Miracle-dz/UniFAR-FTUs huggingface dataset:
Adversarial Evaluation for Models of Natural Language

We now have a rich and growing set of modeling tools and algorithms for inducing linguistic structure from text that is less than fully annotated. In this paper, we discuss some of the weaknesses of our current methodology. We present a new abstract framework for evaluating natural language processing (NLP) models in general and unsupervised NLP models in particular. The central idea is to make explicit certain adversarial roles among researchers, so that the different roles in an evaluation are more clearly defined and performers of all roles are offered ways to make measurable contributions to the larger goal. Adopting this approach may help to characterize model successes and failures by encouraging earlier consideration of error analysis. The framework can be instantiated in a variety of ways, simulating some familiar intrinsic and extrinsic evaluations as well as some new evaluations. This paper presents a new approach to evaluating computational models of natural language, based on adversarial roles performed by different researchers or their models. We begin inx2 with a brief review of current evaluation strategies in NLP. We then turn to coupled adversarial evaluations inspired by perplexity (x3) and the traditional roles of linguists (x4). The two-performer setup is formalized inx5. We then consider the origins of the data and growing awareness of the importance of context on language use (x6) and provide a three-performer setup, in which a third performer manages data selection (x7). We close with a few open questions (x8).
Experimental Investigation of Friction Coefficient and Wear Rate of Stainless Steel 202 Sliding against Smooth and Rough Stainless Steel 304 Couter-faces

In the present study, friction coefficient and wear rate of stainless steel 202 (SS 202) sliding against mild steel are investigated experimentally using a pin on disc apparatus designed and fabricated. Experiments are carried out when smooth or rough SS 304 pin slides on SS 202 disc. Experiments are conducted at normal load 10, 15 and 20 N, sliding velocity 1, 1.5 and 2 m/s and relative humidity 70%. Variations of friction coefficient with the duration of rubbing at different normal loads and sliding velocities are investigated. Results show that friction coefficient is influenced by duration of rubbing, normal load and sliding velocity. In general, friction coefficient increases for a certain duration of rubbing and after that it remains constant for the rest of the experimental time. The obtained results reveal that friction coefficient decreases with the increase in normal load for SS 202 mating with smooth or rough SS 304 counter-face. On the other hand, it is also found that friction coefficient increases with the increase in sliding velocity. Moreover, wear rate increases with the increase in normal load and sliding velocity. The magnitudes of friction coefficient and wear rate are different depending on sliding velocity and normal load for both smooth and rough counter-face pin materials.
A Population of planetary systems characterized by short-period, Earth-sized planets

Significance Characterizing the variety of planets and planetary systems orbiting distant stars (exoplanets) is a key ingredient to improving our understanding of the Solar System and of planet formation in general. One important observable property of a planetary system is its architecture—the sizes and orbital periods of the planets in a system and how they are related to each other. From a statistical analysis of the planet candidate catalog from NASA’s Kepler mission, we identify a population of planetary systems characterized by a unique system architecture. Differences in system architecture indicate different paths in the formation or dynamical history of a planetary system—giving clues to the physical conditions or processes that drive systems along those paths. We analyze data from the Quarter 1–17 Data Release 24 (Q1–Q17 DR24) planet candidate catalog from NASA’s Kepler mission, specifically comparing systems with single transiting planets to systems with multiple transiting planets, and identify a population of exoplanets with a necessarily distinct system architecture. Such an architecture likely indicates a different branch in their evolutionary past relative to the typical Kepler system. The key feature of these planetary systems is an isolated, Earth-sized planet with a roughly 1-d orbital period. We estimate that at least 24 of the 144 systems we examined (≳17%) are members of this population. Accounting for detection efficiency, such planetary systems occur with a frequency similar to the hot Jupiters.
3D Selection Strategies for Head Tracked and Non-Head Tracked Operation of Spatially Immersive Displays

We present an investigation of selection strategies designed specifically for the spatially immersive display (SID), CAVE-like situation. We address two common contexts of use of SID displays: single user head tracked, and two person with one non-head tracked demonstrator and a visitor. This second context is, in our experience, a common use scenario of SIDs, but it, and other issues specific to SIDs, are largely ignored in the literature, which has concentrated on head-mounted displays. We introduce a novel interaction technique, Shadow Cone Selection, which was designed for the situation of non-head tracked interaction. Through analysis and experiment, we show that it might be preferred over standard cone and ray-based selection techniques for some applications.
Prion Protein Prolines 102 and 105 and the Surrounding Lysine Cluster Impede Amyloid Formation*

