Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of mortality rates between top height trees and average site trees

Abstract• Although comparisons between methods of selecting trees for site index estimates are well documented in the literature, little is known on mortality rates of different canopy tree cohorts used for that purpose. • This study was initiated to test the hypothesis that the mortality rates of top height trees are lower than those of codominants only or a combination of codominant and dominant trees. To test this hypothesis, we used records from a network of permanent sample plots in Québec and studied the fate of different cohorts of site trees for five different species. • Our results did not show clear evidence of lower mortality rates for top height trees. Instead we found that depending on the species, top height trees have lower (Populus tremuloides, Pinus banksiana), higher (Picea mariana, Abies balsamea) or equal mortality rates (Betula papyrifera) than codominant trees or codominant and dominant trees combined. • These results suggest a tendency for shade intolerant species to maintain lower top height tree mortality rates over time when compared to shade tolerant species. In the latter case, it is also shown that spruce budworm epidemics (Choristoneura fumiferana) did not change the pattern of mortality rates of site trees of A. balsamea. Résumé• Bien que des études comparatives sur les méthodes servant à déterminer l’indice de qualité de station sont disponibles dans la littérature, on connaît peu de choses sur les taux de mortalité de différentes cohortes d’arbres utilisées à cette fin. • Cette étude a été initiée dans le but de tester l’hypothèse selon laquelle les taux de mortalité de arbres dominants sont plus faibles que ceux des arbres codominants ou de ceux d’une combinaiso d’arbres codominants et dominants. Afin de tester cette hypothèse, nous avons utilisé la base de don nées des placettes-échantillons permanentes du Québec et nous avons suivi la destinée de différente cohortes d’arbres indicateurs de la station pour cinq espèces différentes. • Nos résultats n’ont pas montré de façon tranchée que les arbres dominants ont un taux de mortalit inférieur à celui des autres cohortes à l’étude. Nos résultats démontrent plutôt que selon les espèces, les arbres dominants ont un taux de mortalité inférieur (Populus tremuloides, Pinus banksiana), suérieur (Picea mariana, Abies balsamea) ou égal (Betula papyrifera) au taux de mortalité des arbre codominants ou à une combinaison d’arbres codominants ou dominants. • Ces résultats suggèrent que les taux de mortalité des espèces classées intolérantes à l’ombre ont ten dance à demeurer plus faibles dans le temps lorsqu’on les compare aux taux de mortalité des espèce tolérantes à l’ombre. Pour ces dernières, les résultats démontrent de plus que l’effet des épidémie de la tordeuse des bourgeons de l’épinette (Choristoneura fumiferana) n’ont eu aucun effet sur le patrons de mortalité des différentes cohortes d’arbres indicateurs de la station en ce qui concern A. balsamea.
Reinforcement learning based power management for hybrid electric vehicles

Compared to conventional internal combustion engine (ICE) propelled vehicles, hybrid electric vehicles (HEVs) can achieve both higher fuel economy and lower pollution emissions. The HEV consists of a hybrid propulsion system containing one ICE and one or more electric motors (EMs). The use of both ICE and EM increases the complexity of HEV power management, and therefore requires advanced power management policies to achieve higher performance and lower fuel consumption. Towards this end, our work aims at minimizing the HEV fuel consumption over any driving cycle (without prior knowledge of the cycle) by using a reinforcement learning technique. This is in clear contrast to prior work, which requires deterministic or stochastic knowledge of the driving cycles. In addition, the proposed reinforcement learning technique enables us to (partially) avoid reliance on complex HEV modeling while coping with driver specific behaviors. To our knowledge, this is the first work that applies the reinforcement learning technique to the HEV power management problem. Simulation results over real-world and testing driving cycles demonstrate the proposed HEV power management policy can improve fuel economy by 42%.
Young apple tree responses to crop load

