Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronically implanted hyperdrive for cortical recording and optogenetic control in behaving mice

Neural stimulation technology has undergone a revolutionary advance with the introduction of light sensitive ion channels and pumps into genetically identified subsets of cells. To exploit this technology, it is necessary to incorporate optical elements into traditional electrophysiology devices. Here we describe the design, construction and use of a “hyperdrive” capable of simultaneous electrical recordings and optical stimulation. The device consists of multiple microdrives for moving electrodes independently and a stationary fiber for delivering light to the tissue surrounding the electrodes. We present data demonstrating the effectiveness of inhibitory recruitment via optical stimulation and its interaction with physiological and behavioral states, determined by electrophysiological recording and videographic monitoring.
An automatic control model for rat-robot

In this paper, a control model is developed to automate the process of navigation in rat-robot-a new type of bio-robot based on BCI(Brain-Computer Interface) technique. Because of the particular difficulties in rat-robot control, we design a novel control model to ‘learn’ and ‘imitate’ the control behavior of human guidance. General Regression Neural Network (GRNN) model is used to analyze the control commands made by human operators, with the locomotion information of rat-robot recorded and analyzed in a video-based experimental system. The results of the control model shows that the human control process could be well understood and predicted, and expected to generate control commands automatically in future real-time rat-robot navigation experiments.
Expansion stimulated emission depletion microscopy (ExSTED)

Stimulated emission depletion (STED) microscopy is routinely used to resolve the ultra-structure of cells with a ∼10-fold higher resolution compared to diffraction limited imaging. While STED microscopy is based on preparing the excited state of fluorescent probes with light, the recently developed expansion microscopy (ExM) provides sub-diffraction resolution by physically enlarging the sample before microscopy. Expansion of fixed cells by crosslinking and swelling of hydrogels easily enlarges the sample ∼4-fold and hence increases the effective optical resolution by this factor. To overcome the current limits of these complimentary approaches, we here combined ExM with STED (ExSTED) and demonstrate an increase in resolution of up to 30-fold compared to conventional microscopy (<10 nm lateral and ∼50 nm isotropic). While the increase in resolution is straight forward, we found that high fidelity labelling via multi-epitopes is required to obtain emitter densities that allow to resolve ultra-structural details with ExSTED. Our work provides a robust template for super resolution microscopy of entire cells in the ten nanometer range.
An accelerated constant modulus algorithm for space-time blind equalization

We address the problem of signal separation using space-time blind equalization techniques. A novel blind algorithm, denoted ACMA (Accelerated Constant Modulus Algorithm), is proposed. It minimizes the constant modulus cost function and is based on a tuner used in adaptive control that sets the second derivative (“acceleration ”) of the coefficient estimates. Both the convergence speed and computational complexity of Multiuser ACMA lie between those of the Multiuser Constant Modulus and the Multiuser Shalvi-Weinstein algorithms. Some preliminary results show that the proposed algorithm presents a robust behavior with respect to global minima and tracking capability.
Toss-up wear leveling: Protecting Phase-Change Memories from inconsistent write patterns

Limited write endurance is one of major obstacles to adopt Phase Change Memories (PCMs) in practice as future main memory. Considering process variation (PV) and non-uniform write intensity, PCM cells with low endurance (i.e. weak cells) can wear out in seconds under intensive writes. To prolong PCMs' lifetime, many PV-aware wear leveling schemes have been proposed following a common idea: intensive writes are predicted and allocated to cells with high endurance (i.e. strong cells) based on the write intensity distribution, which should be consistent at predicted intervals. However, we discover that this idea leaves a serious vulnerability against a malicious program, which is designed to have an inconsistent write intensity distribution. Prior wear-leveling schemes can even be leveraged to speed up wearing out weak cells. To counteract this attack, we propose Toss-up Wear Leveling (TWL), a novel scheme that randomly allocates writes between two bond blocks discounting the consistency of write distribution. Experiment results demonstrate that, compared to prior works, TWL can improve lifetime substantially with negligible overhead in performance and hardware cost.
Glucocorticoid receptor isoform‐specific regulation of development, circadian rhythm, and inflammation in mice

