Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between VEGFR-3 expression and lymph node metastasis in non-small-cell lung cancer

Vascular endothelial growth factor receptor (VEGFR)-3 is considered to be associated with lymphangiogenesis. The aim of the present study was to identify the clinical significance of VEGFR-3 expression and lymph node metastasis in patients with non-small-cell lung cancer (NSCLC). Lung tumor tissue samples and 196 lymph nodes from 52 patients with NSCLC were analyzed. In addition, lung tissue samples and 8 lymph nodes from 10 patients with lung diseases other than cancer were included as controls. Semiquantitative multiplex reverse transcription technology was applied to measure the mRNA expression levels of VEGFR-3, while VEGFR-3 protein expression levels were assessed immunohistochemically. The total number of lymphatic vessels was counted and the microlymphatic vessel density (MLVD) was calculated. The results indicated that the VEGFR-3 mRNA expression level in lymph node tissue from the group with lymph node metastasis was significantly lower compared with the group without lymph node metastasis (0.281±0.166 vs. 0.158±0.158; t=4.849; P<0.001). The VEGFR-3 mRNA expression levels in the lung tumor tissue of the NSCLC patients exhibited no statistically significant difference between the lymph node metastasis and lymph node non-metastasis groups (0.139±0.137 vs. 0.142±0.123; t=0.08; P>0.05). In addition, in the lymph node metastasis group, there was no statistically significant difference between the metastasis-positive and -negative lymph nodes (0.158±0.158 vs. 0.123±0.115; t=0.993; P>0.05) with regard to VEGFR-3 mRNA expression. Morphologically, VEGFR-3 immunoreactivity was primarily localized in the cytoplasm of the lymphatic endothelial cells, as well as a number of the cancer cells. MLVD was much higher in the lung tissue surrounding the tumor than in the tumor tissue, and was significantly higher in the lymph node metastasis group than in the lymph node non-metastasis group. VEGFR-3 expression levels were shown to correlate with lymph node metastasis in NSCLC patients, thus, may be a useful biomarker for lymph node metastasis prediction in NSCLC. MLVD is a key indictor of lymphatic vessel metastasis in NSCLC. An enhanced MLVD indicates lymphangiogenesis and lymphatic node metastasis, and may be an important predictor for tumor monitoring and prognosis.
Quantifying the timescales over which exogenous and endogenous conditions affect soil respiration.

Understanding how exogenous and endogenous factors and above-ground-below-ground linkages modulate carbon dynamics is difficult because of the influences of antecedent conditions. For example, there are variable lags between above-ground assimilation and below-ground efflux, and the duration of antecedent periods are often arbitrarily assigned. Nonetheless, developing models linking above- and below-ground processes is crucial for estimating current and future carbon dynamics. We collected data on leaf-level photosynthesis (Asat ) and soil respiration (Rsoil ) in different microhabitats (under shrubs vs under bunchgrasses) in the Sonoran Desert. We evaluated timescales over which endogenous and exogenous factors control Rsoil by analyzing data in the context of a semimechanistic temperature-response model of Rsoil that incorporated effects of antecedent exogenous (soil water) and endogenous (Asat ) conditions. For both microhabitats, antecedent soil water and Asat significantly affected Rsoil , but Rsoil under shrubs was more sensitive to Asat than that under bunchgrasses. Photosynthetic rates 1 and 3 d before the Rsoil measurement were most important in determining current-day Rsoil under bunchgrasses and shrubs, respectively, indicating a significant lag effect. Endogenous and exogenous controls are critical drivers of Rsoil , but the relative importance and the timescale over which each factor affects Rsoil depends on above-ground vegetation and ecosystem structure characteristics.
PHENOTYPIC PLASTICITY IN POLYGONUM PERSICARIA. I. DIVERSITY AND UNIFORMITY IN GENOTYPIC NORMS OF REACTION TO LIGHT

Several aspects of genotype‐environment interaction may act to modulate natural selection in populations that encounter variable environments. In this study the norms of reaction (phenotypic responses) of 20 cloned genotypes from two natural populations of the annual plant Polygonum persicaria were determined over a broad range of controlled light environments (8%‐100% full sun). These data reveal both the extent of functionally adaptive phenotypic plasticity expressed by individual genotypes, and the patterns of diversity among genotypes for characters relevant to fitness, in response to an environmental factor that is both highly variable within populations and critical to growth and reproduction.
Consumption of gold kiwifruit reduces severity and duration of selected upper respiratory tract infection symptoms and increases plasma vitamin C concentration in healthy older adults

