Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel mechanism of self-primed reverse transcription defines a new family of retroelements

Retroviruses and long terminal repeat (LTR)-containing retrotransposons initiate reverse transcription by using a specific tRNA primer than anneals to the primer-binding site of the retroelement transcript. Sequences from a large number of retroviruses and LTR-containing retrotransposons had indicated that the role of tRNAs in priming reverse transcription is universal among these LTR-containing retroelements. Data presented here strongly support the surprising conclusion that Tf1, a highly active LTR-containing retrotransposon isolated from Schizosaccharomyces pombe, undergoes a novel self-priming process that requires hybridization between the primer-binding site and the first 11 bases of the Tf1 transcript. Single-base mutations in these regions block transposition and reverse transcription, while compensatory mutations that reestablish complementarily rescue both defects. In addition, the sequence of the minus-strand RNA primer of reverse transcription was consistent with its being derived from the 5' end of the Tf1 transcript. Evidence that this mechanism defines a new family of retroelements is presented.
A Systematic Qualitative Review of Risk and Protective Factors for Sexual Violence Perpetration

The current review summarized results of 191 published empirical studies that examined the risk and protective factors for sexual violence perpetration. Studies in the review examined factors for perpetration by and against adolescents and adults, by male and female perpetrators, and by those who offended against individuals of the same sex or opposite sex. Factors associated with child sexual abuse (CSA) perpetration were not included. In all, 2 societal and community factors, 23 relationship factors, and 42 individual-level factors were identified. Of these 67 factors, consistent significant support for their association with SV was found for 35, nonsignificant effects were found for 10, 7 factors had limited or sample-specific evidence that they were associated with SV but were in need of further study, and 15 demonstrated mixed results. The factors identified in the review underscore the need for comprehensive prevention programs that target multiple risk and protective factors as well as factors that occur across the social ecology. Moreover, we identified two domains of factors—the presence and acceptance of violence and unhealthy sexual behaviors, experiences, or attitudes—that had consistent significant associations with SV but are not typically addressed in prevention programs. Therefore, SV prevention may also benefit from learning from effective strategies in other areas of public health, namely sexual health and youth violence prevention.
Evaluation of Moderate Traumatic Brain Injury

Introduction:Traumatic brain injury (TBI) affects nearly 1.4 million Americans annually with an estimated 5.3 million US citizens living with disability. There is no standardized course of treatment for individuals with moderate TBI. This study aims to evaluate the patient demographics and acute care course for those with moderate TBI. Methods:This is a descriptive study of 40 persons diagnosed with moderate TBI to examine demographic, clinical, and discharge variables associated with this injury. Results:Falls, the most frequent mechanism of injury, were seen in more than 50% of individuals 65 years and older. The 21-to 64-year age group was more likely to be injured from motor vehicle crashes. Fifty percent of the patients were discharged; however, only 1 in 9 patients older than 65 years was discharged. Glasgow Coma Scale was not correlated with discharge destination. Cognitive status was screened in the hospital setting on 9 patients, and orders for outpatient screening/evaluation were done on an additional 17 patients. Conclusion:Moderate TBI is a unique subset of brain injury. Having a better understanding of its course of recovery will help develop appropriate management guidelines for this group.
Significantly different bcl‐2 expression profiles in gastric and non‐gastric primary extranodal high‐grade B‐cell lymphomas

Fifty‐five cases of primary extranodal high‐grade B‐cell non‐Hodgkin's lymphoma were investigated for bcl‐2 and p53 protein expression as well as for t(14;18) translocations and p53 mutations. Phenotypic and genotypic profiles were compared between tumours of gastric (27 cases) and non‐gastric (28 cases) origin. bcl‐2 protein expression was significantly lower in gastric (11/27) than in non‐gastric (28/28) lymphomas (p<0.0001), while nuclear p53 protein expression did not differ significantly between these two groups. In the stomach, there were no significant differences in either bcl‐2 or p53 expression profiles between high‐grade lymphomas with (n=14) and without (n=13) evidence of a low‐grade component of MALT type. However, secondary high‐grade lymphomas showed a significant down‐regulation of bcl‐2 protein (p<0.0001) and, conversely, an up‐regulation of p53 protein (p<0.0001) as compared with their low‐grade tumour components. In extranodal high‐grade B‐cell lymphomas, bcl‐2 protein expression was not associated with t(14;18) translocation. Only one gastric lymphoma had a p53 point mutation with potential alteration of the amino acid sequence. These findings indicate that primary gastric high‐grade B‐cell lymphomas are immunohistologically distinct from primary extranodal high‐grade B‐cell lymphomas of an origin other than in the stomach. Copyright © 2000 John Wiley & Sons, Ltd.
Evolution of nevi during treatment with natalizumab: A prospective follow-up of patients treated with natalizumab for multiple sclerosis.

