Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower within Japonica relative to Indica, which is consistent with the known population bottleneck during Japonica domestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.
WHAT TEACHERS THINK ABOUT ASSESSMENT AND HOW IT INFLUENCES THEIR CLASSROOM-BASED ASSESSMENT PRACTICES – THE RESULTS OF A GLOBAL SURVEY

This paper considers teachers’ attitudes to assessment. The attitudes were explored through Borg’s (2015) Language Teacher Cognition Framework. A mixed-methods approach of questionnaire and interview was adopted. The online survey was completed by English language teachers working in 57 different countries worldwide. The questionnaire was divided into 3 sections. The first section included questions which related to the participants’ experiences of assessment at school. The second section explored the participants’ assessment training experiences both in their initial teaching training and in any professional development sessions they had attended. The third and final section explored the participants’ assessment practices and their beliefs about assessment. These three sections are based on the Language Teacher Cognition Framework. The interviews were conducted to explore the reasoning behind the responses given to the questionnaire. The framework also informed the data analysis process. Classroom experiences and professional development sessions were found to have the most influence on the teachers’ attitudes to assessment. The participants were influenced by their experiences of assessment at school as they choose to avoid replicating the assessment practices which had been used when they were being assessed.
Estimation of Nutrient Load from Aquaculture Farms in Manila Bay, Philippines

Waste from aquaculture is considered as one of the possible causes of water quality deterioration in Manila Bay. Aquaculture in the area accounts for almost 30% of the total production in the Philippines. This high production entails intensified application of inputs that could possibly contribute to the nutrient (nitrogen, N and phosphorus, P) load in the bay. Thus, estimation of the N, P and SO4 loaded from aquaculture farms is necessary to develop more responsive intervention to reduce nutrient load in Manila Bay. Water samples were collected throughout the rearing period from different aquaculture systems in Cavite, Bulacan, Pampanga, and Bataan. The annual estimated N and P loaded from aquaculture farms were 12, 696.66 MT and 2, 363.01 MT, respectively. Fish pens/cages recorded the highest contribution accounting for 88% N and 86% P of the total load. It can be attributed to the direct release of uneaten feeds into the bodies of water. Roughly, 12% N and 14% P were obtained from the fishponds. Furthermore, the annual SO4 loaded from fishponds was estimated at 36,917.54 MT. Results of the study suggested that there should be an extensive monitoring of the environmental impacts and annual load of aquaculture farms for the sustainable regulations and management of aquaculture activities to reduce nutrient load and improve the aquaculture production as well. Finally, strict compliance to the regulatory guidelines and ordinances must be imposed to achieve the effluent quality standards.
Mixed evidence for adaptation to environmental pollution

Adaptation to pollution has been studied since the first observations of heavy metal tolerance in plants decades ago. To document micro‐evolutionary responses to pollution, researchers have used phenotypic, molecular genetics, and demographic approaches. We reviewed 258 articles and evaluated the evidence for adaptive responses following exposure to a wide range of pollutants, across multiple taxonomic groups. We also conducted a meta‐analysis to calculate the magnitude of phenotypic change in invertebrates in response to metal pollution. The majority of studies that reported differences in responses to pollution were focused on phenotypic responses at the individual level. Most of the studies that used demographic assays in their investigations found that negative effects induced by pollution often worsened over multiple generations. Our meta‐analysis did not reveal a significant relationship between metal pollution intensity and changes in the traits studied, and this was probably due to differences in coping responses among different species, the broad array of abiotic and biotic factors, and the weak statistical power of the analysis. We found it difficult to make broad statements about how likely or how common adaptation is in the presence of environmental contamination. Ecological and evolutionary responses to contamination are complex, and difficult to interpret in the context of taxonomic, and methodological biases, and the inconsistent set of approaches that have been used to study adaptation to pollution in the laboratory and in the field. This review emphasizes the need for: (a) long‐term monitoring programs on exposed populations that link demography to phenotypic, genetic, and selection assays; (b) the use of standardized protocols across studies especially for similar taxa. Approaches that combine field and laboratory studies offer the greatest opportunity to reveal the complex eco‐evolutionary feedback that can occur under selection imposed by pollution.
Concurrent action of salinity and water stress on leaf gas exchange and water relations in tomato

