Miracle-dz/UniFAR-FTUs huggingface dataset:
Introducing proteins into cultured animal cells.

Improved methods of protein purification and antibody production, together with a burgeoning array of techniques for single-cell analysis, have led increasing numbers of cell biologists to try microinjecting functional proteins, or antibodies raised against them, into living cells. This has highlighted the shortcomings of available techniques, and encouraged attempts to develop new methodologies. Here I present a brief appraisal of available microinjection procedures, and give examples of their application. I have limited my scope to the transfer of proteins into cultured animal cells. The term microinjection is usually associated with direct pressure injection of proteins or other molecules into cells through glass microcapillaries ('needle microinjection'). This is one of the simplest microinjection procedures, and the one most frequently used, but the term is commonly applied to other methods of introducing macromolecules into cells. Most of the other methods fall into two categories: (1) membrane-vesicle methods in which pre-loaded membrane vesicles (erythrocyte ghosts, liposomes, protoplasts) are caused to fuse with cultured cells and release their contents into the cytoplasm; and (2) physical methods, which rely on macromolecules entering cells by diffusion through holes transiently introduced in their plasma membranes by mechanical means (scraping from the substratum, agitating with glass beads).
Preliminary Findings Exploring the Social Determinants of Black Males’ Lay Health Perspectives

The unequal discussion of Black males’ health is a pressing social problem. This study addressed Black males’ lay perspectives regarding their health, illness, and mortality, with attention to the determinants of men’s health, prevention, lifestyle, and opportunities for health promotion using an exploratory/qualitative research methodology. Participants were 68 Black males aged 15 to 68 years, with an average age of 44 years (SD = 14.5). The narratives represented a complex interplay of biopsychosocial factors, ranging from intrapersonal attitudes, interpersonal experiences to discussions about community and public policy injustices. Five prominent themes emerged: (a) lack of chronic disease awareness, (b) fatalism, (c) fear and anxiety of academic–medical settings, (d) hyperactive masculinity fatigue, and (e) the gay–straight divide. The term Tired Black Male Health syndrome was coined in the forum. Implications of these findings are discussed in the context of culturally relevant strategies for improving Black male community health engagement.
Strain effect on the device characteristics of vertical tunneling graphene heterostructure-based transistor

In this work, the compressive normal strain effect on the performance and device characteristics of vertical tunneling graphene FET (VTGFET) is theoretically investigated. The vertical tunneling FET is made of the heterostructure of graphene and hexagonal boron nitride. Molecular dynamic simulation is used to calculate the stress-strain characteristic of the device. An atomistic tight-binding model along with the NEGF formalism is used to investigate the on and off state current and on/off current ratio of VTGFET under strain. Moreover, the effect of different number of hBN layers on the device characteristics is studied. It can be inferred from the results that the compressive normal strain leads to significant decrease in on/off current ratio of device. In addition, the results show that the increase of the number of hBN layers leads to larger strain-induced current variation.
Endoscopic electrocautery incision therapy for benign lower gastrointestinal tract anastomotic strictures

Benign anastomotic strictures can occur in up to 22% of patients who undergo colonic or rectal resection. Traditionally, surgery was the preferred method of treatment, but, over time, endoscopic techniques, such as balloon dilation, have become the preferred modality. However, a high stricture recurrence rate of up to 18-20% and the increased risk of perforation due to uncontrolled stretching are its major drawbacks. Endoscopic electrocautery incision (EECI) allows for controlled mucosal incision in predetermined locations of stricture. In this meta-analysis, we have summarized case reports, case series, retrospective studies and prospective studies describing the different endoscopic EECI techniques used for benign lower gastrointestinal tract anastomotic strictures. Our analysis showed that EECI, either alone or in combination with other modalities (e.g. balloon dilation, steroid injection or argon plasma coagulation) is an effective treatment option for both treatment-naïve and refractory short non-inflammatory strictures. The overall success rate for EECI-based therapy for benign colorectal stricture was 98.4%, with a stricture recurrence rate of 6.0%. No major adverse event (bleeding, infection or perforation) was reported. Only minor adverse events (abdominal pain) were reported in 3.8% of the population.
Activation via Nrf2 in Macrophages TLR-Dependent Heme Oxygenase-1 Gene Bruton's Tyrosine Kinase Is Required for

