Miracle-dz/UniFAR-FTUs huggingface dataset:
Variable Patterning of Chromatin Remodeling, Telomere Positioning, Synapsis, and Chiasma Formation of Individual Rye Chromosomes in Meiosis of Wheat-Rye Additions

Meiosis, the type of cell division that halves the chromosome number, shows a considerable degree of diversity among species. Unraveling molecular mechanisms of the meiotic machinery has been mainly based on meiotic mutants, where the effects of a change were assessed on chromosomes of the particular species. An alternative approach is to study the meiotic behavior of the chromosomes introgressed into different genetic backgrounds. As an allohexaploid, common wheat tolerates introgression of chromosomes from related species, such as rye. The behavior of individual pairs of rye homologues added to wheat has been monitored in meiotic prophase I and metaphase I. Chromosome 4R increased its length in early prophase I much more than other chromosomes studied, implying chromosome specific patterns of chromatin organization. Chromosome conformation affected clustering of telomeres but not their dispersion. Telomeres of the short arm of submetacentric chromosomes 4R, 5R, and 6R failed more often to be included in the telomere cluster either than the telomeres of the long arms or telomeres of metacentrics such as 2R, 3R, and 7R. The disturbed migration of the telomeres of 5RS and 6RS was associated with failure of synapsis and chiasma formation. However, despite the failed convergence of its telomere, the 4RS arm developed normal synapsis, perhaps because the strong increase of its length in early prophase I facilitated homologous encounters in intercalary regions. Surprisingly, chiasma frequencies in both arms of 4R were reduced. Similarly, the short arm of metacentric chromosome 2R often failed to form chiasmata despite normal synapsis. Chromosomes 1R, 3R, and 7R showed a regular meiotic behavior. These observations are discussed in the context of the behavior that these chromosomes show in rye itself.
Identification and antibiotic resistance profiling of bacterial isolates from septicaemic soft-shelled turtles (Pelodiscus sinensis)

The present study sought to identify pathogens associated with septicaemia in the Chinese softshelled turtle (Pelodiscus sinensis) and to characterise antibiotic resistance in these pathogens. Twenty-three isolates recovered from the livers of diseased soft-shelled turtles were genetically identified as Aeromonas hydrophila (n = 8), A. veronii (n = 3), Citrobacter freundii (n = 4), Morganella morganii (n = 3), Edwardsiella tarda (n = 2), Wohlfahrtiimonas chitiniclastica (n = 1), Chryseobacterium sp. (n = 1), and Comamonas sp. (n = 1). Most isolates (n = 21) were resistant to ampicillin whereas a low percentage of isolates was susceptible to aminoglycosides (amikacin, gentamicin, and tobramycin). PCR assays and sequence analysis revealed the presence of the qnrS2 and blaTEM antibiotic resistance genes in all isolates. The blaDHA-1, blaCTX-M-14 and blaCMY-2 genes were harboured by 17.4% (n = 4), 13.5% (n = 3) and 8.7% (n = 2) of the strains, respectively. One or more tetracycline resistance genes were detected in 60.9% (n = 14) of the isolates. Four isolates (17.4%) harboured single or multiple class 1 integron cassettes. Collectively, a variety of bacterial pathogens were involved in the occurrence of septicaemia in Chinese soft-shelled turtles and most of the isolates had multi-antibiotic resistant phenotypes. To our knowledge, the present report is the first to identify W. chitiniclastica and Comamonas sp. as causes of septicaemia in softshelled turtles and the first to identify Aeromonas spp. with blaCTX-M-14 and blaDHA-1 resistance genes.
The influence of experimentally-induced endotoxaemia on clinical variables and markers of systemic inflammation in donkeys (Equus asinus)

