Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans

ABSTRACT Single-nucleotide polymorphisms (SNPs) are essential tools for studying a variety of organismal properties and processes, such as recombination, chromosomal dynamics, and genome rearrangement. This paper describes the development of a genome-wide SNP map for Candida albicans to study mitotic recombination and chromosome loss. C. albicans is a diploid yeast which propagates primarily by clonal mitotic division. It is the leading fungal pathogen that causes infections in humans, ranging from mild superficial lesions in healthy individuals to severe, life-threatening diseases in patients with suppressed immune systems. The SNP map contains 150 marker sequences comprising 561 SNPs and 9 insertions-deletions. Of the 561 SNPs, 437 were transition events while 126 were transversion events, yielding a transition-to-transversion ratio of 3:1, as expected for a neutral accumulation of mutations. The average SNP frequency for our data set was 1 SNP per 83 bp. The map has one marker placed every 111 kb, on average, across the 16-Mb genome. For marker sequences located partially or completely within coding regions, most contained one or more nonsynonymous substitutions. Using the SNP markers, we identified a loss of heterozygosity over large chromosomal fragments in strains of C. albicans that are frequently used for gene manipulation experiments. The SNP map will be useful for understanding the role of heterozygosity and genome rearrangement in the response of C. albicans to host environments.
The thread form detection based on SVM

This paper presents a detection method of thread image based on support vector machine. This method is to obtain a training sample set by collecting every concrete sub-image of thread form from the standard thread images as positive examples, and unqualified thread images as negative examples; and to train support vector machine with sequential minimal optimization algorithm, detect the thread with the optimal decision function that was obtained. Experiments show that by this method the detection result is reliable, and it is easy to accomplish the online detection. In addition, this paper also briefly discusses how to reduce point dimension and how to speed up operation.
The 3C architecture: an XML topic maps-based framework for integrating content, context and common knowledge about multimedia

We present an XML topic maps (XTM) based framework for the integration of three "Cs" of the media: content, context and common (background/domain) knowledge. The framework incorporates content analysis modules such as object detectors, context analysis modules such as named entity extractors and common knowledge analysis modules to extract key pieces of knowledge about media elements such as images, sound recordings, videos, graphic illustrations and animations. The extracted pieces of knowledge are integrated via a uniform and extensible knowledge representation method: XML topic maps. The framework allows for the automatic generation of multimedia queries and the automatic population of multimedia databases. The framework also facilitates conceptual indexing of multimedia elements in digital libraries. Key components of the framework are implemented in an automatic presentation generation system.
Quadriceps Function and Gait Kinetics after Anterior Cruciate Ligament Reconstruction.

PURPOSE Chronic quadriceps dysfunction has been implicated as a contributor to knee osteoarthritis (OA) development after anterior cruciate ligament reconstruction (ACLR). This dysfunction potentially leads to impulsive/high-rate loading during gait, thus accelerating cartilage degradation. The purpose of this study was to examine relationships between several indices of quadriceps function and gait biomechanics linked to knee OA development in individuals with ACLR. METHODS Gait biomechanics and quadriceps function were assessed in 39 individuals with ACLR. Indices of quadriceps function included isometric peak torque and rate of torque development (RTD), isokinetic peak torque and power, and the central activation ratio. Gait biomechanics included the peak vertical ground reaction force and loading rate, and the heel strike transient (HST) magnitude and loading rate. RESULTS Isometric peak torque was not associated with any of the gait biomechanical variables. However, greater RTD was associated with lesser peak vertical ground reaction force linear (r = -0.490, P = 0.003) and instantaneous (r = -0.352, P = 0.031) loading rates, as well as a lesser HST magnitude (r = -0.312, P = 0.049) and instantaneous loading rate (r = -0.355, P = 0.029). Greater central activation ratio was associated with greater HST instantaneous (r = 0.311, P = 0.050) and linear (r = 0.328, P = 0.033) loading rates. Isokinetic peak torque and power were not associated with any of the biomechanical variables. CONCLUSION Poor quadriceps function, especially RTD, is associated with gait kinetics linked to cartilage degradation in individuals with ACLR. These results highlight the likely role of chronic quadriceps dysfunction in OA development after ACLR and the need to emphasize improving quadriceps function as a primary rehabilitation goal.
Total Procedural Requirements as Indication for Emergency Department Sedation

