Miracle-dz/UniFAR-FTUs huggingface dataset:
Vascular segmentation algorithm using locally adaptive region growing based on centerline estimation

In this paper, we propose a new region-based approach on the basis of centerline estimation, to segment vascular networks in 3D CTA/MRA images. The proposed algorithm is applied repeatedly to newly updated local cubes. It consists of three tasks; local region growing, surfacic connected component labeling, and next local cube detection. The cube size is adaptively determined according to the estimated diameter. After region growing inside a local cube, we perform the connected component labeling procedure on all 6 faces of the current local cube (surfacic component labeling). Then the detected surfacic components are put into a queue to serve as seeds of following local cubes. Contrary to conventional centerline-tracking methods, the proposed algorithm can detect all bifurcations without any restriction because a region-based method is used at every local cube. And by confining region growing to a local cube, it can be more effective in producing prospective results. It should be noticed that the segmentation result is divided into several branches, so a user can easily edit the result branch-by-branch. The proposed method can automatically generate a flyway in a virtual angioscopic system since it provides a tree structure of the detected branches.
Circulating cell free DNA as the diagnostic marker for colorectal cancer: a systematic review and meta-analysis

Background Quantitative analyses of circulating cell-free DNA (cfDNA) are suggested to be a promising method for the detection of colorectal cancer, validated clinical relevance of cfDNA has not been published so far. Though some of the inconsistent results were published. This study is the first meta-analysis to systematically evaluate the diagnostic accuracy of circulating cfDNA as non-invasive biomarkers for colorectal cancer. Results Fourteen studies concerning a quantitative analysis of circulating cfDNA for the diagnosis of colorectal cancer met the inclusion criteria. Data includes 1,258 patients with colorectal cancer and 803 healthy individuals as control was analyzed. The summary estimates were as follow: sensitivity, 0.735 (95% CI 0.713–0.757); specificity, 0.918 (95% CI, 0.900–0.934); positive likelihood ratio, 8.295 (95% CI, 5.037–13.659); negative likelihood ratio, 0.300 (95% CI, 0.231–0.391); diagnostic odds ratio, 30.783 (95% CI, 16.965–55.856); and area under the curve, 0.8818 (95% CI, 0.88–0.93), respectively. Publication bias was not evident with Deeks’ funnel plot asymmetry test (p = 0.197). Materials and Methods A systematic literature was searched in PubMed, EMBASE, Cochrane Library and Chinese National Knowledge Infrastructure from their inception to August 07, 2017. Analyses were conducted by Meta-DiSc 1.4 and Stata 12.0. Diagnostic accuracy in sensitivity, specificity and aspects were pooled. Subgroup analyses and meta-regression were performed to identify the sources of heterogeneity. Clinical utility of the cfDNA was evaluated by Fagan nomogram. Conclusions Our meta-analysis suggested that the diagnostic accuracy of circulating cfDNA has unsatisfactory sensitivity but acceptable specificity for diagnosis of colorectal cancer. Furthermore, the integrity index (ALU247/ALU115) is better than absolute DNA concentration in diagnostic accuracy of colorectal cancer.
Uncoupling Protein 2 and Peroxisome Proliferator-Activated Receptor γ Gene Polymorphisms in Association with Diabetes Susceptibility in Chinese Han Population with Variant Glucose Tolerance

