Miracle-dz/UniFAR-FTUs huggingface dataset:
QTL analysis of the photoperiodic response and clinal distribution of period alleles in Nasonia vitripennis

In seasonal environments, organisms synchronize their life cycle with the annual cycle of environmental factors. In many insect species, this includes a diapause response: a timed dormant stage that allows to survive harsh winter conditions. Previously, we have shown that larval diapause in the parasitic wasp Nasonia vitripennis is induced by the mother upon exposure to a threshold number of short photoperiods (named switch point) and diapause response follows a latitudinal cline in natural populations. Here, we present a QTL analysis using two lines derived from the extremes of this clinal distribution: a northern line from Oulu, Finland and a southern line from Corsica, France. A genomic region on chromosome 1 and one on chromosome 5 were found to be associated with photoperiodic diapause induction. Interestingly, these regions contain the putative clock genes period, cycle (chromosome 1) and cryptochrome (chromosome 5). An analysis of period polymorphisms in seven European populations showed a clinal distribution of two main haplotypes that correlate with the latitudinal cline for diapause induction.
Ontology quality assurance through analysis of term transformations

Motivation: It is important for the quality of biological ontologies that similar concepts be expressed consistently, or univocally. Univocality is relevant for the usability of the ontology for humans, as well as for computational tools that rely on regularity in the structure of terms. However, in practice terms are not always expressed consistently, and we must develop methods for identifying terms that are not univocal so that they can be corrected. Results: We developed an automated transformation-based clustering methodology for detecting terms that use different linguistic conventions for expressing similar semantics. These term sets represent occurrences of univocality violations. Our method was able to identify 67 examples of univocality violations in the Gene Ontology. Availability: The identified univocality violations are available upon request. We are preparing a release of an open source version of the software to be available at http://bionlp.sourceforge. net. Contact: karin.verspoor@ucdenver.edu
(1, 3)-β-D-glucan assay for diagnosing invasive fungal infections in critically ill patients with hematological malignancies

Invasive fungal infections (IFIs) are life-threatening complications of hematological malignancies that must be diagnosed early to allow effective treatment. Few data are available on the performance of serum (1–3)-β-D-glucan (BG) assays for diagnosing IFI in patients with hematological malignancies admitted to the intensive care unit (ICU). In this study, 737 consecutive patients with hematological malignancies admitted to 17 ICUs routinely underwent a BG assay at ICU admission. IFIs were diagnosed using standard criteria applied by three independent specialists. Among the 737 patients, 439 (60%) required mechanical ventilation and 273 (37%) died before hospital discharge. Factors known to alter BG concentrations were identified in most patients. IFIs were documented in 78 (10.6%) patients (invasive pulmonary aspergillosis, n = 54; Pneumocystis jirovecii pneumonia, n = 13; candidemia, n = 13; and fusarium infections, n = 3). BG concentrations (pg/mL) were higher in patients with than without IFI (144 (77–510) vs. 50 (30–125), < 0.0001). With 80 pg/mL as the cutoff, sensitivity was 72%, specificity 65%, and area-under-the-curve 0.74 (0.68–0.79). Assuming a prevalence of 10%, the negative and positive predictive values were 94% and 21%. By multivariable analysis, factors independently associated with BG > 80 pg/mL were IFI, admission SOFA score, autologous bone-marrow or hematopoietic stem-cell transplantation, and microbiologically documented bacterial infection. In conclusion, in unselected critically ill hematology patients with factors known to affect serum BG, this biomarker showed only moderate diagnostic performance and rarely detected IFI. However, the negative predictive value was high. Studies are needed to assess whether a negative BG test indicates that antifungal de-escalation is safe.
Analytical modeling of low cost single and dual gate organic transistor and their parameters extraction

This research paper analyzes the electrical behavior of single gate (SG) and dual gate (DG) organic thin film transistors (OTFTs). To better understand the device physics and conduction mechanism, an analytical model for drain current is derived incorporating the empirical parameters. The effect of two gate insulator capacitances along with depletion capacitance of the organic semiconductor active layer is incorporated. To validate the models, the OTFT in both structures is simulated and thus the analytical model parameters are compared with the simulation results. DG-OTFT exhibits improved performance by means of current, mobility, threshold voltage and transconductance than that of SG-OTFT. Consequently, a substantial improvement of 67%, 50%, 19% and 54%, respectively is observed. Realization of such improved performance device structure using organic materials demonstrates the possibility of producing low cost digital and analog circuits on the bendable substrates and thus establishes a stepping stone towards low cost flexible organic electronics.
Uniform image and camera access

