Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Various Quality Attributes of Sunflower and Soybean Plants by Near Infrared Reflectance Spectroscopy: Development and Validation Calibration Models

Soybean and sunflower are summer annuals that can be grown as an alternative to corn and may be particularly useful in organic production systems for forage in addition to their traditional use as protein and/or oil yielding crops. Rapid and low cost methods of analyzing plant forage quality would be helpful for nutrition management of livestock. We developed and validated calibration models using Near-infrared Reflectance Spectroscopic (NIRS) analysis for 27 different forage quality parameters of organically grown sunflower and soybean leaves or reproductive parts. Crops were managed under conventional tillage or no-till with a cover crop of wheat before soybean and rye-crimson clover before sunflower. From a population of 120 samples from both crops, covering multiple sampling dates within the treatments, calibration models were developed utilizing spectral information covering both visible and NIR region of 61 - 85 randomly chosen samples using modified partial least-squares (MPLS) regression with internal cross validation. Within MPLS protocol, we compared nine different math treatments on the quality of the calibration models. The math treatment “2,4,4,1” yielded the best quality models for all but starch and simple sugars (r2 = 0.699 - 0.999; where the 1st digit is the number of the derivative with 0 for raw spectra, 1 for first derivative, and 2 for second derivative, the 2nd digit is the gap over which the derivative is calculated, the 3rd digit is the number of data points in a running average or smoothing, and the 4th digit is the second smoothing). Prediction of an independent validation set of 28-35 samples with these models yielded excellent agreement between the NIRS predicted values and the reference values except for starch (r2 = 0.8260 - 0.9990). The results showed that the same model was able to adequately quantify a particular forage quality of both crops managed under different tillage treatments and at different stages of growth. Thus, these models can be reliably applied in the routine analysis of soybean and sunflower forage quality for the purposes of livestock nutrient management decisions.
Optimizing Preventive Service of Software Products

The implementer of a large, complex software system cannot make it completely defect free, so he must normally provide fixes for defects found after the code is put into service. A system user may do preventive service by installing these fixes before the defects cause him problems. Preventive service can benefit both the software developer and the software user to the extent that it reduces the number of operational problems caused by software errors, but it requires the expenditure of the resources required to prepare, disseminate, and install fixes; and it can be the cause of additional software problems caused by design errors introduced into the code by fixes. The benefit from removing a given defect depends on how many problems it would otherwise cause. Benefits may be estimated by modeling problem occurrence as a random process in execution time governed by a distribution of characteristic rates. It is found that most of the benefit to be realized by preventive service comes from removing a relatively small number of high-rate defects that are found early in the service life of the code. For the typical user corrective service would seem preferable to preventive service as a way of dealing with most defects found after code has had some hundreds of months of usage.
DPC4/Smad4: No Mutations, Rare Allelic Imbalances, and Retained Protein Expression in Pancreatic Endocrine Tumors

Several chromosomal loci involved in tumorigenesis of pancreatic endocrine tumors (PET) have been identified. To date, the only gene known to be frequently altered is the MEN1 gene. Recently, DPC4 mutations and homozygous deletions have been described in 5/9 (55%) non-functioning PET, thus representing the most frequent genetic aberration described in PET. However, these data are in discordance with comparative genomic hybridization (CGH) results that rarely show genetic losses on chromosome 18. They have also been challenged by immunohistochemical data. We performed a detailed combined DPC4 mutation and deletion analysis in 34 benign and malignant PET. Mutations of the conserved C-terminal exons were not found in all examined PET and allelic loss (LOH) was found to be rare (<6%) by combined microsatellite PCR and FISH analysis. In addition, DPC4 protein expression was retained in all PET that were examined by immunohistochemistry. Therefore, DPC4 inactivation by mutation or deletion appears to be very rare in PET, which confirms the current concept of unrelated mechanisms of tumorigenesis of endocrine versus exocrine pancreatic tumors.
Pollination efficiency and reproductive patterns in relation to local plant density, population size, and floral display in the rewarding Listera ovata (Orchidaceae)