BACKGROUND Natalizumab is a monoclonal antibody directed against α₄ integrin used in the treatment of multiple sclerosis (MS). Four cases of melanomas occurring in patients prescribed natalizumab to treat MS were recently reported. Although some fundamental data suggested that α₄β1 integrin could be linked to the invasiveness of melanoma, none showed any relation with the transformation of melanocytes. OBSERVATIONS We performed a prospective follow-up of a cohort of patients with MS treated with natalizumab to assess the evolution of nevi under treatment. Clinical dermatologic examination and videodermoscopy were performed every 6 months. Nevi were compared side-by-side with baseline photographs, and histologic analysis was proposed based on clinical and dermoscopic criteria. Forty-four patients were included, and 248 nevi were examined and followed up. The mean duration of follow-up was 14 months (range, 6-20 months). Seventeen lesions (6.8%) showed modifications over time. Only 12 (4.8%) presented substantial dermoscopic changes. Five lesions were removed. All of them were classified as benign after histologic examination. CONCLUSIONS Our results showed the same rate of clinical and dermoscopic changes of nevi during treatment with natalizumab compared with the spontaneous evolution of nevi reported in literature. In accordance with fundamental data, those results suggest that the inhibition of the α₄ integrin does not promote the transformation of melanocytic lesions.
The coccoid forms of Helicobacter pylori. Criteria for their viability

Summary The fact that Helicobacter pylori can revert to a coccoid form has stimulated speculation about its role in transmission and as a possible cause of reinfection in duodenal ulcer disease. Bismuth subcitrate (32 μg/ml), bismuth subsalicylate (64 μg/ml), amoxicillin (0·05 μg/ml) and erythromycin (4 μg/ml) inhibited the growth of H. pylori and stimulated the formation the formation of basically respiring but non-culturable coccoid structures. The presence of polyphosphates as energy and phosphorus source permits a certain level of endogenous metabolism to preserve RNA and DNA, as well as structural components like cell wall, cell membrane and cytoplasma for at least 3 months. However, the applied standard laboratory methods were insufficient for regrowth of H. pylori out of the coccoid form.
A two-dimensional medium access control protocol based on OFDMA and CSMA/CA

In this paper we present a two-dimensional medium access control (MAC) protocol. Orthogonal frequency division multiple access (OFDMA) can make multiple stations (STA) transmit simultaneously on different sub-channels. On the other hand, carrier sense multiple access with collision avoidance (CSMA/CA) could make different stations contend the available channel from the time domain to avoid collision with each other. We propose a two-dimensional MAC protocol based on OFDMA and CSMA/CA in broadband systems. With the new designed MAC protocol different stations will access the channel from the time-frequency domain without interference and collision. The combination of OFDMA with CSMA/CA will improve the system throughput with efficient MAC and decrease the collision probability. We design that different stations will contend the available time-frequency resources dynamically under fairness. The system throughput of the designed protocol is analyzed and simulation results are presented to show the performance under our designed protocol far better than the conventional CSMA/CA protocol.
Muscle MRS detects elevated PDE/ATP ratios prior to fatty infiltration in Becker muscular dystrophy

