Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Susceptibility to Methyl Donor Deficiency: From Fetal Programming to Aging Outcome in Rats

Deficiencies in methyl donors, folate, and vitamin B12 are known to lead to brain function defects. Fetal development is the most studied but data are also available for such an impact in elderly rats. To compare the functional consequences of nutritional deficiency in young versus adult rats, we monitored behavioral outcomes of cerebellum and hippocampus circuits in the offspring of deficient mother rats and in adult rats fed a deficient diet from 2 to 8 months-of-age. We present data showing that the main deleterious consequences are found in young ages compared to adult ones, in terms of movement coordination and learning abilities. Moreover, we obtained sex and age differences in the deleterious effects on these functions and on neuronal layer integrity in growing young rats, while deficient adults presented only slight functional alterations without tissue damage. Actually, the cerebellum and the hippocampus develop and maturate according to different time lap windows and we demonstrate that a switch to a normal diet can only rescue circuits that present a long permissive window of time, such as the cerebellum, whereas the hippocampus does not. Thus, we argue, as others have, for supplements or fortifications given over a longer time than the developmental period.
Article Asparagine synthesis during tobacco leaf curingLucien Bovet*†

Senescence is a genetically controlled mechanism that modifies leaf chemistry. This involves significant changes in the accumulation of carbonand nitrogen-containing compounds, including asparagine through the activity of asparagine synthetases. These enzymes are required for nitrogen re-assimilation and remobilization in plants; however, their mechanisms are not fully understood. Here, we report how leaf curing—a senescence-induced process that allows tobacco leaves to dry out—modifies the asparagine metabolism. We show that leaf curing strongly alters the concentration of the four main amino acids, asparagine, glutamine, aspartate, and glutamate. We demonstrate that detached tobacco leaf or stalk curing has a different impact on the expression of asparagine synthetase genes and accumulation of asparagine. Additionally, we characterize the main asparagine synthetases involved in the production of asparagine during curing. The expression of ASN1 and ASN5 genes is upregulated during curing. The ASN1-RNAi and ASN5RNAi tobacco plant lines display significant alterations in the accumulation of asparagine, glutamine, and aspartate relative to wild-type plants. These results support the idea that ASN1 and ASN5 are key regulators of asparagine metabolism during leaf curing.
Tegretol (Carbamazepine): A Controlled Trial of a New Anti-Convulsant

Tegretol (carbamazepine; 5-carbamyl-5H-dibenz (b, f) azepine) has been under investigation since 1958 in the treatment of epilepsy on the continent of Europe, following the demonstration of its anticonvulsant properties in animals by Theobald and Kunz (1963). Clinical reports have been enthusiastic (Lorgé, 1963, Bonduelle et al., 1963). The present investigation was undertaken with a view to a more critical appraisal of this drug, avoiding the dangers of sudden alteration of anticonvulsant therapy in epileptic patients, documented by Schwab et al. (1959), while still maintaining the double-blind nature of the trial.
Unraveling the Teleconnection Mechanisms that Induce Wintertime Temperature Anomalies over the Northern Hemisphere Continents in Response to the MJO

Significant extratropical surface air temperature variations arise as a result of teleconnections induced by the Madden–Julian oscillation (MJO). The authors elucidate the detailed physical processes responsible for the development of temperature anomalies over Northern Hemisphere continents in response to MJOinduced heating using an intraseasonal perturbation thermodynamic equation and a wave activity tracing technique. A quantitative assessment demonstrates that surface air temperature variations are due to dynamical processes associated with a meridionally propagating Rossby wave train. Over East Asia, a local Hadley circulation causes adiabatic subsidence following MJO phase 3 to be a main driver for the warming. Meanwhile, for North America and eastern Europe, horizontal temperature advection by northerlies or southerlies is the key process for warming or cooling. A ray-tracing analysis illustrates that Rossby waves with zonal wavenumbers 2 and 3 influence the surface warming over North America and a faster wavenumber 4 affects surface temperature over eastern Europe. Although recent studies demonstrate the impacts of the Arctic Oscillation, Arctic sea ice melting, and Eurasian snow cover variations on extremely cold wintertime episodes over the NH extratropics, the weather and climate there are still considerably modulated through teleconnections induced by the tropical heat forcing. In addition, the authors show that the MJO is a real source of predictability for strong warm/cold events over these continents, suggesting a higher possibility of making a skillful forecast of temperature extremes with over 1 month of lead time.
Automated Wrist Pulse diagnosis of Pancreatitis via Autoregressive Discriminant models

