Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-walled carbon nanotubes promote rat vascular adventitial fibroblasts to transform into myofibroblasts by SM 22-α expression

Correspondence: Zhuge Xi Institute of Hygiene and Environmental Medicine, Academy of Military Medical Sciences, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Road Dali 1#, District Heping, Tianjin Province, China, 300050 Email zhugexi2003@sina.com Abstract: The aim of this study was to explore whether single-wall carbon nanotubes (SWCNTs) can be used as artery tissue-engineering materials by promoting vascular adventitial fibroblasts (VAFs) to transform into myofibroblasts (MFs) and to find the signal pathway involved in this process. VAFs were primary cultured and incubated with various doses of SWCNTs suspension (0, 0.8, 3.2, 12.5, 50, and 200 μg/mL). In the present study, we used three methods (MTT, WST-1, and WST-8) at the same time to detect the cell viability and immunofluorescence probe technology to investigate the effects of oxidative injury after VAFs incubated with SWCNTs. Immunocytochemical staining was used to detect SM 22 -α expression to confirm whether VAFs transformed into MFs. The protein levels were detected by western blotting. The results of immunocytochemical staining showed that SM 22 -α was expressed after incubation with 50 μg/mL SWCNTs for 96 hours, but with oxidative damage. The mRNA and protein levels of SM 22 -α, C-Jun N-terminal kinase, TGF-β 1 , and TGF-β receptor II in VAFs increased with the dose of SWCNTs. The expression of the p-Smad2/3 protein was upregulated while the Smad7 protein was significantly down-regulated. Smad4 was translocated to the nucleus to regulate SM 22 -α gene expression. In conclusion, SWCNTs promoted VAFs to transform into MFs with SM 22 -α expression by the C-Jun N-terminal kinase/Smads signal pathway at the early stage (48 hours) but weakened quickly. SWCNTs also promoted the transformation by the TGF-β l /Smads signal pathway at the advanced stage in a persistent manner. These results indicate that SWCNTs can possibly be used as artery tissue-engineering materials.
Moment-Generating Function Method Used to Evaluate the Performance of a Linear Optical Communication System

The moment-generating function (MGF) of the received photoelectric current is evaluated for a linear optical communication system consisting of distributed amplified spontaneous emission (ASE), polarization-mode dispersion (PMD), and polarization dependent loss (PDL). Using this function, optical performance characterization based on the bit error rate (BER), Q-factor, and signal-to-noise ratio (SNR), can be evaluated. As an example of the applicability to binary differential phase-shift keying (DPSK) systems with defined PDL, the BER results predicted by linked model and lumped model are compared. Our results indicate that the difference can be orders of magnitude when the PDL is larger than 2.5 dB. Additionally, random PDL induced statistical feature of the BER is entirely different for these two models. Finally, relations between the statistical variations of other performance parameters ( Q-factor and SNR) and link model parameters (input signal polarization, average PDL value, and link number K) are also investigated.
FURTHER CONSIDERATION OF THE STUDY ‘ BRONCHIAL HYPER-RESPONSIVENESS AND ATOPY IN URBAN , PERI-URBAN AND RURAL SOUTH AFRICAN CHILDREN ’

Over two decades ago, the prevalence of sensitisation to allergens and asthma in rural Xhosa children was almost unheard of, as documented in the seminal studies of Van Niekerk et al. Recently, PAI published our findings examining the bronchial hyper-responsiveness (BHR) and atopy in urban, peri-urban and rural South African children, documenting the rising prevalence of these conditions in these various groups and reporting a dramatic increase of atopy in rural Xhosa children. The findings of this paper are reviewed here and contrasted with a fourth component of the study, not published before, which examined BHR in a group of children living in an area in close proximity to a petrol refinery, which documented a disproportionately high prevalence of BHR.
Sparsity analysis using a mixed approach with greedy and LS algorithms on channel estimation

