Miracle-dz/UniFAR-FTUs huggingface dataset:
The ARiBo tag: a reliable tool for affinity purification of RNAs under native conditions

Although RNA-based biological processes and therapeutics have gained increasing interest, purification of in vitro transcribed RNA generally relies on gel-based methods that are time-consuming, tedious and denature the RNA. Here, we present a reliable procedure for affinity batch purification of RNA, which exploits the high-affinity interaction between the boxB RNA and the N-peptide from bacteriophage λ. The RNA of interest is synthesized with an ARiBo tag, which consists of an activatable ribozyme (the glmS ribozyme) and the λBoxB RNA. This ARiBo-fusion RNA is initially captured on Glutathione-Sepharose resin via a GST/λN-fusion protein, and the RNA of interest is subsequently eluted by ribozyme self-cleavage using glucosamine-6-phosphate. Several GST/λN-fusion proteins and ARiBo tags were tested to optimize RNA yield and purity. The optimized procedure enables one to quickly obtain (3 h) highly pure RNA (>99%) under native conditions and with yields comparable to standard denaturing gel-based protocols. It is widely applicable to a variety of RNAs, including riboswitches, ribozymes and microRNAs. In addition, it can be easily adapted to a wide range of applications that require RNA purification and/or immobilization, including isolation of RNA-associated complexes from living cells and high-throughput applications.
Joint Inertial Sensor Orientation Drift Reduction for Highly Dynamic Movements

Inertial sensor drift is usually corrected on a single-sensor unit level. When multiple sensor units are used, mutual information from different units can be exploited for drift correction. This study introduces a method for a drift-reduced estimation of three dimensional (3-D) segment orientations and joint angles for motion capture of highly dynamic movements as present in many sports. 3-D acceleration measured on two adjacent segments is mapped to the connecting joint. Drift is estimated and reduced based on the mapped accelerations’ vector orientation differences in the global frame. Algorithm validity is assessed on the example of alpine ski racing. Shank, thigh, and trunk inclination as well as knee and hip flexion were compared to a multicamera-based reference system. For specific leg angles and trunk segment inclination mean accuracy and precision were below 3.9° and 6.0°, respectively. The errors were similar to errors reported in other studies for lower dynamic movements. Drift increased axis misalignment and mainly affected joint and segment angles of highly flexed joints such as the knee or hip during a ski turn.
Research Statement

I am interested in building secure systems. Leakage of confidential data plagues many computing systems today and my Ph.D. work has focused on protecting data confidentiality against a powerful and common class of attackers: attackers with full access to data stored on servers. Such attackers occur in numerous settings. First, due to the recent shift towards cloud computing, an increasing number of companies and users host data at external cloud providers, so their sensitive data becomes readily available to cloud administrators. Indeed, recent surveys show that security remains one of the top concerns for customers of cloud computing and an impediment to adopting clouds for potential customers. Second, hackers notoriously break into systems and gain access to a part or to all of the data stored on a server. Third, we know from recent news that the government has been accessing a lot of private data even without a subpoena. Finally, even inside a local data center, insider attackers are responsible for many data leaks. Most existing systems today do not protect confidentiality against these attackers. For systems that need to compute on sensitive data, the common approach has been to assume that a part of the server is trusted, either uncompromisable or inaccessible to the adversary, such as the database or the operating system; then, they prevent attacks to the application by using techniques such as static or dynamic analysis, language-based enforcement, or information flow control. Unfortunately, this assumption does not hold for the attackers we described, because they can have access to all server components and can simply read the data from the trusted component (e.g, from the database or main memory). My work provides confidentiality guarantees against this powerful and relevant class of attackers.
An asynchronous finite state machine controller for integrated buck-boost power converters in wideband signal-tracking applications

In this paper, a simple, fully digital, asynchronous finite state machine controller for buck-boost power converters is introduced and simulated. With the addition of only two analog voltage comparators and six power MOS switches, the circuit can generate an output voltage that is able to track a dynamic reference with a 1 MHz bandwidth with good efficiency using a 0.35 mum CMOS process. The controller also provides adiabatic charging and discharging of capacitive loads.
Hierarchical functional modularity in the resting‐state human brain

