Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical transfection and injection techniques applied to mammalian and embryonic cells

The delivery of biomolecules into living cells is an important methodology in cell and molecular biology. Optical methods using lasers are attractive tools for such application. However, the interaction of the laser with the cell depends on the laser type and the parameters used. Hence, in this thesis, optical transfection and injection of both mammalian and embryonic cells is demonstrated using a variety of laser sources. Furthermore, some key issues are addressed by demonstrating alternative configurations of optoinjection and transfection systems to develop a robust, user-friendly device with potential for commercialisation. Most optical methods for the delivery of molecules rely on complex and expensive laser systems that occupy a large footprint. In order for the system to be accessible to end-users, transient transfection of plasmid DNA into mammalian cells using an inexpensive continuous wave 405 nm diode laser is demonstrated. In this work, the laser parameters are varied in order to optimise the transfection efficiency. By calculating the temperature change upon irradiation of the focused violet light, the mechanism of violet diode laser transfection is elucidated. Furthermore, the system is used to deliver small interfering RNA molecules to specifically knock down a particular protein within the cell. This work is a major step towards an inexpensive and portable optical transfection system. The critical issue of accurate targeting of the cell membrane is also addressed in conventional near-infrared femtosecond optical transfection systems. A near-infrared femtosecond holographic system is built utilising a spatial light modulator in order to provide fast three dimensional beam translation. Computer control of dosage and targeting allows us to explore the potential of different targeting modalities. An enhanced optoinjection and transfection on mammalian cells is demonstrated. Furthermore, the system is applied to optically manipulate a developing Pomatoceros lamarckii embryo. The holographic system can be employed to optoinject a variety of macromolecules into the embryo, as well as orient and position the embryo by switching to the continuous wave mode of the laser. Such development of optical techniques to deliver biomolecules and orient embryos will benefit the field of developmental biology. Lastly, to achieve controlled cavitation, limiting the mechanical effects of a nanosecond laser source, an optically trapped microsphere undergoes laser induced breakdown in the presence of a cell monolayer. Laser induced breakdown of a trapped microsphere allows control over several parameters, such as the microsphere material, position of the breakdown from the monolayer and the size of the microsphere. Optimising these parameters provide limited mechanical effects, particularly suited for cell transfection. This technique is an excellent tool for plasmid-DNA trans-
Successive Convex Approximation for Transmit Power Minimization in SWIPT-Multicast Systems

We propose a novel technique for total transmit power minimization and optimal precoder design in wireless multi-group (MG) multicasting (MC) systems. The considered framework consists of three different systems capable of handling heterogeneous user types viz., information decoding (ID) specific users with conventional receiver architectures, energy harvesting (EH) only users with non-linear EH module, and users with joint ID and EH capabilities having separate units for the two operations, respectively. Each user is categorized under unique group(s), which can be of MC type specifically meant for ID users, and/or an energy group consisting of EH explicit users. The joint ID and EH users are a part of the (last) EH group as well as any one of the MC groups distinctly. In this regard, we formulate an optimization problem to minimize the total transmit power with optimal precoder designs for the three aforementioned scenarios, under constraints on minimum signal-to-interference-plus-noise ratio and harvested energy by the users with respective demands. The problem may be adapted to the well-known semi-definite program, which can be typically solved via relaxation of rank-l constraint. However, the relaxation of this constraint may in some cases lead to performance degradation, which increases with the rank of the solution obtained from the relaxed problem. Hence, we develop a novel technique motivated by the feasible-point pursuit and successive convex approximation method in order to address the rank-related issue. The benefits of the proposed method are illustrated under various operating conditions and parameter values, with comparison between the three above-mentioned scenarios.
Role of oxidative stress in seasonal and daily vertical migration of three krill species in the Gulf of California

Vertical distribution and abundance of three numerically dominant krill species (Nyctiphanes simplex, Nematoscelis difficilis, and Euphausia eximia) were surveyed in the Gulf of California to understand the role of oxidative stress in their daily vertical migration (DVM) and zoogeographic patterns. Superoxide radical production, lipid peroxidation, and antioxidant enzyme activities were analyzed from krill collected with stratified nets from the surface down to 200 m during January, July, and October 2007. The upper boundary of the oxygen minimum zone (OMZ) was significantly shallower during October than during January. N. simplex was always distributed above the hypoxic layers, mostly in coastal upwelling areas. Ne. difficilis and E. eximia were relatively abundant during January, but detected mostly during their ascending migration. N. simplex was the most sensitive species to high temperatures and low oxygen concentrations, showing evidence of oxidative stress during summer (100 times more lipid peroxidation and 30 times more antioxidant enzyme activities than in winter). Ne. difficilis had higher glutathione peroxidase activity than N. simplex, which could facilitate its larger DVM. Low abundance of Ne. difficilis at 100 m during summer suggests that high temperature was also an environmental limiting factor. Oxidative stress indicators could explain the absence of N. simplex and Ne. difficilis in the eastern tropical Pacific and the ability of E. eximia to live in the OMZ and the eastern tropical Pacific. The latter had higher superoxide radical production and smaller lipid peroxidation during October. This suggests that E. eximia antioxidant enzyme activities are enough to avoid oxidative damage when exposed to hypoxic conditions during DVM.
Spatial prediction of demersal fish distributions: enhancing our understanding of species–environment relationships