Various channels can be denoted by sparse channels and many algorithms have been proposed to exploit their sparsity. In this paper, we propose a mixed algorithm based on Greedy and LS algorithms for sparse channel estimation. Analyses of the proposed and commonly used algorithms in terms of performance and complexity are performed considering the channel's sparsity, the length of training sequence and the stopping criterion. Our results show that a suitable trade-off can be found and effective channel estimations can be obtained with a low-cost algorithm.
Online Support Vector Regression based value function approximation for Reinforcement Learning

This paper proposes the online Support Vector Regression (SVR) based value function approximation method for Reinforcement Learning (RL). This approach conserves the Support Vector Machine (SVM)'s good property, the generalization which is a key issue of function approximation. Online SVR can do incremental learning and automatically track variation of environment with time-varying characteristics. Using the online SVR, we can obtain the fast and good estimation of value function and achieve RL objective efficiently. Throughout simulation tests, the feasibility and usefulness of the proposed approach is demonstrated by comparison with SARSA and Q-learning.
Power loss for multiallelic transmission/disequilibrium test when errors introduced: GAW11 simulated data

Many researchers are considering the use of transmission/disequilibrium tests (TDT) for trios of genotypes (father, mother, child) as a method for localizing genes associated with complex diseases. We evaluate the effect of random errors (allele changes) in trios on the power to detect linkage. For a marker in the simulated data set, one allele is associated with the fictitious disease in a certain subpopulation. For the data as given (no errors), our power to detect linkage using the multiallelic TDT (TDTmhet) is 68% (critical p‐value set at 0.0001). We introduce errors into trios at various rates (1%, 5%, or 10%), remove only trios displaying mendelian inconsistencies, and recalculate power to detect linkage. Our principal finding is that there is power loss to detect linkage with the TDTmhet when errors are introduced. We observe power losses of 8%, 16%, and 48% for error rates of 1%, 5%, and 10%, respectively. To determine the source of the power loss, we perform Monte Carlo simulations. At the 1% and 5% rates, we conclude that power loss is due primarily to loss in sample size. At the 10% rate, we observe substantial power loss due to error introduction in addition to sample size reduction. We also determine, given a particular error rate, the probability that we detect errors if we use only mendelian consistency as a check. We find that the mean detection rates for the data sets with 1%, 5%, or 10% error rates are 58%, 60%, and 62%, respectively. As a result, the apparent error rate appears to be almost half the true error rate. Based on these results, we recommend that researchers maintain error rates below 5% when using the TDTmhet for linkage, use additional methods beyond mendelian consistency checks when searching for errors in their data, and modify sample size calculations when accounting for errors in their genotype data.
Propofol in paediatric anaesthesia

Purpose of review In this review we intend to ascertain trends in propofol administration for paediatric anaesthesia and sedation. Recent findings Propofol is being ‘discovered’ by non-anaesthesiologist practitioners of paediatric sedation. However it appears that the drug is not infrequently administered alone for painful procedures, necessitating large doses that result in uncontrolled general anaesthesia with a high potential for adverse events. An elegant technique comprises small doses of short-acting opioid (e.g. fentanyl 1 μg/kg) with low-dose propofol infusion. This does not result in worsening of pre-existing right-to-left intracardiac shunts. The dilemma is to educate non-anaesthesiologists about propofol pharmacokinetics and pharmacodynamics and in particular about the advantages of combined drug therapy. A paediatric target-controlled system for propofol has undergone preliminary clinical evaluation and it is hoped that administration according to pharmacokinetic principles will refine administration to infants and children. Sporadic cases of the propofol infusion syndrome in patients receiving prolonged sedation in intensive care units continue to be reported (characterized by metabolic acidosis, rhabdomyolysis and myocardial failure). It appears that one mechanism may be a deficiency of mitochondrial oxidatative processes possibly induced by a dialyzable substance, perhaps a propofol metabolite. Propofol has been used with some success in treating postoperative laryngospasm and for tracheal intubation without muscle relaxants. Summary Propofol should be used with extreme caution for prolonged sedation in intensive care unit patients, at dose rates of below 5 mg/kg per h, while maintaining extreme vigilance for signs of developing propofol infusion syndrome. If used correctly propofol is a suitable drug for sedation outside the operating room.
Combining evolution and machine learning for functional annotation and classification of remote homologous proteins. (Evolution et apprentissage automatique pour l'annotation fonctionnelle et la classification des homologies lointains en protéines)

