Miracle-dz/UniFAR-FTUs huggingface dataset:
Disulfide Mapping of the Cyclotide Kalata B1

The cyclotides are a recently discovered family of plant proteins that have the fascinating structural feature of a continuous cyclic backbone and, putatively, a knotted arrangement of their three conserved disulfide bonds. We here show definite chemical proof of the I-IV, II-V, III-VI knotted disulfide connectivity of the prototypic cyclotide kalata B1. This has been achieved by a new approach for disulfide analysis, involving partial reduction and stepwise alkylation including introduction of charges and enzymatic cleavage sites by aminoethylation of cysteines. The approach overcomes the intrinsic difficulties for disulfide mapping of cyclotides, i.e. the cyclic amide backbone, lack of cleavage sites between cysteines, and a low or clustered content of basic amino acids, and allowed a direct determination of the disulfide bonds in kalata B1 using analysis by mass spectrometry. The established disulfide connectivity is unequivocally shown to be cystine knotted by a topological analysis. This is the first direct chemical determination of disulfides in native cyclotides and unambiguously confirms the unique cyclic cystine knot motif.
A novel agent-based modelling framework for travel time reliability analysis

ABSTRACT Under transportation network supply and demand uncertainty, travel time reliability emerges from non-linear interactions among numerous travellers who are driven by self-interest, learn and adapt in changing situations, and therefore can be modelled as an emergent network property. This paper proposes a novel theoretical framework for the study of complexity regarding travel time reliability on the basis of empirically derived individual decision rules, and develops an agent-based evolutionary model for travel time reliability analysis. Findings show that actual route choice behaviours related to network reliability are often non-optimal, and that these behaviours themselves are important determinants of travel time reliability under network supply and demand uncertainty. While many travellers search for alternative routes under uncertainty, few travellers actually change routes. Route choice rules employed by travellers can successfully improve travel time reliability in most tested uncertainty scenarios, but they do not necessarily reduce absolute travel time. While reducing demand uncertainty improves travel time and planning under uncertainty, the model provides a theoretically sound tool for analysing the impact of traveller information systems on individual travel behaviour and network performance. It can also serve as an empirically estimated router for microscopic traffic simulators or act as a behavioural assignment algorithm for activity-based travel demand models.
Environment Kuznets Curve for CO2 Emissions:A Coin- tegration Analysis for China *

This study examines the long-run relationship between CO2 emissions and per capita energy consumption, income and foreign trade in the case of China by employing time series data of 1978-2008 and autoregressive distributed lag(ARDL) methodology. The conclusions indicate that there is a very strong long-term relationship between CO2 emissions and economic development of China, and the char- acteristics of China's CO2 emissions is in accordance with EKC. To reduce CO2 emissions, We can take the following measures: Increasing government investment, Strengthening the R & D of energy technology, solving the problem of energy price, encouraging and supporting new energy, reducing energy consump- tion of products and improving export structure.
An Analysis of the Food Metaphor in EkeGusii HIV and AIDS Discourse

HIV represents one of the greatest public health challenges confronting Kenyans. Whereas Kenya has made significant progress in the fight against HIV and AIDS, the prevalence rates in Gusii are very high and this calls for investigation. The HIV and AIDS prevalence rates in Kisii and Nyamira Counties stand approximately at 26% which is higher than the provincial and national rates. HIV is a social issue, therefore issues dealing with language use and communication cannot be ignored. There are a number of linguistic expressions related to food that are employed when one is speaking about HIV and AIDS its related terminologies. The article investigates the food metaphors that EkeGusii speakers use in relation to HIV and AIDS. We argue that metaphors are used in EkeGusii discourse on HIV and AIDS because metaphors are ubiquitous in nature and AbaGusii culture places restrictions on words and expressions which directly refer to HIV and AIDS and sex related issues. Some of such direct words and expressions are considered taboo while others instill fear or create stigma. Hence, EkeGusii speakers find metaphors handy to use in such situations. Most concepts are understood in terms of other concepts and it could therefore be invaluable to analyze food metaphors in relation to HIV and AIDS and sex related issues. This study reveals how the food metaphor reflects and structures our understanding of reality in relation to sexuality and HIV and AIDS in EkeGusii.
Method to remove the interference in reflected wave of passive radar based on the improved FastICA

