Miracle-dz/UniFAR-FTUs huggingface dataset:
UC San Francisco UC San Francisco Previously Published Works Title Robustness and modular design of the Drosophila segment polarity network

Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in relation to a patterning function in Drosophila embryogenesis. We found that while the vast majority of topologies can either not perform the required function or only do so very fragilely, a small fraction of topologies emerges as particularly robust for the function. The topology adopted by Drosophila, that of the segment polarity network, is a top ranking one among all topologies with no direct autoregulation. Furthermore, we found that all robust topologies are modular—each being a combination of three kinds of modules. These modules can be traced back to three sub-functions of the patterning function and their combinations provide a combinatorial variability for the robust topologies. Our results suggest that the requirement of functional robustness drastically reduces the choices of viable topology to a limited set of modular combinations among which nature optimizes its choice under evolutionary and other biological constraints.
Ecological assessment of executive functions in mild cognitive impairment and mild Alzheimer’s disease

Abstract Although memory deficits are typically the earliest and most profound symptoms of Alzheimer’s disease (AD) and mild cognitive impairment (MCI), there is increasing recognition of subtle executive dysfunctions in these patients. The purpose of the present study was to determine the sensitivity of the Behavioral Assessment of the Dysexecutive Syndrome (BADS), and to detect early specific signs of the dysexecutive syndrome in the transition from normal cognition to dementia. The BADS was administered to 50 MCI subjects, 50 mild AD patients, and 50 normal controls. Statistically significant differences were found among the three groups with the AD patients performing most poorly, and the MCI subjects performing between controls and AD patients. The Rule Shift Cards and the Action Program subtests were the most highly discriminative between MCI and controls; the Zoo Map and Modified Six Elements between MCI and AD; and the Action Program, Zoo Map, and Modified Six Elements between AD and controls. These results demonstrate that the BADS is clinically useful in discriminating between normal cognition and progressive neurodegenerative conditions. Furthermore, these data confirm the presence of a dysexecutive syndrome even in mildly impaired elderly subjects. (JINS, 2009, 15, 751–757.)
GLUT1 glucose transporter expression in the diabetic and nondiabetic human eye.

PURPOSE The GLUT1 glucose transporter is expressed in endothelial and epithelial barriers, including the retinal capillary endothelium and the retinal pigment epithelium (RPE) of the eye. The present studies were undertaken to determine whether GLUT1 is expressed in additional cell types within the human eye and whether retinal endothelial GLUT1 is aberrantly expressed in diabetic proliferative retinopathy in humans. METHODS Immunohistochemical staining of sections of human eyes obtained at surgery or autopsy from patients with and without diabetes was performed with polyclonal antisera directed against the human GLUT1 glucose transporter. RESULTS In the course of this study, an unexpected multicellular localization of GLUT1 in different cellular barriers of the human eye was observed. In the nondiabetic eye, specific staining for GLUT1 was seen in the nerve fiber layer, the ganglion and photoreceptor cell bodies, the capillaries and the RPE of the retina, the basal infoldings of the pigmented and nonpigmented layers of the ciliary body, the capillary endothelium and posterior epithelium of the iris, the corneal epithelium and endothelium, and the endothelium lining of the canal of Schlemm. Müller cells, a type of retinal glial cell identified by morphology and by parallel staining for glial fibrillary acidic protein, also stained intensely positive for GLUT1. The pattern of GLUT1 immunoreactivity in the diabetic eyes was virtually identical to that in the nondiabetic specimens, with the notable exception that the neovascular endothelium of proliferative retinopathy did not stain for GLUT1. CONCLUSIONS These studies describe the heretofore unrecognized expression of immunoreactive GLUT1 in the ganglion cell layer of the retina, the endothelium lining the canal of Schlemm, the corneal endothelium, and the basal cells of the corneal epithelium of the human eye. The present study also provides evidence for immunoreactive GLUT1 in glial cells of the central nervous system. Because the expression of GLUT1 is characteristic of tissues that possess a barrier function, the absence of GLUT1 immunoreactivity in the neovascular tissue of proliferative diabetic retinopathy suggests that the loss of selective permeability is associated with an absence of facilitated glucose transport in this disorder.
Get IT Scored Using AutoSAS - An Automated System for Scoring Short Answers

In the era of MOOCs, online exams are taken by millions of candidates, where scoring short answers is an integral part. It becomes intractable to evaluate them by human graders. Thus, a generic automated system capable of grading these responses should be designed and deployed. In this paper, we present a fast, scalable, and accurate approach towards automated Short Answer Scoring (SAS). We propose and explain the design and development of a system for SAS, namely AutoSAS. Given a question along with its graded samples, AutoSAS can learn to grade that prompt successfully. This paper further lays down the features such as lexical diversity, Word2Vec, prompt, and content overlap that plays a pivotal role in building our proposed model. We also present a methodology for indicating the factors responsible for scoring an answer. The trained model is evaluated on an extensively used public dataset, namely Automated Student Assessment Prize Short Answer Scoring (ASAP-SAS). AutoSAS shows state-of-the-art performance and achieves better results by over 8% in some of the question prompts as measured by Quadratic Weighted Kappa (QWK), showing performance comparable to humans.
Deconstructing death in paleodemography.

