Miracle-dz/UniFAR-FTUs huggingface dataset:
Relative Immunogenicity of PorA Subtypes in a Multivalent Neisseria meningitidis Vaccine Is Not Dependent on Presentation Form

ABSTRACT The hexavalent meningococcal vaccine HexaMen, containing six PorAs on two vesicles, was tested in clinical studies. Although fourfold increases in serum bactericidal activity (SBA) titers against all of the PorAs were observed, there were significant differences between PorA-specific SBA titers. SBA titers were mainly directed against one PorA from each vesicle, P1.5-2,10 and P1.5-1,2-2, and were lower against the other PorAs, especially P1.7-2,4 and P1.19,15-1. We investigated whether these differences were due to immunological interference that resulted in competition between the three PorAs on the same vesicle or whether they were caused by a difference in the immunogenicities of the separate PorAs. Therefore, mice were immunized either with HexaMen, with six monovalent outer membrane vesicles (OMVs) representing the same six PorAs simultaneously (HexaMix), or with only one of the monovalent OMVs. The immunoglobulin G and SBA titers after HexaMen immunization in mice resembled the results obtained in clinical studies. Although immunization with HexaMix gave higher titers than immunization with HexaMen for some PorAs, the pattern of high and low titers was the same. Similar differences in immunogenicity between subtypes were seen after monovalent immunization when interference was eliminated as a cause of the differences. Monovalent immunization resulted in higher titers for P1.5-1,2-2 and P1.7,16 than immunization with HexaMen. However, no significant differences were found for the weakly immunogenic PorAs, P1.7-2,4 and P1.19,15-1. Since immunization with the six PorAs in the trivalent presentation form (HexaMen) and in the mixture of monovalent vesicles (HexaMix) resulted in the same pattern of high and low titers, we concluded that the differences between the PorA-specific responses are due to differences in the immunogenicities of the various PorAs and not due to interference that results in competition between different PorAs.
A novel mutant-enriched liquidchip technology for the qualitative detection of somatic mutations in KRAS gene from both serum and tissue samples

Abstract Background: Somatic mutations in the KRAS gene have been reported to confer drug resistance to epidermal growth factor receptor tyrosine kinase inhibitors and some monoclonal antibodies. However, current DNA mutation detection technologies are primarily DNA sequencing-based and not high throughput, nor sensitive enough to meet clinical needs. Methods: A mutant-enriched PCR method was designed by introducing a unique restriction enzyme site to the PCR product. This allowed the wild-type KRAS sequence to be selectively removed by restriction enzyme digestion before application to the Luminex liquidchip system. Results: A total of 100 copies of mutant KRAS DNA fragment mixed with 1×105 copies of the wild-type KRAS DNA could be detected to achieve a sensitivity of 0.1%. This technology is currently used for clinical testing of KRAS somatic mutations for the purpose of pharmacogenomic evaluation. Serum samples from 109 patients with non-small cell lung cancer were tested and 34 mutations were detected (34/109). The formalin-fixed and paraffin-embedded samples from 60 patients with colorectal cancer were tested and 19 mutations were detected (19/60). Conclusions: A novel, qualitative, sensitive, reliable and high throughput liquidchip technology has been developed for detecting KRAS mutations using clinical serum and formalin-fixed and paraffin-embedded samples. Clin Chem Lab Med 2010;48:1103–6.
Microgeographic genetic diversity of wild steelhead trout 10 ( Oncorhynchus mykiss ) in a conservation hatchery operated coastal 11 river : How wild are they ? 12 13 14

