Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonstructural Carbohydrate Concentrations of Pine Trees as a Function of Evolutionary History

Nonstructural carbohydrates (NSC) can supply substrate during periods when current photosynthate is unavailable or inadequate to meet metabolic demands. I hypothesized that natural selection has favored higher nonstructural carbohydrate concentrations ([NSC]) in species that have an evolutionary history of frequent disturbance and tested this using three southern pine species that have evolved under a continuum of disturbance frequencies (evolutionary history of fire ~ longleaf > slash > loblolly). Stem and root samples were collected from 12 similar-sized individual trees of each species during time periods that reflect the annual minimum and maximum [NSC]. A modified colorimetric method was performed on the samples to determine [NSC]. Both [sugar] and [starch] differed among species, between organs, and exhibited seasonal patterns; however, these individual effects were not always independent of each other. Longleaf roots exhibited higher [sugar] than loblolly and slash; however, [sugar] in the stems were similar among species. Both [sugar] and [starch] of roots were higher than stems in March. Roots exhibited seasonal changes in [sugar] and [starch] (higher in October for sugar and higher in March for starch). The results suggest that evolutionary history of disturbance partly explains patterns of [NSC] observed in southern pines as longleaf—the species with an evolutionary history of frequent fire—exhibited the highest [NSC] in roots; however, similarities between slash and loblolly indicate that other factors must also be considered. The results are likely explained by the 2 different life histories exhibited in the juvenile stages of these pines; specifically, patterns of allocation to aboveand belowground tissues. I suggest that the increased belowground storage observed in adult longleaf pine may simply be a relic of selective pressures imposed at the juvenile stage. INDEX WORDS: nonstructural carbohydrates, stored carbon, longleaf, slash, loblolly, disturbance history, evolutionary history, fire, insect 3 NONSTRUCTURAL CARBOHYDRATE CONCENTRATIONS OF PINE TREES AS A FUNCTION OF EVOLUTIONARY HISTORY
Disparities in gestational age e speci fi c fetal mortality rates in the United States , 2009 e 2013

Purpose: Although studies have examined overall temporal changes in gestational ageespecific fetal mortality rates, there is little information on the current status of racial/ethnic differences. We hypothesize that differences exist between racial/ethnic groups across gestational age and that these differences are not equally distributed. Methods: Using the 2009e2013 data from US fetal death and live birth files for non-Hispanic white (NHW); non-Hispanic black (NHB); Hispanic; and American Indian/Alaska Native (AIAN) women, we conducted analyses to examine fetal mortality rates and estimate adjusted prevalence rate ratios and 95% confidence intervals (CIs). Results: There were lower risks of fetal mortality among NHB women (aPRR 1⁄4 0.76; 95% CI 1⁄4 0.71e0.81) and Hispanic women (aPRR 1⁄4 0.89; 95% CI 1⁄4 0.83e0.96) compared with NHWs at 22e23 weeks’ gestation. For NHB women, the risk was higher starting at 32e33 weeks (aPRR 1⁄4 1.11; 95% CI 1⁄4 1.04 e1.18) and continued to increase as gestational age increased. Hispanic and AIAN women had lower risks of fetal mortality compared with NHW women until 38e39 weeks. Conclusions: Further examination is needed to identify causes of fetal death within the later pregnancy period and how those causes and their antecedents might differ by race and ethnicity. 2017 Elsevier Inc. All rights reserved.
Taurolidine susceptibility of methicillin-resistant Staphylococcus pseudintermedius isolates

Infections caused by methicillin-resistant Staphylococcus pseudintermedius (MRSP) can be challenging to treat because they are often resistant to many other antimicrobial agents. We assessed the susceptibility of 29 MRSP isolates from dogs to taurolidine in vitro. There was no growth at 0.12% taurolidine and light growth at 0.06% for all isolates. Taurolidine was reliable at inhibiting growth of MRSP at a concentration of 1,200 µg/mL.
Phase II study of neo-adjuvant chemotherapy with paclitaxel and cisplatin given every 2 weeks for patients with a resectable squamous cell carcinoma of the esophagus.

