Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating absorption coefficients of colored dissolved organic matter (CDOM) using a semi-analytical algorithm for southern Beaufort Sea waters: application to deriving concentrations of dissolved organic carbon from space

A series of papers have suggested that freshwater discharge, including a large amount of dissolved organic matter (DOM), has increased since the middle of the 20th century. In this study, a semi-analytical algorithm for estimating light absorption coefficients of the colored fraction of DOM (CDOM) was developed for southern Beaufort Sea waters using remote sensing reflectance at six wavelengths in the visible spectral domain corresponding to MODIS ocean color sensor. This algorithm allows the separation of colored detrital matter (CDM) into CDOM and non-algal particles (NAP) through the determination of NAP absorption using an empirical relationship between NAP absorption and particle backscattering coefficients. Evaluation using independent datasets, which were not used for developing the algorithm, showed that CDOM absorption can be estimated accurately to within an uncertainty of 35% and 50% for oceanic and coastal waters, respectively. A previous paper (Matsuoka et al., 2012) showed that dissolved organic carbon (DOC) concentrations were tightly correlated with CDOM absorption in our study area ( r 2 = 0.97). By combining the CDOM absorption algorithm together with the DOC versus CDOM relationship, it is now possible to estimate DOC concentrations in the near-surface layer of the southern Beaufort Sea using satellite ocean color data. DOC concentrations in the surface waters were estimated using MODIS ocean color data, and the estimates showed reasonable values compared to in situ measurements. We propose a routine and near real-time method for deriving DOC concentrations from space, which may open the way to an estimate of DOC budgets for Arctic coastal waters.
Sub-state national identities among minority groups in Britain

Using data from a new question in the 2011 UK census, national identities across minority ethno-religious groups in England, Wales and Scotland are compared. The findings not only substantiate earlier work showing high levels of British identification among minority groups but also demonstrate that this does not extend to sub-state national identities. The extent of sub-state national identification varies between different minorities, but the nature of this variation also depends on the specific (sub-state) national context. The findings may be understood in relation to key biographical ‘markers’ of national identity. These markers help explain variations in sub-state national identities to a much greater extent than British identity, but their effect also varies across the different nations. The analysis demonstrates the importance of examining sub-state as well as state (British) identities and heeding differences in the ways in which these identities might be conceived and asserted across national borders within the same state.
A Big Data Analytical Framework for Sports Behavior Mining and Personalized Health Services

Mobile healthcare has become an important trend in medical and healthcare domains. With the rapid development of wearable and sensing technologies, various health-related information can now be recorded, forming valuable big health data. Physical activities are considered to have a great impact on heart rate, and the analysis of heart rate data now is widely used in medical/healthcare researches. The analysis of exercise records and heart rate data have been used for the research of the exercise intensity in many institutes. Heart rate patterns refers to a symbol of health status of heart, which is based on the current rate, and other physiological parameters. An effective heart rate pattern discovering is very helpful for the healthcare and cardiovascular prevention. In this work, we aim to build a big data analytics framework for sports behavior mining and personalized health services. We analyzed users' exercise data including heart rate and GPS data, which were collected in a practical sports and social platform, to discover users' periodic sports patterns and the trend of heart rate change during exercise. Since the dataset is not only very huge but also growing very quickly, we adopt Apache Spark as the development framework to address this Velocity issue in Big Data. The analytical results can serve as important core for personalized healthcare applications. Moreover, we also group the individual result to discover the clustering result, which can be further applied for advanced healthcare applications.
Single Nucleotide Polymorphisms Identifi cation, Characterization, and Linkage Mapping in Chenopodium quinoa

Chenopodium, commonly known as the goosefoot genus, includes a wide array of species native to all inhabited continents. Many Chenopodium species are adapted to arid and/or saline environments and are notorious as invasive weed species, including C. album (lambsquarters) and C. berlandieri (pigweed). At least four species in the genus were domesticated anciently, either as vegetable or seed crops. One of these, the Andean species C. quinoa has risen from a neglected subsistence crop of indigenous farmers to become an important export commodity of the Andean nations of Bolivia, Peru, and Chile. Notable is the 2011 declaration of the Food and Agriculture Organization that 2013 is the offi cial International Year of Quinoa. Maughan et al. report the identifi cation of 14,178 putative single nucleotide polymorphisms (SNPs) using a genomic reduction protocol, as well as the development of 511 functional SNP assays. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map. The SNPs identifi ed here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.
Reaching All Families: Family, School, and Community Partnerships Amid Homelessness and High Mobility in an Urban District

