Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-treated Yeast Cells*

The target of rapamycin (TOR) kinase senses the availability of nutrients and coordinates cellular growth and proliferation with nutrient abundance. Inhibition of TOR mimics nutrient starvation and leads to the reorganization of many cellular processes, including autophagy, protein translation, and vesicle trafficking. TOR regulates cellular physiology by modulating phosphorylation and ubiquitylation signaling networks; however, the global scope of such regulation is not fully known. Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified. The phosphoproteome was extensively modulated by rapamycin treatment, with more than 900 up-regulated sites one hour after rapamycin treatment. Dynamically regulated phosphoproteins were involved in diverse cellular processes, prominently including transcription, membrane organization, vesicle-mediated transport, and autophagy. Several hundred ubiquitylation sites were increased after rapamycin treatment, and about half as many decreased in abundance. We found that proteome, phosphorylation, and ubiquitylation changes converged on the Rsp5-ubiquitin ligase, Rsp5 adaptor proteins, and Rsp5 targets. Putative Rsp5 targets were biased for increased ubiquitylation, suggesting activation of Rsp5 by rapamycin. Rsp5 adaptor proteins, which recruit target proteins for Rsp5-dependent ubiquitylation, were biased for increased phosphorylation. Furthermore, we found that permeases and transporters, which are often ubiquitylated by Rsp5, were biased for reduced ubiquitylation and reduced protein abundance. The convergence of multiple proteome-level changes on the Rsp5 system indicates a key role of this pathway in the response to rapamycin treatment. Collectively, these data reveal new insights into the global proteome dynamics in response to rapamycin treatment and provide a first detailed view of the co-regulation of phosphorylation- and ubiquitylation-dependent signaling networks by this compound.
Imaging Dedicated and Multifunctional Neural Circuits Generating Distinct Behaviors

Central pattern generators (CPGs) control both swimming and crawling in the medicinal leech. To investigate whether the neurons comprising these two CPGs are dedicated or multifunctional, we used voltage-sensitive dye imaging to record from ∼80% of the ∼400 neurons in a segmental ganglion. By eliciting swimming and crawling in the same preparation, we were able to identify neurons that participated in either of the two rhythms, or both. More than twice as many cells oscillated in-phase with crawling (188) compared with swimming (90). Surprisingly, 84 of the cells (93%) that oscillated with swimming also oscillated with crawling. We then characterized two previously unidentified interneurons, cells 255 and 257, that had interesting activity patterns based on the imaging results. Cell 255 proved to be a multifunctional interneuron that oscillates with and can perturb both rhythms, whereas cell 257 is an interneuron dedicated to crawling. These results show that the swimming and crawling networks are driven by both multifunctional and dedicated circuitry.
Privacy-Preserving Social DNA-Based Recommender

This research studies current privacy-preserving and familiarity-based recommender systems and introduces a new recommender system based on these existing techniques that uses DNA-similarity between users of the system as a basis for generating recommendations. Techniques for privacy-preserving DNA-matching are researched and incorporated in the setting of a privacy-preserving recommender system. Somewhat homomorphic encryption is used as the standard encryption for both the privacy-preserving DNA-matching and the recommendation generation. The system is first devised in a semi-honest security model and is then extended to the malicious user model. The recommender system is implemented in both security models and its performance is compared to existing privacy-preserving recommender systems.
An Improved Forwarding of Diverse Events with Mobile Sinks in Underwater Wireless Sensor Networks

In this paper, a novel routing strategy to cater the energy consumption and delay sensitivity issues in deep underwater wireless sensor networks is proposed. This strategy is named as ESDR: Event Segregation based Delay sensitive Routing. In this strategy sensed events are segregated on the basis of their criticality and, are forwarded to their respective destinations based on forwarding functions. These functions depend on different routing metrics like: Signal Quality Index, Localization free Signal to Noise Ratio, Energy Cost Function and Depth Dependent Function. The problem of incomparable values of previously defined forwarding functions causes uneven delays in forwarding process. Hence forwarding functions are redefined to ensure their comparable values in different depth regions. Packet forwarding strategy is based on the event segregation approach which forwards one third of the generated events (delay sensitive) to surface sinks and two third events (normal events) are forwarded to mobile sinks. Motion of mobile sinks is influenced by the relative distribution of normal nodes. We have also incorporated two different mobility patterns named as; adaptive mobility and uniform mobility for mobile sinks. The later one is implemented for collecting the packets generated by the normal nodes. These improvements ensure optimum holding time, uniform delay and in-time reporting of delay sensitive events. This scheme is compared with the existing ones and outperforms the existing schemes in terms of network lifetime, delay and throughput.
Security of neuromorphic computing: Thwarting learning attacks using memristor's obsolescence effect

