Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of embryo developmental stage and culture conditions on number and quality of ovine in vitro produced blastocysts

Summary This study evaluated the final output and quality of in vitro produced blastocysts derived from in vivo recovered sheep embryos cultured at various early developmental stages to blastocyst. A total of 270 embryos were recovered from the oviduct, at different days of the early luteal phase, and were classified into three different developmental stages: 2- to 4-cell (n = 93); 5- to 8-cell (n = 92) and 9- to 12-cell (n = 85). The effect of culture conditions was studied, at the same time, by randomly allocating the embryos to one of four groups: three groups of culture with fresh oviduct monolayers (2, 4 and 5 days old) and a fourth group with 2-day monolayers derived from frozen-thawed oviduct cells. Two control groups were established: first, embryos cultured in semi-defined medium (n = 29) and, second, blastocysts obtained in vivo and cryopreserved (n = 43). Influence on blastocyst yield of embryo developmental stage at the start of culture was statistically significant (p < 0.001). Two- to four-cell embryos showed a significantly lower developmental rate (67.7%) than the 5- to 8-cell (83.6%; p < 0.001) and 9- to 12-cell groups (90.5%; p < 0.0001) and lower quality in terms of blastocyst cryotolerance (56.0 vs. 83.7%; p < 0.005). There were no detected effects relating to the age or handling of the monolayer on the embryo developmental rate, but the day of blastocyst appearance was different between embryos cultured on monolayers derived from fresh or frozen-thawed cells (p < 0.0001); the main influence was on the group of 9- to 12-cell embryos (p < 0.0001). Current results confirm the temporal sensitivities of sheep embryos to in vitro culture, regardless of the culture conditions.
Advantages of embedment‐free section transmission electron microscopy

The usefulness of embedment‐free section transmission electron microscopy (TEM) is stressed for present and future morphological analyses, and several examples are demonstrated which are revealed in sections for the first time by this method: en‐face views of slit diaphragm of renal glomerulus and fenestrated diaphragm of capillary endothelium, transparency of neural myelin, attenuated endothelium and some basement laminae, labyrinth architecture of vacuoles within lipid droplets, and enhanced 3D effect of ultrastructures, the latter of which is the case in electron tomography. In addition, the biological significance of structured appearance (microtrabecular lattices) of the cytoplasmic matrix, which is disclosed by this method, are briefly reviewed in relation to the sol–gel transition of cytoplasmic heterogenous proteins. Since the ultrastructures of various cells and tissues in this method are confirmed to be well correspondent to those in conventional epoxy section TEM except for isotropic dimensional changes, and because there is no necessity for any special expensive equipments other than those for the conventional TEM, the embedment‐free section TEM method with these advantages, deserves much more wide application to the morphological research including electron tomography. Microsc. Res. Tech. 76:1257–1265, 2013. © 2013 Wiley Periodicals, Inc.
[Association of the ratio of regulatory and effector T cells with recurrence and chronic graft-versus-host disease after allogeneic hematopoietic stem cell transplantation].

OBJECTIVE To investigate the association of the ratio of regulatory and effector T cells with recurrence and chronic graft-versus-host disease (cGVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS Thirty patients with hematological malignancies who underwent allo-HSCT were classified as recurrence with cGVHD (n=4), non-recurrence with cGVHD (n=14), recurrence without cGVHD (n=5) and non-recurrence without cGVHD (n=7). The different percentage of CD4⁺CD25⁻CD69⁺ regulatory T cells in bone marrow and CD4⁺CD25⁺FoxP3⁺ regulatory T cells, Th1 cells and Th17 cells in peripheral blood were analyzed by flow cytometry. RESULTS There were no significant differences in all these T-cell subsets among different groups (P>0.05). While the ratio of CD4⁺CD25⁻CD69⁺ regulatory T cells and Th1 cells (0.211±0.177) in 9 recurrence patients was significant higher than that (0.133±0.160) in 21 non-recurrence patients (P=0.033). The ratio were also significance between recurrence without cGVHD and non-recurrence without cGVHD patients (0.167±0.073 vs 0.073±0.057, P=0.048), and between recurrence with cGVHD and non-recurrence without cGVHD patients (0.218±0.113 vs 0.073±0.057, P=0.024). Furthermore, the ratio of CD4⁺CD25⁺FoxP3⁺ regulatory T cells and Th17 cells was significant lower (1.975±2.045) in 18 cGVHD patients than that of 12 without cGVHD patients (3.198±1.132, P=0.010), and the ratio was also significant lower in non-recurrence patients with cGVHD (1.695±1.178) than that of without cGVHD (3.446±1.376, P=0.028). CONCLUSION Our results show that the ratio of CD4⁺CD25⁻CD69⁺ regulatory T cells and Th1 cells raise in recurrence patients, and the ratio of CD4⁺CD25⁺FoxP3⁺ regulatory T cells and Th17 decrease in cGVHD patients, which suggest that the ratio of regulatory and effector T cells had association with recurrence and cGVHD in patients with allo-HSCT.
Changes in perlecan during chondrocyte differentiation in the fetal bovine rib growth plate

