Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

Managing Trade-Offs Most organisms experience selection on a host of traits to determine their likelihood to succeed evolutionarily. However, specific traits may experience trade-offs in determining an organism's optimal phenotype. Shoval et al. (p. 1157; see the Perspective by Noor and Milo) relate physical traits to the task that they are optimizing using a Pareto curve, a power law probability distribution, to show that a single set of trait values optimizes performance at a given task and that performance decreases as an organism's phenotype moves away from this set of trait values. The results suggest how selection makes the best trade-offs for an arbitrary number of tasks and traits and may explain examples of evolutionary variation. The fitness of an organism can be modeled graphically to determine how phenotypic trade-offs are maximized. Biological systems that perform multiple tasks face a fundamental trade-off: A given phenotype cannot be optimal at all tasks. Here we ask how trade-offs affect the range of phenotypes found in nature. Using the Pareto front concept from economics and engineering, we find that best–trade-off phenotypes are weighted averages of archetypes—phenotypes specialized for single tasks. For two tasks, phenotypes fall on the line connecting the two archetypes, which could explain linear trait correlations, allometric relationships, as well as bacterial gene-expression patterns. For three tasks, phenotypes fall within a triangle in phenotype space, whose vertices are the archetypes, as evident in morphological studies, including on Darwin’s finches. Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes.
Functional properties of corticotectal neurons in the monkey's frontal eye field.

1. We examined the activity of identified corticotectal neurons in the frontal eye field of awake behaving rhesus monkeys (Macaca mulatta). Corticotectal neurons were antidromically excited using biphasic current pulses passed through monopolar microelectrodes within the superior colliculus. The activity of single corticotectal neurons was studied while the monkey performed behavioral tasks designed to test the relation of the neuron's discharge to visual and oculomotor events. 2. Fifty-one frontal eye field corticotectal neurons were examined in two monkeys. Current thresholds for antidromic excitation ranged from 6 to 1,200 microA, with a mean of 330 microA. Antidromic latencies ranged from 1.2 to 6.0 ms, with a mean of 2.25 ms. 3. Fifty-three percent of the identified corticotectal neurons were classified as having movement-related activity. They had little or no response to visual stimuli, but very strong activity before both visually guided and memory-guided saccades. An additional 6% of corticotectal neurons had visuomovement activity, combining both a visual- and a saccade-related response. In each case, visuomovement neurons antidromically excited from the superior colliculus had movement-related activity, which was much stronger than the visual component of their response. 4. Twenty-two percent of the corticotectal neurons were primarily responsive to visual stimulation of the fovea. These included both neurons responding to the onset and neurons responding to the disappearance of a light flashed on the fovea. 5. The remaining 20% of the corticotectal neurons were a heterogeneous group whose activity could not be classified as movement, visuomovement or foveal. Their responses included postsaccadic, anticipatory, and reward-related activity, as well as activity modulated during certain directions of smooth-pursuit eye movements. One neuron was unresponsive during all of the behavioral tasks used. There were no corticotectal neurons that could be classified as primarily responsive to peripheral visual stimuli. 6. Histological reconstructions of electrode penetrations localized corticotectal neurons to layer V of the frontal eye field. For 22 corticotectal neurons tested, each had its minimum threshold for antidromic excitation within the superior colliculus, as judged by either histological confirmation, or surrounding neuronal responses recorded through the stimulation microelectrode. The majority of these neurons had minimum threshold sites within the intermediate layers, a few minimum threshold sites were located within the superficial or deep collicular layers. (ABSTRACT TRUNCATED AT 400 WORDS)
Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design

Six helix surface positions of protein G (Gβ1) were redesigned using a computational protein design algorithm, resulting in the five fold mutant Gβ1m2. Gβ1m2 is well folded with a circular dichroism spectrum nearly identical to that of Gβ1, and a melting temperature of 91 °C, ∼6°C higher than that of Gβ1. The crystal structure of Gβ1m2 was solved to 2.0 Å resolution by molecular replacement. The absence of hydrogen bond or salt bridge interactions between the designed residues in Gβ1m2 suggests that the increased stability of Gβ1m2 is due to increased helix propensity and more favorable helix dipole interactions.
Emergent Intentionality in Perception-Action Subsumption Hierarchies

A cognitively-autonomous artificial agent may be defined as one able to modify both its external world-model and the framework by which it represents world, requiring two simultaneous optimization objectives. This presents deep epistemological issues centered on the question of how a framework for representation (as opposed to the entities it represents) may be objectively validated. In this summary paper, formalizing previous work in this field, it is argued that subsumptive perception-action learning uniquely has the capacity to resolve these issues by a) building the perceptual hierarchy from the bottom up so as to ground all proposed representations and b) maintaining a bijective coupling between proposed percepts and projected action possibilities to ensure empirical falsifiability of these grounded representations. In doing so, we will show that such subsumptive perception-action learners intrinsically incorporate a model for how intentionality emerges from randomized exploratory activity in the form of 'motor babbling'. Moreover, such a model of intentionality also naturally translates into a model for human-computer interfacing that makes minimal assumptions as to cognitive states.
Insulin-like growth factor 1 treatment via hydrogels rescues cochlear hair cells from ischemic injury

