Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of in vitro produced porcine embryos according to serum types as macromolecule

This study was conducted to establish an in vitro maturation (IVM) system by selection of efficient porcine serum during porcine in vitro production. To investigate the efficient porcine serum (PS), different types of PS [newborn pig serum, prepubertal gilt serum (PGS), estrus sow serum, and pregnancy sow serum] were used to supplement IVM media with or without gonadotrophin (GTH) and development rates of parthenogenetic activation (PA) and in vitro fertilization (IVF) embryos were then compared. The maturation rates of the PGS group was significantly higher when GTH was not added. Additionally, during development of PA embryos without GTH, the PGS group showed significantly higher cleavage and blastocyst formation rates. Moreover, the cleavage rates of IVF embryos were significantly higher in the PGS group, with no significant differences in the blastocyst formation. However, when GTH was supplemented into the IVM media, there were no significant differences among the four groups in the cleavage rates, development rates of the blastocyst, and cell number of the blastocyst after PA and IVF. In conclusion, PGS is an efficient macromolecule in porcine IVM, and GTH supplementation of the IVM media is beneficial when PS is used as macromolecule, regardless of its origin.
Robust superhydrophobic attapulgite coated polyurethane sponge for efficient immiscible oil/water mixture and emulsion separation

Separation of oil/water mixtures has become an increasingly important subject worldwide because of frequent oil spill incidents and industrial oily wastewater. The filter materials for the mixtures separation need to collect first and then filter, which is energy-intensive and cumbersome. Utilization of adsorbents appears to be an economical and direct way for mixture disposal. In this study, the superhydrophobic polyurethane (PU) sponge is fabricated by coating superhydrophobic attapulgite (APT) onto its skeleton surface. The coated PU sponges exhibit robust superhydrophobicity and high adsorption capability under a series of harsh conditions, which are used for the separation of mixtures of oil and various corrosive solutions and hot water. Moreover, the coated PU sponges can selectively adsorb oils from mixtures under extreme and harsh turbulent conditions. Furthermore, the coated PU sponge connected to a vacuum system could remove up to 3200 times its self-weight in kerosene within 20 s under a vacuum degree of about 30 kPa. More importantly, the coated PU sponges can separate tiny oil droplets from surfactant-stabilized oil-in-water emulsions with a separation efficiency of over 99.87% by employing a compression and agitation procedure. All of these characteristics make the coated PU sponge a promising adsorbent for realizing oil and organic pollutant removal in realistic aquatic environments.
High-performance, inexpensive setup for simultaneous multisite recording of electrophysiological signals and mesoscale voltage imaging in the mouse cortex

Abstract. Simultaneous recording of optical and electrophysiological signals from multiple cortical areas may provide crucial information to expand our understanding of cortical function. However, the insertion of multiple electrodes into the brain may compromise optical imaging by both restricting the field of view and interfering with the approaches used to stabilize the specimen. Existing methods that combine electrophysiological recording and optical imaging in vivo implement either multiple surface electrodes, silicon probes, or a single electrode for deeper recordings. To address such limitation, we built a microelectrode array (hyperdrive, patent US5928143 A) compatible with wide-field imaging that allows insertion of up to 12 probes into a large brain area (8 mm diameter). The hyperdrive is comprised of a circle of individual microdrives where probes are positioned at an angle leaving a large brain area unobstructed for wide-field imaging. Multiple tetrodes and voltage-sensitive dye imaging were used for acute simultaneous registration of spontaneous and evoked cortical activity in anesthetized mice. The electrophysiological signals were used to extract local field potential (LFP) traces, multiunit, and single-unit spiking activity. To demonstrate our approach, we compared LFP and VSD signals over multiple regions of the cortex and analyzed the relationship between single-unit and global cortical population activities. The study of the interactions between cortical activity at local and global scales, such as the one presented in this work, can help to expand our knowledge of brain function.
Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis

This study used a next-generation sequencing approach to identify the bacterial taxa occurring in the advanced front of caries biofilms associated with pulp exposure and irreversible pulpitis. Samples were taken from the deepest layer of dentinal caries lesions associated with pulp exposure in 10 teeth diagnosed with symptomatic irreversible pulpitis. DNA was extracted and the microbiome was characterized on the basis of the V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. Bacterial taxa were mapped to 14 phyla and 101 genera composed by 706 different OTUs. Three phyla accounted for approximately 98% of the sequences: Firmicutes, Actinobacteria and Proteobacteria. These phyla were also the ones with most representatives at the species level. Firmicutes was the most abundant phylum in 9/10 samples. As for genera, Lactobacillus accounted for 42.3% of the sequences, followed by Olsenella (13.7%), Pseudoramibacter (10.7%) and Streptococcus (5.5%). Half of the samples were heavily dominated by Lactobacillus, while in the other half lactobacilli were in very low abundance and the most dominant genera were Pseudoramibacter, Olsenella, Streptococcus, and Stenotrophomonas. High bacterial diversity occurred in deep dentinal caries lesions associated with symptomatic irreversible pulpitis. The microbiome could be classified according to the relative abundance of Lactobacillus. Except for Lactobacillus species, most of the highly prevalent and abundant bacterial taxa identified in this study have been commonly detected in infected root canals. The detected taxa can be regarded as candidate pathogens for irreversible pulpitis and possibly the pioneers in pulp invasion to initiate endodontic infection.
The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data

Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S). Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively. Furthermore, we present the first analyses of a substantial protein-coding data set (4.6 kb from one mitochondrial and four nuclear genes). Our results indicate that previous studies may have suffered from inflated support values due to subjective alignment of the ribosomal sequences, but apparently not from significant biases. The protein data provide independent confirmation of several earlier results, including the monophyly of non-xyelid hymenopterans, Pamphilioidea + Unicalcarida, Unicalcarida, Vespina, Apocrita, Proctotrupomorpha and core Proctotrupomorpha. The protein data confirm that Aculeata are nested within a paraphyletic Evaniomorpha, but cast doubt on the monophyly of Evanioidea. Combining the available morphological, ribosomal and protein-coding data, we examine the total-evidence signal as well as congruence and conflict among the three data sources. Despite an emerging consensus on many higher-level hymenopteran relationships, several problems remain unresolved or contentious, including rooting of the hymenopteran tree, relationships of the woodwasps, placement of Stephanoidea and Ceraphronoidea, and the sister group of Aculeata.
Wonky worlds: Listeners revise world knowledge when utterances are odd

World knowledge enters into pragmatic utterance interpretation in complex ways, and may be defeasible in light of speakers’ utterances. Yet there is to date a surprising lack of systematic investigation into the role of world knowledge in pragmatic inference. In this paper, we show that a state-of-the-art model of pragmatic interpretation greatly overestimates the influence of world knowledge on the interpretation of utterances like Some of the marbles sank. We extend the model to capture the idea that the listener is uncertain about the background knowledge the speaker is bringing to the conversation. This extension greatly improves model predictions of listeners’ interpretation and also makes good qualitative predictions about listeners’ judgments of how ‘normal’ the world is in light of a speaker’s statement. Theoretical and methodological implications are discussed.
Pioglitazone could induce remission in major depression: a meta-analysis