Pollination efficiency and reproductive success vary strongly among populations of most animal-pollinated plant species, depending on their size and local density, whereas individual plants within populations experience varying levels of reproductive output as a result of differences in floral display. Although most orchid species have been shown to be severely pollination limited, few studies have investigated the impact of the above-mentioned factors on pollination success and reproduction, especially in rewarding species. In this study, the impact of population size, local density of flowering plants, and floral display on the rates of pollinia export and fruit production was investigated in 13 natural populations of the rewarding terrestrial orchid Listera ovata. In addition, an emasculation experiment was set up to examine how floral display and local density of flowering plants affected the relative importance of cross- vs. geitonogamous pollination in determining fruit set. In the studied populations, pollination efficiency, pollen removal, and fruit set increased with increasing population size until a threshold value of 30‐40 flowering plants was reached, above which pollination efficiency and reproductive output decreased again. On average, plants with large floral displays showed higher proportional pollinia removal and fruit set compared with smaller plants. Fruit production was also significantly and positively related to local plant density, whereas emasculation did not affect the relationship between local plant density and fruit set, suggesting that geitonogamous pollination did not affect the outcome of female function. The results of this study are discussed in the light of the flowering mechanism of the species and its generalized pollination system. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157, 713‐721.
Association Between High Variability of Gait Speed and Mild Cognitive Impairment: A Cross‐Sectional Pilot Study

from the Research Institute for Humanity and Nature from the Japanese Ministry of Education, Science and Culture. Author Contributions: Kiyohito Okumiya, Taizo Wada, Ryota Sakamoto, Kuniaki Otsuka, Kozo Matsubayashi, Tetsuya Inamura, and Patricia J Garcia: Concept and design the project. Kiyohito Okumiya, Eriko Fukutomi, Yumi Kimura, Yasuko Ishimoto, Wen-ling Chen, Motonao Ishikawa, Reiko Hozo, Tetsuya Inamura, Marcela Lazo, Jose Perez Lu, and Kozo Matsubayashi: Participation in the medical surveys in Peru. Kiyohito Okumiya, Taizo Wada, Ryota Sakamoto, Patricia J Garcia, and Kozo Matsubayashi: Analysis and interpretation of data, and preparation of the manuscript. Sponsor’s Role: None.
Application of machine learning : automated trading informed by event driven data

Models of stock price prediction have traditionally used technical indicators alone to generate trading signals. In this paper, we build trading strategies by applying machine-learning techniques to both technical analysis indicators and market sentiment data. The resulting prediction models can be employed as an artificial trader used to trade on any given stock exchange. The performance of the model is evaluated using the S&P 500 index.
Norovirus outbreak associated with undercooked oysters and secondary household transmission

SUMMARY During December 2009, over 200 individuals reported gastrointestinal symptoms after dining at a North Carolina restaurant. An outbreak investigation included a case-control study of restaurant patrons, a secondary household transmission study, environmental assessment of the restaurant facilities and operations, and laboratory analysis of stool and food samples. Illness was primarily associated with consumption of steamed oysters (odds ratio 12, 95% confidence interval 4·8–28) and 20% (8/41 households) reported secondary cases, with a secondary attack rate of 14% among the 70 susceptible household contacts. Norovirus RNA was detected in 3/5 stool specimens from ill patrons; sequencing of RT–PCR products from two of these specimens identified identical genogroup II genotype 12 sequences. Final cooked temperatures of the steamed oysters were generally inadequate to inactivate norovirus, ranging from 21°C to 74°C. Undercooked contaminated oysters pose a similar risk for norovirus illness as raw oysters and household contacts are at risk for secondary infection.
Replication of Mouse Hepatitis Viruses with High and Low Virulence in Cultured Hepatocytes

