Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinal proteomics of experimental glaucoma model reveal intraocular pressure‐induced mediators of neurodegenerative changes

Current evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3 ± 0.1 vs 20.8 ± 1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using a multiplexed quantitative proteomics approach (TMT‐MS3). Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated (≤0.83) while the expression of 109 proteins was upregulated (≥1.2‐fold change) under glaucoma conditions (P ≤ .05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton, and actin filament organisation, along with increased expression of proteins in coagulation cascade, apoptosis, oxidative stress, and RNA processing. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport, and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism, and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins were exclusive to human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.
Both CD45Rlow and CD45Rhigh "revertant" CD4 memory T cells provide help for memory B cells

During a primary response to thymus dependent antigens, B cells undergo a number of qualitative changes to become memory B cells — processes that require co‐stimulatory signals and cytokine help from CD4 T cells. The question of whether distinct, antigen‐experienced memory CD4 T cells are subsequently needed to program memory B cells into antibody synthesis has not been clearly resolved.Using an adoptive transfer model in which memory but not naive B cells were stimulated, we evaluated CD4 T cell help using lymphocytes obtained from primed or unprimed thymectomized donors and expressing a naive (CD45Rhigh) or a memory (CD45Rlow) phenotype. Memory B cells, most of which were committed to the IgG1 (Th2) subclass, could be stimulated to produce antibody using help transferred by the CD45Rhigh naive subset of unprimed donors (slow onset of response), the CD45Rlow subset of 7 day primed donors (large, rapid antibody response) or by both the CD45Rlow and the CD45Rhigh "revertant" subsets of 6 month primed donors. We found that antigen primed CD45Rlow CD4 T cells reverted (defaulted) with time to a CD45Rhigh resting state, a change that was prevented by persisting antigen. The evidence suggests that CD4 memory T cells are partitioned into two different functional states (CD45Rhigh and CD45Rlow) and that these determine the characteristics of the memory B cell response in terms of speed, size and longevity.
Combatting the evolution of antifungal resistance in Cryptococcus neoformans

Fungal infections are a global concern and the evolution of intrinsic resistance to current antifungals presents an alarming problem. For Cryptococcus neoformans, a human fungal pathogen of primarily immunocompromised individuals, resistance toward treatment strategies demands alternative approaches. Given the prevalence of virulence factor production during cryptococcal infection, an emerging and important field of research encompasses the development of novel antivirulence therapies proposed to improve host immune responses and promote fungal clearance. To accomplish this task, information regarding the presence and role of virulence factors, the mechanisms of action within the host, and the ability to influence fungal susceptibility to antifungals is pertinent. Research into mechanisms of antifungal resistance for C. neoformans is limited but extrapolation from successful studies in other fungal species can improve our understanding of mechanisms employed by C. neoformans and suggest targeted strategies to enhance our ability to combat the pathogen. In this Review, we highlight antifungal therapy options against Cryptococcus, explore current knowledge of underlying mechanisms promoting resistance, and present new opportunities for novel and effective strategies to overcome fungal infections and reduce, or possibly even reverse, the effects of resistance evolution.
Nicotine increases alcohol self‐administration in male rats via a μ‐opioid mechanism within the mesolimbic pathway

Alcohol and nicotine use disorders are commonly comorbid. Both alcohol and nicotine can activate opioid systems in reward‐related brain regions, leading to adaptive changes in opioid signalling upon chronic exposure. The potential role of these adaptations for comorbidity is presently unknown. Here, we examined the contribution of μ and κ‐opioid receptors to nicotine‐induced escalation of alcohol self‐administration in rats.
The Effect of Extra Food on Fitness in Breeding Carrion Crows

Food limitation during the nestling stage was experimentally investigated in an urban population of Carrion Crows. Parents were offered supplemental food during the nestling period and the following variables compared with those from non food-supple- mented pairs: (1) nesting success, (2) fledgling number, (3) fledgling mass and linear body size, (4) proportion of fledglings resighted (a) after transition to independence from the parents, and (b) after the first winter postfledging, and (5) the probability that a fledgling became a breeder. Food-supplemented pairs had a higher nesting success and produced more fledglings. The fledglings of food-supplemented pairs were heavier and bigger in tarsus length than controls, but experimental and control fledglings were seen in equal proportions both after transition to independence and after the first winter. The production of potential breeders was increased ninefold in food-supplemented pairs. The study demonstrates that in this urban habitat food limitation causes low fitness not through lowered survival, but through the production of a low number of potential breeders.
Herbivory and fire interact to affect forest understory habitat, but not its use by small vertebrates

