Miracle-dz/UniFAR-FTUs huggingface dataset:
Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes)

Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.
Comparative Proteomic Analysis of Gossypium thurberi in Response to Verticillium dahliae Inoculation

Verticillium wilt is threatening cotton productivity globally. This disease is caused by soil-borne Verticillium dahliae which directly infects cotton roots, and exclusively colonizes and occludes xylem vessels, finally resulting in necrosis, defoliation, and most severely, plant death. For the first time, iTRAQ (isobaric tags for relative and absolute quantification) was applied to screen the differentially expressed proteins of Gossypium thurberi inoculated with V. dahliae. A total of 6533 proteins were identified from the roots of G. thurberi after inoculation with V. dahliae, and 396 showed up- and 279 down-regulated in comparison to a mock-inoculated roots. Of these identified proteins, the main functional groups were those involved in cell wall organization and reinforcement, disease-resistant chemicals of secondary metabolism, phytohormone signaling, pathogenesis-related proteins, and disease-resistant proteins. Physiological and biochemical analysis showed that peroxidase activity, which promotes the biosynthesis and accumulation of lignin, was induced early in the hypocotyl after inoculation with V. dahliae. Similarly, salicylic acid also accumulated significantly in hypocotyl of the seedlings after inoculation. These findings provide an important knowledge of the molecular events and regulatory networks occurring during G. thurberi-V. dahliae interaction, which may provide a foundation for breeding disease-resistance in cotton.
New Calibration Estimators in Stratified Sampling

Calibration approach is widely used survey sampling that incorporates auxiliary information to increase the precision of survey estimates. In this manuscript, we propose two new calibration estimators of population mean in stratified sampling, using the known auxiliary information on mean and coefficient of variation in each stratum. A numerical example is presented to illustrate the application and computational details of the proposed calibration estimators. Moreover, a simulation study is carried out to compare the performance of the proposed calibration estimators.
Predicting Adolescent Deviant Behaviors through Data Mining Techniques

Adolescence is the time during which people develop and form their crucial values, personality traits, and beliefs. Hence, as deviant behaviors occur during adolescence, it is important to guide adolescents away from such behaviors and back to normal behaviors. Moreover, although there are various kinds of deviant behavior, most of them would either directly or indirectly affect youths’ academic learning progresses. Therefore, many researchers have endeavored to explore the issues of juvenile delinquency. In this study, we focus on providing methods that could assist counseling officers in discovering symptoms and pre-symptoms of youth delinquency. The study proposes a framework for mining associations from “memo-type” records without supervision of senior experts. In addition, we apply this approach to retrieve associations among deviant behaviors from the counseling records stored in databases. The contributions to adolescent counseling are as follows: (1) A keyword tree of deviant behaviors is constructed and verified; (2) the general and time sequence associations of deviant behaviors are mined from memo-type records and also verified. Finally, (3) an information system is recommended to help junior counselors performing counseling works. Consequently, without experienced consultants, the proposed framework could discover valuable knowledge from consulting records effectively and many efforts are therefore saved.
Organic vs. psychogenic? The Manichean diagnosis in sexual medicine.

INTRODUCTION The Manichean diagnosis, psychogenic or organic, is the first and most frequent diagnostic scope managing sexual disorders. The aim of this Controversy is to discuss if this philosophy is still useful both in the conceptual and clinical perspective. METHODS Five scientists (an endocrinologist, two psychologist, and two urologists) with expertise in the area of psychosexology and sexual medicine were asked to contribute with their opinions. MAIN OUTCOME MEASURE Expert opinion supported by the critical review of the currently available literature. RESULT Expert # 1, who is Controversy's section Editor, suggests that the term psychogenic is redundant, because all sexual dysfunctions involve the mind and the relationship with (at least) one partner. Furthermore, he is strongly against the exclusion diagnosis, in agreement with the Expert # 5. The idea that the psychogenic etiology is always present is also sustained with good arguments by the Expert # 2. On the other hand, the two Experts # 3 and 4 argue that a pharmacological treatment such as type 5 phosphodiesterase inhibitors or dapoxetine work in both organic and psychogenic conditions and that the attempt to perform a diagnostic effort is frequently useless. Last but not least, the Expert # 5 concludes that the mind-body dualism is to be considered obsolete and unhelpful in a modern approach to the patient with a sexual dysfunction. CONCLUSIONS The reader of the Journal will judge if there is still a room for the Manichean diagnosis of different sexual dysfunctions or if it is time to completely change our perspective on this essential aspect of clinical sexual medicine.
MONETARY UNCERTAINTY AND DEMAND FOR MONEY IN KOREA