Moore, C. H. , Harvey, E. S. , and Van Niel, K. P. 2009. Spatial prediction of demersal fish distributions: enhancing our understanding of species-environment relationships. - ICES Journal of Marine Science, 66: 2068-2075.We used species distribution modelling to identify key environmental variables influencing the spatial distribution of demersal fish and to assess the potential of these species-environment relationships to predict fish distributions accurately. In the past, predictive modelling of fish distributions has been limited, because detailed habitat maps of deeper water (>10 m) have not been available. However, recent advances in mapping deeper marine environments using hydroacoustic surveys have redressed this limitation. At Cape Howe Marine National Park in southeastern Australia, previously modelled benthic habitats based on hydroacoustic and towed video data were used to investigate the spatial ecology of demersal fish. To establish the influence of environmental variables on the distributions of this important group of marine fish, classification trees (CTs) and generalized additive models (GAMs) were developed for four demersal fish species. Contrasting advantages were observed between the two approaches. CTs provided greater explained variation for three of the four species and revealed a better ability to model species distributions with complex environmental interactions. However, the predictive accuracy of the GAMs was greater for three of the four species. Both these modelling techniques provided a detailed understanding of demersal fish distributions and landscape linkages and an accurate method for predicting species distributions across unsampled locations where continuous spatial benthic data are available. Information of this nature will permit more-targeted fisheries management and more-effective planning and monitoring of marine protected areas.
Models of Capitalism: Growth and Stagnation in the Modern Era

Preface. 1. Capitalist Models and Economic Growth. Part I: Capitalist Models: The Arguments: . 2. Liberal Capitalism: Retreat and Revival? 3. 'Trust-Based' Capitalism: Revival and Retreat. Part II: Capitalist Models: The Evidence: . 4. The Power of Organized Labour. 5. Education, Training and Culture. 6. The Organization of Capital in the Pursuit of Growth. 7. The State as an Element in the Growth Equation. Part III: Conclusion: . 8. Capitalist Models and the Politics of the Left. Appendix: Theories of Growth. References. Index.
Response: the hypothalamus–pituitary–testis axis in cryptorchid boys

Dear Sir, We are grateful for the interest of Professors Hadziselimovic, Emmons and Snyder (Hadziselimovic et al., 2008) for our paper on hormone levels in normal boys and boys with cryptorchidism or hypospadias (Pierik et al., 2008). They point out a controversy between our above mentioned paper and an earlier paper of Dr De Muinck Keizer-Schrama et al. (1988) in which HPT hormones were measured in another group of cryptorchid boys and in controls. In the latter study, no significant difference between the testosterone levels in the two groups was detected, whereas in our more recent study a significant difference was found. Prof Hadziselimovic and co-authors enquire: ‘‘What changed in the last 20 years? ’’. We would like to point out that the population-based selection of boys in our recent study was different from the hospital-based design in the previous study. The boys in our recent study were aged between 35 and 184 days (mean: 80 days) at the time of blood collection. This contrasts with the group reported earlier in which samples were collected from the cryptorchid boys between 80 and 420 days-of-age. In the earlier paper, it is stated ‘‘the sign test revealed no significant differences in the three groups (controls, and boys with persistent or transient cryptorchidism) from the age of 80 to 180 days’’. We now stated that ‘‘the lower testosterone in the cryptorchid boys was mainly due to a higher proportion of testosterone levels below the detection limit among boys that were 100 or more days old, suggesting that in cryptorchidism cases the androgen nadir may be reached more rapidly’’. Because the levels of hypothalamus–pituitary–testis axis hormones change dramatically in the first 6 months of life, we adjusted for the ‘time since birth’ in the latter study, applying statistical techniques that were not available in 1988. As we adjusted for the country of origin, we do not think that the increase of the Turkish population in Rotterdam during the last 20 years plays an important role. As described in the paper, we reached identical conclusions when the statistics was applied to the subjects of Dutch origin only. Finally, we already stated that we did not have data on the severity of the cryptorchidism in all cases. In conclusion, the differences in population characteristics (e.g. the age distribution) and in the statistical techniques used are likely to explain the difference between the results of the two studies as far as the question asked is concerned. We do not see how the histology of the testes could be of help in deciding if testosterone levels in control and cryptorchid boys are different.
Duration of diapause in the stem borers, Busseola fusca and Chilo partellus

