Miracle-dz/UniFAR-FTUs huggingface dataset:
A High-Frequency Null Mutant of an Odorant-Binding Protein Gene, Obp57e, in Drosophila melanogaster

We have found a null mutant of an odorant-binding protein, Obp57e, in Drosophila melanogaster. This frameshift mutation, which is a 10-bp deletion in the coding region, is at a high frequency in the Kyoto population and is also present in Taiwan and Africa. We have sequenced a 1.5-kb region including the tandemly duplicated gene, Obp57d, from 16 inbred lines sampled in Kyoto, Japan. The analyses showed a peak of nucleotide diversity and strong linkage disequilibrium around this mutation. This pattern suggests an elevated mutation rate or an influence of balancing selection in this region. The level of nucleotide divergence between D. melanogaster and D. simulans does not support the former possibility. Thus, this presence/absence polymorphism may be due to balancing selection, which takes advantage of the relatively weak functional constraint in members of a large gene family. In addition, the Obp57d gene region showed an excess of high-frequency-derived mutants that is consistent with a pattern predicted under positive natural selection.
A Nonline-of-Sight Error-Mitigation Method for TOA Measurements

In wireless location, nonline-of-sight (NLOS) errors are a major error source. To improve positional performance, these errors should be identified and mitigated before measurements are used in position computations. A novel NLOS mitigation algorithm is proposed in this paper. Employing system redundancy, the algorithm derives from the distribution function of hyperbolic intersections, which is an intermediate mobile location. Cost functions based on the intermediate position are then created for each time-of-arrival measurement. NLOS errors are detected and mitigated via hypothesis tests performed on the cost functions. Simulation tests are presented in this paper, and the results verify the effectiveness of this NLOS-error-mitigation method. This paper also demonstrates that algorithm performance depends closely on receiver noise. Reducing receiver noise or providing the intermediate mobile location via external aiding can improve performance
Eiger, a TNF superfamily ligand that triggers the Drosophila JNK pathway

Drosophila provides a powerful genetic model for studying the in vivo regulation of cell death. In our large‐scale gain‐of‐function screen, we identified Eiger, the first invertebrate tumor necrosis factor (TNF) superfamily ligand that can induce cell death. Eiger is a type II transmembrane protein with a C‐terminal TNF homology domain. It is predominantly expressed in the nervous system. Genetic evidence shows that Eiger induces cell death by activating the Drosophila JNK pathway. Although this cell death process is blocked by Drosophila inhibitor‐of‐apoptosis protein 1 (DIAP1), it does not require caspase activity. We also show genetically that Eiger is a physiological ligand for the Drosophila JNK pathway. Our findings demonstrate that Eiger can initiate cell death through an IAP‐sensitive cell death pathway via JNK signaling.
Ecological Assessment of Executive Function in Traumatic Brain Injury

Executive dysfunction is a common outcome in children who have sustained traumatic brain injury (TBI). Appropriate assessment of these complex interrelated regulatory functions is critical to plan for the necessary interventions yet present a challenge to our traditional methodologies. Ecological validity has become an increasingly important focus in neuropsychological assessment with particular relevance for the executive functions, which coordinate one's cognitive and behavioral capacities with real-world demand situations. The Behavior Rating Inventory of Executive Function (BRIEF) was developed to capture the real-world behavioral manifestations of executive dysfunction. Its development and various forms of validity, including ecological validity, are described. Application of the BRIEF's methodology to the assessment of executive dysfunction in TBI is provided. We advocate a multilevel approach to understanding executive function outcome in TBI, including traditional test-based measures of executive function, real-world behavioral manifestation of executive dysfunction, and the environmental system factors that impact the child. In this model, ecologically valid assessment of executive dysfunction provides an important bridge toward understanding the impact of component-level (i.e., test-based) deficits on the child's everyday adaptive functioning, which can assist the definition of targets for intervention.
High HIV seroprevalence and increased HIV‐associated mortality among hospitalized patients with deep bacterial infections in Dar es Salaam, Tanzania

