Miracle-dz/UniFAR-FTUs huggingface dataset:
Anatomy of Escherichia coli ribosome binding sites.

During translational initiation in prokaryotes, the 3' end of the 16S rRNA binds to a region just upstream of the initiation codon. The relationship between this Shine-Dalgarno (SD) region and the binding of ribosomes to translation start-points has been well studied, but a unified mathematical connection between the SD, the initiation codon and the spacing between them has been lacking. Using information theory, we constructed a model that treats these three components uniformly by assigning to the SD and the initiation region (IR) conservations in bits of information, and by assigning to the spacing an uncertainty, also in bits. To build the model, we first aligned the SD region by maximizing the information content there. The ease of this process confirmed the existence of the SD pattern within a set of 4122 reviewed and revised Escherichia coli gene starts. This large data set allowed us to show graphically, by sequence logos, that the spacing between the SD and the initiation region affects both the SD site conservation and its pattern. We used the aligned SD, the spacing, and the initiation region to model ribosome binding and to identify gene starts that do not conform to the ribosome binding site model. A total of 569 experimentally proven starts are more conserved (have higher information content) than the full set of revised starts, which probably reflects an experimental bias against the detection of gene products that have inefficient ribosome binding sites. Models were refined cyclically by removing non-conforming weak sites. After this procedure, models derived from either the original or the revised gene start annotation were similar. Therefore, this information theory-based technique provides a method for easily constructing biologically sensible ribosome binding site models. Such models should be useful for refining gene-start predictions of any sequenced bacterial genome.
Talk the talk and walk the walk. Evaluation of autonomy in aging and Alzheimer disease by simulating instrumental activities of daily living: the S-IADL

Objective The autonomy of individuals is linked to the achievement of instrumental activities of daily living that require complex behavior. In the elderly, the assessment of autonomy is usually based on questionnaires that have strong subjective constraints. Considering this fact, we tested elderly healthy adults and Alzheimer disease patients using a new measure, the S-IADL (Simulation of Instrumental Activities for Daily Living), to assess the ability to perform effectively activities of daily living. Method The S-IADL shares many items with the well-known IADL questionnaire proposed by Lawton & Brody (1969). However, as opposed to the IADL, the assessment of autonomy is not based on the completion of a questionnaire but requires the realization or simulation of various activities of daily living. Eighty-three participants (69 healthy elderly, and 14 Alzheimer Disease patients) completed the IADL and performed the S-IADL assessment. Results Results revealed that, like the IADL, the S-IADL is able to identify AD patients who are likely to encounter difficulties in performing everyday activities, and no major differences were found between the IADL and the S-IADL. Conclusions We outlined some advantages for prefering, in certain situation, this new tool based on simulation of activities in functional evaluation. Finally, we discuss the main limits of the S-IADL that should be investigated prior to its utilization by clinicians.
Characterization of a common wheat (Triticum aestivum L.) TaSnRK2.7 gene involved in abiotic stress responses

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) plays a key role in the plant stress signalling transduction pathway via phosphorylation. Here, a SnRK2 member of common wheat, TaSnRK2.7, was cloned and characterized. Southern blot analysis suggested that the common wheat genome contains three copies of TaSnRK2.7. Subcellular localization showed the presence of TaSnRK2.7 in the cell membrane, cytoplasm, and nucleus. Expression patterns revealed that TaSnRK2.7 is expressed strongly in roots, and responds to polyethylene glycol, NaCl, and cold stress, but not to abscisic acid (ABA) application, suggesting that TaSnRK2.7 might participate in non-ABA-dependent signal transduction pathways. TaSnRK2.7 was transferred to Arabidopsis under the control of the CaMV-35S promoter. Function analysis showed that TaSnRK2.7 is involved in carbohydrate metabolism, decreasing osmotic potential, enhancing photosystem II activity, and promoting root growth. Its overexpression results in enhanced tolerance to multi-abiotic stress. Therefore, TaSnRK2.7 is a multifunctional regulatory factor in plants, and has the potential to be utilized in transgenic breeding to improve abiotic stress tolerance in crop plants.
A new human antitumor immunoreagent specific for ErbB2.

