Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

Ethical fashion : the human stories driving a fashion movement

This paper examines and compares two stories, the novel Helen Fleetwood (Elizabeth, 1841) and the film China Blue (Teddy Bear Films, 2005), in relation to the Ethical Fashion movement. In 2005, more than 50 designers from around the world took part in The Ethical Fashion Show in Paris. This movement dictates that designers ensure that their garments are produced in an ethical manner, rather than support the ‘sweatshop’ environments of some industrialists determined to make a profit at the expense of workers rights. The momentum of the Ethical Fashion movement suggests that it is possible for fashion to be ethical, desirable and profitable in the 21st century. In 1841, after extensive research, Charlotte Elizabeth Tonna (using the pseudonym Charlotte Elizabeth) began to write about the atrocities of the factory system in industrialised England. Her novel, Helen Fleetwood, is one of the earliest examples of this kind of work, providing the reader with an extensive insight into the life of English factory workers in the mid-19th century. The story is about the Widow Green and her orphan dependents who are led, through circumstance, to leave their rural home and take up employment in the cotton mills of Manchester, with the hope of having an independent existence. Instead they discover the realities of factory life – extremely long hours, unsafe conditions, poor wages and a steady decline into extreme poverty. In his film China Blue (Teddy Bear Films, 2005), director Micha X. Peled tells an alarmingly similar tale set in 21st century China. This ‘docu-drama’ (a recreation from actual interviews and diary entries) tells the story of ‘Little Jasmine’ who leaves her family’s farm to pursue an independent life in Southern China’s manufacturing district. It is not long before the realities of modern factory life are revealed to the teenage ‘heroine’ – crowded dormitories, long working hours, arbitrary fines and wages that do not compare with those of workers in the Western world. While much of the human story remains unchanged, there have been significant improvements in technology and safety in the last 165 years that result in the reality that not all clothing manufacture is performed in ‘sweatshop’ conditions. After a recent visit to a manufacturing plant in China, consultation with peers in the industry and having worked in the Australian fashion industry for many years, the author compares these stories with her own experiences.

Human-body shadowing effects on indoor MIMO-OFDM channels at 5.2 GHz

Pedestrian movement is known to cause significant effects on indoor MIMO channels. In this paper, a statistical characterization of the indoor MIMO-OFDM channel subject ot pedestrian movement is reported. The experiment used 4 sending and 4 receiving antennas and 114 sub-carriers at 5.2 GHz. Measurement scenarios varied from zero to ten pedestrians walking randomly between transmitter (tx) and receiver (Rx) arrays. The empirical cumulative distribution function (CDF) of the received fading envelope fits the Ricean distribution with K factors ranging from 7dB to 15 dB, for the 10 pedestrians and vacant scenarios respectively. In general, as the number of pedestrians increase, the CDF slope tends to decrease proportionally. Furthermore, as the number of pedestrians increase, increasing multipath contribution, the dynamic range of channel capacity increases proportionally. These results are consistent with measurement results obtained in controlled scenarios for a fixed narrowband Single-Input Single-Output (SISO) link at 5.2 GHz in previous work. The described empirical characterization provides an insight into the prediction of human-body shadowing effects for indoor MIMO-OFDM channels at 5.2 GHz.

