Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Layer and Recursive Neural Networks for Metagenomic Classification

Recent advances in machine learning, specifically in deep learning with neural networks, has made a profound impact on fields such as natural language processing, image classification, and language modeling; however, feasibility and potential benefits of the approaches to metagenomic data analysis has been largely under-explored. Deep learning exploits many layers of learning nonlinear feature representations, typically in an unsupervised fashion, and recent results have shown outstanding generalization performance on previously unseen data. Furthermore, some deep learning methods can also represent the structure in a data set. Consequently, deep learning and neural networks may prove to be an appropriate approach for metagenomic data. To determine whether such approaches are indeed appropriate for metagenomics, we experiment with two deep learning methods: i) a deep belief network, and ii) a recursive neural network, the latter of which provides a tree representing the structure of the data. We compare these approaches to the standard multi-layer perceptron, which has been well-established in the machine learning community as a powerful prediction algorithm, though its presence is largely missing in metagenomics literature. We find that traditional neural networks can be quite powerful classifiers on metagenomic data compared to baseline methods, such as random forests. On the other hand, while the deep learning approaches did not result in improvements to the classification accuracy, they do provide the ability to learn hierarchical representations of a data set that standard classification methods do not allow. Our goal in this effort is not to determine the best algorithm in terms accuracy-as that depends on the specific application-but rather to highlight the benefits and drawbacks of each of the approach we discuss and provide insight on how they can be improved for predictive metagenomic analysis.
Evaluation of vegetable-faba bean (Vicia faba L.) intercropping under Latvian agro-ecological conditions.

BACKGROUND Monoculture is used mostly in conventional agriculture, where a single crop is cultivated on the same land for a period of at least 12 months. In an organic and integrated growing approach, more attention is paid to plant-environment interactions and, as a result, diverse growing systems applying intercropping, catch crops, and green manure are being implemented. Thus, field experiments for evaluation of vegetable/faba bean full intercropping efficiency, in terms of vegetable and faba bean yield and protein content, were set up during two consecutive growing seasons (2014 and 2015). RESULTS Data obtained showed that the most efficient intercropping variants were cabbage/faba bean (cabbage yield 1.27-2.91 kg m-2 , immature faba bean pods 0.20-0.43 kg m-2 ) and carrot/faba bean (carrot yield 1.67-2.28 kg m-2 , immature faba bean pods 0.10-0.52 kg m-2 ), whilst onion and faba bean intercrop is not recommended for vegetable growing since it induces a very low onion yield (0.66-1.09 kg m-2 ), although the highest immature faba bean pod yield was found in the onion/faba bean intercropping scheme (up to 0.56 kg m-2 ). CONCLUSION Vegetable/faba bean intercropping can be used in practical horticulture for carrot and cabbage growing in order to ensure sustainable farming and environmentally friendly horticultural production. © 2017 Society of Chemical Industry.
Individual patterns of functional reorganization in the human cerebral cortex after capsular infraction

We have previously shown bilateral activation of motor pathways and the recruitment of additional motor areas in studies of groups of patients with recovery from motor stroke. We have now deveoloped a new positron emission tomographic technique to measure the changes in regional cerebral blood flow elicated duringsd a motor task in individual patients, relative to the cerebral activatuion found in normal subjects. The patterns of cerebral activation in each of 8 individual patients with capuslar lesion of the pyramidal tract and complete recovery from hemiplegia are described by compression with the pattern found in a representative sample of 10 normal subjects. We found a large ventral extension of the hand field of the contralateral (sensori)motor cortex in all patients with lesions of the posterior limb of the internal capsule. Greater activation than in normal subjects was found in varible combination of the supplementray motor areas, the insula, the frontal operculum, and the paterial cortex. Structures belonging to motor pathways ipsilateral to the recovered limb were also more activated in the patients than in normal subjects. However, additional activation of the ipsilateral (sensori)motor cortex was only found in the 4 patients who exhibited associated movements of the unaffected hand when the recovered hand performed the motor task. We conclude that recovery from motor stroke due to striatocapsular damage is associated with individually different patterns of functional reorganization of the brain. These patterns are dependent on the site of the subcortical lesion and the somatotopicorganization of the pyramidal tract, both of which may determine the precise poetntial for recovery of limb function following this type of brain injury.
State-Based Delay Representation and Its Transfer from a Game of Pong to Reaching and Tracking

