Miracle-dz/UniFAR-FTUs huggingface dataset:
Capturing cooperative interactions with the PSI-MI format

The complex biological processes that control cellular function are mediated by intricate networks of molecular interactions. Accumulating evidence indicates that these interactions are often interdependent, thus acting cooperatively. Cooperative interactions are prevalent in and indispensible for reliable and robust control of cell regulation, as they underlie the conditional decision-making capability of large regulatory complexes. Despite an increased focus on experimental elucidation of the molecular details of cooperative binding events, as evidenced by their growing occurrence in literature, they are currently lacking from the main bioinformatics resources. One of the contributing factors to this deficiency is the lack of a computer-readable standard representation and exchange format for cooperative interaction data. To tackle this shortcoming, we added functionality to the widely used PSI-MI interchange format for molecular interaction data by defining new controlled vocabulary terms that allow annotation of different aspects of cooperativity without making structural changes to the underlying XML schema. As a result, we are able to capture cooperative interaction data in a structured format that is backward compatible with PSI-MI–based data and applications. This will facilitate the storage, exchange and analysis of cooperative interaction data, which in turn will advance experimental research on this fundamental principle in biology. Database URL: http://psi-mi-cooperativeinteractions.embl. de/
Skin penetration and UV‐damage prevention by nanoberries

Ethanolic extract from blueberry (Vaccinium myrtillus) is rich in anthocyanins and thus exhibits antioxidant activity. On the other hand, ultradeformable liposomes are capable of penetrating to the impermeable barrier of skin. Nanoberries are ultradeformable liposomes carrying blueberry extract.
An Evaluation of Digital Elevation Models for Upgrading New Zealand Land Resource Inventory Slope Data

Slope is a key environmental parameter which influences land use and erosion hazard. Digital elevation models (DEMs) are often used to map important topographic parameters such as slope. However, the quality of such maps depends on the quality of the DEM’s representation of the earth’s surface. In many cases errors in this representation are neither measured nor estimated. In this paper a real-time differential GPS is used to acquire ground truth data. This ground truth is compared with DEMs generated from contours. This analysis shows that three commonly used contour-based interpolation procedures all produce good quality DEMs.
Exploring the Association Between Cognitive Functioning and Anxiety in Children With Autism Spectrum Disorders: The Role of Social Understanding and Aggression

This study examined relations between anxiety, aggression, social understanding, IQ, and diagnosis in a sample of 231 children (ages 2–9) diagnosed with Autism Spectrum Disorders (ASDs; Autistic Disorder, Asperger's Disorder, Pervasive Developmental Disorder Not Otherwise Specified) in a hospital setting. Children were administered tests of IQ, and parents completed measures of remaining variables. ASD diagnosis was associated with level of anxiety, and level of IQ explained this relation. IQ was significantly and positively associated with anxiety. Tests of a developmental model to explain the relation between IQ and anxiety showed that social understanding and aggression mediated the relation for toddlers. For preschool- and early elementary school-aged children, respectively, three-way interactions between IQ, social understanding, and aggression predicted anxiety, and graphs of the interactions suggest that the association between IQ and anxiety is increasingly driven by either aggression or social understanding over the course of childhood.
A New Very-High-Pressure Silica Mineral in the Shergotty SNC Meteorite: Implications for Shock Metamorphism and the Earth's Lower Mantle

IMPLICATIONS FOR SHOCK METAMORPHISM AND THE EARTH’S LOWER MANTLE; A. El Goresy1, T. G. Sharp2, B. Wopenka3, and M. Chen4; 1Max-Planck-Institut für Kernphysik, Postfach 103980, 69029 Heidelberg, Germany; 2Dept. of Geology, Arizona State University, Tempe, AZ 85287 USA; 3Dept. of Earth and Planetary Sciences, Washington University, St. Louis, MO 63130, USA; 4Guangzhou Institute of Geochemistry, Academia Sinica, Guangzhou, China.
The Global Zonally Integrated Ocean Circulation, 1992–2006: Seasonal and Decadal Variability

Abstract The zonally integrated meridional and vertical velocities as well as the enthalpy transports and fluxes in a least squares adjusted general circulation model are used to estimate the top-to-bottom oceanic meridional overturning circulation (MOC) and its variability from 1992 to 2006. A variety of simple theories all produce time scales suggesting that the mid- and high-latitude oceans should respond to atmospheric driving only over several decades. In practice, little change is seen in the MOC and associated heat transport except very close to the sea surface, at depth near the equator, and in parts of the Southern Ocean. Variability in meridional transports in both volume and enthalpy is dominated by the annual cycle and secondarily by the semiannual cycle, particularly in the Southern Ocean. On time scales longer than a year, the solution exhibits small trends with complicated global spatial patterns. Apart from a net uptake of heat from the atmosphere (forced by the NCEP–NCAR reanalysis, which.
11–AN ALTERNATIVE APPROACH TO TWO-FOLD WEAVING YARN PART II: THE THEORETICAL MODEL

