Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 1 Bioremediation of Polluted Waters Using Microorganisms

Water pollution is an issue of great concern worldwide, and it can be broadly divided into three main categories, that is, contamination by organic compounds, inorganic compounds (e.g., heavy metals), and microorganisms. In recent years, the number of research studies concerning the use of efficient processes to clean up and minimize the pollution of water bodies has been increasing. In this context, the use of bioreme‐ diation processes for the removal of toxic metals from aqueous solutions is gaining considerable attention. Bioremediation can be defined as the ability of certain biomolecules or types of biomass to bind and concentrate selected ions or other molecules present in aqueous solutions. Bioremediation using microorganisms shows great potential for future development due to its environmental compatibility and possible cost-effectiveness. A wide range of microorganisms, including bacteria, fungi, yeasts, and algae, can act as biologically active methylators, which are able to at least modify toxic species. Many microbial detoxification processes involve the efflux or exclusion of metal ions from the cell, which in some cases can result in high local concentrations of metals at the cell surface, where they can react with biogenic ligands and precipitate. Although microorganisms cannot destroy metals, they can alter their chemical properties via a surprising array of mechanisms. The main purpose of this chapter is to provide an update on the recent literature concerning the strategies available for the remediation of metal-contaminated water bodies using microorganisms and to critically discuss their main advantages and weaknesses. The focus is on the heavy metals associated with environmental contamination, for © 2015 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. instance, lead (Pb), cadmium (Cd), and chromium (Cr), which are potentially hazardous to ecosystems. The types of microorganisms that are used in bioremedia‐ tion processes due to their natural capacity to biosorb toxic heavy metal ions are discussed in detail. This chapter summarizes existing knowledge on various aspects of the fundamentals and applications of bioremediation and critically reviews the obstacles to its commercial success and future perspectives.
Genetic and molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a cysteine protease

Upon delivery to the plant cell during infection, the Pseudomonas syringae effector protein AvrRpt2 undergoes proteolytic processing, enhances pathogen virulence and causes the elimination of the Arabidopsis RIN4 protein. A structure‐prediction method was employed in order to investigate possible biochemical functions of AvrRpt2. Results of a secondary structure prediction algorithm suggest that the functional C‐terminal portion of AvrRpt2 is a cysteine protease. Mutation of predicted catalytic residues within this portion of AvrRpt2 abolished in planta processing, elimination of Arabidopsis RIN4, and the ability to trigger an RPS2‐specific resistance response. These data indicate that AvrRpt2 is most likely a sequence divergent cysteine protease whose activity is required for elimination of RIN4 during infection.
Inhibition of growth and guanylate cyclase activity of an undifferentiated prostate adenocarcinoma by an extract of the balsam pear (Momordica charantia abbreviata).

We have recently described the presence of a guanylate cyclase [GTP pyrophosphate-lyase (cyclizing), EC 4.6. 1.2] inhibitor (GCI) in an aqueous extract of the balsam pear (Momordica charantia abbreviata). Because the guanylate cyclase-cyclic GMP system is though to be involved in cell growth, DNA and RNA synthesis, and possible malignant transformation, we examined the effect of the aqueous extract containing GCI on an undifferentiated adenocarcinoma of the rat prostate and concanavalin-A-stimulated [3H]thymidine incorporation into cultured splenic lymphocytes, a process thought to be mediated by cyclic GMP. The results demonstrate that the extract of the balsam pear blocks both the growth of the rat prostatic adencarcinoma in vitro and [3H]thymidine incorporation into DNA. DNA histograms from flow cytometry indicated that the extract containing GCI inhibited in the G2 + M phase of the cell cycle, a presumed locus of cyclic GMP effects. In addition, guanylate cyclase activity was significantly greater in the tumor than normal prostate tissue and was decreased by the extract containing GCI. Cyclic GMP levels in the tumor in culture wer also decreased by addition of the extract. It remains to be determined whether or not the anti-tumor agent and GCI are the same substance.
Defect formation and crossover behavior in the dynamic scaling properties of molecular-beam epitaxy.

