bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre‐isolation Molecular Screening for High‐throughput Sampling and Sequencing of Bacterial Microbes from the Environment
Authors: Wee Soon Keong , Chan Mark Boon Pho , Sivalingam Suppiah Paramalingam , Yap Eric Peng Huat 
Published: May 2023

AbstractEnvironmental studies often require culture and characterization to understand the prevalence, distribution, persistence and functions of target microorganisms in ecological habitats. Isolating pure microbiological monocultures allows the phenotypic characterization of microorganisms to study their functional properties. For efficient isolation of low‐prevalence organisms, enrichment followed by PCR screening is performed to identify positive samples for subsequent culture. Molecular characterization, strain‐typing, and genotyping of isolated microorganisms is best comprehensively performed using whole‐genome sequencing. This article outlines end‐to‐end protocols for screening, isolation, and sequencing of microbes from environmental samples. We provide systematic methods for environmental study design, enrichment, screening, and isolation of target microorganisms. Species identification is performed using qPCR or MALDI‐TOF MS. Genomic DNA is extracted for whole‐genome sequencing using the Oxford Nanopore platform. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Designing and conducting an environmental soil sampling studyBasic Protocol 2: Enrichment of microbes from environmental soil samplesAlternate Protocol 1: Collection and enrichment of microbes from environmental water samplesBasic Protocol 3: Screening of enriched samples by direct qPCRBasic Protocol 4: Enumeration and isolation of enriched samples using selective mediumBasic Protocol 5: Species confirmation using colony qPCRAlternate Protocol 2: Species identification using a MALDI‐TOF MS BiotyperAlternate Protocol 3: Species identification of bacterial isolates using universal PCR primers and Sanger sequencingBasic Protocol 6: Cryostorage of bacterial isolatesBasic Protocol 7: Extraction of genomic DNABasic Protocol 8: Quality check of extracted genomic DNABasic Protocol 9: Whole‐genome sequencing using the Oxford Nanopore MinION Platform
Molecular analysis and comparison of CD34+ and CD133+ very small embryonic‐like stem cells purified from umbilical cord blood
Authors: Bujko Kamila , Ciechanowicz Andrzej K. , Kucia Magdalena , Ratajczak Mariusz Z. 
Published: May 2023

AbstractVery small embryonic like stem cells (VSELs) are a dormant population of stem cells that, as proposed, are deposited during embryogenesis in various tissues, including bone marrow (BM). These cells are released under steady state conditions from their tissue locations and circulate at a low level in peripheral blood (PB). Their number increases in response to stressors as well as tissue/organ damage. This increase is evident during neonatal delivery, as delivery stress prompts enrichment of umbilical cord blood (UCB) with VSELs. These cells could be purified from BM, PB, and UCB by multiparameter sorting as a population of very small CXCR4+Lin−CD45− cells that express the CD34 or CD133 antigen. In this report, we evaluated a number of CD34+Lin−CD45− and CD133+Lin−CD45− UCB‐derived VSELs. We also performed initial molecular characterization of both cell populations for expression of selected pluripotency markers and compared these cells at the proteomic level. We noticed that CD133+Lin−CD45− population is more rare and express, at a higher level, mRNA for pluripotency markers Oct‐4 and Nanog as well as the stromal‐derived factor‐1 (SDF‐1) CXCR4 receptor that regulates trafficking of these cells, however both cells population did not significantly differ in the expression of proteins assigned to main biological processes.
Leaf volatile and nonvolatile metabolites show different levels of specificity in response to herbivory
Authors: Mezzomo Priscila , Weinhold Alexander , Aurová Klára , Jorge Leonardo R. , Kozel Petr , Michálek Jan , Nováková Nela , Seifert Carlo L. , Volfová Tereza , Engström Marica , Salminen Juha‐Pekka , Sedio Brian E. , Volf Martin 
Published: May 2023

