Miracle-dz/UniFAR-FTUs huggingface dataset:
Flux and flexibility : a comparative institutional analysis of evolving university-industry relationships in MIT, Cambridge and Tokyo

University-industry relationships are in a state of flux. They represent important strategic issues for universities, for industry, and for governments alike. This confluence of interests has led to experimentation in which universities and industry seek to work together, often with strong government support. And yet partnerships are not easy. Academics and industrialists live in two different worlds, and universities are not known for their organizational flexibility. Some universities appear to change flexibly, while others change more slowly and with difficulty. The purpose of this dissertation is three-fold: to identify the nature of change taking place in university-industry relationships; to understand the underlying factors that influence that change; and to explore the underlying process of change. Three cases of MIT, Cambridge University, and Tokyo University are examined to compare their experiences in developing new types of university-industry relationships. I argue that internal and external organizational boundaries have influenced the evolution of the new types of relationships, and that the three universities have defined these boundaries differently. MIT's regulated external boundaries permitted close but bounded relationships with industry, but, on the other hand, its one-way permeable internal boundaries enabled its administration to amplify and institutionalize initiatives. This is contrasted with Cambridge's fuzzy boundaries, which appeared to elicit deeper and more informal and personal relationships in specific local settings. Tokyo's apparently impermeable boundaries, in contrast, led both to formal arm's length relationships as well as to informal but closer and invisible relationships. The emergence of these relationships has not been a mechanical and deterministic process. Individuals have played an active and important role through "storytelling" to persuade different players to participate in the new relationships. Individuals also developed individual sub-stories that explained the rationale for their own participation. I argue that there are three different types of compatibility between role-stories as told by the players: individual role compatibility, partnership compatibility and organizational compatibility. I then argue that it is these three types of compatibility that have determined the overall strengths of the new behavioral patterns, their ultimate sustainability over time and their replicability across space:
Quadratic volume preserving maps

We study quadratic, volume preserving diffeomorphisms whose inverse is also quadratic. Such maps generalize the Henon area preserving map and the family of symplectic quadratic maps studied by Moser. In particular, we investigate a family of quadratic volume preserving maps in three space for which we find a normal form and study invariant sets. We also give an alternative proof of a theorem by Moser classifying quadratic symplectic maps.
IS CR Elements : Novel Gene-Capturing Systems of the 21 st Century ?

INTRODUCTION . 296 CRs AND THEIR DISCOVERY . 298 CHARACTERIZATION OF CRs.301 CRs ARE IS91-LIKE TRANSPOSABLE ELEMENTS.302 ISCR ELEMENTS AND ASSOCIATED GENES . 305 ISCR1.305 ISCR1 association with trimethoprim resistance genes . 305 ISCR1 association with plasmid-mediated quinolone resistance . 305 ISCR1 association with aminoglycoside resistance genes . 305 ISCR1 association with class A -lactamases.305 ISCR1 association with blaCTX-M genes . 305 ISCR1 association with other class A -lactamase genes . 306 ISCR1 association with class C -lactamase genes . 306 ISCR2.307 Involvement of ISCR2 with SXT.307 ISCR2 association with other resistance mechanisms.307 ISCR3.308 Involvement of ISCR3 and ISCR1 with the Salmonella genomic island 1 genetic element.308 ISCR4.309 ISCR5.309 ISCR6.309 ISCR7 and ISCR8.309 Other ISCR Elements.309 ISCRs MOBILIZE AND CONSTRUCT COMPLEX CLASS 1 INTEGRONS . 310 SIMILARITIES AND DIFFERENCES BETWEEN ISCR AND IS91-LIKE TRANSPOSASES . 312 SPECIFICITY OF INSERTION OF IS91 AND ISCR ELEMENTS.312 ISCR ELEMENTS AND PROMOTER SEQUENCES . 312 ORIGINS OF CR ELEMENTS . 313 IS91 AND VIRULENCE FACTORS.313 CONCLUSIONS . 313 REFERENCES . 313
Oops! where did that code snippet come from?