Ten strains of mouse hepatitis virus with different levels of virulence and hepatotropism were examined for the ability to replicate in cultured mouse hepatocytes. All of these viruses multiplied well in hepatocytes, attaining a maximum of 105 to 107 PFU per 0.2 ml, with cytopathic effects characterized by the formation of polykaryocytes. However, in nonparenchymal adherent cells of the liver (liver macrophages), highly virulent mouse hepatitis virus type 2 multiplied to a titer 1,000 times higher than that of mouse hepatitis virus S with a low virulence. These results suggest that the virulence of mouse hepatitis virus in infected mice is determined by its potential for replication not in hepatocytes, but in macrophages, including Kupffer cells in the liver.
OPTIMAL SEQUENTIAL DETECTION WITH COMPRESSIVE SENSING

We propose a new framework that combines stochastic optimization and compressive sensing tools to recover the support of a portion of an unknown vector and acquire a utility which decreases linearly with the number of measurement, and increases with the reward associated to a given state of each component. We model a utility function to strive the trade-off between number of measurements and number of entries a decision-maker aims to recover and accrue a given utility from. We characterize the optimal policy and show that for our problem a double greedy maximization allows to achieve a constant factor approximation (≥ 1 3 ) of the optimal value. Numerical simulations corroborate our claims and show the reliability of our assumptions to simplify the compressive recovery performances.
Directing the differentiation of embryonic stem cells to neural stem cells

Embryonic stem cells (ESCs) are a potential source of neural derivatives that can be used in stem cell‐based therapies designed to treat neurological disorders. The derivation of specific neuronal or glial cell types from ESCs invariably includes the production of neural stem cells (NSCs). We describe the basic mechanisms of neural induction during vertebrate embryogenesis and how this information helped formulate several protocols used to generate NSCs from ESCs. We highlight the advantages and disadvantages of each approach and review what has been learned about the intermediate stages in the transition from ESC to NSC. Recent data describing how specific growth factors and signaling molecules regulate production of NSCs are described and a model synthesizing this information is presented. Developmental Dynamics 236:3255–3266, 2007. © 2007 Wiley‐Liss, Inc.
Pathogenesis-related proteins in plants

This invention is directed to the regulatory sequences of the pathogenesis-related (PR) protein genes of the PR-1 group, specifically an inducible PR-1 promoter and, preferably, PR-1 secretion signal se­quences, and to genetic constructs containing the regulatory sequences. This invention also relates to the construction and use of a recombinant DNA molecule that includes a PR protein gene, and its regulatory sequences, including the promoter and secretion signal sequences. More specifically, the invention concerns the use of the recombinant DNA molecule that includes a PR-protein gene operably linked to PR protein regulatory sequences that upon expression in a plant will enhance the hypersensitive response of the plant to an invading pathogen.
Contrast‐enhanced power Doppler of the intestinal wall in the evaluation of patients with Crohn disease

Background: Crohn disease (CD) manifests with highly variable signs and symptoms, and assessment of the status of the disease in the single patient can be difficult. This study was conducted to evaluate the efficacy of power colour Doppler ultrasonography, with and without echo‐enhancement, in distinguishing active from quiescent CD. Methods: Resistance Index (RI) of the superior mesenteric artery (SMA), bowel thickness of the affected loops and the presence of colour signals at power Doppler analysis prior to and after ultrasonography contrast agent injection (Levovist®) were evaluated in 48 patients with CD. Results: In our series, 26/48 patients had active and 22/48 had quiescent CD. A CDAI score ≥150 and a pathological (>5 mg/dL) C reactive protein were significantly correlated with active disease (P < 0.001 and P = 0.004, respectively). Intestinal wall thickness showed no significant correlation with disease status (7.5 ± 1.3 mm in active disease versus 6.8 ± 1.3 mm in quiescent disease; P = 0.11). Vascular signals in the affected loops were revealed in 11/22 patients (50%) with active disease and in 5/26 (20%) with quiescent disease (P = 0.052). After Levovist injection, colour signals were found in 22/22 with active and in 8/26 with quiescent CD (P < 0.001). SMA RI was significantly lower in active CD patients (0.81 ± 0.01 versus 0.83 ± 0.02; P = 0.001). Conclusions: Our data suggest that in patients with CD a finding of a SMA RI ≤ 0.81, or the presence of a colour signal in the wall of the affected loops, at power Doppler sonography, is indicative of active disease. Utilization of echo‐enhancer media can greatly improve the diagnostic sensitivity of intestinal wall power Doppler scan. A finding of intestinal wall thickening is not associated with active disease in our series.
Business value of IT capabilities: effects on processes and firm performance in a developing country

