Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Cloning and Characterization of a cDNA for Pterocarpan 4-Dimethylallyltransferase Catalyzing the Key Prenylation Step in the Biosynthesis of Glyceollin, a Soybean Phytoalexin1[W]

Glyceollins are soybean (Glycine max) phytoalexins possessing pterocarpanoid skeletons with cyclic ether decoration originating from a C5 prenyl moiety. Enzymes involved in glyceollin biosynthesis have been thoroughly characterized during the early era of modern plant biochemistry, and many genes encoding enzymes of isoflavonoid biosynthesis have been cloned, but some genes for later biosynthetic steps are still unidentified. In particular, the prenyltransferase responsible for the addition of the dimethylallyl chain to pterocarpan has drawn a large amount of attention from many researchers due to the crucial coupling process of the polyphenol core and isoprenoid moiety. This study narrowed down the candidate genes to three soybean expressed sequence tag sequences homologous to genes encoding homogentisate phytyltransferase of the tocopherol biosynthetic pathway and identified among them a cDNA encoding dimethylallyl diphosphate: (6aS, 11aS)-3,9,6a-trihydroxypterocarpan [(−)-glycinol] 4-dimethylallyltransferase (G4DT) yielding the direct precursor of glyceollin I. The full-length cDNA encoding a protein led by a plastid targeting signal sequence was isolated from young soybean seedlings, and the catalytic function of the gene product was verified using recombinant yeast microsomes. Expression of the G4DT gene was strongly up-regulated in 5 to 24 h after elicitation of phytoalexin biosynthesis in cultured soybean cells similarly to genes associated with isoflavonoid pathway. The prenyl part of glyceollin I was demonstrated to originate from the methylerythritol pathway by a tracer experiment using [1-13C]Glc and nuclear magnetic resonance measurement, which coincided with the presumed plastid localization of G4DT. The first identification of a pterocarpan-specific prenyltransferase provides new insights into plant secondary metabolism and in particular those reactions involved in the disease resistance mechanism of soybean as the penultimate gene of glyceollin biosynthesis.
THE WASHBACK EFFECT OF TEFL UNIVERSITY ENTRANCE EXAM ON ACADEMIC BEHAVIOR OF STUDENTS AND PROFESSORS

The present study was an attempt to investigate the washback effect of the TEFL MA University Entrance Exam on the teaching and learning behaviors of students and professors. The TEFL MA UEE consists of three subcomponents that deal with particular aspects of applied linguistics; each of these parts measures the participants’ knowledge in linguistics, language testing, and teaching methodology. To realize the effects of the TEFL test, the researchers developed an observation checklist and two questionnaires based on the underlying theories of washback. The questionnaires were answered by 32 professors and 210 students. In addition, 13 linguistics, testing, and methodology classes were also observed. Finally, to find answers to research questions, Chi–square test and frequency analyses were conducted using SPSS. The results of this study indicated that TEFL MA UEE had a negligible effect on the students’ and professors’ academic behavior.
Imaging of Carbon Translocation to Fruit Using Carbon-11-Labeled Carbon Dioxide and Positron Emission Tomography

Carbon kinetics into the fruit is an agricultural issue on the growth and development of the sink organs to be harvested. Particularly, photoassimilate translocation and distribution are important topics for understanding the mechanism. In the present work, carbon-11 (11C) labeled photoassimilate translocation into fruits of tomato has been imaged using carbon-11-labeled carbon dioxide and the positron emission tomography (PET). Dynamice PET data of gradual increasing of 11C activity and its distribution is acquired quantitatively in intact plant body. This indicates that the 3-D photoassimilate translocation into the fruits is imaged successfully and carbon kinetics is analyzable to understand the plant physiology and nutrition.
Environmental influences on familial resemblance for drug abuse in first-cousin pairs: a Swedish national study

