Miracle-dz/UniFAR-FTUs huggingface dataset:
Implication of exofacial thiol groups in the reducing activity of Listeria monocytogenes

Listeria monocytogenes growing in BHI in anaerobic condition leads a decrease of redox potential at pH7 (Eh7) from 0 to −250 mV. An investigation of mechanisms involved in this reducing activity shows the implication of thiol groups located on the bacterial cell surface. Indeed, after reduction of media to −250 mV, only thiol-reactive reagents could restore the initial Eh7 value. Moreover, the growth of L. monocytogenes in anaerobic condition is characterized by a reduction then acidification phases. This suggests a sensor mechanism of environmental Eh7 to convert the metabolism way from the first phase to the second. Finally, the concentration of exofacial thiol still increase strongly during the acidification phase of L. monocytogenes, even after reach the minimal value of Eh7. These results suggest that maintaining the exofacial thiol (−SH) groups in a reduced state do not depend on an active mechanism. Thiol groups appear to be displayed by membrane proteins or cell wallbound proteins and may participate in protecting cells against oxidative stress.
Citizen science data enhance spatio-temporal extent and resolution of animal population studies

Informed management and conservation decisions for animal populations often require data at sufficient geographic, temporal, and demographic resolutions for precise and unbiased estimates of parameters including population size and demographic rates. Recently developed integrated population models estimate such parameters by unifying population presence-absence and demographic data, and we demonstrate how citizen science offers a cost-efficient mechanism to collect such data. We describe the early results of iSeeMammals, a citizen science project that collects opportunistic data on the black bear population in New York State by enlisting volunteers to collect data through observations, hikes, and trail cameras. In 10 months, iSeeMammals increased the spatio-temporal extent of data collection by approximately fourfold and reduced cost by 83% compared to systematic sampling. In combination with other datasets in integrated population model frameworks, large, spatiotemporally extensive datasets from citizen science projects like iSeeMammals can help improve inferences about population-level structure and dynamics.
Disappearing edge: the flowering period changes the distribution of insect pollinators in invasive goldenrod patches

The response of animals to the edge reveals the potential mechanism underlying the impact of invasive plants on native pollinators. Many invasive plants flower only during a part of the growing season, which creates a temporal pattern of the availability of resources. This can lead to the emergence or disappearance of the edge effect in the pollinator community in the patches dominated by alien plants. We tested whether the variability in the supply of flower resources created by dense stands of flowering invasive goldenrods could create a temporal edge effect for pollinating insects in a grassland landscape. We surveyed pollinator communities along transects perpendicular to the goldenrod‐grassland edge. To understand the variation in edge effects, we surveyed the number of flowers, which are the main food resources for pollinators. We found positive edge responses of abundance and species richness of all pollinator groups from the edges to the grassland interior before the goldenrod flowering period. During the goldenrod flowering period abundance and species richness of bees showed a neutral edge response, the response of butterflies and hoverflies towards the centre of the goldenrod patch were negative and positive respectively. Our results revealed that the emergence of the edge effect in a pollinating insect community is associated with temporal usability of invasive plants as a food source. Thus, the combined outcome of the available resources and invasion of alien plants can help to understand the edge effect on pollinator distributions in the invaded landscapes.
Genetic variability for yield and yield components in Jerusalem artichoke (Helianthus tuberosus L.)

Investigation of quantitative traits of Jerusalem artichoke populations was conducted on the experimental field of the Agricultural Institute of the Republic of Srpska in Banja Luka, during 2013 and 2014. The material was collected in the wider area of Republic of Srpska. The following populations were analyzed: Srbac, Modriča, Pivara, Lazarevo, Bosna, Vrbas, Gradiška and Aleksići. The trial was arranged in a randomized complete block design with three replications. The following parameters were analyzed: tuber weight (g), plant height (cm), stem number/plant, average stem thickness (cm), green mass yield/plant (kg), and dry mass yield/plant (kg). Average tuber weight ranged from 36.7 g (Bosna) to 61.0 g (Lazarevo). Plant height ranged from 1.55 m (Lazarevo) to 2.20 m (Aleksići). Stem number/plant varied from 2.2 (Aleksici) artichoke populations with better quantitative traits, and their inclusion in the program of creating new varieties .
Morphology and Flowering Responses of Four Bedding Plant Species to a Range of Red to Far Red Ratios

