Miracle-dz/UniFAR-FTUs huggingface dataset:
Setting Up Decision-Making Tools toward a Quality-Oriented Participatory Maize Breeding Program

Previous studies have reported promising differences in the quality of kernels from farmers' maize populations collected in a Portuguese region known to produce maize-based bread. However, several limitations have been identified in the previous characterizations of those populations, such as a limited set of quality traits accessed and a missing accurate agronomic performance evaluation. The objectives of this study were to perform a more detailed quality characterization of Portuguese farmers' maize populations; to estimate their agronomic performance in a broader range of environments; and to integrate quality, agronomic, and molecular data in the setting up of decision-making tools for the establishment of a quality-oriented participatory maize breeding program. Sixteen farmers' maize populations, together with 10 other maize populations chosen for comparison purposes, were multiplied in a common-garden experiment for quality evaluation. Flour obtained from each population was used to study kernel composition (protein, fat, fiber), flour's pasting behavior, and bioactive compound levels (carotenoids, tocopherols, phenolic compounds). These maize populations were evaluated for grain yield and ear weight in nine locations across Portugal; the populations' adaptability and stability were evaluated using additive main effects and multiplication interaction (AMMI) model analysis. The phenotypic characterization of each population was complemented with a molecular characterization, in which 30 individuals per population were genotyped with 20 microsatellites. Almost all farmers' populations were clustered into the same quality-group characterized by high levels of protein and fiber, low levels of carotenoids, volatile aldehydes, α- and δ-tocopherols, and breakdown viscosity. Within this quality-group, variability on particular quality traits (color and some bioactive compounds) could still be found. Regarding the agronomic performance, farmers' maize populations had low, but considerably stable, grain yields across the tested environments. As for their genetic diversity, each farmers' population was genetically heterogeneous; nonetheless, all farmers' populations were distinct from each other's. In conclusion, and taking into consideration different quality improvement objectives, the integration of the data generated within this study allowed the outline and exploration of alternative directions for future breeding activities. As a consequence, more informed choices will optimize the use of the resources available and improve the efficiency of participatory breeding activities.
Human Cytomegalovirus IE86 Attenuates Virus- and Tumor Necrosis Factor Alpha-Induced NFκB-Dependent Gene Expression

ABSTRACT Human cytomegalovirus (HCMV) infection regulates a number of genes involved in the host antiviral response. We have previously reported that HCMV attenuates the expression of beta interferon (IFN-β) and a number of proinflammatory chemokines, and this attenuation is mediated by the HCMV immediate-early protein IE86. The present study seeks to identify the mechanism by which IE86 blocks IFN-β expression. We demonstrate that the induction of IFN-β during HCMV infection requires the activation of both the IRF-3 and the NFκB pathways. Therefore, IE86 may target either pathway to block IFN-β expression. Our results show that IE86 does not block IRF-3 phosphorylation, dimerization, nuclear translocation, or target gene expression. However, using gel shift analysis, we demonstrate that IE86 efficiently inhibits virus-induced binding of NFκB to the IFN-β promoter, resulting in attenuation of IFN-β and NFκB-dependent gene expression. Furthermore, IE86 expression inhibits tumor necrosis factor alpha-induced NFκB DNA binding and target gene expression. Together, these results identify IE86 as a NFκB antagonist, which results in the suppression of NFκB-dependent cytokine and chemokine gene expression.
Remote Health Monitoring of Heart Failure With Data Mining via CART Method on HRV Features

Disease management programs, which use no advanced information and computer technology, are as effective as telemedicine but more efficient because less costly. We proposed a platform to enhance effectiveness and efficiency of home monitoring using data mining for early detection of any worsening in patient's condition. These worsenings could require more complex and expensive care if not recognized. In this letter, we briefly describe the remote health monitoring platform we designed and realized, which supports heart failure (HF) severity assessment offering functions of data mining based on the classification and regression tree method. The system developed achieved accuracy and a precision of 96.39% and 100.00% in detecting HF and of 79.31% and 82.35% in distinguishing severe versus mild HF, respectively. These preliminary results were achieved on public databases of signals to improve their reproducibility. Clinical trials involving local patients are still running and will require longer experimentation.
Prognostic Factors in Terms of the Number of Metastatic Nodules in Patients With Colorectal Cancer Liver Metastases