Schools often struggle to build partnerships with homeless and highly mobile (HHM) families. These families are not homogeneous; they live in and engage with schools from diverse residential contexts. Using Epstein’s theory and framework and drawing from 132 interviews with HHM parents, school personnel, and community stakeholders in an urban district, results suggest that (a) interviewees had divergent experiences with family, school, and community partnerships; (b) some school actors were better positioned to engage HHM families than others; and (c) the diverse residential context of HHM families molded partnership building in unique ways. Theoretical implications and recommendations for practice and policy are discussed.
Identification of wheat genotypes tolerant to the effects of heat stress on grain quality

High-temperature stress (>35°C) during the grain-filling period has the potential to modify grain quality. A consequent weakening of dough properties has been reported for many wheat genotypes. The experiment described in this article was designed to identify wheat genotypes that might be tolerant to the effects of heat stress on grain quality and to further assess the molecular basis of these changes. A diverse set of 45 wheat genotypes was exposed to 10 hr of 40°C on each of three consecutive days in a phytotron. Mean values for all genotypes (with unheated control samples, all in duplicate) showed highly significant changes (P < 0.001) in 1,000 kernel weight (-17% difference for heat stressed minus control), protein content (17% increase), dough mixing time in a 2-g Mixograph (-13%), and resistance breakdown (17%). The general weakening of dough due to heat was accompanied by a decrease in glutenin-to-gliadin ratio and in the percentage of very large glutenin polymers. Bound lipid content increased, and there was a general reduction (-9%) in the proportion of small (B-type) starch granules. For all these attributes, reactions for individual genotypes ranged from little change (tolerance to heat stress) to considerable change (susceptible to heat stress). A group of genotypes was thus identified that should be useful in breeding attempts to stabilize wheats against heat-related variations in grain quality. Markers identified as potentially useful in breeding for tolerance include the presence of the Glu-Dld allele (glutenin subunits 5 and 10), and increases in glutenin-to-gliadin ratio and in the percentage of very large glutenin polymers.
Electrode-Shared Differential Configuration for Pressure Sensor Made of Carbon Nanotube-Filled Silicone Rubber Composites

To develop the differential pressure sensor made of carbon nanotube-filled silicone rubber composites with a simplified structure, an electrode-shared differential configuration is designed. The configuration includes the top and bottom sandwich layers. The top sandwich layer is composed of the top film, the intermediate film, and the composite film with low carbon nanotube content between them. The bottom sandwich layer is composed of the intermediate film, the bottom film, and the composite film with high carbon nanotube content between them. The electrode in the intermediate film is shared by the top and bottom sandwich layers, which can make the sensor probe more concise. The electrical resistance of the composite film with high/low carbon nanotube content increases/decreases with the increase of the pressure, and increases with the increase of the temperature. The top and bottom sandwich layers are connected to the neighboring arms of an electrical bridge to construct a differential system. The experiments verify the feasibility of using the electrode-shared configuration to construct the differential piezoresistive sensor made of the composite to decrease the temperature-induced drift and increase the sensitivity.
Expression and activity of 3-hydroxy-3-methylglutaryl-CoA synthase and reductase in the fat body of ovariectom ized and al latectom ized Blaftella germanica

3-Hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase and HMG-CoA reductase show coordinated regulation in the fat body of Blurtella germanica females. Since the profile of activity is parallel to the cycle of vitellogenin production, we postulated a link between the mevalonate pathway and vitellogenesis. Here we have studied both enzymes in females of B.gennanicu modified by ovariectomy (which leads to a saturable accumulation of vitellogenin) and allatectomy (which supresses vitellogenesis). Protein levels and enzymatic activity for both enzymes in ovariectomized specimens rose early in the first days of imaginal life and remained high until the end of the period studied, whereas controls showed cyclic profiles. In allatectomized specimens the same parameters were measured on day 4 of adult life and values were much lower with respect to controls. The parallelism between the patterns of HMG-CoA synthase and reductase, and that of vitellogenin, suggests a functional relationship between the mevalonate pathway and the glycosylation of vitellogenin through dolichol intermediates.
Cross-tissue Methylomic Profiling Strongly Implicates a Role for Cortex-specific Deregulation of Ank1 in Alzheimer's Disease Neuropathology Cross-tissue Methylomic Profiling Strongly Implicates a Role for Cortex-specific Deregulation of Ank1 in Alzheimer's Disease Neuropathology Hhs Public Access On