Detection of remote homologous proteins is essential for functional and structural classification of protein sequences and for the completion of the annotation for highly divergent genomes. Here, we present two new methods to address these problems. For the first prob- lem, we introduce ILP-SVM Homology that combines inductive logic programming (ILP) and propositional models. It proposes a novel logical representation of physico-chemical properties, conserved amino acid positions and conserved physico-chemical positions in sequence alignments. Based on these signals, ILP finds the most frequent patterns and uses them to train models, such as decision trees and support vector machines. ILP-SVM Homology achieves at least equal performance when compared with other methods. To address the second problem, we propose CASH, a large-scale pipeline to annotate highly divergent genomes. CASH was applied to the Plasmodium falciparum, but it is applicable to any species. In CASH we explore different evolutionary pathways including those that are phylogenetically distant from P. falciparum. As a result, each known domain is represented by an ensemble of heterogeneous models, and the outputs are combined through a meta-classifier that assigns a confidence score to each prediction. Based on this score and on properties as domain co-occurrence, CASH finds the most probable architecture for each query sequence by resolving a multi-objective optimization problem. CASH provides domain annotation for 70% of proteins in P. falciparum, while its competitors achieve at most 58%. We find additional domains into already annotated proteins, and predict domains for proteins with unknown function.
Outpatient high-dose chemotherapy with autologous stem-cell rescue for hematologic and nonhematologic malignancies.

PURPOSE A prospective study to determine the feasibility of high-dose chemotherapy (HDC) and autologous stem-cell rescue (ASCR) in the outpatient setting. METHODS One hundred thirteen consecutive patients underwent 165 cycles of HDC/ASCR for a variety of malignancies. HDC regimens were disease-specific. Initially, patients were hospitalized for HDC, discharged on completion, and maintained as outpatients unless toxicities required rehospitalization (subtotal outpatient transplantation [STOT]). Once this was established as safe, a total outpatient transplant (TOT) program was developed in which patients received all of the HDC, as well as supportive care, as outpatients. Patients who declined the outpatient programs received the same HDC and supportive care as inpatients. RESULTS In 140 of 165 (85%) HDC cycles, patients agreed to participate in one of the outpatient transplant programs. Five patients in the STOT program could not be discharged from the hospital because of toxicities that developed during HDC; thus, 135 patients were monitored the outpatient setting, 95 (70%) of whom were never readmitted. The mean +/- SEM total hospital length of stay (LOS), including all readmissions and excess days after chemotherapy, was 18.33 +/- 5.06 days for patients who refused the outpatient program, 8.22 +/- 5.76 days for patients in the STOT program, and 2.81 +/- 7.66 days for those in the TOT program (P < .001). One treatment-related death occurred in each treatment setting: day 120 inpatient, day 17 STOT, and day 110 TOT. CONCLUSION Outpatient management of HDC/ASCR is safe and acceptable for the vast majority of patients. The STOT program resulted in significant reduction in hospital LOS, while the TOT program appears equally safe and further reduces LOS. Hospitalization for HDC/ASCR is unnecessary in most patients.
A low power low phase noise wide switched tuned band LC VCO for S band applications