In the elderly, immunosenescence and malnourishment can contribute to increased risk and severity of upper respiratory tract infections (URTI). Gold kiwifruit (Actinidia chinensis ‘Hort16A’) contains nutrients important for immune function and mitigation of symptoms of infection, including vitamins C and E, folate, polyphenols and carotenoids. The objective of the present study was to evaluate whether regular consumption of gold kiwifruit reduces symptoms of URTI in older people, and determine the effect it has on plasma antioxidants, and markers of oxidative stress, inflammation and immune function. A total of thirty-two community-dwelling people ( ≥ 65 years) participated in a randomised crossover study, consuming the equivalent of four kiwifruit or two bananas daily for 4 weeks, with treatments separated by a 4-week washout period. Participants completed the Wisconsin Upper Respiratory Symptom Survey-21 daily, and blood samples were collected at baseline and at the end of each treatment and washout period. Gold kiwifruit did not significantly reduce the overall incidence of URTI compared with banana, but significantly reduced the severity and duration of head congestion, and the duration of sore throat. Gold kiwifruit significantly increased plasma vitamin C, α-tocopherol and lutein/zeaxanthin concentrations, and erythrocyte folate concentrations, and significantly reduced plasma lipid peroxidation. No changes to innate immune function (natural killer cell activity, phagocytosis) or inflammation markers (high-sensitivity C-reactive protein, homocysteine) were detected. Consumption of gold kiwifruit enhanced the concentrations of several dietary plasma analytes, which may contribute to reduced duration and severity of selected URTI symptoms, offering a novel tool for reducing the burden of URTI in older individuals.
Practice guidelines for tumor marker use in the clinic.

BACKGROUND Increasing interest in implementing the practice of evidence-based medicine in oncology has encouraged the development of clinical guidelines, many of which include recommendations about the appropriate use of serum tumor markers. METHODS Recent national and international guidelines relating to the use of tumor markers in germ cell, colorectal, breast, ovarian, prostate, lung, neuroendocrine, and thyroid cancers were identified from the scientific literature and other sources and tabulated. RESULTS Guideline recommendations developed by national and international groups and relating to the use of tumor markers for specific cancers are reviewed and compared, considering the recommendations made for their use in screening, diagnosis, prognosis, and monitoring of therapy. Potential advantages and disadvantages of clinical guidelines, how best to implement them, and means of auditing their effectiveness are also considered. CONCLUSIONS Excellent clinical guidelines, including recommendations for the most appropriate use of tumor markers, are already available for many cancers. Many questions relating to optimal use of these important tests remain to be answered, but current guidelines already contain much valuable information and advice. Further dissemination and implementation of the guidelines should encourage better use of tumor markers in clinical practice. Careful audit studies are also required to establish the impact of these guidelines on the practice of evidence-based medicine.
Toluene Monooxygenase-Catalyzed Epoxidation of Alkenes

ABSTRACT Several toluene monooxygenase-producing organisms were tested for their ability to oxidize linear alkenes and chloroalkenes three to eight carbons long. Each of the wild-type organisms degraded all of the alkenes that were tested. Epoxides were produced during the oxidation of butene, butadiene, and pentene but not hexene or octadiene. A strain of Escherichia coli expressing the cloned toluene-4-monooxygenase (T4MO) of Pseudomonas mendocina KR1 was able to oxidize butene, butadiene, pentene, and hexene but not octadiene, producing epoxides from all of the substrates that were oxidized. A T4MO-deficient variant of P. mendocina KR1 oxidized alkenes that were five to eight carbons long, but no epoxides were detected, suggesting the presence of multiple alkene-degrading enzymes in this organism. The alkene oxidation rates varied widely (ranging from 0.01 to 0.33 μmol of substrate/min/mg of cell protein) and were specific for each organism-substrate pair. The enantiomeric purity of the epoxide products also varied widely, ranging from 54 to >90% of a single epoxide enantiomer. In the absence of more preferred substrates, such as toluene or alkenes, the epoxides underwent further toluene monooxygenase-catalyzed transformations, forming products that were not identified.
TUTA1 at the NTCIR-11 IMine Task