AbstractPlants produce diverse chemical defenses with contrasting effects on different insect herbivores. Deploying herbivore‐specific responses can help plants increase their defensive efficiency. Here, we explore how variation in induced plant responses correlates with herbivore species, order, feeding guild, and level of specialization. In a greenhouse experiment, we exposed 149 plants of Salix fragilis (Linnaeus, 1753) to 22 herbivore species naturally associated with this host. The insects belonged to four orders (Coleoptera, Lepidoptera, Hemiptera, and Hymenoptera), three feeding guilds (external leaf‐chewers, leaf‐tying chewers, and sap‐sucking), and included both dietary specialists and generalists. Following herbivory, we quantified induced changes in volatiles and nonvolatile leaf metabolites. We performed multivariate analyses to assess the correlation between herbivore order, feeding guild, dietary specialization, chewing damage by herbivores, and induced responses. The volatile composition was best explained by chewing damage and insect order, with Coleoptera and Lepidoptera eliciting significantly different responses. Furthermore, we recorded significant differences in elicited volatiles among some species within the two orders. Variation in nonvolatile leaf metabolites was mainly explained by the presence of insects, as plants exposed to herbivores showed significantly different metabolites from controls. Herbivore order also played a role to some extent, with beetles eliciting different responses than other herbivores. The induction of volatile and nonvolatile leaf metabolites shows different levels of specificity. The specificity in volatiles could potentially serve as an important cue to specialized predators or parasitoids, increasing the efficacy of volatiles as indirect defenses. By contrast, the induction of nonvolatile leaf metabolites was largely unaffected by herbivore identity. Most nonvolatile metabolites were downregulated, possibly indicating that plants redirected their resources from leaves in response to herbivory. Our results demonstrate how diverse responses to herbivores can contribute to the diversity of plant defensive strategies.
Exploring paths and innovation in Norwegian carbon capture and storage policy
Authors: Wettestad Jørgen , Inderberg Tor Håkon Jackson , Gulbrandsen Lars H. 
Published: May 2023

AbstractNorway, a significant petroleum producer and exporter, has been a frontrunner within policies for carbon capture and storage (CCS). As CCS is recognized as a key technology for achieving the Paris climate policy targets, there is a clear need for more knowledge about how to design successful projects. Norway's first CCS policy initiative, the ambitious Mongstad project, was the result of a political compromise that was imposed from above, basically with one single company in control. The project was largely seen as a failure and was terminated in 2013. However, instead of dropping ambitions for developing CCS projects, the authorities launched a new policy soon afterwards. This policy evolved with the differently organized Longship CCS project as its core. Using a path‐dependency perspective, we find that established institutional structures from the Mongstad project, combined with national interests and expertise, help to explain the fundamental continuity of CCS policies in Norway. This explanation is supplemented by a policy‐learning perspective, which helps to explain policy changes and differences between the two flagship CCS projects. The Longship project developed gradually ‘from below’; linked project responsibilities close to competences and interests; dealt with key risks separately to reduce the inherent complexity; and organized clear requirements up front. We hold that this way of designing CCS projects is of relevance to other countries considering CCS projects. Furthermore, by placing the Norwegian case in context of the development of EU and international climate policy we contribute a theoretical framework relevant also for subsequent research.
Adrenomedullin peptides and precursor levels in relation to haemodynamics and prognosis after heart transplantation
Authors: Ahmed Abdulla , Kania Kriss , Abdul Rahim Hebba , Ahmed Salaheldin , Rådegran Göran 
Published: May 2023

AbstractAimsHeart failure (HF) is a frequent condition in the elderly, further complicated by associated pulmonary hypertension (PH), with impact on morbidity and mortality. Plasma proteins associated with cardiovascular disease, related to inflammation, neurohormonal changes, and myocyte stress, pathways recognized in the pathophysiology of HF, may provide information on disease severity and prognosis. We aimed to investigate such cardiovascular proteins and their relationship to haemodynamics before and 1 year after heart transplantation (HT), as well as their prognostic value in advanced HF with PH.Methods and resultsIn 20 healthy controls and 67 patients with HF and PH, before and 1 year after HT, N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) and 18 cardiovascular proteins were analysed with proximity extension assay. Right heart catheterization was used to measure the haemodynamics of the HF patients pre‐operatively and at 1 year follow‐up after HT. Prognosis was estimated using Kaplan–Meier and Cox regression analyses. Out of 18 plasma proteins, 11 proteins including adrenomedullin peptides and precursor levels (ADM) and protein suppression of tumourigenicity 2 receptor were elevated before HT compared with healthy controls and had decreased 1 year after HT. The decrease in plasma levels 1 year after HT was towards the healthy controls' levels. The decrease in ADM levels before vs. after HT correlated with decreased mean right atrial pressure (rs = 0.61; P = 0.0077), decreased NT‐proBNP (rs = 0.75; P = 0.00025), and decreased stroke volume index (rs = −0.52; P = 0.022). High levels of pre‐operative plasma ADM were associated with worse event‐free survival (HT or death), as well as survival compared with low ADM levels (log‐rank P value = 0.023 and 0.0225, respectively). Univariable Cox regression analysis demonstrated that ADM levels were associated with survival, hazard ratio (HR) 1.007 (95% confidence interval (CI): 1.00–1.015, P = 0.049), and the association remained after adjusting for NT‐proBNP, HR 1.01 (95% CI: 1.00–1.021, P = 0.041).ConclusionsElevated plasma levels of ADM may be a marker of pressure/volume overload in HF patients with PH, as well as long‐term prognosis after HT. In line with previous studies, our findings additionally confirm that ADM may be a marker of venous congestion in HF. Further studies are encouraged to establish a deeper understanding of the properties of ADM and its relationship with HF and PH, in order to potentially facilitate clinical management of HF and associated PH.
How did the female fetus speak? Abortion, sex selection, and national futures in India
Authors: Saha Roy Sayantan 
Published: May 2023

