Miracle-dz/UniFAR-FTUs huggingface dataset:
The last deglaciation of the Norwegian Channel – geomorphology, stratigraphy and radiocarbon dating

Based on high‐resolution TOPAS acoustic data, bathymetric data sets and sediment cores from the Norwegian Channel, the last retreat of the Norwegian Channel Ice Stream has been investigated. Mapping of ice‐marginal features such as grounding‐zone wedges and terminal moraines off western Norway suggest that the retreat of the grounding line in this part of the channel was interrupted by frequent stillstands, whereas the channel south of the threshold at Jæren does not have crossing ice‐marginal landforms. Three main seismic units have been identified, and, based on their seismic characteristics, in addition to study of sediment cores, these units are interpreted as till (U1), glacial marine sediment (U2) and Holocene hemipelagic sediment (U3). Based on new and published radiocarbon dates of the lower part of U2, combined with dates from the adjacent areas, it is concluded that the grounding line started to retreat from the shelf edge at about 19 ka and that the inner part of Skagerrak was ice free at 17.6 ka. This gives an average retreat rate of 450 m a−1, which is generally higher than mean retreat rates estimated for other palaeo‐ice streams (15–310 m a−1).
Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation.

Replication of human immunodeficiency virus requires Tat protein which activates elongation of RNA polymerase II transcription at the HIV-1 promoter through interaction with the cyclin T1 (CycT1) subunit of the positive transcription elongation factor complex (P-TEFb). Tat binds directly through its transactivation domain to the CycT1 subunit of the P-TEFb and induces loop sequence specific binding of the P-TEFb onto nascent HIV-1 TAR RNA. By using a gel electrophoresis method and a comprehensive set of TAR loop mutants, we have identified the sequence and structural determinants for high-affinity CycT1-Tat-TAR ternary complex formation. Our results show that CycT1 and Tat binding to TAR RNA is highly cooperative, and a capacity of 85%, a Hill coefficient of 2.7, and a dissociation constant (K(D)) of 2.45 nM were observed. These results indicate that there are three binding sites on TAR RNA. CycT1 does not bind TAR RNA in the absence of Tat, and Tat binding to TAR, while detectable, is very inefficient in the absence of CycT1. It is conceivable that the CycT1-Tat heterodimer directly binds to TAR RNA in the U-rich RNA bulge region and this binding facilitates the interactions of the CycT1-Tat heterodimer at the other two sites in the RNA loop region. On the basis of our results, we suggest a model where CycT1 interacts with Tat protein and positions the protein complex to make contacts with the G34 region of the loop sequence; G34 is critical for CycT1-Tat binding and forms a C30.G34 base pair. Two functional groups, O6 and N7, at nucleotide positions 32 and 34 in the TAR loop are essential for CycT1-Tat interactions with TAR RNA. The identity of two nucleotides, U31 and G33, is not critical, but they contribute to the stabilization of the RNA-protein complex. The presence of a single-nucleotide bulge of A35 or C35 is essential for distortion of the backbone RNA structure as well as the accessibility of functional groups in the major groove of the double-helical region. CycT1-Tat interaction with TAR RNA represents another example of the flexibility and complexity of RNA structure involved in protein recognition.
Manganese superoxide dismutase (MnSOD) genetic polymorphism is associated with risk of early‐onset prostate cancer

Prostate cancer continues to be the most frequently diagnosed neoplasm, and the second leading cause of cancer‐related mortality in men. Oxidative stress may enhance prostatic carcinogenesis. Manganese superoxide dismutase (MnSOD) is the only known superoxide scavenger in mitochondria. It plays a key role in antioxidant defense as mitochondria are important for oxidative metabolism coupled to the electron transport chain and oxidative phosphorylation and hence, ROS production. A T→C single nucleotide substitution, resulting in a Val→Ala change at position 9 (Ala‐9Val), which alters the secondary structure of the protein, has been noted to affect transport of MnSOD into the mitochondria. We have determined the MnSOD genotype in 85 prostate cancer cases and 151 control subjects. Ala‐9Val polymorphism was determined using real time polymerase chain reaction (PCR) amplification with fluorescently labeled primers. No significant difference was found in prostate cancer susceptibility in the subjects with Ala/Ala and Val/Ala genotype compared with Val/Val genotype (Odds ratio (OR), 1.3; 95% confidence interval (95% CI), 0.69–2.42; p = 0.416). We did not observe an association of the MnSOD genotype or allele frequency between subgroups of cases divided by disease status (aggressive vs. non‐aggressive prostate cancer). However, in the analyses stratified by the age at diagnosis we have observed that men homozygous for Ala had a 5.2‐fold increased risk of early‐onset prostate cancer (under age of 65) compared to men homozygous for Val allele (p = 0.05). These data suggest that Ala/Ala MnSOD genotype in the Macedonian population could have an influence on early onset of prostate cancer, but no impact on the subsequent development of the disease. Copyright © 2008 John Wiley & Sons, Ltd.
Security in networked building automation systems