Tomato plants (Lycopersicon esculentum Mill.) grown in pots were irrigated for four weeks with 0.04,0.08,0.12 molai NaCl solutions and a control solution. Half the plants in each salt treatment were water stressed for five days. Single leaf gas exchange at near ambient C02, water consumption and plant water relations were measured. Both salt and water stress reduced growth, water potential and gas exchange rates. Well watered plants were only slightly stressed by a salt concentration of 0.04 molai, while plant growth continued at a concentration of 0.08 molai. Short-term water stress imposed greater stress than long-term salt stress; carbon exchange rate (CER) was partially limited by stomatal closure in the case of water stress and by mesophyll limitation with longer-term salinity treatments. Osmoregulation in response to salt stress did not impart particular tolerance to transient water stress.
Chamber studies and modeling of secondary organic aerosol formation

Secondary organic aerosol (SOA), formed from atmospheric oxidation of gas-phase hydrocarbons, comprise a large fraction of ambient particulate matter. Significant uncertainties exist in identifying the sources and mechanisms responsible for SOA formation, making it difficult to understand its impact on global climate and local air quality. Laboratory chambers have been a valuable tool to study underlying chemical mechanisms of SOA formation and to quantify SOA formation from select hydrocarbons in a controlled environment. However, a good understanding of the chemical processes involved is required to be able to extrapolate data acquired from smog chamber studies. This thesis presents results from experimental investigation of SOA formation from atmospherically important compounds, and model simulations of kinetic mechanisms involved in SOA formation. The distinguishing mechanism of SOA formation is the partitioning of semivolatile hydrocarbon oxidation products between the gas and aerosol phases. While SOA formation is typically described in terms of partitioning only, the rate of formation and ultimate yield of SOA can also depend on the kinetics of both gas- and aerosol-phase processes. Here a general equilibrium/kinetic model of SOA formation is presented to provide a framework for evaluating the extent to which the controlling mechanisms of SOA formation can be inferred from laboratory chamber data. Current atmospheric models systematically underpredict SOA formation, suggesting that in current models, 1) signicant SOA precursors could be missing and 2) SOA forming processes could be misrepresented. Aerosol formation from oxidation of 2-methyl-3-buten-2-ol (MBO) and polycyclic aromatic hydrocarbons (PAHs), two important classes of compounds previously assumed to be an insignicant SOA source, is studied. Upon photooxidation, MBO produces glyoxal (an important SOA intermediate), but the yields are too low to be atmospherically important. Photooxidation of napthalene and other 2-ring PAHs leads to substantial amounts of aerosol, and can account for a large fraction of SOA formed from oxidation of diesel exhaust and other primary emissions. Isoprene is a signicant source of atmospheric organic aerosol; however, the oxidation pathways that lead to SOA have remained elusive. Under remote low-NOx conditions, epoxydiols are formed from gas-phase photooxidation of isoprene, and are found to undergo reactive uptake to lead to low-volatility compounds, such as C5-methyltetrols and organosulfates observed in ambient particulate matter. Under urban high-NOx conditions, methacrolein, an important C4 aldehyde formed from isoprene oxidation, is found to form SOA via reaction with NO2 to form peroxy methacryloyl nitrate, which subsequently forms low-volatility oligoester products. As a result of radical chemistry of aldehydes, SOA formation from isoprene depends critically on the NO2/NO ratio, and the implications on ambient aerosol formation are discussed.
Effects of macitentan and tadalafil monotherapy or their combination on the right ventricle and plasma metabolites in pulmonary hypertensive rats

Pulmonary arterial hypertension is a severe respiratory disease characterized by pulmonary artery remodeling. RV dysfunction and dysregulated circulating metabolomics are associated with adverse outcomes in pulmonary arterial hypertension. We investigated effects of tadalafil and macitentan alone or in combination on the RV and plasma metabolomics in SuHx and PAB models. For SuHx model, rats were injected with SU5416 and exposed to hypoxia for three weeks and then were returned to normoxia and treated with either tadalafil (10 mg/kg in chow) or macitentan (10 mg/kg in chow) or their combination (both 10 mg/kg in chow) for two weeks. For PAB model, rats were subjected to either sham or PAB surgery for three weeks and treated with above-mentioned drugs from week 1 to week 3. Following terminal echocardiographic and hemodynamic measurements, tissue samples were collected for metabolomic, histological and gene expression analysis. Both SuHx and PAB rats developed RV remodeling/dysfunction with severe and mild plasma metabolomic alterations, respectively. In SuHx rats, tadalafil and macitentan alone or in combination improved RV remodeling/function with the effects of macitentan and combination therapy being superior to tadalafil. All therapies similarly attenuated SuHx-induced changes in plasma metabolomics. In PAB rats, only macitentan improved RV remodeling/function, while only tadalafil attenuated PAB-induced changes in plasma metabolomics.
Using E-Learning to Deliver In-Service Teacher Training in the Vocational Education Sector: Perception and Acceptance in Poland, Italy and Germany