Neuromorphic architectures are widely used in many applications for advanced data processing, and often implements proprietary algorithms. In this work, we prevent an attacker with physical access from learning the proprietary algorithm implemented by the neuromorphic hardware. For this purpose, we leverage the obsolescence effect in memristors to judiciously reduce the accuracy of outputs for any unauthorized user. For a legitimate user, we regulate the obsolescence effect, thereby controlling the accuracy of outputs. We also analyze the security vs. cost trade-offs for different applications. Our methodology is compatible with mainstream classification applications, memristor devices, and security and performance constraints.
Hybrid cooperative MAC protocol for wireless ad hoc networks

In this paper, we propose hybrid cooperative medium access control (MAC) protocol that adaptively uses single relay path or two relay paths for enhanced throughput and delay performance under fast Rayleigh fading conditions. The proposed protocol, termed as 2rcMAC, invokes two best relay (cooperating) paths for improved spatial diversity that offer higher transmission rate compared to the direct transmission path. It transmits through primary relay path for higher throughput performance and uses secondary relay path for reliable backup transmission. In case, only one best relay path (with higher rate than the direct transmission path) is available, the 2rcMAC protocol transmits directly to the destination node and invokes the secondary relay path for backup transmission only. Furthermore, handshaking and single bit feedback in 2rcMAC protocol resolve contentions among relay nodes in close proximity at the time, and further provide source node with rate information on source-to-destination, source-to-relay and relay-to-destination links. Simulation results clearly show average throughput improvement of 7% and 25% and average delay improvement of 94.8% and 98.9% compared to UtdMAC and CoopMAC I, respectively [4], [5], [7].
Reducing the barriers to writing verified specifications

Formally verifying a program requires significant skill not only because of complex interactions between program subcomponents, but also because of deficiencies in current verification interfaces. These skill barriers make verification economically unattractive by preventing the use of less-skilled (less-expensive) workers and distributed workflows (i.e., crowdsourcing). This paper presents VeriWeb, a web-based IDE for verification that decomposes the task of writing verifiable specifications into manageable subproblems. To overcome the information loss caused by task decomposition, and to reduce the skill required to verify a program, VeriWeb incorporates several innovative user interface features: drag and drop condition construction, concrete counterexamples, and specification inlining. To evaluate VeriWeb, we performed three experiments. First, we show that VeriWeb lowers the time and monetary cost of verification by performing a comparative study of VeriWeb and a traditional tool using 14 paid subjects contracted hourly from Exhedra Solution's vWorker online marketplace. Second, we demonstrate the dearth and insufficiency of current ad-hoc labor marketplaces for verification by recruiting workers from Amazon's Mechanical Turk to perform verification with VeriWeb. Finally, we characterize the minimal communication overhead incurred when VeriWeb is used collaboratively by observing two pairs of developers each use the tool simultaneously to verify a single program.
Robust static output feedback control using a Particle Swarm Optimization-DE-linear matrix inequality algorithm hybrid algorithm

Under the multi-objective framework, this paper presents a hybrid algorithm to solve robust static output feedback control problem for continuous poly-topic uncertain system. To obtain static output feedback gain, a new hybrid algorithm is proposed by combination of a hybrid algorithm of the Particle Swarm Optimization and Differential Evolution (DE), and the linear matrix inequality method. The proposed algorithm is used to solve a optimization problem with a bi-linear matrix inequality constraints. The Particle Swarm Optimization-DE hybrid algorithm was used to obtain a population of controllers, and linear matrix inequality approach was used to optimize a performance criterion of the system. Taking a hybrid H 2/H infinite control problem as example, the detailed algorithm is presented to solve robust static output feedback control problem. The simulation results show that the proposed hybrid algorithm improves the convergence rate and accuracy of iterative methods and the original DE-linear matrix inequality algorithm.
Critical Race Theory Counterstory as Allegory: A Rhetorical Trope to Raise Awareness about Arizona's Ban on Ethnic Studies.

