Miracle-dz/UniFAR-FTUs huggingface dataset:
Sorghum Seed Maturity Affects the Weight and Feeding Duration of Immature Corn Earworm, Helicoverpa zea, and Fall Armyworm, Spodoptera frugiperda, in the Laboratory

Abstract Corn earworm, Helicoverpa zea Boddie (Lepidoptera: Noctuidae), and fall armyworm, Spodoptera frugiperda J.E. Smith, are occasional pests in sorghum, Sorghum bicolor L. Moench (Poales: Poaceae), and can be economically damaging when conditions are favorable. Despite the frequent occurrence of mixed-species infestations, the quantitative data necessary for developing yield loss relationships for S. frugiperda are not available. Although these species share similar biological characteristics, it is unknown whether their damage potentials in developing grain sorghum panicles are the same. Using no-choice feeding assays in the laboratory, this study examined larval growth and feeding duration for H. zea and S. frugiperda in the absence of competition. Each species responded positively when exposed to sorghum seed in the soft-dough stage, supporting evidence for the interactions between host-quality and larval growth and development. The results of this study also confirmed the suitability of using laboratory-reared H. zea to develop sorghum yield loss estimates in the field, and provided insights into the biological responses of S. frugiperda feeding on developing sorghum seed.
Pathfinding in angiosperm reproduction: pollen tube guidance by pistils ensures successful double fertilization

Sexual reproduction in flowering plants is unique in multiple ways. Distinct multicellular gametophytes contain either a pair of immotile, haploid male gametes (sperm cells) or a pair of female gametes (haploid egg cell and homodiploid central cell). After pollination, the pollen tube, a cellular extension of the male gametophyte, transports both male gametes at its growing tip and delivers them to the female gametes to affect double fertilization. The pollen tube travels a long path and sustains its growth over a considerable amount of time in the female reproductive organ (pistil) before it reaches the ovule, which houses the female gametophyte. The pistil facilitates the pollen tube's journey by providing multiple, stage‐specific, nutritional, and guidance cues along its path. The pollen tube interacts with seven different pistil cell types prior to completing its journey. Consequently, the pollen tube has a dynamic gene expression program allowing it to continuously reset and be receptive to multiple pistil signals as it migrates through the pistil. Here, we review the studies, including several significant recent advances, that led to a better understanding of the multitude of cues generated by the pistil tissues to assist the pollen tube in delivering the sperm cells to the female gametophyte. We also highlight the outstanding questions, draw attention to opportunities created by recent advances and point to approaches that could be undertaken to unravel the molecular mechanisms underlying pollen tube–pistil interactions. WIREs Dev Biol 2012, 1:96–113. doi: 10.1002/wdev.6
A Tool for Managing Software Architecture Knowledge

This paper describes a tool for managing architectural knowledge and rationale. The tool has been developed to support a framework for capturing and using architectural knowledge to improve the architecture process. This paper describes the main architectural components and features of the tool. The paper also provides examples of using the tool for supporting well-known architecture design and analysis methods.
Justice sociale et performances économiques: de l'alliance cachée au conflit ouvert ?

Basically, this paper investigates how post WWII growth patterns are related to income and, more widely, social unequalities. A brief survey dœs not suggest any clear cut and stable relationship between social justice and Pareto efficiency, neither from theory nor from available empirical or historical studies. Feelings about social justice are built within the historical process and then legitimate a set of institutions designed to fight against some unequalities. After 1945, in France and in most OECD countries, a reduction in income differentials and the rise of Welfare programs have contributed to enhance growth, and skills until the early Seventies. But afterward, the progressive exhaustion of productivity and the rise of the competitiveness objectives have destabilized this virtuous configuration: priority given to efficiency, widening of unequalities and rise and ultimately persistance of unemployment. Thus industrial democracy might possibly give a new content to social justice and help in spurring growth, according to a new alliance between equity and efficiency. Mots clés: Justice sociale, Inégalités (de revenu), Croissance, équité et efficience, crise économique, chômage, France.
The importance of pre-operative needle core breast biopsy results on resected tissue volume, margin status, and cosmesis.