This study was designed to investigate the protective effects of recombinant human insulin-like growth factor 1 (rhIGF1), applied locally via a hydrogel, against ischemic damage of the cochleae in gerbils. A hydrogel was immersed in rhIGF1 or saline and was applied on the round window membrane 30 min after the ischemia. Local rhIGF1 treatment significantly reduced the elevation of auditory brain responses thresholds at a frequency of 8 kHz on days 1, 4, and 7 after ischemia. A histological analysis revealed increased survival of inner hair cells in the animals treated with rhIGF1 via the hydrogel 7 days after ischemia. These findings showed that local rhIGF1 application using a hydrogel has the potential to protect the cochleae from ischemic injury.
Flexible control over optical reflection property of metallic surfaces via pulse laser

The control of fundamental optical properties, such as transmission and reflection, over metallic surfaces plays a significant role in multiple fields like solar cells and aerospace. The direct laser etching in air can perform a variety of flexible control abilities in optical functional metal surfaces. In this paper, the authors use the aluminum alloy as an example of widely metal materials and propose two kinds of controlling strategies: large-range controlling strategy and small-range precise controlling strategy. The former changes the process repeat number of femtosecond lasers or the scanning speed of nanosecond lasers. The latter combines the femtosecond laser and the nanosecond laser. The results show that when the process repeat number of femtosecond lasers is changed from 30 to 1, the height of the induced micropillars on the surface of Al alloy is changed from 80 to 6 μm. As a result, the reflectivity of samples will change from ∼16% to ∼87%. The nanosecond laser-induced micro-/nanostructures achieve the reflectivity changing from ∼18% to ∼79% when the scanning speed changes from 10 to 400 mm/s in a spectrum range of 250–2000 nm. What is more, after being fabricated in the way of two-step controlling strategy, the reflectivity raises from ∼30% to ∼40% when the scanning speed of nanosecond lasers changes from 10 to 200 mm/s, while the reflectivity of samples fabricated simply by nanosecond laser changes from ∼18% to ∼66% when the scanning speed changes in the same range and other parameters are kept the same. In addition, the authors demonstrated that the two-step precise controlling strategy is applicable to a variety of metals such as copper, stainless steel, and titanium.The control of fundamental optical properties, such as transmission and reflection, over metallic surfaces plays a significant role in multiple fields like solar cells and aerospace. The direct laser etching in air can perform a variety of flexible control abilities in optical functional metal surfaces. In this paper, the authors use the aluminum alloy as an example of widely metal materials and propose two kinds of controlling strategies: large-range controlling strategy and small-range precise controlling strategy. The former changes the process repeat number of femtosecond lasers or the scanning speed of nanosecond lasers. The latter combines the femtosecond laser and the nanosecond laser. The results show that when the process repeat number of femtosecond lasers is changed from 30 to 1, the height of the induced micropillars on the surface of Al alloy is changed from 80 to 6 μm. As a result, the reflectivity of samples will change from ∼16% to ∼87%. The nanosecond laser-induced micro-/nanostructures a.
“New”‐clear functions of PDK1: Beyond a master kinase?

Activation of cytosolic phosphoinositide‐3 kinase (PI‐3K) signaling pathway has been well established to regulate gene expression, cell cycle, and survival by feeding signals to the nucleus. In addition, strong evidences accumulated over the past few years indicate the presence of an autonomous inositol lipid metabolism and PI‐3K signaling within the nucleus. Much less, however, is known about the role and regulation of this nuclear PI‐3K pathway. Components of the PI‐3K signaling pathway, including PI 3‐kinase and its downstream kinase Akt, have been identified at the nuclear level. Consistent with the presence of a complete PI‐3K signaling pathway in the nucleus, we have recently found that phosphoinositide‐dependent kinase 1 (PDK1), a kinase functioning downstream of PI‐3K and upstream of Akt, is a nucleo‐cytoplasmic shuttling protein. In the present review, we update our current knowledge on the regulatory mechanisms and the functional roles of PDK1 nuclear translocation. We also summarize some of the kinase‐independent activities of PDK1 in cell signaling. J. Cell. Biochem. © 2005 Wiley‐Liss, Inc.
EXPLORING THE RHEOLOGY OF SOFT GLASSY MATTER June 19 , 2009

