Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

A Statistical Approach for Multilingual Document Clustering and Topic Extraction from Clusters

2000 Mathematics Subject Classification: 62H30

Derivation of base-line geochemistry, petrography, and isotopic data for the host rocks to the Lucky Strike deposit and comparison with data from other alteration zones, Buchans Mining Camp, Newfoundland

The Buchans ore bodies of central Newfoundland represent some of the highest grade VMS deposits ever mined. These Kuroko-type deposits are also known for the well developed and preserved nature of the mechanically transported deposits. The deposits are hosted in Cambro-Ordovician, dominantly calc-alkaline, bimodal volcanic and epiclastic sequences of the Notre Dame Subzone, Newfoundland Appalachians. Stratigraphic relationships in this zone are complicated by extensively developed, brittledominated Silurian thrust faulting. Hydrothermal alteration of host rocks is a common feature of nearly all VMS deposits, and the recognition of these zones has been a key exploration tool. Alteration of host rocks has long been described to be spatially associated with the Buchans ore bodies, most notably with the larger in-situ deposits. This report represents a base-line study in which a complete documentation of the geochemical variance, in terms of both primary (igneous) and alteration effects, is presented from altered volcanic rocks in the vicinity of the Lucky Strike deposit (LSZ), the largest in-situ deposit in the Buchans camp. Packages of altered rocks also occur away from the immediate mining areas and constitute new targets for exploration. These zones, identified mostly by recent and previous drilling, represent untested targets and include the Powerhouse (PHZ), Woodmans Brook (WBZ) and Airport (APZ) alteration zones, as well as the Middle Branch alteration zone (MBZ), which represents a more distal alteration facies related to Buchans ore-formation. Data from each of these zones were compared to those from the LSZ in order to evaluate their relative propectivity. Derived litho geochemical data served two functions: (i) to define primary (igneous) trends and (ii) secondary alteration trends. Primary trends were established using immobile, or conservative, elements (i. e., HFSE, REE, Th, Ti0₂, Al₂0₃, P₂0₅). From these, altered volcanic rocks were interpreted in terms of composition (e.g., basalt - rhyodacite) and magmatic affinity (e.g., calc-alkaline vs. tholeiitic). The information suggests that bimodality is a common feature of all zones, with most rocks plotting as either basalt/andesite or dacite (or rhyodacite); andesitic senso stricto compositions are rare. Magmatic affinities are more varied and complex, but indicate that all units are arc volcanic sequences. Rocks from the LSZ/MBZ represent a transitional to calc-alkalic sequence, however, a slight shift in key geochemical discriminants occurs between the foot-wall to the hanging-wall. Specifically, mafic and felsic lavas of the foot-wall are of transitional (or mildly calc-alkaline) affinity whereas the hanging-wall rocks are relatively more strongly calc-alkaline as indicated by enriched LREE/HREE and higher ZrN, NbN and other ratios in the latter. The geochemical variations also serve as a means to separate the units (at least the felsic rocks) into hanging-wall and foot-wall sequences, therefore providing a valuable exploration tool. Volcanic rocks from the WBZ/PHZ (and probably the APZ) are more typical of tholeiitic to transitional suites, yielding flatter mantlenormalized REE patterns and lower ZrN ratios. Thus, the relationships between the immediate mining area (represented by LSZ/MBZ) and the Buchans East (PHZ/WBZ) and the APZ are uncertain. Host rocks for all zones consist of mafic to felsic volcanic rocks, though the proportion of pyroclastic and epiclastic rocks, is greatest at the LSZ. Phenocryst