Stochastic simulation results, appropriate for molecular-beam epitaxy, involving ballistic deposition and thermally activated Arrhenius diffusion of adatoms, are presented for one- and two-dimensional substrates, allowing for overhangs and bulk vacancies. The asymptotic Kardar-Parisi-Zhang universality is found to be triggered by a sudden nucleation of large-scale defect formation in the growing film that shows a distinct dependence on dimensionality. The prenucleation transient behavior, which may be of experimental relevance due to the low defect content, is associated with standard solid-on-solid univerality classes.
Bootstrapping of a Multilingual Transliteration Dictionary for European Languages

Transliteration dictionaries are an important resource for the development of machine transliteration systems. The paper describes and analyses a large multilingual transliteration dictionary extracted from probabilistic dictionaries for 24 European languages containing approximately 1.25 million transliterated word pairs. The transliteration dictionary is evaluated: 1) manually for the LatvianEnglish language pair and 2) automatically within a statistical machine translation based transliteration task for all 23 language pairs.
110 The mechanism of the specific protein-DNA interactions during DNA lesion search and damaged base recognition by Endonuclease VIII

protein-DNA interactions during DNA lesion search and damaged base recognition by Endonuclease VIII N.A. Kuznetsov*, O.A. Kladova, A.A. Kuznetsova and O.S. Fedorova Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia *Email: Nikita.Kuznetsov@niboch.nsc. ru, Phone: +7-383-3635174
In vitro tests for aerosol deposition. I: Scaling a physical model of the upper airways to predict drug deposition variation in normal humans.

BACKGROUND In vitro-in vivo correlations (IVIVCs) are needed to relate in vitro test results for deposition to mean data from clinical trials, as well as the extremes in a population. Because drug deposition variations are related to differences in airway dimensions and inhalation profiles, this article describes the development and validation of models and methods to predict in vivo results. METHODS Three physical models of the upper airways were designed as small, medium, and large versions to represent 95% of the normal adult human population. The physical dimensions were validated by reference to anatomy literature. The models were constructed by rapid prototyping, housed in an artificial thorax, and used for in vitro testing of drug deposition from 200 μg Budelin Novolizers using a breath simulator to mimic the inhalation profiles used in the clinic. In vitro results were compared to those reported in vivo. RESULTS The "average" model was scaled to produce "small" and "large" versions by multiplying linear dimensions by 0.748 or 1.165, respectively, based on reports of the mean and standard deviation of airway volume across a normal adult population. In vitro deposition variation under fixed test conditions was small. Testing in the model triplet however, using air flow rate versus time profiles based on the mean and the extremes reported in the clinic, produced results for total lung deposition (TLD) in vitro consistent with the complete range of drug deposition results reported in vivo. The effects of variables such as flow rate in vitro were also predictive of in vivo deposition. CONCLUSIONS A new in vitro test method is described to predict the median and range of aerosol drug deposition seen in vivo. The method produced an IVIVC that was consistent with 1:1 predictions of total lung deposition from a marketed powder inhaler in trained normal adults.
Low-Voltage Steep Turn-On pMOSFET Using Ferroelectric High- $\kappa$ Gate Dielectric

Power consumption is the most difficult challenge for CMOS integrated circuits. Here, we demonstrate experimentally a novel steep turn-on pMOSFET for low-voltage operation for the first time, which exhibits 5-60 mV/decade SS, wide voltage range for , sturdy SS at 85°C, faster transistor turn-on at above threshold voltage, and lower off-state leakage by greater than three orders of magnitude. Such improved leakage current is crucial to decrease the OFF-state leakage current in sub-1X nm CMOS. This was achieved using ferroelectric high-κ ZrHfO gate dielectric pMOSFET.
Differences between bispectral index and spectral entropy during xenon anaesthesia: a comparison with propofol anaesthesia

