Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Structural Flexibility of Damaged DNA Using Thiol-Tethered Oligonucleotide Duplexes

Bent structures are formed in DNA by the binding of small molecules or proteins. We developed a chemical method to detect bent DNA structures. Oligonucleotide duplexes in which two mercaptoalkyl groups were attached to the positions facing each other across the major groove were prepared. When the duplex contained the cisplatin adduct, which was proved to induce static helix bending, interstrand disulfide bond formation under an oxygen atmosphere was detected by HPLC analyses, but not in the non-adducted duplex, when the two thiol-tethered nucleosides were separated by six base pairs. When the insert was five and seven base pairs, the disulfide bond was formed and was not formed, respectively, regardless of the cisplatin adduct formation. The same reaction was observed in the duplexes containing an abasic site analog and the (6–4) photoproduct. Compared with the cisplatin case, the disulfide bond formation was slower in these duplexes, but the reaction rate was nearly independent of the linker length. These results indicate that dynamic structural changes of the abasic site- and (6–4) photoproduct-containing duplexes could be detected by our method. It is strongly suggested that the UV-damaged DNA-binding protein, which specifically binds these duplexes and functions at the first step of global-genome nucleotide excision repair, recognizes the easily bendable nature of damaged DNA.
Images encryption using AES and variable permutations

This work proposes a different procedure to encrypt images of 256 grey levels and colour, using the symmetric system Advanced Encryption Standard with a variable permutation in the first round, after the x-or operation. Variable permutation means using a different one for each input block of 128 bits. In this vein, an algorithm is constructed that defines a Bijective function between sets Nm = {n in N, 0 = 2 and Pm = {pi, pi is a permutation of 0, 1, . , m-1}. This algorithm calculates permutations on 128 positions with 127 known constants. The transcendental numbers are used to select the 127 constants in a pseudo-random way. The proposed encryption quality is evaluated by the following criteria: Correlation; horizontal, vertical and diagonal, Entropy and Discrete Fourier Transform. The latter uses the NIST standard 800-22. Also, a sensitivity analysis was performed in encrypted figures. Furthermore, an additional test is proposed which considers the distribution of 256 shades of the three colours; red, green and blue for colour images. On the other hand, it is important to mention that the images are encrypted without loss of information because many banking companies and some safety area countries do not allow the figures to go through a compression process with information loss. i.e., it is forbidden to use formats such as JPEG.
Periodic and Non Periodic (Complex) Behavior of a Model of Bioreactor With Cell Recycling

A structured model of bioreactor for an activated sludge process was presented. The stability and bifurcation characteristics of the model are investigated, the bifurcation analysis of the model shows static and complex dynamic behavior (periodic and complex) over a wide range of the model parameters. The model exhibits a new interesting behavior (in some range of parameters) including four static limit points (turning points) and two Hopf points, that cause different kinds and rich of stability characteristics ranging from asymptotically stable and hysteresis to periodic and complex behavior.
Human rhinovirus C: a newly discovered human rhinovirus species

Although often ignored, human rhinoviruses (HRVs) are the most frequent causes of respiratory tract infections (RTIs). A group of closely related novel rhinoviruses have recently been discovered. Based on their unique phylogenetic position and distinct genomic features, they are classified as a separate species, HRV-C. After their discovery, HRV-C viruses have been detected in patients worldwide, with a reported prevalence of 1.4–30.9% among tested specimens. This suggests that the species contribute to a significant proportion of RTIs that were unrecognized in the past. HRV-C is also the predominant HRV species, often with a higher detection rate than that of the two previously known species, HRV-A and HRV-B. HRV-C infections appear to peak in fall or winter in most temperate or subtropical countries, but may predominate in the rainy season in the tropics. In children, HRV-C is often associated with upper RTIs, with asthma exacerbation and wheezing episodes being common complications. The virus has also been detected in children with bronchitis, bronchiolitis, pneumonia, otitis media, sinusitis and systemic infections complicated by pericarditis. As for adults, HRV-C has been associated with more severe disease such as pneumonia and exacerbation of chronic obstructive pulmonary disease. However, larger clinical studies with asymptomatic controls are required to better define the significance of HRV-C infection in the adult population. On the basis of VP4 sequence analysis, a potential distinct subgroup within HRV-C has also been identified, although more complete genome sequences are needed to better define the genetic diversity of HRV-C.
TROPOMI/S5P total ozone column data: global ground-based validation and consistency with other satellite missions