Functional magnetic resonance imaging (fMRI) studies have shown that anatomically distinct brain regions are functionally connected during the resting state. Basic topological properties in the brain functional connectivity (BFC) map have highlighted the BFC's small‐world topology. Modularity, a more advanced topological property, has been hypothesized to be evolutionary advantageous, contributing to adaptive aspects of anatomical and functional brain connectivity. However, current definitions of modularity for complex networks focus on nonoverlapping clusters, and are seriously limited by disregarding inclusive relationships. Therefore, BFC's modularity has been mainly qualitatively investigated. Here, we introduce a new definition of modularity, based on a recently improved clustering measurement, which overcomes limitations of previous definitions, and apply it to the study of BFC in resting state fMRI of 53 healthy subjects. Results show hierarchical functional modularity in the brain. Hum Brain Mapp, 2009. © 2008 Wiley‐Liss, Inc.
GABA‐Related phenomena, models of nervous system function, and seizures

Models of nervous system function are presented that place particular emphasis on the roles in nervous system function of inhibitory neurons that liberate γ‐aminobutyric acid (GABA) as neurotransmitter. The nervous system is considered to be highly restrained, with inhibitory neurons acting like reins that serve to keep the neuronal “horses” from running away. In behavioral sequences, whether innate or learned, preprogrammed circuits are released to function at varying rates and in various combinations. This release is accomplished largely by the disinhibition of pacemaker neurons whose activities are under the control of tonically active inhibitory command neurons, many of which may use GABA as a transmitter. In addition to their restraining function, local circuit GABA ergic neurons participate in feed‐forward, feedback, surround, and presynaptic inhibition and inpresynaptic facilitation.
Children's Reasoning and the Mind

K.J. Riggs, P. Mitchell, Making Judgements About Mental States: Processes and Inferences. R.P. Hobson, The Grounding of Symbols: A Social Developmental Account. R.W. Mitchell, A Proposal for the Development of Mental Vocabulary, with Special Reference to Pretence and False Belief. P.L. Harris, H.L. Leevers, Reasoning from False Premises. K.J. Riggs, D.M. Peterson, Counterfactual Thinking in Pre-School Children: Mental State and Causal Inferences. E.J. Robinson, S. Beck, What is Difficult About Counterfactual Reasoning? E. Amsel, J. D. Smalley, Beyond Really and Truly: Children's Counterfactual Thinking About Pretend and Possible Worlds. D. Frye, Theory of Mind, Domain Specificity and Reasoning. P.D. Zelazo, Self-reflection and the Development of Consciously Controlled Processing. J.G. de Villiers, P.A. de Villiers, Linguistic Determinism and the Understanding of False Beliefs. T.P. German, A.M. Leslie, Attending to and Learning About Mental States. H. Wimmer, A. Gschaider, Children's Understanding of Belief: Why is it Important to Understand What Happened? W.V. Fabricius, A. Imbens-Bailey, False Beliefs About False Beliefs. P. Mitchell, H. Kikuno, Belief as Construction: Inference and Processing Bias. D. Kuhn, Theory of Mind, Metacognition and Reasoning: A Lifelong Perspective. E. Subbotsky, Causal Reasoning and Behaviour in Children and Adults in a Technologically Advanced Society: Are We Still Prepared to Believe in Magic and Animism? N.H. Freeman, Communication and Representation: Why Mentalistic Reasoning is a Lifelong Endeavour. J. Perner, Commentary.
Exploiting visual information for NAM recognition

Non-audible murmur (NAM) is an unvoiced speech received through body tissue using special acoustic sensors (i.e., NAM microphones) attached behind the talkers ear. Although NAM has different frequency characteristics compared to normal speech, it is possible to perform automatic speech recognition (ASR) using conventional methods. In using a NAM microphone, body transmission and the loss of lip radiation act as a low-pass filter; as a result, higher frequency components are attenuated in NAM signal. A decrease in NAM recognition performance is attributed to spectral reduction. To address the problem of loss of lip radiation, visual information extracted from the talker's facial movements is fused with NAM speech. Experimental results revealed a relative improvement of 39% when fused NAM speech and facial information were used as compared to using only NAM speech. Results also showed that improvements in the recognition rate depend on the place of articulation.
Hypnotic susceptibility revisited.

Abstract The concept and measurement of hypnotic susceptibility are re-examined in their relation to hypnotizability, hypnotic depth and suggestibility. The Stanford Scales and similar instruments are found to have failed to take into account essential features defining traditional hypnosis and suggestibility and to have created confusion in the scientific inquiry into hypnotism. Other available measures have not been particularly successful, but some bear further attention. Recent claims that hypnotizability can be trained have failed to distinguish between hypnotizability proper and accessory processes, leaving some question about what is actually being trained. Possible future directions of work on susceptibility are considered. Attempts to distinquish between “clinical” and “laboratory” hypnotizability are examined and found to have been premature and loosely based on facts.
Structuring of the Open Innovation Field

