Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of p75NTR enhances the cholinergic innervation pattern of the visual cortex

Abstract The cholinergic system is involved in cortical plasticity, attention, and learning. Within the visual cortex the cholinergic system seems to play a role in visual perception. The cholinergic neurons which project into the visual cortex are located in the basal forebrain. It has been shown that mice deficient for the low-affinity neurotrophin receptor p75NTR display increased numbers of cholinergic neurons in the basal forebrain and a denser cholinergic innervation of the hippocampus. This prompted us to analyze whether the cholinergic system is altered in adult p75NTR deficient mice. By analyzing the densities of cholinergic fibers within layer IV as well as within layer V of the visual cortex, we found that adult p75NTR deficient mice display increased cholinergic fiber densities. However, this increase was not accompanied by an increase in the density of local cholinergic neurons within the visual cortex. This indicates that the enhanced cholinergic innervation of the visual cortex is due to alteration of the cholinergic neurons located in the basal forebrain, projecting to the visual cortex. The increased cholinergic innervation of the visual cortex makes the p75NTR deficient mice an attractive model to study the necessity of the cholinergic system for the visual cortex.
Pesticide Residues in Aquatic Invertebrates

Aquatic invertebrates are defined as invertebrate animals that depend on aquatic ecosystems or moist environments for at least a portion of their lifecycle. Occasionally, taxonomists also include the semiaquatic invertebrates, which inhabit shores and vegetation surrounding aquatic environments. Habitats for aquatic invertebrates include wetlands, lakes, streams, rivers, oceans, and other waters (Pechenik 1996). The term aquatic invertebrate refers to swimming nekton, floating plankton, bottom-dwelling benthos, and surfacedwelling neuston. Aquatic invertebrates are diverse species that range widely in size, habitat, behavior, characteristics, food preference, and evolutionary relationships. In the food web, aquatic invertebrates are often divided into herbivores, detritivores, carnivores, and parasites. However, many scientists classify aquatic organisms based on feeding method (shredders, grazers, and suspension feeders) rather than food type. For the purpose of this CONTENTS
Development and Usability Evaluation of a Desktop Software Application for Pain Assessment in Infants

ABSTRACT Background Pain assessment is a key component of pain management and research in infants. We developed software to assist in coding of pain in infants called PAiN (Pain Assessment in Neonates). Aims The aims of this study were to evaluate the usability of PAiN in terms of effectiveness, efficiency, and satisfaction among novice and expert users and to compare the efficiency and satisfaction of PAiN to existing software for coding of infant pain among expert users. Methods A quantitative usability testing approach was conducted with two participant groups, representing novice and expert end-users. Testing included an observed session with each participant completing a pain assessment coding task, followed by administration of the Post Study System Usability Questionnaire and Desirability Toolkit. For comparison, the usability of existing coding software was also evaluated by the expert group. Results Twelve novice and six expert users participated. Novice users committed 14 noncritical navigational errors, and experts committed six. For experts, the median time for completing the coding task was 28.6 min in PAiN, compared to 46.5 min using the existing software. The mean Post Study System Usability Questionnaire score among novice (1.89) and expert users (1.40) was not significantly different (P = 0.0917). Among experts, the score for the existing software (4.83) was significantly (P = 0.0277) higher compared to PAiN (1.40). Lower scores indicate more positive responses. Conclusions Users were highly satisfied with PAiN. Experts were more efficient with PAiN compared to the existing software. The study was critical to ensuring that PAiN is error free and easy to use prior to implementation.
CORRECTION[OPEN]

We inadvertently omitted a double bond in the A ring of several flavonoidmolecules in Figure 1, amistake that was kindly brought to the attention of The Plant Cell by Dr. Guanghui Xu (National Maize Improvement Center of China). In addition, the Figure 1 legend has been corrected to refer to rhamnosylation at “C-2” of the Glc moiety (instead of “C-1”). For ease of comparison, the original and corrected versions of this figure are presented below, with the position of the error and correction marked with red arrows.
Anomaly Detection System in Cloud Computing Network