The critical race counterstory in this essay takes on the form of allegory to raise awareness about Arizona's anti-immigrant/Mexican climate, and pays particular attention to legislation targeted at Tucson Unified School District's Mexican American studies (also RAZA studies) program. Derrick Bell, Allegory, and Rhet/Comp Composing allegorically for publication has proven an effective writing style in fields, such as law and education. For over forty years, prominent critical race theory scholar, Derrick Bell has employed allegory as CRT counterstory. His allegories have been published countless times in law reviews and as two bestsellers. Bell (1987) contends allegory is the most effective style through which to convey his argument because his work seeks "to uncover enduring truths. [and] allegory employs stories that are not true to explore situations that are real enough but, in their many and contradictory dimensions, defy understanding" (p. 6-7). Bell asserts his use of allegory gets at the "truth" about racism and his purpose for writing allegorically coincides with my working definition of allegory. Copeland and Struck cite Jane K. Brown's definition of allegory as "a mode of representation which renders the supernatural visible" (2010, p. 5). Combining the rhetorical understanding of allegory as a trope, Bell's justification for use of allegory in his writing, and Brown's definition, I define allegory as a trope by which to render invisible forms of racism (structural or colorblind), visible. This definition applies to Bell's body of work, but particularly "The Space Traders" (1992), on which the allegory in this article is modeled. In "The Space Traders," Bell weaves his allegory around citations of historical and contemporary American legislation, historical cultural references, and characters that represent existing political and racist ideologies. In my own work, I set my allegory in the present anti-immigrant context that plagues Arizona and the nation at-large, and reference political and media coverage. Modeled after Bell's Gleeson Golightly in "The Space Traders," I have constructed a composite character[1] as a protagonist who is an assimilated conservative person of color and is used (like Golightly) by powerful politicians as a "minority mouthpiece" for their white, right-wing interests. While Bell (1992) allegorically dramatizes the African slave trade, my allegory dramatizes the great event of the U.S. conquest of the southwest. I explore assimilation, especially with regard to the protagonist, and the colonizing effects of an education that conquers the mind, crushes, and essentially obliterates a people's worldview (Villenas & Deyhle, 1999, p. 417). This setting illustrates the imminent threat of cultural erasure posed when a people are denied the right to their history; a real threat in Arizona's anti-ethnic studies climate.
PROX1: A Lineage Tracer for Cortical Interneurons Originating in the Lateral/Caudal Ganglionic Eminence and Preoptic Area

The homeobox-encoding gene Prox1 and its Drosophila homologue prospero are key regulators of cell fate-specification. In the developing rodent cortex a sparse population of cells thought to correspond to late-generated cortical pyramidal neuron precursors expresses PROX1. Using a series of transgenic mice that mark cell lineages in the subcortical telencephalon and, more specifically, different populations of cortical interneurons, we demonstrate that neurons expressing PROX1 do not represent pyramidal neurons or their precursors but are instead subsets of cortical interneurons. These correspond to interneurons originating in the lateral/caudal ganglionic eminence (LGE/CGE) and a small number of preoptic area (POA)-derived neurons. Expression within the cortex can be detected from late embryonic stages onwards when cortical interneurons are still migrating. There is persistent expression in postmitotic cells in the mature brain mainly in the outer cortical layers. PROX1+ve interneurons express neurochemical markers such as calretinin, neuropeptide Y, reelin and vasoactive intestinal peptide, all of which are enriched in LGE/CGE- and some POA-derived cells. Unlike in the cortex, in the striatum PROX1 marks nearly all interneurons regardless of their origin. Weak expression of PROX1 can also be detected in oligodendrocyte lineage cells throughout the forebrain. Our data show that PROX1 can be used as a genetic lineage tracer of nearly all LGE/CGE- and subsets POA-derived cortical interneurons at all developmental and postnatal stages in vivo.
The Role of Dependence in Alcohol Reinforcement: Neurobehavioral Mechanisms

The Role of Dependence in Alcohol Reinforcement: Neurobehavioral Mechanisms by Michal Atzram Adviser: Dr. Michael J. Lewis The motivation to consume alcohol is complex, though physiological dependence has long been implicated in alcohol reinforcement and alcoholism. The research presented here was conducted to examine the role of alcohol dependence on voluntary alcohol consumption and preference, the validity of the Lieber-DeCarli (LD) liquid diet as a procedure to induce dependence, and the effect of alcohol administration on dopamine and endocannabinoids. While the LD diet has been used extensively to induce alcohol toxicity and teratogenic effects, there has not been research that has examined its use in the development of dependence and alcohol reinforcement. This research utilized varying periods of chronic alcohol administration in three cohorts of C57 mice followed by two-bottle choice procedures to examine the role of dependence in alcohol consumption. Chronic oral intake of the alcohol containing LD diet produced moderate symptoms of physical dependence and increased motivation to consume alcohol. In all three cohorts, there were indications of greater alcohol intake or preference in mice that consumed the alcohol diet compared to the control diet. These differences were greatest in the cohort receiving chronic alcohol for 30 days in comparison to 21 and 52 days. Following behavioral data collection, analyses were performed to explore the role of dopamine and endocannabinoid brain systems in dependent mice. While significant differences were not found in the endocannabinoids, AEA or 2AG, there was a trend toward significance for experimental animals
MundoMessage: enabling trustworthy ubiquitous emergency communication