We introduce a work-in-progress camera access scheme we call the Unified Camera Framework. Attempts have been made in the past to provide simple access to cameras, however these are generally OS specific or lacking in functionality. We present a novel interface which works across operating systems, and provides access to native images through a descriptor. A unified configuration model is presented to allow manipulation of camera parameters to the level each camera supports. Validation of the ideas presented is given in the form of a proof-of-concept implementation called the All Seeing Eye.
Self-Replicating Turing Machines and Computer Viruses

This paper reviews self-replication in the context of (partial) recursive functions and Turing computability. By the ChurchTuring thesis, these are equivalent to other models of computation. The theory is linked to applications in the area of computer viruses. We address the views of various authors with respect to the (in)adequacy of Turing machine equivalent models for computer viruses.
The Osteoinductive Activity of Bone Morphogenetic Protein (BMP) Purified by Repeated Extracts of Bovine Bone

Native bone morphogenetic proteins (BMPs) extracted from bone have been used clinically to stimulate bone regeneration and repair. However, preparation of purified BMP is a laborious process. This study investigated the yield, activity and cost effectiveness of repeatedly extracting the same bone matrix to produce purified BMP. While repeated extraction was able to increase the yield 62% the activity of the partially purified BMP in later extracts decreased both in vitro and in vivo. This decline in activity appears to be due to an increase in non-BMP contaminants, such as collagen, in the extracts. When the first three extracts were combined and processed together activity was equivalent to that of the first extract. A simple analysis based on the cost of reagents used and the time required for purification indicates that separate processing of the extracts is inefficient while combining the first and second extracts and processing them together would result in a small cost saving. Based on this study we would recommend that the demineralized bone matrix be extracted no more than twice and that the extracts be combined for further processing.
Growth status of children in rural Mali: Implications for nutrition education programs

In conjunction with a rural development project, a cross‐sectional anthropometric survey and ethnographic research were conducted in six rural villages in southern Mali where food is generally sufficient. A total of 1,132 individuals were measured, and individual and group interviews concerning dietary habits and intra‐familial food distribution patterns were conducted. In this paper, data on the growth status of children under 12 years of age (N=575) are reported and analyzed. As defined by inadequate growth, rates of malnutrition are extremely high in this population. Deficits in growth peak among the 2 year olds, with 67% falling more than 2 SD below the NCHS/WHO standard for weight‐for‐age, and 53% falling more than 2SD below the standard for height‐for‐age. Deficits in weight‐for‐height are highest among the 1 year olds, with 32% falling more than 2 SD below the NCHS/WHO standards. From birth to 23 months, the correlation between age (in months) and weight‐for‐age z‐scores is −. 63 (P=.0001). Between 24 and 47 months, the correlation improves, to +. 36 (P=.0004), indicating that children experience some catch‐up growth. By the age of 11 years, they still have not recovered fully from the combination of poor nutrition and infections in early childhood, however, and malnutrition continues to be a problem throughout childhood. Iodine deficiency is also a problem in two of the six villages. Interview data confirm earlier findings in Mali regarding child feeding practices, specifically, that infants and young children are expected to feed themselves, and that the best foods are reserved for adults. These findings have important implications for the design and implementation of nutrition education programs in southern Mali.
Control of non-Markovian decay and decoherence by measurements and interference.

Novel methods are discussed for the state control of atoms coupled to multi-mode reservoirs with non-Markovian spectra: 1) Excitation decay control : we point out that the quantum Zeno effect, i.e., inhibition of spontaneous decay by frequent measurements, is observable in open cavities and waveguides using a sequence of evolution- interrupting pulses or randomly-modulated CW fields. 2) Location-dependent interference of decay channels - nonadiabatic (resonant) control : We show that the control of populations and coherences of two metastable states is feasible via resonant single-photon absorption to an intermediate state, by controlled spontaneous emission in a cavity. 3) Decoherence control by conditionally interfering parallel evolutions: We demonstrate that an arbitrary internal atomic state can be completely protected from decoherence by interference of its interactions with the reservoir over many different time interals in parallel . Such interference is conditional upon the detection of appropriate atomic-momentum observables. Realization in cavities is suggested. The rich arsenal of control methods described above can improve the performance of single-atom devices. It can also advance the state-of-the-art of quantum information encoding and processing.
The relationship between executive function and joint attention in the second year of life

