Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Evaluation of the Effect of Stimulation with Magnetic Fields on Chondrocytes

Magnetic fields (MFs) have been used as an external stimulus to increase cell proliferation in chondrocytes and extracellular matrix (ECM) synthesis of articular cartilage. However, previously published studies have not shown that MFs are homogeneous through cell culture systems. In addition, variables such as stimulation times and MF intensities have not been standardized to obtain the best cellular proliferative rate or an increase in molecular synthesis of ECM. In this work, a stimulation device, which produces homogeneous MFs to stimulate cell culture surfaces was designed and manufactured using a computational model. Furthermore, an in vitro culture of primary rat chondrocytes was established and stimulated with two MF schemes to measure both proliferation and ECM synthesis. The best proliferation rate was obtained with an MF of 2 mT applied for 3 h, every 6 h for 8 days. In addition, the increase in the synthesis of glycosaminoglycans was statistically significant when cells were stimulated with an MF of 2 mT applied for 5 h, every 6 h for 8 days. These findings suggest that a stimulation with MFs is a promising tool that could be used to improve in vitro treatments such as autologous chondrocyte implantation, either to increase cell proliferation or stimulate molecular synthesis. Bioelectromagnetics. 2020;41:41–51 © 2019 Bioelectromagnetics Society
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

The colored de Bruijn graph (cdbg) and its variants have become an important combinatorial structure used in numerous areas in genomics, such as population-level variation detection in metagenomic samples, large scale sequence search, and cdbg-based reference sequence indices. As samples or genomes are added to the cdbg, the color information comes to dominate the space required to represent this data structure. In this paper, we show how to represent the color information efficiently by adopting a hierarchical encoding that exploits correlations among color classes — patterns of color occurrence — present in the de Bruijn graph (dbg). A major challenge in deriving an efficient encoding of the color information that takes advantage of such correlations is determining which color classes are close to each other in the high-dimensional space of possible color patterns. We demonstrate that the dbg itself can be used as an efficient mechanism to search for approximate nearest neighbors in this space. While our approach reduces the encoding size of the color information even for relatively small cdbgs (hundreds of experiments), the gains are particularly consequential as the number of potential colors (i.e. samples or references) grows to thousands of experiments. We apply this encoding in the context of two different applications; the implicit cdbg used for a large-scale sequence search index, Mantis, as well as the encoding of color information used in population-level variation detection by tools such as Vari and Rainbowfish. Our results show significant improvements in the overall size and scalability of representation of the color information. In our experiment on 10,000 samples, we achieved more than 11× better compression compared to RRR.
Immunological and clinicopathological characteristics of C1RL in 2143 glioma patients

Glioma is a deadly and immunosuppressive brain tumor. Complement C1r Subcomponent Like (C1RL), as a prognostic biomarker in several kinds of tumors, has attracted increasing attention from oncologists. However, the role of C1RL in glioma remains unclear. Through 2143 glioma patients from 5 public datasets, the relationships between C1RL expression and clinicopathological characteristics were analyzed. Furthermore, the C1RL associated genes were screened and GO analysis was conducted to investigate their biological process enrichment. In addition, tumor purity, leukocytes infiltration and overall survival were calculated based on C1RL expression. We found that C1RL expression was upregulated in glioblastoma (GBM), especially mesenchymal GBM and primary GBM. Increased C1RL accompanied IDH1 wt both in lower grade glioma (LGG) and GBM. C1RL associated genes were mainly enriched in biological processes which are related to immune response. C1RL expression was also correlated with less tumor purity and more M2 macrophage infiltration. Higher C1RL expression predicted unfavorable survival for patients with glioma and therapeutic resistance in GBM. Our results implied that C1RL is involved in immunological activities and is an independent unfavorable prognostic biomarker for patients with glioma. C1RL is a potential immunotherapeutic target for glioma in future clinical practice.
Feature selection using mutual information and neural networks

