Miracle-dz/UniFAR-FTUs huggingface dataset:
PISMA: A Visual Representation of Motif Distribution in DNA Sequences

Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas. unam.mx/wp-content/software/pisma.zip and www.biomedicas. unam.mx/wp-content/pdf/manual/pisma.pdf.
Laser speckle and related phenomena

This is the second edition of a widely read book on laser and astronomical speckle. I have, through the years, extensively used the material in the first edition for teaching purposes and for “meaty” homework problems. The book is very readable, with good introductory material for helping the uninitiated “over the hurdles,” and yet, with a development in each subject to the state of the art in depth (as of 1975). The second edition is a handsome soft-bound book identical to the first edition (sans typographical errors), except for a rewritten Chapter 7 on “Stellar Speckle Interferometry” and a new Chapter 8 on “Recent Developments” in the overall field of speckle. Both are by J. C. Dainty. The other chapters are 1) “Introduction” by J . C. Dainty; 2) “Statistical Properties of Laser Speckle Patterns” by J. W .
Does the niche breadth or trade‐off hypothesis explain the abundance–occupancy relationship in avian Haemosporidia?

Two hypotheses have been proposed to explain the abundance–occupancy relationship (AOR) in parasites. The niche breadth hypothesis suggests that host generalists are more abundant and efficient at colonizing different host communities than specialists. The trade‐off hypothesis argues that host specialists achieve high density across their hosts' ranges, whereas generalists incur the high cost of adaptation to diverse immuno‐defence systems. We tested these hypotheses using 386 haemosporidian cytochrome‐b lineages (1894 sequences) recovered from 2318 birds of 103 species sampled in NW Africa, NW Iberia, W Greater Caucasus and Transcaucasia. The number of regions occupied by lineages was associated with their frequency suggesting the presence of AOR in avian Haemosporidia. However, neither hypothesis provided a better explanation for the AOR. Although the host generalist Plasmodium SGS1 was over three times more abundant than other widespread lineages, both host specialists and generalists were successful in colonizing all study regions and achieved high overall prevalence.
Stereocilia displacement induced somatic motility of cochlear outer hair cells.

Outer hair cells, isolated from mammalian cochleas, are known to respond to electrical stimulation with elongation or contraction of the cell's cylindrical soma. It is assumed that such shape changes, when driven by the cell's receptor potential in vivo, are a part of the feedback process that underlies cochlear amplification. To date it has not been possible to demonstrate somatic shape changes upon normal mechanical stimulation of the cell--i.e., the deflection of its hair bundle. We show here that mechanically induced hair-bundle deflection produces somatic motility of the cell. Such motility is dependent upon a functioning forward transducer process and disappears upon interference with transduction. The motile response also reflects the hair bundle's known directional sensitivity. This demonstration of mechanically driven motility indicates that the cell may possess capabilities to affect its mechanical environment under control of its own receptor potential and, thereby, participate in a local cochlear feedback process.
Share communication and energy resources for mobile cloud computing: An optimal cooperative contract approach

In this paper, we propose a cooperative contract approach to study the optimal energy-communication resource sharing for mobile cloud computing between energy-poor mobile devices and data-poor mobile devices. Specifically, an energy-poor mobile device with an energy harvesting module harvests energy from a data-poor mobile device through power splitting policy. In reciprocity, the energy-poor device will help relay the data-poor mobile device's computation task with part of the harvested energy. Firstly, we formulate an optimization model for designing of the optimal cooperative contract, and find that it is a multivariable non-convex optimization problem. Then, we transform it into a solvable convex optimization problem and derive the close-form expressions of the optimal harvest-energy allocation factor, the optimal power splitting factor, and the optimal transmission power through theoretical analysis. Finally, numerical results prove the unification between theoretical analysis and simulation results. Meanwhile, it is shown that our scheme reduces both of the energy consumption and data usage for resource-constrained mobile devices in utilizing mobile cloud computing.
Repetitive and Resonant Control for a Single-Phase Grid-Connected Hybrid Cascaded Multilevel Converter

This paper investigates the use of adaptive repetitive and resonant control approaches for the control of a single-phase hybrid cascaded multilevel converter designed to interface with power grids of highly distorted voltage waveform. The proposed repetitive/resonant control (RPC/RSC) is used for the extraction of clean phase angle, frequency, and magnitude information of the fundamental grid voltage together with the control of the converter current and mitigation of current harmonics under distorted grid voltage and variable frequency. The RPC time period and the RSC resonant frequency are updated adaptively using the estimated grid frequency while interpolation is used to preserve the RPC rejection capability under noninteger number of time steps per period. Detailed modeling and experimental investigation of the proposed control scheme are carried out.
Mobilizing resources for collective action and sustainable development: mobilizing interests or shared values?

