Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse

Previous studies have revealed that the subunit α 2 (Gabra2) of the γ-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.
FPGA based Digital Pulse Width Modulator with Time Resolution under 2 ns

This work proposes a new DPWM architecture that takes advantage of FPGA's advanced characteristics, especially the DLLs (Delay-Locked Loop) present in almost every FPGA. The proposed DPWM combines a synchronous (counter-based) block with an asynchronous block for increased resolution without unnecessarily increasing the clock frequency. The experimental results show an implementation in a low cost FPGA (Xilinx Spartan-3) that uses an external 32 MHz clock for a final time resolution under 2 ns.
Intermediate disturbance in a late‐successional hemlock‐northern hardwood forest

1 An old‐growth mesic forest in northern Michigan, USA, experienced an unusually intense storm in July 2002. Permanent inventory plots and a 2.9‐ha mapped stand allow comparison of effects of this rare disturbance with patterns of ‘baseline’ mortality. 2 Tree mortality attributable to immediate effects of the storm was of similar magnitude to mortality over the previous decade, amounting to about 9% of basal area and 7% of stem density (mean of 88 inventory plots). 3 Storm mortality differed from baseline mortality in patterns related to species and size. Tsuga canadensis suffered little mortality of either type. Betula alleghaniensis had high baseline mortality in all size classes, but very low storm mortality. Acer spp. and Fagus grandifolia showed similar overall levels of baseline and storm mortality, but storm mortality was higher for larger stems. 4 Spatial patterns of mortality differed between baseline and storm‐caused disturbance, with storm mortality patterns related to composition and to substrate variation over the stand. Baseline canopy mortality was hyperdispersed at local scales, but mortality due to the storm was strongly clustered at distances up to 30 m. 5 Properties of rare, intermediate disturbances cannot be predicted by simply scaling up patterns due to frequent, less intense, events. They may have distinctive influences on community dynamics, countering trends towards dominance by shade‐tolerant species, generating demographic and spatial structure in the canopy, and distinctively affecting understorey environment. 6 These results suggest that climate change may induce changes in forest ecosystems by changing disturbance patterns even when species are not close to limits of physiological tolerance. Forest management for natural regeneration may need to take the effects of rare, intermediate disturbance into account.
Hematopoietic transcription factor GATA‐2 activates transcription from HIV‐1 long terminal repeat

Objectives:To study the role of the hematopoietic transcription factor GATA-2 in long terminal repeat (LTR)-directed transcriptional activation of HIV-1 in hematopoietic progenitor cells, and to investigate possible GATA-2 binding sites in HIV-1 LTR. Design and methods:Wild-type HIV-1 LTR, or mutants, ligated to a luciferase reporter gene with or without a GATA-2 expression vector, were transfected into COS cells, and standardized luciferase activity was examined. The binding activity of GATA-2 to these sites was examined by electrophoretic mobility shift assay. These wild-type or mutant reporter genes were also transfected into the murine hematopoietic progenitor cells, BAF3, in which GATA-2 was the predominantly expressed transcription factor of the GATA family, to assay LTR-directed transcription in intact hematopoietic machinery. Using a Tat expression plasmid for cotransfection, the influence of Tat protein on GATA-2-induced transactivation was determined. Results:In COS cells, LTR-dependent transactivation was highly enhanced by the coexpression of GATA-2. Experiments with mutant LTR suggested the presence of multiple GATA-2 binding sites, of which the major sites were identified. Cotransfection of Tat with GATA-2 indicated that GATA-2 and Tat synergistically enhanced the transcriptional activity. Transfection experiments in BAF3 cells showed that the disruption of these GATA sites diminished LTR-driven activity to 40% of the wild-type. Conclusions:GATA-2 may be a key host cell regulator of HIV-1 expression in hematopoietic stem cells. Manipulating this transactivation may represent a valuable approach to controlling virus production in infected hematopoietic progenitors. To elucidate the possible interaction between GATA-2 and Tat protein in vivo might give new insights to the mechanism of impaired hematopoiesis in AIDS patients.
Characteristics of hamadryas-like male baboons living in anubis baboon troops in the Awash hybrid zone, Ethiopia.