Perlecan is a heparan sulfate proteoglycan present in the growth plate and essential for endochondral ossification. We evaluated the synthesis and structure of perlecan in the different zones of the growth plate. The growth plates from fetal bovine ribs were isolated and sequentially sliced into 1‐mm sections containing the hypertrophic zone, lower proliferative zone, upper proliferative zone, intermediate zone, and resting zone, respectively. The slices were then either incubated in culture medium with 35SO4 to measure total sulfated proteoglycan synthesis and perlecan synthesis, extracted for perlecan core protein analysis by Western blot, or extracted for perlecan isolation and subsequent characterization of glycosaminoglycan size and disaccharide composition. 35SO4 incorporation into perlecan was three–fourfold higher in the proliferating/hypertrophic zone than the resting zone. Western blot showed perlecan content was greatest in the lower and upper proliferating zones and that a perlecan fragment lacking portions of the N‐ and C‐terminal domains containing heparan sulfate was also present in all zones. Purified perlecan from the hypertrophic/lower proliferative zone had larger chondroitin sulfate chains and a different composition of CS and HS disaccharides than the perlecan isolated from the resting zone. These results indicate perlecan deposition is increased and is turned over during proliferation to be replaced by a perlecan with a different sulfation pattern. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:1317–1326, 2006
A Sentiment Detection Engine for Internet Stock Message Boards

Financial investors trade on the basis of information, and in particular, on the likelihood that a piece of information will impact the market. The ability to predict this within milliseconds of the information being released would be useful in applications such as algorithmic trading. We present a solution for classifying investor sentiment on internet stock message boards. Our solution develops upon prior work and examines several approaches for selecting features in a messy and sparse data set. Using a variation of the Bayes classifier with feature selection methods allows us to produce a system with better accuracy, execution performance and precision than using conventional Naive Bayes and SVM classifiers. Evaluation against author-selected sentiment labels results in an accuracy of 78.72% compared to a human annotation and conventional Naive Bayes accuracy of 57% and 65.63% respectively.
Dephosphorylation at a Conserved SP Motif Governs cAMP Sensitivity and Nuclear Localization of Class IIa Histone Deacetylases*

Background: Nucleocytoplasmic trafficking of class IIa histone deacetylases is crucial for various biological processes. Results: cAMP induces dephosphorylation at an SP motif conserved in HDAC4, HDAC5, and HDAC9 but not in HDAC7. Conclusion: Dephosphorylation at the SP motif governs cAMP sensitivity and nuclear localization of class IIa histone deacetylases. Significance: Cellular signaling pathways may act upon cAMP to promote dephosphorylation and nuclear localization of class IIa histone deacetylases. Histone deacetylase 4 (HDAC4) and its paralogs, HDAC5, -7, and -9 (all members of class IIa), possess multiple phosphorylation sites crucial for 14-3-3 binding and subsequent nuclear export. cAMP signaling stimulates nuclear import of HDAC4 and HDAC5, but the underlying mechanisms remain to be elucidated. Here we show that cAMP potentiates nuclear localization of HDAC9. Mutation of an SP motif conserved in HDAC4, -5, and -9 prevents cAMP-stimulated nuclear localization. Unexpectedly, this treatment inhibits phosphorylation at the SP motif, indicating an inverse relationship between the phosphorylation event and nuclear import. Consistent with this, leptomycin B-induced nuclear import and adrenocorticotropic hormone (ACTH) treatment result in the dephosphorylation at the motif. Moreover, the modification synergizes with phosphorylation at a nearby site, and similar kinetics was observed for both phosphorylation events during myoblast and adipocyte differentiation. These results thus unravel a previously unrecognized mechanism whereby cAMP promotes dephosphorylation and differentially regulates multisite phosphorylation and the nuclear localization of class IIa HDACs.
High-rosmarinic acid spearmint tea in the management of knee osteoarthritis symptoms.

