Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of mechanical loading in chondrocyte signaling pathways

Wan, Qiaoqiao. Ph.D., Purdue University, August 2016. The Role of Mechanical Loading in Chondrocyte Signaling Pathways. Major Professor: Sungsoo Na. Chondrocytes are a predominant cell type present in articular cartilage, whose integrity is jeopardized in joint degenerative diseases such as osteoarthritis (OA). In the chondrocytes of patients with OA, the elevated levels of inflammatory cytokines such as interleukin 1β (IL1β) and tumor necrosis factor α (TNFα) have been reported. These cytokines contribute to degradation of cartilage matrix by increasing activities of proteolytic enzymes. In addition to their contribution to proteolytic enzymes, these cytokines adversely affect anabolic activity of chondrocytes by inhibiting the production of proteoglycans and type II collagen. Therefore, blocking the action of these cytokines is a potential strategy to prevent cartilage degradation. Accumulating evidence suggests that mechanical loading contributes to the regulation of cartilage homeostasis. However, the underlying mechanisms are not clear as to how varying magnitudes of mechanical loading trigger differential intracellular signaling pathways at sub-cellular levels, which consequently lead to selective matrix synthesis or degradation. Furthermore, it is not known whether the loading-magnitude dependent responses are linked to degenerative diseases such as OA. Tyrosine kinases such as Src and focal adhesion kinase (FAK) are known to play a crucial role in OA progression. We hypothesized that mechanical loading regulates the sub-cellular activation pattern of Src/FAK, and acts as a suppressor of the OAor inflammatory cytokine-driven signaling activities. We used live cell imaging approach in conjunction with fluorescence resonance energy transfer (FRET)-based biosensors to investigate real-time molecular events at the sub-cellular level in live chondrocytes. Using two-dimensional (2D) cell culture and shear stress application, we found that
Performance of salt tolerant mutant rhizobia inoculation with graded levels of nitrogen on the growth and yield attributes of groundnut (arachis hypogaea l.)

Groundnut (Arachis hypogaea L.) is one of the most important oleaginous plants cultivated in globally and particularly in tropical and subtropical areas (Shiyam, 2010). This crop is commonly cultivated in arid and semi-arid regions of India where it plays an important socioeconomical role. In this field experiment focused, the trails performance of salt tolerant mutant strain Bradyrhizobium (GNBJ-9M) at graded levels of nitrogen significantly to improve the growth and yield of groundnut. Among the treatments, T8-GNBJ-9M+100% N recorded the maximum of plant height, leaf area index, dry matter production, number of nodules plant, number of pods plant, test weight of 100 seed (g), pod yield ha, kernel yield t ha, haulm yield t ha at harvesting period and also oil content (%), protein content (%) respectively followed by T7-GNBJ-9M+ 75% N compared to other treatments. The minimum was recorded in the all growth parameters in control treatment of T1 in groundnut plant.
Precipitin Production in Chickens

Aging of chicken antisera at 4°C or at -20°C resulted in: (a) an increase in interfacial titers with tests performed in 1.8% NaCl. (b) a decrease in nitrogen precipitation when the quantitative tests were performed in 8% NaCl. (c) an increase in nitrogen precipitation with most antisera when the quantitative tests were performed in 1% NaCl. Inactivation of chicken complement by versene is to be preferred to heat (56°C, ½ hour) since the latter may contribute to the co-precipitation of nonspecific nitrogen when the quantitative test is performed in 8% NaCl. Treatment with versene decreased the nitrogen precipitation in the antigen excess region of the precipitin curve. This was quite evident in 1% NaCl. Some explanations for the points noted above were given.
Incidence of “Candidatus Liberibacter asiaticus” in a Florida population of Asian citrus psyllid

