Miracle-dz/UniFAR-FTUs huggingface dataset:
RE: Diffusion-Weighted Magnetic Resonance Imaging: A New Approach in Imaging-Guided Biopsies of Cervical Lesions Suspicious for Malignancy

We read with great interest the article recently published by Wu et al. (1) in the 2013 issue of the Korean Journal of Radiology. In this article, CT-guided core needle biopsy is an accurate and efficient method for the historical diagnosis of deep suprahyoid lesions in post-treated head and neck cancer patients with both infrequent and minor complications. We congratulate the authors for the excellent results and we would like to add some complementary comments to the content covered by the authors.Overall, imaging-guided cervical needle biopsy represents a major challenge due to several reasons. Different yet
Cohort Fertility Patterns in the Nordic Countries

Previous analyses of period fertility suggest that the trends of the Nordic countries are sufficiently similar to speak of a common "Nordic fertility regime". We investigate whether this assumption can be corroborated by comparing cohort fertility patterns in the Nordic countries. We study cumulated and completed fertility of Nordic birth cohorts based on the childbearing histories of women born in 1935 and later derived from the population registers of Denmark, Finland, Norway, and Sweden. We further explore childbearing behaviour by women’s educational attainment. The results show remarkable similarities in postponement and recuperation between the countries and very small differences in completed fertility across educational groups. Median childbearing age is about 2−3 years higher in the 1960−64 cohort than in the 1950−54 cohort, but the younger cohort recuperates the fertility level of the older cohort at ages 30 and above. A similar pattern of recuperation can be observed for highly educated women as compared to women with less education. An interesting finding is that of a positive relationship between educational level and the final number of children when women who become mothers at similar ages are compared. Country differences in fertility outcome are generally rather low. Childlessness is highest in Finland and lowest in Norway, and the educational differentials are largest in Norway. Despite such differences, the cohort analyses in many ways support the notion of a common Nordic fertility regime.
Experience with host cell protein impurities in biopharmaceuticals

In the 40‐year history of biopharmaceuticals, there have been a few cases where the final products contained residual host cell protein (HCP) impurities at levels high enough to be of concern. This article summarizes the industry experience in these cases where HCP impurities have been presented in public forums and/or published. Regulatory guidance on HCP impurities is limited to advising that products be as pure as practical, with no specified numerical limit because the risk associated with HCP exposure often depends on the clinical setting (route of administration, dose, indication, patient population) and the particular impurity. While the overall safety and purity track record of the industry is excellent, these examples illustrate several important lessons learned about the kinds of HCPs that co‐purify with products (e.g., product homologs, and HCPs that react with product), and the kinds of clinical consequences of HCP impurities (e.g., direct biological activity, immunogenicity, adjuvant). The literature on industry experience with HCP impurities is scattered, and this review draws in to one reference documented examples where the data have been presented in meetings, patents, product inserts, or press releases, in addition to peer‐reviewed journal articles. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 34:828–837, 2018
Optimality, computation, and interpretation of nonnegative matrix factorizations

The notion of low rank approximations arises from many important applications. When the low rank data are further required to comprise nonnegative values only, the approach by nonnegative matrix factorization is particularly appealing. This paper intends to bring about three points. First, the theoretical Kuhn-Tucker optimality condition is described in explicit form. Secondly, a number of numerical techniques, old and new, are suggested for the nonnegative matrix factorization problems. Thirdly, the techniques are employed to two real-world applications to demonstrate the difficulty in interpreting the factorizations.
iMag: Accurate and Rapidly Deployable Inertial Magneto-Inductive Localisation

Localisation is of importance for many applications. Our motivating scenarios are short-term construction work and emergency rescue. Not only is accuracy necessary, these scenarios also require rapid setup and robustness to environmental conditions. These requirements preclude the use of many traditional methods e.g. vision-based, laser-based, Ultra-wide band (UWB) and Global Positioning System (GPS)-based localisation systems. To solve these challenges, we introduce iMag, an accurate and rapidly deployable inertial magneto-inductive (MI) localisation system. It localises monitored workers using a single MI transmitter and inertial measurement units with minimal setup effort. However, MI location estimates can be distorted and ambiguous. To solve this problem, we suggest a novel method to use MI devices for sensing environmental distortions, and use these to correctly close inertial loops. By applying robust simultaneous localisation and mapping (SLAM), our proposed localisation method achieves excellent tracking accuracy, and can improve performance significantly compared with only using an inertial measurement unit (IMU) and MI device for localisation.
Novel length aware packet aggregation and coding scheme for multi-hop wireless LANs