Heme oxygenase (HO)-1 is the inducible isoform of the rate-limiting enzyme of heme degradation and provides cytoprotection against oxidative stress by its products carbon monoxide and biliverdin. More recently, HO-1 has also been shown to exert immunomodulatory functions via cell type-speciﬁc anti-inﬂammatory effects in myeloid/macrophage cells. In the current study, it is demonstrated that Bruton’s tyrosine kinase (Btk), the gene of which is mutated in the human immunodeﬁciency X-linked agammaglobulinemia, is involved in the upregulation of HO-1 gene expression via TLR signaling in macrophages. The speciﬁc Btk inhibitor LFM-A13 blocked HO-1 induction by the classical TLR4 ligand LPS in cell cultures of RAW264.7 monocytic cells and primary mouse alveolar macrophages. Moreover, upregulation of HO-1 gene expression was abrogated in LPS-stimulated alveolar macrophages from Btk 2 / 2 mice. Transfection studies with luciferase reporter gene constructs demonstrated that LPS-dependent induction of HO-1 promoter activity was attenuated by pharmacological Btk inhibition and by an overexpressed dominant-negative mutant of Btk. This induction was mediated by the transcription factor Nrf2, which is a master regulator of the antioxidant cellular defense. Accordingly, nuclear translocation of Nrf2 in LPS-treated macrophages was reduced by Btk inhibition. The generation of reactive oxygen species, but not that of NO, was involved in this regulatory pathway. Btk-dependent induction of HO-1 gene expression was also observed upon macrophage stimulation with ligands of TLR2, TLR6, TLR7, and LPS-dependent production of ROS is involved in Btk-mediated upregulation of HO-1 macrophages
A Novel Parcellation of Human Cerebral Cortex based on Extrinsic Connectivity

Current theories hold that the human cortex can be subdivided in anatomically and functionally distinct regions, from which interactions cognition arises. In these interactions the long-range axonal connectivity, namely extrinsic connectivity, plays a fundamental role (Passingham et al., 2002). Hence, parceling the cortex taking into account its extrinsic connectivity can help to understand brain’s internal organization. However, current brain atlases are based on cytoarchitecture (Brodmann, 1909) or anatomical landmarks (Desikan et al., 2006), which do not necessarily reflect brain’s connectivity. Even modern approaches, like that of Glasser et al. (2016) did not include connectivity information on their building process. Using such parcellations on studies involving connectivity could introduce a bias, leading to erroneous connections and conclusions. In Gallardo et al. (2016) we presented a hierarchical clustering based technique to parcellate the whole cortex based on its extrinsic connectivity. In this work, we show the consistency of our technique. Then we use it to obtain a novel cortical 55 parcels parcellation based on the extrinsic connectivity of 138 subjects from the Human Connectome Project (HCP). Experiments show that several of our extrinsic parcels are closely related to brain functionality.
VEGF-Trap: A VEGF blocker with potent antitumor effects

Vascular endothelial growth factor (VEGF) plays a critical role during normal embryonic angiogenesis and also in the pathological angiogenesis that occurs in a number of diseases, including cancer. Initial attempts to block VEGF by using a humanized monoclonal antibody are beginning to show promise in human cancer patients, underscoring the importance of optimizing VEGF blockade. Previous studies have found that one of the most effective ways to block the VEGF-signaling pathway is to prevent VEGF from binding to its normal receptors by administering decoy-soluble receptors. The highest-affinity VEGF blocker described to date is a soluble decoy receptor created by fusing the first three Ig domains of VEGF receptor 1 to an Ig constant region; however, this fusion protein has very poor in vivo pharmacokinetic properties. By determining the requirements to maintain high affinity while extending in vivo half life, we were able to engineer a very potent high-affinity VEGF blocker that has markedly enhanced pharmacokinetic properties. This VEGF-Trap effectively suppresses tumor growth and vascularization in vivo, resulting in stunted and almost completely avascular tumors. VEGF-Trap-mediated blockade may be superior to that achieved by other agents, such as monoclonal antibodies targeted against the VEGF receptor.
Retinoic acid-receptor activation of SPB gene transcription in respiratory epithelial cells