Becker muscular dystrophy (BMD) is characterized by progressive muscle weakness. Muscles show structural changes (fatty infiltration, fibrosis) and metabolic changes, both of which can be assessed using MRI and MRS. It is unknown at what stage of the disease process metabolic changes arise and how this might vary for different metabolites. In this study we assessed metabolic changes in skeletal muscles of Becker patients, both with and without fatty infiltration, quantified via Dixon MRI and 31P MRS. MRI and 31P MRS scans were obtained from 25 Becker patients and 14 healthy controls using a 7 T MR scanner. Five lower‐leg muscles were individually assessed for fat and muscle metabolite levels. In the peroneus, soleus and anterior tibialis muscles with non‐increased fat levels, PDE/ATP ratios were higher (P < 0.02) compared with controls, whereas in all muscles with increased fat levels PDE/ATP ratios were higher compared with healthy controls (P ≤ 0.05). The Pi/ATP ratio in the peroneus muscles was higher in muscles with increased fat fractions (P = 0.005), and the PCr/ATP ratio was lower in the anterior tibialis muscles with increased fat fractions (P = 0.005). There were no other significant changes in metabolites, but an increase in tissue pH was found in all muscles of the total group of BMD patients in comparison with healthy controls (P < 0.05). These findings suggest that 31P MRS can be used to detect early changes in individual muscles of BMD patients, which are present before the onset of fatty infiltration. Copyright © 2014 John Wiley & Sons, Ltd.
Analysis of apoptosis-associated genes and pathways in oral cancer cells.

BACKGROUND Cancer cells can resist apoptosis that is induced by stimuli such as detachment or differentiation, but may be more susceptible to apoptosis when exposed to chemotherapeutic drugs. The pattern of gene expression that produces this phenotype is unknown. METHODS We compared gene expression patterns of normal human epidermal keratinocytes (NHEK cells) and the oral cancer cell line Tu183 when the cells were exposed to different apoptosis-inducing stimuli. RESULTS Pathway analysis revealed that the phenotype difference could be best explained by the simultaneous existence of both proapoptosis and antiapoptosis signals in the cancer cells. Microarray analysis, supported by immunoblotting, showed that one gene that was likely to be involved in the proapoptosis signal was TNFRSF5, which encodes the receptor CD40. When Tu183 cells were exposed to the CD40 ligand they showed apoptosis, while NHEK cells did not. CONCLUSIONS The effects of different apoptotic stimuli on normal cells and oral cancer cells can be explained by expression of proapoptosis genes, including the gene that encodes CD40.
On the modeling of a nano communication network using spiking neural architecture

The human neural system is comprised of millions of neural cells which are fully networked through synaptic connections. Each neuron receives the input through dendrites from neighboring nodes, in order to fire an action potential through its axon into the next neurons. In this paper, a biological communication network is modeled and a scenario is implemented to detect the damaged neural cells. For this purpose, the membrane potential of the biological network nodes is monitored and evaluated using spiking neural network algorithm. A spiking Izhikevich neural modeling technique is implemented at nanoscale to model the biological network. A swarm of nanobots is taken into consideration to diagnose the malfunction of the biological communication network by measuring the membrane potential of each firing neuron and the neighboring nodes. After fault occurrence, some nodes will no longer be available to process and communicate in the biological communication network. Therefore, the fully-connected biological network as a small-world network would be a randomly-connected communication network. The idea of this research is to diagnose the defected nano-cells and autonomously cluster to regenerate a small-world network using the available neighboring neural cells. To reestablish the small-world biological communication network, a graph theory scheme is applied considering the membrane potentials and coordination of the neural cells in a two dimensional biological network. The depth-first search algorithm is implemented for clustering and the simulation results are illustrated and discussed.
Relationship between acrosin activity of human spermatozoa and oxidative stress.

AIM To study the association between seminal oxidative stress and human sperm acrosin activity. METHODS It is a prospective study consisting of 30 infertile men and 12 fertile normozoospermic volunteers. A full history, clinical examination and scrotal ultrasound were done to exclude other related factors such as smoking and varicocele. Presence of white blood cells (WBCs) in semen samples was evaluated by peroxidase staining. Lipid peroxidation in spermatozoa was induced after incubating with ferrous sulphate (4 mmol/L) and sodium ascorbate (20 mmol/L). Induced peroxidation of spermatozoa was assessed by determining the production of thiobarbituric acid reactive substances (TBARS). Acrosin activity was measured using the gelatinolysis technique. The halo diameters around the sperm heads and the percentages of spermatozoa showing halo formation were evaluated. An acrosin activity index was calculated by multiplying the halo diameter by the halo formation rate. RESULTS A significant difference was observed in acrosin activity parameters and TBARS levels between samples with WBCs (1 multiply 10(6)/mL of ejaculate) and those without. This difference was also noted between the normozoospermic and the oligoasthenoteratozoospermic semen samples. The TBARS production by spermatozoa had a significant negative correlation with the acrosin activity index (r = -0.89, P 0.001). CONCLUSION The presence of oxidative stress in an individual with leukocytospermia and/or abnormal semen parameters is associated with impaired sperm function as measured by its acrosin activity.
IL‐6 Is the Principal Factor Produced by Synovia of Patients with Rheumatoid Arthritis That Induces B‐Lymphocytes to Secrete Immunoglobulins