BACKGROUND We have previously reported a favourable response rate in patients with advanced esophageal cancer after treatment with a biweekly regimen of paclitaxel and cisplatin. In this study we investigate the feasibility and efficacy of this regimen in a neo-adjuvant setting. PATIENTS AND METHODS Patients with resectable squamous cell carcinoma of the esophagus received paclit-axel 180 mg/m(2) and cisplatin 60 mg/m(2) every 2 weeks. Patients received three courses and responding patients received three additional courses; thereafter, patients were referred for surgery. Patient characteristics of 50 eligible patients were as follows: male, 60%; median age, 62 years (range 45-78); median World Health Organization performance status of 1 (range 0-2). RESULTS Ninety-four per cent of patients received at least three courses of chemotherapy. Haematological toxicity consisted of National Cancer Institute-Common Toxicity Criteria grade 3 or 4 neutropenia in 71% of patients, with neutropenic fever occurring in only two patients (4%). The overall response rate was 59%. Pathological examination showed tumour-free margins in 38 patients. In seven patients no residual tumour was found. The median overall survival was 20 months and the 1- and 3-year survival rates were 68% and 30%, respectively. CONCLUSIONS This dose-dense schedule of paclitaxel and cisplatin administered biweekly is well tolerated and the observed overall and complete response rates are promising.
A bottom‐up approach to discover transition rules of cellular automata using ant intelligence

This paper presents a new method to discover transition rules of geographical cellular automata (CA) based on a bottom‐up approach, ant colony optimization (ACO). CA are capable of simulating the evolution of complex geographical phenomena. The core of a CA model is how to define transition rules so that realistic patterns can be simulated using empirical data. Transition rules are often defined by using mathematical equations, which do not provide easily understandable explicit forms. Furthermore, it is very difficult, if not impossible, to specify equation‐based transition rules for reflecting complex geographical processes. This paper presents a method of using ant intelligence to discover explicit transition rules of urban CA to overcome these limitations. This ‘bottom‐up’ ACO approach for achieving complex task through cooperation and interaction of ants is effective for capturing complex relationships between spatial variables and urban dynamics. A discretization technique is proposed to deal with continuous spatial variables for discovering transition rules hidden in large datasets. The ACO–CA model has been used to simulate rural–urban land conversions in Guangzhou, Guangdong, China. Preliminary results suggest that this ACO–CA method can have a better performance than the decision‐tree CA method.
Range-Based Nearest Neighbor Queries with Complex-Shaped Obstacles

In this paper, we study a novel variant of obstructed nearest neighbor queries, namely, <italic>range-based obstructed nearest neighbor</italic> (RONN) search. As a natural generalization of <italic>continuous obstructed nearest-neighbor</italic> (CONN), an RONN query retrieves a set of <italic>obstructed nearest neighbors</italic> corresponding to every point in a specified range. We propose a new index, namely binary obstructed tree (called <italic>OB-tree</italic>), for indexing complex objects in the obstructed space. The novelty of OB-tree lies in the idea of <italic>dividing the obstructed space into non-obstructed subspaces</italic>, aiming to efficiently retrieve highly qualified candidates for RONN processing. We develop an algorithm for construction of the OB-tree and propose a space division scheme, called <italic>optimal obstacle balance</italic> (OOB2) scheme, to address the tree balance problem. Accordingly, we propose an efficient algorithm, called <italic>RONN by OB-tree Acceleration</italic> (RONN-OBA), which exploits the OB-tree and a binary traversal order of data objects to accelerate query processing of RONN. In addition, we extend our work in several aspects regarding the shape of obstacles, and range-based <inline-formula><tex-math notation="LaTeX">$k$</tex-math><alternatives> <inline-graphic xlink:href="zhu-ieq1-2779487.gif"/></alternatives></inline-formula> NN queries in obstructed space. At last, we conduct a comprehensive performance evaluation using both real and synthetic datasets to validate our ideas and the proposed algorithms. The experimental result shows that the RONN-OBA algorithm outperforms the two R-tree based algorithms and RONN-OA significantly.
Hippocampal Pathophysiology: Commonality Shared by Temporal Lobe Epilepsy and Psychiatric Disorders