Purpose The hepatic resection is the gold-standard treatment for patients with colorectal-cancer liver metastases (CLM). This study aimed to identify prognostic factors in patients with synchronous CLM who underwent a surgical curative (R0) resection with respect to the number of metastatic nodules. Methods Of 1,261 CLM patients treated between January 1991 and December 2010, 339 who underwent a R0 resection for synchronous CLM were included in this retrospective analysis. Patients were grouped according to the number of CLM nodules: 1–2 CLM nodules, n = 272 (group 1) and 3–8 CLM nodules, n = 67 (group 2). Results The 5-year progression-free survival (PFS) rate in group 1was better than that in group 2 (P = 0.020). The multivariate analysis identified lymph-node metastasis (N2), lymphovascular invasion (LVI), and three or more CLM nodules as independent poor prognostic factors for PFS in all patients and lymph-node metastasis (N2) and LVI as independent poor prognostic factors for patients in group 1. No independent prognostic factors were identified for patients in group 2. CLM treatment method and neoadjuvant chemotherapy were not associated with survival. Conclusion Three or more metastatic nodules, lymph-node metastasis (N2), and LVI were independent poor prognostic factors for PFS in patients with synchronous CLM who underwent a R0 resection. The latter 2 factors were also independent prognostic factors for PFS in patients with less than 3 CLM nodules; however, in patients with three or more CLM nodules, the prognosis for PFS may be related only to liver metastasis.
Study of Diseases and the Immune System of Bivalves Using Molecular Biology and Genomics

Environmental chemico-physical factors, pathogens, and biological interactions constantly affect organism physiology and behavior. Invertebrates, including bivalve mollusks do not possess acquired immunity. Their defense mechanisms rely on an innate, non-adaptive immune system employing circulating cells and a large variety of molecular effectors. The mechanisms underlying host defense depend on the presence of functional proteins in appropriate quantities, within a crucial time window. These proteins are encoded by genes whose transcription is tightly coordinated by complex programs of gene expression. Currently available advanced techniques allow the evaluation of this gene expression, expanding our understanding of the behavior and function of cells and tissues under varying conditions. In particular, DNA microarray technology enables measurement of a large predetermined set of known genes or sequences. Expressed sequence tag sequencing from redundant, normalized, subtractive hybridization libraries is a robust method for sampling the protein encoding genes that are expressed within a tissue. The elimination of microorganisms by defense cells is a dynamic process that involves integrating synthesis of granule proteins during differentiation, migration onto sites of infection, phagocytosis and killing of microorganisms, modulation of their effector cells, and finally apoptosis. Understanding how this complex biological process is regulated can best be addressed using a systems biology approach to the study of organisms and populations in order to more effectively decipher the continuous challenge between two genomes, i.e., evolving host-pathogen interactions.
A generating mechanism for apparent fluid slip in hydrophobic microchannels

Fluid slip has been observed experimentally in micro- and nanoscale flow devices by several investigators [e.g., Tretheway and Meinhart, Phys. Fluids 14, L9 (2002); Zhu and Granik, Phys. Rev. Lett. 87, 096105 (2001); Pit et al., Phys. Rev. Lett. 85, 980 (2000); and Choi et al., Phys. Fluids 15, 2897 (2003)]. This paper examines a possible mechanism for the measured fluid slip, for water flowing over a hydrophobic surface. We extend the work of Lum et al. [J. Phys. Chem. B 103, 4570 (1999)], Zhu and Granick [Phys. Rev. Lett. 87, 096105 (2001)], Granick et al. [Nature Materials 2, 221 (2003)], and de Gennes [Langmuir 18, 3413 (2002)], who suggest slip develops from a depleted water region or vapor layer near a hydrophobic surface. By modeling the presence of either a depleted water layer or nanobubbles as an effective air gap at the wall, we calculate slip lengths for flow between two infinite parallel plates. The calculated slip lengths are consistent with experimental values when the gas layer is modeled as a continuum and significantly higher when rarefied gas conditions are assumed. The results suggest that the apparent fluid slip observed experimentally at hydrophobic surfaces may arise from either the presence of nanobubbles or a layer of low density fluid at the surface.
Effect of Different Crop Establishment Methods and Fertilizer Sources on Growth, Yield Attribute and Yield of Rice (Oryza sativa L.)