PURPOSE Our aim was to isolate a novel human mini-antibody(scFv) that specifically targets ErbB2-positive cancer cells. ErbB2, a tyrosinekinase receptor, is overexpressed in clinically significant tumors, such as breast, ovary, and lung carcinomas. In normal tissues, it is expressed only in certain epithelial cell types. EXPERIMENTAL DESIGN A large phagemid library (Griffin.1 library) of human scFv was used for the isolation of the ErbB2-specific scFv. A very effective strategy was developed for the isolation, consisting in a double subtractive selection, the use of two different combinations of "positive," i.e., ErbB2-bearing, and "negative" cell lines. RESULTS Here we report the isolation of the first human anti-ErbB2 mini-antibody endowed with antitumor action. Both in its soluble and phage format, it binds specifically to ErbB2, inhibits its autophosphorylation, is internalized by target cells, and exerts a strong and specific antiproliferative action on ErbB2-positive target cells. A correlation was found between the extent of this antiproliferative effect and the expression levels of ErbB2 on target cells, with a strong cytotoxicity for hyper-expressing cells, such as SKBR3, in which apoptosis was evidenced. CONCLUSIONS This scFv is a potentially effective immunoreagent for diagnostics and therapeutics of certain cancers, both as a readily diffused molecule in solid tumors and as an essential asset for the construction of fully human anticancer drugs.
Guiding the study of brain dynamics by using first-person data: Synchrony patterns correlate with ongoing conscious states during a simple visual task

Even during well-calibrated cognitive tasks, successive brain responses to repeated identical stimulations are highly variable. The source of this variability is believed to reside mainly in fluctuations of the subject's cognitive “context” defined by his/her attentive state, spontaneous thought process, strategy to carry out the task, and so on … As these factors are hard to manipulate precisely, they are usually not controlled, and the variability is discarded by averaging techniques. We combined first-person data and the analysis of neural processes to reduce such noise. We presented the subjects with a three-dimensional illusion and recorded their electrical brain activity and their own report about their cognitive context. Trials were clustered according to these first-person data, and separate dynamical analyses were conducted for each cluster. We found that (i) characteristic patterns of endogenous synchrony appeared in frontal electrodes before stimulation. These patterns depended on the degree of preparation and the immediacy of perception as verbally reported. (ii) These patterns were stable for several recordings. (iii) Preparatory states modulate both the behavioral performance and the evoked and induced synchronous patterns that follow. (iv) These results indicated that first-person data can be used to detect and interpret neural processes.
COMMISSIONING OF THE LNLS X-RAY BPMS

We present experimental results of the commissioning of staggered-pair blade X-Ray beam position monitor (XBPM) recently developed and installed at the diagnostic beamline of the UVX electron storage ring at the Brazilian Synchrotron Light Laboratory (LNLS). The results obtained with a prototype XBPM indicate that the short-term and long-term data are both in agreement with the data from a commercially acquired XBPM installed at the same beamline, as well as with the data of the electron storage ring RF BPMs. In this paper we present the commissioning results of the LNLS XBPM.
ADAPTIVE VISUAL SERVOING CONTROL IN 2 D WITHOUT VELOCITY MEASUREMENTS

This paper considers the problem of position control of robot manipulators via visual servoing in presence of uncertainties associated with the robot dynamics and the vision system. Specifically, an adaptive algorithm is designed to compensate for the uncertainties associated with the mechanical model of the robot manipulator and the intrinsic parameters of the camera. We propose a control law which requires for implementation only joint and image coordinates, also a velocity observer is designed. This is achieved by combining a previous control algorithm designed originally to work Cartesian coordinates and an adaptive control law, to a version which uses image coordinates instead. Simulation results show the good performance of the complete system.
Assessment of Femoral Head Revascularization in Legg-Calvé-Perthes Disease Using Serial Perfusion MRI.