Open Innovation is considered a ‘hot’ concept in research as well as in industry practice. At the same time, at least two critiques have been raised against the notion: that it is based on old theories and that the term is vague and nonprecise. Based on a bibliometrical analysis, this conceptual paper structures the emerging field of open innovation into two interrelated perspectives; the firm perspective and the ecosystem perspective. By that, it introduces an integrated framework for open innovation and shows how various concepts under the umbrella of open innovation are related to each other. A discussion is presented on how the two perspectives relate to earlier innovation management literature and how they are linked by ‘new’ interaction approaches, such as toolkits, innovation contests, crowdsourcing, and innovation intermediaries.
On the structure of the Sun and α Centauri A and B in the light of seismic and non-seismic constraints

The small separation (δ ν01 , δν 02 and δν 13 ) between oscillations with low degree l is dependent primarily on the sound speed profile within the stellar core, where nuclear evolution occurs. The detection of such oscillations in a star offers a very good opportunity to determine the stage of its nuclear evolution, and hence its age. In this context, we investigate the Sun and a Cen A and B. For a Cen A and B, each of the small separations δν 01 , δν 02 and δν 13 gives a different age. Therefore, in our fitting process, we also employ the second difference, defined as ν n,2 - 2ν n,1 + ν n,0 , which is 2δν 01 -δν 02 . In addition to this, we use the frequency ratio (ν n,0 /ν n,2 ). For the Sun, these expressions are equivalent and give an age of about 4.9-5.0 Gyr. For a Cen A and B, however, the small separation and the second difference give very different ages. This conflict may be resolved by the detection of oscillation frequencies that can be measured much more precisely than the current frequencies. When we fit the models to the observations, we find that (i) Z 0 = 0.020, t = 3.50 Gyr and M B =1.006 M ⊙ from the small separations δν 01 , δν 02 and δν 13 of a Cen B; and (ii) a variety of solutions from the non-seismic constraints and 3ν 02 of a Cen A and B, in which the masses of a Cen A and B are slightly modified and the age of the system is about 5.2-5.3 Gyr. For Z = 0.025, the closest masses we find to the observed masses are M B = 0.922 M ⊙ and M A = 1.115 M ⊙ . The differences between these masses and the corresponding observed masses are about 0.01 M ⊙ .
OpenTracker-an open software architecture for reconfigurable tracking based on XML

This paper describes OpenTracker, an open software architecture that provides a generic solution to the different tasks involved in tracking input devices and processing tracking data for virtual environments. It combines a highly modular design with a configuration syntax based on XML, thus taking full advantage of this new technology. OpenTracker is a first attempt towards a "write once, track anywhere" approach to virtual reality application development.
Problem Solving Interventions: Impact on Young Children with Developmental Disabilities.

iii ACKNOWLEDGEMENTS v LIST OF TABLES ix LIST OF FIGURES xi CHAPTER ONE INTRODUCTION 1 Problem Solving Defined 2 Problem Solving Instruction 4 Problem Solving with Students Who are Typical Learners 4 Problem Solving with Students with Developmental Disabilities 8 Statement of the Problem 10 Significance of the Study 13 Definitions 14 Limitations 17 CHAPTER TWO REVIEW OF THE LITERATURE 19 CHAPTER THREE METHODOLOGY 78 Overview 78 Research Questions 80 Participants 83 Setting 90 Instrumentation 91 Materials 92 Instructional Routines 94 Training 99 Problem Solving Instruction 102 Design and Procedures 104 Treatment of the Data 111 CHAPTER FOUR RESULTS 115 Teacher Fidelity to Instruction 117 Interrater Observers 120 Analysis of Problem Solving Measures 125
Biosynthesis and catabolism of 6-deoxy L-talitol by Klebsiella aerogenes mutants

A mutant strain of Klebsiella aerogenes was constructed and, when incubated anaerobically with L-fucose and glycerol, synthesized and excreted a novel methyl pentitol, 6-deoxy L-talitol. The mutant was constitutive for the synthesis of L-fucose isomerase but unable to synthesize L-fuculokinase activity. Thus, it could convert the L-fucose to L-fuculose but was incapable of phosphorylating L-fuculose to L-fuculose 1-phosphate. The mutant was also constitutive for the synthesis of ribitol dehydrogenase, and in the presence of sufficient reducing power this latter enzyme catalyzed the reduction of the L-fuculose to 6-deoxy L-talitol. The reducing equivalents required for this reaction were generated by the oxidation of glycerol to dihydroxyacetone with an anaerobic glycerol dehydrogenase. The parent strain of K. aerogenes was unable to utilize the purified 6-deoxy L-talitol as a sole source of carbon and energy for growth; however, mutant could be isolated which had gained this ability. Such mutants were found to be constitutive for the synthesis of ribitol dehydrogenase and were thus capable of oxidizing 6-deoxy L-talitol to L-fuculose. Further metabolism of L-fuculose was shown by mutant analysis to be mediated by the enzymes of the L-fucose catabolic pathway.
Human infections with Borna disease virus: Seroprevalence in patients with chronic diseases and healthy individuals