This paper proposes a length aware packet aggregation and coding (LAPAC) scheme that uses packet aggregation and network coding (NC) to improve the throughput of single-relay multi-user wireless networks. Besides, this paper clarifies that the throughput is improved by optimizing the minimum contention window sizes in the IEEE 802.11 based single-relay multi-user wireless networks with LAPAC subject to the constraint achieving fairness between uplink and downlink flows. Computer simulation results show that the throughput of the LAPAC scheme is about 10% higher than that of the conventional ones. The optimized minimum contention window sizes are derived by computer simulations and theoretical analysis. The optimized minimum contention window sizes obtained from theoretical analysis are in good agreement with those obtained from computer simulations, when the number of wireless stations is less than or equal to 15. Furthermore this paper shows that LAPAC scheme outperforms the conventional ones in the case of not only single-rate networks but also multi-rate networks.
Macroecology: more than the division of food and space among species on continents

Macroecology is a big-picture, statistical approach to the study of ecology. By focusing on broadly occurring patterns and processes operating at large spatial and temporal scales and ignoring localized and fine-scaled details, macroecology aims to uncover general mechanisms operating at organism, population and ecosystem levels of organization. Although such an approach is evident in writings dating from the mid- to late 1800s, not until 1989 was the domain of macroecology clearly articulated. Since then there has been an exponential growth in publications employing a macroecological perspective. Here we (1) briefly review the history of macroecology, with emphasis on cultural, scientific and technological innovations that made this approach possible, (2) highlight current developments in the field, including its increasing linkages with biogeography and other disciplines, and (3) point to likely future directions. We also touch upon methodological, statistical and institutional challenges faced by this and other highly interdisciplinary approaches. Our review of macroecology is especially timely, since it has been 20 years since the term was coined and the seminal paper published.
Evaluation of cognitive functions and its influencing factors in refractory obsessive-compulsive disorder

Objective:To evaluate the cognitive functions and its influencing factors in refractory obsessive-compulsive disorder(OCD) . Method:55 patients with refractory OCD and 60 healthy person as control were evaluated by neuropsychological test,such as Stroop color-word test,repeatable battery for the assessment of neuropsychological status(RBANS) and Yale-Brown obsessive compulsive scale(YBOCS) . Results:The language score of RBANS in refractory OCD patients were significantly lower than those in healthy controls(P0.01) . Refractory OCD patient's age,onset age were negatively correlated with immediate memory score,attention score and total scores in RBANS(P0.05 or P0.01) ,and were positively correlated with the color interference time in Stroop(P0.05 or P0.01) . YBOCS scores were positively correlated with the word interference time in Stroop(P0.01) . The points and total score in RBANS with the working group(n=30) were significantly higher than non-working group(n=25) (all P0.01) . Conclusion:The language function in refractory OCD patients were impaired,and some cognitive function scores were significantly correlated with the age,onset age and symptom severity.Work may be the protective effect of cognitive function in patients with obsessive-compulsive disorder.
Parallel Evolution of Cortical Areas Involved in Skilled Hand Use

Dexterous hands, used to manipulate food, tools, and other objects, are one of the hallmarks of primate evolution. However, the neural substrate of fine manual control necessary for these behaviors remains unclear. Here, we describe the functional organization of parietal cortical areas 2 and 5 in the cebus monkey. Whereas other New World monkeys can be quite dexterous, and possess a poorly developed area 5, cebus monkeys are the only New World primate known to use a precision grip, and thus have an extended repertoire of manual behaviors. Unlike other New World Monkeys, but much like the macaque monkey, cebus monkeys possess a proprioceptive cortical area 2 and a well developed area 5, which is associated with motor planning and the generation of internal body coordinates necessary for visually guided reaching, grasping, and manipulation. The similarity of these fields in cebus monkeys and distantly related macaque monkeys with similar manual abilities indicates that the range of cortical organizations that can emerge in primates is constrained, and those that emerge are the result of highly conserved developmental mechanisms that shape the boundaries and topographic organizations of cortical areas.
GOME/ERS-2: New Homogeneous Level 1B Data from an Old Instrument

In the framework of ESA’s “GOME Evolution Project”, a reprocessing will be made of the entire 16 year GOME Level 1 dataset. The GOME Evolution Project further includes the generation of a new GOME water vapour product, and a public outreach programme. In this paper we will describe the reprocessing of the Level 1 data, carried out with the latest version of the GOME Data Processor at DLR. The change most visible to the user will be the new product format in NetCDF, plus supporting documentation (ATBD and PUM). Full-mission reprocessed L1b data are expected to be released in the 4th quarter of 2015
Identifying the Authors’ National Variety of English in Social Media Texts

