bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between food-based dietary inflammatory potential and ulcerative colitis: a case–control study
Authors: Khademi Zeinab , Saneei Parvane , Hassanzadeh-Keshteli Ammar , Daghaghzadeh Hamed , Tavakkoli Hamid , Adibi Peyman , Esmaillzadeh Ahmad 
Published: May 2023

AbstractDespite several studies on the link between dietary inflammatory potential and risk of several conditions, limited studies investigated the association between pro-inflammatory diet and ulcerative colitis (UC). The objective of the present study was to examine the link between food-based dietary inflammatory potential (FDIP) and odds of UC in Iranian adults. This case–control study was carried out among 109 cases and 218 randomly chosen healthy controls. UC was diagnosed and confirmed by a gastroenterologist. Patients with this condition were recruited from Iranian IBD registry. Age- and sex-matched controls were selected randomly from participants of a large cross-sectional study. Dietary data were obtained using a validated 106-item semi-quantitative food frequency questionnaire (FFQ). We calculated FDIP score using subjects’ dietary intakes of 28 pre-defined food groups. In total 67% of subjects were female. There was no significant difference in mean age between cases and controls (39.5 vs. 41.5y; p = 0.12). The median (interquartile range) of FDIP scores for cases and controls were − 1.36(3.25) and − 1.54(3.15), respectively. We found no significant association between FDIP score and UC in the crude model (OR 0.93; 95% CIs 0.53–1.63). Adjustment for several potential confounders in multivariate model did not change this association (OR 1.12; 95% CIs 0.46–2.71). We failed to observe any significant association between greater adherence to a pro-inflammatory diet and risk of UC in this study. Prospective cohort studies are needed to further assess this relationship.
New evidence for the Ontong Java Nui hypothesis
Authors: Tejada M. L. G. , Sano T. , Hanyu T. , Koppers A. A. P. , Nakanishi M. , Miyazaki T. , Ishikawa A. , Tani K. , Shimizu S. , Shimizu K. , Vaglarov B. , Chang Q. 
Published: May 2023

AbstractThe formation of the Ontong Java Nui super oceanic plateau (OJN), which is based on the model that the submarine Ontong Java Plateau (OJP), Manihiki Plateau (MP), and Hikurangi Plateau (HP) were once its contiguous fragments, could have been the largest globally consequential volcanic event in Earth’s history. This OJN hypothesis has been debated given the paucity of evidence, for example, the differences in crustal thickness, the compositional gap between MP and OJP basalts and the apparent older age of both plateaus relative to HP remain unresolved. Here we investigate the geochemical and 40Ar-39Ar ages of dredged rocks recovered from the OJP’s eastern margin. Volcanic rocks having compositions that match the low-Ti MP basalts are reported for the first time on the OJP and new ~ 96–116 Ma and 67–68 Ma 40Ar-39Ar age data bridge the temporal gap between OJP and HP. These results provide new evidence for the Ontong Java Nui hypothesis and a framework for an integrated tectonomagmatic evolution of the OJP, MP, and HP. The isotopic data imply four mantle components in the source of OJN that are also expressed in present-day Pacific hotspots sources, indicating origin from (and longevity of) the Pacific Large Low Shear-wave Velocity Province.
Development of a calculated panel reactive antibody calculator for the United Arab Emirates: a proof of concept study
Authors: Alvares Marion , Anwar Siddiq , Hashmi Shahrukh K. , Zaman Muhammad Badar , Al Mahri Ayeda , Alvares Christabelle , Al Katheeri Layla , Purushothaman Ananthanayagi , Ralonya Mesele Emily , Sangalang Marie Glo , Jannang Raysha , Abdulle Abdulkadir , Al Qubaisi Alyazia , Al Ahmed Maitha , Khamis Amar Hassan , Al Seiari Mohamed , Al Obaidli Ali , Al Yafei Zain , ElGhazali Gehad 
Published: May 2023