In this paper we address how actors mobilize resources to realize collective change and innovation to solve common issues. We draw on previous studies anchored within the IMP literature that have offered two perspectives on how actors concerned with a common issue mobilize resources for collective change and innovation. We review these perspectives and challenge them in an empirical setting to arrive at an understanding of how they relate to each other and how they contribute to the mobilization of resources and collective action. One perspective emphasizes the mobilization of interest, and the other the mobilization of shared values as key mechanism to mobilize actors and their resources to contribute to collective action. We draw on an in-depth-case study consisting of two interrelated issue-nets faced to combine environmental with socio-economic issues in a sustainable way. The findings suggest that shared values are important to the extent that they help in raising awareness for the issue and that they can temporarily hold a group together. However, we found that collective action for sustainable development only occurs once actors see how their contribution can benefit their private interest. We theorize on our findings and suggest that interest of actors can only be directed once they can be properly calculated in terms of cost and benefits of their contribution to collective change. We reflect on these findings and conclude with tentative theoretical contributions and implications for further research.
Activity of aminoglycoside antibiotics aganst Pseudomonas aeruginosa: specificity and site of calcium and magnesium antagonism.

Four aminoglycoside antibiotics were tested against five species of gram-negative bacilli in defined media with various concentrations of calcium and magnesium. A species-specific antagonism of antimicrobial action against Pseudomonas aeruginosa was observed. Antibiotics were not inactivated, but the bacilli became unsusceptible. Even after a long incubation in a bactericidal concentration of gentamicin, the addition of calcium stabilized P. aeruginosa and permitted bacterial replication in the presence of an otherwise lethal concentration of drug. Calcium and magnesium exerted their inhibitory effect only if the bacterial cell wall was intact. Also, the action of gentamicin on carbenicillin-induced spheroplasts of P. aeruginosa was not antagonized by calcium. It was concluded that the interaction of magnesium or calcium with P. aeruginosa, which results in its resistance to aminoglycoside antibiotics, is at a locus exterior to the bacterial membrane, probably in the cell wall or a linkage between the cell wall and membrane. Of five common species of gram-negative bacilli tested, the effect is speciesspecific for P. aeruginosa and is similar for all of the aminoglycoside antibiotics.
Construction of navigation map to retrieve semantically information from medical resources

Semantic information retrieval has been a topic of great interest in recent years. Its purpose is to improve the effectiveness of information retrieval methods by exploiting the semantic information in documents and queries. Many approaches have been proposed to retrieval semantically the information. In this article, we propose a new approach based on domain ontology and natural language processing (NLP) techniques. In our approach, we represent resources and queries by a list of concepts. This allows us at the second level to create a semantic map of concepts and terms extracted from resources. Through this map, we propose to the users a proximity champ allowing them to find, in the one time, pertinent resources according to their query and in the second time to discover a new knowledge by navigating in semantic proximity relations.
The impact of cell adhesion changes on proliferation and survival during prostate cancer development and progression

In the normal prostate epithelium, androgen receptor (AR) negative basal epithelial cells adhere to the substratum, while AR expressing secretory cells lose substratum adhesion. In contrast, prostate cancer cells both express AR and adhere to a tumor basement membrane. In this review, we describe the differential expression of integrins, growth factor receptors (GFRs), and AR in normal and cancerous epithelium. In addition, we discuss how signals from integrins, GFRs, and AR are integrated to regulate the proliferation and survival of normal and malignant prostate epithelial cells. While cell adhesion is likely of great importance when considering therapeutic approaches for treatment of metastatic prostate cancer, no data on integrin expression are available from tissues of prostate cancer metastasis. However, several drug targets that are upregulated after androgen ablative therapy regulate cell adhesion and thus novel targeted therapies indirectly interfere with cell adhesion mechanisms in prostate cancer cells. J. Cell. Biochem. 99: 345–361, 2006. © 2006 Wiley‐Liss, Inc.
Hepatocellular Sinusoidal Membrane Organic Anion Transport and Transporters

This review focuses on oatp, a rat liver protein that has been cloned on the basis of its ability to transport organic anions such as bilirubin and sulfobromophthalein (BSP). Although other proteins have been suggested as having bilirubin or BSP transport activity, these data have primarily been indirect, and their cloning and expression have not yet been accomplished. Although preliminary data suggest that organic anion transporting polypeptide (oatp) accounts for a significant amount of BSP transport into the hepatocyte, there is certainly the possibility that other transporters exist. In addition, oatp appears to be a member of a new family of integral membrane transport proteins that may have overlapping substrate specificities. Organic anions such as bilirubin and sulfobromophthalein (BSP) circulate bound tightly to albumin from which they are rapidly extracted by hepatocytes. This process of organic anion uptake has been the subject of extensive investigation over many years. Although details remain unresolved, much has been learned recently regarding the mechanisms of organic anion transport. This article will examine the history and current status of this field.
Audio-Vestibular Findings in Increased Intracranial Hypertension Syndrome.

