Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural features of the nucleotide sequences of virus and organelle genomes

The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P (L) (the probability of the base-distribution at L), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.
EGF Receptor-Dependent Mechanism May be Involved in the Tamm–Horsfall Glycoprotein-Enhanced PMN Phagocytosis via Activating Rho Family and MAPK Signaling Pathway

Our previous studies showed that urinary Tamm–Horsfall glycoprotein (THP) potently enhanced polymorphonuclear neutrophil (PMN) phagocytosis. However, the domain structure(s), signaling pathway and the intracellular events responsible for THP-enhanced PMN phagocytosis remain to be elucidated. THP was purified from normal human urine. The human promyelocytic leukemia cell line HL-60 was induced to differentiate into PMNs by all-trans retinoid acid. Pretreatment with different MAPK and PI3K inhibitors was used to delineate signaling pathways in THP-enhanced PMN phagocytosis. Phosphorylation of molecules responsible for PMN phagocytosis induced by bacterial lipopolysaccharide (LPS), THP, or human recombinant epidermal growth factor (EGF) was evaluated by western blot. A p38 MAPK inhibitor, SB203580, effectively inhibited both spontaneous and LPS- and THP-induced PMN phagocytosis. Both THP and LPS enhanced the expression of the Rho family proteins Cdc42 and Rac that may lead to F-actin re-arrangement. Further studies suggested that THP and EGF enhance PMN and differentiated HL-60 cell phagocytosis in a similar pattern. Furthermore, the EGF receptor inhibitor GW2974 significantly suppressed THP- and EGF-enhanced PMN phagocytosis and p38 and ERK1/2 phosphorylation in differentiated HL-60 cells. We conclude that EGF receptor-dependent signaling may be involved in THP-enhanced PMN phagocytosis by activating Rho family and MAP kinase.
Communication, leadership and coordination failure

We investigate the limits of communication and leadership in avoiding coordination failure in minimum effort games. Our environment is challenging, with low benefits of coordination relative to the effort cost. We consider two leader types: cheap-talk leader-communicators who suggest an effort level, and first-mover leaders who lead by example. Both types of leadership have some ability to increase effort in groups with no history, but are insufficient in groups with a history of low effort. Using the strategy method for followers’ responses, we attribute the persistence of coordination failure to the presence of followers who do not follow the leader.
Novel approaches to the diagnosis and treatment of posttraumatic stress disorder

Posttraumatic stress disorder (PTSD) was officially proposed as separate diagnosis in DSM-III, although the clinical consequences of trauma were recognized since ancient times. After its identification in DSM-III, the neurobiology of chronic PTSD has been area of increasing investigation. Earlier the psychoanalytic model of explanation and treatment mostly prevailed. Epidemiological studies show high prevalence of PTSD in general population and specific groups exposed to the traumatic events (survivors of war trauma, natural disasters, terrorist attacks, etc.). Trauma and its consequences affect significantly individual health and functioning, and whole society. The diagnosis of PTSD may have a several subtypes, including psychotic symptoms, depending upon pre-exiting psychiatric disorder, trauma severity and duration, comorbidity, post-trauma social environment, etc. The role of trauma as an etiological factor in other psychiatric disorders and symptoms remains to be clarified. This paper presents the diagnostic and therapeutic issues in relation to the stress-related disorders with the emphasis on our own experiences in the diagnostic assessment and treatment of psychotraumatized persons (establishing more precious diagnosis of PTSD and comorbid diagnoses, differential diagnoses, different models of treatment in the community and institutions after massive traumatization, including “ Croatian model” , treatment of PTSD with psychotic features with novel antipsychotics, etc.).
SDF1-Induced Antagonism of Axonal Repulsion Requires Multiple G-Protein Coupled Signaling Components That Work in Parallel

SDF1 reduces the responsiveness of axonal growth cones to repellent guidance cues in a pertussis-toxin-sensitive, cAMP-dependent manner. Here, we show that SDF1's antirepellent effect can be blocked in embryonic chick dorsal root ganglia (DRGs) by expression of peptides or proteins inhibiting either Gαi, Gαq, or Gβγ. SDF1 antirepellent activity is also blocked by pharmacological inhibition of PLC, a common effector protein for Gαq. We also show that SDF1 antirepellent activity can be mimicked by overexpression of constitutively active Gαi, Gαq, or Gαs. These results suggest a model in which multiple G protein components cooperate to produce the cAMP levels required for SDF1 antirepellent activity.
Frequencies of the Common MEFV Gene Mutations in Adiyaman, Southeast Anatolia, Turkey