UNLABELLED Individuals with medically diagnosed knee osteoarthritis (OA) participated in a randomized, double-blind study to investigate the effects of a high-rosmarinic acid (rosA) spearmint tea. Sixty-two participants were randomized by sex and screening pain score to consume tea brewed from a high-rosA spearmint variety or a commercially available spearmint twice daily for 16 weeks. Pain, quality of life (QoL), and physical function at baseline and week 16 were assessed using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Short-Form 36-item Health Survey (SF-36), 6-minute walk test (6MWT), and stair climb test (SCT). Data from 46 participants (mean age=60.7; BMI=32.9 kg/m(2)) were analyzed. Pain score significantly decreased from week 0 to 16 for the high-rosA group but not for the control group and scores for stiffness and physical disability significantly decreased from week 0 to 16 for both groups. Increased QoL score on the bodily pain index in the SF-36 was observed at week 16 within the high-rosA group only, although no significant differences were observed between the groups. A nonsignificant improvement was observed in the 6MWT at week 16 in the high-rosA group only. There were no changes in the SCT for either group. Therefore, 16-week daily consumption of the high-rosA and commercial spearmint teas significantly improved stiffness and physical disability scores in adults with knee OA, but only the high-rosA tea significantly decreased pain. Consumption of high-rosA tea warrants further consideration as a potential complementary therapy to reduce pain in OA. CLINICAL TRIAL REGISTRATION NUMBER NCT01380015.
Supersaliency: Predicting Smooth Pursuit-Based Attention with Slicing CNNs Improves Fixation Prediction for Naturalistic Videos

Predicting attention is a popular topic at the intersection of human and computer vision, but video saliency prediction has only recently begun to benefit from deep learning-based approaches. Even though most of the available video-based saliency data sets and models claim to target human observers' fixations, they fail to differentiate them from smooth pursuit (SP), a major eye movement type that is unique to perception of dynamic scenes. In this work, we aim to make this distinction explicit, to which end we (i) use both algorithmic and manual annotations of SP traces and other eye movements for two well-established video saliency data sets, (ii) train Slicing Convolutional Neural Networks (S-CNN) for saliency prediction on either fixation- or SP-salient locations, and (iii) evaluate ours and over 20 popular published saliency models on the two annotated data sets for predicting both SP and fixations, as well as on another data set of human fixations. Our proposed model, trained on an independent set of videos, outperforms the state-of-the-art saliency models in the task of SP prediction on all considered data sets. Moreover, this model also demonstrates superior performance in the prediction of "classical" fixation-based saliency. Our results emphasize the importance of selectively approaching training set construction for attention modelling.
Fabrication and Microstructuring of Hexagonally Ordered Two‐Dimensional Nanopore Arrays in Anodic Alumina