This paper deals with the design problems associated to the implementation of low power wide tuning band low phase noise LC VCOs in low cost Si-integrated technologies. For that, a VCO was developed using a low cost 0.35 mum 2-poly 4-metal standard CMOS technology. The VCO uses a radio frequency switched varactor array (RFSVA) in the tank circuit in order to decrease the influence of the varactor tuning input on the oscillator phase noise. The VCO presents a continuous tuning band from 2.76 GHz to 3.36 GHz, a single-ended output power that ranges from -12 dBm to -6 dBm and a phase noise always lower than -117 dBc/Hz at an offset frequency of 1 MHz. Moreover, the two output ports of the VCO present return losses higher than 12.7 dB in the 600 MHz tuning band. The VCO core works with a voltage supply of 1.5 V and has a current consumption of 5 mA and the output buffers draws 18 mA from a 3 V voltage supply.
Silencing of tuberin enhances photoreceptor survival and function in a preclinical model of retinitis pigmentosa (an american ophthalmological society thesis).

PURPOSE To assess the functional consequences of silencing of tuberin, an inhibitor of the mTOR signaling pathway, in a preclinical model of retinitis pigmentosa (RP) in order to test the hypothesis that insufficient induction of the protein kinase B (PKB)-regulated tuberin/mTOR self-survival pathway initiates apoptosis. METHODS In an unbiased genome-scale approach, kinase peptide substrate arrays were used to analyze self-survival pathways at the onset of photoreceptor degeneration. The mutant Pde6b(H620Q)/Pde6b(H620Q) at P14 and P18 photoreceptor outer segment (OS) lysates were labeled with P-ATP and hybridized to an array of 1,164 different synthetic peptide substrates. At this stage, OS of Pde6b(H620Q)/Pde6b(H620Q) rods are morphologically normal. In vitro kinase assays and immunohistochemistry were used to validate phosphorylation. Short hairpin RNA (shRNA) gene silencing was used to validate tuberin's role in regulating survival. RESULTS At the onset of degeneration, 162 peptides were differentially phosphorylated. Protein kinases A, G, C (AGC kinases), and B exhibited increased activity in both peptide array and in vitro kinase assays. Immunohistochemical data confirmed altered phosphorylation patterns for phosphoinositide-dependent kinase-1 (PDK1), ribosomal protein S6 (RPS6), and tuberin. Tuberin gene silencing rescued photoreceptors from degeneration. CONCLUSIONS Phosphorylation of tuberin and RPS6 is due to the upregulated activity of PKB. PKB/tuberin cell growth/survival signaling is activated before the onset of degeneration. Substrates of the AGC kinases in the PKB/tuberin pathway are phosphorylated to promote cell survival. Knockdown of tuberin, the inhibitor of the mTOR pathway, increased photoreceptor survival and function in a preclinical model of RP.
Ferrocenylnaphthalene Diimide-based Electrochemical Ribonuclease Assay

Messenger RNA (mRNA) poly(A)^+RNA (from mouse kidney) was immobilized on a N -hydroxysuccinimide(NHS)-activated carboxylic acid modified electrode prepared by the treatment of a gold electrode with 3,3′-dithiodipropionic acid, followed by NHS and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). An electrochemical measurement using this mRNA electrode was carried out in an electrolyte containing ferrocenylnaphthalene diimide ( 1 ), and showed an electrochemical signal based on 1 concentrated on immobilized mRNA. After treating this electrode with water containing varied amounts of ribonuclease A (RNase A), the current peak based on 1 decreased with increasing in the amount of RNase A with a linear correlation in the range of 0.2 - 10 pg of RNase A.
The Effect of Hairpin Structure on PCR Amplification Efficiency

Design of primers for efficient DNA amplification using polymerase chain reaction is critical. Therefore, evaluation of hairpin structures while designing position dependent primers needs special attention. Here, we present the data on the effect of hairpins on DNA amplification using polymerase chain reaction. X-antigen of Hepatitis B Virus has been used as a model. Studies showed that hairpin loop with less than three complementary nucleotides did not have any effect whereas primer length is directly proportional to the hairpin size. Most important characteristic of hairpin structure affecting the amplification is loop size. There should be no complementarity among the primers at their 3' end because this greatly increases the possibility of spurious products by amplifying themselves, thereby, decreasing the amplification efficiency. Hairpin structures greatly affect the primer designing theory having direct relation to amplification.
Esophagitis in children: an update on current pharmacotherapy