In allusion to the complexion that the serious harm to passive radar which is based on FM (the resource of frequency modulation) by the multiplex interference in identical frequency, and the average method such as filter couldn't remove it, a novel method to eliminate the interference based on the improved FastICA (fixed point Independent Component Analysis) is presented. This method pick-up the pure signal by blind source separation which is depended on the improved FastICA and eliminate the multiplex interference in identical frequency. The result of blind source separation for the data show that the improved FastICA is a effective method in eliminating the interference. Therefore, this method can improve the precision of orientation for passive radar which is based on the FM.
A New Sensitive, Whole-Cell Hybridization Technique for Detection of Bacteria Involving a Biotinylated Oligonucleotide Probe Targeting rRNA and Tyramide Signal Amplification

A tyramide signal amplification system with biotinylated oligonucleotide probes and streptavidin-horseradish peroxidase was used to increase the sensitivity of fluorescent in situ hybridization techniques. When applied to both gram-negative and -positive bacteria immobilized on glass slides, a 7- to 12-fold amplification of the fluorescence signal was observed relative to that of cells hybridized with fluorescently monolabeled probes. A large proportion (62 to 78%) of bacteria could be detected under starvation conditions and in natural samples from the marine environment. This amplification procedure allows new investigations in marine oligotrophic ecosystems and water quality control.
TweetMT: A Parallel Microblog Corpus

We introduce TweetMT, a parallel corpus of tweets in four language pairs that combine five languages (Spanish from/to Basque, Catalan, Galician and Portuguese), all of which have an official status in the Iberian Peninsula. The corpus has been created by combining automatic collection and crowdsourcing approaches, and it is publicly available. It is intended for the development and testing of microtext machine translation systems. In this paper we describe the methodology followed to build the corpus, and present the results of the shared task in which it was tested.
Caenorhabditis elegans UNC-96 is a new component of M-lines that interacts with UNC-98 and paramyosin and is required in adult muscle for assembly and/or maintenance of thick filaments.

To gain further insight into the molecular architecture, assembly, and maintenance of the sarcomere, we have carried out a molecular analysis of the UNC-96 protein in the muscle of Caenorhabditis elegans. By polarized light microscopy of body wall muscle, unc-96 mutants display reduced myofibrillar organization and characteristic birefringent "needles. " By immunofluorescent staining of known myofibril components, unc-96 mutants show major defects in the organization of M-lines and in the localization of a major thick filament component, paramyosin. In unc-96 mutants, the birefringent needles, which contain both UNC-98 and paramyosin, can be suppressed by starvation or by exposure to reduced temperature. UNC-96 is a novel approximately 47-kDa polypeptide that has no recognizable domains. Antibodies generated to UNC-96 localize the protein to the M-line, a region of the sarcomere in which thick filaments are cross-linked. By genetic and biochemical criteria, UNC-96 interacts with UNC-98, a previously described component of M-lines, and paramyosin. Additionally, UNC-96 copurifies with native thick filaments. A model is presented in which UNC-96 is required in adult muscle to promote thick filament assembly and/or maintenance.
A cross-sectional population-based study of elder self-neglect and psychological, health, and social factors in a biracial community