Yan, Cong, Manely Ghaffari, Jeffrey A. Whitsett, Xin Zeng, Zvjezdana Sever, and Sui Lin. Retinoic acidreceptor activation of SP-B gene transcription in respiratory epithelial cells. Am. J. Physiol. 275 (Lung Cell. Mol. Physiol. 19): L239–L246, 1998. —Retinoids are known to play important roles in organ development of the lung. Retinoids exert their activity by modulating the expression of numerous genes, generally influencing gene transcription, in target cells. In the present work, the mechanism by which retinoic acid (RA) regulates surfactant protein (SP) B expression was assessed in vitro. RA (9-cis-RA) enhanced SP-B mRNA in pulmonary adenocarcinoma cells (H441 cells) and increased transcriptional activity of the SP-B promoter in both H441 and mouse lung epithelial cells (MLE-15). Cotransfection of H441 cells with retinoid nuclear receptor (RAR)-a, -b, and -g and retinoid X receptor (RXR)-g further increased the response of the SP-B promoter to RA. Treatment of H441 cells with RA increased immunostaining for the SP-B proprotein and increased the number of cells in which the SP-B proprotein was detected. An RA responsive element mediating RA stimulation of the human SP-B promoter was identified. RAR-a and -g and RXR-a but not RAR-b or RXR-b and -g were detected by immunohistochemical analysis of H441 cells. RA, by activating RAR activity, stimulated the transcription and synthesis of SP-B in pulmonary adenocarcinoma cells.
Cooperative spectrum sensing, power and throughput tradeoffs in cognitive radio systems

In this paper, we study the throughput optimization problem and obtain the sensing time and transmit power tarde off, regarding high protection on the primary users. Throughput maximization is a key challenge in cognitive radio networks (CRNs) and it is a criterion for the performance assessment of these systems. Cognitive radio is the solution for scarcity of spectrum in use with the ability to sense the spectrum and share it by allowing the coexistence of unlicensed and licensed users without causing harmful interference on primary users (PUs) that leads to the efficient use of the spectrum. We focus on the throughput maximization in single and cooperative CRNs. For this purpose, we assume a spectrum sharing CRN in which we use the energy detector to optimize the sensing time and power allocation. We solve this optimization problem under some constraints on the average transmit and interference power, as well as the minimum probability of detection on the system. We analyze the simulation results which indicate the effect of sensing time, transmit power, channel attenuation and the threshold of the detection probability on the capacity of CRNs. Eventually, we observe that optimizing the transmit power and sensing time plays an important role in the throughput maximization of the system.
Outcomes of Repeat Endothelial Keratoplasty in Patients With Failed Descemet Stripping Endothelial Keratoplasty

Purpose: To report the outcomes of repeat endothelial keratoplasty (EK) in patients with failed Descemet stripping endothelial keratoplasty (DSEK). Methods: The clinical records of patients with failed DSEK who underwent repeat EK surgery at a single institution were reviewed. Results: A total of 20 eyes of 20 patients (8 men and 12 women) were included. The mean age at initial DSEK surgery was 69.9 ± 11.9 years (range, 41–83 years). The causes of DSEK failure included progressive endothelial failure (8 eyes; 40%), primary graft failure (8 eyes; 40%), and endothelial rejection (4 eyes; 20%). The mean duration from primary DSEK to repeat EK was 13.1 ± 10.3 months (range, 2–33 months). Removal of the failed DSEK donor disc was performed in all eyes. Mean preoperative corrected distance visual acuity (logMAR) before repeat EK surgery was 1.76, and this improved to 0.5 (P < 0.001) at the final follow-up at 27 months. Three eyes had limited corrected distance visual acuity secondary to ocular comorbidities (age-related macular degeneration and advanced glaucomatous optic neuropathy). Conclusions: Repeat EK in patients with DSEK failure is an effective treatment modality. This is the preferred management option compared with penetrating keratoplasty because the advantages of EK surgery are maintained with repeat EK surgery.
Joint Effects of Self-Fertilization and Population Structure on Mutation Load, Inbreeding Depression and Heterosis