Allelic variation at 10 microsatellite loci was assayed in potentially wild Oncorhynchus mykiss 32 collected from 11 tributaries and three upper main stem river sites (n=547), and compared to steelhead 33 trout from the hatchery operated in the lower main stem river (n=333). The objective was to investigate 34 microgeographic genetic structure of wild O. mykiss , in the face of large-scale hatchery stocking since 35 1984. Measures of genetic diversity within wild samples indicated diversity were similar to what has 36 previously been documented for wild populations. The level of microgeographic site subdivision (θ) was 37 significant (θ = 0.031), indicating moderate structure, and much higher than among sites located in the 38 lower river where the hatchery operates (θ = 0.004). Bayesian assignment clustering was used to infer 39 genetic ancestry without relying on prior information about sampling sites of individuals, and indicated 40 the existence of five or more, wild O. mykiss populations. The overall spatial pattern, however, identified 41 no clearly separate sites, but what appeared as an overlapping mosaic of modestly genetically divergent 42 localities. We conclude that wild O. mykiss populations exist in the tributaries and the upper main stem 43 river and its tributaries. These upper river populations appear to have retained genetic diversity and 44 differentiation in the face of extensive hatchery releases. 45
Cloning of Gene lon (capR) of Escherichia coli K-12 and Identification of Polypeptides Specified by the Cloned Deoxyribonucleic Acid Fragment

A mutation in the lon (capR) gene of Escherichia coli K-12 results in overproduction of capsular polysaccharide and increased sensitivity to ultraviolet and ionizing radiations. The lon (capR) gene deoxyribonucleic acid was cloned from a new F′ factor. The new plasmids, designated pBZ201 and pBZ203, (i) contained an additional 8.2-megadalton (Md) EcoRI fragment that had the same mobility as one of the EcoRI fragments of the F′, and (ii) conferred repression of capsular polysaccharide synthesis and repression of sensitivity to ultraviolet radiation in a bacterial transformation experiment with capR mutant recipient strains. A capR9 mutant plasmid, pBZ201M9, was also isolated and conferred expression of mucoidy and ultraviolet sensitivity to a capR+ (lon+) strain, indicating that the capR9 allele was dominant. Plasmids pBZ201M80, pBZ201M9-INSA, and pBZ201M9-INSB were characterized by transformation as containing recessive capR mutant alleles. Heteroduplex analyses and agarose gel electrophoresis of restriction endonuclease digests of plasmid DNA preparations revealed that (i) pBZ201M9-INSA and pBZ201M9-INSB each contains a 0.5-Md insertion (probably IS1) in the cloned DNA fragment at the same site, and (ii) pBZ201 and pBZ203, both capR+ plasmids, contain the same 8.2-Md fragment cloned in opposite orientations with respect to the cloning vehicle, pSC101. Plasmid-specified polypeptides were determined by using strain CSR603 maxicells containing each plasmid. Two new polypeptides were coded by the lon+ (capR+) 8.2-Md DNA fragment: Z1, 94 kilodaltons (94K), and Z2, 67K. The maxicells containing recessive capR mutant plasmids were deficient only in synthesis of the 94K polypeptide, and the dominant (capR9) mutant plasmid specified 5 to 10 times more of the 94K polypeptide than the maxicells containing the capR+ plasmid. Other data indicated that the capR9-specified “94K polypeptide” was not identical to the capR+-specified “94K polypeptide. ” Thus the altered mutant polypeptide was synthesized in increased quantities, suggesting a defective mode of autogenous regulation for the capR9 polypeptide and effective autogenous regulation of the capR+ polypeptide.
Salvage Enzymes in Nucleotide Biosynthesis Structural Studies on Three Bacterial Thymidine Kinases and Human Uridine-Cytidine Kinase 1