Reducing the dimensionality of the raw input variable space is an important step in pattern recognition and functional approximation tasks often determined by practical feasibility. The purpose of this study was to investigate an information theoretic approach to feature selection. We will use mutual information (MI) as a pre-processing step for artificial neural networks. The reasons why mutual information is not in wider use currently (except between two scalar variables) lie in computational difficulties. The probability density functions of the variables are required, and MI involves numerical integration of functions of those, which leads to a high computational complexity. Because of the difficulty in directly implementing the maximal dependency condition, we first derive an equivalent form, called minimal redundancy maximal relevance criterion, for first order incremental feature selection. The feature selection methodology is hybridized with three different classification and universal function approximation paradigms: Multilayer Perceptron, Radial Basis Function and Support Vector Machine. We perform extensive experimental comparison of the proposed hybrid algorithm for different problem: breast cancer classification, diabetes in Pima Indians and arrhythmia
CRECIMIENTO REPRODUCTIVO DE Passiflora cincinnata MAST.

Reproductive growth of Passiflora cincinnata Mast. The Passiflora cincinnata Mast. is distributed from the Brazilian Northeast until the North of the Argentina. In Venezuela, it is known as creole or montera passionfruit and is located in Lara and Falcon States. It is used to elaborate drinks and remedies. In order to provide knowledge about its reproductive growth, sixteen 15-month old plants coming from seeds and conducted in 2 m high vertical trellis were evaluated in Tarabana, (10° 00’ N; 510 msnm), Lara state, Venezuela, during the years 2001 and 2002. It was obtained that: a) the second and third order branches presented a reproductive character and the flowering, anthesis, and fructification and ramification areas were identified from apical, intermediate and basal positions, respectively. Ramifications were only observed in second order branches; b) anthesis occurred before 10:00 and its mechanism was similar to the one described for other pasifloras; c) The total quantity of pollen grains was 237.143 ± 10.459 per flower; its viability in artificial medium was of 94 ± 4 % and its germinability was 85 ± 3.5 %; and d) the highest percentages of fruit set corresponded to flowers with free and crossed pollination, while in those with selfpollination the fructification was 7.6 %; which allows to classify it as partially compatible.
Ocean colour validation activities at the Acqua Alta Oceanographic Tower in the northern Adriatic Sea

The development and validation of ocean colour products require the availability of in situ atmospheric and marine data. Since 1995, the Coastal Atmosphere and Sea Time Series (CoASTS) Program ensures the collection of an in situ comprehensive set of measurements taken from an oceanographic tower in the northern Adriatic Sea. An example of a validation exercise is presented through the comparison of in situ and satellite-derived aerosol optical thickness at various wavelengths in the 443–865 nm spectral interval.
Design of Underground Openings in Competent Rock

From Summary: "This report presents methods and principles useful in designing underground mine openings and pillars in competent rock formations. Two types of formations are considered: (1) Massive formations, in which openings are generally mined with an arched roof, and (2) bedded formations, in which openings are generally mined with a flat roof. "
Early Nineteenth‐Century Grasslands of the Midcontinent Plains

Abstract The abundance patterns of native grasses in the Midcontinent Plains may be examined through several lines of evidence, but the patterns are often contradictory. The journals of scientific exploration, early maps of grass cover, contemporary data, and paleobotanical materials in the form of opal phytoliths are examined to resolve the discrepancies among the various sources. The most significant discrepancy is the lack of convergence of evidence on the eastern limit of the shortgrass dominance in the Central Plains. When all data are placed in a temporal context, the emergent pattern of disagreement over the location of the eastern margin of shortgrass dominance suggests a continual westward movement of the boundary between the tall and short, warm-season grasses in the Central Plains. Since the little Ice Age, the westward movement of tall, warm-season grasses that emerges from the data suggests that climate does not determine grass patterns, and that the vegetation cover of the early nineteenth-c.
Influence of White-Coat Hypertension on Left Ventricular Deformation 2- and 3-Dimensional Speckle Tracking Study

