bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of sub‐zero temperatures in MRI using T1 temperature sensitive soft silicone materials: Applications for MRI‐guided cryosurgery
Authors: Hankiewicz Janusz H. , Celinski Zbigniew , Camley Robert E. 
Published: September 2021

AbstractPurposeOne standard method, proton resonance frequency shift, for measuring temperature using magnetic resonance imaging (MRI), in MRI‐guided surgeries, fails completely below the freezing point of water. Because of this, we have developed a new methodology for monitoring temperature with MRI below freezing. The purpose of this paper is to show that a strong temperature dependence of the nuclear relaxation time T1 in soft silicone polymers can lead to temperature‐dependent changes of MRI intensity acquired with T1 weighting. We propose the use of silicone filaments inserted in tissue for measuring temperature during MRI‐guided cryoablations.MethodsThe temperature dependence of T1 in bio‐compatible soft silicone polymers was measured using nuclear magnetic resonance spectroscopy and MRI. Phantoms, made of bulk silicone materials and put in an MRI‐compatible thermal container with dry ice, allowed temperature measurements ranging from –60°C to + 20°C. T1‐weighted gradient echo images of the phantoms were acquired at spatially uniform temperatures and with a gradient in temperature to determine the efficacy of using these materials as temperature indicators in MRI. Ex vivo experiments on silicone rods, 4 mm in diameter, inserted in animal tissue were conducted to assess the practical feasibility of the method.ResultsMeasurements of nuclear relaxation times of protons in soft silicone polymers show a monotonic, nearly linear, change with temperature (R2 > 0.98) and have a significant correlation with temperature (Pearson's r > 0.99, p < 0.01). Similarly, the intensity of the MR images in these materials, taken with a gradient echo sequence, are also temperature dependent. There is again a monotonic change in MRI intensity that correlates well with the measured temperature (Pearson's r < ‐0.98 and p < 0.01). The MRI experiments show that a temperature change of 3°C can be resolved in a distance of about 2.5 mm. Based on MRI images and external sensor calibrations for a sample with a gradient in temperature, temperature maps with 3°C isotherms are created for a bulk phantom. Experiments demonstrate that these changes in MRI intensity with temperature can also be seen in 4 mm silicone rods embedded in ex vivo animal tissue.ConclusionsWe have developed a new method for measuring temperature in MRI that potentially could be used during MRI‐guided cryoablation operations, reducing both procedure time and cost, and making these surgeries safer.
Importance of Coarse Woody Habitat Complexity to Yellow Perch Egg Skein Deposition and Survival
Authors: Grausgruber Stephen J. , Weber Michael J. , Morris Joseph E. 
Published: September 2021

Abstract
Habitat introductions are often implemented in aquatic systems to meet fishery management goals. Conifer trees have been used to augment spawning habitat for Yellow Perch Perca flavescens to support and suspend their unique egg skeins above the lake bottom in hopes of increasing reproduction and recruitment; however, little is known about the influence of tree characteristics on the reproductive success of Yellow Perch. Our objective was to evaluate the effects of tree complexity on the skein deposition and survival rates of Yellow Perch. In February 2020, 30 eastern red cedar Juniperus virginiana trees were manipulated to one of five complexities (from 1 = least complex [all branches removed] to 5 = most complex [all branches retained]; n = 6 per complexity) and placed on the ice. After ice-off and tree submersion, we conducted snorkeling surveys every 2 d from March 31 to May 5, 2020, and recorded the number and viability of the skeins. We observed 35 Yellow Perch egg skeins. Yellow Perch preferred to deposit their egg skeins on tree complexities 4 and 5, whereas deposition on tree complexities 1, 2, and 3 was random. The nest survival models estimated that skeins that were deposited on tree complexities 1, 2, and 5 had a 27-d survival estimate of 0.07 (95% CI = 0.06 to 0.08) that was lower (β = −1.29; 95% CI = −2.32 to −0.27) than that for skeins that were deposited on complexities 3 and 4, with a survival estimate of 0.48 (95% CI = 0.43 to 0.52). Our results indicate that Yellow Perch prefer to deposit their egg skeins on intermediate cedar tree complexities that resulted in increased skein deposition and survival. Given our results, once introduced trees have deteriorated below an intermediate complexity, managers should consider supplemental introductions of more complex trees that benefit the reproduction of Yellow Perch.
Hamiltonian Monte Carlo for Simultaneous Interface and Spatial Field Detection (HMCSISFD) and its application to a piping zone interface detection problem
Authors: Koch Michael Conrad , Osugi Misato , Fujisawa Kazunori , Murakami Akira 
Published: September 2021