In this paper, we present a study for the identification of authors’ national variety of English in texts from social media. In data from Facebook and Twitter, information about the author’s social profile is annotated, and the national English variety (US, UK, AUS, CAN, NNS) that each author uses is attributed. We tested four feature types: formal linguistic features, POS features, lexicon-based features related to the different varieties, and data-based features from each English variety. We used various machine learning algorithms for the classification experiments, and we implemented a feature selection process. The classification accuracy achieved, when the 31 highest ranked features were used, was up to 77.32%. The experimental results are evaluated, and the efficacy of the ranked features discussed.
Does Time-in-Range Matter? Perspectives From People With Diabetes on the Success of Current Therapies and the Drivers of Improved Outcomes

IN BRIEF After assessing patient perspectives on the success of current diabetes therapies and the factors that have the greatest impact on daily life, we show that time-in-range is a crucial outcome for people with diabetes and that current therapies are falling short on this metric. We also show that patients feel significant stress and worry, and they believe they are falling short in diet, exercise, and weight maintenance. In addition, they believe diet and exercise and in-range blood glucose are the biggest drivers of improved diabetes management and mindset. Together, these findings support the need for therapies that improve outcomes including and beyond A1C.
Measuring the Impact of Topic Drift in Scholarly Networks

With the increase in collaboration among researchers of various disciplines, changing the research topic or working on multiple topics is not an unusual behavior. Several comprehensive efforts have been made for predicting, quantifying, and studying the researcher's impact. The question, that how the change in the field of interest over time or working in more than one topics can influence the scientific impact, remains unanswered. In this research, we study the effect of topic drift on the scientific impact of an author. We apply Author Conference Topic (ACT) model to extract topic distribution of individual authors who are working on multiple topics to compare and analyze with authors who work on a single topic. We analyze the productivity of the authors on the basis of publication count, citation count and h-index. We find that authors who stick to one topic, produce a higher impact and gain more attention. To further strengthen our results we gather the h-index of top-ranked authors working on one topic and top-ranked authors working on multiple topics and examine whether there are similar trends in their progress. The results show an evidence of significant impact of topic drift on career choices of researchers.
Predicting Document Creation Times in News Citation Networks

For the temporal analysis of news articles or the extraction of temporal expressions from such documents, accurate document creation times are indispensable. While document creation times are available as time stamps or HTML metadata in many cases, depending on the document collection in question, this data can be inaccurate or incomplete in others. Especially in digitally published online news articles, publication times are often missing from the article or inaccurate due to (partial) updates of the content at a later time. In this paper, we investigate the prediction of document creation times for articles in citation networks of digitally published news articles, which provide a network structure of knowledge flows between individual articles in addition to the contained temporal expressions. We explore the evolution of such networks to motivate the extraction of suitable features, which we utilize in a subsequent prediction of document creation times, framed as a regression task. Based on our evaluation of several established machine learning regressors on a large network of English news articles, we show that the combination of temporal and local structural features allows for the estimation of document creation times from the network.
Drastic reorganization of the bioconvection pattern of Chlamydomonas: quantitative analysis of the pattern transition response

SUMMARY Motile aquatic microorganisms are known to self-organize into bioconvection patterns. The swimming activity of a population of microorganisms leads to the emergence of macroscopic patterns of density under the influence of gravity. Although long-term development of the bioconvection pattern is important in order to elucidate the possible integration of physiological functions of individuals through bioconvection pattern formation, little quantitative investigation has been carried out. In the present paper, we present the first quantitative description of long-term behavior of bioconvection of Chlamydomonas reinhardtii, particularly focusing on the ‘pattern transition response’. The pattern transition response is a sudden breakdown of the steady bioconvection pattern followed by re-formation of the pattern with a decreased wavelength. We found three phases in the pattern formation of the bioconvection of C. reinhardtii: onset, steady-state 1 (before the transition) and steady-state 2 (after the transition). In onset, the wavelength of the bioconvection pattern increases with increasing depth, but not in steady-states 1 or 2. By means of the newly developed two-axis view method, we revealed that the population of C. reinhardtii moves toward the bottom of the experimental chamber just before the pattern transition. This indicates that the pattern transition response could be caused by enhancement of the gyrotaxis of C. reinhardtii as a result of the changes in the balance between the gravitactic and gyrotactic torques. We also found that the bioconvection pattern changes in response to the intensity of red-light illumination, to which C. reinhardtii is phototactically insensitive. These facts suggest that the bioconvection pattern has a potential to drastically reorganize its convection structure in response to the physiological processes under the influence of environmental cues.
Comparative analysis of tissue reconstruction algorithms for 3D histology