Wavefront aberrations and the depth of focus of the human eye

The depth of focus (DOF) can be defined as the variation in image distance of a lens or an optical system which can be tolerated without incurring an objectionable lack of sharpness of focus. The DOF of the human eye serves a mechanism of blur tolerance. As long as the target image remains within the depth of focus in the image space, the eye will still perceive the image as being clear. A large DOF is especially important for presbyopic patients with partial or complete loss of accommodation (presbyopia), since this helps them to obtain an acceptable retinal image when viewing a target moving through a range of near to intermediate distances. The aim of this research was to investigate the DOF of the human eye and its association with the natural wavefront aberrations, and how higher order aberrations (HOAs) can be used to expand the DOF, in particular by inducing spherical aberrations ( 0 4 Z and 0 6 Z ). The depth of focus of the human eye can be measured using a variety of subjective and objective methods. Subjective measurements based on a Badal optical system have been widely adopted, through which the retinal image size can be kept constant. In such measurements, the subject.s tested eye is normally cyclopleged. Objective methods without the need of cycloplegia are also used, where the eye.s accommodative response is continuously monitored. Generally, the DOF measured by subjective methods are slightly larger than those measured objectively. In recent years, methods have also been developed to estimate DOF from retinal image quality metrics (IQMs) derived from the ocular wavefront aberrations. In such methods, the DOF is defined as the range of defocus error that degrades the retinal image quality calculated from the IQMs to a certain level of the possible maximum value. In this study, the effect of different amounts of HOAs on the DOF was theoretically evaluated by modelling and comparing the DOF of subjects from four different clinical groups, including young emmetropes (20 subjects), young myopes (19 subjects), presbyopes (32 subjects) and keratoconics (35 subjects). A novel IQM-based through-focus algorithm was developed to theoretically predict the DOF of subjects with their natural HOAs. Additional primary spherical aberration ( 0 4 Z ) was also induced in the wavefronts of myopes and presbyopes to simulate the effect of myopic refractive correction (e.g. LASIK) and presbyopic correction (e.g. progressive power IOL) on the subject.s DOF. Larger amounts of HOAs were found to lead to greater values of predicted DOF. The introduction of primary spherical aberration was found to provide moderate increase of DOF while slightly deteriorating the image quality at the same time. The predicted DOF was also affected by the IQMs and the threshold level adopted. We then investigated the influence of the chosen threshold level of the IQMs on the predicted DOF, and how it relates to the subjectively measured DOF. The subjective DOF was measured in a group of 17 normal subjects, and we used through-focus visual Strehl ratio based on optical transfer function (VSOTF) derived from their wavefront aberrations as the IQM to estimate the DOF. The results allowed comparison of the subjective DOF with the estimated DOF and determination of a threshold level for DOF estimation. Significant correlation was found between the subject.s estimated threshold level for the estimated DOF and HOA RMS (Pearson.s r=0.88, p<0.001). The linear correlation can be used to estimate the threshold level for each individual subject, subsequently leading to a method for estimating individual.s DOF from a single measurement of their wavefront aberrations. A subsequent study was conducted to investigate the DOF of keratoconic subjects. Significant increases of the level of HOAs, including spherical aberration, coma and trefoil, can be observed in keratoconic eyes. This population of subjects provides an opportunity to study the influence of these HOAs on DOF. It was also expected that the asymmetric aberrations (coma and trefoil) in the keratoconic eye could interact with defocus to cause regional blur of the target. A dual-Badal-channel optical system with a star-pattern target was used to measure the subjective DOF in 10 keratoconic eyes and compared to those from a group of 10 normal subjects. The DOF measured in keratoconic eyes was significantly larger than that in normal eyes. However there was not a strong correlation between the large amount of HOA RMS and DOF in keratoconic eyes. Among all HOA terms, spherical aberration was found to be the only HOA that helped to significantly increase the DOF in the studied keratoconic subjects. Through the first three studies, a comprehensive understanding of DOF and its association to the HOAs in the human eye had been achieved. An adaptive optics system was then designed and constructed. The system was capable of measuring and altering the wavefront aberrations in the subject.s eye and measuring the resulting DOF under the influence of different combination of HOAs. Using the AO system, we investigated the concept of extending the DOF through optimized combinations of 0 4 Z and 0 6 Z . Systematic introduction of a targeted amount of both 0 4 Z and 0 6 Z was found to significantly improve the DOF of healthy subjects. The use of wavefront combinations of 0 4 Z and 0 6 Z with opposite signs can further expand the DOF, rather than using 0 4 Z or 0 6 Z alone. The optimal wavefront combinations to expand the DOF were estimated using the ratio of increase in DOF and loss of retinal image quality defined by VSOTF. In the experiment, the optimal combinations of 0 4 Z and 0 6 Z were found to provide a better balance of DOF expansion and relatively smaller decreases in VA. Therefore, the optimal combinations of 0 4 Z and 0 6 Z provides a more efficient method to expand the DOF rather than 0 4 Z or 0 6 Z alone. This PhD research has shown that there is a positive correlation between the DOF and the eye.s wavefront aberrations. More aberrated eyes generally have a larger DOF. The association of DOF and the natural HOAs in normal subjects can be quantified, which allows the estimation of DOF directly from the ocular wavefront aberration. Among the Zernike HOA terms, spherical aberrations ( 0 4 Z and 0 6 Z ) were found to improve the DOF. Certain combinations of 0 4 Z and 0 6 Z provide a more effective method to expand DOF than using 0 4 Z or 0 6 Z alone, and this could be useful in the optimal design of presbyopic optical corrections such as multifocal contact lenses, intraocular lenses and laser corneal surgeries.

