Ferrous iron oxidation by foam immobilized Acidithiobacillus ferrooxidans: Experiments and modeling

Ferrous iron bio-oxidation by Acidithiobacillus ferrooxidans immobilized on polyurethane foam was investigated. Cells were immobilized on foams by placing them in a growth environment and fully bacterially activated polyurethane foams (BAPUFs) were prepared by serial subculturing in batches with partially bacterially activated foam (pBAPUFs). The dependence of foam density on cell immobilization process, the effect of pH and BAPUF loading on ferrous oxidation were studied to choose operating parameters for continuous operations. With an objective to have high cell densities both in foam and the liquid phase, pretreated foams of density 50 kg/m3 as cell support and ferrous oxidation at pH 1.5 to moderate the ferric precipitation were preferred. A novel basket-type bioreactor for continuous ferrous iron oxidation, which features a multiple effect of stirred tank in combination with recirculation, was designed and operated. The results were compared with that of a free cell and a sheet-type foam immobilized reactors. A fivefold increase in ferric iron productivity at 33.02 g/h/L of free volume in foam was achieved using basket-type bioreactor when compared to a free cell continuous system. A mathematical model for ferrous iron oxidation by Acidithiobacillus ferrooxidans cells immobilized on polyurethane foam was developed with cell growth in foam accounted by an effectiveness factor. The basic parameters of simulation were estimated using the experimental data on free cell growth as well as from cell attachment to foam under nongrowing conditions. The model predicted the phase of both oxidation of ferrous in shake flasks by pBAPUFs as well as by fully activated BAPUFs for different cell loadings in foam. Model for stirred tank basket bioreactor predicted within 5% both transient and steady state of the experiments closely for the simulated dilution rates. Bio-oxidation at high Fe2+ concentrations were simulated with experiments when substrate and product inhibition coefficients were factored into cell growth kinetics.

Inferring neuronal network connectivity from spike data: A temporal data mining approach

Understanding the functioning of a neural system in terms of its underlying circuitry is an important problem in neuroscience. Recent d evelopments in electrophysiology and imaging allow one to simultaneously record activities of hundreds of neurons. Inferring the underlying neuronal connectivity patterns from such multi-neuronal spike train data streams is a challenging statistical and computational problem. This task involves finding significant temporal patterns from vast amounts of symbolic time series data. In this paper we show that the frequent episode mining methods from the field of temporal data mining can be very useful in this context. In the frequent episode discovery framework, the data is viewed as a sequence of events, each of which is characterized by an event type and its time of occurrence and episodes are certain types of temporal patterns in such data. Here we show that, using the set of discovered frequent episodes from multi-neuronal data, one can infer different types of connectivity patterns in the neural system that generated it. For this purpose, we introduce the notion of mining for frequent episodes under certain temporal constraints; the structure of these temporal constraints is motivated by the application. We present algorithms for discovering serial and parallel episodes under these temporal constraints. Through extensive simulation studies we demonstrate that these methods are useful for unearthing patterns of neuronal network connectivity.

Phenotypic and Functional Characterization of Human Mammary Stem/Progenitor Cells in Long Term Culture

Background: Cancer stem cells exhibit close resemblance to normal stem cells in phenotype as well as function. Hence, studying normal stem cell behavior is important in understanding cancer pathogenesis. It has recently been shown that human breast stem cells can be enriched in suspension cultures as mammospheres. However, little is known about the behavior of these cells in long-term cultures. Since extensive self-renewal potential is the hallmark of stem cells, we undertook a detailed phenotypic and functional characterization of human mammospheres over long-term passages. Methodology: Single cell suspensions derived from human breast `organoids' were seeded in ultra low attachment plates in serum free media. Resulting primary mammospheres after a week (termed T1 mammospheres) were subjected to passaging every 7th day leading to the generation of T2, T3, and T4 mammospheres. Principal Findings: We show that primary mammospheres contain a distinct side-population (SP) that displays a CD24(low)/CD44(low) phenotype, but fails to generate mammospheres. Instead, the mammosphere-initiating potential rests within the CD44(high)/CD24(low) cells, in keeping with the phenotype of breast cancer-initiating cells. In serial sphere formation assays we find that even though primary (T1) mammospheres show telomerase activity and fourth passage T4 spheres contain label-retaining cells, they fail to initiate new mammospheres beyond T5. With increasing passages, mammospheres showed an increase in smaller sized spheres, reduction in proliferation potential and sphere forming efficiency, and increased differentiation towards the myoepithelial lineage. Significantly, staining for senescence-associated beta-galactosidase activity revealed a dramatic increase in the number of senescent cells with passage, which might in part explain the inability to continuously generate mammospheres in culture. Conclusions: Thus, the self-renewal potential of human breast stem cells is exhausted within five in vitro passages of mammospheres, suggesting the need for further improvisation in culture conditions for their long-term maintenance.