Kosinska, U. , 2007. Salvage enzymes in nucleotide biosynthesis: Structural studies on three bacterial thymidine kinases and human uridine-cytidine kinase 1. Doctoral dissertation ISSN 1652-6880, ISBN 978-91-576-7348-0 Balanced pools of deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA, and ribonucleoside triphosphates (NTPs), the precursors of RNA, are crucial for a controlled cell proliferation. The dNTPs and NTPs are synthesized de novo via energyconsuming reactions involving low-weight molecules, and through a salvage pathway by recycling (deoxy)ribonucleosides originating from food and degraded DNA and RNA. The enzymes described in this thesis catalyze the first reaction in the salvage biosynthesis of dNTPs and NTPs. The crystal structures of three bacterial thymidine kinases (TKs) are described and the enzymes are investigated as potential targets for antibacterial therapies. TK is a deoxyribonucleoside kinase (dNK) with specificity for thymidine. In addition to the natural substrates, TK can also phosphorylate a number of nucleoside analogs used in antiviral and anticancer therapies. This thesis presents the structures of TKs from three pathogenic microorganisms: Ureaplasma urealyticum (parvum), Bacillus anthracis and Bacillus cereus, and compares them to the human thymidine kinase 1 (hTK1). The bacterial TKs and the hTK1 are structurally very similar and have a highly conserved active site architecture, which may complicate structure-based drug design. However, the different complex structures presented in this work provide information regarding the conformational changes of TK1-like enzymes during the time of reaction. The structure of human uridine-cytidine kinase 1 (UCK1) is also presented. Humans possess two uridine-cytidine kinases, UCK1 and UCK2. The expression pattern of these enzymes is tissue dependent, and despite high sequence as well as structural similarities they possess somewhat diverse substrate specificity. In addition to the natural substrates, uridine and cytidine, UCKs are able to phosphorylate a number of nucleoside analogs. The monomeric structure of UCK comprises four domains: a CORE domain, an NMP-binding domain, a LID domain and a β-hairpin domain, which upon substrate binding undergo dramatic conformational changes. In the structure described in this thesis the enzyme has been trapped in an intermediate conformation between a fully opened and fully closed form, which may represent a sequential mode of substrate binding.
Demographics, farm and reproductive management strategies used in Australian automatic milking systems compared with regionally proximal conventional milking systems

OBJECTIVE To determine the management practices utilised in automatic milking systems (AMS) that affect reproductive management and performance and how these compare with the management practices used in regionally proximal conventional milking systems (CMS). METHODS This study examined demographic and management data from AMS and CMS dairy farms through a survey, with a specific focus on reproductive management procedures. RESULTS Overall, responses from AMS and CMS dairy farms showed little difference in terms of respondent demographics, farm size, herd structure and most farm management strategies. AMS dairies were more likely to use activity meters or other electronic oestrus detection aids than CMS dairies (P < 0.001) and were also more likely to have changed to electronic recording systems (P = 0.007). Although many respondents indicated that they used key monitoring parameters to assess reproductive performance (e.g. days in milk, conception vs pregnancy rate etc.), the format of responses varied significantly, indicating a relatively widespread (among the respondents) lack of knowledge regarding the meaning and usage of some of these common parameters/terminology. CONCLUSIONS Ultimately, reproductive management practices of AMS dairies were largely similar to those of CMS dairies, indicating that such practices can be implemented in a practical sense, even though the resultant reproductive performance is not yet understood. Understanding that the key reproductive management strategies do not need to change vastly is important to ensure that new adoptees are well informed. Further work is needed to objectively measure AMS performance to increase the knowledge base and generate the confidence that will facilitate further adoption of this innovation.
Tracking Coastal Sharks with small boats: Hammerhead Shark Pups as a case study

Acoustic telemetry techniques have been adapted for use with small boats to facilitate tracking of nearshore reef species. In addition to permitting tracking in areas where manoeuvrability and quick responses are required, the system has modest operating costs that make tracking experiments a viable option for a wide range of researchers. Tracking and communication equipment can be powered for several days by a single 12-V 8D truck battery. Current topics in shark biology that are amenable to these tracking techniques are discussed. For instance, hammerhead pups have been tracked on their natal grounds for periods of up to 13 days. Their daytime movements appeared to be restricted to a well defined 'core area' where a school of sharks hovered between 1 and 3 m off the lagoon floor. At night, the sharks became more active, expanding their range of movements before returning to the core area the next morning.
An Exploratory Study On Depression in Iranian Addicts

For the purpose of measuring the degree of depression among drug addicts in Iran, the Beck Depression Inventory was administered to 50 addicts, 46 depressed non-addicts, and 48 normal controls. Statistical comparison of the BDI for the three groups yielded a significant difference between the addicts and the controls, whereas the difference between the addicts and the depressed non-addicts was not significant; this indicates that depression is one of the clinical symptoms of drug addiction in Iran.
Cervical HPV DNA Detection as a Predictor of a Recurrent SIL Diagnosis Among Untreated Women