Efficient emergency communication is of high practical importance, but has specific challenges: unpredictable local emergency situations harden the establishment of communication structures, legal requirements dictate the use of end-to-end secure and documentable approaches, while users demand ease-of-use and privacy protection. Dealing with these challenges, the contribution of this paper is four-fold: first, together with emergency practioners we define realistic security requirements and patterns for ubiquitous emergency communication. Second, we devise techniques for privacy-respecting re-identificaton of pseudonymous receivers. Third, we propose a new hybrid encryption technique for expressive policies, which combines ciphertext-policy attribute-based encryption with location-based encryption. Fourth, building on the new techniques, we introduce MundoMessage, our approach to multilaterally end-to-end secure, user-friendly attribute-based messaging for emergency communication. Finally, we analyze our approach.
Enacting knowledge work : the genealogy of knowledge representations in hospitals

Given that knowledge (intensive) work takes place immersed in truly heterogenous networks of knowledge representations (codified, narrative, embedded in routines, inscribed in artefacts), our analysis is geared towards how the transformation of these resources are enacted in the practise of everyday, knowledge work. First, we discuss the work, strategies and mechanisms implied in the rendering of knowledge as credible, trustworthy and relevant. Second, we analyse how sediments of historically superimposed layers of knowledge need to be enacted through selective repetitions, omittance and highlighting to preserve it as `living` knowledge. Third, supplementing the more intellectually oriented aspects of knowledge work, we discuss the organisational complexity of coordination and delegation and the role of externalised knowledge in achieving this. Empirically, we study clinical work in large hospitals, a type of work, we argue, that unduely has been left out of traditional listings of knowledge workers.
Structured Analysis (SA): A Language for Communicating Ideas

Structured analysis (SA) combines blueprint-like graphic language with the nouns and verbs of any other language to provide a hierarchic, top-down, gradual exposition of detail in the form of an SA model. The things and happenings of a subject are expressed in a data decomposition and an activity decomposition, both of which employ the same graphic building block, the SA box, to represent a part of a whole. SA arrows, representing input, output, control, and mechanism, express the relation of each part to the whole. The paper describes the rationalization behind some 40 features of the SA language, and shows how they enable rigorous communication which results frorn disciplined, recursive application of the SA maxim: "Everything worth saying about anything worth saying something about must be expressed in six or fewer pieces. "
Learning spatial relationships between objects

Although a manipulator must interact with objects in terms of their full complexity, it is the qualitative structure of the objects in an environment and the relationships between them which define the composition of that environment, and allow for the construction of efficient plans to enable the completion of various elaborate tasks. In this paper we present an algorithm which redescribes a scene in terms of a layered representation, from labeled point clouds of the objects in the scene. The representation includes a qualitative description of the structure of the objects, as well as the symbolic relationships between them. This is achieved by constructing contact point networks of the objects, which are topological representations of how each object is used in that particular scene, and are based on the regions of contact between objects. We demonstrate the performance of the algorithm, by presenting results from the algorithm tested on a database of stereo images. This shows a high percentage of correctly classified relationships, as well as the discovery of interesting topological features. This output provides a layered representation of a scene, giving symbolic meaning to the inter-object relationships useful for subsequent commonsense reasoning and decision making.
ANTIOXIDANT EFFECT OF ALOE VERA IN EXPERIMENTALLY INDUCED DIABETES MELLITUS

The aim of the present study was to evaluate antidiabetic and antioxidant potential of Aloe vera (AV) in alloxan induced diabetes in albino rabbits. Experimental Diabetes was induced in rabbits with alloxan(80mg/Kg body weight)and animals showing fasting blood glucose levels more than 250mg/dl were considered as diabetics and divided into four groups of six each (n=6). Group I: Normal control rabbits, Group II: Alloxan induced diabetic rabbits, Group III: Diabetic rabbits received AV gel extract (300 mg/Kg) in aqueous solution for 21 days, Group IV: diabetic rabbits given glibenclamide (600ug/kg) in aqueous solution. All the drugs were administered orally (using an intra gastric tube) in a single dose in the morning for 21 days. Blood samples were collected from the marginal vein of pinna of overnight fasted rabbits (Blood sugar, glycosylated hemoglobin (HbA1c), Malondialdehyde (MDA), reduced glutathione (GSH), total thiols (PSH) and Superoxide dismutase (SOD). Oral administration of AV showed potent antihyperglycemic and anti-lipidperoxidative effect in diabetic animals. Simultaneously, the levels of protective antioxidant enzymes (SOD, GSH and PSH) were significantly increased with AV supplementation. The results suggest potent antidiabetic and antioxidant potential of AV in experimental diabetes, and thus Aloe vera can be used as an alternative remedy for treatment of diabetes mellitus and its complications.