We sought to compare left ventricular deformation in subjects with white-coat hypertension to normotensive and sustained hypertensive patients. This cross-sectional study included 139 untreated subjects who underwent 24-hour ambulatory blood pressure monitoring and completed 2- and 3-dimensional examination. Two-dimensional left ventricular multilayer strain analysis was also performed. White-coat hypertension was diagnosed if clinical blood pressure was elevated and 24-hour blood pressure was normal. Our results showed that left ventricular longitudinal and circumferential strains gradually decreased from normotensive controls across subjects with white-coat hypertension to sustained hypertensive group. Two- and 3-dimensional left ventricular radial strain, as well as 3-dimensional area strain, was not different between groups. Two-dimensional left ventricular longitudinal and circumferential strains of subendocardial and mid-myocardial layers gradually decreased from normotensive control to sustained hypertensive group. Longitudinal and circumferential strains of subepicardial layer did not differ between the observed groups. We concluded that white-coat hypertension significantly affects left ventricular deformation assessed by 2-dimensional traditional strain, multilayer strain, and 3-dimensional strain.
Estimating the reproducibility of psychological science

INTRODUCTION: Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research of exemplary quality may have irreproducible empirical findings because of random or systematic error.
Environmental factors influential to the duration and intensity of tornadoes in simulated supercells

Simulations were performed using an idealized cloud model to investigate the environmental conditions influential to tornado duration and intensity. The results from twenty‐one tornadic simulations are presented—far more than any previous study. The results show a nearly linear relationship between storm relative environmental helicity (SREH) and simulated tornado duration. A multiple linear regression analysis was performed showing that, in addition to SREH, convective available potential energy (CAPE), convective inhibition (CIN), and precipitable water (Pwat) are useful predictor variables for simulated tornado duration. Similar results were found for simulated tornado intensity, as represented by the maximum central pressure drop.
Training Spiking Neural Networks for Cognitive Tasks: A Versatile Framework Compatible to Various Temporal Codes

Conventional modeling approaches have found limitations in matching the increasingly detailed neural network structures and dynamics recorded in experiments to the diverse brain functionalities. On another approach, studies have demonstrated to train spiking neural networks for simple functions using supervised learning. Here, we introduce a modified SpikeProp learning algorithm, which achieved better learning stability in different activity states. In addition, we show biological realistic features such as lateral connections and sparse activities can be included in the network. We demonstrate the versatility of this framework by implementing three well-known temporal codes for different types of cognitive tasks, which are MNIST digits recognition, spatial coordinate transformation, and motor sequence generation. Moreover, we find several characteristic features have evolved alongside the task training, such as selective activity, excitatory-inhibitory balance, and weak pair-wise correlation. The coincidence between the self-evolved and experimentally observed features indicates their importance on the brain functionality. Our results suggest a unified setting in which diverse cognitive computations and mechanisms can be studied.
HIF-1 α in heart: remodeling nucleotide metabolism

These studies have examined the effect of hypoxia inducible factor 1 α (HIF-1 α ) on nucleotide metabolism in the ischemic heart using a genetic mouse model with heart-specific and regulated expression of a stable form of HIF-1 α . We find that AMP deaminase (AMPD), the entry point of the purine nucleotide cycle (PNC), is induced by HIF-1 α at the level of mRNA, protein, and activity. AMP that accumulates during ischemia can be metabolized to adenosine by 5 ′ nucleotidase or to IMP by AMPD. Consistent with the finding of AMPD induction, adenosine accumulation during ischemia was much attenuated in HIF-1 α -expressing hearts. Further investigation of nucleotide salvage enzymes found that hypoxanthine phosphoribosyl transferase (HPRT) is also upregulated in HIF-1 α -expressing hearts. Treatment of hearts with an inhibitor of the PNC, hadacidin, hastens the fall of the adenylate energy charge during ischemia and the accumulation of AMP. The results provide new insight into the role of the PNC in heart, especially as it relates to ischemia, and indicate that HIF-1 α regulates nucleotide metabolism as a compensatory response to hypoxia.
High‐resolution magnetics reveal the deep structure of a volcanic‐arc‐related basalt‐hosted hydrothermal site (Palinuro, Tyrrhenian Sea)