The influence of different crop establishment methods and fertilizer sources on growth attributes and yield of rice was studied during Kharif season of 2009 and 2010 on lateritic soils. The experiment was laid out in split plot design replicate thrice with five crop establishment methods (transplanting, pre-monsoon dibbling of seeds, dibbling of seeds with the onset of monsoon, transplanting of seedling by Thomba method and system of rice intensification) in main plots and three fertilizer sources (recommended dose of fertilizers-120:60:60 kg NPK ha-1, placement of urea-DAP briquettes and placement of urea-suphala briquettes) in sub plots. From the present investigation, it can be concluded that for growing kharif rice under upland situation, crop need to be established by transplanting method and amended with urea-DAP briquettes (@ 168.75 kg ha-1), to obtain higher yield. However, under inadequate rainwater for puddling, Thomba method with urea-DAP briquettes (@ 168.75 kg ha-1) is suitable, and under labour scarcity condition, pre-monsoon dibbling of seeds with urea-DAP briquettes (@ 168.75 kg ha-1) is one of the alternatives to conventional transplanting method under upland conditions.
Comprehensive Small Animal Imaging Strategies on a Clinical 3 T Dedicated Head MR-Scanner; Adapted Methods and Sequence Protocols in CNS Pathologies

Background Small animal models of human diseases are an indispensable aspect of pre-clinical research. Being dynamic, most pathologies demand extensive longitudinal monitoring to understand disease mechanisms, drug efficacy and side effects. These considerations often demand the concomitant development of monitoring systems with sufficient temporal and spatial resolution. Methodology and Results This study attempts to configure and optimize a clinical 3 Tesla magnetic resonance scanner to facilitate imaging of small animal central nervous system pathologies. The hardware of the scanner was complemented by a custom-built, 4-channel phased array coil system. Extensive modification of standard sequence protocols was carried out based on tissue relaxometric calculations. Proton density differences between the gray and white matter of the rodent spinal cord along with transverse relaxation due to magnetic susceptibility differences at the cortex and striatum of both rats and mice demonstrated statistically significant differences. The employed parallel imaging reconstruction algorithms had distinct properties dependent on the sequence type and in the presence of the contrast agent. The attempt to morphologically phenotype a normal healthy rat brain in multiple planes delineated a number of anatomical regions, and all the clinically relevant sequels following acute cerebral ischemia could be adequately characterized. Changes in blood-brain-barrier permeability following ischemia-reperfusion were also apparent at a later time. Typical characteristics of intra-cerebral haemorrhage at acute and chronic stages were also visualized up to one month. Two models of rodent spinal cord injury were adequately characterized and closely mimicked the results of histological studies. In the employed rodent animal handling system a mouse model of glioblastoma was also studied with unequivocal results. Conclusions The implemented customizations including extensive sequence protocol modifications resulted in images of high diagnostic quality. These results prove that lack of dedicated animal scanners shouldn't discourage conventional small animal imaging studies.
Predictive Role of p53 Protein as a Single Marker or Associated to Ki67 Antigen in Oral Carcinogenesis