Abstract Motivation Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches. Availability and implementation Code: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702. Supplementary information Supplementary data are available at Bioinformatics online.
Application of Dried Blood Spot Testing for Hepatitis C Virus RNA Amplification

Background/Aim : Hepatitis C Virus (HCV) infection represent a major public health problem because of the ability of HCV to cause a chronic carrier state. Even though chronic carriers remain largely asymptomatic, a large number of these individuals subsequently develop cirrhosis and primary hepatocellular carcinomas. Dried Blood Spot (DBS) samples are a simple and inexpensive sampling method, especially useful for blood collection in resource poor settings with limited access to diagnostic facilities. The main advantage of DBS samples over routine blood samples is that only a small quantity of blood is required, easy to obtain, stable and can be transported to a reference laboratory at minimal cost. The Aim of the work was to evaluate the feasibility of DBS samples as an alternative sample type to serum for the detection of HCV RNA. Results obtained from DBS samples were compared with results of serum using the same technique. Methods : This study was carried out on 50 anti-HCV–positive serum samples, from patients whom attending Arar Central Hospital and Prince Hospital, Arar, kingdom of Saudi Arabia. , during November 2011 to February 2012. Results: . HCV RNA was detected in 49/50 (98%) of the DBS samples, with Sensitivity 98% and Specificity 100 %, in comparisons to serum samples. Also there was no statistical significant difference in hepatitis C viral load between the two different samples among the patients. We demonstrated that there is no statistical significant different between the two samples when viral load is both less than and also more than 100000 IU. Concluded that the use of DBS for extraction and amplification of HCV RNA was reliable, specific, sensitive, cheap and appropriate method to monitor the HCV infected patients.
Microreview Cell signalling and Trypanosoma cruzi invasion

Mammalian cell invasion by the protozoan pathogen Trypanosoma cruzi is critical to its survival in the host. To promote its entry into a wide variety of nonprofessional phagocytic cells, infective trypomastigotes exploit an arsenal of heterogenous surface glycoproteins, secreted proteases and signalling agonists to actively manipulate multiple host cell signalling pathways. Signals initiated in the parasite upon contact with mammalian cells also function as critical regulators of the invasion process. Whereas the full spectrum of cellular responses modulated by T. cruzi is not yet known, mounting evidence suggests that these pathways impinge on a number of cellular processes, in particular the ubiquitous wound-repair mechanism exploited for lysosomemediated parasite entry. Furthermore, differential engagement of host cell signalling pathways in a cell type-specific manner and modulation of host cell gene expression by T. cruzi are becoming recognized as essential determinants of infectivity and intracellular survival by this pathogen.
Building institutional capacities and competencies for systemic learning analytics initiatives

The last five years have brought an explosion of research in the learning analytics field. However, much of what has emerged has been small scale or tool-centric. While these efforts are vitally important to the development of the field, in order to truly transform education, learning analytics must scale and become institutionalized at multiple levels throughout an educational system. Many institutions are currently undertaking this grand challenge and this panel will highlight cases from: the University of Wisconsin System, the Society for Learning Analytics Research, the University of New England, and Rio Salado College.
DOES NOT REQUIRE INEQUALITY 1 Trade-offs between Equity and Excellence in Academic Performance : Evidence from 27 Countries

Educational policy makers traditionally perceived there to be a trade-off between educational excellence and educational equity. With the rise of cross-national comparative datasets, however, research has begun to suggest such a trade-off does not exist and indeed, higher variance in achievement and more segregated school systems may be associated with lower performance. However, such research has tended to focus on between nation analysis for which important covariates are not controlled (e.g., response set differences, latent cultural differences, etc.). Likewise, relatively little consideration has been given to whether a trade-off may exist for high or low performing students. Using five cycles of the PISA database, the current research explores within country trajectories in achievement and inequality measures to test the hypothesis of an excellence/equity trade-off in academic performance. Rejecting the trade-off hypothesis, we find a robust negative relationship between performance and inequality which is of statistical and practical significance. Detailed analysis of countries with large changes in average achievement from 2000 to 2012 suggest a focus on low and average performers may be critical to successful policy interventions within a given country.