AbstractCalculated panel reactive antibody (CPRA) is used to help increase sensitized patient’s access to transplantation. United Arab Emirates (UAE) has a diverse resident population hence we developed a UAE–CPRA calculator based on HLA antigen frequencies of the different ethnic groups that represent the UAE population. HLA antigen frequencies at serological split antigen level for HLA-A, -B, -C, -DRB1 and -DQB1 of 1002 healthy unrelated donors were performed. We subsequently compared the performance of the UAE CPRA calculator with the Organ Procurement and Transplantation Network (OPTN) and the Canadian CPRA calculators in 110 Kidney Transplant waitlist patients from January 2016 to December 2018. Lin’s concordance correlation coefficient showed a moderate agreement between the UAE and OPTN calculator (Rc = 0.949, 95% CI 0.929–0.963) and the UAE and Canadian calculators (Rc = 0.952, 95% CI 0.932–0.965). While there continued to be a moderate agreement (Rc = 0.937, UAE versus OPTN calculator) in the lower sensitized group, a poor agreement (Rc = 0.555, UAE versus OPTN calculator) was observed in the higher sensitized group. In this study, we provide a template for countries to develop their own population-specific CPRA calculator. Implementation of the CPRA algorithm based on HLA frequencies of the multi-ethnic UAE population will be more fitting to increase access to transplantation and improve transplant outcomes. Our study demonstrates that the CPRA calculators developed using the data from the western population had poor correlation in our higher sensitized patients disadvantaging them in potential organ allocations systems. We plan to further refine this calculator by using high resolution HLA typing to address the problem of a genetically diverse population.
Transcriptomic and metabolic studies on the role of inorganic and organic iodine compounds in lettuce plants
Authors: Smoleń Sylwester , Czernicka Małgorzata , Kęska-Izworska Kinga , Kowalska Iwona , Grzebelus Dariusz , Pitala Joanna , Halka Mariya , Skoczylas Łukasz , Tabaszewska Małgorzata , Liszka-Skoczylas Marta , Grzanka Marlena , Ledwożyw-Smoleń Iwona , Koronowicz Aneta , Krzemińska Joanna , Sularz Olga , Kiełbasa Daniel , Neupauer Jakub , Kováčik Peter 
Published: May 2023

AbstractIodine (I) is considered a beneficial element or even micronutrient for plants. The aim of this study was to determine the molecular and physiological processes of uptake, transport, and metabolism of I applied to lettuce plants. KIO3, KIO3 + salicylic acid, 5-iodosalicylic acid and 3,5-diiodosalicylic acid were applied. RNA-sequencing was executed using 18 cDNA libraries constructed separately for leaves and roots from KIO3, SA and control plants. De novo transcriptome assembly generated 1937.76 million sequence reads resulting in 27,163 transcripts with N50 of 1638 bp. 329 differentially expressed genes (DEGs) in roots were detected after application of KIO3, out of which 252 genes were up-regulated, and 77 were down-regulated. In leaves, 9 genes revealed differential expression pattern. DEGs analysis indicated its involvement in such metabolic pathways and processes as: chloride transmembrane transport, phenylpropanoid metabolism, positive regulation of defense response and leaf abscission, and also ubiquinone and other terpenoid-quinone biosynthesis, protein processing in endoplasmic reticulum, circadian rhythm including flowering induction as well as a putative PDTHA (i.e. Plant Derived Thyroid Hormone Analogs) metabolic pathway. qRT-PCR of selected genes suggested their participation in the transport and metabolism of iodine compounds, biosynthesis of primary and secondary metabolites, PDTHA pathway and flowering induction.
Simple combination of multiple somatic variant callers to increase accuracy
Authors: Trevarton Alexander J. , Chang Jeffrey T. , Symmans W. Fraser 
Published: May 2023

AbstractPublications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior standard, combinations or ensembles of variant callers have appeared in the literature. In this study, a whole genome somatic reference standard was used to derive principles to guide strategies for combining variant calls. Then, manually annotated variants called from the whole exome sequencing of a tumor were used to corroborate these general principles. Finally, we examined the ability of these principles to reduce noise in targeted sequencing.
Effect of modified waste introduction methods over short-term and long-term use of onsite sanitation systems
Authors: Astete Vasquez L. , Mladenov N. 
Published: May 2023

