Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping open chromatin by ATAC-seq in bread wheat

Gene transcription is largely regulated by cis-regulatory elements. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an emerging technology that can accurately map cis-regulatory elements in animals and plants. However, the presence of cell walls and chloroplasts in plants hinders the extraction of high-quality nuclei, thereby affects the quality of ATAC-seq data. Meanwhile, it is tricky to perform ATAC-seq with different tissue types, especially for those with limited size and amount. Moreover, with rapid growth of ATAC-seq datasets from plants, powerful and easy-to-use data analysis pipelines for ATAC-seq, especially for wheat is lacking. Here, we provided an all-in-one solution for mapping open chromatin in wheat including both experimental and data analysis procedure. We efficiently obtained nuclei with less cell debris from various wheat tissues. High-quality ATAC-seq data from young spike and ovary, which are hard to harvest were generated. We determined that the saturation sequencing depth of wheat ATAC-seq is about 16 Gb. Particularly, we developed a powerful and easy-to-use online pipeline to analyze the wheat ATAC-seq data and this pipeline can be easily extended to other plant species. The method developed here will facilitate plant regulatory genome study not only for wheat but also for other plant species.
Neuroimaging in schizophrenia: A review article

In this review article we have consolidated the imaging literature of patients with schizophrenia across the full spectrum of modalities in radiology including computed tomography (CT), morphologic magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), magnetic resonance spectroscopy (MRS), positron emission tomography (PET), and magnetoencephalography (MEG). We look at the impact of various subtypes of schizophrenia on imaging findings and the changes that occur with medical and transcranial magnetic stimulation (TMS) therapy. Our goal was a comprehensive multimodality summary of the findings of state-of-the-art imaging in untreated and treated patients with schizophrenia. Clinical imaging in schizophrenia is used to exclude structural lesions which may produce symptoms that may mimic those of patients with schizophrenia. Nonetheless one finds global volume loss in the brains of patients with schizophrenia with associated increased cerebrospinal fluid (CSF) volume and decreased gray matter volume. These features may be influenced by the duration of disease and or medication use. For functional studies, be they fluorodeoxyglucose positron emission tomography (FDG PET), rs-fMRI, task-based fMRI, diffusion tensor imaging (DTI) or MEG there generally is hypoactivation and disconnection between brain regions. However, these findings may vary depending upon the negative or positive symptomatology manifested in the patients. MR spectroscopy generally shows low N-acetylaspartate from neuronal loss and low glutamine (a neuroexcitatory marker) but glutathione may be elevated, particularly in non-treatment responders. The literature in schizophrenia is difficult to evaluate because age, gender, symptomatology, comorbidities, therapy use, disease duration, substance abuse, and coexisting other psychiatric disorders have not been adequately controlled for, even in large studies and meta-analyses.
A prospective marker for the prediction of postoperative deep venous thrombosis: Neutrophil extracellular traps

Deep venous thrombosis (DVT) is a common medical complication in patients with lumbar fractures. The current study aimed to investigate the predictive value of neutrophil extracellular traps (NETs) in postoperative DVT formation in patients with lumbar fractures and to develop a nomogram relating clinical admission information for prediction. Patients who underwent open reduction and pedicle screw internal fixation in the treatment of single-segment lumbar fracture in the Department of Spine Surgery, the First Affiliated Hospital of Nanjing Medical University, from December 2020 to June 2022 were enrolled in this study. Baseline data and laboratory results were collected from enrollees, and the primary study endpoint event was the occurrence of DVT in patients after surgery. Multivariable logistic regression analysis was used to identify risk factors associated with higher odds of DVT after surgery. A nomogram was constructed using the results of the multivariable model. The calibration plot and receiver operating characteristics (ROC) curve were used to show the satisfactory predictive capacity of the model. Of these 393 patients who did not have DVT preoperatively, 79 patients developed it postoperatively, and 314 did not, respectively. Multivariate analysis showed that higher body mass index (BMI) (BMI between 24 and 28: RR = 1.661, 95% CI = 0.891–3.094; BMI ≤28: RR = 5.625, 95% CI = 2.590–12.217; reference: BMI <24), neutrophils (RR = 1.157, 95% CI 1.042–1.285), D-dimer (RR = 1.098, 95% CI 1.000–1.206), and citrullinated histone H3 (CitH3) (RR = 1.043, 95% CI 1.026–1.060) were independent risk factors for postoperative DVT. Using the multivariable analysis, we then constructed a nomogram to predict DVT, which was found to have an area under the curve of 0.757 (95% CI = 0.693–0.820). Calibration plots also showed the satisfied discrimination and calibration of the nomogram. In conclusion, patients with lumbar fractures with postoperative DVT had higher levels of NETs in the circulation preoperatively compared to those without postoperative DVT. Furthermore, based on BMI, D-dimer, neutrophils, and CitH3, we developed a predictive model to predict postoperative DVT incidence in these patients.
College students’ exercise experience and aggression during COVID-19: A chain mediating model

