Miracle-dz/UniFAR-FTUs huggingface dataset:
CONVERGENCE AND REMARKABLY CONSISTENT CONSTRAINT IN THE EVOLUTION OF CARNIVORE SKULL SHAPE

Abstract Phenotypic similarities between distantly related marsupials and placentals are commonly presented as examples of convergence and support for the role of adaptive evolution in shaping morphological and ecological diversity. Here we compare skull shape in a wide range of carnivoran placentals (Carnivora) and nonherbivorous marsupials using a three-dimensional (3-D) geometric morphometric approach. Morphological and ecological diversity among extant carnivorans is considerably greater than is evident in the marsupial order Dasyuromorphia with which they have most commonly been compared. To examine convergence across a wider, but broadly comparable range of feeding ecologies, a dataset inclusive of nondasyuromorphian marsupials and extinct taxa representing morphotypes no longer present was assembled. We found support for the adaptive paradigm, with correlations between morphology, feeding behavior, and bite force, although skull shape better predicted feeding ecology in the phylogenetically diverse marsupial sample than in carnivorans. However, we also show that remarkably consistent but differing constraints have influenced the evolution of cranial shape in both groups. These differences between carnivorans and marsupials, which correlate with brain size and bite force, are maintained across the full gamut of morphologies and feeding categories, from small insectivores and omnivores to large meat-specialists.
A Configurable Interface and Software Architecture for Robot Rescue

This paper describes the Swarthmore College entry in the 2004 Urban Search and Rescue [USAR] Event at the 2004 American Association for Artificial Intelligence Robot Competition. The primary focus of Swarthmore’s entry was the development of a fast, responsive user interface for effectively tele-operating a robot with some autonomous capability. This interface was inspired by first-person video game interfaces, and enabled Swarthmore to place first in the 2004 USAR competition.
Disturbance legacies and climate jointly drive tree growth and mortality in an intensively studied boreal forest

Most North American forests are at some stage of post‐disturbance regrowth, subject to a changing climate, and exhibit growth and mortality patterns that may not be closely coupled to annual environmental conditions. Distinguishing the possibly interacting effects of these processes is necessary to put short‐term studies in a longer term context, and particularly important for the carbon‐dense, fire‐prone boreal forest. The goals of this study were to combine dendrochronological sampling, inventory records, and machine‐learning algorithms to understand how tree growth and death have changed at one highly studied site (Northern Old Black Spruce, NOBS) in the central Canadian boreal forest. Over the 1999–2012 inventory period, mean tree diameter increased even as stand density and basal area declined significantly. Tree mortality averaged 1.4 ± 0.6% yr−1, with most mortality occurring in medium‐sized trees; new recruitment was minimal. There have been at least two, and probably three, significant influxes of new trees since stand initiation, but none in recent decades. A combined tree ring chronology constructed from sampling in 2001, 2004, and 2012 showed several periods of extreme growth depression, with increased mortality lagging depressed growth by ~5 years. Higher minimum and maximum air temperatures exerted a negative influence on tree growth, while precipitation and climate moisture index had a positive effect; both current‐ and previous‐year data exerted significant effects. Models based on these variables explained 23–44% of the ring‐width variability. We suggest that past climate extremes led to significant mortality still visible in the current forest structure, with decadal dynamics superimposed on slower patterns of fire and succession. These results have significant implications for our understanding of previous work at NOBS, the carbon sequestration capability of old‐growth stands in a disturbance‐prone landscape, and the sustainable management of regional forests in a changing climate.
A Guide to Functional Analytic Psychotherapy: Awareness, Courage, Love, and Behaviorism