Abstract To accurately estimate the state of the body, the nervous system needs to account for delays between signals from different sensory modalities. To investigate how such delays may be represented in the sensorimotor system, we asked human participants to play a virtual pong game in which the movement of the virtual paddle was delayed with respect to their hand movement. We tested the representation of this new mapping between the hand and the delayed paddle by examining transfer of adaptation to blind reaching and blind tracking tasks. These blind tasks enabled to capture the representation in feedforward mechanisms of movement control. A Time Representation of the delay is an estimation of the actual time lag between hand and paddle movements. A State Representation is a representation of delay using current state variables: the distance between the paddle and the ball originating from the delay may be considered as a spatial shift; the low sensitivity in the response of the paddle may be interpreted as a minifying gain; and the lag may be attributed to a mechanical resistance that influences paddle’s movement. We found that the effects of prolonged exposure to the delayed feedback transferred to blind reaching and tracking tasks and caused participants to exhibit hypermetric movements. These results, together with simulations of our representation models, suggest that delay is not represented based on time, but rather as a spatial gain change in visuomotor mapping.
Visual and confocal microscopic interpretation of patch tests to benzethonium chloride and benzalkonium chloride

Quaternary ammonium compounds (Quats), such as benzalkonium chloride (BAC) and benzethonium chloride (BEC), are widely used as antibacterial active ingredients and preservatives in personal care products, disinfectants, and ophthalmic preparations. BAC is known to be a marginal irritant when patch tested at 0.15% aq. Data on BEC are limited.
Milk protein intake, the metabolic-endocrine response, and growth in infancy: data from a randomized clinical trial.

BACKGROUND Protein intake in early infancy has been suggested to be an important risk factor for later obesity, but information on potential mechanisms is very limited. OBJECTIVE This study examined the influence of protein intake in infancy on serum amino acids, insulin, and the insulin-like growth factor I (IGF-I) axis and its possible relation to growth in the first 2 y of life. DESIGN In a multicenter European study, 1138 healthy, formula-fed infants were randomly assigned to receive cow-milk-based infant and follow-on formulas with lower protein (LP; 1.77 and 2.2 g protein/100 kcal) or higher protein (HP; 2.9 and 4.4 g protein/100 kcal) contents for the first year. Biochemical variables were measured at age 6 mo in 339 infants receiving LP formula and 333 infants receiving HP formula and in 237 breastfed infants. RESULTS Essential amino acids, especially branched-chain amino acids, IGF-I, and urinary C-peptide:creatinine ratio, were significantly (P < 0.001) higher in the HP group than in the LP group, whereas IGF-binding protein (IGF-BP) 2 was lower and IGF-BP3 did not differ significantly. The median IGF-I total serum concentration was 48.4 ng/mL (25th, 75th percentile: 27.2, 81.8 ng/mL) in the HP group and 34.7 ng/mL (17.7, 57.5 ng/mL) in the LP group; the urine C-peptide:creatinine ratios were 140.6 ng/mg (80.0, 203.8 ng/mg) and 107.3 ng/mg (65.2, 194.7 ng/mg), respectively. Most essential amino acids, IGF-I, C-peptide, and urea increased significantly in both the LP and HP groups compared with the breastfed group. Total IGF-I was significantly associated with growth until 6 mo but not thereafter. CONCLUSIONS HP intake stimulates the IGF-I axis and insulin release in infancy. IGF-I enhances growth during the first 6 mo of life. This trial was registered at clinicaltrials.gov as NCT00338689.
Analysis of patients with bodyboarding injuries transported by physician-staffed emergency helicopter

