Miracle-dz/UniFAR-FTUs huggingface dataset:
Context-Aware Service Input Ranking by Learning from Historical Information

Users visit on-line services and compose them to accomplish on-line tasks, such as shopping on-line. Quite often, users enter the same information into various on-line services to finish on-line tasks. However, repetitively typing the same information into web forms is a tedious job for users. In this paper, we propose a context-aware ranking framework to rank values for input parameters. We propose 6 categories of ranking features constructed from various types of information, such as user contexts and patterns of user inputs. Our framework adopts learning-to-rank (LtR) algorithms that consist of a set of machine learned models to automatically construct ranking models by integrating the ranking features. When a user enters a value to an input parameter, an interaction between the user input and the input parameter is established. Our framework learns information relevant to such interactions and ranks user inputs in different contexts. Through empirical studies on the real-world on-line services, we obtain the following main results: (1) Among the 8 state-of-the-art learning-to-rank models, RankBoost can outperform other LtR models on ranking user inputs for input parameters; (2) Our framework using IRSVM that performs the worst among the LtR models outperforms the two baseline conventional ranking models and Google Chrome Autofilling, an industrial tool, on ranking user inputs to input parameters; and (3) We observe that the textual information of user inputs and input parameters is the most influential factor on ranking user inputs. Among the various types of contextual data, user locations and time matter the most to the ranking of user inputs.
Bioaccumulation, Ionome and Physiological Responses to Copper Toxicity of Iranian Grapevine Rootstocks Grafted with ‘Asgari’ Seedless Grape

ABSTRACT Use of proper rootstocks has the potential to improve copper (Cu) tolerance of grape. To evaluate the rootstock ability to reduce Cu transfer in the aerial portion of a grapevine, a glasshouse experiment was conducted to determine the physiological impact of Cu soil application in ‘Asgari’ seedless grape, either non-grafted or grafted onto different rootstocks. Vines were supplied with a nutrient solution at four levels of CuSO4 concentrations (0, 10, 25 and 50 µM). Cu toxicity symptoms in leaves and reduced plant growth rate were evident in the non-grafted ‘Asgari’ and less pronounced in grapevines grafted onto ‘Shahani’ rootstock. Moreover, ‘Asgari’ grafted onto ‘Shahani’ rootstock had lower rate of Cu accumulation in the leaves when compared to the roots than those of non-grafted and ‘Asgari’ with ‘Keshmeshi’ rootstock. Although significant reduction of P in non-grafted ‘Asgari’ leaf tissue was found under Cu toxicity, ‘Shahani’ rootstock reported the highest amount of P (5.94 mg g−1) in the leaves of ‘Asgari’ scion. However, significant fluctuations in terms of Ca and Fe were reported in leaves of both grafted and non-grafted ‘Asgari’. When exposed to Cu toxicity, ‘Shahani’ rootstock induced significant increase in chlorophyll content, Fv/Fm ratio and a noticeable reduction in electrolyte leakage, H2O2 and malondialdehyde (MDA) compared to those having ‘Keshmeshi’ rootstock and non-grafted ‘Asgari’. ‘Shahani’ rootstock improved ‘Asgari’ performance under Cu toxicity by slowly reducing the activity of antioxidant enzymes, preventing Cu accumulation in the aerial parts and maintaining a balanced scion nutritional status.
Uncoupling the roles of firing rates and spike bursts in shaping the GPe-STN beta band oscillations

The STN-GPe circuit is integral to generation and modulation of β oscillations in basal ganglia. However, how do their firing rates and spike bursting affect the oscillations is unclear. In order to uncouple their effects, we performed spiking neural network simulations of STN-GPe using a neuron model, where firing rates and spike bursting can be independently controlled. We find that the presence of oscillations are reliant on STN firing rates but not on GPe rates. The effect of GPe/STN bursting is state-dependent i.e only in network states on the border of oscillatory and non-oscillatory regime, an increase in GPe bursting strengthens the oscillations whereas an equivalent proportion of STN bursting suppresses them. We propose that these incursions into oscillatory and back to non-oscillatory state constitutes what we know as “β bursts”. During PD, however, the network shifts deeper into oscillatory regime where this mechanism fails leading to run away oscillations.
Leishmaniasis in Northern Morocco: Predominance of Leishmania infantum Compared to Leishmania tropica

