Miracle-dz/UniFAR-FTUs huggingface dataset:
The borders of cis-regulatory DNA sequences harbor the divergent transcription factor binding motifs in the human genome

Changes in the cis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources that shape the gene regulatory evolution in eukaryotes. However, it is currently unclear how dynamic change of DNA sequences introduce various divergence level of TF binding motifs in the genome over evolutionary time. Here, we estimated the evolutionary divergence level of the TF binding motifs, and quantified their occurrences in the DNase I hypersensitive sites. Results from our in silico motif scan and empirical TF-ChIP (chromatin immunoprecipitation) demonstrate that the divergent motifs tend to be introduced at the borders of the cis-regulatory regions, that are likely accompanied with the expansion through evolutionary time. Accordingly, we propose that an expansion by incorporating divergent motifs within the cis-regulatory regions provides a rationale for the evolutionary divergence of regulatory circuits.
BDNF-Induced Release of Endogenous Cannabinoids at Inhibitory and Excitatory Synapses

Endocannabinoids (eCBs) are important mediators of synaptic plasticity, acting as retrograde messengers because they are released on demand from postsynaptic sites and activate presynaptic type I cannabinoid (CB1) receptors to suppress neurotransmitter release at both excitatory and inhibitory synapses. Similarly, brain derived neurotrophic factor (BDNF) is also a potent neuromodulator of synaptic transmission. The effect of BDNF on synaptic transmission is mediated by tropomyosin receptor kinase B (trkB) receptors. Both CB1 and trkB receptors are highly expressed at synapses throughout the neocortex and hippocampus. There is a growing evidence of cross talk between eCB and BDNF signaling. In particular, studies in our lab have shown that BDNF can trigger the release of endogenous endocannabinoids via phospholipase C signaling at inhibitory synapses in somatosensory cortex. It is not known whether BDNF-induced eCB release also occurs at excitatory synapses and in regions other than the neocortex. In the present studies, we examined a potential crosstalk between BDNF and eCB release at excitatory synapses in neocortex and inhibitory synapses in the hippocampus.
Thermosensitive Brinzolamide in situ Gel Nanoemulsions, in vitro and ex vivo Evaluation

Brinzolamide (BZ) is a carbonic anhydrase inhibitor with selectivity and affinity for the carbonic anhydrase type II isoenzyme that administrated topically as an ophthalmic suspension for reducing intraocular pressure. In this study, BZ in situ gel nanoemulsions (NEs) were developed and evaluated for transcorneal permeation via the bovine corneal membrane. The spontaneous emulsification method was employed to prepare BZ in situ gel NEs. Various physicochemical characteristics, including particle size, polydispersity index, pH, refractive index, and viscosity, were evaluated. Accelerated physical stability and in vitro drug release, as well as transcorneal permeation studies was performed by applying the Franz-type diffusion cells. Thermosensitive BZ in situ gel NEs with desired physicochemical features and sustained release profiles were designed in the current study. Optimized Formulations exhibited physical stability under different conditions. The transcorneal permeation of formulations was higher than that of suspension, especially for F3b formulation. According to the present in vitro and ex vivo evaluations, it is concluded that in situ gel NEs could be a topical administration of BZ as a suitable ocular drug delivery system.
The challenges of cross-linguistic parsing

is short paper aims at outlining the present state of cross-linguistic parsing, which, in the context of computational linguistics,1 can be dened as “the process of automatically analyzing a given sentence, viewed as a sequence of words, in order to determine its possible underlying syntactic structures” (Nederhof & Saa 2010: 105, cf. Naumann & Langer 1994: 3). Parsing is an essential component of machine translation and question answering systems, amongst others (cf. Naumann & Langer 1994: 13). Figure 1 is an example2 of parsing based on phrase structure rules.
Heat and mass transfer enhancement strategies by impinging jets: A literature review

Heat and mass transfer can be greatly increased when using impinging jets, regardless the application. The reason behind this is the complex behavior of the impinging jet flow which is leading to the generation of a multitude of flow phenomena, like: large-scale structures, small scale turbulent mixing, large curvature involving strong normal stresses, and strong shear, stagnation, separation, and re-attachment of the wall boundary-layers, increased heat transfer at the impinged plate. All these listed phenomena have highly unsteady nature and even though a lot of scientific studies have approached this subject, the impinging jet is not fully understood due to the difficulties of carrying out detailed experimental and numerically investigations. Nevertheless, for heat transfer enhancement in impinging jet applications, both passive and active strategies are employed. The effect of nozzle geometry and the impinging surface macro-structure modification are some of the most prominent passive strategies. On the other side, the most used active strategies utilize acoustical and mechanical oscillations in the exit plane of the flow, which in certain situations favors mixing enhancement. This is favored by the intensification of some instabilities and by the onset of large scale vortices with important levels of energy.
The Effect of Salinity and Different Rootstocks on Fruit and Photosynthetic Parameters in Grafted Cucumber