p53 over-expression has been proposed as a reliable marker associated to oral carcinogenesis, although only about 50% of oral carcinomas (OSCC) are associated with p53 over-expression and even p53-negative lesions can progress to OSCC. The aim of the study was to determine whether the combination of p53 over-expression and p53 low-expression associated with Ki67 over-expression (high Ki67/p53 ratio) could lead to a more sensitive parameter. Immunohistochemical expression of Ki67 and p53 was measured in 54 specimens from OSCC; 27 specimens from moderate/severe epithelial dysplasia; 32 specimens from oral leukoplakias without epithelial dysplasia, and 13 specimens with normal epithelium. p53 over-expression was found in 31 (53%) samples from OSCC, in 10 (37%) samples from severe dysplasias, and in 5 (15%) samples from non-dysplastic lesions, while the combination of high p53 values with high Ki67/p53 ratio was observed in 93% of OSCC, in 81% of dysplastic lesions, and in 50% of non-dysplastic lesions. This parameter may have a clinical implication to detect early lesions with an impairment of p53 pathway, and probably at risk of progress to OSCC.
Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly

Wheat Stem Sawfly (WSS), Cephus Cinctus Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant’s resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regulatory functions on gene expression, tuning protein production by controlling transcriptional and post-transcriptional activities. A transcriptome-guided approach was followed in order to identify miRNAs, lncRNAs, and mRNA of WSS, and their interaction networks. A total of 1,893 were presented here as differentially expressed between larva and adult WSS insects. There were 11 miRNA families detected in WSS transcriptome. Together with the annotation of 1,251 novel mRNAs, the amount of genetic information available for WSS was expanded. The network between WSS miRNAs, lncRNAs, and mRNAs suggested miRNA-mediated regulatory roles of lncRNAs as competing endogenous RNAs. In the light of the previous evidence that small RNA molecules of a pathogen could suppress the immune response of host plant, we analyzed the putative interactions between larvae and wheat at the miRNA level. Overall, this study provides a profile of larva and adult WSS life stages in terms of coding and non-coding elements. These findings also emphasize the potential roles of wheat and larval miRNAs in wheat resistance to infestation and in the suppression of resistance which is critical for the development of effective pest control strategies.
Climatology of medium‐scale traveling ionospheric disturbances observed by a GPS network in central China

[1] The 15-month climatology of medium-scale traveling ionospheric disturbances (MSTIDs) during a solar minimum period has been constructed from observations of a dense GPS receiver array in Central China. In total, 793 MSTID events are identified, with peaks in occurrence at 1500 LT and 0100 LT. The occurrence of MSTIDs decreases following an increase in geomagnetic activity, with 46% of the MSTIDS occurring in the daytime. Daytime MSTIDs are characterized by a major occurrence maximum around the winter solstice and by an equatorward propagation direction. The period, phase velocity, azimuth, and amplitude of daytime MSTIDs are 20–60 min, 100–400 m/s, 130°–270°, and 0.8–1.5%, respectively. The remaining 54% of the MSTIDs occurred at night, and were characterized by a peak in occurrence at the summer solstice and by a southwestward propagation direction. The period, phase velocity, azimuth, and amplitude of nighttime MSTIDs are 20–70 min, 50–230 m/s, 170°–300°, and 2–7%, respectively. The propagation directions and the seasonal behaviors support the view that daytime MSTIDs are an ionospheric manifestation of atmospheric gravity waves from the lower atmosphere, while a possible excitation mechanism of nighttime MSTIDs is the electrodynamics process caused by plasma instability in the F layer.
Dual Mutation Events in the Haemagglutinin-Esterase and Fusion Protein from an Infectious Salmon Anaemia Virus HPR0 Genotype Promote Viral Fusion and Activation by an Ubiquitous Host Protease

