bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of MLH1 constitutional methylation for Lynch syndrome diagnosis in patients with tumor MLH1 downregulation
Authors: Pinto Diana , Pinto Carla , Guerra Joana , Pinheiro Manuela , Santos Rui , Vedeld Hege Marie , Yohannes Zeremariam , Peixoto Ana , Santos Catarina , Pinto Pedro , Lopes Paula , Lothe Ragnhild , Lind Guro Elisabeth , Henrique Rui , Teixeira Manuel R. 
Published: January 2018

AbstractConstitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, has been identified as an alternative mechanism that predisposes to the development of Lynch syndrome. In the present work, we aimed to investigate the prevalence of MLH1 constitutional methylation in colorectal cancer (CRC) patients with abnormal expression of the MLH1 protein in their tumors. In a series of 38 patients who met clinical criteria for Lynch syndrome genetic testing, with loss of MLH1 expression in the tumor and with no germline mutations in the MLH1 gene (35/38) or with tumors presenting the BRAF p.Val600Glu mutation (3/38), we screened for constitutional methylation of the MLH1 gene promoter using methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) in various biological samples. We found four (4/38; 10.5%) patients with constitutional methylation in the MLH1 gene promoter. RNA studies demonstrated decreased MLH1 expression in the cases with constitutional methylation when compared with controls. We could infer the mosaic nature of MLH1 constitutional hypermethylation in tissues originated from different embryonic germ layers, and in one family we could show that it occurred de novo. We conclude that constitutional MLH1 methylation occurs in a significant proportion of patients who have loss of MLH1 protein expression in their tumors and no MLH1 pathogenic germline mutation. Furthermore, we provide evidence that MLH1 constitutional hypermethylation is the molecular mechanism behind about 3% of Lynch syndrome families diagnosed in our institution, especially in patients with early onset or multiple primary tumors without significant family history.
Mechanism underlying the negative effect of prostate volume on the outcome of extensive transperineal ultrasound‐guided template prostate biopsy
Authors: Demura Takayoshi , Takada Takenori , Shimoda Naohiko , Hioka Takaya , Iwaguchi Yoshihumi , Ichihara Shin , Gotoda Hiroko 
Published: January 2018

AbstractPrevious studies have indicated a possible relationship between increased prostate volume (PV) and decreased biopsy yield, although the mechanism involved is unclear. We evaluated 1650 patients who underwent template biopsy. The distribution of 993 cancer lesions in 302 prostatectomy specimens was compared with the biopsy data to determine whether each lesion was detected. A receiver operating characteristic (ROC) model was used to determine the diagnostic accuracy of prostate‐specific antigen (PSA) and related markers. A medical record number (MRN) was used as a negative control. The cancer positive rate did not change as PSA increased in patients with PV ≥50 mL (P = 0.466), although it increased as PSA increased in patients with PV<50 mL (P = 0.001). The detection rate of cancer lesions decreased as the diameter of the lesions decreased (P = 0.018), but remained unchanged with respect to PV. The diameters of the maximum lesions in patients with PV ≥ 50 mL were significantly smaller than those in patients with PV<50 mL (P = 0.003). In patients with PV ≥ 50 mL, the areas under the ROC curves for PSA‐related markers did not differ significantly from that for MRN, although they were significantly greater than that for MRN in patients with PV<50 mL (P < 0.001). These results suggest that an increase in PV is associated with a decrease in size and detectability of cancer lesions resulting in a decrease in biopsy yield. Loss of diagnostic accuracy of markers in patients with PV ≥ 50 mL indicates a decrease in serum levels of PSA produced by prostate cancer, which suggests growth inhibition of the cancer.
Clinical outcomes of carbon ion radiotherapy with concurrent chemotherapy for locally advanced uterine cervical adenocarcinoma in a phase 1/2 clinical trial (Protocol 1001)
Authors: Okonogi Noriyuki , Wakatsuki Masaru , Kato Shingo , Karasawa Kumiko , Kiyohara Hiroki , Shiba Shintaro , Kobayashi Daijiro , Nakano Takashi , Kamada Tadashi , Shozu Makio ,   the Working Group of Gynecological Tumors
Published: January 2018