In Morocco, Leishmania infantum species is the main causative agents of visceral leishmaniasis (VL). However, cutaneous leishmaniasis (CL) due to L. infantum has been reported sporadically. Moreover, the recent geographical expansion of L. infantum in the Mediterranean subregion leads us to suggest whether the nonsporadic cases of CL due to this species are present. In this context, this review is written to establish a retrospective study of cutaneous and visceral leishmaniasis in northern Morocco between 1997 and 2018 and also to conduct a molecular study to identify the circulating species responsible for the recent cases of leishmaniases in this region. Data concerning leishmaniases cases were collected from the Epidemiology and Disease Control Directorate from 1997 to 2018. Human samples obtained from peripheral laboratories were examined using PCR-ITS1 method. The ITS1 products were subjected to digestion with the restriction endonuclease Mn1-I. Between 1997 and 2018, a total of 1,255 cases of cutaneous and visceral leishmaniasis were recorded in Tangier-Tetouan-Al Hoceima Region, i.e., 1.56% of the reported cases in Morocco (1,255/80,299). Concerning the geographical study covering the period 2007-2018, 79.5% (105/132) of the sectors were affected by leishmaniases. The molecular results showed that Humans were found to be infected with the L. infantum species with a high infection rate compared to L. tropica infection. Moreover, molecular characterization using ITS1 PCR-RFLP showed that the density of L. infantum was significantly higher (n = 68/81; 84%) than that of L. tropica (n = 13/81; 16%) (P-value 9.894e-10). While regarding visceral leishmaniasis, L. infantum was the only species responsible of this form. These findings of this study showed the emergence of L. infantum in Morocco and suggest that this species might be more prevalent than previously thought. Furthermore, the molecular determination of L. infantum will be helpful for control strategies by taking into consideration the reservoir of this species.
Poor Glycaemic Control Is Associated with Increased Lipid Peroxidation and Glutathione Peroxidase Activity in Type 2 Diabetes Patients

Glycaemic control is the main focus of managing diabetes and its complications. Hyperglycaemia induces oxidative stress favouring cellular damage and subsequent diabetic complications. The present study was conducted to compare the plasma total antioxidant capacity (TAC) and individual antioxidant marker antioxidant status of type 2 diabetics (T2D) with good ((+) GC) and poor ((-) GC) glycaemic control with prediabetic (PDM) and normoglycaemic (NG) individuals. T2D (n = 147), PDM (n = 47), and NGC (n = 106) were recruited as subjects. T2D and PDM had lower plasma TAG than NG subjects. T2D and PDM had significantly higher GPx activity and plasma MDA concentrations than NG. PDM showed the highest SOD activity. T2D (-) GC showed significantly elevated GPx activity and higher MDA level and significantly lower SOD activity among all study groups. Lower plasma TAC and higher plasma MDA indicate the presence of oxidative stress in T2D and PDM. Elevated GPx activity in T2D, PDM, and particularly in T2D (-) GC suggests a compensatory response to counteract excess lipid peroxidation in the hyperglycaemic state. Decline in SOD activity advocates the presence of glycation and excess lipid peroxidation in T2D.
RAD sequencing rejects a long‐distance disjunction in
 Stellaria
 (Caryophyllaceae) and yields support for a new southern Rocky Mountains endemic