Salinity is a vital factor in reducing cucumber yield and quality. Grafting on the resistant rootstock could keep growth near to optimum condition. The present research aimed to investigate the characteristics of different rootstocks on the physiology and fruit characteristics of cucumber. Treatments were rootstocks [‘Rn’: Nongrafted (Cucumis sativus v. DAVOSII), ‘Rt’: Tanbal (Cucurbita maxima), ‘Rg’: Ghalyani (Lagenaria siceraria), ‘Rk’: Karela (Momordica charantia), ‘Rkh’: Khoreshi (Cucurbita pepo)] and salinity concentration included 0 (S1), 30 (S2) and 60 (S3) mM with three replications. Most of the fruit characteristics and physiology parameters like fruit weight and firmness, fruit length/diameter, photosynthesis rate, transpiration decreased with salinity. When grafted plants were used, physiological parameters improved in ‘Rkh’, ‘Rk’ at salinity compare with ‘Rn’. Transpiration decreased with salinity in Rkh and Rg and did not change in ‘Rn’. The highest transpiration was seen in ‘Rn’ in all salinity levels. Fruit quality is mostly improved at ‘Rg’ in salinity. TSS increased in ‘Rg’ and ‘Rkh’ in S2. Firmness decreased with S3 in ‘Rg’ and Rkh significantly. Na absorption was highest in ‘Rn’ and conversely, K concentration was lowest in ‘Rn’. Na concentration did not affect salinity levels in other rootstock and was lower than ‘Rn’. On the other hands, K concentration increased in ‘Rk’ and ‘Rkh’ in all salinity levels. Generally, using rootstocks like ‘Rk’, ‘Rkh’, and ‘Rg’ improved fruit quality and physiological aspect of grafted cucumber in saline soil.
Determination of Resistance in Winter Wheat Genotypes to the Dryland Root Rots caused by Fusarium culmorum in Turkey

The dryland root rot (foot/crown) caused by Fusarium spp. attacks cereals especially wheat and causes severe yield loss by reducing both grain quantity and quality. Among those Fusarium species attacking wheat crop is the Fusarium culmorum species which has been reported as the main crown rot causal agent in Turkey. Unfortunately, up-to-date, there is only some wheat genotypes with partial resistant to Fusarium spp. Therefore, this study was carried out to find new sources of resistance in diverse wheat genotypes to limit the damage caused by Fusarium disease. In this study, a total of 141 genotypes and breeding lines were obtained from 19 different countries, provided via the International Winter Wheat Improvement Program (IWWIP) and screened for their resistance reactions to a local isolate of Fusarium culmorum under three different environmental conditions (growth room, greenhouse and field) in Turkey in 2012. The best performed genotypes in terms of resistant were then rescreened in 2013 for data validation. Out of the 141 phenotyped wheat genotypes, 17 genotypes (12 %) ranked as moderately resistant (MR) at seedling and/or adult growth stage. The genotypes from Mexico seemed to have adult plant resistant rather than seedling resistance which was higher in the USA genotypes. Winter bread wheats PATWIN YR5 and TAST/SPRW//ZAR/5/YUANDONG 3/4/PPB8-68/CHRC/3/PYN//TAM101/AMIGO which possess high level of resistance seem promising for breeding for foot rot.
A Typology of Democratic Innovations

A variety of institutions and processes, collectively termed ‘democratic innovations’ are increasingly being utilised around the world in order to increase, diversify, and deepen opportunities for citizen participation in governance, policy, and public administration processes and are attracting substantial academic interest as a result. Despite this there is little agreement in the academy about which governance processes should be classified as ‘democratic innovations’ and a lack of clarity and precision in the use of the term. Indeed, democracy itself is widely regarded as an ‘essentially contested concept’ and ‘innovation’ is interpreted in a number of different ways across different countries and policy areas. This article seeks to survey the history of the term’s use and critically review the different and dominant definitions currently employed, in order to produce an analytical typology that can provide greater clarity and coherence. Drawing on Freeden’s morphological analysis of political concepts a set of ineliminable, quasi-contingent, and contextual features of democratic innovations are offered to enable a degree of consistency to be achieved in the understanding of ‘democratic innovations’ independent of specific contexts. Following this it is argued that democratic innovations can be seen as Wittgensteinian ‘families’ of conceptual clusters that include spaces and processes that have certain resemblance but, also differences determined by context. They are similar because they all reimagine the role of citizens in governance processes, and thus renegotiate the relationship between government and civil society.
An Iterative Learning Control Architecture For Precision Machining Processes

