Miracle-dz/UniFAR-FTUs huggingface dataset:
The study of DNA damage repair in Arabidopsis thaliana

DNA is the major storage of genetic information common to all cellular organisms. Endogenous and exogenous factors may damage DNA and affect plant growth and fitness. To dissect the genetic variation of Arabidopsis thaliana to DNA replication stress, 400 Arabidopsis natural accessions were exposed to hydroxyurea (HU), a drug interfering with deoxyribonucleotide synthesis. This revealed a great variation in relative survival of Arabidopsis accessions to HU. However, extremely hypersensitive accessions were rare. To identify the molecular basis of this natural variation, quantitative trait locus (QTL) mapping with the recombinant inbred line population derived from crosses between HU-sensitive and resistant parents was performed. Two significant QTLs with additive effects and one minor QTL with epistatic effect were identified. Using heterogeneous inbred family analysis, one QTL was validated and fine mapped to a 22 kb region containing eight candidate genes which require further analysis. Genes involved in related biological processes or pathways are often expressed coordinately, thus the uncharacterized candidate genes might be co-expressed with the functionally known genes. This co-expression strategy was applied to search for novel DNA damage repair genes in Arabidopsis and revealed increased sensitivity of mutants in CHROMATIN REMODELING 31 to DNA inter-strand cross-linker, mitomycin C. Furthermore, the chr31 mutant showed delayed cell cycle progression and increased frequencies of somatic homologous recombination (HR). This provides a novel connection between chromatin remodeling and DNA damage responses by so far unknown mechanisms. Nucleoside analogues are frequently used in basic and medical research. However, their mode of action and spectra of effects are not well understood. Analysis of the molecular effects of non-methylable cytidine analogue zebularine in Arabidopsis revealed induction of DNA damage response, post-replicative cell cycle arrest, and increased endoreduplication, but without obvious changes in DNA methylation. Molecular and genetic data suggested that zebularine-induced damage specifically occur during DNA replication in the course of DNA strand synthesis. The signaling of this damage was mediated by additive activity of ATAXIA TELANGIECTASIA MUTATED and ATAXIA_TELANGIECTASIA MUTATED AND RAD3-RELATED kinases. The repair required a functional STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC) 5-SMC6 complex and was accomplished predominantly by synthesis-dependent strand annealing type of HR. Hence, commonly used “epigenetic inhibitor” zebularine causes specific type of DNA damage.
Habitat Preferences of a European Bison (Bison bonasus) Population in the Carpathian Mountains

We assessed habitat selection patterns of the European bison (Bison bonasus) reintroduced to the Bieszczady Mountains (the Eastern Carpathians, Poland) using presence data and Ecological Niche Factor Analysis. During the growing season, bison selected habitats at higher elevations close to natural grasslands, coniferous forest, and stands with broken canopy, while in winter — lower elevations, close to agricultural areas and alder or pine stands. In both seasons, bison avoided busy roads. The use of low-elevation valleys in winter can be a trade-off between the access to good habitats with milder climate, and the risk associated with close proximity to people. Relative tolerance to proximity to infrastructure indicates that good quality habitats in its vicinity can be considered suitable for further expansion of the species' range. Optimal sites for bison introductions in the Carpathians should include areas at lower elevations, providing winter refuges, and allow unrestricted access to summer habitats at higher elevations.
Individual variation in dental characteristics for estimating age of African lions

Countries that allow sport hunting of African lions, Panthera leo, increasingly are mandating minimum age regulations for harvested individuals that require accurate aging techniques. However, individual variation in dental characteristics used for aging could result in errors and has not been quantified. We assessed individual variation in three dental methods for estimating age of lions using left and right paired PM2s from 31 free-ranging lions of unknown age from Zambia. Assignment of individuals to age class based on crown wear was largely consistent (87%) between paired PM2s; measures of pulp chamber closure also were highly consistent (< 4% variation) between pairs. Though pulp chamber closure varied little between pairs, calibrating pulp closure with known-aged lions is needed to fully develop this method. In contrast, cementum line counts differed between paired PM2s in 94% of lions, ranging from 1 to 7 cementum lines (i.e. 0.5–3.5 years). Of lions with cementum lion counts that differed between teeth, 45% were estimated as meeting the 5- or 6-year-old minimum age used in trophy lion monitoring programs with one PM2, but not the paired PM2. Though individual variation in cementum line counts may render this technique unsuitable for aging lions, using the maximum or average count from both PM2s warrants further investigation. Individual variation in dental characteristics should be considered when developing lion aging techniques based on dentition.
Yield Enhancement and Insect Suppression with Chlordimeform (Fundal) on Dryland Cotton

