Miracle-dz/UniFAR-FTUs huggingface dataset:
Error-Prone Translesion DNA Synthesis by Escherichia coli DNA Polymerase IV (DinB) on Templates Containing 1,2-dihydro-2-oxoadenine

Escherichia coli DNA polymerase IV (Pol IV) is involved in bypass replication of damaged bases in DNA. Reactive oxygen species (ROS) are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ROS induce various kinds of base damage in DNA. It is important to examine whether Pol IV is able to bypass oxidatively damaged bases. In this study, recombinant Pol IV was incubated with oligonucleotides containing thymine glycol (dTg), 5-formyluracil (5-fodU), 5-hydroxymethyluracil (5-hmdU), 7,8-dihydro-8-oxoguanine (8-oxodG) and 1,2-dihydro-2-oxoadenine (2-oxodA). Primer extension assays revealed that Pol IV preferred to insert dATP opposite 5-fodU and 5-hmdU, while it inefficiently inserted nucleotides opposite dTg. Pol IV inserted dCTP and dATP opposite 8-oxodG, while the ability was low. It inserted dCTP more effectively than dTTP opposite 2-oxodA. Pol IV's ability to bypass these lesions decreased in the order: 2-oxodA > 5-fodU~5-hmdU > 8-oxodG > dTg. The fact that Pol IV preferred to insert dCTP opposite 2-oxodA suggests the mutagenic potential of 2-oxodA leading to A:T→G:C transitions. Hydrogen peroxide caused an ~2-fold increase in A:T→G:C mutations in E. coli, while the increase was significantly greater in E. coli overexpressing Pol IV. These results indicate that Pol IV may be involved in ROS-enhanced A:T→G:C mutations.
Molecular profiling of endometrial carcinoma precursor, primary and metastatic lesions suggests different targets for treatment in obese compared to non-obese patients

Obesity is linked to increased incidence of endometrioid endometrial cancer (EEC) and complex atypical hyperplasia (CAH). We here explore pattern and sequence of molecular alterations characterizing endometrial carcinogenesis in general and related to body mass index (BMI), to improve diagnostic stratification and treatment strategies. We performed molecular characterization of 729 prospectively collected EEC and CAH. Candidate biomarkers were identified in frozen samples by whole-exome and Sanger sequencing, oligonucleotide gene expression and Reverse Phase Protein Arrays (investigation cohort) and further explored in formalin fixed tissues by immunohistochemistry and Fluorescent in Situ Hybridization (validation cohort). We here demonstrate that PIK3CA mutations, PTEN loss, PI3K and KRAS activation are early events in endometrial carcinogenesis. Molecular changes related to KRAS activation and inflammation are more common in obese CAH patients, suggesting different prevention and systemic treatment strategies in obese and non-obese patients. We also found that oncoprotein Stathmin might improve preoperative diagnostic distinction between premalignant and malignant endometrial lesions.
Wavelet Feature Extraction for the Recognition and Verification of Handwritten Numerals

Two kinds of wavelet features are proposed: (a) Kirsch edge enhancement based 2D wavelets and (b) 2D complex wavelets. The two sets of hybrid features are congregated by combining them with the geometrical features for the recognition of handwritten numerals. Experiments conducted on handwritten numeral recognition and verification show that the two hybrid feature sets can achieve high recognition and verification performance. In addition, the merits of the proposed wavelet feature extraction methods are discussed.
Not only priming: Soil microbiota may protect tomato from root pathogens

Abstract An increasing number of studies have investigated soil microbial biodiversity. However, the mechanisms regulating plant responses to soil microbiota are largely unknown. A previous work tested the hypothesis that tomato plants grown on native soils with their complex microbiotas respond differently from tomato growing in a sterile substrate. Two soils, suppressive or conducive to Fusarium oxysporum f. sp. lycopersici (FOL), and two genotypes susceptible and resistant to the same pathogen were considered. The work highlighted that the two tested soil microbiotas, irrespectively of their taxonomic composition, elicit the PAMP-triggered Immunity Pathway, the first level of plant defence, as well as an increased lignin synthesis, leading to an active protection when FOL is present in the soil. Here, we tested the expression of a panel of genes involved in Effector-Triggered Immunity (ETI), demonstrating that soil microbiota, beside genotype, affects plant resistance to FOL also modulating this pathway.
A Feasible Power Saving Scheduling Approach in WiMAX 802 . 16 e Networks