BACKGROUND Legg-Calvé-Perthes disease is a juvenile form of osteonecrosis of the femoral head. The purpose of this study was to use serial perfusion magnetic resonance imaging (MRI) to determine the pattern and rate of revascularization of the femoral heads of patients with the active stage of Legg-Calvé-Perthes disease. METHODS We performed a prospective study of 29 patients (30 hips) with a mean age (and standard deviation) of 8.4 ± 1.9 years who were diagnosed with Waldenström Stage-1 or 2 Legg-Calvé-Perthes disease. All patients had ≥2 perfusion MRIs, and 21 patients (22 hips) had ≥3. Perfusion percentages of the femoral epiphyses were measured by 2 independent observers. Statistical analyses included calculation of the intraclass correlation coefficient, the paired t test, the Mann-Whitney U test, and the Kruskal-Wallis test. RESULTS Initial perfusion MRIs showed the percent perfusion in the affected femoral heads to range from 5% to 70%. The average percent perfusion (and standard deviation) was 35% ± 16% on the first MRI, which increased to 77% ± 14% on the follow-up MRI acquired at an average of 10.5 ± 2.9 months later (p < 0.01). Serial assessment showed a general pattern of revascularization starting from the periphery of the posterior, lateral, and medial aspects of the femoral epiphysis and converging toward the anterocentral region. The average rate of revascularization was 4.9% ± 2.3% per month with a wide range among the patients (0.6% to 10.4% per month). CONCLUSIONS Revascularization of the necrotic femoral head increased over time in a horseshoe pattern, starting from the posterior, lateral, and medial aspects of the femoral epiphysis. The rate of revascularization was highly variable among patients. LEVEL OF EVIDENCE Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Adaptive PDE Observer for Battery SOC/SOH Estimation

This paper develops an adaptive PDE observer for battery state-of-charge (SOC) and state-of-health (SOH) estimation. Real-time state and parameter information enables operation near physical limits without compromising durability, thereby unlocking the full potential of battery energy storage. SOC/SOH estimation is technically challenging because battery dynamics are governed by electrochemical principles, mathematically modeled by partial differential equations (PDEs). Simultaneous state and parameter estimation is extremely challenging in PDE models. Consequently, several new theoretical ideas are developed, integrated together, and tested. These include a backstepping PDE state estimator, a Pade-based parameter identifier, nonlinear parameter sensitivity analysis, and adaptive inversion of nonlinear output functions. The end result is the first combined SOC/SOH battery estimation algorithm that identifies physical system variables via an electrochemical model, from measurements of voltage and current only.Copyright © 2012 by ASME
Clinical and Aesthetic Outcome with Post-Extractive Implants with or without Soft Tissue Augmentation: A 2-Year Randomized Clinical Trial.

BACKGROUND The aesthetic outcome of an implant-supported restoration is first of all dependent on the soft tissue volume. Because the labial bone plate resorbs in every direction after tooth extraction, even when an implant is placed immediately, most patients end up with compromised aesthetics. MATERIALS AND METHODS In this parallel-designed, randomized clinical trial, participants were randomly assigned to the test group (immediate load post-extractive implant treated with subepithelial connective tissue graft placed using the tunnel technique in the labial area) and control group (immediate load post-extractive implant treated without raising a flap) with an allocation ratio of 1:1. Both groups received deproteinized bovine bone mineral. Patients were observed at baseline, crown insertion, 1-year follow-up, and 2-year follow-up. Clinical, radiological and aesthetic parameters were recorded to assess primary treatment outcomes. A random permuted block system was blindly generated ensuring uniformity of the patient allocation during the trial by randomly distributing three participants to the test and three participants to the control group every six treated patients. RESULTS At the 2-year examination, all 47 implants were successfully integrated, demonstrating stability and healthy peri-implant soft tissues as documented by standard clinical parameters. The results showed a soft tissue remodeling of -10% in thickness and -18% in highness in the non-grafted group, whereas in the grafted group there was a gain of 35% in thickness and a slight reduction of -11% in highness. Test group reported an increase of aesthetic result (mean pink aesthetic score [PES] 8) compared with control group (mean PES 6.65). CONCLUSIONS This prospective study demonstrates the effectiveness of placing a soft tissue graft at the time of immediate implant placement in the aesthetic zone. At the 2-year follow-up, test group revealed a better aesthetic outcomes and stable facial soft tissues compared with control group.
Is multicell interference coordination worthwhile in indoor wireless broadband systems?