Objective: Elder self-neglect is an important public health issue; however, its association with psychological, health, and social factors remains unclear. This study aimed to (1) examine the associations between self-neglect severity and psychological, health, and social factors (2) examine the racial/ethnic differences in these associations. Methods: We conducted a biracial population-based study in a geographically defined community in Chicago: Chicago Health Aging Project. We identified 1094 persons who had been identified by social services agency as suspected elder self-neglect from 1993 to 2005. Self-neglect severity was assessed on a 0–45 scale. The psychological, health, and social factors were assessed using Center for Epidemiological Studies of Depression (CESD), poor mental health, health status, unhealthy days, poor physical health, days away from usual activities, social network, and social engagement. Linear regression was used to assess associations between self-neglect and psychological, health, and social factors. Interaction terms (Self-neglect × Race) were used to assess the black (non-Hispanic black) and white (non-Hispanic white) differences in these associations. Results: There were significant associations between self-neglect severity with health and social factors. After adjusting for confounders, greater self-neglect severity was associated with lower health status (PE = 0.001, p = 0.002), higher unhealthy days (PE = 0.139, p < 0.001), poor physical health (PE = 0.141, p < 0.001), and more days away from usual activities (PE = 0.120, p = 0.030). Interaction term (Self-Neglect × Race) indicates black compared with white older adults, had more days away from usual activities (PE = 0.321, p = 0.045) and lower social engagement (PE = −0.04, p = 0.003). Conclusion: Greater self-neglect severity is associated with lower levels of health and social wellbeing. These associations may be stronger for black than white older adults.
Short pulse High Power Microwave surface flashover

High Power Microwave (HPM) induced surface flashover is investigated in order to gain a better understanding of this phenomenon and reduce the limitations it imposes on transmitted power levels. This work builds on previous testing using a magnetron producing 5 MW for 4 µs at 2.85 GHz. Both the previous and current experimental setups are designed to produce a flashover on the high pressure side of a transmission window without the influence of a triple point. Limitations of the previous experiment included a maximum power of 5 MW and a pulse rise time of 50 ns. The current HPM source is an experimental virtual cathode oscillator (vircator), the output of which has been extensively characterized. The vircator is capable of producing 50 MW peak for 100 ns with an adjustable frequency from 3 to 5 GHz and a rise time of ≪ 4 ns. The dominant modes of the vircator and magnetron are the circular TE11 and rectangular TE10 modes respectively, with the major electric field component in both setups normal to the direction of propagation, yielding comparable field geometries at the transmission window. The experimental setup permits the study of factors including gas pressure, composition, temperature, and air speed. Diagnostic equipment allows the analysis of power levels and flashover luminosity with sub-nanosecond resolution.
Of the Origin of Government

Man, born in a family, is compelled to maintain society, from necessity, from natural inclination, and from habit. The same creature, in his farther progress, is engaged to establish political society, in order to administer justice; without which there can be no peace among them, nor safety, nor mutual intercourse. We are, therefore, to look upon all the vast apparatus of our government, as having ultimately no other object or purpose but the distribution of justice, or, in other words, the support of the twelve judges. Kings and parliaments, fleets and armies, officers of the court and revenue, ambassadors, ministers, and privy-counsellors, are all subordinate in their end to this part of administration. Even the clergy, as their duty leads them to inculcate morality, may justly be thought, so far as regards this world, to have no other useful object of their institution.
Arthrogryposis Wrist Deformities: Results of Infantile Serial Casting

Arthrogryposis multiplex congenita involving the upper extremity can be associated with significant contractures of major joints. Treatment options to maximize upper extremity motion and function include passive joint stretching, serial casting, or surgical intervention. This study reviewed all patients at Carrie Tingley Hospital with arthrogrypotic wrist flexion contractures treated with passive stretching, serial casting, and custom wrist orthotics to determine the effect on wrist position and function. Seventeen infant patients with distal and classic arthrogryposis used this regimen. Average follow-up was 6 years. The greatest gain in wrist motion occurred after the first casting session for both groups. Patients with distal arthrogryposis had the largest improvement in passive wrist motion, were more functionally independent at final follow-up, and had no recurrence of deformity. Patients with classic arthrogryposis had rigid wrist flexion contractures and a 75% incidence of deformity recurrence after casting. At final follow-up, these patients remained functionally dependent, requiring >50% assistance with activities of daily living, and had less improvement in wrist motion. The authors recommend early casting of infant wrist deformities for both forms of arthrogryposis. If the wrist deformity recurs, repeat serial casting is unlikely to improve wrist extension. Other treatment options may be considered in the older child.
Plasma levels of retinoids, carotenoids and tocopherols in patients with mild obstructive sleep apnoea

