Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon source-dependent expansion of the genetic code in bacteria

Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNAPyl is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ∼5% of ORFs, whereas Pyl-decoding bacteria (∼20% of ORFs contain in-frame TAGs) regulate Pyl-tRNAPyl formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases.
Pronunciation Proficiency in the First and Second Languages of Korean-English Bilinguals.

This study examined pronunciation proficiency in both the first (Korean) and second (English) languages of bilinguals. The participants were adult immigrants whose age of arrival in the USA ranged from 1–23 years. English and Korean sentences were rated by native listeners to obtain measures of pronunciation proficiency. English pronunciation of participants with ages of arrival of 1–5 years was close to monolinguals, heavier accents were noted as ages of arrival increased from 6 to 23 years. Korean pronunciation of participants with ages of arrival of 1–7 years was distinctly accented, while those with ages of arrival of 12–23 years were rated the same as monolinguals. Participants with ages of arrival of 1–9 years pronounced English better than Korean, whereas the reverse was true for ages of arrival of 12–23 years. Overall, the results were more consistent with the view that deviations from native pronunciation result from interactions between the languages of bilinguals rather than with the view of a maturationally defined critical period for language learning.
On Experimental and Philosophical Investigations of Mental Timing: A Response to Commentary

Reinterpretations of Libet's results have received support from most commentaries. Libet's arguments against alternative hypotheses are contested. Latency depends on intensity. Integration of intensity and duration explains the Minimum Train Duration. Analogies of Libet's timing of intentions with control (flash-lag-like) experiments indicate biases of opposite signs, according to intramodal or intermodal results. Rosenthal's view of nonconscious intentions (or sensations) becoming conscious after a delay is favored. Compatibilist free will is discussed.
Altruism in Humans

Introduction Part I: A Theory of Altruistic Motivation 1. The Empathy-Altruism Hypothesis 2. Antecedents of Empathic Concern 3. Behavioral Consequences of Empathy-Induced Altruism Part II: Empirical Evidence 4. Turning to Experiments 5. Testing the Empathy-Altruism Hypothesis 6. Two Further Challenges to the Empathy-Altruism Hypothesis Part III: Altruism in Action 7. Benefits of Empathy-Induced Altruism 8. Liabilities 9. Toward a Pluralism of Prosocial Motives-and a More Humane Society Summary and Conclusion References
Design and Implementation of a Monocular Vision Sensor Model for Mobile Robot Localization

General availability of inexpensive, all-terrain, lightweight autonomous mobile robots would drive innovation in many application areas such as security, remote sensing, inspection, and landmine detection. Many of these tasks require accurate 6-DOF robot localization, and cameras are potentially ideal for this purpose, but most current techniques use stereo vision sensors, which are expensive or difficult to calibrate. Towards flexible and low cost vision-based robot localization, we have designed, implemented, and evaluated a prototype system incorporating SIFT feature detection and factorization-based methods for sparse Euclidean reconstruction from three uncalibrated views. We test the system on synthetic data, in a virtual world, and in a real-world outdoor environment, using three different reconstruction algorithms. We find that of the algorithms tested, Han and Kanade’s algorithm achieves the best reconstruction. We conclude that SIFT combined with factorizationbased structure from motion is suitable for single-camera mobile robot
DNA methylation biomarkers in cancer: progress towards clinical implementation

Altered DNA methylation is ubiquitous in human cancers and specific methylation changes are often correlated with clinical features. DNA methylation biomarkers, which use those specific methylation changes, provide a range of opportunities for early detection, diagnosis, prognosis, therapeutic stratification and post-therapeutic monitoring. Here we review current approaches to developing and applying DNA methylation biomarkers in cancer therapy. We discuss the obstacles that have so far limited the routine use of DNA methylation biomarkers in clinical settings and describe ways in which these obstacles can be overcome. Finally, we summarize the current state of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including SEPT9, VIM, SHOX2, PITX2 and MGMT.
Design and Development of a Low-Cost Multisensor Inertial Data Acquisition System for Sailing

This paper presents the development of an inertial measurement data acquisition system intended for use in sailboats. The variables of interest are three-axis acceleration, three-axis rotation, Global Positioning System (GPS) position/velocity, magnetic compass bearing, and wind speed/direction. The design focus is on low-cost microelectromechanical systems-based technology and demonstrating the validity of these technologies in a scientific application. A prototype is constructed and submitted to a series of tests to demonstrate functionality and soundness of the design. Contributions of this paper include the novel application of inertial measurement unit technology to a sailboat racing application, the integration of all instrumentation, creative ruggedized packaging, and emphasizing the use of low-cost commercial off-the-shelf technology.
Common sites and etiologies of residents' misinterpretation of head CT scans in the emergency department of a level I trauma center.

