bluuebunny/crossref_metadata_2025_split huggingface dataset:
Productive biofilms: from prokaryotic to eukaryotic systems
Authors: Schmeckebier Andrea , Zayed Ahmed , Ulber Roland 
Published: August 2022

AbstractBiofilms have great potential for producing valuable products more efficiently than suspended cultivations when it comes to yield and productivity. In addition, biofilms have the advantage of cell protection and increased resistance to environmental influences. Therefore, productive biofilms are used in biofilm reactors to produce value‐added products. A summary of possible applications for biofilm reactors is given here. In addition, the surfaces on which biofilms are cultivated are briefly explained. The possibility of using biofilms is not limited to prokaryotic systems. Thus, eukaryotic systems can also be cultivated as biofilms to produce valuable products. Therefore, both prokaryotic and eukaryotic productive biofilms will be described in this review. In the case of eukaryotic systems, fungal biofilms and plant biofilms will be discussed. The biofilm formation of the different cell types is listed and the productivity of a cell line on a corresponding substrate is summarized. Finally, the investigation methods of biofilms are discussed, as these methods are essential to understanding biofilms. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).
The combined cartilage growth – calcification patterns in the wing‐fins of Rajidae (Chondrichthyes): A divergent model from endochondral ossification of tetrapods
Authors: Pazzaglia Ugo E. , Reguzzoni Marcella , Manconi Renata , Zecca Piero Antonio , Zarattini Guido , Campagnolo Monica , Raspanti Mario 
Published: August 2022

AbstractThe relationship between cartilage growth – mineralization patterns were studied in adult Rajidae with X‐ray morphology/morphometry, undecalcified resin‐embedded, heat‐deproteinated histology and scanning electron microscopy. Morphometry of the wing‐fins, nine central rays of the youngest and oldest specimens documented a significant decrement of radials mean length between inner, middle and outer zones, but without a regular progression along the ray. This suggests that single radial length growth is regulated in such a way to align inter‐radial joints parallel to the wing metapterygia curvature. Trans‐illumination and heat‐deproteination techniques showed polygonal and cylindrical morphotypes of tesserae, whose aligned pattern ranged from mono‐columnar, bi‐columnar, and multi‐columnar up to the crustal‐like layout. Histology of tessellated cartilage allowed to identify of zones of the incoming mineral deposition characterized by enhanced duplication rate of chondrocytes with the formation of isogenic groups, whose morphology and topography suggested a relationship with the impending formation of the radials calcified column. The morphotype and layout of radial tesserae were related to mechanical demands (stiffening) and the size/mass of the radial cartilage body. The cartilage calcification pattern of the batoids model shares several morphological features with tetrapods' endochondral ossification, that is, (chondrocytes' high duplication rate, alignment in rows, increased volume of chondrocyte lacunae), but without the typical geometry of the metaphyseal growth plates.Research Highlights1. The wing‐fins system consists of stiff radials, mobile inter‐radial joints and a flat inter‐radial membrane adapted to the mechanical demand of wing wave movement.2. Growth occurs by forming a mixed calcified‐uncalcified cartilage texture, developing intrinsic tensional stresses documented by morphoanatomical data.
Characterization of protein complexes in extracellular vesicles by intact extracellular vesicle crosslinking mass spectrometry (iEVXL)
Authors: Bauzá‐Martinez Julia , Armony Gad , Pronker Matti F. , Wu Wei 
Published: August 2022

AbstractExtracellular vesicles (EVs) are blood‐borne messengers that coordinate signalling between different tissues and organs in the body. The specificity of such crosstalk is determined by preferential EV docking to target sites, as mediated through protein‐protein interactions. As such, the need to structurally characterize the EV surface precedes further understanding of docking selectivity and recipient‐cell uptake mechanisms. Here, we describe an intact extracellular vesicle crosslinking mass spectrometry (iEVXL) method that can be applied for structural characterization of protein complexes in EVs. By using a partially membrane‐permeable disuccinimidyl suberate crosslinker, proteins on the EV outer‐surface and inside EVs can be immobilized together with their interacting partners. This not only provides covalent stabilization of protein complexes before extraction from the membrane‐enclosed environment, but also generates a set of crosslinking distance restraints that can be used for structural modelling and comparative screening of changes in EV protein assemblies. Here we demonstrate iEVXL as a powerful approach to reveal high‐resolution information, about protein determinants that govern EV docking and signalling, and as a crucial aid in modelling docking interactions.
Molecular characterization‐based multi‐omics analyses in primary liver cancer using the Japanese version of the genome atlas
Authors: Imamura Taisuke , Okamura Yukiyasu , Ohshima Keiichi , Uesaka Katsuhiko , Sugiura Teiichi , Yamamoto Yusuke , Ashida Ryo , Ohgi Katsuhisa , Nagashima Takeshi , Yamaguchi Ken 
Published: August 2022