Herbivory and fire are two disturbances that often co‐occur, but studies of their interactive effects are rare outside of grassland ecosystems. We experimentally tested the interactive effects of prescribed fire and macropod herbivory on forest understory vegetation and its vertebrate fauna. Fire and herbivory interacted synergistically to affect forest understory vegetation, with palatable plants showing poor post‐fire recovery in unfenced sites compared with herbivore exclusion sites. Despite this strong interactive effect on vegetation, small vertebrates responded to the individual, and not the interactive effects of disturbance. The native insectivorous mammal Antechinus stuartii was more frequently encountered on large herbivore exclusion sites, as was the introduced European rabbit. In contrast, the small skink Lampropholis delicata was more common on sites with high densities of large herbivores. Skinks, snakes and European rabbits were also more active on burnt than unburnt sites. Our results suggest that it may be necessary to manage the macropod herbivore population after fire to prevent the decline of palatable plants, and maintain the dense habitat required by some small mammals. However, as the invasive rabbit was most active in macropod‐free sites after fire, any management must include control of both types of herbivores. A mix of understory densities may also need to be maintained to ensure the persistence of species preferring more open habitats. Our study demonstrates that interactive effects of disturbance on vegetation communities may not lead to predictable effects on animals, and highlights the importance of considering both multiple stressors, and multiple species, in the management of disturbance regimes.
Electrophoretic Detection of Proteases from Selected Strains of Flexibacter psychrophilus and Assessment of Their Variability

Abstract The cell-free extracellular products of a reference isolate of Flexibacter psychrophilus were analyzed by substrate gel electrophoresis (SDS-PAGE), and proteases with apparent molecular masses (AMM) of 114 and 152 kiloDaltons (kDa), which had activity against both casein and gelatin, were identified. Proteases with AMMs from 32 to 86 kDa, which were active against gelatin but not casein, were also observed. Analysis of 28 additional isolates of F. psychrophilus indicated that the isolates formed four groups based on the presence or absence of certain proteases visualized by substrate SDS-PAGE. Seven F. psychrophilus isolates from coho salmon Oncorhynchus kisutch and ayu Plecoglossus altivelis reared in Japan were included in the study. These isolates had protease patterns similar to isolates from the USA and could also be grouped. There was a correlation between protease group and the host from which the bacterium was isolated. Of the 29 isolates studied, all 11 group-1 isolates were from coho sa.
"Fungal Disease Control in Banana, a Tropical Monocot : Transgenic Plants in the Third World?"

In a recent lecture, the plant breeder Norman Borlaug (1970 Nobel Peace Prize Laureate) underlined that plant biotechnology is likely to be instrumental in dealing with the complexities of "feeding a world of 10 billion people" (1) that the current populat ion o f 5.8 billion would certainly reach during the next century before stabilizing. Agricultural biotechnology is expected to play a particular role i n the less developed countries (LDCs) where s t i l l 800 million underfed people are concentrated but where special constraints and challenges are faced with. For example, the population in the Third World relies to a large extent on staple crops as cassava, sweet potato and tropical fruits that are hardly known in the developed countries. As a result, highquality scientific research is scarce with these crops. In addition, the tropical climate that prevails in most LDCs causes a number of significant consequences, e.g. due to the absence of dormancy, (i) many tropical crops propagate (exclusively) vegetatively which makes classical breeding extremely difficult, and (ii) pathogens and pests can permanently damage their hosts.
Characterizing Consciousness: From Cognition to the Clinic?-ReadingSample