IEEE 802.16 is a novel broadband wireless access standard. Quality of service (QoS) guarantee and power saving are two important factor in IEEE 802.16 standard. Unsolicited grant service (UGS) is a constant bit rate QoS service and is defined in IEEE 802.16 standard. Power saving classes of type II (PSCs-II) is provided in IEEE 802.16 standard for repeat fixed active and sleep frames. However, IEEE 802.16 standard does not define how to develop an approach for power saving. This paper aims to provide a solution that provides a power saving schedule for one mobile station with multi UGS connections. The proposed approach is named Bucket Checker (BC) that follows the IEEE 802.16 standard definitions, UGS and PSCs-II. In addition, BC aims to provide a best power saving efficiency. By the numerical results, it shows that the proposed approach has better power saving efficiency and always follows QoS requirements. Key-Words: WiMAX, 802.16, power saving, schedule, UGS, PSCs
Avatar and Extended Self in Online Gaming

Meyers-Levy, John and Durairaj Maheswaran (2004), “Exploring Message Framing Outcomes When Systematic, Heuristic or Both Types of Processing Occur,” Journal of Consumer Psychology, 14(1-2), 159-167. and Laura A. Peracchio (1996), “Moderators of the Impact of Self-Reference on Persuasion,” Journal of Consumer Research, 22(March), 408-423. Otker, Ton and Peter Hayes (1987), “Judging the Efficiency of Sponsorship,” European Research, 15 (4), 53-8. Pham, Michel Tuan (1992), “Effects of Involvement, Arousal, and Pleasure on the Recognition of Sponsorship Stimuli,” Advances in Consumer Research, 19, 85-93. Smith, Gareth (2004), “Brand Image Transfer through Sponsorship: A Consumer Learning Perspective,” Journal of Marketing Management, 20, 457-474. Speed, Richard and Peter Thompson (2000), “Determinants of Sports Sponsorship Response,” Journal of The Academy of Marketing Science. 28 (2), 226-238. Walliser, Bjorn (2003), “An International Review of Sponsorship Research: Extension and Update,” International Journal of Advertising, 22 (1), 5–40. Zeithaml, Valarie A. (1988), “Consumer Perceptions of Price, Quality, and Value: A Means-End Model and Synthesis of Evidence,” Journal of Marketing, 52 (July), 2-22.
Magnetic Fields and the Triaxiality of Molecular Cloud Cores

We make the hypothesis that molecular cloud fragments are triaxial bodies with a large-scale magnetic field oriented along the short axis. While consistent with theoretical expectations, this idea is supported by magnetic field strength data, which show strong evidence for flattening along the direction of the mean magnetic field. It is also consistent with early submillimeter polarization data, which show that the projected direction of the magnetic field is often slightly misaligned with the projected minor axis of a molecular cloud core; i.e., the offset angle Ψ is nonzero. We calculate distributions of Ψ for various triaxial bodies, when viewed from a random set of viewing angles. The highest viewing probability always corresponds to Ψ = 0°, but there is a finite probability of viewing all nonzero Ψ, including even Ψ = 90°; the average offset typically falls in the range of 10°-30° for triaxial bodies most likely to satisfy observational and theoretical constraints.
Regulation of Radial Glial Survival by Signals from the Meninges

Radial glial cells (RGCs) in the developing cerebral cortex are progenitors for neurons and glia, and their processes serve as guideposts for migrating neurons. So far, it has remained unclear whether RGC processes also control the function of RGCs more directly. Here, we show that RGC numbers and cortical size are reduced in mice lacking β1 integrins in RGCs. TUNEL stainings and time-lapse video recordings demonstrate that β1-deficient RGCs processes detach from the meningeal basement membrane (BM) followed by apoptotic death of RGCs. Apoptosis is also induced by surgical removal of the meninges. Finally, mice lacking the BM components laminin α2 and α4 show defects in the attachment of RGC processes at the meninges, a reduction in cortical size, and enhanced apoptosis of RGC cells. Our findings demonstrate that attachment of RGC processes at the meninges is important for RGC survival and the control of cortical size.
OH regeneration from methacrolein oxidation investigated in the atmosphere simulation chamber SAPHIR