Objective To investigate the association of polymorphisms in uncoupling protein 2 (UCP2) and peroxisome proliferator-activated receptor (PPARγ) with glucolipid metabolism in Chinese Han population. Methods Five hundred eighty-nine subjects were divided into normal glucose tolerance (NGT) group (n = 198) and abnormal glucose tolerance group (n = 358). HbA1c, blood lipid profile, plasma glucose, and insulin were determined. Insulin sensitivity (HOMA-IR and Matsuda index (ISIM)) and insulin secretion indexes (HOMA-β, early and total phase disposition index) were evaluated. Eight potential functional SNPs in UCP2 and 7 in PPARγ were selected. SNPs were genotyped on Sequenom MassARRAY platform. Results The GG genotype of rs2920502 in PPARγ was associated with decreased risk of impaired glucose tolerance (G allele: OR: 0.818, 95%CI: 0.526–0.969, P = 0.042; GG: OR: 0.715, 95%CI: 0.527–0.97, P = 0.031). The TT genotype of rs3856806 in PPARγ was associated with increased risk of impaired glucose tolerance (T allele: OR: 1.46, 95%CI: 1.055–2.017, P = 0.022; TT: OR: 1.58, 95%CI: 1.104–2.761, P = 0.032). The GG genotype of rs2920502 in PPARγ had better blood glucose and increased insulin secretion and had lower HOMA-IR than GC/CC genotypes. Conclusion It probably could prevent insulin resistance in early stage by classifying the genotype of rs649446 and rs7109266 in UCP2. The GG genotype of rs2920502 in PPARγ had a decreased risk for diabetes. The TT genotype of rs3856806 in PPARγ had an increased risk for diabetes.
Variable uptake and elimination of stable nitrogen isotopes between tissues in fish

We conducted a diet-switching experiment using freshwater ocellate river stingrays (Potamotrygon motoro) fed a novel earthworm (Eisenia foetida) diet to establish the relative contributions of growth and metabolism to δ 15 N values in an elasmobranch species. We specifically controlled for the potential effects of protein composition of experi- mental diets on δ 15 N turnover to determine whether δ 15 N turnover after a low to high δ 15 N diet switch (uptake) and a high to low δ 15 N diet switch (elimination) will occur at the same rate within each consumer tissue. Our results showed that the turnover of δ 15 N from metabolism and growth differed between uptake and elimination phases in the liver, blood, cartilage, and muscle of freshwater stingrays. During uptake, liver was found to track dietary δ 15 N more closely than the other tissues, with the highest metabolic turnover rate of δ 15 N (0.015 day -1 ), whereas cartilage had the slowest rate of metabolic δ 15 N turnover (0.0022 day -1 ) relative to a constant rate of growth among tissues (0.003 day -1 ). We propose that estimates of trophic position from muscle sampling alone have considerable uncertainty, particularly for scavenging or omnivorous species. We suggest that multitissue sampling can identify this problem and lead to a more robust evaluation of trophic dynamics for individual species. Resume : Nous avons mene une experience de changement de regime alimentaire chez la pastenague d'eau douce ocellee (Potamotrygon motoro) nourrie d'un regime inusite de vers de terre (Eisenia foetida) afin d'etablir les contribu- tions relatives de la croissance et du metabolisme aux valeurs de 15 N chez une espece d'elasmobranches. Nous avons
Routing Metrics Depending on Previous Edges: The Mn Taxonomy and Its Corresponding Solutions

The routing algorithms used by current operators aim at coping with the demanded QoS requirements while optimizing the use of their network resources. These algorithms rely on the optimal substructure property (OSP), which states that an optimal path contains other optimal paths within it. However, we show that QoS metrics such as queuing delay and buffer consumption do not satisfy this property, which implies that the used algorithms lose their optimality and/or completeness. This negatively impacts the operator economy by causing a waste of network resources and/or violating Service Level Agreements (SLAs). In this paper, we propose a new so-called Mn taxonomy defining new metric classes. An Mn metric corresponds to a metric which requires the knowledge of the n previously traversed edges to compute its value at a given edge. Based on this taxonomy, we present three solutions for solving routing problems with the newly defined classes of metrics. We show that state-of- the-art algorithms based on the OSP indeed lose their original optimality and/or completeness properties while our proposed solutions do not, at the price of an increased computation time.
A Comparative Study for Classification on Different Domain

There is no individual classification technique has been shown to deal with all kinds of classification problems. The objective is to select the technique which more possibly reaches the best performance for any domain of data set. We focus on classifying datasets in different domains and properties such as numerical, categorical, and textual. We deal with one versus all strategy to handle multi-class problems. In the experiment, we compared the performance of 4 classification techniques namely Boosted C5.0, KNN, Naïve Bayes, and SVM on 10-fold cross-validation on different number of features. For numerical data set (low and high dimensional data set), the performance of KNN was better than other classification methods. For a categorical and textual data set, Naïve Bayes and SVM were outperformed, respectively.
Seroprevalence of hantaviruses and Leptospira in muskrat and coypu trappers in the Netherlands, 2016