Both the spatial distribution of organisms and their mode of reproduction have important effects on the change in allele frequencies within populations. In this article, we study the combined effect of population structure and the rate of partial selfing of organisms on the efficiency of selection against recurrent deleterious mutations. Assuming an island model of population structure and weak selection, we express the mutation load, the within- and between-deme inbreeding depression, and heterosis as functions of the frequency of deleterious mutants in the metapopulation; we then use a diffusion model to calculate an expression for the equilibrium probability distribution of this frequency of deleterious mutants. This allows us to derive approximations for the average mutant frequency, mutation load, inbreeding depression, and heterosis, the simplest ones being Equations 35–39 in the text. We find that population structure can help to purge recessive deleterious mutations and reduce the load for some parameter values (in particular when the dominance coefficient of these mutations is <0.2–0.3), but that this effect is reversed when the selfing rate is above a given value. Conversely, within-deme inbreeding depression always decreases, while heterosis always increases, with the degree of population subdivision, for all selfing rates.
Cytochrome P-450 mediates bioactivation of organic nitrates.

The cellular mechanism of bioactivation underlying guanylate cyclase activation by organic nitrates was investigated. In cultured rat lung fibroblasts (RFL-6 cells), the inhibitor of cytochrome P-450 proadifen (0.1 mM) decreased cyclic GMP stimulation by glyceryl trinitrate (GTN, 1-100 microM) by up to 81%. Cyclic GMP stimulation by isoidide dinitrate was inhibited to a similar degree under these conditions. However, proadifen did not affect cyclic GMP stimulation by sodium nitroprusside that spontaneously releases nitric oxide. Cyclic GMP stimulation in RFL-6 cells by GTN remained unaltered in the presence of the inhibitor of glutathione S-transferase sulfobromophthalein. In the same cell type, a 24-hr pretreatment with the inducer of cytochrome P-450 3-methylcholanthrene (10 microM) augmented cyclic GMP stimulation by GTN or isoidide dinitrate by up to 102%. Cultured porcine aortic endothelial cells were found to be without a cyclic GMP response to GTN, although sodium nitroprusside produced a marked cyclic GMP elevation in these cells. The endothelial cells remained unresponsive to GTN even in the presence of N-acetylcysteine (5 mM). Moreover, in a cell-free preparation from rat liver, glutathione-dependent biotransformation of GTN was not accompanied by activation of soluble guanylate cyclase. These findings suggest that in intact cells bioactivation of, i.e., nitric oxide formation from organic nitrates is mediated by a cytochrome P-450 enzyme system rather than by glutathione S-transferase or free thiols.
Mapping the (R-)Evolution of Technological Fields -- A Semantic Network Approach

The aim of this paper is to provide a framework and novel methodology geared towards mapping technological change in complex interdependent systems by using large amounts of unstructured data from various recent on- and offline sources. Combining techniques from the fields of natural language processing and network analysis, we are able to identify technological fields as overlapping communities of knowledge fragments. Over time persistence of these fragments allows to observe how these fields evolve into trajectories, which may change, split, merge and finally disappear. As empirical example we use the broad area of Technological Singularity, an umbrella term for different technologies ranging from neuroscience to machine learning and bioengineering, which are seen as main contributors to the development of artificial intelligence and human enhancement technologies. Using a socially enhanced search routine, we extract 1,398 documents for the years 2011-2013. Our analysis highlights the importance of generic interface that ease the recombination of technology to increase the pace of technological progress. While we can identify consistent technology fields in static document collections, more advanced ontology reconciliation is needed to be able to track a larger number of communities over time.
Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain

Zebrafish pou5f1, also known as pou2, encodes a POU‐family transcription factor that is transiently expressed in the prospective midbrain and anterior hindbrain during gastrulation, governing brain development. In the present study, we found that the main regulatory elements reside in the proximal upstream DNA sequence from −2.2 to −0.12 kb (the −2.2/−0.1 region). The electrophoretic gel mobility shift assay (EMSA) revealed four functional octamer sequences that can associate with zebrafish Pou2/Pou5f1. The expression of mutated reporter constructs, as well as EMSA, suggested that these four octamer sequences operate in a cooperative manner to drive expression in the mid/hindbrain. We also identified a retinoic acid (RA) ‐responsive element in this proximal region, which was required to repress transcription in the posterior part of the embryo. These data provide a scheme wherein pou2/pou5f1 expression in zebrafish embryos is regulated by both an autoregulatory loop and repression by RA emanating from the posterior mesoderm. Developmental Dynamics 237:1373‐1388, 2008. © 2008 Wiley‐Liss, Inc.
Transformerless Single Phase Inverter Design for LCD Television

A LCD (liquid crystal display) has the CCFL (cold cathode fluorescent lamp) for backlight illumination. The CCFL is fed at high voltage and high frequency voltage by an inverter in the LCD TVs. The backlight unit consumes almost %40 of input power. The inverter with step-up transformer for this unit is commonly supplied from the switch mode power supply. In this work, a parallel resonance inverter without a step-up transformer is used to eliminate the transformer power loss. The circuit is analyzed in PSPICE package program and the results are compared with implementation.
Development of a rapid diagnostic assay based on magnetic bead purification of OXA-β-lactamase mRNA.

AIM To countermeasure the global spread of β-lactamases, we developed a rapid molecular test for the highly variable OXA-β-lactamases that allows minimizing the time to effective treatment. METHODS OXA-mRNA was specifically enriched from total RNA using group-specific biotinylated DNA probes and streptavidin-coated magnetic beads. Phylogenetic OXA groups were distinguished by PCR product size. RESULTS This mRNA fishing method is highly sensitive, yielding specific results from as little as 1 ng total RNA. It enables discrimination of OXA-extended substrate spectrum β-lactamases and carbapenemases and the semi-quantitative detection of highly expressed ISAba1-controlled variants. CONCLUSION Targeting mRNA with specific probes on magnetic beads will allow for adaptation to automated systems, such as point-of-care diagnostics.
Studies on the growth of Eikenella corrodens strain 23834.

The growth characteristics and nutritional requirements of Eikenella corrodens strain 23834 were studied. Generation times, growth rates, and cell yields were determined employing a basal medium supplemented with yeast extract (YE), vitamins, amino acids, phosphate, nitrogen, and sulfate. Incubation was in a variety of air, CO2, and N2 atmospheres. Incubation statically in air or in 10% CO2+ 90% air did not affect the growth rate, while Na2CO3, bubbling with various atmospheres, shaking, or anaerobic incubation all decreased the growth rate. Atmospheric CO2 was found not to be a requirement for growth. The addition of 1-2.5% YE decreased the generation time and increased the cell yield. The growth-promoting factor(s) of YE was a low molecular weight, water-soluble, dialyzable substance which is stable to and not extractable by chloroform-methanol. Vitamins and amino acids singly or in combination were slightly growth-promoting and purines, pyrimidines, and acetate had no effect on Eikenella growth. Increasing concentrations of phosphate inhibited growth, while nitrate but not sulfate proved essential for growth.
Multiple Kernel Learning and Optical Flow for Action Recognition in RGB-D Video

Recognizing human action is valuable for many real world applications such as video surveillance, human computer interaction, smart home and gaming. In this paper, we present a method of action recognition based on hypothesizing that the classification of action can be boosted by motion information using optical flow. Emergence of automatic RGBD video analysis, we propose fusing optical flow is extracted from both RGB and depth channels for action representation. Firstly, we extract optical flow from RGB and depth data. Secondly, motion descriptor with spatial pyramid is computed from histogram of optical flow of RGB and depth. Then, feature pooling technique is used in order to accumulate RGB and depth feature into set of feature vectors for each action. Finally, we use the Multiple Kernel Learning (MKL) technique at the kernel level for action classification from RGB and depth feature pooling. To demonstrate generalizability, our proposed method has been systematically evaluated on two benchmark datasets shown to be more effective and accurate for action recognition compared to the previous work. We obtain overall accuracies of: 97.5 % and 92.8 % with our proposed method on the 3D Action Pairs and MSR-Daily Activity 3D dataset, respectively.