Machining processes, although presenting a cyclic behaviour, cannot exploit control strategies such as Iterative Learning Control (ILC) or Repetitive Control (RC) to improve tracking performance, since the initial position of the tool at the beginning of each cycle depends on the material removed during the previous cycles. This paper proposes a solution to this weakness by introducing a new control strategy that merges the ability of ILC to support the re-initialization of the initial conditions, with the ability of RC to support the dependencies of the initial conditions from previous cycles.
An abstract interpretation for SPMD divergence on reducible control flow graphs

Vectorizing compilers employ divergence analysis to detect at which program point a specific variable is uniform, i.e. has the same value on all SPMD threads that execute this program point. They exploit uniformity to retain branching to counter branch divergence and defer computations to scalar processor units. Divergence is a hyper-property and is closely related to non-interference and binding time. There exist several divergence, binding time, and non-interference analyses already but they either sacrifice precision or make significant restrictions to the syntactical structure of the program in order to achieve soundness. In this paper, we present the first abstract interpretation for uniformity that is general enough to be applicable to reducible CFGs and, at the same time, more precise than other analyses that achieve at least the same generality. Our analysis comes with a correctness proof that is to a large part mechanized in Coq. Our experimental evaluation shows that the compile time and the precision of our analysis is on par with LLVM's default divergence analysis that is only sound on more restricted CFGs. At the same time, our analysis is faster and achieves better precision than a state-of-the-art non-interference analysis that is sound and at least as general as our analysis.
EXPERIENCE, KNOWLEDGE AND THE TECHNOLOGY CHOICES OF SHRIMP FARMERS IN THAILAND AND VIETNAM

It is frequently asserted that as farmers gain in experience or obtain more accurate and scientific knowledge that their capacity to manage shrimp ponds more sustainable is enhanced. Conversely, those with little experience and poor knowledge are often characterized by unsustainable practices. In this paper we explore the relationships between information, sources and quality of knowledge about the environment and the technology choices and practices of shrimp farming businesses in Thailand and Vietnam. We do this by developing an initial set of indicators of ecological, social, and economic sustainability of pond-level practices and explore associations with experience, knowledge, and technology variables with alternative explicit path models. Our findings suggest that information directly affect sources and quality of knowledge, as well as subsequent technology choice and the relative sustainability of farming practices in terms of ecological, social, and economic sustainability. Relationships were not identical in Vietnam and Thailand reflecting differences in access to and sources of information and the overall structure of the industry in the two countries.
REV IEW AND SYNTHES IS The biogeography of marine plankton traits

Andrew D. Barton,* Andrew J. Pershing, Elena Litchman, Nicholas R. Record, Kyle F. Edwards, Zoe V. Finkel, Thomas Kiørboe, and Ben A. Ward Abstract Changes in marine plankton communities driven by environmental variability impact the marine food web and global biogeochemical cycles of carbon and other elements. To predict and assess these community shifts and their consequences, ecologists are increasingly investigating how the functional traits of plankton determine their relative fitness along environmental and biological gradients. Laboratory, field and modelling studies are adopting this trait-based approach to map the biogeography of plankton traits that underlies variations in plankton communities. Here, we review progress towards understanding the regulatory roles of several key plankton functional traits, including cell size, N2-fixation and mixotrophy among phytoplankton, and body size, ontogeny and feeding behaviour for zooplankton. The trait biogeographical approach sheds light on what structures plankton communities in the current ocean, as well as under climate change scenarios, and also allows for finer resolution of community function because community trait composition determines the rates of significant processes, including carbon export. Although understanding of trait biogeography is growing, uncertainties remain that stem, in part, from the paucity of observations describing plankton functional traits. Thus, in addition to recommending widespread adoption of the trait-based approach, we advocate for enhanced collection, standardisation and dissemination of plankton functional trait data.
Revision of the theoretical and observational grounds of the seismic hazard estimates at a national scale

Introduction We would like to point out that this re-proposed project received the present year funds only around the half of January 2003. For this reason this report will reflect activities formally carried out in a time period definitely shorter than one year. In particular, for the peculiar nature of the collaboration with the private research company SGA, the planned activities in the ambit of Task 1 are still at a very early stage and will be presented here in a preliminary form. We thus reserve ourselves to complete the reporting at a successive time. On the contrary the activities concerning the other research lines were pursued almost exactly according to the initial program, due to the voluntary effort of the contributors, although with some difficulties. The objectives of the project, as also described in the re-proposition proposal, have been resized with relation to the referees’ comments and to the amount of assigned funds. The corresponding activities affects only 4 of the tasks initially proposed. This strongly reduced the unitariness and coherency of the project that originally was thought to have, as final product, the revision of hazard estimates at national scale. We tried however to develop a proposal that, starting from the activities that the Evaluation Commission have judged new and innovative, was able to give results directly usable by other GNDT project. In this ambit, as also suggested by the Commission, we tried to integrate our project with the one coordinated by A. Amato through information exchanges, in order to avoid superposition or duplication of objectives. For this reason some researches we proposed have been thought to give products that can be easily used by anyone. Among the others we want to mention the “Boxer” code to analyze macroseismic data and the database of Earthquake Mechanism of Mediterranean Area (EMMA). These are tools designed for a free usage by Italian and foreigner investigators and for which we also prepared a reference manual. In the following we synthetically report, for each of the active tasks, the planned activities, the expected results in the two years (second and third) of the reproposition and those effectively achieved in the second year.
The prevalence of hearing loss in infants hospitalized in the neonatal intensive care units