Background and objective: OSA is associated with increased incidence of cardiovascular diseases. Pathogenic mechanisms of vascular diseases include thickened vascular walls due to the increased number of smooth muscle cells (SMC). Retinoic acid (RA) suppresses the growth of SMC, and reduced retinoid levels are associated with vascular diseases. Oxidant signalling promotes SMC growth, thus antioxidant levels may also influence the development of cardiovascular diseases. The present study tested the hypothesis that plasmas from OSA patients contain altered levels of retinoids, carotenoids and tocopherols.
Lemongrass-Incorporated Tissue Conditioner Against Candida albicans Culture.

BACKGROUND Tissue conditioner is applied popularly with dental prosthesis during wound healing process but it becomes a reservoir of oral microbiota, especially Candida species after long-term usage. Several antifungal drugs have been mixed with this material to control fungal level. In this study, lemongrass essential oil was added into COE-COMFORT tissue conditioner before being determined for anti-Candida efficacy. MATERIALS AND METHODS Lemongrass (Cymbopogon citratus) essential oil was primarily determined for antifungal activity against C. albicans American type culture collection (ATCC) 10231 and MIC (minimum inhibitory concentration) value by agar disk diffusion and broth microdilution methods, respectively. COE-COMFORT tissue conditioner was prepared as recommended by the manufacturer after a fixed volume of the oil at its MIC or higher concentrations were mixed thoroughly in its liquid part. Antifungal efficacy of the tissue conditioner with/without herb was finally analyzed. RESULTS Lemongrass essential oil displayed potent antifungal activity against C. albicans ATCC 10231and its MIC value was 0.06% (v/v). Dissimilarly, the tissue conditioner containing the oil at MIC level did not cease the growth of the tested fungus. Both reference and clinical isolates of C. albicans were completely inhibited after exposed to the tissue conditioner containing at least 0.25% (v/v) of the oil (approximately 4-time MIC). The tissue conditioner without herb or with nystatin was employed as negative or positive control, respectively. CONCLUSION COE-COMFORT tissue conditioner supplemented with lemongrass essential oil obviously demonstrated another desirable property as in vitro anti-Candida efficacy to minimize the risk of getting Candidal infection.
Martin Loginov Beyond decoding : representational similarity analysis on fMRI data

Representational similarity analysis is a novel data analysis technique in neuroscience first proposed by Kriegeskorte et al. in [KMB08]. It aims to connect different branches of neuroscience by providing a framework for comparing activity patterns in the brain that represent some cognitive processes. These activity patterns can come from various sources, like different subjects, species or modalities like electroencephalography (EEG) or functional magnetic resonance imaging (fMRI). The central concept of RSA lies in measuring the similarity between these activity patterns. One of the open questions regarding RSA is what distance measures are best suited for measuring the similarity between activation patterns in neuronal or fMRI data. In this thesis RSA is implemented on a well known fMRI dataset in neuroscience, that was produced by a studying the categorical representations of objects in the ventral temporal cortex of human subjects [HGF01]. We carry out RSA on this dataset using different notions of distance and give an overview of how the end results of the analysis are affected by each distance notion. In total 9 different distance measures were evaluated for calculating the similarity between activation patterns in fMRI data. The results provided in this thesis can be used by researchers leveraging RSA to select distance measures for their studies that are most relevant to their particular research questions at hand. In addition to the comparison of distance notions, we also present a novel use case for RSA as a tool to visualize the global effects different transformations can have on the input dataset.
Costs of resistance in insect-parasite and insect-parasitoid interactions