A kernel oops is an error report that logs the status of the Linux kernel at the time of a crash. Such a report can provide valuable first-hand information for a Linux kernel maintainer to conduct postmortem debugging. Recently, a repository has been created that systematically collects kernel oopses from Linux users. However, debugging based on only the information in a kernel oops is difficult. We consider the initial problem of finding the offending line, i.e., the line of source code that incurs the crash. For this, we propose a novel algorithm based on approximate sequence matching, as used in bioinformatics, to automatically pinpoint the offending line based on information about nearby machine-code instructions, as found in a kernel oops. Our algorithm achieves 92% accuracy compared to 26% for the traditional approach of using only the oops instruction pointer.
Towards persuasive social recommendation: knowledge model

The exponential growth of social networks makes fingerprint let by users on the Internet a great source of information, with data about their preferences, needs, goals, profile and social environment. These data are distributed across different sources of information (social networks, blogs, databases, etc.) that may contain inconsistencies and their accuracy is uncertain. Paradoxically, this unprecedented availability of heterogeneous data has meant that users have more information available than they actually are able to process and understand to extract useful knowledge from it. Therefore, new tools that help users in their decision-making processes within the network (e.g. which friends to contact with or which products to consume) are needed. In this paper, we show how we have used a graph-based model to extract and model data and transform it in valuable knowledge to develop a persuasive social recommendation system.
Se) former à enseigner les langues aux enfants

Ce chapitre a pour finalite de sensibiliser a la problematique des enseignements linguistiques et culturels dans le cadre des cours de langues dispenses aux jeunes apprenants en situation institutionnelle, que ce soit en France ou dans d'autres pays. Il vise a guider les etudiants, assistants de langues, formateurs et conseillers pedagogiques dans la decouverte de la specificite des apprentissages des langues/cultures par les enfants, des approches les plus connues et des demarches privilegiees pour ce faire, en reference aux recherches du domaine. Il construit la reflexion sur les competences attendues des enseignants de langues et leur mise en œuvre en formation avec de jeunes publics.
Are Temporal Concepts Embodied? A Challenge for Cognitive Neuroscience

Is time an embodied concept? People often talk and think about temporal concepts in terms of space. This observation, along with linguistic and experimental behavioral data documenting a close conceptual relation between space and time, is often interpreted as evidence that temporal concepts are embodied. However, there is little neural data supporting the idea that our temporal concepts are grounded in sensorimotor representations. This lack of evidence may be because it is still unclear how an embodied concept of time should be expressed in the brain. The present paper sets out to characterize the kinds of evidence that would support or challenge embodied accounts of time. Of main interest are theoretical issues concerning (1) whether space, as a mediating concept for time, is itself best understood as embodied and (2) whether embodied theories should attempt to bypass space by investigating temporal conceptual grounding in neural systems that instantiate time perception.
A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions.

More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large ( > 4000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points and experimenting with both fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ∼ 23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineage would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kb of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events explain present-day distributions better than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World (OW) to New World (NW) dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s. , which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within the last ∼ 20 myr even though Acanthaceae s.s is over 3 times as old. A simulation study confirmed that these dispersal events were significantly skewed toward the present and not simply a chance occurrence. Finally, we review reports of fossils that have been assigned to Acanthaceae that are substantially older than the lower Cretaceous estimate for Angiosperms as a whole (i.e., the general consensus that has resulted from several recent dating and fossil-based studies in plants). This is the first study to reconstruct divergence times among clades of Acanthaceae and sets the stage for comparative evolutionary research in this and related families that have until now been thought to have extremely poor fossil resources.
Phonation in Tonal Contrasts.