The duration of diapause in the stem borers Busseola fusca (Fuller) and Chilo partellus (Swinhoe) was studied in South Africa by collecting diapausing larvae from the field throughout winter (April–August). B. fusca larvae emerged as moth around the middle of October regardless of the date of collection and the length of time they were kept in the laboratory under constant 21 °C. C. partellus larvae collected in April‐June emerged in November, those collected in July emerged in October, and those collected in August emerged in September. Regardless of the collection date C. partellus started to emerge from diapause earlier and moth emergence lasted up to twice as long as in B. fusca. Under laboratory conditions at 60% RH both borer larvae lost about 50% of their body mass during diapause. When provided with water B. fusca larvae lost about 30% of their body mass and adults emerged 20 days earlier than when kept dry. C. partellus, on the other hand, lost only 13% of their body weight and emerged 34 days earlier. The differences between the two species are discussed in light of different types of diapause; i.e., obligatory diapause in B. fusca and facultative diapause in C. partellus.
Palaemonella dijonesae sp. nov. (Crustacea: Decapoda: Pontoniinae) from Western Australia

A recent publication by Bruce (2008a) reported the presence of Palaemonella spinulata Yokoya, 1936 in the Dampier Archipelago, Western Australia. This report noted that “The holotype specimen from Misaki, Japan, is considered to be lost (Holthuis 1952; Bruce 1970; Okuno pers. comm.). The designation of a neotype would appear useful but one from Japanese or nearby waters would be more appropriate than one of the present specimens”. The brief description provided by Yokoya (1936), with only a single figure showing the whole specimen, antennule, antenna, mandible, second maxilliped and posterior telson, is inadequate for comparison with other species of the genus. This deficiency has now been rectified by Hayashi (2009) who has provided a detailed and well illustrated description of P. spinulata and designated a neotype from Sagami Bay, near Misaki, the type locality. This re-description immediately indicated that the Western Australian specimens were not conspecific and they are now described as a new species. The specimens are held in the collections of the Western Australian Museum, Perth.
Old World Monkeys: The molecular systematics of the Cercopithecidae

Introduction George H.F. Nuttall (1904:4) wrote: “The persistence of the chemical blood-relationship between the various groups of animals serves to carry us back into geological times, and I believe we have but begun the work along these lines, and that it will lead to valuable results in the study of various problems of evolution. ” While enormous strides have been made in the field of molecular genetics, Nuttall's statement is still true. Our knowledge of the systematics of Old World monkeys, gleaned from both morphological and molecular approaches, is still poorer than many would admit. In the 1960s, Nuttall's immunological approach was enhanced and used extensively by anthropologists and biochemists studying primates (Goodman, 1961, 1963; Sarich and Wilson, 1966, 1967). Karyological research by, for example, Chiarelli (1966) and Dutrillaux (1979) has also played a major role in primate evolutionary studies. The recognition of the potential of a “molecular clock” by Zuckerkandl and Pauling (1962) led to studies of protein sequences (Goodman et al ., 1987). Research on primate DNA itself, and not merely its products, began in the late 1960s and early 1970s (Kohne et al ., 1972; Benveniste et al ., 1976), and was followed by restriction enzyme analyses of relationships among and between primate species and populations (Templeton, 1983; Melnick et al ., 1993). The mapping and sequencing of portions of primate mitochondrial and nuclear genomes has also contributed greatly to primate systematics and population genetics (reviewed in Honeycutt and Wheeler, 1989; Koop et al ., 1989; Melnick and Hoelzer, 1993).
Children's interpretation of ambiguous pronouns based on prior discourse.

In conversation, individual utterances are almost always ambiguous, with this ambiguity resolved by context and discourse history (common ground). One important cue for disambiguation is the topic under discussion with a particular partner (e.g., "want to pick? " means something different in a conversation with a bluegrass musician vs. with a book club partner). Here, we investigated 2- to 5-year-old American English-speaking children's (N = 131) reliance on conversational topics with specific partners to interpret ambiguous or novel words. In a tablet-based game, children heard a speaker consistently refer to objects from a category without mentioning the category itself. In study 1, 3- and 4-year-olds interpreted the ambiguous pronoun "it" as referring to another member of the same category. In study 2, only 4-year-olds interpreted the pronoun as referring to the implied category when talking to the same speaker but not when talking to a new speaker. Thus, children's conception of what constitutes common ground in discourse develops substantially between age 2 and 5.
Model Checking Trust-based Multi-Agent Systems