Indications for pediatric procedural sedation and analgesia are generally based on the need to manage pain or elicit cooperation for a single major procedure in the emergency department setting. However, multiple minor procedures such as vascular access, urethral catheterization, lumbar puncture, or superficial abscess drainage may be required in the care of a single child, and combining these activities may produce as much stress as a single major procedure. The use of procedural sedation in children based on total procedural requirements is proposed with 2 illustrative cases as examples of this concept.
MANAGEMENT OF THE BILE DUCT STONE: CURRENT SITUATION IN JAPAN

Endoscopic treatment is now recognized as the standard treatment for common bile duct stones worldwide. Endoscopic treatment routinely involves endoscopic sphincterotomy in most countries including Japan and endoscopic papillary balloon dilation is also a widely used alternative to endoscopic sphincterotomy in Japan. Surgery in any form, including laparoscopic surgery, is mainly performed when endoscopic treatments are unsuccessful or unfavorable. Other therapeutic modalities considered under certain circumstances include lithotripsy under the guidance of percutaneous transhepatic cholangioscopy, peroral cholangioscopy, or enteroscopy; electrohydraulic lithotripsy or laser lithotripsy; and extracorporeal shock‐wave lithotripsy.
α-Glucosidase inhibitory and cytotoxic botryorhodines from mangrove endophytic fungus Trichoderma sp. 307

Abstract One new depsidone, botryorhodine H (1), together with three known analogues, botryorhodines C, D and G (2–4), were obtained from the mangrove endophytic fungus Trichoderma sp. 307 by co-culturing with Acinetobacter johnsonii B2. Structures were determined by 1D and 2D NMR analyses and high-resolution mass spectrum. Compounds 1–3 showed α-glucosidase inhibitory activity with IC50 ranging from 8.1 to 11.2 μM, and compound 1 exhibited potent cytotoxicity against rat prolactinoma MMQ and rat pituitary adenoma GH3 cell lines (IC50 = 3.09 and 3.64 μM).
Anti‐inflammatory property of the cannabinoid receptor‐2‐selective agonist JWH‐133 in a rodent model of autoimmune uveoretinitis

Previous studies have shown that cannabinoids have anti‐inflammatory and immune‐modulating effects, but the precise mechanisms of action remain to be elucidated. In this study, we investigated the effect of JWH 133, a selective agonist for cannabinoid receptor 2, the main receptor expressed on immune cells, in a model of autoimmune disease, experimental autoimmune uveoretinitis (EAU). JWH 133 suppressed EAU in a dose‐dependent manner (0.015–15 mg/kg), and the suppressive effect could be achieved in the disease‐induction stage and the effector stage. Leukocytes from mice, which had been treated with JWH 133, had diminished responses to retinal peptide and mitogen Con A stimulation in vitro. In vivo JWH 133 treatment also abrogated leukocyte cytokine/chemokine production. Further in vitro studies indicated that JWH 133 down‐regulated the TLR4 via Myd88 signal transduction, which may be responsible for its moderate, suppressive effect on antigen presentation. In vivo JWH 133 treatment (1 mg/kg) also suppressed leukocyte trafficking (rolling and infiltration) in inflamed retina as a result of an effect on reducing adhesion molecules CD162 (P‐selectin glycoprotein ligand 1) and CD11a (LFA‐1) expression on T cells. In conclusion, the cannabinoid agonist JWH 133 has a high in vivo, anti‐inflammatory property and may exert its effect via inhibiting the activation and function of autoreactive T cells and preventing leukocyte trafficking into the inflamed tissue.
Spatiotemporal hurdle models for zero-inflated count data: Exploring trends in emergency department visits