Abstract. Hydroxyl radicals (OH) are the most important reagent for the oxidation of trace gases in the atmosphere. OH concentrations measured during recent field campaigns in isoprene-rich environments were unexpectedly large. A number of studies showed that unimolecular reactions of organic peroxy radicals (RO2) formed in the initial reaction step of isoprene with OH play an important role for the OH budget in the atmosphere at low mixing ratios of nitrogen monoxide (NO) of less than 100 pptv. It has also been suggested that similar reactions potentially play an important role for RO2 from other compounds. Here, we investigate the oxidation of methacrolein (MACR), one major oxidation product of isoprene, by OH in experiments in the simulation chamber SAPHIR under controlled atmospheric conditions. The experiments show that measured OH concentrations are approximately 50% larger than calculated by the Master Chemical Mechanism (MCM) for conditions of the experiments (NO mixing ratio of 90 pptv). The analysis of the OH budget reveals an OH source that is not accounted for in MCM, which is correlated with the production rate of RO2 radicals from MACR. In order to balance the measured OH destruction rate, 0.77 OH radicals (1σ error: ± 0.31) need to be additionally reformed from each reaction of OH with MACR. The strong correlation of the missing OH source with the production of RO2 radicals is consistent with the concept of OH formation from unimolecular isomerization and decomposition reactions of RO2. The comparison of observations with model calculations gives a lower limit of 0.03 s−1 for the reaction rate constant if the OH source is attributed to an isomerization reaction of MACR-1-OH-2-OO and MACR-2-OH-2-OO formed in the MACR + OH reaction as suggested in the literature (Crounse et al., 2012). This fast isomerization reaction would be a competitor to the reaction of this RO2 species with a minimum of 150 pptv NO. The isomerization reaction would be the dominant reaction pathway for this specific RO2 radical in forested regions, where NO mixing ratios are typically much smaller.
ELECTRONIC STRUCTURE AND SPECTROSCOPY OF CADMIUM THIOLATE CLUSTERS

The singly excited configuration interaction (CIS) approximation and the CNDO model Hamiltonian have been employed to calculate the optical spectra of [Cd(SPh)4]2-, [Cd2(SPh)6]2-, and [Cd4(SPh)10]2- and the artificial defect models [Cd2(SPh)5]- and [Cd4(SPh)9]- (Ph = phenyl). The electronic transitions have been characterized by evaluating changes in orbital electron population between ground and excited states; this allows clear assignment of the nature of the optical transitions. The simulated spectra are able to reproduce well the main features of experimental optical transition bands. The lowest energy bands for the first three compounds are due to both intraligand and ligand-to-metal charge transfer transitions. The terminal thiolate levels lie insignificantly higher in energy than the bridging ones. Both experimental and simulated spectra show a blue shift with increasing sizes, directly opposed to simple predictions based on quantum confinement. This can be explained by the Jahn−Teller effect. Inco.
Phase 1 study of the PI3Kδ inhibitor INCB040093 ± JAK1 inhibitor itacitinib in relapsed/refractory B-cell lymphoma.

