroidism status in Brazil: Brazilian census of parathyroidectomy.

INTRODUCTION Secondary hyperparathyroidism (SHP) is a common and serious complication of chronic kidney disease (CKD), with a negative impact on morbidity and mortality. Despite advances in the clinical management of SHP, treatment failure still occurs in a significant number of patients. In such cases, parathyroidectomy (PTx) is indicated. OBJECTIVE To have an overview of the prevalence of severe SHP and of its surgical treatment in hemodialysis (HD) patients in Brazil. METHODS This was an observational and descriptive study. Data were obtained from questionnaires posted to 660 dialysis units (DU). RESULTS Results are expressed in absolute values and percentages, or means and standard deviation, as appropriate. 226 (34%) DU answered the questionnaire, providing data about 32,264 HD patients. The prevalence rate of severe SHP (PTH > 1,000 pg/mL) was 10.7 % (n = 3,463). 68 hospitals countrywide perform PTX. Around 40% of them are university centers. 49 (21.7%) DU reported not to have a specialized medical center to refer their patients with severe SHP. 74 (33%) DU reported that the time interval between surgery indication and its performance was over 6 months. The main recognized obstacles to surgery performance were: difficulty to perform the preoperative exams, lack of head and neck surgeons and the long waiting time. CONCLUSIONS Although severe SHP is highly prevalent in Brazil, a significant number of patients do not have access to PTx. Better public health policies and liaison between nephrologists and head and neck surgeons are urgently required to change this reality.
Analysis of cell growth and diffusion in a scaffold for cartilage tissue engineering

Developments in tissue engineering over the past decade have offered promising future for the repair and reconstruction of damaged tissues. To regenerate three dimensional and weight‐bearing implants, advances in biomaterials and manufacturing technologies prompted cell cultivations with natural or artificial scaffolds, in which cells are allowed to proliferate, migrate, and differentiate in vitro. In this article, we develop a mathematical model for cell growth in a porous scaffold. By treating the cell‐scaffold construct as a porous medium, a continuum model is set up based on basic principles of mass conservation. In addition to cell growth kinetics, we incorporate cell diffusion in the model to describe the effects of cell random walks. Computational results are compared to experimental data found in the literature. With this model, we are able to investigate cell motility, heterogeneous cell distributions, and non‐uniform seeding for tissue engineering applications. Results show that random walks tend to enhance uniform cell spreads in space, which in turn increases the probabilities for cells to acquire nutrients; therefore random walks are likely to be a positive contribution to the overall cell growth on scaffolds. © 2006 Wiley Periodicals, Inc.
Lifestyle intervention by group-based rehabilitation versus individual counseling in type 2 diabetes: 1-year follow-up of the Copenhagen type 2 diabetes rehabilitation project

Background: Today most guidelines on the management of type 2 diabetes incorporate lifestyle intervention including patient education, physical activity and dietary modification. However, the content and organization of lifestyle intervention programs are still debatable. Aims: To compare the longer term effectiveness of a group-based rehabilitation program with an individual counseling program at improving glycemic control, cardiovascular risk factors and quality of life among type 2 diabetes patients. Methods: We randomized 143 type 2 diabetes patients to either a 6-month group-based rehabilitation program, including patient education, supervised exercise, and diet intervention, or a 6-month individual counseling program. Follow-up time was 12 months after baseline. Outcome measures were glycated hemoglobin (HbA1c), cardiovascular risk factors, quality-of-life and self-rated health. Results: In the rehabilitation group, HbA1c decreased 0.2%-point (95% confidence interval [CI] = -0.4, -0.03), systolic blood pressure decreased 6 mmHg (95% CI = -9.3, -2.5), diastolic blood pressure decreased 4 mmHg (95% CI = -6.3, -2.4), weight decreased 2.2 kg (95% CI = -3.2, -1.3), and waist circumference decreased 2.0 cm (95% CI = -2.9, -1.1). In the individual group, HbA1c decreased 0.4% (95% CI = -0.6, -0.1), systolic blood pressure decreased 3 mmHg (95% CI = -6.3, -0.7), diastolic blood pressure decreased 3 mmHg (95% CI = -4.7, -0.7), weight decreased 1.6 kg (95% CI = -2.6, -.7]), and waist circumference decreased 1.6 cm (95% CI = -2.5, -0.6). Vitality, fatigue distress, physical functioning and cardiovascular distress improved over time (P < 0.05) in the two groups combined. Repeated measurement analysis did not result in significant differences between the groups of any outcome. Conclusions: This study demonstrates that group-based rehabilitation in a primary healthcare center is a comparable alternative to individual counseling in an outpatient clinic. However, the resource use of the rehabilitation program was twice as much as the individual program.
The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods

We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. Author Summary Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, the genetic impact associated with this cultural transformation has not yet been estimated. In order to investigate this, we sequence Neolithic and Bronze Age samples from Portugal, which we compare to other ancient and present-day individuals. Genome-wide imputation of a large dataset of ancient samples enabled sensitive methods for detecting population structure and selection in ancient samples. We revealed subtle genetic differentiation between the Portuguese Neolithic and Bronze Age samples suggesting a markedly reduced influx in Iberia compared to other European regions. Furthermore, we predict individual height in ancients, suggesting that stature was reduced in the Neolithic and affected by subsequent admixtures. Lastly, we examine signatures of strong selection in important traits and the timing of their origins.
Comparison of arterial stiffness in preeclamptic and normotensive pregnant women from a semi-rural region of South Africa

ABSTRACT Background: Preeclampsia is associated with arterial stiffness and endothelial dysfunction. The pathophysiology of arterial tone in preeclampsia has not been well described in rural African population, where the incidence is higher. Objective: The aim of the study was to compare arterial tone of preeclamptic with pregnant normotensive women assessed with noninvasive techniques, using applanation tonometry with SphygmoCor. Method: This was a cross-sectional study. Participants were recruited from Mthatha General Hospital complex Antenatal clinics during their third trimester. A hundred and twelve (112) normotensive and 85 preeclamptic women (PE) were recruited into the study. Arterial stiffness was assessed using applanation tonometry with SphygmoCor device; central aortic pressures, peripheral and central augmentation index (Alx), and carotid–femoral pulse wave velocity (PWV) were then calculated. Data were analyzed using STATISTICA version 10 software. Results: Pulse wave velocity was significantly higher in preeclamptic than normotensive women (6.6 IQR 1.8 versus 5.0 IQR 1.2; p = 0.000). Central augmentation index corrected to heart rate of 75 was significant higher in preeclamptic than normotensives women (23.4 ± 12.4 versus 12.8 ± 12) with p < 0.002. Early-onset preeclampsia had significantly higher brachial diastolic blood pressure (87 IQR 79-101.5 versus 82 IQR 65-88; p = 0.0198) than late-onset preeclampsia. Conclusion: This study has demonstrated that women of rural Eastern Cape with preeclampsia have increased pulse wave velocity and peripheral augmentation index. This shows that preeclamptic women from rural Eastern Cape of South Africa have increased arterial stiffness.
A New Particle Weighting Strategy for Robot Mapping FastSLAM

Nowadays, FastSLAM filters are the most widely used methods to solve the Simultaneous Localization and Mapping (SLAM) problem. In general, these approaches can use complex matrix formulation for computing the particle weighting procedure, during the execution of the SLAM algorithm. In this paper, we describe a new particle weight strategy for the FastSLAM filter, which can maintain the generation of particles in its most simplified form. Thus, this approach tries to estimate the robot poses and build the environment map using a simple geometric formulation for executing the particle weighting procedure. This method is capable of reducing the processing time and keeping the accuracy of the robot pose. Both simulation and experimental results demonstrate the feasibility of the proposed approach at enabling a robotic vehicle to accomplish the mapping of an unknown environment and also navigate through it.
Enzymatic Inactivation of W-NÃ¬troso Compounds in Murine Blood Plasma1

Murine blood plasma rapidly inactivates nitrosamides and nitrosocarbamates but not nitrosoureas. The mechanism of this inactivation in murine blood plasma has been investigated. The vast majority of activity (>97%) was inhibited by serine hydroxylase inhibitors. Also, 92% of the activity was inhibited by bis(pnitrophenyl)phosphate, a selective inhibitor of carboxy(esterases. Decomposition products formed after blood plasma action on Nethyl-N-nitrosoacetamide or W-methyl-A/-nitrosoethylcarbamate were separated and identified by gas chromatography. The products formed were consistent with a hydrolytic cleavage of the amidic bond. These observations are consistent with the idea that the major active faetonÂ» in plasma is a carboxylester
A Review of Presence and Performance in Virtual Environments

This article provides a review of the literature related to presence and performance within virtual environments. Summary tables are provided to present the reader with a general framework in which to evaluate the type of studies that have been run, as well as representative findings across different tasks and virtual environments. Within the general area of performance, the topics of navigation and knowledge acquisition have been expanded, as they are seen as important aspects of tasks performed within virtual environments drawing much attention from researchers. In addition, given that a sense of presence is an important aspect of the virtual environment experience, the literature related to presence within virtual environments is also reviewed. The summary tables provided can be used to indicate areas where additional research efforts are needed to more fully explain how human performance and presence are affected by use of virtual environment technology. This article concludes with a discussion of potential relations between presence and performance and directions for future research.
A 3.1 to 5 GHz CMOS DSSS UWB transceiver for WPANs

A DSSS UWB transceiver using the 3.1 to 5 GHz band is implemented in 0.18 /spl mu/m CMOS and includes a programmable pulse shaping circuit in the transmitter, an LNA with a NF of 4 dB and a 6/sup th/-order active LPF with a bandwidth of 500 MHz in the receiver. Die area of the transceiver is around 9 mm/sup 2/. and the transceiver consumes 105 mW in the transmit mode and 280 mW in the receive mode from a 1.8 V supply.