In the twenty-two years since the Awash baboon hybrid zone was first described, about 25-30 hamadryas or hamadryas-like hybrid males have taken up residence in anubis baboon groups. Most enter as mature adults, though some may immigrate as juvenile followers. Long-term tracking of known immigrants indicates that they may reside for four years or more in their adopted troop, during which time they establish a series of comparatively short-term harems, and probably sire hybrid offspring. "Abductions" of anubis females to hamadryas troops, as postulated by early observers, were not seen, though their occurrence cannot be ruled out. Younger, more recent immigrants tend to be "purer" hamadryas in phenotype, perhaps reflecting a more distant origin, or a change in the composition of neighboring hamadryas populations. Coexisting hamadryas and anubis show no signs of reproductive isolation by behavioral barriers, and evidently belong to a single "recognition species. "
Joint detection, segmentation, and registration of elastically deformable objects

We present a new approach to the general problem of template-based detection, segmentation, and registration of elastically deformable objects. This joint problem is highly nonlinear and high dimensional, due to the large space of possible geometric transformations between a given template and its observed signature. Hence, any attempt to directly solve it inevitably leads to a high dimensional, nonlinear, nonconvex optimization procedure. We propose a novel parametric solution to this problem, by showing that it can be equivalently represented by a low dimensional model, which is linear in the deformation parameters, and biased by the unknown observation background. Linear Bayesian estimation is then employed to estimate the deformation parameters, and a likelihood ratio test is utilized to detect a deformed instance of the template, thus providing an explicit closed-form solution for the joint problem.
Characterization of non-methane hydrocarbons emitted from open burning of wheat straw and corn stover in China

Field measurements were conducted to determine the characteristics of non-methane hydrocarbons (NMHCs) emitted from open burning of wheat straw and maize stover, two major agricultural residues in China. The headfire ignition technique was used with sampling downwind from the agricultural fire. Fifty-two NMHC species were quantified using gas chromatography/mass spectrometry. A carbon mass balance method was used to determine NMHC emission factors. The emission factors of the total speciated NMHCs from wheat straw and maize stover are 1690 ± 580 mg kg−1 and 1590 ± 430 mg kg−1, respectively. Propane, n-pentane, 2,3-dimethylbutane, 2-methylpentane, propene, benzene and toluene are the main species, together accounting for 55.3%–68.0% of the total NMHCs. On the basis of measured emission factors and the published maximum incremental reactivity values for NMHCs, we estimated the ozone forming potential (OFP) of speciated NMHCs. The results indicate that propene, 1-butene, isoprene, toluene and m,p-xylene have high OFP values and account for about 50% of the total OFP. Alkenes played the most important role in potential ozone formation, followed by aromatics and alkanes.
Management of mass casualty of incidents using an autonomous sensor network

The introduction of information and communication technologies (ICTs) to the management of catastrophes give us the opportunity to significantly increase the effectiveness of the rescue forces. Current state of the art, hanging triage cards and white boards, require a significant level of effort and stress to achieve the organization of the operation. In this paper we discuss a solution based on an autonomous sensor network and the necessity of its implementation on such scenarios. Scalability properties, robustness, ultra low-power consumption and user acceptance were aspects considered during the development. We studied as well the real time tracking of valuable patient information like the status of vital parameters and its location. By observing the interaction with the end user, we finalized out tests to prove the reliability, efficiency and effort-reduction of our technology during simulation exercises.
Upregulation of Annexin A 1 Expression by Butyrate in Human Colon Adenocarcinoma Cells : Role of p 53 , NF-Y , and p 38 Mitogen-Activated Protein Kinase

Annexin A1 is a member of a phospholipid and calcium binding family of proteins; it is involved in anti-inflammation and in the regulation of differentiation, proliferation, and apoptosis. Here, we show the existence of a functional binding site for the tumor suppressor p53 near the proximal CCAAT box and the fact that the basal expression of annexin A1 in human colon adenocarcinoma cells is driven by p53 at the transcriptional level. Posttranscriptional mechanisms may also play an important role in maintaining constitutive annexin A1 expression. In addition, a p53/NF-Y complex is detected bound to the p53 binding site on its promoter. Butyrate is a natural product of fiber degradation in the colon and a key regulator of colonic epithelium homeostasis. We show that butyrate, a class I and II histone deacetylase inhibitor, induces transcriptional activation of annexin A1 expression correlated with differentiation. The effect of butyrate is mediated through a release of NF-Y from the proximal CCAAT box and an enhancement of p53 binding. The interaction of p53 with the promoter is dependent on p38 MAPK activity either in the absence or in the presence of butyrate. Further, activation of p38 MAPK by this agent is required to increase annexin A1 promoter activity and to increase protein expression.
A Hybrid Entity-Mention Pronoun Resolution Model for German Using Markov Logic Networks

