Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental regulation of the glyoxylate cycle in the human pathogen Penicillium marneffei

Penicillium marneffei is a thermally dimorphic opportunistic human pathogen with a saprophytic filamentous hyphal form at 25°C and a pathogenic unicellular yeast form at 37°C. During infection. P. marneffei yeast cells exist intracellularly in macrophages. To cope with nutrient deprivation during the infection process, a number of pathogens employ the glyoxylate cycle to utilize fatty acids as carbon sources. The genes which constitute this pathway have been implicated in pathogenesis. To investigate acetate and fatty acid utilization, the acuD gene encoding a key glyoxylate cycle enzyme (isocitrate lyase) was cloned. The acuD gene is regulated by both carbon source and temperature in P. marneffei, being strongly induced at 37°C even in the presence of a repressing carbon source such as glucose. When introduced into the non‐pathogenic monomorphic fungus Aspergillus nidulans, the P. marneffei acuD promoter only responds to carbon source. Similarly, when the A. nidulans acuD promoter is introduced into P. marneffei it only responds to carbon source suggesting that P. marneffei possesses both cis elements and trans‐acting factors to control acuD by temperature. The Zn(II)2Cys6 DNA binding motif transcriptional activator FacB was cloned and is responsible for carbon source‐, but not temperature‐, dependent induction of acuD. The expression of acuD at 37°C is induced by AbaA, a key regulator of morphogenesis in P. marneffei, but deletion of abaA does not completely eliminate temperature‐dependent induction, suggesting that acuD and the glyoxylate cycle are regulated by a complex network of factors in P. marneffei which may contribute to its pathogenicity.
Gene frequencies of the HPA‐15 (Gov) platelet alloantigen system in Brazilians

Summary. The HPA‐15 (Gov) alloantigen is a biallelic co‐dominant system on human platelets, and its allele HPA‐15a and HPA‐15b differ by an A→C single nucleotide polymorphism at nucleotide 2108 of the coding sequence resulting in a Tyr682Ser substitution in the mature CD109 glycoprotein.
Meeting the Healthy People 2020 Objectives to Reduce Cancer Mortality

Introduction Healthy People 2020 (HP2020) calls for a 10% to 15% reduction in death rates from 2007 to 2020 for selected cancers. Trends in death rates can be used to predict progress toward meeting HP2020 targets. Methods We used mortality data from 1975 through 2009 and population estimates and projections to predict deaths for all cancers and the top 23 cancers among men and women by race. We apportioned changes in deaths from population risk and population growth and aging. Results From 1975 to 2009, the number of cancer deaths increased among white and black Americans primarily because of an aging white population and a growing black population. Overall, age-standardized cancer death rates (risk) declined in all groups. From 2007 to 2020, rates are predicted to continue to decrease while counts of deaths are predicted to increase among men (15%) and stabilize among women (increase <10%). Declining death rates are predicted to meet HP2020 targets for cancers of the female breast, lung and bronchus, cervix and uterus, colon and rectum, oral cavity and pharynx, and prostate, but not for melanoma. Conclusion Cancer deaths among women overall are predicted to increase by less than 10%, because of, in part, declines in breast, cervical, and colorectal cancer deaths among white women. Increased efforts to promote cancer prevention and improve survival are needed to counter the impact of a growing and aging population on the cancer burden and to meet melanoma target death rates.
nfluence of β-t ricalcium Phosphate on the Biomechanical Dynamics of Healing of Experimental Defect of the Compact Bone

