Miracle-dz/UniFAR-FTUs huggingface dataset:
Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

ABSTRACT Lineage segregation in the mouse embryo is a finely controlled process dependent upon coordination of signalling pathways and transcriptional responses. Here we employ a conditional deletion system to investigate embryonic patterning and lineage specification in response to loss of Oct4. We first observe ectopic expression of Nanog in Oct4-negative postimplantation epiblast cells. The expression domains of lineage markers are subsequently disrupted. Definitive endoderm expands at the expense of mesoderm; the anterior-posterior axis is positioned more distally and an ectopic posterior-like domain appears anteriorly, suggesting a role for Oct4 in maintaining the embryonic axis. Although primitive streak forms in the presumptive proximal-posterior region, epithelial-to-mesenchymal transition is impeded by an increase of E-cadherin, leading to complete tissue disorganisation and failure to generate germ layers. In explant and in vitro differentiation assays, Oct4 mutants also show upregulation of E-cadherin and Foxa2, suggesting a cell-autonomous phenotype. We confirm requirement for Oct4 in self-renewal of postimplantation epiblast ex vivo. Our results indicate a role for Oct4 in orchestrating multiple fates and enabling expansion, correct patterning and lineage choice in the postimplantation epiblast. Highlighted Article: Ectopic expression of Nanog, expansion of the presumptive endodermal domain and trapping of cells in the primitive streak ultimately result in consistent disrupted phenotype with loss of embryonic structures.
Methane in groundwater before, during, and after hydraulic fracturing of the Marcellus Shale

Significance This study incorporates time series sampling of groundwater before, during, and after drilling, hydraulic fracturing, and initiation of shale gas production. Using monitoring wells installed next to gas well pads and above gas well laterals, previously undocumented responses to drilling and a gas well casing breach were observed, although groundwater impacts arising from the process of hydraulic fracturing were not detected. We discover considerable temporal variability in methane concentrations in deeper horizons of freshwater aquifers and attribute this to persistent shifts in aquifer recharge that influence mixing between shallow freshwater and comparatively saline and methane-rich deep groundwater. These results have implications for attribution of groundwater contamination to specific stages of shale gas development or natural processes and improving regulatory monitoring. Concern persists over the potential for unconventional oil and gas development to contaminate groundwater with methane and other chemicals. These concerns motivated our 2-year prospective study of groundwater quality within the Marcellus Shale. We installed eight multilevel monitoring wells within bedrock aquifers of a 25-km2 area targeted for shale gas development (SGD). Twenty-four isolated intervals within these wells were sampled monthly over 2 years and groundwater pressures were recorded before, during, and after seven shale gas wells were drilled, hydraulically fractured, and placed into production. Perturbations in groundwater pressures were detected at hilltop monitoring wells during drilling of nearby gas wells and during a gas well casing breach. In both instances, pressure changes were ephemeral (<24 hours) and no lasting impact on groundwater quality was observed. Overall, methane concentrations ([CH4]) ranged from detection limit to 70 mg/L, increased with aquifer depth, and, at several sites, exhibited considerable temporal variability. Methane concentrations in valley monitoring wells located above gas well laterals increased in conjunction with SGD, but CH4 isotopic composition and hydrocarbon composition (CH4/C2H6) are inconsistent with Marcellus origins for this gas. Further, salinity increased concurrently with [CH4], which rules out contamination by gas phase migration of fugitive methane from structurally compromised gas wells. Collectively, our observations suggest that SGD was an unlikely source of methane in our valley wells, and that naturally occurring methane in valley settings, where regional flow systems interact with local flow systems, is more variable in concentration and composition both temporally and spatially than previously understood.
CMU-AML Submission to Moments in Time Challenge 2018

In this report, we describe our solution for Moments in Time Challenge 2018. We employed both visual and audio features in the submission. For visual features, we utilize the preprocessed RGB and optical flow data for training or fine-tuning 2D (e.g. Temporal Segment Network (TSN) and 3D (e.g. Inflated 3D ConvNets (I3D). For audio features, we use raw waveforms as the input modality and fine-tune the feature extracted from the last pooling layer of SoundNet. We achieve 31.56% in terms of Top-1 accuracy and 59.75% in terms of Top-5 accuracy on the validation set.
A qualitative study on primary health care responses to intimate partner violence during the economic crisis in Spain