assemblages and textures are common in all zones, with minor exceptions, and are not useful for discrimination purposes. Felsic rocks from all zones are dominated by sericiteclay+/- silica alteration, whereas mafic rocks are dominated by chlorite- quartz- sericite alteration. Pyrite is ubiquitous in all moderately altered rocks and minor associated base metal sulphides occur locally. The exception is at Lucky Strike, where stockwork quartzveining contains abundant base-metal mineralization and barite. Rocks completely comprised of chlorite (chloritite) also occur in the LSZ foot-wall. In addition, K-feldspar alteration occurs in felsic volcanic rocks at the MBZ associated with Zn-Pb-Ba and, notably, without chlorite. This zone represents a peripheral, but proximal, zone of alteration induced by lower temperature hydrothermal fluids, presumably with little influence from seawater. Alteration geochemistry was interpreted from raw data as well as from mass balanced (recalculated) data derived from immobile element pairs. The data from the LSZ/MBZ indicate a range in the degree of alteration from only minor to severe modification of precursor compositions. Ba tends to show a strong positive correlation with K₂0, although most Ba occurs as barite. With respect to mass changes, Al₂0₃, Ti0₂ and P₂0₅ were shown to be immobile. Nearly all rocks display mass loss of Na₂O, CaO, and Sr reflecting feldspar destruction. These trends are usually mirrored by K₂0-Rb and MgO addition, indicating sericitic and chloritic alteration, respectively. More substantial gains ofK₂0 often occur in rocks with K-feldspar alteration, whereas a few samples also displayed excessive MgO enrichment and represent chloritites. Fe₂0₃ indicates both chlorite and sulphide formation. Si0₂ addition is almost always the case for the altered mafic rocks as silica often infills amygdules and replaces the finer tuffaceous material. The felsic rocks display more variability in Si0₂. Silicic, sericitic and chloritic alteration trends were observed from the other zones, but not K-feldspar, chloritite, or barite. Microprobe analysis of chlorites, sericites and carbonates indicate: (i) sericites from all zones are defined as muscovite and are not phengitic; (ii) at the LSZ, chlorites ranged from Fe-Mg chlorites (pycnochlorite) to Mg-rich chlorite (penninite), with the latter occurring in the stockwork zone and more proximal alteration facies; (iii) chlorites from the WBZ were typical of those from the more distal alteration facies of the LSZ, plotting as ripidolite to pycnochlorite; (iv) conversely, chlorite from the PHZ plot with Mg-Al-rich compositions (chlinochlore to penninite); and (v) carbonate species from each zone are also varied, with calcite occurring in each zone, in addition to dolomite and ankerite in the PHZ and WBZ, respectively. Lead isotope ratios for galena separates from the different various zones, when combined with data from older studies, tend to cluster into four distinctive fields. Overall, the data plot on a broad mixing line and indicate evolution in a relatively low-μ environment. Data from sulphide stringers in altered MBZ rocks, as well as from clastic sulphides (Sandfill prospect), plot in the Buchans ore field, as do the data for galena from altered rocks in the APZ. Samples from the Buchans East area are even more primitive than the Buchans ores, with lead from the PHZ plotting with the Connel Option prospect and data from the WBZ matching that of the Skidder prospect. A sample from a newly discovered debris flow-type sulphide occurrence (Middle Branch East) yields lead isotope ratios that are slightly more radiogenic than Buchans and plot with the Mary March alteration zone. Data within each cluster are interpreted to represent derivation from individual hydrothermal systems in which metals were derived from a common source.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.