High‐resolution magnetic surveys have been acquired over the partially sedimented Palinuro massive sulfide deposits in the Aeolian volcanic arc, Tyrrhenian Sea. Surveys flown close to the seafloor using an autonomous underwater vehicle (AUV) show that the volcanic‐arc‐related basalt‐hosted hydrothermal site is associated with zones of lower magnetization. This observation reflects the alteration of basalt affected by hydrothermal circulation and/or the progressive accumulation of a nonmagnetic deposit made of hydrothermal and volcaniclastic material and/or a thermal demagnetization of titanomagnetite due to the upwelling of hot fluids. To discriminate among these inferences, estimate the shape of the nonmagnetic deposit and the characteristics of the underlying altered area—the stockwork—we use high‐resolution vector magnetic data acquired by the AUV Abyss (GEOMAR) above a crater‐shaped depression hosting a weakly active hydrothermal site. Our study unveils a relatively small nonmagnetic deposit accumulated at the bottom of the depression and locked between the surrounding volcanic cones. Thermal demagnetization is unlikely but the stockwork extends beyond the limits of the nonmagnetic deposit, forming lobe‐shaped zones believed to be a consequence of older volcanic episodes having contributed in generating the cones.
Identifying adolescent protective factors that disrupt the intergenerational transmission of cannabis use and disorder.

Adolescent cannabis use is common, has been associated with several deleterious outcomes, and is often associated with previous parent cannabis use. Therefore, identifying protective factors that prevent this intergenerational transmission of cannabis use is increasingly important given shifting contemporary policies around cannabis use. The present study examines 3 protective factors in adolescence (active coping, positive activity involvement, and school grades) that may disrupt patterns of intergenerational cannabis use. The present study uses data from a high-risk longitudinal sample followed for over 30 years that includes Generation 1 (G1) parents (54.19% with lifetime alcohol use disorder, 8.15% with lifetime cannabis use disorder), their Generation 2 (G2) children, and their Generation 3 (G3) grandchildren and therefore provides the opportunity to replicate effects across 2 intergenerational cohorts (a G1-G2 cohort and a G2-G3 cohort). Results from ordered logistic regression models reveal that in both intergenerational cohorts, greater midadolescent active coping, higher positive activity involvement, and higher grades prospectively predict lower late adolescent cannabis use at significant (p < .05) or marginal (p < .10) levels, even after powerful control variables, such as parent cannabis use and alcohol use, as well as previous early adolescent cannabis use, are accounted for. Additionally, in both intergenerational cohorts, midadolescent high levels of active coping disrupt intergenerational transmission of cannabis use. Results indicate replication in the intergenerational transmission of cannabis use and in the protective effects of coping, grades, and, to a lesser extent, positive activity involvement across generational cohorts. Implications for prevention programming are discussed. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Residence times and mixing of water in river banks: implications for recharge and groundwater–surface water exchange

Bank exchange processes within 50 m of the Tambo River, southeast Australia, have been investigated through the combined use of 3 H and 14 C. Groundwater residence times increase towards the Tambo River, which suggests the absence of significant bank storage. Major ion concentrations and δ 2 H and δ 18 O values of bank water also indicate that bank infiltration does not significantly impact groundwater chemistry under baseflow and post-flood conditions, suggesting that the gaining nature of the river may be driving the return of bank storage water back into the Tambo River within days of peak flood conditions. The covariance between 3 H and 14 C indicates the leakage and mixing between old (~17 200 years) groundwater from a semi-confined aquifer and younger groundwater (<100 years) near the river, where confining layers are less prevalent. It is likely that the upward infiltration of deeper groundwater from the semi-confined aquifer during flooding limits bank infiltration. Furthermore, the more saline deeper groundwater likely controls the geochemistry of water in the river bank, minimising the chemical impact that bank infiltration has in this setting. These processes, coupled with the strongly gaining nature of the Tambo River are likely to be the factors reducing the chemical impact of bank storage in this setting. This study illustrates the complex nature of river groundwater interactions and the potential downfall in assuming simple or idealised conditions when conducting hydrogeological studies.
Stratigraphy and ammonite fauna of the Graneros Shale and Greenhorn Limestone near Pueblo, Colorado