Background Pioglitazone, a selective agonist of the nuclear transcription factor peroxisome proliferator-activated receptor-gamma (PPAR-γ), prescribed for the treatment of type 2 diabetes, could have antidepressant properties. However, its potential to induce remission of major depressive episodes, the optimal clinical target for an antidepressant drug, is a matter of concern. Indeed, only one out of four double-blind randomized controlled trials show higher remission rates with pioglitazone than with control treatments. Hence, the main aim of this study was to perform a meta-analysis of the efficacy of pioglitazone for the treatment of MDE, focusing on remission rates. Methods Four double-blind randomized controlled trials, comprising 161 patients with an MDE, were included in this meta-analysis. Pioglitazone was studied either alone (one study) or as add-on therapy to conventional treatments (antidepressant drugs or lithium salts). It was compared either to placebo (three studies) or to metformin (one study). Remission was defined by a Hamilton Depression Rating Scale score <8 after treatment. Results Pioglitazone could induce higher remission rates than control treatments (27% versus 10%, I2=17.3%, fixed-effect model: odds ratio [OR] =3.3, 95% confidence interval [95% CI; 1.4; 7.8], P=0.008). The OR was even higher in the subgroup of patients with major depressive disorder (n=80; 23% versus 8%, I2=0.0%; fixed-effect model: OR =5.9, 95% CI [1.6; 22.4], P=0.009) and in the subgroup of patients without metabolic comorbidities (n=84; 33% versus 10%, I2=0.0%; fixed-effect model: OR =5.1, 95% CI [1.5; 17.9], P=0.01). As compared to control treatments, results suggest six patients would need to be treated with pioglitazone in order to achieve the possibility of one more remission. Conclusion Pioglitazone, either alone or as add-on therapy to conventional treatments, could induce remission of MDE, suggesting that drugs with PPAR-γ agonist properties may be true and clinically relevant antidepressants, even in patients without metabolic comorbidities.
Vitamin D Modulates Expression of the Airway Smooth Muscle Transcriptome in Fatal Asthma

Globally, asthma is a chronic inflammatory respiratory disease affecting over 300 million people. Some asthma patients remain poorly controlled by conventional therapies and experience more life-threatening exacerbations. Vitamin D, as an adjunct therapy, may improve disease control in severe asthma patients since vitamin D enhances glucocorticoid responsiveness and mitigates airway smooth muscle (ASM) hyperplasia. We sought to characterize differences in transcriptome responsiveness to vitamin D between fatal asthma- and non-asthma-derived ASM by using RNA-Seq to measure ASM transcript expression in five donors with fatal asthma and ten non-asthma-derived donors at baseline and with vitamin D treatment. Based on a Benjamini-Hochberg corrected p-value <0.05, 838 genes were differentially expressed in fatal asthma vs. non-asthma-derived ASM at baseline, and vitamin D treatment compared to baseline conditions induced differential expression of 711 and 867 genes in fatal asthma- and non-asthma-derived ASM, respectively. Functional gene categories that were highly represented in all groups included extracellular matrix, and responses to steroid hormone stimuli and wounding. Genes differentially expressed by vitamin D also included cytokine and chemokine activity categories. Follow-up qPCR and individual analyte ELISA experiments were conducted for four cytokines (i.e. CCL2, CCL13, CXCL12, IL8) to measure TNFα-induced changes by asthma status and vitamin D treatment. Vitamin D inhibited TNFα-induced IL8 protein secretion levels to a comparable degree in fatal asthma- and non-asthma-derived ASM even though IL8 had significantly higher baseline levels in fatal asthma-derived ASM. Our findings identify vitamin D-specific gene targets and provide transcriptomic data to explore differences in the ASM of fatal asthma- and non-asthma-derived donors.
Evaluation of Mammography Screening and Awareness Health Promotion Interventions Targeting Women with Disabilities: A Systematic Literature Review

Research evaluating the effectiveness of health promotion interventions that aim to increase mammography utilization and or awareness among women with disabilities is extremely limited. The purpose of this thesis was to systematically review the literature that does exist, and examine the effectiveness and methodological rigor of various health promotion interventions, that aim to increase mammography utilization among women with disabilities. This thesis followed a five-step systematic review process: framing of the research question, identification of relevant work, extraction of relevant data on outcomes and quality, summarization of evidence, and interpretation of evidence. The sample consisted of eight articles that were evaluated and examined with the use of three tools: comparative matrix tool, quality assessment tool, and level of evidence pyramid. The results of the review revealed various health promotion intervention formats, among women with either a mobility impairment, intellectual disability, or learning disability.
Effects of invasion history on physiological responses to immune system activation in invasive Australian cane toads