Author(s): Kuang, Jianjing | Advisor(s): Keating, Patricia | Abstract: Phonation is used in many tonal languages, but how it should be incorporated into tonal systems is not well understood. The purpose of this dissertation thus is to examine the role of phonation in tonal contrasts, and to investigate how phonation and pitch interact in the tonal space. This dissertation presents close studies of tonal contrasts from three language families that provide different answers to these questions. From the case of Yi languages, where the tense/lax phonation ("register") contrast is orthogonal to the tone contrast, we show that phonation production can be independent from tonal production. Phonation in these languages is not only phonologically contrastive, but phonetically completely independent. Tone is purely pitch, and phonation is purely voice quality. From the case of Mandarin, where non-modal phonation (specifically, creaky voice) is known to be an allophonic cue to the low-dipping Tone 3, we show that the presence of creak in Mandarin is purely driven by pitch range, and can occur with any of the low-pitch targets. Moreover, we show that in a corpus of pitch sweeps that rose or fell over large pitch ranges, Mandarin speakers' voice quality co-vary with pitch in a wedge-shaped function. Finally, we investigate the case of Black Miao, a language with five-level-tone contrasts, the case of maximum use of pitch contrast attested among languages. Due to limitations on pitch production and perception, it should be very hard to make these contrasts purely by pitch. Both production and perception experiments show that non-modal phonations provide very important cues in both tonal production and perception, but in different ways. On the one hand, the three mid-range tones (T22, T33, T44) have very similar pitch cues, but T33 is quite distinct from T22 and T44 by its breathy voice quality. On the other hand, the extra-high (T55) and extra-low (T11) tones show the same kind of pitch-dependent voice quality that was found in Mandarin: the extra-low pitches tend to be creaky while the extra-high pitches tend to be tense. Taking these cases together, we establish: 1) there are two different uses of phonation types, based on their relationship with pitch: pitch-dependent and pitch-independent, which can either enhance the perceptual distinctiveness of extreme pitch targets, or serve as a contrastive dimension for tones with similar pitch values; 2) tonal contrast is multidimensional, and the dimensionality of tonal contrasts in part depends on the size of the tonal inventory. We propose a new tone space model, and principles for good dispersion of tonal contrasts. This dissertation thus extends our knowledge about tonal contrasts, and provides a better understanding of the interaction between phonation and pitch in tone languages.
Asymmetric Proteome Equalization of the Skeletal Muscle Proteome Using a Combinatorial Hexapeptide Library

Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.
Effect of interface states on spin-dependent tunneling in Fe/MgO/Fe tunnel junctions

The electronic structure and spin-dependent tunneling in epitaxial $\mathrm{Fe}∕\mathrm{Mg}\mathrm{O}∕\mathrm{Fe}(001)$ tunnel junctions are studied using first-principles calculations. For small MgO barrier thickness the minority-spin resonant bands at the two interfaces make a significant contribution to the tunneling conductance for the antiparallel magnetization, whereas these bands are, in practice, mismatched by disorder and/or small applied bias for the parallel magnetization. This explains the experimentally observed decrease in tunneling magnetoresistance (TMR) for thin MgO barriers. We predict that a monolayer of Ag epitaxially deposited at the interface between Fe and MgO suppresses tunneling through the interface band and may thus be used to enhance the TMR for thin barriers.
Observational constraints on an inflation model with a running mass

We explore a model of inflation where the inflaton mass-squared is generated at a high scale by gravity-mediated soft supersymmetry breaking, and runs at lower scales to the small value required for slow-roll inflation. The running is supposed to come from the coupling of the inflaton to a non-Abelian gauge field. In contrast with earlier work, we do not constrain the magnitude of the supersymmetry breaking scale, and we find that the model might work even if squark and slepton masses come from gauge-mediated supersymmetry breaking. With the inflaton and gaugino masses in the expected range, and $\ensuremath{\alpha}{=g}^{2}/4\ensuremath{\pi}$ in the range ${10}^{\ensuremath{-}2}\char21{}{10}^{\ensuremath{-}3}$ (all at the high scale), the model can give the observed cosmic microwave anisotropy and a spectral index in the observed range. The latter has a significant variation with scale, which can confirm or rule out the model in the foreseeable future.
Regression of Replication Forks Stalled by Leading-strand Template Damage

