Vrishabhavathi Valley Wastewater Treatment Plant System Upgrade

Sixteen activated sludge tanks, eight secondary clarifiers, and four return pump stations were designed for the Vrishabhavathi Wastewater Treatment plant in Bangalore India. The design included tank dimensions, mechanical equipment associated with each component, pipe sizes for the piping system, and a cost estimate with a construction schedule. The activate sludge tanks were designed to be made of reinforced concrete with a mechanical air diffuser system installed for oxidation purposes. The secondary clarifiers were designed using reinforced concrete and a mechanical sweeping mechanism to scrape up the sludge as it settles to the bottom of the tank. Return pump stations were designed to transport the sludge into recirculation pipes or to a waste activated sludge stream. The treated water from the expanded facility will be discharged back into the river or transported to a tertiary treatment facility on site. The effluent will act as a source of non-potable water for local urban and agricultural use. Construction of the proposed facility will not interfere with the operation of the existing plant. This expansion to the existing facility will provide the city of Bangalore with an additional 71.33 million gallons per day of fresh, not-potable water

Time vs. Information Tradeoffs for Leader Election in Anonymous Trees

The leader election task calls for all nodes of a network to agree on a single node. If the nodes of the network are anonymous, the task of leader election is formulated as follows: every node $v$ of the network must output a simple path, coded as a sequence of port numbers, such that all these paths end at a common node, the leader. In this paper, we study deterministic leader election in anonymous trees. Our aim is to establish tradeoffs between the allocated time $\tau$ and the amount of information that has to be given $\textit{a priori}$ to the nodes to enable leader election in time $\tau$ in all trees for which leader election in this time is at all possible. Following the framework of $\textit{algorithms with advice}$, this information (a single binary string) is provided to all nodes at the start by an oracle knowing the entire tree. The length of this string is called the $\textit{size of advice}$. For an allocated time $\tau$, we give upper and lower bounds on the minimum size of advice sufficient to perform leader election in time $\tau$. We consider $n$-node trees of diameter $diam \leq D$. While leader election in time $diam$ can be performed without any advice, for time $diam-1$ we give tight upper and lower bounds of $\Theta (\log D)$. For time $diam-2$ we give tight upper and lower bounds of $\Theta (\log D)$ for even values of $diam$, and tight upper and lower bounds of $\Theta (\log n)$ for odd values of $diam$. For the time interval $[\beta \cdot diam, diam-3]$ for constant $\beta >1/2$, we prove an upper bound of $O(\frac{n\log n}{D})$ and a lower bound of $\Omega(\frac{n}{D})$, the latter being valid whenever $diam$ is odd or when the time is at most $diam-4$. Finally, for time $\alpha \cdot diam$ for any constant $\alpha <1/2$ (except for the case of very small diameters), we give tight upper and lower bounds of $\Theta (n)$

Intellectual Honesty

Until recently, almost nothing had been written about the moral virtue of honesty in the past 50 years of Western analytic philosophy. Slowly, this is beginning to change. But moral honesty is not the only kind of honesty there is. In this paper, I focus specifically on the intellectual cousin to moral honesty, and offer a preliminary account of its behavioral and motivational dimensions. The account will be centered on not intentionally distorting the facts as the person takes them to be, for one of a variety of intellectually virtuous motivating reasons

Gene regulation during stress response transcription in Saccharomyces Cerevisiae

DYNAMIC TRANSCRIPTOME ANALYSIS MEASURES RATES OF MRNA SYNTHESIS AND DECAY IN YEAST To obtain rates of mRNA synthesis and decay in yeast, we established dynamic transcriptome analysis (DTA). DTA combines non-perturbing metabolic RNA labeling with dynamic kinetic modeling. DTA reveals that most mRNA synthesis rates are around several transcripts per cell and cell cycle, and most mRNA half-lives range around a median of 11 min. DTA can monitor the cellular response to osmotic stress with higher sensitivity and temporal resolution than standard transcriptomics. In contrast to monotonically increasing total mRNA levels, DTA reveals three phases of the stress response. During the initial shock phase, mRNA synthesis and decay rates decrease globally, resulting in mRNA storage. During the subsequent induction phase, both rates increase for a subset of genes, resulting in production and rapid removal of stress-responsive mRNAs. During the recovery phase, decay rates are largely restored, whereas synthesis rates remain altered, apparently enabling growth at high salt concentration. Stress-induced changes in mRNA synthesis rates are predicted from gene occupancy with RNA polymerase II. Thus, DTA realistically monitors the dynamics in mRNA metabolism that underlie gene regulatory systems.MEDIATOR PHOSPHORYLATION PREVENTS STRESS RESPONSE TRANSCRIPTION DURING NON STRESS CONDITIONS The multiprotein complex Mediator is a coactivator of RNA polymerase (Pol) II transcription that is required for the regulated expression of protein-coding genes. Mediator serves as an endpoint of signaling pathways and regulates Pol II transcription, but the mechanisms it uses are not well understood. Here we used mass spectrometry and dynamic transcriptome analysis to investigate a functional role of Mediator phosphorylation in gene expression. Affinity purification and mass spectrometry revealed that Mediator from the yeast S. cerevisiae is phosphorylated at multiple sites a 17 out of its 25 subunits. Mediator phosphorylation levels change upon an external stimulus set by exposure of cells to high salt concentrations. Phosphorylated sites in the Mediator tail subunit Med15 are required for suppression of stress-induced changes in gene expression under non-stress conditions. Thus dynamic and differential Mediator phosphorylation contributes to gene regulation in eukaryotic cells