Several theories of cognitive control or executive function (EF) propose that EF development corresponds to children's ability to form and reflect on represented stimuli in the environment. However, research on early EF is primarily conducted with preschoolers, despite the fact that important developments in representation (e.g., language, gesture) occur within the first years of life within a social context (e.g., to share, communicate, and collaborate, see Tomasello, Carpenter, Call, Behne, & Moll, 2005). In the current study, children's EF performance and the relationship between EF and early representation (i.e., joint attention, language) were longitudinally examined in 47 children at 14 and 18 months of age. Results provided support for a unidirectional relationship in which earlier joint attention behavior at 14 months was related to better EF at 18 months. Specifically, higher level initiation of joint attention behaviors at 14 months (e.g., pointing to manipulate another's attention) were related to stronger, more cohesive EF performance at 18 months. Children's performance on EF tasks was low at 14 months and improved from 14 to 18 months. Although EF performance during this period revealed patterns dissimilar to later EF development in preschool (e.g., low inter-task correlations, few significant relations to language), by 18 months of age a subset of children consistently passed the majority of EF tasks, possibly indicating the emergence of a unified EF in the second year of life. These results provide evidence that preverbal means of representation (i.e., initiation of joint attention) are related to early EF (e.g., Zelazo, 2004). Further, early representation that emerges within a social context (e.g., to communicate information to another person) may underlie the emergence of a unified EF ability, as only children demonstrating higher-level initiation of joint attention behaviors were able to guide behavior across multiple EF contexts.
Copper(II)-induced Conformational Changes and Protease Resistance in Recombinant and Cellular PrP

While PrPC rearranges in the area of codons 104–113 to form PrPSc during prion infections, the events that initiate sporadic Creutzfeldt-Jakob disease are undefined. As Cu(II) is a putative ligand for PrPC and has been implicated in the pathogenesis of Creutzfeldt-Jakob disease and other neurodegenerative diseases, we investigated the structural effects of binding. Incubation of brain microsomes with Cu(II) generated ∼30-kDa proteinase K-resistant PrP. Cu(II) had little effect on fresh recombinant PrP23-231, but aged protein characterized by conversion of Asn-107 to Asp decreased α-helical content by ∼30%, increased β-sheet content 100%, formed aggregates, and acquired proteinase K resistance in the presence of Cu(II). These transitions took place without need for acid pH, organic solvents, denaturants, or reducing agents. Since conversion of Asn to Asp proceeds by a spontaneous pathway involving deamidation, our data suggest that covalent variants of PrPC arising in this manner may, in concert with Cu(II), generate PrPSc-like species capable of initiating sporadic prion disease.
Neurolipofuscin Is a Measure of Age in Panulirus argus, the Caribbean Spiny Lobster, in Florida

Accurate age estimates for Panulirus argus, the commercially important Caribbean spiny lobster, would greatly enhance life history and population analyses. Most age approximations of P. argus are based on size and growth data, but size is generally considered a poor proxy for age of crustaceans in the field because of numerous environmental, density-dependent, and fishery-related factors. An established technique for aging crustaceans, employing histologically determined lipofuscin content in the nervous system, was investigated using known-age lobsters reared in the laboratory at ambient temperatures. We verified the presence of lipofuscin in eyestalk neural tissue by using autofluorescence and Sudan black staining and described its distribution in cell cluster A of the hemiellipsoid body. Neurolipofuscin accumulated with age; the overall trend was linear with indications of seasonal oscillation, whereas growth began to approach an asymptote after 3 years. Differences in the neurolipofuscin concentrations in the two eyestalks from the same animal were statistically insignificant. There was also no difference in the neurolipofuscin concentrations of males and females of the same age. The present data suggest a maximum potential lifespan for P. argus of about 20 years. These results also suggest that the neurolipofuscin technique will be valuable for estimating age of wild-caught specimens of P. argus.
LPA: a new location-based privacy-preserving authentication protocol in VANET

In this paper, we introduce a location-based privacy-preserving authentication protocol (LPA) in vehicular ad hoc networks (VANETs) to address the issue on conditional privacy preservation in which safety messages can be anonymously authenticated by peer vehicles while an authority can trace the sender in a dispute. Specifically, in the LPA protocol, we propose a top-down security system: the top authority (TA) authorizes the roadside units (RSUs) to issue group certificates to the onboard units (OBUs). In addition, we also introduce RSU neighbor set to enhance security and efficiency. We demonstrate the merits of the proposed scheme through extensive analysis and performance evaluation. Copyright © 2011 John Wiley & Sons, Ltd.
Pr&#233;cis: The Essence of a Query Answer