Purpose –This article proposes an integrated three-stage model, which tests the impact of IT capabilities at the firm level. Design/methodology/approach – The measurement model was constructed from the following research phases: i) assessment of the variables by experts in the fields of IS and business; ii) survey pretest; and iii) pilot survey. The full survey was applied to managers from IT and business fields in Brazil’s largest organizations, and was analyzed through Structural Equation Modelling. Findings – The results of the full survey allow us to conclude about the relationships that exist between IT capabilities, information quality and performance processes. Performance processes partially mediate the impact of IT capabilities on firm performance. Originality/value – The results presented contribute to the academic and management aspects, for they allow: i) to replicate the model in other research contexts (national, international) and evaluating incremental improvements of IT capabilities on firm performance; ii) the identification of intermediate performance indicators, associated with the use of IT, and the concentration of energy of organizations in the measurement of IT effects on business processes; iii) the adoption of the model for horizontal analysis of IT performance in large companies, from the perspective of business and IT managers.
Blood pressure variability is more important than blood pressure level in determination of end-organ damage in rats

Objective This study was designed to determine how important a novel risk factor of elevated blood pressure variability (BPV) is in the determination of end-organ damage by comparison with the classic risk factor of a high blood pressure (BP) level. Methods and results The effects of haemodynamics on cardiovascular morphology were evaluated by univariate and multivariate regression analysis in two different rat models with an enlarged distribution of haemodynamics. In male sham-operated and sinoaortic-denervated Wistar–Kyoto rats and spontaneously hypertensive rats (n = 34), BPV was more important than BP in cardiac and renal damage and aortic hypertrophy. BPV and BP had independent effects, explaining 59.4% of the variation in damage to these organs. In male (n = 44) and female (n = 46) F1 hybrids of Sprague–Dawley rats and spontaneously hypertensive rats, the greater importance of BPV than BP was further demonstrated in left ventricular hypertrophy, glomerular damage and aortic hypertrophy. The phenomenon was more evident in females than males for cardiovascular hypertrophy. BPV and BP or BPV alone had independent effects, explaining 46.9% (male) or 37.5% (female) of the variation in damage to these organs. Conclusion BPV is a more critical determinant than BP level for cardiac damage, renal lesions and aortic hypertrophy in rats, strongly suggesting the significance of BPV control for the protection of these organs.
The effect of glucocorticoid replacement therapy on bone mineral density in children with congenital adrenal hyperplasia

Abstract Objectives: 1) To evaluate the effects of glucocorticoid (GC) doses on bone mineral density (BMD) in children with congenital adrenal hyperplasia (CAH), 2) Investigate other factors influencing BMD. Methods: Twenty-six children with CAH and 11 healthy controls included in the study. All of the patients were examined with dual-energy X-ray absorptiometry (DXA) using a Hologic QDR 1000/W densitometer. The metabolic control state, age at diagnosis GC dose (mg/m2/day), pubertal status, 17 hydroxyprogesterone (17 OHP) levels, bone age (BA), and lumber BMD were evaluated in all cases. BMD (g/cm2), BMD z-score corrected to National Standards (cNS-BMD z-score), BMD z-score corrected to BA (cBABMD), bone mineral content (BMC), BMC corrected to puberty (cPBMC), and bone area (BAR) values were determined. Patients were grouped according to mean on-therapy serum 17 OHP levels as tight control (17 OHP<10 nmol/L) (n:13) and poor control (17 OHP>10 nmol/L) (n:13). All groups were compared with each other. Results: The age range was 2.1–15.7 years and the mean age (±SD) 9.3 (±3.5) years. There were no significant differences between the groups in terms of GC doses, lumbar BMD values [BMD (g/cm2), BMD z-score corrected to National Standards (cNS-BMD z-score), BMD z-score corrected to BA (cBABMD), bone mineral content (BMC), BMC corrected to puberty (cPBMC), and bone area (BAR)]. However, the BMI value was higher in children with CAH than normal healthy controls. The BA of the poor control, late diagnosed groups and male patients were higher than tight control, early diagnosed group and female patients, respectively. BMC and BA were lower than the control group in tight control with early diagnosed patients. The cBABMD z-score was lower in males with poor control than males with tight control. There were no similar results in female patients. Conclusions: Although GC treatment seems not to influence BMD in CAH patients in our study, further studies are needed to additionally evaluate daily calcium (Ca) intake, polymorphism of vitamin D receptor, ethnic factors (strict Islamic dress, etc.), socioeconomic status, and 24-h urinary free cortisol level.
Convergent inputs from electrically and topographically distinct orexin cells to locus coeruleus and ventral tegmental area