The theoretical model underlying a two-strand spinning system is given. It is shown that, for an idealized model, the equilibrium twist in the strands is dependent upon a torsion balance existing between an individual strand above the convergence point and the strand as it lies in th plied structure. As a consequence, at equilibrium, twist in the strands relies solely on ply-twist and the helix radius of the strands in the ply. Basic equations are derived that lead to a method of evaluating trapped strand-twist in the resultant yarn that is produced by changes in twist in the strands when equilibrium is deliberately perturbed.
Placental‐like alkaline phosphatase as a marker of carcinoma‐in‐situ of the testis. Comparison with monoclonal antibodies M2A and 43–9F

In an immunohistochemical study of 59 routinely processed tissue specimens from 48 adult testes with isolated carcinoma‐in‐situ (CIS) changes and of 66 specimens from adult testes without neoplasia, placental‐like alkaline phosphatase (PIAP) was shown to be a reliable marker of CIS cells preceding the development of a testicular tumour. Thus, a positive reaction was encountered in all 36 biopsies treated with formaldehyde, or Bouin's or Stieve's fluid. However, only 11 of 23 specimens fixed with Cleland's fluid were immunoreactive for PIAP. None of the non‐malignant components of seminiferous tubules, including the large abnormal spermatogonia, reacted with the antibody against PIAP. Besides the antibody against PIAP, monoclonal antibodies M2A and 43–9F were tested on CIS specimens fixed with the above‐mentioned fixatives. In the 17 specimens fixed with Stieve's or Bouin's fluid, a positive reaction was obtained in all sections with all three antibodies tested. However, for each antibody at least two specimens gave a weak staining reaction. When all three immunostainings were performed, in each case at least one of them gave a moderate or strong reaction, thus making CIS cells easily detectable. In the samples fixed with Cleland's fluid, a negative reaction was found in one to three specimens, depending on the antibody used. However, at least one of the three antibodies gave a positive reaction if all three immunostainings were applied. In only one of the formaldehyde‐fixed paraffin specimens did CIS cells react with the monoclonal antibody 43–9F, whereas M2A gave no positive reaction at all if this method of fixation was used. Thus, the sensitivity of the immunohistochemical staining procedure in the detection of CIS is dependent on the fixative used and increases when immunostainings with all three markers are performed simultaneously.
Massachusetts Institute of Technology Department of Economics Working Paper Series the China Syndrome: Local Labor Market Effects of Import Competition in the United States the China Syndrome: Local Labor Market Effects of Import Competition in the United States *

We analyze the effect of rising Chinese import competition between 1990 and 2007 on local U.S. labor markets, exploiting cross-market variation in import exposure stemming from initial differences in industry specialization while instrumenting for imports using changes in Chinese imports by industry to other high-income countries. Rising exposure increases unemployment, lowers labor force participation, and reduces wages in local labor markets. Conservatively, it explains one-quarter of the contemporaneous aggregate decline in U.S. manufacturing employment. Transfer benefits payments for unemployment, disability, retirement, and healthcare also rise sharply in exposed labor markets. and numerous seminar and conference participants for valuable suggestions that improved the paper.
Using terminological feedback for web search refinement: a log-based study

Although interactive query reformulation has been actively studied in the laboratory, little is known about the actual behavior of web searchers who are offered terminological feedback along with their search results. We analyze log sessions for two groups of users interacting with variants of the AltaVista search engine - a baseline group given no terminological feedback and a feedback group to whom twelve refinement terms are offered along with the search results. We examine uptake, refinement effectiveness, conditions of use, and refinement type preferences. Although our measure of overall session "success" shows no difference between outcomes for the two groups, we find evidence that a subset of those users presented with terminological feedback do make effective use of it on a continuing basis.
The Timing Hypothesis and Hormone Replacement Therapy: A Paradigm Shift in the Primary Prevention of Coronary Heart Disease in Women. Part 2: Comparative Risks