Background: One of the important criteria for successful treatment of bone defects with calcium phosphate osteoplastic materials is a full-fledged recovery of the biomechanical characteristics of the injured bone. However, the information regarding the effect of β-tricalcium phosphate on the biomechanical dynamics of the healing of the defect compact bone in the scientific literature is not presented. Aim and Objectives: This study was focused on the biomechanical assessment of the healing of experimental defect of the compact bone tissue after the implantation of calcium phosphate osteoplastic material "ChronOSTM" (β-tricalcium phosphate block), with identifying the dynamics of the changes of the microhardness and Young's modulus forming the regenerate with the implanted material. Material and Methods: In the middle third of the femoral shaft of 48 white Wistar rats eight months of age with the weight of 250 ± 10 g were produced perforated defect to the medullary canal, which in the animals of the experimental group was filled with β-tricalcium phosphate, and in the control animals was left unfilled. th th th Fragments of injured bones examined at 15 , 30 , 60 th and 120 day by the method of kinetic identication with the definition of the microhardness and Young's modulus of the site of the defect and adjacent to it maternal bone. Results: It was found out that throughout the observation period the site of implantation of osteoplastic material "ChronOSTM" by the microhardness and Young's modulus greatly dominated over the area of the defect in animals of the th control group, till the 60 day it was inferior to the th maternal bone, and on the 120 day of the experimentInfluence of β-tricalcium Phosphate on the Biomechanical Dynamics of Healing of Experimental Defect of the Compact Bone
AnOverview on Image Forensics

e aim of this survey is to provide a comprehensive overview of the state of the art in the area of image forensics. ese techniques have been designed to identify the source of a digital image or to determine whether the content is authentic or modi�ed, without the knowledge of any prior information about the image under analysis �and thus are de�ned as passive�. All these tools work by detecting the presence, the absence, or the incongruence of some traces intrinsically tied to the digital image by the acquisition device and by any other operation aer its creation. e paper has been organized by classifying the tools according to the position in the history of the digital image in which the relative footprint is le: acquisition-based methods, coding-based methods, and editing-based schemes.
Vascular function and sphingosine-1-phosphate regulate development of the dorsal pancreatic mesenchyme

Early growth and differentiation of the pancreatic endoderm is regulated by soluble factors from the pancreatic mesenchyme. Previously, we demonstrated that N-cadherin-deficient mice lack a dorsal pancreas, due to a critical role of N-cadherin in dorsal pancreatic mesenchymal cell survival. Here, we show that restoring cardiac and circulatory function in N-cadherin null mice by cardiac-specific expression of N-cadherin, rescues formation of the dorsal pancreas, indicating that the phenotype is secondary to defects related to cardiac/vascular function. Based on this observation, we demonstrate that soluble factors present in plasma, such as sphingosine-1-phosphate, rescue formation of the dorsal pancreas in N-cadherin-deficient mice. We also show that sphingosine-1-phosphate indirectly promotes budding of the pancreatic endoderm by stimulating pancreatic mesenchymal cell proliferation. Finally, we identify sphingosine-1-phosphate receptors within the mesenchyme and show that pertussis toxin blocks the sphingosine-1-phosphate-induced actions, suggesting the involvement of G-protein-coupled sphingosine-1-phosphate receptors. Thus, we propose a new model where blood vessel-derived sphingosine-1-phosphate stimulates growth and budding of the dorsal pancreatic endoderm by induction of mesenchymal cell proliferation.
Optimization Based Tumor Classification from Microarray Gene Expression Data

Background An important use of data obtained from microarray measurements is the classification of tumor types with respect to genes that are either up or down regulated in specific cancer types. A number of algorithms have been proposed to obtain such classifications. These algorithms usually require parameter optimization to obtain accurate results depending on the type of data. Additionally, it is highly critical to find an optimal set of markers among those up or down regulated genes that can be clinically utilized to build assays for the diagnosis or to follow progression of specific cancer types. In this paper, we employ a mixed integer programming based classification algorithm named hyper-box enclosure method (HBE) for the classification of some cancer types with a minimal set of predictor genes. This optimization based method which is a user friendly and efficient classifier may allow the clinicians to diagnose and follow progression of certain cancer types. Methodology/Principal Findings We apply HBE algorithm to some well known data sets such as leukemia, prostate cancer, diffuse large B-cell lymphoma (DLBCL), small round blue cell tumors (SRBCT) to find some predictor genes that can be utilized for diagnosis and prognosis in a robust manner with a high accuracy. Our approach does not require any modification or parameter optimization for each data set. Additionally, information gain attribute evaluator, relief attribute evaluator and correlation-based feature selection methods are employed for the gene selection. The results are compared with those from other studies and biological roles of selected genes in corresponding cancer type are described. Conclusions/Significance The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers.
Expression of the ATP-binding cassette transporter gene ABCG1 (ABC8) in Tangier disease.