OBJECTIVE Idiopathic intracranial hypertension (IIH) can be manifested by audiological and vestibular complaints. The aim of the present study is to determine the audio-vestibular pathologies and their pathophysiologies in this syndrome by performing current audio-vestibular tests. MATERIALS AND METHODS The study was performed prospectively on 40 individuals (20 IIH patients, 20 healthy volunteers). Pure tone audiometry, tympanometry, vestibular evoked myogenic potentials, and electronystagmography tests were performed in both groups and the results were compared. RESULTS The mean age of both groups was found to be 30.2±18.7. There were 11 females and 9 males in each group. The study group patients had significantly worse hearing levels. Pure tone averages were significantly higher in both ears of the study group (p<0.05). Ten patients (50%) in the study group and one healthy volunteer (5%) had pathologic ENG, possibly related to central pathologies (p=0.008). Eight patients (40%) and one (5%) control had variable abnormal VEMP records (p=0008). CONCLUSION Many IIH patients initially visit otolaryngology clinics since cochlear and vestibular systems are frequently affected in this condition. Our test results suggest inner ear pathologies in these patients. Higher incidence of inferior vestibular nerve and/or saccule dysfunction is detected as a novelty. Increased intracranial pressure may affect the inner ear with similar mechanisms as in hydrops.
Understanding Playlist Creation on Music Streaming Platforms

Music streaming platforms enable people to access millions of tracks using computers and mobile devices. The latter allow users consume different music during different activities. Both, the sheer amount of music and the mobile access to music makes music organization an interesting topic for multimedia researchers. Assisting users to organize their music and make the music they like easily available in the right moment, contributes to increased usability of music streaming platforms. To get a deeper understanding of how users organize music nowadays, we analyze user-created playlists crawled from the music streaming platform Spotify. Using this new data set we find an explanation of differences in the playlists using audio features and based on this compute playlist clusters. We find that 91% of all users create at least one playlist in the “feel good music”-cluster and classical music or rap music can be considered as niche music with respect to the number of playlists, however not as niche music when considering the number of users. To foster research in this field, we make our analysis tool publicly available.
Examination of Precise Measurement of DC Magnetic Properties of Permalloy Under Low Flux Density More Than a Few mT

Permalloy is used in a magnetically shielded room to inhibit the penetration of external magnetic field, etc. The flux density in permalloy used in the shielded room is of the order of a few mT or lower. In order to examine the performance of such a shielded room, the dc magnetic properties at low flux density is necessary. In this paper, we developed a measurement method of dc (5 mHz) magnetic properties of permalloy under such a low flux density. It is shown that the dc magnetic properties could be measured more than 4 mT by paying the attention to the degaussing of specimen and applying the correction of drift and offset of measurement system.
Treatment of prostatic calculi.

Prostatic calculi are classified as exogenous or endogenous, depending on the point of origin. Exogenous calculi come from urinary salts and may originate as ureteral or bladder stones and become lodged in the prostatic urethra. In a sense they are not true prostatic stones, but they have been classed as such. This type of stone has been seen after prostatectomy and may become quite large. Deposition of urinary salts in prostatic diverticula may also lead to formation of calculi in the prostate. These stones are frequently seen during endoscopic examinations and are often just below the mucous membrane of the prostatic urethra. True prostatic stones, on the other hand, are found in the deeper structures of the prostate and are usually multiple. One case has been reported in which there were 1,247 stones, and in other reported cases several hundred calculi have been found at operation. Although true prostatic calculi
Effect of Alcohol Consumption on Oxidative Stress Markers and its Role in the Pathogenesis and Progression of Liver Cirrhosis