Background: We investigated how pathogenic prion protein mutations P102L and P105L lead to misfolding. Results: Mutations of these proline and adjacent lysine residues accelerated in vitro formation of amyloid with properties reminiscent of PrPSc. Conclusion: Specific proline and lysine residues might delay spontaneous prion disease by hindering PrP conversion into amyloid. Significance: These findings suggest mechanisms for genetic prion diseases. Human prion diseases can have acquired, sporadic, or genetic origins, each of which results in the conversion of prion protein (PrP) to transmissible, pathological forms. The genetic prion disease Gerstmann-Straussler-Scheinker syndrome can arise from point mutations of prolines 102 or 105. However, the structural effects of these two prolines, and mutations thereof, on PrP misfolding are not well understood. Here, we provide evidence that individual mutations of Pro-102 or Pro-105 to noncyclic aliphatic residues such as the Gerstmann-Straussler-Scheinker-linked leucines can promote the in vitro formation of PrP amyloid with extended protease-resistant cores reminiscent of infectious prions. This effect was enhanced by additional charge-neutralizing mutations of four nearby lysine residues comprising the so-called central lysine cluster. Substitution of these proline and lysine residues accelerated PrP conversion such that spontaneous amyloid formation was no longer slower than scrapie-seeded amyloid formation. Thus, Pro-102 and Pro-105, as well as the lysines in the central lysine cluster, impede amyloid formation by PrP, implicating these residues as key structural modulators in the conversion of PrP to disease-associated types of amyloid.
Late Pleistocene and Holocene environmental history of the Iguala Valley, Central Balsas Watershed of Mexico

The origin of agriculture was a signal development in human affairs and as such has occupied the attention of scholars from the natural and social sciences for well over a century. Historical studies of climate and vegetation are closely associated with crop plant evolution because they can reveal the ecological contexts of plant domestication together with the antiquity and effects of agricultural practices on the environment. In this article, we present paleoecological evidence from three lakes and a swamp located in the Central Balsas watershed of tropical southwestern Mexico that date from 14,000 B.P. to the modern era. [Dates expressed in B.P. years are radiocarbon ages. Calibrated (calendar) ages, expressed as cal B.P., are provided for dates in the text. ] Previous molecular studies suggest that maize (Zea mays L.) and other important crops such as squashes (Cucurbita spp.) were domesticated in the region. Our combined pollen, phytolith, charcoal, and sedimentary studies indicate that during the late glacial period (14,000–10,000 B.P.), lake beds were dry, the climate was cooler and drier, and open vegetational communities were more widespread than after the Pleistocene ended. Zea was a continuous part of the vegetation since at least the terminal Pleistocene. During the Holocene, lakes became important foci of human activity, and cultural interference with a species-diverse tropical forest is indicated. Maize and squash were grown at lake edges starting between 10,000 and 5,000 B.P., most likely sometime during the first half of that period. Significant episodes of climatic drying evidenced between 1,800 B.P. and 900 B.P. appear to be coeval with those documented in the Classic Maya region and elsewhere, showing widespread instability in the late Holocene climate.
Nonlinear viscoelastic materials : bioinspired applications and new characterization measures

Viscoelastic materials, such as biomaterials and non-Newtonian fluids, typically experience mechanical loading which evokes a nonlinear rheological response. Rheologically complex materials can provide novel functionality in biological and engineered systems. However, it is found that standard characterization techniques are insufficient to appropriately describe nonlinear viscoelasticity. The goal of this thesis is to transcend the limitations of current characterization methods as well as demonstrate applications of nonlinear viscoelastic materials, including reversible adhesion and snail-like wall climbing. PART ONE of this thesis introduces a complete language and framework (or ontology) for characterizing nonlinear viscoelasticity using large amplitude oscillatory shear (LAOS) deformation. The LAOS protocol spans the 2D parameter space of deformation amplitude and frequency, known as a Pipkin space. Physically meaningful material measures are proposed, corresponding to clearly defined language such as strain-stiffening/softening and shear-thickening/thinning. The new ontology is general enough to be applied to any viscoelastic material, mapping behaviors from purely elastic to purely viscous, and any complex response in-between. The framework has been packaged into a distributable data analysis program (MITlaos) to widen its use in both academic and industrial settings. PART TWO examines the nonlinear rheological response of various soft materials and constitutive models. The new framework is illustrated by examining prototypical nonlinear constitutive models (Giesekus, pseudoplastic Carreau, and elastoplastic Bingham). Various soft materials are tested experimentally, including pedal mucus gel from terrestrial gastropods, a wormlike micelle solution, ultrasoft hagfish slime, and an oilfield drilling fluid. PART THREE describes the use of nonlinear rheological behavior to enable unique functionality, specifically for bioinspired snail-like wall climbing and tunable adhesion using magnetorheological fluids. Yield stress fluids are examined here to enable the bioinspired adhesive locomotion of a self-contained mechanical device (Robosnail, developed by Brian Chan, Ph.D. ’09). Field-responsive magnetorheological fluids are analyzed in the context of providing fast-switching reversible adhesion for use with adhesive locomotion devices and shape-changing soft robots. In conclusion, interest in soft materials is increasing across many disciplines. The contributions presented here provide the means to a better understanding of biological and engineered systems which involve complex viscoelastic materials. Thesis Supervisor: Gareth H. McKinley Title: Professor, Mechanical Engineering Thesis Supervisor: Anette E. Hosoi Title: Associate Professor, Mechanical Engineering
The use of explicit intermediate representations in intelligent tutoring systems