Glucocorticoids are primary stress hormones, and their synthetic derivatives are widely used clinically. The therapeutic efficacy of these steroids is limited by side effects and glucocorticoid resistance. Multiple glucocorticoid receptor (GR) isoforms are produced from a single gene by alternative translation initiation; however, the role individual isoforms play in tissue‐specific responses to glucocorticoids is unknown. We have generated knockin mice that exclusively express the most active receptor isoform, GR‐C3. GR‐C3 knockin mice die at birth due to respiratory distress. Microarray analysis of fibroblasts from wild‐type and GR‐C3 mice indicated that most genes regulated by GR‐C3 were unique to this isoform. Antenatal glucocorticoid administration rescued GR‐C3 knockin mice from neonatal death. Dual‐energy X‐ray absorptiometry revealed no major alterations in body composition for rescued knockin mice. Rescued female, but not male, GR‐C3 mice exhibited increased wheel running activity in the light portion of the day. LPS administration induced premature mortality in rescued GR‐C3 knockin mice, and gene expression studies revealed a deficiency in the ability of GR‐ C3 to repress a large cohort of immune and inflammatory response genes. These findings demonstrate that specific GR translational isoforms can influence development, circadian rhythm, and inflammation through the regulation of distinct gene networks. —Oakley, R. H. , Ramamoorthy, S. , Foley, J. F. , Busada, J. T. , Lu, N. Z. , Cidlowski, J. A. Glucocorticoid receptor isoform‐specific regulation of development, circadian rhythm, and inflammation in mice. FASEB J. 32, 5258–5271 (2018). www.fasebj. org
Time-predictable memory arbitration for a Java chip-multiprocessor

In this paper, we propose an approach to calculate worst-case execution times (WCET) of tasks running on a homogeneous Java multiprocessor. These processors access a shared main memory. Hence, the tasks running on different CPUs may influence the execution times of each other. Therefore, we implemented a time division multiple access arbiter that divides the memory access time into equal time slots, one time slot for each CPU. This memory arbitration allows calculating upper bounds for the execution time of Java bytecodes depending on the number of CPUs, the size of the time slot, and the memory access time. A WCET analysis tool can utilize these results and generate temporal, upper bounds for application tasks. We further explore how the size of the time slot and the number of CPUs in the system influence the WCET results. Furthermore, a real-world application task is used to compare the analyzed results with measured execution times. This paper describes the timing analysis of a time-predictable Java multiprocessor with shared memory.
High expression of long non-coding RNA GHET 1 is associated with unfavorable prognosis in hepatocellular carcinoma

Background: Recently, emerging evidence has suggested the role of long non-coding RNAs (lncRNAs) in human carcinogenesis. Herein, we aimed to detect the expression profiles and functional implications of lncRNA GHET1 in human HCC. Methods: GHET1 levels in a cohort of 179 pairs of HCC tissues and pair-matched noncancerous hepatic tissues were tested using quantitative real-time PCR (qRT-PCR). The correlations of GHET1 expression with clinicopathologic features and prognostic outcomes were also analyzed in these HCC patients. The effects of GHET1 on HCC cell proliferation, cell-cycle profiles, Cyclin D1 expression and cell migration/invasion in vitro were investigated through CCK-8, flow cytometer, Western blot and transwell assays, respectively. Results: We verified that GHET1 was significantly up-regulated in HCC compared with corresponding non-tumor tissues, and a high level of GHET1 was correlated with larger tumor size, advanced TNM stage, and positive vascular invasion. HCC patients with high GHET1 expression level had shorter OS and DFS than the low GHET1 expression group, and multivariate logistic regression analysis considered high GHET1 expression as an independent factor of unsatisfactory prognosis. Functionally, knock-down of GHET1 attenuated HCC cell proliferation in vitro through inducing G0/G1 arrest and inhibiting Cyclin D1 expression. In addition, knock-down of GHET1 also inhibited migration and invasion ability of HCC cells in vitro. Conclusions: Collectively, these data demonstrated that GHET1 is obviously increased in HCC tissues, and uncontrolled GHET1 overexpression might drive HCC progression. Therefore, GHET1 might serve as a novel indicator of unsatisfactory prognosis and a promising therapeutic target for HCC patients.
Burnout in Health Professionals According to Their Self-Esteem, Social Support and Empathy Profile