AbstractInsufficiently treated wastes contained within onsite sanitation systems (OSS) commonly used by disadvantaged and developing communities contribute to public and environmental health concerns, calling for practical alternative solutions. At the basic level, an improved understanding of the evolution of chemical and physical constituents under different waste introduction methods and for short-term and long-term operation is needed. While receiving non-dilute waste under mixed, unmixed, toilet paper exclusion, and urine diversion (UD) regimes, self-flushing OSS simulated using anaerobic digesters (ADs) were compared during three operational stages: (1) 0–1 month service for unsheltered encampments; (2) 1–3 month disaster relief scenario; and (3) ≥ 3 months representing refugee camps and long-term household use. Although stratification was found to promote suitable conditions for short-term use of self-flushing toilets, mixing increased beneficial biodegradation of organic constituents. Urine-containing ADs demonstrated a shift from sulfide to ammonia odor accompanied by high pH (> 8) after ~ 240 d. E. coli reduction following elevated nitrogen and dissolved solids levels pointed to decreased pathogen survival in ADs with urine. The benefits of bacterial disinfection, reduction of sulfurous odors, and heightened organics degradation in mixed, urine-containing ADs suggest this format as more desirable for prolonged use of self-flushing OSS over unmixed or urine-diverting formats.
Unravelling the resilience of the KGK VI population from the Gumelnița site (Romania) through stable isotopes
Authors: García-Vázquez Ana , Bălășescu Adrian , Vasile Gabriel , Golea Mihaela , Radu Valentin , Opriș Vasile , Ignat Theodor , Culea Mihaela , Covătaru Cristina , Sava Gabriela , Lazăr Cătălin 
Published: May 2023

AbstractThe Gumelnița site belongs to the Kodjadermen-Gumelnița-Karanovo VI (KGK VI) communities (c. 4700–3900 cal BC) and comprises the tell-type settlement and its corresponding cemetery. This paper reconstructs the diet and lifeways of the Chalcolithic people in the northeastern Balkans using archaeological remains found at the Gumelnița site (Romania). A multi-bioarchaeological investigation (archaeobotany, zooarchaeology, anthropology) was conducted on vegetal, animal, and human remains, alongside radiocarbon dating and stable isotope analyses (δ13C, δ15N) of humans (n = 33), mammals (n = 38), reptiles (n = 3), fishes (n = 8), freshwater mussels shells (n = 18), and plants (n = 24). According to the results of δ13C and δ15N values and FRUITS, the inhabitants of Gumelnița had a diet based on crops and using natural resources, such as fish, freshwater molluscs and game. Although domestic fauna was occasionally exploited for meat, it had a role in providing secondary products. Crops were heavily manured, and chaff and other crop waste may have been necessary fodder for cattle and sheep. Dogs and pigs fed on human waste, although the diet of the latter is more similar to that of wild boars. Foxes had a diet close to dogs, which may indicate synanthropic behaviour. Radiocarbon dates were calibrated with the percentage of freshwater resources obtained by FRUITS. As a result, the corrected dates for the freshwater reservoir effect (FRE) have a delay of an average of 147 years. According to our data, this agrarian community developed a subsistence strategy under the pressure of some climatic changes that started after 4300 cal BC, corresponding to KGK VI rapid collapse/decline episode tracked recently (that begins around 4350 cal BC). This matching of our data in the two models (climatic and chrono-demographic) allowed us to capture the economic strategies that led to the resilience of those people more than other contemporary KGK VI communities.
The nonlinear energy model and stress–strain model of sandstone
Authors: Zheng Zhiming , Yang Yu , Pan Cheng 
Published: May 2023

AbstractThe relationship between strain and elastic energy is simplified by introducing a stress state parameter based on the generalised Hooke’s law. It is assumed that the micro-element strengths satisfy the Weibull distribution and a new model for the non-linear evolution of energy is developed by introducing the concept of rock micro-element strengths. A sensitivity analysis of the model parameters is carried out on this basis. The results show that the model agrees well with the experimental data. The model is close to the deformation and damage laws of the rock and is able to reflect the relationship between the elastic energy and strain of the rock. By comparing with other model curves, the model of this paper is more suitable for the experimental curve. They show that the improved model could better describe the stress–strain relationship of rock. Finally, according to the analysis of the influence of the distribution parameter on the variation pattern of the elastic energy of the rock, the magnitude of the distribution parameter can directly reflect the peak energy of the rock.
Uric acid level in climacteric women and its association with clinical and metabolic parameters
Authors: Cota e Souza Laura Alves , D’Angelo Georgia Carvalho de Oliveira , da Silva Glenda Nicioli , Lima Angélica Alves 
Published: May 2023