PURPOSE This study aimed to evaluate the relationship between pre-operative image-guided large needle core biopsy (LNCB) histopathology results and surgical resection volumes in breast conserving surgery (BCS), with attention to both margin status and cosmetic outcome. METHODS Breast volumes (BV) were calculated using the elliptical cone based formula on mammography images for each patient. Initial resected volume (IRV), final resected volume (FRV), and resected volume ratio (RVR) were calculated and compared according to histopathological diagnosis and cosmetic outcomes. Final pathology results were classified as benign, high risk lesion (HRL), ductal carcinoma in situ (DCIS), or invasive cancer. The cosmetic results were graded based on the Harvard breast cosmesis grading scale. RESULTS A total of 217 women underwent BCS by the same experienced breast surgeon. The resected volumes (mean, cm3) were higher among patients who underwent LNCB than those who did not (54.3 vs 26.5 ;p=0.005). The LNCB diagnoses were 16% benign, 19% HRLs, 16% DCIS, and 49% invasive cancers. Reexcision rates were 15.6% and 25.8% for DCIS and invasive cancer, respectively. Cosmesis was excellent in 79.8%. Age, pathological tumor size, IRV and FRV were different among the benign, HRLs and carcinoma groups (p= 0.001). CONCLUSION The diagnosis of carcinoma by LNCB leads to the planning of a wider resection, but the need for reexcision is no different than less resection. HRLs are best approached with diagnostic excision, as there is no strong evidence that larger resections reduce the incidence of involved resection margins.
Prognostic significance of p 53 and epidermal growth factor receptor expression in resected surgical-pathologic t 1 non-small cell lung cancer : analysis in combination with histopathological factors

Introduction Lung cancer is the leading cause of cancer death in United States of America and throughout the world. Non-small cell lung carcinoma accounts for about 80% of all lung cancers. The current management of NSCLC is largely guided by tumor stage. Pateints with early stage (I and II) tumor are treated by surgical resection with or without adjuvant chemotherapy, and stage III patients require combined modality approaches that may include chemotherapy, radiation and surgery. Nevertheless, the overall 5-year survival rates of Prognostic significance of p53 and epidermal growth factor receptor expression in resected surgical-pathologic t1 non-small cell lung cancer: analysis in combination with histopathological factors
Lempel-Zip Complexity Reference

The aim of this note is to provide some reference facts for LZW---mostly from Thomas and Cover \cite{Cover:2006aa} and provide a reference for some metrics that can be derived from it. LZW is an algorithm to compute a Kolmogorov Complexity estimate derived from a limited programming language that only allows copy and insertion in strings (not Turing complete set). Despite its delightful simplicity, it is rather powerful and fast. We then focus on definitions of LZW derived complexity metrics consistent with the notion of descriptive length, and discuss different normalizations, which result in a set of metrics we call $\rho_0$, $\rho_1$ and $\rho_2$, in addition to the Description Length $l_{LZW}$ and the Entropy Rate.
Modeling a Predictive Energy Equation Specific for Maintenance Hemodialysis

BACKGROUND Hypermetabolism is theorized in patients diagnosed with chronic kidney disease who are receiving maintenance hemodialysis (MHD). We aimed to distinguish key disease-specific determinants of resting energy expenditure to create a predictive energy equation that more precisely establishes energy needs with the intent of preventing protein-energy wasting. MATERIALS AND METHODS For this 3-year multisite cross-sectional study (N = 116), eligible participants were diagnosed with chronic kidney disease and were receiving MHD for at least 3 months. Predictors for the model included weight, sex, age, C-reactive protein (CRP), glycosylated hemoglobin, and serum creatinine. The outcome variable was measured resting energy expenditure (mREE). Regression modeling was used to generate predictive formulas and Bland-Altman analyses to evaluate accuracy. RESULTS The majority were male (60.3%), black (81.0%), and non-Hispanic (76.7%), and 23% were ≥65 years old. After screening for multicollinearity, the best predictive model of mREE (R2 = 0.67) included weight, age, sex, and CRP. Two alternative models with acceptable predictability (R2 = 0.66) were derived with glycosylated hemoglobin or serum creatinine. Based on Bland-Altman analyses, the maintenance hemodialysis equation that included CRP had the best precision, with the highest proportion of participants' predicted energy expenditure classified as accurate (61.2%) and with the lowest number of individuals with underestimation or overestimation. CONCLUSIONS This study confirms disease-specific factors as key determinants of mREE in patients on MHD and provides a preliminary predictive energy equation. Further prospective research is necessary to test the reliability and validity of this equation across diverse populations of patients who are receiving MHD.
Example-based video color transfer