In greenhouse ornamental crop production, bedding plants grown below high densities of hanging baskets (HBs) tend to be of lower quality. Hanging basket crops can decrease the red to far red ratio (R:FR) of the growing environment below; however, the extent to which decreased R:FR affects plant morphology and ﬂowering of the lower-level crops is unknown. The present study examined effects of R:FR on morphology and ﬂowering of marigold ‘Antigua Orange’ ( Tagetes erecta ), petunia ‘Duvet Red’ ( Petunia 3 hybrida ), calibrachoa ‘Kabloom Deep Blue’ ( Calibrachoa 3 hybrida ), and geranium ‘Pinto Premium Salmon’ ( Pelargonium 3 hortorum ). Five R:FR light treatments were provided ranging from R:FR 1.1 (representing unﬁltered sunlight) to R:FR 0.7 (representing shaded conditions under HBs) using light-emitting diodes (LEDs) in growth chambers, each with identical photosynthetically active radiation ( PAR ) (400– 700 nm) and FR added to achieve the target R:FR ratio. Two experiments using the same R:FR treatments were conducted with day/night temperature regimes of 20 8 C/18 8 C and 25 8 C/21 8 C, respectively. In the second experiment, a ﬂuorescent light treatment was included. The results of the second experiment were more dramatic than the ﬁrst, where reducing R:FR from 1.1 to 0.7 increased height by 11%, 22%, and 32% in marigold, petunia, and calibrachoa,
Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reaction

Sargassum species are one of the major alginate‐producing seaweed species in Asian countries. Alginate is widely used in food, feed, pharmaceutical and medical industries as thickening and stabilizing agents. To establish a set of consistently expressed genes as reference genes for quantitative real‐time polymerase chain reaction (qRT‐PCR) studies of Sargassum polycystum (Fucales, Ochrophyta) in samples collected at two distinct time points from the field, four candidate reference genes, namely ribosomal protein L3 (RPL3), ribosomal protein S15 (RPS15), alpha‐tubulin (α‐TUB) and eukaryotic translation elongation factor 1 alpha (TEF1α), were analyzed using geNorm and NormFinder. The results showed that RPL3, α‐TUB and TEF1α were the most stable genes using both programs, whereas RPS15 gene was shown to be the least stable. Identification of stably expressed reference genes is crucial for qRT‐PCR studies to allow accurate quantification of target gene expression levels. In addition, the expression of key enzyme in the final step of alginate biosynthesis pathway mannuronan C5 epimerase‐SP01411 (MC5E‐SP01411) and mannuronan C5 epimerase‐SP02271 (MC5E‐SP02271) were differentially expressed in the seaweeds collected at two distinct time points from the field. To our knowledge, this is the first report on validation of reference genes for any Sargassum species. Our data provide a basis for the selection of reference genes for future biological research in related studies.
Instability in 18S and 5.8S rDNA copy numbers and 18S:5.8S ratios in longitudinally-collected human DNA samples detected by monochrome multiplex qPCR

Ribosomal DNA encodes the structural RNAs of the ribosomes. Ribosomal DNA instability is a major contributor to aging in yeast, but its role in human aging and longevity is largely unknown. Human 45S rDNA encodes the 18S, 5.8S, and 28S ribosomal RNAs; ranges in copy number from 60 to > 800 per cell, distributed as tandem repeats along the short arms of the five acrocentric chromosomes (p13, p14, p15, p21, and p22); and is prone to frequent homologous and non-homologous recombination. Here we present two multiplex quantitative PCR assays, one for 18S rDNA normalized to the single copy gene beta-globin (HBB), and the other for 5.8S rDNA normalized to the single copy gene albumin (ALB). Longitudinally-collected pairs of DNAs from bloods drawn approximately 16 years apart from 40 females and 39 males, aged < 1 to 77 years at first blood draw, from the Utah CEPH families were assayed. Ribosomal DNA copy number varied over a four-fold range between subjects and increased approximately 14% across the lifespan. Longitudinal within-individual gains in copy number up to +68% and losses down to ‐25% were observed, while repeated assays of single DNA samples varied approximately +/- 10%. While 18S and 5.8S rDNA tended to be gained and lost together, the 18S:5.8S ratio was also unstable longitudinally, with increases up to +19% and decreases down to ‐15% observed. The 18S:5.8S ratio at second draw, relative to that at first draw, increased significantly across the lifespan in males, but not in females. To our knowledge this is the first report of within-individual longitudinal changes in the human 18S and 5.8S rDNA copy numbers. These assays will facilitate investigations of the biology of ribosomal RNA genes and their roles in health and disease across the human lifespan.
Heavy use of antibiotics in aquaculture: Emerging human and animal health problems – A review