Abstract. In October 2017, the Sentinel-5 Precursor (S5P) mission was launched, carrying the TROPOspheric Monitoring Instrument (TROPOMI), which provides a daily global coverage at a spatial resolution as high as 7 km × 3.5 km and is expected to extend the European atmospheric composition record initiated with GOME/ERS-2 in 1995, enhancing our scientific knowledge of atmospheric processes with its unprecedented spatial resolution. Due to the ongoing need to understand and monitor the recovery of the ozone layer, as well as the evolution of tropospheric pollution, total ozone remains one of the leading species of interest during this mission. In this work, the TROPOMI near real time (NRTI) and offline (OFFL) total ozone column (TOC) products are presented and compared to daily ground-based quality-assured Brewer and Dobson TOC measurements deposited in the World Ozone and Ultraviolet Radiation Data Centre (WOUDC). Additional comparisons to individual Brewer measurements from the Canadian Brewer Network and the European Brewer Network (Eubrewnet) are performed. Furthermore, twilight zenith-sky measurements obtained with ZSL-DOAS (Zenith Scattered Light Differential Optical Absorption Spectroscopy) instruments, which form part of the SAOZ network (Système d'Analyse par Observation Zénitale), are used for the validation. The quality of the TROPOMI TOC data is evaluated in terms of the influence of location, solar zenith angle, viewing angle, season, effective temperature, surface albedo and clouds. For this purpose, globally distributed ground-based measurements have been utilized as the background truth. The overall statistical analysis of the global comparison shows that the mean bias and the mean standard deviation of the percentage difference between TROPOMI and ground-based TOC is within 0 –1.5 % and 2.5 %–4.5 %, respectively. The mean bias that results from the comparisons is well within the S5P product requirements, while the mean standard deviation is very close to those limits, especially considering that the statistics shown here originate both from the satellite and the ground-based measurements. Additionally, the TROPOMI OFFL and NRTI products are evaluated against already known spaceborne sensors, namely, the Ozone Mapping Profiler Suite, on board the Suomi National Polar-orbiting Partnership (OMPS/Suomi-NPP), NASA v2 TOCs, and the Global Ozone Monitoring Experiment 2 (GOME-2), on board the Metop-A (GOME-2/Metop-A) and Metop-B (GOME-2/Metop-B) satellites. This analysis shows a very good agreement for both TROPOMI products with well-established instruments, with the absolute differences in mean bias and mean standard deviation being below +0.7 % and 1 %, respectively. These results assure the scientific community of the good quality of the TROPOMI TOC products during its first year of operation and enhance the already prevalent expectation that TROPOMI/S5P will play a very significant role in the continuity of ozone monitoring from space.
Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding

We recently identified a set of chromosome domains that are early replicating uniquely in pluripotent cells. Their switch from early to late replication occurs just prior to germ layer commitment, associated with a stable form of gene silencing that is difficult to reverse. Here, we discuss results demonstrating that these domains are among the least sensitive regions in the genome to global digestion by either MNase or restriction enzymes. This inaccessible chromatin state persists whether these regions are in their physically distended early replicating or compact late replicating configuration, despite dramatic changes in 3D chromatin folding and long-range chromatin interactions, and despite large changes in transcriptional activity. This contrasts with the strong correlation between early replication, accessibility, transcriptional activity and open chromatin configuration that is observed genome-wide. We put these results in context with findings from other studies indicating that many structural (DNA sequence) and functional (density and activity of replication origins) properties of developmentally regulated replication timing (“switching”) domains resemble properties of constitutively late replicating domains. This suggests that switching domains are a type of late replicating domain within which both replication timing and transcription are subject to unique or additional layers of control not experienced by the bulk of the genome. We predict that understanding the unusual structure of these domains will reveal a novel principle of chromosome folding.
Dynamic modeling and simulation of rowing with a robotics formalism

This paper presents a robotics framework intended to be used for rowing simulation. It provides kinematic and inverse dynamic models for the system composed of boat, rowers and oars. The inverse dynamic model is based on the Recursive Newton-Euler Algorithm with free-floating base dealing with tree-structured systems with kinematic loops. Examples of simulations of a rowing-like model are given along with external force models. It is composed of a total of 6 links for the rower and the oars, the floating boat, and 7 joints. It presents a branched structure with one loop enabling to test the ability of the framework regarding its goals.
Driver Distraction through Conversation Measured with Pupillometry

Assessing a driver´s mental workload during tasks that are not visual-manual is a challenging endeavor. Especially with the rapid development of speech systems, this is becoming increasingly important. Pupillometry promises to be a suitable physiological measurement method, sensitive to variations of cognitive workload. This driving simulator study shows that the pupillometry data indicate a significant increase in cognitive activity during conversation tasks regardless of the acoustic channel used.
Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

