Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization of digestive proteases of the yellow mealworm, Tenebrio molitor L.

United States Department of Agriculture-Cooperative State Research, Education, and Extension Service-Risk Avoidance and Mitigation Program, Civilian Research and Development Foundation, Russian Foundation for Basic Research, North Atlantic Treaty Organization-Russia Collaborative Linkage Grant, Kansas State University-Department of Entomology.
Transcriptional Analysis of the Bacteroides fragilis Starch Utilization Operon, osuA

The opportunistic pathogen Bacteroides fragilis is a symbiotic organism that inhabits the human gastrointestinal tract where it utilizes dietary and host-derived polysaccharides as carbon and energy sources. If abdominal injury occurs this otherwise commensal organism can migrate from the anaerobic environment of the large intestine to the more aerobic peritoneum. In this new extraintestinal environment B. fragilis frequently contributes to the development of intra-abdominal abscesses and is often the most common isolate from such anaerobic infections which can lead to systemic infections and death if left untreated. The organism's ability to shift from commensalist to pathogen is inextricably linked with the complex oxidative stress response (OSR) it has evolved. The studies described in this thesis have focused on the characterization of the promoter for the oxidative starch utilization operon osu and the identification of regulatory sequences involved in transcription activation during growth in maltose or exposure to oxygen. The results of this promoter deletional analysis study have demonstrated that the osu promoter is indeed responsive to both maltose and oxygen and that regulatory regions important for activation of transcription in response to both stimuli are likely found within the same 50 bp region of the promoter. Consistent with this observation was the discovery of a LacI-type binding region in this site. In addition studies demonstrated that there is the possibility of an additional weak oxygen-responsive promoter that exists in a separate region of the osu promoter. The previously identified transcriptional activator OsuR may also play a critical role in transcription activation of the osu promoter regardless of whether the inducing agent is maltose or oxygen. The mechanism of osu protection during oxidative stress is not fully understood but results of this thesis offer a more complex model of transcriptional activation of the osu operon than was initially theorized. More studies will be necessary to further elucidate the role of osu in maintaining the OSR of B. fragilis during oxygen exposure.
Sightings of Delphinus delphis (Cetacea, Odontoceti) in the Otranto Channel (Southern Adriatic Sea and Northern Ionian Sea) / Avvistamenti di Delphinus delphis (Cetacea, Odontoceti) nel Canale d'Otranto (Mar Adriatico Meridionale e Mar Ionio Settentrionale)

Abstract Two sightings of Common dolphin Delphinus delphis in the Channel of Otranto are reported, and the status of this species in the Mediterranean Sea is briefly discussed. Riassunto Sono riportati due avvistamenti di Delfino comune Delphinus delphis nel Canale d'Otranto, lungo la costa greca e quella italiana. Viene inoltre brevemente commentata la frequenza degli avvistamenti e degli spiaggiamenti di tale specie nel Mar Mediterraneo.
Low Reproductive Success of Mallards in a Grassland-Dominated Landscape in The Sandhills of Nebraska

The Sandhills of Nebraska comprise approximately 5,000,000 ha of native grassland interspersed with numerous groundwater-fed wetlands. A substantial population of the mallard (Anas platyrhynchos) nests in this region. Previous investigations of nest survival probability of ducks in the Sandhills have estimated surprisingly low rates of nest survival for a grassland-dominated landscape. These investigations were conducted on public lands and most nest searching took place near wetlands where activity of nest predators might be highest. We predicted that mallards would nest at varying distances from wetlands and that survival probability of a representative sample of duck nests would increase with distance from wetlands. We decoy-trapped and radio-marked 71 female mallards, 32 during the 2005 nesting season and 39 during the 2006 nesting season, and monitored their individual choice of nest habitats, their survival during the nesting season, and survival of their nests. Mallards nested in various habitats, both near and far from wetlands. Nest survival probability (O = 0.03, SE = 0.02) was low relative to other studies regardless of distance to wetlands. Survival of females during the nesting season (O = 0.84, SE = 0.08), however, was high relative to other studies. This pattern could have resulted from the combination of a diverse community of nest predators, few predators of nesting females, and a population of largely second year females that put little effort into nesting. ____________________ Corresponding author. E-mail address: jwalker@ducks.org 2 The Prairie Naturalist 40(1/2): March/June 2008
Performance analysis of numerical schemes in highly swirling turbulent flows in cyclones

