Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico and Biochemical Analysis of Physcomitrella patens Photosynthetic Antenna: Identification of Subunits which Evolved upon Land Adaptation

BACKGROUND In eukaryotes the photosynthetic antenna system is composed of subunits encoded by the light harvesting complex (Lhc) multigene family. These proteins play a key role in photosynthesis and are involved in both light harvesting and photoprotection. The moss Physcomitrella patens is a member of a lineage that diverged from seed plants early after land colonization and therefore by studying this organism, we may gain insight into adaptations to the aerial environment. PRINCIPAL FINDINGS In this study, we characterized the antenna protein multigene family in Physcomitrella patens, by sequence analysis as well as biochemical and functional investigations. Sequence identification and analysis showed that some antenna polypeptides, such as Lhcb3 and Lhcb6, are present only in land organisms, suggesting they play a role in adaptation to the sub-aerial environment. Our functional analysis which showed that photo-protective mechanisms in Physcomitrella patens are very similar to those in seed plants fits with this hypothesis. In particular, Physcomitrella patens also activates Non Photochemical Quenching upon illumination, consistent with the detection of an ortholog of the PsbS protein. As a further adaptation to terrestrial conditions, the content of Photosystem I low energy absorbing chlorophylls also increased, as demonstrated by differences in Lhca3 and Lhca4 polypeptide sequences, in vitro reconstitution experiments and low temperature fluorescence spectra. CONCLUSIONS This study highlights the role of Lhc family members in environmental adaptation and allowed proteins associated with mechanisms of stress resistance to be identified within this large family.
A hybrid AANN-KPCA approach to sensor data validation

In this paper two common methods for nonlinear principal component analysis are compared. These two methods are Auto-associative Neural Network (AANN) and Kernel PCA (KPCA). The performance of these methods in sensor data validation are discussed, finally a methodology which takes advantage of both of these methods is presented. The result is a unique approach to nonlinear component mapping of a given set of data obtained from a nonlinear quasi-static system. This method is finally compared with AANN and KPCA for sensor data validation and shows a better performance in terms of predicting/reconstructing the missing or corrupted channels of data.
Bruised Inside Out: The Adverse and Abusive Life Histories of Incarcerated Women as Pathways to PTSD and Illicit Drug Use

The majority of incarcerated women who suffer from diverse traumatic life histories including abusive home lives and intimate partner violence (IPV), develop post-traumatic stress disorder (PTSD) and struggle with heavy illicit drug use. While many have offered examinations of these relationships, the current study is among the first to utilize an integrated feminist pathways and general strain theory (GST) approach to explain them. Using data from a stratified random sample of all incarcerated women in Oklahoma (N = 334), we explore the links between, adverse childhood experiences, including physical, sexual, emotional, and childhood neglect, IPV, PTSD, and heavy illicit drug use. Our findings indicate that the effects of IPV on heavy illicit drug use are mediated by PTSD symptoms suggesting that PTSD plays a significant role in the pathway to illicit drug use among Oklahoma women prisoners. Implications for the importance of utilizing an integrated feminist pathways and GST approach in future research are offered.
The nature and dynamics of learning among caregivers in a national certificate training programme

In this research study I investigate the nature and dynamics of learning amongst learners in a National Certificate Training Programme for community health workers who are caregivers in a home-based care prgoramme. The study analyses the relationship between experience, participation and learning and seeks to establish how the experience of adult learners can be mobilised through active participation and how situational conditions can either facilitate or inhibit participation and learning amongst the learners. Another dimension of the study seeks to establish what caregivers learn and the processes through which they learn and how such learning contributes to changes in behaviour and relationships. In this study, the nature and dynamics of learning amongst adult learners in the NCTP programme at community level is explored as an example of socio-cultural theory and situated learning which hold that learning results from participation in various socio-cultural situations – the act of participation is seen as crucial in the learning. The study focused on a group of 10 learners in the National Certificate Training Programme for community health workers who are also caregivers in the Nokuthembeka Home-based Care Programme in New Crossroads in the Cape Town metropole and used a qualitative research design and interpretive approach to understand the situations in which they learn. An interpretive approach allowed for deeper insight into the socio-cultural contexts that influence the social interactions of caregivers with peers as well as their learning. In the study I argue that the experience of caregivers forms a critical resource and the foundational basis for learning. The research study confirmed that the training programme in which caregivers interact and engage with peers and facilitators creates a learning context and that active participation in the situation facilitates learning. The study further confirmed that the informal settings of the home and community are important sites for learning and gaining experience and that situational conditions such as language, personal attributes and culture of learning/teaching can influence participation and learning.
High-Temperature Compressive Resistance and Mechanical Properties Improvement of Strain-Induced Melt Activation-Processed Al-Mg-Si Aluminum Alloy