CONTEXT There have been no reports that have studied the characteristics specific to bodyboard injuries. AIMS To clarify characteristics to bodyboard injuries. SETTINGS AND DESIGN A retrospective medical chart review. MATERIALS AND METHODS A medical chart review was retrospectively performed for all patients with spinal cord injuries transported via physician-staffed emergency helicopters between January 2009 and October 2013. The subjects were divided into two groups based on whether they had a spinal cord injury induced by bodyboarding (Bodyboard group, n = 14) or not (Control group, n = 14). STATISTICAL ANALYSIS USED Using a χ(2)-test, Mann-Whitney U-test and non-paired Student's t-test. RESULTS All but one of the subjects had spinal canal stenosis. The age of the patients in the Bodyboard group was younger than that of the Control group. The ratio of males and Glasgow Coma Scale of the Bodyboard group were higher than those on the Control group. The spinal cord injury induced by bodyboarding typically occurred after impacts of the head or face with the sea bottom while the subject was being buffeted by the waves. The severity of the spinal cord injury in the Bodyboard group was lower than that in the Control group. CONCLUSION Bodyboarding tended to induce spinal cord injuries after the head or face collided with the sea bottom, and was more common in middle-aged males during the summer season, and was associated with a favorable outcome.
Ischemia in Rats

The mechanisms of selective neuronal loss after short-term global ischemia remain undefined, but processes including increased proteolytic activity, impaired protein synthesis, and oxidative damage have been proposed to contribute. A decrease in activity of the pyruvate dehydrogenase complex in the dorsolateral striatum, an ischemia-susceptible region, is one change apparently differentiating this region from ischemia-resistant areas during early recirculation. To provide an insight into processes contributing to postischemic cell damage, the changes in thepyruvate dehydrogenase complex during early recirculation have been further characterized. These studies provide clear confirmation that the activity of the pyruvate dehydrogenase complex is reduced in mitochondria from the dorsolateral striatum by 3 h of recirculation. The decrease in activity wasnot accompanied by a loss of antigenic sites or by changes in electrophoretic mobilityof the components of the complex. A reduction in activity of the El component of the complex (39— 42% decrease), but not the E2 and E3 components, was observed that was apparently sufficient to explain the decrease in activity of the whole complex. These results indicate that the changes in activity of the pyruvate dehydrogenase complex in the dorsolateral striatum are not due to loss orgross disruption of the constituent proteins but rather most likely reflect a selective inactivation of a specific component of the complex.
The Impact of Fine-Scale Disturbances on the Predictability of Vegetation Dynamics and Carbon Flux

Predictions from forest ecosystem models are limited in part by large uncertainties in the current state of the land surface, as previous disturbances have important and lasting influences on ecosystem structure and fluxes that can be difficult to detect. Likewise, future disturbances also present a challenge to prediction as their dynamics are episodic and complex and occur across a range of spatial and temporal scales. While large extreme events such as tropical cyclones, fires, or pest outbreaks can produce dramatic consequences, small fine-scale disturbance events are typically much more common and may be as or even more important. This study focuses on the impacts of these smaller disturbance events on the predictability of vegetation dynamics and carbon flux. Using data on vegetation structure collected for the same domain at two different times, i.e. “repeat lidar data”, we test high-resolution model predictions of vegetation dynamics and carbon flux across a range of spatial scales at an important tropical forest site at La Selva Biological Station, Costa Rica. We found that predicted height change from a height-structured ecosystem model compared well to lidar measured height change at the domain scale (~150 ha), but that the model-data mismatch increased exponentially as the spatial scale of evaluation decreased below 20 ha. We demonstrate that such scale-dependent errors can be attributed to errors predicting the pattern of fine-scale forest disturbances. The results of this study illustrate the strong impact fine-scale forest disturbances have on forest dynamics, ultimately limiting the spatial resolution of accurate model predictions.
Brainstem Axonal Degeneration in Mice with Deletion of Selenoprotein P