Several members of the ATP-binding cassette (ABC) transporter family are involved in cholesterol efflux from cells. A defect in one member, ABCA1, results in Tangier disease, a condition characterized by cholesterol accumulation in macrophages and virtual absence of mature circulating high-density lipoproteins. Expression of a second member, ABCG1, is increased by cholesterol-loading in human macrophages. We now show that ABCG1, which we identified by differential display RT-PCR in foamy macrophages, is overexpressed in macrophages from patients with Tangier disease compared to control macrophages. On examination by confocal laser scanning microscopy, ABCG1 was present in perinuclear structures within the cell. In addition, a combination of in situ hybridization and indirect immunofluorescence microscopy revealed that ABCG1 is expressed in foamy macrophages within the atherosclerotic plaque. These data indicate that not only ABCA1 but also ABCG1 may play a role in the cholesterol metabolism of macrophages in vitro and in the atherosclerotic plaque.
Cooperative distributed algorithm for AUV teams: A minimum entropy approach

Autonomous Underwater Vehicles (AUVs) have found their application in exploration and surveillance. This paper proposes a cooperative distributed search algorithm based on a minimum entropy approach for AUVs with capabilities like multi agent exploration. The work is motivated by the project “Thesaurus”, whose among its own purposes has the survey of marine areas of archaeological interest in the Tuscan Archipelago. The cooperative algorithm is developed to move each vehicle on the exploration area taking into account communication constraints and a prior prediction probability map, which is updated on line during the mission. The prior probability map over the exploration area is built through Gaussian kernel approximation, on the basis of previous findings and historical archival data.
Decoupled teleoperation of a holonomic mobile-manipulator system using automatic switching

Mobile-manipulator systems (MMS) are extremely useful tools in teleoperation tasks. However, the current command strategy is strenuous and difficult and requires extensive training. A new command strategy is presented where control of the entire MMS is done using a single joystick. Rather than modeling the system as a redundant manipulator, control of the manipulator and mobile base is decoupled. In two separate states, the operator either controls the manipulator or the base. The system automatically switches between states based on the configuration of the manipulator. Testing is performed using the Omnibot MMS, a holonomic platform with a 3-DOF manipulator. The results showed that less time is required for completion of the tasks. In addition, the tasks are completed with greater accuracy and lower power consumption. Operators who used the system agreed the new command strategy was easier and more intuitive.
Adaptive Pacing, Cognitive Behaviour Therapy, Graded Exercise, and Specialist Medical Care for Chronic Fatigue Syndrome: A Cost-Effectiveness Analysis

Background The PACE trial compared the effectiveness of adding adaptive pacing therapy (APT), cognitive behaviour therapy (CBT), or graded exercise therapy (GET), to specialist medical care (SMC) for patients with chronic fatigue syndrome. This paper reports the relative cost-effectiveness of these treatments in terms of quality adjusted life years (QALYs) and improvements in fatigue and physical function. Methods Resource use was measured and costs calculated. Healthcare and societal costs (healthcare plus lost production and unpaid informal care) were combined with QALYs gained, and changes in fatigue and disability; incremental cost-effectiveness ratios (ICERs) were computed. Results SMC patients had significantly lower healthcare costs than those receiving APT, CBT and GET. If society is willing to value a QALY at £30,000 there is a 62.7% likelihood that CBT is the most cost-effective therapy, a 26.8% likelihood that GET is most cost effective, 2.6% that APT is most cost-effective and 7.9% that SMC alone is most cost-effective. Compared to SMC alone, the incremental healthcare cost per QALY was £18,374 for CBT, £23,615 for GET and £55,235 for APT. From a societal perspective CBT has a 59.5% likelihood of being the most cost-effective, GET 34.8%, APT 0.2% and SMC alone 5.5%. CBT and GET dominated SMC, while APT had a cost per QALY of £127,047. ICERs using reductions in fatigue and disability as outcomes largely mirrored these findings. Conclusions Comparing the four treatments using a health care perspective, CBT had the greatest probability of being the most cost-effective followed by GET. APT had a lower probability of being the most cost-effective option than SMC alone. The relative cost-effectiveness was even greater from a societal perspective as additional cost savings due to reduced need for informal care were likely.
Reduction of incidence and relapse or recrudescence cases of malaria in the western region of the Brazilian Amazon.