Vibration characteristics of slender structures under human induced loads

This paper presents the outcome of investigations and studies of the vibratioon characteristics and response of low frequency structural systems for a composite concrete steel floor plate and a reverse profiled cable tensioned foot bridge. These highly dynamic and slender structure are the engineering response to planning, aesthetic and environmental influences, but are prone to excessive and complex vibration. A number of design codes and practice guides provided information to engineers for vibration mitigation However, they are limited to very simple load function applied to a few uncoupled translational modes of excitation. Motivated by the need to address the knowledge gaps in this area, the investigations described in this paper focused on synchronous multi-modal and coupled excitation of the floor plate and footbridge with considerations for torsinal effects. The results showed the potential for adverse dynamic response from multi-modal and coupled excitation influenced by patterned loading, structure geometry, stiffness distribution, directional effects, forcing functions based on activity frequency and duration of foot contact, and modal participation. It was also shown that higher harmonics of the load frequency can excite higher modes in the composite floor structure. Such responsive behaviour is prevalent mainly in slender and lightweight construction and not in stiffer and heavier structural systems. The analytical techniques and methods used in these investigations can supplement the current limited code and best practice provisions for mitigating the impact of human induced vibrations in slender structural systems.

Long-term effects of hydrogel properties on human chondrocyte behavior

Hydrogels provide a 3-dimensional network for embedded cells and offer promise for cartilage tissue engineering applications. Nature-derived hydrogels, including alginate, have been shown to enhance the chondrocyte phenotype but are variable and not entirely controllable. Synthetic hydrogels, including polyethylene glycol (PEG)-based matrices, have the advantage of repeatability and modularity; mechanical stiffness, cell adhesion, and degradability can be altered independently. In this study, we compared the long-term in vitro effects of different hydrogels (alginate and Factor XIIIa-cross-linked MMP-sensitive PEG at two stiffness levels) on the behavior of expanded human chondrocytes and the development of construct properties. Monolayer-expanded human chondrocytes remained viable throughout culture, but morphology varied greatly in different hydrogels. Chondrocytes were characteristically round in alginate but mostly spread in PEG gels at both concentrations. Chondrogenic gene (COL2A1, aggrecan) expression increased in all hydrogels, but alginate constructs had much higher expression levels of these genes (up to 90-fold for COL2A1), as well as proteoglycan 4, a functional marker of the superficial zone. Also, chondrocytes expressed COL1A1 and COL10A1, indicative of de-differentiation and hypertrophy. After 12 weeks, constructs with lower polymer content were stiffer than similar constructs with higher polymer content, with the highest compressive modulus measured in 2.5% PEG gels. Different materials and polymer concentrations have markedly different potency to affect chondrocyte behavior. While synthetic hydrogels offer many advantages over natural materials such as alginate, they must be further optimized to elicit desired chondrocyte responses for use as cartilage models and for development of functional tissue-engineered articular cartilage.