AbstractBackgroundPrimary liver cancer (PLC) is classified into hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC), and combined hepatocellular and intrahepatic cholangiocarcinoma (CHC). We investigated the genomic landscape of PLC according to the histological classification and established a cross‐histological molecular subtyping for PLC by a multi‐omics analysis.MethodsWe analyzed 265 PLC cases with whole‐exome sequencing and DNA copy number analyses and 251 cases with gene expression profiling.ResultsThe cohort included HCC (n = 223, 84%), ICC (n = 34, 13%), and CHC (n = 8, 3%). Mutation analyses identified histological type‐specific driver genes, such as CTNNB1 in HCC and KRAS, IDH1, and PIK3CA in ICC, and ARID1A and KMT2C in CHC. The tumor suppressor gene TP53 mutation was detected in 21.1% of HCC, 16.1% of ICC, and 25.0% of CHC cases. Other well‐characterized tumor suppressor genes included RB1, which was mutated in 2.8% of HCC and 3.2% of ICC; and PTEN, which was mutated in 1.4% of HCC, 3.2% of ICC, and 12.5% of CHC cases. DNA copy number analyses identified focal amplifications, with NUF2 (1q23.3) the most frequently detected as an amplified gene in all 3 types (HCC, 3.8%; CHC, 12.5%, ICC, 3.2%). Molecular subtyping for PLC based on the multi‐omics analysis identified three subtypes, one of which was associated with recurrence after resection and amplified genes located at chromosome 8q.ConclusionsOur dataset serves as a fundamental resource for genomic medicine for PLC in Japan and identified amplified genes located at chromosome 8q as promising therapeutic targets for the subgroup with a poor prognosis.
Efficacy of shear wave elastography for the diagnosis of chronic pancreatitis
Authors: Kojima Hiroyuki , Sofuni Atsushi , Sugimoto Katsutoshi , Tsuchiya Takayoshi , Ishii Kentaro , Tanaka Reina , Tonozuka Ryosuke , Yamamoto Kenjiro , Hirakawa Noriyuki , Itoi Takao 
Published: August 2022

AbstractBackground/PurposeShear wave elastography (SWE) is a clinical method used to evaluate liver hardness. In this study, we assessed its applicability in assessing the pancreas and its potential for diagnosing chronic pancreatitis.MethodsWe performed SWE on 59 patients who underwent abdominal ultrasound, and measured the computed tomography (CT) values of the pancreas. Patients were classified as having a normal pancreas (NP), early chronic pancreatitis (ECP), or chronic pancreatitis (CP). SW elasticity (SWe), SW dispersion (SWd), and CT values between groups were analyzed.ResultsSWe significantly differed between the CP and NP/ECP groups (NP vs CP; P = 0.001, ECP vs CP; P = 0.026,), while SWd showed a significant difference only between the NP and CP group (NP vs CP; P = 0.001). The CT values were significantly different between the CP and NP/ECP groups (NP vs CP; P = 0.0006, ECP vs CP; P = 0.0027).ConclusionPancreatic SWE and CT values were helpful in the diagnosis of chronic pancreatitis. SWd may reveal status changes in ECP.
Contribution of κ‐/ι‐carrageenan on the gelling properties of shrimp myofibrillar protein and their interaction mechanism exploration
Authors: Li Shuang , Lin Songyi , Jiang Pengfei , Bao Zhijie , He Xueqing , Sun Na 
Published: August 2022