Chlordimeform was evaluated in four large-plot field tests over 2 years to determine its effect on yield enhancement for a short-season, dryland cotton system under typical insect pest management. Four or seven applications of chlordimeform (0.14 kg [AI]/ha) were made at the sixth true leaf stage and reapplied at 5-day intervals. Densities of early season cotton fleahoppers, Pseudatomoscelis Seriatus (Reuter), and blasted squares were reduced as much as 50% by multiple applications of chlordimeform. Fleahopper nymph densities were reduced 85%. Predaceous insects and spiders were not significantly affected. Chlordimeform increased early square and boll counts, earliness of harvest, and total bolls (12.2%)and lint harvested (6.4%) per ha, but had no measurable effect on lint per boll or boll diameter. Significant increases in yield and earliness of fruit set were attributed, in part, to reduced insect damage in the chlordimeform-treated plots.
Population Genetic Analysis by Randomly Amplified Polymorphic DNA Markers in Pecan

This article is concerned with population genetic diversity in pecan, Carya illinoensis , based on randomly amplified polymorphic DNA markers or RAPDs. Seed nuts from 45 trees of 9 populations collected from southeastern, northern, western USA and eastern, southeastern, central and western China were used for DNA isolation with the improved CTAB process. In PCR amplification, 10 Operon arbitrary primers were selected. A total of 42 polymorphic loci were detected, with which the population genetic diversity was analyzed in terms of the proportion of polymorphic loci, Shannon's index of phenotypic diversity, Virk's genetic distance, and Nei's similarity coefficient. Results have indicated a significant variation in pecan populations. While the inter population variation is greater than the intra population, the genetic distances between China located populations are longer than the American populations.
Effects of Bailing Capsule on the Cellular Immune Function of Type 2 Diabetic Nephropathy Patients

Aim To explore the impact of Bailing capsule on the cellular immune function of type 2 diabetic nephropathy patients. Methods 108 patients with type 2 diabetic nephropathy were randomly divided into treatment group and control group,and 40 cases of healthy person were classified as healthy group. Patients in the control group were treated with conventional therapy,and patients in the treatment group received Bailing capsule additionally. All of them were treated for 12 weeks. The main biochemical indicators were detected. The levels of T cells( CD3 +,CD3 + CD4 +,CD3 + CD8 +),B cells( CD3- CD19 +),NK cells( CD3- CD16 + CD56 +),and NKT cells( CD3 + CD16 + CD56 +) were detected by flow cytometry. Results After treatment,serum CysC and 24 h urinary protein decreased greatly( P 0. 05),and those of the treatment group decreased more obviously( P 0. 05). As far as the peripheral blood lymphocyte subsets distribution was concerned,there were obvious differences between healthy group and type 2 diabetic nephropathy patients. After treatment,the lymphocyte subsets distribution in control group did not change obviously; in the treatment group,CD3 +,CD3 + CD4 +,CD3 + CD8 +,CD3- CD16 + CD56 +,CD3 + CD16 + CD56 + cell percentage increased,CD3- CD19 + cell percentage and the ratio of CD4 + / CD8 + decreased( P 0. 05),and there were significant differences between the treatment group and the control group( P 0. 05). Conclusion Bailing capsule can regulate the cellular immune dysfunction of type 2 diabetic nephropathy.
Genotypic Diversity of Strains of Flavobacterium columnare from Diseased Fishes

Genetic variability among strains of Flavobacterium columnare (formerly Flexibacter columnaris) was characterized using restriction fragment length polymorphism (RFLP) analysis of 16S rDNA, 16S rDNA sequencing, and DNA-DNA hybridization. A total of 23 Fl. columnare strains isolated from diseased fishes in various areas were divided into three distinct genomic groups. The main group, genomovar 1 consisted of 20 strains, including the type strain. Two strains were assigned to genomovar 2, and one to genomovar 3. However, as we found their phenotypic characteristics to be identical, there is no evidence to classify strains of these genomovars as belonging to new species or sub-species.
Cesarean section in dogs: Physiology and perioperative considerations