Accumulating evidence points to the association of epilepsy, particularly, temporal lobe epilepsy (TLE), with psychiatric disorders, such as schizophrenia. Among these illnesses, the hippocampus is considered the regional focal point of the brain, playing an important role in cognition, psychosis, and seizure activity and potentially suggesting common etiologies and pathophysiology of TLE and schizophrenia. In the present review, we overview abnormal network connectivity between the dentate gyrus (DG) and the Cornus Ammonis area 3 (CA3) subregions of the hippocampus relative to the induction of epilepsy and schizophrenia. In light of our recent finding on the misguidance of hippocampal mossy fiber projection in the rodent model of schizophrenia, we discuss whether ectopic mossy fiber projection is a commonality in order to evoke TLE as well as symptoms related to schizophrenia.
4D CT image acquisition errors in SBRT of liver identified using correlation

In the AAPM Report 80,( 1 ) the imaging modality of 4D CT and respiration‐correlated CT was declared a “promising solution for obtaining high‐quality CT data in the presence of respiratory motion”. To gather anatomically correct data over time, the existence of correlation between the internal organ movement and an external surrogate has to be assumed. For the in‐house evaluation of such correlation, we retrospectively analyzed 21 four‐dimensional computer tomography (4D CT) scans of five patients, out of which the artifacts experienced in three patients are shown here. To provide context and a baseline for the analysis of patient motion, a real‐tissue liver phantom was used with a solid water block and liver tissue. The superior–inferior motion of fiducials in phantom and patients was correlated to the recorded anterior–posterior motion of an external surrogate marker on the chest. The use of a solid water block yielded a measurable correlation coefficient of 0.98 or better using a sinusoidal animation pattern. With sinusoidally‐animated liver tissue, the minimum correlation observed was 0.96. Comparing this to retrospective patient data, we found three cases of a change in the correlation coefficient, or simply a low correlation. The source of this low correlation was investigated by careful examination of the breathing traces and the CT‐phase assignments used to reconstruct the datasets. Consequences of nonregular breathing are elaborated on. We demonstrate the impact of wrong phase assignments and missing image information in the 4D CT phase sampling processes. We also show how daily patient‐based correlation analysis can indicate changes in breathing traces, which can be significant enough to decrease, or completely eliminate, previously existing correlation. PACS numbers: 87.57. ‐s, 87.57. Q‐, 87.57. cp, 87.57. N‐, 87.55. Qr
MALDI Spectra Database for Rapid Discrimination and Subtyping of Mycobacterium kansasii

Mycobacterium kansasii is an emerging non-tuberculous mycobacterial (NTM) pathogen capable of causing severe lung disease. Of the seven currently recognized M. kansasii genotypes (I-VII), genotypes I and II are most prevalent and have been associated with human disease, whereas the other five (III-VII) genotypes are predominantly of environmental origin and are believed to be non-pathogenic. Subtyping of M. kansasii serves as a valuable tool to guide clinicians in pursuing diagnosis and to initiate the proper timely treatment. Most of the previous rapid diagnostic tests for mycobacteria employing the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology focused on species-level identification. The purpose of this study was to establish MALDI-TOF MS reference spectra database for discrimination of M. kansasii at the genotype level. A panel of 32 strains, representatives of M. kansasii genotypes I-VI were selected, whole cell proteins extracted and measured with MALDI-TOF MS. A unique main spectra (MSP) library was created using MALDI Biotyper Compass Explorer software. The spectra reproducibility was assessed by computing composite correlation index and MSPs cross-matching. One hundred clinical M. kansasii isolates used for testing of the database resulted in 90% identification at genus-level, 7% identification at species-level and 2% identification was below the threshold of log score value 1.7, of which all were correct at genotype level. One strain could not be identified. On the other hand, 37% of strains were identified at species level, 40% at genus level and 23% was not identified with the manufacturer's database. The MALDI-TOF MS was proven a rapid and robust tool to detect and differentiate between M. kansasii genotypes. It is concluded that MALDI-TOF MS has a potential to be incorporated into the routine diagnostic workflow of M. kansasii and possibly other NTM species.
Low-Cost High-Speed Interpolation Method to Minimize Jagged Artifacts on Mobile Devices