Aim This study aimed to explore to how exercise experience affects the aggression of college students and the mediating effects of mood and exercise attitude in COVID-19. Methods A questionnaire survey [The Subjective Exercise Experience Scale (SEES); Profile of Mood State (POMS); Exercise Attitude Scale; and Aggression Questionnaire (AQ)] was conducted among 1,006 college students. Results Exercise experience had a significant effect on aggression. The direct effect of exercise well-being was not significant, but indirectly affected the aggression through independent mediation and chain mediation of mood and exercise attitude. The direct effect of exercise distress was not significant, but indirectly affected the aggression through independent mediation and chain mediation of mood and exercise attitude. Conclusion Mood and exercise attitude are powerful factors to alleviate the impact of exercise experience on aggression during the pandemic. Actively adjusting the mood and exercise attitude from a cognitive perspective may be an effective way to promote college students’ physical exercise and reduce aggression.
Optimal decision-making model for selecting residential green building technologies in China

China is expected to have an annual demand of 1 billion square meters of new residential floor areas in the next few years. Housing developers have adopted various green building technologies (GBTs) in building designs to meet the constantly rising green building (GB) standards. However, they often ignore users’ satisfaction and perception of these GBTs and doubt the cost-benefit assessment of GBTs. This study first constructed GBTs commonly used in residential construction in the Yangtze River Delta region, China. In particular, it adopted the Kano model and the Customer Satisfaction Coefficient (CSC) model to conduct questionnaire surveys on 171 Ningbo households to analyze the differences between developers’ and users’ perceptions of GBTs. Further, a zero-one integer programming (ZOIP) approach was used to build an optimal decision-making model for housing developers to select GBTs that take into account developers’ incremental cost and benefit assessment. The results showed that residents focus on technologies related to comfort and health issues, followed by energy-efficient technologies with lower costs. High-cost and low-scoring GBTs, such as new air systems and Low-E center louvered glass, will be excluded. The decision model clarifies the differences between developers’ and users’ perceptions of GBTs and effectively assists developers in rationalizing the selection of GBTs. Furthermore, it is suggested that the proposed model can be widely applied to other projects in different regions in the future to promote GB markets in China.
Gestural communication of wild bonnet macaques in the Bandipur National Park, Southern India

Nonhuman primate gestures are believed to be crucial evolutionary precursors of human language. Comparative studies on primate gestures in an evolutionary framework have, however, remained largely restricted to the great apes and the potential flexibility and richness of gestural communication in monkeys, especially in the wild, continue to be virtually unknown. In this paper, we followed several criteria, adapted from ape gesture studies, to identify gestures and evaluate their contexts of usage in the repertoire of wild bonnet macaques Macaca radiata in the Bandipur National Park of southern India. This report is the first of its kind to systematically identify gestures in any wild, non-ape species, thus providing a platform for comparative studies across primate taxa, particularly in our efforts to trace out the phylogenetic origins of language-like markers in the primate lineage, earlier than in the great apes.
INFLUENCE OF ARBUSCULAR MYCORRHIZAL FUNGI , RHIZOBIUM INOCULATION AND ROCK PHOSPHATE ON GROWTH AND QUALITY OF LENTIL