Introduction: Professionals in the healthcare field are in situations that could be a source of stress and sometimes develop burnout syndrome. Self-esteem, social support, and empathy are variables which intervene and influence the appearance of this syndrome. Objective: Identify healthcare professional profiles based on self-esteem, empathy and perceived social support, and analyze the extent to which these profiles show differences in developing burnout. Method: The sample was made up of 719 healthcare professionals with a mean of 38.52 years of age. The Short Questionnaire of Burnout, the Rosenberg Self-Esteem Scale, the Perceived Social Support Questionnaire and the Basic Empathy Scale were used. Results: The results of a cluster analysis with self-esteem, empathy, and perceived social support showed four groups/profiles. Two of them, which included professionals with low self-esteem, differed in the rest of the characteristics. Furthermore, significant differences in burnout scores were found among the groups identified. Conclusion: The results show the need to study burnout with attention to individual and or social characteristics, where self-esteem is shown to be one of the explanatory variables making the main differences among the groups.
Microgastrinae (Hymenoptera: Braconidae) parasitizing Epirrita autumnata (Lepidoptera: Geometridae) larvae in Fennoscandia with description of Cotesia autumnatae Shaw, sp. n.

The microgastrine subset of hymenopteran parasitoids of the geometrid Epirrita autumnata is investigated in Fennoscandia. Ecology, including population dynamics, of the moth has been intensively studied in northern and mountainous Finland, Norway and Sweden. Recently supported hypotheses about the causes of its cyclic population dynamics stress the role of parasitoids, while the parasitoid complex with some 15 species is insufficiently known. The complex includes four solitarymicrogastrine species, Protapanteles anchisiades (Nixon), P. immunis (Wesmael), Cotesia salebrosa (Marshall) and C. autumnatae Shaw, sp. n. Here, we provide detailed figures for the latter, which is morphologically close to C. jucunda (Marshall), and describe the species as new to science. We also providemore general habitus figures of the other three species, as well as an identification key for the four species, aiming to aid recognition of these species by ecologists dealingwithmicrogastrine parasitoids of E. autumnata and their alternative geometrid hosts.
Relationship between bovine endometrial thickness and plasma progesterone and estradiol concentrations in natural and induced estrus

The objective of this study was to investigate cyclical changes in endometrial thickness in relation to progesterone (P4) and estradiol-17β (E2) concentrations during natural and induced estrus in 15 cows. In the prostaglandin (PG) F2α-induced estrus group, ultrasonography (USG) at 6-h intervals was used to determine endometrial thickness 48–24 h before the PGF2α treatment until 24 h after ovulation (ovulation = Day 0). In the natural estrus group, USG was performed every 48 h from Day 3 to Days 15–18 after the first ovulation, and then every 6 h until 24 h after ovulation. Endometrial thickness was standardized using Day 13 as a reference day. Blood was collected during every USG examination and plasma P4 and E2 concentrations were determined. Endometrial thickness of the induced estrus group (n = 11) was greater than that of the natural estrus group (n = 9) between 60 and 12 h before ovulation (P < 0.05). In the natural estrus group, prior to an increase in endometrial thickness, a decrease in P4 and an increase in E2 were detected. In the induced estrus group, based on the time of ovulation, an increase in endometrial thickness was detected at the same time of a decrease in P4 before an increase in E2. These results suggest that decreases in P4 concentrations may be a cue to changes in endometrial thickness, while increases in E2 concentrations appear to sustain and/or enhance these changes.
Efficient Expression of Genes in the Drosophila Germline Using a UAS Promoter Free of Interference by Hsp70 piRNAs

