Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of Seed Soundness in Conifers Cryptomeria japonica and Chamaecyparis obtusa Using Narrow-Multiband Spectral Imaging in the Short-Wavelength Infrared Range

Regeneration of planted forests of Cryptomeria japonica (sugi) and Chamaecyparis obtuse (hinoki) is the pressing importance to the forest administration in Japan. Low seed germination rate of these species, however, has hampered low-cost production of their seedlings for reforestation. The primary cause of the low germinability has been attributed to highly frequent formation of anatomically unsound seeds, which are indistinguishable from sound germinable seeds by visible observation and other common criteria such as size and weight. To establish a method for sound seed selection in these species, hyperspectral imaging technique was used to identify a wavelength range where reflectance spectra differ clearly between sound and unsound seeds. In sound seeds of both species, reflectance in a narrow waveband centered at 1,730 nm, corresponding to a lipid absorption band in the short-wavelength infrared (SWIR) range, was greatly depressed relative to that in adjacent wavebands on either side. Such depression was absent or less prominent in unsound seeds. Based on these observations, a reflectance index SQI, abbreviated for seed quality index, was formulated using reflectance at three narrow SWIR wavebands so that it represents the extent of the depression. SQI calculated from seed area-averaged reflectance spectra and spatial distribution patterns of pixelwise SQI within each seed area were both proven as reliable criteria for sound seed selection. Enrichment of sound seeds was accompanied by an increase in germination rate of the seed lot. Thus, the methods described are readily applicable toward low-cost seedling production in combination with single seed sowing technology.
Poisson Statistics for Eigenvalues of Continuum Random Schr

We show absence of energy levels repulsion for the eigenvalues of random Schr\"odinger operators in the continuum. We prove that, in the localization region at the bottom of the spectrum, the properly rescaled eigenvalues of a continuum Anderson Hamiltonian are distributed as a Poisson point process with intensity measure given by the density of states. We also obtain simplicity of the eigenvalues. We derive a Minami estimate for continuum Anderson Hamiltonians. We also give a simple and transparent proof of Minami's estimate for the (discrete) Anderson model.
Effect of implantation on engineered skeletal muscle constructs

The development of engineered skeletal muscle would provide a viable tissue for replacement and repair of muscle damaged by disease or injury. Our current tissue‐engineering methods result in three‐dimensional (3D) muscle constructs that generate tension but do not advance phenotypically beyond neonatal characteristics. To develop to an adult phenotype, innervation and vascularization of the construct must occur. In this study, 3D muscle constructs were implanted into the hindlimb of a rat, along the sciatic nerve, with the sural nerve isolated, transected and sutured to the construct to encourage innervation. Aortic ring anchors were sutured to the tendons of the biceps femoris muscle so that the construct would move dynamically with the endogenous muscle. After 1 week in vivo, the constructs were explanted, evaluated for force production and stained for muscle, nerve and collagen markers. Implanted muscle constructs showed a developing capillary system, an epimysium‐like outer layer of connective tissue and an increase in myofibre content. The beginning of α‐bungarotoxin clustering suggests that neuromuscular junctions (NMJs) could form on the implanted muscle, given more time in vivo. Additionally, the constructs increased maximum isometric force from 192 ± 41 μN to 549 ± 103 μN (245% increase) compared to in vitro controls, which increased from 276 ± 23 μN to 329 ± 27μN (25% increase). These findings suggest that engineered muscle tissue survives 1 week of implantation and begins to develop the necessary interfaces needed to advance the phenotype toward adult muscle. However, in terms of force production, the muscle constructs need longer implantation times to fully develop an adult phenotype. Copyright © 2012 John Wiley & Sons, Ltd.
Liver resection with bipolar radiofrequency device: Habib 4X.