A major misperception concerning postmenopausal hormone replacement therapy (HRT) is that the associated risks are large in magnitude and unique to HRT, but over the past 10 years, sufficient data have accumulated so that the magnitude and perspective of risks associated with the primary coronary heart disease prevention therapies of statins, aspirin, and postmenopausal HRT have become more fully defined. Review of randomized controlled trials indicates that the risks of primary prevention therapies and other medications commonly used in women's health are of similar type and magnitude, with the majority of these risks categorized as rare to infrequent (<1 event per 100 treated women). Evidence‐based data show that the risks of postmenopausal HRT are predominantly rare (<1 event per 1,000 treated women) and certainly no greater than other commonly used medications in women's health, including statins and aspirin. These risks, including breast cancer, stroke, and venous thromboembolism are common across medications and are rare, and even rarer when HRT is initiated in women younger than 60 or who are less than 10 years since menopause. In Part 1 of this series, the sex‐specificity of statins and aspirin and timing of initiation of HRT as modifiers of efficacy in women were reviewed. Herein, the comparative risks of primary prevention therapies in women are discussed.
Local Anesthetics in the Surgical Wound-Is the Pendulum Swinging Toward Increased Use?

Surgical pain originates from the surgical wound, and a rational approach to perioperative pain treatment has therefore been directed toward the use of local anesthetics at the site of surgery. Although single-dose local anesthetic infiltration has been documented to be effective and remains the optimal anesthetic technique for certain minor procedures, a more widespread use has been hindered owing to the well-documented short duration for approximately 4 to 6 hrs and the limited effects in major procedures. In recent years, efforts have therefore been made to improve local anesthetic wound analgesia with other approaches such as continuous local anesthetic wound infusion, highvolume local anesthetic wound infiltration, and development of different carrier systems for extended release of the local anesthetic from a single administration.
Genetic evidence that the Tat proteins of human immunodeficiency virus types 1 and 2 can multimerize in the eukaryotic cell nucleus

The formation of dimers or higher-order multimers is critical to the biological activity of many eukaryotic regulatory proteins. However, biochemical analyses of the multimerization capacity of the Tat trans activator of human immunodeficiency virus types 1 (HIV-1) and 2 (HIV-2) have yielded contradictory results. We used the two-hybrid genetic assay for protein-protein interactions in the eukaryote Saccharomyces cerevisiae (S. Fields and O.-K. Song, Nature [London] 340:245-246, 1989) to examine the multimerization of Tat in vivo. Both HIV-1 and HIV-2 Tat are shown to form specific homo- but not heteromultimers in the yeast cell nucleus. Mutational analysis indicates a critical role for the essential core motif of Tat in mediating this interaction but demonstrates that efficient Tat multimerization does not require an intact cysteine motif. These data raise the possibility that the multimerization of Tat may be important for Tat function in higher eukaryotes.
Context-Dependent Cleavage of the Capsid Protein by the West Nile Virus Protease Modulates the Efficiency of Virus Assembly

ABSTRACT The molecular mechanisms that define the specificity of flavivirus RNA encapsulation are poorly understood. Virions composed of the structural proteins of one flavivirus and the genomic RNA of a heterologous strain can be assembled and have been developed as live attenuated vaccine candidates for several flaviviruses. In this study, we discovered that not all combinations of flavivirus components are possible. While a West Nile virus (WNV) subgenomic RNA could readily be packaged by structural proteins of the DENV2 strain 16681, production of infectious virions with DENV2 strain New Guinea C (NGC) structural proteins was not possible, despite the very high amino acid identity between these viruses. Mutagenesis studies identified a single residue (position 101) of the DENV capsid (C) protein as the determinant for heterologous virus production. C101 is located at the P1′ position of the NS2B/3 protease cleavage site at the carboxy terminus of the C protein. WNV NS2B/3 cleavage of the DENV structural polyprotein was possible when a threonine (Thr101 in strain 16681) but not a serine (Ser101 in strain NGC) occupied the P1′ position, a finding not predicted by in vitro protease specificity studies. Critically, both serine and threonine were tolerated at the P1′ position of WNV capsid. More extensive mutagenesis revealed the importance of flanking residues within the polyprotein in defining the cleavage specificity of the WNV protease. A more detailed understanding of the context dependence of viral protease specificity may aid the development of new protease inhibitors and provide insight into associated patterns of drug resistance. IMPORTANCE West Nile virus (WNV) and dengue virus (DENV) are mosquito-borne flaviviruses that cause considerable morbidity and mortality in humans. No specific antiflavivirus therapeutics are available for treatment of infection. Proteolytic processing of the flavivirus polyprotein is an essential step in the replication cycle and is an attractive target for antiviral development. The design of protease inhibitors has been informed by insights into the molecular details of the interactions of proteases and their substrates. In this article, studies of the processing of WNV and DENV capsid proteins by the WNV protease identified an unexpected contribution of the sequence surrounding critical residues within the cleavage site on protease specificity. This demonstration of context-dependent protease cleavage has implications for the design of chimeric flaviviruses, new therapeutics, and the interpretation of flavivirus protease substrate specificity studies.
A new achievable scheme for interference relay channels