Even though the high-temperature formability of Al alloys can be enhanced by the strain-induced melt activation (SIMA) process, the mechanical properties of the formed alloys are necessary for estimation. In this research, a modified two-step SIMA (TS-SIMA) process that omits the cold working step of the traditional SIMA process is adopted for the 6066 Al-Mg-Si alloy to obtain globular grains with a short-duration salt bath. The high-temperature compressive resistance and mechanical properties of TS-SIMA alloys were investigated. The TS-SIMA alloys were subjected to artificial aging heat treatment to improve their mechanical properties. The results show that the TS-SIMA process can reduce compression loading by about 35%. High-temperature compressive resistance can be reduced by the TS-SIMA process. After high-temperature compression, the mechanical properties of the TS-SIMA alloys were significantly improved. Furthermore, artificial aging treatment can be used to enhance formed alloys via the TS-SIMA process. After artificial aging treatment, the mechanical properties of TS-SIMA alloys are comparable to those of general artificially-aged materials.
A Traffic Knowledge Aided Vehicle Motion Planning Engine Based on Space Exploration Guided Heuristic Search

A real-time vehicle motion planning engine is presented in this paper, with the focus on exploiting the prior and online traffic knowledge, e.g., predefined roadmap, prior environment information, behaviour-based motion primitives, within the space exploration guided heuristic search (SEHS) framework. The SEHS algorithm plans a kinodynamic vehicle motion in two steps: a geometric investigation of the free space, followed by a grid-free heuristic search employing primitive motions. These two procedures are generic and possible to take advantage of traffic knowledge. In this paper, the space exploration is supported by a roadmap and the heuristic search benefits from the behaviour-based primitives. Based on this idea, a light weighted motion planning engine is built, with the purpose to handle the traffic knowledge and the planning time in real-time motion planning. The experiments demonstrate that this SEHS motion planning engine is flexible and scalable for practical traffic scenarios with better results than the baseline SEHS motion planner regarding the provided traffic knowledge.
Comment on "Conceptual Inadequacy of Shannon Information ..." by C. Brukner and A. Zeilinger

It is pointed out that the case for Shannon entropy and von Neumann entropy, as measures of uncertainty in quantum mechanics, is not as bleak as suggested in quant-ph/0006087. The main argument of the latter is based on one particular interpretation of Shannon's H-function (related to consecutive measurements), and is shown explicitly to fail for other physical interpretations. Further, it is shown that Shannon and von Neumann entropies have in fact a common fundamental significance, connected to the existence of a unique geometric measure of uncertainty for classical and quantum ensembles. Some new properties of the ``total information'' measure proposed in quant-ph/0006087 are also given.
Angiotensin II stimulates intercellular adhesion molecule-1 (ICAM-1) expression by human vascular endothelial cells and increases soluble ICAM-1 release in vivo.

BACKGROUND We evaluated whether angiotensin II (Ang II) influenced intercellular adhesion molecule (ICAM)-1 expression by human vascular endothelial cells derived from umbilical cord veins (HUVECs) and plasma soluble ICAM-1 levels in vivo. METHODS AND RESULTS Cultured HUVECs were incubated with Ang II (from 10(-9) to 10(-6) mol/L) with or without candesartan and PD12319 (inhibitors of Ang II AT(1) and AT(2) receptors, respectively) for various times up to 4 hours. Total RNA was then extracted from HUVECs, and Northern blots were probed with a 1.9-kb ICAM-1 cDNA fragment. HUVEC supernatants were used to assess soluble ICAM-1 release by ELISA. Northern blot analysis detected a strong increase of ICAM-1 mRNA after 2-hour incubation with Ang II. The response was inhibited by candesartan. Soluble ICAM-1 release by HUVECs also increased (P<0. 002) after 2-hour Ang II stimulation. In vivo, Ang II (at an initial rate of 1.0 ng. kg(-1). min(-1), to be increased each 30 minutes by 2.0 ng. kg(-1). min(-1) to the final rate of 7.0 ng. kg(-1). min(-1)) was infused in 8 normotensive and 12 essential hypertensive individuals. In the latter, Ang II was reinfused after 4 weeks on either placebo (n=3), losartan (50 mg UID, n=5), or atenolol (50 mg UID, n=4) treatment. Plasma soluble ICAM-1 levels increased after Ang II infusion in hypertensives and normotensives (P<0.0001 after 90 minutes). Losartan reduced baseline soluble ICAM-1 levels (P<0.05) and Ang II-related ICAM-1 increments. CONCLUSIONS Ang II upregulates ICAM-1 expression by HUVECs and stimulates in vitro and in vivo soluble ICAM-1 release. AT(1) receptor blockade inhibits such endothelial effects of Ang II.
Clock buffer and wire sizing using sequential programming