This paper presents a hybrid pronoun reso- lution system for German. It uses a simple rule-driven entity-mention formalism to in- crementally process discourse entities. An- tecedent selection is performed based on Markov Logic Networks (MLNs). The hy- brid architecture yields a cheap problem formulation in the MLNs w.r. t. inference complexity but pertains their expressive- ness. We compare the system to a rule- driven baseline and an extension which uses a memory-based learner. We find that the MLN hybrid outperforms its competi- tors by large margins.
Review of the long‐term effectiveness of cognitive behavioral therapy compared to medications in panic disorder

Panic disorder is a recurrent and disabling illness. It is believed that Cognitive Behavioral Therapy (CBT) has a long‐term protective effect for this disorder. This would offer CBT considerable advantage over medication management of panic disorder, as patients often relapse when they are tapered off their medications. This is a review of the literature about the long‐term effectiveness of CBT. We searched for follow‐up studies of panic disorder using CBT. Of the 78 citations produced in the initial search, most had major methodological flaws, including ignoring losses to follow‐up, not accounting for interval treatment, and unclear reporting. Three papers met strict methodological criteria, and two of these demonstrated a modest protective effect of CBT in panic disorder patients. We make recommendations for well‐designed studies involving comparisons of medications and cognitive behavior therapy. Depression and Anxiety 17:58–64, 2003. © 2003 Wiley‐Liss, Inc.
Impact of High Ratios of Plasma–to–Red Cell Concentrate on the Incidence of Acute Respiratory Distress Syndrome in UK Transfused Combat Casualties

ABSTRACT Trauma transfusion strategies, which incorporate balanced red-cell concentrate (RCC)–to–fresh frozen plasma (FFP) ratios, may be associated with improved survival in massively transfused patients. However, the use of this approach in nonmassively transfused patients has led to concern regarding an increase in acute respiratory distress syndrome (ARDS). The aim of this study was to assess the incidence of ARDS in transfused UK military casualties. All UK military casualties receiving an RCC transfusion within a 16-month period were identified from the UK Trauma Registry, and chest radiographs retrieved. If bilateral infiltrates were present, case notes were retrieved to calculate the PaO2/FIO2 ratio in accordance with the American-European Consensus Conference criteria. Patients were divided into massively transfused (≥10 U/24 h) and nonmassively transfused (<10 U/24 h) receiving a high ratio (≥0.75) or low (<0.75) RCC:FFP ratio. The primary outcome was the development of ARDS within 7 days of transfusion. Primary blast lung injury was excluded. Of 145 patients identified, 144 had records available for analysis with a median injury severity score of 21. The majority were injured by explosion (76%), and the remainder by gunshot (24%). There were 60 nonmassively transfused patients with 18 in the low and 42 in the high RCC:FFP ratio groups. Of the remaining 80 massively transfused patients, 11 were in the low and 73 were in the high-ratio groups. There was no difference in the incidence of ARDS between low- and high-ratio groups in either nonmassively transfused (22.2% vs. 9.5%; P = 0.232) or massively transfused (18.2% vs. 23.3%; P = 1.000) casualties. There was no statistically significant increase in the incidence of ARDS in UK casualties treated with high, compared with low, ratios of plasma to RCC.
A software framework for the microscopic modelling of pedestrian movement

A town planner, faced with the task of designing attractive walking spaces, needs a tool that will allow different designs to be compared in terms of their attractiveness as well as their effectiveness. PEDFLOW is an attempt to create such a tool. It is an agent-based, microscopic model of pedestrian flow where virtual pedestrians navigate a virtual environment. On their way towards a goal the agents, representing pedestrians, interact with features of the environment and with other agents. The microscopic, rule-based actions result in an emergent behaviour that mimics that of real pedestrians. Pedestrians are subjected to a multitude of influences when walking. The majority of existing models only focus on a single aspect, typically the avoidance of obstructions or other pedestrians. PEDFLOW uses an implementation of context-mediated behaviour to enable the agents to deal with multiple cause-effect relations in a well-defined and flexible yet highly efficient manner. A variety of mobile and immobile entities can be modelled by objects in an object-oriented environment. The model is informed by an empirical study of pedestrian behaviour and the parameters of the agents are derived from measures of observed pedestrian movement. PEDFLOW’s suitability for pedestrian modelling in the described context is evaluated in both qualitative and quantitative terms. Typical macroscopic movement patterns from the real world such as "platooning" and "walking with a partner" are selected and the corresponding emergent model behaviours investigated. Measures of service (MOS) are defined end extracted from the model for comparison with real world measures. As PEDFLOW was created as an interactive tool to be used in an office environment rather than in a high performance lab, the scalability and performance limitations are explored with regards to the size of the modelled area, the number of modelled pedestrians and the complexity of the interactions between them. It is shown that PEDFLOW can be a useful tool in the urban design process.
Spin dependent disorder in a junction device with spin orbit couplings