Color transfer is an image processing technique commonly used to fix images with wrong colors, enhance the lighting conditions, or produce special styles to express specific emotions. With the aid of a reference image, the intended color characteristics can be properly transferred to the source images or videos. Since the applications start growing popular, many image color transfer methods have emerged; However, only few video color transfer algorithms have been proposed so far. In this paper, we propose an efficient example-based color transfer algorithm for both images and videos, which preserves the gradient details of the source by building Laplacian pyramids and improves the spatio-temporal consistency by employing patch matching method. Other than the existing quality metrics, we further propose a video quality metric regarding temporal consistency and compare our algorithm with other color transfer methods. The experimental results show that our algorithm generally produces outputs with high fidelity in terms of colors, scene details, and also spatiotemporal consistency.
Large-scale multiple sequence alignment visualization through gradient vector flow analysis

Multiple sequence alignment (MSA) is essential as an initial step in studying molecular phylogeny as well as during the identification of genomic rearrangements. Recent advances in sequencing techniques have led to a tremendous increase in the number of sequences to be analyzed. As a result, a greater demand is being placed on visualization techniques, as they have the potential to reveal the underlying information in large-scale MSAs. In this work, we present a novel visualization technique for conveying the patterns in large-scale MSAs. By applying gradient vector flow analysis to the MSA data, we can extract and visually emphasize conservations and other patterns that are relevant during the MSA exploration process. In contrast to the traditional visual representation of MSAs, which exploits color-coded tables, the proposed visual metaphor allows us to provide an overview of large MSAs as well as to highlight global patterns, outliers, and data distributions. We will motivate and describe the proposed algorithm, and further demonstrate its application to large-scale MSAs.
Performance Metric Ensemble for Multiobjective Evolutionary Algorithms

Evolutionary algorithms have been successfully exploited to solve multiobjective optimization problems. In the literature, a heuristic approach is often taken. For a chosen benchmark problem with specific problem characteristics, the performance of multiobjective evolutionary algorithms (MOEAs) is evaluated via some heuristic chosen performance metrics. The conclusion is then drawn based on statistical findings given the preferable choices of performance metrics. The conclusion, if any, is often indecisive and reveals no insight pertaining to which specific problem characteristics the underlying MOEA could perform the best. In this paper, we introduce an ensemble method to compare MOEAs by combining a number of performance metrics using double elimination tournament selection. The double elimination design allows characteristically poor performance of a quality algorithm to still be able to win it all. Experimental results show that the proposed metric ensemble can provide a more comprehensive comparison among various MOEAs than what could be obtained from a single performance metric alone. The end result is a ranking order among all chosen MOEAs, but not quantifiable measures pertaining to the underlying MOEAs.
Resonant absorption of cosmic-ray neutrinos by the relic-neutrino background

Within the framework of standard big-bang cosmology and the standard electroweak model, it is shown that . nu.nu-bar annihilation on the Z resonance is the only cosmic-ray process sensitive to relic neutrinos. For massive (m/sub .nu./> or approx. =10/sup -3/ eV) neutrinos originating from a zapprox.3 red-shifted source, a 15% to 50% absorption dip is predicted at E/sub . nu. /approx.10/sup 11/ GeV.
Language engineering for the recovery of requirements from legacy documents

Legacy documents, such as requirements documents or manuals of business procedures, can sometimes offer an important resource for informing what features of legacy software are redundant, need to be retained or can be reused. This situation is particularly acute where business change has resulted in the dissipation of human knowledge through staff turnover or redeployment. Exploiting legacy documents poses formidable problems, however, since they are often incomplete, poorly structured, poorly maintained and voluminous. This report proposes that language engineering using tools that exploit probabilistic natural language processing (NLP) techniques offer the potential to ease these problems. Such tools are available, mature and have been proven in other domains. The document provides a review of NLP and a discussion of the components of probabilistic NLP techniques and their potential for requirements recovery from legacy documents. The report concludes with a summary of the preliminary results of the adaptation and application of these techniques in the REVERE project.
Efficient Deterministic Replay Using Complete Race Detection