Abstract Familial Mediterranean fever (FMF) is an autosomal recessive disorder characterized by fever and serosal inflammation. The reasons for the disorder are mutations in the Mediterranean fever (MEFV) gene; the most common of which are M694V, M680I, M694I and V726A. In this study, we aimed to screen these common mutations of the MEFV gene and then determine the prevalence of FMF according to these mutations in Adıyaman, Southeast Anatolia, Turkey. Seven hundred and sixty-seven healthy individuals from the region of Adıyaman participated in the study. Polymerase chain reaction-amplification refractory mutation system (PCR-ARMS) methods were used to determine the common mutations of the MEFV gene. Twenty-six (3.9%) individuals had only one mutation in the MEFV gene, 25 individuals were heterozygous and one person was homozygous for the V726A mutation (0.15%). In the present study, the V726A mutation (50.0%) was the most frequent, followed by M694V (38.5%), M680I (7.7%) and M694I (3.8%). It was seen that the carrier rate was very low and the prevalence of FMF was 0.15%, according to the common mutations of the MEFV gene in Adıyaman, Southeast Anatolia, Turkey.
Hubungan Antara Tingkat Pengetahuan Dengan Perilaku Bullying Pada RemajaDi SMK PGRI Semarang

Latar Belakang: Bullying adalah perilaku agresif yang dilakukan secara sengaja terjadi berulang-ulang untuk menyerang seorang target atau korban yang lemah, mudah dihina dan tidak bisa membela diri sendiri . Penelitian yang dilakukan oleh SEJIWA (2008) tentang kekerasan bullying di tiga kota besar di Indonesia, yaitu Yogyakarta, Surabaya, dan Jakarta mencatat terjadinya tingkat kekerasan sebesar 67,9% di tingkat Sekolah Menengah Atas (SMA) dan 66,1% di tingkat Sekolah Menengah Pertama (SMP). Tujuan dari penelitian ini adalah untuk mengidentifikasi hubungan antara tingkat pengetahuan dengan perilaku bullying pada remaja di SMK PGRI Semarang. Metode: Penelitian kuantitatif, desain penelitian yang digunakan adalah deskriptif dengan jenis studi korelasional. Pendekatan yang digunakan cross-sectional Teknik pengambilan sampel yaitu simple random sampling. Jumlah responden 75 siswa terdiri dari kelas XI berjumlah 35 siswa dan kelas XII berjumlah 40 siswa. Data diolah secara statistik menggunakan rumus Rank Spearman. Hasil: Berdasarkan hasil penelitian dari 75 responden menyatakan tingkat pengetahuan rendah tentang bullying sebanyak 1,3%, tingkat pengetahuan sedang sebanyak 54,7% dan tingkat pengetahuan tinggi sebanyak 44,0%. Dari 75 responden, responden yang tidak pernah melakukan perilaku bullying sebanyak 0%, responden yang jarang melakukan perilaku bullying sebanyak 60,0% dan responden yang sering melakukan perilaku bullying sebanyak 40,0% dengan P value = 0,001 (p <0,05). Simpulan: Ada hubungan antara tingkat pengetahuan dengan perilaku bullying Kata kunci: Tingkat Pengetahuan, Perilaku Bullying, Remaja
Self-Portraits: Smartphones Reveal a Side Bias in Non-Artists

According to surveys of art books and exhibitions, artists prefer poses showing the left side of the face when composing a portrait and the right side when composing a self-portrait. However, it is presently not known whether similar biases can be observed in individuals that lack formal artistic training. We collected self-portraits by naïve photographers who used the iPhone™ front camera, and confirmed a right side bias in this non-artist sample and even when biomechanical constraints would have favored the opposite. This result undermines explanations based on posing conventions due to artistic training or biomechanical factors, and is consistent with the hypothesis that side biases in portraiture and self-portraiture are caused by biologically- determined asymmetries in facial expressiveness.
Gods, Guides and Gardeners: Preservice Music Educators' Personal Teaching Metaphors