Expression pattern of Oct-4, Sox2, and c-Myc in the primary culture of human dental pulp derived cells

Dental pulp cells (DPCs) have shown promising potential in dental tissue repair and regeneration. However, during in vitro culture, these cells undergo replicative senescence and result in significant alteration in cell proliferation and differentiation. Recently, the transcription factors of Oct-4, Sox2, c-Myc, and Klf4 have been reported to play a regulatory role in the stem cell self-renewal process, namely cell reprogramming. Therefore, it is interesting to know whether the replicative senescence during the culture of dental pulp cells is related to the diminishing of the expression of these transcription factors. In this study, we investigated the expression of the reprogramming markers Oct-4, Sox2, and c-Myc in the in vitro explant cultured dental pulp tissues and explant cultured dental pulp cells (DPCs) at various passages by immunofluorescence staining and real-time polymerase chain reaction analysis. Our results demonstrated that Oct-4, Sox2, and c-Myc translocated from nucleus in the first 2 passages to cytoplasm after the third passage in explant cultured DPCs. The mRNA expression of Oct-4, Sox2, and c-Myc elevated significantly over the first 2 passages, peaked at second passage (P < .05), and then decreased along the number of passages afterwards (P < .05). For the first time we demonstrated that the expression of reprogramming markers Oct-4, Sox2, and c-Myc was detectable in the early passaged DPCs, and the sequential loss of these markers in the nucleus during DPC cultures might be related to the cell fate of dental pulp derived cells during the long-term in vitro cultivation under current culture conditions.

Building a software architecture for a human-robot team using the ORCA framework

This paper considers the problem of building a software architecture for a human-robot team. The objective of the team is to build a multi-attribute map of the world by performing information fusion. A decentralized approach to information fusion is adopted to achieve the system properties of scalability and survivability. Decentralization imposes constraints on the design of the architecture and its implementation. We show how a Component-Based Software Engineering approach can address these constraints. The architecture is implemented using Orca – a component-based software framework for robotic systems. Experimental results from a deployed system comprised of an unmanned air vehicle, a ground vehicle, and two human operators are presented. A section on the lessons learned is included which may be applicable to other distributed systems with complex algorithms. We also compare Orca to the Player software framework in the context of distributed systems.

A forensic investigation of single human hair fibres using FTIR-ATR spectroscopy and chemometrics

Human hair fibres are ubiquitous in nature and are found frequently at crime scenes often as a result of exchange between the perpetrator, victim and/or the surroundings according to Locard's Principle. Therefore, hair fibre evidence can provide important information for crime investigation. For human hair evidence, the current forensic methods of analysis rely on comparisons of either hair morphology by microscopic examination or nuclear and mitochondrial DNA analyses. Unfortunately in some instances the utilisation of microscopy and DNA analyses are difficult and often not feasible. This dissertation is arguably the first comprehensive investigation aimed to compare, classify and identify the single human scalp hair fibres with the aid of FTIR-ATR spectroscopy in a forensic context. Spectra were collected from the hair of 66 subjects of Asian, Caucasian and African (i.e. African-type). The fibres ranged from untreated to variously mildly and heavily cosmetically treated hairs. The collected spectra reflected the physical and chemical nature of a hair from the near-surface particularly, the cuticle layer. In total, 550 spectra were acquired and processed to construct a relatively large database. To assist with the interpretation of the complex spectra from various types of human hair, Derivative Spectroscopy and Chemometric methods such as Principal Component Analysis (PCA), Fuzzy Clustering (FC) and Multi-Criteria Decision Making (MCDM) program; Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and Geometrical Analysis for Interactive Aid (GAIA); were utilised. FTIR-ATR spectroscopy had two important advantages over to previous methods: (i) sample throughput and spectral collection were significantly improved (no physical flattening or microscope manipulations), and (ii) given the recent advances in FTIR-ATR instrument portability, there is real potential to transfer this work.s findings seamlessly to on-field applications. The "raw" spectra, spectral subtractions and second derivative spectra were compared to demonstrate the subtle differences in human hair. SEM images were used as corroborative evidence to demonstrate the surface topography of hair. It indicated that the condition of the cuticle surface could be of three types: untreated, mildly treated and treated hair. Extensive studies of potential spectral band regions responsible for matching and discrimination of various types of hair samples suggested the 1690-1500 cm^-1 IR spectral region was to be preferred in comparison with the commonly used 1750-800 cm^-1. The principal reason was the presence of the highly variable spectral profiles of cystine oxidation products (1200-1000 cm^-1), which contributed significantly to spectral scatter and hence, poor hair sample matching. In the preferred 1690-1500 cm^-1 region, conformational changes in the keratin protein attributed to the α-helical to β-sheet transitions in the Amide I and Amide II vibrations and played a significant role in matching and discrimination of the spectra and hence, the hair fibre samples. For gender comparison, the Amide II band is significant for differentiation. The results illustrated that the male hair spectra exhibit a more intense β-sheet vibration in the Amide II band at approximately 1511 cm^-1 whilst the female hair spectra displayed more intense α-helical vibration at 1520-1515cm^-1. In terms of chemical composition, female hair spectra exhibit greater intensity of the amino acid tryptophan (1554 cm^-1), aspartic and glutamic acid (1577 cm^-1). It was also observed that for the separation of samples based on racial differences, untreated Caucasian hair was discriminated from Asian hair as a result of having higher levels of the amino acid cystine and cysteic acid. However, when mildly or chemically treated, Asian and Caucasian hair fibres are similar, whereas African-type hair fibres are different. In terms of the investigation's novel contribution to the field of forensic science, it has allowed for the development of a novel, multifaceted, methodical protocol where previously none had existed. The protocol is a systematic method to rapidly investigate unknown or questioned single human hair FTIR-ATR spectra from different genders and racial origin, including fibres of different cosmetic treatments. Unknown or questioned spectra are first separated on the basis of chemical treatment i.e. untreated, mildly treated or chemically treated, genders, and racial origin i.e. Asian, Caucasian and African-type. The methodology has the potential to complement the current forensic analysis methods of fibre evidence (i.e. Microscopy and DNA), providing information on the morphological, genetic and structural levels.