Motivated by a study exploring spatiotemporal trends in emergency department use, we develop a class of two-part hurdle models for the analysis of zero-inflated areal count data. The models consist of two components—one for the probability of any emergency department use and one for the number of emergency department visits given use. Through a hierarchical structure, the models incorporate both patient- and region-level predictors, as well as spatially and temporally correlated random effects for each model component. The random effects are assigned multivariate conditionally autoregressive priors, which induce dependence between the components and provide spatial and temporal smoothing across adjacent spatial units and time periods, resulting in improved inferences. To accommodate potential overdispersion, we consider a range of parametric specifications for the positive counts, including truncated negative binomial and generalized Poisson distributions. We adopt a Bayesian inferential approach, and posterior computation is handled conveniently within standard Bayesian software. Our results indicate that the negative binomial and generalized Poisson hurdle models vastly outperform the Poisson hurdle model, demonstrating that overdispersed hurdle models provide a useful approach to analyzing zero-inflated spatiotemporal data.
Relative messenger RNA abundance in bovine oocytes collected in vitro or in vivo before and 20 hr after the preovulatory luteinizing hormone surge

In the cyclic cow, final maturation of the ovulatory follicle is initiated by the preovulatory luteinizing hormone (LH) surge. During the subsequent 24 hr period, the oocyte nucleus undergoes meiotic progression to metaphase II and several changes in cytoplasmic organization take place. We have previously shown that oocytes recovered at the time of the LH peak and matured in vitro are less competent to reach the blastocyst stage than their counterparts recovered 20 hr later following in vivo maturation, despite both groups undergoing IVF and culture in parallel. The objective of this study was to compare, using real‐time quantitative RT‐PCR, the relative abundance of various developmentally important gene transcripts in these oocytes. The groups used were mature bovine oocytes originating from: (1) 2–6 mm follicles from slaughterhouse ovaries; (2) preovulatory follicles punctured by ovum pick‐up just before the LH surge (i.e., immature) and matured in vitro; or (3) preovulatory follicles punctured 20 hr later, just prior to ovulation (i.e., in vivo matured). In addition, immature oocytes from 2–6 mm follicles were examined. We examined the relative mRNA expression of five enzymes involved in protection against free oxygen radicals (mitochondrial Mn‐superoxide dismutase, MnSOD, cytosolic Cu/Zn superoxide dismutase, Cu/ZnSOD, γ‐glutamyl‐cysteine transferase, GCS, glutathione peroxidase, GPX, sarcosine oxidase, SOX), a transcript involved in follicular development (growth differentiation factor‐9, GDF‐9), transcripts involved in glucose metabolism (glucose‐6‐phosphate dehydrogenase, G6PDH, glucose transporter type ‐1 and ‐8, Glut‐1, Glut‐8) and genes involved in cell cycle events, Cyclin A and B, and poly(A) polymerase (PAP). Transcripts for all genes were detected, irrespective of oocyte origin. While differences were not significant in all cases, variations in levels of transcript abundance between the groups were related to developmental competence. In particular, transcripts for GDF‐9 were expressed at significantly higher levels in oocytes recovered at the LH peak and matured in vitro than in those matured in vivo. The observations with GDF‐9 are interesting as this gene is believed to be essential for normal folliculogenesis and may be important in the regulation of early follicle and oocyte growth. In conclusion, the results of this study demonstrate differences in the relative mRNA abundance of several developmentally important gene transcripts in bovine oocytes which may be related to developmental competence. Mol. Reprod. Dev. 66: 297–305, 2003. © 2003 Wiley‐Liss, Inc.
High-Efficiency Angled-Dipole Antennas for Millimeter-Wave Phased Array Applications

A high-efficiency microstrip-fed endfire angled-dipole antenna has been developed for millimeter-wave phased array applications. The antenna is built on both sides of a Teflon substrate (epsivr = 2.2) and this allows a wideband feed from the single-ended microstrip line to the differential dipole. The design results in wide radiation patterns for scanning purposes with a gain of around 2.5 dB at 20-26 GHz and a cross-polarization level of < -15 dB at 24 GHz. A mutual coupling of < -23 dB is measured between adjacent elements with 6.8 mm center-to center spacing (0.50-0.54 lambda0 at 22-24 GHz). A variant of the angled-dipole antenna with a magnetic ground plane edge was also developed, and shows a measured gain of > 6 dB at 23.2-24.6 GHz and very low mutual coupling between elements (<-23 dB for a 6.8 mm spacing). Both antennas result in a radiation efficiency of > 93% when referenced to the microstrip line feed (including mismatch loss). The usefulness of these antennas as phased array radiators is demonstrated by several eight-element linear arrays at 22-24 GHz with scan angle up to 50 degrees. The application areas are in automotive radars and high data-rate communication systems.
Exclusion of linkage of schizophrenia to the gene for the dopamine D2 receptor (DRD2) and chromosome 11q translocation sites