This study explores the use of metaphor in preservice teachers' representations of themselves as teachers and their relationships to conceptions of practice. Specifically, we sought to identify through self-generated pictorial and narrative metaphors the teaching roles and assumptions that preservice music teachers use to characterize themselves. Our main research questions were: What do preservice teachers imagine teaching to be? What representations do they use to characterize teachers? Data analysis used a descriptive approach that included the construction of a category-classification scheme built upon patterning and comparing responses. Analysis of preservice teachers 'pictorial metaphors suggests a wide range of responses with images of growth, transmission, facilitating, nurturing, and sharing emerging as broad categories, supported by analysis of narratives. Interpretation of preservice teachers' images suggests three root metaphors: production, growth and travel. Implications for music education are drawn specifically within the context of music teacher education. Areas for further research are suggested.
Parathyroid carcinoma with lung metastasis in a thirteen-year-old girl

Parathyroid carcinoma is a rare disease in pediatric patients. We present a case of a 13-year-old girl who presented to the Thyroid Department for an asymptomatic palpable neck mass for 1 year. The high levels of calcium, ionized calcium, and parathyroid hormone level along with parathyroid scintigraphy studies suggested primary hyperparathyroidism. Parathyroid carcinoma was confirmed by biopsy and pathologic examination after resection. Six months postoperatively, persistent hypercalcemia and multiple lung metastases were found on computed tomography. Bilateral lung wedge resection was performed. En bloc resection for primary parathyroid carcinoma and aggressive resection of metastatic disease is the most effective treatment to control hypercalcemia.
Media effects: Marshall McLuhan, television culture, and "The X-Files"

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Procedural and declarative database update languages

INTRODUCTION. While query languages have been extensively stu&ed, update languages have only recently become the ObJect of formal lnvesngaaon Recent results focused on the computanonal power of update transactions [AVl, AV2] and on the use of transacnons as speckanon tools [AVl, Br, CCF] In [AVl], we mtroduced a procedural, non-detenmmstlc update transacnon language (TL) and proved certam completeness propemes of this language with respect to updaang and speclficaaon power In tis paper, we mtmduce a determuusnc counterpart of TL, as well as non-detemumsnc and detenmmsuc declaranve update languages, and show that these languages are computationally complete wth respect to database updates We also define resmcttons of the complete languages, and charactenze ther power Several of the resmcted languages correspond to natural complexity classes of updates Our results pro-de mslght mto the connections between procedural and declarative languages, and between non-detemmstic and determmutlc languages
Autoantibodies to Tumor-Associated Antigens in Breast Carcinoma

Autoantibodies (AAbs) to tumor-associated antigens (TAAs) have been identified in the circulation of patients with cancer. This paper will focus on recent knowledge related to circulating AAbs to TAAs in breast carcinoma. So far, the following TAAs have been identified to elicit circulating AAbs in breast carcinoma: p53, MUC-1, heat shock proteins (HSP-27, HSP-60, and HSP-90), HER2/neu/c-erb B2, GIPC-1, c-myc, c-myb, cancer-testis antigens (NY-ESO-1), BRCA1, BRCA2, endostatin, lipophilin B, cyclin B1, cyclin D1, fibulin, insulin-like growth factor binding protein 2 (IGFBP-2), topoisomerase II alpha (TOPO2α), and cathepsin D. Measurement of serum AAbs to one specific TAA only is of little value for screening and early diagnosis of breast carcinoma; however, assessment of AAbs to a panel of TAAs may have promising diagnostic potential.
Light increases the gap junctional coupling of retinal ganglion cells

We examined the effect of light adaptation on the gap junctional coupling of α‐ganglion cells (α‐GCs) in rabbit and mouse retinas. We assayed changes in coupling by measuring parameters of tracer coupling following injection of α‐GCs with Neurobiotin and the concerted spike activity of α‐GC neighbours under dark‐ and light‐adapted conditions. We found that light adaptation using mesopic or photopic background lights resulted in a dramatic increase in the labelling intensity, number, and spatial extent of ganglion and amacrine cells coupled to OFF α‐GCs when compared to levels seen under dark adaptation. While this augmentation of coupling by light did not produce an increase in the concerted spontaneous activity of OFF α‐GC neighbours, it did significantly increase correlated light‐evoked spiking. This was seen as an increase in the number of correlated spikes for α‐GC neighbours and an extension of correlations to second‐tier neighbours that was not seen under dark‐adapted conditions. Pharmacological studies in the rabbit retina indicated that dopamine mediates the observed changes in coupling by differentially activating D1 and D2 receptors under different adaptation states. In this scheme, activation of dopamine D1 receptors following light exposure triggers cAMP‐mediated intracellular pathways resulting in an increase in gap junctional conductance. Overall, our results indicate that as we move from night to day there is an enhanced electrical coupling between α‐GCs, thereby increasing the concerted activity believed to strengthen the capacity and efficiency of information flow across the optic nerve.
Influence of thymic genotype on the systemic lupus erythematosus-like disease and T cell proliferation of MRL/Mp-lpr/lpr mice