Because both phosphatidylinositol 3-kinase δ (PI3Kδ) and Janus kinase (JAK)-signal transducer and activator of transcription pathways contribute to tumor cell proliferation and survival in B-cell malignancies, their simultaneous inhibition may provide synergistic treatment efficacy. This phase 1 dose-escalation/expansion study assessed the safety, efficacy, pharmacokinetics, and pharmacodynamics of INCB040093, a selective PI3Kδ inhibitor, as monotherapy or combined with itacitinib (formerly INCB039110), a selective JAK1 inhibitor, in adult patients with relapsed or refractory (R/R) B-cell lymphomas. Final results are reported. Overall, 114 patients were treated (monotherapy, n = 49; combination therapy, n = 72 [7 patients crossed over from monotherapy to combination]). INCB040093 100 mg twice daily (monotherapy) and INCB040093 100 mg twice daily + itacitinib 300 mg once daily (combination) were the recommended phase 2 doses. One dose-limiting toxicity (gastrointestinal bleed secondary to gastric diffuse large B-cell lymphoma [DLBCL] regression) occurred with monotherapy. The most common serious adverse events with monotherapy were pneumonia (n = 5) and pyrexia (n = 4), and with combination Pneumocystis jiroveci pneumonia (n = 5), pneumonia (unrelated to P jiroveci; n = 5), and pyrexia (n = 4). Grade 3 or higher transaminase elevations were less common with combination. INCB040093 was active across the B-cell lymphomas; 63% of patients (5/8) with follicular lymphoma responded to monotherapy. Adding itacitinib provided promising activity in select subtypes, with responses of 67% (14/21) in classic Hodgkin lymphoma (vs 29% [5/17] with monotherapy) and 31% (4/13) in nongerminal center B-cell-like DLBCL. INCB040093 with/without itacitinib was tolerated and active in this study, and is a promising treatment strategy for patients with select R/R B-cell lymphomas. This trial was registered at www.clinicaltrials. gov as #NCT01905813.
Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience

Noble metal quantum clusters (NMQCs) are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature.
Ultrasound-guided Supraclavicular Brachial Plexus Block

Purpose: To evaluate the effect of adding dexamethasone 5mg or dexmedetomedine 1ug/kg on levobupivacaine action during ultrasound guided supraclavicular brachial plexus block technique. Material and Methods: In this prospective randomaized double blind clinical study, 120 patients were equally divided into four groups according to the injectate LA into: Group B: 30ml of bupivacaine 0.25%. Group L: 30ml of levobupivacaine 0.25%. Group L +D: 30ml of levobupivacaine 0.25% + 5mg of dexamethasone. Group L + DEX: 3 0ml of levobupivacaine 0.25% + 1ug/kg of dexmedetomedine. All patients had recievied single shot ultrasound guided supraclavicular brachial plexus block with using nerve stimulation. Parameters recorded in the study include the following: Onset and duration of both sensory and motor block and duration of analgesia. Haemodynamic changes (blood pressure and heart rate) and a verbal numerical pain rating scale (V.N.P.R.S.) during the first 24 hours. Serum cortisol level at 1 and 4 hour post injection. Total analgesic requirements calculated. Any evidence of complication. The patients satisfaction with the anesthetic technique was assessed. Data were analyzed with the paired sample t-test, analysis of variance ANOVA, post hoc test and the Chi-square test. p<0.05 was considered statistically significant. p<0.00 1 was considederd highly significant. Results: Regarding onset of sensory and motor block there was high significance between the four groups being shorter onset of block in Group L, Group L +D and Group L +DEX than Group B with no significance in between Group L, Group L +D and Group L + DEX. The duration of sensory, motor block and the duration of analgesia were significantly longer in Group L +D than Group L + DEX, Group L and Group B respectively. Haemodynamics were better cotrolled in Group L +D and Group L + DEX than Group B and Group L but in Group L + DEX there was significant hypotension and decrease heart rate. Also pain scores were significantly low in Group L + D and Group L + DEX than Group L and Group B. Serum cortisol levels at 1 and 4 hours were non significantly changed in Group L + D and Group L + DEX denoting better suppression of stress reponse to surgery than Group L and Group B. Patients were satisfied with the anesthetic technique. Correspondence to: Dr. Hazem A. Essa, The Department of Anesthesiology, Faculty of Medicine, Benha University, Egypt Conclusions: The addition of dexamethasone or dexmedetomedine to levopubivacaine prolongs sensory and motor block duration and duration of analgesia with no effect on onset of block and better control of haemodynamics and serum cortisol.
U-model Based Adaptive Tracking Scheme for Unknown MIMO Bilinear Systems