(Table 3, page 8) Chemical composition and physical cahracteristics of manganese nodules from the Pacific Ocean

This paper reviews the state of the art in processing and extraction of ocean floor manganese nodules. It briefly reviews the mining sites where the abundant rich nodules occur and also discusses the metal distribution in nodules in view of economical processing and extraction of these metal values. The paper discloses in a detailed manner the physical and chemical characteristics of nodules, including porosity, surface area, water content and the effect of temperature on crystal structure of major constituents of nodules. In the extraction aspect of nodules, the paper reviews two different extraction schemes revealed in the literature, namely hydrometallurgical treatment and pyrometallurgical treatment. The hydrometallurgical treatments include acid leaching, ammonia leaching, leaching with reducing agents and leaching after high temperature pre-treatments such as in sulfating rousting, while the pyrometallurgical processes include smelting, chlorination-vaporization and segregation. The paper also covers metal recovery processes from leach liquor. An economic survey of processing nodules has been made in terms of problems associated with metal-marketing, and impact of metal production from nodules on mineral industries.

Biogeochemical and physico-chemical characteristics in the gulf of Trieste, Italy

In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea).

Seeing Turkish state formation processes: Mapping language and education census data

Language provides an interesting lens to look at state-building processes because of its cross-cutting nature. For example, in addition to its symbolic value and appeal, a national language has other roles in the process, including: (a) becoming the primary medium of communication which permits the nation to function efficiently in its political and economic life, (b) promoting social cohesion, allowing the nation to develop a common culture, and (c) forming a primordial basis for self-determination. Moreover, because of its cross-cutting nature, language interventions are rarely isolated activities. Languages are adopted by speakers, taking root in and spreading between communities because they are legitimated by legislation, and then reproduced through institutions like the education and military systems. Pádraig Ó’ Riagáin (1997) makes a case for this observing that “Language policy is formulated, implemented, and accomplishes its results within a complex interrelated set of economic, social, and political processes which include, inter alia, the operation of other non-language state policies” (p. 45). In the Turkish case, its foundational role in the formation of the Turkish nation-state but its linkages to human rights issues raises interesting issues about how socio-cultural practices become reproduced through institutional infrastructure formation. This dissertation is a country-level case study looking at Turkey’s nation-state building process through the lens of its language and education policy development processes with a focus on the early years of the Republic between 1927 and 1970. This project examines how different groups self-identified or were self-identified (as the case may be) in official Turkish statistical publications (e.g., the Turkish annual statistical yearbooks and the population censuses) during that time period when language and ethnicity data was made publicly available. The overarching questions this dissertation explores include: 1.What were the geo-political conditions surrounding the development and influencing the Turkish government’s language and education policies? 2.Are there any observable patterns in the geo-spatial distribution of language, literacy, and education participation rates over time? In what ways, are these traditionally linked variables (language, literacy, education participation) problematic? 3.What do changes in population identifiers, e.g., language and ethnicity, suggest about the government’s approach towards nation-state building through the construction of a civic Turkish identity and institution building? Archival secondary source data was digitized, aggregated by categories relevant to this project at national and provincial levels and over the course of time (primarily between 1927 and 2000). The data was then re-aggregated into values that could be longitudinally compared and then layered on aspatial administrative maps. This dissertation contributes to existing body of social policy literature by taking an interdisciplinary approach in looking at the larger socio-economic contexts in which language and education policies are produced.

Extraction and purification of immunoglobulin G with aqueous biphasic systems

The immune system is able to produce antibodies, which have the capacity to recognize and to bind to foreign molecules or pathogenic organisms. Currently, there are a diversity of diseases that can be treated with antibodies, like immunoglobulins G (IgG). Thereby, the development of cost-efficient processes for their extraction and purification is an area of main interest in biotechnology. Aqueous biphasic systems (ABS) have been investigated for this purpose, once they allow the reduction of costs and the number of steps involved in the process, when compared with conventional methods. Nevertheless, typical ABS have not showed to be selective, resulting in low purification factors and yields. In this context, the addition of ionic liquids (ILs) as adjuvants can be a viable and potential alternative to tailor the selectivity of these systems. In this work, ABS composed of polyethylene glycol (PEG) of different molecular weight, and a biodegradable salt (potassium citrate) using ILs as adjuvants (5 wt%), were studied for the extraction and purification of IgG from a rabbit source. Initially, it was tested the extraction time, the effect on the molecular weight of PEG in a buffer solution of K3C6H5O7/C6H8O7 at pH≈7, and the effect of pH (59) on the yield (YIgG) and extraction efficiency (EEIgG%) of IgG. The best results regarding EEIgG% were achieved with a centrifugation step at 1000 rpm, during 10 min, in order to promote the separation of phases followed by 120 min of equilibrium. This procedure was then applied to the remaining experiments. The results obtained in the study of PEGs with different molecular weights, revealed a high affinity of IgG for the PEG-rich phase, and particularly for PEGs of lower molecular weight (EEIgG% of 96 % with PEG 400). On the other hand, the variation of pH in the buffer solution did not show a significant effect on the EEIgG%. Finally, it was evaluated the influence of the addition of different ILs (5% wt) on the IgG extraction in ABS composed of PEG 400 at pH≈7. In these studies, it was possible to obtain EEIgG% of 100% with the ILs composed of the anions [TOS]-, [CH3CO2]-and Cl-, although the obtained YIgG% were lower than 40%. On the other hand, the ILs composed of the anions Br-, as well as of the cation [C10mim]+, although not leading to EEIgG% of 100%, provide an increase in the YIgG%. ABS composed of PEG, a biodegradable organic salt and ILs as adjuvants, revealed to be an alternative and promising method to purify IgG. However, additional studies are still required in order to reduce the loss of IgG.

