bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential extracellular vesicle protein markers altered in osteosarcoma from public databases
Authors: Zhang Jinhe , Li Huiyan 
Published: December 2022

AbstractPurposeExtracellular vesicles (EVs) have become promising biomarkers for cancer management. Particularly, the molecular cargo such as proteins carried by EVs are similar to their cells of origin, providing important information that can be used for cancer diagnostics, prognosis, and treatment monitoring. However, to date, molecular analysis on EVs is still challenging, limited by the availability of efficient analytical technologies, largely due to the small size of EVs. In this work, we developed a computational workflow for in silico identification of potential EV protein markers from genomic and proteomic databases, and applied it for the discovery of osteosarcoma (OS) EV protein markers.Experimental designBoth mRNA and protein data were computed and compared from publicly accessible databases, and top markers with high differential expression levels were selected.ResultsThirty nine markers were identified overexpressed and seven found to be downregulated. These identified markers have been found to be associated with OS on different aspects in literature, demonstrating the usability of this workflow.Conclusions and clinical relevanceThis work provides a list of potential EV protein markers that are either overexpressed or downregulated in OS for further experimental validation for improved clinical management of OS.
Molecular insights into alginate β‐lactoglobulin A multivalencies—The foundation for their amorphous aggregates and coacervation
Authors: Madsen Mikkel , Prestel Andreas , Madland Eva , Westh Peter , Tøndervik Anne , Sletta Håvard , Peters Günther H. J. , Aachmann Finn L. , Kragelund Birthe B. , Svensson Birte 
Published: December 2022

AbstractFor improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β‐lactoglobulin A (β‐LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β‐LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β‐LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β‐LgA, as concluded from saturation transfer difference and 1H‐ligand‐targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016‐1 revealed the orientation of AOSs to only vary slightly at the preferred β‐LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β‐LgA complexes may help explain the first steps toward disordered β‐LgA alginate coacervate structures.
Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry
Authors: Wei Jun , Beebe‐Dimmer Jennifer , Shi Zhuqing , Sample Christopher , Yan Guifang , Rifkin Andrew S. , Sadeghpour Azita , Gielzak Marta , Choi Sodam , Moon David , Zheng S. Lilly , Helfand Brian T. , Walsh Patrick C. , Xu Jianfeng , Cooney Kathleen A. , Isaacs William B. 
Published: December 2022

AbstractBackgroundAlthough men of African ancestry (AA) have the highest mortality rate from prostate cancer (PCa), relatively little is known about the germline variants that are associated with PCa risk in AA men. The goal of this study is to systematically evaluate rare, recurrent nonsynonymous variants across the exome for their association with PCa in AA men.MethodsWhole exome sequencing (WES) of germline DNA in two AA PCa patient cohorts of Johns Hopkins Hospital (N = 960) and Wayne State University (N = 747) was performed. All nonsynonymous variants present in both case cohorts, with a carrier rate between 0.5% and 1%, were identified. Their carrier rates were compared with rates from 8128 African/African American (AFR) control subjects from The Genome Aggregation Database (gnomAD) using Fisher's exact test. Significant variants, defined as false discovery rate (FDR) adjustedp‐value ≤ 0.05, were further evaluated in AA PCa cases (N = 132) and controls (N = 1184) from the UK Biobank (UKB).ResultsTwo variants reached a pre‐specified statistical significance level. The first was p.R14Q inGPRC5C(found in 0.47% of PCa cases and 0.01% of population controls); odds ratio (OR) for PCa was 37.46 (95% confidence interval CI 4.68–299.72), pexact = 7.01E‐06, FDR‐adjustedp‐value = 0.05. The second was p.R511Q inIGF1R(found in 0.53% of PCa cases and 0.01% of population controls); OR for PCa was 21.54 (95%CI 4.65–99.76), pexact = 5.51E‐06, FDR‐adjustedp‐value = 0.05. The mean percentage of African ancestry was similar between variant carriers and noncarriers of each variant,p > 0.05. In the UKB AA men,GPRC5CR14Q was 0.76% and 0.08% in cases and controls, respectively, OR for PCa was 9.00 (95%CI 0.56–145.23), pexact = 0.19. However,IGF1RR511Q was not found in cases or controls.ConclusionsThis WES study identified two rare, recurrent nonsynonymous PCa risk‐associated variants in AA. Confirmation in additional large populations of AA PCa cases and controls is required.
Responses of arbuscular mycorrhizal fungi to rice–upland crop rotations in an 8‐year paddy ecosystem
Authors: Wang Qingfeng , Zhou Deping , Chu Changbin , Zhao Zheng , Zhou Jing , Wu Shuhang 
Published: December 2022