washed three times with water, and dried over MgSO4. After removing the solvent, chromatography is carried out on the residue on neutral alox. First, unreacted compound 4 and monoadduct 8 are eluted with pentane, and then bis-adduct 5 with petrolether/ethyl acetate. (54 %, m.p.: 191 C). H NMR (CDCl3, ppm) 3.64 (s, 8 H, CH2), 4.33 (dd, 2 H, CH), 6.99 (dd, 2 H, CH), 7.14 (s, 8 H, aromatic); C NMR (CDCl3, ppm) 33.72, 54.79, 126.37, 129.22, 134.8, 139.74, 140.72. Compound 2: Compound 5 (0.8 g, 2.64 mmol) and chloranil (1.28 g, 5.28 mmol) are dissolved in toluene (150 mL), and heated for 1.5 h under reflux. After removing the solvent, the residue is purified via chromatography (neutral alox/toluene) (75 %, m.p.: 239 C). H NMR (CDCl3, ppm) 5.33 (dd, 2 H, CH), 7.06 (dd, 2 H, CH), 7.37 (AA¢BB¢, 4 H, aromatic), 7.71 (AA¢BB¢, 4 H, aromatic), 7.73(s, 4 H, aromatic); C NMR (CDCl3, ppm) 50.74, 121.71, 126, 127.92, 132.25, 138.73, 142.66. Compound 6a: A solution of compound 2 (100 mg, 0.32 mmol) and 2,3,4,5-tetrachlorothiophenedioxide (167 mg, 0.64 mmol) in CH2Cl2 (4 mL) is heated for 3 days at 70 C under a pressure of 6 kbar. After the reaction is complete, the solvent is removed under vacuum. Chromatography is carried out on the residue on silica gel with hexane/toluene 4/1 as eluent. The first fraction gives the desired product (75 %). The material can be further purified by recrystallization from dichloroethane/ethyl acetate. H NMR (CD2Cl2, ppm) 3.54 (s, 2 H, CH), 5.13 (s, 2 H, CH), 7.45 (AA¢BB¢, 4 H, aromatic), 7.80 (s, 2 H, aromatic), 7.82 (AA¢BB¢, 4 H, aromatic), 7.86 (s, 2 H, aromatic); C NMR (CD2Cl2, ppm) 48.08, 48.86, 122.91, 123.93, 124.29, 126.24, 126.35, 128.02, 128.07, 131.38, 132.91, 133.07, 137.47, 139.58. Compound 6b: Using the procedure described for the synthesis of compound 6a, compound 6b is obtained in a yield of 70 %. H NMR (CD2Cl2, ppm) 3.58 (s, 2 H, CH), 5.19 (s, 2 H, CH), 7.46 (AA¢¢BB¢, 4 H, aromatic), 7.82 (s, 2 H, aromatic), 7.84 (AA¢BB¢, 4 H, aromatic), 7.86 (s, 2 H, aromatic); C NMR (CD2Cl2, ppm) 49.74, 51.89, 120.49, 122.87, 123.96, 126.22, 126.33, 128.02, 128.08, 128.72, 132.90, 133.06, 137.51, 139.73.
AFLP variation in wild barley (Hordeum spontaneum C. Koch) with reference to salt tolerance and associated ecogeography.

Thirty-nine genotypes of Hordeum spontaneum were selected from three geographically separated areas (southwestern, northern, and southeastern) of the Fertile Crescent. The lines were subject to AFLP (amplified fragment length polymorphism) analysis from which a similarity matrix was produced. A dendrogram of the data showed, with two exceptions, that the genotypes grouped together according to area of origin. This was confirmed by principal coordinate analysis in which the first principal coordinate separated the genotypes of the southwestern area from the other two areas, which in turn could be separated by the second principal coordinate. While genotypes from the same site of origin can exhibit very similar AFLP profiles, sharp genetic differences were detected between genotypes separated by relatively short distances. Thirty of the 39 genotypes were subjected to hydroculture salt tolerance tests. These were analysed for shoot Na+ content and carbon isotope composition (δ13C) after 4 weeks of treatment (100 mol∙m−3 NaCl). Shoot Na+ content and δ13C were highly correlated. Twelve AFLP markers were found to be associated with both shoot Na+ content and shoot δ13C and were also associated with site of origin ecogeographic data, particularly longitude. The most salt tolerant genotype came from Ilam in the southeastern area and the most salt sensitive genotype originated in the southwestern area. The 12 markers were partitioned into groups that showed significant associations within groups but no significant association between groups. In a multiple regression analysis, three AFLP markers, from separate groups, accounted for more than 60% of the variation for shoot Na+ content and δ13C. The results demonstrate the effectiveness of AFLP fingerprinting in genetic studies of complex traits at the wild species and (or) population level.
A Note on Local Scoring and Weighted Local Polynomial Regression in Generalized Additive

A new variety of pear rootstock selected from a family of seedling pear trees germinated from seed collected from a wild pear tree. The subject variety produces hearty pear trees having high yield. The rootstock is compatible with all major commercial pear varieties. The variety roots easily and reproduces readily by hardwood cuttings.
Transportation Mode Detection on Mobile Devices Using Recurrent Nets

We present an approach to the use of Recurrent Neural Networks (RNN) for transportation mode detection (TMD) on mobile devices. The proposed model, called Control Gate-based Recurrent Neural Network (CGRNN), is an end-to-end model that works directly with raw signals from an embedded accelerometer. As mobile devices have limited computational resources, we evaluate the model in terms of accuracy, computational cost, and memory usage. Experiments on the HTC transportation mode dataset demonstrate that our proposed model not only exhibits remarkable accuracy, but also is efficient with low resource consumption.
Paying Attention: Overnight Returns and the Hidden Cost of Buying at the Open