Security in cloud computing poses higher challenges due to modern day distributed computing architectures. Cloud computing is a quickly developing IT show for the trade and conveyance of various administrations through the Internet. Be that as it may, there are a plenty of security worries in cloud computing which still should be handled (e.g., confidentiality, auditability and Privileged User Access). To recognize and avoid such issues, the Intrusion Detection System (IDS) and Intrusion Prevention System (IPS) are powerful instruments against assaults, for example, SQL Injection. Monitoring such a highly complex network environment needs a system capable of handling passive monitoring efficiently with less human intervene. Intrusion detection is a versatile security paradigm which can avert most of the computer and network related attacks if efficiently employed. In this paper, we propose a modern security monitoring framework capable of detecting security attacks through data intelligence. The results of experiments prove that the average time taken to predict attacks by K-means algorithm is better than Naive Bayes, MLP, and SVM algorithms.
A Modified Sesamol Derivative Inhibits Progression of Atherosclerosis

Objective—Sesamol, a phenolic component of lignans, has been previously shown to reduce lipopolysaccharide-induced oxidative stress and upregulate phosphatidylinositol 3-kinase/Akt/endothelial nitric oxide synthase pathways. In the present study, we synthesized a modified form of sesamol (INV-403) to enhance its properties and assessed its effects on atherosclerosis. Methods and Results—Watanabe heritable hyperlipidemic rabbits were fed with high-cholesterol chow for 6 weeks and then randomized to receive high-cholesterol diet either alone or combined with INV-403 (20 mg/kg per day) for 12 weeks. Serial MRI analysis demonstrated that INV-403 rapidly reduced atherosclerotic plaques (within 6 weeks), with confirmatory morphological analysis at 12 weeks posttreatment revealing reduced atherosclerosis paralleled by reduction in lipid and inflammatory cell content. Consistent with its effect on atherosclerosis, INV-403 improved vascular function (decreased constriction to angiotensin II and increased relaxatio.
Efficient Alignment Algorithms for DNA Sequencing Data

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space. Many new genome alignment algorithms are proposed over time and one of the key differentiators among these algorithms is the efficiency of the genome alignment process. I present a new algorithm for efficiently finding Maximal Exact Matches (MEMs) between two genomes: E-MEM (Efficient computation of maximal exact matches for very large genomes). Computing MEMs is one of the most time consuming step during the alignment process. E-MEM can be used to find MEMs which are used as seeds in a genome aligner to increase its efficiency. The E-MEM program is the most efficient algorithm as of today for computing MEMs, and it surpasses all competitors by large margins. There are many genome assembly algorithms available for use, but none produces perfect genome assemblies. It is important that assemblies produced by these algorithms are evaluated accurately and efficiently.This is necessary to make the right choice of the genome assembler to be used for all the downstream research and analysis. A fast genome assembly evaluator is a key factor when a new genome assembler is developed, to quickly evaluate the outcome of the algorithm. I present a fast and efficient genome assembly evaluator called LASER (Large genome ASsembly EvaluatoR), which is based on a leading genome assembly evaluator QUAST, but significantly more efficient both in terms of memory and run time. The NGS technologies limit the potential of genome assembly algorithms because of short read lengths and nonuniform coverage. Recently, third generation sequencing technologies have been proposed which promise very long reads and a uniform coverage. However, this
Optimising Flexibility of Temporal Problems with Uncertainty