In 1992 in this Journal (Konigsberg and Frankenberg [1992] Am. J. Phys. Anthropol. 89:235-256), we wrote about the use of maximum likelihood methods for the "estimation of age structure in anthropological demography. " More specifically, we presented a particular method (the "iterated age-length key") from the fisheries literature and suggested that the method could be used in human and primate demography and paleodemography as well. In our paper (section titled "Some Future Directions"), we spelled out two broad areas that we expected to see develop over the ensuing years. First, we felt that the use of explicit likelihood methods would open up interest in basic estimation issues, such as the calculation of standard errors for demographic estimates and the formulation of tests for whether samples differed in their demographic structure. Second, we felt that the time was ripe for hazards analyses that would incorporate the uncertainty in estimation that follows from using age "indicators" rather than known ages. While some of these developments have occurred during the last decade, few have been reported in the American Journal of Physical Anthropology. In this paper we resolve some issues from our 1992 paper, and attempt to redress this deficit in the literature by reviewing some recent developments in paleodemography over the past decade.
Addressing Teaching Practices Regarding Software Quality: Testing and Debugging in the Classroom

Software quality is seen as an integral part of CS education. Two of the key concepts concerning software quality are testing and debugging. Testing is considered important to verify the students' underlying model or algorithm. Debugging is an approach related to computational thinking which is distinct from general programming skills and fosters abilities like logical reasoning and independent problem solving. However, approaches, teaching materials, and studies on how to teach and integrate those concepts effectively into K12 classrooms are lacking. Therefore, both debugging and testing are often neglected in teaching practice, despite them being represented in many (but not all) curricula. In the following, we present a research project with the intention of providing adequate and evaluated strategies for addressing software quality in the classroom and its rationale. For this purpose, the model of Beizer's testing levels has been utilized and didactically transposed, thereby making it applicable to CS education in K12. The resulting categories may provide a basis for teaching and research.
A general probabilistic framework for detecting community structure in networks

Based on Newman's fast algorithm [13], in this paper we develop a general probabilistic framework for detecting community structure in a network. The key idea of our generalization is to characterize a network (graph) by a bivariate distribution that specifies the probability of the two vertices appearing at both ends of a randomly selected path in the graph. With such a bivariate distribution, we give a probabilistic definition of a community and a definition of a modularity index. To detect communities in a network, we propose a class of distribution-based clustering algorithms that have comparable computational complexity to that of Newman's fast algorithm. Our generalization provides the additional freedom to choose a bivariate distribution and a correlation measure. As such, we obtain significant performance improvement over the original Newman fast algorithm in the computer simulations of random graphs with known community structure.
Design and Implementation of a Wireless SensorNetwork for Agricultural Applications

We present the design and implementation of a shortest path tree based, energy efficient data collection wireless sensor network to sense various parameters in an agricultural farm using in-house developed low cost sensors. Nodes follow a synchronized, periodic sleep-wake up schedule to maximize the lifetime of the network. The implemented network consists of 24 sensor nodes in a 3 acre maize farm and its performance is captured by 7 snooper nodes for different data collection intervals: 10 minutes, 1 hour and 3 hours. The almost static nature of wireless links in the farm motivated us to use the same tree for a long data collection period(3 days). The imbalance in energy consumption across nodes is observed to be very small and the network architecture uses easy-to-implement protocols to perform different network activities including handling of node failures. We present the results and analysis of extensive tests conducted on our implementation, which provide significant insights.
AnoA: A Framework for Analyzing Anonymous Communication Protocols

Protecting individuals' privacy in online communications has become a challenge of paramount importance. To this end, anonymous communication (AC) protocols such as the widely used Tor network have been designed to provide anonymity to their participating users. While AC protocols have been the subject of several security and anonymity analyses in the last years, there still does not exist a framework for analyzing complex systems such as Tor and their different anonymity properties in a unified manner. In this work we present AnoA: a generic framework for defining, analyzing, and quantifying anonymity properties for AC protocols. AnoA relies on a novel relaxation of the notion of (computational) differential privacy, and thereby enables a unified quantitative analysis of well-established anonymity properties, such as sender anonymity, sender unlinkability, and relationship anonymity. While an anonymity analysis in AnoA can be conducted in a purely information theoretical manner, we show that the protocol's anonymity properties established in AnoA carry over to secure cryptographic instantiations of the protocol. We exemplify the applicability of AnoA for analyzing real-life systems by conducting a thorough analysis of the anonymity properties provided by the Tor network against passive attackers. Our analysis significantly improves on known anonymity results from the literature.
MIXS: A Mixed Level Simulator for Large Digital System Logic Verification

A mixed level simulator, MIXS, is a logic verification tool which has multiple simulation capabilities. Main MIXS techniques are time wheel and selective trace algorithm for functional level simulation based on 'node' model concept and the linkage function of functional models, described in different detail, with network information. The mixed level simulation for large digital systems can be achieved very efficiently by using the above techniques.
The Discrete Logarithm Problem and Ternary Functional Graphs

Encryption is essential to the security of transactions and communications, but the algorithms on which they rely might not be as secure as we all assume. In this paper, we investigate the randomness of the discrete exponentiation function used frequently in encryption. We show how we used exponential generating functions to gain theoretical data for mapping statistics in ternary functional graphs. Then, we compare mapping statistics of discrete exponentiation functional graphs, for a range of primes, with mapping statistics of the respective ternary functional graphs.
Analysis of Dimensionality Reduction in Intrusion Detection

Intrusion detection system is an important technology in the market sector as well as in the area of research. Intrusion detection is considered a useful security tool that assists in preventing attacker’s access to networks or systems. The determination of genuineness of packets is a key issue and various approaches of classification have been presented. The complexity of a classifier is greatly reduced if the numbers of attributes in a data set are reduced. Analysis of dimensionality reduction and it is impacting thereof is the objective of our study. An experimental study is carried out to build up a classifier on a standard dataset of network traffic data that includes normal packets and abnormal packets. A rough set theory and information gain approaches are employed to reduce dimensionality of network traffic data set. The features obtained by the rough set theory and information gain are used to train and test the J48 classifier. A comparative analysis of the results obtained a reduced attribute set and original attributes are presented. The results shows that the performance of J48 classifier with the reduced attributes (rough set and information gain) is better, which is at the cost of time KeywordIntrusion Detection System, Rough Set Theory, Information Gain, J48 Classifier
Usage of the memory of mobile phones by illiterate people

A large number of illiterate people all around the world is using mobile phones for serving different purposes of their day-to-day life. Since most of the operations in a typical mobile phone require a minimum level of literacy, it has become interesting to know how these illiterate people manage to operate these phones. Understanding this usage pattern would help us design an effective user interface for these people. At the same time, it would help us understand the human learning behavior while interacting with a technical artifact. In this short communication, we present the initial findings of our ongoing project on investigating many of the questions related to this issue. Here we try to get an idea of how illiterate people use the memory of mobile phones. We present here our initial findings from our investigation upon 15 illiterate mobile phone users in Bangladesh. This study revealed a number of interesting facts about how illiterate people "unbox" mobile technology.
Enhanced distributed explicit rate allocation for ABR services in ATM networks

Rate allocation for available bit-rate (ABR) services in ATM networks has received a considerable amount of attention, but important issues such as bandwidth fairness, MCR rate guarantees, and queue control still require further investigation. In light of these concerns, an enhanced rate allocation algorithm is proposed for congestion management using explicit rate feedback control. The algorithm uses fast, exact rate computations and is capable of achieving a variety of MCR-related fairness criteria. The scheme handles transient effects and can function in heterogeneous networks carrying higher priority real-time traffic. Simulation results for a wide range of network scenarios demonstrate that the algorithm effectively controls queue buildups and achieves good fairness. Performance scalability to large networks under challenging conditions is also shown for a given control parameter set.
Effects of intraperitoneally administered ubiquinone on the level of total lipid and fatty acids in rat liver

The purpose of the present study was to evaluate the effect of ubiquinone (coenzyme Q‐10) on total lipid and fatty acid composition of liver tissues in rats. Twenty male wistar rats were randomly divided into two groups. The first group was used as a control. The second group received ubiquinone (8 mg/every other day) intraperitoneally. This administration was done for a period of 38 days. Body weight increases in animals fed diets for 38 days were on average 35 g in control group (C), and only 11 g in the ubiquinone group. Total lipid content of liver tissues in the ubiquinone group (UB) decreased significantly (p < 0.0001) compared to the control group (C). The ratio of 22:6 and total ω3 fatty acid in the UB increased (p < 0.01) compared to C. While the level of oleic acid (18:1), palmitoleic acid (16:1) and total monounsaturated fatty acid (MUFA) in UB significantly decreased (p < 0.01, p < 0.001, p < 0.001, respectively), the level of stearic acid (18:0) in liver tissue increased (p < 0.05) in the same group when compared to C. Stearoyl‐CoA desaturase (SCD) is the rate‐limiting enzyme catalyzing the synthesis of monounsaturated fatty acid mainly oleate (18:1). We speculate that ubiquinone inhibits SCD activity. SCD is an important metabolic control point in body weight regulation. Our results indicate that ubiquinone supplementation may have an inhibitory effect on obesity and it seems that the level of 22:6 in liver increased due to ubiquinone. Copyright © 2005 John Wiley & Sons, Ltd.
Enabling Fog Computing using Self-Organizing Compute Nodes

The emergence of fog computing has led to the design of multi-layer fog computing models which are organized hierarchically. These models commonly dictate the hierarchical structure to all the participating compute nodes. However, organizing the compute nodes by adding customized connections that do not abide by the hierarchical approach, may result in improved performance due to the network’s properties i.e., latency or bandwidth between the nodes. For this reason, in this paper we propose an alternative to the hierarchical approach, which is the self-organizing compute nodes. These nodes organize themselves into a flat model which leverages on the network’s properties to provide improved performance. The results of the evaluation show that this approach reduces bandwidth utilization (~30%) by using optimized messaging instead of direct messaging. Furthermore, we show that following a flat model, enables the design of mechanisms for fault tolerance which has been mostly neglected in existing hierarchical models.
Generative Agent-Based Modeling and Empirical Validation of the Size Distribution of Hospitals

The hospital system is a complex service system in which patients and hospitals interact and make their decisions based on bounded rationality and information. In this paper, we develop a generative agent-based model to simulate the behavior of a hospital service system. Our model combines agent-based simulation and queueing models to mimic the hospital service processes. Our goal is to simulate and understand the growth and size distribution of hospitals. This simulation model includes agents for supply elements (i.e., hospitals with different resources and expansion strategies) and demand elements (i.e., patients with different preferences for their hospital selections) in a hospital service system. Three important questions are investigated: 1) what is the emergent size distribution of hospitals? 2) what key factors influence the size distribution? and 3) how sensitive is the size distribution to these key factors? Simulation results show that the size distribution is neither power law nor lognormal. Rather, the distribution is leptokurtic, and more skewed than normal but less skewed than lognormal. This result contradicts those in extant literature on the size distributions of human and natural systems, including cities, firms, power-grids, and citation network. We conduct a set of experiments to identify the generative mechanisms for the hospital size distribution and to test the robustness of the results. The model was validated empirically by using a U.S. hospital size dataset.
Puriﬁcation and Biochemical Characterization of the F 1 F o -ATP Synthase from Thermoalkaliphilic Bacillus sp. Strain TA2.A1

We describe here puriﬁcation and biochemical characterization of the F 1 F o -ATP synthase from the ther- moalkaliphilic organism Bacillus sp. strain TA2.A1. The puriﬁed enzyme produced the typical subunit pattern of an F 1 F o -ATP synthase on a sodium dodecyl sulfate-polyacrylamide gel, with F 1 subunits (cid:1) , (cid:2) , (cid:3) , (cid:4) , and (cid:5) and F o subunits a, b, and c. The subunits were identiﬁed by N-terminal protein sequencing and mass spectroscopy. A notable feature of the ATP synthase from strain TA2.A1 was its speciﬁc blockage in ATP hydrolysis activity. ATPase activity was unmasked by using the detergent lauryldimethylamine oxide (LDAO), which activated ATP hydrolysis >15-fold. This activation was the same for either the F 1 F o holoenzyme or the isolated F 1 moiety, and therefore latent ATP hydrolysis activity is an intrinsic property of F 1 . ATP-dependent proton translocation was determined at 45°C by quenching of 9-amino-6-chloro-2-methoxyacridine (ACMA) in proteoliposomes. The 1.5-ml reaction mixture contained 5 mM potassium phosphate buffer (pH 7.5), 5 mM MgCl 2 , 1 (cid:11) M ACMA, and 50 (cid:11) l of reconstituted proteoliposomes. After the ﬂuorescence signal had stabilized (100%), the reaction was initiated by addition of neutralized ATP (1.7 mM). Fluorescence was measured with an excitation wavelength of 410 nm and an emission wavelength of 480 nm (slit width, 10 nm). Protein concentrations were determined by using a bicinchoninic acid protein assay kit from Pierce, with bovine serum albumin as the standard.
A relaxation system adapting to user's condition-identification of relationship between massage intensity and heart rate variability

The purpose of the study is to build a relaxation system which can control a user's body condition, changing the operation mode and intensity of the massage seat according to the user's current condition. Heart rate is an index of human conditions which can be easily measured, and it has chaotic dynamics. We show relations between the intensity of the massage operation and two indices which express chaotic properties such as correlation dimension and Lyapunov exponent. These data are indispensable for building a feedback loop between the relaxation system and a user.