Miracle-dz/UniFAR-FTUs huggingface dataset:
Systemic Cold Stress Adaptation of Chlamydomonas reinhardtii*

Chlamydomonas reinhardtii is one of the most important model organisms nowadays phylogenetically situated between higher plants and animals (Merchant et al. 2007). Stress adaptation of this unicellular model algae is in the focus because of its relevance to biomass and biofuel production. Here, we have studied cold stress adaptation of C. reinhardtii hitherto not described for this algae whereas intensively studied in higher plants. Toward this goal, high throughput mass spectrometry was employed to integrate proteome, metabolome, physiological and cell-morphological changes during a time-course from 0 to 120 h. These data were complemented with RT-qPCR for target genes involved in central metabolism, signaling, and lipid biosynthesis. Using this approach dynamics in central metabolism were linked to cold-stress dependent sugar and autophagy pathways as well as novel genes in C. reinhardtii such as CKIN1, CKIN2 and a hitherto functionally not annotated protein named CKIN3. Cold stress affected extensively the physiology and the organization of the cell. Gluconeogenesis and starch biosynthesis pathways are activated leading to a pronounced starch and sugar accumulation. Quantitative lipid profiles indicate a sharp decrease in the lipophilic fraction and an increase in polyunsaturated fatty acids suggesting this as a mechanism of maintaining membrane fluidity. The proteome is completely remodeled during cold stress: specific candidates of the ribosome and the spliceosome indicate altered biosynthesis and degradation of proteins important for adaptation to low temperatures. Specific proteasome degradation may be mediated by the observed cold-specific changes in the ubiquitinylation system. Sparse partial least squares regression analysis was applied for protein correlation network analysis using proteins as predictors and Fv/Fm, FW, total lipids, and starch as responses. We applied also Granger causality analysis and revealed correlations between proteins and metabolites otherwise not detectable. Twenty percent of the proteins responsive to cold are uncharacterized proteins. This presents a considerable resource for new discoveries in cold stress biology in alga and plants.
Cam deformity and hip degeneration are common after fixation of a slipped capital femoral epiphysis

Background and purpose — Slipped capital femoral epiphysis is thought to result in cam deformity and femoroacetabular impingement. We examined: (1) cam-type deformity, (2) labral degeneration, chondrolabral damage, and osteoarthritic development, and (3) the clinical and patient-reported outcome after fixation of slipped capital femoral epiphysis (SCFE). Methods — We identified 28 patients who were treated with fixation of SCFE from 1991 to 1998. 17 patients with 24 affected hips were willing to participate and were evaluated 10–17 years postoperatively. Median age at surgery was 12 (10–14) years. Clinical examination, WOMAC, SF-36 measuring physical and mental function, a structured interview, radiography, and MRI examination were conducted at follow-up. Results — Median preoperative Southwick angle was 22o (IQR: 12–27). Follow-up radiographs showed cam deformity in 14 of the 24 affected hips and a Tönnis grade > 1 in 1 affected hip. MRI showed pathological alpha angles in 15 affected hips, labral degeneration in 13, and chondrolabral damage in 4. Median SF-36 physical score was 54 (IQR: 49–56) and median mental score was 56 (IQR: 54–58). These scores were comparable to those of a Danish population-based cohort of similar age and sex distribution. Median WOMAC score was 100 (IQR: 84–100). Interpretation — In 17 patients (24 affected hips), we found signs of cam deformity in 18 hips and early stages of joint degeneration in 10 hips. Our observations support the emerging consensus that SCFE is a precursor of cam deformity, FAI, and joint degeneration. Neither clinical examination nor SF-36 or WOMAC scores indicated physical compromise.
Adaptive decision fusion for multi-sample speaker verification over GSM networks

In speaker verification, a claimant may produce two or more utterances. In our previous study [1], we proposed to compute the optimal weights for fusing the scores of these utterances based on their score distribution and our prior knowledge about the score statistics estimated from the mean scores of the corresponding client speaker and some pseudo-impostors during enrollment. As the fusion weights depend on the prior scores, in this paper, we propose to adapt the prior scores during verification based on the likelihood of the claimant being an impostor. To this end, a pseudo-imposter GMM score model is created for each speaker. During verification, the claimant’s scores are fed to the score model to obtain a likelihood for adapting the prior score. Experimental results based on the GSM-transcoded speech of 150 speakers from the HTIMIT corpus demonstrate that the proposed prior score adaptation approach provides a relative error reduction of 15% when compared with our previous approach where the prior scores are non-adaptive.
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.