Antibiotics have been extensively and effectively used in aquaculture due to accelerated growth of aquaculture and this has resulted in the development of serious health problems in aquaculture, other animals, and human. The use of a wide variety of antibiotics in large amounts, including non-biodegradable antibiotics, ensures that they remain in the aquatic environment for a long time. This has resulted; the emergence of antibiotic-resistant bacteria in the environments, an increase of antibiotic resistance in fish pathogens, transfer of these resistance determinants to bacteria and then land animals and finally become human pathogens along with alterations of the bacterial ﬂora both in sediments and in the water column. Thus, the global efforts are needed to promote more judicious use of prophylactic antibiotics in aquaculture as accumulating evidence indicates that unrestricted use is detrimental to fish, terrestrial animals and human health.
SCREENING OF ENDOPHYTIC BACTERIA PRODUCING ANTIFUNGAL ISOLATED FROM INDONESIA MEDICINAL PLANT, JAVA GINSENG (TALINUM TRIANGULARE) (JACQ.) WILLD

Objective: The objective of this research was to isolate and characterize endophytic bacteria from Talinum triangulare having antifungal activity. Methods: The endophytic bacteria were isolated from roots tissue of Talinum triangulare by surface sterilization method. The isolates were cultured in Trypticase Soybean agar and antagonist activities were evaluated by dual culture assay against Fusarium oxysporum, Trichoderma reesei and Candida albicans . For metabolite antifungal activities, bacterial isolates were grown for 4 d in TS broth at 35 °C under shaking condition. The antifungal activities of the supernatant extract were determined by using the disk agar diffusion. Polyketide synthase (PKS I) and NRPS genes fragments of all isolates were amplified. Results: The result reveals that 4 of 23 endophytic bacterial isolates demonstrated great antifungal potentiality against many tested fungi. Polyketide synthase (PKS I) and NRPS genes amplification were showed 10 and 4 of endophytic isolates detected harboring PKS type I and NRPS genes, respectively. In general, high frequencies of positive PCR amplification were obtained for PKS I (43.47%). Phylogenetic analyses based on the 16S rRNA gene sequence, morphological, physiological and biochemical showed that the isolates were identified as a member of genus Bacillus and Brevibacillus . Conclusion: These results indicated that the endophytic bacteria from java ginseng could be used as an alternative source of antifungal agents.
Detection of Canine Herpesvirus Infection on Dogs

Canine herpesvirus (CHV) seems to be present worldwide in both domestic and wild dogs. Serologic surveys have shown a relatively high prevalence of CHV in household and colony-bred dogs. Blood samples were collected from dogs in dog shelters or dog collection centres in Konya and Antalya that showed clinical signs of the disease. In total, 141 blood samples were examined for antibodies to CHV by commercial enzyme-linked immunosorbent assay, whereas the blood leukocyte samples obtained from the dogs were assessed by immunoflouresence test (IFT) for isolation of CHV. Madin-Darby canine kidney cells were used for virus isolation. Ninety-seven samples (68.8%) were detected as seropositive; while no positive results were identified using IFT. In conclusion, the high seropositivity may indicate that CHV infection is common in dog shelters or dog collection centres in Turkey and infected animals with CHV need to be identified and quarantined.
Fish in the diet of the Long-eared Owl Asio otus

ABSTRACT Capsule: Analysis of regurgitated pellets showed that fish were a very rare prey in the diet of the Long-eared Owl Asio otus. Remains of 38 individual fish were found at 8 of 121 nests and only in 2 out of 11 years. Occurrence tended to be more frequent in warm dry periods, when water ditches were dry.
The Role of Inositol 1,4,5-Trisphosphate Receptor-Interacting Proteins in Regulating Inositol 1,4,5-Trisphosphate Receptor-Dependent Calcium Signals and Cell Survival