AbstractIn practice, inverse problems related to explicit interface detection rely on scarcely available information of the background continuous spatial fields. To accurately carry on inversion in such cases, a method called Hamiltonian Monte Carlo for Simultaneous Interface and Spatial Field Detection (HMCSISFD) is developed. Update of the interface parameters is done in a reversible mesh moving framework leading to a change in domain geometry which forces a recomputation of the spatial field covariance function as it is domain dependent. The eigenvalue problem and its derivatives w.r.t. the parameters are solved again on the updated domain to enable dimensionality reduction of the spatial field parameters through the use of the truncated Karhunen‐Loève expansion. This simultaneous parameter update procedure is applied to the detection of the interface and spatial field properties of a piping zone. Inversion is done considering hydraulic head and discharge rate data, with a priori known observation noise, from a carefully designed laboratory seepage flow experiment in a domain consisting a predefined piping zone. The static pipe in the experiment is representative of a pipe in equilibrium beneath an embankment/levee where the current hydraulic gradient isn't sufficient to cause further pipe progression. Markov chains obtained from the HMCSISFD method show convergence and the true interface and spatial field parameters are found to lie well within the 95% high probability density regions and the 0.05 and 0.95 quantiles, respectively, provided a proper choice for the observation noise is made.
Long‐term lower urinary tract sequelae following AUS cuff erosion
Authors: Chertack Nathan A. , Caldwell Kelly M. , Joice Gregory A. , Kavoussi Mehraban , Dropkin Benjamin M. , Ortiz Nicolas M. , Baumgarten Adam S. , Shakir Nabeel A. , Sanders Sarah C. , Hudak Steven J. , Morey Allen F. 
Published: September 2021

AbstractAimsTo examine the rate of lower urinary tract complications (LUTC) and urinary diversion (UD) after artificial urinary sphincter (AUS) explantation with the acute reconstruction of AUS cuff erosion defects.MethodsWe performed a retrospective study of patients who underwent in‐situ urethroplasty (ISU) for AUS cuff erosion from June 2007 to December 2020. Outcomes included LUTC (urethral stricture, diverticulum, fistula), AUS reimplantation, and UD. Defect size was prospectively estimated acutely and a subanalysis was performed to determine the impact of erosion severity (small erosions [<33% circumferential defect] and large erosions [≥33%]) on these outcomes. Kaplan–Meier curves were created to compare survival between the two groups.ResultsA total of 40 patients underwent ISU for urethral cuff erosion. The median patient age was 76 years old with a median erosion circumference of 46%. The overall LUTC rate was 30% (12/40) with 35% (14/40) of patients requiring permanent UD. Secondary AUS placement occurred in 24/40 (60%) patients with 11/24 (46%) leading to repeat erosion. On subanalysis, small erosion was associated with improved LUTC‐free and UD‐free survival but not associated with AUS reimplantation.ConclusionsLower urinary tract complications are common after AUS cuff erosion and can lead to the need for permanent UD. Patients with larger erosions are more likely to undergo UD and reach this end‐stage condition earlier compared to patients with small erosions.
Communication‐based predictive energy management strategy for a hybrid powertrain
Authors: Deng Junpeng , Adelberger Daniel , del Re Luigi 
Published: September 2021

AbstractPredictive information can significantly improve energy efficiency in a hybrid powertrain, especially for a long drive. Ideally the prediction of a sufficiently long horizon can bring the maximum benefit, however during this horizon the traffic can change, making it impossible to continue the chosen optimal strategy. Due to the limited vision of vehicles' sensors, it is difficult to acquire information far away. Against this background, this article proposes a predictive optimal control strategy in the connected environment. It combines real‐world vehicle‐to‐everything (V2X) information and cloud communication to allow for swift reaction and loss mitigation. More specifically, V2X information is used to detect impending changes on the route and the cloud is used to map these changes onto new constraints on the operation of the HEV. Instead of using “static” V2X information directly, a more realistic prediction method considering the dynamic of traffic is developed. Besides, an update strategy is adopted to timely cope with uncertainties. The performance of the approach is shown by a case study based on real driving cycles in Austria. The results show that the proposed structure is able to improve the performance (mainly fuel efficiency) up to .
Molecular genetic evidence supporting diverse histogenic origins of germ cell tumors
Authors: Jung Seung‐Hyun , Park Hyeon‐Chun , Choi Youn Jin , Song Sang Yong , Chung Yeun‐Jun , Lee Sug Hyung 
Published: September 2021

