bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen (N) use efficiency and yield in rice under varying types and rates of N source: chemical fertilizer, livestock manure compost and food waste-livestock manure compost
Authors: Sung Jwakyung , Kim Woojin , Oh Taek-Keun , So Yoon-Sup 
Published: January 2023

AbstractAn optimal use of organic composts derived from animal and food wastes could provide an opportunity to achieve both sustainable crop production and soil quality, and a lot of research has provided the evidence. The nitrogen use efficiencies (NUEs) is a definition to evaluate the interaction between crop and nitrogen (N), and, due to this reason, widely used in agriculture. The current work tried to evaluate NUEs as an indicator of N acquisition capacity and physiological responses of rice grown under varying N levels. To do this, we employed different types and rates of nitrogen source, chemical fertilizer, livestock manure-based compost and food waste and livestock manure-containing compost. Despite of the enhanced rice growth and yield by fertilization, a difference by types and rates of fertilization was not observed. Net photosynthetic rate was significantly higher in the treatments of 90–317 N kg ha-1. The NUE (N uptake efficiency × N utilization efficiency) was the highest in lower N application groups, and sharply reduced with an increase in fertilization rates. In contrast, the nitrogen harvest index (NHI, grain N/total biomass N, kg kg-1) showed higher (0.71– 0.76 kg kg-1) in greater N application treatments (≤ 317 N kg ha-1). Accordingly, in terms of NUE, our result suggest that rice may be affordable of the application of less than 300 kg N ha-1 (combination with chemical fertilizer and organic compost). Nevertheless, it should be investigated how excess N application affects soil quality, and how long rice plant and soil can accept excess N without an environmental load.
Suppression of Phytophthora capsici using double-stranded RNAs targeting NLP effector genes in Nicotiana benthamiana
Authors: Park Minsu , Kweon Yujin , Lee Dowhan , Shin Chanseok 
Published: January 2023

AbstractRNA interference (RNAi) is a gene regulatory mechanism that involves the interaction of small interfering RNAs (siRNAs) and RNA-induced silencing complex (RISC). Dicer cleaves exogenous double-stranded RNA (dsRNA) into siRNAs, which get incorporated into RISC and bind to complementary sequences on the target mRNA to induce its degradation. In this study, we adopted RNAi technology using dsRNAs to suppress Phytophthora capsici, which causes diseases in solanaceous crops, including pepper. We designed and synthesized dsRNAs targeting the P. capsici effector genes PcNLP2 and PcNLP6, respectively. These genes encode necrosis and ethylene-inducing peptide 1-like proteins in P. capsici, which are known to promote oomycete infection. Nicotiana benthamiana leaves were first infiltrated with dsRNAs and inoculated with P. capsici 2 days later. We confirmed significant suppression of P. capsici and PcNLP2, PcNLP6 expression in dsRNA-treated leaves. In addition, we found that downregulation of PcNLP2 and PcNLP6 distinctly affected the expression of some defense-related genes. These results suggest that dsRNA mediated RNAi technology can be used to suppress various pathogens, and may contribute toward crop protection.
Are bacterial coinfections really rare in COVID-19 intensive care units?
Authors: Karaca Banu , Aksun Murat , Karahan Nagihan Altıncı , Girgin Senem , Ormen Bahar , Tuzen Ahmet Salih , Demirdal Tuna , Sencan Atilla 
Published: January 2023

Abstract
Objectives
There are limited data about nosocomial coinfections of COVID-19 cases monitored in the intensive care unit. This study aims to investigate coinfections in COVID-19 patients followed in an intensive care unit of a university hospital.

Methods
This study analyzed retrospectively the data of coinfections of 351 COVID-19 patients in the period 28.02.2020–15.01.2021 in a tertiary care intensive care unit in a university hospital.