This paper investigates methods for clock skew minimization using buffer and wire sizing. First, a technique that significantly improves solution quality and stability of sequential programming-based buffer/wire sizing is used. Then, a new formulation of clock skew minimization that uses quadratic programming and considers sub-critical skews in addition to the most critical skews is presented. The quality of results is verified to be more robust using Monte Carlo simulations to account for process sensitivity. For the same power budget, the sequential quadratic programming (SQP) method has better expected skew, standard deviation, and overall CPU time on average
Efficacy of psychosocial interventions for psychological and pregnancy outcomes in infertile women and men: a systematic review and meta-analysis

Objective To evaluate the evidence on the efficacy of psychosocial interventions for improving pregnancy rates and reducing distress for couples in treatment with assisted reproductive technology (ART). Design Systematic review and meta-analysis. Data sources PsycINFO, PubMed, EMBASE, CINAHL, Web of Science and The Cochrane Library between 1978 and April 2014. Study selection Studies were considered eligible if they evaluated the effect of any psychosocial intervention on clinical pregnancy and/or distress in infertile participants, used a quantitative approach and were published in English. Data extraction Study characteristics and results were extracted and the methodological quality was assessed. Effect sizes (ES; Hedges g) were pooled using a random effects model. Heterogeneity was assessed using the Q statistic and I2, and publication bias was evaluated using Egger’s method. Possible moderators and mediators were explored with meta-analyses of variances (ANOVAs) and meta-regression. Results We identified 39 eligible studies (total N=2746 men and women) assessing the effects of psychological treatment on pregnancy rates and/or adverse psychological outcomes, including depressive symptoms, anxiety, infertility stress and marital function. Statistically significant and robust overall effects of psychosocial intervention were found for both clinical pregnancy (risk ratio=2.01; CI 1.48 to 2.73; p<0.001) and combined psychological outcomes (Hedges g=0.59; CI 0.38 to 0.80; p=0.001). The pooled ES for psychological outcomes were generally larger for women (g: 0.51 to 0.73) than men (0.13 to 0.34), but the difference only reached statistical significance for depressive symptoms (p=0.004). Meta-regression indicated that larger reductions in anxiety were associated with greater improvement in pregnancy rates (Slope 0.19; p=0.004). No clear-cut differences were found between effects of cognitive–behavioural therapy (CBT; g=0.84), mind–body interventions (0.61) and other intervention types (0.50). Conclusions The present meta-analysis suggests that psychosocial interventions for couples in treatment for infertility, in particular CBT, could be efficacious, both in reducing psychological distress and in improving clinical pregnancy rates.
Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.
Multiresolution Isosurface Fitting on a Surface Octree

The Surface Octree (SO) is an extension of the Classical Octree used to maintain a decimated codification of a surface while preserving volume data information. Constrained by a region of maximal interest, we present an algorithm to extract a multiresolution surface from a SO data structure. This algorithm reconstructs the surface with maximal precision in the focus of interest and at progressively lower resolution away from it.
Tactical performance changes with equal vs unequal numbers of players in small-sided football games

This study investigated the effects of equal (GK+4-vs-4+GK) and unequal (GK+4-vs-3+GK) numbers of outfield players on tactical behaviour of players and teams in small-sided football games. Thirty sequences of play without transitions in ball possession captured from six games of five minutes duration were selected for analysis from each game condition. The movement trajectories of players, teams and ball were expressed using polar coordinates referenced on centre location of the defending goal. Tactical performance was expressed by the degree of coupling of players and teams as indicated by the relative phase for different dyad combinations and by spatial-temporal relations between players and teams using various kinematic metrics. Results showed stronger couplings in the defending dyads, defending player ball pairs and the defending team and ball (p < 0.05) for the unequal numbers game condition. Also, decreased distances between players to their team geometric centre, decreased surface areas but increased distances between team geometric centres was observed for unequal playing numbers (p<0.05). Thus, results demonstrated that numerical advantage for the attacking team changed the tactical performances of the defending and attacking players and teams, particularly the former. Knowledge on this matter provides support for coaches manipulating small-sided football games for training purposes.
A novel PCA-based authentication watermarking scheme with superior localization and security

In this paper, a Novel PCA-based authentication watermarking scheme with superior localization and security is proposed. The input image is partitioned into non-overlapping 8×8 image blocks. An alternate representation of these image blocks is obtained based on principal component analysis (PCA). The authentication watermark bits are generated from the first m coefficients among these blocks. In order to resist vector quantization (VQ) attack and collage attack, and tolerate incidental manipulation, each bit of the block's authentication watermark is redundancy embedded into another block which is selected by its corresponding secret key. Theoretic analysis and experimental results have proved that the proposed algorithm not only has superior localization and security to all kinds of attack, but also tolerate incidental manipulations while keep sensitive to malicious manipulations.
ReForm: Integrating Physical and Digital Design through Bidirectional Fabrication