The aim of this study is to investigate the suitability of various numerical schemes and turbulence models in highly complex swirling flows which occur in tangential inlet cyclones. Three-dimensional steady governing equations for incompressible turbulent flow inside a cyclone were solved numerically using Fluent CFD (computational fluid dynamics) code. The Reynolds stress turbulence model, the Standard k-e and the RNG k-e turbulence models together with various combinations of numerical schemes are used to obtain axial and tangential velocity profiles, pressure drop and turbulent quantities. Computational results were compared with experimental and numerical values given in the literature, so as to evaluate the performance of the numerical schemes and turbulent models. Comparison of CFD results with experimental data shows that the Reynolds Stress turbulence model yields a reasonably good prediction. Results obtained from the numerical tests have demonstrated that the use of the Presto interpolation scheme for pressure, the Simplec algorithm for pressure-velocity coupling and the quadratic upstream interpolation for convective kinetics (quick) scheme for momentum variables gives satisfactory results for highly swirling flows in cyclones.
Straightening out the mechanisms of axial elongation using mouse mutant analysis

Understanding the mechanisms that lead to axial elongation in the mouse has direct relevance to elucidating the etiology of vertebral defects in humans. Through the characterization of a spontaneous mouse mutant, kinked tail, and the analysis of Tbx6 protein modulation in vivo, I uncovered two distinct mechanisms affecting axial elongation in the mouse. The kinked tail mutation is a spontaneous mutation, inherited dominantly, that results in a kinky tail phenotype in heterozygotes and early embryonic lethality in homozygotes. Defective axial elongation in kinked tail heterozygotes is displayed as shortened tails and multiple tail kinks resulting from wedge, hemi- and fused vertebrae, similar to those observed in scoliosis patients. These vertebral defects are likely due to a primary notochord defect that is thickened and branched. Kinked tail homozygotes fail to undergo gastrulation due to defective distal visceral endoderm cell migration, ultimately resulting in lethality by embryonic day 8.5. The defective cell migration is further compounded by basement membrane defects and gross dysmorphology of the mutant embryo. Tbx6, a T-box transcription factor, is essential for posterior somite formation, patterning and viability of the mouse embryo. I sought to understand Tbx6 protein regulation and the phenotypic consequences of modulating Tbx6 protein levels in vivo. In vitro analyses revealed that Tbx6 is a relatively stable protein that appears to be regulated in part by the proteasome in addition to other mechanisms. In vivo, less than heterozygous levels of Tbx6 protein results in rib and vertebral defects, enlarged tailbuds and axial shortening while greater than wildtype levels of Tbx6 protein results in small embryonic tailbuds, axial shortening, and lethality. I further examined the consequences of Tbx6 misexpression using a 3-component transgenic system. The primitive streak and presomitic mesoderm are affected in those embryos that misexpress Tbx6.Altogether, my analysis of the spontaneous mutation, kinked tail, demonstrated a possible role of the notochord in proper axial elongation, and the analysis of Tbx6 protein modulation further clarified the importance of maintaining proper levels of Tbx6 for normal axis elongation and embryonic development.
Advanced Neuropsychological Diagnostics Infrastructure (ANDI): A Normative Database Created from Control Datasets

In the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), datasets of several research groups are combined into a single database, containing scores on neuropsychological tests from healthy participants. For most popular neuropsychological tests the quantity, and range of these data surpasses that of traditional normative data, thereby enabling more accurate neuropsychological assessment. Because of the unique structure of the database, it facilitates normative comparison methods that were not feasible before, in particular those in which entire profiles of scores are evaluated. In this article, we describe the steps that were necessary to combine the separate datasets into a single database. These steps involve matching variables from multiple datasets, removing outlying values, determining the influence of demographic variables, and finding appropriate transformations to normality. Also, a brief description of the current contents of the ANDI database is given.
The assessment of omega 3 oilsources for use in aquaculture –alternatives to the unsustainableharvest of wild fish stocks