For teachers in vocational education and training (VET), lifelong learning and related further training is important to meet the growing demands of the teaching profession. This paper analyses the perception of technology and e-learning of teachers in Poland, Italy and Germany. The innovative aspect of this study lies in its combination of general perceptions of online learning and technology on the one hand and findings in relation to a specific online Teacher Training Tool on the other hand. The aims of this study are to show the relevance of e-learning in teacher training and to measure the perception and acceptance of this form of further training by VET teachers. The results should provide support for the further design and development of online education formats for teachers. The evaluation was carried out using a quantitative cross-cutting study using a standardised questionnaire. The results of an online questionnaire show that the approach of online learning as a form of teacher training was met with great interest among VET teachers and that the perception of one’s own benefit from such a training option was positive. The quality of the online learning units is decisive for the acceptance of e-learning opportunities. One limitation of this study is that the diverse country-specific cultural aspects and systems of teacher training could only be taken into account to a limited extent. This paper enables international comparative research on teacher training to be integrated using e-learning formats.
Interactive Effect of School principals’ Leadership Styles and Teacher Characteristics on Curriculum Implementation at Public Secondary Schools of Punjab

The research was conducted in the positivist paradigm to determine the interactive effect of school principals' leadership style and the teaching characteristics (traditional Vs. Progressive) of school teachers on curriculum implementation. The research further explores how teaching characteristics mediate between school principals' leadership style and curriculum implementation. Higher secondary school teachers' perceptions were collected from 600 teachers teaching at secondary schools in six districts of Punjab. Multistage sampling was used to draw a sample from a large and diverse population. Descriptive and inferential statistics were used to determine the relationship among various constructs leadership styles, teacher characteristics, and strategies used for the curriculum implementation at secondary schools of Punjab. Path analysis using Structure Equation Modeling with AMOS yielded unique relationships among leadership styles of school principals and teacher characteristics for curriculum implementation. Democratic style of school principals was found to exert maximum direct influence on curriculum implementation with no teacher characteristics mediation. However, it is found that both teacher characteristics play a significant mediating role in curriculum implementation; the visionary style was best mediated through progressive characteristics, and 2) commanding style was mediated through traditional characteristics. The research draws attention to existing gaps in developing teacher expertise for curriculum implementation, which need to be addressed to prepare future teacher leadership in Pakistan.
Interpreting Accent Marks as Hiatus Indicators: Syllabification Intuitions for io Sequences in US Spanish

This study considers the syllabification perceptions of heritage speakers of Spanish (HSS), second language learners, and monolingual speakers in words with io sequences in order to understand the differences between HSS and the other two groups. Participants completed a reading task and then a listening task in which they indicated the number of syllables in each stimulus perceived. Three different lexical stress patterns were tested: stress on i (like río), stress on o (like pidió), and atonic syllables (like folio). The results show that heritage participants behave like monolinguals with audio stimuli, but in the reading task they interpret orthographic accent marks as indicators that two vowels should be divided into separate syllables. This leads to accurate interpretations of stimuli with stress on i, since Spanish phonology dictates that stressed high vowels are syllabified in hiatus. Atonic syllables, which lack an orthographic accent, are correctly syllabified as diphthongs. However, heritage participants were less accurate with stress on o because they treated these stimuli like those with stress on i. These findings have implications for both linguistic theory and for pedagogy.
Individual listening success explained by synergistic interaction of two distinct neural filters

Successful speech comprehension requires the listener to differentiate relevant from irrelevant sounds. Recent neurophysiological studies have typically addressed one of two candidate neural filter solutions for this problem: the selective neural tracking of speech in auditory cortex via the modulation of phase-locked cortical responses, or the suppression of irrelevant inputs via alpha power modulations in parieto-occipital cortex. However, empirical evidence on their relationship and direct relevance to behavior is scarce. Here, a large, age-varying sample (N=76, 39–70 years) underwent a challenging dichotic listening task. Irrespective of listeners’ age, measures of behavioral performance, neural speech tracking, and alpha power lateralization all increased in response to spatial-attention cues. Under most challenging conditions, individual listening success was predicted best by the synergistic interaction of these two distinct neural filter strategies. Trial-by-trial fluctuations of lateralized alpha power and ignored-speech tracking did not co-vary, which demonstrates two neurobiologically distinct filter mechanisms.
Contribution à la quantification 3D de réseaux fibreux par microtomographie au rayonnement synchrotron : applications aux papiers