AbstractThe debate around abortion is often constituted in terms of a tension between fetal personhood on the one hand and the right to bodily autonomy on the other. The supposed personhood of the fetus is widely invoked to restrict the right to abortion. In India however, one sees a paradoxical situation. Not only is there wide legal access to abortion, but this also exists simultaneously with an active legal imperative to protect the female fetus. How did the Indian state allow access to abortion while protecting a unique fetus? This paper argues that the question of reproduction and abortion in India is intimately tied to imaginations of national futures and risks and reproductive bodies have been entangled in those futures. The discourse around the legalization of abortion and the criminalization of sex‐selection offered differing but stark visions of national endangerment which played a critical role in authorizing different state actions targeting reproductive bodies while sustaining this paradox. This paper expands the anthropological understanding of the different grounds of abortion debates globally.
Acrylamide‐induced autophagy‐lysosomal pathway dysfunction contributing to neurotoxicity through targeting transcription factor EB
Authors: Yang Liuqing , Dong Li , Zhang Lujia , Li Daotong , Luo Yinghua , Chen Fang 
Published: May 2023

AbstractAutophagy‐lysosomal pathway (ALP), a lysosome‐mediated self‐renewal process, is crucial for cell survival and death. Acrylamide (AA) is a neurotoxic compound produced during food thermal processing, and the mechanism underlying AA‐induced neurotoxicity remains elusive. In this study, we explored whether dysregulated ALP was involved in AA‐induced neurotoxicity and the underlying mechanism. We first evaluated the toxic effects of AA on the activation of apoptosis and NLRP3 pathway in human glioma U251 cells. We found that AA‐induced autophagy activation with the accumulation of an autophagy substrate P62, which implies the occurrence of autophagy‐lysosomal disorders. By using autophagy agonist PP242 and siRNA interfering ATG5, we demonstrated that ALP dysregulation contributed to AA‐induced apoptosis and NLRP3 inflammasome pathway activation. In addition, AA triggered ALP dysfunction by decreasing the expression of transcription factor EB (TFEB), and TFEB overexpression restored the lysosomal‐associated proteins and protected against AA‐induced apoptosis and inflammasome activation. Moreover, the autophagy agonist rapamycin restored AA‐induced ALP dysfunction by upregulating TFEB and prevented neurotoxicity. Overall, our study provides novel insights into the role of disrupted ALP in AA‐induced neurotoxicity and highlights that TFEB can be developed as a promising intervention target against AA‐induced neurotoxicity.
OpenMindat: Open and FAIR mineralogy data from the Mindat database
Authors: Ma Xiaogang , Ralph Jolyon , Zhang Jiyin , Que Xiang , Prabhu Anirudh , Morrison Shaunna M. , Hazen Robert M. , Wyborn Lesley , Lehnert Kerstin 
Published: May 2023