Effective inoculation of legumes has the ability not only to ensure nutrients availability to plants particularly in N & Plimiting (due to improvement in nutrients fixation) environments but also can manipulate the environmental hazards associated with over inorganic fertilization. To support this view, the current experiment was conducted to study the influence of rock phosphorus fertilization, Arbuscular Mycorrhizae (AM) and Rhizobium inoculation on growth and yield parameters of Lens culinaris (NARC.2008-4). In addition, the current experiments aimed to evaluate the effect of different inoculation practices on crop quality in comparison with control (no inoculation). The experiment was laid out in randomized complete block design with four replications during winter (2010-11 and 2012-13) at the Department of Botany University of Peshawar Pakistan. Overall, inoculated plant performed superior in terms of plant growth and quality over control. All plants measured parameters (Leaf chlorophyll content, seed protein, fiber and ash content, plant height, number of seed pod , leaves plant, flowers plant, pods plant, pod length and thousand seed weight) were highest in plant samples inoculated with VAM and Rhizobium in combination as compared to sole application of VAM or Rhizobium. Combined inoculation of VAM and Rhizobium caused 10, 24, 17, 21 and 14% increase in seed protein content, leaf chlorophyll content, seed fiber content, seed ash content and number of seed pod over sole application of VAM and Rhizobium when averaged over two years. Combined application of Rhizobium + VAM enhanced seed yield plant by 45% over control and 24% and 28% over sole inoculation of VAM and Rhizobium respectively. It is therefore concluded that dual inoculation of VAM + Rhizobium and rock phosphate may be of only limited consequence in high input agricultural systems.
Prevalence of Zoonotic bovine tuberculosis and associated risk factors among cattle herds in North Central Nigeria | University of Abuja Open Education Resources (OER)

Prevalence of Bovine Tuberculosis (BTB) was investigated among 600 lactating cows in 48 herds in North Central Nigeria using tuberculin skin test, culture, acid fast stain and biochemical characterization, well structured questionnaire was administered to 200 cattle farmers and non cattle farmers respectively to determine risk factors associated with BTB in the study area. Forty five (7.5%) lactating cows tested positive for tuberculin skin test, 11 (1.8%) were inconclusive reactors, 544 (90.6%) tested negative, 30 (5%) milk samples from tuberculin positive cows were cultured on LowensteinJensen media, while 33 (5.5%) were acid-fast positive. Biochemical test identified 19 isolates of M. bovis indicating prevalence of 3.2% for M. bovis in the study area. Cattle farmers indicated close association with cattle and consumed unpasteurized cow milk for years, while 42 non cattle farmers consumed unpasteurized cow milk. Milking maids processed cow milk by boiling under uncontrolled temperatures and sometimes sell raw cow milk to the public. Biochemical test identified 3.2% prevalence for Bovine Tuberculosis while close association with cattle and prolonged consumption of unpasteurized milk were identified as risk factors. Further studies using molecular test to identify M. bovis strains is recommended where similar risk factors exist. KEYWORDS
Lightning measurements on radiocommunication towers

Orange and Meteorage have unified their skills to set up an experiment related to the lightning storms. It consists in measuring the current values when direct strokes hit the air termination system on two radio telecommunication towers and in addition to check the way it is distributed within the structure. For Orange the results will be precious to contribute to the ITUT Standardization in order to optimize the engineering rules for the radio communication towers electromagnetic protection. For Meteorage the interest is to strengthen and validate the algorithms of the stormy activity geo-localization, knowing that for a given lightning stroke Orange has this information. The two experimental sites are located in the Rhône-Durance (France) area. Each one is equipped with a field mill to register the electrostatic field in an area of 15km around the site, 24h a day, and with a digital oscilloscope to which are connected four current transformers dedicated to the direct lightning stroke current, to the current flowing through the surge arrestors, to the electric line and to the grounding system. The control of both instrumentations is performed through the 3G network. The paper focuses on the main objectives of this experiment, the difficulties encountered for the installation of the measuring equipment and the solution which have been implemented to fix them. Then the outcomes of the experiment will be discussed with regard to the ongoing work in standardization. Keywords—Lightning current; Lightning Locating System (LLS); Radio-telecommunication towers; standardization;
Serum interleukin 1-βlevels among salivary secretary ABO blood group chronic periodontitis subjects