Abstract We find a strong tendency for positive returns during the overnight period followed by reversals during the trading day. This behavior is driven by an opening price that is high relative to intraday prices. It is concentrated among stocks that have recently attracted the attention of retail investors, it is more pronounced for stocks that are difficult to value and costly to arbitrage, and it is greater during periods of high overall retail investor sentiment. The additional implicit transaction costs for retail traders who buy high-attention stocks near the open frequently exceed the effective half spread.
Mediation of vertebrate life histories via insulin‐like growth factor‐1

Life‐history traits describe parameters associated with growth, size, survival, and reproduction. Life‐history variation is a hallmark of biological diversity, yet researchers commonly observe that one of the major axes of life‐history variation after controlling for body size involves trade‐offs among growth, reproduction, and longevity. This persistent pattern of covariation among these specific traits has engendered a search for shared mechanisms that could constrain or facilitate production of variation in life‐history strategies. Endocrine traits are one candidate mechanism that may underlie the integration of life history and other phenotypic traits. However, the vast majority of this research has been on the effects of steroid hormones such as glucocorticoids and androgens on life‐history trade‐offs. Here we propose an expansion of the focus on glucocorticoids and gonadal hormones and review the potential role of insulin‐like growth factor‐1 (IGF‐1) in shaping the adaptive integration of multiple life‐history traits. IGF‐1 is a polypeptide metabolic hormone largely produced by the liver. We summarize a vast array of research demonstrating that IGF‐1 levels are susceptible to environmental variation and that IGF‐1 can have potent stimulatory effects on somatic growth and reproduction but decrease lifespan. We review the few studies in natural populations that have measured plasma IGF‐1 concentrations and its associations with life‐history traits or other characteristics of the organism or its environment. We focus on two case studies that found support for the hypothesis that IGF‐1 mediates adaptive divergence in suites of life‐history traits in response to varying ecological conditions or artificial selection. We also examine what we view as potentially fruitful avenues of research on this topic, which until now has been rarely investigated by evolutionary ecologists. We discuss how IGF‐1 may facilitate adaptive plasticity in life‐history strategies in response to early environmental conditions and also how selection on loci controlling IGF‐1 signaling may mediate population divergence and eventual speciation. After consideration of the interactions among androgens, glucocorticoids, and IGF‐1 we suggest that IGF‐1 be considered a suitable candidate mechanism for mediating life‐history traits. Finally, we discuss what we can learn about IGF‐1 from studies in free‐ranging animals. The voluminous literature in laboratory and domesticated animals documenting relationships among IGF‐1, growth, reproduction, and lifespan demonstrates the potential for a number of new research questions to be asked in free‐ranging animals. Examining how IGF‐1 mediates life‐history traits in free‐ranging animals could lead to great insight into the mechanisms that influence life‐history variation.
Pilot Distribution Optimization and Power Control in Multi-Cellular Large Scale MIMO Systems

Massive MIMO communication systems have been identified as one of the most prominent technologies of the next generation wireless standards, such as 5G, due to the large gains in energy and spectral efficiency that can be achieved. In the asymptotic condition of infinite number of antennas at the base station (BS), the performance bottleneck of these systems is due to the pilot contamination effect, i.e., the directional interference arising from users in adjacent cells that reuse the same set of orthogonal training sequences, and thus the interference seen by each user is determined by the pilot sequence assigned to him. We show in this paper that the system performance can be improved by appropriately assigning the pilot sequences to the users, in the so-called pilot allocation scheme. Depending on the optimization metric adopted, it is more advantageous to a user with certain long- term fading coefficient be assigned to a specific pilot sequence, whose interference can be completely estimated in advance by the BS by only knowing the long term fading coefficients of users in adjacent cells. Besides, if the objective is to maximize the number of users with a target quality of service, we have shown that the pilot allocation schemes can be combined with power control algorithms, resulting in much more improvements for the system. For unitary frequency reuse factor, we have found that the data throughput provided for 95% of the users increases when applying power control algorithm from 134kbps to 1.461Mbps with no pilot allocation, while this performance gain provided by power control changes from 793kbps to 6.743Mbps when pilot allocation is employed. If the reuse factor increases to 3, a 95%-likely data throughput of 17.310Mbps can be assured when pilot allocation and power control are suitably combined.