In this paper I will review some of the recent results that have been obtained in the soft glassy materials rhology. I will concentrate my attention on the formulation of two main models for soft materials: Soft Glassy Material (SRG) model proposed by Peter Sollich that quanti es the mechanical response of these systems and predicts aging under suitable conditions and a time recurrence model (called Hop eld-Herz model by me) for earthquakes. I will discuss in particular that if the shear stress is small, it is possible characterize the system through linear rheology.
Multirelational Social Recommendations via Multigraph Ranking

Recommender systems aim to identify relevant items for particular users in large-scale online applications. The historical rating data of users is a valuable input resource for many recommendation models such as collaborative filtering (CF), but these models are known to suffer from the rating sparsity problem when the users or items under consideration have insufficient rating records. With the continued growth of online social networks, the increased user-to-user relationships are reported to be helpful and can alleviate the CF rating sparsity problem. Although researchers have developed a range of social network-based recommender systems, there is no unified model to handle multirelational social networks. To address this challenge, this paper represents different user relationships in a multigraph and develops a multigraph ranking model to identify and recommend the nearest neighbors of particular users in high-order environments. We conduct empirical experiments on two real-world datasets: 1) Epinions and 2) Last.fm, and the comprehensive comparison with other approaches demonstrates that our model improves recommendation performance in terms of both recommendation coverage and accuracy, especially when the rating data are sparse.
Improving gate level fault coverage by RTL fault grading

A practical RTL level testability analysis methodology is presented in the paper. Both RTL models and functional verification patterns are used in the RTL testability analysis. An RTL fault simulator which is the core of the methodology, is developed to support RTL testability analysis. It is able to generate quantitative RTL fault coverage and provide information for test pattern improvement to improve fault coverage and design modifications to improve testability at the RTL level. Experimental results show that RTL fault coverage is quite close to fault coverage achieved at the gate level when designs are completed and mapped to a technology library. The results also show that effort to improve fault coverage at the RTL level very likely results in corresponding improvement of fault coverage at the gate level. An investigation of some of the causes of difference between RTL fault coverage and actual gate level fault coverage is also reported in the paper.
Concussion Nondisclosure During Professional Career Among a Cohort of Former National Football League Athletes

Background: Despite a focus on the incidence and effects of concussion, nondisclosure of sports-related concussions among retired players from the National Football League (NFL) has yet to be examined. Purpose: Examine the prevalence of and factors associated with nondisclosure of sports-related concussions in former NFL athletes. Study Design: Cross-sectional study; Level of evidence, 3. Methods: A sample of 829 former NFL players completed a general health survey. This historical cohort included players who had played before World War II to 2001. Respondents retrospectively recalled sports-related concussions that they sustained during their professional careers and whether at least one of these sports-related concussions was not reported to medical staff. We computed the prevalence of nondisclosure among those recalling sport-related concussions during their professional careers. Multivariable binomial regression estimated adjusted prevalence ratios (PR) with 95% confidence intervals (CIs) controlling for race/ethnicity, number of years played, primary position played, professional career concussion history, and playing era. Playing era was categorized by whether the majority of a player’s career was before or after a 1976 rule change to limit contact (“spearing”). Results: Overall, 417 (50.3%) respondents reported they had sustained a concussion and did not inform medical staff at least once during their professional playing career. Nonwhite respondents had a higher prevalence of nondisclosure than white/non-Hispanic respondents (adjusted PR = 1.19; 95% CI, 1.02-1.38). An interaction between professional career concussion history and playing era was also found (P = .08). Compared with those in the pre–spearing rule change group with 1 or 2 concussions, all other groups had larger prevalences of nondisclosure (increases ranging from 41% to 153% in multivariable models). Across concussion strata, nondisclosure prevalence was generally higher in the post–spearing rule change group than the pre–spearing rule change group, with the largest differences found among those with 1 or 2 concussions or those with 3 or 4 concussions. Conclusion: A large proportion of former NFL players in this historical cohort reported at least one instance of not disclosing sports-related concussions to medical staff. Future research on concussion nondisclosure needs to identify mechanisms to improve football players’ intentions to disclose concussion-related symptoms to health care providers and to equip health care providers with more effective strategies for timely identification of concussion.
Human Telomerase Reverse Transcriptase Motifs Required for Elongation of a Telomeric Substrate*

The reverse transcriptase telomerase copies an internal RNA template to synthesize telomeric simple-sequence repeats. In the cellular context, telomerase must elongate its few intended substrates (authentic chromosome ends) without spurious activity on other potential substrates (chromosome ends created by damage, repair, or recombination). Many mechanisms have been proposed to account for the biological substrate specificity of telomerase, with most models focusing on protein-protein interactions between telomerase and telomeric chromatin. Telomerase activity assays testing the elongation of model oligonucleotide substrates have revealed that in addition to hybridization with the RNA template, optimal DNA substrates also engage telomerase protein-based interaction sites. The physiological significance of these non-template interaction sites has not been established. We used in vivo reconstitution to assemble telomerase enzymes with variant telomerase reverse transcriptase proteins. Several telomerase enzyme variants retained a wild-type level of catalytic function in vitro when assayed using an artificial sequence substrate but exhibited reduced activity on a more physiological telomeric-sequence substrate. Telomerases that demonstrated this defect in telomeric substrate usage in vitro also failed to support telomere length maintenance in vivo. Our findings suggest that non-template interactions of the telomerase ribonucleoprotein with telomeric DNA play a critical role in supporting telomerase function on its appropriate cellular substrates.
Tardive Dyskinesia: Treatment with Aripiprazole