ObjectivesTo correlate deep bacterial infections with HIV infection and evaluate the influence of HIV on clinical picture and outcome in patients with meningitis, pneumonia or pyomyositis. DesignCase-control comparison of HIV seroprevalence between patients and an age- and sex-matched control group in a prospective cross-sectional study of hospitalized patients. ParticipantsOne hundred and sixty-five patients admitted to hospital with either purulent meningitis, pneumonia or pyomyositis and 165 age- and sex-matched controls from orthopaedic/trauma wards. SettingUniversity Hospital, Dar es Salaam, Tanzania. Outcome measuresDifferences in HIV seroprevalence and mortality. ResultsOf 78 patients with purulent meningitis, 19 (24%) were HIV-seropositive, compared with 13 (17%) in the control group (P = 0.345). Of 36 patients with meningitis seen before a meningococcal epidemic affected Dar es Salaam, there was a statistically significant association with HIV infection (P = 0.013). Ten out of 19 (53%) HIV-seropositives died, compared with nine out of 59 (15%) seronegatives (P = 0.028). Of patients with pneumococcal meningitis, five out of six (83%) seropositives died, compared with two out of 12 (17%) seronegatives (P = 0.013). Fifteen out of 45 (33%) patients with pneumonia were HIV-seropositive, compared with four (9%) in the control group (P = 0.001). There was no difference in mortality between seropositive and seronegative patients with pneumonia. HIV seroprevalence was 62% among 42 patients with pyomyositis and 12% among 42 controls (P<0.0001). Eighteen out of 25 (72%) seropositive patients with pyomyositis fulfilled the World Health Organization (WHO) clinical case definition for AIDS. Response to recommended antibiotic treatment was satisfactory among patients with pneumonia and pyomyositis. ConclusionsThese results show a strong association between pyomyositis, pneumonia and HIV infection. They also indicate an increased mortality associated with HIV infection in patients with pyogenic meningitis, especially pneumococcal meningitis. Pyomyositis should be considered an indicator of stage III HIV disease in the proposed WHO clinical staging system.
Role and complexity of next‐generation sequencing in melanoma

Michael A. Davies, MD, PhD, is an associate professor of the Departments of Melanoma Medical Oncology and Systems Biology at The University of Texas MD Anderson Cancer Center. He is a physician-scientist whose research focus is the regulation and clinical significance of oncogenic signaling networks in melanoma. Dr. Davies has been the principal investigator of both individual and team science grants from the National Cancer Institute, the American Society of Clinical Oncology, the Melanoma Research Alliance, and the Melanoma Research Foundation, and he has led multiple clinical trials. He is a member of the Melanoma Research Foundation Breakthrough Consortium and the International Melanoma Working Group, and is the codirector of MD Anderson Cancer Center’s MelCore, one of the largest clinically annotated melanoma tissue banks in the world.
THE CARE SPAN: In The Netherlands, rich interaction among professionals conducting disease management led to better chronic care

Disease management programs based on the Chronic Care Model are expected to improve the quality of chronic care delivery. However, evidence to date for such improvement and how it is achieved is scarce. In 2010 and again in 2011, we surveyed professionals in twentytwo primary care practices in the Netherlands that had implemented the Chronic Care Model of disease management beginning in 2009. The responses showed that, over time, chronic illness care delivery improved to advanced levels. The gains were attributed primarily to improved relational coordination-that is, raising the quality of communication and task integration among professionals from diverse disciplines who share common objectives. These findings may have implications for other disease management efforts by collaborative care teams, in that they suggest that diverse health care professionals must be strongly connected to provide effective, holistic care.
Building Cognition: The Construction of Computational Representations for Scientific Discovery

Novel computational representations, such as simulation models of complex systems and video games for scientific discovery (Foldit, EteRNA etc.), are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a theoretical analysis of the cognitive roles such representations play, based on an ethnographic study of the building of computational models in a systems biology laboratory. Specifically, we focus on a case of model-building by an engineer that led to a remarkable discovery in basic bioscience. Accounting for such discoveries requires a distributed cognition (DC) analysis, as DC focuses on the roles played by external representations in cognitive processes. However, DC analyses by and large have not examined scientific discovery, and they mostly focus on memory offloading, particularly how the use of existing external representations changes the nature of cognitive tasks. In contrast, we study discovery processes and argue that discoveries emerge from the processes of building the computational representation. The building process integrates manipulations in imagination and in the representation, creating a coupled cognitive system of model and modeler, where the model is incorporated into the modeler's imagination. This account extends DC significantly, and we present some of the theoretical and application implications of this extended account.
A Base Station Controlled Simple Sensor Network Protocol

In this paper, we propose a <i>base</i> <i>station</i> <i>controlled</i> <i>simple</i> <i>sensor</i> <i>network</i> <i>protocol</i> <i>(BCSP)</i>, which does not use the location information of each sensor node but the information of remaining energy to prolong lifetime of a sensor network.
A DSOM hierarchical model for reflexive processing: an application to visual trajectory classificati

Any intelligent system, whether human or robotic, must be capable of dealing with patterns over time. Temporal pattern processing can be achieved if the system has a short-term memory capacity (STM) so that diierent representations can be maintained for some time. In this work we propose a neural model wherein STM is realized by leaky integrators in a self-organizing system. The model exhibits compo-sitionality, that is, it has the ability to extract and construct progressively complex and structured associations in an hierarchical manner, starting with basic and primitive (temporal) elements. An important feature of the proposed model is the use of temporal correlations to express dynamic bindings.
Migrating anterior mesoderm cells and intercalating trunk mesoderm cells have distinct responses to Rho and Rac during Xenopus gastrulation