Cesarean section is common in small animal veterinary practice.The goal of cesarean section is delivery of healthy, vigorous pups and provision of surgical anesthesia, appropriate analgesia, and rapid return to consciousness for the dam. Changes in maternal respiratory and cardiovascular physiology that occur during pregnancy and neonatal physiology and circulation have a significant impact on anesthetic pharmacokinetics and pharmacodynamics. Various risk factors for maternal mortality and neonatal mortality and vigor have been identified and should influence the perioperative and anesthetic management of patients undergoing cesarean section. Intensive neonatal resuscitation techniques can lead to decreased periparturient neonatal mortality. CESAREAN SECTION IN DOGS Send comments/questions via email editor@CompendiumVet.com or fax 800-556-3288. Visit CompendiumVet.com for full-text articles, CE testing, and CE
Dental microwear texture analysis of extant African Bovidae

Abstract Bovids are often used as paleoenvironmental proxies because they are among the most commonly recovered large mammals at many fossil hominin sites and because modern African bovids occupy a wide range of dietary and environmental niches. This study uses dental microwear texture analysis to examine 25 species of extant African bovids, representing six dietary categories and with an emphasis on various levels of mixed feeding. The results show significant differences among the dietary classifications and confirm previous work suggesting that grazing taxa have less complex, more anisotropic surfaces with smaller features than browsing taxa. The results also indicate that dental microwear texture analysis can distinguish beyond the classic grazer-browser-mixed feeder trichotomy and accurately separate variable grazers, generalists, browser-grazer intermediates and frugivores from obligate grazers and browsers, as well as from one another. Some differences among taxa within dietary categories were also found, probably reflecting seasonal and/or geographic differences in diet. In addition to demonstrating the effectiveness of the technique at differentiating between different levels of mixed feeding in bovids, this study also provides a comprehensive comparative dataset of extant bovid microwear textures that can be applied to fossil taxa from sites and time periods across Africa.
Injury effects of LPS on mesencephalic neuron-glia cultures of rats

Aim:To investigate the injury effects of dopaminergic neurons induced by LPS in rat mesencephalic neuron-glia cultures.Methods:Rat mesencephalic neuron-glia cultures were obtained from timed pregnant SD-rats on embryonic 14 d. Ⅰ:The mesencephalic neuron-glia cultures were categorized into five groups:control and LPS(0.01,0.10,1.00,and 10.00 mg/L)group.On the 7th day of culture,different concentrations of LPS were incubated for 72 h.Dopaminergic neurons were identified and counted by using tyrosine hydroxylase(TH)immunochemistry. Ⅱ:The mesencephalic neuron-glia cultures were categorized into two groups:control and LPS group(0.1 mg/L). On the 7th day of culture,0.1 mg/L LPS was incubated for different times(8,24,and 72 h). After administration supernatants were collected,IL-6 levels were detected by using ELISA.Dopaminergic neurons and actived microglias were identified and counted by using TH and ionized calcium binding adaptor molecule 1(Iba1)immunochemistry.Results:The number of TH positive cells reduced significantly with shorter cell processes showing bead-like.The IL-6 levels in 0.1 mg/L LPS-treated groups of 8,24 and 72 h after administration,increased significantly(t was 15.787,16.712 and 15.910,P0.001). The number of actived microglias were(40.0±6.1),(76.0±3.4),and(69.0±5.2),respectively(F=387.820,P0.001). The number of dopaminergic neurons were(18.0±5.3)and(10.0±3.2)in 0.1 mg/L LPS-treated groups of 24 and 72 h after administration,respectively(F=94.840,P0.001). Conclusion:Microglias may play an important role in injury effects of dopaminergic neurons,activated by LPS to release IL-6.
The thread-legged bugs (Hemiptera: Heteroptera: Reduviidae: Emesinae) of Lord Howe and Norfolk Islands

