Miracle-dz/UniFAR-FTUs huggingface dataset:
Reasoning with bio-ontologies: using relational closure rules to enable practical querying

MOTIVATION Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as a semi-automated process in three steps: (i) defining a logic-based representation language; (ii) building a consistent ontology using that language; and (iii) exploiting the ontology through querying. RESULTS Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological Resource Description Framework knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases. AVAILABILITY SPARUL code, a query end point and curated relation types in OBO Format, RDF and OWL 2 DL are freely available at http://www.semantic-systems-biology.org/metarel.
Improved Visualization and Specific Binding for Metabotropic Glutamate Receptor Subtype 1 (mGluR1) Using [11C]ITMM with Ultra-High Specific Activity in Small-Animal PET

Metabotropic glutamate receptor subtype 1 (mGluR1) is a crucial target in the development of new medications to treat central nervous system (CNS) disorders. Recently, we developed N-[4-[6-(isopropylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl]-4-[11C]methoxy-N-methyl-benzamide ([11C]ITMM) as a useful positron emission tomography (PET) probe for mGluR1 in clinical studies. Here, we aimed to improve visualization and threshold of specific binding for mGluR1 using [11C]ITMM with ultra-high specific activity (SA) of > 3,500 GBq/μmol in rat brains. A two-tissue compartment model indicated large differences between the two SAs in the constants k3 and k4, representing binding ability for mGluR1, while constants K 1 and k2 showed no differences. The total distribution volume (VT) values of conventional and ultra-high SA were 9.1 and 11.2 in the thalamus, 7.7 and 9.7 in the striatum, and 6.4 and 8.5 mL/cm3 in the substantia nigra, respectively. The specific binding of [11C]ITMM with ultra-high SA was significantly higher than the conventional SA, especially in the basal ganglia. Parametric PET images scaled with VT of the ultra-high SA clearly identified regional differences in the rat brain. In conclusion, PET studies using [11C]ITMM with ultra-high SA could sufficiently improve visualization and specific binding for mGluR1, which could help further understanding for mGluR1 functions in CNS disorders.
Three's company, or a crowd?: The effects of robot number and behavior on HRI in Japan and the USA

In everyday applications of robotics, people will likely interact with groups of robots. Most human-robot interaction (HRI) research to date, however, has studied humans interacting with individual robots. Initial research suggests that humans respond differently to individual robots and robots in groups, making responses to groups of robots critical to study. This paper presents a study performed in a public setting familiar to participants (university cafeterias) to examine how participants respond when robots, individually and in groups, enter their space. We examined participant survey and behavioral responses to different numbers of robots (Single or Group) with different behaviors (Social or Functional). Because robots will be used across cultures, we performed the study in Japan and the USA. Across cultures, we found that people interact more with robots in groups than single robots, yet report similar levels of liking for both; participants also rated social robots as more friendly and helpful than functional robots in general. They rated single social robots more positively than a group of social robots, but a group of functional robots more positively than single functional robots. Japanese participants reported liking the robots more than USA participants. This suggests that researchers and designers should be aware of how robot characteristics influence group effects. Social human-robot interaction, group effects, robot behavior, cross-cultural study
Modification of tumor cells by a low dose of Newcastle Disease Virus.

The present study elucidates the mechanism whereby viral xenogenization of highly metastatic ESb lymphoid tumor cells increases tumor immunogenicity and syngeneic tumor‐specific T cell responses in comparison to nonmodified tumor cells. It was found that the frequency of cytotoxic T lymphocytes specific for the ESb tumor‐associated transplantation antigen (TATA) and the cytotoxic anti‐tumor activity in bulk cultures of immune spleen cells were significantly increased (by factor 3 and 25, respectively) when using virus‐modified tumor cells. An amplified response was observed both in vivo and in vitro which might explain the demonstrated effectiveness of this approach for postoperative immunotherapy of ESb metastases.
Reconstructing drought variability for Mongolia based on a large‐scale tree ring network: 1520–1993

[1] Previous tree ring based hydrologic studies in Mongolia have been regional in scale. Here, we present a large-scale summer drought reconstruction for Mongolia that reveals the main summer moisture patterns of the past. This reconstruction is based on a network of tree ring chronologies that span the country. The resulting drought model explains 61% of the variance and is extended to cover 1520-1993 by using a nested approach to modeling. Severe droughts and harsh winter conditions occurred in Mongolia from ~1999-2002 and contributed to massive livestock mortality and economic loss. These droughts were extreme in the context of the past several hundred years. Significant periodicities are found at 40 (90%), 19.3-25 (99%), 11.6 (95%), 6.4-7.2 (95%), and 2.8 years (99%). This high-resolution drought reconstruction and associated tree ring chronologies supplement and extend the sparse meteorological data in Mongolia and can be used to better understand climate variability and potential forcings of climate.
Dose–response association between maternal body mass index and small for gestational age: a meta-analysis