Introduction: A common diagnostic entity in children is Esophagitis with multiple etiologies and complex immuno-pathogenic mechanisms. Our understanding of these mechanisms and of the pharmacotherapy of esophagitis is still evolving. Areas covered: Areas of focus for this review were chosen based on recent clinical practice and research interest in esophagitis in infants and children. A literature search was conducted with the relevant keywords (‘gastroesophageal reflux disease' in pediatric age group, ‘eosinophilia', ‘esophageal eosinophilia', ‘esophagitis', ‘eosinophilic esophagitis', ‘proton pump inhibitors'). Use, safety and efficacy of proton pump inhibitors in young infants and older children, the concepts of esophageal eosinophilia and overlap of reflux and eosinophilic esophagitis are discussed here. Expert opinion: Proton pump inhibitors are effective in healing reflux esophagitis in children of all ages but do not improve gastroesophageal reflux related symptoms in infants. An overlap in clinical and histological features of reflux and eosinophilic esophagitis exists, and proton pump inhibitors may exert their action in pathways other than just acid suppression. The role of weakly acidic/alkaline reflux in gastroesophageal reflux symptoms, development of newer reflux modifying medications and tools to assess efficacy of therapeutic intervention in eosinophilic esophagitis are promising areas for further research and developing knowledge.
MULTIPLE-INTERNAL-REFLECTION POLY(DIMETHYLSILOXANE) SYSTEMS FOR ON-LINE pH MONITORING

We present an improved method for on-line pH monitoring in nL-to-�L volumes of complex cell medium using two different multiple-internal-reflection photonic systems. Preliminary absorbance tests of the complex culture medium showed significant peaks at two different wavelengths (450 and 560 nm) due to the presence of phenol red pH indicator. This observed absorbance may be exploited for non-invasive optical monitoring applications. A full characterization of the photonic systems using a surrogate culture medium yielded a maximum sensitivity of 0.20 ± 0.00 and lowest LOD of 0.04 ± 0.00 pH units in the pH range between 6 and 8 (standard in mammalian cell culture).
Mobile Self-Splicing Group I Introns from thepsbA Gene of Chlamydomonas reinhardtii: Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter

ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.
Smad-interacting Protein 1 Is a Repressor of Liver/Bone/Kidney Alkaline Phosphatase Transcription in Bone Morphogenetic Protein-induced Osteogenic Differentiation of C2C12 Cells*

Up-regulation of liver/bone/kidney alkaline phosphatase (LBK-ALP) has been associated with the onset of osteogenesis in vitro. Its transcription can be up-regulated by bone morphogenetic proteins (BMPs), constitutively active forms of their cognate receptors, or appropriate Smads. The promoter of LBK-ALP has been characterized partially, but not much is known about its transcriptional modulation by BMPs. A few Smad-interacting transcriptional factors have been isolated to date. One of them, Smad-interacting protein 1 (SIP1), belongs to the family of two-handed zinc finger proteins binding to E2-box sequences present, among others, in the promoter of mouse LBK-ALP. In the present study we investigated whether SIP1 could be a candidate regulator of LBK-ALP transcription in C2C12 cells. We demonstrate that SIP1 can repress LBK-ALP promoter activity induced by constitutively active Alk2-Smad1/Smad5 and that this repression depends on the binding of SIP1 to the CACCT/CACCTG cluster present in this promoter. Interestingly, SIP1 and alkaline phosphatase expression domains in developing mouse limb are mutually exclusive, suggesting the possibility that SIP1 could also be involved in the transcriptional regulation of LBK-ALP in vivo. Taken together, these results offer an intriguing possibility that ALP up-regulation at the onset of BMP-induced osteogenesis could involve Smad/SIP1 interactions, resulting in the derepression of that gene.