ABSTRACT Worldwide harvest of wild marine fisheries for fish oil cannot increase. However, the demand for fish oil is increasing due to a rapidly expanding aquaculture industry and is further increased by nutraceutical/biomedical and agricultural companies. Aquaculture uses fish oil as a source for essential fatty acids in particular omega-3 long chainpolyunsaturated fatty acids (ω3 LC-PUFA) and for energy. Other novel sources of renewable, environmentally sustainable oil that provide these nutritional requirements for Atlantic salmon (Salmo salar L.) are needed. This research looked at alternate sources of oil containing the ω3 LC-PUFA that are associated with the many health benefits of eating Atlantic salmon. This thesis also contributed to the development of three techniques for use in aquaculture lipid nutrition research: 1) advanced chromatography and mass spectroscopy to examine intact molecular membrane lipids; 2) nuclear magnetic resonance (13C NMR) to assess the regiospecific distribution of ω3 LC-PUFA in oil, and 3) molecular RT-PCR to investigate endogenous ω3 LC-PUFA production.
Genetic Fingerprinting of Goldenseal (Hydrastis canadensis) Using AFLP Markers: An Update

Our earlier publication indicated 3 accessions of goldenseal (Hydrastis canadensis L. [Ranunculaceae]) originated in Florida, although our results indicated they were more closely related to Tennessee and Georgia genotypes. After further investigation with our plant supplier, it appears that 2 of the 3 accessions purportedly from Florida were indeed from Tennessee and Georgia—AFLP is a robust method for correctly identifying the source of goldenseal genotypes.
Pain and Power Doppler Ultrasonographic Evaluation according to Bursal Preservation after Arthroscopic Rotator Cuff Repair: Comparison between Complete and Minimal Bursectomy in Early 3 Months

“This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ” The Journal of the Korean Orthopaedic Association Volume 53 Number 3 2018 Received February 22, 2017 Revised June 13, 2017 Accepted August 26, 2017 Correspondence to: Byung Hoon Kwack, M.D. Department of Orthopaedic Surgery, Daegu Catholic University Medical Center, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Korea TEL: +82-53-650-4054 FAX: +82-53-626-4272 E-mail: kwackbyunghoon@nate.com ORCID: https://orcid.org/0000-0003-4795-8294 관절경하 회전근 개 봉합술 시 윤활낭 절제 정도에 따른 통증 및 파워 도플러 초음파 결과: 전절제술과 최소 절제술 시 초기 3개월간의 비교
Investigating allosteric regulation of ABL and BCR-ABL kinases: Implications for small molecule inhibitors

BCR-ABL is the oncogenic protein-tyrosine kinase responsible for the pathogenesis of chronic myelogenous leukemia (CML). Clinical management of CML has been revolutionized by imatinib, a selective ATP-competitive inhibitor of BCR-ABL kinase activity. Despite this clinical success, imatinib is less effective in advanced disease due to the emergence of drug resistant BCR-ABL mutants. Resistant mutations often arise in the drug binding site and include the most recalcitrant gatekeeper mutation, T315I. Other mutations arise outside the active site and allosterically reduce imatinib binding by promoting the active kinase conformation. Recently, a new class of allosteric BCR-ABL inhibitors, of which GNF-2 is the prototype, has been reported that targets the myristate-binding pocket of ABL. These compounds stabilize the inactive conformation of ABL and work in concert with ATP-competitive inhibitors to overcome imatinib resistance. Mounting evidence supports a regulatory influence of the non-catalytic SH3 and SH2 domains on BCR-ABL kinase domain. The major focus of this study was to exploit the intramolecular SH3:linker interaction, to stabilize the downregulated kinase domain conformation of BCR-ABL and sensitize the kinase to both imatinib and GNF-2. To achieve this goal, I engineered High Affinity Linker (HAL) variants of both ABL and BCR-ABL in which SH3:linker interaction was tightened through sequential addition of proline residues to the linker. Enhanced SH3:linker interaction induced long-range suppressive effects on the kinase activity in c-ABL, allosterically stabilized both the active site and the myristate-binding pocket, and sensitized BCR-ABL to small molecule inhibitors. Src family kinases (SFKs) are important mediators of BCR-ABL signal transduction and oncogenesis in CML. SFKs also play important roles in clinical resistance to imatinib in the absence of BCR-ABL mutations. In the second part of my project, I explored the effect of SFK- selective inhibitor, pyrazolopyrimidine A-419259, on myeloid cells transformed with clinically relevant imatinib resistant BCR-ABL mutants. While proliferation of cells expressing BCR-ABL E255V and Y253H was inhibited by A-419259, BCR-ABL T315I cells were not. Surprisingly, cells expressing BCR-ABL-T315I maintained SFK activity in the presence of the inhibitor. This observation suggests that BCR-ABL-T315I induces cross-resistance to drugs that inhibit SFKs in CML through direct phosphorylation of the SFKs.
EVALUATION OF THE PHYSIOLOGICAL FUNCTIONS OF BLEOMYCIN HYDROLASE IN THE MURINE CNS