AbstractThe open data movement has brought revolutionary changes to the field of mineralogy. With a growing number of datasets made available through community efforts, researchers are now able to explore new scientific topics such as mineral ecology, mineral evolution and new classification systems. The recent results have shown that the necessary open data coupled with data science skills and expertise in mineralogy will lead to impressive new scientific discoveries. Yet, feedback from researchers also reflects the needs for better FAIRness of open data, that is, findable, accessible, interoperable and reusable for both humans and machines. In this paper, we present our recent work on building the open data service of Mindat, one of the largest mineral databases in the world. In the past years, Mindat has supported numerous scientific studies but a machine interface for data access has never been established. Through the OpenMindat project we have achieved solid progress on two activities: (1) cleanse data and improve data quality, and (2) build a data sharing platform and establish a machine interface for data query and access. We hope OpenMindat will help address the increasing data needs from researchers in mineralogy for an internationally recognized authoritative database that is fully compliant with the FAIR guiding principles and helps accelerate scientific discoveries.
Effect of obesity on outcomes after open laryngeal surgery including total laryngectomy: A NSQIP database analysis
Authors: Chen Tiffany , Meng Marvin L. , Hong Ellen M. , Durrant Frederick , Talmor Guy , Park Richard Chan Woo , Benson Brian 
Published: May 2023

AbstractBackgroundThe impact of obesity on outcomes after open laryngeal surgery has not been well‐described.MethodsThe NSQIP database was queried for all open laryngeal surgeries including total laryngectomies between 2005 and 2018. Outcomes of patients identified as obese or nonobese by BMI were compared.ResultsOf 1865 patients, 20.1% classified as obese. The most common operation performed was total laryngectomy with or without radical neck dissection (73.2%). Operation time and length of hospital stay were significantly less for obese patients. On multivariate analysis, obesity was associated with less bleeding transfusions occurrences (aOR, 0.395, p = 0.0052), surgical complications (aOR, 0.604, p < 0.001), and any complication (aOR, 0.730, p = 0.0019).ConclusionThough there may be an inverse association of obesity with complications and bleeding transfusion occurrences, as well as decreased operation time and length of hospital stay, several confounders and bias may exist; therefore, it is difficult to conclude that the obesity paradox is present.
A numerical study integrated with RSM for hydrothermal and entropy performance of porous jet impingement
Authors: Al‐damook Amer , Azzawi Itimad D. J. 
Published: May 2023

AbstractThe thermohydraulic and thermodynamic performance of porous jet impingement under pressure drop effect has not yet been jointly published. Thus, the novelty of this work computationally along with the response surface methodology (RSM) optimization approach considers the porous jet impingement performance linked with a pressure drop simultaneously. Also, the current study used a novel multiobjective optimum design study for various design parameters, such as porosity (ε), Darcy number (Da), and pore per inch (PPI), under numerical simulation assessment of forced laminar convection of jet impingement with full and partial metal foam. The influence of various base plate thicknesses (t = 0, 1, 2, and 3 mm), various nanofluids (Al2O3, CuO, SiO2, and ZnO), and the metal foam size percentage (W/L = 0, 0.25, 0.5, 0.75, and 1) on the improvement of the thermohydraulic and thermodynamic performance is also simulated. Results indicated that utilizing pure water and a metal foam size (W/L) of 1 along with a base plate thickness of 0 mm produced the preferable thermohydraulic and thermodynamic performance. Furthermore, according to an optimization analysis, the current study's objective for the thermohydraulic and thermodynamic performance of jet impingement can be achieved using the parameters porosity ε = 0.1, Darcy number, Da = 1, and the PPI = 15. Therefore, this investigation integrating computational fluid dynamics and RSM offers considerable innovation and useful reference for the optimum design of a porous jet impingement cooling.
A phase II trial of nifurtimox combined with topotecan and cyclophosphamide for refractory or relapsed neuroblastoma and medulloblastoma
Authors: Eslin Don , Zage Peter E. , Bergendahl Genevieve , Lewis Elizabeth , Roberts William , Kraveka Jacqueline , Mitchell Deanna , Isakoff Michael S. , Rawwas Jawhar , Wada Randal K. , Fluchel Mark , Brown Valerie I. , Ginn Kevin , Higgins Timothy , BeeravallyNagulapally Abhinav , Dykema Karl , Hanna Gina , Ferguson William , Saulnier Sholler Giselle L. 
Published: May 2023

