Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling via Multigene Concatemers

We established a novel method, Gene Expression Profiling via Multigene Concatemers (MgC-GEP), to study multigene expression patterns simultaneously. This method consists of the following steps: (1) cDNA was obtained using specific reverse primers containing an adaptor. (2) During the initial 1–3 cycles of polymerase chain reaction (PCR), the products containing universal adaptors with digestion sites at both termini were amplified using specific forward and reverse primers containing the adaptors. (3) In the subsequent 4–28 cycles, the universal adaptors were used as primers to yield products. (4) The products were digested and ligated to produce concatemers. (5) The concatemers were cloned into the vector and sequenced. Then, the occurrence of each gene tag was determined. To validate MgC-GEP, we analyzed 20 genes in Saccharomyces cerevisiae induced by weak acid using MgC-GEP combined with real-time reverse transcription (RT)-PCR. Compared with the results of real-time RT-PCR and the previous reports of microarray analysis, MgC-GEP can precisely determine the transcript levels of multigenes simultaneously. Importantly, MgC-GEP is a cost effective strategy that can be widely used in most laboratories without specific equipment. MgC-GEP is a potentially powerful tool for multigene expression profiling, particularly for moderate-throughput analysis.
Traction Force Microscopy in 3‐Dimensional Extracellular Matrix Networks

Cell migration through a three‐dimensional (3‐D) matrix depends strongly on the ability of cells to generate traction forces. To overcome the steric hindrance of the matrix, cells need to generate sufficiently high traction forces but also need to distribute these forces spatially in a migration‐promoting way. This unit describes a protocol to measure spatial maps of cell traction forces in 3‐D biopolymer networks such as collagen, fibrin, or Matrigel. Traction forces are computed from the relationship between measured force‐induced matrix deformations surrounding the cell and the known mechanical properties of the matrix. The method does not rely on knowledge of the cell surface coordinates and takes nonlinear mechanical properties of the matrix into account. © 2017 by John Wiley & Sons, Inc.
PKG II effectively reversed EGF‐induced protein expression alterations in human gastric cancer cell lines

Epidermal growth factor receptor (EGFR) plays an important role in gastric cancer (GC) progression. Our previous data demonstrated that type II cGMP‐dependent protein kinase (PKG II) could block the EGF‐EGFR axis as well as down‐stream signaling pathways, for example, MAPK, PI3 K, and PLC in GC cells. However, the exact mechanisms of PKG II against cancer remain unclear. Therefore, the present work was to address the above question. Human GC cell line AGS was infected with adenoviral construct encoding cDNA of PKG II (Ad‐PKG II) to up‐regulate PKG II and then treated with 8‐pCPT‐cGMP. Two‐dimensional electrophoresis (2‐DE) was used to analyze the changes of protein expression in the cells. The results showed that 17 proteins had more than twofold changes in EGF‐treated group compared with control. However, Ad‐PKG II could effectively reversed the changes. Furthermore, far upstream element‐binding protein 1 (FUBP1) and MarvelD3 were chosen and PKG II activation reversed EGF/EGFR‐induced up‐regulation of FUBP1 and downregulation of MarvelD3, respectively. MarvelD3 silence effectively abolished the inhibitory effect of PKG II on EGF‐triggered migration. These data indicated that the inhibitory effect of PKG II partially was associated with MarvelD3.
Self-Reported Visual Perceptual Abnormalities Are Strongly Associated with Core Clinical Features in Psychotic Disorders

Background Past studies using the Bonn Scale for the Assessment of Basic Symptoms (hereafter, Bonn Scale) have shown that self-reported perceptual/cognitive disturbances reveal which persons have or will soon develop schizophrenia. Here, we focused specifically on the clinical value of self-reported visual perceptual abnormalities (VPAs) since they are underexplored and have been associated with suicidal ideation, negative symptoms, and objective visual dysfunction. Method Using the 17 Bonn Scale vision items, we cross-sectionally investigated lifetime occurrence of VPAs in 21 first-episode psychosis and 22 chronic schizophrenia/schizoaffective disorder (SZ/SA) patients. Relationships were probed between VPAs and illness duration, symptom severity, current functioning, premorbid functioning, diagnosis, and age of onset. Results Increased VPAs were associated with: earlier age of onset; more delusions, hallucinations, bizarre behavior, and depressive symptoms; and worse premorbid social functioning, especially in the childhood and early adolescent phases. SZ/SA participants endorsed more VPAs as compared to those with schizophreniform or psychotic disorder-NOS, especially in the perception of color, bodies, faces, object movement, and double/reversed vision. The range of self-reported VPAs was strikingly similar between first-episode and chronic patients and did not depend on the type or amount of antipsychotic medication. As a comparative benchmark, lifetime occurrence of visual hallucinations did not depend on diagnosis and was linked only to poor premorbid social functioning. Conclusion A brief 17-item interview derived from the Bonn Scale is strongly associated with core clinical features in schizophrenia. VPAs hold promise for clarifying diagnosis, predicting outcome, and guiding neurocognitive investigations.
Proceedings of the 5th Symposium on Operating Systems Design and Implementation an Analysis of Internet Content Delivery Systems