We enrolled 114 patients, aged 65–83 years, undergoing elective surgery (duration > 2h) into a randomised, controlled study to evaluate the performance of bispectral index and spectral entropy for monitoring depth of xenon versus propofol anaesthesia. In the propofol group, bispectral index and state entropy values were comparable. In the xenon group, bispectral index values resembled those in the propofol group, but spectral entropy levels were significantly lower. Mean arterial blood pressure was higher and heart rate was lower in the xenon group than in the propofol group. Bispectral index and spectral entropy considerably diverged during xenon but not during propofol anaesthesia. We therefore conclude that these measures are not interchangeable for the assessment of depth of hypnosis and that bispectral index is likely to reflect actual depth of anaesthesia more precisely compared with spectral entropy.
High nontransferrin bound iron levels and heart disease in thalassemia major

Although the presence of nontransferrin bound plasma iron (NTBI) in transfusional iron overload is well documented, knowledge about its clinical significance is limited. We assessed NTBI levels in a large and homogeneous series of thalassemia patients on regular transfusion and chelation and explored the hypothesis that NTBI levels may be associated with relevant clinical outcomes: in particular, heart disease. Among 174 patients with thalassemia major and intermedia, we showed the presence NTBI in 145 of 174 or 83.3% of cases. NTBI levels correlated with transferrin saturation, age, and ALT, and not with serum ferritin or liver iron concentrations. At a multiple regression analysis, transferrin saturation and heart disease but not age was independent predictors of NTBI. Patients with heart disease had NTBI levels significantly higher than those without. All patients with heart disease had transferrin saturation above 70%, and all were NTBI positive. Conversely, none of the patients without NTBI and/or with transferrin saturation less than 70% had preclinical or clinical heart disease. To our knowledge, this is the first documentation of a link between the presence of NTBI in thalassemic patients with transfusional iron overload and heart disease. Further investigation from these preliminary findings may clarify whether NTBI assessment may have a role in evaluating the risks and optimizing treatment for transfusion‐dependent patients. Am. J. Hematol. , 2009. © 2008 Wiley‐Liss, Inc.
Text modeling in adaptive educational chat room based on Madamira tool

This paper discusses how to enhance the ability of text modeling in Arabic during chat sessions. Hanini and Jabari et al. modeled the text in chat sessions, but there is still a problem when using Arabic, because the Arabic language is very difficult to comprehend, has complex derivative and many ambiguities. This paper enhanced the previous study and added MADAMIRA tool to analyze the Arabic text. Monitoring and modeling has been completed through the text modeling process by evaluating the student expressions within the chat session using MADAMIRA tool and machine learning. MADAMIRA tool enables the modeling process to categorize Arabic text into different categories, which makes it easier to use the levels of the used expressions and discover the importance of the chat session between two peers. The process of the student modeling using MADAMIRA and Machine learning will update the student model which gathers information about the student achievements within the AVCM.
Correction: Archaeal Tuc1/Ncs6 Homolog Required for Wobble Uridine tRNA Thiolation Is Associated with Ubiquitin-Proteasome, Translation, and RNA Processing System Homologs

Ap, ampicillin resistance; Nv, novobiocin resistance; flag‐, N‐terminal Flag‐tag coding sequence; ‐strepII, C‐terminal StrepII coding sequence. Plasmids were constructed as follows: The QuikChange Lightning site directed mutagenesis kit (Agilent Technologies) was used to generate plasmids pJAM1111 and pJAM1118 by PCR with primers P11/P12 and pJAM1111 (Flag‐SAMP2K64R) as template and primers P13/P14 and pJAM949 as template, respectively (See Table S2 for details on all primers used in this study). Plasmid pJAM1910 was generated by T4 DNA ligation of DNA fragments generated by PCR with primer pairs P1/P2 and P3/P4 with Hfx. volcanii DS70 genomic DNA as template into the KpnI‐XhoI‐XbaI sites of pTA131. Plasmid pJAM2812 was generated by T4 DNA ligation of a PCR product encoding NcsA (with primer pairs P5/P5 and Hfx. volcanii DS70 genomic DNA as template) into the NdeI to KpnI sites of plasmid pJAM809. DNA fragment containing nscA‐strepII of pJAM2812 was isolated by restriction enzyme digestion with BamHI and BlpI and blunt‐end ligated into the BlpI site of pJAM947 to generate pJAM2813, pJAM949 to generate pJAM2814, and pJAM1118 to generate pJAM2818. Plasmid pJAM555 was generated by T4 DNA ligation of a 1.9 kb DNA fragment encoding aCSPF generated by PCR with primers P9/P10 and Hfx. volcanii DS70 genomic DNA into the KpnI to BlpI sites of pJAM947. Plasmid pJAM556 was generated by T4 DNA ligation of 1.1 kb NdeI to BlpI DNA fragment of pJAM2812 carrying ncsA into the BlpI site of pJAM555 by treating DNA with Klenow DNA polymerase prior to ligation. Fidelity of all PCR products ligated into plasmids was confirmed by Sanger DNA sequencing (UF ICBR Sequencing Core). Strain, plasmid Description Source or reference E. coli strains:
Case Report Niemann-Pick disease: report of two cases and review of literature