BACKGROUND Intraoperative blood loss has been shown to be an important factor correlating with morbidity and mortality in liver surgery. In spite of the technological advances in hepatic parenchymal transection devices, bleeding remains the single most important complication of liver surgery. The role of radiofrequency (RF) in liver surgery has been expanded from tumour ablation to major hepatic resections in the last decade. Habib 4X, a new bipolar RF device designed specifically for liver resection is described here. METHODS Habib 4X is a bipolar, handheld, disposable RF device and consists of two pairs of opposing electrodes which is introduced perpendicularly into the liver, along the intended transection line. It produces controlled RF energy between the electrodes and the heat produced seals even major biliary and blood vessels and enables resection of the liver parenchyma with a scalpel without blood loss or biliary leak. RESULTS Three hundred and eleven patients underwent 384 liver resections from January 2002 to October 2007 with this device. There were 109 major resections and none of the patients had vascular inflow occlusion (Pringle's manoeuvre). Mean intraoperative blood loss was 305 ml (range 0-4300) ml, with less than 5% (n=18) rate of transfusion. CONCLUSION Habib 4X is an additional device for hepatobiliary surgeons to perform liver resections with minimal blood loss and low morbidity and mortality rates.
Learnable Pooling Regions for Image Classification

Biologically inspired, from the early HMAX model to Spatial Pyramid Matching, pooling has played an important role in visual recognition pipelines. Spatial pooling, by grouping of local codes, equips these methods with a certain degree of robustness to translation and deformation yet preserving important spatial information. Despite the predominance of this approach in current recognition systems, we have seen little progress to fully adapt the pooling strategy to the task at hand. This paper proposes a model for learning task dependent pooling scheme -- including previously proposed hand-crafted pooling schemes as a particular instantiation. In our work, we investigate the role of different regularization terms showing that the smooth regularization term is crucial to achieve strong performance using the presented architecture. Finally, we propose an efficient and parallel method to train the model. Our experiments show improved performance over hand-crafted pooling schemes on the CIFAR-10 and CIFAR-100 datasets -- in particular improving the state-of-the-art to 56.29% on the latter.
A STUDY OF PATIENTS ATTENDING EMERGENCY OUT-PATIENT SERVICES OF A LARGE TEACHING INSTITUTION

SUMMARY Authors have studied the pattern of psychiatric morbidity at the general emergency out-patient services and at the emergency psychiatric services being run concurrently at a large teaching institution. The percentage of psychotics was observed to be maximum at emergency psychiatric services. Non-psychiatric medical officers were observed to deal with non-psychotic psychiatric emergencies themselves rather than referring them to emergency psychiatric services.
Transfer Entropy as a Tool for Hydrodynamic Model Validation

The validation of numerical models is an important component of modeling to ensure reliability of model outputs under prescribed conditions. In river deltas, robust validation of models is paramount given that models are used to forecast land change and to track water, solid, and solute transport through the deltaic network. We propose using transfer entropy (TE) to validate model results. TE quantifies the information transferred between variables in terms of strength, timescale, and direction. Using water level data collected in the distributary channels and inter-channel islands of Wax Lake Delta, Louisiana, USA, along with modeled water level data generated for the same locations using Delft3D, we assess how well couplings between external drivers (river discharge, tides, wind) and modeled water levels reproduce the observed data couplings. We perform this operation through time using ten-day windows. Modeled and observed couplings compare well; their differences reflect the spatial parameterization of wind and roughness in the model, which prevents the model from capturing high frequency fluctuations of water level. The model captures couplings better in channels than on islands, suggesting that mechanisms of channel-island connectivity are not fully represented in the model. Overall, TE serves as an additional validation tool to quantify the couplings of the system of interest at multiple spatial and temporal scales.
Transmission Estimation in Underwater Single Images

This paper proposes a methodology to estimate the transmission in underwater environments which consists on an adaptation of the Dark Channel Prior (DCP), a statistical prior based on properties of images obtained in outdoor natural scenes. Our methodology, called Underwater DCP (UDCP), basically considers that the blue and green color channels are the underwater visual information source, which enables a significant improvement over existing methods based in DCP. This is shown through a comparative study with state of the art techniques, we present a detailed analysis of our technique which shows its applicability and limitations in images acquired from real and simulated scenes.
Restraint and seclusion in psychiatric inpatient wards