Artisanal extraction and traditional knowledge associated with medicinal use of Crabwood Oil (Carapa guianensis Aublet.) in a peri-urban Várzea environment in the Amazon Estuary.

Varzea forests of the Amazon estuary contain species of importance to riverine communities. For example, the oil extracted from the seeds of crabwood trees is traditionally used to combat various illnesses and as such artisanal extraction processes have been maintained. The objectives of this study were to (1) describe the process involved in artisanal extraction of crabwood oil in the Fazendinha ProtectedArea, in the state ofAmap´a; (2) characterise the processes of knowledge transfer associated with the extraction and use of crabwood oil within a peri-urban riverine community; and (3) discern medicinal uses of the oil.The data were obtained using semistructured interviews with 13 community members involved in crabwood oil extraction and via direct observation.The process of oil extraction is divided into four stages: seed collection; cooking and resting of the seeds; shelling of the seeds and dough preparation; and oil collection. Oil extraction is carried out within the home for personal use, with surplus marketed within the community. More than 90% of the members of the community involved in extraction of crabwood oil highlighted the use of the oil to combat inflammation of the throat. Knowledge transfer occurs via oral transmission and through direct observation.

Emerging plant-based proteins: comparison from extraction to functional properties and food application

The increasing demand for alternatives to meat food products, which is linked to ethical and environmental reasons, highlights the necessity of using different protein sources. Plant proteins provide a valid option, thanks to the relative low costs, high availability and wide supply sources. The current process used to produce plant concentrates and isolates is the alkaline extraction followed by isoelectric precipitation. However, despite the high purity of the proteins, it presents some drawbacks. Innovative protein extraction processes are emerging, with the aim of reducing the environmental impact and the costs, as well as improving the functional properties. In this study, the traditional wet protein extraction and another simplified wet process were used to obtain protein-rich extracts out of different plants. The sources considered in the project were de-oiled sunflower and canola, chickpea, lentils, and the camelina meal, an emerging oleaginous seed interesting for its high content of omega 3. The extracts obtained from the two processes were then analysed for their capacities to hold water and fat, to form gel and a stable foam. Results highlighted strong differences concerning the protein content, yield and functionalities. The extracts obtained with the alkaline process confirmed the literature data about the four plant sources (sunflower, canola, chickpea and lentils) and allow to obtain a camelina concentrate with a protein content of 63 % and a protein recovery of 41 %. The second easiest process was not effective to obtain a protein enrichment in oleaginous sources, whereas an enrichment of 10 and 15 % was obtained in chickpea and lentils, respectively. The functional properties were also completely different: the easiest process produced protein ingredients completely water-soluble at pH 7, with a discrete foaming capacity compared to the extracts obtained with alkaline process. These characteristics could make these extracts suitable for the plant milk-analogue products.

Construction Of A Manual Of Work Processes And Techniques From Centro De Dispensação De Medicamentos De Alto Custo (cedmac), Hospital De Clínicas, Unicamp.