The incidence of a bacterium “Candidatus Liberibacter asiaticus” was assessed in a Florida population of Asian citrus psyllid, Diaphorina citri. The bacterium is the presumed causal agent of Asiatic huanglongbing, a serious citrus disease. Adult D. citri were periodically collected between May 2010 and September 2012 in a block of diseased trees located in east‐central Florida. The psyllids were individually subjected to molecular analyses (quantitative polymerase chain reaction assays using HLBaspr primers) to determine whether the bacterium was present and, if so, the population level of the pathogen based on qPCR cycle threshold (CT) values. Significantly greater percentages of females tested positive for the pathogen than males, but there were no significant differences between females and males with respect to population levels of the pathogen within the psyllids. No significant differences were found among the three D. citri colour morphs with respect to percentages of adults testing positive for the pathogen. Among 47 sample dates, a mean of 17.5% of adults per sample date tested positive (CT < 36) for the pathogen with a mean CT value of 31.1. The incidence of the pathogen was generally higher during late fall or early winter and often lower during mid‐ to late summer. There was a significant negative correlation between percentages of D. citri testing positive and air temperature. Increases in the incidence of the pathogen may not necessarily correspond to increases in transmission, as a number of factors both internal and external to D. citri can influence transmission. Transmission rates may be highest during periods when D. citri infestation levels are large, a high percentage of adults carry a high population of the pathogen in their salivary glands, and citrus flush is abundant.
Thermal and mechanical properties of POSS-Cyanate ester/epoxy nanocomposites

A new cyanate ester functionalized polyhedral oligomeric silsesquioxane (POSS-Cy) monomer was prepared by reacting hydroxyl functionalized POSS-OH with cyanogen bromide (CNBr) in the presence of triethylamine (Et3N). The precursor POSS-OH and the corresponding cyanate ester POSS-Cy were characterized by Fourier transform infrared (FTIR), 1H and 13C nuclear magnetic resonance (13C-NMR) spectral techniques. Nanocomposites were prepared by reacting diglycidylether of bisphenol-A, POSS-Cy and 4,4’-diaminodiphenylmethane (DDM). The structure of the cross-linked networks was confirmed by FT-IR. The POSS particles formed clusters in some regions leading to phase separation as revealed by scanning electron microscopy (SEM) analysis. Dynamic mechanical analysis (DMA) shows that the glass transition temperature decreases from 161oC to 155oC when the POSS-Cy content was increased from 0% to 15%. But, the T10% of the epoxy resin (369oC) increased significantly (404°C) on incorporating 15% of POSS-Cy. The LOI values indicate that these blends have good flame-retardant properties.
Preparatory enquiry on cephalic abnormality in hatchery raised Heterobranchus longifilis and its aquacultural consequence

Cephalic abnormality (gill arch malformation) in four mating combinations involving cephalic and noncephalic male and female Heterobranchus longifilis broodstocks were investigated in order to assess its frequency of level of occurrence in the offsprings and if it has any genetic basis. Percentage fertilization and hatchability were not significantly different (P0.05) in all the mating combinations. Weight gain (4.4 g) and survival (75%) were highest in mating combinations involving the non-cephalic male × non-cephalic female and non-cephalic male × cephalic female respectively which were significantly different (P<0.05) at the end of six weeks in outdoor growth studies. The offsprings of the cephalic male × non-cephalic female had the highest frequency of cephalic abnormality (2%) which was very low and not significantly different (P>0.05) from the other mating combinations. The very low level of cephalic abnormality observed in the offspring of all the mating combinations at 12 weeks possibly indicate the involvement of other factors rather than genotype in the occurrence of this morphological aberration.
Supplementation of lactic and citric acid in antibiotic free diets and their influence on performance, meat yield and immune response of broiler chickens

The present study aimed at evaluating two organic acids, lactic acid (LA) and citric acid (CA), each at 1.0 and 2.0% levels for replacing antibiotic (AB-Virginiamycin 11 mg/kg) in diets. In a feeding trial with 270 broiler chicks (Vencobb) LA and CA were tested in 2 x 2 factorial design, and compared with AB and control diets from day-one to 42 d of age in battery cages. Each of the 6 test diets was offered to 9 replicates of 5 chicks, and their growth performance, carcass attributes, bone morphology and immune response were recorded. Supplemental LA or CA at 2% level in diets significantly (p 3.1%) and breast meat yield (>9.7%) with desirable decline in abdominal fat. LA even at 1% level supported higher tibia weight (5.96 g), length (8.11 cm) and low leg scores (1.08), indicating better bone condition. LA and CA at 2% level improved immune competence in broilers measured as humoral and cell mediated response, compared to the AB and control diets. It is concluded that LA and CA supplementation at 2% level improved the broiler performance, meat yields, bone conformation and immune response over AB and control diets, implying that organic acids could replace antibiotic from broiler diets effectively and beneficially.
Field evaluation of a live vaccine against porcine reproductive and respiratory syndrome in fattening pigs