Eye-view: A retinal image acquisition system

This paper presents a low cost but high resolution retinal image acquisition system of the human eye. The images acquired by a CMOS image sensor are communicated through the Universal Serial Bus (USB) interface to a personal computer for viewing and further processing. The image acquisition time was estimated to be 2.5 seconds. This system can also be used in telemedicine applications.

Error Checking Digit for Nonconventional Chemical Codes

In handling large volumes of data such as chemical notations, serial numbers for books, etc., it is always advisable to provide checking methods which would indicate the presence of errors. The entire new discipline of coding theory is devoted to the study of the construction of codes which provide such error-detecting and correcting means.l Although these codes are very powerful, they are highly sophisticated from the point of view of practical implementation

Drosophila indirect flight muscle specific Act88F actin mutants as a model system for studying congenital myopathies of the human ACTA1 skeletal muscle actin gene

Most human ACTA1 skeletal actin gene mutations cause dominant, congenital myopathies often with severely reduced muscle function and neonatal mortality. High sequence conservation of actin means many mutated ACTA1 residues are identical to those in the Drosophila Act88F, an indirect flight muscle specific sarcomeric actin. Four known Act88F mutations occur at the same actin residues mutated in ten ACTA1 nemaline mutations, A138D/P, R256H/L, G268C/D/R/S and R372C/S. These Act88F mutants were examined for similar muscle phenotypes. Mutant homozygotes show phenotypes ranging from a lack of myofibrils to almost normal sarcomeres at eclosion. Aberrant Z-disc-like structures and serial Z-disc arrays, ‘zebra bodies’, are observed in homozygotes and heterozygotes of all four Act88F mutants. These electron-dense structures show homologies to human nemaline bodies/rods, but are much smaller than those typically found in the human myopathy. We conclude that the Drosophila indirect flight muscles provide a good model system for studying ACTA1 mutations.

Parallelization of an unstructured data based cell centre finite volume code, HIFUN-3D

This work describes the parallelization of High Resolution flow solver on unstructured meshes, HIFUN-3D, an unstructured data based finite volume solver for 3-D Euler equations. For mesh partitioning, we use METIS, a software based on multilevel graph partitioning. The unstructured graph used for partitioning is associated with weights both on its vertices and edges. The data residing on every processor is split into four layers. Such a novel procedure of handling data helps in maintaining the effectiveness of the serial code. The communication of data across the processors is achieved by explicit message passing using the standard blocking mode feature of Message Passing Interface (MPI). The parallel code is tested on PACE++128 available in CFD Center

On Minimization of Test Application Time for RAS

Conventional Random access scan (RAS) for testing has lower test application time, low power dissipation, and low test data volume compared to standard serial scan chain based design In this paper, we present two cluster based techniques, namely, Serial Input Random Access Scan and Variable Word Length Random Access Scan to reduce test application time even further by exploiting the parallelism among the clusters and performing write operations on multiple bits Experimental results on benchmarks circuits show on an average 2-3 times speed up in test write time and average 60% reduction in write test data volume

Toward Effective Scalar Hardware for Highly Vectorizable Applications

The performance of a program will ultimately be limited by its serial (scalar) portion, as pointed out by Amdahl′s Law. Reported studies thus far of instruction-level parallelism have mixed data-parallel program portions with scalar program portions, often leading to contradictory and controversial results. We report an instruction-level behavioral characterization of scalar code containing minimal data-parallelism, extracted from highly vectorized programs of the PERFECT benchmark suite running on a Cray Y-MP system. We classify scalar basic blocks according to their instruction mix, characterize the data dependencies seen in each class, and, as a first step, measure the maximum intrablock instruction-level parallelism available. We observe skewed rather than balanced instruction distributions in scalar code and in individual basic block classes of scalar code; nonuniform distribution of parallelism across instruction classes; and, as expected, limited available intrablock parallelism. We identify frequently occurring data-dependence patterns and discuss new instructions to reduce latency. Toward effective scalar hardware, we study latency-pipelining trade-offs and restricted multiple instruction issue mechanisms.