ABSTRACT Aims: Seoul orthohantavirus (SEOV) and Leptospira spp. are zoonotic pathogens with rats as main reservoir. Recently, the presence of SEOV in brown rats was reported in one region in the Netherlands. Brown rats are a frequent bycatch in traps placed to catch muskrats (Ondatra zibethicus) and coypus (Myocastor coypus), and thus are a potential health risk for trappers. It was our aim to determine the seroprevalence of orthohantavirus, specifically SEOV, and Leptospira spp in Dutch trappers. Methods and results: Participating trappers provided serum samples and completed an online questionnaire. The serum was tested for the presence of antibodies against six orthohantaviruses and eight Leptospira serovars. Two hundred-sixty trappers completed the online questionnaire (65%), and 246 (61%) and 162 (40%) serum samples were tested for relevant orthohantaviruses and Leptospira spp. , respectively. The seroprevalence of Puumala orthohantavirus in Dutch trappers was 0.4% (95% CI: 0.1–2.3%). None of the participants tested positive for SEOV. The seroprevalence of leptospirosis was 1.2% (95% CI: 0.3–4.4%), although Leptospira spp. are present in brown rats in the Netherlands.Significance of study: The results indicate that the infections with orthohantaviruses and leptospires is low for muskrat and coypu trappers.
Title Global Analysis of Cellular Proteolysis by Selective Enzymatic Labeling of Protein N-Termini Permalink

Proteolysis is a critical modification leading to alteration of protein function with important outcomes in many biological processes. However, for the majority of proteases, we have an incomplete understanding of both cellular substrates and downstream effects. Here, we describe detailed protocols and applications for using the rationally engineered peptide ligase, subtiligase, to specifically label and capture protein N-termini generated by proteases either induced or added to complex biological samples. This method allows identification of the protein targets as well as their precise cleavage locations. This approach has revealed >8000 proteolytic sites in healthy and apoptotic cells including >1700 caspase cleavages. One can further determine substrate preferences through rate analysis with quantitative mass spectrometry, physiological substrate specificities, and even infer the identity of proteases operating in the cell. In this chapter, we also describe how this experimental method can be generalized to investigate proteolysis in any biological sample.
An Analysis of Cross-Document Linking Mechanisms

Physical and digital documents do often not exist in isolation but are implicitly or explicitly linked. Previous research in Human-Computer Interaction and Personal Information Management has revealed certain user behaviour in associating information across physical and digital documents. Nevertheless, there is a lack of empirical studies on user needs and behaviour when defining these associations. In this paper, we address this lack of empirical studies and provide insights into strategies that users apply when associating information across physical and digital documents. In addition, our study reveals the limitations of current practices and we suggest improvements for associating information across documents. Last but not least, we identify a set of design implications for the development of future cross-document linking solutions.
Oncology monoclonal antibodies expenditure trends and reimbursement projections in the emerging Balkan market

Monoclonal antibodies applied in clinical oncology present a therapeutic promise for many patients with cancer. Nevertheless these expensive protocols are associated with extremely high acquisition and administration costs. The issue of societal affordability of such treatment options is particularly at stake among middle income European economies. Medicines Agency of Serbia issues regular annual reports on public expenditure on pharmaceuticals since 2004. According to these official data total public expenditure on drugs doubled from 2004-2012 (from € 339,279,304 to € 742,013,976). During the same nine years public expenditure on antineoplastic pharmaceuticals was rising at much faster pace, approximately five times from € 10,297,616 in 2004 to € 51,223,474 in 2012. Absolutely record growth belongs to the value of turnover of monoclonal antibodies indicated in diverse malignancies. These costs became almost twenty times higher in 2012 compared to 2004 (€ 19,687,454 towards € 1,033,313 in the past). National pharmaceutical expenditure trend projections in this country show strong recovery in 2012 after severe blow to the overall health care market imposed by the worldwide crisis. Universal health insurance coverage and sustainable health care financing provision will remain difficult issues for Balkan economies in years to come. Although monoclonal antibodies exhibit undisputed therapeutic efficiency in certain malignant disorders, cost-effectiveness estimates must be taken into consideration by policy makers deciding on reimbursement.
Incidence and predictive factors for additional opioid prescription after endoscopic sinus surgery