Using the yeast GAL4 transcription factor to control expression in Drosophila melanogaster has long been ineffective in female germ cells during oogenesis. Here, DeLuca and Spradling show that the expression problem of most Drosophila molecular tools. Controlling the expression of genes using a binary system involving the yeast GAL4 transcription factor has been a mainstay of Drosophila developmental genetics for nearly 30 years. However, most existing GAL4 expression constructs only function effectively in somatic cells, but not in germ cells during oogenesis, for unknown reasons. A special upstream activation sequence (UAS) promoter, UASp was created that does express during oogenesis, but the need to use different constructs for somatic and female germline cells has remained a significant technical limitation. Here, we show that the expression problem of UASt and many other Drosophila molecular tools in germline cells is caused by their core Hsp70 promoter sequences, which are targeted in female germ cells by Hsp70-directed Piwi-interacting RNAs (piRNAs) generated from endogenous Hsp70 gene sequences. In a genetic background lacking genomic Hsp70 genes and associated piRNAs, UASt-based constructs function effectively during oogenesis. By reducing Hsp70 sequences targeted by piRNAs, we created UASz, which functions better than UASp in the germline and like UASt in somatic cells.
NMF: A Modeling Framework for the .NET Platform

For its promises in terms of increased productivity, Modeldriven engineering (MDE) is getting applied increasingly often in both industry and academia. However, most tools currently available are based on the Eclipse Modeling Framework (EMF) and hence based on the Java platform whereas tool support for other platforms is limited. This leads to a language and tool adoption problem for developers of other platforms such as . NET. As a result, few projects on the . NET platform adopt MDE. Furthermore, the limited tool availability introduces a technical barrier in the interoperability between EMF and . NET applications. In this paper, we present the . NET Modeling Framework (NMF), a tool set for model repositories, model-based incrementalization, model transformation, model synchronization and code generation. The framework makes intensive use of the C# language as host language for model transformation and synchronization languages, whereas the model repository serialization is compatible with EMF. This solves the language adoption problem for C# programmers and creates a bridge to the EMF platform.
The ability of streptomycin-loaded chitosan-coated magnetic nanocomposites to possess antimicrobial and antituberculosis activities

Magnetic nanoparticles (MNPs) were synthesized by the coprecipitation of Fe2+ and Fe3+ iron salts in alkali media. MNPs were coated by chitosan (CS) to produce CS-MNPs. Streptomycin (Strep) was loaded onto the surface of CS-MNPs to form a Strep-CS-MNP nanocomposite. MNPs, CS-MNPs, and the nanocomposites were subsequently characterized using X-ray diffraction and were evaluated for their antibacterial activity. The antimicrobial activity of the as-synthesized nanoparticles was evaluated using different Gram-positive and Gram-negative bacteria, as well as Mycobacterium tuberculosis. For the first time, it was found that the nanoparticles showed antimicrobial activities against the tested microorganisms (albeit with a more pronounced effect against Gram-negative than Gram-positive bacteria), and thus, should be further studied as a novel nano-antibiotic for numerous antimicrobial and antituberculosis applications. Moreover, since these nanoparticle bacteria fighters are magnetic, one can easily envision magnetic field direction of these nanoparticles to fight unwanted microorganism presence on demand. Due to the ability of magnetic nanoparticles to increase the sensitivity of imaging modalities (such as magnetic resonance imaging), these novel nanoparticles can also be used to diagnose the presence of such microorganisms. In summary, although requiring further investigation, this study introduces for the first time a new type of magnetic nanoparticle with microorganism theranostic properties as a potential tool to both diagnose and treat diverse microbial and tuberculosis infections.
Comparing a passive-elastic and a powered prosthesis in transtibial amputees