Background and AimStudies have shown that several factors affect the hearing loss of infants hospitalized in the neonatal intensive care unit (NICU). These factors include hyperbilirubinemia, low birth weight, asphyxia, and prematurity. This study aimed to investigate the prevalence of hearing loss and its risk factors in NICU infants.MethodsThis is a cross-sectional study. Samples were 159 infants admitted to the NICU in Fatemieh and Shahid Beheshti hospitals in Hamadan, Iran, who were selected using a convenience sampling method. Their hearing was screened using transient evoked otoacoustic emission (TEOAE) and automated auditory brainstem response (AABR) tests; in case of failure in these tests, auditory brainstem response (ABR) was performed.ResultsOf 159 infants, 9 (5.66%) were identified with different types of hearing loss where 4 (2.51%) had sensory-neural hearing loss, one (0.62%) had auditory neuropathy and 4 (2.51%) had conductive hearing loss. There was a statistically significant relationship between hearing loss and birth weight < 1500 g, hyperbilirubine mia, antibiotic therapy, family history of hearing loss, asphyxia and Apgar score < 5.ConclusionPrevalence of hearing loss in NICU infants is noticeable so hearing assessment after discharge is necessary. Due to the presence of auditory neuropathy, simultaneous use of TEOAE and AABR tests in these infants is recommended.
Quantifying Intimacy in Language

Intimacy is a fundamental aspect of how we relate to others in social settings. Language encodes the social information of intimacy through both topics and other more subtle cues (such as linguistic hedging and swearing). Here, we introduce a new computational framework for studying expressions of the intimacy in language with an accompanying dataset and deep learning model for accurately predicting the intimacy level of questions (Pearson's r=0.87). Through analyzing a dataset of 80.5M questions across social media, books, and films, we show that individuals employ interpersonal pragmatic moves in their language to align their intimacy with social settings. Then, in three studies, we further demonstrate how individuals modulate their intimacy to match social norms around gender, social distance, and audience, each validating key findings from studies in social psychology. Our work demonstrates that intimacy is a pervasive and impactful social dimension of language.
Automated approach to measure stellar inclinations: validation through large-scale measurements on the red giant branch

Measuring stellar inclinations is fundamental to understand planetary formation and dynamics as well as physical conditions during star formation. Oscillation spectra of red giant stars exhibit mixed modes that have both a gravity component from the radiative interior and a pressure component from the convective envelope. Gravity-dominated (g-m) mixed modes split by rotation are well separated inside frequency spectra, making possible accurate measurements of stellar inclinations. This work aims at developing an automated and general approach to measure stellar inclinations, that can be applied to any solar-type pulsator for which oscillation modes are identified, and at validating it using red giant branch stars observed by Kepler. We use the mean height-to-background ratio of dipole mixed modes with different azimuthal orders to measure stellar inclinations. The underlying statistical distribution of inclinations is recovered in an unbiased way using a probability density function for the stellar inclination angle. We derive stellar inclination measurements for 1139 stars on the red giant branch, for which Gehan et al. (2018) have identified the azimuthal order of dipole g-m mixed modes. Raw measured inclinations exhibit strong deviation with respect to isotropy which is expected for random inclinations over the sky. When taking uncertainties into account, the reconstructed distribution of inclinations actually follows the expected isotropic distribution of the rotational axis. This work highlights the biases that affect inclination measurements and provides the way to infer their underlying statistical distribution. When the star is seen either pole-on or equator-on, measurements are challenging and result in a biased distribution. Correcting biases that appear at the low- and high inclination regimes allows us to recover the underlying inclination distribution.
QMUL-SDS @ DIACR-Ita: Evaluating Unsupervised Diachronic Lexical Semantics Classification in Italian (short paper)

In this paper, we present the results and main findings of our system for the DIACR-ITA 2020 Task. Our system focuses on using variations of training sets and different semantic detection methods. The task involves training, aligning and predicting a word's vector change from two diachronic Italian corpora. We demonstrate that using Temporal Word Embeddings with a Compass C-BOW model is more effective compared to different approaches including Logistic Regression and a Feed Forward Neural Network using accuracy. Our model ranked 3rd with an accuracy of 83.3%.