Excessive postoperative opioid prescription is a source of prescription diversion in the United States opioid crisis and may contribute to chronic opioid use. Efficient prescription by the surgeon can mitigate opioid abuse and improve postoperative pain control. In this study we sought to better characterize the incidence and predictive baseline characteristics associated with the need for additional opioid prescription after endoscopic sinus surgery (ESS) for chronic rhinosinusitis.
Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model With Interval-Censored Data

ABSTRACT For semiparametric survival models with interval-censored data and a cure fraction, it is often difficult to derive nonparametric maximum likelihood estimation due to the challenge in maximizing the complex likelihood function. In this article, we propose a computationally efficient EM algorithm, facilitated by a gamma-Poisson data augmentation, for maximum likelihood estimation in a class of generalized odds rate mixture cure (GORMC) models with interval-censored data. The gamma-Poisson data augmentation greatly simplifies the EM estimation and enhances the convergence speed of the EM algorithm. The empirical properties of the proposed method are examined through extensive simulation studies and compared with numerical maximum likelihood estimates. An R package “GORCure” is developed to implement the proposed method and its use is illustrated by an application to the Aerobic Center Longitudinal Study dataset. Supplementary material for this article is available online.
Differential effect of manganese on the germination of Triglochin striata ( Juncaginaceae ) and C otula coronopifolia ( Asteraceae ) in Laguna

1Laboratorio de Ecología y Biodiversidad, Departamento de Biología, Universidad de Santiago de Chile. Casilla 40, Correo 33, Santiago. Avenida Libertador Bernardo O’Higgins 3363, Santiago, Chile. 2Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, 917-0124. Avenida Libertador Bernardo O’Higgins 3363, Santiago, Chile. 3Laboratorio de Bioquímica Vegetal y Fitorremediación, Departamento de Biología, Universidad de Santiago de Chile. Casilla 40, Correo 33, Santiago. Avenida Libertador Bernardo O’Higgins 3363, Santiago, Chile. *guerreroleiva.nicole@gmail.com
Reconsidering the importance of context for the success of digital government: the case of legal vulnerability and extreme poverty in the provision of migration services at the Southern Mexican border

This case study proposes to rethink context as a determinant of digital government success and elaborate on the variables that affect these initiatives in specific contexts. When talking about contextual variables, researchers often categorize them as social, political, and economic. Regarding social conditions, the digital divide is probably the most studied concept, although the conceptualization can vary for authors from different disciplines and theoretical traditions. For instance, many authors use the digital divide to not only refer to access to the Internet and related technologies, but also the skills and capabilities of users and how they use technologies to generate value in their daily lives. This case study argues, however, that the social context goes well beyond the digital divide and includes additional important factors like extreme poverty and legal vulnerability. Using the case of immigration services in the southern border of Mexico, this paper shows how multiple variables from the social environment affect digital government success and its impact on multiple users.
Management of Genu Varum/Valgum in Shwachman-Diamond Syndrome: A Report of Two Cases