The cane toad (Rhinella marina) has undergone rapid evolution during its invasion of tropical Australia. Toads from invasion front populations (in Western Australia) have been reported to exhibit a stronger baseline phagocytic immune response than do conspecifics from range core populations (in Queensland). To explore this difference, we injected wild-caught toads from both areas with the experimental antigen lipopolysaccharide (LPS, to mimic bacterial infection) and measured whole-blood phagocytosis. Because the hypothalamic-pituitary-adrenal axis is stimulated by infection (and may influence immune responses), we measured glucocorticoid response through urinary corticosterone levels. Relative to injection of a control (phosphate-buffered saline), LPS injection increased both phagocytosis and the proportion of neutrophils in the blood. However, responses were similar in toads from both populations. This null result may reflect the ubiquity of bacterial risks across the toad’s invaded range; utilization of this immune pathway may not have altered during the process of invasion. LPS injection also induced a reduction in urinary corticosterone levels, perhaps as a result of chronic stress.
Python based framework for HDSLs with an underlying formal semantics: (Invited paper)

Although Moore's law is slowing down, design productivity is still a big issue in semiconductor industry. Drivers are the trend to 3D integration, the addition of design goals such as ultra-low power and safety, and an increasing number of designs in IoT and automotive areas. EDA tools such as high-level synthesis cover a small design area only. Also, the impact of IP reuse is overestimated since IP integration often requires complex configuration and additional software to be developed. To continuously increase design productivity, Infineon heavily relies on an in-house automation framework that utilizes Python as language for automation and synthesis. It supports (and makes use of) classical HDSLs to describe specific design aspects. Mostly structured specification formalisms such as tables, requirements or diagrams (e.g. SysML subsets) are used. These formalisms can be seen as HDSLs with the additional benefit that they exist as a result of a specification process, i.e. need not be coded explicitly. To be able to deal with several formalisms, Infineon's automation framework follows OMG's MDA vision and utilizes meta-models e.g. for generation of infrastructure code. This work focuses on the aspect of combining DSLs, defining a formal semantic for HDSLs and using this definition to validate the correctness of the mapping of HDSLs to HDLs, an essential pillar to connect HDSLs to today's design flows.
Caveolar Fatty Acids and Acylation of Caveolin-1

Purpose Caveolae are cholesterol and sphingolipids rich subcellular domains on plasma membrane. Caveolae contain a variety of signaling proteins which provide platforms for signaling transduction. In addition to enriched with cholesterol and sphingolipids, caveolae also contain a variety of fatty acids. It has been well-established that acylation of protein plays a pivotal role in subcellular location including targeting to caveolae. However, the fatty acid compositions of caveolae and the type of acylation of caveolar proteins remain largely unknown. In this study, we investigated the fatty acids in caveolae and caveolin-1 bound fatty acids. Methods Caveolae were isolated from Chinese hamster ovary (CHO) cells. The caveolar fatty acids were extracted with Folch reagent, methyl esterificated with BF3, and analyzed by gas chromatograph-mass spectrometer (GC/MS). The caveolin-1bound fatty acids were immunoprecipitated by anti-caveolin-1 IgG and analyzed with GC/MS. Results In contrast to the whole CHO cell lysate which contained a variety of fatty acids, caveolae mainly contained three types of fatty acids, 0.48 µg palmitic acid, 0.61 µg stearic acid and 0.83 µg oleic acid/caveolae preparation/5×107 cells. Unexpectedly, GC/MS analysis indicated that caveolin-1 was not acylated by myristic acid; instead, it was acylated by palmitic acid and stearic acid. Conclusion Caveolae contained a special set of fatty acids, highly enriched with saturated fatty acids, and caveolin-1 was acylated by palmitic acid and stearic acid. The unique fatty acid compositions of caveolae and acylation of caveolin-1 may be important for caveolae formation and for maintaining the function of caveolae.
Primary breast cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.