The overall hypothesis of this thesis project was that bleomycin hydrolase (BLMH) has biologically specific and unique functions in the central nervous system (CNS). BLMH is a multifaceted papain superfamily cysteine protease that has importance in drug metabolism. The physiological functions of this protease are unknown as are factors regulating its expression. Immunohistochemical examination of B6.129Blmhtm1Geh/J null and control animals showed no gross abnormalities; however, marked global astrogliosis was observed in the null aged animals. To define the role of BLMH in the brain, the behavioral phenotype of hybrid [129S6-Blmhtm1Geh/J X B6.129 Blmhtm1Geh/J]F1 null and littermate controls was characterized using multiple behavioral paradigms. Deletion of Blmh was found to result in deficits among young animals in water maze probe trials. Retention of target platform location during the probe trials requires both learning and memory as well as sensory and locomoter skills. No overt sensory or motor deficits were noted in Blmh null F1 hybrids. The profile of BLMH expression and its regulation in the CNS was studied next. Inducible transcription of BLMH was evaluated in the context of a putative role in the processing of MHC I epitopes. BLMH was found to be differentially regulated in microglia and astrocytes. In microglia, Blmh protein was significantly induced by gamma interferon or tumor necrosis factor a, whereas in astrocytes, no change in protein expression was observed. Treatment of microglial derived cell lines with both gamma interferon and tumor necrosis factor a revealed synergistic effects between the cytokines. BLMH protein induction was accompanied by increased Blmh mRNA. These results suggest that cell specific regulation of BLMH is an important control mechanism for this protease. These data also provide further evidence for a targeted immune related biological function for BLMH. It is concluded that BLMH potentially has multiple unique and biologically important functions within the brain.
TETHERED IL-15 TO AUGMENT THE THERAPEUTIC POTENTIAL OF T CELLS EXPRESSING CHIMERIC ANTIGEN RECEPTOR: MAINTAINING MEMORY POTENTIAL, PERSISTENCE, AND ANTITUMOR ACTIVITY

vi TABLE OF CONTENTS . viii LIST OF FIGURES . xii LIST OF TABLES . xiv LIST OF ABBREVIATIONS . xv CHAPTER 1: Background . 1 1.1 B-cell Acute Lymphoblastic Leukemia . 1 1.2 CD8 T Cell Differentiation During Immune Response . 1 1.3 Harnessing the Immune System to Target ALL Minimal Residual Disease . 4 1.4 Adoptive Immunotherapy: Redirecting T Cell Specificity . 6 1.5 Improving Adoptively Transferred T Cell Persistence . 8 1.6 Cytokines Support Adoptively Transferred T Cell Persistence . 9 1.7 Specific Aims . 12 CHAPTER 2: Generation of Clinically Relevant CD19-specific T Cells Co-expressing mIL15 . 14 2.
IDENTIFCATION OF THE CAUSES OF CYTOKINESIS FAILUREIN CANCER CELLS