AbstractArbuscular mycorrhizal fungi (AMF), which can form symbiotic associations with many terrestrial plants, are critical for crop yields and agroecosystem sustainability. In this study, we assessed the influence of rice–upland crop rotations on soil AMF diversity and composition. We also explored the mechanisms of rice (Oryza sativa L.)–upland crop rotations that affect AMF using trait‐based guild methods. We found that rotations of rice with different plants differentially influenced soil AMF. Rice–wheat (Triticum aestivum L.) (RW) and rice–Chinese milk vetch (Astragalus sinicus L.) (RV) rotations significantly altered the soil AMF composition, with RW and RV significantly increasing and decreasing AMF diversity, respectively, compared with the rice–fallow treatment. In addition, RW and RV affected AMF abundance in intra‐ and extra‐radical portions in different ways. For example, both the RW and RV treatments increased AMF spore density, but decreased AMF colonization rate. Different AMF guilds showed different responses to rice–upland crop rotations. The RW treatment increased the rhizophilic guild by 4.9% and decreased the edaphophilic guild by 27.9%, whereas the RV treatment produced opposite trends. Thus, rice–upland crop rotations changed soil AMF diversity, AMF composition, and trait‐based guilds in different ways, and rice yield was mainly correlated with AMF colonization rate.
Printing Crack‐Free Microporous Structures by Combining Additive Manufacturing with Colloidal Assembly
Authors: Winhard Benedikt F. , Maragno Laura G. , Gomez‐Gomez Alberto , Katz Julian , Furlan Kaline P. 
Published: December 2022

AbstractTo date high printing resolution and scalability, i.e., macroscale component dimensions and fast printing, are incompatible characteristics for additive manufacturing (AM) processes. It is hereby demonstrated that the combination of direct writing as an AM process with colloidal assembly enables the breaching of this processing barrier. By tailoring printing parameters for polystyrene (PS) microparticle‐templates, how to avoid coffee ring formation is demonstrated, thus printing uniform single lines and macroscale areas. Moreover, a novel “comb”‐strategy is introduced to print macroscale, crack‐free colloidal coatings with low viscous colloidal suspensions. The printed templates are transformed into ceramic microporous channels as well as photonic coatings via atomic layer deposition (ALD) and calcination. The obtained structures reveal promising wicking capabilities and broadband reflection in the near‐infrared, respectively. This work provides guidelines for printing low viscous colloidal suspensions and highlights the advancements that this printing process offers toward novel applications of colloidal‐based printed structures.
What divides the first and second generations? Family time of arrival and educational outcomes for immigrant youth
Authors: Hull Marie C. 
Published: December 2022

AbstractIn this article, I develop a measure of host country experience, which I call “relative time of arrival,” to explore differences between first‐ and second‐generation immigrants. This measure is finer than immigrant generation and expands on the widely used measures of years since migration and age at migration. It is scaled so that zero indicates that a child was born in the same year that the family migrated, and the negative side of the scale measures parents' host country experience before the child's birth. I then use relative time of arrival to assess whether parents' host country experience before birth matters and generally find that it does not. I also study the dividing line between the first and second generations, specifically, whether there are differences in educational outcomes between early arriving first‐generation immigrants and second‐generation immigrants whose parents arrived shortly before birth. For most outcomes considered, I find that the transition between the first and second generations is relatively smooth, indicating that these groups are not as distinct as often thought. Thus, observed differences between the first and second generations are driven by the lower performance of late‐arriving first‐generation children.
IoT‐based smart UV meter for domestic and hospital UV sterilization devices
Authors: Dash Satya Prakash , Tripathy Hara Prasada , Nayak Gargi Priyadarshini , Das Sidhant , Nayak Amit Kumar , Mishra Dilip Kumar , Pattanaik Priyabrata 
Published: December 2022

AbstractIn the current circumstances, when lakhs of people are dying as a result of the COVID‐19 Pandemic, imposing lockdown and shutdown disrupts the socioeconomic conditions of the entire globe to the point that the country's backbone is compromised. A highly modified, effective sterilizing and disinfection system is essential to improve the country or human civilization. To combat the many adverse effects of radiation, not only on human health but also on the environment, ultra violet technology has been introduced. UV technology is also a source of radiation that has health risks; however, changes in wavelength can make the risk low. UVM‐30A sensor module is used in the sanitization to detect UV irradiation in this study effort. An IoT‐based system based on Arduino uno microcontroller, GSM A6 WiFi module, and UVM‐30A is presented to create an automated implanted UV radiation detection device.
Distributed Computing
Authors: Wang Liang , Zhao Jianxin 
Published: December 2022