INTRODUCTION Malaria is one of the major parasitic diseases in the State of Rondônia, located in the western Brazilian Amazon. The basic treatment scheme for this disease is chloroquine and primaquine. This study evaluated the epidemiological profile of malaria in Rondônia between 2008 and 2012. METHODOLOGY The epidemiological data were provided by the Health Surveillance Agency from the State of Rondônia, and socioeconomic indicators were obtained from the Brazilian Institute of Geography and Statistics, Department of Informatics of the Unified Health System, and from the National Institute for Space Research. The analyzed variables included year of diagnosis, gender, age group, main activity performed in the 15 days previous to the diagnosis, parasite species, level of parasitemia, number of relapse/recrudescence cases, and socioeconomic and environmental data for Rondônia. RESULTS A total of 238,626 cases of malaria were recorded in Rondônia during the study period. Of this total, 65.6% were men and the most prevalent age group was 20-39 years. Plasmodium vivax was the most common parasite (89.8%), followed by Plasmodium falciparum (9.4%). An average of 30.9% of the individuals who were tested presented with relapse/recrudescence malaria. The API value was highest in 2008 and lowest in 2012, corresponding to 42.3 cases and 19.2 cases per 1,000 inhabitants, respectively. CONCLUSIONS A 58% reduction in the number of malaria cases and a 36.2% reduction in the number of relapse/recrudescence malaria cases were observed, due to increases in the economy, improvements in the health system, and reduction of deforestation in this region.
Evolution of Sucrose Synthesis [w]

Cyanobacteria and proteobacteria (purple bacteria) are the only prokaryotes known to synthesize sucrose (Suc). Suc-P synthase, Suc-phosphatase (SPP), and Suc synthase activities have previously been detected in several cyanobacteria, and genes coding for Suc-P synthase ( sps ) and Suc synthase ( sus ) have been cloned from Synechocystis sp. PCC 6803 and Anabaena ( Nostoc ) spp. , respectively. An open reading frame in the Synechocystis genome encodes a predicted 27-kD polypeptide that shows homology to the maize ( Zea mays ) SPP. Heterologous expression of this putative spp gene in Escherichia coli , reported here, confirmed that this open reading frame encodes a functional SPP enzyme. The Synechocystis SPP is highly specific for Suc-6 F -P ( K m (cid:1) 7.5 (cid:1) m ) and is Mg 2 (cid:2) dependent ( K a (cid:1) 70 (cid:1) m ), with a specific activity of 46 (cid:1) mol min (cid:3) 1 mg (cid:3) 1 protein. Like the maize SPP, the Synechocystis SPP belongs to the haloacid dehalogenase superfamily of phosphatases/hydrolases. Searches of sequenced microbial genomes revealed homologs of the Synechocystis sps gene in several other cyanobacteria ( Nostoc punctiforme , Prochlorococcus marinus strains MED4 and MIT9313, and Synechococcus sp. WH8012), and in three proteobacteria ( Acidithiobacillus ferrooxidans , Magnetococcus sp. MC1, and Nitrosomonas europaea ). Homologs of the Synecho- cystis spp gene were found in Magnetococcus sp. MC1 and N. punctiforme , and of the Anabaena sus gene in N. punctiforme and N. europaea . From analysis of these sequences, it is suggested that Suc synthesis originated in the proteobacteria or a common ancestor of the proteobacteria and cyanobacteria.
Popular Performance Metrics for Evaluation of Interaction in Virtual and Augmented Reality

Augmented and Virtual Reality applications provide environments in which users can immerse themselves in a fully or partially virtual world and interact with virtual objects or user interfaces. User-based, formal evaluation is needed to objectively compare interaction techniques, and find their value in different use cases, and user performance metrics are the key to being able to compare those techniques in a fair and effective manner. In this paper we explore evaluation principles used for or developed explicitly for virtual environments, and survey quality metrics, based on 15 current, important publications on interaction techniques for virtual environments. We check, categorize and analyze the formal user studies, and establish and present baseline performance metrics used for evaluation on interaction techniques in VR and AR.
Pfetin as a prognostic biomarker in gastrointestinal stromal tumor: novel monoclonal antibody and external validation study in multiple clinical facilities.