In this paper, we detail our participation in two subtasks: subtopic mining and document ranking of the NTCIR-11 IMine task. In the subtopic mining subtask, to discover the latent hierarchy among query-like strings, our key idea is to structurally parse query-like strings by characterizing pairwise dependency in the bag-of-units perspective. Then the clustering algorithm (i
Flow availability analysis in two-layer networks with dedicated path protection at the upper layer

We propose an analytical model that computes availability of upper-layer flows in two-layer networks with dedicated path protection deployed at the upper layer. Our proposed model reduces overestimation of the existing model caused by the ignorance of upper-layer failure correlations. We compute the flow availability by properly taking into account such correlation, and tracing upper-layer failures to lower-layer root causes. Our simulation results show that our proposed model reduces overestimation on upper-layer flow unavailability by about 30%, and thus significantly relaxes unnecessary high-availability requirements on lower-layer links without compromising the availability of upper-layer flows.
Fossil evidence for serpentinization fluids fueling chemosynthetic assemblages

Among the deep-sea hydrothermal vent sites discovered in the past 30 years, Lost City on the Mid-Atlantic Ridge (MAR) is remarkable both for its alkaline fluids derived from mantle rock serpentinization and the spectacular seafloor carbonate chimneys precipitated from these fluids. Despite high concentrations of reduced chemicals in the fluids, this unique example of a serpentinite-hosted hydrothermal system currently lacks chemosynthetic assemblages dominated by large animals typical of high-temperature vent sites. Here we report abundant specimens of chemosymbiotic mussels, associated with gastropods and chemosymbiotic clams, in approximately 100 kyr old Lost City-like carbonates from the MAR close to the Rainbow site (36 °N). Our finding shows that serpentinization-related fluids, unaffected by high-temperature hydrothermal circulation, can occur on-axis and are able to sustain high-biomass communities. The widespread occurrence of seafloor ultramafic rocks linked to likely long-range dispersion of vent species therefore offers considerably more ecospace for chemosynthetic fauna in the oceans than previously supposed.
Adjuvant radiotherapy for gastric carcinoma: 10 years follow-up of 244 cases from a single institution.

BACKGROUND Postoperative chemoradiotherapy (CRT) of gastric carcinoma improves survival among high- risk patients. This study was undertaken to analyse long-term survival probability and the impact of certain covariates on the survival outcome in affected individuals. MATERIALS AND METHODS Between January 2000 and December 2005, 244 patients with gastric cancer underwent adjuvant radiotherapy (RT) in our institution. Data were retrieved retrospectively from patient files and analysed with SPSS version 21.0. RESULTS A total of 244 cases, with a male to female ratio of 2.2:1, were enrolled in the study. The median age of the patients was 52 years (range, 20-78 years). Surgical margin status was positive or close in 72 (33%) out of 220 patients. Postoperative adjuvant RT dose was 46 Gy. Median follow-up was 99 months (range, 79-132 months) and 23 months (range, 2-155 months) for surviving patients and all patients, respectively. Actuarial overall survival (OS) probability for 1-, 3-, 5- and 10-year was 79%, 37%, 24% and 16%, respectively. Actuarial progression free survival (PFS) probability was 69%, 34%, 23% and 16% in the same consecutive order. AJCC Stage I-II disease, subtotal gastrectomy and adjuvant CRT were significantly associated with improved OS and PFS in multivariate analyses. Surgical margin status or lymph node dissection type were not prognostic for survival. CONCLUSIONS Postoperative CRT should be considered for all patients with high risk of recurrence after gastrectomy. Beside well-known prognostic factors such as stage, lymph node status and concurrent chemotherapy, the type of gastrectomy was an important prognostic factor in our series. With our findings we add to the discussion on the definition of required surgical margin for subtotal gastrectomy. We consider that our observations in gastric cancer patients in our clinic can be useful in the future randomised trials to point the way to improved outcomes.
Is There a Relationship between Research Sponsorship and Publication Impact? An Analysis of Funding Acknowledgments in Nanotechnology Papers

This study analyzes funding acknowledgments in scientific papers to investigate relationships between research sponsorship and publication impacts. We identify acknowledgments to research sponsors for nanotechnology papers published in the Web of Science during a one-year sample period. We examine the citations accrued by these papers and the journal impact factors of their publication titles. The results show that publications from grant sponsored research exhibit higher impacts in terms of both journal ranking and citation counts than research that is not grant sponsored. We discuss the method and models used, and the insights provided by this approach as well as it limitations.
Evaluation of FLT-PET/CT usefulness in diagnosis and qualification for surgical treatment of gastric cancer