Digital fabrication machines such as 3D printers and laser-cutters allow users to produce physical objects based on virtual models. The creation process is currently unidirectional: once an object is fabricated it is separated from its originating virtual model. Consequently, users are tied into digital modeling tools, the virtual design must be completed before fabrication, and once fabricated, re-shaping the physical object no longer influences the digital model. To provide a more flexible design process that allows objects to iteratively evolve through both digital and physical input, we introduce bidirectional fabrication. To demonstrate the concept, we built ReForm, a system that integrates digital modeling with shape input, shape output, annotation for machine commands, and visual output. By continually synchronizing the physical object and digital model it supports object versioning to allow physical changes to be undone. Through application examples, we demonstrate the benefits of ReForm to the digital fabrication process.
Binding binding: Departure points for a different version of the perceptual retouch theory

In the perceptual retouch theory, masking and related microgenetic phenomena were explained as a result of interaction between specific cortical representational systems and the non-specific sub-cortical modulation system. Masking appears as deprivation of sufficient modulation of the consciousness mechanism suffered by the target-specific signals because of the temporal delay of non-specific modulation (necessary for conscious representation), which explicates the later-coming mask information instead of the already decayed target information. The core of the model envisaged relative magnitudes of EPSPs of single cortical cells driven by target and mask signals at the moment when the nonspecific, presynaptic, excitatory input arrives from the thalamus. In the light of the current evidence about the importance of synchronised activity of specific and non-specific systems in generating consciousness, the retouch theory requires perhaps a different view. This article presents some premises for modification of the retouch theory, where instead of the cumulative presynaptic spike activities and EPSPs of single cells, the oscillatory activity in the gamma range of the participating systems is considered and shown to be consistent with the basic ideas of the retouch theory. In this conceptualisation, O-binding refers to specific encoding which is based on gamma-band synchronised oscillations in the activity of specific cortical sensory modules that represent features and objects; C-binding refers to the gamma-band oscillations in the activity of the non-specific thalamic systems, which is necessary for the O-binding based data to become consciously experienced.
Overexpression of BDNF Increases Excitability of the Lumbar Spinal Network and Leads to Robust Early Locomotor Recovery in Completely Spinalized Rats

Strategies to induce recovery from lesions of the spinal cord have not fully resulted in clinical applications. This is a consequence of a number of impediments that axons encounter when trying to regrow beyond the lesion site, and that intraspinal rearrangements are subjected to. In the present study we evaluated (1) the possibility to improve locomotor recovery after complete transection of the spinal cord by means of an adeno-associated (AAV) viral vector expressing the neurotrophin brain-derived neurotrophic factor (BDNF) in lumbar spinal neurons caudal to the lesion site and (2) how the spinal cord transection and BDNF treatment affected neurotransmission in the segments caudal to the lesion site. BDNF overexpression resulted in clear increases in expression levels of molecules involved in glutamatergic (VGluT2) and GABAergic (GABA, GAD65, GAD67) neurotransmission in parallel with a reduction of the potassium-chloride co-transporter (KCC2) which contributes to an inhibitory neurotransmission. BDNF treated animals showed significant improvements in assisted locomotor performance, and performed locomotor movements with body weight support and plantar foot placement on a moving treadmill. These positive effects of BDNF local overexpression were detectable as early as two weeks after spinal cord transection and viral vector application and lasted for at least 7 weeks. Gradually increasing frequencies of clonic movements at the end of the experiment attenuated the quality of treadmill walking. These data indicate that BDNF has the potential to enhance the functionality of isolated lumbar circuits, but also that BDNF levels have to be tightly controlled to prevent hyperexcitability.
Intersample and Finite Wordlength Eeects in Sampled-data Problems 1 2

We consider the behaviour of digital control systems from the point of view of modeling intersample behavior , and the eeects of quantizations and nite wordlength computations. Our purpose in this paper is to investigate the dependence of these two eeects on the sampling rate. We show that there is essentialy a tradeoo between guarding against these two eeects, in that fast sampling will generaly improve intersample behavior, while it makes the system more sensitive to nite arithmetic eeects. We develop quantitative measures for performance under these two combined eeects using input-output norms. We address the problem of intersample behavior using the by now well known lifting technique, while we investigate roundoo error effects by modeling them as feedback with certain types of switching nonlinearities. We present examples that exhibit these tradeoos.