In view of the frequent involvement of endotoxins in the pathogenesis of equine diseases, the present study set out to gain preliminary insight into the challenge caused by lipopolysaccharide (LPS) exposure in donkeys and into the responses of animals to LPS challenge. To the best of our knowledge, this is the first study to determine the susceptibility and response of donkeys to LPS administration and the first to describe the extent to which donkeys can tolerate a state of endotoxaemia. For this purpose, 18 clinically healthy, native breed donkeys were randomly allocated into three groups of equal size. The first and second groups received E. coli O55:B5 endotoxin at a dose rate of 20 ng/kg (Low dose group), and 5.0 μg/kg (High dose group), respectively, after dilution in 500 ml of 0.9% normal saline, while the third group (Control) received 500 ml of 0.9% isotonic saline solution. Blood samples were drawn from each animal before exposure to LPS and hourly for 6 h subsequently to measure the circulating levels of inflammatory cytokines as well as the cellular response. All animals were clinically monitored throughout the study period. Following LPS exposure, donkeys in both treated groups had quite different temporal patterns of clinical manifestations. The high dose of LPS yielded a statistically significant (P < 0.001 and P < 0.001, respectively) increase in heart rate, and respiratory rate, as well as hypothermia and poor outcome compared with animals receiving the low dose. The severity of colic was, in general, mild in donkeys receiving the low dose of LPS, while the signs were overt in those receiving the high dose. Donkeys of both treated groups exhibited marked cellular alterations and up-regulation of tumour necrosis factor alpha, interleukin (IL)-12 and IL-10 with a marginal increase in the values of serum amyloid A compared with controls (P < 0.05). The results described herein demonstrate that donkeys can respond to even a physiological dose of E. coli O55:B5 endotoxin, while a high dose can elicit overt clinical alterations and marked inflammatory responses. Further studies with an extended follow-up time are needed to verify and generalise the obtained findings and to evaluate novel medications to minimise the deleterious consequences of endotoxaemia in equine patients.
Effect of glide path preparation on apical debris extrusion of rotary and reciprocating single-file systems: OneShape versus WaveOne

12.00 Objective To assess the effect of glide path on the amount of apically extruded debris after instrumentation with WaveOne and OneShape. Methods. Forty-eight extracted human mandibular incisors were assigned to 4 groups. In groups 1 and 2, preparation was completed with WaveOne In groups 3 and 4, canals were prepared with OneShape. Before instrumentation, in groups 1 and 3, glide path was created with PathFile 1, 2, and 3 at working length, whereas in groups 2 and 4, glide path was not performed. The weight of the extruded debris for each group was calculated by comparing the pre- and post-instrumentation weights of the eppendorf tubes. The time required for reaching full WL was also recorded. Data were analyzed by Kruskal–Wallis and Mann–Whitney U tests. Results. There was no difference in the amount of debris extruded between the single file systems ( P =0.234). Time required to reach full WL was significantly decreased by creating a glide path ( P < 0.05). Conclusion . C reation of a glide path does not significantly affect the apically extruded debris. Normal 0 21 false false false TR X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normal Tablo"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:. 0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}
CXCL 14 antagonizes the CXCL 12-CXCR 4 signaling axis

CXCL12 and CXCL14 are evolutionarily conserved members of the CXC-type chemokine family. CXCL12 binds specifically to the G-protein-coupled receptor CXCR4 to induce the migration of primordial germ cells, hematopoietic stem cells, and inflammation-associated immune cells. In addition, CXCL12-CXCR4 signaling is often enhanced in malignant tumor cells and facilitates increased proliferation as well as metastasis. Although macrophage migration inhibitory factor and extracellular ubiquitin interact with CXCR4 as agonistic factors, CXCL12 was believed to be the sole chemokine ligand for CXCR4. However, a very recent report revealed that CXCL14 binds to CXCR4 with high affinity and efficiently inhibits CXCL12-mediated chemotaxis of hematopoietic progenitor and leukemia-derived cells. CXCL14 does not directly cross-compete with CXCL12 for the CXCR4 binding but instead inactivates CXCR4 via receptor internalization. Because both CXCL12 and CXCL14 are expressed during embryogenesis and brain development in mice, these two chemokines could function in an interactive fashion. We propose that the CXCL14 gene has been conserved from fish to man due to its role in fine-tuning the strength of CXCL12-mediated signal transduction. In addition to its biological implications, the above finding will be important for designing anti-cancer compounds targeting the CXCL12-CXCR4 signaling axis. In fact, a stabilized dimeric peptide containing the C-terminal 51–77 amino acid residues of CXCL14 has been shown to have stronger CXCL12 antagonistic activity than full-length CXCL14.
Statistical Disclosure Control and Protecting Privacy within a Clinical Data Warehouse