Friedman’s volatility hypothesis asserts that increased volatility of money supply can lower the velocity of money or increase the demand for money. Previous studies have tested this hypothesis by using data from a few industrialized countries. In this paper, we estimate the demand for money in Korea after including a measure of volatility of nominal money supply. We provide support for Friedman’s hypothesis in the short run as well as in the long run.
A Framework to Construct Three-Dimensional Complementary Codes for Multiuser MIMO Systems

This paper proposes a framework to construct 3-D complementary codes (3DCCs), which enable chip-level space-time coding to integrate multiantenna and multiple-access techniques in a unified platform. The 3DCCs are generated based on an extension method with the help of traditional complementary codes and well-designed matrices. The relationship between the correlation properties and flock size of the constructed 3DCCs is analyzed, and the proposed framework provides a generic way to construct different families of 3DCCs with a controllable tradeoff between their correlation properties and flock sizes. As examples, three families of 3DCCs with different characteristic features are constructed using the framework, and their correlation properties are simulated to validate their properties. The general architecture of the 3DCC-based multiple-input multiple-output (MIMO) system is also proposed in this paper. The simulated bit-error-rate (BER) performance of the corresponding system over both flat and multipath fading channels show that the constructed 3DCCs can eliminate both multiuser and multipath interferences in multiuser MIMO communications. The property to provide both transmit diversity and multiplexing with its uniquely flexible tradeoff between the two also makes it particularly well suited for futuristic wireless communications to fit to varying channel conditions and application requirements.
A Non-generative Approach for Face Recognition Across Aging

Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.
Rates of Digestion of Bacteria by Marine Phagotrophic Protozoa: Temperature Dependence

The effect of temperature on length of time for digestion of bacteria was evaluated, by using fluorescently labeled bacteria (FLB), for phagotrophic flagellates and ciliates isolated from coastal northwest Mediterranean waters. Accumulation of FLB in protozoan food vacuoles was followed until a plateau of FLB per cell occurred; then after a 1:10 dilution of FLB with unlabeled bacteria, disappearance of FLB in food vacuoles was monitored. For both 3- to 5-μm flagellates and 10- to 40-μm ciliates, the absolute linear slopes of FLB uptake and disappearance were nearly identical in individual experiments over a temperature range of 12 to 22°C. We inferred from these results that the leveling off of the uptake curves resulted when equilibrium between ingestion and digestion of bacteria was attained. The time to leveling off then represented the average time needed for complete digestion of the bacteria ingested at the start of the experiment, and the inverse of this time represented a bacterial digestion rate. The digestion rate increased exponentially from 12 to 22°C for both a mixed flagellate assemblage and the oligotrichous ciliate Strombidium sulcatum, with a Q10 of 2.8 for the flagellates and 2.0 for the ciliate. Although bacterial ingestion rates varied greatly, depending on protozoan cell size, total bacterial abundance, and temperature, digestion times appeared to be significantly influenced only by protozoan cell size (or type of protozoan) and by temperature.
Malleable Embodiment: Changing Sense of Embodiment by Spatial-Temporal Deformation of Virtual Human Body

We hypothesize that replacing the visual perception of one's body with a spatial-temporal deformed state would change sensations associated with the body. We developed a system that captures full-body movement and generates estimated past and future body movement by deformation. With a head mounted display, people could see their bodies as slightly deformed. We then investigated 1) how human movement is physically changed, and 2) how humans feel about the change in physical and emotional views of the body due to virtual body deformation. Our results show that spatial-temporal deformation of a virtual body actually changes the sense of body as well as physical movement. For instance, a body image generated at approximately 25-100 ms in the future induced a "lighter weight" sensation. On the basis of our findings, we discuss the design implication of computational control for the physical and emotional sense of body.
A role for N‐glycanase in the cytosolic turnover of glycoproteins