SYNOPSIS There have been previous reports of a 1q43;11q21 translocation cosegregating with schizophrenia and a 9p22;11q22.3 translocation cosegregating with manic depression. In addition, the genes for the dopamine D2 receptor and for tyrosinase both map to chromosome 11q. Three 11q DNA markers were used to investigate 23 pedigrees containing multiple cases of schizophrenia. Strongly negative lod scores were obtained, providing evidence against linkage over a 70 cM region which included both translocation sites and both candidate genes.
Economic Approaches to Understanding Scientific Norms

A theme of much work taking an “economic approach” to the study of science is the interaction between the norms of individual scientists and those of society at large. Though drawing from the same suite of formal methods, proponents of the economic approach offer what are in substantive terms profoundly different explanations of various aspects of the structure of science. The differences are illustrated by comparing Strevens's explanation of the scientific reward system (the “priority rule”) with Max Albert's explanation of the prevalence of “high methodological standards” in science. Some objections to the economic approach as a whole are then briefly considered.
Mitochondria Influence CDR1 Efflux Pump Activity, Hog1-Mediated Oxidative Stress Pathway, Iron Homeostasis, and Ergosterol Levels in Candida albicans

ABSTRACT Mitochondrial dysfunction in Candida albicans is known to be associated with drug susceptibility, cell wall integrity, phospholipid homeostasis, and virulence. In this study, we deleted CaFZO1, a key component required during biogenesis of functional mitochondria. Cells with FZO1 deleted displayed fragmented mitochondria, mitochondrial genome loss, and reduced mitochondrial membrane potential and were rendered sensitive to azoles and peroxide. In order to understand the cellular response to dysfunctional mitochondria, genome-wide expression profiling of fzo1Δ/Δ cells was performed. Our results show that the increased susceptibility to azoles was likely due to reduced efflux activity of CDR efflux pumps, caused by the missorting of Cdr1p into the vacuole. In addition, fzo1Δ/Δ cells showed upregulation of genes involved in iron assimilation, in iron-sufficient conditions, characteristic of iron-starved cells. One of the consequent effects was downregulation of genes of the ergosterol biosynthesis pathway with a commensurate decrease in cellular ergosterol levels. We therefore connect deregulated iron metabolism to ergosterol biosynthesis pathway in response to dysfunctional mitochondria. Impaired activation of the Hog1 pathway in the mutant was the basis for increased susceptibility to peroxide and increase in reactive oxygen species, indicating the importance of functional mitochondria in controlling Hog1-mediated oxidative stress response. Mitochondrial phospholipid levels were also altered as indicated by an increase in phosphatidylserine and phosphatidylethanolamine and decrease in phosphatidylcholine in fzo1Δ/Δ cells. Collectively, these findings reinforce the connection between functional mitochondria and azole tolerance, oxidant-mediated stress, and iron homeostasis in C. albicans.
Use of Stem Cells in Dental Implants and Enamel Regenerative Therapies

Present review article emphasizes use of various stem cell types, biological scaffold materials, genes and factors essentially required in wound healing, transplantation and regeneration of tooth implants. All recent developments in tooth engineering used for successful regeneration of tooth, induction of enamel and formation of dentin complexes are highlighted. In addition, genes, factors and minerals required in vascularization and maintenance of microenvironment for responsiveness to cells are also elucidated as most attractive candidates for regeneration therapy. Present review also elucidates use of stable and durable biodegradable polymer scaffolds materials and cementum/periodontal-ligament complex formation. There is a need to widen the horizon of bio-root engineering technology for successful repairing of tooth injuries and replacement of fractured or traumatized tooth. For this purpose, use of implantation of cultured stem cells, adhesion factors and biomaterials can provide stable attachment of dental implants. This review also sketch upon need of newer technologies and more adhesive biocompatible biomaterials for successful dental implants and enamel regenerative therapies.
Early Transcriptional Responses during Heat Stress in the Coral Acropora hyacinthus