Aim of the study Evaluation of FLT/PET/ CT usefulness in diagnosis and qualification for surgical treatment of gastric cancer. Material and methods The FLT/PET/CT test was carried out in a group of 50 gastric cancer patients. Based on the test result, a decision followed about the therapeutic procedure to be applied. A comparison was made with regards to the consistency of the cancer growth advancement degree evaluation in the initial preoperative FLT/PET/CT test against the evaluation of postoperative degree of cancer advancement in histopathology. Results In the group of 50 diagnosed patients a surgical treatment was used for 37 patients. 21 resections were performed out of which 19 operations were radical In the group of 16 non-resective operations 2 post-laparotomic patients were selected for inductive treatment. In the group of 13 patients who did not undergo any surgery, 10 were directed to palliative care and 3 for inductive treatment. In the group of 50 patients, the applied FLT-PET/CT test confirmed presence of primary tumor in 49 patients. The presence of increased uptake of FLT in the local lymph nodes during the preoperative FLT-PET/CT test was confirmed in 22 cases. In 14 patients with FLT-PET/Ct N(+) with the M(–) feature resection surgery was performed. The increased uptake of FLT in localizing metastases (nodal and non-nodal) FLT-PET/CT (M+) was detected in 22 patients. The presence of nodal metastases in the postoperative histopathology examination (hpN+) was detected in 14 cases. In these cases preoperative FLT-PET/CT test proved the N(+) feature in 11 patients. The result FLT-PET/CT N(–) was truly negative in 2 patients, and false negative in 1 patient. In the group of 7 operated hpN(–) patients, in 3 patients a preoperative result FLT-PET/ CT N(+) (false positive result) was obtained. The consistency (positive) of nodal metastases identification in FLT-PET/CT as compared to post-surgical histopathology examination scored 11/15, which equals 73.3%. In the group of patients in whom resection surgery was performed, 4 false negative results were obtained [hp(N+), FLT-PET/CT (N–)] and 3 false positive results [hp(N–), FLT-PET/CT N(+)]. Conclusions The initial test results indicate that FLT-PET/CT is an effective method in evaluating the primary tumor and the regional lymph nodes and is useful and beneficial in the diagnosis and further treatment evaluation of gastric cancer. FLT-PET/CT examination facilitates making proper therapeutic decisions – it allows the number of unnecessary laparotomies to be lowered.
High‐speed gel microelectrophoresis, a new and easy approach for detection of PCR‐amplified microbial DNA from environmental and clinical samples in microgels using conventional equipment

Aims: Microelectrophoresis allows the detection of DNA bands using minimal amounts of sample in a short time, but commonly requires the use of special equipment which is not available in all laboratories. This fact has limited the application of this technique in microbiology despite its advantages. In this work, we describe a new approach to perform gel microelectrophoresis, named high‐speed gel microelectrophoresis (HSGME), and its application for rapid detection of bacteria, protozoa and viruses in clinical, vegetal and environmental samples.
The GIP Receptor Displays Higher Basal Activity than the GLP-1 Receptor but Does Not Recruit GRK2 or Arrestin3 Effectively