Background Using three independent methods, prior studies in Swedish sibling pairs indicate that environmental factors contribute substantially to familial aggregation for drug abuse (DA). Could we replicate these results in cousin pairs? Method Using multiple Swedish public databases (1964–2011), we defined DA using medical, legal or pharmacy registry records and examined concordance in full cousin pairs as a function of age differences, younger–older relationships and geographical proximity while growing up. Results Replicating prior results in siblings, cousin pairs were significantly more similar in their history of DA if they were (i) closer versus more distant in age and (ii) grew up in high versus low geographical proximity to one another. Furthermore, controlling for background factors, having an older cousin with DA conveys a greater risk for DA than having a younger drug-abusing cousin. The greater transmission of DA from older to younger versus younger to older cousin was more prominent in pairs who grew up close to one another. In age difference and geographical proximity analyses, effects were consistently strongest in male–male cousin pairs. In analyses of older → younger versus younger → older transmission, effects were stronger in male–male and male–female than in female–female or female–male relative pairs. Conclusions In accord with prior results in siblings, environmental factors contribute substantially to the familial aggregation of DA in cousins and these effects are, in general, stronger in males than in females.
IMPROVED FUNCTIONAL IMMOBILIZATION OF LLAMA SINGLE-DOMAIN ANTIBODY FRAGMENTS TO POLYSTYRENE SURFACES USING SMALL PEPTIDES

We studied the effect of different fusion domains on the functional immobilization of three llama single-domain antibody fragments (VHHs) after passive adsorption to polystyrene in enzyme-linked immunosorbent assays (ELISA). Three VHHs produced without any fusion domain were efficiently adsorbed to polystyrene, which, however, resulted in inefficient antigen binding. Functional VHH immobilization was improved by VHH fusion to a consecutive myc-His6-tag and was even more improved by fusion to the llama antibody long hinge region containing an additional His6-tag (LHc-His6). The partial dimerization of VHH-LHc-His6 fusion proteins through LHc-mediated disulfide-bond formation was not essential for their improved functional immobilization. VHH fusions to specific polystyrene binding peptides, hydrophobins, or other, unrelated VHH domains were less suitable for increasing functional VHH immobilization because of reduced microbial expression levels. Thus, VHH-LHc-His6 fusion proteins are most suited for functional passive adsorption in ELISA.
Video Captioning with Guidance of Multimodal Latent Topics

The topic diversity of open-domain videos leads to various vocabularies and linguistic expressions in describing video contents, and therefore, makes the video captioning task even more challenging. In this paper, we propose an unified caption framework, M&M TGM, which mines multimodal topics in unsupervised fashion from data and guides the caption decoder with these topics. Compared to pre-defined topics, the mined multimodal topics are more semantically and visually coherent and can reflect the topic distribution of videos better. We formulate the topic-aware caption generation as a multi-task learning problem, in which we add a parallel task, topic prediction, in addition to the caption task. For the topic prediction task, we use the mined topics as the teacher to train a student topic prediction model, which learns to predict the latent topics from multimodal contents of videos. The topic prediction provides intermediate supervision to the learning process. As for the caption task, we propose a novel topic-aware decoder to generate more accurate and detailed video descriptions with the guidance from latent topics. The entire learning procedure is end-to-end and it optimizes both tasks simultaneously. The results from extensive experiments conducted on the MSR-VTT and Youtube2Text datasets demonstrate the effectiveness of our proposed model. M&M TGM not only outperforms prior state-of-the-art methods on multiple evaluation metrics and on both benchmark datasets, but also achieves better generalization ability.
Comparison of clinical manifestations, outcomes and cerebrospinal fluid findings between herpes simplex type 1 and type 2 central nervous system infections in adults

In previous reports on the viral causes of central nervous system (CNS) infections, it has been generally recognized that HSV‐1 is a major cause of encephalitis, while HSV‐2 is the predominant cause of aseptic meningitis in adults. To examine this matter, the clinical characteristics in the two types of HSV CNS infections were investigated. In a retrospective cohort study which included all adult patients (≥16 years) between January 1999 and December 2013 in a 2,700‐bed tertiary care hospital, all the patients in whom PCR of the CSF for HSV was positive were identified. Ninety‐five patients with positive CSF PCR results for HSV were included, 21 with HSV‐1 and 74 with HSV‐2. Many patients with HSV‐1 had encephalitis (13/21, 61.9%), whereas most patients with HSV‐2 had meningitis (62/74, 83.8%). However, HSV‐1 and HSV‐2 accounted for similar proportion of patients with HSV encephalitis (13/25, 52.0% vs. 12/25, 48.0%). Neurological sequelae were more frequent among patients with HSV‐1 (9/21, 42.9% vs. 6/74, 8.1%; P = 0.001). The present study suggests that HSV‐2 is not only a major cause of aseptic meningitis, but also it may cause serious manifestation as HSV‐1 encephalitis in adults. J. Med. Virol. 86: 1766–1771, 2014. © 2014 Wiley Periodicals, Inc.
Secondary User Friendly TDMA Scheduling for Primary Users in Cognitive Radio Networks