AbstractGerm cell tumors (GCTs) originate during the histogenesis of primordial germ cells to mature gametes. Previous studies identified five histogenic mechanisms in ovarian mature teratomas (type I: failure of meiosis I; type II: failure of meiosis II; type III: duplication of the genome of a mature gamete; type IV: no meiosis; and type V: fusion of two different ova), but those of other GCTs remain elusive. In this study, we analyzed 84 GCTs of various pathologic types to identify the histogenesis using single‐nucleotide polymorphism array by analyzing copy‐neutral loss of heterozygosity (CN‐LOH) and copy number alterations (CNAs). We detected types I and II in ovarian teratomas, type III in ovarian teratomas and yolk sac tumors (YSTs), and type IV in all GCT types. The GCTs with multiple‐type histogenesis (I–IV) (ovarian mature/immature teratomas and YST) show meiotic CN‐LOH with scant CNAs. Type IV‐only GCTs are either with mitotic CN‐LOH and abundant CNAs (seminoma, dysgerminoma, testicular mixed GCTs) or with scant CNAs and no CN‐LOH (pediatric testicular and mediastinal teratomas). The development sequences of CN‐LOH and CNA are different between the multiple type (I–IV) GCTs and type IV‐only GCTs. We analyzed two different histologic areas in eight GCTs (one mature teratoma with a mucin‐secreting adenoma, two immature teratomas, and five mixed GCTs). We found that GCTs (mature teratoma, immature teratoma, and mixed GCT) showed different genomic alterations between histologic areas, suggesting that genomic differences within a GCT could accompany histologic differentiation. Of note, we found evidence for collision tumors in a mixed GCT. Our data indicate that GCTs may have various histogenesis and intratumoral genomic differences, which might provide important information for the identification of GCTs, especially for those with different histologic areas. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Weakly supervised annotation‐free cancer detection and prediction of genotype in routine histopathology
Authors: Schrammen Peter Leonard , Ghaffari Laleh Narmin , Echle Amelie , Truhn Daniel , Schulz Volkmar , Brinker Titus J , Brenner Hermann , Chang‐Claude Jenny , Alwers Elizabeth , Brobeil Alexander , Kloor Matthias , Heij Lara R , Jäger Dirk , Trautwein Christian , Grabsch Heike I , Quirke Philip , West Nicholas P , Hoffmeister Michael , Kather Jakob Nikolas 
Published: September 2021

AbstractDeep learning is a powerful tool in computational pathology: it can be used for tumor detection and for predicting genetic alterations based on histopathology images alone. Conventionally, tumor detection and prediction of genetic alterations are two separate workflows. Newer methods have combined them, but require complex, manually engineered computational pipelines, restricting reproducibility and robustness. To address these issues, we present a new method for simultaneous tumor detection and prediction of genetic alterations: The Slide‐Level Assessment Model (SLAM) uses a single off‐the‐shelf neural network to predict molecular alterations directly from routine pathology slides without any manual annotations, improving upon previous methods by automatically excluding normal and non‐informative tissue regions. SLAM requires only standard programming libraries and is conceptually simpler than previous approaches. We have extensively validated SLAM for clinically relevant tasks using two large multicentric cohorts of colorectal cancer patients, Darmkrebs: Chancen der Verhütung durch Screening (DACHS) from Germany and Yorkshire Cancer Research Bowel Cancer Improvement Programme (YCR‐BCIP) from the UK. We show that SLAM yields reliable slide‐level classification of tumor presence with an area under the receiver operating curve (AUROC) of 0.980 (confidence interval 0.975, 0.984; n = 2,297 tumor and n = 1,281 normal slides). In addition, SLAM can detect microsatellite instability (MSI)/mismatch repair deficiency (dMMR) or microsatellite stability/mismatch repair proficiency with an AUROC of 0.909 (0.888, 0.929; n = 2,039 patients) and BRAF mutational status with an AUROC of 0.821 (0.786, 0.852; n = 2,075 patients). The improvement with respect to previous methods was validated in a large external testing cohort in which MSI/dMMR status was detected with an AUROC of 0.900 (0.864, 0.931; n = 805 patients). In addition, SLAM provides human‐interpretable visualization maps, enabling the analysis of multiplexed network predictions by human experts. In summary, SLAM is a new simple and powerful method for computational pathology that could be applied to multiple disease contexts. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
A review on extraction, chemical treatment, characterization of natural fibers and its composites for potential applications
Authors: Jagadeesh Praveenkumara , Puttegowda Madhu , Mavinkere Rangappa Sanjay , Siengchin Suchart 
Published: September 2021