In the span of only a few years, the Internet has experienced an astronomical increase in the use of specialized content delivery systems, such as content delivery networks and peer-to-peer file sharing systems. Therefore, an understanding of content delivery on the Internet now requires a detailed understanding of how these systems are used in practice. This paper examines content delivery from the point of view of four content delivery systems: HTTP web traffic, the Akamai content delivery network, and Kazaa and Gnutella peer-to-peer file sharing traffic. We collected a trace of all incoming and outgoing network traffic at the University of Washington, a large university with over 60,000 students, faculty, and staff. From this trace, we isolated and characterized traffic belonging to each of these four delivery classes. Our results (1) quantify the rapidly increasing importance of new content delivery systems, particularly peer-to-peer networks, (2) characterize the behavior of these systems from the perspectives of clients, objects, and servers, and (3) derive implications for caching in these systems.
Prioritizing Consumers in Smart Grid: A Game Theoretic Approach

This paper proposes an energy management technique for a consumer-to-grid system in smart grid. The benefit to consumers is made the primary concern to encourage consumers to participate voluntarily in energy trading with the central power station (CPS) in situations of energy deficiency. A novel system model motivating energy trading under the goal of social optimality is proposed. A single-leader multiple-follower Stackelberg game is then studied to model the interactions between the CPS and a number of energy consumers (ECs), and to find optimal distributed solutions for the optimization problem based on the system model. The CPS is considered as a leader seeking to minimize its total cost of buying energy from the ECs, and the ECs are the followers who decide on how much energy they will sell to the CPS for maximizing their utilities. It is shown that the game, which can be implemented distributedly, possesses a socially optimal solution, in which the sum of the benefits to all consumers is maximized, as the total cost to the CPS is minimized. Numerical analysis confirms the effectiveness of the game.
Longitudinal outcomes of patients enrolled in a phase Ib clinical trial of the adipose‐derived stromal cells‐stromal vascular fraction in idiopathic pulmonary fibrosis

Cell‐based therapies have been used for the management of several diseases, holding promising results. Few studies have evaluated their use in chronic lung diseases. Idiopathic pulmonary fibrosis (IPF) remains a lethal disease although new therapies have emerged the recent years. We have recently published a phase I study of 14 patients receiving endobronchially adipose‐derived stem cells (ADSCs). The aim of this report is to assess the outcome for our patients' population.
Investigation of Antibacterial Properties of Silver Nanoparticle-loaded Poly ( acrylamide-co-itaconic acid )-Grafted Cotton Fabric

Cotton fabric was grafted with a poly (acrylamide-co-itaconic acid) co-polymer via ceric ammonium nitrate (CAN) induced graft co-polymerization in an aqueous medium. The grafted cotton fabric was loaded with Ag nanoparticles by entrapment of Ag+ ions into a grafted polymer network, followed by borohydride reduction. The resulting Ag nanoparticle-loaded grafted fabric was characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) analysis. The Ag nanoparticles were almost monodisperse in nature and their average diameter was approximately 12.5 nm. The fabric shows antibacterial activity against Escherichia coli depending upon the extent of grafting of the polymer network onto the fabric and the amount of nano Ag loaded into the grafted fabric. Finally, the Ag-loaded grafted fabric is found to suppress the bacterial growth approximately 3 h after the immersion of the fabric into a nutrient broth at 37 oC.
Face check development in veneered furniture panels

This project studied check develop in 1-foot square veneered furniture panels. Wood species used were flat-sliced red oak and hard maple cut on a half-round machine. The veneer flitches were clipped to 6-inch widths with the cathedral centered, book matched, and spliced. The resulting faces were 12 inches by the length of the veneer flitch. One set of veneer faces was conditioned at 35 percent relative humidity (RH) and 72°F. The second set of veneer faces was conditioned at 65 percent RH and 72°F. The panel core used was 11/16-inch southern pine particleboard. The particleboard core stock was all taken from the same bundle. The particleboard core was conditioned at 35 percent RH and 72°F. The adhesives used were urea-formaldehyde (UF) and precatalyzed cross-linked PVA. The assembly times were 1 minute and 10 minutes. The panels were first exposed for 3 weeks at 75 to 80 percent RH and then 3 additional weeks at 20 to 25 percent RH. This cycle was repeated three times. After every 3-week exposure, the panels were examined for the number of veneer checks. The panels were also evaluated for veneer checking as they were removed from the hot-press. Thus, the panels were evaluated seven times. The Student-Newman-Keuls test was used to evaluate the presence of face checks. The combination of factors resulting in the fewest face checks for red oak veneered panels was UF adhesive, loose side out, faces conditioned at 35 percent RH, and 1-minute assembly time. Six of the panels in this test were check free and two panels developed just one check each. For hard maple veneered panels, the combination of UF adhesive, tight side out, faces conditioned at 35 percent RH, and 1-minute assembly time resulted in no face check development.
Identification and human exposure prediction of two aldehyde oxidase-mediated metabolites of a methylquinoline-containing drug candidate