AbstractWe conducted a phase 1/2 study to evaluate the efficacy and safety of carbon ion radiotherapy (C‐ion RT) with concurrent chemotherapy for locally advanced uterine cervical adenocarcinoma. Thirty‐three patients were enrolled between April 2010 and March 2014. Treatment consisted of C‐ion RT with concurrent weekly cisplatin at a dose of 40 mg/m2. In the phase 1 component, the total dose was escalated from 68.0 Gy (relative biological effectiveness [RBE]) to 74.4 Gy (RBE) to determine the maximum tolerated dose of C‐ion RT. In the phase 2 component, the efficacy and safety of C‐ion RT with concurrent chemotherapy were evaluated using the dose determined in the phase 1 component. The median follow‐up duration was 30 months. Two patients did not receive chemotherapy because of anemia or leukocytopenia immediately prior to commencing treatment; 31 patients were analyzed. None of the patients developed dose‐limiting toxicities. The recommended dose (RD) was determined to be 74.4 Gy (RBE). In the phase 2 component, two patients developed Grade 3–4 toxicities in the gastrointestinal tract, due to repeated laser coagulation or peritonitis caused by appendicitis. In the patients treated with the RD, the 2‐year local control, progression‐free survival, and overall survival rates were 71%, 56%, and 88%, respectively. C‐ion RT with concurrent weekly cisplatin was well tolerated in patients with locally advanced uterine cervical adenocarcinoma. Our findings support further investigations into the efficacy of this strategy.
Real‐Time Gas Quality Data for On‐Demand Production of Biogas
Authors: Bierer Benedikt , Nägele Hans-Joachim , Perez Alvaro Ortiz , Wöllenstein Jürgen , Kress Philipp , Lemmer Andreas , Palzer Stefan 
Published: January 2018

AbstractThe flexible production of biogas makes it a promising candidate to become the first renewable, on‐demand energy source. One appealing possibility to achieve an on‐demand supply of methane is to adjust the output of the biogas plant itself. As a consequence, the biological process will be partially overloaded and might fail. Hence, a prerequisite to avoid cost‐intensive failure is a fast, reliable, and cost‐efficient analytical technology for quickly determining the biogas quality. A low‐cost, robust, in‐situ online measurement system for the real‐time determination of carbon dioxide and methane concentrations is presented. The approach makes use of photoacoustic detectors, allowing for the development of gas sensors with reduced size that do not show cross‐sensitivities towards water vapor. The system's readings may be used as input for a novel type of control system that enables an active, demand‐driven control of actuators, such as feeding machinery or mixers.
Gaseous ozone decomposition over high silica zeolitic frameworks
Authors: Brodu Nicolas , Manero Marie‐Hélène , Andriantsiferana Caroline , Pic Jean‐Stéphane , Valdés Héctor 
Published: January 2018

AbstractFor several decades, it has been known that ozone emissions are harmful to humans, plants, and animals. Heterogeneous catalytic decomposition is an efficient process for removing ozone from air. This study examines the effect of the zeolite's framework and pore width on efficiency for decomposing gaseous ozone. Four highly hydrophobic zeolites are used: a large cavity zeolite (Faujasite/H‐FAU), a medium pore zeolite with parallel channel (Mordenite/H‐MOR), and two medium pore zeolites with interconnected channels (H‐ZSM‐5/H‐MFI and Na‐ZSM‐5/Na‐MFI). Experiments were conducted in fixed‐bed flow reactors loaded with zeolite at ambient conditions (20 °C and 101 kPa). Zeolite surfaces were analyzed during the experiments in order to understand the influence of physical and chemical surface properties on the ozone decomposition mechanism. A higher amount of ozone is eliminated using H‐MOR, compared with the zeolite samples H‐FAU, H‐MFI, and Na‐MFI. Pore width and micropore framework size distribution (channel and cages) appear to be key factors. A narrow channel or cage, slightly larger than the ozone molecule size, seems to promote ozone interactions with Lewis acid sites. Fourier transform infrared spectroscopy shows that Lewis acid sites (LAS), located on the walls of zeolite pores, decompose ozone. This leads to the formation of atomic oxygen species that could react with another ozone molecule to form dioxygen. Hence, LAS are regenerated, ready to decompose another ozone molecule once more.
Anthropogenic nitrogen deposition ameliorates the decline in tree growth caused by a drier climate
Authors: Ibáñez Inés , Zak Donald R. , Burton Andrew J. , Pregitzer Kurt S. 
Published: January 2018