Background The objective of this study was to explore how health professionals perceived the effect of the economic crisis and associated austerity measures on the detection of and cares for intimate partner violence (IPV) in primary care in Spain. Methods Qualitative study designed using semi-structured interviews carried out with 145 health professionals in 16 primary health care centres in different regions of Spain. An inductive thematic analysis was made of the transcriptions. Results Three main themes were identified: 'Women endure more violence during times of economic crisis', 'Fewer resources, fewer professionals and less time to respond to IPV' and 'Professionals' motivation as a requirement to respond to IPV'. Professionals perceived that economic precariousness triggered violence against women and made women more hesitant to put an end to violent relationships. They also reported that the austerity measures applied to primary health care negatively affected their ability to detect and adequately care for cases of IPV due to a heavy workload, reduced human resources, difficulties in training and the loss of resources to which women could be referred. To counteract these obstacles, health professionals' motivation played a vital role in the response to IPV. Conclusions Institutional efforts to organize awareness programmes and training in order to improve and promote early diagnosis, care and rehabilitation of these women cannot stop during times of crisis and primary health care centres should facilitate health professionals' access to these programmes.
Diphtheria Outbreak in Amerindian Communities, Wonken, Venezuela, 2016–2017

In February 2017, a diphtheria outbreak occurred among Amerindians of the Pemón ethnic group in Wonken, Venezuela. A field investigation revealed ≈10 cases; clinical presentation did not include cutaneous or neurologic signs or symptoms. To prevent future outbreaks in Venezuela, Amerindian communities need better access to vaccination and healthcare.
Conditions and strategies high school students living in lodgings experience as important and helpful for their well-being

ABSTRACT Many 15- to 16-year-old adolescents in Scandinavian countries have to move away from home to live in lodgings during senior high school. This transition might affect the adolescents’ well-being and mental health, with the risk of dropping out of school and/or potential mental health problems. This study aims to explore what adolescents experience to be of importance and helpful for their well-being through their lives in lodgings during senior high school. Qualitative, in-depth interviews were performed among 21 adolescents from the ages of 16 to 18 of both genders living in lodgings in a Norwegian county. Eleven interviews were performed in 2008 and 10 interviews performed in 2016. Interviews were analysed using qualitative content analysis. Two main categories and six subcategories were identified as important for well-being: (1) Conditions for well-being, me and my surroundings: (a) practical support; (b) relational support; (c) convenient housing; and (d) supportive class environment. (2) Strategies for well-being, me and myself: (a) practical strategies, and (b) strategies facing challenges. Adolescents living in lodgings experience several conditions in their surroundings to be of importance for their well-being, based on which they develop their own strategies to feel well. Implications towards promoting and strengthen their well-being are discussed.
Associations of object control motor skill proficiency, game play competence, physical activity and cardiorespiratory fitness among primary school children

ABSTRACT This study investigated if object control relates to children’s game play competence, and examined these competencies as correlates of physical activity and cardiorespiratory fitness. Game play (Game Performance Assessment Instrument), object control (The Test Gross Motor Development-3), moderate-to-vigorous physical activity (Accelerometry), and cardiorespiratory fitness (20-metre shuttle) assessments were completed for 107 children (57% Female, 43% Male) aged 9–12 years (M 10.53, SD 0.65). Two-level regression of object control on game play competence, and object control and game play competence on physical activity and cardiorespiratory fitness assessed associations. Object control competence was positively associated with game play competence (Std. B = 0.25, t (104.77) = 2.38, p = 0.001). Game play competence (Std. B = 0.33, t (99.81) = 5.21, p < 0.000) was more strongly associated with moderate-to-vigorous physical activity than object control competence (Std. B = 0.20, t (106.93) = 2.96, p = 0.003). Likewise, game competence (Std. B = 0.39, t (104.41) = 4.36, p < 0.000) was more strongly associated with cardiorespiratory fitness than object control competence (Std. B = 0.22, t (106.69) = 2.63, p = 0.002). Object control and game competence are both important as correlates of physical activity and cardiorespiratory fitness in children.
Joint bottleneck feature and attention model for speech recognition