AbstractDistributed computing has been playing a significant role in current smart applications in various fields. In this chapter, we first briefly give a bird’s-eye view of this topic, introducing various programming paradigms. Next, we introduce Actor, an OCaml-based distributed computing engine, and how it works together with Owl. We then focus on one key element in distributed computing: the synchronization. We introduce four different types of synchronization methods or “barriers” that are commonly used in current systems. Next, we elaborate how these barriers are designed and provide illustrations from the theoretical perspective. Finally, we use evaluations to show the performance trade-offs in using different barriers.
Testing Framework
Authors: Wang Liang , Zhao Jianxin 
Published: December 2022

AbstractEvery proper software requires testing, and so is Owl. All too often, we have found that testing can help us discover potential errors we failed to notice during development. In this chapter, we briefly introduce the philosophy of testing in Owl, the tool we use for conducting the unit test, and examples to demonstrate how to write unit tests. Issues such as using functors in tests and other things to notice in writing test code for Owl, etc. are also discussed in this chapter.
Rigidity properties of the hypercube via Bakry–Émery curvature
Authors: Liu Shiping , Münch Florentin , Peyerimhoff Norbert 
Published: December 2022

AbstractWe give rigidity results for the discrete Bonnet–Myers diameter bound and the Lichnerowicz eigenvalue estimate. Both inequalities are sharp if and only if the underlying graph is a hypercube. The proofs use well-known semigroup methods as well as new direct methods which translate curvature to combinatorial properties. Our results can be seen as first known discrete analogues of Cheng’s and Obata’s rigidity theorems.
Two discretisations of the time-dependent Bingham problem
Authors: Carstensen C. , Schedensack M. 
Published: December 2022

AbstractThis paper introduces two methods for the fully discrete time-dependent Bingham problem in a three-dimensional domain and for the flow in a pipe also named after Mosolov. The first time discretisation is a generalised midpoint rule and the second time discretisation is a discontinuous Galerkin scheme. The space discretisation in both cases employs the non-conforming first-order finite elements of Crouzeix and Raviart. The a priori error analyses for both schemes yield certain convergence rates in time and optimal convergence rates in space. It guarantees convergence of the fully-discrete scheme with a discontinuous Galerkin time-discretisation for consistent initial conditions and a source term $$f\in H^1(0,T;L^2(\Omega ))$$

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Estradiol-dependent hypocretinergic/orexinergic behaviors throughout the estrous cycle
Authors: Kim Hye Ji J. , Dickie Samuel A. , Laprairie Robert B. 
Published: December 2022

Abstract
Rationale
The female menstrual or estrous cycle and its associated fluctuations in circulating estradiol (E2), progesterone, and other gonadal hormones alter orexin or hypocretin peptide production and receptor activity. Depending on the estrous cycle phase, the transcription of prepro-orexin mRNA, post-translational modification of orexin peptide, and abundance of orexin receptors change in a brain region-specific manner. The most dramatic changes occur in the hypothalamus, which is considered the starting point of the hypothalamic-pituitary–gonadal axis as well as the hub of orexin-producing neurons. Thus, hypothalamus-regulated behaviors, including arousal, feeding, reward processing, and the stress response depend on coordinated efforts between E2, progesterone, and the orexin system. Given the rise of orexin therapeutics for various neuropsychiatric conditions including insomnia and affective disorders, it is important to delineate the behavioral outcomes of this drug class in both sexes, as well as within different time points of the female reproductive cycle.

Objectives
Summarize how the menstrual or estrous cycle affects orexin system functionality in animal models in order to predict how orexin pharmacotherapies exert varying degrees of behavioral effects across the dynamic hormonal milieu.
Comprehensive two-dimensional gas chromatography-time of flight mass spectrometry as a tool for tracking roasting-induced changes in the volatilome of cold-pressed rapeseed oil
Authors: Drabińska Natalia , Siger Aleksander , Jeleń Henryk 
Published: December 2022

AbstractThe aim of this study was to track changes in the volatilome of cold-pressed oil and press cakes obtained from roasted seeds and to combine it with the profile of non-volatile metabolites in a single study, in order to understand pathways of volatile organic compound (VOC) formation caused by thermal processing. Comprehensive two-dimensional gas chromatography-time of flight mass spectrometry was used for the analysis of VOCs in cold-pressed oils and corresponding press cakes obtained after roasting of seeds at 140 and 180 °C prior to pressing. Contents of primary metabolites (amino acids, saccharides, fatty acids) as well as selected secondary metabolites (glucosinolates, polyphenols) were determined, as many of them serve as precursors to volatile compounds formed especially in thermal reactions. After roasting, the formation of Maillard reaction products increased, which corresponded to the reduction of free amino acids and monosaccharides. Moreover, levels of the products of thermal oxidation of fatty acids, such as aldehydes and ketones, increased with the increasing temperature of roasting, although no significant changes were noted for fatty acids. Among sulphur-containing compounds, contents of the products and intermediates of methionine Strecker degradation increased significantly with the increasing temperature of roasting. Degradation of glucosinolates to nitriles occurred after thermal treatment. The results of this study confirmed that seed roasting before cold pressing has a significant effect on the volatiles, but also indicated roasting-induced changes in non-volatile metabolites of oil and press cake. Such an approach helps to understand metabolic changes occurring during rapeseed processing in cold-pressed oil production.
Graphical Abstract
Causes of Increased Use of Closed Reduction and Internal Fixation for High‐Energy‐Related Traumatic Sacral Fractures
Authors: Yu Yi‐Hsun , Tsai Ping‐Jui , Liu Chang‐Heng , Chen I.‐Jung , Hsu Yung‐Heng , Chou Ying‐Chao , Tseng I.‐Chuan 
Published: December 2022