Results
Bacterial coinfections were present in 216 of the 351 cases. One hundred and thirty of these cases were evaluated as nosocomial infections. On the third day the Sequential Organ Failure Assessment Score, usage of invasive mechanical ventilation and presence of septic shock were significantly higher in the coinfected group. The neutrophil/lymphocyte ratio, polymorphonuclear leukocyte count, procalcitonin, ferritin, and blood urea nitrogen values were significantly higher in the coinfection group. White blood cells (WBC) (OR: 1.075, 95% CI 1.032–1.121, p = 0.001) and ICU hospitalization day (OR: 1.114, 95% CI 1.063–1.167, p < 0.001) were found to be independent risk factors for coinfection in the multivariate logistic regression analysis. The rates of hospitalization day on the day of arrival, the 21st day, as well as total mortality (p = 0.004), were significantly higher in the coinfected group.

Conclusion
Bacterial coinfections of COVID-19 patients in the intensive care unit remain a problem. Identifying the infectious agent, classifying colonizations and infections, and using the proper treatment of antibiotics are of great importance in the case management of COVID-19 patients in the intensive care unit.
The global prevalence of primary central nervous system tumors: a systematic review and meta-analysis
Authors: Salari Nader , Ghasemi Hooman , Fatahian Reza , Mansouri Kamran , Dokaneheifard Sadat , Shiri Mohammad hossain , Hemmati Mahvan , Mohammadi Masoud 
Published: January 2023

Abstract
Background
Primary central nervous system (CNS) tumors are a heterogeneous group of neoplasms, including benign and malignant tumors. Since there are many heterogeneities in the prevalence reported in previous studies on this type of tumor, this study was performed to determine the overall prevalence of different primary CNS tumors.

Method
The study was conducted as a systematic review and meta-analysis by searching international databases, including PubMed, Scopus, Science Direct, Web of science, and the Google Scholar search engine until August 2020. After transferring the studies to information management software (EndNote) and eliminating duplicate studies, the remaining studies were reviewed based on inclusion and exclusion criteria according to three stages of primary and secondary evaluation and qualitative evaluation. Comprehensive Meta-Analysis software, Begg, Mazumdar, and I2 tests were used for data analysis, publication bias analysis, and heterogeneity analysis, respectively.

Results
After performing the systematic review steps, 80 studies were included for final analysis. Based on 8 studies, the prevalence of brain tumors was 70.9%. Also, studies on 7 other studies showed that the prevalence of spinal tumors was 12.2%. A review of 14 studies showed that the prevalence of neuroepithelial tumors was 34.7%. The analysis of 27 studies reported a prevalence of glioma tumors of 42.8%. Analyses performed on other studies showed that the prevalence of pituitary adenomas was 12.2%, embryonal tumors 3.1%, ependymal tumors 3.2%, meningiomas 24.1%, glial tumors 0.8%, astrocytic 20.3%, oligodendroglial 3.9%, glioblastoma 17.7%, schwannoma 6.7%, medulloblastoma 7.7% and Polycystic astrocytomas 3.8%.

Conclusion
As a result, it can be stated that brain tumors are the most common type of primary CNS tumors. It was also observed that tumors involving neuroepithelial cells are more common in patients than other types of tumors.
siRNA-E6 sensitizes HPV-16-related cervical cancer through Oxaliplatin: an in vitro study on anti-cancer combination therapy
Authors: Shiri Aghbash Parisa , Hemmat Nima , Baradaran Behzad , Bannazadeh Baghi Hossein 
Published: January 2023

Abstract
Background
Persistent infection with high-risk Human papillomaviruses (HPV), such as hr-HPV-16 and hr-HPV-18, lead to cervical cancer, the fourth most common cancer in the world. In the present study, we investigated the alteration of E6 oncogene expression by E6-specific short interfering RNA (siRNA) combined with Oxaliplatin.

Methods
The cervical cancer cell line, CaSki, was transfected with E6-siRNA, then treated with Oxaliplatin. The cellular genes, such as p53, MMP9, Nanog, and caspases expression, were assessed by quantitative real-time PCR. The cell death rate, cell cycle, and cell viability were assessed by Annexin V/PI staining, DAPI staining, and MTT test, respectively. Furthermore, colony formation assay and scratch test determined the stemness ability and cell metastasis, respectively.