Recently, attention based sequence-to-sequence model become a research hotspot in speech recognition. The attention model has the problem of slow convergence and poor robustness. In this paper, a model that jointed a bottleneck feature extraction network and attention model is proposed. The model is composed of a Deep Belief Network as bottleneck feature extraction network and an attention-based encoder-decoder model. DBN can store the priori information from Hidden Markov Model so that increasing convergence speed of and enhancing both robustness and discrimination of features. Attention model utilizes the temporal information of feature sequence to calculate the posterior probability of phoneme. Then the number of stack recurrent neural network layers in attention model is reduced in order to decrease the calculation of gradient. Experiments in the TIMIT corpus showed that the phoneme error rate is 17.80% in test set, the average training iteration decreased 52%, and the number of training iterations decreased from 139 to 89. The word error rate of WSJ eval92 is 12.9% without any external language model.
Uncertainty Shocks, Financial Frictions and Business Cycle Asymmetries Across Countries

This paper explores the interaction of uncertainty shocks and financial frictions in explaining the excess volatility of real variables in emerging countries vis-à-vis advanced countries. I use an open economy DSGE model augmented with the financial accelerator mechanism, nominal rigidities and uncertainty evolving as the time-varying volatility of exogenous shocks. The model is solved using perturbation techniques about a third order approximation to the equilibrium conditions of the model. An uncertainty shock in the model triggers a precautionary response among agents and generates the simultaneous decline in GDP, investment and consumption in this open economy environment. Financial frictions interact with uncertainty to generate the amplified responses in emerging countries along with producing a strong countercyclical response in trade balances. Using this feature of the model I estimate key behavioral parameters that guide differences in business cycle characteristics across advanced and emerging countries using a sample of 8 countries (U.S., U.K., Canada, France, Mexico, Chile, Argentina and South Korea). The results from estimation suggest that borrowing costs for non-financial debt in emerging countries are 270-288 basis points higher compared to advanced countries. While heightened uncertainty is common for both groups of countries in recessions, differences in financial development captured through financial frictions is key towards generating the amplified responses in emerging countries. JEL Classification Codes: C32, E32, F41, E37, F44, G15
Research on Urban Greenway Planning based on Big Data of Bus Smart Card

Location Based Service data has provided a new perspective for urban space research which has been applied in urban planning and geography and seldom in landscape planning and design. The authors study the way of greenway planning based on secondary data of bus smart card data in Beijing,combined with the current land use. The authors make connections between bus smart card data and travel distribution law in Beijing,determine the connected area of greenway in different urban functional areas and establish a evaluation index system for selection of connection carriers based on the landscape,cultural and ecological features of green space. And then greenway network is planned by service function optimization. The authors expand the function of greenway connecting different urban functional areas and promote the formation of urban compact layout.
The Relationship between Disordered Eating Pathology, Sense of Coherence and Body Image among Adolescent Boys in Israel.

BACKGROUND Disordered eating pathology (DEP) and body dissatisfaction are well-documented risk factors for eating disorders and have become more prevalent among adolescent males. METHOD The sample consisted of 256 Israeli boys, in grades 8-12. Participants completed questionnaires measuring, Sense of Coherence (SOC), Body Shape (BSQ), Eating attitudes (EAT-26), and the Eating Disorder Inventory (EDI-2). RESULTS Findings revealed low levels of DEP among adolescent boys. Younger adolescents (grade 8-9) had higher levels of clinically relevant DEP than older adolescents (grade 10-12). SOC was negatively associated with DEP and a significant interaction for age and SOC emerged with younger age being associated with both lower levels of SOC and higher DEP. CONCLUSION These results demonstrate a low overall prevalence rate of DEP among adolescent boys and is consistent with the developmental literature relating to SOC and mental health and in contrast with a similar population of girls documented in Israel and the US.
Trehalose reduces retinal degeneration, neuroinflammation and storage burden caused by a lysosomal hydrolase deficiency