BACKGROUND Misinterpretation of head computerized tomographic (CT) scans by radiology residents in the emergency department (ED) can result in delayed and even erroneous radiology diagnoses. Better knowledge of pitfalls and environmental factors may decrease the occurrence of these errors. OBJECTIVES To evaluate common misinterpretations of head CT scans by radiology residents in a level I trauma center ED. METHODS We studied 955 head CT scans of patients admitted to our ED from January 2010 to May 2011. They were reviewed separately by two senior neuroradiologists and graded as being unimportant (score of 1), important but not requiring emergent treatment (score of 2), and important requiring urgent treatment (score of 3). We recorded the time of day the examination was performed, the year of residency, the site, subsite and side of the lesion, the pathology, the anatomical mistake, false-positive findings, and the attending neuroradiologists' score. RESULTS A total of 955 examinations were interpreted of which 398 had misinterpreted findings that were entered into the database, with the possibility of multiple errors per examination. The overall misinterpretation rate was 41%. The most commonly missed pathologies were chronic infarcts, hypodense lesions, and mucosal thickening in the paranasal sinuses. The most common sites for misdiagnosis were brain lobes, sinuses and deep brain structures. The highest percentage of misinterpretation occurred between 2.30 p.m. and 8 p.m. and the lowest between midnight and 8 a.m. (P < 0.05). The overall percentage of errors involving pathologies with a score of 3 by at least one of the neuroradiologists was 4.7%. Third-year residents had an overall higher error rate and first-year residents had significantly more false-positive misinterpretations compared to the other residents. CONCLUSIONS The percentage of errors made by our residents in cases that required urgent treatment was comparable to the published data. We believe that the intense workload of radiology residents contributes to their misinterpretation of head CT findings.
Rate Region of the Vector Gaussian CEO Problem With the Trace Distortion Constraint

We establish a new extremal inequality, which is further leveraged to give a complete characterization of the rate region of the vector Gaussian CEO problem with the trace distortion constraint. The proof of this extremal inequality hinges on a careful analysis of the Karush-Kuhn-Tucker necessary conditions for the non-convex optimization problem associated with the Berger-Tung scheme, which enables us to integrate the perturbation argument by Wang and Chen and the distortion projection method by Rahman and Wagner.
GENETIC DIFFERENTIATION AND SHELL MORPHOLOGY OF TROCHULUS OREINOS (WAGNER, 1915) AND T. HISPIDUS (LINNAEUS, 1758) (PULMONATA: HYGROMIIDAE) IN THE NORTHEASTERN ALPS

Trochulus oreinos oreinos and T. oreinos scheerpeltzi are two land snail taxa endemic to the Northeastern Austrian Alps, which have been regarded as subspecies of the highly variable, widespread land snail T. hispidus. We analysed these three taxa morphologically and genetically to evaluate whether a delimitation between them is possible and, if so, to resolve their phylogenetic relationships. Shell morphological results revealed high similarity between the two T. oreinos taxa, and that they are clearly separated from T. hispidus. Additionally, the T. oreinos subspecies concur with respect to their habitat preferences, as they are both restricted to rocky high alpine areas, whereas the local form of T. hispidus is distributed over a wider altitudinal range in moist areas and scrubby perennial herb vegetation near water bodies. While the morphological and ecological results allow clear differentiation between T. hispidus and T. oreinos only, analyses of the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed high sequence divergences between all three taxa, which indicates that they represent old lineages. The two T. oreinos taxa appear as distantly related sister groups, well separated from T. hispidus. Whether T. o. oreinos and T. o. scheerpeltzi should be considered as species cannot be decided at the current state of knowledge.
Row-Action Methods for Compressed Sensing

Compressed sensing uses a small number of random, linear measurements to acquire a sparse signal. Nonlinear algorithms, such as 11 minimization, are used to reconstruct the signal from the measured data. This paper proposes row-action methods as a computational approach to solving the 11 optimization problem. This paper presents a specific row-action method and provides extensive empirical evidence that it is an effective technique for signal reconstruction. This approach offers several advantages over interior-point methods, including minimal storage and computational requirements, scalability, and robustness
THE EFFECT OF LIGHT ON THE ELECTRICAL POLARITY AND THE RATE OF ELONGATION OF THE AVENA COLEOPTILE.