, FAP has developed a strong following among therapists interested in the relational and interpersonal aspects of psychotherapy and human functioning, yet who are too strongly committed to testable hypotheses and integration with basic science to forego their behavioral roots. FAP is a comprehensive, ground-up approach to behaviorally conceptualizing therapist behavior within sessions to create optimal contingencies for client change and treatment implementation. The uniqueness of FAP lies in the recognition that no specific therapist behavior will serve to heighten intimacy and trust in the therapeutic relationship when provided by therapists that differ by appearance, gender, ethnicity, or temperament; genuine behaviors arise from contingent responses to client behavior, and a mindful awareness of which client behaviors require a response. For this reason, there is a certain difficulty in capturing the sense of a FAP intervention due to the importance of both the functional assessment and the therapist’s use of her own style and self as an instrument of change; for example, a disclosure of a clinically relevant personal loss will vary by therapist (e.g., Tsai et al., 2010), and a reaction that one client perceives as warm or encouraging by one therapist might sound strained or disingenuous coming from a different clinician. Though increasingly labeled a “third wave” behavioral therapy, FAP is fundamentally grounded in the Skinnerian tradition of a strong behavioral assessment (i.e., the titular functional analysis) of the client’s interpersonal repertoire as experienced by the therapist.
Optimization of geometric multigrid for emerging multi- and manycore processors

Multigrid methods are widely used to accelerate the convergence of iterative solvers for linear systems used in a number of different application areas. In this paper, we explore optimization techniques for geometric multigrid on existing and emerging multicore systems including the Opteron-based Cray XE6, Intel® Xeon® E5-2670 and X5550 processor-based Infiniband clusters, as well as the new Intel® Xeon Phi coprocessor (Knights Corner). Our work examines a variety of novel techniques including communication-aggregation, threaded wavefront-based DRAM communication-avoiding, dynamic threading decisions, SIMDization, and fusion of operators. We quantify performance through each phase of the V-cycle for both single-node and distributed-memory experiments and provide detailed analysis for each class of optimization. Results show our optimizations yield significant speedups across a variety of subdomain sizes while simultaneously demonstrating the potential of multi- and manycore processors to dramatically accelerate single-node performance. However, our analysis also indicates that improvements in networks and communication will be essential to reap the potential of manycore processors in large-scale multigrid calculations.
A Recommender System for Business Process Models

Process modeling facilitates understanding and restructuring of activities used to achieve business goals. However, manual process modeling is time-consuming and error-prone. In this paper, we describe a recommender system that suggests a list of correct and fitting process fragments for an edited business process model, which can be used to complete the process model being edited. The recommender system supports the user during the process modeling phase and reduces the number of structural modeling errors.
Anti-DNA antibodies from autoimmune mice arise by clonal expansion and somatic mutation

The proximate cause of autoantibodies characteristic of systemic autoimmune diseases has been controversial. One hypothesis is that autoantibodies are the result of polyclonal nonspecific B cell activation. Alternatively, autoantibodies could be the result of antigen-driven B cell activation, as observed in secondary immune responses. We have approached this question by studying monoclonal anti- DNA autoantibodies derived from unmanipulated spleen cells of the autoimmune MRL/lpr mouse strain. This analysis shows that anti-DNAs, like rheumatoid factors (19), are the result of specific antigen-driven stimulation. In addition, correlation of sequences with fine specificity shows that: (a) somatic mutations can cause specificity for dsDNA and that such mutations are selected for; (b) arginine residues play an important role in determining specificity; and (c) anti- idiotypes that recognize the majority of anti-DNA are probably not specific for any one family of V regions.
A Write-Aware STTRAM-Based Register File Architecture for GPGPU

The massively parallel processing capacity of GPGPUs requires a large register file (RF), and its size keeps increasing to support more concurrent threads from generation to generation. Using traditional SRAM-based RFs, there are concerns in both area cost and energy consumption, and soon they will become unrealistic. In this work, we analyze the feasibility of using STTRAM-based RF designs, which have benefits in terms of smaller silicon area and zero standby leakage power. However, STTRAM long write latency and high write energy bring new challenges. Therefore, we propose a write-aware STTRAM-based RF architecture (WarRF), which contains two techniques: Split Bank Write modifies the arbitrator design to increase the parallelism of read and write accesses in the same bank; Write Pool reduces the number of repeated write accesses to RFs. Our experiment shows that the performance of STTRAM-based RF is improved by 13% and up to 23% after adopting WarRF. In addition, the energy consumption is reduced by 38% on average compared to SRAM-based RFs.
Cerebral Blood Flow Measurement in Children With Sickle Cell Disease Using Continuous Arterial Spin Labeling at 3.0-Tesla MRI