ABSTRACT The accumulation of undegraded molecular material leads to progressive neurodegeneration in a number of lysosomal storage disorders (LSDs) that are caused by functional deficiencies of lysosomal hydrolases. To determine whether inducing macroautophagy/autophagy via small-molecule therapy would be effective for neuropathic LSDs due to enzyme deficiency, we treated a mouse model of mucopolysaccharidosis IIIB (MPS IIIB), a storage disorder caused by deficiency of the enzyme NAGLU (alpha-N-acetylglucosaminidase [Sanfilippo disease IIIB]), with the autophagy-inducing compound trehalose. Treated naglu–/ – mice lived longer, displayed less hyperactivity and anxiety, retained their vision (and retinal photoreceptors), and showed reduced inflammation in the brain and retina. Treated mice also showed improved clearance of autophagic vacuoles in neuronal and glial cells, accompanied by activation of the TFEB transcriptional network that controls lysosomal biogenesis and autophagic flux. Therefore, small-molecule-induced autophagy enhancement can improve the neurological symptoms associated with a lysosomal enzyme deficiency and could provide a viable therapeutic approach to neuropathic LSDs. Abbreviations: ANOVA: analysis of variance; Atg7: autophagy related 7; AV: autophagic vacuoles; CD68: cd68 antigen; ERG: electroretinogram; ERT: enzyme replacement therapy; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFAP: glial fibrillary acidic protein; GNAT2: guanine nucleotide binding protein, alpha transducing 2; HSCT: hematopoietic stem cell transplantation; INL: inner nuclear layer; LC3: microtubule-associated protein 1 light chain 3 alpha; MPS: mucopolysaccharidoses; NAGLU: alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB); ONL: outer nuclear layer; PBS: phosphate-buffered saline; PRKCA/PKCα: protein kinase C, alpha; S1BF: somatosensory cortex; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; VMP/VPL: ventral posterior nuclei of the thalamus
Exchange Market Pressure in Central European Countries from the Eurozone Membership Perspective

Exchange Market Pressure in Central European Countries from the Eurozone Membership Perspective This paper estimates the exchange market pressure (EMP) in four Central European countries (Czech Republic, Hungary, Poland, Slovakia) over the period 1993-2006. Therefore, it is one of very few studies focused on this region and the very first paper applying concurrently model-dependent as well as model-independent approaches to EMP estimation to these countries. The results obtained suggest that the approaches lead to inconsistent findings. They often differ in identification of the principal development trends, as well as the magnitude and direction of the pressure. The paper provides evidence that a shift in the exchange rate regime towards the quasi-fixed ERM II should not stimulate EMP growth. However, it is highly probable that some episodes of the excessive EMP will make the fulfillment of the exchange rate stability criterion more difficult in all of the countries analyzed.
Nutritional status is associated with the degree of cognitive impairment and depressive symptoms in a Greek elderly population

Introduction: Cognitive impairment and malnutrition are two important public health issues in the elderly, which have been associated with their mental health. Aims: This study aims to evaluate the nutritional status of an elderly population in Greece, and its association with the grade of cognitive decline, anthropometric measures and psychological status. Materials and Methods: A total of 2092 elderly men and women were enrolled from seven Greek cities. Mini Nutritional Assessment (MNA), Mini Mental State Examination (MMSE) and Geriatric Depression Scale (GDS) questionnaires were used to assess the impact of nutritional status on cognitive abilities and psychological status of the participants. Results: Of the elderly, 35.0% were at risk of malnutrition and 11.3% were malnourished, while 34.4% of the participants had impaired cognitive function, and 32.3% showed depressive symptoms. Malnutrition was more frequently observed in participants presenting cognitive impairment, and depressive symptoms. In multiple regression analysis, nutritional status was independently associated with cognitive and psychological status. Conclusions: A high prevalence of malnutrition was recorded in this elderly population sample, which was directly associated with cognitive impairment and depression. Diagnostic tools such as MNA, MMSE, and GDS are strongly recommended to be applied as a routine clinical practice in the elderly to timely and effectively address these health problems.
Sulfur and Calcium Simultaneously Regulate Photosynthetic Performance and Nitrogen Metabolism Status in As-Challenged Brassica juncea L. Seedlings