node; HER2, human epidermal growth factor 2 receptor. DCIS, ductal carcinoma in situ; BCS, breast-conserving surgery; WBRT, whole breast radiation therapy; G-CSF, granulocyte colony-stimulating factor; BCT, breast-conserving therapy; RT, radiotherapy; SLNB, sentinel lymph node biopsy; DFS, disease-free survival; AI, aromatase inhibitor; ET, endocrine therapy; uPA-PAI1, urokinase plasminogen activator-plasminogen activator inhibitor 1.
Two-dimensional rheological characteristics of poly(dimethylsiloxane) at the interface of two immiscible liquids

The rheological and thermodynamic characteristics of interfacial adsorption layers of α-(carboxy-ethyl)-ω-(trimethylsiloxy))-poly(dimethylsiloxane) at the interface of two immiscible liquid phases are studied. The formation of a two-dimensional self-organizing poly(dimethylsiloxane) structure at the water-m-xylene interface is discovered; this structure occurs in the LC state and displays thixotropic properties. These properties of interfacial adsorption layers are important for the use of poly(dimethylsiloxane) as a stabilizer in the synthesis of polystyrene suspensions with a narrow particle size distribution, because they not only enhance the stability of dispersions but also ensure healing of defects emerging in protective shells during the deformation of interfacial adsorption layers; that is, a structural-mechanical barrier (according to Rehbinder) is formed. A model of the two-dimensional structure of poly(dimethylsiloxane) formed at the water-m-xylene interface is proposed.
A Thermodynamic Model for Predicting Wax Formation in Jet and Diesel Fuels

A thermodynamic model to predict wax formation and the low-temperature phase behavior of different types of fuel is proposed. The model is based on an accurate description of the nonideality of the phases in equilibrium using modified UNIFAC for the liquid phase and the UNIQUAC equation for the description of the solid phase. A comparison of the model predictions with literature data for the low-temperature behavior of a number of jet fuels, ship propulsion distillate fuels, and diesel fuels is presented to validate the model. It is shown that it provides an excellent description of both the composition of the phases in equilibrium and the fraction of solids in partly crystallized fuels, for all types of fuels studied, in the temperature range from 200 to 300 K. This model should help in designing the new generation of fuels to meet the European standards and in preventing many of the problems associated with wax deposition during the handling of refined products.
Genetically engineered microelectronic infrared filters

A genetic algorithm is used for design of infrared filters and in the understanding of the material structure of a resonant tunneling diode. These two components are examples of microdevices and nanodevices that can be numerically simulated using fundamental mathematical and physical models. Because the number of parameters that can be used in the design of one of these devices is large, and because experimental exploration of the design space is unfeasible, reliable software models integrated with global optimization methods are examined. The genetic algorithm and engineering design codes have been implemented on massively parallel computers to exploit their high performance. Design results are presented for the infrared filter showing new and optimized device design.
PET Imaging of Integrin αVβ3 Expression

PET imaging of integrin αvβ3 expression has been studied intensely by the academia and recently also by the industry. Imaging of integrin αvβ3 expression is of great potential value, as the integrin αvβ3 is a key player in tumor metastasis and angiogenesis. Therefore PET imaging of this target might be a suitable in-vivo biomarker of angiogenesis and metastatic potential of tumors. In this manuscript, the various strategies for PET imaging of the integrin αvβ3 will be summarized, including monomeric and multimeric radiolabelled RGD peptides and nanoparticles. While most experiments have been performed using preclinical tumor models, more and more clinical results on PET imaging of αvβ3 expression are available and will be discussed in detail. However, while a multitude of radiotracer strategies have been successfully evaluated for PET imaging of αvβ3, the ultimate clinical value of this new imaging biomarker still has to be evaluated in large clinical trials.