Consciousness encompasses a variety of functions and properties, such as awakening, awareness, and subjective aspects of both perception and volition (e.g., qualia and authorship, respectively). It remains to be seen whether these diverse functions are related to one another through common neural mechanisms, and if so how. Here, we advance the thesis that the neural mechanisms that give rise to conscious states share features with neural mechanisms that underlie simpler forms of decisions. The neurobiology of decision-making provides detailed insight into how the brain deliberates and reasons from evidence to make choices. The underlying mechanisms, mainly studied in animals, could support a variety of complex cognitive functions that probably operate independently of many aspects of consciousness. For example, many complex decisions in humans rely upon wakefulness but not upon awareness or authorship. In animal studies, decisions are typically embodied: they can be described as selection among possible actions. By substituting “circuits” for “actions” in the preceding phrase, we generalize from “deciding to do” to “deciding to consider” or, more generally, “deciding to decide to. ” This is an appealing notion from the perspective of brain evolution, because it allows us to recognize ideation as an elaboration of a simpler sensory-motor design. We propose that many of the functions of consciousness are simply ways of engaging the environment. Thus consciousness might be mediated by (nonconscious) decisions to engage, as in awakening, or to engage in a certain way, as when attaching narrative to action. Although the neural mechanisms underlying “decisions to engage” are unknown, they are likely to involve intralaminar (and matrix) thalamus and processes that “decide” to turn other circuits on. This idea invites an analogy between the functions of brain regions that project to M.N. Shadlen (*) HHMI and Department of Physiology and Biophysics, University of Washington, Seattle, WA 98115, USA e-mail: shadlen@u.washington. edu S. Dehaene and Y. Christen (eds.), Characterizing Consciousness: From Cognition to the Clinic? Research and Perspectives in Neurosciences, DOI 10.1007/978-3-642-18015-6_2, # Springer-Verlag Berlin Heidelberg 2011 27 matrix thalamus, including the “default system”, and the role of parietal cortex in perceptual decisions. While highly speculative, we think “decision to engage” provides a biologically plausible and computationally coherent hypothesis about the neural correlates of consciousness.
Hyperactivated motility patterns of ram spermatozoa recovered from the oviducts of mated ewes

The contents of the oviducts of ewes were recovered by flushing with small volumes of culture medium, 22½–24¼ hr after mating. The ampulla was flushed separately from the uterotubal junction and isthmus. Among the motile spermatozoa recovered, a proportion exhibited “hyperactivated” motility, also known as “activated”, or “whiplash” motility. This was characterized by increased flexion of the neck, increased amplitude of the flagellar waves, and marked asymmetry of beat. Two types of hyperactivation appeared: in the first, spermatozoa swam in a repetitive, nonprogressive circling pattern and appeared to have intact acrosome caps; in the second, the spermatozoa showed a propensity to stick to glass by the equatorial segment and most had modified or missing acrosome caps. The proportions of motile spermatozoa exhibiting hyperactivation were greatest in the ampullae, as were the proportions with modified or absent acrosomes. Hyperactivation is a capacitation‐associated phenomenon that has now been reported for one or more species from seven orders of eutherian mammals. It may well be a universal aspect of the prefertilization behavior of mammalian spermatozoa and is probably of advantage to the fertilizing spermatozoon within the oviduct.
The Effect of the Prebiotic Inulin and the Probiotic Bifidobacterium longum on the Fecal Microflora of Healthy Volunteers Measured by FISH and DGGE

The effect of pre- and probiotics on the human intestinal microflora was investigated by fluorescent in situ hybridization (FISH) with specific 16S rRNA-targeted oligonucleotide probes, and by denaturing gradient gel electrophoresis (DGGE) of specifically PCR-amplified 16S rRNA genes. The prebiotic inulin was orally administered in the form of Raftiline® HP (Orafti, Belgium). Daily doses of 9 g were taken for 14 days by 10 healthy adult volunteers. The probiotic Bifidobacterium longum, encapsulated in gelatin/pectin capsules, was orally administered in the form of Bifina® (Morishita Jintan, Japan). Nine capsules were taken each day for 14 days by 14 healthy adult volunteers. For the prebiotic study, FISH probes were used to enumerate all bacteria, bifidobacteria, the Eubacterium rectale - Clostridium coccoides group (Erec group), Bacteroides, and eubacteria of the low G+C group. No significant changes were found in the total population of bacteria, the Bacteroides nor in the low G+C group during the study. The population of bifidobacteria increased significantly, while there was a significant decrease in numbers of the Erec group. The FISH analysis of the probiotic study focused on the enumeration of bifidobacteria only, which did not increase significantly during the study. Samples collected in both studies were analyzed by Bifidobacterium -specific PCR and DGGE. The results showed that a stable bifidobacterial population was present throughout each study. Using both FISH and DGGE, we have shown that for modulation of the bifidobacterial populations in the gut, prebiotics are better candidates than probiotics, since inulin increased bifidobacterial numbers without changing the species composition, whilst the probiotic had almost no effect.
Trust and Privacy Considerations in Participant Selection for Social Participatory Sensing