Results
Combination therapy increased the re-expression of genes involved in the p53-dependent apoptosis pathway (increase in apoptosis to 44.2%), and reduced stemness and metastasis ability compared to either siRNA or Oxaliplatin monotherapy. Together, our results demonstrate that E6-siRNA and Oxaliplatin combination increased the cervical cancer cells’ sensitivity to Oxaliplatin and decreased the survival rate, proliferation, and metastasis, and consequently escalated apoptosis rate, induced cell cycle arrest in the sub-G1 stage, and reduced the chemotherapy drug dosage.

Conclusion
Inhibition of E6 oncogene expression and subsequent E6-siRNA with Oxaliplatin combination therapy could be a novel strategy for cervical cancer treatment.

Graphical Abstract
The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet
Authors: Lin Limei , Lai Zheng , Zhang Jiyou , Zhu Weiyun , Mao Shengyong 
Published: January 2023

Abstract
Background
Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal tract (GIT) microbiota to digest plant feed. However, the region-specific taxonomic composition and function of the GIT microbiome in dairy cattle and the mechanistic basis for the diet-induced effects remain to be elucidated.

Results
We collected 120 digesta samples from 10 GIT regions of 12 Holstein cows fed forage- and grain-based diets and characterized their GIT microbiome via functional shotgun metagenomics and the resolution of metagenome-assembled genomes. Our results demonstrated that the GIT microbiome was mainly partitioned into three distinct clusters, four-chambered stomach, small intestine, and large intestine. Moreover, we found that the four-chambered stomach microbiome with the highest diversity had a strong ability to degrade recalcitrant polysaccharide substrates, underpinned by the prevalence of potential cellulosome-­producing and plant-derived polysaccharide utilization loci-encoding consortia. In contrast, the post-gastric intestinal microbiome orchestrated alternative fermentation pathways to adapt to nutrient availability and energy acquisition. Diet shifts selectively modified the metabolic cascades of the microbiome in specific GIT regions, evidenced by the loss of fiber-degrading taxa and increased hydrogen sinks in propionate after grain introduction.

Conclusions
Our findings provide new insights into GIT microbial organization and function in dairy cattle by GIT regions and diet regimes, which offers clues for improving animal production and health in the future.
The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome
Authors: Chamankar Bahar , Maleki-Ravasan Naseh , Karami Mohsen , Forouzan Esmaeil , Karimian Fateh , Naeimi Sabah , Choobdar Nayyereh 
Published: January 2023

Abstract
Background
Paederus fuscipes is medically the most famous rove beetle, which causes dermatitis or conjunctivitis in humans, as well as gastrointestinal toxicosis in livestock, via releasing toxic hemolymph containing pederin. Pedrin biosynthesis genes have been identified in uncultured Pseudomonas-like endosymbionts that are speculated to be acquired through a horizontal transfer. However, the composition of the P. fuscipes microbial community, especially of the gut and genital microbiome, remains unclear. This study was aimed to characterize the structure and diversity of P. fuscipes-associated bacterial communities in terms of gender, organ, and location using the Illumina HiSeq platform in the southern littorals of Caspian Sea.

Results
The OTUs identified from P. fuscipes specimens were collapsed into 40 phyla, 112 classes, 249 orders, 365 families, 576 genera, and 106 species. The most abundant families were Pseudomonadaceae, Spiroplasmataceae, Weeksellaceae, Enterococcaceae, and Rhizobiaceae, respectively. Thirty top genera made up > 94% of the P. fuscipes microbiome, with predominating Pseudomonas, followed by the Spiroplasma, Apibacter, Enterococcus, Dysgonomonas, Sebaldella, Ruminococcus, and Wolbachia. Interesting dissimilarities were also discovered within and between the beetle microbiomes in terms of genders and organs. Analyses showed that Spiroplasma / Apibacter as well as Pseudomonas / Pseudomonas were the most abundant in the genitals / intestines of male and female beetles, respectively. Bacterial richness did not display any significant difference in the three provinces but was higher in male beetles than in females and more in the genitals than intestines.