Structural inquiry, human agency and the contribution of Harre and Bhaskar : a case study of Wright’s “Classes”

This paper examines the contribution of aspects of critical and referential realism to the “logic” of structural explanation through an analysis of Erik Olin Wright’s Classes and the debate surrounding this work. Wright’s Classes has been selected as a case study because it offers an opportunity to examine issues pertaining to “objective” and “subjective” determinations of class and related questions of agency and structure at the level of actual methodological strategies. A close examination of the structure of Wright’s inquiry reveals a number of places where Harre’s and Bhaskar’s approaches may contribute to the prescription of methodological strategies which could overcome some of the antinomies on which the debate on Classes is based. As a case study, the paper underlines the important “underlabourer” role of critical and referential realism and their contribution to questions of agency and structure in the context of actual stages involved in structural explanation

Human resource behaviour simulation in business processes

The structure and dynamics of a modern business environment are very hard to model using traditional methods. Such complexity raises challenges to effective business analysis and improvement. The importance of applying business process simulation to analyze and improve business activities has been widely recognized. However, one remaining challenge is the development of approaches to human resource behavior simulation. To address this problem, we describe a novel simulation approach where intelligent agents are used to simulate human resources by performing allocated work from a workflow management system. The behavior of the intelligent agents is driven a by state transition mechanism called a Hierarchical Task Network (HTN). We demonstrate and validate our simulator via a medical treatment process case study. Analysis of the simulation results shows that the behavior driven by the HTN is consistent with design of the workflow model. We believe these preliminary results support the development of more sophisticated agent-based human resource simulation systems.

Correlation of the expression of human kallikrein-related peptidases 4 and 7 with the prognosis in oral squamous cell carcinoma

Background Very few articles have been written about the expression of kallikreins (KLK4 and KLK7) in oral cancers. Therefore, the purpose of this study was to examine and report on their prognostic potential. Methods Eighty archival blocks of primary oral cancers were sectioned and stained for KLK4 and KLK7 by immunohistochemistry. The percentage and the intensity of malignant keratinocyte staining were correlated with patient survival using Cox regression analysis. Results Both kallikreins were expressed strongly in the majority of tumor cells in 68 of 80 cases: these were mostly moderately or poorly differentiated neoplasms. Staining was particularly intense at the infiltrating front. Patients with intense staining had significantly shorter overall survival (p < .05). Conclusion This is the first observation on the patient survival influenced by kallikrein expression in oral carcinoma. The findings are consistent with those for carcinomas at other sites, in particular the prostate and ovary. KLK4 and/or KLK7 immunohistochemistry seems to have diagnostic and prognostic potential in this disease.