Biochemical reactors (BCRs) using complex organics for bioremediation of mine-influenced water must operate successfully year round. In cold climates, where many mines in Canada are located, survival of the important microorganisms through the winter months is a concern. In this work, broad phylogenetic surveys, using metagenomics, of the microbial populations in pulp mill biosolids used to remediate metal leachate containing As, Zn, Cd and sulfate were performed to see if the types of microorganisms present changed over the seasons of one year (August 2008 to July 2009). Despite temperature variations between 0 and 17 °C the overall structure of the microbial population was fairly consistent. A cyclical pattern in relative abundance was detected in certain taxa. These included fermenter-related groups, which were out of phase with other taxa such as Desulfobulbus that represented potential consumers of fermentation byproducts. Sulfate-reducers in the BCR biosolids were closely related to psychrotolerant species. Temperature was not a factor that shaped the microbial population structure within the BCR biosolids. Kinetics of organic matter degradation by these microbes and the rate of supply of organic carbon to sulfate-reducers would likely affect the metal removal rates at different temperatures.
Eurocentrism and the Contribution of Ibn Khaldun to the Growth of Sociology

It is generally believed that sociology originated in Europe in the 19th century and the paternity of the discipline is commonly attributed to the French sociologist August Comte. However, reflections of a sociological nature were observed and found in the work of 14th century North African historian and philosopher Ibn Khaldun. However, such contribution of Ibn Khaldun is little acknowledged by European scholars in their works. Therefore, this paper attempts to examine how Eurocentrism is embedded in the writing of the European scholars and unpacks the contribution of Ibn Khaldun in the growth of Sociology. In the first part of essay, I argue that the perspective of European scholars are mainly Eurocentric and parochial in their accounts on culture, language and other aspects of non-European society. In the second part of the essay, I argue Ibn Khaldun’s contribution to the field of sociology is largely ignored, though his contributions dealt with the society and human character, political organization and government, differences between rural and urban populations, kinship, social solidarity, and the interplay between economic conditions and social organizations. Nevertheless, I argue that though Ibn Khaldun’s ideas have hugely impressed some of European thinkers in the 19th century prompting them to regard him as the progenitor of sociology, question remains as to how his ideas and theories have been appropriated by contemporary social scientists in their works.
Dynamics of DNA Damage Induced Pathways to Cancer

Chemotherapy is commonly used in cancer treatments, however only 25% of cancers are responsive and a significant proportion develops resistance. The p53 tumour suppressor is crucial for cancer development and therapy, but has been less amenable to therapeutic applications due to the complexity of its action, reflected in 66,000 papers describing its function. Here we provide a systematic approach to integrate this information by constructing a large-scale logical model of the p53 interactome using extensive database and literature integration. The model contains 206 nodes representing genes or proteins, DNA damage input, apoptosis and cellular senescence outputs, connected by 738 logical interactions. Predictions from in silico knock-outs and steady state model analysis were validated using literature searches and in vitro based experiments. We identify an upregulation of Chk1, ATM and ATR pathways in p53 negative cells and 61 other predictions obtained by knockout tests mimicking mutations. The comparison of model simulations with microarray data demonstrated a significant rate of successful predictions ranging between 52% and 71% depending on the cancer type. Growth factors and receptors FGF2, IGF1R, PDGFRB and TGFA were identified as factors contributing selectively to the control of U2OS osteosarcoma and HCT116 colon cancer cell growth. In summary, we provide the proof of principle that this versatile and predictive model has vast potential for use in cancer treatment by identifying pathways in individual patients that contribute to tumour growth, defining a sub population of “high” responders and identification of shifts in pathways leading to chemotherapy resistance.
Feedback on Grammatical Accuracy: Comparing Perceptions and Practices on the Teachers’ and Learners’ Parts

An advantage of the communication-based instruction in an EFL situation is prioritizing fluency and meaning negotiation though of course at the cost of accuracy. Researchers have, therefore, found feedback on the learners’ erroneous utterances quite appealing so that form can be attended to against the wider backdrop of meaning-focused involvement in communication. This present study qualitatively and quantitatively sought to investigate the teachers’ and intermediate learners’ perceptions as well as the teachers’ practices concerning corrective feedback types, sources of feedback, and types of grammatical errors that occur and need to be attended to during the classroom conversations. The study was conducted in two private language institutes in Tabriz, Eastern Azerbaijan Province, Iran. The instructional materials were Top Notch course books. For the purpose of the study, 6 teachers and 60 EFL learners were focused on. First, the classes of 6 teachers were observed. Then, the teachers and learners completed a questionnaire on corrective feedback. The results indicated that learners showed strong agreement toward using explicit feedback. On the contrary, teachers usually neglected the learners’ grammatical errors at the classroom to maintain the flow of interaction. Another important finding about sources of feedback was that teachers and learners preferred teacher correction to peer correction or self-correction. Finally, both teachers and learners expressed strong agreement about feedback on serious grammatical errors during conversation though the former tended to agree more with the feedback on less serious and frequent grammatically erroneous utterances.
Torsionfree dimension of modules and self-injective dimension of rings