Objectives This study was conducted to test whether patient history of untreated cervical intraepithelial neoplasia (CIN) 1 or low-grade squamous intraepithelial lesions (LGSIL) modifies the interpretation of a positive HPV DNA result with regards to subsequent squamous intraepithelial lesions (SIL). Methods Seventy-three women with recurrent SIL were compared to 105 controls who remain cytologically normal during follow up. Cervical samples collected at enrollment were assayed for HPV DNA in the subject and control groups. Results Women with and without a history of LGSIL who tested positive for HPV DNA were at a similarly increased risk of having (recurrent) LGSIL as compared to controls. However, in women with a history of LGSIL, HPV DNA appeared to be less predictive for high-grade squamous intraepithelial lesions (HGSIL) than in women without a history of disease. Conclusions Past history of untreated CIN1 or LGSIL does not modify the predictive value of a positive HPV DNA test for subsequent LGSIL. The observed difference of the predictive value of a positive HPV DNA test for the risk of recurrent HSIL compared to incident HSIL should be pursued.
Clusters and Features from Combinatorial Stochastic Processes

In partitioning—a.k. a. clustering—data, we associate each data point with one and only one of some collection of groups called clusters or partition blocks. Here, we formally develop an analogous problem, called feature allocation, for associating data points with arbitrary non-negative integer numbers of groups, now called features or topics. We review known combinatorial stochastic process representations of clustering and develop analogous representations for the feature allocation case. We illustrate the clustering representations with examples that include the canonical nonparametric Bayesian clustering prior: the Chinese restaurant process or Dirichlet process. We not only illustrate the feature allocation representations with the canonical nonparametric Bayesian feature prior—the Indian buffet process or beta process—but also simultaneously discover new connections between the different representations for the Indian buffet process. We thereby bring the same level of completeness to the treatment of the Indian buffet that has previously been developed for the Chinese restaurant.
State of charge of lead acid battery

Lead acid batteries are used in hybrid vehicles and telecommunications power supply. For reliable operation of these systems, an indication of state of charge of battery is essential. To determine the state of charge of battery, current integration method combined with open circuit voltage, is being implemented. To reduce the error in the current integration method the dependence of available capacity as a function of discharge current is determined. The current integration method is modified to incorporate this factor. The experimental setup built to obtain the discharge characteristics of the battery is presented.
Tinospora cordifolia Chemical Constituents and Medicinal Properties : A Review

Since the beginning of human civilization, medicinal plants have been used by mankind for its therapeutic value. Nature has been a source of medicinal agents for thousands of years and an impressive number of modern drugs have been isolated from natural sources. Traditional medicine has remained as the most affordable and easily accessible source of treatment in the primary healthcare system of resource poor communities in India. A huge interest always exists in exploring nutraceuticals from plant materials to replace synthetic drugs in order to overcome their adverse effects and also for economic reasons. Tinospora cordifolia is a widely used shrub in folk and Ayurvedic systems of medicine all over India. Though almost all of its parts are used in traditional systems of medicines, leaves stem and roots are the most important parts which are used medicinally. Tinospora cordifolia is a versatile resource for all forms of life. It belongs to family Menispermaceae. It contains many different chemicals that affect the body. The present review aims to summarize the information concerning the chemical constituents and medicinal aspects of the Tinospora cordifolia plant.
Automated chicken processing: machine vision and water-jet cutting for optimized performance

Deboned chicken, especially breast meat, is a fast-growing segment of the poultry industry. This trend has placed new challenges on automation in poultry plants for deboning and portioning pieces of meat. In particular, poultry processors are looking for ways to maximize their profits by efficiently using each piece of deboned meat. Automating the portioning and cutting processes is challenging due to variations in thickness, shape, size, and positions of defects. Moreover, the equipment must tolerate the harsh environment in the plant such as cold temperatures, debris from the portioning process, and daily washing of the equipment. This paper presents the DSI Accura portioning system, made by FMC FoodTech. This portioning system uses high-speed image processing and automated water jets to cut chicken fillets into portions, nuggets, and strips of specified sizes and shapes. The system takes images of fillets moving on a conveyor belt and, for each fillet, determines an optimal pattern for the cuts. The cuts are made by focused water jets. These machines have four basic algorithmic tasks: imaging, portioning, path planning for the cutters, and control loops.
Detection of Pneumocystis carinii sequences by polymerase chain reaction: animal models and clinical application to noninvasive specimens