Selenoprotein P is an abundant extracellular protein that is expressed in liver, brain, and other tissues. Studies in mice with the selenoprotein P gene deleted (Sepp −/− mice) have implicated the protein in maintaining brain selenium. Sepp −/− mice fed a normal or low selenium diet develop severe motor impairment and die, but Sepp −/− mice fed a high selenium diet remain clinically unimpaired. As an initial step to evaluate the effect of selenoprotein P deletion on central nervous system architecture, the brains and cervical spinal cords of Sepp −/− and Sepp + / + mice fed low or high selenium diets were examined by light and electron microscopy. Brains of Sepp −/− mice demonstrated no gross abnormalities. At the light microscopic level, however, Sepp −/− mice fed either the selenium deficient diet or the high selenium diet had enlarged dystrophic axons and degenerated axons in their brainstems and cervical spinal cords. No axonal lesions were observed in the Sepp + / + mice fed either diet. Electron microscopy demonstrated that the enlarged axons in the Sepp −/− mice were packed with organelles, suggesting a deficit in fast axonal transport. The similar severity of axonal lesions observed in Sepp −/− mice fed the 2 diets suggests that axonal dystrophy is a common phenotype for deletion of selenoprotein P regardless of selenium intake and that additional studies will be required to determine the pathogenesis of the neurological signs and mortality observed in Sepp −/−mice fed a low selenium diet.
Corporate cash holding during crisis and beyond: what matters the most

Purpose The purpose of this paper is to examine the cash holding of firms during a crisis and test the widely accepted determinants of corporate cash holding (CCH) for their consistency across periods of crisis, stability and recovery, and across firm categories, in the emerging market context of India. Design/methodology/approach The study employs panel data and Fama–Macbeth regression techniques on publicly listed ﬁrms during 2001–2015, amid controls for idiosyncratic factors. Further empirical analysis is carried out through the disaggregation of ﬁrms based on group affiliation, controlling stake of promoters, financial constraints and firm size. Findings The study reports that cash levels are significantly higher during crisis periods for Indian firms. Moreover, promoter holding is observed to be a strong predictor of CCH, which is an addition to the list of predictors in existing literature. Additionally, most of the predictors of cash holding turn out to be consistent through periods of financial crisis, stability and recovery. A firm’s age and growth prospects do not determine cash levels for Indian firms; however, cash-flow volatility, firm size, leverage and non-cash working capital requirements help to determine the cash levels of the firm consistently through different periods. Group-affiliated firms are less likely to engage in cash accumulation as opposed to firms that are large and financially constrained and have high promoter stakes. Originality/value The study is unique because it examines the consistency of determinants of cash holding across good and turbulent times and across firm classifications. Moreover, the study uses a broad sample of firms and investigates the topic for a relatively long period in an emerging market setup.
Microflora Trigger Colitis in Mice Deficient in Selenium-Dependent Glutathione Peroxidase and Induce Gpx2 Gene Expression

Abstract Selenium-dependent glutathione peroxidase isoenzymes-1 and -2 are the major glutathione-dependent H2O2-reducing activities in the epithelium of the mid to lower gastrointestinal tract. The two isoenzymes protect mice against ileocolitis. We have found that luminal microflora are required for colitis to develop in mice deficient in GPX-1 and GPX-2 activity (GPX-DKO). Within 7 days of association with microflora, previously asymptomatic germfree GPX-DKO mice developed severe acute colitis while their littermates with at least one wildtype Gpx1 or Gpx2 gene remained virtually symptomfree. Microflora also affected Gpx2 gene expression. Gpx2, but not Gpx1, mRNA levels were elevated 4-5 fold in the ileum and colon in conventionally reared or microflora-associated adult mice compared with germ-free mice. Since the gastrointestinal tract microflora undergo major changes 2-3 weeks after birth, from relatively benign to a potentially stressful composition, we examined postnatal Gpx2 gene expression. The jejunal and ileal GPX-2 activity levels were low in two to three weekold mice and increased 5-7 fold during the next two weeks. GPX-2 activity levels were correlated with the mRNA levels. Colon Gpx2 mRNA levels held steady at about 50% of adult levels from 12-21 days of age but were several times higher than ileal levels. Our results suggest that ileal Gpx2 mRNA and GPX-2 activity levels are induced by luminal microflora. This response is consistent with a role for GPX as an antiinflammatory activity.
Gene expression profiling of peripheral blood mononuclear cells in endometriosis identifies genes altered in non-gynaecologic chronic inflammatory diseases.