Biennial bearing is a common and important issue facing apple growers that can result in losses in production of up to 30%, depending on cultivar. To study this issue, a collaborative project focusing on molecular, biochemical and whole tree physiological responses to variable crop loads was established between German research institutions and Agriculture Victoria, Australia. The whole tree physiological component of the project was performed in the Yarra Valley in Victoria, Australia. In spring 2015, a series of crop loads, ranging from almost no fruit on the trees to double normal grower practice, were applied to the biennial bearing cultivar ‘Nicoter’ (Kanzi®) and to the non-biennial bearing cultivar ‘Rosy Glow’ (Pink Lady®). Trees were three years old, grafted on M9 EMLA rootstock and trained as Open Tatura. Several tree growth (shoot length and winter wood pruning) and productivity (fruit maturity, size, soluble solids concentration and firmness, and return bloom) factors were measured to understand the effect of crop load. Strength of the response varied depending on the cultivar and factor investigated. In general, all the measured characteristics responded to crop load with the trend inversely proportional to the number of fruit remaining on the trees. Particularly interesting was the return bloom that showed a stronger response in the non-biennial bearing Cripps Pink cultivar than the biennial bearing ‘Nicoter’. This could imply that the response of young trees to thinning may be more important than the inherent tendency of the cultivar to biennial bearing.
A theoretical framework for performance characterization of elastography: the strain filter

This paper presents a theoretical framework for performance characterization in strain estimation, which includes the effect of signal decorrelation, quantization errors due to the finite temporal sampling rate, and electronic noise. An upper bound on the performance of the strain estimator in elastography is obtained from a strain filter constructed using these limits. The strain filter is a term used to describe the nonlinear filtering process in the strain domain (due to the ultrasound system and signal processing parameters) that allows the elastographic depiction of a limited range of strains from the compressed tissue. The strain filter predicts the elastogram quality by specifying the elastographic signal-to-noise ratio (SNR/sub e/), sensitivity, and the strain dynamic range at a given resolution. The dynamic range is limited by decorrelation errors for large tissue strain values, and electronic noise for low strain values. Tradeoffs between different techniques used to enhance elastogram image quality may also be analyzed using the strain filter.
Interleukin‐10‐induced gene expression and suppressive function are selectively modulated by the PI3K‐Akt‐GSK3 pathway

Interleukin‐10 (IL‐10) is an immunosuppressive cytokine that inhibits inflammatory gene expression. Phosphatidylinositol 3‐kinase (PI3K) ‐mediated signalling regulates inflammatory responses and can induce IL‐10 production, but a role for PI3K signalling in cellular responses to IL‐10 is not known. In this study we investigated the involvement of the PI3K‐Akt‐GSK3 signalling pathway in IL‐10‐induced gene expression and IL‐10‐mediated suppression of Toll‐like receptor‐induced gene expression in primary human macrophages. A combination of loss and gain of function approaches using kinase inhibitors, expression of constitutively active Akt, and RNA interference in primary human macrophages showed that expression of a subset of IL‐10‐inducible genes was dependent on PI3K‐Akt signalling. The effects of PI3K‐Akt signalling on IL‐10 responses were mediated at least in part by glycogen synthase kinase 3 (GSK3). In accordance with a functional role for PI3K pathways in contributing to the suppressive actions of IL‐10, PI3K signalling augmented IL‐10‐mediated inhibition of lipopolysaccharide‐induced IL‐1, IL‐8 and cyclo‐oxygenase‐2 expression. The PI3K signalling selectively modulated IL‐10 responses, as it was not required for inhibition of tumour necrosis factor expression or for induction of certain IL‐10‐inducible genes such as SOCS3. These findings identify a new mechanism by which PI3K‐mediated signalling can suppress inflammation by regulating IL‐10‐mediated gene induction and anti‐inflammatory function.
The accuracy of a new confidence interval method

Confidence intervals for the median of estimators or other quantiles were proposed as a substitute for usual confidence intervals in terminating and steady-state simulation. This is adequate since for many estimators the median and the expectation are close together or coincide, particularly if the sample size is large. Grouping data into batches is useful for median confidence intervals. The novel confidence intervals are easy to obtain, the variance of the estimator is not used. They are well suited for correlated simulation output data, apply to functions of estimators, and in simulation they seem to be particularly accurate, namely they follow the confidence level better than other confidence intervals. This paper states their accuracy which is the difference between the nominal confidence level and the actual coverage. The accuracy is evaluated with analytical models and simulation. For the estimation of quantiles by order statistics, the new confidence intervals are exact.
A Prospective Evaluation of Early Detection Biomarkers for Ovarian Cancer in the European EPIC Cohort