Cognitive radio technology is widely accepted as an efficient approach to solve the problem that the wireless spectrum has been getting scarcer and scarcer due to the rapid growth in the ubiquitous wireless applications. Several cognitive medium access control (MAC) protocols have been proposed for the secondary users (non-licensed users) to take advantage of the vacant channels whenever they are not occupied by the primary users (licensed users) in the wireless time division multiple access (TDMA)-based networks. In this paper, by exploiting the unique property of the wireless fading channel and cross-layer design technique, we develop a packet scheduling scheme for the primary users in the context of wireless TDMA networks, which is set up to operate friendly towards the secondary users in terms of vacant-channel probability. Our proposed scheme can be implemented with just slight modification on the traditional TDMA scheduling algorithm. We develop a rigorous queuing model and then quantitatively analyze the tradeoff among multiple performance metrics to identify when and where the cost for favoring the secondary users is worthy. The analytical results show that our proposed scheme can generate more vacant-channel opportunities for secondary users, at the expense of little increasing packet delay, as compared with the traditional wireless TDMA scheduling algorithm. In addition, since the implementation of our proposed scheme only needs little modification on the existing TDMA scheduling algorithm, our proposed scheme is a practical and cost-effective approach to increase the wireless spectrum utilization.
Development and evaluation of the Osteoporosis Self-Efficacy Scale.

The Osteoporosis Self-Efficacy Scale was developed as a measure of self-efficacy, or confidence, for behaviors related to physical activity and calcium intake. An item pool of 21 statements, responded to on a visual analog self-report format, was reviewed by a panel of expert judges. The revised item stems were tested with a sample of 201 women, ages 35 to 95. Concurrent data on sport, leisure, and exercise activity and calcium in diet and dietary supplements were collected from the respondents. Factor analysis of responses to the self-efficacy items revealed a logical, theoretically meaningful two-factor structure, one for physical activity and one for calcium intake. Internal consistency estimates for each of the two factors were in the . 90s. Convergent and discriminant validity analyses as well as hierarchical regression analyses to explain self-reports of physical activity and calcium intake were supportive. The final version of the brief, psychometrically sound scale contains items reflecting initiation, maintenance, and persistence at osteoporosis preventive behaviors; thus, the Osteoporosis Self-Efficacy Scale is a potentially beneficial research instrument.
Ror2 Signaling and Its Relevance in Breast Cancer Progression

Breast cancer is a heterogeneous disease and has been classified into five molecular subtypes based on gene expression profiles. Signaling processes linked to different breast cancer molecular subtypes and different clinical outcomes are still poorly understood. Aberrant regulation of Wnt signaling has been implicated in breast cancer progression. In particular Ror1/2 receptors and several other members of the non-canonical Wnt signaling pathway were associated with aggressive breast cancer behavior. However, Wnt signals are mediated via multiple complex pathways, and it is clinically important to determine which particular Wnt cascades, including their domains and targets, are deregulated in poor prognosis breast cancer. To investigate activation and outcome of the Ror2-dependent non-canonical Wnt signaling pathway, we overexpressed the Ror2 receptor in MCF-7 and MDA-MB231 breast cancer cells, stimulated the cells with its ligand Wnt5a, and we knocked-down Ror1 in MDA-MB231 cells. We measured the invasive capacity of perturbed cells to assess phenotypic changes, and mRNA was profiled to quantify gene expression changes. Differentially expressed genes were integrated into a literature-based non-canonical Wnt signaling network. The results were further used in the analysis of an independent dataset of breast cancer patients with metastasis-free survival annotation. Overexpression of the Ror2 receptor, stimulation with Wnt5a, as well as the combination of both perturbations enhanced invasiveness of MCF-7 cells. The expression–responsive targets of Ror2 overexpression in MCF-7 induced a Ror2/Wnt module of the non-canonical Wnt signaling pathway. These targets alter regulation of other pathways involved in cell remodeling processing and cell metabolism. Furthermore, the genes of the Ror2/Wnt module were assessed as a gene signature in patient gene expression data and showed an association with clinical outcome. In summary, results of this study indicate a role of a newly defined Ror2/Wnt module in breast cancer progression and present a link between Ror2 expression and increased cell invasiveness.
Improved surgical results for hilar cholangiocarcinoma with procedures including major hepatic resection.