Using the multi-probe Landauer-BUttiker formula and Green's function approach, we calculate the longitudinal conductance (LC) and spin Hall conductance (SHC) numerically in a two-dimensional junction system with the Rashba and Dresselhaus spin orbit coupling (SOC) and spin dependent disorder (SDD) in presence of both random onsite and hopping disorder strengths. It has been found that when the strengths of the RSOC and DSOC are same, the SHC vanishes. Further in presence of random onsite or hopping disorder, the SHC is still zero when the strengths of the two types of SOC, that is Rashba and Dressselhaus are the same. This indicates that the cancellation of SHC is robust even in the presence of random disorder. Only with the inclusion of SDD (onsite or hopping), a non-zero SHC is found and it increases as the strength of SDD increases. The physical implication of the existence of a non-zero SHC has been explored in this work. Finally, we have compared the effect of onsite SDD and hopping SDD on both longitudinal and spin Hall conductances.
Hybrid geo-spatial query processing on the semantic web

SemanticWeb data sources such as DBpedia are a rich resource of structured representations of knowledge about geographical features and provide potential data for computing the results of Question Answering System queries that require geo-spatial computations. Retrieval from these resources of all content that is relevant to a particular spatial query of, for example, containment, proximity or crossing is not always straightforward as the geometry is usually confined to point representations and there is considerable inconsistency in the way in which geographical features are referenced to locations. In DBpedia, some geographical feature instances have point coordinates, others have qualitative properties that provide explicit or implicit spatial relationships between named places, and some have neither of these. This thesis demonstrates that structured geo-spatial query, a form of question answering, on DBpedia can be performed with a hybrid query method that exploits quantitative and qualitative spatial properties in combination with a high quality reference geo-dataset that can help to support a full range of geo-spatial query operators such as proximity, containment and crossing as well as vague directional queries such as Find airports north of London? A quantitative model based on the spatial directional relations in DBpedia has been used to assist in query processing. Evaluation experiments confirm the benefits of combining qualitative and quantitative methods for containment queries and of employing high-quality spatial data, as opposed to DBpedia points, as reference objects for proximity queries, particularly for linear features. The high quality geo-data also enabled answering questions impossible to answer with SemanticWeb resources alone, such as finding geographic features within some distance from a region boundary. The contributions were validated by a prototype geo-spatial query system that combined qualitative and quantitative processing and included ranking answers for directional queries based on models derived from DBpedia contributed data.
Participative development and training for business processes in industry: review of 88 simulation games

A tool for participative business process development is the so-called social simulation game method. The social simulation game method is like a "role-play" but is tailored to an organisation's own business processes. The main purpose is to develop business processes, i.e., to analyse present processes, to test alternative process modes and to train employees. The authors have carried out and studied simulation games in different industrial organisations over the past ten years, though these have been more focused during the last four years. According to these research results, the participative simulation game method has proven to be an effective facilitator in business process development and training in industrial organisations. This article is based on 32 case studies, including 88 simulation games, which are briefly described. Our primary aim is to describe how the social simulation game method is used in training and participative development for different processes and purposes. Results indicate that the method enables individual learning as well as promotes both single-loop and double-loop types of organisational learning. The simulation game method underscores the problems and development needs of the simulated business processes. The short-term and long-term qualitative (soft) and quantitative (hard) as well as the so-called future results and implications of the cases in implementation are reported and discussed. The concept of tacit and explicit change as a result of the interplay of tacit and explicit knowledge and soft, hard and future results has been created.
Use of trans-pleural hydrogel foam plugs for reducing pneumothorax complicating CT-guided lung biopsy

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