In Infectious salmon anaemia virus (ISAV), deletions in the highly polymorphic region (HPR) in the near membrane domain of the haemagglutinin-esterase (HE) stalk, influence viral fusion. It is suspected that selected mutations in the associated Fusion (F) protein may also be important in regulating fusion activity. To better understand the underlying mechanisms involved in ISAV fusion, several mutated F proteins were generated from the Scottish Nevis and Norwegian SK779/06 HPR0. Co-transfection with constructs encoding HE and F were performed, fusion activity assessed by content mixing assay and the degree of proteolytic cleavage by western blot. Substitutions in Nevis F demonstrated that K276 was the most likely cleavage site in the protein. Furthermore, amino acid substitutions at three sites and two insertions, all slightly upstream of K276, increased fusion activity. Co-expression with HE harbouring a full-length HPR produced high fusion activities when trypsin and low pH were applied. In comparison, under normal culture conditions, groups containing a mutated HE with an HPR deletion were able to generate moderate fusion levels, while those with a full length HPR HE could not induce fusion. This suggested that HPR length may influence how the HE primes the F protein and promotes fusion activation by an ubiquitous host protease and/or facilitate subsequent post-cleavage refolding steps. Variations in fusion activity through accumulated mutations on surface glycoproteins have also been reported in other orthomyxoviruses and paramyxoviruses. This may in part contribute to the different virulence and tissue tropism reported for HPR0 and HPR deleted ISAV genotypes.
Physical Health of the Long-Term Mentally Ill in the Community

A clinical assessment was made of 145 long-term users of hospital and social-services day psychiatric facilities, and 84 consented to laboratory pathological screening. We recorded data on relevant medical care where that was being provided. Based on clinical assessment, 59 patients (41%) were judged to have medical problems potentially requiring care. Based on pathological screening 39 (44% of those assessed) had unmet needs, and this rating was associated with poor compliance with attendance and treatment plans. Altogether, 12 patients had important unmet needs, mainly for detailed medical investigation, although none required immediate hospital admission. Long-term patients should be medically reassessed and supervised at appropriate intervals.
S T U D I E S ON AN E P I T H E L I A L (GLAND) CELL J U N C T I O N II. Surface Structure

The surface structure of a gland cpithclium (Drosophila salivary gland), particularly that at the junction bctwcen cells, was cxamined under the electron microscope. The junctional surface, which in the preceding paper was shown to bc highly permeable to ions, has the following structural characteristics. About two-thirds of it are profuscly infolded; the surface mcmbrancs of adjoining cells interdigitatc and present desmosomcs. Thc width of the intcrccllular space varies considerably. Thc remainder of the junctional surfacc, the third that abuts on the lumcn, is rather straight. Here, the cell membranes are aligned parallel at a distance of 150 A, and interconnected at regular intcrvals of 100 A. The connccting material has a high electron opacity, and is about as thick as the cell mcmbrancs, but, unlike the latter, has no resolvable unit mcmbrane structure. Thc surface at thc cell base, which in the preceding paper was shown to be rather impcrmcablc, is infolded and resembles the infolded junctional region. The luminal surface exhibits microvilli. Critical surface dimcnsions arc given, and thc implications of surfacc structure in intcrcellular permeabili ty are discusscd. I N T R O D U C T I O N Evidcnce has been prcscnted in the preceding paper that ions move rather frccly from cell to ccll in a gland epithelium (l). I t was shown that there is no substantial diffusion barrier in the ccll-to-ccll direction, but that thcrc is a strong barrier bctween the intcrccllular space and cell cxtcrior. Two observations called for an explanation at thc structural level: the lack of ion leakage along thc intercellular space and the low diffusion resistance across the contact surfaces of adjaccnt cells. The former implies that the intercellular space is obstructed or very narrow; and the latter, that either the membrane area at the contact surface is large in relation to that of the rest of the cell surface, or that the permeability of the contact surface is high. One may expect to find information on at least two of these points at the fine structural level. The present study has been undertaken to provide this information and to correlate the structure with the electrophysiological measurements of the preceding article (1). M A T E R I A L S A N D M E T H O D S Salivary glands of third instar larvae of Drosophila flavorepleta wcrc used in these studies. Thc glands were fixed for 3 hours in cold buffered 6.25 per ccnt