There is increasing interest in the development and research use of large scale repositories of clinical data, known as Clinical Data Warehouses (CDWs). CDWs facilitate the pooling of data from one or more electronic health record systems, providing a potentially useful resource for clinical research. Whether or not there is consent for the data to be used for research, there is almost always a need to protect the privacy of the individuals whose data is stored within the data warehouse. Formal identifiers such as name and address are usually not directly relevant to research questions and can be removed before data is released for research purposes. However, this alone does not preclude the identification of individuals within a CDW or the discovery of sensitive information about such individuals. By examining an example clinical data warehouse, developed during the Clinical E-Science Framework (CLEF) project, the authors have been able to consider these disclosure risks in detail. This paper describes the purposes of clinical data warehouses (CDWs), the risks posed through statistical disclosure, how these can be limited by appropriate use of statistical disclosure control (SDC) methods, and discusses how these can be applied in the context of clinical data warehousing.
Susceptibility of the topmouth gudgeon (Pseudorasbora parva) to CyHV-3 under no-stress and stress conditions

Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus, is the causative agent of the highly contagious koi herpesvirus disease, which is restricted to koi and common carp and causes significant losses in both fish stock. Some experimental investigations have shown that other cyprinid or non-cyprinid species may be asymptomatically susceptible to this virus and might play roles as potential carriers of CyHV-3 or might contribute to persistence of this virus in environment. Therefore, it seems important to verify not only the susceptibility of other cyprinid or non-cyprinid species, but also their ability to transmit CyHV-3 infection to susceptible species. Our previous investigation of the susceptibility of the topmouth gudgeon (Pseudorasbora parva) did not reveal the presence of CyHV-3 DNA in the tissues of this species after cohabitation with infected koi. Consequently, we changed the experimental conditions and applied two stress factors (removal of skin mucus and scaring) which would presumably mimic the stress most commonly encountered in the wild. Both experiments (without and with stress factors) consisted of primary and secondary challenges. In both the no-stress and stress experiments, the first challenge was focused only on testing the susceptibility of the topmouth gudgeon to the virus. With the secondary challenge, we investigated potential viral transmission from the topmouth gudgeon to healthy naive koi after exposure to stress factors. All fish (dead, surviving and sacrificed) were tested for the presence of CyHV-3 DNA using nested PCR (no-stress experiment) and real-time PCR (stress experiment). After the primary challenge of the no-stress experiment, PCR did not reveal the presence of CyHV-3 DNA in any specimen of cohabitated topmouth gudgeon, but all specimens of dead koi were CyHV-3 DNA-positive. PCR of fish tissues subjected to the secondary challenge did not show the transfer of virus to naive fish. After exposure to stress (removal of skin mucus), qPCR revealed four out of five samples (80%) of topmouth gudgeon to be positive for CyHV-3 DNA. Two out of five samples (40%) of topmouth gudgeon treated by scaring were found to be positive for the presence of viral DNA. Real-time PCR after the secondary challenge did not reveal any viral DNA positivity in specimens of topmouth gudgeon from groups previously exposed to stress. The stress experiments show that removal of skin mucus might potentially lead to susceptibility of topmouth gudgeon to CyHV-3 infection, but the transmission of the virus to koi carp was not observed.
Malware modeling and experimentation through parameterized behavior

Experimentation is critical to understanding the malware operation and to evaluating potential defenses. However, constructing the controlled environments needed for this experimentation is both time-consuming and error-prone. In this study, we highlight several common mistakes made by researchers and conclude that existing evaluations of malware detection techniques often lack in both flexibility and transparency. For instance, we show that small variations in the malware’s behavioral parameters can have a significant impact on the evaluation results. These variations, if unexplored, may lead to overly optimistic conclusions and detection systems that are ineffective in practice. To overcome these issues, we propose a framework to model malware behavior and guide systematic parameter selection. We evaluate our framework using a synthetic botnet executed within the CyberVAN testbed. Our study is intended to foster critical evaluation of proposed detection techniques and stymie unintentionally erroneous experimentation.
Recreational fisheries in inland waters