The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax.
Dietary n-6:n-3 ratio and Vitamin E improve motility characteristics in association with membrane properties of boar spermatozoa

This study was aimed to evaluate the effects of dietary n-6:n-3 ratio and Vitamin E on the membrane properties and motility characteristics of spermatozoa in boars. Forty Duroc boars were randomly distributed in a 2 × 2 factorial design with two n-6:n-3 ratios (14.4 and 6.6) and two Vitamin E levels (200 and 400 mg kg−1 ). During 16 weeks of treatment, fresh semen was collected at weeks 0, 8, 12, and 16 for measurements of motility characteristics, contents of fatty acids, membrane properties (membrane fluidity and membrane integrity), and lipid peroxidation of the spermatozoa. The semen was diluted in Beltsville Thawing Solution (BTS) extender and stored at 17°C, and the sperm motility was assessed at 12, 36, 72, and 120 h of storage. The 6.6 n-6:n-3 dietary ratio increased the contents of n-3 polyunsaturated fatty acids (PUFAs) and docosahexaenoic acid (DHA) and improved the membrane integrity and membrane fluidity of the spermatozoa, resulting in notably increased total motility, sperm progressive motility, and velocity parameters of fresh semen. Feeding diet with Vitamin E (400 mg kg−1 ) prevented sperm lipid peroxidation, and resulted in higher total motility and sperm progressive motility in fresh and liquid stored semen. In conclusion, the adjustment of n-6:n-3 ratio (6.6) and supply of Vitamin E (400 mg kg−1 ) successfully improved sperm motility characteristics and thus may be beneficial to the fertility of boars, which might be due to the modification of the physical and functional properties of spermatozoa membrane in response to dietary supplementation.
Cardassian Expansion: Constraints from Compact Radio Source Angular Size versus Redshift Data

The "Cardassian Expansion Scenario" was recently proposed by Freese & Lewis as an alternative to a cosmological constant in explaining the current accelerating universe. In this paper we investigate observational constraints on this scenario from recent measurements of the angular size of high-z compact radio sources compiled by Gurvits and coworkers. We show that the allowed intervals for n and zeq, the two parameters of the Cardassian model, are heavily dependent on the value of the mean projected linear size l. However, the best fit to the current angular size data prefers the conventional flat Λ cold dark matter model to this Cardassian expansion proposal, though the latter is cosmologically credible and compatible with the Θ-z diagram for some values of l.
Using Strong Lines to Estimate Abundances in Extragalactic H II Regions and Starburst Galaxies

We have used a combination of stellar population synthesis and photoionization models to develop a set of ionization parameter and abundance diagnostics based only on the use of the strong optical emission lines. These models are applicable to both extragalactic H II regions and star-forming galaxies. We show that, because our techniques solve explicitly for both the ionization parameter and the chemical abundance, the diagnostics presented here are an improvement on earlier techniques based on strong emission-line ratios. Our techniques are applicable at all metallicities. In particular, for metallicities above half solar, the ratio [N II]/[O II] provides a very reliable diagnostic since it is ionization parameter independent and does not have a local maximum. This ratio has not previously been used historically because of worries about reliable calibration over such a long baseline, and reddening correction concerns. However, we show that the use of classical reddening curves and standard calibration are quite sufficient to allow this [N II]/[O II] diagnostic to be used with confidence as a reliable abundance indicator. As we had shown, the commonly used abundance diagnostic R23 depends strongly on the ionization parameter, while the commonly used ionization parameter diagnostic [O III]/[O II] depends strongly on abundance. The iterative method of solution presented here allows both of these parameters to be obtained without recourse to the use of temperature-sensitive line ratios involving faint emission lines. We compare three commonly used abundance diagnostic techniques and show that individually, they contain systematic and random errors. This is a problem affecting many abundance diagnostics, and the errors generally have not been properly studied or understood due to the lack of a reliable comparison abundance, except for very low metallicities, where the [O III] λ4363 auroral line is used. Here we show that the average of these techniques provides a fairly reliable comparison abundance indicator against which to test new diagnostic methods. The cause of the systematic effects are discussed, and we present a new "optimal" abundance diagnostic method based on the use of line ratios involving [N II], [O II], [O III], [S II], and the Balmer lines. This combined diagnostic appears to suffer no apparent systematic errors, can be used over the entire abundance range and significantly reduces the random error inherent in previous techniques. Finally, we give a recommended procedure for the derivation of abundances in the case that only spectra of limited wavelength coverage are available so that the optimal method can no longer be used.
Well begun but not yet done : progress and emerging challenges for poverty reduction in Vietnam