Purpose of review Despite the controversy over the use of seclusion and restraint, these measures are commonly used to treat and manage disruptive and violent behaviour. This review summarizes recent research on the use of seclusion and restraint, and measures taken to reduce their use. Recent findings Lately, prominent international recommendations have aimed to restrict the use of seclusion and restraint, and reminded that they should only be used in exceptional cases, where there are no other means of remedying the situation and under the supervision of a doctor. The use of seclusion and restraint has remained prevalent, but there are serveral innovative programmes that have succeeded in controlling and reducing their use. Staff attitudes about seclusion and restraint have changed little in the last few years. Summary There is a need for novel methods to treat violence and the threat of violence on psychiatric wards. Violence is a complex phenomenon that needs to be met with a multiprofessional approach. Customer involvement in this work is required. The assessment of the effectiveness of programmes aiming to minimizing seclusion and restraint has been hampered by the lack of parallel control groups and there is a need for cluster-randomized trials. When studying these interventions, the safety of staff and patients should be included as on outcome measure.
Carbon Fiber-Reinforced Polymer Wraps for Corrosion Control and Rehabilitation of Reinforced Concrete Columns

This paper discusses the use of carbon fiber-reinforced polymer (CFRP) wraps as a rehabilitation technique for corroded reinforced concrete columns. The effect of applying the wraps at early ages of the columns and its effect on corrosion propagation is addressed. Interaction between corrosion phenomena and the CFRP wrapping is studied through simple combinations of both factors. The lab work included testing of 52 reinforced concrete cylinders. The testing procedures are described. It was concluded that applying CFRP wraps significantly decreases corrosion activity when applied over the entire specimen. The application of the wraps before corrosion propagation will prevent corrosion from taking place, while the application of the wraps after corrosion occurrence will drop the rate of corrosion sharply. This effect is likely due to the epoxy saturant used to apply the CFRP sheets and not from the fibers themselves.
Tetrameric Structure of Centromeric Nucleosomes in Interphase Drosophila Cells

Centromeres, the specialized chromatin structures that are responsible for equal segregation of chromosomes at mitosis, are epigenetically maintained by a centromere-specific histone H3 variant (CenH3). However, the mechanistic basis for centromere maintenance is unknown. We investigated biochemical properties of CenH3 nucleosomes from Drosophila melanogaster cells. Cross-linking of CenH3 nucleosomes identifies heterotypic tetramers containing one copy of CenH3, H2A, H2B, and H4 each. Interphase CenH3 particles display a stable association of approximately 120 DNA base pairs. Purified centromeric nucleosomal arrays have typical "beads-on-a-string" appearance by electron microscopy but appear to resist condensation under physiological conditions. Atomic force microscopy reveals that native CenH3-containing nucleosomes are only half as high as canonical octameric nucleosomes are, confirming that the tetrameric structure detected by cross-linking comprises the entire interphase nucleosome particle. This demonstration of stable half-nucleosomes in vivo provides a possible basis for the instability of centromeric nucleosomes that are deposited in euchromatic regions, which might help maintain centromere identity.
A Genomic Background Based Method for Association Analysis in Related Individuals

Background Feasibility of genotyping of hundreds and thousands of single nucleotide polymorphisms (SNPs) in thousands of study subjects have triggered the need for fast, powerful, and reliable methods for genome-wide association analysis. Here we consider a situation when study participants are genetically related (e.g. due to systematic sampling of families or because a study was performed in a genetically isolated population). Of the available methods that account for relatedness, the Measured Genotype (MG) approach is considered the ‘gold standard’. However, MG is not efficient with respect to time taken for the analysis of genome-wide data. In this context we proposed a fast two-step method called Genome-wide Association using Mixed Model and Regression (GRAMMAR) for the analysis of pedigree-based quantitative traits. This method certainly overcomes the drawback of time limitation of the measured genotype (MG) approach, but pays in power. One of the major drawbacks of both MG and GRAMMAR, is that they crucially depend on the availability of complete and correct pedigree data, which is rarely available. Methodology In this study we first explore type 1 error and relative power of MG, GRAMMAR, and Genomic Control (GC) approaches for genetic association analysis. Secondly, we propose an extension to GRAMMAR i.e. GRAMMAR-GC. Finally, we propose application of GRAMMAR-GC using the kinship matrix estimated through genomic marker data, instead of (possibly missing and/or incorrect) genealogy. Conclusion Through simulations we show that MG approach maintains high power across a range of heritabilities and possible pedigree structures, and always outperforms other contemporary methods. We also show that the power of our proposed GRAMMAR-GC approaches to that of the ‘gold standard’ MG for all models and pedigrees studied. We show that this method is both feasible and powerful and has correct type 1 error in the context of genome-wide association analysis in related individuals.
Extracting informative genes from unprocessed microarray data