Enriching Building Automation Systems (BAS) with new services formerly provided by separate subsystems promises synergies, but increases demands on the BAS architecture. In particular, the integration of security subsystems significantly tightens security requirements on the protocol of a networked control system. First, this paper gives a survey on security in BAS. Possible threats and attacks are discussed. Weaknesses in the security mechanisms of important open networked BAS (LonWorks, BACnet, KNX/EIB) are summarized. Then, a security extension to KNX/EIB is presented. It includes several security mechanisms that guarantee data integrity, confidentiality and freshness, as well as authentication to provide secure process data and management communication. Relevant configuration related issues such as key management and distribution are also addressed.
Seasonal growth dynamic of Norway spruce at the study site of Rájec (Drahanská vrchovina Highland)

The circumference increment assessment of Norway spruce focused on the effect of inter tree competition in the mature spruce stand was made at the study site of Rájec (Drahanská vrchovina Highland) over a 5-year period. Data were collected from 49 trees, which were monitored continuously with mechanical band dendrometers from 2010 to 2014. The dependency of the circumference increment on competition index, diameter at breast height, Lang’s rain factor, mean temperature of various periods and sum of precipitation of various periods was evaluated. Climatic conditions of the study site are characterised with warm and wet summers and cold-dry winters. In 5 years average around 61% of the annual precipitation falls during growing season. There was highly significant correlation between relative increment and temperature (p=2.324e–13) and significant correlation between relative increment and precipitation (p=0.0439). These results confirmed that inter–tree competition and diameter at breast height are sufficient variables for circumference increment estimation of unmeasured trees in the particular year. Coefficient of determination reached 0.25–0.63 for competition and 0.40–0.84 for tree diameter at breast height. The present investigation brings important results about tree growth and seasonal growth dynamics and its relation with competition and microclimatic conditions in mature spruce stand.
Algorithm discovery by protein folding game players

Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.
Loss of Fas expression and high expression of HLA-E promoting the immune escape of early colorectal cancer cells

Previous studies have investigated the mechanisms of immune evasion of tumor cells in numerous types of advanced solid malignant tumor, and several types of immune preparations have been administered as antitumor adjuvant therapies. However, in the majority of studies, the efficacy of therapies has been revealed to be limited. The present study aimed to investigate the immune evasion mechanisms employed by early colorectal cancer cells and the expression of the molecules associated with immune evasion during the malignant transformation process of normal colorectal epithelial cells to measure the effects of immune intervention for early colorectal cancer, and to improve the efficacy of immunotherapy. A total of 60 colorectal tissues, including 15 normal mucosa, 15 adenoma, 15 early cancer and 15 advanced cancer tissues, from patients undergoing endoscopic procedures in Huadong Hospital Affiliated to Fudan University (Shanghai, China) were collected. A comparison of baseline characteristics among these four groups was performed. The expression levels of human leukocyte antigen-A (HLA-A), apoptosis antigen 1 (Fas), c-c chemokine receptor type 5 (CCR5), Fas ligand (FasL) and HLA-E in each group were detected by immunohistochemical analysis. Furthermore, 15 patients with advanced colorectal cancer were enrolled into the present study. Advanced cancer and paracancer tissues (normal mucosal tissues 3 cm away from the margin of cancer tissues) were collected from each patient by colonoscopic biopsy. The expression levels of HLA-A, Fas, CCR5, FasL and HLA-E in each group were detected by western blot analysis. During the malignant transformation process of normal colorectal epithelial cells, the expression levels of CCR5, FasL and HLA-E increased significantly (P<0.001), whilst the expression levels of Fas reduced significantly (P=0.0271). In the early cancer group, the expression levels of Fas reduced significantly (P=0.0239), whilst the expression levels of HLA-E increased significantly (P<0.001) compared with adenoma group. In conclusion, a loss of Fas expression and high expression levels of HLA-E may promote the immune evasion of early colorectal cancer cells.
Hold Me Tight: Role of the Heat Shock Protein Family of Chaperones in Cardiac Disease