Background and Purpose— Cerebral infarction is an important complication of sickle cell disease (SCD) and occurs in one third of the patients with SCD. The risk of infarction is commonly attributed to the hyperemia that is associated with anemia and reduces the cerebral vascular reserve. We measured regional cerebral blood flow (rCBF) by continuous arterial spin labeling MRI, which is a noninvasive method that does not require ionizing radiation. The purpose of this study was to examine rCBF in children with SCD and compare it with rCBF in healthy children. Methods— rCBF was measured at 3-T continuous arterial spin labeling MRI in 24 neurological normal patients with SCD and in 12 healthy children matched for ethnicity and age (mean age in both groups 13 years). rCBF was calculated for 6 vascular territories (left and right anterior, middle and posterior cerebral artery). Asymmetry in rCBF was evaluated by measuring differences in flow between left and right hemispheres. The definition of asymmetry (>11.7 mL/100 g/min) was based on a repeatability study performed in 6 healthy adults. Results— The rCBF was of similar magnitude in patients with SCD and control subjects in the frontal, middle, and posterior territories. The majority of patients with SCD (58%) demonstrated a left–right asymmetry of rCBF in one or more vascular territories, whereas none of the control subjects did. Conclusion— In contrast to previous studies, we found no difference in cerebral blood flow between patients and control subjects. We did observe an asymmetry in rCBF in the majority of patients with SCD that was not present in healthy control subjects.
Bilingual Segmented Topic Model

This study proposes the bilingual segmented topic model (BiSTM), which hierarchically models documents by treating each document as a set of segments, e.g., sections. While previous bilingual topic models, such as bilingual latent Dirichlet allocation (BiLDA) (Mimno et al., 2009; Ni et al., 2009), consider only cross-lingual alignments between entire documents, the proposed model considers cross-lingual alignments between segments in addition to document-level alignments and assigns the same topic distribution to aligned segments. This study also presents a method for simultaneously inferring latent topics and segmentation boundaries, incorporating unsupervised topic segmentation (Du et al., 2013) into BiSTM. Experimental results show that the proposed model signiﬁcantly out-performs BiLDA in terms of perplexity and demonstrates improved performance in translation pair extraction (up to +0.083 extraction accuracy).
From Autism to Eating Disorders and More: The Role of Oxytocin in Neuropsychiatric Disorders

Oxytocin (oxy) is a pituitary neuropeptide hormone synthesized from the paraventricular and supraoptic nuclei within the hypothalamus. Like other neuropeptides, oxy can modulate a wide range of neurotransmitter and neuromodulator activities. Additionally, through the neurohypophysis, oxy is secreted into the systemic circulation to act as a hormone, thereby influencing several body functions. Oxy plays a pivotal role in parturition, milk let-down and maternal behavior and has been demonstrated to be important in the formation of pair bonding between mother and infants as well as in mating pairs. Furthermore, oxy has been proven to play a key role in the regulation of several behaviors associated with neuropsychiatric disorders, including social interactions, social memory response to social stimuli, decision-making in the context of social interactions, feeding behavior, emotional reactivity, etc. An increasing body of evidence suggests that deregulations of the oxytocinergic system might be involved in the pathophysiology of certain neuropsychiatric disorders such as autism, eating disorders, schizophrenia, mood, and anxiety disorders. The potential use of oxy in these mental health disorders is attracting growing interest since numerous beneficial properties are ascribed to this neuropeptide. The present manuscript will review the existing findings on the role played by oxy in a variety of distinct physiological and behavioral functions (Figure 1) and on its role and impact in different psychiatric disorders. The aim of this review is to highlight the need of further investigations on this target that might contribute to the development of novel more efficacious therapies. Figure 1 Oxytocin regulatory control of different and complex processes.
Remarks on the racetrack scheme: Stabilizing the moduli of string theory