AbstractIn recent days, natural fiber reinforced polymer composite is more popular due to its extensive properties suitable for various potential applications. The attention towards natural fibers is because of low cost, biodegradable, recyclability, nonabrasive, combustible, lightweight, and nontoxic properties. However, there is a need for furthermore fundamental knowledge for the raw materials processing and fabrication of composite structures, which is still challenging in current days. Natural fiber sources exist all over the world, which is obtained from animals, plants and minerals. The quality of the natural fibers depends on the extraction methods and different processing techniques. These natural fibers surface characteristics could be enhanced by selecting suitable surface treatment and chemical treatment. These fiber treatments reduce the water intake percentage, improve the adhesive nature, and enhance the overall performance of resulting polymer composites. Among all the chemical treatments, alkaline treatment (NaOH) is the most preferred chemical treatment because of its effectiveness and its low cost. This review article proposes the natural fibers detailed classification, composition, structure, properties, and extraction methods, chemical and surface treatments. We also summarize the previous research work findings on the fibers treatment, properties of natural/natural hybrid polymer composites and natural/synthetic hybrid polymer composites with applications.
Grafting of poly(ε‐caprolactone) from Abaca cellulose fibers via ring‐opening polymerization resulting in facile one‐pot biocomposites
Authors: Roy Bernice Lorraine F. , Heinrich Lydia A. , Tayo Lemmuel L. , Malmström Eva , Engström Joakim 
Published: September 2021

AbstractAs efforts to replace nonsustainable plastics increase, biocomposites from cellulose fibers and biodegradable polymers like poly(ε‐caprolactone) (PCL) are promising candidates. The necessary adhesion between fibers and matrix can be achieved by grafting polymeric chains onto the fibers. Herein, we report grafting of PCL onto Abaca fibers (AFs), a one‐pot method to obtain a composite containing grafted fiber and free PCL, and the characterization of prepared composite films. Three parameters for pretreatment (disintegration, drying, and solvent exchange) of AF were compared. Short and long PCL chains with molecular weights below and close to the chain entanglement weight of PCL were grafted from AFs. Using benzyl alcohol as an additional initiator, free PCL was simultaneously prepared. The unreacted monomer was removed by precipitation in water, resulting in ready‐made one‐pot composites. The biocomposites containing the free PCL and PCL‐grafted AFs were further processed by a combination of compounding and hot‐pressing. The analyzed mechanical (tensile) and rheological properties show a large dependence on the lengths of the PCL grafts. The herein‐reported composites pave the way for interesting bio‐based alternatives to plastic, especially looking at the tailoring of material properties.
Characterization of HLA‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS
Authors: Khan Amir , Shin Ji‐Yon , So Min Kyung , Na Jung‐Hyun , Justesen Sune , Ansari Adnan Ahmad , Ko Byoung Joon , Ahn Sung‐Min 
Published: September 2021

AbstractHuman leukocyte antigen (HLA) class I has more than 18,000 alleles, each of which binds to a set of unique peptides from the cellular degradome. Deciphering the interaction between antigenic peptides and HLA proteins is crucial for understanding immune responses in autoimmune diseases and cancer. In this study, we aimed to characterize the peptidome that binds to HLA‐A*33:03, which is one of the most prevalent HLA‐A alleles in the Northeast Asian population, but poorly studied. For this purpose, we analyzed the HLA‐A*33:03 monoallelic B cell line using immunoprecipitation of HLA‐A and peptide complexes, followed by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). In this study, we identified 5731 unique peptides that were associated with HLA A*33:03, and experimentally validated the affinity of 40 peptides for HLA‐A*33:03 and their stability in HLA A*33:03‐peptides complexes. To our knowledge, this study represents the largest dataset of peptides associated with HLA‐A*33:03. Also, this is the first study in which HLA A*33:03‐associated peptides were experimentally validated.
Prevalence of collusion in cancer communications: A meta‐analysis
Authors: Sutar Roshan , Chaudhary Pooja , Yadav Vikas 
Published: September 2021