AbstractBACKGROUNDThe contribution and mechanism of κ‐/ι‐carrageenan (CG) with different hydration characteristics on the gelling properties of shrimp myofibrillar protein (MP) gelation was studied.RESULTSThe gel strength, water‐holding capacity and viscoelastic properties of MP gels were significantly enhanced by 1.0% κ‐/ι‐CG (P < 0.05), but the microstructure showed that excessive carrageenan caused fragmentation of the gel network and a corresponding decrease in gel properties. Compared to MP‐ιCG, MP‐κCG showed larger breaking force and shorter breaking distance, thus enhancing the hardness and brittleness of the gel, which might be ascribed to a reinforced network skeleton and a tighter binding of κCG‐myosin. However, MP‐ιCG stabilized more moisture in the gel network, thereby improving the tenderness of the gel, which might be related to the electrostatic repulsion observed between the sulfate groups of ιCG and the myosin observed by molecular docking. In addition, the β‐sheet content and intermolecular interactions might be positively correlated with gel properties.CONCLUSIONIn this study, a composite gel system was constructed based on the interaction of MP and CG. The quality differences of two kinds of CG‐MP gels were clarified, which will provide guidance for the application of different kinds of carrageenan and the development of recombinant meat products with specific quality. © 2022 Society of Chemical Industry.
The Correlation Between the HEAD‐US‐C Score and HJHS in Hemophilic Arthropathy of the Knee
Authors: Fang Yunmei , Guo Yulin , Qin Ting , Luan Yuting , Zhang Cuiming 
Published: August 2022

ObjectivesWe aimed to discuss the correlation between the Hemophilia Early Detection Ultrasound in China (HEAD‐US‐C) score and the Hemophilia Joint Health Score version 2.1 (HJHS 2.1) of the knee joint in patients with hemophilia.MethodsWe included 70 male patients with hemophilia admitted to The Second Hospital of Shanxi Medical University; the patients' bilateral knee joints were evaluated using the HEAD‐US‐C score and HJHS. We analyzed factors influencing hemophilia arthropathy of the knee and examined the correlation between the HEAD‐US‐C score and HJHS.ResultsThe joint injury severity was positively correlated with age and the number of bleeds (P < .001). Further, the HEAD‐US‐C score and HJHS differed according to the severity (both P < .001), but not type (P = .163 and P = .283, respectively), of hemophilia. There was a significant correlation between the HEAD‐US‐C score and HJHS (P < .001).ConclusionsOverall, all joint lesions observed on ultrasound corresponded to clinical joint functional abnormalities. Therefore, the HEAD‐US‐C is important for hemophilic arthropathy evaluation and is useful in explaining abnormal joint function.
Improved predictions and forecasts of chronic wasting disease occurrence using multiple mechanism dynamic occupancy modeling
Authors: Cook Jonathan D. , Williams David M. , Porter William F. , Christensen Sonja A. 
Published: August 2022

AbstractDiseases spread and persist according to complex interactions among hosts, pathogens, and their shared environments. In actively managed wildlife diseases, unanticipated disease spread and persistence can challenge mitigation efforts, necessitating modeling approaches that elucidate and integrate multiple mechanisms. Dynamic occupancy models (DOMs) can predict and forecast species occurrence patterns; however, they have not been extended to explain the complex spread and persistence patterns of chronic wasting disease (CWD). We used a DOM to predict and forecast the persistence, and localized and long‐distance spread of CWD in white‐tailed deer (Odocoileus virginianus) according to distinct ecological relationships that we hypothesized were important. We estimated large differences between the probabilities of disease persistence and localized and long‐distance CWD spread in Wisconsin, USA. Chronic wasting disease was more likely to persist in areas with low clay content in soils, to spread locally as the amount of localized disease increased, and to occur in areas far removed from prior positives in places with a higher proportion of agriculture. Across all landscape compositions, the probability of occurrence decayed by distance from prior positives in a manner consistent with transient movement distances of white‐tailed deer. Finally, a multi‐mechanism DOM was able to produce spatially accurate predictions and forecasts of disease occurrence using only data collected during the first 2 days of the firearm harvest season. Thus, our multi‐mechanism DOM offers advantages over simple linear models that can improve our understanding of the complex ecology driving CWD dynamics and lead to better surveillance and management strategies moving forward.
Free Tissue Transfer for Skull Base Osteoradionecrosis: A Novel Approach in the Endoscopic Era
Authors: Sreenath Satyan B. , Grafmiller Kevin T. , Tang Dennis M. , Roof Scott A. , Woodard Troy D. , Kshettry Varun R. , Recinos Pablo F. , Sindwani Raj , Fritz Michael A. 
Published: August 2022