Most, if not all, organisms face attack by natural enemies and will be selected to evolve some form of defence. Resistance may have costs as well as its obvious benefits. These costs may be associated with actual defence or with the maintenance of the defensive machinery irrespective of whether a challenge occurs. In this paper, the evidence for costs of resistance in insect-parasite and insect-parasitoid systems is reviewed, with emphasis on two host-parasitoid systems, based on Drosophila melanogaster and pea aphids as hosts. Data from true insect-parasite systems mainly concern the costs of actual defence; evidence for the costs of standing defences is mostly circumstantial. In pea aphids, the costs of standing defences have so far proved elusive. Resistance amongst clones is not correlated with life-time fecundity, whether measured on good or poor quality plants. Successful defence by a D. melanogaster larva results in a reduction in adult size and fecundity and an increased susceptibility to pupal parasitoids. Costs of standing defences are a reduction in larval competitive ability though these costs only become important when food is limited. It is concluded that costs of resistance can play a pivotal role in the evolutionary and population dynamic interactions between hosts and their parasites.
Relationship between ceftriaxone use and resistance of Enterobacter species

We investigated the relationship between the amount of ceftriaxone used in our hospital and the evolution of the rate of resistance among Enterobacter species isolates. We reviewed all positive microbiological reports for Enterobacter species and the pharmacy records for the ceftriaxone consumption during four semesters over 4 consecutive years. The resistance to ceftriaxone among Enterobacter species rose from 10 to 27% while the amount of ceftriaxone used almost trebled during the study period. In order to investigate the relationship between the use of an antibiotic and the emergence of resistance to it, we studied the development of ceftriaxone resistance in Enterobacter species and the use of this drug at the Centre Hospitalier Universitaire Vaudois (CHUV) each year between 1983 and 1986. The consumption of ceftriaxone more than doubled between 1983 and 1984, and since then has increased only slowly. Within 2 years the rate of Enterobacter species resistance to ceftriaxone has jumped from about 10% between 1983 and 1985 to 27% in 1986. As no particular modification in the preventive methods of hospital hygiene and no epidemics occurred during the period of our study, we conclude that the increase in the prescribing of ceftriaxone probably played a central role in the increased number of resistant strains of Enterobacter species.
Differential induction of apoptosis and necrosis in monocytes from patients with tuberculosis and healthy control subjects.

BACKGROUND Mycobacterium tuberculosis and purified protein derivative (PPD) induce apoptosis in murine macrophages and apoptosis and necrosis in human monocytes and alveolar epithelial cells. Macrophages from bronchoalveolar lavages and granulomas from patients with tuberculosis (TB) present both types of cell death; however, the significance of the type of cell death in TB remains uncertain. METHODS Monocytes from PPD-positive control subjects and from patients with TB were exposed to PPD or M. tuberculosis. Apoptosis, necrosis, and the percentage of tumor necrosis factor (TNF)-alpha -positive and interleukin (IL)-10-positive cells were determined cytofluorometrically. Levels of lactate dehydrogenase, TNF-alpha, and IL-10 were measured in culture supernatants. The role of TNF-alpha and IL-10 was tested by blockade experiments. RESULTS PPD and M. tuberculosis induced apoptosis in monocytes from PPD-positive control subjects, whereas cells from patients with TB presented apoptosis and necrosis. Cells from PPD-positive control subjects produced mainly TNF-alpha, whereas cells from patients with TB produced mainly IL-10. Blockade experiments suggest that TNF-alpha and IL-10 regulate the type of cell death occurring in response to M. tuberculosis. CONCLUSIONS Results suggest that apoptosis of monocytes exposed to mycobacteria may partly explain the protective immune response found in PPD-positive control subjects, whereas necrosis may be determinant of the bacterial dissemination and tissue damage that occur in patients with active TB.