Background and Objectives Glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) are important regulators of insulin secretion, and their functional loss is an early characteristic of type 2 diabetes mellitus (T2DM). Pharmacological levels of GLP-1, but not GIP, can overcome this loss. GLP-1 and GIP exert their insulinotropic effects through their respective receptors expressed on pancreatic β-cells. Both the GLP-1 receptor (GLP-1R) and the GIP receptor (GIPR) are members of the secretin family of G protein-coupled receptors (GPCRs) and couple positively to adenylate cyclase. We compared the signalling properties of these two receptors to gain further insight into why GLP-1, but not GIP, remains insulinotropic in T2DM patients. Methods GLP-1R and GIPR were transiently expressed in HEK-293 cells, and basal and ligand-induced cAMP production were investigated using a cAMP-responsive luciferase reporter gene assay. Arrestin3 (Arr3) recruitment to the two receptors was investigated using enzyme fragment complementation, confocal microscopy and fluorescence resonance energy transfer (FRET). Results GIPR displayed significantly higher (P<0.05) ligand-independent activity than GLP-1R. Arr3 displayed a robust translocation to agonist-stimulated GLP-1R but not to GIPR. These observations were confirmed in FRET experiments, in which GLP-1 stimulated the recruitment of both GPCR kinase 2 (GRK2) and Arr3 to GLP-1R. These interactions were not reversed upon agonist washout. In contrast, GIP did not stimulate recruitment of either GRK2 or Arr3 to its receptor. Interestingly, arrestin remained at the plasma membrane even after prolonged (30 min) stimulation with GLP-1. Although the GLP-1R/arrestin interaction could not be reversed by agonist washout, GLP-1R and arrestin did not co-internalise, suggesting that GLP-1R is a class A receptor with regard to arrestin binding. Conclusions GIPR displays higher basal activity than GLP-1R but does not effectively recruit GRK2 or Arr3.
Observations Concerning the Locking Range in a Complementary Differential $LC$  Injection-Locked Frequency Divider—Part II: Design Methodology

An intuitive approach to analyze the behavior of an Injection-Locked Frequency Divider was presented in Part I of this work; that paper provided insight into the locking behavior in the valid design area of the circuit. In this paper, we present a rigorous design methodology which provides a closed form equation showing where the locking range is wider. Theoretical predictions of the locked regions are verified by simulations of the circuit in Spectre RF using 0.35-CMOS technology models.
UvA-DARE (Digital Measurement of the W±Z boson pair-production cross section in pp collisions at √s=13 TeV with the ATLAS detector

The production of W ± Z events in proton–proton collisions at a centre-of-mass energy of 13 TeV is measured with the ATLAS detector at the LHC. The collected data correspond to an integrated luminosity of 3 . 2 fb − 1 . The W ± Z candidates are reconstructed using leptonic decays of the gauge bosons into electrons or muons. The measured inclusive cross section in the detector ﬁducial region for leptonic decay modes is σ ﬁd. W ± Z → (cid:4) (cid:4) ν (cid:4)(cid:4) = 63 . 2 ± 3 . 2 (stat.) ± 2 . 6 (sys.) ± 1 . 5 (lumi.) fb. In comparison, the next-to-leading-order Standard Model prediction is 53 . 4 + 3 . 6 − 2 . 8 fb. The extrapolation of the measurement from the ﬁducial to the total phase space yields σ tot. W ± Z = 50 . 6 ± 2 . 6 (stat.) ± 2 . 0 (sys.) ± 0 . 9 (th.) ± 1 . 2 (lumi.) pb, in agreement with a recent next-to-next-to-leading-order calculation of 48 . 2 + 1 . 1 − 1 . 0 pb. The cross section as a function of jet multiplicity is also measured, together with the charge-dependent W + Z and W − Z cross sections and their ratio. © The
Effect of Safflower Oil on the Protective Properties of the in situ Formed Salivary Pellicle

Aim: The prevalence of dental erosion is still increasing. A possible preventive approach might be rinsing with edible oils to improve the protective properties of the pellicle layer. This was tested in the present in situ study using safflower oil. Methods: Pellicle formation was carried out in situ on bovine enamel slabs fixed buccally to individual upper jaw splints (6 subjects). After 1 min of pellicle formation subjects rinsed with safflower oil for 10 min, subsequently the samples were exposed in the oral cavity for another 19 min. Enamel slabs without oral exposure and slabs exposed to the oral cavity for 30 min without any rinse served as controls. After pellicle formation in situ, slabs were incubated in HCl (pH 2; 2.3; 3) for 120 s, and kinetics of calcium and phosphate release were measured photometrically (arsenazo III, malachite green). Furthermore, the ultrastructure of the pellicles was evaluated by transmission electron microscopy (TEM). Results: Pellicle alone reduced erosive calcium and phosphate release significantly at all pH values. Pellicle modification by safflower oil resulted in an enhanced calcium loss at all pH values and caused an enhanced phosphate loss at pH 2.3. TEM indicated scattered accumulation of lipid micelles and irregular vesicle-like structures attached to the oil-treated pellicle layer. Acid etching affected the ultrastructure of the pellicle irrespective of oil rinsing. Conclusion: The protective properties of the pellicle layer against extensive erosive attacks are limited and mainly determined by pH. The protective effects are modified and reduced by rinses with safflower oil.