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are channels located on the endoplasmic reticulum (ER) that release calcium (Ca2+) ions into the cytosol during intracellular signaling cascades. By initiating and shaping Ca2+ signals, IP3Rs play key roles in many essential processes. Consequently, cells have evolved complex mechanisms to control IP3R-mediated Ca2+ signals, including regulation by interacting proteins. In this dissertation, the regulation of IP3Rs by interacting proteins was investigated in order to: (1) further establish the identities and roles of IP3R-interacting proteins in controlling Ca2+ release and cell survival; and, (2) evaluate the possibility of targeting protein-IP3R interactions for the treatment of cancers. Reported herein is the discovery that the glycolytic enzyme pyruvate kinase M2 (PKM2) localizes in part to the ER and interacts with IP3Rs. By controlling IP3R-mediated Ca2+ release, IP3R-associated PKM2 governs Ca2+ transfer from ER to mitochondria, regulating cellular bioenergetics and suppressing Ca2+ signals capable of inducing cell death. The control of Ca2+ homeostasis by PKM2 is thus a novel mechanism by which PKM2 promotes cell survival. Notably, these findings suggest that PKM2 serves as a gatekeeper of the
Differences in structure of northern Australian hypolithic communities according to location, rock type, and gross morphology

Hypolithic communities (under translucent rocks) were compared between a semi-arid site (Wave Hill) and a site with considerably higher rainfall (Lake Bennett) to test the hypothesis that the communities at the higher rainfall site would be more diverse. A total of 153 cyanobacteria operational taxonomic units (OTUs) were identified, and only 50 of those were found at both sites. Of these, only two were core OTUs, as defined as being present in ≥90% of samples, highlighting the extreme differences in the cyanobacterial communities at the two sites. At Wave Hill, we compared the composition of the cyanobacterial components under two different rock types (quartz and prehnite) to determine if the different minerals would result in different hypolithic communities, but no differences were found. Of the 42 core OTUs found at Wave Hill, 22 (52%) were shared between the two rock types. As hypothesised, the diversity of both cyanobacteria and eukaryotes in the hypolithic communities was significantly higher at Lake Bennett. Some hypolithic communities were thin and tightly adhered to the rock surface, but others were thicker and could be peeled off the rock in sheets. However, the two types were not significantly different in OTU composition. Metazoans, primarily nematodes, were ubiquitous, raising the possibility that nematodes may act as vectors to transport the components of hypolithic communities from rock to rock as a mechanism of colonization.
Lidar based 3D Tracking and State Estimation of Dynamic Objects

State estimation of oncoming vehicles: Earlier research has been based on determining states like position, velocity, orientation , angular velocity, etc of ego-vehicle. Our approach focuses on estimating the states of non-ego vehicles which is crucial for Motion planning and decision-making. Dynamic Scene Based Localization: Our project will work on dynamic scenes like moving ego (self) and non-ego vehicles. Previous methods were focused on static environments.
The Effectiveness of Using Marginal Annotations in Reading Comprehension for FL Learners

Name: Dr. Elham Sweilam Ahmad Desouky Lecturer of Curriculum & Instruction (TEFL), Faculty of Education, October 6 University Email: elesweilam@gmail.com Abstract Current research randomly allocated 104 FL learners to investigate whether there is any positive effect of marginal annotations on their reading comprehension performance and some other issues related to their learning. Learners were divided into two groups: the experimental group, which used marginal annotations, and the control group, which did not use marginal annotations. To achieve the goal of the study, both a pre-test and immediate post-test were used in two sessions, while the other two sessions used the delayed post-test design. English unaccusativity and 10 pseudoword items were the goal features; thus, the current study utilized meaning recognition test, a word form and grammaticality judgment tests to evaluate the target features learning. The findings revealed that marginal annotations have no significant impact on reading comprehension outcomes, but they facilitate learning the target features to a great extent.
GENETIC DIVERSITY AT EACH HABITAT OF PSEUDOLABRUS SIEBOLDI, USUAL FISH SPECIES IN A WESTERN JAPAN COASTAL AREA