Tardive dyskinesia is characterized by choreiform movements, or rhythmic abnormal involuntary movements of the face, mouth, tongue, trunk, and limbs. It is frequently associated with the use of neuroleptic medications. The choreiform movements are irreversible in some patients, even after the drug is withdrawn. Although no reliable treatment for tardive dyskinesia exists, atypical antipsychotics are associated with a significantly lower incidence of tardive dyskinesia than typical antipsychotics. Moreover, recent reports suggest that atypical antipsychotics may have a beneficial effect on tardive dyskinesia remission. Until recently, evidence for the effectiveness of aripiprazole on tardive dyskinesia has been mixed. Aripiprazole has a unique mechanism of action and has various effects in tardive dyskinesia. The drug acts as a partial D2 receptor agonist that can stabilize D2 up-regulation, and as a partial 5-HT1A receptor agonist and a 5-HT2A receptor antagonist, and can increase the release of dopamine in the striatum.
A practical guide and software for analysing pairwise comparison experiments

Most popular strategies to capture subjective judgments from humans involve the construction of a unidimensional relative measurement scale, representing order preferences or judgments about a set of objects or conditions. This information is generally captured by means of direct scoring, either in the form of a Likert or cardinal scale, or by comparative judgments in pairs or sets. In this sense, the use of pairwise comparisons is becoming increasingly popular because of the simplicity of this experimental procedure. However, this strategy requires non-trivial data analysis to aggregate the comparison ranks into a quality scale and analyse the results, in order to take full advantage of the collected data. This paper explains the process of translating pairwise comparison data into a measurement scale, discusses the benefits and limitations of such scaling methods and introduces a publicly available software in Matlab. We improve on existing scaling methods by introducing outlier analysis, providing methods for computing confidence intervals and statistical testing and introducing a prior, which reduces estimation error when the number of observers is low. Most of our examples focus on image quality assessment.
The LIMSI QAst systems: Comparison between human and automatic rules generation for question-answering on speech transcriptions

In this paper, we present two different question-answering systems on speech transcripts. These two systems are based on a complete and multi-level analysis of both queries and documents. The first system uses handcrafted rules for small text fragments (snippet) selection and answer extraction. The second one replaces the handcrafting with an automatically generated research descriptor. A score based on those descriptors is used to select documents and snippets. The extraction and scoring of candidate answers is based on proximity measurements within the research descriptor elements and a number of secondary factors. The preliminary results obtained on QAst (QA on speech transcripts) development data are promising ranged from 72% correct answer at 1 st rank on manually transcribed meeting data to 94% on manually transcribed lecture data.
Thoracic aortic atheroma severity predicts high-risk coronary anatomy in patients undergoing transesophageal echocardiography

Introduction We hypothesized a relationship between severity of thoracic aortic atheroma (AA) and prevalence of high-risk coronary anatomy (HRCA). Material and methods We investigated AA diagnosed by transesophageal echocardiography and HRCA diagnosed by coronary angiography in 187 patients. HRCA was defined as ≥ 50% stenosis of the left main coronary artery or significant 3-vessel coronary artery disease (≥ 70% narrowing). Results HRCA was present in 45 of 187 patients (24%). AA severity was grade I in 55 patients (29%), grade II in 71 patients (38%), grade III in 52 patients (28%), grade IV in 5 patients (3%), and grade V in 4 patients (2%). The area under receiver operating characteristic curve for AA grade predicting HRCA was 0.83 (p = 0.0001). The cut-off points of AA to predict HRCA was > II grade. The sensitivity and specificity of AA > grade II to predict HRCA were 76% and 81%, respectively. After adjustment for 10 variables with significant differences by univariate regression, AA > grade II was related to HRCA by multivariate regression (odds ratio = 7.5, p< 0.0001). During 41-month follow-up, 15 of 61 patients (25%) with AA >grade II and 10 of 126 patients (8%) with AA grade ≤ 2 died (p= 0.004). Survival by Kaplan-Meier plot in patients with AA > grade II was significantly decreased compared to patients with AA ≤ grade II (p= 0.002). Conclusions AA > grade II is associated with a 7.5 times increase in HRCA and with a significant reduction in all-cause mortality.