Current Position Professor, School of Information Sciences, University of Illinois at Urbana-Champaign (2009-date). Director, Master of Science in Information Management degree Zero-time courtesy appointment with Computer Science, UIUC UIUC Academy of Entrepreneurial Leadership Faculty Fellow Member of the UIUC Information Trust Institute Affiliate Faculty, Beckman Institute Human Perception and Performance Research Group NCSA Fellow Visiting Professor, University of Nottingham Adjunct Professor, University of Tasmania
Activation of Dopaminergic D2/D3 Receptors Modulates Dorsoventral Connectivity in the Hippocampus and Reverses the Impairment of Working Memory after Nerve Injury

Dopamine plays an important role in several forms of synaptic plasticity in the hippocampus, a crucial brain structure for working memory (WM) functioning. In this study, we evaluated whether the working-memory impairment characteristic of animal models of chronic pain is dependent on hippocampal dopaminergic signaling. To address this issue, we implanted multichannel arrays of electrodes in the dorsal and ventral hippocampal CA1 region of rats and recorded the neuronal activity during a food-reinforced spatial WM task of trajectory alternation. Within-subject behavioral performance and patterns of dorsoventral neuronal activity were assessed before and after the onset of persistent neuropathic pain using the Spared Nerve Injury (SNI) model of neuropathic pain. Our results show that the peripheral nerve lesion caused a disruption in WM and in hippocampus spike activity and that this disruption was reversed by the systemic administration of the dopamine D2/D3 receptor agonist quinpirole (0.05 mg/kg). In SNI animals, the administration of quinpirole restored both the performance-related and the task-related spike activity to the normal range characteristic of naive animals, whereas quinpirole in sham animals caused the opposite effect. Quinpirole also reversed the abnormally low levels of hippocampus dorsoventral connectivity and phase coherence. Together with our finding of changes in gene expression of dopamine receptors and modulators after the onset of the nerve injury model, these results suggest that disruption of the dopaminergic balance in the hippocampus may be crucial for the clinical neurological and cognitive deficits observed in patients with painful syndromes.
Direct induction of cyclin D2 by Myc contributes to cell cycle progression and sequestration of p27

Ectopic expression of Myc induces Cdk2 kinase activity in quiescent cells and antagonizes association of p27kip1 with Cdk2. The target gene(s) by which Myc mediates this effect is largely unknown. We now show that p27 is rapidly and transiently sequestered by cyclin D2–Cdk4 complexes upon activation of Myc and that cyclin D2 is a direct target gene of Myc. The cyclin D2 promoter is repressed by Mad–Max complexes and de‐repressed by Myc via a single highly conserved E‐box element. Addition of trichostatin A to quiescent cells mimics activation of Myc and induces cyclin D2 expression, suggesting that cyclin D2 is repressed in a histone deacetylase‐dependent manner in quiescent cells. Inhibition of cyclin D2 function in established cell lines, either by ectopic expression of p16 or by antibody injection, inhibits Myc‐dependent dissociation of p27 from Cdk2 and Myc‐induced cell cycle entry. Primary mouse fibroblasts that are cyclin D2‐deficient undergo accelerated senescence in culture and are not immortalized by Myc; induction of apoptosis by Myc is unimpaired in such cells. Our data identify a downstream effector pathway that links Myc directly to cell cycle progression.
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs. ubc.ca/labs/beta/Software/HotKnots.
Aspen: A domain specific language for performance modeling

We present a new approach to analytical performance modeling using Aspen, a domain specific langauge. Aspen (Abstract Scalable Performance Engineering Notation) fills an important gap in existing performance modeling techniques and is designed to enable rapid exploration of new algorithms and architectures. It includes a formal specification of an application's performance behavior and an abstract machine model. We provide an overview of Aspen's features and demonstrate how it can be used to express a performance model for a three dimensional Fast Fourier Transform. We then demonstrate the composability and modularity of Aspen by importing and reusing the FFT model in a molecular dynamics model. We have also created a number of tools that allow scientists to balance application and system factors quickly and accurately.
The patent paradox revisited: an empirical study of patenting in the U