Background: Stalled replication forks are foci for genomic instability. Results: RecA can only regress a stalled fork in the absence of SSB. Conclusion: Regression by RecA in vivo is likely to require additional activities. Significance: Replication fork regression is a major step in processing stalled forks. Stalled replication forks are sites of chromosome breakage and the formation of toxic recombination intermediates that undermine genomic stability. Thus, replication fork repair and reactivation are essential processes. Among the many models of replication fork reactivation is one that invokes fork regression catalyzed by the strand exchange protein RecA as an intermediate in the processing of the stalled fork. We have investigated the replication fork regression activity of RecA using a reconstituted DNA replication system where the replisome is stalled by collision with leading-strand template damage. We find that RecA is unable to regress the stalled fork in the presence of the replisome and SSB. If the replication proteins are removed from the stalled fork, RecA will catalyze net regression as long as the Okazaki fragments are sealed. RecA-generated Holliday junctions can be detected by RuvC cleavage, although this is not a robust reaction. On the other hand, extensive branch migration by RecA, where a completely unwound product consisting of the paired nascent leading and lagging strands is produced, is observed under conditions where RuvC activity is suppressed. This branch migration reaction is inhibited by SSB, possibly accounting for the failure of RecA to generate products in the presence of the replication proteins. Interestingly, we find that the RecA-RuvC reaction is supported to differing extents, depending on the template damage; templates carrying a cyclopyrimidine dimer elicit more RecA-RuvC product than those carrying a synthetic abasic site. This difference could be ascribed to a higher affinity of RecA binding to DNAs carrying a thymidine dimer than to those with an abasic site.
Counter Strike: Generic Top-Down Join Enumeration for Hypergraphs

Finding the optimal execution order of join operations is a crucial task of today's cost-based query optimizers. There are two approaches to identify the best plan: bottom-up and top-down join enumeration. But only the top-down approach allows for branch-and-bound pruning, which can improve compile time by several orders of magnitude while still preserving optimality. For both optimization strategies, efficient enumeration algorithms have been published. However, there are two severe limitations for the top-down approach: The published algorithms can handle only (1) simple (binary) join predicates and (2) inner joins. Since real queries may contain complex join predicates involving more than two relations, and outer joins as well as other non-inner joins, efficient top-down join enumeration cannot be used in practice yet. We develop a novel top-down join enumeration algorithm that overcomes these two limitations. Furthermore, we show that our new algorithm is competitive when compared to the state of the art in bottom-up processing even without playing out its advantage by making use of its branch-and-bound pruning capabilities.
Sickle cell disease telemedicine network for rural outreach

The Medical College of Georgia (MCG) Sickle Cell Center in Augusta, Georgia, USA, provides consultation and (in some cases) primary-care services to more than 1000 patients with sickle cell disease (SCD). Three SCD telemedicine clinic sites were established in rural areas of middle and southern Georgia, based on clinical need; a fourth site had been proposed. Over a 36-month study period, 77 telemedicine SCD clinics were held. There was a mean of 6.1 (SD 2.5) encounters per clinic and 466 total encounters among 128 SCD patients. By using telemedicine, the productivity of the MCG adult sickle cell clinic increased from 1413 to 1889 encounters a year, with an increase in rural outreach activity from 271 to 745 encounters a year. This was accomplished with the addition of a single physician assistant during the last 12 months of the study period; otherwise provider staffing was unchanged. A formal cost-benefit analysis now needs to be carried out.
Identification and compensation of inverter dead-time effect on zero speed sensorless control of AC machines based on voltage pulse injection

In this paper the influence of the non-ideal behavior of power electronics, sensors, and signal processing on pulse signal injection based speed sensorless control is addressed and investigated. The speed sensorless control signals are obtained from the transient current response resulting from an excitation of the machine with voltage pulses. The investigation is focused on sensorless control of induction machines however, the results are applicable also for other types of ac machines. By using pulse width modulation in combination with voltage source inverters the inverter interlock dead-time is essential necessary to prevent the short circuit of the dc link. A new approach to identify the interlook dead-time by utilizing the transient voltage pulses and the current response is presented. The disturbing influences and effects of the inverter interlock dead-time on the resulting signal include the deviation of the operating point during the pulse injection, as well as additional resulting harmonics in the control signal. For the specific problem of compensating these effects on the signal injection measurement a new approach is applied in this paper. After identifying the effective dead time the switching commands are adapted in order to clearly reduce the disturbing effects. Further simulation results and additionally measurement results are presented to show the influence on the resulting control signals.