Whereas the eastern North American–eastern Asian floristic connection represents one of the most widely studied biogeographical relationships in flowering plant evolution, connections between western North America and Asia have been comparatively rarely investigated, especially through genetic approaches. Stellaria irrigua is one of several plants that has been treated as an exceptionally dramatic example of a disjunction between floristically similar, high alpine biotas of the southern Rocky Mountains and south-central Siberia. We here employ numerous new field collections and ddRADseq data to test the hypothesis that S. irrigua—a species that has been known for over 180 years—represents a long-distance disjunction between the southern Rocky Mountains and central Asia. Extensive fieldwork, review and perusal of herbarium materials, and phylogenomic analyses indicate that S. irrigua is broadly distributed across an amphi-Beringian arc extending from southern and central Asia, east through Beringia, and south throughout mountainous regions of western North America. Sampled Asian populations formed two clades, and North American individuals all formed a clade embedded within this broader Asian lineage. Stellaria irrigua is, however, rendered non-monophyletic by a lineage that is embedded within the North American populations and is ecologically and morphologically distinctive from S. irrigua. The identity of this newly recognized lineage, which was in prior works attributed to S. irrigua, has been confused since plants of the former were first collected in the San Juan Mountains of Colorado in the late 1800s under Arenaria and Alsine. We provide a new name for this taxon, Stellaria sanjuanensis, a charismatic starwort of dry alpine scree slopes of the southern Rocky Mountains. Additionally, two lectotypes are designated, one holotype and one isotype are identified, and two new synonymies are proposed, to help stabilize the taxonomy and nomenclature of this long-confused species complex. A key to the starworts of the southern Rocky Mountains is also provided, and Stellaria alsine is reported as new to the region.
Dynamic Ins2 gene activity defines β-cell maturity states

Transcriptional and functional cellular specialization has been described for insulin-secreting β-cells of the endocrine pancreas. However, it is not clear whether β-cell heterogeneity is stable or reflects dynamic cellular states. We investigated the temporal kinetics of endogenous insulin gene activity using live cell imaging, with complementary experiments employing FACS and single cell RNA sequencing, in β-cells from Ins2GFP knock-in mice. In vivo staining and FACS analysis of islets from Ins2GFP mice confirmed that at a given moment, ~25% of β-cells exhibited significantly higher activity at the conserved insulin gene Ins2. Live cell imaging captured Ins2 gene activity dynamics in single β-cells over days. Autocorrelation analysis revealed a subset of cells with oscillating behavior, with mean oscillation periods of 17 hours. Increased glucose concentrations stimulated more cells to oscillate and resulted in higher average Ins2 gene activity per cell. Single cell RNA sequencing showed that Ins2(GFP)HIGH β-cells were enriched for markers of β-cell maturity. Ins2(GFP)HIGH β-cells were also significantly less viable at all glucose concentrations and in the context of ER stress. Collectively, our results demonstrate that the heterogeneity of insulin production, observed in mouse and human β-cells, can be accounted for by dynamic states of insulin gene activity. Blurb Previously reported pancreatic β-cell heterogeneity reflects β-cell state transitions.
Distributed neural replay of decision confidence mediates informational conformity

We occasionally receive conflicting views from others. To maximize accuracy, we should exercise informational conformity by changing our mind proportional to our confidence about our initial view. This account predicts that neural correlates of confidence in the private decision should be replayed as the private and social information are integrated. In a perceptual estimation task (N=120), influence from others was proportional to private confidence. Human fMRI (N=20) showed that consistent with the replay hypothesis, confidence covaried with temporally distributed activity during private estimate (Precuneus and dorsal anterior cingulate cortex, dACC), social change of mind (dACC) and social outcome (dorsolateral prefrontal cortex and dACC). During social change of mind and only when paired with alleged human (but not with computer) partners, left temproparietal junction carried information about participants9 social use of confidence. Our study reveals the neuronal substrates of the role of confidence in computational implementation of informational conformity.
Mechanistic Insights of Phenobarbital-Mediated Activation of Human but Not Mouse Pregnane X Receptor