Wrist pulse signals, commonly used in traditional oriental medicine, reflects important pathological changes in the body which may be utilized to characterize an individual’s health status. Being one of the ‘four pillars of clinical evaluation’, pulse diagnosis plays a critical role in traditional Chinese medicine (TCM), informing the physician about crucial information such as the state of balance of the body and the state of internal organs. The traditional method of examination is via palpation in which the practitioner uses fingertips to feel the radial pulse of the patient. It is thus highly subjective and depends heavily on the practitioner’s experience. With the aid of technology, modern measurements of pulse signal can be taken in a more objective manner. However, there is a lack of tools and standards for analysing and interpreting these computerized pulse signals. In particular, diagnosis of inflammation is challenging and current clinical approaches via other methods (such as blood test, urine test, and X-ray) are time-consuming and often inaccurate. This paper proposes an automated procedure for distinguishing patients with inflammation using their digitized wrist pulse signals, based on a two-stage time-series classification technique involving autoregressive models followed by common classification methods such as Linear Discriminant Analysis (AR-LDA) and Logistic regression (AR-LR). We focus on one of the major inflammation symptoms – pancreatitis, a condition that can potentially lead to fatal complications in severe cases. We work with wrist pulse signals captured from patients using a Doppler ultrasonic blood analyser. After pre-processing, features derived from fitted AR models were fed to train a LDA and a LR classifier. The effectiveness of our approach is demonstrated using a subset of the wrist pulse database from Chen et al. (2009), consisting of 100 healthy persons and 54 Pancreatitis patients. To evaluate the classification performance, the models are trained on 50% of the data while the remaining observations were reserved for testing. An overall accuracy of 83% and 91% was achieved from AR-LR and AR-LDA respectively, both with an area under curve of 0.88. AR-LDA achieved a higher sensitivity (81%) and specificity (96%) with a positive predictive value of 92%. These results showed that AR-LDA is a promising approach for classifying time-series wrist pulse signals. It provides a relatively low-cost, easy-to-implement, and reliable tool for modern computerized wrist pulse diagnosis.
MULTI SIZE EYE DETECTION ON DIGITIZED COMIC IMAGE

Metadata extraction on Comic: Manga, Japanese Style Comic is a key technology for comic distribution systems and user centric comic viewers. One of the most important metadata for that is a comic character’s face position. However character’s face are often deformed and occluded fatally. Thus, to become efficient face detection, eye position detection is focused on. Generally, Comic image is drawn by monochrome, and eye size has many variations. In this paper, we utilized reformed HOG feature to treat Manga image and to be able to handle size variation. HOG feature on digitized comic image is affected by image resolution condition. In our approach, the resolution of calculating HOG feature is fixed, and block size is determined according to input image. Thus, even if input image has resolution variation, HOG feature space is stable. Finally, the resolution fixed approach is compared to image resolution converting approach by experiment.
Phenotypic Plasticity in the Structure of Fine Adventitious Metasequoia glyptostroboides Roots Allows Adaptation to Aquatic and Terrestrial Environments