Recreational fisheries represent the dominant fisheries sector targeting wild freshwater fishes in all industrialized nations and are becoming increasingly popular in some emerging economies. The socio‐economic benefits of recreational fisheries are numerous and substantial. Recreational fisheries through their practices (e.g. overharvest, habitat change, release mortality, stocking and dispersal of non‐native fishes), however, have been implicated in negative effects on populations and ecosystems. In inland waters, fish populations also face a variety of threats that are external to the recreational fisheries sector such that recreational fisheries often operate on top of already imperilled resources. This chapter characterizes the scope and magnitude of inland recreational fisheries globally, explores recreational fisheries as a coupled social–ecological system, reviews management strategies, identifies the main issues faced by inland recreational fisheries and discusses the future of recreational fishing in inland waters with an emphasis on research and information needs to ensure their long‐term sustainability.
A Possible Association between Cervical Erosion in Pregnant Women and Congenital Abnormalities in Their Children-A Population-Based Case-Control Study

Objective to study the possible association between erosion of cervix in pregnant women (ECP) and structural birth defects, i.e. congenital abnormalities (CA) in their offspring. Study design: Comparison of cases with CA and all matched controls without any CA born to wo- men with prospectively and medical record ECP in the population-based large data set of the Hungarian Case-Control Surveillance of Congenital Abnormalities (HCCSCA). Results: HCC- SCA contained 22,843 cases and 38,151 matched controls, the informative offspring of 40 (0.18%) case mothers and the newborns of 25 control mothers (0.07%) with ECP were compared and the higher risk for total CA (adjusted OR with 95% CI: 2.7, 1.6-4.4) was found explained by the higher risk of 9 cases with hypospadias (OR with 95% CI: 4.5, 2.1-9.7) and 10 cases with car-diovascular CAs (OR with 95% CI: 3.4, 1.6-7.1), particularly with conotruncal CAs. Conclusions: An unexpected possible association of ECP with higher risk for hypospadias and conotrun-cal cardiovascular CAs was found and these findings are considered as signals that need confirmation or rejection
Sayı 2 , 2015 173 CO 2 EMISSIONS , ENERGY CONSUMPTION AND ECONOMIC GROWTH IN THE USA AND THE UNITED KINGDOM : ARDL APPROACH

This study investigates the effects of energy consumption and the economic growth on the carbon dioxide emissions and causality in a multivariate model, which includes nuclear energy generation, foreign trade and urbanization variables, in the UK and the USA by employing data of 1960-2004. Cointegration test results support that there is a long-term relationship among the variables. While the economic growth in the UK has a positive effect on CO2 emissions in the short term and long term, the economic growth in the USA does not affect CO2 emissions. In both countries, there is a positive relationship between energy consumption and CO2 emissions and a negative relationship between nuclear energy generation and CO2 emissions. There is a unidirectional causality from CO2 to economic growth in the UK and from energy consumption to CO2 emissions in the USA. In both countries, we have detected no causal relationship between energy consumption and the economic growth.
Optimized Complex Power Quality Classifier Using One vs. Rest Support Vector Machines

Nowadays, power quality issues are becoming a significant research topic because of the increasing inclusion of very sensitive devices and considerable renewable energy sources. In general, most of the previous power quality classification techniques focused on single power quality events and did not include an optimal feature selection process. This paper presents a classification system that employs Wavelet Transform and the RMS profile to extract the main features of the measured waveforms containing either single or complex disturbances. A data mining process is designed to select the optimal set of features that better describes each disturbance present in the waveform. Support Vector Machine binary classifiers organized in a “One Vs Rest” architecture are individually optimized to classify single and complex disturbances. The parameters that rule the performance of each binary classifier are also individually adjusted using a grid search algorithm that helps them achieve optimal performance. This specialized process significantly improves the total classification accuracy. Several single and complex disturbances were simulated in order to train and test the algorithm. The results show that the classifier is capable of identifying >99% of single disturbances and >97% of complex disturbances.
Clonal variation in the Caucasian rock lizard Lacerta armeniaca and its origin