Orexin/hypocretin (orx/hcrt) neurons are thought to ensure that reward‐seeking is accompanied by alertness, but the underlying circuit organization is unclear. Reports of differential regulation of lateral versus medial orx/hcrt cells produced a hypothesis of ‘efferent dichotomy’, in which lateral orx/hcrt cells innervate the ventral tegmental area (VTA) and control reward, while medial orx/hcrt cells innervate locus coeruleus (LC) and control arousal. Two distinct types of orx/hcrt cells also emerged from analysis of intrinsic and input‐driven single‐cell electrical activity. To examine the projections of these emerging orx/hcrt subtypes to LC and VTA, we injected retrograde tracer into these regions in the mouse brain in vivo, and then examined the properties of tracer‐containing orx/hcrt cells in hypothalamic slices. VTA‐ and LC‐projecting orx/hcrt cells were found across the entire orx/hcrt field, including the zona incerta, perifornical area, dorsomedial/anterior and lateral hypothalamus. Within these areas, orx/hcrt cells had similar probabilities of projecting to VTA or LC. Examination of lateral versus medial sections revealed that VTA and LC received inputs from both lateral and medial orx/hcrt cells, but, unexpectedly, lateral orx/hcrt cells were more likely to project to LC than medial orx/hcrt cells. Finally, patch‐clamp recordings revealed that VTA and LC received projections from both electrical classes of orx/hcrt cells, which had similar likelihoods of projecting to VTA or LC. Contrary to previous predictions, our data suggest that medial and lateral orx/hcrt cells, and the different electrical and morphological subclasses of orx/hcrt cells identified to date, send projections to both LC and VTA.
Histogenetic compartments of the mouse centromedial and extended amygdala based on gene expression patterns during development

The amygdala controls emotional and social behavior and regulates instinctive reflexes such as defense and reproduction by way of descending projections to the hypothalamus and brainstem. The descending amygdalar projections are suggested to show a cortico‐striato‐pallidal organization similar to that of the basal ganglia (Swanson [2000] Brain Res 886:113–164). To test this model we investigated the embryological origin and molecular properties of the mouse centromedial and extended amygdalar subdivisions, which constitute major sources of descending projections. We analyzed the distribution of key regulatory genes that show restricted expression patterns within the subpallium (Dlx5, Nkx2.1, Lhx6, Lhx7/8, Lhx9, Shh, and Gbx1), as well as genes considered markers for specific subpallial neuronal subpopulations. Our results indicate that most of the centromedial and extended amygdala is formed by cells derived from multiple subpallial subdivisions. Contrary to a previous suggestion, only the central—but not the medial—amygdala derives from the lateral ganglionic eminence and has striatal‐like features. The medial amygdala and a large part of the extended amygdala (including the bed nucleus of the stria terminalis) consist of subdivisions or cell groups that derive from subpallial, pallial (ventral pallium), or extratelencephalic progenitor domains. The subpallial part includes derivatives from the medial ganglionic eminence, the anterior peduncular area, and possibly a novel subdivision, called here commissural preoptic area, located at the base of the septum and related to the anterior commissure. Our study provides a molecular and morphological foundation for understanding the complex embryonic origins and adult organization of the centromedial and extended amygdala. J. Comp. Neurol. 506:46–74, 2008. © 2007 Wiley‐Liss, Inc.