Niemann-Pick Disease (NPD) refers to a group of disorders with deficiency in lipid storage, causing accu - mulation of fats in brain and liver that lead to serious damage or dysfunction of mentioned tissues. Its pathogenesis is still unclear, very rarely it has been associated with genetic disorders. Herein we report two cases: one is a 5-year- old boy and another is a 23-year-old woman.
Keratinocyte growth factor accelerates wound closure in airway epithelium during cyclic mechanical strain

The airway epithelium may be damaged by inhalation of noxious agents, in response to pathogens, or during endotracheal intubation and mechanical ventilation. Maintenance of an intact epithelium is important for lung fluid balance, and the loss of epithelium may stimulate inflammatory responses. Epithelial repair in the airways following injury must occur on a substrate that undergoes cyclic elongation and compression during respiration. We have previously shown that cyclic mechanical strain inhibits wound closure in the airway epithelium (Savla and Waters, 1998b). In this study, we investigated the stimulation of epithelial wound closure by keratinocyte growth factor (KGF) in vitro and the mechanisms by which KGF overcomes the inhibition due to mechanical strain. Primary cultures of normal human bronchial epithelial cells (NHBE) and a cell line of human airway epithelial cells, Calu 3, were grown on Silastic membranes, and a wound was scraped across the well. The wells were then exposed to cyclic strain using the Flexercell Strain Unit, and wound closure was measured. While cyclic elongation (20% maximum) and cyclic compression (∼2%) both inhibited wound closure in untreated wells, treatment with KGF (50 ng/ml) significantly accelerated wound closure and overcame the inhibition due to cyclic strain. Since wound closure involves cell spreading, migration, and proliferation, we investigated the effect of cyclic strain on cell area, cell‐cell distance, and cell velocity at the wound edge. While the cell area increased in unstretched monolayers, the cell area of monolayers in compressed regions decreased significantly. Treatment with KGF increased the cell area in both cyclically elongated and compressed cells. Also, when cells were treated with KGF, cell velocity was significantly increased in both static and cyclically strained monolayers, and cyclic strain did not inhibit cell migration. These results suggest that KGF is an important factor in epithelial repair that is capable of overcoming the inhibition of repair due to physiological levels of cyclic strain. J. Cell. Physiol. 181:424–432, 1999. © 1999 Wiley‐Liss, Inc.
Smoking habits in the randomised Danish Lung Cancer Screening Trial with low-dose CT: final results after a 5-year screening programme

Background We present the final results of the effect of lung cancer screening with low-dose CT on the smoking habits of participants in a 5-year screening trial. Methods The Danish Lung Cancer Screening Trial (DLCST) was a 5-year screening trial that enrolled 4104 subjects; 2052 were randomised to annual low-dose CT (CT group) and 2052 received no intervention (control group). Participants were current and ex-smokers (≥4 weeks abstinence from smoking) with a tobacco consumption of ≥20 pack years. Smoking habits were determined annually. Missing values for smoking status at the final screening round were handled using two different models. Results There were no statistically significant differences in annual smoking status between the CT group and control group. Overall the ex-smoker rates (CT + control group) significantly increased from 24% (baseline) to 37% at year 5 of screening (p<0.001). The annual point prevalence quit rate increased from 11% to 24% during the five screening rounds; the ex-smokers’ relapse rate remained stable, around 11%, across the same period. Conclusions Screening with low-dose CT had no extra effect on smoking status compared with the control group, but overall the screening programme probably promoted smoking cessation. Clinical Trial Registration: The DLCST is registered in Clinical Trials.gov Protocol Registration System (identification no. NCT00496977).
Differential variations in Ca2+ entry, cytosolic Ca2+ and membrane capacitance upon steady or action potential depolarizing stimulation of bovine chromaffin cells