__________________________. Introduction ______________________________________ Acknowledgments _________________. _____ Previous work _______________________________ Stratigraphy _____________________________________ Graneros Shale _______________________________ Lower barren unit ________________________ Thatcher Limestone Member _______________ Upper fossiliferous unit ___________________ Regional variation of thickness _. __________ Greenhorn Limestone _________________________ Lincoln Limestone Member ________________ Hartland Shale Member __________________ Bridge Creek Limestone Member ___________ Supplemental stratigraphic sections ____________ Faunal zonation __________________________________ Fossil zones and age of the Graneros Shale ______ Fossil zones and age of the Greenhorn Limestone ^ Zonation in the western interior ________________ Geographic distribution of fossils __________________ Systematic descriptions ____________________________ Family Ptychoceratidae Meek, 1876 ____________ Genus Worthoceras Adkins, 1928 ___________ Worthoceras gibbosum Moreman __ Worthoceras vermiculum (Shumard)_ Family Hamitidae Hyatt, 1900 ________________ Genus Stomohamites Breistroffer, 1940 ______ Stomohamites cf. S. simplex (d'Orbigny) ____________________ Genus Hemiptychoceras Spath, 1925 ________ Hemiptychoceras reesidei Cobban and Scott, n. sp. ___________ Genus Puebloites Cobban and Scott, n. gen _ Puebloites corrugatus (Stanton) ___ Puebloites spiralis Cobban and Scott, n. sp ____________________ Puebloites greenhornensis Cobban and Scott, n. sp ________________ Family Baculitidae Meek, 1876 ________________ Genus Sciponoceras Hyatt, 1894 ____________ Sciponoceras gracile (Shumard) ____ Genus Baculites Lamarck, 1799 ____________ Baculites cf. B. yokoyamai Tokunaga and Shimizu _________ Baculites calamus Morrow ________ Family Anisoceratidae Hyatt, 1900 _____________ Genus Anisoceras Pictet, 1854______________ Anisoceras cf. A. plicatile (J. Sowerby) _______ ______ Anisoceras sp _ _____________ Genus Idiohamites Spath, 1925 ____________ Idiohamites sp ___________________ Genus Allocrioceras Spath, 1926 ____________ Allocrioceras annulatum (Shumard)Page
Modulation of functional connectivity folowing visual adaptation : homeostasis in V 1

Sensory neurons exhibit remarkable adaptability in acquiring new optimal selectivity to unfamiliar features when a new stimulus becomes prevalent in the environment. In conventionaly prepared adult anesthetized cats, we used visual adaptation to change the preferred orientation selectivity in V1 neurons. Cortical circuits are dominated by complex and intricate connections between neurons. Cross-correlation of celular spike-trains discloses the putative functional connection between two neurons. We sought to investigate changes in these links folowing a twelve minute uninterrupted application of a specific, usualy non-preferred, orientation. We report that visual adaptation, mimicking training, modulates the magnitude of cross-correlograms suggesting that the strength of inter-neuronal relationships is modified. While individual cel-pairs exhibit changes in their response correlation strength, the average correlation of the recorded cel cluster remains unchanged. Hence, visual adaptation induces plastic changes that impact the connectivity between neurons. Author's post-print published in Brain Research Vol. 1594 , pp. 136-153, 2015 http://dx.doi. org/10.1016/j.brainres. 2014.10. 054
Discriminating Between Coherent and Incoherent Light with Metasurfaces

Metasurfaces represent a powerful paradigm of optical engineering that enables one to control the flow of light across material interfaces. We report on a discovery that metallic metasurfaces of a certain type respond differently to spatially coherent and incoherent light, enabling robust speckle-free discrimination between different degrees of coherence. The effect has no direct analogue in conventional optics and may find applications in compact metadevices enhancing imaging, vision, detection, communication and metrology.