Metasequoia glyptostroboides (Cupressaceae) is a rare deciduous conifer which grows successfully in both aquatic and terrestrial environments. This tree has a narrow natural distribution in central China but is cultivated worldwide. Using histochemical staining and microscopy (both brightfield and epifluorescent), we investigated whether the phenotypic anatomical and histochemical plasticity in the fine adventitious roots of M. glyptostroboides has promoted the adaptation of this plant to aquatic and terrestrial environments. The fine root development and cortex sloughing of M. glyptostroboides occurs later in aquatic habitats than in terrestrial habitats. Anatomical and histochemical analyses have revealed that the apoplastic barriers in the primary growth of the fine roots consist of the endodermis and exodermis with Casparian bands, suberin lamellae, and secondarily lignified cell walls. There were also lignified phi (Φ) thickenings in the cortex. In both aquatic and terrestrial roots, secondary growth was observed in the vascular cambium, which produced secondary xylem and phloem, as well as in the phellogen, which produced cork. As compared to terrestrial adventitious roots, aquatic adventitious roots had multiple lignified Φ thickenings throughout the cortex, larger air spaces, dilated parenchyma, and dense suberin and lignin depositions in the exodermis. Our results thus indicate that phenotypic plasticity in the anatomical features of the fine adventitious roots, including apoplastic barriers, air spaces, and lignified Φ thickenings, might support the adaptation of M. glyptostroboides to both aquatic and terrestrial environments.
Cohomology and Subcohomology for expansive geodesic flows

We show that there are examples of expansive, non-Anosov geodesic flows of compact surfaces with non-positive curvature, where the Livsic Theorem holds in its classical (continuous, Hölder) version. We also show that such flows have continuous subaction functions associated to Hölder continuous observables. Instituto de Matemática, UFRGS, Porto Alegre, Brasil Departamento de Matemática, U. N. de San Agust́ın de Arequipa Peru. Departamento de Matemática PUC Rio de Janeiro Brasil
Qualitative and Quantitative Differences in Osmolytes Accumulation and Antioxidant Activities in Response to Water Deficit in Four Mediterranean Limonium Species

Limonium is a genus represented in the Iberian Peninsula by numerous halophytic species that are affected in nature by salinity, and often by prolonged drought episodes. Responses to water deficit have been studied in four Mediterranean Limonium species, previously investigated regarding salt tolerance mechanisms. The levels of biochemical markers, associated with specific responses—photosynthetic pigments, mono- and divalent ions, osmolytes, antioxidant compounds and enzymes—were determined in the control and water-stressed plants, and correlated with their relative degree of stress-induced growth inhibition. All the tested Limonium taxa are relatively resistant to drought on the basis of both the constitutive presence of high leaf ion levels that contribute to osmotic adjustment, and the stress-induced accumulation of osmolytes and increased activity of antioxidant enzymes, albeit with different qualitative and quantitative induction patterns. Limonium santapolense activated the strongest responses and clearly differed from Limonium virgatum, Limonium girardianum, and Limonium narbonense, as indicated by cluster and principal component analysis (PCA) analyses in agreement with its drier natural habitat, and compared to that of the other plants. Somewhat surprisingly, however, L. santapolense was the species most affected by water deficit in growth inhibition terms, which suggests the existence of additional mechanisms of defense operating in the field that cannot be mimicked in greenhouses.
BIOfid Dataset: Publishing a German Gold Standard for Named Entity Recognition in Historical Biodiversity Literature

The Specialized Information Service Biodiversity Research (BIOfid) has been launched to mobilize valuable biological data from printed literature hidden in German libraries for over the past 250 years. In this project, we annotate German texts converted by OCR from historical scientific literature on the biodiversity of plants, birds, moths and butterflies. Our work enables the automatic extraction of biological information previously buried in the mass of papers and volumes. For this purpose, we generated training data for the tasks of Named Entity Recognition (NER) and Taxa Recognition (TR) in biological documents. We use this data to train a number of leading machine learning tools and create a gold standard for TR in biodiversity literature. More specifically, we perform a practical analysis of our newly generated BIOfid dataset through various downstream-task evaluations and establish a new state of the art for TR with 80.23% F-score. In this sense, our paper lays the foundations for future work in the field of information extraction in biology texts.
Compiler support for the Fortran 2003 standard

This is a standing article in Fortran Forum. The first version appeared in Fortran Forum Volume 26, Number 1, April 2007. The basis for the entries in the list of features was a report by John Reid The original report can be found at: ftp://ftp.nag. co.uk/sc22wg5/N1551-N1600/N1579.pdf An updated version of this report was included in Fortran Forum. An electronic version can be found at: ftp://ftp.nag. co.uk/sc22wg5/N1601-N1650/N1648.pdf If you are a compiler vendor and would like to be included in future versions of this table please email one of us with details and they will be added to the table and published in Fortran Forum.
Machine translation for information access across the language barrier: the MuST system