Aims: This study looks into the physiology of the exocytosis of catecholamines released by adrenal medullary chromaffin cells. We have comparatively explored the exocytotic responses elicited by two different patterns of depolarizing stimulation: the widely employed square depolarizing pulses (DPs) and trains of acetylcholine‐like action potentials (APs), likely the physiological mode of stimulation in the intact innervated adrenal medulla. APs were applied at 30 Hz, a frequency similar to that produced in a stressful situation.
Parent–Child Interaction Therapy in a Community Setting: Examining Outcomes, Attrition, and Treatment Setting

Objectives: The purpose of this study was to evaluate Parent-Child Interaction Therapy (PCIT) deployed in a community setting comparing in-home with the standard office-based intervention. Child behavior, parent stress, parent functioning, and attrition were examined. Methods: Using a quasi-experimental design, standardized measures at three time points were collected from parent-child dyads (n=120) with thirty-seven families completing treatment. Results: Growth modeling analyses indicate significant improvements in child and parent outcomes in both treatment settings with more rapid improvements in parent outcomes within office-based treatment. Attrition was predicted by income and parent functioning. Conclusion: PCIT delivered in the community can produce measureable improvements. In-home PCIT is a feasible option but future research should consider benefits and costs. Treatment completion remains a challenge.
Coinfection with HIV an d hepatitis C virus in 229 children and young adults living in Europe The European Paediatric HIV / HCV Co-infection Study Group in the European Pregnancy and Paediatric HIV Cohort Collaboration ( EPPICC )

Results: Of 229 patients included, 142 (62%) had vertically acquired infection. Median age at last follow-up was 16.2 years. Most children had HCV genotype 1 (101/184, 55%) or 3 (57/184, 31%). One-fifth (46/214) had a previous AIDS diagnosis (data missing on prior AIDS diagnoses for 15). At their last clinic visit, 70% (145/208) had no/mild immunosuppression (Centers for Disease Control and Prevention stage 1), and 131 of 179 on antiretroviral therapy had undetectable HIV RNA (assay thresholds varied from <20 to <150 copies/ml). Overall, 42% (86/204) had hepatomegaly in the previous year, and 55% (116/213) had alanine aminotransferase more than 40 IU/l at their last test. Of 97 patients with transient elastography, 12 had results more than 9 kPa; this was associated with duration of HCV infection (P1⁄40.033), but not with CD4þ cell count, antiretroviral therapy use or sex in univariable analysis. Of 17 patients with liver biopsies, six had bridging fibrosis and one had cirrhosis. Twenty-five (11%) had been treated successfully for HCV.
Surveillance of Parapoxvirus Among Ruminants in Virginia and Connecticut

In 2008, two deer hunters in Virginia and Connecticut were infected with a unique strain of pseudocowpox virus, a parapoxvirus. To estimate the prevalence of this virus, and in an attempt to define the reservoir, Parapoxvirus surveillance was undertaken between November 2009 and January 2010. 125 samples from four ruminant species (cows, goat, sheep and white‐tailed deer) were collected in Virginia, and nine samples from white‐tailed deer were collected in Connecticut. We found no evidence that the parapoxvirus species that infected the deer hunters is circulating among domesticated ruminants or white‐tailed deer. However, parapoxvirus DNA of a different parapoxvirus species, bovine papular stomatitis virus (BPSV), was detected in 31 samples obtained from asymptomatic cattle in Virginia. Parapoxvirus DNA–positive cattle originated from the same counties indicating probable transmission among animals. Molecular analysis identified BPSV as the parapoxvirus affecting animals. Asymptomatic parapoxvirus infections in livestock, particularly young animals, may be common, and further investigation will inform our knowledge of virus transmission.