Στη μeλέτη αυτή eξeτάστηκe η αποτeλeσματικότητα σe eπίπeδο eκτροφής, eνός ζωντανού eμβολίου (Porcilis PRRS, Intervet), που προέρχeται από στέλeχος του ιού του αναπαραγωγικού και αναπνeυστικού συνδρόμου του χοίρου (ΑΑΣΧ) που απομονώθηκe στον eυρωπαϊκό χώρο. Συγκeκριμένα διeρeυνήθηκe η eνeργητική προστασία που παρέχeι το eμβόλιο αυτό έναντι της αναπνeυστικής μορφής του συνδρόμου σe αναπτυσσόμeνους/παχυνόμeνους χοίρους. Ο πeιραματισμός έγινe σe μια eκτροφή προσβλημένη από το ΑΑΣΧ, όπου eμβολιάστηκαν 10.000 χοίροι στην ηλικία των 6 eβδομάδων και στη συνέχeια έγινe σύγκριση μeταξύ eμβολιασμένων και ανeμβολίαστων χοίρων που αφορούσe στην κατάσταση της υγeίας τους, στη θνησιμότητα, στις παραγωγικές παραμέτρους (μέση ημeρήσια αύξηση βάρους, μέση ημeρήσια κατανάλωση τροφής, δeίκτης μeτατρeψιμότητας τροφής) και στην πιθανή παρουσία παθογόνων βακτηρίων στους πνeύμονeς. Τα αποτeλέσματα έδeιξαν ότι τόσο η συχνότητα eμφάνισης της νόσου όσο και η θνησιμότητα ήταν χαμηλότeρeς στα eμβολιασμένα σe σχέση μe τα ανeμβολίαστα ζώα. Eπίσης, οι eμβολιασμένοι χοίροι eίχαν καλύτeρeς αποδόσeις από τους ανeμβολίαστους σe ό,τι αφορά στη μέση ημeρήσια αύξηση βάρους (Ρ 0.05). Από τις μικροβιολογικές eξeτάσeις προέκυψe σημαντικά μικρότeρη προσβολή των πνeυμόνων από δeυτeρογeνeίς βακτηριακές λοιμώξeις στα ζώα που eμβολιάστηκαν σe σύγκριση μe τα ανeμβολίαστα. Σe ό,τι αφορά τη χυμική ανοσοαπάντηση των eμβολιασμένων ζώων, αυτά έδeιξαν γρηγορότeρα τάση αύξησης των τίτλων των αντισωμάτων σe σύγκριση μe τους μάρτυρeς. Eπίσης δeν παρατηρήθηκe κλινικά καμία παρeνέργeια από τη χρησιμοποίηση του πeιραματικού αυτού eμβολίου. Συμπeρασματικά, τα αποτeλέσματα της eργασίας αυτής δeίχνουν ότι η ανοσοποίηση των αναπτυσσόμeνων/παχυνόμeνων χοίρων μe το ζωντανό eμβόλιο Porcilis PRRS παρέχeι πολύ καλή προστασία έναντι της αναπνeυστικής μορφής του ΑΑΣΧ.
Optimization of Enrichment Protocol for Campylobacter Detection

ii Acknowledgements.iv List of Tables . vii List of Figures . viii Chapter I. General Introduction . 1 Chapter II. Literature Review . 5 Characteristics of Campylobacter . 8 Virulence Factors and Pathogenesis . 10 Survival Mechanisms of Campylobacter jejuni . 13 Antibiotic Resistance in Campylobacter . 19 Poultry Colonization with Campylobacter . 23 Strategies to Control Campylobacter during Poultry Production and Processing . 24 Campylobacter Isolation and Culture Techniques . 30 Literature Cited . 37 Chapter III. Materials and Methods . 53 Bacterial Culture Preparation . 53 Selection of Media Used to Evaluate Campylobacter jejuni Growth . 53 Evaluation of Campylobacter jejuni Growth in Enrichment Media . 55
Modification of pumice with HCl and NaOH enhancing its fluoride adsorption capacity: Kinetic and isotherm studies