In this paper we describe the design and implementation of MuST, a multilingual information retrieval, summarization, and translation system. MuST integrates machine translation and other text processing services to enable users to perform cross-language information retrieval using available search services such as commercial Internet search engines. To handle non-standard languages, a new Internet indexing agent can be deployed, specialized local search services can be built, and shallow MT can be added to provide useful functionality. A case study of augmenting MuST with Indonesian is included. MuST adopts ubiquitous web browsers as its primary user interface, and provides tightly integrated automated shallow translation and user biased summarization to help users quickly judge the relevance of documents.
Design and Synthesis of Ag Nanocluster Molecular Beacon for Adenosine Triphosphate Detection

This study presents a fluorescence method for detecting adenosine triphosphate (ATP) based on a label-free Ag nanocluster molecular beacon (MB) with high sensitivity. The sensor contains a hairpin-shaped MB, two short single-stranded DNA strands, and T4 DNA ligase. The MB consists of three parts, which are the template DNA sequence for synthesizing Ag nanoclusters at the 5′ end, the middle DNA with a hairpin-shaped structure, and the guanine base-rich DNA sequence at the 3′ end. The sensor exhibits high fluorescence intensity in the absence of ATP. However, when the probe is used for ATP detection, the two short DNA sequences in the sensor would form a long sequence by enzymatic ligation reaction; this long sequence opens the hairpin-shaped structure of the MB and decreases the fluorescence of the system. Under optimal analytical conditions, a clear linear relationship is observed between ATP concentration and fluorescence intensity in the range of 0.1–10 μM. The interference presented by other small molecules during ATP detection is evaluated, and results confirm the good selectivity of the proposed sensor. Compared with traditional methods, the sensor is label free, easy to operate, inexpensive, and highly sensitive.
Indigo Naturalis Suppresses Colonic Oxidative Stress and Th1/Th17 Responses of DSS-Induced Colitis in Mice

Indigo naturalis (also known as Qing-dai, or QD), a traditional Chinese medicine, has been widely used as an anticolitis regimen in the clinical practice of Chinese medicine. However, the precise mechanisms behind its efficacy remain unknown. We investigated the protective effects and associated molecular mechanisms of QD in DSS-induced colitis in mice. We found that QD administration attenuated DSS-induced colon shortening, tissue damage, and the disease activity index during the onset of colitis. Moreover, QD administration significantly suppressed colonic MPO activity and increased the activities of colonic T-SOD, CAT, and GSH-Px, as well the expression of p-AMPK and Nrf-2 in colon tissues of colitic mice. In addition, QD was capable of reducing the colonic Th1 and Th17 cell cytokines, the frequencies of Th1 and Th17 cells, and the phosphorylation of p-STAT1 and p-STAT3 in the mesenteric lymph nodes of colitic mice. An in vitro assay showed that QD significantly suppressed the differentiation of Th1 and Th17 cells. These findings suggest that QD has the potential to alleviate experimental colitis by suppressing colonic oxidative stress and restraining colonic Th1/Th17 responses, which are associated with activating AMPK/Nrf-2 signals and inhibiting STAT1/STAT3 signals, respectively. These findings also support QD as an effective regimen in the treatment of IBD.
Community Paramedicine: Higher Education as An Enabling Factor

The aim of this case study was to describe one rural community paramedic model and identify enablers related to the implementation of the model. It was undertaken in the County of Renfrew, Ontario, Canada where a community paramedicine role has emerged in response to demographic changes and broader health system reform. Qualitative data was collected through direct observation of practice, informal discussions, interviews and focus groups. The crucial role of education in the effective and sustainable implementation of the community paramedicine model was identified as one of four enablers. Traditional paramedicine education programs are narrowly focused on emergency response, with limited education in health promotion, aged care and chronic disease management. Educational programs hoping to include a wider range of topics face the twin challenges of an already crowded curriculum and predominately young students who fail to see the relevance of community primary care content. A closer match between the paramedicine curriculum and the emerging roles of paramedics, whether they are community paramedics, extended care paramedics, or as yet unformed roles is needed if paramedics are to become valued members of the health care team.
Structural insights into a HECT-type E3 ligase AREL1 and its ubiquitination activities in vitro