Successful maturation determines the intracellular fate of secretory and membrane proteins in the endoplasmic reticulum (ER). Failure of proteins to fold or assemble properly can lead to their retention in the ER and redirects them to the cytosol for degradation by the proteasome. Proteasome inhibitors can yield deglycosylated cytoplasmic intermediates that are the result of an N‐glycanase activity, believed to act prior to destruction of these substrates by the proteasome. A gene encoding a yeast peptide:N‐glycanase, PNG1, has been cloned, but this N‐glycanase and its mammalian homolog were reported to be incapable of deglycosylating full‐length glycoproteins. We show that both the yeast PNG1 enzyme and its mammalian homolog display N‐glycanase activity towards intact glycoproteins. As substrates, cytosolic PNGase activity prefers proteins containing high‐mannose over those bearing complex type oligosaccharides. Importantly, PNG1 discriminates between non‐native and folded glycoproteins, consistent with a role for N‐glycanase in cytoplasmic turnover of glycoproteins.
Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus

ABSTRACT One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in Brucella, and genomic island 3 (GI-3) is shared by two pathogenic species, B. melitensis and B. abortus. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. abortus from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abortus from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of B. abortus were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of B. abortus, demonstrating the high stability of gene cluster GI-3 in Chilean field strains.
Left ventricular hypertrophy: pathogenesis, detection, and prognosis.

When the heart faces a hemodynamic burden, it can do the following to compensate: (1) use the Frank-Starling mechanism to increase crossbridge formation; (2) augment muscle mass to bear the extra load; and (3) recruit neurohormonal mechanisms to increase contractility. The first mechanism is limited in its scope, and the third is deleterious as a chronic adjustment. Thus, increasing mass assumes a key role in the compensation for hemodynamic overload. This increase in mass is due to the hypertrophy of existing myocytes rather than hyperplasia, because cardiomyocytes become terminally differentiated soon after birth. In response to pressure overload in conditions such as aortic stenosis or hypertension, the parallel addition of sarcomeres causes an increase in myocyte width, which in turn increases wall thickness. This remodeling results in concentric hypertrophy (increase in ratio of wall thickness/chamber dimension). According to LaPlace’s Law, the load on any region of the myocardium is given as follows: (pressure×radius)/(2×wall thickness); thus, an increase in pressure can be offset by an increase in wall thickness. Because systolic stress (afterload) is a major determinant of ejection performance, the normalization of systolic stress helps maintain a normal ejection fraction even when needing to generate high levels of systolic pressure.1 Volume overload in conditions such as chronic aortic regurgitation, mitral regurgitation, or anemia engenders myocyte lengthening by sarcomere replication in series and an increase in ventricular volume. This pattern of eccentric hypertrophy (cavity dilatation with a decrease in ratio of wall thickness/chamber dimension) is also initially compensatory, such that the heart can meet the demand to sustain a high stroke volume. However, chronic hypertrophy may be deleterious because it increases the risk for the development of heart failure and premature death. This review will focus on the pathogenesis of pressure- versus volume-overload types of left ventricular hypertrophy (LVH), detection, …
Gestion de connaissances personnelles et contextuelles, et respect de la vie privée

Nous montrons comment les mecanismes de confidentialite peuvent evoluer pour exploiter les modeles orientes ontologie et suivre le deploiement de Webs semantiques. Testee dans le projet myCampus, l'architecture distribuee que nous presentons ici repose sur des regles pour le Web semantique et le respect de la confidentialite ainsi que des services Web pour representer les ressources personnelles et publiques. Des agents logiciels gerent les echanges, notamment les agents e-Wallets responsables des ressources des utilisateurs.
Lower Skin Cancer Risk in Women with Higher Body Mass Index: The Women's Health Initiative Observational Study