Pneumocystis carinii is a eukaryotic microbe which causes fatal pneumonia in patients with AIDS. Oligonucleotide primers were used to amplify the 5S rDNA sequence of P. carinii by the polymerase chain reaction (PCR) in various clinical and animal samples. Of 35 independent lung specimens tested, PCR detected the P. carinii sequence in all 23 cases which were known to be P. carinii infected, i.e., 15 from mice, 1 from rat, 3 from human autopsy, and 4 from biopsy of AIDS patients by needle aspiration. The results were consistent with clinical and microscopic diagnosis. The detection was highly sensitive and specific. Direct sequencing of these amplified DNAs revealed homogeneity of 5S rDNA sequences of independent isolates from mice, rats, and humans. Preliminary trials manifested efficacy of the PCR method to detect P. carinii sequences in induced sputum or blood from AIDS patients, the latter case suggesting that P. carinii might enter peripheral blood via phagocytosis or direct intrusion. Development of less-invasive or noninvasive PCR diagnostic techniques to detect P. carinii infection would greatly facilitate therapeutic and prophylactic management of P. carinii pneumonia.
Tethering the N‐terminus of the prion protein compromises the cellular response to oxidative stress

The role of the N‐terminal half of the prion protein (PrPC) in normal cellular function and pathology remains enigmatic. To investigate the biological role of the N‐terminus of PrP, we examined the cellular properties of a construct of murine PrP, PrP‐DA, in which the N‐terminus is tethered to the membrane by an uncleaved signal peptide and which retains the glycosyl‐phosphatidylinositol anchor. Human neuroblastoma SH‐SY5Y cells expressing PrP‐DA were more susceptible to hydrogen peroxide and copper induced toxicity than wtPrP expressing cells. The PrP‐DA expressing cells had an increased level of intracellular free radicals and reduced levels of superoxide dismutase and glutathione peroxidase as compared to the wtPrP expressing cells. The membrane topology, cell surface location, lipid raft localisation, intracellular trafficking and copper‐mediated endocytosis of PrP‐DA were not significantly different from wtPrP. However, cells expressing PrP‐DA accumulated an N‐terminal fragment that was resistant to proteinase K. The data presented here are consistent with the N‐terminal region of PrPC having a role in the cellular response to oxidative stress, and that tethering this region of the protein to the membrane compromises this function through the accumulation of a protease‐resistant N‐terminal fragment, similar to that seen in some forms of human prion disease.
Dry fingerprint detection for multiple image resolutions using ridge features

Dry and wet fingers lead to poor fingerprint quality, which means that it has impact for fingerprint recognition and matching. Recognition methods that are based on the feature of ridge, valley, minutiae or pore are affected by skin conditions. In this paper, we propose a novel dry fingerprint detection method for images with different resolutions using ridge features. The dry fingerprints have vague pores and discontinuous and fragmented ridges. Therefore, the features that we adopt for detection are ridge continuity, ridge fragmentation and ridge/valley ratio. These features can be observed clearly under different image resolutions, so our proposed method can work on 500∼1200 dpi. We propose several ridge features and use the support vector machine to classify into two groups, dry and normal. The NASIC database (1200dpi) and FVC2002 DB1 (500dpi) are used in our experiments, the SVM classification accuracy are 99.00%, and 99.09% relatively.
Fusarium Wilt Suppression and Agglutinability of Pseudomonas putida

Mutants of Pseudomonas putida (Agg−) that lack the ability to agglutinate with components present in washes of bean and cucumber roots showed limited potential to protect cucumber plants against Fusarium oxysporum f. sp. cucumerinum. However, a higher level of protection was observed against Fusarium wilt in cucumber plants coinoculated with the parental bacterium (Agg+), which was agglutinable. The Agg− mutants did not colonize the roots of cucumber plants as extensively as the Agg+ parental isolate did. In competition experiments involving bean roots inoculated with a mixture of Agg+ and Agg− bacteria, the Agg+ strains colonized roots to a greater extent than the Agg− cells did. These data suggest that the Agg+ phenotype provides additional interactions that aid in the beneficial character of P. putida.