Abstract 1. Aldehyde oxidase (AO enzymes)-mediated oxidation predominantly occurs at a carbon atom adjacent to the nitrogen on aromatic azaheterocycles. In the current report, we identified that AO enzymes oxidation took place at both the C-2 and C-4 positions of the methylquinoline moiety of Compound A based on data from mass spectrometric analysis, AO enzymes “litmus” test, and comparison with authentic standards. 2. To assess the potential for inadequate coverage for these two AO enzyme-mediated metabolites in nonclinical safety studies, given concerns due to differences in AO enzymes expression between preclinical species and humans, the human circulating levels of the two AO enzyme-mediated metabolites were predicted prospectively using in vitro and in vivo models. Both formation clearance and elimination clearance of the two metabolites were predicted based on in vitro to in vivo correlation and comparison with in vivo data from rats. 3. The result showed that the 4-OH metabolite of Compound A would account for less than 3% of the total drug-related exposure in human plasma, while the exposure to the 2-oxo metabolite would be relatively high (∼70%). 4. The predicted human exposure levels for the two metabolites are in similar ranges as those observed in monkeys. These data taken together support the advancement to clinical development of Compound A.
Attenuation of lung fibrosis in mice with a clinically relevant inhibitor of glutathione-S-transferase π.

Idiopathic pulmonary fibrosis (IPF) is a debilitating lung disease characterized by excessive collagen production and fibrogenesis. Apoptosis in lung epithelial cells is critical in IPF pathogenesis, as heightened loss of these cells promotes fibroblast activation and remodeling. Changes in glutathione redox status have been reported in IPF patients. S-glutathionylation, the conjugation of glutathione to reactive cysteines, is catalyzed in part by glutathione-S-transferase π (GSTP). To date, no published information exists linking GSTP and IPF to our knowledge. We hypothesized that GSTP mediates lung fibrogenesis in part through FAS S-glutathionylation, a critical event in epithelial cell apoptosis. Our results demonstrate that GSTP immunoreactivity is increased in the lungs of IPF patients, notably within type II epithelial cells. The FAS-GSTP interaction was also increased in IPF lungs. Bleomycin- and AdTGFβ-induced increases in collagen content, α-SMA, FAS S-glutathionylation, and total protein S-glutathionylation were strongly attenuated in Gstp-/- mice. Oropharyngeal administration of the GSTP inhibitor, TLK117, at a time when fibrosis was already apparent, attenuated bleomycin- and AdTGFβ-induced remodeling, α-SMA, caspase activation, FAS S-glutathionylation, and total protein S-glutathionylation. GSTP is an important driver of protein S-glutathionylation and lung fibrosis, and GSTP inhibition via the airways may be a novel therapeutic strategy for the treatment of IPF.
Whole‐exome sequencing of sickle cell disease patients with hyperhemolysis syndrome suggests a role for rare variation in disease predisposition

Hyperhemolysis syndrome (HHS) is an uncommon, but life‐threatening, transfusion‐related complication of red blood cell transfusion. HHS has predominantly been described in patients with sickle cell disease (SCD) and is difficult to diagnose and treat. The pathogenesis of HHS, including its occurrence in only a subset of apparently susceptible individuals, is poorly understood. We undertook whole‐exome sequencing (WES) of 12 SCD‐HHS patients to identify shared genetic variants that might be relevant to the development of HHS.
Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.
Innate and Adaptative Immunity in the Sea-Star Asterias Rubens

The axial organ of the sea star Asterias rubens is a primitive immune organ. The B-like cells, when stimulated by various antigens, produce antibody substances correlating with Mouse Ig Kappa genes. On the other hand elements of the innate immunity are present in Asterias rubens such as Toll-like receptors, interleukin receptors, complement components which contribute to initiate the «antibody factor».
Video In Sentences Out

We present a system that produces sentential descriptions of video: who did what to whom, and where and how they did it. Action class is rendered as a verb, participant objects as noun phrases, properties of those objects as adjectival modifiers in those noun phrases,spatial relations between those participants as prepositional phrases, and characteristics of the event as prepositional-phrase adjuncts and adverbial modifiers. Extracting the information needed to render these linguistic entities requires an approach to event recognition that recovers object tracks, the track-to-role assignments, and changing body posture.
Self-Evaluations and Performance: Evidence from Adolescence