The unclear relationship of obesity to incident melanoma and nonmelanoma skin cancer (NMSC) risks was evaluated in the large, geographically diverse longitudinal, prospective Women's Health Initiative (WHI) observational study. Risks of melanoma and NMSC in normal weight women were compared with risks in overweight [body mass index (BMI) = 25–29.0 kg/m2] and obese (BMI ≥ 30 kg/m2) women, using Cox proportional hazards models for melanoma and logistic regression for NMSC. Over a mean 9.4 years of follow-up, there were 386 melanoma and 9,870 NSMC cases. Risk of melanoma did not differ across weight categories (P = 0.86), whereas in fully adjusted models, NMSC risk was lower in overweight [OR, 0.93; 95% confidence interval (CI), 0.89–0.99] and obese (OR, 0.85; 95% CI, 0.80–0.91) women (P < 0.001). Excess body weight was not associated with melanoma risk in postmenopausal women but was inversely associated with NMSC risk, possibly due to lower sun exposure in overweight and obese women. This supports previous work demonstrating the relationship between excess body weight and skin cancer risk. Cancer Epidemiol Biomarkers Prev; 22(12); 2412–5. ©2013 AACR.
Orthoptic Changes following Photorefractive Keratectomy

Purpose To report orthoptic changes after photorefractive keratectomy (PRK). Methods This interventional case series included 297 eyes of 150 patients scheduled for PRK. Complete ophthalmologic evaluations focusing on orthoptic examinations were performed before and 3 months after PRK. Results Before PRK, 2 (1.3%) patients had esotropia which remained unchanged; 3 (2%) patients had far exotropia which improved after the procedure. Of 12 cases (8%) with initial exotropia at near, 3 (2%) cases became orthophoric, however 6 patients (4%) developed new near exotropia. A significant reduction in convergence and divergence amplitudes (P < 0.001) and a significant increase in near point of convergence (NPC) (P < 0.006) were noticed after PRK. A reduction ≥ 10 PD in convergence amplitude and ≥ 5 PD in divergence amplitude occurred in 10 and 5 patients, respectively. Four patients had initial NPC > 10 cm which remained unchanged after surgery. Out of 9 (6%) patients with baseline stereopsis > 60 seconds of arc, 2 (1.33%) showed an improvement in stereopsis following PRK. No patient developed diplopia postoperatively. Conclusion Preexisting strabismus may improve or remain unchanged after PRK, and new deviations can develop following the procedure. A decrease in fusional amplitudes, an increase in NPC, and an improvement in stereopsis may also occur after PRK. Preoperative evaluation of orthoptic status for detection of baseline abnormalities and identification of susceptible patients seem advisable.
Wireless Sensor Networks: Performance Analysis in Indoor Scenarios

We evaluate the performance of realistic wireless sensor networks in indoor scenarios. Most of the considered networks are formed by nodes using the Zigbee communication protocol. For comparison, we also analyze networks based on the proprietary standard Z-Wave. Two main groups of network scenarios are proposed: (i) scenarios with direct transmissions between the remote nodes and the network coordinator, and (ii) scenarios with routers, which relay the packets between the remote nodes and the coordinator. The sensor networks of interest are evaluated considering different performance metrics. In particular, we show how the received signal strength indication (RSSI) behaves in the considered scenarios. Then, the network behavior is characterized in terms of end-to-end delay and throughput. In order to confirm the experiments, analytical and simulation results are also derived.
Developing sustainable food supply chains

This paper reviews the opportunities available for food businesses to encourage consumers to eat healthier and more nutritious diets, to invest in more sustainable manufacturing and distribution systems and to develop procurement systems based on more sustainable forms of agriculture. The important factors in developing more sustainable supply chains are identified as the type of supply chain involved and the individual business attitude to extending responsibility for product quality into social and environmental performance within their own supply chains. Interpersonal trust and working to standards are both important to build more sustainable local and many conserved food supply chains, but inadequate to transform mainstream agriculture and raw material supplies to the manufactured and commodity food markets. Cooperation among food manufacturers, retailers, NGOs, governmental and farmers’ organizations is vital in order to raise standards for some supply chains and to enable farmers to adopt more sustainable agricultural practices.