OBJECTIVE To evaluate the long-term outcome of aggressive surgery incorporating hepatic resection and systematic nodal dissection for advanced carcinoma involving the hepatic hilus. SUMMARY BACKGROUND DATA Few long-term results are available regarding radical surgery incorporating major hepatectomy and nodal dissection. METHODS A retrospective analysis was undertaken in 107 patients with carcinoma involving the hepatic hilus treated between 1980 and 1997. Resectional surgery was performed in 65 patients, 52 of whom underwent major hepatectomies. The effects of clinical and pathologic factors were assessed by univariate and multivariate analyses. RESULTS Sixty percent of the patients with resectional surgery had stage IVA or IVB disease, and 92.3% of them underwent major hepatectomies. No in-hospital deaths were encountered in the 35 most recent resections, whereas there were six deaths in the early period. Resectional surgery was associated with a survival benefit, especially when resection margins were free from cancerous infiltration. The estimated 5-year survival rate after resection, including all deaths, was 34.8%; this was 51.6% when the margins were clear. Nodal involvement was documented in 44.6% of the resections. However, patients with metastases limited to the regional nodes showed a survival rate similar to that in patients without nodal involvement. Significant predictive factors for survival after resection were extension to the gallbladder, nodal status, resectional margins, histologic type, and gender. CONCLUSIONS The combination of major hepatectomy with systematic nodal dissection gave a good chance of prolonged survival for patients with carcinoma involving the hepatic hilus, even when the disease was advanced. Less-extensive procedures were also beneficial for less-advanced disease if clear resectional margins were secured.
Risk of oral and gastrointestinal mucosal injury in patients with solid tumors treated with ramucirumab: a systematic review and meta-analysis

Background: We performed a systematic review and meta-analysis of the risk of oral and gastrointestinal (GI) mucosal injury associated with ramucirumab. Patients and methods: Eligible studies included randomized Phase II and III trials of patients with solid tumors on ramucirumab: describing events of stomatitis, diarrhea, GI perforation and GI hemorrhage. Results: Our search strategy yielded 167 potentially relevant citations from Pubmed/Medline, CENTRAL Cochrane registry, European society of medical oncology meeting abstracts and American Society of Clinical Oncology meeting library. After exclusion of ineligible studies, a total of 11 clinical trials were considered eligible for the meta-analysis. The RR of all-grade stomatitis, diarrhea, GI perforation and GI hemorrhage were 1.62 (95% CI 1.31 – 2.00; p < 0.00001), 1.15 (95% CI 1.07 – 1.24; p < 0.0001), 3.29 (95% CI 1.54 – 7.04; p = 0.002) and 1.92 (95% CI 1.03 – 3.57; p = 0.04), respectively. The RR of high-grade stomatitis, diarrhea, GI perforation and GI hemorrhage were 2.72 (95% CI 1.76 – 4.19; p < 0.00001), 1.28 (95% CI 0.96 – 1.71; p = 0.09), 3.37 (95% CI 1.51 – 7.54; p = 0.03) and 1.26 (95% CI 0.79 – 2.01; p = 0.34), respectively. Conclusions: Our meta-analysis has demonstrated that ramucirumab-based combination treatment is associated with an increased risk of high-grade stomatitis and GI perforation compared to control treatment.
Relaxation-Time Determination from Continuous-Microwave Saturation of EPR Spectra