Conclusions
The present study identified Pseudomonas-like endobacterium as a common symbiont of P. fuscipes beetles; this bacterium begins its journey from gut and genitalia of females to reach the male rove beetles. Additionally, male and female rove beetles were characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes. Evidence of the extension of P. fuscipes microbiome from the environmental paradigm to the pathobiome was also presented herein. A comprehensive survey of P. fuscipes microbiome components may eventually lead to ecological insights into the production and utilization of defensive compound of pederin and also the management of linear dermatitis with the use of available antibiotics against bacterial pathogens released by the beetles.
Lab and field evaluation of tagging methods for the use of acoustic telemetry to observe sea urchin movement behaviour at ecologically relevant spatio-temporal scales
Authors: MacGregor Kathleen A. , Lavoie Marie-France , Robinson Shawn M. C. , Simard Émilie , McKindsey Christopher W. 
Published: January 2023

Abstract
Background
Acoustic telemetry allows detailed observations of the movement behaviour of many species and as tags get smaller, smaller organisms may be tagged. The number of studies using acoustic telemetry to evaluate marine invertebrate movement is growing, but novel attachment methods include unknowns about the effects of tagging procedures on individual survival and behaviour. This study compared methods of tag attachment on green sea urchins (Strongylocentrotus droebachiensis) to determine the feasibility of using acoustic transmitters to track echinoid movement. Four tagging methods were compared in the lab and tag retention, urchin condition, and survival analysed. Two tagging methods (Dyneema® fishing line and T-bar tags) were evaluated in the field using an existing acoustic telemetry array. Urchins were tagged and the study area revisited one week and 2 months post-release by scuba divers to estimate movement and tag retention.

Results
The best methods in the lab, with high tag retention, survival, and minimal effects on urchin condition, were fishing line methods. T-bar tags, although showing high tag retention, caused significant mortality and had deleterious long-term effects on urchin condition and behaviour. After 2 months in the field, as in the lab, fishing line was a more effective tagging method. Urchins tagged with fishing line showed increased estimates of space occupancy compared to T-bar-tagged urchins and a single fishing-line tagged individual was found by divers in good health after 80 days. Combined, these laboratory and field results demonstrate the feasibility of using acoustic telemetry to observe urchin movement.

Conclusions
Results strongly suggest that surgical attachment methods that minimize injuries at the attachment site should be prioritized for echinoid tagging studies. Together, lab and field tests indicate that acoustic telemetry is a promising method to examine marine echinoid movement over ecologically relevant spatial and temporal scales.
Negative association between harsh parenting and life satisfaction: negative coping style as mediator and peer support as moderator
Authors: Ma Chensen , Song Jingjing 
Published: January 2023

AbstractBackgroundPrevious research has demonstrated that harsh parenting negatively affects children’s psychological development. This study examined the association between harsh parenting during childhood and life satisfaction of Chinese college students. We further looked at whether this association is explained in part by negative coping styles, and whether peer support lessens the potential effect of harsh parenting on negative coping styles and life satisfaction.MethodThe sample included 609 Chinese students (aged 17–21 years,M = 18.39,SD = 0.82). The participants responded to questionnaires measuring past experiences with harsh parenting, life satisfaction, negative coping styles, and peer support.ResultsRegression analysis showed that harsh parenting negatively contributed to students’ life satisfaction via the mediator of negative coping styles, and peer support moderated this negative relationship. Specifically, the negative impact of harsh parenting on life satisfaction was only significant when there was low peer support. The effect of harsh parenting on negative coping styles was higher in individuals with high peer support than in those with low peer support.ConclusionThis study highlights the roles of intrinsic (negative coping style) and extrinsic (peer support) factors in understanding the negative effects of harsh parenting on adolescents’ life satisfaction. These results provide insight into how to enhance adolescents’ life satisfaction by reducing harsh parenting and negative coping styles and by promoting peer support.
Functional testing, coronary artery calcifications, and outcomes in Hodgkin lymphoma survivors treated with chest radiation
Authors: Divakaran Sanjay , Lopez Diana M. , Parks Sean M. , Hainer Jon , Ng Andrea K. , Blankstein Ron , Di Carli Marcelo F. , Nohria Anju 
Published: January 2023