Phenobarbital (PB), a broadly used antiseizure drug, was the first to be characterized as an inducer of cytochrome P450 by activation of the constitutive androstane receptor (CAR). Although PB is recognized as a conserved CAR activator among species via a well-documented indirect activation mechanism, conflicting results have been reported regarding PB regulation of the pregnane X receptor (PXR), a sister receptor of CAR, and the underlying mechanisms remain elusive. Here, we show that in a human CAR (hCAR)-knockout (KO) HepaRG cell line, PB significantly induces the expression of CYP2B6 and CYP3A4, two shared target genes of hCAR and human PXR (hPXR). In human primary hepatocytes and hCAR-KO HepaRG cells, PB-induced expression of CYP3A4 was markedly repressed by genetic knockdown or pharmacological inhibition of hPXR. Mechanistically, PB concentration dependently activates hPXR but not its mouse counterpart in cell-based luciferase assays. Mammalian two-hybrid assays demonstrated that PB selectively increases the functional interaction between the steroid receptor coactivator-1 and hPXR but not mouse PXR. Moreover, surface plasmon resonance binding affinity assay showed that PB directly binds to the ligand binding domain of hPXR (KD = 1.42 × 10−05). Structure-activity analysis further revealed that the amino acid tryptophan-299 within the ligand binding pocket of hPXR plays a key role in the agonistic binding of PB and mutation of tryptophan-299 disrupts PB activation of hPXR. Collectively, these data reveal that PB, a selective mouse CAR activator, activates both hCAR and hPXR, and provide novel mechanistic insights for PB-mediated activation of hPXR.
Effects of physical training on sarcomere lengths and muscle-tendon interface of the cervical region in an experimental model of menopause

The aim of this study was to describe the structural and ultrastructural aspects of the myotendinous junction (MTJ) and the proximal and distal sarcomeres of the sternomastoid of aged Wistar rats subjected to an experimental model of menopause and swimming training. A total of 20 female elderly rats were divided into the following four groups (n=5 in each group): sedentary/no-menopausal (SNM), trained/nomenopausal (TNM), sedentary/menopausal (SM), and trained/menopausal (TM). The MTJ samples were dissected and analyzed using transmission electron microscopy. We showed that the TNM Group rats exhibited changes in morphological characteristics as a consequence of physical exercise, which included an increase of 36.60% (P<0.001) in the evagination length of the MTJ and a reduction in the length of the distal (77.38%) (P<0.0001) and proximal (68.15%) (P<0.0001) sarcomeres. The SM Group exhibited a reduction of about 275.93% (P<0.001) in the muscle-tendon interface and in the lengths of distal sarcomeres (55.87%) (P<0.0001) compared with SNM Group. Our results suggest that the swimming training under experimental model of menopause promoted tissue reorganization and increased muscle-tendon interaction with a drastic development in the length and thickness of the sarcoplasmatic invaginations and evaginations. In addition, the sarcomeres exhibited different lengths and a reduction in both groups subjected to swimming training.
Prediction of girdle beetle (Oberiopsis brevis) infestation through pest-weather model in soybean

Girdle beetle happens to be a serious insect pest causing yield losses between 14 to 42 per cent in soybean. The incidence of this insect pest is related to the prevailing weather conditions. It is in this context, we intended to ascertain pertinent weather parameters that directly influence the girdle beetle incidence and the appropriate stage it infests and therefore necessary curative measures can be addressed to. Therefore, data survey was conducted on girdle beetle damage on soybean crop under Crop Pest Surveillance and Advisory Project (CROPSAP) in 20 districts of Maharashtra state during 2010-2015. The weekly data collected so were used for the analysis. The correlation analysis of girdle beetle damage with climatic variables showed the significant negative correlation with maximum temperature during current (TMax0 =-0.44**) and previous two lag weeks (TMax-1= -0.61**; TMax-2=-0.54**) and significant positive correlation with relative humidity in current (RH0=0.24*) and first lag week (RH1=0.29*). Separate models pertaining to two peak weeks were developed using multiple regression and assessed for its prediction accuracy. The first peak (33 SMW) model explained 54.2% variation in percent damage and the variables significantly influencing its infestation were TMin0, TMax-1, TMin-1, and TMin-2. The second peak model (36 SMW) could explain 53.52% variability and TMax-1, RF-2, and TMin-2 were significantly influencing the infestation. The favorable pre-disposing conditions for peak damage were found to be related to maximum temperature (27.29-31.65 oC), minimum temperature (19.73-24.74) oC, relative humidity (82.96-93.75%), and weekly total rainfall (15.03-141.46 mm). Weather based prediction models were also validated satisfactorily using cross-validation approach using two years (2014 and 2015) independent dataset. Small RMSE value, standardized residuals between ±3 and insignificant value of t-test signifies that there was no significant difference between observed and predicted values of girdle beetle damage. In conclusion, maximum and minimum temperature, and rainfall determine the severity of girdle beetle incidence.
Using a novel web application for thermodynamic characterization of Tel22 G-quadruplex unfolding