Vietnam has built a remarkable record of economic growth and poverty reduction over the last two decades. Using a poverty line set in the 1990s and since updated, Vietnams poverty rate fell from 58 percent in the early 1990s to 14 percent by 2008 and had fallen to well below 10 percent in 2010. Vietnam has also made substantial progress in other dimensions of well-being, ranging from high primary and secondary school enrollment rates to improvements in health outcomes and reductions in morbidity and mortality. Consequently, Vietnam has achieved, and in some cases surpassed, most of the Millennium Development Goals (MDGs). A new poverty assessment for Vietnam, entitled well begun, not yet done: Vietnams remarkable progress on Poverty Reduction and the Emerging Challenges, was finalized in December 2012. It was led by the World Bank (WB) and the Vietnam Academy of Social Sciences (VASS), working in collaboration with the General Statistics Office (GSO) and a team of local and international consultants. This new poverty assessment, presented in this book, takes a fresh look at the lives of poor men, women, and children and explores the constraints and opportunities they face in rising out of poverty. Building on a rich body of poverty analysis and an excellent base of knowledge from previous poverty assessments (in 1995, 2000, 2003, and 2008), it has three aims. First, it proposes revisions to Vietnam's poverty monitoring system, including better data, updated welfare aggregates, and new poverty lines, to bring the system more in line with economic and social conditions in present-day Vietnam. Second, it revisits the stylized facts about poverty and deprivation in Vietnam and develops an updated profile of poverty using data from the 2010 Vietnam Household Living Standards Survey (VHLSS) and new qualitative field studies. Third, it aims to forge a consensus around some of the key challenges for poverty reduction in the next decade, including changing regional patterns of poverty and wealth, high and persistent poverty among ethnic minorities, and rising inequality in outcomes and opportunities.
Timing Embryo Segmentation: Dynamics and Regulatory Mechanisms of the Vertebrate Segmentation Clock

All vertebrate species present a segmented body, easily observed in the vertebrate column and its associated components, which provides a high degree of motility to the adult body and efficient protection of the internal organs. The sequential formation of the segmented precursors of the vertebral column during embryonic development, the somites, is governed by an oscillating genetic network, the somitogenesis molecular clock. Herein, we provide an overview of the molecular clock operating during somite formation and its underlying molecular regulatory mechanisms. Human congenital vertebral malformations have been associated with perturbations in these oscillatory mechanisms. Thus, a better comprehension of the molecular mechanisms regulating somite formation is required in order to fully understand the origin of human skeletal malformations.
Computer Usage & Constructivist Approach of the Basic Class: Abilities & Skills and Attitudes of Pre-Service Teachers

Computers are the most significant tools of information age, have increasingly been used in each stage of education system. The participants were two hundred and forty (240) pre-service teachers who have participated in this study. The implications discussed for ASCUAC and suggestions for pre-service teachers' opinions and attitudes. This paper has designed to study the adoption of the pre-service teachers of the basic class towards the computer usage in three dimensions of their abilities, skills and attitudes. The interaction between these dimensions is the key purpose of this study to integrate technology in existing educational approach and introduce computer technology as an important tool to support new ways of teaching and learning. A model, which explains the effect of CU, AC and ASCU on learning, is established and tested. Using AMOS 18 (Analysis of Moment Structures) program, it explains 55% of CU TOOLS, 77% of ASCU TECHNOLOGY and 55% of AC, with good model fit. As a result, the effectiveness of attitude towards computer (AC) on computer usage (CU) is stronger than other factors in this study.
The origin of extended disc galaxies at z= 2

Galaxy formation models typically assume that the size and rotation speed of galaxy discs are largely dictated by the mass, concentration and spin of their surrounding dark matter haloes. Equally important, however, is the fraction of baryons in the halo that collect into the central galaxy, as well as the net angular momentum that they are able to retain during its assembly process. We explore the latter using a set of four large cosmological N-body/gasdynamical simulations drawn from the OverWhelmingly Large Simulations project. These runs differ only in their implementation of feedback from supernovae (SNe). We find that, when expressed as fractions of their virial values, galaxy mass and net angular momentum are tightly correlated. Galaxy mass fractions, m(d) = M(gal)/M(vir), depend strongly on feedback but only weakly on halo mass, or spin over the halo mass range explored here (M(vir) > 10(11) h(-1) M(circle dot)). The angular momentum of a galaxy, expressed in units of that of its surrounding halo, j(d) = J(gal)/J(vir), correlates with m(d) in a manner that is insensitive to feedback and that deviates strongly from the simple j(d) = m(d) assumption often adopted in semi-analytic models of galaxy formation. The m(d)-j(d) correlation implies that, in a given halo, galaxy disc size is maximal when the central galaxy makes up a substantial fraction (similar to 20-30 per cent) of all baryons within the virial radius (i.e. m(d) similar to 0.03-0.05). At z = 2, such systems may host gaseous discs with radial scalelengths as large as those reported for star-forming discs by the SINS survey, even in moderately massive haloes of average spin. Extended discs at z = 2 may thus signal the presence of systems where galaxy formation has been particularly efficient, rather than the existence of haloes with unusually high spin parameter.
Uncertainties and Systematic Effects on the estimate of stellar masses in high z galaxies