Purpose: About 60% of ovarian cancers are diagnosed at late stage, when 5-year survival is less than 30% in contrast to 90% for local disease. This has prompted search for early detection biomarkers. For initial testing, specimens taken months or years before ovarian cancer diagnosis are the best source of information to evaluate early detection biomarkers. Here we evaluate the most promising ovarian cancer screening biomarkers in prospectively collected samples from the European Prospective Investigation into Cancer and Nutrition study. Experimental Design: We measured CA125, HE4, CA72.4, and CA15.3 in 810 invasive epithelial ovarian cancer cases and 1,939 controls. We calculated the sensitivity at 95% and 98% specificity as well as area under the receiver operator curve (C-statistic) for each marker individually and in combination. In addition, we evaluated marker performance by stage at diagnosis and time between blood draw and diagnosis. Results: We observed the best discrimination between cases and controls within 6 months of diagnosis for CA125 (C-statistic = 0.92), then HE4 (0.84), CA72.4 (0.77), and CA15.3 (0.73). Marker performance declined with longer time between blood draw and diagnosis and for earlier staged disease. However, assessment of discriminatory ability at early stage was limited by small numbers. Combinations of markers performed modestly, but significantly better than any single marker. Conclusions: CA125 remains the single best marker for the early detection of invasive epithelial ovarian cancer, but can be slightly improved by combining with other markers. Identifying novel markers for ovarian cancer will require studies including larger numbers of early-stage cases. Clin Cancer Res; 22(18); 4664–75. ©2016 AACR. See related commentary by Skates, p. 4542
Developmental Changes in Opioid Peptides and Their Receptors inCpe fat/Cpe fatMice Lacking Peptide Processing Enzyme Carboxypeptidase E

Carboxypeptidase E (CPE) is involved in the biosynthesis of a number of neuropeptides including opioid peptides. A point mutation in this gene results in a loss of enzyme activity, decrease in mature neuroendocrine peptides, and development of late onset obesity as seen in Cpe fat/Cpe fatmice. In this study, we examined the processing of peptides derived from prodynorphin and proenkephalin in various brain regions of these mice during development. At 6 to 8 weeks, an age prior to the onset of obesity, levels of dynorphin peptides are decreased in all brain regions, whereas levels of ir-Met-enkephalin are differentially altered. There is an accumulation of C-terminally extended forms of all three opioid peptides inCpe fat/Cpe fatmice, consistent with a lack of CPE activity. Thus, it appears that there is no direct correlation between the level of mature opioid peptides and the development of obesity in these mice. Since altered levels of peptides can influence the opioid receptor system, we examined the functional activity of μ and κ opioid receptors using [35S]guanosine-5′-O-(γ-thio)-triphosphate binding assays. We find no differences in κ receptor activity inCpe fat/Cpe fatcompared with control littermate mice. In contrast, the μ receptor activity is differentially altered in select regions ofCpe fat/Cpe fatmice in response to a μ-specific ligand. Taken together, these results suggest that the lack of CPE activity leads to alterations in the level of opioid peptides during development and that changes in peptide levels differentially affect opioid receptor activity in vivo.
Locally Advanced Rectal Cancer

Locally advanced rectal cancer is a complex disease that requires a multidisciplinary treatment team to carefully evaluate each patient before prescribing a treatment plan. The current standard of care in the United States is multimodal therapy, consisting of chemotherapy, radiation, and surgery. Commonly, this involves neoadjuvant long-course chemoradiation, followed by total mesorectal excision and then adjuvant systemic chemotherapy. However, alternative regimens using chemotherapy first, followed by chemoradiation and then surgery (total neoadjuvant therapy), may allow for better tolerance of therapy. Short-course radiation is also acceptable but is rarely used in the United States. Minimally invasive surgical techniques such as laparoscopy, robotic surgery, and transanal total mesorectal excision offer several potential advantages over conventional open surgery, but their oncologic equivalence has not been determined. The role of nonoperative management for locally advanced rectal cancer is still evolving, and additional studies are needed to improve patient selection and evaluate long-term outcomes of a watch-and-wait approach. This review contains 1 figure, 2 table and 58 references Key words: colorectal cancer, locally advanced rectal cancer, minimally invasive surgery, nonoperative management, radical proctectomy, robotic surgery, total mesorectal excision, total neoadjuvant therapy, transanal total mesorectal excision, watch and wait
Dominance of the Inducible State in Strains of Staphylococcus aureus Containing Two Distinct Penicillinase Plasmids