Numerous feature selection methods have been developed to identify informative genes from a large pool of genes that are not involved in the array experiments. However, the integrity of the reported genes is still uncertain due to the applications of various pre-processing techniques to the microarray data by these methods and a lack of standard validation procedures to validate the significance of the genes. In this paper, we developed a feature extraction framework based on the hybrid genetic algorithm (GA) and neural network (ANN) to extract informative genes from the raw (unprocessed) microarray data. This approach has showed its efficacy in extracting informative genes for microarray data.
Circle theorem-based realization of nonlinear force control for teleoperation under time delay

The communication delay is one of the major problems existing in the bilateral teleoperation system since it largely degrades the performance. This study treats the acceleration-based bilateral control (ABC) as a basic controller. According to the analyses, it is shown that a trade-off between the operationality and the reproduction performance of the kinesthetic contact exists in designing the ABC under time delay. For addressing this, adjustment of the force control gain according to the situations of the bilateral control is proposed. For ensuring the stability of the system with the nonlinear controller, circle theorem is applied to the proposed system. Experimental results show that the proposed system can realize stable operation as well as the improved performance over the bilateral control system with constant gain.
The exonuclease ISG20 mainly localizes in the nucleolus and the Cajal (Coiled) bodies and is associated with nuclear SMN protein‐containing complexes

We have previously shown that ISG20, an interferon (IFN)‐induced gene, encodes a 3′ to 5′ exoribonuclease member of the DEDD superfamily of exonucleases. ISG20 specifically degrades single‐stranded RNA. In this report, using immunofluorescence analysis, we demonstrate that in addition to a diffuse cytoplasmic and nucleoplasmic localization, the endogenous ISG20 protein was present in the nucleus both in the nucleolus and in the Cajal bodies (CBs). In addition, we show that the ectopic expression of the CBs signature protein, coilin, fused to the red fluorescent protein (coilin‐dsRed) increased the number of nuclear dots containing both ISG20 and coilin‐dsRed. Using electron microcopy analysis, ISG20 appeared principally concentrated in the dense fibrillar component of the nucleolus, the major site for rRNA processing. We also present evidences that ISG20 was associated with survival of motor neuron (SMN)‐containing macromolecular nuclear complexes required for the biogenesis of various small nuclear ribonucleoproteins. Finally, we demonstrate that ISG20 was associated with U1 and U2 snRNAs, and U3 snoRNA. The accumulation of ISG20 in the CBs after IFN treatment strongly suggests its involvement in a new route for IFN‐mediated inhibition of protein synthesis by modulating snRNA and rRNA maturation. J. Cell. Biochem. 98: 1320–1333, 2006. © 2006 Wiley‐Liss, Inc.
Mutation and evolutionary analyses identify NR2E1-candidate-regulatory mutations in humans with severe cortical malformations