Illumination of plants causes their electrical polarity and growth rate to change. These facts were observed years ago, but the relationship, if any, between these two changes has not been established. The experiments to be presented are concerned with this relationship. It appears that HAAKE (9) was the first investigator to observe alterations in the electrical polarities of plants caused by changes in illumination. WALLER (16), who cites the literature to 1925, presented evidence for associating the electrical changes of green leaves with the activity of chlorophyll. The etiolated seedlings used by him gave little if any electrical response when illuminated. Since 1925, GLASS (8) and BROWN (5) have shown that the electrical polarity of Elodea leaves and internodes of Chara vulgaris manifest notable changes when their illumination is varied. SHEARD (12) exposed leaves of the sunflower and Poinsettia to both ultra-violet and infrared light and obtained potential changes as high as 0.3 volt. Effects of light on the bioelectric potentials of Halicystis and Valonia have also been noted (2, 10, 11). It happens, however, that the effect of radiant energy on the bioelectrical potentials of etiolated plants has rarely been observed. CLARK (6) uniformly illuminated 30to 40-mm. etiolated Avena seedlings with 600,000 meter-candle-seconds of incandescent light and recorded changes in the longitudinal electrical polarity. His data show a diphasic electrical variation in which the polarity first decreases, then increases before returning to the original value. Numerous experiments have been performed to show the influence of il-lumination on the growth of the Avena coleoptile. One aspect of this problem deals with the inhibition of growth (3). VAN DILLEWIJN (7) subjected the Avena coleoptile to uniform illumination and noted effects on the growth rates by both continued and short-period irradiation. After a latent period, he observed a period of depressed growth showing two types of responses. In the first and short response, the maximum growth-rate depression was reached after 30 minutes. The second and longer, reaction reached the maximum growth-rate depression after 90 minutes. It has been demonstrated that the second depression can be detected only when the apex of the plant is illuminated. [WENT (17) : tip response. ] The short period of depressed growth rate can be observed when either the basal portion or the entire coleoptile is illuminated. (WENT: base response.) The present exSupported by the University of Texas Research Institute. 467
From technology to activity development: the challenge of using students as participants in a PD project

The interest of evaluating new information technologies in real-life conditions "in the wild" has recently been increasing. For this new direction, researchers and technology developers need to find the real-life context in which to intervene and the users willing to test the prototype technologies in their everyday practices. Additional complications follow from the ecology of several applications used together. In this paper, experiences from a complex real-life experiment with a set of three research prototypes are analyzed. Based on the results, master-level students are competent users when evaluating individual prototypes but less suitable for integrating separate prototypes into meaningful ecology and envisioning a transition from a traditional way of working to a new one. For this task, users are needed who have a vision of the new and who recognize the problems and tensions between the old and the nascent new.
Making the invisible visible: near-infrared spectroscopy and phlebotomy in children.

AIM Phlebotomy and venous cannulation are the most frequently performed and the most distressing invasive procedures in pediatrics. The aim of this pilot study was to assess whether a novel vein imaging system was advantageous for the identification of superficial veins, thus reducing the number of skin punctures. METHODS The Vein Viewer was trialled in 50 children <16 years of age who required venous blood sampling or peripheral venous catheterization as part of their standard clinical care. A questionnaire with 10 questions about their experience of using this equipment was distributed to the pediatric doctors and nurses performing the procedures. RESULTS During a 9-month period, 38 venipunctures and 12 cannulations were performed in 50 children (mean age 6.67 years). On average, 1.7 puncture attempts per child were necessary. Fifty questionnaires were completed by 11 consultants, 16 registrars, 20 senior house officers, and 3 nurses. Seventy-two percent rated the imaging device as useful, 8% as not useful, and 20% remained neutral. Visibility of the peripheral veins was improved in 76% of children, and the same as with room light in 24%. CONCLUSIONS Near-infrared technology facilitated venipuncture and venous cannulation in a pediatric cohort. Further, controlled trials are required including children of specific age groups and those from ethnic minorities.
Model Formulation: The BRIDG Project: A Technical Report

OBJECTIVES The Biomedical Research Integrated Domain Group (BRIDG) project is a collaborative initiative between the National Cancer Institute (NCI), the Clinical Data Interchange Standards Consortium (CDISC), the Regulated Clinical Research Information Management Technical Committee (RCRIM TC) of Health Level 7 (HL7), and the Food and Drug Administration (FDA) to develop a model of the shared understanding of the semantics of clinical research. DESIGN The BRIDG project is based on open-source collaborative principles and an implementation-independent, use-case driven approach to model development. In the BRIDG model, declarative and procedural knowledge are represented using the Unified Modeling Language (UML) class, activity and state diagrams. MEASUREMENTS The BRIDG model currently contains harmonized semantics from four project use cases: the caXchange project and the patient study calendar project from caBIG; the standard data tabular model (SDTM) from CDISC; and the regulated products submission model (RPS) from HL7. Scalable harmonization processes have been developed to expand the model with content from additional use cases. RESULTS The first official release of the BRIDG model was published in June 2007. Use of the BRIDG model by the NCI has supported the rapid development of semantic interoperability across applications within the caBIG program. CONCLUSIONS The BRIDG project has brought together different standards communities to clarify the semantics of clinical research across pharmaceutical, regulatory, and research organizations. Currently, the NCI uses the BRIDG model to support interoperable application development in the caBIG, and CDISC and HL7 are using the BRIDG model to support standards development.
Involvement of Cell Cycle Elements, Cyclin-dependent Kinases, pRb, and E2F·DP, in B-amyloid-induced Neuronal Death*