We establish an achievable rate region for discrete memoryless interference relay channels that consist of two source-destination pairs and one or more relays. We develop an achievable scheme combining Han-Kobayashi and noisy network coding. We apply our achievability to two cases. First, we characterize the capacity region of some classes of discrete memoryless interference relay channels. These classes naturally generalize the injective deterministic discrete memoryless interference channel by El Gamal and Costa and the discrete memoryless relay channel. Moreover, for the Gaussian interference relay channel with orthogonal receiver components, we show that our scheme achieves a better sum rate than that of noisy network coding.
Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2–rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.
A Logic Based Approach to Multi-Agent Systems

The research group at CENTRIA UNL in Lisbon, in collaboration with Ferrara and Linköping, has been quite active in the field of Logic Programming (LP) geared towards rational agents over several years, and has investigated a spate of rational agent functionalities and their implementations. In particular, the Lisbon group has been active in the fields of learning, abduction, updating, argumentation, paraconsistency, belief revision, soft LP, contradicition removal, diagnosis, and debugging. These research directions are all included in the broader long term research avenue of building evolving and collaborative rational epistemic agents, whose overarching objective is to establish a flexible declarative language for the specification and implementation of dynamic knowledge construction in a society of agents. In [32, 33], the philosophical foundations and the general line of approach to the definition of rational agents, based on and building upon the strengths of LP, have been put forward. Other recent results by the team include the combination of various pieces of knowledge, possibly originating in various agents, each of which with ascribed priorities over the others, the totality being organized via an acyclic graph [25, 28]. The long term objective of the group specifically includes the building of rational epistemic agents capable, in an integrated fashion, of reacting to a dynamic environment comprising other agents; managing and revising their goals,
MapReduce Performance Models for Hadoop 2.x

MapReduce is a popular programming model for distributed processing of large data sets. Apache Hadoop is one of the most common open-source implementations of such paradigm. Performance analysis of concurrent job executions has been recognized as a challenging problem, at the same time, that it may provide reasonably accurate job response time at significantly lower cost than experimental evaluation of real setups. In this paper, we tackle the challenge of defining MapReduce performance models for Hadoop 2.x. While there are several efficient approaches for modeling the performance of MapReduce workloads in Hadoop 1.x, the fundamental architectural changes of Hadoop 2.x require that the cost models are also reconsidered. The proposed solution is based on an existing performance model for Hadoop 1.x, but it takes into consideration the architectural changes of Hadoop 2.x and captures the execution flow of a MapReduce job by using queuing network model. This way the cost model adheres to the intra-job synchronization constraints that occur due the contention at shared resources. The accuracy of our solution is validated via comparison of our model estimates against measurements in a real Hadoop 2.x setup. According to our evaluation results, the proposed model produces estimates of average job response time with error within the range of 11% - 13.5%.
Field Trial Evaluating the Influence of Prophylactic and Therapeutic Antimicrobial Administration on Antimicrobial Resistance of Fecal Escherichia coli in Dairy Calves

ABSTRACT The objective of this study was to describe the influence of in-feed and therapeutic antimicrobials on resistance in commensal fecal Escherichia coli isolated from preweaned calves. Four groups of 30, day-old calf-ranch calves were enrolled and raised until 4 weeks of age. Groups 1 to 3 were raised without antimicrobials in the feed. Group 1 was isolated from the other groups and received no antimicrobial therapy. Group 2 was housed on the calf ranch and did not receive antimicrobial therapy, whereas groups 3 and 4 could be treated with antimicrobials. Group 4 was fed neomycin and tetracycline HCl in the milk replacer. Fecal samples were collected from calves on days 1, 14, and 28. Three E. coli isolates per sample were evaluated for susceptibility to 12 antimicrobials. Cluster analysis was used to group isolates having similar susceptibility patterns. Cumulative logistic regression was used to evaluate factors associated with increasing levels of multiple antimicrobial resistance. In-feed antimicrobials were associated with higher levels of multiple antimicrobial resistance in fecal E. coli.f In calves not receiving in-feed antimicrobials, older calves had higher levels of resistance compared to day-old calves. Individual antimicrobial therapy increased resistance in these calves but appeared to be transient. There was no environmental influence on resistance in E. coli populations among study groups.