Nuclear receptor 2E1 (NR2E1) is expressed in human fetal and adult brains; however, its role in human brain–behavior development is unknown. Previously, we have corrected the cortical hypoplasia and behavioral abnormalities in Nr2e1−/− mice using a genomic clone spanning human NR2E1, which bolsters the hypothesis that NR2E1 may similarly play a role in human cortical and behavioral development. To test the hypothesis that humans with abnormal brain–behavior development may have null or hypomorphic NR2E1 mutations, we undertook the first candidate mutation screen of NR2E1 by sequencing its entire coding region, untranslated, splice site, proximal promoter and evolutionarily conserved non‐coding regions in 56 unrelated patients with cortical disorders, namely microcephaly. We then genotyped the candidate mutations in 325 unrelated control subjects and 15 relatives. We did not detect any coding region changes in NR2E1; however, we identified seven novel candidate regulatory mutations that were absent from control subjects. We used in silico tools to predict the effects of these candidate mutations on neural transcription factor binding sites (TFBS). Four candidate mutations were predicted to alter TFBS. To facilitate the present and future studies of NR2E1, we also elucidated its molecular evolution, genetic diversity, haplotype structure and linkage disequilibrium by sequencing an additional 94 unaffected humans representing Africa, the Americas, Asia, Europe, the Middle East and Oceania, as well as great apes and monkeys. We detected strong purifying selection, low genetic diversity, 21 novel polymorphisms and five common haplotypes at NR2E1. We conclude that protein‐coding changes in NR2E1 do not contribute to cortical and behavioral abnormalities in the patients examined here, but that regulatory mutations may play a role.
Drug Development in Alzheimer’s Disease: The Contribution of PET and SPECT

Clinical trials aiming to develop disease-altering drugs for Alzheimer’s disease (AD), a neurodegenerative disorder with devastating consequences, are failing at an alarming rate. Poorly defined inclusion-and outcome criteria, due to a limited amount of objective biomarkers, is one of the major concerns. Non-invasive molecular imaging techniques, positron emission tomography and single photon emission (computed) tomography (PET and SPE(C)T), allow visualization and quantification of a wide variety of (patho)physiological processes and allow early (differential) diagnosis in many disorders. PET and SPECT have the ability to provide biomarkers that permit spatial assessment of pathophysiological molecular changes and therefore objectively evaluate and follow up therapeutic response, especially in the brain. A number of specific PET/SPECT biomarkers used in support of emerging clinical therapies in AD are discussed in this review.
An Osteopontin–NADPH Oxidase Signaling Cascade Promotes Pro–Matrix Metalloproteinase 9 Activation in Aortic Mesenchymal Cells

Osteopontin (OPN) is a cytokine upregulated in diabetic vascular disease. To better understand its role in vascular remodeling, we assessed how OPN controls metalloproteinase (MMP) activation in aortic adventitial myofibroblasts (AMFs) and A7r5 vascular smooth muscle cells (VSMCs). By zymography, OPN and tumor necrosis factor (TNF)-&agr; preferentially upregulate pro–matrix metalloproteinase 9 (pro-MMP9) activity. TNF-&agr; upregulated pro-MMP9 in AMFs isolated from wild-type (OPN+/+) mice, but pro-MMP9 induction was abrogated in AMFs from OPN−/− mice. OPN treatment of VSMCs enhanced pro-MMP9 activity, and TNF-&agr; induction of pro-MMP9 was inhibited by anti-OPN antibody and apocynin. Superoxide and the oxylipid product 8-isoprostaglandin F2 &agr;-isoprostane (8-IsoP) were increased by OPN treatment, and anti-OPN antibody suppressed 8-IsoP production. Like OPN and TNF-&agr;, 8-IsoP preferentially activated pro-MMP9. Superoxide, 8-IsoP, and NADPH oxidase 2 (Nox2) subunits were reduced in OPN−/− AMFs. Treatment of A7r5 VSMCs with OPN upregulated NADPH oxidase subunit accumulation. OPN structure/function studies mapped these activities to the SVVYGLR heptapeptide motif in the thrombin-liberated human OPN N-terminal domain (SLAYGLR in mouse OPN). Treatment of aortic VSMCs with SVVYGLR upregulated pro-MMP9 activity and restored TNF-&agr; activation of pro-MMP9 in OPN−/− AMFs. Injection of OPN-deficient OPN+/− mice with SVVYGLR peptide upregulated pro-MMP9 activity, 8-IsoP levels, and Nox2 protein levels in aorta and increased panmural superoxide production (dihydroethidium staining). At equivalent hyperglycemia and dyslipidemia, 8-IsoP levels and aortic pro-MMP9 were reduced with complete OPN deficiency in a model of diet-induced diabetes, achieved by comparing OPN−/−/LDLR−/− versus OPN+/−/LDLR−/− siblings. Thus, OPN provides a paracrine signal that augments vascular pro-MMP9 activity, mediated in part via superoxide generation and oxylipid formation.