Previous evidence by others has indicated that a variety of cell cycle-related molecules are up-regulated in brains of Alzheimer’s disease patients. The significance of this increase, however, is unclear. Accordingly, we examined the obligate nature of cyclin-dependent kinases and select downstream targets of these kinases in death of neurons evoked by B-amyloid (AB) protein. We present pharmacological and molecular biological evidence that cyclin-dependent kinases, in particular Cdk4/6, are required for such neuronal death. In addition, we demonstrate that the substrate of Cdk4/6, pRb/p107, is phosphorylated during AB treatment and that one target of pRb/p107, the E2F·DP complex, is required for AB-evoked neuronal death. These results provide evidence that cell cycle elements play a required role in death of neurons evoked by AB and suggest that these elements play an integral role in Alzheimer’s disease-related neuronal death.
Mapping the pathways of information processing from sensation to action in four distinct sensorimotor tasks

Two sensorimotor tasks that share neither sensory nor motor modality can interfere with one another when they are performed simultaneously. A possible cause for this interference is the recruitment of common brain regions by these two tasks, thereby creating a bottleneck of information processing. This hypothesis predicts that such “bottleneck” regions would be activated by each task even when they are performed separately. To test this prediction, we sought to identify, with fMRI, brain regions commonly activated by sensorimotor tasks that share neither sensory input nor motor output. One group of subjects was scanned while they performed in separate runs an auditory‐vocal (AVo) task and a visuo‐manual (ViM) task, while a second group of subjects performed the reversed sensorimotor mapping tasks (AM and ViVo). The results revealed strong activation preferences in specific sensory and motor cortical areas for each sensory and motor modality. By contrast, the posterior portion of the lateral prefrontal cortex (pLPFC), anterior insula, and, less consistently, the anterior cingulate, presupplementary and supplementary motor areas, and subcortical areas were commonly activated across all four sensorimotor tasks. These results were observed in both blocked and event‐related fMRI designs, in both 3D‐group averaged and 2D‐individual subject analyses, and were replicated within individuals across scanning sessions. These findings not only suggest that these brain regions serve a common amodal function in sensorimotor tasks, they also point to these regions—particularly, the pLPFC and anterior insula—as candidate neural substrates underlying a central hub of information processing in the human brain. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
Idioms-Proverbs Lexicon for Modern Standard Arabic and Colloquial Sentiment Analysis

the fair amount of works in sentiment analysis (SA) and opinion mining (OM) systems in the last decade and with respect to the performance of these systems, but it still not desired performance, especially for morphologically-Rich Language (MRL) such as Arabic, due to the complexities and challenges exist in the nature of the languages itself. One of these challenges is the detection of idioms or proverbs phrases within the writer text or comment. An idiom or proverb is a form of speech or an expression that is peculiar to itself. Grammatically, it cannot be understood from the individual meanings of its elements and can yield different sentiment when treats as separate words. Consequently, In order to facilitate the task of detection and classification of lexical phrases for automated SA systems, this paper presents AIPSeLEX a novel idioms/ proverbs sentiment lexicon for modern standard Arabic (MSA) and colloquial. AIPSeLEX is manually collected and annotated at sentence level with semantic orientation (positive or negative). The efforts of manually building and annotating the lexicon are reported. Moreover, we build a classifier that extracts idioms and proverbs, phrases from text using n-gram and similarity measure methods. Finally, several experiments were carried out on various data, including Arabic tweets and Arabic microblogs (hotel reservation, product reviews, and TV program comments) from publicly available Arabic online reviews websites (social media, blogs, forums, e-commerce web sites) to evaluate the coverage and accuracy of AIPSeLEX.
Lightweight Directory Access Protocol

The protocol described in this document is designed to provide access to the X.500 Directory while not incurring the resource requirements of the Directory Access Protocol (DAP). This protocol is specifically targeted at simple management applications and browser applications that provide simple read/write interactive access to the X.500 Directory, and is intended to be a complement to the DAP itself.