Abstract Objective: This study was performed to determine the dose–response relationships between maternal anthropometric variables and risk of small for gestational age (SGA). Methods: Linear and nonlinear dose–response meta-analyses were performed to summarize the adjusted relative risks of SGA. Ten databases, including PubMed (MEDLINE), were searched. Study quality was assessed using the Newcastle–Ottawa scale. Results: A total of 323 243 subjects were extracted from high-quality studies to evaluate maternal body mass index (BMI) (n = 9). The generalizability of the findings regarding height and weight (n = 3 and 2, respectively) was limited. The non-linear model (p for non-linearity < 0.05) showed a significant and inverse association of maternal BMI with risk of SGA, although only two of nine studies involved obese women (i.e. BMI ≥ 30 kg/m2). The slope of the dose–response curve between maternal BMI and SGA (i.e. the amount of reduction in SGA risk) decreased gradually. Conclusions: SGA risk may be reduced by increasing BMI of normal (i.e. 18.5 kg/m2 ≤ BMI < 25 kg/m2) and overweight women (i.e. 25 kg/m2 ≤ BMI < 30 kg/m2), but the most marked reduction is achieved by increasing BMI of underweight women (i.e. BMI < 18.5 kg/m2).
Effects of Bay k 8644, a Dihydropyridine Analog, on [3H]Nitrendipine Binding to Canine Cardiac Sarcolemma and the Relationship to a Positive Inotropic Effect

Equilibrium dissociation constants of Bay k 8644, a calcium agonist, and nitrendipine, a calcium antagonist, were determined in canine cardiac sarcolemma. The equilibrium dissociation constant for Bay k 8644 was compared to the concentration that produced a fifty percent increase, and the equilibrium dissociation constant for nitrendipine was compared to the concentration that produced a fifty percent decrease, in contractile force in canine heart trabecular muscle. Both saturation and inhibition binding data suggest that Bay k 8644 and nitrendipine bind to and compete for a high affinity dihydropyridine-binding site present in isolated cardiac sarcolemma preparations. The equilibrium dissociation constant (7–10 NM) and concentration that produced a fifty percent increase in contractile force in the canine trabecular muscle (30 ± 8 nM) of Bay k 8644 were in a similar concentration range, but the equilibrium dissociation constant (0.29 ± 0.025 nM) of nitrendipine binding was more than a thousand-fold lower than the concentration that produced a fifty percent decrease in contractile force in canine trabecular muscle (613 ± 109 n). These data suggest that binding of Bay k 8644 to high affinity binding sites is pharmacologically relevant, and is related to a positive inotropic effect.
Effect of interleukin 17 on proteoglycan degradation in murine knee joints

OBJECTIVE To evaluate the effect of murine interleukin 17 (IL17) on cartilage catabolism and joint inflammation by direct intra-articular injection of the cytokine into murine knee joints. METHODS Knees of normal C57 Bl mice were injected once or repeatedly with recombinant IL17 or IL1β. Inflammation was estimated by technetium-99m pertechnetate (99Tc) uptake and histological scoring of tissue sections. Proteoglycan depletion was evaluated by histological scoring of safranin O stained sections. Effects on proteoglycan synthesis were studied by 35SO4incorporation. RESULTS A single intra-articular injection of IL17 (10 ng/knee) produced effects very similar to those of IL1β (10 ng/knee). No inflammation was detected at six or 24 hours by 99Tc uptake. However, safranin O staining showed depletion of proteoglycan at 48 hours. Repeated injections of IL17 induced joint inflammation and cartilage proteoglycan depletion as shown by histological scoring. Unlike IL1β, proteoglycan depletion induced by IL17 seemed to be the result of increased degradation only, as no suppression of35SO4 incorporation was seen. CONCLUSION These findings confirm, in vivo, the catabolic effects of IL17 on cartilage. IL17 is thus the first T cell cytokine showing a direct catabolic effect on cartilage in addition to stimulatory effects on macrophages and synoviocytes, making it a potentially important cytokine in the pathogenesis of arthritis.
Mesh reduction with error control