AbstractClimacteric women often experience unfavorable metabolic changes. Consequently, identifying markers that may contribute to such undesirable changes is imperative. This study aimed to evaluate serum uric acid (UA) concentration and its association with metabolic and clinical parameters in climacteric women. We selected 672 women between 40 and 65 years and performed interviews, biochemical analyses, blood pressure, and anthropometric measurements. UA levels were determined using the enzymatic-colorimetric method. We compared variables according to the quartiles of UA using the Kruskal–Wallis test. The mean UA level was 4.9 ± 1.5 mg/dl, ranging from 2.0 to 11.6 mg/dl. We found that UA levels greater than 4.8 mg/dl were associated with adverse metabolic parameters in climacteric women. For all anthropometric and biochemical variables, we observed significantly better results in women who had lower UA levels (p < 0.05). Similarly, we observed a significant increase in blood pressure, frequency of metabolic syndrome, and cardiovascular risk as UA levels increased (p < 0.05). Our findings showed that climacteric women with high levels of UA were more likely to have adverse metabolic and clinical parameters than those with lower UA levels. Further studies may determine the causal relationship between UA and metabolic changes in climacteric women.
Effect of far-infrared radiation on inhibition of colonies on packaging during storage of sterilised surgical instruments
Authors: Fann Li-Yun , Cheng Chih-Chien , Chien Yung-Chen , Hsu Cheng-Wei , Chien Wu-Chien , Huang Yao-Ching , Chung Ren-Jei , Huang Shi-Hao , Jiang Ying-Hua , Yin Shih-Han , Cheng Kai-Wen , Wu Yi-Ping , Hsiao Sheng-Huang , Hsu Shao-Yuan , Huang Ying-Che , Chu Chi-Ming 
Published: May 2023

AbstractThe sterilisation of surgical instruments is a major factor in infection control in the operating room (OR). All items used in the OR must be sterile for patient safety. Therefore, the present study evaluated the effect of far-infrared radiation (FIR) on the inhibition of colonies on packaging surface during the long-term storage of sterilised surgical instruments. From September 2021 to July 2022, 68.2% of 85 packages without FIR treatment showed microbial growth after incubation at 35 °C for 30 days and at room temperature for 5 days. A total of 34 bacterial species were identified, with the number of colonies increasing over time. In total, 130 colony-forming units were observed. The main microorganisms detected wereStaphylococcusspp. (35%) andBacillusspp. (21%) ,Kocuria marinaandLactobacillusspp. (14%), and mould (5%). No colonies were found in 72 packages treated with FIR in the OR. Even after sterilisation, microbial growth can occur due to movement of the packages by staff, sweeping of floors, lack of high-efficiency particulate air filtration, high humidity, and inadequate hand hygiene. Thus, safe and simple far-infrared devices that allow continuous disinfection for storage spaces, as well as temperature and humidity control, help to reduce microorganisms in the OR.
Subpopulations of hypocretin/orexin neurons differ in measures of their cell proliferation, dynorphin co-expression, projections, and response to embryonic ethanol exposure
Authors: Yasmin Nushrat , Collier Adam D. , Karatayev Olga , Abdulai Abdul R. , Yu Boyi , Fam Milisia , Khalizova Nailya , Leibowitz Sarah F. 
Published: May 2023

AbstractNumerous studies in animals demonstrate that embryonic exposure to ethanol (EtOH) at low-moderate doses stimulates neurogenesis and increases the number of hypothalamic neurons expressing the peptide, hypocretin/orexin (Hcrt). A recent study in zebrafish showed that this effect on the Hcrt neurons in the anterior hypothalamus (AH) is area specific, evident in the anterior (aAH) but not posterior (pAH) part of this region. To understand specific factors that may determine the differential sensitivity to EtOH of these Hcrt subpopulations, we performed additional measures in zebrafish of their cell proliferation, co-expression of the opioid dynorphin (Dyn), and neuronal projections. In association with the increase in Hcrt neurons in the aAH but not pAH, EtOH significantly increased only in the aAH the proliferation of Hcrt neurons and their number lacking Dyn co-expression. The projections of these subpopulations differed markedly in their directionality, with those from the pAH primarily descending to the locus coeruleus and those from the aAH ascending to the subpallium, and they were both stimulated by EtOH, which induced specifically the most anterior subpallium-projecting Hcrt neurons to become ectopically expressed beyond the aAH. These differences between the Hcrt subpopulations suggest they are functionally distinct in their regulation of behavior.
Fabrication of plane-type axon guidance substrates by applying diamond-like carbon thin film deposition
Authors: Ban Masahito , Chen Jing 
Published: May 2023