AbstractMost forest ecosystems are simultaneously affected by concurrent global change drivers. However, when assessing these effects, studies have mainly focused on the responses to single factors and have rarely evaluated the joined effects of the multiple aspects of environmental change. Here, we analyzed the combined effects of anthropogenic nitrogen (N) deposition and climatic conditions on the radial growth of Acer saccharum, a dominant tree species in eastern North American forests. We capitalized on a long‐term N deposition study, replicated along a latitudinal gradient, that has been taking place for more than 20 yr. We analyzed tree radial growth as a function of anthropogenic N deposition (ambient and experimental addition) and of summer temperature and soil water conditions. Our results reveal that experimental N deposition enhances radial growth of this species, an effect that was accentuated as temperature increased and soil water became more limiting. The spatial and temporal extent of our data also allowed us to assert that the positive effects of growing under the experimental N deposition are likely due to changes in the physiological performance of this species, and not due to the positive correlation between soil N and soil water holding capacity, as has been previously speculated in other studies. Our simulations of tree growth under forecasted climate scenarios specific for this region also revealed that although anthropogenic N deposition may enhance tree growth under a large array of environmental conditions, it will not mitigate the expected effects of growing under the considerably drier conditions characteristic of our most extreme climatic scenario.
Non‐volant mammals from the Upper Paraná River Basin: a data set from a critical region for conservation in Brazil
Authors: Gonçalves Fernando , Hannibal Wellington , Godoi Mauricio N. , Martins Fernando I. , Oliveira Roniel F. , Figueiredo Valquiria V. , Casella Janaina , de Sá Érica F. G. G. 
Published: January 2018

AbstractThe data set represents the first attempt at a large‐scale inventory of non‐volant mammals, with potential applications to performing macroecological studies, developing conservation strategies, and undertaking population and community ecology research, but also to evaluate the ecological consequences of fragmentation and defaunation. Our objectives for compiling these data were to summarize information about inventories of non‐volant mammals in the critically important area of the Upper Paraná River Basin by focusing on species richness and index of frequency of occurrence and to identify gaps in knowledge regarding non‐volant mammal communities in order to guide future sampling efforts. The data set comprises studies on communities of non‐volant mammals from 52 locations covering more than 1,000 km2 and comprises portion of four Brazilian states in the Upper Paraná River Basin. We listed 81 species of non‐volant mammals distributed among 58 genera, 22 families, and 9 orders. Rodentia (28 species) was the richest order, followed by Carnivora (17 spp.) and Didelphimorphia (15 spp.). The richest family was Cricetidae (20 spp.), followed by Didelphidae (15 spp.), and Dasypodidae and Felidae (six spp.). Considering national conservation status, one species are considered endangered and 16 vulnerable. Considering global conservation status, 7 species are considered vulnerable, 10 are considered near threatened, and 6 are data deficient. According to the index of frequency of occurrence, Myrmecophaga tridactyla was the most frequent species, occurring at 88.64% of all sites, while 25 species were considered very restricted, occurring in just 2.56% of all sites. In general, the non‐volant mammal fauna was composed of mainly very restricted (VR, 25 species) and localized species (L, 25 species), which account for 61.7% of the known species, while 38.3% are restricted (R, 8 species), common (C, 16 species), and widespread (W, 7 species). Seven marsupials and five small rodents had their distributions extended in the central‐south of Brazil. All of these species are considered data deficient or threatened, which highlights the importance of these records. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.
Fate, uptake, and distribution of nanoencapsulated pesticides in soil–earthworm systems and implications for environmental risk assessment
Authors: Mohd Firdaus Mohd Anuar , Agatz Annika , Hodson Mark E. , Al-Khazrajy Omar S.A. , Boxall Alistair B.A. 
Published: January 2018