We discuss the uncertainties and the systematic effects that exist in the estimates of the stellar masses of high redshift galaxies, using broad band photometry, and how they affect the deduced galaxy stellar mass function. We use at this purpose the latest version of the GOODS‐MUSIC catalog. In particular, we discuss the impact of different synthetic models, of the assumed initial mass function and of the selection band. Using Chariot & Bruzual 2007 and Maraston 2005 models we find masses lower than those obtained from Bruzual & Chariot 2003 models. In addition, we find a slight trend as a function of the mass itself comparing these two mass determinations with that from Bruzual & Chariot 2003 models. As consequence, the derived galaxy stellar mass functions show diverse shapes, and their slope depends on the assumed models. Despite these differences, the overall results and scenario is observed in all these cases. The masses obtained with the assumption of the Chabrier initial mass function are in avera.
Characterization of a Novel Hemolytic Activity of Human IgG Fractions Arising from Diversity in Protein and Oligosaccharide Components

Human IgG is a well-established multifunctional antigen specific immunoglobulin molecule of the adaptive immune system. However, an antigen nonspecific immunological function of human IgG has never been reported. In this study, human IgG was isolated using ammonium sulfate fractional precipitation and diethylaminoethanol (DEAE) cellulose 52 ion exchange chromatography, from which h-IgG and hs-IgG fractions were purified on the basis of their differential binding to rabbit anti-shrimp hemocyanin antibody (h) and rabbit anti-shrimp hemocyanin's small subunit antibody (hs), respectively. We found that h-IgG had a higher hemolytic activity than hs-IgG against erythrocytes from humans, rabbits, mice and chickens, whereas the control IgG showed negligible activity. h-IgG could interact directly with erythrocyte membranes, and this interaction was suppressed by high molecular weight osmoprotectants, showing that it may follow a colloid-osmotic mechanism. In comparative proteomics and glycomics studies, h-IgG and hs-IgG yielded 20 and 5 significantly altered protein spots, respectively, on a 2-D gel. The mean carbohydrate content of h-IgG and hs-IgG was approximately 3.6- and 2-fold higher than that of IgG, respectively, and the α-d-mannose/α-d-glucose content was in the order of h-IgG>hs-IgG>IgG. In this study, a novel antigen nonspecific immune property of human IgG was investigated, and the diversity in the protein constituents and glycosylation levels may have functional signficance.
Image Classification via fusing the latent deep CNN feature

In recent years, the convolutional neural network (CNN) has made great achievements in image classification. It can extract features of image and classify them from a large number of image data automatically. Compared with these traditional feature extraction techniques (e.g., SIFT, HOG, GIST), the convolutional neural network can make better performance and does not need hand designed image features. However, how to further enhance the algorithm performance is still a hot spot in academic research. Therefore, in this paper, we propose a method to fuse the latent features extracted from the middle layers in a CNN to train a more robust classifier. First, we utilize the pretrained CNN models by caffe to extract visual features of 3-layer.Then, we use the SVM classifier for 3-layer features respectively, and we get their trained classifier. Finally, we combine three pretrained classifier into a classifier which is compared with 3-layer SVM classifier. The experiment is performed on Caltech-256 datasets. The experimental result shows that the combined classifier obtains good performance compared with the conventional CNN.
Initial soil moisture retrievals from AMSR‐E: Multiscale comparison using in situ data and rainfall patterns over Iowa

Coupled with information from the North American Land Data Assimilation System (NLDAS), standard soil datasets and vegetation and land surface parameters, a land surface microwave emission model (LSMEM) is employed using AMSR‐E brightness temperatures at X‐band (10.7 GHz) to determine soil moisture over Iowa for June and July 2002. Comparisons of calculated soil moisture with in situ validation data collected from a densely monitored watershed as part of the SMEX02 campaign, indicate that accuracies in the order of 3% vol./vol. are achievable, even where agricultural surfaces such as corn and soybean dominate. Additionally, to qualitatively evaluate the derived product and identify the level of coherence between related hydrometeorological data, a comparison of soil moisture retrievals with precipitation patterns is undertaken. Consistent spatial correlation is observed between these two fields, illustrating not only that remotely sensed soil moisture has potential to provide improved characterisation of large scale precipitation patterns, but that such patterns may also offer a pathway towards enhanced assessment of soil moisture retrievals.