There are only a small number of ideas for stabilizing the moduli of string theory. One of the most appealing of these is the racetrack mechanism, in which a delicate interplay between two strongly interacting gauge groups fixes the value of the coupling constant. In this note, we explore this scenario. We find that quite generally, some number of discrete tunings are required in order that the mechanism yield a small gauge coupling. Even then, there is no sense in which a weak coupling approximation is valid. On the other hand, certain holomorphic quantities can be computed, so such a scheme is in principle predictive. Searching for models which realize this mechanism is thus of great interest. We also remark on cosmology in these schemes.
Molecular characterization of Saccharomyces cerevisiae Sco2p reveals a high degree of redundancy with Sco1p

The Saccharomyces cerevisiae gene SCO1 has been shown to play an essential role in the transfer of copper to the CuA‐centre of the mitochondrial cytochrome c oxidase subunit Cox2p. By contrast, the function of Sco2p, the gene product of the highly homologous SCO2 gene, remains to be elucidated. Deletion of the SCO2 gene does not affect growth on a variety of carbon sources, including glycerol, lactate and ethanol. We report here, that Sco2p is anchored in the mitochondrial membrane by a single transmembrane segment and displays a similar tripartite structure as Sco1p. Most parts of Sco1p can be replaced by the homologous parts of Sco2p without loss of function. A short stretch of 13 amino acids, immediately adjacent to the transmembrane region, is crucial for Sco1p function and cannot be replaced by its Sco2p counterpart. We propose that this region is relevant for the correct spatial orientation of the C‐terminal part of the protein. Immunoprecipitation and in vitro binding assays show that Sco2p interacts with the C‐terminal portion of Cox2p. This interaction is neither dependent on bound copper ions nor on the presence of Sco1p. Furthermore we report on in vitro binding assays which show that Sco2p can form homomeric complexes, but also heteromeric complexes with Sco1p. Our data suggest that Sco2p is involved in the transfer of copper to Cox2p, but that this activity is insufficient for oxidative growth and not able to substitute for Sco1p activity. Copyright © 2002 John Wiley & Sons, Ltd.
Beyond the Individual: The Dynamic Features of Distributed Affect

Affect has been identified as an important component of the communication practices of distributed teams. Our emerging theory of distributed affect moves beyond the individual as the primary unit of analysis, focusing instead on affect as a dynamic group process. Drawing upon a data set of over four years of chat logs from a distributed scientific collaboration relying on text-based communication to coordinate their work, we expand upon the framework of distributed affect and characterize the concept through five features: transference, resonance, pervasiveness, persistence, and representation. These features provide a set of descriptive components for interactions between people and their environment, their tools, and their present and historical references as part of a dynamical system of affect. We examine specific events in the group's history which highlight the dynamic way affect is operating in this context, and how it influences factors such as creative problem solving. The framework we describe offers a unique analytic lens for the study of computer-supported group work, and a useful tool for framing questions about the continued study of affect in collaborative teams.
Exploratory visualizations and statistical analysis of large, heterogeneous epigenetic datasets