Let R be a left and right Noetherian ring. We introduce the notion of the torsionfree dimension of finitely generated R-modules. For any n 0, we prove that R is a Gorenstein ring with self-injective dimension at most n if and only if every finitely generated left R-module and every finitely generated right R-module have torsionfree dimension at most n, if and only if every finitely generated left (or right) R-module has Gorenstein dimension at most n. For any n 1, we study the properties of the finitely generated R-modules M with Ext i R (M, R) 0 for any 1 i n. Then we investigate the relation between these properties and the s elf-injective dimension of R.
Meeting the Needs of the Foster Child: Perceptions of the K–6 Teacher

A growing number of children are entering the foster care system every year. The trauma experienced by these children negatively impacts them. This current study sought to determine the perceptions of foster children by thirty-six teacher participants. The results indicate a need to increase teacher’s awareness of foster children and the unique challenges they face. This study has brought a heightened awareness of the teachers’ perceptions towards this growing population of students relative to the challenges facing foster children. Teachers must be aware of the issues these students face while providing adequate interventions to meet the needs of these students.
Adherence in adults with type 1 diabetes mellitus correlates with treatment satisfaction but not with adverse events

Purpose Diabetes self-care and self-monitoring adherence has a positive effect on the metabolic control of the disease. The aim of this study was to analyze the adherence to self-care recommendations and to identify its correlates in adults with type 1 diabetes mellitus. Patients and methods One hundred and eleven patients with type 1 diabetes were enrolled in an observational cross-sectional study conducted at the Diabetes Center of the University Hospital in Hradec Králové, Czech Republic. Diabetes self-care adherence was measured by the Self Care Inventory-Revised, and treatment satisfaction by the Diabetes Treatment Satisfaction Questionnaire-status version. Additional data were collected from self-administered questionnaires and medical records. The Mann–Whitney test, Spearman correlations, and multiple linear regressions were used in the statistical analysis. Results The mean age of patients was 42.4 years; 59.5% of them were females and 53.2% of all patients used an insulin pump. The mean glycosylated hemoglobin (HbA1c) was 66.2 ± 15.3 mmol/mol and the mean insulin dosage was 0.6 ± 0.3 IU insulin/kg/day. The number of hypoglycemic episodes (including severe) that patients had in the last month before taking the survey was 3.6 ± 3.2. Self-care adherence was associated with treatment satisfaction (0.495; P = 0.004) along with frequency of self-monitoring of before meal blood glucose (0.267; P = 0.003). It was not associated with the incidence of hypoglycemic events or any other insulin therapy-related problems or with socio-demographic or clinical characteristics. Conclusion Treatment satisfaction is one of the key factors that need to be targeted to maximize benefits to patients. Self-care adherence in adults with type 1 diabetes did not correlate with socio-demographic and clinical characteristics, nor with adverse events.
Regional Frontal Cortical Volumes Decrease Differentially in Aging: An MRI Study to Compare Volumetric Approaches and Voxel-Based Morphometry

Recent neuroimaging studies suggest that the frontal lobes are the part of the brain most profoundly affected by the aging process. The present study investigated whether subregions within the frontal cortex show different patterns of brain aging. Magnetic resonance images of 57 healthy participants between 21 and 81 years old were used to measure regional frontal gray matter volumes in three ways: a manual tracing method, a semiautomatic "Talairach boxes" volumetric method, and voxel-based morphometry. Seven regions within each hemisphere were manually traced: precentral gyrus, inferior frontal gyrus, dorsolateral frontal cortex, ventral medial region, lateral orbital region, anterior cingulate, and frontal pole. With the semiautomatic approach, four regions were measured: lateral, orbital, and medial frontal regions and frontal pole. Advancing age was strongly associated with decreases in the volume of the whole frontal cortex. Differential age effects on the volumes of frontal subregions were dependent on the method applied. According to the manual approach, age-related volume decreases were strongest in the lateral and orbital frontal gray matter. The semiautomatic and voxel-based analyses found that age effects were most prominent within the lateral frontal and cingulate regions. Overall, it was concluded that although semiautomated and voxel-based methods can provide a reasonable estimate of regional brain volume, they cannot serve as a substitute for manual volumetry.