In young adulthood, MRL/Mp-lpr/lpr mice develop severe systemic lupus erythematosus (SLE)-like syndrome associated with massive T cell proliferation. The congenic MRL/Mp- mice lack the lpr gene and develop chronic SLE late in life. We have exchanged thymic transplants between these substrains so as to determine the role of the thymus in the development of early, severe SLE and of lymphoproliferation. The median survival times of unmanipulated lpr/lpr and mice were 160 and 510 d, respectively. The lpr/lpr and mice thymectomized when newborn and transplanted at 1 mo with the opposite type of thymus retained the diseases phenotype of their unmanipulated counterparts with 50% mortality at 186 and 498 d, respectively. In contrast, lpr/lpr mice thymectomized when newborn but not transplanted with thymus did not develop lymphoid hyperplasia and glomerulonephritis, and 100% of them were alive at 390 d. Serologically, the thymectomized but untransplanted lpr/lpr mice had significantly reduced levels of autoantibodies, whereas thymectomized and transplanted mice of either substrain were similar to unmanipulated controls. The results indicate that: (a) a thymus is essential for expression of lymphoproliferation and early SLE-like disease in the lpr/lpr phenotype; (b) the lpr/lpr disease is not a result of a unique hormonal or microenvironmental defect(s) of the thymus of this substrain because the genotype of the thymus is irrelevant for the development of T cell proliferation and early SLE; (c) differentiation of stem cells under the hormonal or microenvironmental influences of a thymus that possesses the lpr genotype does not lead to abnormal T cell differentiation or early autoimmunity; and (d) the lpr/lpr disease cannot be caused exclusively by an intrinsic B cell defect or environmental stimuli that cause B cell polyclonal activation.
Colocalization of GWAS and eQTL Signals Detects Target Genes

The vast majority of genome-wide association studies (GWAS) risk loci fall in non-coding regions of the genome. One possible hypothesis is that these GWAS risk loci alter the individual’s disease risk through their effect on gene expression in different tissues. In order to understand the mechanisms driving a GWAS risk locus, it is helpful to determine which gene is affected in specific tissue types. For example, the relevant gene and tissue may play a role in the disease mechanism if the same variant responsible for a GWAS locus also affects gene expression. Identifying whether or not the same variant is causal in both GWAS and eQTL studies is challenging due to the uncertainty induced by linkage disequilibrium (LD) and the fact that some loci harbor multiple causal variants. However, current methods that address this problem assume that each locus contains a single causal variant. In this paper, we present a new method, eCAVIAR, that is capable of accounting for LD while computing the quantity we refer to as the colocalization posterior probability (CLPP). The CLPP is the probability that the same variant is responsible for both the GWAS and eQTL signal. eCAVIAR has several key advantages. First, our method can account for more than one causal variant in any loci. Second, it can leverage summary statistics without accessing the individual genotype data. We use both simulated and real datasets to demonstrate the utility of our method. Utilizing publicly available eQTL data on 45 different tissues, we demonstrate that computing CLPP can prioritize likely relevant tissues and target genes for a set of Glucose and Insulin-related traits loci. eCAVIAR is available at http://genetics.cs. ucla.edu/caviar/
Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species

The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA)/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru)/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+) bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells.
The Assembly of the Self from Sensory and Motor Foundations

The problem of the self has captivated philosophers and psychologists for centuries. While the self is clearly a central facet of the human psyche, to date we have a limited understanding of the cognitive and neural mechanisms underlying this construct. The fundamental, pre-reflexive level of self-representation, often termed the minimal self has been the focus of recent work in psychology and neuroscience. This article will review recent advances in the study of the minimal self and its grounding in sensory and motor processing. I will suggest that the minimal self arises from unconscious integration of sensorimotor signals in specific brain systems, and that these same mechanisms may be of relevance to understanding disorders of the self such as schizophrenia. Finally, some influences of the minimal self on social cognition and future challenges will be discussed.