Trust has been the focus of many research projects, both theoretical and practical, in the recent years, particularly in domains where open multi-agent technologies are applied (e.g., Internet-based markets, Information retrieval, etc.). The importance of trust in such domains arises mainly because it provides a social control that regulates the relationships and interactions among agents. Despite the growing number of various multi-agent applications, they still encounter many challenges in their formal modeling and the verification of agents’ behaviors. Many formalisms and approaches that facilitate the specifications of trust in Multi-Agent Systems (MASs) can be found in the literature. However, most of these approaches focus on the cognitive side of trust where the trusting entity is normally capable of exhibiting properties about beliefs, desires, and intentions. Hence, the trust is considered as a belief of an agent (the truster) involving ability and willingness of the trustee to perform some actions for the truster. Nevertheless, in open MASs, entities can join and leave the interactions at any time. This means MASs will actually provide no guarantee about the behavior of their agents, which makes the capability of reasoning about trust and checking the existence of untrusted computations highly desired. This thesis aims to address the problem of modeling and verifying at design time trust in MASs by (1) considering a cognitive-independent view of trust where trust ingredients are seen from a non-epistemic angle, (2) introducing a logical language named Trust Computation Tree Logic (TCTL), which extends CTL with preconditional, conditional, and graded trust operators along with a set of reasoning postulates in order to explore its capabilities, (3) proposing a new accessibility relation which is needed to define the semantics of the trust modal operators. This accessibility relation is defined so that it captures the intuition of trust while being easily computable, (4) investigating the most intuitive and efficient algorithm for computing the trust set by developing, implementing, and experimenting different model checking techniques in order to compare between them in terms of memory consumption, efficiency, and scalability with regard to the number of considered agents, (5) evaluating the performance of the model checking techniques by analyzing the time and space complexity. The approach has been applied to different application domains to evaluate its computational performance and scalability. The obtained results reveal the effectiveness of the proposed approach, making it a promising methodology in practice.
Banks Grass Mite (Acari: Tetranychidae) Suppression May Add to the Benefit of Drought-Tolerant Corn Hybrids Exposed to Water Stress

Abstract Spider mite (Acari: Tetranychidae) outbreaks are common on corn grown in the arid West. Hot and dry conditions reduce mite development time, increase fecundity, and accelerate egg hatch. Climate change is predicted to increase drought incidents and produce more intense temperature patterns. Together, these environmental shifts may cause more frequent and severe spider mite infestations. Spider mite management is difficult as many commercially available acaricides are ineffective due to the development of resistance traits in field mite populations. Therefore, alternative approaches to suppress outbreaks are critically needed. Drought-tolerant plant hybrids alleviate the challenges of growing crops in water-limited environments; yet, it is unclear if drought-tolerant hybrids exposed to water stress affect mite outbreaks under these conditions. We conducted a greenhouse experiment to evaluate the effect of drought-tolerant corn hybrids on Banks grass mite [Oligonychus pratensis Banks (Acari:Tetranychidae)], a primary pest of corn, under optimal irrigation and water-stress irrigation. This was followed by a 2-yr field study investigating the effect of drought-tolerant corn hybrids exposed to the same irrigation treatments on Banks grass mite artificially infested on hybrids and resident spider mite populations. Results showed that water-stressed drought-tolerant hybrids had significantly lower Banks grass mite and resident spider mite populations than water-stressed drought-susceptible hybrids. Interestingly, water-stressed drought-tolerant hybrids had equal Banks grass mite populations to drought-susceptible and drought-tolerant hybrids under optimal irrigation. We posit that planting drought-tolerant hybrids may suppress spider mite outbreaks in water-challenged areas.
Probability Paths and the Structure of Predictions over Time

In settings ranging from weather forecasts to political prognostications to financial projections, probability estimates of future binary outcomes often evolve over time. For example, the estimated likelihood of rain on a specific day changes by the hour as new information becomes available. Given a collection of such probability paths, we introduce a Bayesian framework -- which we call the Gaussian latent information martingale, or GLIM -- for modeling the structure of dynamic predictions over time. Suppose, for example, that the likelihood of rain in a week is 50 %, and consider two hypothetical scenarios. In the first, one expects the forecast to be equally likely to become either 25 % or 75 % tomorrow; in the second, one expects the forecast to stay constant for the next several days. A time-sensitive decision-maker might select a course of action immediately in the latter scenario, but may postpone their decision in the former, knowing that new information is imminent. We model these trajectories by assuming predictions update according to a latent process of information flow, which is inferred from historical data. In contrast to general methods for time series analysis, this approach preserves important properties of probability paths such as the martingale structure and appropriate amount of volatility and better quantifies future uncertainties around probability paths. We show that GLIM outperforms three popular baseline methods, producing better estimated posterior probability path distributions measured by three different metrics. By elucidating the dynamic structure of predictions over time, we hope to help individuals make more informed choices.