The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. et al. 2014. " Cross-tissue methylomic profiling strongly implicates a role for cortex-specific deregulation of ANK1 in Alzheimer's disease neuropathology. Abstract * CJ provided brain tissue for analysis. PDJ, GS and DB provided replication data. ZK provided help with cellular heterogeneity correction. LH provided help with the alternative splicing assays. JM, KL and LS drafted the manuscript. All authors read and approved the final submission. Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive neuropathology and cognitive decline. We describe a cross-tissue analysis of methylomic variation in AD using samples from three independent human post-mortem brain cohorts. We identify a differentially methylated region in the ankyrin 1 (ANK1) gene that is associated with neuropathology in the entorhinal cortex, a primary site of AD manifestation. This region was confirmed as significantly hypermethylated in two other cortical regions (superior temporal gyrus and prefrontal cortex) but not in the cerebellum, a region largely protected from neurodegeneration in AD, nor whole blood obtained pre-mortem, from the same individuals. Neuropathology-associated ANK1 hypermethylation was subsequently confirmed in cortical samples from three independent brain cohorts. This study represents the first epigenome-wide association study (EWAS) of AD employing a sequential replication design across multiple tissues, and highlights the power of this approach for identifying methylomic variation associated with complex disease. Alzheimer's disease (AD) contributes significantly to the global burden of disease affecting in excess of 26 million people worldwide 1,2. The pathogenesis associated with AD is characterized by the accumulation of amyloid plaques, tangles of intracellular hyperphosphorylated tau, gliosis, synaptic dysfunction and eventually cell death 3,4. Although the neuropathological manifestation of AD is well characterized in post-mortem brain, little is known about the underlying risk factors or mechanism(s) involved in disease progression. Of note, different parts of the brain show differential vulnerability to AD; although there is progressive neurodegeneration across the cortex with areas such as the entorhinal cortex (EC) being characterized by considerable and early neuropathology, regions such as the cerebellum (CER) are relatively resistant to neuronal damage, with little or no plaque or neurofibrillary tangle pathology 5. Contemporary research aimed at exploring the etiology of AD has focused primarily on DNA sequence variation, with some notable success 6. Increasing knowledge about the biology of the genome 7 also implicates an important role for epigenetic variation …
Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)

Eastern North American plant biogeography has traditionally focused on two primary issues: (i) the location of temperate Pleistocene refugia and their proximity to the southern margin of the ice sheet during the last glacial maximum, and (ii) the origin of the temperate element of northern Latin America. While numerous population genetic and phylogeographical studies have focused on the first issue, few (if any) have considered the second. We addressed these issues by surveying 117 individuals from 24 populations of Liquidambar styraciflua (American sweetgum; Altingiaceae) across the southeastern USA, eastern Mexico, and Guatemala, using more than 2200 bp of chloroplast DNA sequence data. To specifically address the issue of timing, we estimated intraspecific divergence times on the basis of multiple fossil‐based calibration points, using taxa from Altingiaceae (Liquidambar and Altingia) and Hammamelidaceae (Hamamelis) as outgroups. More than half of the sampled localities exhibited multiple haplotypes. Remarkably, the greatest variation was observed within the USA, with Mexico and Guatemala sharing widespread haplotypes with Texas, Mississippi, Kentucky, Ohio, and northern Virginia. This lack of differentiation suggests shared ancestral polymorphisms, and that the genetic signal we observed is older than the disjunction itself. Our data provide support for previously proposed hypotheses of Pleistocene refugia in peninsular Florida and along the eastern Atlantic, but also for deeper divergences (~8 million years ago) within the USA. These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study.
A Novel Zinc-Binding Domain Is Essential for Formation of the Functional Junín Virus Envelope Glycoprotein Complex