AbstractChildren with relapsed/refractory (R/R) neuroblastoma (NB) and medulloblastoma (MB) have poor outcomes. We evaluated the efficacy of nifurtimox (Nfx) in a clinical trial for children with R/R NB and MB. Subjects were divided into three strata: first relapse NB, multiply R/R NB, and R/R MB. All patients received Nfx (30 mg/kg/day divided TID daily), Topotecan (0.75 mg/m2/dose, days 1‐5) and Cyclophosphamide (250 mg/m2/dose, days 1‐5) every 3 weeks. Response was assessed after every two courses using International Neuroblastoma Response Criteria and Response Evaluation Criteria in Solid Tumors (RECIST) criteria. One hundred and twelve eligible patients were enrolled with 110 evaluable for safety and 76 evaluable for response. In stratum 1, there was a 53.9% response rate (CR + PR), and a 69.3% total benefit rate (CR + PR + SD), with an average time on therapy of 165.2 days. In stratum 2, there was a 16.3% response rate, and a 72.1% total benefit rate, and an average time on study of 158.4 days. In stratum 3, there was a 20% response rate and a 65% total benefit rate, an average time on therapy of 105.0 days. The most common side effects included bone marrow suppression and reversible neurologic complications. The combination of Nfx, topotecan and cyclophosphamide was tolerated, and the objective response rate plus SD of 69.8% in these heavily pretreated populations suggests that this combination is an effective option for patients with R/R NB and MB. Although few objective responses were observed, the high percentage of stabilization of disease and prolonged response rate in patients with multiply relapsed disease shows this combination therapy warrants further testing.
Management of large paravaginal hematomas with the Zhukovsky vaginal catheter
Authors: Barinov Sergey , Di Renzo Gian Carlo , Kadtsyna Тatyana , Nadezhina Еvgenia , Lazareva Оksana , Kochev Dmitry 
Published: May 2023

AbstractObjectiveTo ameliorate the treatment of large paravaginal hematomas postpartum using the Zhukovsky vaginal catheter.MethodsA retrospective, controlled study including puerperas with large paravaginal hematomas. To assess the effectiveness of the proposed treatment, a group of patients underwent traditional obstetric surgery. A second group of puerperas underwent an integrated approach: the surgical stage (pararectal incision) and the application of the Zhukovsky vaginal catheter. The effectiveness of treatment was assessed according to the following criteria: blood loss volume and hospital admission time.ResultsIn total, 30 puerperas were included in the study; 15 in each treatment group. Large paravaginal hematomas were reported most often in primiparas (50.0%), in 36.7% were combined with rupture of the vagina and the cervix, and in 10.0% of cases an episiotomy was performed during delivery. In 40.0% of primiparas, the blood loss volume was more than 1000 mL, whereas in multiparous and in multiple pregnancies, blood loss did not exceed 1000 mL (r = –0.49; P = 0.022). In 25.0% of puerperas with a blood loss of up to 1000 mL there were no obstetric injuries; in the group with a blood loss of more than 1000 mL, 83.3% of patients had obstetric injuries. An integrated approach reduced the blood loss volume (r = –0.22; P = 0.29), compared with the traditional surgery, and reduced the hospital admission time from 12 (11.5; 13.5) days to 9 (7.5; 10.0) days (P < 0.001).ConclusionIn patients with large paravaginal hematomas treated by an integrated approach we reported a decrease in bleeding, less risk of postoperative complications, and a reduction in the time of the hospital stay.
Hybrid‐Patch‐Alex: A new patch division and deep feature extraction‐based image classification model to detect COVID‐19, heart failure, and other lung conditions using medical images
Authors: Erdem Kenan , Kobat Mehmet Ali , Bilen Mehmet Nail , Balik Yunus , Alkan Sevim , Cavlak Feyzanur , Poyraz Ahmet Kursad , Barua Prabal Datta , Tuncer Ilknur , Dogan Sengul , Baygin Mehmet , Erten Mehmet , Tuncer Turker , Tan Ru‐San , Acharya U. Rajendra 
Published: May 2023

AbstractCOVID‐19, chronic obstructive pulmonary disease (COPD), heart failure (HF), and pneumonia can lead to acute respiratory deterioration. Prompt and accurate diagnosis is crucial for effective clinical management. Chest X‐ray (CXR) and chest computed tomography (CT) are commonly used for confirming the diagnosis, but they can be time‐consuming and biased. To address this, we developed a computationally efficient deep feature engineering model called Hybrid‐Patch‐Alex for automated COVID‐19, COPD, and HF diagnosis. We utilized one CXR dataset and two CT image datasets, including a newly collected dataset with four classes: COVID‐19, COPD, HF, and normal. Our model employed a hybrid patch division method, transfer learning with pre‐trained AlexNet, iterative neighborhood component analysis for feature selection, and three standard classifiers (k‐nearest neighbor, support vector machine, and artificial neural network) for automated classification. The model achieved high accuracy rates of 99.82%, 92.90%, and 97.02% on the respective datasets, using kNN and SVM classifiers.