The Centers for High Cost Medication (Centros de Medicação de Alto Custo, CEDMAC), Health Department, São Paulo were instituted by project in partnership with the Clinical Hospital of the Faculty of Medicine, USP, sponsored by the Foundation for Research Support of the State of São Paulo (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP) aimed at the formation of a statewide network for comprehensive care of patients referred for use of immunobiological agents in rheumatological diseases. The CEDMAC of Hospital de Clínicas, Universidade Estadual de Campinas (HC-Unicamp), implemented by the Division of Rheumatology, Faculty of Medical Sciences, identified the need for standardization of the multidisciplinary team conducts, in face of the specificity of care conducts, verifying the importance of describing, in manual format, their operational and technical processes. The aim of this study is to present the methodology applied to the elaboration of the CEDMAC/HC-Unicamp Manual as an institutional tool, with the aim of offering the best assistance and administrative quality. In the methodology for preparing the manuals at HC-Unicamp since 2008, the premise was to obtain a document that is participatory, multidisciplinary, focused on work processes integrated with institutional rules, with objective and didactic descriptions, in a standardized format and with electronic dissemination. The CEDMAC/HC-Unicamp Manual was elaborated in 10 months, with involvement of the entire multidisciplinary team, with 19 chapters on work processes and techniques, in addition to those concerning the organizational structure and its annexes. Published in the electronic portal of HC Manuals in July 2012 as an e-Book (ISBN 978-85-63274-17-5), the manual has been a valuable instrument in guiding professionals in healthcare, teaching and research activities.

Intensification Of Bioactive Compounds Extraction From Medicinal Plants Using Ultrasonic Irradiation.

Extraction processes are largely used in many chemical, biotechnological and pharmaceutical industries for recovery of bioactive compounds from medicinal plants. To replace the conventional extraction techniques, new techniques as high-pressure extraction processes that use environment friendly solvents have been developed. However, these techniques, sometimes, are associated with low extraction rate. The ultrasound can be effectively used to improve the extraction rate by the increasing the mass transfer and possible rupture of cell wall due the formation of microcavities leading to higher product yields with reduced processing time and solvent consumption. This review presents a brief survey about the mechanism and aspects that affecting the ultrasound assisted extraction focusing on the use of ultrasound irradiation for high-pressure extraction processes intensification.

Leaf-, Panel- And Latex-expressed Sequenced Tags From The Rubber Tree (hevea Brasiliensis) Under Cold-stressed And Suboptimal Growing Conditions: The Development Of Gene-targeted Functional Markers For Stress Response.

Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding.

Chasing Cardiac Physiology And Pathology Down The Camkii Cascade.

Calcium dynamics is central in cardiac physiology, as the key event leading to the excitation-contraction coupling (ECC) and relaxation processes. The primary function of Ca(2+) in the heart is the control of mechanical activity developed by the myofibril contractile apparatus. This key role of Ca(2+) signaling explains the subtle and critical control of important events of ECC and relaxation, such Ca(2+) influx and SR Ca(2+) release and uptake. The multifunctional Ca(2+)-calmodulin-dependent protein kinase II (CaMKII) is a signaling molecule that regulates a diverse array of proteins involved not only in ECC and relaxation, but also in cell death, transcriptional activation of hypertrophy, inflammation and arrhythmias. CaMKII activity is triggered by an increase in intracellular Ca(2+) levels. This activity can be sustained, creating molecular memory after the decline in Ca(2+) concentration, by autophosphorylation of the enzyme, as well as by oxidation, glycosylation and nitrosylation at different sites of the regulatory domain of the kinase. CaMKII activity is enhanced in several cardiac diseases, altering the signaling pathways by which CaMKII regulates the different fundamental proteins involved in functional and transcriptional cardiac processes. Dysregulation of these pathways constitutes a central mechanism of various cardiac disease phenomena, like apoptosis and necrosis during ischemia/reperfusion injury, digitalis exposure, post-acidosis and heart failure arrhythmias, or cardiac hypertrophy. Here we summarize significant aspects of the molecular physiology of CaMKII and provide a conceptual framework for understanding the role of the CaMKII cascade on Ca(2+) regulation and dysregulation in cardiac health and disease.