Wide spread use of database systems in modern society has brought the need to provide inexperienced users with the ability to easily search a database with no specific knowledge of a query language. Several recent research efforts have focused on supporting keyword-based searches over relational databases. This paper presents an alternative proposal and introduces the idea of précis queries. These are free-form queries whose answer (a précis) is a synthesis of results, containing not only information directly related to the query selections but also information implicitly related to them in various ways. Our approach to précis queries includes two additional novelties: (a) queries do not generate individual relations but entire multi-relation databases; and (b) query results are personalized to user-specific and/or domain requirements. We develop a framework and system architecture for supporting such queries in the context of a relational database system and describe algorithms that implement the required functionality. Finally, we present a set of experimental results that evaluate the proposed algorithms and show the potential of this work.
Comparison and evaluation of anthropogenic emissions of SO 2 and NO x over China

Abstract. Bottom-up emission inventories provide primary understanding of sources of air pollution and essential input of chemical transport models. Focusing on SO2 and NOx, we conducted a comprehensive evaluation of two widely used anthropogenic emission inventories over China, ECLIPSE and MIX, to explore the potential sources of uncertainties and find clues to improve emission inventories. We first compared the activity rates and emission factors used in two inventories and investigated the reasons of differences and the impacts on emission estimates. We found that SO2 emission estimates are consistent between two inventories (with 1 % differences), while NOx emissions in ECLIPSE's estimates are 16 % lower than those of MIX. The FGD (flue-gas desulfurization) device penetration rate and removal efficiency, LNB (low-NOx burner) application rate and abatement efficiency in power plants, emission factors of industrial boilers and various vehicle types, and vehicle fleet need further verification. Diesel consumptions are quite uncertain in current inventories. Discrepancies at the sectorial and provincial levels are much higher than those of the national total. We then examined the impacts of different inventories on model performance by using the nested GEOS-Chem model. We finally derived top-down emissions by using the retrieved columns from the Ozone Monitoring Instrument (OMI) compared with the bottom-up estimates. High correlations were observed for SO2 between model results and OMI columns. For NOx, negative biases in bottom-up gridded emission inventories (−21 % for MIX, −39 % for ECLIPSE) were found compared to the satellite-based emissions. The emission trends from 2005 to 2010 estimated by two inventories were both consistent with satellite observations. The inventories appear to be fit for evaluation of the policies at an aggregated or national level; more work is needed in specific areas in order to improve the accuracy and robustness of outcomes at finer spatial and also technological levels. To our knowledge, this is the first work in which source comparisons detailed to technology-level parameters are made along with the remote sensing retrievals and chemical transport modeling. Through the comparison between bottom-up emission inventories and evaluation with top-down information, we identified potential directions for further improvement in inventory development.
Pathological basis of diffusely abnormal white matter: insights from magnetic resonance imaging and histology

Background: The pathological basis of diffusely abnormal white matter (DAWM) in multiple sclerosis (MS) has not been elucidated in detail, but may be an important element in disability and clinical progression. Methods: Fifty-three subjects with MS were examined with T1, multi-echo T2 and magnetization transfer (MT). Twenty-three samples of formalin-fixed MS brain tissue were examined with multi-echo T2 and subsequently stained for myelin phospholipids using luxol fast blue, for axons using Bielschowsky, immunohistochemically for the myelin proteins myelin basic protein (MBP) and 2′,3′-cyclic nucleotide 3′ phosphohydrolase (CNP) and for astrocytes using glial fibrillary acidic protein (GFAP). Regions of interest in DAWM were compared with normal appearing white matter. Results: Fourteen of 53 subjects with MS in the in vivo study showed the presence of DAWM. Subjects with DAWM were found to have a significantly lower Expanded Disability Status Scale (EDSS) and shorter disease duration (DD) when compared with subjects without DAWM (EDSS: 1.5 versus 3.0, p = 0.031; DD: 5.4 versus 10.3 years, p = 0.045). DAWM in vivo had reduced myelin water and MT ratio, and increased T2 and water content. Histological analysis suggests DAWM, which shows a reduction of the myelin water fraction, is characterized by selective reduction of myelin phospholipids, but with a relative preservation of myelin proteins and axons. Conclusions: These findings suggest that the primary abnormality in DAWM is a reduction or perturbation of myelin phospholipids that correlates with a reduction of the myelin water fraction.