Tetraploidy and chromosomal instability are common phenotypes of malignant cells and cytokinesis failure is a known source of tetraploidy. However, the causes of cytokinesis failure are not yet identified. An essential step in the process of cytokinesis is phosphorylation of myosin regulatory light chain (MLC), required for actin–myosin interaction and the formation of the cleavage furrow. Our data indicate that cancer cells are deficient in MLC phosphorylation and this deficiency is the cause of cytokinesis failure. Myosin light chain kinase (MLCK) is a key enzyme that phosphorylates MLC during cytokinesis and is inhibited in cancer cells. Aurora B kinase is an essential regulator of cytokinesis that is commonly over-expressed in cancer cells and can phosphorylate MLCK in vitro. Therefore we hypothesize that Aurora B over-expression is the cause of MLCK inhibition in cancer cells. Consistent with our hypothesis, we demonstrate that Aurora B kinase indeed is an MLCK inhibitor in vitro and in cultured mammalian cells. Cytokinesis failure resulting from Aurora B over-expression can largely be suppressed by constitutively active MLCK or phosphomimetic MLC and reducing protein levels of Aurora B in cancer cells increases MLCK activity and decreases cytokinesis failure. These data thus describe a novel pathway that drives Aurora B induced cytokinesis failure. Cytokinesis failure is often observed in only a subset of cancer cells but the trigger for this divisional failure in that subset is unknown. One strong possibility is the presence of lingering chromatin at the cleavage site that has been previously proposed to block cytokinesis completion. However, the mechanism linking lingering chromatin and cytokinesis failure is still a mystery. In this study we demonstrate that lingering chromatin causes cytokinesis failure by inducing over-expression of Aurora B and the resultant inhibition of MLCK and phosphorylated MLC. Together, my results define a novel pathway for Aurora B mediated regulation of cytokinesis and contribute to our understanding of the genomic destabilizing events of tumorigenesis.
Use of a helicopter to capture flighted cranes

Using a helicopter, we pursued 12 sandhill cranes (Grus canadensis) and captured 6. In forested habitat, cranes could be forced down, but we were unable to deploy the pursuit team, so cranes could not be captured. In open habitat, every crane we pursued was captured. Target cranes were forced to the ground in 0.3-14 minutes (x= 6 minutes). Adjusting pursuit distance (50-150 m) was essential in promoting fatigue and in preventing escape of target cranes.
Response of biofertilizers and pesticides on yield and quality of cabbage, radish and brinjal in vegetable-based rotation system

Microbial biotechnology has emerged as an effective tool in offering tremendous potential to increase productivity under biodynamic production system. To ascertain the effects of different biofertilizers and biopesticides used in combination with organic nutrient on different vegetable crops viz. cabbage, radish and brinjal, an experiment was planned to find ideal microbial strains for specific crop and suitable biopesticides against major vegetable pests so as to develop a complete package of organic farming. The treatments comprised of five combine sources of microbial fertilizers, including chemical fertilizer, and four sources microbial pesticides including chemical pesticides. Among the tested biofertilizers, Azospirillium bresilence manifested better response for each included crop under mid-hill conditions of Himachal Pradesh, India. Though the yield in organic produce was at par with produce obtained under conventional method but the produce was superior in protein and vitamin C contents with better shelf life under ambient storage conditions. The nitrate content, which has an ill effect on health, was also quite low in these treatments. In case of biopesticides Bacillus thurigenisis (Bio-lap & Elcar) and Neem-based pesticide Neemarin were found equally effective in controlling Diamond moth of cabbage, leaf caterpillar of radish and shoot and fruit borer of brinjal as chemical pesticide Endosulfan.
Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 pig population1

An experimental F 2 cross between Iberian and Landrace pig strains was performed to map quantitative trait loci (QTL) for diverse productive traits. Here we report results for meat quality traits from 369 F 2 animals with records for pH 24 h postmortem (pH 24 h), muscle color Minolta measurements L* (lightness), a* (redness), and b* (yellowness), H* (hue angle), C* (chroma), intramuscular fat (IMF) and haematin pigment content measured in the longissimus thoracis. Pigs were genotyped for 92 markers covering the 18 porcine autosomes (SSC). Results of the genome scan show evidence for QTL for IMF (SSC6; F = 27.16), pH 24 h (SSC3; F = 7.73), haematin pigments (SSC4 and SSC7; F = 8.68 and 9.47 respectively) and Minolta color measurements L* (SSC4 and SSC7; F = 16.42 and 7.17 respectively), and a* (SSC4 and SSC8; F = 8.05 and 7.36 respectively). No QTL were observed for the color measurements b*, H*, and C*. Alternative models fitting epistasis between QTL were also tested, but detected epistatic interactions were not significant at a genome-wise level. In this work we identify genomic regions related with meat quality traits. Improvement by traditional selection methods is complicated, and finer mapping would be required for their application in introgression programs.