Collections from Lord Howe and Norfolk Islands include three new species and one new locality record of emesine reduviid bugs. From Lord Howe Island Emesopsis cirratus n. sp. the first record of this genus from Lord Howe and Atisne reidi n. sp. are described. Ploiaria weiri n. sp. is described from Norfolk Island. This paper brings the emesine fauna of Lord Howe Island to eight species in six genera and three tribes, and that of Norfolk Island to four species in four genera and three tribes. Our findings support the hypothesis that many invertebrate species are limited in their distributions on these islands, and provide evidence of altitudinal segregation among sisterspecies of the genus Atisne.
Hydraulic Conductivity, Immobile Water Content, and Exchange Coefficient in Three Soil Profiles

We used tension disk infiltrometers to determine the hydraulic conductivity at the matric potential of -0.1 kPa (K -0.1 ), the immobile water fraction (θ im / θ ), and the mass exchange coefficient (a) in three soil profiles of an agricultural field cropped with winter wheat (Triticum aestivum L.). A significant effect of soil horizonation was found for K -0.1 , θ im /θ, and a and could be related to soil structure as determined either by tillage for surface horizons or by pedogenetic factors for subsurface horizons. The seedbed had lower K -0.1 values (31 to 99 mm h -1 ) than the plowed layer under the seedbed (94-430 mm h -1 ). The θ im /θ was highly variable in the seedbed (0.213 to 0.882), while a had values ranging from 0.0006 to 0.0115 h -1 . Values of θ im /θ and α in the plow layer under the seedbed were similar but less variable than those found in the seedbed. In the subsoil, clay-enriched illuvial horizons had K -0.1 values similar to those found in the seedbed, but lower than those of the heavy clay horizon (average value of 260 mm h -1 ) and the limestone horizons (average value of 450 mm h -1 ). In the illuvial and heavy clay horizons, both θ im /θ and a parameters had a small variability. In the limestone, we found a high variability of both θ im /θ values (0.506-0.933) and α values (0.0006-0.0424 h -1 ) associated with high average values. The presence of subsoil horizons with large θ im /θ and low a values may have a significant impact on ground water contamination.
Fatigue Analysis of Riveted Railway Bridges.

There is a large number of old riveted railway bridges that are still in use in the UK and around the world. Due to their considerable age, which in many cases is over 100 years, their useful life-span may be close to its end. Fatigue cracking has been observed in riveted bridge connections over the years, confirming that the connections in these bridges are susceptible to fatigue damage. Although considerable research has been conducted on the fatigue behaviour of riveted bridges, only a small percentage of this research has concentrated on riveted connections. In this thesis, a general methodology for the fatigue assessment of riveted railway bridges is presented by concentrating on the fatigue behaviour of their connections. The methodology is developed through the fatigue analysis of a finite element model of a 10 m span riveted railway bridge, typical of a very large number of old railway bridges in the UK. As a first step of such a methodology, a global finite element analysis of the bridge is performed in order to identify, on an S-N basis, the most fatigue-critical connections. Probabilistic methods are also employed in order to determine the reliability of those connections. The global analysis is then followed by a detailed investigation of a refined finite element model of this connection, which is developed with the aid of benchmark studies on simple finite element models of riveted lap joints. This second step of the methodology aims at identifying, on an S-N basis, the hot spots and potential crack initiation sites in the connection itself. In both steps, the analysis is carried out in terms of present day and historical train loading. In the context of these investigations, the most important parameters that affect fatigue damage, estimated on an S-N basis, are found to be the connection stiffness, the detail S-N classification and the rivet clamping force. By ranking the bridge connections according to their fatigue damage, the inner stringer-to-cross-girder connections are identified as the most fatigue-critical. The fatigue life of these connections is found to be governed by stress levels which are close and below the fatigue limit of the relevant detail. The rivet holes and the angle fillet are identified as the most fatigue-critical locations on the connection where fatigue cracking may initiate. Quantitative results are obtained for the critical connections under various scenarios. The results obtained in this thesis can also be used in planning effective inspection regimes for these bridges.
Prognostic value of ERCC1, thymidylate synthase and glutathione S-transferase π for 5-FU/oxaliplatin chemotherapy in advanced colorectal cancer.