Data races can significantly affect the executions of multi-threaded programs. Hence, one has to recur the results of data races to deterministically replay a multi-threaded program. However, data races are concealed in enormous number of memory operations in a program. Due to the difficulty of accurately identifying data races, previous multi-threaded deterministic record/replay schemes for commodity multi-processor system give up to record data races directly. Consequently, they either record all shared memory operations, which brings remarkable slowdown to the production run, or record the synchronization only, which introduces significant efforts to replay. Inspired by the advances in data race detection, we propose an efficient software-only deterministic replay scheme for commodity multi-processor systems, which is named RacX. The key insight of RacX is as follows: although it is NP-hard to accurately identify the existence of data races between a pair of memory operations, we can find out all potential data races in a multi-threaded program, in which the false positives can be reduced to a small amount with our automatic false positive reduction techniques. As a result, RacX can efficiently monitor all potential data races to deterministically replay a multi-threaded program. To evaluate RacX, we have carried out experiments over a number of well-known multi-threaded programs from SPLASH-2 benchmark suite and large-scale commercial programs. RacX can precisely recur production runs of these programs with value determinism. Averagely, RacX causes only about 1.21%, 1.89%, 2.20%, and 8.41% slowdown to the original run during recording (for 2-, 4-, 8- and 16-thread programs, respectively). The soundness, efficiency, scalability, and portability of RacX well demonstrate its superiority.
An upstream repressor element that contributes to hepatocyte-specific expression of the rat serum amyloid A1 gene.

Serum amyloid A (SAA) is a major acute-phase protein whose expression can be dramatically induced in response to tissue damage, infection, and inflammation. Its expression is highly tissue-specific, restricted almost exclusively to liver hepatocytes. We have shown that a 320-bp fragment of the rat SAA1 promoter could confer liver-cell-specific expression on a reporter gene when transfected into cultured cells. Here we report the identification of a 29-bp regulatory element that possesses inhibitory activities on SAA1 promoter in HeLa cells but has no such effects in liver cells. Moreover, this regulatory element has properties of a transcriptional repressor; in that, it can function with a heterologous promoter and is independent of orientation and distance from the transcription initiation site. Protein binding studies showed that this regulatory element can form specific protein-DNA complexes with nuclear proteins from several nonliver cell lines (HeLa, 10T(1/2), and C2) and placenta. However, the same DNA-protein complex was not detected in extracts from liver or liver-derived cell lines (HepG2 and Hep3B). Taken together, our results demonstrate the presence of a DNA-binding protein, termed tissue-specific repressor, found only in nonhepatocytes which may function to repress SAA1 gene expression by interacting with a repressor element. Thus, liver-specific expression of the SAA1 gene is apparently regulated by both positive and negative regulatory elements and their interacting transcription factors to ensure that it is expressed only in suitable cell types.
Rapid disuse atrophy of diaphragm fibers in mechanically ventilated humans.

BACKGROUND The combination of complete diaphragm inactivity and mechanical ventilation (for more than 18 hours) elicits disuse atrophy of myofibers in animals. We hypothesized that the same may also occur in the human diaphragm. METHODS We obtained biopsy specimens from the costal diaphragms of 14 brain-dead organ donors before organ harvest (case subjects) and compared them with intraoperative biopsy specimens from the diaphragms of 8 patients who were undergoing surgery for either benign lesions or localized lung cancer (control subjects). Case subjects had diaphragmatic inactivity and underwent mechanical ventilation for 18 to 69 hours; among control subjects diaphragmatic inactivity and mechanical ventilation were limited to 2 to 3 hours. We carried out histologic, biochemical, and gene-expression studies on these specimens. RESULTS As compared with diaphragm-biopsy specimens from controls, specimens from case subjects showed decreased cross-sectional areas of slow-twitch and fast-twitch fibers of 57% (P=0.001) and 53% (P=0.01), respectively, decreased glutathione concentration of 23% (P=0.01), increased active caspase-3 expression of 100% (P=0.05), a 200% higher ratio of atrogin-1 messenger RNA (mRNA) transcripts to MBD4 (a housekeeping gene) (P=0.002), and a 590% higher ratio of MuRF-1 mRNA transcripts to MBD4 (P=0.001). CONCLUSIONS The combination of 18 to 69 hours of complete diaphragmatic inactivity and mechanical ventilation results in marked atrophy of human diaphragm myofibers. These findings are consistent with increased diaphragmatic proteolysis during inactivity.
Genetically distinct and clinically relevant classification of hepatocellular carcinoma: putative therapeutic targets.