In the present study, the role of sulfur (K2SO4: S; 60 mg S kg-1 sand) and/or calcium (CaCl2: Ca; 250 mg Ca kg-1 sand) applied alone as well as in combination on growth, photosynthetic performance, indices of chlorophyll a fluorescence, nitrogen metabolism, and protein and carbohydrate contents of Indian mustard (Brassica juncea L.) seedlings in the absence and presence of arsenic (Na2HAsO4.7H2O: As1; 15 mg As kg-1 sand and As2; 30 mg As kg-1 sand) stress was analyzed. Arsenic with its rising concentration negatively affected the fresh weight, root/shoot ratio, leaf area, photosynthetic pigments content, photosynthetic oxygen yield, and chlorophyll a fluorescence parameters: the O–J, J–I and I–P rise, QA- kinetic parameters, i.e., ΦP0, Ψ0, ΦE0, and PIABS, along with Fv/F0 and Area while increased the energy flux parameters, i.e., ABS/RC, TR0/RC, ET0/RC, and DI0/RC along with F0/Fv and Sm due to higher As/S and As/Ca ratio in test seedlings; however, exogenous application of S and Ca and their combined effect notably counteracted on As induced toxicity on growth and other important growth regulating processes. Moreover, inorganic nitrogen contents, i.e., nitrate (NO3-) and nitrite (NO2-) and the activities of nitrate assimilating enzymes, viz., nitrate reductase (NR) and nitrite reductase (NiR) and ammonia assimilating enzymes, viz., glutamine synthetase (GS) and glutamate synthase (GOGAT) along with protein and carbohydrate contents were severely affected with As toxicity; while under similar condition, ammonium (NH4+) content and glutamate dehydrogenase (GDH) activity in both root and leaves showed reverse trend. Furthermore, S and Ca supplementation alone and also in combination to As stressed seedlings ameliorated these parameters except NH4+ content and GDH activity, which showed an obvious reduction under similar conditions. These findings point out that exogenous application of S and/or Ca particularly S+Ca more favorably regulated the photosynthesis, contents of protein, carbohydrate and inorganic nitrogen, and the activities of nitrate and ammonia assimilating enzymes, which might be linked with the mitigation of As stress. Our results suggest that exogenous application of S+Ca more efficiently defends Brassica seedlings by declining As accumulation in root and shoot tissues and by maintaining the photosynthesis and nitrogen metabolism as well.
Enhanced Indexing and Querying of Trajectories in Road Networks via String Algorithms

In this article, we propose a novel indexing and querying method for trajectories constrained in a road network. We aim to provide efficient algorithms for various types of spatiotemporal queries that involve routing in road networks, such as (1) finding moving objects that have traveled along a given path during a given time interval, (2) extracting all paths traveled after a given spatiotemporal context, and (3) enumerating all paths between two locations traveled during a certain time interval. Unlike the existing methods in spatial database research, we employ indexing techniques and algorithms from string processing. This idea is based on the fact that we can represent spatial paths as strings, because trajectories in a network are represented as sequences of road segment IDs. The proposed SNT-index (suffix-array-based network-constrained trajectory index) introduces two novel concepts to trajectory indexing. The first is FM-index, which is a compact in-memory data structure for pattern matching. The second is an inverse suffix array, which allows the FM-index to be integrated with the temporal information stored in a forest of B+-trees. Thanks to these concepts, we can reduce the number of B+-tree accesses required by the query processing algorithms to a constant number, something that cannot be achieved with existing methods. Although an FM-index is essentially a static index, we also propose a practical method of appending new data to the index. Finally, experiments show that our method can process the target queries for more than 1 million trajectories in a few tens of milliseconds, which is significantly faster than what the baseline algorithms can achieve without string algorithms.