During the development of cardiac hypertrophy, heart failure, and ischemia reperfusion challenge, the heart accumulates misfolded proteins as a result of cellular stresses.1,–,4 Although the compensatory increases in chaperones/cochaperones work to prevent misfolding, refold denatured proteins, and/or target them for degradation, this system can become overwhelmed, leading to worsening of cardiac function. In fact, recent studies have demonstrated experimentally that increasing the burden of misfolded proteins in the heart can contribute to the development of cardiac dysfunction.5 In this review, we discuss the role of heat shock proteins (HSPs) in common cardiac diseases, including cardiac hypertrophy, heart failure, and ischemia/reperfusion injury. Furthermore, we delineate the many specific mechanisms by which these chaperones, cochaperones, and heat shock factor (HSF) transcription factors have been found to be cardioprotective in experimental models. Lastly, we review recent studies involving drugs that are being developed (and currently used) to increase the expression (and presumably function) of chaperone/cochaperone systems that may be applicable to the treatment of common cardiac diseases and familial cardiac diseases with a pathogenesis that includes a major component of misfolded proteins (eg, desminopathies). There are several general families of molecular chaperones in the cytoplasm of mammalian cells, including HSP90, HSP70, chaperonin containing TCP1 (CCT; also called TCP1-ring complex [TRiC]), and small HSP (sHSP) family proteins (the Figure, A). Members of the HSP90 family of chaperones are the most abundant chaperones located in the cytosol. They form dimers consisting of HSP90α and HSP90β subunits and are inducible with stress, although they also are quite abundant without stress.8,9 HSP90 assists many proteins involved with signal transduction, including >40 kinases and many steroid hormone receptors, with a supporting role in conformational changes involved in ATP hydrolysis.10,11 The HSP70 chaperone family consists of …
Enhanced predictive zonal search for single and multiple frame motion estimation

Motion Estimation (ME) for video coding has taken an entirely different direction with the emergence of zonal algorithms. These algorithms made it possible to significantly reduce, if not almost eliminate, the tremendous computational overhead of motion estimation that was incurred in a video encoding system, while having little if any loss in quality. In this paper we further improve on these algorithms with the introduction of the Enhanced Predictive Zonal Search Algorithm (EPZS). By considering an additional set of predictors, improving the thresholding process, and simplifying the search pattern employed by these algorithms, we not only manage in achieving better output quality, but also reduce complexity of the motion estimation process even further. Our algorithm was compared with the algorithms accepted in the Optimization Model 1.0 of MPEG-4, and our simulations prove its outright superiority versus the existing algorithms. Furthermore we present a 3-Dimensional implementation of EPZS, which can be easily applied in the case of multiple frame motion estimation (ITU H.263++ and H.26L).
Fatty Acids Decrease in Pearl Millet Forage from Relative Increases of Pseudostem

Fatty acid content and composition of lamina and pseudostem are markedly different. Whole plant fatty acid analysis is a non‐ideal presentation for warm‐season annuals. Lamina mass ratio is an important correlate of fatty acids in warm‐season annuals. Managing for greater lamina intake may greatly influence animal fatty acid supply.
Effects of Unsaturated Flow on Hillslope Recession Characteristics

Recession flow analysis is usually conducted to infer hydraulic parameters of hillslope aquifers. Various Boussinesq equation‐based models, both linear and nonlinear, have been used to analyze the recession curves for sloping aquifers, with a focus on the long‐time recession behavior. Based on a modified Boussinesq equation with capillarity incorporated, we demonstrate the significant effect of unsaturated flow on the recession curve, which result in three (instead of two) power law regimes with two transition points (instead of one) corresponding to the formation of a fully unsaturated zone at the adjacent area of the upslope boundary and across the whole domain, respectively. The results show that the power of the second and third recession regime is variable, depending on the slope angles, soil types, and hillslope geometries. The unsaturated flow effects also lead to the absence of drastic drop of −dQ/dt at the transition between the first and second regime, which was predicted by previous numerical models but has not been observed in the field or laboratory experiments. These findings have important implications for recession flow analysis in studies of hillslope aquifers.
Scalable Algorithms for Association Mining

Association rule discovery has emerged as an important problem in knowledge discovery and data mining. The association mining task consists of identifying the frequent itemsets, and then forming conditional implication rules among them. We present efficient algorithms for the discovery of frequent itemsets which forms the compute intensive phase of the task. The algorithms utilize the structural properties of frequent itemsets to facilitate fast discovery. The items are organized into a subset lattice search space, which is decomposed into small independent chunks or sublattices, which can be solved in memory. Efficient lattice traversal techniques are presented which quickly identify all the long frequent itemsets and their subsets if required. We also present the effect of using different database layout schemes combined with the proposed decomposition and traversal techniques. We experimentally compare the new algorithms against the previous approaches, obtaining improvements of more than an order of magnitude for our test databases.
Visual information-processing impairments in deficit and nondeficit schizophrenia.