Methods and apparatus are disclosed for continuous mixing of formulations for urethane products. A hydroxyl mixture and isocyanate, the major foam components, are supplied to a mixer. In the mixer, the components are mixed by transverse shearing and agitation means. The degree of agitation is varied along the length of the mixer, which runs at a constant speed, by varying the shearing pin configuration. The flow path through the mixer is arranged to control pressure on the fluid as well as minimize the tendency of internal foam build-up to occur.
Endothelial Nitric Oxide Synthase Limits Left Ventricular Remodeling After Myocardial Infarction in Mice

Background—To investigate the role of endothelial nitric oxide synthase (NOS3) in left ventricular (LV) remodeling after myocardial infarction (MI), the impact of left anterior descending coronary artery ligation on LV size and function was compared in 2- to 4-month-old wild-type (WT) and NOS3-deficient mice (NOS3−/−). Methods and Results—Two days after MI, both strains of mice had a similar LV size, fractional shortening, and ejection fraction by echocardiography. Twenty-eight days after MI, both strains had dilated LVs with decreased fractional shortening and lower ejection fractions. Although the infarcted fraction of the LV was similar in both strains, LV end-diastolic internal diameter, end-diastolic volume, and mass were greater, but fractional shortening, ejection fraction, and the maximum rate of developed LV pressure (dP/dtmax) were lower in NOS3−/− than in WT mice. Impairment of diastolic function, as measured by the time constant of isovolumic relaxation (&tgr;) and the maximum rate of LV pressure decay (dP/dtmin), was more marked in NOS3−/− than in WT mice. Mortality after MI was greater in NOS3−/− than in WT mice. Long-term administration of hydralazine normalized blood pressure in NOS3−/− mice, but it did not prevent the LV dilatation, impaired systolic and diastolic function, and increased LV mass that followed MI. In WT mice, capillary density and myocyte width in the nonischemic portion of the LV did not differ before and 28 days after MI, whereas in NOS3−/− mice, capillary density decreased and myocyte width increased after MI, whether or not hydralazine was administered. Conclusions—These results suggest that the presence of NOS3 limits LV dysfunction and remodeling in a murine model of MI by an afterload-independent mechanism, in part by decreasing myocyte hypertrophy in the remote myocardium.
Fournier’s Gangrene: Lessons Learned from Multimodal and Multidisciplinary Management of Perineal Necrotizing Fasciitis

Background Fournier’s gangrene (FG) is a rapidly evolving necrotizing fasciitis of the perineum and the genital area, the scrotum as it most commonly affects man in the vast majority of cases. It is polymicrobial in origin, due to the synergistic action of anaerobes and aerobes and has a very high mortality. There are many predisposing factors including diabetes mellitus, alcoholism, immunosuppression, renal, and hepatic disease. The prognosis of the disease depends on a lot of factors including but not limited to patient age, disease extent, and comorbidities. The purpose of the study is to describe the experience of a general surgery department in the management of FG, to present the multimodal and multidisciplinary treatment of the disease, to identify predictors of mortality, and to make general surgeons familiar with the disease. Methods The current retrospective study is presenting the experience of our general surgery department in the management of FG during the last 20 years. The clinical presentation and demographics of the patients were recorded. Also we recorded the laboratory data, the comorbidities, the etiology, and microbiology and the therapeutic interventions performed, and we calculated the various severity indexes. Patients were divided to survivors and non-survivors, and all the collected data were statistically analyzed to assess mortality factors using univariate and then multivariate analysis. Results In our series, we treated a total of 24 patients with a mean age 58.9 years including 20 males (83.4%) and 4 females (16.6%). In most patients, a delay between disease onset and seeking of medical help was noted. Comorbidities were present in almost all patients (87.5%). All patients were submitted to extensive surgical debridements and received broad-spectrum antibiotics until microbiological culture results were received. Regarding all the collected data, there was no statistically significant difference between survivors and non-survivors except the presence of malignancy in non-survivors (p = 0.036) and the lower hemoglobin (p < 0.001) and hematocrit (p = 0.002) in non-survivors. However, multivariate analysis did not reveal any predictor of mortality. Conclusion Early diagnosis, aggressive thorough surgical treatment, and administration of the proper antibiotic treatment comprise the cornerstone for the outcome of this disease. In small populations like in the present study, it is difficult to recognize any predictors of mortality and even the severity indexes, which take into account a lot of data cannot predict mortality.