Clonal variation in Lacerta armeniaca was investigated using allozyme electrophoresis and morphol- ogy. Among the 35 allozyme loci examined, three were variable, which divided L. armeniaca into four clones. One rare clone of L. armeniaca made up the majority of two populations. This contrasts to rare clones in other parthenogenetic Caucasian rock lizards which typically consist of only one or two individuals. Another rare clone, which showed a striking colouration difference, had different allelic composition at two loci. Although mutation is a possible explanation of the origin of the clonal variation, the alternative, multiple origin, is equally likely.
Behaviour and survival of wild Atlantic salmon Salmo salar captured and released while surveillance angling for escaped farmed salmon

: In many Norwegian rivers, spawning stocks are surveyed for escaped farmed salmon with surveillance fishing by rod and reel after the recreational angling season. However, the benefits of surveillance fishing depend on the ability of wild salmon to return to the spawning stock. To evaluate the impacts of surveillance fishing, we captured, radio-tagged and released wild Atlantic salmon Salmo salar in the River Lakselva, Norway, in a surveillance fishery occurring just prior to the spawning period. Among 39 salmon captured, 36 wild fish were tagged and released, whereas 3 were not released (1 bleeding from the gills, 1 farmed, 1 farmed and bleeding). Survival of fish captured by surveillance fishing was high (95% total survival, 100% catch-and-release sur-vival). Tagged fish were tracked on average 1.2 ± 2.8 (SD) km from the release site at the end of the experiment during the spawning season, not significantly different from the distance moved by salmon radio tagged throughout the summer during a similar interval (15 September to 24 October 2014). Total movement within 3 d of release was inferred to average 1.9 ± 2.1 km, exclud-ing 1 individual that exited the river. Tracking data revealed an immediate behavioural reaction of salmon to surveillance catch-and-release angling, the long-term consequences of which are uncertain. Surveillance fishing may be problematic in rivers with small and vulnerable wild stocks in which a high proportion of the spawning populations is sampled. Surveillance fishing completed with ample time before spawning would be a precautious approach to minimize potential effects during spawning.
Micromorphological analysis of Aranda Broga Blue orchid PLBs for Agrobacterium- mediated transformation system

Aims: The aim of this work was to analyse the morphological aspects of ABB’s PLBs and interaction between ABB’s PLBs and Agrobacterium. Methodology and results: Aranda Broga Blue’s (ABB) protocorm-like bodies (PLB) proliferated on Vacin and Went medium by incubating at 25 ± 2°C under 16 h semi-photoperiod was used to study the micromorphology of PLB, bacterial attachment and chemotaxis studies. The anatomy and micromorphology study indicates that ABB’s PLBs provide the platform for attachment of Agrobacterium tumefaciens strain LBA 4404. Successful propagation of ABB’s PLBs was achieved on modified Vacin and Went solid media supplemented with organic homogenates. Histological analysis of the development of ABB’s PLBs shows it is a meristematic tissue and contains actively dividing cells. Transmission electron microscope (TEM) studies signify the presence of specialized organelles to indicate PLB is similar to a mature plant. Scanning electron microscope (SEM) observation on ABB’s PLBs and bacterial attachment studies proves that trichomes and stomata on the surface facilitate the interaction with A. tumefaciens. Quantification of the attachment of Agrobacterium to ABB’s PLBs using spectrophotometric system displayed higher affinity compared to the attachment mutant Escherichia coli DH5α. The interaction of Agrobacterium to ABB’s PLBs was also evaluated based on chemotaxis studies. Highest motility respond of Agrobacterium was recorded (1.6 unit) towards severely wounded PLBs indicating wounding is necessary for the interaction between bacterium and PLB. Conclusion, significance and impact study: Micromorphology of protocorm-like bodies (PLBs) enhances the physical interaction with bacteria proved that PLB is a suitable explant for the Agrobacterium-mediated genetic transformation.