A positive view of the self is often portrayed as a valuable asset in the sense that it can have performance enhancing properties. Using data on self-esteem - the most fundamental manifestation of positive self evaluations - and high school grade point averages of American students we produce results in line with this idea and find a positive link between favorable self-evaluations and higher levels of educational performance. However, when we exploit exogenous variation in self-esteem due to adolescent skin problems in order to account for the possible endogeneity of self-esteem, this finding is reversed and we obtain a negative effect on performance. We discuss mechanisms that may generate such an adverse causal effect of positive self-evaluations, and conclude that self-esteem and effort need not always be complements but can actually be substitutes.
Incorporating D2D to Current Cellular Communication System

A device-to-device (D2D) group works as relay nodes to aid the information delivery from a source to a destination in cellular communication network. Within this system, we propose a communication mechanism to aid traditional cellular communication and correspondingly borrow some channel resource from traditional cellular communication system for D2D communication. On one side, to aid cellular communication, we propose a modified Alamouti scheme which does not modify the operation at the base station. This makes our proposed scheme consistent with previous cellular communication system. On the other side, there are many competitive D2D groups that want to potentially utilize the borrowed channel resource from traditional cellular system for delivering their own information. We model this competition as a game and utilize game theory technique to solve this competition problem.
A Lipid-Anchored NAC Transcription Factor Is Translocated into the Nucleus and Activates Glyoxalase I Expression during Drought Stress[OPEN]

Under drought stress, lipid-anchored MfNACsa translocates to the nucleus by thioesterase MtAPT1-dependent de-S-palmitoylation, regulating GlyI gene expression and GSH/GSSG ratio. The plant-specific NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) play a vital role in the response to drought stress. Here, we report a lipid-anchored NACsa TF in Medicago falcata. MfNACsa is an essential regulator of plant tolerance to drought stress, resulting in the differential expression of genes involved in oxidation reduction and lipid transport and localization. MfNACsa is associated with membranes under unstressed conditions and, more specifically, is targeted to the plasma membrane through S-palmitoylation. However, a Cys26-to-Ser mutation or inhibition of S-palmitoylation results in MfNACsa retention in the endoplasmic reticulum/Golgi. Under drought stress, MfNACsa translocates to the nucleus through de-S-palmitoylation mediated by the thioesterase MtAPT1, as coexpression of APT1 results in the nuclear translocation of MfNACsa, whereas mutation of the catalytic site of APT1 results in colocalization with MfNACsa and membrane retention of MfNACsa. Specifically, the nuclear MfNACsa binds the glyoxalase I (MtGlyl) promoter under drought stress, resulting in drought tolerance by maintaining the glutathione pool in a reduced state, and the process is dependent on the APT1-NACsa regulatory module. Our findings reveal a novel mechanism for the nuclear translocation of an S-palmitoylated NAC in response to stress.
Estrogen receptor β ligands: Recent advances and biomedical applications

Recent work elucidating the role that the estrogen receptor β (ERβ), a member of the nuclear receptor superfamily, plays in regulating various physiological functions has highlighted the potential of this receptor subtype as a therapeutic target for several pathologies. In fact, molecules that are able to selectively activate ERβ hold promise for the treatment of certain cancers, as well as endometriosis, inflammatory diseases including rheumatoid arthritis, and cardiovascular and CNS conditions. Nevertheless, ERβ remains a challenging target because its ligand‐binding cavity is very similar to that present in ERα, and this makes it difficult to develop ligands having sufficient levels of ERβ selectivity for therapeutic use. Nevertheless, considerable advances have recently been made in developing both nonsteroidal and steroidal ERβ‐selective agonists. These molecules constitute not only important tools to probe the biological effects of the selective stimulation of ERβ, but some of them appear to be agents with considerable therapeutic potential. This study provides a detailed review of selective ERβ ligands that have been developed recently. After a brief introduction to the structure and nature of the two ERs and the biology of ERβ and its isoforms, the ligands are classified on the basis of their structures and activities. Common pharmacophore elements are highlighted throughout the description of the various chemical classes analyzed, and these elements are presented in a concluding summary overview along with a discussion of potential therapeutic applications of these agents in biomedicine. © 2009 Wiley Periodicals, Inc. Med Res Rev, 31, No. 3, 364–442, 2011
The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin

Expression of the neuronal kinase DCLK3 is reduced in Huntington’s disease. Galvan et al. report that DCLK3 silencing in the mouse striatum exacerbates the toxicity of mutant huntingtin, whereas DCLK3 overexpression is neuroprotective, and show that DCLK3 regulates the expression of many genes involved in transcription regulation and chromatin remodelling.