Abstract Lund, A. , Sagstuen, E. , Sanderud, A. and Maruani, J. Relaxation-Time Determination from Continuous-Microwave Saturation of EPR Spectra. Based on the theories of Portis and of Castner 50 years ago, different continuous-wave measurement procedures for analyzing the microwave saturation power dependence of inhomogeneously broadened EPR lines were developed. Although these procedures have been refined, they still use only a few selected points on the saturation curve. A non-linear least-squares procedure for analyzing the microwave-power dependence of inhomogeneously broadened lines using all data points on a saturation curve has been developed. This procedure provides a simple alternative method to obtain magnetic relaxation data when the more direct pulse-saturation techniques are not available or are less suitable. The latter includes applications of quantitative EPR such as dosimetry. Then microwave saturation data should be obtained under conditions similar to those used in the quantitative measurements, which are usually made on first derivative spectra recorded using continuous-wave spectrometers. Selected applications to benchmark literature data and within the field of EPR dosimetry are discussed. The results obtained illustrate that relaxation times comparable to those yielded by various pulse-saturation EPR techniques can be obtained. It appears as a systematic feature that, whenever the pulse EPR data are fitted using bi-exponential functions, the shortest relaxation times obtained are those that correspond best to those measured using the current continuous-wave saturation method.
Conserved and divergent expression patterns of markers of axial development in the laboratory opossum, Monodelphis domestica

Background: Previous comparative studies suggest that the requirement for Nodal in epiblast and hypoblast development is unique to mammalians. Expression of anterior visceral endoderm (AVE) genes in the visceral endoderm and of their orthologs in the hypoblast may be unique to mammalians and avians, and is absent in the reptilian hypoblast. Axis formation in reptiles is signaled by the formation of the posterior marginal epiblast (PME), which expresses a series of primitive streak genes. To assess the phylogenetic origin of Nodal and AVE gene expression and axis formation in amniotes, we examined marker gene expression in gray short‐tailed opossum, a metatherian. Results: Nodal was expressed in neither epiblast nor hypoblast of opossum embryos. No AVE genes were expressed in the opossum hypoblast. Attainment of polarity in the embryonic disk was signaled by Nodal, Wnt3a, Fgf8, and Bra expression in the PME at 8.5 days post‐coitus. Conclusions: Nodal expression in epiblast or hypoblast may be unique to eutherians. AVE gene expression in visceral endoderm and hypoblast may have been independently acquired in eutherian and avian lineages. PME formation appears to be the event that signals axis formation in reptilian and metatherian embryos, and thus may be an ancestral characteristic of basal amniotes. Developmental Dynamics 245:1176–1188, 2016. © 2016 Wiley Periodicals, Inc.
Aurora kinase inhibitors: identification and preclinical validation of their biomarkers

Aurora kinases are key regulators of mitosis and inhibitors being developed by a wide range of pharmaceutical and biotechnology companies for the treatment of cancer. Tumor cells respond differentially on inhibition of different Aurora kinase family members and these differences have to be considered in the clinical development of small-molecule inhibitors with respect to the chosen indications, the schedules or the selection of appropriate end points and they should also guide the development of biomarkers. Preclinical validation of potential biomarkers for Aurora kinase inhibitors led to a first application in clinical trials, as exemplified for the phosphorylation of histone H3 to follow Aurora-B inhibition. This review discusses the criteria for translation into the clinic and the value of pharmacodynamic biomarkers and their potential, but also their limitations to be used as surrogate markers for clinical end points.
Task-specific modulation of memory for object features in natural scenes

The influence of visual tasks on short and long-term memory for visual features was investigated using a change-detection paradigm. Subjects completed 2 tasks: (a) describing objects in natural images, reporting a specific property of each object when a crosshair appeared above it, and (b) viewing a modified version of each scene, and detecting which of the previously described objects had changed. When tested over short delays (seconds), no task effects were found. Over longer delays (minutes) we found the describing task influenced what types of changes were detected in a variety of explicit and incidental memory experiments. Furthermore, we found surprisingly high performance in the incidental memory experiment, suggesting that simple tasks are sufficient to instill long-lasting visual memories.