ABSTRACT Fluoride concentration, if exceeds the standard levels in drinking water, can lead to adverse effects on human health. Adsorption is one of the widely considered appropriate technologies for water defluoridation. In this study, modified pumice with HCl and NaOH were used for the fluoride removal from aqueous solution, and two linear forms of the Langmuir and Freundlich isotherms model were applied to determine the best fit of equilibrium expressions. Several experimental parameters including pH (2–10), temperature (20–60°C), adsorbent dosage (2–10 g/L), fluoride concentration (5–20 mg/L), and contact time were studied. Results showed that removal efficiency improved with increase in contact time, initial fluoride concentration, and adsorbent dosage. The maximum removal efficiency (96%) was observed at pH 6, 10 g/L adsorbent dosage, 20°C solution temperature, 90-min reaction time, and 20 mg/L of fluoride concentration. The kinetic studies indicated that the adsorption equilibrium and kinetic data were in good agreement with the Langmuir Model (R2 = 0.95) with qmax = 65.5 mg/g and pseudo-second-order reaction (R2 = 0.99). According to the results, the modified pumice was found to be able to remove fluoride from aqueous environments with good removal efficiency and adsorption capacity.
First record of two new species of genus Tetraponera (Hymenoptera: Pseudomyrmecinae: Formicidae) from Pakistan

Two species of genus Tetraponera, T. allaborans (Walker, 1859) and T. nigra (Jerdon, 1851) have been reported for the first time from Pakistan. These species have been described giving main identification characters supported with microphotographs, and their distribution range. GPS position of surveyed localities has also been given for both species.
Who's who in the fleabane (Conyza spp.) family?

Flaxleaf fleabane (Conyza bonariensis (L.) Cronquist) has become a problem weed throughout the entire cropping belt of south-eastern Australia. One of the barriers for effective control of C. bonariensis is the morphological confusions with other fleabane species. This study used the scanning electron microscopic technique to investigate the differences in trichome and stomatal densities between C. bonariensis and tall fleabane (C. sumatrensis (Retz.) E.Walker). Results showed that C. bonariensis had significantly higher trichome densities than C. sumatrensis. The trichome densities in C. bonariensis ranged from 67.2 to 221.9 trichomes mm−2 on the adaxial leaf surface and from 74.0 to 168.1 trichomes mm−2 on the abaxial leaf surface, while the trichome densities in C. sumatrensis ranged from 40.3 to 147.9 trichomes mm−2 on the adaxial surface and from 53.8 to 134.5 trichomes mm−2 on the abaxial surface. There were no significant differences in trichome densities between the adaxial and abaxial surfaces in both species. For the stomatal density, C. bonariensis had an average 314.3 ± 12.5 stomata mm−2 on the adaxial surface, which was significantly higher than that on the abaxial surface (237.4 ± 9.1 stomata mm−2). However, C. sumatrensis had a lower adaxial stomatal density (217.7 ± 8.5 stomata mm−2) compared to the abaxial surface (275.1 ± 15.3 stomata mm−2). Both the trichomes and stomata can influence the herbicide control of this weed, with the high trichome numbers potentially restricting herbicide uptake and the high stomatal numbers facilitating the uptake. The restrictive trichome barrier should be overcome to increase the leaf penetrability and herbicide uptake, thereby improving foliar herbicide efficacy on C. bonariensis.
Controlling Herbicide-Resistant Annual Bluegrass (Poa annua) Phenotypes with Methiozolin

Methiozolin is an isoxazoline herbicide being investigated for selective POST annual bluegrass control in managed turfgrass. Research was conducted to evaluate methiozolin efficacy for controlling two annual bluegrass phenotypes with target-site resistance to photosystem II (PSII) or enolpyruvylshikimate-3-phosphate synthase (EPSPS)-inhibiting herbicides (i.e., glyphosate), as well as phenotypes with multiple resistance to microtubule and EPSPS or PSII and acetolactate synthase (ALS)-inhibiting herbicides. All resistant phenotypes were established in glasshouse culture along with a known herbicide-susceptible control and treated with methiozolin at 0, 125, 250, 500, 1000, 2000, 4000, or 8000 g ai ha-1. Methiozolin effectively controlled annual bluegrass with target-site resistance to inhibitors of EPSPS, PSII, as well as multiple resistance to EPSPS and microtubule inhibitors. Methiozolin rates required to reduce aboveground biomass of these resistant phenotypes 50% (GR50 values) were not significantly different from the susceptible control, ranging from 159 to 421 g ha-1. A phenotype with target-site resistance to PSII and ALS inhibitors was less sensitive to methiozolin (GR50 = 862 g ha-1) than a susceptible phenotype (GR50 = 423 g ha-1). Our findings indicate that methiozolin is an effective option for controlling select annual bluegrass phenotypes with target-site resistance to several herbicides. Nomenclature: Methiozolin, annual bluegrass, Poa annua L.
Correlation and Path Analysis Studies in Aerobic Rice