Borna disease virus (BDV) is as yet an unclassified infectious agent which causes a neurologic disease in horses and sheep and is transmissible to other animal species. Human sera were tested for BDV‐specific antibodies by immunofluorescence and immunoprecipitation. The sera were collected from three thousand subjects in Europe, the USA, and Africa classified by clinical syndromes/infectious diseases, and from healthy controls. In all three continents, positive serum samples were detected which recognized the major BDV antigen of 38/40 KD present in the nuclei of infected cells. In contrast to 2% of se‐ropositives among the normal population, significantly higher prevalences (13‐14%) were present among patients with chronic progressive diseases of the brain and the immune system. In children, antibody frequencies were two to four times higher than in adults. The results suggest a latent infection with BDV in humans leading to low antigen expression in healthy subjects and frequent reactivation events in chronically ill patients.
Efficient Skyline Query Processing on Peer-to-Peer Networks

Skyline query has been gaining much interest in database research communities in recent years. Most existing studies focus mainly on centralized systems, and resolving the problem in a distributed environment such as a peer-to-peer (P2P) network is still an emerging topic. The desiderata of efficient skyline querying in P2P environment include: 1) progressive returning of answers, 2) low processing cost in terms of number of peers accessed and search messages, 3) balanced query loads among the peers. In this paper, we propose a solution that satisfies the three desiderata. Our solution is based on a balanced tree structured P2P network. By partitioning the skyline search space adaptively based on query accessing patterns, we are able to alleviate the problem of "hot" spots present in the skyline query processing. By being able to estimate the peer nodes within the query subspaces, we are able to control the amount of query forwarding, limiting the number of peers involved and the amount of messages transmitted in the network. Load balancing is achieved in query load conscious data space splitting/merging during the joining/departure of nodes and through dynamic load migration. Experiments on real and synthetic datasets confirm the effectiveness and scalability of our algorithm on P2P networks.
How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. This is exemplified for Escherichia coli by the increase of its ribosomal protein‐fraction with growth rate, which precisely matches the increased protein synthesis demand. These findings and others have led to the hypothesis that E. coli aims to maximize its growth rate in environments that support growth. However, what kind of regulatory strategy is required for a robust, optimal adjustment of the ribosome concentration to the prevailing condition is still an open question. In the present study, we analyze the ppGpp‐controlled mechanism of ribosome expression used by E. coli and show that this mechanism maintains the ribosomes saturated with its substrates. In this manner, overexpression of the highly abundant ribosomal proteins is prevented, and limited resources can be redirected to the synthesis of other growth‐promoting enzymes. It turns out that the kinetic conditions for robust, optimal protein‐partitioning, which are required for growth rate maximization across conditions, can be achieved with basic biochemical interactions. We show that inactive ribosomes are the most suitable ‘signal’ for tracking the intracellular nutritional state and for adjusting gene expression accordingly, as small deviations from optimal ribosome concentration cause a huge fractional change in ribosome inactivity. We expect to find this control logic implemented across fast‐growing microbial species because growth rate maximization is a common selective pressure, ribosomes are typically highly abundant and thus costly, and the required control can be implemented by a small, simple network.
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

Internal friction, which reflects the “roughness” of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners.
Native Wisdom on Belonging.

Our worldviews are shaped by our cultural and family at­ tachments. Each of us drags around a cultural tail a thou­ sand years long, as well as our more personal family tale. My Lakota (Sioux) grandfather was born in the mid-1800s and did not see his first White man until after the en­ croachments of Custer 's cavalry. He proudly carried the name Brokenleg, which memorialized an injury incurred in his job of training wild horses. Up until his death at 99 years of age, he only spoke Lakota as he would tell us, his grandchildren, stories of our culture before we were subjugated by European settlers.
Intricate Isohedral Tilings of 3D Euclidean Space

Various methods to create intricate tilings of 3D space are presented. They include modulated extrusions of 2D Escher tilings, free-form deformations of the fundamental domain of various 3D symmetry groups, highly symmetrical polyhedral toroids of genus 1, higher-genus cage structures derived from the cubic lattice as well as from the diamond and triamond lattices, and finally interlinked tiles with the connectivity of simple knots.