In many cases the surfaces of geometric models consist of a large number of triangles. Several algorithms were developed to reduce the number of triangles required to approximate such objects. Algorithms that measure the deviation between the approximated object and the original object are only available for special cases. We use the Hausdorff distance between the original and the simplified mesh as a geometrically meaningful error value which can be applied to arbitrary triangle meshes. We present a new algorithm to reduce the number of triangles of a mesh without exceeding a user defined Hausdorff distance between the original and simplified mesh. As this distance is parameterization independent, its use as error measure is superior to the use of the L/sup /spl infin//-Norm between parameterized surfaces. Furthermore the Hausdorff distance is always less than the distance induced by the L/sup /spl infin//-Norm. This results in higher reduction rates. Excellent results were achieved by the new decimation algorithm for triangle meshes that has been used in different application areas such as volume rendering, terrain modeling and the approximations of parameterized surfaces. The key advantages of the new algorithm are: it guarantees a user defined position dependent approximation error; it allows one to generate a hierarchical geometric representation in a canonical way; it automatically preserves sharp edges.
Engaging with Young People's Conceptions of the Political

In many states, there are concerns about declining levels of political engagement and participation among young people. Our understanding of this decline, however, is limited because much of the research on youth politics is based on a narrow conception of 'the political', little attempt is made to explore how people themselves define politics, non-participation is not adequately problematised, and there are in sufficient youth-specific explanations for declining participation among young people. Drawing on fieldwork carried out in Britain, I argue there is a need to develop an approach and research methodology that engages with young people's conceptions of the political.
On the Partial Inclusion Protocol for Multi Level Cache Hierarchy in Disk Controller

The Inclusion protocol is important in reducing the cache coherence complexity for disk controller with multilevel cache hierarchies. We proposed a two kind of partial inclusion protocol called space inclusion and mapping inclusion for fully associative caches and set associative caches which allow different block sizes at different levels of the hierarchy. The disk controller structures with a two-level cache hierarchy are examined. The feasibility of this protocol in this controller is discussed. From the performance measurement results of benchmark test, we can see the performance of the proposed protocol can be 10% better than conventional inclusion protocol
Which Part of the Conductor's Body Conveys Most Expressive Information? A Spatial Occlusion Approach

This study investigated the perception of conductors' body movements under different viewing conditions with a multi-modal within-subjects design. Five conductors with different levels of experience each conducted four excerpts from a Beethoven symphony that varied in musical expressiveness. Video recordings were manipulated according to three occlusion conditions: a) only the face was visible, b) only the arms were visible and c) the whole body was visible in simulated peripheral vision. 127 musically trained or untrained participants first watched, without sound, randomly presented video sequences according to these conditions. For each sequence, they were asked to rate affective and communicative items. Complete video sequences with sound were then presented as a reference and rated similarly. Video sequences that presented the conductors' faces resembled the reference significantly better than the arms-only or the peripheral conditions in terms of expressiveness ratings. Sequences showing the arms were judged higher in amount of information. For the movements of all conductors, clear interpretation differences between the four musical excerpts appeared even for conditions without sound. Differences between conductors were related to their general affective behaviour and to evaluations of four conducting experts. The findings generally highlight the importance of facial affective behaviour for expressive conducting.
Circulating matrix metalloproteinases and their inhibitors in inguinal hernia and abdominal aortic aneurysm.

AIM There is evidence supporting the role of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) in aortic and abdominal wall connective tissue degeneration, resulting in aneurysm and hernia formation. Furthermore, clinical association studies have demonstrated increased prevalence of abdominal wall hernias in patients with aortic aneurysms. Our objective was to estimate the levels of MMPs and TIMPs in the blood of patients with aortic aneurysm and inguinal hernia, in order to investigate whether there is potential pathogenic linkage of impaired collagen metabolism. METHODS Plasma concentrations of MMP-9, MMP-2, TIMP-1 and TIMP-2 were quantified using ELISA in 33 male patients with abdominal aortic aneurysm and 91 male patients with inguinal hernia. They were consecutive patients undergoing repair during the study period. The same substances were measured in 35 healthy male controls. RESULTS MMP-9 and MMP-2 concentrations were lower in the plasma of patients with inguinal hernia and abdominal aortic aneurysm than controls, with hernia patients having the lowest circulating levels. The levels of TIMP-2 were significantly elevated in patients with inguinal hernia and significantly reduced in patients with aortic aneurysm, whereas opposite correlations were found for circulating TIMP-1. CONCLUSION Different patterns of circulating MMP and TIMP levels were found in patients with aneurysm and hernia compared with controls. Underlying pathogenic processes implicating MMPs and TIMPs in connective tissue metabolism are expressed by differing plasma levels in the two disease states. Further research including combined plasma and tissue analyses is required to further investigate potential common pathogenesis of these diseases.
Protein design automation