ObjectivesOsteoradionecrosis (ORN) of the skull base and craniovertebral junction is a challenging complication of radiation therapy (RT). Severe cases often require surgical intervention through a multi‐modal approach. With the evolution in endoscopic surgery and advances in skull base reconstruction, there is an increasing role for microvascular free tissue transfer (MFTT). We describe an endoscopic‐assisted approach for the management of ORN of the skull base using fascia lata for MFTT.Study DesignRetrospective case series.MethodsBetween 2017 and 2021, a review of all cases in which fascia lata MFTT was utilized for skull base ORN was performed. Patient demographics, preoperative characteristics, and postoperative outcomes with long‐term follow‐up were reviewed.ResultsFive patients were identified. Mean duration to onset of ORN was 17 months following RT. A trial of antibiotics, hyperbaric oxygen (HBO), and/or limited debridement was attempted without success. Refractory pain and progressive osteomyelitis were unifying symptoms. All patients underwent endoscopic debridement of the affected region of ORN prior to MFTT. Vascularized fascia lata was inset through a combined endonasal and transoral corridor. There was improvement in chronic pain in the postop setting with no patients requiring continued antibiotics or HBO therapy. Mean post‐op follow‐up was 23 months.ConclusionsWith continued evolution in endoscopic, minimally invasive approaches, there is an expanding indication for early surgical management in refractory ORN. Fascia lata MFTT is a novel and effective strategy for the management of ORN of the skull base and upper cervical spine with excellent postoperative outcomes and limited patient morbidity.Level of Evidence4 Laryngoscope, 133:562–568, 2023
Directly Determining Orbital Angular Momentum of Ultrashort Laguerre–Gauss Pulses via Spatially‐Resolved Autocorrelation Measurement
Authors: Yu Bing‐Shi , Li Chun‐Yu , Yang Yuanjie , Rosales‐Guzmán Carmelo , Zhu Zhi‐Han 
Published: August 2022

AbstractAutocorrelation measurement based on second‐harmonic generation (SHG), the best‐known technique for measuring the temporal duration of ultrashort pulses, dates back to the birth of ultrafast lasers. Here, it is proposed and experimentally demonstrated that such well‐established technique can be used to measure the orbital angular momentum of ultrashort Laguerre–Gauss (LG) pulses. By analyzing the spatial spectrum (i.e., the far‐field pattern) of the SHG signal with a spatially‐resolved detector, the full spatial structure of ultrashort LG pulses, including both azimuthal and radial indices, are unambiguously determined. The results provide an important advancement for the well‐established autocorrelation technique by extending it to reach its full potential in laser characterization, especially for structured ultrashort pulses.
CBKmodel composition using paired web services and executable functions: A demonstration for individualizing preventive services
Authors: Flynn Allen , Taksler Glen , Caverly Tanner , Beck Adam , Boisvert Peter , Boonstra Philip , Gittlen Nate , Meng George , Raths Brooke , Friedman Charles P. 
Published: August 2022

AbstractIntroductionLearning health systems are challenged to combine computable biomedical knowledge (CBK) models. Using common technical capabilities of the World Wide Web (WWW), digital objects called Knowledge Objects, and a new pattern of activating CBK models brought forth here, we aim to show that it is possible to compose CBK models in more highly standardized and potentially easier, more useful ways.MethodsUsing previously specified compound digital objects called Knowledge Objects, CBK models are packaged with metadata, API descriptions, and runtime requirements. Using open‐source runtimes and a tool we developed called the KGrid Activator, CBK models can be instantiated inside runtimes and made accessible via RESTful APIs by the KGrid Activator. The KGrid Activator then serves as a gateway and provides a means to interconnect CBK model outputs and inputs, thereby establishing a CBK model composition method.ResultsTo demonstrate our model composition method, we developed a complex composite CBK model from 42 CBK submodels. The resulting model called CM‐IPP is used to compute life‐gain estimates for individuals based their personal characteristics. Our result is an externalized, highly modularized CM‐IPP implementation that can be distributed and made runnable in any common server environment.DiscussionCBK model composition using compound digital objects and the distributed computing technologies is feasible. Our method of model composition might be usefully extended to bring about large ecosystems of distinct CBK models that can be fitted and re‐fitted in various ways to form new composites. Remaining challenges related to the design of composite models include identifying appropriate model boundaries and organizing submodels to separate computational concerns while optimizing reuse potential.ConclusionLearning health systems need methods for combining CBK models from a variety of sources to create more complex and useful composite models. It is feasible to leverage Knowledge Objects and common API methods in combination to compose CBK models into complex composite models.
Epigenetic Clock Acceleration Is Linked to Age at Onset of Parkinson's Disease
Authors: Tang Xuelin , Gonzalez‐Latapi Paulina , Marras Connie , Visanji Naomi P. , Yang Wanli , Sato Christine , Lang Anthony E. , Rogaeva Ekaterina , Zhang Ming 
Published: August 2022