Temporal networks have been applied in many autonomous systems. In real situations, we cannot ignore the uncertain factors when using those autonomous systems. Achieving robust schedules and temporal plans by optimising flexibility to tackle the uncertainty is the motivation of the thesis. This thesis focuses on the optimisation problems of temporal networks with uncertainty and controllable options in the field of Artificial Intelligence Planning and Scheduling. The goal of this thesis is to construct flexibility and robustness metrics for temporal networks under the constraints of different levels of controllability. Furthermore, optimising flexibility for temporal plans and schedules to achieve robust solutions with flexible executions. When solving temporal problems with uncertainty, postponing decisions according to the observations of uncertain events enables flexible strategies as the solutions instead of fixed schedules or plans. Among the three levels of controllability of the Simple Temporal Problem with Uncertainty (STPU), a problem is dynamically controllable if there is a successful dynamic strategy such that every decision in it is made according to the observations of past events. In the thesis, we make the following contributions. (1) We introduce an optimisation model for STPU based on the existing dynamic controllability checking algorithms. Some flexibility and robustness measures are introduced based on the model. (2) We extend the definition and verification algorithm of dynamic controllability to temporal problems with controllable discrete variables and uncertainty, which is called Controllable Conditional Temporal Problems with Uncertainty (CCTPU). An entirely dynamically controllable strategy of CCTPU consists of both temporal scheduling and variable assignments being dynamically decided, which maximize the flexibility of the execution. (3) We introduce optimisation models of CCTPU under fully dynamic controllability. The optimisation models aim to answer the questions how flexible, robust or controllable a schedule or temporal plan is. The experiments show that making decisions dynamically can achieve better objective values than doing statically. The thesis also contributes to the field of AI planning and scheduling by introducing robustness metrics of temporal networks, proposing an envelope-based algorithm that can check dynamic controllability of temporal networks with uncertainty and controllable discrete decisions, evaluating improvements from making decisions strongly controllable to temporally dynamically controllable and fully dynamically controllable and comparing the runtime of different implementations to present the scalability of dynamically controllable strategies.
Homeobox Protein Hex Facilitates Serum Responsive Factor–Mediated Activation of the SM22α Gene Transcription in Embryonic Fibroblasts

Objective— Hex (hematopoietically expressed homeobox), a member of homeobox family of transcription factors, has been implicated in the vascular development because of its expression in hemangioblast, a hypothetical stem cell that gives rise to both angioblasts and hematopoietic lineages. In the present study, we examined the role of Hex in the differentiation of vascular smooth muscle cells. Methods and Results— We constructed adenovirus expressing Hex, to which we refer to as AxCA/Hex, and transduced murine embryonic fibroblasts, 10T1/2 cells. Northern blot analyses showed that Hex increased the mRNA levels of smooth muscle α-actin and SM22α but not of calponin and smooth muscle myosin heavy chain. Transient transfection assays showed that Hex activates the transcription from the SM22α promoter in a CArG box-dependent manner. Electrophoretic mobility shift assays demonstrate that Hex is not able to bind to CArG box, but binding of serum responsive factor (SRF) to CArG box is enhanced in AxCA/Hex-transdu.
Les gardiens de nos rêves identifiés - Une cible neuronale de la maladie de Parkinson ?

m/s n° 10, vol. 33, octobre 2017 DOI : 10.1051/medsci/20173310006 infect mouse colonies and protect against highly-pathogenic C. difficile. Gut 2017 ; pii : gutjnl-2016-313510. 11. Etienne-Mesmin L, Chassaing B, Adekunle O, et al. Genome sequence of a toxin-positive Clostridium difficile strain isolated from murine feces. Genome Announc 2017 ; 5 : pii : e00088-17. 12. Nagaro KJ, Phillips ST, Cheknis AK, et al. Nontoxigenic Clostridium difficile protects hamsters against challenge with historic and epidemic strains of toxigenic BI/NAP1/027 C. difficile. Antimicrob Agents Chemother 2013 ; 57 : 5266-70. 13. Gerding DN, Meyer T, Lee C, et al. Administration of spores of nontoxigenic Clostridium difficile strain M3 for prevention of recurrent C. difficile infection: a randomized clinical trial. JAMA 2015 ; 313 : 1719-27. understanding transmission. Nat Rev Gastroenterol Hepatol 2016 ; 13 : 206-16. 6. Buffie CG, Bucci V, Stein RR, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 2015 ; 517 : 205-8. 7. Rupnik M, Wilcox MH, Gerding DN. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol 2009 ; 7 : 526-36. 8. Chen X, Katchar K, Goldsmith JD, et al. A mouse model of Clostridium difficile-associated disease. Gastroenterology 2008 ; 135 : 1984-92. 9. Reeves AE, Koenigsknecht MJ, Bergin IL, Young VB. Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect Immun 2012 ; 80 : 3786-94. 10. Etienne-Mesmin L, Chassaing B, Adekunle O, et al. Toxin-positive Clostridium difficile latently RÉFÉRENCES
Estimating point-of-interest rating based on visitors geospatial behaviour