We have conceived and implemented a cyclical protein design strategy that couples theory, computation, and experimental testing. The combinatorially large number of possible sequences and the incomplete understanding of the factors that control protein structure are the primary obstacles in protein design. Our protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead‐End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry from the vast number of possible solutions. Rotamer sequences were scored for steric complementarity using a van der Waals potential. A Monte Carlo search was then executed, starting at the optimal sequence, in order to find other high‐scoring sequences. As a test of the design methodology, high‐scoring sequences were found for the buried hydrophobic residues of a homodimeric coiled coil based on GCN4‐p1. The corresponding peptides were synthesized and characterized by CD spectroscopy and size‐exclusion chromatography. All peptides were dimeric and nearly 100% helical at 1 °C, with melting temperatures ranging from 24 °C to 57 °C. A quantitative structure activity relation analysis was performed on the designed peptides, and a significant correlation was found with surface area burial. Incorporation of a buried surface area potential in the scoring of sequences greatly improved the correlation between predicted and measured stabilities and demonstrated experimental feedback in a complete design cycle.
Offshoring: What Can Go Wrong?

Offshoring has sustained much criticism, mainly over the issue of whether shipping IT work abroad is good for the US as a whole. Does it benefit a US firm to offshore its IT work - specifically software development and maintenance? This paper discusses several reasons for firms to be wary of this practice. For some managers, these considerations might tip the balance against offshoring. For those who wish to offshore anyway, this article can serve as a map of the pitfalls to try to avoid.
A Systems Immunology Approach to Plasmacytoid Dendritic Cell Function in Cytopathic Virus Infections

Plasmacytoid dendritic cell (pDC)-mediated protection against cytopathic virus infection involves various molecular, cellular, tissue-scale, and organism-scale events. In order to better understand such multiscale interactions, we have implemented a systems immunology approach focusing on the analysis of the structure, dynamics and operating principles of virus-host interactions which constrain the initial spread of the pathogen. Using high-resolution experimental data sets coming from the well-described mouse hepatitis virus (MHV) model, we first calibrated basic modules including MHV infection of its primary target cells, i.e. pDCs and macrophages (Mφs). These basic building blocks were used to generate and validate an integrative mathematical model for in vivo infection dynamics. Parameter estimation for the system indicated that on a per capita basis, one infected pDC secretes sufficient type I IFN to protect 103 to 104 Mφs from cytopathic viral infection. This extremely high protective capacity of pDCs secures the spleen's capability to function as a ‘sink’ for the virus produced in peripheral organs such as the liver. Furthermore, our results suggest that the pDC population in spleen ensures a robust protection against virus variants which substantially down-modulate IFN secretion. However, the ability of pDCs to protect against severe disease caused by virus variants exhibiting an enhanced liver tropism and higher replication rates appears to be rather limited. Taken together, this systems immunology analysis suggests that antiviral therapy against cytopathic viruses should primarily limit viral replication within peripheral target organs.
Inverted‐U relationship between the level of peripheral corticosterone and the magnitude of hippocampal primed burst potentiation

Studies have shown that peripheral levels of corticosterone correlate with the magnitudes of two well‐described physiological models of memory, long‐term potentiation (LTP) and primed burst (PB) potentiation. In the present experiments, the authors investigated the effects of experimenter‐controlled manipulations of the levels of corticosterone on the magnitude of hippocampal PB potentiation in urethane‐anesthetized rats. Primed burst potentiation is a long‐lasting (at least 30 minutes) increase in the amplitude of the CA1 population spike and EPSP slope in response to physiologically patterned stimulation of the hippocampal commissure. The levels of serum corticosterone were controlled by implanting corticosterone pellets in adrenalectomized rats (ADX/PELLET). In the first experiment, a significant negative linear correlation between elevated (stress) levels of serum corticosterone (greater than 20 μm/dL) and the magnitude of PB potentiation in ADX/PELLET subjects (r = 0.60, P <.05) was found. In the second experiment, the shape of the corticosterone‐PB potentiation function was different at low and intermediate levels of corticosterone than it was at high levels of corticosterone: There was a positive correlation at low levels (0–10 μm/dL), a peak response at intermediate levels (11–20 μm/dL), and a negative correlation at high levels (21–93 μm/dL) of corticosterone. Thus, the overall relationship between corticosterone and PB potentiation is an inverted‐U function. These findings provide strong support for the hypothesis that corticosterone exerts a concentration‐dependent biphasic influence on the expression of hippocampal plasticity.
A random fault injector for CAN Network

This paper presents a fault injector for CAN network. The injector is capable of generating random errors in the CAN bus from the send of a bit sequence that violate operational rules of the CAN protocol. The time between errors follows an exponential distribution with a specific mean. The injector was implemented and validated successfully. Finally, an experimental study of a CAN network was developed to examine the impact of faults in the worst case response time of messages. As expected, the worst case response time of messages increased with the injection of faults on the bus. Accordingly, the fault injector proposed can be used to test CAN applications in real time in order to check the time requirements will be fulfilled.