Abstract

Nanopesticides are novel plant protection products offering numerous benefits. Because nanoparticles behave differently from dissolved chemicals, the environmental risks of these materials could differ from conventional pesticides. We used soil–earthworm systems to compare the fate and uptake of analytical-grade bifenthrin to that of bifenthrin in traditional and nanoencapsulated formulations. Apparent sorption coefficients for bifenthrin were up to 3.8 times lower in the nano treatments than in the non-nano treatments, whereas dissipation half-lives of the nano treatments were up to 2 times longer. Earthworms in the nano treatments accumulated approximately 50% more bifenthrin than those in the non-nano treatments. In the non-nano treatments, most of the accumulated material was found in the earthworm tissue, whereas in the nano treatments, the majority resided in the gut. Evaluation of toxicokinetic modeling approaches showed that models incorporating the release rate of bifenthrin from the nanocapsule and distribution within the earthworm provided the best estimations of uptake from the nano-formulations. Overall, our findings indicate that the risks of nanopesticides may be different from those of conventional formulations. The modeling presented provides a starting point for assessing risks of these materials but needs to be further developed to better consider the behavior of the nanoencapsulated pesticide within the gut system. Environ Toxicol Chem 2018;37:1420–1429. © 2018 SETAC
Abstract
An interuser interference suppression approach in full‐duplex wireless communications
Authors: Wu Fei , Pu Xumin , Zhang Mintao , Li Si , Ma Wanzhi 
Published: January 2018

AbstractConsidering that a full‐duplex network is composed of a full‐duplex base station (BS) and 2 half‐duplex users, one user transmits on the uplink channel and the other receives through the downlink channel on the same frequency. The uplink user will generate interuser interference (IUI) on the downlink user through the interference channel. In this paper, we propose a novel IUI suppression scheme when the BS knows the full channel state information. The main idea of this scheme is to retransmit the weighted uplink signal as soon as it has been received by the BS. For the narrowband case, we first assess the performance of the proposed scheme through simulation with residual self‐interference at the BS. Specially, we derive the closed‐form expression of the optimum weighted coefficient when self‐interference is perfectly canceled at the BS and then discuss the performance of the proposed IUI suppression scheme in practical considerations. Furthermore, the proposed IUI suppression scheme can be extended to the broadband case using a time‐domain weighted filter. Simulation results show the advantage over existing IUI suppression schemes.
Evaluation of marine zooplankton community structure through environmental DNA metabarcoding
Authors: Djurhuus Anni , Pitz Kathleen , Sawaya Natalie A. , Rojas‐Márquez Jaimie , Michaud Brianna , Montes Enrique , Muller‐Karger Frank , Breitbart Mya 
Published: January 2018

AbstractZooplankton dominate the abundance and biomass of multicellular animals in pelagic marine environments; however, traditional methods to characterize zooplankton communities are invasive and laborious. This study compares zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) and 18S rRNA genes to traditional morphological identification by microscopy. Triplicates of three different sample types were collected from three coral reef sites in the Florida Keys National Marine Sanctuary: (1) 1 L surface seawater samples prefiltered through 3 μm filters and subsequently collected on 0.22 μm filters for eDNA (PF‐eDNA); (2) 1 L surface seawater samples filtered on 0.22 μm pore‐size filters (environmental DNA; eDNA), and (3) zooplankton tissue samples from 64 μm, 200 μm, and 500 μm mesh size net tows. The zooplankton tissue samples were split, with half identified morphologically and tissue DNA (T‐DNA) extracted from the other half. The COI and 18S rRNA gene metabarcoding of PF‐eDNA, eDNA, and T‐DNA samples was performed using Illumina MiSeq. Of the families detected with COI and 18S rRNA gene metabarcoding, 40% and 32%, respectively, were also identified through morphological assessments. Significant differences in taxonomic composition were observed between PF‐DNA, eDNA, and T‐DNA with both genetic markers. PF‐eDNA resulted in detection of fewer taxa than the other two sample types; thus, prefiltering is not recommended. All dominant copepod taxa (> 5% of total abundance) were detected with eDNA, T‐DNA, and morphological assessments, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.
Novel Making of Bacterial Cellulose Blended Polymeric Fiber Bandages
Authors: Altun Esra , Aydogdu Mehmet Onur , Koc Fatma , Crabbe‐Mann Maryam , Brako Francis , Kaur‐Matharu Rupy , Ozen Gunes , Kuruca Serap Erdem , Edirisinghe Ursula , Gunduz Oguzhan , Edirisinghe Mohan 
Published: January 2018