With the development of multimedia technology, the demand for images of various sizes has increased. People zoom-in on low-resolution images to get high-resolution images. Simple interpolation techniques were utilized to generate high-resolution images from low-resolution images for low-power consumer electronics. This simple approach, however, had the disadvantage of creating jagged artifacts at the edges of the image. In this paper, a low-cost high-speed image interpolation method is proposed to reduce jagging defects in mobile devices. When the image is enlarged, the proposed method uses edge preservation interpolation, has better performance and processing speed than conventional methods, and suppresses blurry and jagged edges of one-pixel components.
Investigating the clinical advantages of a robotic linac equipped with a multileaf collimator in the treatment of brain and prostate cancer patients

The purpose of this study was to evaluate the performance of a commercially available CyberKnife system with a multileaf collimator (CK‐MLC) for stereotactic body radiotherapy (SBRT) and standard fractionated intensity‐modulated radiotherapy (IMRT) applications. Ten prostate and ten intracranial cases were planned for the CK‐MLC. Half of these cases were compared with clinically approved SBRT plans generated for the CyberKnife with circular collimators, and the other half were compared with clinically approved standard fractionated IMRT plans generated for conventional linacs. The plans were compared on target coverage, conformity, homogeneity, dose to organs at risk (OAR), low dose to the surrounding tissue, total monitor units (MU), and treatment time. CK‐MLC plans generated for the SBRT cases achieved more homogeneous dose to the target than the CK plans with the circular collimators, for equivalent coverage, conformity, and dose to OARs. Total monitor units were reduced by 40% to 70% and treatment time was reduced by half. The CK‐MLC plans generated for the standard fractionated cases achieved prescription isodose lines between 86% and 93%, which was 2%–3% below the plans generated for conventional linacs. Compared to standard IMRT plans, the total MU were up to three times greater for the prostate (whole pelvis) plans and up to 1.4 times greater for the intracranial plans. Average treatment time was 25 min for the whole pelvis plans and 19 min for the intracranial cases. The CK‐MLC system provides significant improvements in treatment time and target homogeneity compared to the CK system with circular collimators, while maintaining high conformity and dose sparing to critical organs. Standard fractionated plans for large target volumes (>100 cm3) were generated that achieved high prescription isodose levels. The CK‐MLC system provides more efficient SRS and SBRT treatments and, in select clinical cases, might be a potential alternative for standard fractionated treatments. PACS numbers: 87.56. nk, 87.56. bd
A multi‐institutional study for tolerance and action levels of IMRT dose quality assurance measurements in Korea

The purpose of this study was to suggest tolerance levels for IMRT DQA measurements using confidence limits determined by a multi‐institutional study in Korea. Ten institutions were grouped into LINAC (seven linear accelerators) and TOMO (three tomotherapy machines). The DQA processes consisted of point (high‐ and low‐dose regions) and planar (per‐field and composite‐field) dose measurements using an ion chamber and films (or 2D detector array) inserted into a custom‐made acryl phantom (LINAC) or a cheese phantom (TOMO). The five mock structures developed by AAPM TG‐119 were employed, but the prostate as well as the H&N structures were modified according to Korean patients' anatomy. The point measurements were evaluated in a ratio of measured and planned doses, while the planar dose distributions were assessed using two gamma criteria of 2 mm/2% and 3 mm/3%. The confidence limit (|mean + 1.96 σ|) for point measurements was determined to be 3.0% in high‐dose regions and 5.0% in low‐dose regions. The average percentage of points passing the gamma criteria of 2 mm/2% and 3 mm/3% for per‐field measurements was 92.7 ±6.5% and 98.2 ±2.8%, respectively. Thus, the corresponding confidence limit was 79.1% and 92.7%, respectively. The gamma passing rate averaged over all mock tests and institutions for composite‐field measurements was 86.1 ±6.5% at 2 mm/2% and 95.3 ±3.8% at 3 mm/3%, leading to the confidence limit of 73.3% and 87.9%, respectively. There was no significant difference in the tolerance levels of point dose measurements between LINAC and TOMO groups. In spite of the differences in mock structures and dosimetry tools, our tolerance levels were comparable to those of AAPM and ESTRO guidelines. PACS number: 87.55. Qr
A Smart Visual Analysis Solution for MOOC Data