AbstractBackgroundAging is the strongest risk factor for Parkinson's disease (PD), which is a clinically heterogeneous movement disorder with highly variable age at onset. DNA methylation age (DNAm age) is an epigenetic clock that could reflect biological aging.ObjectivesThe aim was to evaluate whether PD age at onset is associated with DNAm‐age acceleration (difference between DNAm age and chronological age).MethodsWe used the genome‐wide Infinium MethylationEPIC array to assess DNAm age in discovery (n = 96) and replication (n = 182) idiopathic PD cohorts and a unique longitudinal LRRK2 cohort (n = 220) at four time points over a 3‐year period, comprising 91 manifesting and 129 nonmanifesting G2019S carriers at baseline. Cox proportional hazard regression and multivariate linear regression were used to evaluate the relation between DNAm‐age acceleration and PD age at onset, which was highly variable in manifesting G2019S carriers (36–75 years) and both idiopathic PD cohorts (26–77 and 35–81 years).ResultsDNAm‐age acceleration remained steady over the 3‐year period in most G2019S carriers. It was strongly associated with age at onset in the LRRK2 cohort (P = 2.25 × 10−15) and discovery idiopathic PD cohort (P = 5.39 × 10−9), suggesting that every 5‐year increase in DNAm‐age acceleration is related to about a 6‐year earlier onset. This link was replicated in an independent idiopathic PD cohort (P = 1.91 × 10−10). In each cohort, the faster‐aging group has an increased hazard for an earlier onset (up to 255%).ConclusionsThis study is the first to demonstrate that DNAm‐age acceleration is related to PD age at onset, which could be considered in disease‐modifying clinical trials. Future studies should evaluate the stability of DNAm‐age acceleration over longer time periods, especially for phenoconverters from nonmanifesting to manifesting individuals. © 2022 International Parkinson and Movement Disorder Society.
Timing of Postfertilization Pressure Shock Treatment for the Production of Mitotic Gynogens in Six Salmonid Species
Authors: Biagi Carlo A. , Leggatt Rosalind A. , Sakhrani Dionne , Wetklo Mike , Vandersteen Wendy E. , Christensen Kris A. , Rondeau Eric B. , Watson Breanna M. , Wellband Kyle W. , Koop Ben F. , Withler Ruth E. , Devlin Robert H. 
Published: August 2022

Abstract
Doubled haploid gynogens are individuals whose genetic material consists of two identical maternal chromosome sets and who lack paternal genetic contributions. These individuals can be useful in whole-genome sequence assembly to eliminate allelic variation in an individual that otherwise complicates the discrimination of SNPs and paralogs in regular diploids. This is particularly important in salmonid species, which have extensive remnants of an ancestral whole-genome duplication. Further, doubled haploid individuals are fully homozygous and can be used to generate clonal lines. Here, successful timing was determined for late pressure shocking for producing doubled haploid gynogens in five Oncorhynchus species (Chinook Salmon O. tshawytscha, Coho Salmon O. kisutch, Chum Salmon O. keta, Pink Salmon O. gorbuscha, and Sockeye Salmon O. nerka) and one Salvelinus species (domesticated Artic Char Salvelinus alpinus). For this study, sperm was treated with UV irradiation to inactivate the paternal nuclear DNA and used to fertilize eggs. The resulting zygotes were pressure shocked at various times following fertilization to form doubled haploid embryos via inhibition of the first cell division (mitotic gynogenesis). At an incubation temperature of 10.5°C, successful postfertilization pressure shock times for maximal survival of confirmed gynogens were 2.41–2.83 accumulated thermal units (ATUs) for Coho Salmon, 2.63–2.84 ATUs for Chum Salmon, 2.84–3.06 ATUs for Pink Salmon, 2.19 ATUs for Sockeye Salmon, and 2.63–3.06 ATUs for Chinook Salmon, whereas for Arctic Char a shock time of 2.29–2.54 ATUs at 4°C incubation was successful. Survival to fry stage ranged from less than 1% to 11.7%. Survivors were genotyped using microsatellite markers to assess nonpaternity and maternal homozygosity and were found to be 92.5% gynogens when averaged across all treatments and species. Mitotic gynogenetic individuals were produced in all six salmonid species and were used in subsequent studies to generate whole-genome sequences for Chinook, Coho, Chum, and Sockeye salmons.