First, IL-6 is produced by synovial tissue of patients with rheumatoid arthritis (RA) and is the principal mediator produced by that tissue inducing differentiation of B-lymphocytes into antibody-forming cells. The Leu-1+ subset of B-lymphocytes is induced by IL-6 to secrete rheumatoid factor (IgM with anti-Fc gamma specificity). Second, the main cell types producing IL-6 in cells dissociated from RA synovial tissue are mononuclear leukocytes. Connective tissue type cells (synoviocytes) cultured from RA synovial tissue produce IL-6 in response to IL-1 beta, and IL-6 formation is increased by TGF-beta. Glucocorticoids strongly inhibit and PGE2 slightly inhibits IL-1-induced IL-6 mRNA expression in synoviocytes. Production of IL-6 increases when undissociated RA synovial tissue is maintained in culture, thus suggesting release from inhibition by a factor or factors not yet identified. Third, the major known local effect of IL-6 in RA synovial tissue is the augmentation of antibody formation and the major known systemic effect is the induction of the synthesis by the liver of acute-phase proteins, especially C-reactive protein. Levels of circulating C-reactive protein are reported to decrease in RA patients receiving long-acting antirheumatic drugs, which would be consistent with the interpretation that immature monocyte-derived macrophages are major producers of IL-6 in these patients.
Diversity in prokaryotic glycosylation: an archaeal‐derived N‐linked glycan contains legionaminic acid

VP4, the major structural protein of the haloarchaeal pleomorphic virus, HRPV‐1, is glycosylated. To define the glycan structure attached to this protein, oligosaccharides released by β‐elimination were analysed by mass spectrometry and nuclear magnetic resonance spectroscopy. Such analyses showed that the major VP4‐derived glycan is a pentasaccharide comprising glucose, glucuronic acid, mannose, sulphated glucuronic acid and a terminal 5‐N‐formyl‐legionaminic acid residue. This is the first observation of legionaminic acid, a sialic acid‐like sugar, in an archaeal‐derived glycan structure. The importance of this residue for viral infection was demonstrated upon incubation with N‐acetylneuraminic acid, a similar monosaccharide. Such treatment reduced progeny virus production by half 4 h post infection. LC‐ESI/MS analysis confirmed the presence of pentasaccharide precursors on two different VP4‐derived peptides bearing the N‐glycosylation signal, NTT. The same sites modified by the native host, Halorubrum sp. strain PV6, were also recognized by the Haloferax volcanii N‐glycosylation apparatus, as determined by LC‐ESI/MS of heterologously expressed VP4. Here, however, the N‐linked pentasaccharide was the same as shown to decorate the S‐layer glycoprotein in this species. Hence, N‐glycosylation of the haloarchaeal viral protein, VP4, is host‐specific. These results thus present additional examples of archaeal N‐glycosylation diversity and show the ability of Archaea to modify heterologously expressed proteins.
Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy

Macroautophagy (hereafter autophagy) is a ubiquitous process in eukaryotic cells that is integrally involved in various aspects of cellular and organismal physiology. The morphological hallmark of autophagy is the formation of double-membrane cytosolic vesicles, autophagosomes, which sequester cytoplasmic cargo and deliver it to the lysosome or vacuole. Thus, autophagy involves dynamic membrane mobilization, yet the source of the lipid that forms the autophagosomes and the mechanism of membrane delivery are poorly characterized. The TRAPP complexes are multimeric guanine nucleotide exchange factors (GEFs) that activate the Rab GTPase Ypt1, which is required for secretion. Here we describe another form of this complex (TRAPPIII) that acts as an autophagy-specific GEF for Ypt1. The Trs85 subunit of the TRAPPIII complex directs this Ypt1 GEF to the phagophore assembly site (PAS) that is involved in autophagosome formation. Consistent with the observation that a Ypt1 GEF is directed to the PAS, we find that Ypt1 is essential for autophagy. This is an example of a Rab GEF that is specifically targeted for canonical autophagosome formation.
Object Extraction Using an Edge-Based Feature for Query-by-Sketch Image Retrieval

We previously proposed a query-by-sketch image retrieval system that uses an edge relation histogram (ERH). However, it is difficult for this method to retrieve partial objects from an image, because the ERH is a feature of the entire image, not of each object. Therefore, we propose an object-extraction method that uses edge-based features in order to enable the query-by-sketch system to retrieve partial images. This method is applied to 20,000 images from the Corel Photo Gallery. We confirm that retrieval accuracy is improved by using the edge-based features for extracting objects, enabling the query-by-sketch system to retrieve partial images. key words: query-by-sketch image retrieval, object extraction, partial image retrieval, edge-based feature
ColorFingers: improved multi-touch color picker

ColorFingers is a WYSIWYG, Location Independent Touch (LIT) based color picking tool aimed to give unique and swift interaction in choosing color on touch based devices. It makes use of touch interface and the touch information of two fingers to select almost 16 million colors. This tool is a model to prove how touch can be interpreted in different ways to achieve performance improvements in HCI. In this paper, we propose ColorFingers which is a color picker and briefly discuss the working of it. We show, how it achieves around 54% reduction in color selection time and 53% improvement in accuracy when compared to existing models. The proposed model emphasizes on Multi-touch, Quick feedback and Location Independency.
Estadísticas de juego que discriminan las selecciones participantes en los Campeonatos del Mundo de 2006 de Baloncesto, en función del nivel y género de los equipos

espanolEl objetivo del articulo fue identificar las diferencias de juego en funcion del genero, (hombres y mujeres) y la categoria o nivel de juego (junior y senior). Se clasifican los partidos en funcion del resultado final del encuentro, utilizandose los partidos ajustados para el analisis de los datos (N=131, 1 a 6 puntos de diferencia). Las estadisticas de juego se normalizan a 100 posesiones para minimizar el efecto ritmo de juego. El analisis discriminante se utilizo para identificar las estadisticas de juego que mejor discriminan entre genero y nivel de competicion. Se encontraron estadisticas de juego que permiten diferenciar el juego de hombres y mujeres, asi como entre los equipos junior y senior. Los resultados indican que las principales diferencias en funcion del genero de los participantes se deben a la mejor habilidad de los equipos masculinos para lanzar a canasta (encestan mas lanzamientos de 1 y 3 puntos) y dar pases de canasta (asistencias), aunque realizan mas faltas personales. Las diferencias en funcion del nivel de los jugadores se encuentran en los lanzamientos de campo fallados (2 y 3 puntos) y los rebotes (ofensivos y defensivos). EnglishThe purpose of this study was to identify the differences according to game-related statistics by sex (male and female), and level (junior and senior). For the analysis only closed games were used in this study (N=131, 1 a 6 points). Gamerelated statistics were normalized to 100 possessions to minimize game rhythm contamination. Discriminant analysis was used to identify the game-related statistics that maximize mean differences between sex and level of competition. The results showed the differences between male and female teams and junior and senior teams. The mean differences between men and women are based on of physical development and a better ability for long shots. The young players made more shots and are less efficient than the experts.
Almost Periodic Parameters for the Second Moment Stability of Linear Stochastic Systems

The technical note presents conditions to assure the uniform second moment stability for a class of linear time-varying stochastic systems. The system parameters are assumed to be almost periodic, a concept that is weaker than the periodic one. Under the existence of the long-run average cost associated with the stochastic system, we apply the almost periodicity to prove the desired stability result. An application illustrates the usefulness of the approach by implementing an almost periodic state-feedback strategy to control the velocity of a DC motor device.