ABSTRACT The envelope glycoprotein of the Junín arenavirus (GP-C) mediates entry into target cells through a pH-dependent membrane fusion mechanism. Unlike other class I viral fusion proteins, the mature GP-C complex retains a cleaved, 58-amino-acid signal peptide (SSP) as an essential subunit, required both for trafficking of GP-C to the cell surface and for the activation of membrane fusion. SSP has been shown to associate noncovalently in GP-C via the cytoplasmic domain (CTD) of the transmembrane fusion subunit G2. In this report we investigate the molecular basis for this intersubunit interaction. We identify an invariant series of six cysteine and histidine residues in the CTD of G2 that is essential for incorporation of SSP in the GP-C complex. Moreover, we show that a CTD peptide fragment containing His-447, His-449, and Cys-455 specifically binds Zn2+ at subnanomolar concentrations. Together, these results suggest a zinc finger-like domain structure in the CTD of G2. We propose that the remaining residues in the series (His-459, Cys-467, and Cys-469) form an intersubunit zinc-binding center that incorporates Cys-57 of SSP. This unusual motif may act to retain SSP in the GP-C complex and position the ectodomain loop of SSP for its role in modulating membrane fusion activity. The unique tripartite organization of GP-C could provide novel molecular targets for therapeutic intervention in arenaviral disease.
Measuring Everything You’ve Ever Wanted to Know About an Ultrashort Light Pulse

We review the problem of measuring an ultrashort laser pulse and then describe several experimentally simple, accurate, and very reliable methods for measuring both very simple laser pulses and very complex ultrashort light pulses. Each of these methods comprises only a few easily aligned components, and they allow the measurement of a wide range of pulses, including those with time-bandwidth products greater than 1000 and those with energies of only a few hundred photons. Finally, two recently introduced very simple methods allow the measurement of the complete spatio-temporal intensity and phase of even complex pulses on a single shot or at a tight focus. In short, pulse-measurement technology is now so powerful and easy to use that it is time to use these methods and to focus on their applications.
Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.

Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.
Sampling Bias in Respirometry

Comparisons of the metabolic rates of species, populations, and treatment groups of animals are common. However, the data used in these comparisons may not be truly equivalent. We report the effects of varying (1) total time from which minimum metabolism is selected and (2) time over which metabolic rate is calculated (calculation interval) on estimates of oxygen consumption for Microtus agrestis and Apodemus sylvaticus. Oxygen consumption was measured at 10°, 20°, and 30° C, using open-circuit respirometry. The lowest 15 min of metabolism were 13% and 65% higher for Microtus and Apodemus, respectively, when selected from a total monitoring period of 30 min than when selected from a period of 6 h. This demonstrates the importance of standardizing the duration of time from which minimal estimates of metabolism are selected (i. e., the amount of time for which metabolism is measured). For Microtus, minimum oxygen consumption was 12% higher when calculated over 60 min than when calculated over 15 min. We suggest that analyses relying on minimal (e.g., basal) metabolic rates include calculation interval as a potential covariate.
Characterization of materials and film stacks for accurate surface topography measurement using a white-light optical profiler

Pupil-Plane Scanning White-Light Interferometry measures reflectivity as a function of angle of incidence, wavelength and polarization in one location of an object surface. This information is converted into ellipsometric information and allows the characterization of material optical properties and layer thickness in the case of layered structures. We illustrate the capability of the method by measuring the thickness and refractive index of thin film standards. The information is also used to create accurate 3D topography maps of complex object structures.
Clustering Social News Based on User Affection

Recently, several news aggregation services have emerged to deal with the problem of information overload and news personalization. These news providers are able to organize news based on content similarity as a strategy to improve the user reading experience. However, organizing news solely on content fails to consider actual human reading behavior, and in turn ignores the importance of user perception in news personalization. We propose an enhanced news clustering technique based on an user affect model, which is a feasible framework for news categorization that can contribute to building more human-centric interactive systems. Empirical results demonstrate the effectiveness of clustering news articles through the enrichment of a user affect model when compared to traditional keyword-based clustering.