Introduction: Periodontal disease is defined as inflammatory destruction of periodontal tissue and alveolar bone supporting the teeth. The key role for inflammation in periodontitis is interleukins; the important one is IL1β. Limited efforts have been made to inspect the association between periodontal disease and secretor status ABO blood group. The aim of this study was to show if there is any relationship between secretors ABO group and IL-1B in chronic periodontitis subjects in comparison to control. Materials and methods: the saliva and serum were collected from 21patients with chronic periodontitis in comparison to 18 healthy subjects with the average age about 35-55 years for both groups. Clinical periodontal parameters (PLI, GI and BOP) for both studied groups were taken and probing pocket depth (PPD) for only chronic periodontitis group. Determination of serum IL-1β level was done by ELISA. The secretary ABO blood group from saliva by using Blood Typing Kit # 11. Results: The means of all clinical periodontal parameters were higher in chronic periodontitis group. While the mean for periodontal pocket depth was (4.9 ±1.36). The results show non significance difference between chronic periodontitis and control group for O secretary blood group in mean concentration of serum IL-1β and significance difference for A secretary blood group while for the B secretary blood group it was highly significance. There were no statistical differences for AB secretary blood group because there was only one subject from chronic periodontitis AB secretary blood group Conclusion: the concentration of serum interleukin 1-β in chronic periodontitis differs according to secretary status ABO blood group and this play a role in the extent of the severity of periodontal disease.
Do Developmental Mathematics Courses Develop the Mathematics ? Addressing Missing Outcome Problem in Regression Discontinuity Design ∗

Many students are unprepared for college-level math in spite of many attempts to improve the math skills of high-school students. In community colleges, developmental mathematics courses are designed to help those students make up for the gaps in highschool math. However, there are few studies on the effect of developmental mathematics on mathematics achievement despite the vast quantity of research on the courses’ effects on various outcomes. Developmental mathematics consists of various courses in a tight sequence where course assignments are determined by a rigid placement rule based on students’ test scores, and in which students must master the assigned course before taking the next level of math. A course’s effectiveness can be measured by the letter grade or other test scores in its subsequent course. However, such an effect is difficult to investigate because of missing outcome problems; achievement in the subsequent course is only observed for those who enrolled and finished it. Enrollment may be affected by assignment to a prerequisite course since those assigned to the prerequisite are less likely to enroll in the subsequent course compared to those assigned directly to the subsequent course. In regression discontinuity design (RDD), usual methods such as the control function approach cannot address these missing outcome problems as the outcome’s propensity to be observable is also discontinuous. Applying a bounding approach in RDD, this study partially identifies the causal effects of developmental mathematics, and computes their bounds. Using the data from a community college in California, I find that assignment to developmental courses would increase achievement and learning efficiency in the subsequent math courses. ∗I am deeply indebted to my advisor Geert Ridder for his enormously valuable advice and comments. I would also like to thank to Hyungsik Roger Moon for his valuable comments and suggestions. Finally, I am especially grateful to Tatiana Melguizo for her valuable comments and generous provision of the data used in this study. I am solely responsible for any remaining errors. †Department of Economics, University of Southern California, Kaprielian Hall 300, Los Angeles, CA 90089. (E-mail: bokim@usc.edu.)
Effect of hydrofluoric acid etching on bond strength of composite luting agent to lithium disilicate ceramic material