Oxidative stress has been increasingly implicated in the pathogenesis and progression of liver cirrhosis. Chronic ethanol consumption induces an oxidative stress resulting in increased ferritin levels and thereby iron over load. The study was aimed at evaluating the relation between alcohol consumption and erythrocyte superoxide dismutase (SOD), Glutathione peroxidase (GPx), Malondialdehyde (MDA) activities in liver cirrhosis patients. The study included two groups based on alcohol consumption; subjects taking low alcohol content (Less than 150 g/day.), those consuming high alcohol content (More than 150 g/day), diagnosed as suffering from liver cirrhosis and control group who do not take alcohol and are not suffering from liver cirrhosis. All cirrhotic patients on high alcohol intake in the study group had lower serum SOD (P < 0.0001), GPx (0.0001) and significantly higher MDA levels (P<0.001) than those with subjects taking low alcohol and control group. These results suggest that the decrease in erythrocyte SOD, GPx and increase in MDA levels are related to the alcohol consumption and that may be associated with pathogenesis and progression of liver disease.
Analysis of the defence phosphoproteome of Arabidopsis thaliana using differential mass tagging

Despite recent advances in proteomic technologies, quantitative analysis of the proteome remains a challenging task. Phosphorylation of proteins is central to signal transduction pathways and plays an important role in plant defence against pathogens, although the immediate targets of kinases remain elusive. Determining changes in the phosphoproteome during the defence response is a major goal in molecular plant pathology. In this first description of the novel mass tagging strategy (iTRAQ™ Applied Biosystems) applied to plant pathogen interactions, we describe early changes to the phosphoproteome of Arabidopsis thaliana during the defence response to Pseudomonas syringae pv. tomato DC3000. We identified five proteins which showed reproducible differences between a control and three different bacterial challenges, thus identifying proteins potentially phosphorylated as part of a plant basal defence response. Four of the five proteins a dehydrin, a putative p23 co‐chaperone, heat shock protein 81 and a plastid‐associated protein (PAP)/fibrillin, are known to be phosphorylated or have potential phosphorylation sites. One further protein, the large subunit of Rubisco, showed a significant difference between tissue undergoing the hypersensitive response and a basal defence response. We document the reproducibility, utility and problems associated with this approach.
Introduction to the theory of neural computation

From the Publisher: This book is a comprehensive introduction to the neural network models currently under intensive study for computational applications. It is a detailed, logically-developed treatment that covers the theory and uses of collective computational networks, including associative memory, feed forward networks, and unsupervised learning. It also provides coverage of neural network applications in a variety of problems of both theoretical and practical interest.
“Mark the Gene”: a Method for Nondestructive Introduction of Marker Sequences Inside the Gene Frame of Transgenes

ABSTRACT A specific marking and detection technique is a fundamental requirement for the safer use of genetically modified (GM) organisms. Here we propose a simple and effective method for directly marking functional transgenes in GM organisms. For that purpose, we introduced nucleotide substitutions (NS), based on the degeneracy of codons as markers (NS markers), into the bphC (2,3-dihydroxybiphenyl dioxygenase) and tomA3 (toluene-ortho-monooxygenase) gene frames using a PCR-based method. No change was observed in the enzyme activity of translated proteins, and alignments with homologous genes showed the uniqueness of the NS markers. Furthermore, we constructed tomA3 variations harboring NS markers in different positions. Although the translational products were identical, the constructed variation genes could be distinguished through their marker patterns by multiplex PCR, showing that NS markers could serve as product-specific tags for identifying individual GM organisms. This direct method of marking the functional transgene provides a simple, low-risk, and robust marking method without causing the gene functions to deteriorate.
Domain- and sequence-specific phosphorylation of vimentin induces disassembly of the filament structure.

We reported that stoichiometric phosphorylation by either cAMP-dependent protein kinase or protein kinase C induces disassembly of vimentin filaments [Inagaki, M. , Nishi, Y. , Nishizawa, K. , Matsuyama, M. , & Sato, C. (1987) Nature 328, 649-652; Inagaki, M. , Gonda, Y. , Matsuyama, M. , Nishizawa, K. , Nishi, Y. , & Sato, C. (1988) J. Biol. Chem. 263, 5970-5978]. In the present work, we attempted to identify the sites of vimentin phosphorylated by each protein kinase. Sequential analysis of the purified phosphopeptides, together with the known primary sequence, revealed that Ser-8, Ser-9, Ser-20, Ser-25, Ser-33, and Ser-41 were specifically phosphorylated by protein kinase C, whereas Ser-46 was phosphorylated preferentially by cAMP-dependent protein kinase. Both kinases reacted with Ser-6, Ser-24, Ser-38, Ser-50, and Ser-65. Specific phosphorylation sites for protein kinase C are mostly located close to the amino-terminal side of arginine while those for cAMP-dependent protein kinase are located close to the carboxyl-terminal side of arginine. The phosphorylation sites exclusively occur in the amino-terminal non-alpha-helical head domain, particularly at the beta-turn region. These results provide clues to the molecular mechanisms of phosphorylation-dependent disassembly of vimentin filaments.