OBJECTIVE The clinical course of gastrointestinal stromal tumor (GIST) spans a wide spectrum from a curable disorder to a highly malignant disease that leads to metastasis and death. To develop prognostic modalities for GIST patients, we developed a mouse monoclonal antibody against pfetin, the prognostic value of which has been previously reported. METHODS The reactivity of the monoclonal antibody against pfetin was examined by western blotting and immunohistochemistry. RESULTS Western blotting demonstrated that the monoclonal antibody was specific to pfetin. The immunohistochemical study demonstrated that the 5-year disease-free survival rate was 93.2% and 94.5% for GIST patients with pfetin-positive tumors and 70.0% and 80.7% for those with pfetin-negative tumors in the 159 cases from the National Cancer Center Hospital (P < 0.0001) and in the 100 cases from Niigata University Medical and Dental Hospital (P < 0.0001), respectively. Uni- and multivariate analyses revealed that pfetin expression was a powerful prognostic factor among the clinico-pathological parameters examined. CONCLUSIONS These results establish pfetin as a practical prognostic marker for GIST patients after surgery. Pfetin may also present a novel therapeutic target to prevent recurrence of GIST.
Breast Reconstruction with a Transverse Abdominal Island Flap

: A rectus abdominis musculocutaneous island flap for breast reconstruction following mastectomy is presented. The vascular anatomy of the abdominal wall has been clinically studied in patients undergoing abdominal lipectomy. Cadaver dissections are shown, demonstrating the anatomy, arc of rotation, and design alternatives of the rectus abdominis flap. The surgical technique is demonstrated and representative patients are shown.
Regional biotechnology regulations: Design options and implications for good governance

"Many developing countries are currently in the process of designing regulatory systems that should allow them to use genetically modified organisms (GMOs) for agricultural development, while also managing the food safety and environmental risks potentially associated with these technologies. Various regions of the developing world are seeking to establish regional systems of biotechnology regulation. However, considerable costs are associated with biotechnology regulation, and biosafety specialists are scarce. In addition, there is no consistent understanding of how regional systems of biotechnology regulation can be designed to be effective and efficient, while also fulfilling the principles of good governance, such as transparency, voice and accountability, control of corruption, and avoidance of special interest capture. There are a wide variety of possible regional approaches, differing with regard to the level of centralization, the scope of the regional system, the types of regional institutions and processes, and the types of financing mechanisms. Here, based on findings in the fields of environmental and fiscal federalism and transaction costs economics, we develop a conceptual framework for the assessment of regional systems of biotechnology regulation. The framework specifies design options and assessment criteria, and identifies major trade-offs and their mediating factors. We use the case of West Africa to illustrate this framework, and refer to the European Union for comparison. Our analysis indicates that involving regional experts, stakeholders and policy-makers in the design of a regional regulatory system will help fill knowledge gaps and generate conclusions regarding the trade-offs involved in regional biotechnology regulation. " from Author's Abstract
GRID matching in Monte Carlo Bayesian compressive sensing

Sparse signal reconstruction from compressive measurements assumes a grid of possible support points from which to estimate the signal support set. However, reconstruction of high measurement resolution waveforms is very sensitive to small grid offsets and assuming a fixed grid may result to information loss. On the other hand, identifying sparse elements over a very fine grid to minimize information loss is computationally prohibitive. In this work grid matching is performed via a computationally efficient multi-stage Monte Carlo sampling approach. The multistage sampling method identifies sparse signal elements and chooses the appropriate grid using information from compressively acquired measurements and any prior information on the signal structure. The effectiveness of the method in reconstructing high resolution waveforms, after compressive acquisition, is demonstrated via a simulation study.