Bilinear systems are attractive candidates for many dynamical processes, since they allow a significantly larger class of behaviour than linear systems, yet retain a rich theory which is closely related to the familiar theory of linear systems. A new technique for the control of unknown MIMO bilinear systems is introduced. The scheme is based on the U-model with identification based on radial basis functions neural networks which is known for mapping any nonlinear function. U-model is a control oriented model used to represent a wide range of non-linear discrete time dynamic plants. The proposed tracking scheme is presented and verified using simulation examples
Tratamientos actuales del trastorno por atracón

Introduction: Although binge eating disorder (bed) is a major health problem, less than half of sufferers receive treatment. Objective: To review recent literature on interventions carried out in bed cases. Method: In order to conduct this narrative review, the databases PubMed, Medline and Scielo have been consulted. Only articles in indexed journals in the Web of Science were chosen. The literature reviewed corresponds to the most cited articles published in the period between 2010-2015. Results and conclusions: The results show that the most commonly used interventions are those of psychological nature, including cognitive behavioral therapy and interpersonal therapy, the latter recommended in patients with a more severe pathology. The behavioral therapy for weight loss is less effective by not reducing binge eating; therefore, it is not the treatment of choice. Although some antidepressant and antiepileptic drugs have shown some utility in reducing binge eating, weight and comorbidities, there is no evidence that pharmacological intervention alone is more effective than psychological intervention, or that it improves the results of the latter when both are applied together.
Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants

It is assumed that microbial communities involved in the biological treatment of different wastewaters having a different chemical composition harbor different microbial populations which are specifically adapted to the environmental stresses encountered in these systems. Yet, little is known about the composition of these microbial communities. Therefore, the aim of this study was to assess the microbial community composition over two seasons (winter and summer) in activated sludge from well‐operating textile wastewater treatment plants (WWTPs) in comparison with municipal WWTPs, and to explain observed differences by environmental variables. 454‐pyrosequencing generated 160 archaeal and 1645 bacterial species‐level Operational Taxonomic Units (OTUs), with lower observed richness in activated sludge from textile WWTPs compared to municipal WWTPs. The bacterial phyla Planctomycetes, Chloroflexi, Chlorobi, and Acidobacteria were more abundant in activated sludge samples from textile WWTPs, together with archaeal members of Thaumarchaeota. Nonmetric multidimensional scaling analysis of the microbial communities showed that microbial communities from textile and municipal WWTPs were significantly different, with a seasonal effect on archaea. Nitrifying and denitrifying bacteria as well as phosphate‐accumulation bacteria were more abundant in municipal WWTPs, while sulfate‐reducing bacteria were almost only detected in textile WWTPs. Additionally, microbial communities from textile WWTPs were more dissimilar than those of municipal WWTPs, possibly due to a wider diversity in environmental stresses to which microbial communities in textile WWTPs are subjected to. High salinity, high organic loads, and a higher water temperature were important potential variables driving the microbial community composition in textile WWTPs. This study provides a general view on the composition of microbial communities in activated sludge of textile WWTPs, and may provide novel insights for identifying key players performing important functions in the purification of textile wastewaters.
Asymmetries in Long-Distance Extraction in a Tree-Adjoining Grammar

In recent papers (Kroch and Joshi 1985, Kroch 1987) we claimed that, if one adopts the Tree Adjoining Grammar (TAG) formalism of Joshi, Levi, and Takahashi (1975) as the formal language of syntax, the ungrammaticality of extractions from whislands can be made to follow in a straightforward way from the nonexistence of multiple whfronting in simple questions. The analysis we gave was oversimplified, however, because it wrongly predicted all whisland extractions to be ungrammatical, and we know that certain of them are well-formed, not only in languages like Swedish or Italian, but also in English (Chomsky 1986, Grimshaw 1986). Nevertheless, the analysis we gave had the attraction of providing a simple structural explanation for the whisland effect, and it generalized directly to such other manifestations of subjacency as the Complex Noun Phrase Constraint (CNPC). In this paper we show that the analysis presented in our earlier papers can be extended in a reasonable way to several cases that were unaccounted for in the original discussion. In particular, we discuss such well-known examples as the following: