Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of a HEPN-MNT family type II toxin–antitoxin in Shewanella oneidensis

Toxin–antitoxin (TA) systems are prevalent in bacteria and archaea. However, related studies in the ecologically and bioelectrochemically important strain Shewanella oneidensis are limited. Here, we show that SO_3166, a member of the higher eukaryotes and prokaryotes nucleotide‐binding (HEPN) superfamily, strongly inhibited cell growth in S. oneidensis and Escherichia coli. SO_3165, a putative minimal nucleotidyltransferase (MNT), neutralized the toxicity of SO_3166. Gene SO_3165 lies upstream of SO_3166, and they are co‐transcribed. Moreover, the SO_3165 and SO_3166 proteins interact with each other directly in vivo, and antitoxin SO_3165 bound to the promoter of the TA operon and repressed its activity. Finally, the conserved Rx4‐6H domain in HEPN family was identified in SO_3166. Mutating either the R or H abolished SO_3166 toxicity, confirming that Rx4‐6H domain is critical for SO_3166 activity. Taken together, these results demonstrate that SO_3166 and SO_3165 in S. oneidensis form a typical type II TA pair. This TA pair plays a critical role in regulating bacterial functions because its disruption led to impaired cell motility in S. oneidensis. Thus, we demonstrated for the first time that HEPN‐MNT can function as a TA system, thereby providing important insights into the understanding of the function and regulation of HEPNs and MNTs in prokaryotes.
Fungal Community Ecology: A Hybrid Beast with a Molecular Master

ABSTRACT Fungi play a major role in the function and dynamics of terrestrial ecosystems, directly influencing the structure of plant, animal, and bacterial communities through interactions that span the mutualism-parasitism continuum. Only with the advent of deoxyribonucleic acid (DNA)-based molecular techniques, however, have researchers been able to look closely at the ecological forces that structure fungal communities. The recent explosion of molecular studies has greatly advanced our understanding of fungal diversity, niche partitioning, competition, spatial variability, and functional traits. Because of fungi's unique biology, fungal ecology is a hybrid beast that straddles the macroscopic and microscopic worlds. While the dual nature of this field presents many challenges, it also makes fungi excellent organisms for testing extant ecological theories, and it provides opportunities for new and unanticipated research. Many questions remain unanswered, but continuing advances in molecular techniques and field and lab experimentation indicate that fungal ecology has a bright future.
Simultaneous radio and X-ray observations of Galactic center low-mass X-ray binaries

We have performed simultaneous X-ray and radio observations of 13 Galactic Centre low-mass X-ray binaries in 1998 April using the Wide Field Cameras on board BeppoSAX and the Australia Telescope Compact Array, the latter simultaneously at 4.8 and 8.64 GHz. We detect two Z sources, GX 17+2 and GX 5−1, and the unusual ‘hybrid’ source GX 13+1. Upper limits, which are significantly deeper than previous non-detections, are placed on the radio emission from two more Z sources and seven atoll sources. Hardness–intensity diagrams constructed from the Wide Field Camera data reveal GX 17+2 and GX 5−1 to have been on the lower part of the horizontal branch and/or the upper part of the normal branch at the time of the observations, and the two non-detected Z sources, GX 340+0 and GX 349+2, to have been on the lower part of the normal branch. This is consistent with the previous empirically determined relation between radio and X-ray emission from Z sources, in which radio emission is strongest on the horizontal branch and weakest on the flaring branch. For the first time we have information on the X-ray state of atoll sources, which are clearly radio-quiet relative to the Z sources, during periods of observed radio upper limits. We place limits on the linear polarization from the three detected sources, and use accurate radio astrometry of GX 17+2 to confirm that it is probably not associated with the optical star NP Ser. Additionally we place strong upper limits on the radio emission from the X-ray binary 2S 0921−630, disagreeing with suggestions that it is a Z-source viewed edge-on.
Preventing Germinal Matrix Layer Rupture and Intraventricular Hemorrhage

The etiology of intraventricular hemorrhage (IVH) in extremely low birth weight preterm infants is multifactorial with circulatory instability and hemostasis being preeminent. This study sought to determine if the germinal matrix layer remained intact when platelets were above 200 × 109/L, a near normal level, and fell below that when IVH occurred. This was a retrospective study of platelets and head ultrasounds (HUS) in infants 23–28 weeks gestation. Analyses were descriptive, one way analysis of variance, Pearson Chi-square tests, and t-tests. Platelet counts and HUS were linked in 114 infants during the first 3 days when 90% of IVHs occur. Mean platelet levels were >200 × 109/L in 68% of infant 23–24 weeks gestation and 78% of those 25–26 weeks when there were no IVHs. These findings, if confirmed, suggest that improving hemostasis in high risk preterm infants by keeping platelet levels >200 × 109/L may maintain the integrity of the germinal matrix layer and prevent IVHs.
Evaluation: An Integrated Framework for Understanding, Guiding, and Improving Policies and Programs

A Brief Overview of the Evaluation Enterprise A Framework for Describing and Planning Evaluations Social Betterment Realist Foundations for Sensemaking Through Evaluation Aligning Betterment, Purposes, Modes of Inquiry, and Methods for Sensemaking in a Realist World Evaluation Planning for Sensemaking in a Real(ist) World Methods for Description Classification Methods for Causal Analysis Values Inquiry Evaluation as Assisted Sensemaking: A Reprise
Domain and Keyword Specific Data Extraction from Invisible Web Databases

Web information access today primarily relies on search engines. Current search engines cannot make index to the pages which are generated automatically by the back -- end databases called invisible web or deep web. The information is hidden behind HTML forms and is only available in response to user's request. In this paper a system based on domain and keyword specific information extraction is described.
Multijav: a Distributed Shared Memory System Based on Multiple Java Virtual Machines

Current distributed shared memory systems suuer from portability problems which hinder popularity. We present a distributed shared memory system as a distributed implementation of the Java Virtual Machine. The proposed system is unique in that it provides a user-friendly, exible programming model based on pure Java. It is an object-based memory system which maintains the synchronization scope as the whole address space, like page-based systems. MultiJav demonstrates that it is possible to design an eecient, portable, distributed shared memory system for running parallel and distributed applications written in a standard language.
Political Economy of Financial Integration in Europe: The Battle of the Systems

Few aspects of the great European integration project have been as difficult and fraught with political conflict as the creation of a single financial market and monetary union. It is clear, however, that monetary union and financial integration are now on the front-burner in Europe, and will remain so until at least the year 2000. This timely volume traces the political, financial, and economic steps toward financial union in Europe, focusing on the political economy of the process—notably the dynamics of a Europe of sovereign states. It is the first integrated view of the issue, combining political, economic, and financial perspectives. Authoritative, comprehensive, and accessible, the volume is essential reading for students, researchers, policy makers, journalists, and anyone who needs to know about financial integration in Europe.
Structure Identification and Anti-Cancer Pharmacological Prediction of Triterpenes from Ganoderma lucidum

Ganoderma triterpenes (GTs) are the major secondary metabolites of Ganoderma lucidum, which is a popularly used traditional Chinese medicine for complementary cancer therapy. In the present study, systematic isolation, and in silico pharmacological prediction are implemented to discover potential anti-cancer active GTs from G. lucidum. Nineteen GTs, three steroids, one cerebroside, and one thymidine were isolated from G. lucidum. Six GTs were first isolated from the fruiting bodies of G. lucidum, including 3β,7β,15β-trihydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid methyl ester (1), 3β,7β,15β-trihydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid (2), 3β,7β,15α,28-tetrahydroxy-11,23-dioxo-lanost-8,16-dien-26-oic acid (3), ganotropic acid (4), 26-nor-11,23-dioxo-5α-lanost-8-en-3β,7β,15α,25-tetrol (5) and (3β,7α)-dihydroxy-lanosta-8,24-dien- 11-one (6). (4E,8E)-N-d-2′-hydroxypalmitoyl-l-O-β-d-glucopyranosyl-9-methyl-4,8-spingodienine (7), and stigmasta-7,22-dien-3β,5α,6α-triol (8) were first reported from the genus Ganodema. By using reverse pharmacophoric profiling of the six GTs, thirty potential anti-cancer therapeutic targets were identified and utilized to construct their ingredient-target interaction network. Then nineteen high frequency targets of GTs were selected from thirty potential targets to construct a protein interaction network (PIN). In order to cluster the pharmacological activity of GTs, twelve function modules were identified by molecular complex detection (MCODE) and gene ontology (GO) enrichment analysis. The results indicated that anti-cancer effect of GTs might be related to histone acetylation and interphase of mitotic cell cycle by regulating general control non-derepressible 5 (GCN5) and cyclin-dependent kinase-2 (CDK2), respectively. This research mode of extraction, isolation, pharmacological prediction, and PIN analysis might be beneficial to rapidly predict and discover pharmacological activities of novel compounds.
Walk-Unlock: Zero-Interaction Authentication Protected with Multi-Modal Gait Biometrics

Zero-interaction authentication (ZIA) refers to a form of user-transparent login mechanism using which a terminal (e.g., a desktop computer) can be unlocked by the mere proximity of an authentication token (e.g., a smartphone). Given its appealing usability, ZIA has already been deployed in many real-world applications. However, ZIA contains one major security weakness - unauthorized physical access to the token, e.g., during lunch-time or upon theft, allows the attacker to have unfettered access to the terminal. In this paper, we address this gaping vulnerability with ZIA systems by (un)locking the authentication token with the user's walking pattern as she approaches the terminal to access it. Since a user's walking or gait pattern is believed to be unique, only that user (no imposter) would be able to unlock the token to gain access to the terminal in a ZIA session. While walking-based biometrics schemes have been studied in prior literature for other application settings, our main novelty lies in the careful use of: (1) multiple sensors available on the current breed of devices (e.g., accelerometer, gyroscope and magnetometer), and (2) multiple devices carried by the user (in particular, an "in-pocket" smartphone and a "wrist-worn" smartwatch), that all capture unique facets of user's walking pattern. Our contributions are three-fold. First, we introduce, design and implement WUZIA ("Walk-Unlock ZIA"), a multi-modal walking biometrics approach tailored to enhance the security of ZIA systems (still with zero interaction). Second, we demonstrate that WUZIA offers a high degree of detection accuracy, based on multi-sensor and multi-device fusion. Third, we show that WUZIA can resist active attacks that attempt to mimic a user's walking pattern, especially when multiple devices are used.
An All-pay Auction Approach to Reallocation 4 the Auction Metaphor

The auction has been advocated as a valuable metaphor in the design of decentralized mechanisms for various problems. The walrasian auction was proposed as a suitable mechanism for resource reallocation in distributed planning. Economic theory ooers ample opportunities to develop distributed walrasian mechanisms for reallocation in \mar-kets" with many agents and innnitely divisible resources. However , in cases where resources are essentially indivisible and markets relatively small, the perspective is considerably worse. In this paper, we address such reallocation problems. After pointing out the deeciencies of walrasian-like mechanisms in the chosen problem context, we propose an alternative mechanism based on the metaphor of an all-pay auction. The key feature of this Informed Gambling mechanism is that agents are required to commit themselves to exchange proposals in the face of uncertainty about the market situation. We present an example that illustrates how the mechanism renders acceptable reallocations where walrasian mechanisms fail. 1 TOOL REALLOCATION We investigate auction-based mechanisms for a class of problems that can be described as \tool reallocation problems". A tool is a resource that is essentially indivisible. Typical examples of indivisible resource types are computer workstationss5], oil tankers, and low-capacity communication channels. The essential characteristic here is that agents generally require only a small number of resources of the types they desire. Tool reallocation problems constitute a subclass of resource reallocation problems, for which mechanism design is particularly diicult, because the standard assumptions of economic equilibrium theory (viz., innnite resource divisibility and negligible innuence of individual agents) are violated. At the other hand, many real-world problems in the area of distributed planning are in this category. These problems therefore deserve to be attended to within DAI. In this paper, we do so by assessing the performance of our Informed Gambling (IG) mechanism in comparison with an established micro-economic equilibrium notion, the walrasian equilibrium. We measure global performance in a relative-utilitarian fashion 4], that is, community welfare is deened to be the mean of the agents' relative utilities. These relative utilities equal the fraction of the utility an agent would attain if it possessed all the tools in the community. 2 TOOL TYPES Reallocation problems where agents need multiple tools of different types to accomplish a given task are the primary target problem for our Informed Gambling (IG) mechanism. For an account on this general reallocation problem, we refer to 3]. In this paper, we focus on a simpliied …
Estimation of the absolute position of mobile systems by an optoelectronic processor

A method that determines the absolute position of a mobile system with a hybrid optoelectronic processor has been developed. Position estimates are based on an analysis of circular landmarks that are detected by a TV camera attached to the mobile system. The difference between the known shape of the landmark and its image provides the information needed to determine the absolute position of the mobile system. For robust operation, the parameters of the landmark image are extracted at high speeds using an optical processor that performs an optical Hough transform. The coordinates of the mobile system are computed from these parameters in a digital coprocessor using fast algorithms. Different sources of position estimation errors have also been analyzed, and consequent algorithms for improving the navigation performance of the mobile system have been developed and evaluated by both computer simulation and experiments. >
USE OF DISTILLERS GRAINS AND CO-PRODUCTS IN RUMINANT DIETS

The fermentation of grains to produce alcohol yields whole spent stillage from which wet distillers grains (WDG) and thin stillage are obtained by screening and pressing or centrifugation. Usually, WDG are dried to yield dried distillers grains (DDG), or dried distillers grains with solubles (DDGS) if solubles in the thin stillage are added back to the grains at drying. The solubles in the thin stillage may also be partially or totally dried to make condensed distillers solubles (CDS) or dried distillers solubles (DDS), respectively. Of these co-products, DDG and DDGS are the most commonly used, probably because of ease of handling, storage, and shipping. However, the high cost of drying has led people to investigate the possibility of feeding wet distillers byproducts to ruminants.
Fluid Flow-Induced Mesenchymal Stem Cell Migration: Role of FAK and ROCK Mechanosensors

The study of mesenchymal stem cell (MSC) migration under mechanical stimulation conditions with investigation of the underlying molecular mechanism could lead to a better understanding and outcomes in stem cell-based regenerative medicine. MSCs having multipotent regenerative capability exist in niches in the bone marrow, muscle, vasculature, and in other tissues throughout the body, and their migration through tissues and vasculature for the repair of damaged tissue is a key process of cell and tissue homeostasis, remodeling, and regeneration. While cell migration in response to cytokines and other chemo-attractants is relatively well understood, little is revealed in regard to the effect of mechanical cues. In this study, we investigated the migration of C3H10T1/2 murine MSCs in response to fluid flow-induced shear stress in vitro. MSCs were subjected to steady flows with physiologically relevant shear stresses of 2, 15, and 25 dyne/cm 2 and compared with static control. Fluid shear induced cell migration following the flow direction, which effect was greater at higher shear stresses. To test the molecular mechanism, MSCs with stable knockdown of focal adhesion kinase (FAK) and RhoA kinase (ROCK), each constituting the key component of focal adhesion signaling and cytoskeletal tension signaling respectively, were fluid-sheared. FAK-silenced MSCs showed decreases in fluid shear-induced migration, for example, decreases in migration length, confinement ratio, and motility coefficient. Interestingly, in the presence of ROCK silencing, MSCs were more responsive to fluid shear, showing increases in such migration parameters. Our data may suggest a different role of focal adhesion and cytoskeletal tension in mechanical induction of MSC migration. iii Acknowledgements Thank you to Dr. Jung Yul Lim for the opportunity to conduct this research and for providing guidance and support. From you I have learned much about peer reviewed research and how to participate in the scientific community. Working in your lab has been the most enriching experience. my thesis committee. I appreciate the time and effort you have spent in reviewing this thesis and providing valuable feedback. To the student the education experience may at times seem to be a solitary endeavor but I recognize that this journey is not possible without enormous support and encouragement. I would like to thank my parents, family, and mentors for your investment in my life and education. Thank you to the educators who inspired me to love learning and who insisted I take the difficult classes. I am most grateful to the Susan Thompson Buffett …
Development and application of a DNA microarray-based yeast two-hybrid system

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms.
Lyman-break galaxies at z ~ 5 – I. First significant stellar mass assembly in galaxies that are not simply z ~ 3 LBGs at higher redshift

We determine the ensemble properties of z ∼ 5 Lyman-break galaxies (LBGs) selected as V-band dropouts to i AB < 26.3 in the Chandra Deep Field-South using their rest-frame UV-to-visible spectral energy distributions. By matching the selection and performing the same analysis that has been used for z ∼ 3 samples, we show clear differences in the ensemble properties of two samples of LBGs which are separated by 1 Gyr in look-back time. We find that z ∼ 5 LBGs are typically much younger (<100Myr) and have lower stellar masses (∼10 9 M ⊙ ) than their z ∼ 3 counterparts (which are typically ∼ few x 10 10 M ⊙ and ∼320 Myr old). The difference in mass is significant even when considering the presence of an older, underlying population in both samples. Such young and moderately massive systems dominate the luminous z ∼ 5 LBG population (≥70 per cent), whereas they comprise ≤30 per cent of LBG samples at z ∼ 3. This result, which we demonstrate is robust under all reasonable modelling assumptions, shows a clear change in the properties of the luminous LBGs between z ∼ 5 and z ∼ 3. These young and moderately massive z ∼ 5 LBGs appear to be experiencing their first (few) generations of large-scale star formation and are accumulating their first significant stellar mass. Their dominance in luminous LBG samples suggests that z ∼ 5 witnesses a period of wide-spread, recent galaxy formation. As such, z ∼ 5 LBGs are the likely progenitors of the spheroidal components of present-day massive galaxies. This is supported by their high stellar mass surface densities, and is consistent with their core phase-space densities, as well as the ages of stars in the bulge of our Galaxy and other massive systems. With implied formation redshifts of z ∼ 6-7, these luminous z ∼ 5 LBGs could have only contributed to the UV photon budget at the end of reionization. However, their high star formation rates per unit area suggest these systems host outflows or winds that enrich the intragalactic and intergalactic media with metals, as has been established for z ∼ 3 LBGs. Their estimated young ages are consistent with inefficient metal-mixing on galaxy-wide scales. Therefore these galaxies may contain a significant fraction of Population III stars as proposed for z ∼ 3 LBGs by Jiminez & Haimann.