Rating of different services, products and experiences plays an important role in our digitally assisted day-to-day life. It helps us make decisions when we are indecisive, uninformed or inexperienced. Traditionally, ratings depend on the willingness of existing customers to provide them. This often leads to biased (due to the insufficient number of votes) or nonexistent ratings. This was the motivation for our research, which aims to provide automatic star rating. The paper presents an approach to extracting points-of-interest from various sources and a novel approach to estimating point-of-interest ratings, based on geospatial data of their visitors. Our research is applied to campsite dataset where the community is still developing and more than thirty percent of camps are unrated. Our study use case addresses a realword problem of motorhome users visiting campsites in European countries. The dataset includes GPS traces from 10 motorhomes that were collected over a period of 2 years. To estimate star ratings of points-of-interest we applied machine learning methods including support vector machine, linear regression, random forest and decision trees. Our experimental results show that the duration of visit, which is a crucial part of the proposed approach, is an indicative feature for predicting camp ratings.
Expression of dehydrin and antioxidant genes and enzymatic antioxidant defense under drought stress in wild relatives of wheat

Abstract The aims of this study were to investigate different species of Triticum and Aegilops in terms of the expression pattern of ascorbate peroxidase, superoxide dismutase, and guaiacol peroxidase encoding genes along with the wheat dehydrin gene, wdhn13, which is involved in the induction of tolerance to drought stress. The study also explored the enzyme activity of these three antioxidant enzymes under drought stress. There was a significant difference in the expression level of the four studied genes, Wdhn13, APX, SOD and GPX, between the well-watered and drought stress (FC = 100% and FC = 25%) treatments and among the examined species. The relative expression of Wdhn13 under conditions of drought was higher in T. boeoticum and Ae. crassa compared to the tolerant reference cultivar (Sirvan) and the rest of the wild species. Ae. tauschii showed the highest expression of the APX gene, and the SOD and GPX genes were up-regulated in Ae. tauschii and T. boeoticum at the drought-stressed conditions. The highest APX, GPX and SOD enzyme activities under the drought-stressed conditions were observed in Ae. crassa, T. boeoticum and Ae. neglecta, respectively. The results indicated that there was relevant correspondence between the genetically determined tolerance of wheat species (i.e. the gene transcript levels) and their antioxidant enzyme activities. The species having Ab (T. boeoticum), D (Ae. tauschii) and D (Ae. tauschii and Ae.crassa) genomes had a higher expression of GPX, SOD, and APX genes, respectively.
A preliminary study to describe two wild phenotypes of (Myrtus communis) spread in some sites north of Lattakia Governorate

The study was aimed to describe two wild phenotypes, where exist as scattered groups of shrubs in villages (Ras auj, Slayeb al-Bahaouliah, Al-Rasteen), Lattakia governorate . This study was carried out during the years 2013 – 2014 . first phenotype has a bluish black fruits, gave symbol A. Second phenotype with spherical and white fruits, gave symbol B. phenotype (B) was exceeded in average of shrub height opposite to phenotype (A) , where recorded in mean (2.7 – 2.3 m) respectively, as well as it was exceeded in the length ,width, leaf area ,in addition to weight , length , and width of the fruit and its size , fruit size for A and B phenotypes gave in mean (0.801,1.032 cm 3 ) respectively. While the symbol A was exceeded on symbol B in the average number of main branches (six branches on A, three branches on B). Thick leaf for phenotypes A and B were (0.019, 0.024 cm) respectively, whereas no differences between two phenotypes in the average number of branching angle where was recorded approximately (79°). The date of the beginning of the flowering of the two phenotypes, was between (9-16) June and the number of stamens in the flower was big which recorded between (125, 150) stamen in both phenotypes. دراسة أولية لتوصيف طرازين بريين من نبات الريحان (الآس الشائع) Myrtus communis L. المنتشر في بعض المواقع شمال محافظة اللاذقية هدفت هذه الدراسة إلى توصيف طرازين بريين منتشرين بشكل تجمعات مبعثرة في قرى (رأس عوج ، صليب البهلولية ، الرستين) التابعة لمنطقة اللاذقية- ناحية البهلولية ، وتمت هذه الدراسة خلال عامي 2013- 2014 . أعطي الرمز ((A للطراز الأول ذو الثمار السوداء المزرقة ، وأعطي الرمز ((B للطراز الثاني ذو الثمار الكروية البيضاء . بينت الدراسة تفوق الطراز (B) على الطراز((A في متوسط ارتفاع الشجيرة حيث سجلت (2.7 – 2.3 م) على التوالي، وكذلك تفوق في متوسطات طول وعرض ومساحة الورقة إضافة إلى متوسط وزن وطول وعرض الثمرة وحجمها إذ كان حجم الثمرة للطرازين A، B على التوالي (0.801، 1.032) سم 3 على التوالي ، بينما تفوق الطراز ((A على الطراز ((B بعدد الفروع الهيكلية على الساق الرئيسة ( 6 فروع هيكلية للطراز A ، 3 فروع هيكلية للطراز B) ، كانت متوسط سماكة الورقة للطرازين A و B ( 0.019، 0.024 سم) على التوالي ، بينما لم يكن هناك أي اختلاف بين الطرازين في زاوية التفرع حيث سجلت تقريبا (80o )، كان تاريخ بدء الإزهار للطرازين بين (9-16) حزيران ، و كان عدد الأسدية في الزهرة كبير في كلا الطرازين حيث سجل مابين (120-150) سداة.
Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