The main idea behind social participatory sensing is to leverage social friends to participate in mobile sensing tasks. A main challenge, however, is the identiﬁcation and recruitment of sufﬁcient number of well-suited participants. This becomes especially more challenging for large-scale online social networks where the network topology and friendship relations are not known to the applications. Moreover, the potential sparseness of the friendship network may result in insufﬁcient participation, thus reducing the validity of the obtained information. In this paper, we propose a participant selection framework which aims to address the aforementioned limitations. The framework has two main modules. The nomination module makes use of a customized random surfer to crawl the social graph and identify suitable nominees among the re-quester’s friends and friends-of-friends. The nominee selection is determined as a function of the suitability score of members and pairwise trust perception among members. The selection module is responsible for selecting the required participants from the set of nominees. The selection is done based on the nominee’s timeliness, the number of participants selected so far and the task’s remaining time. Moreover, to prevent any possible collusion, a further check is performed to determine whether the selection of a new participant may result in the formation of a colluding group among the selected participants. Simulation results demonstrate the efﬁcacy of our proposed participant selection framework in terms of selecting a large number of reputable participants with high suitability scores, in comparison with state-of-the-art methods.
Project scope management through multiple perspectives: A critical review of concepts

Project scope management is a main function in project management process. Moreover, it is a critical function because any changes or modifications in scope will cause extra cost on the total project development expenses. In addition, scope management ensures the successful management of other key project management areas, including time, cost, and quality. There are six main steps in scope management process namely; plan the scope, collect the requirements, define the scope, create work breakdown structure (WBS), validate scope and control the scope. These processes been highlighted in different scale in project methods and standards.
All the fundamental massless fields in bosonic string theory

A systematic analysis of the massless fields in the mass spectra of bosonic strings is carried in arbitrary spacetime dimension D > 2. The emphasis is put on the derivations of their propagators, their polarization aspects and the underlying constraints involved. The treatment is given, in the presence of external sources, in the celebrated Coulomb gauge for the second rank tensors and vector fields, which ensures positivity – a result which is also established in the process. No constraints are imposed on the external sources so that their components may be varied independently generating complete expressions for the propagators. This latter condition is an important one in the generation of dynamical theories with constraints involving such modifications as Faddeev‐Popov factors.
Depolarization‐controlled parameters of the ciliary cycle and axonemal function

Depolarization-induced cycles of a frontal cirrus of Stylonychia were investigated by applying methods of axial-view analysis of the cilia, high-speed microcinematography, and step voltage-clamp. Rising depolarization (from 3 mV to 7ge; 30mV) increased the rate of beating from zero to maximally 58 Hz. During cyclic activity, the axis of the beat cone of a proximal segment of the cirrus was inclined by 60° (0° = perpendicular to cell surface), and was always oriented 90° counterclockwise to the power stroke. With the stimulus amplitude rising, the orientations of the power stroke and inclination were increasingly shifted in more counterclockwise directions by up to 80° After correction for inclination ( = normalization), and following planification of the track of the segment, we determined the following properties of the cycle during depolarization: The course of the cycle tended to be rounded, i.e., the ratio of major over minor amplitudes (= spatial polarity) approximated a value of 1.6 which is only two thirds of maximal spatial polarity observed during hyperpolarization. The angular velocity generally increased with rising steps of depolarization; up to +5 mV (and comparable to hyperpolarization-induced responses), the velocity maximum occurred during the return stroke. With depolarizations ≥7 mV the angular velocity maximum shifted to the power stroke so that the temporal polarity (rates of power stroke over rates of return stroke) increased from 0.4 to 1.6. Calculations of the angular velocity as referred to the proximal ciliary segment level suggest active sliding rates (between 5 and 30 nm/ms) of identified pairs of doublet microtubules. Ciliary frequency is a function of the rate of reorientation of the cyclic track; this parameter, which corresponds to the rate of translocation of active sliding between pairs of doublets, grew with the amplitude of depolarization. Translocation rates were high during transitions between the beat phases (power stroke, return stroke), and were reduced during these phases. Orientational polarograms of the mean rates of both active sliding and sliding translocation show properties of discreteness as well as continuity. The depolarization-induced changes in inclination, and the inferred patterns of sliding rate and sliding translocation rate, are compared with previous results from hyperpolarization-dependent activation of the same motor organelle.
Advances in Selective Chemical Syntheses of Complex Oligosaccharides

A wide variety of complex oligosaccharides has now been made accessible as a result of methodological improvements in the sphere of chemical synthesis, which can be used for the study of conformations and interactions with protein-receptor molecules. Such work is of particular importance because the oligosaccharide chains of glycoproteins and glycolipids anchored to the plasma membrane are important in cell-cell interactions and are receptors for enzymes, hormones, proteins, and viruses; furthermore, they determine the antigen properties of cells. The methods of synthesis available for the production of selective linkages in oligosaccharides are dealt with, particular attention being paid to conversion of saccharides into oligosaccharides, which are important from the biological point of view.