Test Application Time Minimization for RAS using Basis Optimization of Column Decoder

Random Access Scan, which addresses individual flip-flops in a design using a memory array like row and column decoder architecture, has recently attracted widespread attention, due to its potential for lower test application time, test data volume and test power dissipation when compared to traditional Serial Scan. This is because typically only a very limited number of random ``care'' bits in a test response need be modified to create the next test vector. Unlike traditional scan, most flip-flops need not be updated. Test application efficiency can be further improved by organizing the access by word instead of by bit. In this paper we present a new decoder structure that takes advantage of basis vectors and linear algebra to further significantly optimize test application in RAS by performing the write operations on multiple bits consecutively. Simulations performed on benchmark circuits show an average of 2-3 times speed up in test write time compared to conventional RAS.

Studies on multi-metal ion tolerance of Thiobacillus ferrooxidans

The influence of different concentrations of base metal ions, such as CU2+, Zn2+ and Fe3+, when present either alone or in different possible binary and ternary combinations in a 9K medium, on the fel rous ion oxidation ability of Thiobacillus ferrooxidans was studied. Levels and degree of toxicity of these ions have been quantified in terms of toxicity index (TI). Copper and zinc tolerant strains of the bacteria were developed through serial subculturing and their activity tested in the presence of the above metal ions in comparison with the behavior of wild unadapted cells under similar conditions. Copper tolerant strains (25 g/L Cu2+) were found to be more efficient in the bioleaching of both copper and zinc concentrates than wild unadapted strains, while zinc tolerant strains (40 g/L Zn2+) exhibited better leaching efficiency only in the bioleaching of sphalerite concentrates. The significance and relevance of multi-metal ion tolerance in Thiobacillus ferrooxidans has been highlighted with respect to bioleaching of sulphide mineral concentrates. (C) 1997 Published by Elsevier Science Ltd.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

Static Balancing of Spring-loaded Planar Revolute-joint Linkages without Auxiliary Links

We present a method to statically balance a general treestructured,planar revolute-joint linkage loaded with linear springs or constant forces without using auxiliary links. The balancing methods currently documented in the literature use extra links; some do not apply when there are spring loads and some are restricted to only two-link serial chains. In our method, we suitably combine any non-zero-free-length load spring with another spring to result in an effective zero-free-length spring load. If a link has a single joint (with the parent link), we give a procedure to attach extra zero-free-length springs to it so that forces and moments are balanced for the link. Another consequence of this attachment is that the constraint force of the joint on the parent link becomes equivalent to a zero-free-length spring load. Hence, conceptually,for the parent link, the joint with its child is removed and replaced with the zero-free-length spring. This feature allows recursive application of this procedure from the end-branches of the tree down to the root, satisfying force and moment balance of all the links in the process. Furthermore, this method can easily be extended to the closed-loop revolute-joint linkages, which is also illustrated in the paper.

Eye-View: A retinal image capture system

This paper presents a low cost but high resolution retinal image acquisition system of the human eye. The images acquired by a CMOS image sensor are communicated through the Universal Serial Bus (USB) interface to a personal computer for viewing and further processing. The image acquisition time was estimated to be 2.5 seconds. This system can also be used in telemedicine applications.

Analog/RF Built-in-Self-Test Subsystem for a Mobile Broadcast Video Receiver in 65-nm CMOS

A built-in-self-test (BIST) subsystem embedded in a 65-nm mobile broadcast video receiver is described. The subsystem is designed to perform analog and RF measurements at multiple internal nodes of the receiver. It uses a distributed network of CMOS sensors and a low bandwidth, 12-bit A/D converter to perform the measurements with a serial bus interface enabling a digital transfer of measured data to automatic test equipment (ATE). A perturbation/correlation based BIST method is described, which makes pass/fail determination on parts, resulting in significant test time and cost reduction.