Massive Open Online Courses (MOOCs) have been the focus of online education in recent years. Compared to traditional courses, indirect communication and trans normal number of students in MOOCs bring great difficulties for instructors in knowing how much and how well students have learned. In this paper, a smart visual analysis solution for MOOC data is proposed. The solution contains four views, Demographics Distribution View, Activeness Calendar View, Progress Distribution View and Personal Footprints View. We also integrate data mining results into visualization to help instructors quickly build an insight. Our solution provides a direct, explicit, vivid and interactive way for instructors to know about students' learning progress in multiple scales, which was commented as very helpful in the case study.
5′-Phospho-RNA Acceptor Specificity of GDP Polyribonucleotidyltransferase of Vesicular Stomatitis Virus in mRNA Capping

ABSTRACT The GDP polyribonucleotidyltransferase (PRNTase) domain of the multifunctional L protein of rhabdoviruses, such as vesicular stomatitis virus (VSV) and rabies virus, catalyzes the transfer of 5′-phospho-RNA (pRNA) from 5′-triphospho-RNA (pppRNA) to GDP via a covalent enzyme-pRNA intermediate to generate a 5′-cap structure (GpppA). Here, using an improved oligo-RNA capping assay with the VSV L protein, we showed that the Michaelis constants for GDP and pppAACAG (VSV mRNA-start sequence) are 0.03 and 0.4 μM, respectively. A competition assay between GDP and GDP analogues in the GpppA formation and pRNA transfer assay using GDP analogues as pRNA acceptors indicated that the PRNTase domain recognizes the C-2-amino group, but not the C-6-oxo group, N-1-hydrogen, or N-7-nitrogen, of GDP for the cap formation. 2,6-Diaminopurine-riboside (DAP), 7-deazaguanosine (7-deaza-G), and 7-methylguanosine (m7G) diphosphates efficiently accepted pRNA, resulting in the formation of DAPpppA, 7-deaza-GpppA, and m7GpppA (cap 0), respectively. Furthermore, either the 2′- or 3′-hydroxyl group of GDP was found to be required for efficient pRNA transfer. A 5′-diphosphate form of antiviral ribavirin weakly inhibited the GpppA formation but did not act as a pRNA acceptor. These results indicate that the PRNTase domain has a unique guanosine-binding mode different from that of eukaryotic mRNA capping enzyme, guanylyltransferase. IMPORTANCE mRNAs of nonsegmented negative-strand (NNS) RNA viruses, such as VSV, possess a fully methylated cap structure, which is required for mRNA stability, efficient translation, and evasion of antiviral innate immunity in host cells. GDP polyribonucleotidyltransferase (PRNTase) is an unconventional mRNA capping enzyme of NNS RNA viruses that is distinct from the eukaryotic mRNA capping enzyme, guanylyltransferase. In this study, we studied the pRNA acceptor specificity of VSV PRNTase using various GDP analogues and identified chemical groups of GDP as essential for the substrate activity. The findings presented here are useful not only for understanding the mechanism of the substrate recognition with PRNTase but also for designing antiviral agents targeting this enzyme.
Lessons Learned from Protective Immune Responses to Optimize Vaccines against Cryptosporidiosis

In developing countries, cryptosporidiosis causes moderate-to-severe diarrhea and kills thousands of infants and toddlers annually. Drinking and recreational water contaminated with Cryptosporidium spp. oocysts has led to waterborne outbreaks in developed countries. A competent immune system is necessary to clear this parasitic infection. A better understanding of the immune responses required to prevent or limit infection by this protozoan parasite is the cornerstone of development of an effective vaccine. In this light, lessons learned from previously developed vaccines against Cryptosporidium spp. are at the foundation for development of better next-generation vaccines. In this review, we summarize the immune responses elicited by naturally and experimentally-induced Cryptosporidium spp. infection and by several experimental vaccines in various animal models. Our aim is to increase awareness about the immune responses that underlie protection against cryptosporidiosis and to encourage promotion of these immune responses as a key strategy for vaccine development. Innate and mucosal immunity will be addressed as well as adaptive immunity, with an emphasis on the balance between TH1/TH2 immune responses. Development of more effective vaccines against cryptosporidiosis is needed to prevent Cryptosporidium spp. -related deaths in infants and toddlers in developing countries.