The rapid growth in demand for mobile and nomadic wireless access forces the use of more and more base stations (BSs). In such dense networks, various techniques for multicell interference coordination have been investigated. However, whether or not the interference coordination provides cost benefit compared with a loosely coordinated system is not obvious because the tight coordination at PHY-layer is likely to need an expensive high-speed backbone infrastructure. In this paper, we assess the worthiness of the tight interference coordination, referred to as coordination gain, in various indoor environments. We compare a hypothetical interference-free system as an upper bound with a simple interference-limited system opportunistically avoiding interference. The range of possible coordination gain is examined for various wall losses, path loss exponents, building shapes, and deployment density. Results show that substantial gain can be achieved in dense deployment at open areas with low path loss exponent, e.g., lightly furnished offices partitioned with soft walls. Nevertheless, the coordination gain significantly drops in the presence of marginal wall loss regardless of the other environmental factors.
Single event upset mitigation in low power SRAM design

Technology advancements in recent years have led to an increase in the employment of integrated circuits in space applications. However, these applications operate in a highly radiated environment, causing a high probability of single event upsets (SEU). Continuous transistor scaling exacerbates the situation, as susceptibility to SEUs is increased in advanced process technologies. The most vulnerable of these circuits are memory arrays that cover large areas of the silicon die and often store critical data. Accordingly, maintaining data integrity in light of SEUs has become an integral aspect of memory cell design. This paper introduces recently proposed methods for mitigating SEUs, and reviews the advantages and disadvantages of leading memory radiation hardening solutions. A brief comparison of radiation hardened bitcells is provided, based on Monte Carlo simulations in a 65nm CMOS process under slightly scaled supply voltages.
Evaluation of a Prediction Protocol to Identify Potential Targets of Epigenetic Reprogramming by the Cancer Associated Epstein Barr Virus

Background Epstein Barr virus (EBV) infects the majority of the human population, causing fatal diseases in a small proportion in conjunction with environmental factors. Following primary infection, EBV remains latent in the memory B cell population for life. Recurrent reactivation of the virus occurs, probably due to activation of the memory B-lymphocytes, resulting in viral replication and re-infection of B-lymphocytes. Methylation of the viral DNA at CpG motifs leads to silencing of viral gene expression during latency. Zta, the key viral protein that mediates the latency/reactivation balance, interacts with methylated DNA. Zta is a transcription factor for both viral and host genes. A sub-set of its DNA binding sites (ZREs) contains a CpG motif, which is recognised in its methylated form. Detailed analysis of the promoter of the viral gene BRLF1 revealed that interaction with a methylated CpG ZRE (RpZRE3) is key to overturning the epigenetic silencing of the gene. Methodology and Principal Findings Here we question whether we can use this information to identify which host genes contain promoters with similar response elements. A computational search of human gene promoters identified 274 targets containing the 7-nucleotide RpZRE3 core element. DNA binding analysis of Zta with 17 of these targets revealed that the flanking context of the core element does not have a profound effect on the ability of Zta to interact with the methylated sites. A second juxtaposed ZRE was observed for one promoter. Zta was able to interact with this site, although co-occupancy with the RpZRE3 core element was not observed. Conclusions/Significance This research demonstrates 274 human promoters have the potential to be regulated by Zta to overturn epigenetic silencing of gene expression during viral reactivation from latency.
Effect of Polycyclic Aromatic Hydrocarbons and Carbon Black Particles on Pro-Inflammatory Cytokine Secretion: Impact of PAH Coating Onto Particles