Epigenetic marks, such as DNA methylation and histone modifications, are important regulatory mechanisms that allow a single genomic sequence to give rise to a complex multicellular organism. When studying mechanisms of epigenetic regulation, the analyses depend on the experimental technologies and the available data. Recent advancements in sequencing technologies allow for the efficient extraction of genome-wide maps of epigenetic marks. A number of large-scale mapping projects, such as ENCODE and IHEC, intensively produce data for different tissues and cell cultures. The increasing quantity of data highlights a major bottleneck in bioinformatic research, namely the lack of bioinformatic tools for analyzing these data. To date, there are bioinformatics tools for detailed (mostly visual) inspection of single genomic loci, allowing biologists to focus research on regions of interest. Also, efficient tools for manipulation and analysis of the data have been published, but often they require computer science abilities. Furthermore, the available tools provide solutions to only already well formulated biological questions. What is missing, in our opinion, are tools (or pipelines of tools) to explore the data interactively, in a process that would facilitate a trained biologist to recognize interesting aspects and pursue them further until concrete hypotheses are formulated. A possible solution stems from the best practices in the fields of information retrieval and exploratory search. In this thesis, I propose EpiExplorer, a paradigm for integration of state-of-the-art information retrieval methods and indexing structures, applied to offer instant interactive exploration of large epigenetic datasets. The algorithms we use are developed for semi-structured text data, but we apply them on bioinformatic data through clever textual mapping of biological properties. We demonstrate the power of EpiExplorer in a series of studies that address interesting biological problems. We also present in this manuscript EpiGRAPH, a bioinformatic software that we developed with colleagues. EpiGRAPH helps identify and model significant biological associations among epigenetic and genetic properties for sets of regions. Using EpiExplorer and EpiGRAPH, independently or in a pipeline, provides the bioinformatic community with access to large databases of annotations, allows for exploratory visualizations or statistical analysis and facilitates reproduction and sharing of results.
Delay dependent stability condition for the port Hamiltonian systems with time varying delay

This paper proposes the delay dependent stability condition for the nonlinear port Hamiltonian (pH) systems with time varying delay. A modified Lyapunov-Krasovskii functional is used to derive a sufficient condition for asypmtotical stablity in terms of LMIs. The derived sufficient condition is less conservative than ones shown in the literature. Numerical example is given to show effectiveness of the proposed method.
Inhibition of MEK Induces Fas Expression and Apoptosis in Lymphomas Overexpressing Ras

Published results implicate PI3 kinase as a target of oncogenic Ras activity leading to the suppression of Fas but whether other Ras targets (e.g. Raf-1) are also involved is unclear. Here we report that thymic lymphomas overexpressing Ras and Raf-1 exhibit low expression of Fas. We show that expression of Fas in these lymphomas can be increased not only in the presence of a specific inhibitor (LY294002) of PI3 kinase, but also in the presence of specific inhibitor (PD98059) of MEK, downstream target of Raf-1. Both treatments result in accumulation of ERK in cytosol of lymphoma cells suggesting cross-talk between these two pathways regulating Fas expression. Treatment with PD98059 also results in apoptosis of the lymphoma cells but not of normal thymocytes expressing low Raf-1 levels. These observations provide evidence for involvement of Raf-1/MEK/ERK pathway in Ras-mediated inhibition of Fas expression and in selective promotion of survival of lymphoma cells.
Why do we like frightening: Psychophysiology of horror movies

The horror film industry brings in viewers from all over the world and from every caste of life. But, people differ greatly in their enjoyment of horror movies. Biologically fear is a warning signal that death, injury or destruction is imminent, and it is designed to cause the perceiver to avoid the dangerous situation. Fear, psychologically, is also a warning, and it basically functions to prevent the possibility of personality disintegration. Specific parts of the brain work together to trigger our reactions to fear stimuli. These include: • Amygdala • Hippocampus • Hypothalamus • Sensory cortex • Thalamus Studies of neuronal activity in the brain have suggested that the prefrontal cortex, a cognitive and emotional learning center that helps interpret sensory stimuli, is responsible for the conscious assessment of danger. After passing through the amygdala, sensory information is sent on to the cortex. There, the frightening stimulus is examined in detail to determine whether or not a real threat exists. The primary purpose of this papaer was to look at the individual differences in people's horror film viewing behavior; furthermore, whether certain personality traits predicted physiological reactions to horror film viewing. These paper also suggest personality differences in people that watch horror movies and people that do not. Furthermore, it suggests psycho-physiological differences within and between those that watch horror films.