AbstractIntroductionCollusion is the non‐disclosure of information about diagnosis or prognosis, frequently encountered in cancer care and palliative services. Unraveling collusion is a skill and differences among communication techniques by Health Care Workers have maintained the process of non‐disclosure to patients and caregivers. Identifying the prevalence of collusion in cancer care is required to improve the existing strategies across the world.MethodsA systematic review of the literature from 1991 to 2020 in the English language was conducted with the protocol registration on PROSPERO ID (CRD 42021249216.) to identify the pooled prevalence of collusion.ResultsBy using random effect model, the pooled prevalence estimate among patients for the diagnostic and prognostic collusion was 24.15, (95% CI [17.09; 32.96], Tou2 = 1.0801, I2 = 97.9%, Cochran's Q = 1058.22, df = 21, p‐value < 0.001) and 37.92, (95% CI [22.46; 56.30], Tou2 = 1.9641, I2 = 98.6%, Cochran's Q = 944.26, df = 13, p‐value < 0.001) respectively. There was no difference across subgroups with different types of setting for the interview, WHO regions and trend over the years.ConclusionsSubstantial prevalence of collusion goes unnoticed in cancer care. A meaningful understanding of such a large prevalence requires inquiry into the existing communication paradigm in cancer care across the world. The findings also question the need of formulating uniform interview techniques and structured assessment tools or questionnaires in cancer care to improve the disclosure rates.
Holocene ice wedges of the Kolyma Lowland and January paleotemperature reconstructions based on oxygen isotope records
Authors: Vasil'chuk Yurij K. , Budantseva Nadine A. 
Published: September 2021

AbstractIce wedges in the Holocene deposits of alases and floodplains have been studied in the Kolyma Lowland region. Most ice wedges have been found within alases dated to between 11 and 4.2 cal kyr BP, corresponding to the Greenlandian and Northgrippian stages of the Holocene. This study confirms that the greatest intensity of ice wedge growth occurred during ~10.5–6 cal kyr BP. A decrease in their growth was mainly caused by alas draining and reduced sedimentation. In the last 4–4.5 cal kyr BP (defined as the Meghalayan stage of the Holocene), ice wedges continued to grow in old alases, sometimes as a younger generation, as well as within young alases and floodplains of the Kolyma River and its tributaries. Mean January air temperatures were quite stable during the Holocene and varied usually approximately between −33 and −41°C, with a slight cooling during the Meghalayan stage. Minor variations in mean January air temperature may indicate a stability of winter climate of northern Yakutia, probably as a result of the stable influence of the Siberian anticyclone.
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry
Authors: Wang Ziying , Li Long , Hu Rongting , Zhong Peiyu , Zhang Yiran , Cheng Shihao , Jiang He , Liu Rui , Ding Yu 
Published: September 2021

AbstractRed fluorescent proteins (RFPs) are powerful tools used in molecular biology research. Although RFP can be easily monitored in vivo, manipulation of RFP by suitable nanobodies binding to different epitopes of RFP is still desired. Thus, it is crucial to obtain structural information on how the different nanobodies interact with RFP. Here, we determined the crystal structures of the LaM2‐mCherry and LaM4‐mCherry complexes at 1.4 and 1.9 Å resolution. Our results showed that LaM2 binds to the side of the mCherry β‐barrel, while LaM4 binds to the bottom of the β‐barrel. The distinct binding sites of LaM2 and LaM4 were further verified by isothermal titration calorimetry, fluorescence‐based size exclusion chromatography, and dynamic light scattering assays. Mutation of the residues at the LaM2 or LaM4 binding interface to mCherry significantly decreased the binding affinity of the nanobody to mCherry. Our results also showed that LaM2 and LaM4 can bind to mCherry simultaneously, which is crucial for recruiting multiple operation elements to the RFP. The binding of LaM2 or LaM4 did not significantly change the chromophore environment of mCherry, which is important for fluorescence quantification assays, while several GFP nanobodies significantly altered the fluorescence. Our results provide atomic resolution interaction information on the binding of nanobodies LaM2 and LaM4 with mCherry, which is important for developing detection and manipulation methods for RFP‐based biotechnology.