The HECT E3 ligase family comprises three subfamilies: NEDD4 E3 ubiquitin protein ligase (NEDD4), HECT and RLD domain–containing E3 ubiquitin protein ligase (HERC), and “other. ” Most previous studies have focused on the NEDD4 subfamily. Apoptosis-resistant E3 ligase 1 (AREL1) belongs to “other” subfamily HECT that inhibits apoptosis by ubiquitinating and degrading proapoptotic proteins. Here, we report the crystal structure of the extended HECT domain of AREL1 (amino acids (aa) 436–823) at 2.4 Å resolution and its ubiquitination of the proapoptotic protein second mitochondria-derived activator of caspase (SMAC). We found that the extended HECT domain adopts an inverted, T-shaped, bilobed conformation and harbors an additional loop (aa 567–573) absent in all other HECT members. We also show that the N-terminal extended region (aa 436–482) preceding the HECT domain is indispensable for its stability and activity and that without this region, the HECT domain becomes inactive. AREL1 ubiquitinated SMAC, primarily on Lys62 and Lys191. We solved the crystal structure of the tetrameric form of SMAC to 2.8 Å resolution, revealing the Lys62 and Lys191 locations. The AREL1 HECT domain assembled Lys33-, Lys48-, and Lys63-linked polyubiquitin chains. Moreover, E701A substitution in the AREL1 HECT domain substantially increased its autopolyubiquitination and SMAC ubiquitination activity, whereas deletion of the last three amino acids at the C terminus completely abrogated AREL1 autoubiquitination and reduced SMAC ubiquitination. Finally, an AREL1-specific ubiquitin variant inhibited SMAC ubiquitination in vitro. Our findings may assist in the development of AREL1 inhibitors that block its anti-apoptotic activity in cancer.
Label-free visualization and characterization of extracellular vesicles in breast cancer

Significance Direct in vivo identification and characterization of extracellular vesicles (EVs) in the authentic tumor microenvironment is essential for understanding cancer progression and developing new clinical biomarkers. Here, we introduce an optical-signature-based approach for visualizing, characterizing, and tracking EVs in unperturbed living systems by profiling their intrinsic metabolic and structural contrasts. Imaging of living tumor-bearing animals and fresh excised human breast tissue revealed abundance of NAD(P)H-rich EVs within the tumor, near the tumor boundary, and around vessel structures. In addition, the percentage of NAD(P)H-rich EVs is highly correlated with the human breast cancer diagnosis, which emphasizes the important role of metabolic imaging for EV characterization as well as for clinical applications. Despite extensive interest, extracellular vesicle (EV) research remains technically challenging. One of the unexplored gaps in EV research has been the inability to characterize the spatially and functionally heterogeneous populations of EVs based on their metabolic profile. In this paper, we utilize the intrinsic optical metabolic and structural contrast of EVs and demonstrate in vivo/in situ characterization of EVs in a variety of unprocessed (pre)clinical samples. With a pixel-level segmentation mask provided by the deep neural network, individual EVs can be analyzed in terms of their optical signature in the context of their spatial distribution. Quantitative analysis of living tumor-bearing animals and fresh excised human breast tissue revealed abundance of NAD(P)H-rich EVs within the tumor, near the tumor boundary, and around vessel structures. Furthermore, the percentage of NAD(P)H-rich EVs is highly correlated with human breast cancer diagnosis, which emphasizes the important role of metabolic imaging for EV characterization as well as its potential for clinical applications. In addition to the characterization of EV properties, we also demonstrate label-free monitoring of EV dynamics (uptake, release, and movement) in live cells and animals. The in situ metabolic profiling capacity of the proposed method together with the finding of increasing NAD(P)H-rich EV subpopulations in breast cancer have the potential for empowering applications in basic science and enhancing our understanding of the active metabolic roles that EVs play in cancer progression.