AbstractBacterial cellulose (BC) is a very promising biological material. However, at present its utilization is limited by difficulties in shape forming it. In this Communication, it is shown how this can be overcome by blending it with poly(methylmethacrylate) (PMMA) polymer. BC:PMMA fibers are produced by pressurized gyration of blended BC:PMMA solutions. Subsequently, BC:PMMA bandage‐like scaffolds are generated with different blends. The products are investigated to determine their morphological and chemical features. Cell culture and proliferation tests are performed to obtain information on biocompatibility of the scaffolds.
Resveratrol Influences Pancreatic Islets by Opposing Effects on Electrical Activity and Insulin Release
Authors: Brouwer Simone , Hoffmeister Theresa , Gresch Anne , Schönhoff Lisa , Düfer Martina 
Published: January 2018

ScopeResveratrol is suggested to improve glycemic control by activation of sirtuin 1 (SIRT1) and has already been tested clinically. Our investigation characterizes the targets of resveratrol in pancreatic beta cells and their contribution to short‐ and long‐term effects on insulin secretion.Methods and resultsIslets or beta cells are isolated from C57BL/6N mice. Electrophysiology is performed with microelectrode arrays and patch‐clamp technique, insulin secretion and content are determined by radioimmunoassay, cAMP is measured by enzyme‐linked immunosorbent assay, and cytosolic Ca2+ concentration by fluorescence methods. Resveratrol (25 μmol L–1) elevates [Ca2+]c and potentiates glucose‐stimulated insulin secretion. These effects are associated with increased intracellular cAMP and are sensitive to the SIRT1 blocker Ex‐527. Inhibition of EPAC1 by CE3F4 also abolishes the stimulatory effect of resveratrol. The underlying mechanism does not involve membrane depolarization as resveratrol even reduces electrical activity despite blocking KATP channels. Importantly, after prolonged exposure to resveratrol (14 days), the beneficial influence of the polyphenol on insulin release is lost.ConclusionResveratrol addresses multiple targets in pancreatic islets. Potentiation of insulin secretion is mediated by SIRT1‐dependent activation of cAMP/EPAC1. Considering resveratrol as therapeutic supplement for patients with type 2 diabetes mellitus, the inhibitory influence on electrical excitability attenuates positive effects.
Data‐assisted protein structure modeling by global optimization in CASP12
Authors: Joo Keehyoung , Heo Seungryong , Joung InSuk , Hong Seung Hwan , Lee Sung Jong , Lee Jooyoung 
Published: January 2018

AbstractIn CASP12, 2 types of data‐assisted protein structure modeling were experimented. Either SAXS experimental data or cross‐linking experimental data was provided for a selected number of CASP12 targets that the CASP12 predictor could utilize for better protein structure modeling. We devised 2 separate energy terms for SAXS data and cross‐linking data to drive the model structures into more native‐like structures that satisfied the given experimental data as much as possible. In CASP11, we successfully performed protein structure modeling using simulated sparse and ambiguously assigned NOE data and/or correct residue‐residue contact information, where the only energy term that folded the protein into its native structure was the term which was originated from the given experimental data. However, the 2 types of experimental data provided in CASP12 were far from being sufficient enough to fold the target protein into its native structure because SAXS data provides only the overall shape of the molecule and the cross‐linking contact information provides only very low‐resolution distance information. For this reason, we combined the SAXS or cross‐linking energy term with our regular modeling energy function that includes both the template energy term and the de novo energy terms. By optimizing the newly formulated energy function, we obtained protein models that fit better with provided SAXS data than the X‐ray structure of the target. However, the improvement of the model relative to the 1 modeled without the SAXS data, was not significant. Consistent structural improvement was achieved by incorporating cross‐linking data into the protein structure modeling.