Rho GTPases have been shown recently to be important for cell polarity and motility of the trunk mesoderm during gastrulation in Xenopus embryos. This work demonstrated that Rho and Rac have both distinct and overlapping roles in regulating cell shape, and the dynamic properties, polarity, and type of protrusive activity of these cells. Overexpression of activated or inhibitory versions of these GTPases also disrupts development of the head in Xenopus embryos. In this study, we have undertaken a detailed analysis of Rho and Rac function in migrating anterior mesendoderm cells. Scanning electron micrographs of these cells in situ revealed that their normal shingle arrangement is disrupted and both the cells and their lamellipodia are disoriented. Anterior mesendoderm explants plated on their natural blastocoel roof matrix, however, still migrated towards the animal pole, although the tendency to move in this direction is reduced compared to controls. Analysis of a number of parameters in time‐lapse recordings of dissociated cells indicated that Rho and Rac also have both distinct and overlapping roles in the motility of the prospective head mesoderm; however, their effects differ to those previously seen in the trunk mesoderm. Both GTPases appear to modulate cell polarization, migration, and protrusive activity. Rho alone, however, regulates the retraction of the lagging edge of the cell. We propose that within the gastrulating Xenopus embryo, two types of mesoderm cells that undergo different motilities have distinct responses to Rho GTPases. Developmental Dynamics 235:1090–1099, 2006. © 2006 Wiley‐Liss, Inc.
Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021

Sinorhizobium meliloti is an α-proteobacterium that forms agronomically important N2-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.
ON ESTIMATING THE HIGH-ENERGY CUTOFF IN THE X-RAY SPECTRA OF BLACK HOLES VIA REFLECTION SPECTROSCOPY

The fundamental parameters describing the coronal spectrum of an accreting black hole are the slope Γ of the power-law continuum and the energy Ecut at which it rolls over. Remarkably, this latter parameter can be accurately measured for values as high as 1 MeV by modeling the spectrum of X-rays reflected from a black hole accretion disk at energies below 100 keV. This is possible because the details in the reflection spectrum, rich in fluorescent lines and other atomic features, are very sensitive to the spectral shape of the hardest coronal radiation illuminating the disk. We show that by fitting simultaneous NuSTAR (3–79 keV) and low-energy (e.g., Suzaku) data with the most recent version of our reflection model relxill one can obtain reasonable constraints on Ecut at energies from tens of keV up to 1 MeV, for a source as faint as 1 mCrab in a 100 ks observation.
Capturing Complexity Through Agent-Based Models and the Quest for the Enterprise

Identify the mechanism that creates organizations and structures in the social realm represent a useful approach to capture the complexity of economic systems. Indeed, the use of simulation techniques can help in understanding the dynamics of the system while fully preserving the complexity of the context. This research has the goal of employing agent based models to simulate a single enterprise or a system of enterprises (e.g. within a network or in a market). This Ph.D. thesis tries to explore how markets institutions and organizations can arise from processes of coordination, or laws of organization, that are fundamentally the same universal laws of economic coordination that apply within and across the layers of organizational structure in the economy.
Psychotherapy clients’ attitudes to personal psychotherapy for psychotherapists

ABSTRACT A mixed-method online-survey study was conducted to explore psychotherapy clients’ (N = 230) attitudes to psychotherapists engaging in personal therapy. 61% of participants strongly favoured psychotherapists engaging in personal therapy, while only 9% opposed mandating personal therapy as a professional requirement for psychotherapist training. 75% would feel more comfortable seeking treatment from therapists who had experienced their own psychotherapy. Participants believed that undertaking personal therapy creates more empathic, trustworthy and self-aware psychotherapists and that personal therapy is an important resource in psychotherapist self-care and experiential learning. A minority of participants indicated that therapist education obviates the need for personal therapy, and that mandating it could be counterproductive.
Determining Cooperation in Multiagent Systems with Cultural Traits

Achieving cooperation among autonomous and rational agents is still a major challenge. In the past, altruistic cooperation was generally explained through genetic kinship relations. However, the theory of ‘cultural kin’ is an approach that tries to explain altruism through cultural relatedness. To promote cooperation among autonomous and rational agents, this work transfers the idea of cultural characteristics, which benefits social behaviour, to multiagent systems (MAS). Accordingly, agents are characterised by cultural traits, which they can imitate from their neighbours and are supposed to solve tasks, for which they need the cooperation of other agents in most cases. The interaction of cooperation and cultural trait propagation will be investigated in a theoretical analysis and in an empirical simulation in a particular developed framework. As a novelty, schemata will be analysed that are beyond the well-studied one-to-one interaction.
Czech MWE Database