Dans cette these, nous nous sommes interesses a la quantification 3D de materiaux fibreux cellulosiques(papiers et cartons). Afin de lier les parametres de fabrications des papiers a leurs structures et leurs proprietes d'usage, les echantillons analyses ont ete images par microtomographie a rayonnement synchrotron. Des outils de traitement de l'image ont ete developpes et appliques pour quantifier la microstructure (porosite, surface specifique, taux de charges, orientation des fibres). Il a ete demontre que les donnees obtenues sont representatives d'un point de vue structural. Ainsi, les informations 3D obtenues par ces techniques peuvent etre comparees aux modeles trouves dans la litterature. Des dispositifs experimentaux ont egalement ete developpes pour analyser in-situ l'influence de la compression et de l'humidite sur la structure des papiers. De plus, l'equation de transfert radiatif a ete appliquee pour l'etude des proprietes optiques (opacite et blancheur).
First hybrid complete genome of Aeromonas veronii reveals chromosome-mediated novel structural variant mcr-3.19 from human clinical specimen

Background Recent findings substantiate the origin of plasmid-mediated colistin resistance gene mcr-3 from Aeromonads. The present study aimed to screen the plasmid-mediated colistin resistance among 30 clinical multidrug resistant (MDR) Aeromonas spp. Results The presence of mcr-1, mcr-2, mcr-3, and mcr-4 were screened by PCR, which revealed mcr-3 in a colistin susceptible isolate (FC951). All other isolates were negative for mcr genes. Sequencing of FC951 revealed that mcr-3 (mcr-3.19) identified was different from previously reported variants and had 95.62 and 95.28% nucleotide similarity with mcr-3.3 and mcr-3.10 gene. A hybrid assembly using IonTorrent and MinION reads revealed structural genetic information of mcr-3.19 with an insertion of ISAs18 within the gene. Due to this, mcr-3.19 was non-expressive which makes FC951 susceptible to colistin. Further, in silico sequence and protein structural analysis confirmed the new variant. To the best of our knowledge, this is the first report on novel mcr-3 variant (mcr-3.19). Conclusions The significant role of mcr-like genes in different Aeromonas species remains unknown and needs additional investigation to understand the insights on colistin resistance mechanism.
Predictability of Analyst Earnings Forecast Errors and Institutional and Individual Investors’ Reactions to Earnings News

We decompose analysts’ earnings forecast error into predictable and unpredictable components and investigate individual vis-à-vis institutional investors’ reactions to each of these components. We find that in the immediate post-earnings announcement window, only individuals under-react to the predictable component, while both individuals and institutions under-react to the unpredictable component. The price drift in this window is driven primarily by investors’ under-reaction to the unpredictable component. This drift remains highly significant in larger firms and intensifies in firms with complex financial reports, suggesting that it likely represents the slow and noisy process of price discovery. Around the next quarterly earnings announcement, only individuals under-react to the previous quarter’s predictable component, and this fixation drives the entire price drift in this window. This drift disappears in larger firms and gets exacerbated in firms with greater forecast error autocorrelations, suggesting that it is likely attributable to incomplete processing of earnings information by individuals.
EFFECT OF FEEDING WITH DRIED DISTILLERS GRAINS WITH SOLUBLES AND RICE POLISHINGS ON SCROTAL CIRCUMFERENCE AND SEMEN PARAMETERS OF RAM LAMBS

The effects of level of dried distillers grains with solubles (DDGS) and rice polishings (RP) on the scrotal circumference and semen parameters were examined in 22 crossbred (Pelibuey x Dorper) ram lambs (average live weight 24.84 ± 2.07 kg, approx. 5 months of age). The lambs were randomly allotted to four treatments in a 2 x 2 factorial design. The two factors were dietary levels of RP (0 and 15%) and of DDGS (0 and 30%). The experiment lasted 52 days. The animals were weighed on days 0, 34 and 52, and semen variables were measured on days 34 and 52. Semen evaluation included sperm morphology, mass and progressive motility, and sperm concentration. On day 34, sperm concentration showed an interaction of both effects (P=0.01) and was greater in rams in group 4 (both RP and DDGS) than in those in groups T2 (RP alone) or T3 (DDGS alone). Sperm morphology (% normal cells) was higher (main treatment effect) in rams fed with 30% DDGS than in those not fed with DDGS (P<0.05). The other variables showed no treatment effect. On day 52, none of the ejaculate variables varied with treatments. In conclusion, the diets did not affect body weight of ram lambs, but did affect the percentage of normal spermatozoa at 34 d of the trial, although this effect was not observed after 52 d of the trial; thus, in the long run, these diets do not alter scrotal circumference or semen parameters of young Pelibuey x Dorper ram lambs.