Characterizing the Cellular Function of Protein Phosphatase 1 Isoforms

A protein phosphatase is an enzyme that removes a phosphate group from a specific amino acid residue on a target protein substrate. This protein phosphatase-regulated dephosphorylation is an important mechanism for many different processes and regulations inside mammalian cells (Rebleo, 2015). One of the major classes of protein phosphatases is the Ser/Thr-specific family. These phosphatases target the amino acids serine and threonine. There are many different members of the Ser/Thr-specific family, but the phosphatase that this study focuses on is called protein phosphatase 1 (PP1). PP1 has three different isoforms: alpha, beta, and gamma. These isoforms share roughly 90% of their amino acid composition (Liu, 2015). The main distinguishing factor between the isoforms are the unique sequences that each has at the C and N termini (Liu, 2015). Previous studies of neural cells have shown that PP1 may play a role in regulating and inactivating the nuclear transcription factor, cAMP regulatory element binding (CREB) (Bernhard, 2001). Other studies have indicated that PP1 may have an indirect function in the inactivation histone deacetylase, a group of enzymes that help regulate genes by removing an acetyl group from DNA histones (Gao, 2009). It is not yet known which of the PP1 isoforms is the main agent for dephosphorylation in these cases. Other studies have also shown that PP1 may affect heart failure and that inhibition of PP1 beta appears to benefit the performance of cardiac contractility and relaxation in the short-term (Liu, 2015). The primary purpose of this study is to investigate whether the alpha and beta isoforms of protein phosphatase 1 exhibit specific localization in either the nucleus or the cytoplasm of cells. Furthermore, we wanted to examine the role that protein phosphatase 1 plays in terms of gene regulation and expression in the nucleus, as well as investigate other possible substrate targets. From this study, we have evidence that the beta isoform of PP1 is localized to the nucleus and that the alpha isoform is localized to the cytoplasm. Additionally, we also found that PP1 beta is the isoform that is primarily responsible for the regulation of histone deacetylase 7 in the nucleus. We also considered the effect that the overexpression of the isoforms would have on the enzyme phospholamban (PLB), which is an enzyme that plays a regulatory role in cardiac myocytes (Koss 1996). We found that the overexpression of PP1 alpha decreased the overall phosphorylation level of PLB, whereas PP1 beta had no effect. Possible implications of this study include providing a better idea of the mechanisms of PP1, which grants us a clearer understanding of the functions that PP1 may have in cardiac cells. Moreover, this study may provide the baseline of knowledge necessary for future potential therapeutic interventions to treat heart disease. For example, if PP1 isoforms are also demonstrated to be localized in the nucleus to influence gene expression for cardiac disease, we can inhibit its activity by disrupting its binding with regulatory proteins while their cytosolic activities are still intact. *This scholar and faculty mentor have requested that only an abstract be published

The Cognitive Atlas: Employing Interaction Design Processes to Facilitate Collaborative Ontology Creation

The Cognitive Atlas is a collaborative knowledge-building project that aims to develop an ontology that characterizes the current conceptual framework among researchers in cognitive science and neuroscience. The project objectives from the beginning focused on usability, simplicity, and utility for end users. Support for Semantic Web technologies was also a priority in order to support interoperability with other neuroscience projects and knowledge bases. Current off-the-shelf semantic web or semantic wiki technologies, however, do not often lend themselves to simple user interaction designs for non-technical researchers and practitioners; the abstract nature and complexity of these systems acts as point of friction for user interaction, inhibiting usability and utility. Instead, we take an alternate interaction design approach driven by user centered design processes rather than a base set of semantic technologies. This paper reviews the initial two rounds of design and development of the Cognitive Atlas system, including interactive design decisions and their implementation as guided by current industry practices for the development of complex interactive systems