In this paper we deal with a recently developed large Czech MWE database containing at the moment 160,000 MWEs (treated as lexical units). It was compiled from various resources such as encyclopedias and dictionaries, public databases of proper names and toponyms, collocations obtained from Czech WordNet, lists of botanical and zoological terms and others. We describe the structure of the database and compare the built MWEs database with the corpus data from Czech National Corpus SYN2000 (approx. 100 mil. tokens) and present results of this comparison in the paper. These MWEs have not been obtained from the corpus since their frequencies in it are rather low. To obtain a more complete list of MWEs we propose and use a technique exploiting the Word Sketch Engine, which allows us to work with statistical parameters such as frequency of MWEs and their components as well as with the salience for the whole MWEs. We also discuss exploitation of the database for working out a more adequate tagging and lemmatization. The final goal is to be able to recognize MWEs in corpus text and lemmatize them as complete lexical units, i.e. to make tagging and lemmatization more adequate.
SHAPE STABILIZER USING AN ARTICULATION-TYPE PASSIVE ELEMENT

An articulation-type passive element is a planate bag containing articulating thin plates. It can be freely contracted and bent to fit an arbitrary rounded surface. Evacuation of the internal air renders the bag rigid so that it maintains whatever shape it has been given. The stiffness of the articulation-type passive element is proportional to the reduction in internal pressure below atmospheric pressure. Experimental results show that the stiffness is higher and more stable than that of other passive elements that function by vacuum pressure. As an application of the new passive element, we developed an orthopedic cast that is easy to remove or change in shape. The passive element is also applicable to wearable force displays. Passive elements fixed on an operator provide a sensation of reaction force by constraining his or her motion. The new passive element is suitable for wearable mechanisms, by virtue of being lightweight, soft, and safe.
Remote Sensing-Based Estimates of Annual and Seasonal Emissions from Crop Residue Burning in the Contiguous United States

ABSTRACT Crop residue burning is an extensive agricultural practice in the contiguous United States (CONUS). This analysis presents the results of a remote sensing-based study of crop residue burning emissions in the CONUS for the time period 2003–2007 for the atmospheric species of carbon dioxide (CO2), methane (CH4), carbon monoxide (CO), nitrogen dioxide (NO2), sulfur dioxide (SO2), PM2.5 (particulate matter [PM] ≤ 2.5 μm in aerodynamic diameter), and PM10 (PM ≤ 10 μm in aerodynamic diameter). Cropland burned area and associated crop types were derived from Moderate Resolution Imaging Spectroradiometer (MODIS) products. Emission factors, fuel load, and combustion completeness estimates were derived from the scientific literature, governmental reports, and expert knowledge. Emissions were calculated using the bottom-up approach in which emissions are the product of burned area, fuel load, and combustion completeness for each specific crop type. On average, annual crop residue burning in the CONUS emitted 6.1 Tg of CO2, 8.9 Gg of CH4, 232.4 Gg of CO, 10.6 Gg of NO2, 4.4 Gg of SO2, 20.9 Gg of PM2.5, and 28.5 Gg of PM10. These emissions remained fairly consistent, with an average interannual variability of crop residue burning emissions of ±10%. The states with the highest emissions were Arkansas, California, Florida, Idaho, Texas, and Washington. Most emissions were clustered in the southeastern United States, the Great Plains, and the Pacific Northwest. Air quality and carbon emissions were concentrated in the spring, summer, and fall, with an exception because of winter harvesting of sugarcane in Florida, Louisiana, and Texas. Sugarcane, wheat, and rice residues accounted for approximately 70% of all crop residue burning and associated emissions. Estimates of CO and CH4 from agricultural waste burning by the U.S. Environmental Protection Agency were 73 and 78% higher than the CO and CH4 emission estimates from this analysis, respectively. This analysis also showed that crop residue burning emissions are a minor source of CH4 emissions (<1%) compared with the CH4 emissions from other agricultural sources, specifically enteric fermentation, manure management, and rice cultivation. IMPLICATIONS Current national emission inventories for the United States do not include targeted emission calculations from crop residue burning and rely on expert knowledge for crop residue burned area and subsequent emission estimates. The objective of this study is to quantify crop residue burning emissions in the CONUS through the use of remote sensing-based products. The results of this study represent the first emission estimates from crop residue burning in the CONUS derived from the independent source of satellite data and can be used to revise existing emissions inventories of agricultural sources at a near-national level.