It has been suggested that the organic fraction of particulate matter in air pollution has a major role in the toxicity of this pollutant, notably via its effects on inflammation. The major organic compounds adsorbed onto these particles are polycyclic aromatic hydrocarbons (PAH), among which benzo[a]pyrene (B[a]P), benzo[b]fluoranthene (B[b]F), and pyrene (Pyr) are quantitatively the most important. Generally, cells or organisms are exposed to organic extracts of the particles rather than the native particles in order to study the effects of these PAH. In this study, B[a]P, B[b]F, and Pyr were tested alone and/or adsorbed onto carbon black (CB) particles differing in size in order to evaluate their impact on cytokine production (with or without LPS stimulation) by THP-1 macrophage-like cells. PAH induced significant secretion of IL-1β, IL-8, and IL-12 after 24 or 48 hr of treatment, an effect reinforced by LPS stimulation; no effect on IL-10 secretion was noted. Fine CB particles (260 nm diameter) induced secretion of each cytokine. In general, coating the CB with PAH did not modify the effect of the CB alone; the exception was that LPS-induced IL-1β secretion was reduced. In contrast, ultrafine CB (14 nm diameter: ufCB) caused a decrease in cytokine secretion; this effect was modified by PAH coating. For example, PAH coating on ufCB amplified the inhibitory effect of ufCB against IL-1β secretion but did not modify IL-8 formation. Moreover, PAH coating on ufCB tended to minimize the effect of LPS stimulation; this included (i) inhibition of the decrease in IL-12 secretion induced by uncoated ufCB and (ii) stimulation of IL-10 production. It was concluded that adsorption of PAH onto these particles could decrease their bioavailability and so their abilities to affect cell cytokine production. The results also showed that when PAH were adsorbed onto the fine particles, any observed increases in cytokine secretion consistently appeared to be due to the particles themselves. In contrast, while ufCB alone almost uniformly led to decreases in cytokine formation by the cells, the added presence of the test PAHs led to variable effects – depending on whether stimulation with LPS took place or not. Thus, while some PAHs likely to be associated with PM are clearly immunomodulants, their ultimate effects in situ will likely depend on the properties of the particles themselves, in particular, their size.
Dynamic Model of Heat Inactivation Kinetics for Bacterial Adaptation

ABSTRACT The Weibullian-log logistic (WeLL) inactivation model was modified to account for heat adaptation by introducing a logistic adaptation factor, which rendered its “rate parameter” a function of both temperature and heating rate. The resulting model is consistent with the observation that adaptation is primarily noticeable in slow heat processes in which the cells are exposed to sublethal temperatures for a sufficiently long time. Dynamic survival patterns generated with the proposed model were in general agreement with those of Escherichia coli and Listeria monocytogenes as reported in the literature. Although the modified model's rate equation has a cumbersome appearance, especially for thermal processes having a variable heating rate, it can be solved numerically with commercial mathematical software. The dynamic model has five survival/adaptation parameters whose determination will require a large experimental database. However, with assumed or estimated parameter values, the model can simulate survival patterns of adapting pathogens in cooked foods that can be used in risk assessment and the establishment of safe preparation conditions.
Response of red cell and plasma volume to prolonged training in humans.

To clarify the role of progressive heavy training on vascular volumes and hematologic status, seven untrained males [maximal O2 uptake (VO2max) = 45.1 +/- 1.1 (SE) ml.kg-1.min-1] cycled 2 h/day at an estimated 62% of VO2max. Training was conducted five to six times per week for approximately 8 wk. During this time, VO2max increased (P less than 0.05) by 17.2%. Plasma volume (PV) measured by 125I increased (P less than 0.05) from 3,068 +/- 104 ml at 0 wk to 3,490 +/- 126 ml at 4 wk and then plateaued during the remaining four wk (3,362 +/- 113 ml). Red cell (RBC) mass (RCM) measured by 51Cr-labeled RBC did not change during the initial 4 wk of training (2,247 +/- 66 vs. 2,309 +/- 128 ml). As well, no apparent change occurred in RCM during the final 4 wk of training when RCM was estimated using PV and hematocrit (Hct). Collectively, PV plus RCM, expressed as total blood volume (TBV), increased (P less than 0.05) by 10% at 4 wk and then stabilized for the final 4 wk. During the initial phase of training, reductions (P less than 0.05) were also noted in Hct (4.6%), hemoglobin (Hb, 4.0%), and RBC count (6.3%). In contrast, an increase in mean cell volume (MCV, 1.7%) and mean cell Hb (2.3%) was observed (P less than 0.05). From 4 to 8 wk, no further changes (P greater than 0.05) in Hb, RBC, and MCV were found, whereas both mean cell Hb and Hct returned to pretraining levels. (ABSTRACT TRUNCATED AT 250 WORDS)