Pseudolabrus sieboldi is a very common labrid fish in Japan coastal region, so the species wasn't being watched so much up to now. Therefore, the habitats of P. sieboldi have been developed easily. But it's pointed out that genetic isolation easily occurred due to being polygyny in their mating system. In order to investigate the genetic diversity of usual species, we sampled 6 populations of the species form western Japan coastal area, and studied them for allelic variation at 24 enzyme loci. In comparison with other sea fishes, the total genetic diversity is standard. Though sex ratio was inclined to females and inbreeding were easy to be performed, the gene diversity was not decreasing. In fact, there was inbreeding mating within the population. Moreover, standard genetic distance within populations along the Japan Sea is high and standard genetic distance within Pacific Ocean area is low. The fry of the species dispersed to the Pacific or the Japan Sea. When they grew adults, they returned to rocky shores for mating. The populations along the Pacific Ocean did not return exactly at their birth area. On the other hand, the populations along the Japan Sea returned more exactly at their birth area.
Analysis of endothelial progenitor subpopulation cells, oxidative DNA damage, and their role in coronary artery disease

Background: Endothelial dysfunction has been associated for the cause of atherosclerosis or cardiovascular diseases (CVDs). Endothelial progenitor cells (EPCs) are exposed to oxidative stress during vascular injury as residents of blood vessel walls or as circulating cells homing to the sites of neovascularization. The current study was designed to analyze various subpopulations of EPCs and their DNA damage in CVDs. Methods: The study included 50 coronary artery disease (CAD) patients which was confirmed by angiography and 50 age-matched healthy controls without CAD. Flow cytometric analysis performed to measure subpopulations in EPCs in the peripheral blood using markers such as CD34, CD133, VEGFR2, and CD45. Oxidative DNA damage was analyzed in CD34+ cells. Mean EPC count was expressed as a percentage of total white blood cells. Three different subpopulations with CD45−/CD133+/VEGFR2+, CD45−/CD34+/VEGFR2+, and CD45−/CD34+/CD133+ coexpressions were measured with various percentages. Results: Subpopulation of CD45−/CD34+/VEGFR2+ cells had shown significant (P = 0.001) decrease in CAD patients in comparison with the healthy controls. There was no significant difference in the subpopulations of CD45−/CD34+/CD133+ cells (P = 0.005) and CD45−/CD133+/VEGFR2+ cells (P = 0.005) in CAD and healthy controls. The CD45−/CD34+/VEGFR2+ subpopulation EPC showed positive correlation with the severity of coronary stenosis (r = 0.35, P = 0.026), while other EPC subpopulation count did not show any correlation. Oxidative DNA damage was higher in CAD compared with controls. The number of EPC subpopulation CD45−/CD34+/VEGFR2+ was inversely correlated with oxidative DNA damage (P = 0.001), hypertension (P = 0.001), and diabetes mellitus (P = 0.004). Conclusion: We observed an association between CD45−/CD34+/VEGFR2 subpopulation EPCs and DNA damage in CAD condition. These findings support a cell biologist in searching the role of EPC populations in the pathophysiology or diagnosis of the disease by a clinician.
Discovery of problematic probes in illumina DNA methylation microarrays

In humans, there are hundreds of cell types, each with specialized functions that make up different tissues and organs. All these cells share the same genetic makeup but exhibit different patterns of gene expression contributing to their specialized functions. It is now known that such varying gene expression patterns are regulated by epigenetic mechanisms, one of which is DNA methylation where a methyl group is covalently added to cytosine. The Illumina DNA methylation microarrays are the most widely used platforms for genome-wide DNA methylation study in humans. Significant findings regarding human developments and disease mechanisms have been reported using the Illumina microarrays. This thesis describes the discovery of problematic probes in the Illumina microarrays. These probes generate unreliable array signals that, when misinterpreted, can lead to false discoveries. By recognizing the existence of problematic probes, data generated by the Illumina microarrays can be more reliably interpreted for biological meaning.
Linkage and Inheritance in Lettuce (Lactuca sativa L.)1

Achene color and leaf-type genes are linked, with p = 0.34. Achene color and male-sterility genes are linked, with p = 0.39. Leaf-type and male-sterility genes are independently inherited. Achene color and virescent chlorophyll-deficiency genes are linked, with p = 0.03. Thirty-four other linkage comparisons showed independent inheritance. Endive-type leaf and chlorophyll deficiency are each regulated by recessive alleles. Three separate recessive alleles control albinism.