Shwachman’s syndrome is a rare autosomal recessive disorder characterized by exocrine pancreatic insufficiency, bone marrow failure and skeletal abnormalities. The skeletal defects in the knees are related to the asymmetrical development of the growth plates that can result in varum/valgum deformities. We describe two cases of knee deformity in SDS patients surgically treated. In case n.1, because of a severe deformity, an osteotomy of the distal femur was performed by removing a lateral wedge and stabilizing with a staple, plus lateral tibial hemiepiphysiodesis. In case n. 2 first a medial hemiepiphysiodesis of the proximal tibia with Blount staples was performed. After 18 months the staples were removed from the tibia and a medial femoral hemiepiphysiodesis was performed. In both patients satisfactory angular alignment of the knees was obtained. In patients with genu varu/valgum in SDS the general condition of the patient (values of neutropenia and thrombocytopenia) determines the timing of surgical treatment because the risk of infection is always lurking. Traditional methods, such as osteotomy or hemiepiphysiodesis, have proved to be effective in the treatment of these deformities, but must be finely adjusted, by repeating or combining these procedures to adapt to the conditions of the pathologic physes.
A critical view of the general public's awareness and physicians' opinion of the trends and potential pitfalls of genetic testing in Greece.

AIM Progress in deciphering the functionality of the human genome sequence in the wake of technological advances in the field of genomic medicine have dramatically reduced the overall costs of genetic analysis, thereby facilitating the incorporation of genetic testing services into mainstream clinical practice. Although Greek genetic testing laboratories offer a variety of different genetic tests, relatively little is known about how either the general public or medical practitioners perceive genetic testing services. MATERIALS & METHODS We have therefore performed a nationwide survey of the views of 1717 members of the general public, divided into three age groups, from all over Greece, and residing in both large and small cities and villages, in order to acquire a better understanding of how they perceive genetic testing. We also canvassed the opinions of 496 medical practitioners with regard to genetic testing services in a separate survey that addressed similar issues. RESULTS Our subsequent analysis indicated that a large proportion of the general public is aware of the nature of DNA, genetic disorders and the potential benefits of genetic testing, although this proportion declines steadily with age. Furthermore, a large proportion of the interviewed individuals would be willing to undergo genetic testing even if the cost of analysis was not covered by healthcare insurance. However, a relatively small proportion of the general public has actually been advized to undergo genetic testing, either by relatives or physicians. Most physicians believe that the regulatory and legal framework that governs genetic testing services in Greece is rather weak. Interestingly, the vast majority of the general public strongly opposes direct-access genetic testing, and most would prefer referral from a physician than from a pharmacist. CONCLUSION Overall, our results provide a critical evaluation of the views of the general public with regard to genetics and genetic testing services in Greece and should serve as a model for replication in other populations.
You Say 'What', I Hear 'Where' and 'Why'? (Mis-)Interpreting SQL to Derive Fine-Grained Provenance

SQL declaratively specifies what the desired output of a query is. This work shows that a non-standard interpretation of the SQL semantics can, instead, disclose where a piece of the output originated in the input and why that piece found its way into the result. We derive such data provenance for very rich SQL dialects---including recursion, windowed aggregates, and user-defined functions---at the fine-grained level of individual table cells. The approach is non-invasive and implemented as a compositional source-level SQL rewrite: an input SQL query is transformed into its own interpreter that wields data dependencies instead of regular values. We deliberately design this transformation to preserve the shape of both data and query, which allows provenance derivation to scale to complex queries without overwhelming the underlying database system.
A Study on Utilization of Blockchain for Electricity Trading in Microgrid

The conventional electric power system is a unidirectional configuration that delivers electricity to the consumer in the power plant, but as the prosumers emerges, microgrid technology that enables bi-directional configuration has been developed. By applying the data distribution processing technology called the blockchain to the microgrid, time and cost can be saved compared with the conventional microgrid system. Through the related research, we analyze the structure of the microgrid and the utilization of the blockchain, study the pros and cons of applying the public blockchain and the private (consortium) blockchain, and propose the possible scenarios.
On Accelerated Singular Value Thresholding Algorithm for Matrix Completion

An accelerated singular value thresholding (SVT) algorithm was introduced for matrix completion in a recent paper [1], which applies an adaptive line search scheme and improves the convergence rate from O(1/N) for SVT to O(1/N2), where N is the number of iterations. In this paper, we show that it is the same as the Nemirovski’s approach, and then modify it to obtain an accelerate Nemirovski’s technique and prove the convergence. Our preliminary computational results are very favorable.