Measuring and quantifying thermodynamic parameters that determine stability of and interactions between biological macromolecules is an essential and necessary complement to structural studies. Although several laboratories are able to obtain basic thermodynamic parameters for the observed process, the data interpretation and analysis quality of reported data can be extremely tedious. We have started to develop a web application that will help users to perform thermodynamic characterization of G-quadruplex unfolding. The application can perform global fitting of calorimetric and spectroscopic data, and it uses a three-state equilibrium model to obtain thermodynamic parameters for each transition step: the Gibbs energy, the enthalpy, and the heat capacity. As well as these, the application can define the number of K+ ions and the number of water molecules being released or taken up during the unfolding. To test our application, we used UV spectroscopy, circular dichroism, and differential scanning calorimetry, to monitor folding and unfolding of a model 22-nucleotide-long sequence of human 3’-telomeric overhang, known as Tel22. The obtained data was fed to the web application and global fit revealed that unfolding of Tel22 involves at least one intermediate state, and that K+ ions are released during the unfolding, whereas water molecules are taken up. STATEMENT OF SIGNIFICANCE The laws of thermodynamics provide tools for the use of elegant mathematical expressions to describe stabilities and interactions of biological macromolecule. Even though thermodynamic profiles of simple transitions (e.g., two state) can be obtained in a relatively straightforward manner, performing thermodynamic analysis of complex/ multistep transitions or global analysis of several experimental data requires some experiences and skills. In the present study we are demonstrating how newly developed web application can be used to provide better understanding of driving forces responsible for the structural interconversion of G-quadruplex structures. We have tested this web application with experimental data obtained from monitoring thermal folding/ unfolding of the 5’-AG3T2AG3T2AG3T2AG3-3’ (Tel22) DNA sequence. We believe that this application can be used as a research and/or teaching tool, and it will allow comparisons of the thermodynamic parameters obtained between different laboratories.
Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval

Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades resolution with increasing depth. We propose a method that enables the construction of an in situ 3D response of single emitters directly from single-molecule blinking datasets, and therefore allows their locations to be pinpointed with precision that achieves the Cramér-Rao lower bound and uncompromised fidelity. We demonstrate this method, named in situ PSF retrieval (INSPR), across a range of cellular and tissue architectures, from mitochondrial networks and nuclear pores in mammalian cells to amyloid-β plaques and dendrites in brain tissues and elastic fibers in developing cartilage of mice. This advancement expands the routine applicability of super-resolution microscopy from selected cellular targets near coverslips to intra- and extracellular targets deep inside tissues. In situ point spread function (PSF) retrieval (INSPR) enables precise single-molecule localization in 3D single-molecule localization microscopy of whole cells and tissues. It directly determines PSF from a single-molecule blinking dataset, removing errors associated with sample-induced aberrations.
Molecular evidence of Helicobacter suis infection in pigs in Nigeria

Helicobacter suis mainly colonizes the stomach of pigs and occasionally infects humans. It is a prevalent cause of gastritis and gastric ulcers in both species. This study was designed to determine the colonization rate of H. suis in the stomach of pigs in Nigeria. Pig slaughter house surveys were conducted and stomach mucosa samples were collected from the fundus of the stomach of a total of 160 pigs in four locations in Nigeria (Lagos, Delta, Enugu and Plateau States). In each location, 50% of the samples were collected from stomachs with ulceration in the fundus, while the rest were from those with no gross lesions. DNA was extracted and PCR assay was conducted using standard primers. Data was analyzed by descriptive statistics and Chi-square test (p< 0.05). H. suis was detected in 8.75% of the samples across the four locations at a frequency of 15, 7.5, 10 and 2.5% in Lagos, Delta, Enugu and Plateau states, respectively. H suis was detected in 12.5 and 5% of the stomachs with ulcers and without ulcers, respectively. H suis colonizes pigs in Nigeria at a relatively low rate with its colonization rate being higher in stomachs with ulcers. There is need for characterization of the strains of the organism in Nigeria for a better understanding of its possible role in gastric ulceration in pigs. Key words: Gastric ulcer, Helicobacter suis, pigs, stomach.