Passive-elastic foot prostheses cannot produce net work. Consequently, passive-elastic foot prostheses are limited in their ability to enable a biologically-realistic gait pattern in transtibial amputees. This shortcoming results in difficulties in balance and walking and leads to high levels of oxygen consumption during locomotion. A powered prosthesis has the potential for overcoming these problems and allowing transtibial amputees to achieve a biologically-realistic gait pattern. In this study, we compared the effects of the Ceterus by Össur, a traditional passive-elastic prosthesis, with those of the PowerFoot Biom (iWalk, Cambridge, MA), a recently-developed powered prosthesis. Gait biomechanics and metabolic cost were compared in a group of 5 transtibial amputees during level-ground walking. The results provided preliminary evidence that the use of a powered prosthesis leads to a decrease in the level of oxygen consumption during ambulation due to improvements in ankle kinematics and kinetics primarily during late stance. An average decrease in oxygen consumption of 8.4% was observed during the study when subjects used the PowerFoot compared to the Ceterus. An average increase of 54% was observed in the peak ankle power generation during late stance. Our results suggest that powered prostheses have the potential for significantly improving ambulation in transtibial amputees.
Silicon dioxide nanoparticle exposure affects small intestine function in an in vitro model

Abstract The use of nanomaterials to enhance properties of food and improve delivery of orally administered drugs has become common, but the potential health effects of these ingested nanomaterials remain unknown. The goal of this study is to characterize the properties of silicon dioxide (SiO2) nanoparticles (NP) that are commonly used in food and food packaging, and to investigate the effects of physiologically realistic doses of SiO2 NP on gastrointestinal (GI) health and function. In this work, an in vitro model composed of Caco-2 and HT29-MTX co-cultures, which represent absorptive and goblet cells, was used. The model was exposed to well-characterized SiO2 NP for acute (4 h) and chronic (5 d) time periods. SiO2 NP exposure significantly affected iron (Fe), zinc (Zn), glucose, and lipid nutrient absorption. Brush border membrane intestinal alkaline phosphatase (IAP) activity was increased in response to nano-SiO2. The barrier function of the intestinal epithelium, as measured by transepithelial electrical resistance, was significantly decreased in response to chronic exposure. Gene expression and oxidative stress formation analysis showed NP altered the expression levels of nutrient transport proteins, generated reactive oxygen species, and initiated pro-inflammatory signaling. SiO2 NP exposure damaged the brush border membrane by decreasing the number of intestinal microvilli, which decreased the surface area available for nutrient absorption. SiO2 NP exposure at physiologically relevant doses ultimately caused adverse outcomes in an in vitro model.
Political journalists’ corporate and personal identities on Twitter profile pages: A comparative analysis in four Westminster democracies

The practice for journalists to present an identity and brand the self on social media has become common across many newsrooms, yet its practice is still poorly understood. Focusing on journalists’ self-representations on the social network site Twitter, this study aims to address the lack of empirical understanding through an analysis of the identities which political journalists present on their Twitter profile pages. A total of 679 accounts of parliamentary press gallery journalists in Australia, Canada, New Zealand and the United Kingdom were analyzed, with a focus on various textual and visual pieces of professional and personal information. The article develops scales of corporate and personal identity, finding that UK and Canadian journalists most strongly differentiate between personal and corporate identities. Differences across countries are linked to political and economic aspects of the respective media systems.
Dose‐Finding with Two Agents in Phase I Oncology Trials

Summary. We propose an adaptive two‐stage Bayesian design for finding one or more acceptable dose combinations of two cytotoxic agents used together in a Phase I clinical trial. The method requires that each of the two agents has been studied previously as a single agent, which is almost invariably the case in practice. A parametric model is assumed for the probability of toxicity as a function of the two doses. Informative priors for parameters characterizing the single‐agent toxicity probability curves are either elicited from the physician(s) planning the trial or obtained from historical data, and vague priors are assumed for parameters characterizing two‐agent interactions. A method for eliciting the single‐agent parameter priors is described. The design is applied to a trial of gemcitabine and cyclophosphamide, and a simulation study is presented.