AbstractBackgroundReasons for the increased use of closed reduction and internal fixation (CRIF) for traumatic sacral fractures (SFs) are unclear in the literature. Therefore, we aimed to report the annual changes in the number of patients, mechanisms of injury, fracture patterns, and fixation methods.MethodsIn this retrospective study, we extracted data of 271 patients (mean age, 37.5 years) from the trauma register over an 8‐year period. Annual records regarding the number of patients, injury mechanisms, fracture types, and treatment options were statistically analyzed to examine the interactions among these factors.ResultsThe number of patients with SFs increased significantly each year. The rate of admission to the intensive care unit after resuscitation was high (64.9%). Arbeitsgemeinschaft für Osteosynthesefragen (AO) type C pelvic ring injury (PRI), Dennis zone II injury, Roy‐Camille type 2 injury, and U/H‐type injury were the most common fracture types. Trans‐iliac trans‐sacral screws were mainly used in AO type B PRI, and their use significantly increased each year. For AO type C PRI, open reduction and internal fixation (ORIF) with rigid fixation was the main treatment, and the use of CRIF with iliosacral screws decreased each year. Stepwise statistical analysis revealed that the increase in AO type B PRI and ORIF for anterior PRI were the factors contributing to the increased use of CRIF for SFs.ConclusionsWhile the use of osteosynthesis for SFs is increasing, an increased use of CRIF for traumatic SFs has also been observed in clinical practice. This increase can be attributed to the increase in AO type B PRIs and ORIF for anterior PRIs.
Age class composition and growth of Atlantic cod (Gadus morhua) in the shallow water zone of Kongsfjorden, Svalbard
Authors: Brand Markus , Spotowitz Lisa , Mark Felix Christopher , Berge Jørgen , Langhelle Erlend Lindau , Węsławski Jan Marcin , Godiksen Jane Aanestad , Fischer Philipp 
Published: December 2022

AbstractAlthough Atlantic cod has been observed in Svalbard waters since the 1880s, knowledge about the presence in the Arctic shallow water zone is limited. The regular catch of juvenile Atlantic cod in Kongsfjorden since 2008 is in line with an overall northward shift of boreal fish species toward the Arctic. This is the first study showing the age class composition, growth rates, and stomach content of Atlantic cod in the shallow water zone of Kongsfjorden, Svalbard. From 2012 to 2014 a total of 721 specimens were sampled in 3 to 12 m water depth. The primary age classes were identified as 0+, 1+, and 2+ using otolith age analysis. The different cohorts of these specimens show stable growth rates during the polar day and night. By stomach content analysis, we show that these specimens primarily feed on benthic food sources. These observations support the assumption that the shallow water zone of Kongsfjorden is likely to be a nursery ground for Atlantic cod.
Intralesional Candida albicans antigen versus intralesional zinc sulfate in treatment of cutaneous warts
Authors: Youssef Eman M. Kamal , Eissa Maha A. A. , Bakr Radwa M. 
Published: December 2022

AbstractImmunotherapy represents a promising therapeutic option for treatment of warts. Different concentrations of Candida antigen (1/100 and 1/1000) and zinc sulfate 2% were not previously compared regarding their efficacy in treatment of cutaneous warts. The present study compared the safety and efficacy of intralesional candida antigen versus intralesional 2% zinc sulfate for treatment of cutaneous warts. This prospective controlled clinical trial included one hundred and five patients presented with common, plantar, and plane warts. Patients were divided randomly into three groups, each group included 35 patients. Group 1 were treated with intralesional candida antigen (Ag) 1/100, Group 2 were treated with intralesional candida Ag 1/1000, and Group 3 were treated with intralesional zinc sulfate 2%. This study found that target warts of group 1 displayed higher rate of complete clearance compared to group 2 and group 3 (94.3%, 77.1, 74.2%), respectively. The present study concluded that intralesional immunotherapy with Candida antigen was more effective than Intralesional 2% zinc sulfate in treatment of cutaneous warts and less painful. Clinical trial registration number is (Clinical Trials.gov Identifier: NCT03158168).