Richmond, Mark H. (National Institute for Medical Research, Mill Hill, London, England). Dominance of the inducible state in strains of Staphylococcus aureus containing two distinct penicillinase plasmids. J. Bacteriol. 90:370–374. 1965. —The phenotypic expression of penicillinase synthesis is studied in a strain of S. aureus containing two distinct plasmids, each carrying the penicillinase structural gene and its associated control (inducibility) gene. One plasmid in the heterodiploid carries the genes responsible for the normal, fully inducible synthesis of a structural mutant of type A penicillinase, and the second plasmid carries the genes required for constitutive synthesis of C-type enzyme. The heterodiploid is phenotypically fully inducible, indicating that the inducible state dominates the constitutive in penicillinase synthesis. The heterodiploid synthesizes approximately equal quantities of A- and C-type enzyme when fully induced. Parental types are obtained from the heterodiploid by spontaneous segregation at a frequency of about 1 per 1,000 divisions of each character. Recombination between the two plasmids in such a persistent heterodiploid is a rare event.
miRNA Expression in Colon Polyps Provides Evidence for a Multihit Model of Colon Cancer

Changes in miRNA expression are a common feature in colon cancer. Those changes occurring in the transition from normal to adenoma and from adenoma to carcinoma, however, have not been well defined. Additionally, miRNA changes among tumor subgroups of colon cancer have also not been adequately evaluated. In this study, we examined the global miRNA expression in 315 samples that included 52 normal colonic mucosa, 41 tubulovillous adenomas, 158 adenocarcinomas with proficient DNA mismatch repair (pMMR) selected for stage and age of onset, and 64 adenocarcinomas with defective DNA mismatch repair (dMMR) selected for sporadic (n = 53) and inherited colon cancer (n = 11). Sporadic dMMR tumors all had MLH1 inactivation due to promoter hypermethylation. Unsupervised PCA and cluster analysis demonstrated that normal colon tissue, adenomas, pMMR carcinomas and dMMR carcinomas were all clearly discernable. The majority of miRNAs that were differentially expressed between normal and polyp were also differentially expressed with a similar magnitude in the comparison of normal to both the pMMR and dMMR tumor groups, suggesting a stepwise progression for transformation from normal colon to carcinoma. Among the miRNAs demonstrating the largest fold up- or down-regulated changes (≥4), four novel (miR-31, miR-1, miR-9 and miR-99a) and two previously reported (miR-137 and miR-135b) miRNAs were identified in the normal/adenoma comparison. All but one of these (miR-99a) demonstrated similar expression differences in the two normal/carcinoma comparisons, suggesting that these early tumor changes are important in both the pMMR- and dMMR-derived cancers. The comparison between pMMR and dMMR tumors identified four miRNAs (miR-31, miR-552, miR-592 and miR-224) with statistically significant expression differences (≥2-fold change).
DNA sequence compression using the Burrows-Wheeler Transform

We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns is an important phenomenon in biological sequences. Here, we propose off-line methods to compress DNA sequences that exploit the different repetition structures inherent in such sequences. Repetition analysis is performed based on the relationship between the BWT and important pattern matching data structures, such as the suffix tree and suffix array. We discuss how the proposed approach can be incorporated in the BWT compression pipeline.
Optimization of QHE-devices for metrological applications

In the framework of an European project aiming at the realization of a system for the calibration of capacitance standards based on the quantum Hall effect (QHE), optimized QHE devices for the metrological application as dc as well as ac standards of resistance are developed. The present paper describes the dc characterization of a large number of devices with different layouts, contact configurations, carrier concentrations, and mobilities. The results demonstrate the influence of the device parameters on the critical current, the width of the quantized plateaus, the longitudinal voltages along the device and the quantized Hall resistance. Recommendations are given for the layout and mobility of QHE devices in view of their use as dc standards of resistance.
Design and Evaluation of EdgeWrite Alphabets for Round Face Smartwatches