BACKGROUND & AIMS The biological aggressiveness of hepatocellular carcinoma (HCC) and the lack of optimal therapeutic strategies have rendered the disease a major challenge. Highly heterogeneous genetic alteration profiles of HCC have made it difficult to identify effective tailor-made molecular therapeutic targets. Therefore, classification of HCC into genetically homogeneous subclasses would be of great worth to develop novel therapeutic strategies. METHODS We clarified genome-scale chromosomal copy number alteration profiles and mutational statuses of p53 and beta-catenin in 87 HCC tumors. We investigated the possibility that HCC might be classifiable into a number of homogeneous subclasses based solely on their genetic alteration profiles. We also explored putative molecular therapeutic targets specific for each HCC subgroup. RESULTS Unsupervised hierarchical cluster analysis based on chromosomal alteration profiles suggested that HCCs with heterogeneous genetic backgrounds are divisible into homogeneous subclasses that are highly associated with a range of clinicopathologic features of the tumors and moreover with clinical outcomes of the patients (P < .05). These genetically homogeneous subclasses could be characterized distinctively by pathognomonic chromosomal amplifications (eg, c-Myc-induced HCC, 6p/1q-amplified HCC, and 17q-amplified HCC). An in vitro experiment raised a possibility that Rapamycin would significantly inhibit the proliferative activities of HCCs with 17q amplification. CONCLUSIONS HCC is composed of several genetically homogeneous subclasses, each of which harbors characteristic genetic alterations that can be putative tailor-made molecular therapeutic targets for HCCs with specific genetic backgrounds. Our results offer an opportunity for developing novel individualized therapeutic modalities for distinctive genome types of HCC.
Effects of Isoflurane and Halothane on Contractility and the Cyclic 3′, 5′‐Adenosine Monophosphate System in the Rat Aorta

The effects of isoflurane and halothane on the contractility and on the cyclic 3′, 5′-adenosine monophosphate (cAMP) system of the vascular smooth muscle of rat aorta were studied in citro. Isoflurane and halothane inhibited phenylephrineinduced aortic contraction in a dose-dependent manner. Halothane-induced relaxation was greater than that induced by isoflurane. One and 2 per cent halothane caused approximately the same degree of relaxation as 4 and 6 per cent isoflurane, respectively. Propranolol (10−6 M) failed to block this action. Isoflurane and halothane also stimulated the formation of cyclic AMP. In the aorta prelabeled with 14C-adenine, isoflurane in concentrations of 2, 4, 6, and 8 per cent increased the labeled cAMP/ATP ratio 10, 17, 41, and 72 per cent, respectively. Halothane in concentrations of 1, 2, and 5 per cent increased the labeled cyclic AMP/ATP ratio 19, 37, and 58 per cent, respectively. Only the increases with 6 and 8 per cent isoflurane and with 2 and 5 per cent halothane were statistically significant. The anesthetic-induced increase in the labeled cAMP/ATP ratio was not altered by propranolol (10−6 M). Isoflurane and halothane did not change the phosphodiesterase activity. These results support the hypothesis that the cardiovascular depression during isoflurane and halothane anesthesia results, at least in part, from their direct relaxing action on vascular smooth muscle. The stimulation of cAMP formation may explain the mechanism of the anesthetic-induced relaxation. This action does not appear to be mediated through the beta-adrenergic receptors.