Corals respond to heat pulses that cause bleaching with massive transcriptional change, but the immediate responses to stress that lead up to these shifts have never been detailed. Understanding these early signals could be important for identifying the regulatory mechanisms responsible for bleaching and how these mechanisms vary between more and less resilient corals. Using RNA sequencing (RNAseq) and sampling every 30 minutes during a short-term heat shock, we found that components of the transcriptome were significantly upregulated within 90 min and after a temperature increase of +2 °C. The developmental transcription factor, Krüppel-like factor 7, was highly expressed within 60 min, and stress-related transcription factors such as Elk-3 were highly expressed starting at 240 min. The sets of genes enriched for early transcriptional response to heat stress included heat shock proteins, small GTPases, and proteasome genes. Retrovirus-related Pol polyproteins from transposons were significantly expressed throughout the whole experiment. Lastly, we propose a model for early transcriptional regulation of protein degradation and cell adhesion response that may ultimately lead to the bleaching and stress response.
The relation between expected returns and volatility in the Brazilian stock market

This paper applies the Markov switching regression model of stock returns with volatility feedback of Turner, Startz and Nelson (1989), suitably extended to incorporate endogenous regime shifts, as in Kim, Piger and Startz (2008), to examine the intertemporal relationship between the risk premium and volatility in the Brazilian stock market over the period 1995-2011. The results suggest that there is a positive relationship between the risk premium and the expected volatility once the volatility feedback effect is taken into account. Unanticipated increases in volatility, in contrast, have a negative impact on the risk premium. This negative impact increasesby 50% when I account for endogeneity of regime shifts.
Plasma Hyaluronan-binding Protein Is a Serine Protease*

CTCF is an essential factor for optimal transcription from the amyloid β-protein precursor promoter. A proteolytic activity detected in bovine, rabbit, horse, and human serum cleaves CTCF at three major sites, resulting in a modified mobility shift pattern of the fragments that retain DNA binding ability. The protease was purified to electrophoretic homogeneity, partially sequenced, and identified as the plasma hyaluronan-binding protein. The proteolytic activity was selectively abolished by various serine protease inhibitors, including the Kunitz-type protease inhibitor domain of amyloid β-protein precursor. Reduction with β-mercaptoethanol showed that the 70-kDa protein consists of two polypeptides with apparent molecular masses of 44 and 30 kDa. The serine protease domain was localized to the 30-kDa polypeptide as determined by [3H]diisopropylfluorophosphate binding.
Solid pseudopapillary tumor of the pancreas: a review of 553 cases in Chinese literature.

AIM To sum up the clinical and pathological characteristics of solid pseudopapillary tumor (SPT) and the experience with it. METHODS A total of 553 SPT patients reported in Chinese literature between January 1996 and January 2009 were retrospectively reviewed and analyzed. RESULTS The mean age of the 553 SPT patients included in this review was 27.2 years, and the male to female ratio was 1:8.37. Their symptoms were non-specific, and nearly one third of the patients were asymptomatic. Computed tomography and ultrasonography were performed to show the nature and location of SPT. Most of the tumors were distributed in the pancreatic head (39.8%), tail (24.1%), body and tail (19.5%). Forty-five patients (9.2%) were diagnosed as malignant SPT with metastasis or invasion. None of the clinical factors was closely related to the malignant potential of SPT. Surgery was the main therapeutic modality for SPT. Local resection, distal pancreatectomy and pancreatoduodenectomy were the most common surgical procedures. Local recurrence and hepatic metastasis were found in 11 and 2 patients, respectively, after radical resection. Four patients died of tumor progression within 4 years after palliative resection of SPT. The prognosis of SPT patients was good with a 5-year survival rate of 96.9%. CONCLUSION SPT of the pancreas is a rare indolent neoplasm that typically occurs in young females. It is a low-grade malignancy and can be cured with extended resection. The prognosis of such patients is good although the tumor may recur and metastasize.