This study presents a project aimed at designing and evaluating a unistroke gesture set of alphanumeric characters targeting round-face smartwatches. We conducted a user study with 10 participants to generate the basic gesture design for 40 characters. For each character, we measured the preference and agreement scores and uncovered any challenges faced in designing unistroke gestures for round-face smartwatches. We developed a gesture recognizer using machine learning, which used a backpropagation mechanism to evaluate the designed gestures. Using the gesture recognizer, we collected 80,000 gesture data, and evaluated them with 5-fold cross-validation. The obtained mean recognition rate was 92.14%.
Emotional modulation of attention orienting by gaze varies with dynamic cue sequence

ABSTRACT Recent gaze cueing studies using dynamic cue sequences have reported increased attention orienting by gaze with faces expressing fear, surprise or anger. Here, we investigated whether the type of dynamic cue sequence used impacted the magnitude of this effect. When the emotion was expressed before or concurrently with gaze shift, no modulation of gaze-oriented attention by emotion was seen. In contrast, when the face cue averted gaze before expressing an emotion (as if reacting to the object after first localizing it), the gaze orienting effect was clearly increased for fearful, surprised and angry faces compared to neutral faces. Thus, the type of dynamic sequence used, and in particular the order in which the gaze shift and the facial expression are presented, modulate gaze-oriented attention, with maximal modulation seen when the expression of emotion follows gaze shift.
Innovation and education in the digital age: reconciling the roles of pedagogy, technology, and the business of learning

Terms such as "digital divide," normally understood to mean the gap in access between technologically disenfranchised populations and the information elite, take on a different resonance when the focus of university faculty, administrators, and an increasing number of potential students is on how education is to be conducted. This paper discusses the pedagogical, technological, and business trends that together affect the direction of innovation in virtual education. A discussion is presented on how traditional higher education (campus-based, lecture-bound, and faculty-driven) can benefit from the explosion of opportunities born of technological innovation and development by adopting changes in operational models: both administrative and pedagogical. Also addressed are the scope of services that comprise the engagement of information technology in academic environments necessary to fulfill evolving charters and missions that respond to current trends and future demands of educational innovations in the digital age where education and business - in their operational models and management styles - are moving toward complementary, even comparable strategies.
Oncothanin, a Peptide from the α 3 Chain of Type IV Collagen, Modifies Endothelial Cell Function and Inhibits Angiogenesis

Previous reports from our laboratory have shown that basement membrane (BM) collagen from anterior lens capsule type IV collagen (ALC-COL IV) and peptides from the noncollagenous domain of the α 3(IV) chain, corresponding to residues 185-203 and 179-208, inhibit tumor cell proliferation, specifically through the interaction of the -SNS- tripeptide (residues 189-191) with the CD47/αv β3 integrin receptor complex. Data presented here demonstrate that the α 3(IV)185-203 and the α 3(IV)179-208 peptides, designated as oncothanin, regulate endothelial cell (EC) proliferation, adhesion, and motility that ultimately influence angiogenesis. The data also indicate that oncothanin, when used as a chemoattractant, greatly enhanced EC chemotaxis. In contrast, pretreatment of EC with oncothanin inhibited chemotaxis toward several different chemoattractants. When oncothanin was used as a substrate, it enhanced EC adhesion that was inhibited when pretreated with same. Analysis of angiogenesis by EC differentiation (tube formation), aortic ring microvessel formation, and the chorioallantoic membrane assay demonstrate that oncothanin, but not the control medium or peptides, inhibits angiogenesis. In the EC differentiation assay, oncothanin completely inhibited tube formation at 25 μ g/ml, whereas peptides with comparable sequences, lacking the -SNS- sequence, from ALC-COL IV NC1 domains α 1 and α 2 chains failed to inhibit tube formation. The data support the hypothesis that ALC-COL IV and oncothanin inhibit angiogenesis by modulation of EC function.