BACKGROUND Pelvic inflammatory phenomena have been suggested as critical players in the natural history of endometriosis. However, to what extent these events could affect the systemic immunologic status remains to be clarified. Here, we compared the gene expression profile in peripheral blood mononuclear cells from endometriosis patients in the severe diseased stage with the profile after a conventional surgical treatment for removal of endometriotic lesions and adhesions. METHODS Microarray analysis included four patients suffering from severe endometriosis in which blood samples were obtained few days before the surgical intervention and again 6 months later. Real-time quantitative PCR analyses on a larger population were performed for some genes up-regulated in the diseased stage in a case-control approach. RESULTS Among the 17,665 probe signals detected in the microarray, n = 26 genes resulted up-regulated and n = 15 were down-regulated in the diseased stage. Five genes up-regulated in diseased stage (FBJ Murine osteosarcoma viral oncogene homolog gene, dual specificity phosphatase 1, pre-B-cell colony enhancing factor 1, adrenomedullin and S100 calcium binding protein P) were exactly those shown as up-regulated in peripheral leukocytes of psoriasis patients in a very similar study design (diseased versus 'cured' stage), with a 5.2 × 10(-11) hypergeometric probability that this event could occur by chance. CONCLUSIONS Endometriosis induces the expression of genes in peripheral leukocytes already identified in non-gynaecologic chronic inflammatory diseases, thus revealing the disease as a local affliction with relevant consequences at the systemic level. Although the commonality of gene expression with other inflammatory diseases prevents the use of these genes as non-invasive diagnostic markers, from a clinical standpoint, the idea that the surgical intervention may reduce the expression of peripheral leukocyte genes represents a novel finding.
The relation between religiosity, selected health behaviors, and blood pressure among adult females.

BACKGROUND This study examined the association between blood pressure (BP), selected health behaviors, and various dimensions of religiosity among females. METHODS Data were obtained on 112 females who were at least 35 years of age and of Judeo-Christian faith. Resting BP measures were taken with an automated sphygmomanometer, height and weight were measured to determine body mass index (BMI), and intermediate health variables (e.g., physical activity, smoking, diet, and alcohol consumption) were measured by questionnaire. A multifactorial questionnaire was used to assess various dimensions of religiosity. Multiple regression path analyses were conducted to determine the direct and indirect effects of religiosity on BP with age and BMI controlled statistically. RESULTS The direct effects of religiosity on SBP and DBP were more substantial than the indirect effects through the intermediate health variables, suggesting that religiosity may be associated with lower levels of BP via a direct pathway, such as improving the ability to cope with stress. In general, DBP was more influenced by religiosity than SBP and the dimensions of "intrinsic religiosity" and "religious coping" were most influential. Results also indicated that "religious experiences" may exert a greater beneficial effect on DBP in older (50-80 years) age groups. CONCLUSIONS These results support a direct relationship between religiosity and BP, rather than an indirect effect through intermediate health behaviors.
Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli

The DNA sequence encoding the rbs repressor protein, RbsR, has been determined. Amino acid sequence analyses of the product of an rbsR‐lacZ fusion and of affinity‐purified RbsR demonstrate that translation begins at an unusual codon, TTG, and that the initial amino acid is removed during maturation of the protein. DNA‐binding assays indicate that RbsR binds to a region of perfect dyad symmetry spanning the rbs operon transcriptional start site and that the affinity for the rbs operator is reduced by addition of ribose, consistent with ribose being the inducer of the operon. RbsR is a member of a family of homologous repressor proteins having very similar DNA‐binding sites and binding to similar operator sequences. [RbsR PIR accession number A41828. ]