AbstractThis research aims to fabricate plane-type substrates for evaluating the axon behaviors of neuronal cells in vitro toward the development of brain-on-chip models by applying the functions of diamond-like carbon (DLC) thin film deposition, which helped to eliminate the costly and time-consuming lithography process by utilizing a shadow mask. The DLC thin films were partially deposited on stretched polydimethylsiloxane (PDMS) substrates covered with a metal mask by the plasma chemical vaper deposition method, and using the substrates culture teats with human neuroblastoma cells (SH-SY5Y) were performed. Three patterns of interconnection structures of axons were created on the substrates with disordered and regular linear wrinkle structures with several μm size formed by the depositions. The patterns were characterized by the structure that the aggregations of axons formed on the linear DLC thin film deposited areas were separately placed in regular intervals and connected each other by plenty of axons, which were individually taut in a straight line at about 100 to over 200 μm in length. The substrates expected of uses for evaluation of axon behaviors are available without fabricating guiding grooves by conventional soft lithographic methods requiring multiple stages and their treating times.
The distribution and diversity of eukaryotic phytoplankton in the Icelandic marine environment
Authors: Cerfonteyn Mia , Groben René , Vaulot Daniel , Guðmundsson Kristinn , Vannier Pauline , Pérez-Hernández María Dolores , Marteinsson Viggó Þór 
Published: May 2023

AbstractPhytoplankton play a crucial role in the marine food web and are sensitive indicators of environmental change. Iceland is at the center of a contrasting hydrography, with cold Arctic water coming in from the north and warmer Atlantic water from the south, making this geographical location very sensitive to climate change. We used DNA metabarcoding to determine the biogeography of phytoplankton in this area of accelerating change. Seawater samples were collected in spring (2012–2018), summer (2017) and winter (2018) together with corresponding physico-chemical metadata around Iceland. Amplicon sequencing of the V4 region of the 18S rRNA gene indicates that eukaryotic phytoplankton community composition is different between the northern and southern water masses, with some genera completely absent from Polar Water masses. Emiliania was more dominant in the Atlantic-influenced waters and in summer, and Phaeocystis was more dominant in the colder, northern waters and in winter. The Chlorophyta picophytoplankton genus, Micromonas, was similarly dominant to the dominant diatom genus, Chaetoceros. This study presents an extensive dataset which can be linked with other 18s rRNA datasets for further investigation into the diversity and biogeography of marine protists in the North Atlantic.
Chemical modification of AAV9 capsid with N-ethyl maleimide alters vector tissue tropism
Authors: Mulcrone Patrick L. , Lam Anh K. , Frabutt Dylan , Zhang Junping , Chrzanowski Matthew , Herzog Roland W. , Xiao Weidong 
Published: May 2023

AbstractAlthough more adeno-associated virus AAV-based drugs enter the clinic, vector tissue tropism remains an unresolved challenge that limits its full potential despite that the tissue tropism of naturally occurring AAV serotypes can be altered by genetic engineering capsid vie DNA shuffling, or molecular evolution. To further expand the tropism and thus potential applications of AAV vectors, we utilized an alternative approach that employs chemical modifications to covalently link small molecules to reactive exposed Lysine residues of AAV capsids. We demonstrated that AAV9 capsid modified with N-ethyl Maleimide (NEM) increased its tropism more towards murine bone marrow (osteoblast lineage) while decreased transduction of liver tissue compared to the unmodified capsid. In the bone marrow, AAV9-NEM transduced Cd31, Cd34, and Cd90 expressing cells at a higher percentage than unmodified AAV9. Moreover, AAV9-NEM localized strongly in vivo to cells lining the calcified trabecular bone and transduced primary murine osteoblasts in culture, while WT AAV9 transduced undifferentiated bone marrow stromal cells as well as osteoblasts. Our approach could provide a promising platform for expanding clinical AAV development to treat bone pathologies such as cancer and osteoporosis. Thus, chemical engineering the AAV capsid holds great potential for development of future generations of AAV vectors.