OBJECTIVE Previous studies of covert visuospatial attention in schizophrenia suggest a subtle form of right hemispatial neglect in acutely ill patients but not in chronic, stable patients. Because of previous work documenting various visual information-processing abnormalities in deficit schizophrenia, the authors investigated whether the deficit/nondeficit categorization would help clarify the presence of visual attentional asymmetries in schizophrenia. METHOD Performance on a covert visuospatial attention task was examined in clinically stable outpatients with schizophrenia (17 in a deficit subgroup and 28 in a nondeficit subgroup) and 25 normal subjects. Peripheral cue and central cue versions of the covert visuospatial attention task, at 100-, 200-, and 800-msec intervals between cue and target, were administered a week apart. RESULTS The nondeficit patients exhibited a significant and abnormal asymmetry, with slower reaction time to targets presented in the right visual field than in the left visual field. This right visual field disadvantage was found with both versions of the task, but only at the 100-msec cue-target interval. The deficit patients were slowest in overall reaction time but, similar to the normal subjects, showed no asymmetry. CONCLUSIONS The results are consistent with slower visual information processing in the left compared to the right cerebral hemisphere in nondeficit schizophrenia. This finding cannot be accounted for by differences between the deficit and nondeficit subgroups in demographic characteristics, chronicity, or medication effects, nor is it secondary to generalized cognitive impairment.
Analysis and improved compact modeling of the breakdown behavior of sub-0.25 micron ESD protection ggNMOS devices

The work focuses on a better understanding of the sub-quater micron ggNMOS device breakdown, compact modeling of the band-to-band tunneling enhanced substrate current and the observed gate hot hole injection current. Simple implications of the improved subbreakdown current model on the ggnNMOS model behaviour are shown. Finally, the observed TLP failure mode of the investigated devices is discussed.
Potential Greenhouse Gas Mitigation through Temperate Tree-Based Intercropping Systems

Increasing awareness of global climate change has pressured agricultural producers to reduce greenhouse gas (GHG) emissions while at the same time encouraging them to maintain food production needed for an increasing popula- tion. Tree-based intercropping (TBI) systems are believed to be useful in climate change mitigation, especially in temper- ate regions, due to their potential to reduce GHG emissions from agricultural practices. The purpose of this paper is there- fore to review some of the research conducted on GHG mitigation in TBI in southern Ontario and Quebec, Canada. Re- search conducted at the University of Guelph Agroforestry Research Station (GARS) indicated that TBI systems had the potential to lower N2O emissions by 1.2 kg ha -1 y -1 compared to a conventional agricultural field cropping system. Trees can assimilate residual nitrate (NO3 - ) left from nitrogen (N) fertilizer applications, thereby leaving less NO3 - available for denitrification and subsequently reducing N2O losses. Carbon sequestration is also enhanced in TBI systems as carbon (C) is stored in both above and below ground tree components. Soil Organic Carbon (SOC) is higher in systems incorporating trees because tree litter decomposes slowly, therefore reducing CO2 loss to the atmosphere. The C sequestration potential of TBI systems and the possibility to include fast-growing tree species for bioenergy production in TBI systems make it a valid solution to mitigate climate change in temperate regions. The opportunity of C trading credits to offset the costs of implementing a TBI system and provide additional income to farmers could facilitate the adoption of TBI amidst agricul- tural producers in temperate regions.
Testing Multi-Alternative Decision Models with Non-Stationary Evidence

Recent research has investigated the process of integrating perceptual evidence toward a decision, converging on a number of sequential sampling choice models, such as variants of race and diffusion models and the non-linear leaky competing accumulator (LCA) model. Here we study extensions of these models to multi-alternative choice, considering how well they can account for data from a psychophysical experiment in which the evidence supporting each of the alternatives changes dynamically during the trial, in a way that creates temporal correlations. We find that participants exhibit a tendency to choose an alternative whose evidence profile is temporally anti-correlated with (or dissimilar from) that of other alternatives. This advantage of the anti-correlated alternative is well accounted for in the LCA, and provides constraints that challenge several other models of multi-alternative choice.
The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between Genes

The spatial organization of eukaryotic genomes is thought to play an important role in regulating gene expression. The recent advances in experimental methods including chromatin capture techniques, as well as the large amounts of accumulated gene expression data allow studying the relationship between spatial organization of the genome and co-expression of protein-coding genes. To analyse this genome-wide relationship at a single gene resolution, we combined the interchromosomal DNA contacts in the yeast genome measured by Duan et al. with a comprehensive collection of 1,496 gene expression datasets. We find significant enhancement of co-expression among genes with contact links. The co-expression is most prominent when two gene loci fall within 1,000 base pairs from the observed contact. We also demonstrate an enrichment of inter-chromosomal links between functionally related genes, which suggests that the non random nature of the genome organization serves to facilitate coordinated transcription in groups of genes.