3607 Background: The aim of this study was to determine whether expressions of the excision cross-complementing (ERCC1), thymidylate synthase (TS) and glutathione S-transferase π (GSTπ) predict clinical outcome in patients with advanced colorectal cancer treated with fluorouracil (5-FU)/oxaliplatin chemotherapy. METHODS The study population consisted of 70 advanced colorectal cancer patients (median age, 53 years). Patients were treated with oxaliplatin 85 mg/m2 as a 2-hour infusion at days 1 plus LV 20 mg/m2 over 10 minutes, followed by 5-FU bolus 400 mg/m2 and 22 hour continuous infusion of 600 mg/m2 at day 1-2. Treatment was repeated in 2 week intervals. The expressions of ERCC1, TS and GSTπ of primary tumors were examined by immunohistochemistry. RESULTS The positive rates of ERCC1, TS, and GSTπ were 55.7%, 68.6%, and 71.4%, respectively. The patients without TS expression were more likely to respond to chemotherapy (p=0.009). There were no significant differences between response and ERCC1 or GSTπ expression pattern (p=0.768, p=0.589, respectively). Median overall survival (OS) was significantly longer in patients without ERCC1 expression (p=0.0474). Patients with ERCC1 positive combined with TS positive, or those with ERCC1 positive combined with TS positive and GSTπ positive had poor OS (p=0.0017, p=0.0323, respectively). Multivariate analysis revealed that both ERCC1 and TS expression significantly impacted on OS (Hazard ratio 1.72, p=0.023). CONCLUSIONS Immunohistochemical studies for ERCC1 and TS may be useful in prediction of the clinical outcome of advanced colorectal cancer patients treated with 5-FU and oxaliplatin. No significant financial relationships to disclose.
A Preliminary Study of the Lizard Fauna and Their Habitats in Northwestern Iran

Northwestern Iran has unique geographical and climatic conditions that support a rich flora and fauna. In view of the lack of in-depth studies on the lizards of the region, an investigation was started in the northern part of Ardabil Province for an inventory of this component of the fauna and their habitats. Collections were made from October 2003 to June 2005 and 165 specimens were collected and identified. Five families, 12 genera and 15 species are represented, including Agamidae: Laudakia caucasia, Phrynocephalus persicus, Trapelus ruderatus; Lacertidae: Lacerta media media, Lacerta strigata, Lacerta brandtii, Darevskia raddei raddei, Eremias strauchi strauchi, Eremias arguta, Ophisops elegans; Scincidae: Mabuya aurata transcaucasica, Eumeces schneiderii princeps, Abelepharus bivittatus; Anguidae: Pseudopus apodus and Gekkonidae: Cyrtopodion caspium caspium. Comparing this list to the data provided by Anderson (1999), it seems that most of the lizards are being reported for the Province for the first time. The families Gekkonidae and Anguidae are newly recorded, and the gecko Cyrtopodion caspium is first recorded from the west and northwest of Iran. With seven species represented in the area, lacertids have the high- est species diversity among the lizard families and need further study. Habitat features also have been given for all species.
GENETIC DIVERSITY ANALYSIS OF CHINESE THREE-KEELED POND TURTLE (CHINEMYS REEVESII) BY RAPD

Chinese three-keeled pond turtle (Chinemys reevesii Gray) is a member of the family Emydidae and widely ranges in southern China, especially in the regions of the lower and middle Yangtze River. It has high values for food, traditional Chinese medicine and pet trade, and is one of the turtles for aquaculture in China. But the genetic background of Chinese three-keeled pond turtle is still not very clear. In order to realize its population genetic structure and the diversity for the conservation of its germ plasm and prevention of gene loss, genetic diversity analysis was carried out using RAPD-PCR technique. In this paper, genetic diversity of 24 individuals of Chinese three-keeled pond turtle from Hubei province was analyzed by the random amplified polymorphic DNA (RAPD) technique, using 20 10-nucleotide-long primers. Twenty primers produced 3288 well-amplified DNA fragments with reproducible banding patterns and averaged 137 DNA fragments in one individual. 119 of 137 loci detected are polymorphic, amounting to 86.9%. The DNA fragments were from 0.2kb to 3kb. The genetic distance between two individuals was from 0.168 to 0.467. The average genetic distance was 0.324±0.0631 among the 24 individuals. The phylogenetic tree of the 24 individuals was obtained by NJTREE analysis in the RAPDistance program and the 24 individuals were divided into several clusters and it indicated the turtle maybe have two populations at least. In conclusion, genetic diversity of Chinese three-keeled pond turtle was high.