The rice environments in India are extremely diverse. Of the 44.2 million ha of harvested area, about 30.8% are rainfed lowland, 44.9% irrigated, 17.4% rainfed uplands & 6.9% flood prone which profoundly influence the overall rice productivity of the country. Water consumption per kg of rough rice ranges from 1000 to 5000 litres depending on climate, soil conditions, and crop management, and is about two to three times that of other cereals such as wheat or maize. Irrigation for agriculture consumes 2/3 of world’s fresh water and rice alone consumes more than 50 percent of the water used for irrigation in Asia. A fundamental approach to reduce water inputs in rice is to grow the crop aerobically like an irrigated upland crop such as wheat and maize. Early experiments on aerobic rice reveals that the water input in aerobic rice was 50 percent lower (only 470650mm) and water productivity was higher by 64-88 percent than irrigated lowland rice (Bouman, 2001). Aerobic rice is a production system in which specially developed varieties are grown in well drained, non-puddled and non-saturated soils. Aerobic rice is a new way of cultivating rice that requires less water than lowland rice. It entails the growing of rice in aerobic soil, with the use of external inputs such as supplementary irrigation and fertilizers and aiming at high yields (Wang et al., 2000). International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 8 (2017) pp. 2851-2856 Journal homepage: http://www.ijcmas. com
Drop-coating deposition and surface-enhanced Raman spectroscopies (DCDRS and SERS) provide complementary information of whole human tears

Raman spectroscopy has received increasing interest in biomedical applications because of its label-free and in vivo detection capabilities. The main challenge for a wider application lies in its low detection sensitivity, especially for biomolecules. Various strategies have been employed to improve the detection sensitivity of Raman spectroscopy. In this work, we systematically compared two Raman techniques with improved sensitivity for the detection of microliter quantities of whole human tears: drop-coating deposition Raman spectroscopy (DCDRS) and surface-enhanced Raman spectroscopy (SERS). High-quality and highly reproducible DCDR spectra of tears can be obtained in the ring zone of the dried coffee-ring deposit. The major contribution is from the high-abundant proteins, including lysozyme, lactoferrin, and albumin. Good SER spectra with excellent reproducibility can also be acquired in the deposit area and are contributed by uric acid and hypoxanthine in tears with a low abundance but strong interactions with the silver nanoparticles. The result demonstrates that DCDRS is advantageous for detection of some high-abundant components and SERS for some low-abundant components in the whole tears. A combination of both techniques is able to extract multiparameter information for a systematic analysis of clinical tears and can be further extended to the analysis of other body fluids. Copyright © 2014 John Wiley & Sons, Ltd.
The Analysis of Oxytetracycline Residue in Tissues of Cultured Rainbow Trout (Oncorhynchus Mykiss)

Background: Oxytetracycline (OTC) is commonly used in aquaculture industry and has high potency against bacterial diseases. Objectives: The present study aimed at examining the rate of oxytetracycline (OTC) antibiotic residue in the tissues of cultured rainbow trout (Oncorhynchus mykiss). Methods: Samples were taken randomly from the livers and fillets of 45 rainbow trout from 15 large aquaculture ponds in Hamadan province, West of Iran. The OTC residue was measured using high performance liquid chromatography (HPLC). Data analysis was performed with SPSS (V.18) (mean and standard deviation), and Man-Whitney test was employed for statistical analysis. Results: The results revealed that OTC residue were 389 to 641 ppb in the livers and 175 to 295 ppb in the fillets, respectively. However, in 86.66% of the samples (liver and fillet) the amounts of OTC residue was found to be higher than the maximum residue limits (MRLs) in codex alimentarius commission, and 13.33% of the samples (liver and fillet) were within the standard range. Analysis of input and output data using Man-Whitney test showed significant differences in liver and fillet (P < 0.05). Conclusions: This research determined that the use of OTC must be reduced to an acceptable level in aquaculture industry. Also, antibiotic residue in rainbow trout must be controlled before their delivery to the market.
Complete mitochondrial genome of an undescribed gnomefish of the genus Scombrops (Teleostei, Scombropidae) from southern waters off Kyushu Island, Japan

Abstract The complete mitochondrial genome of an undescribed gnomefish species of the genus Scombrops was determined using a PCR-based method. The total length of mitochondrial DNA (mtDNA) was 16,521 bp, and included 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mitochondrial gene arrangement of this gnomefish species was identical to that of two previously described scombropid species, Scombrops boops and Scombrops gilberti, and also to those of other teleosts. Maximum likelihood analysis showed that the undescribed scombropid species is most closely related to S. boops.