Purpose: The purpose of the current study was to evaluate the effect of surface preparation on bond strength of a composite luting agent joined to a heat-pressed ceramic material. Materials and Methods: Two sizes of disk specimens were made from a lithium disilicate-based ceramics (IPS Empress 2) and their surfaces were separately prepared with three methods: etching with phosphoric acid (PE), etching with hydrofluoric acid (HF), and air-borne particle abrasion with alumina (AA). Each group was further divided into two sub-groups: bonding with the Panavia F material (PF), and silane treatment followed by bonding with the Panavia F material. Shear testing was performed both before and after 20,000 thermocycles. Results: Bond strength varied from 14.2 MPa to 46.6 MPa for the pre-thermocycling groups, whereas post-thermocycling bond strength ranged from 0.3 MPa to 37.5 MPa. Conclusion: Hydrofluoric acid etching effectively enhanced bond strength of the Panavia luting agent to the ceramic material, regardless of the application of silane primer. (Int Chin J Dent 2004; 4: 100-106.)
Analysis of surface wave climate in the North Atlantic by satellite altimeter and scatterometer

Numerous activities require predictions of global ocean wave conditions. It is of growing concern by government officials for decision-making regarding the prediction and mitigation of ocean disasters, as well as sea-going rescue activities. The coastal and marine industry is another community to which wind and wave information is extremely important. This work describes how the wind sea and swell index can be used to analyze the sea surface wave fields. The methodology is to enable the use of collocated wind speed and significant wave height simultaneous satellite scatterometer measurements and sources altimeter to observe the spatial and temporal dominant pattern of swell and wind wave zones in the North Atlantic. The results shows strong distribution of swell fields for the entire study region, with “swell pools” located in areas near the east coast of Africa. In these major swell zones, with swell index of more than 97%. The seasonal maps of the wind sea index shows that wave growth is generally weak in major swell pools. However, the opposite statement is not always true, that is, there is not necessarily strong wave generation in weak swell zones. Given the reasonable results obtained and their general consistency with field observations and model predictions, the proposed scheme appears to be efficient in characterizing the swell and wind sea climate.
Teachers of Color and Urban Charter Schools: Race, School Culture, and Teacher Turnover in the Charter Sector

This article explores working conditions in charter schools with varying rates of teacher turnover. Ethnographic data with 28 racially diverse teachers explores teachers’ experiences, their explanations for moving charter schools, and patterns of movement when teachers leave a charter school for another school. A brief conceptual framework was used to understand multiple dimensions of working conditions in charter schools for teachers of color. Findings indicate teachers most often made structural moves between charter types, primarily from charters managed by nonprofit organizations to standalone charter schools. Teachers of color describe tensions with sociocultural conditions that limited culturally inclusive practices. Discussion includes implications for policies that push to replicate charter schools in communities of color, particularly schools with poor working conditions associated with high turnover and weak propensities to retain teachers of color.
Chapter 14 Antifungals : Mechanism of Action and Drug Resistance

There are currently few antifungals in use which show efficacy against fungal diseases. These antifungals mostly target specific components of fungal plasma membrane or its biosynthetic pathways. However, more recent class of antifungals in use is echinocandins which target the fungal cell wall components. The availability of mostly fungistatic antifungals in clinical use, often led to the development of tolerance to these very drugs by the pathogenic fungal species. Thus, the development of clinical multidrug resistance (MDR) leads to higher tolerance to drugs and its emergence is helped by multiple mechanisms. MDR is indeed a multifactorial phenomenon wherein a resistant organism possesses several mechanisms which contribute to display reduced susceptibility to not only single drug in use but also show collateral resistance to several drugs. Considering the limited availability of antifungals in use and the emergence of MDR in fungal infections, there is a continuous need for the development of novel broad spectrum antifungal drugs with better efficacy. Here, we briefly present an overview of the current understanding of the antifungal drugs in use, their mechanism of action and the emerging possible novel antifungal drugs with great promise.