Populations often encounter changed environments that remove selection for the maintenance of particular phenotypic traits. The resulting genetic decay of those traits under relaxed selection reduces an organism’s fitness in its prior environment. However, whether and how such decay alters the subsequent evolvability of a population upon restoration of selection for a previously diminished trait is not well understood. We addressed this question using Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in the absence of antibiotics. We first confirmed that these derived strains are typically more sensitive to various antibiotics than their common ancestor. We then subjected the ancestral and derived strains to various concentrations of these drugs to examine their potential to evolve increased resistance. We found that evolvability was idiosyncratic with respect to initial genotype; that is, the derived strains did not generally compensate for their greater susceptibility by “catching up” to the resistance level of the ancestor. Instead, the capacity to evolve increased resistance was constrained in some backgrounds, implying that evolvability depended upon prior mutations in a historically contingent fashion. We further subjected a time-series of clones from one LTEE population to tetracycline and determined that an evolutionary constraint arose early in that population, corroborating the role of contingency. In summary, relaxed selection not only can drive populations to increased antibiotic susceptibility, but it can also affect the subsequent evolvability of antibiotic resistance in an unpredictable manner. This conclusion has potential implications for public health, and it underscores the need to consider the genetic context of pathogens when designing drug-treatment strategies.
Overexpression of miRNA-125a-5p inhibits the growth and angiogenesis of hepatocellular carcinoma by regulating the expression of VEGF-A

Abstract The aim of the present study was to investigate whether miRNA (miRNA or miR)-125a-5p regulates angiogenesis in hepatocellular carcinoma (HCC) via VEGF-A. Reverse transcription-quantitative polymerase chain reaction was used to determine the expression of miRNA or mRNA. Western blotting was used to determine the expression of target protein in cells, while ELISA was employed to measure the secretion of target protein by cells. Dual luciferase reporter assay was performed to identify the direct interaction between miRNA and the 3’-untranslated region of its target mRNA. CCK-8 assay was carried out to evaluate the proliferation of cells. MTT assay was performed to examine the migration of cells. The results showed that decreased expression of miR-125a-5p in HHC HepG2 cells was potentially related to the increased expression of VEGF-A. The expression of miR-125a-5p regulated VEGF-A expression and secretion of HepG2 cells. miR-125a-5p could bind with the 3’-UTR seed region of VEGF-A mRNA to inhibit its expression. miR-125a-5p increased the expression and secretion of VEGF-A by HepG2 cells, which subsequently promoted the proliferation of HUVECs by increasing the phosphorylation of Akt. miR-125a-5p regulated the migration of HUVECs via the VEGF-A/VEGFR2/Akt signalling pathway, which was affected by the expression and secretion of VEGF-A by HepG2 cells. Thus, the present study demonstrates that overexpression of miR-125a-5p inhibits the growth and angiogenesis of HCC by regulating the expression of VEGF-A.