Abstract
Background
Consensus guidelines recommend periodic screening for coronary artery disease (CAD) in Hodgkin lymphoma (HL) survivors treated with radiation therapy (RT) to the chest. However, the prognostic utility of screening strategies in this population remains unclear. We evaluated the association between functional testing, coronary artery calcifications (CAC), and guideline-based risk assessment and major adverse cardiovascular events (MACE) in HL survivors treated with RT.

Methods
We retrospectively studied HL survivors treated with RT who underwent functional testing between 2003 and 2020 and chest computed tomography (CT) within 12 months of each other at our center. CAC was assessed semi-quantitatively from CT images. Cardiovascular risk was estimated using the 2019 ACC/AHA Guideline on the Primary Prevention of Cardiovascular Disease. Diagnostic test characteristics were calculated using major adverse cardiac events (MACE) during follow-up as the gold standard.

Results
The study included 159 patients (median age at functional testing 48 years, median age at HL diagnosis 27 years, 62.9% female). Abnormal functional testing had the highest specificity (94.2% (95% CI 88.4%-97.6%)) and positive likelihood ratio (4.55 (95% CI 1.86–11.13)) while CAC had the highest sensitivity (63.2% (95% CI 46.0%-78.2%)) and lowest negative likelihood ratio (0.52 (95% CI 0.34–0.80)). Specificity for ACC/AHA risk assessment was also high (88.5% (95% CI 81.1%-93.7%)). Over 3.3 years of follow-up, abnormal functional testing (adjusted subdistribution hazard ratio (SHR) 5.10, 95% CI 2.41 – 10.78, p < 0.001) and CAC (adjusted SHR 3.58, 95% CI 1.35 – 9.47, p = 0.010) were both significantly associated with MACE.

Conclusions
In HL survivors treated with RT, both abnormal functional testing and ACC/AHA risk assessment had high specificity for subsequent MACE, but CAC had higher sensitivity. Further research is needed to inform CAD screening and primary prevention strategies in this population.
“You need a team”: perspectives on interdisciplinary symptom management using patient-reported outcome measures in hemodialysis care—a qualitative study
Authors: Baragar Brigitte , Schick-Makaroff Kara , Manns Braden , Love Shannan , Donald Maoliosa , Santana Maria , Corradetti Bonnie , Finlay Juli , Johnson Jeffrey A. , Walsh Michael , Elliott Meghan J. 
Published: January 2023

AbstractBackgroundPatient-reported outcome measures (PROMs) are standardized instruments used for assessing patients’ perspectives on their health status at a point in time, including their health-related quality of life, symptoms, functionality, and physical, mental, and social wellbeing. For people with kidney failure receiving hemodialysis, addressing high symptom burden and complexity relies on care team members integrating their expertise to achieve common management goals. In the context of a program-wide initiative integrating PROMs into routine hemodialysis care, we aimed to explore patients’ and clinicians’ perspectives on the role of PROMs in supporting interdisciplinary symptom management.MethodsWe employed a qualitative descriptive approach using semi-structured interviews and observations. Eligible participants included adult patients receiving intermittent, outpatient hemodialysis for > 3 months, their informal caregivers, and hemodialysis clinicians (i.e., nurses, nephrologists, and allied health professionals) in Southern Alberta, Canada. Guided by thematic analysis, team members coded transcripts in duplicate and developed themes iteratively through review, refinement, and discussion.ResultsThirty-three clinicians (22 nurses, 6 nephrologists, 5 allied health professionals), 20 patients, and one caregiver participated in this study. Clinicians described using PROMs to coordinate care across provider types using the resources available in their units, whereas patients tended to focus on the perceived impact of this concerted care on symptom trajectory and care experience. We identified 3 overarching themes with subthemes related to the role of PROMs in interdisciplinary symptom management in this setting: (1) Integrating care for interrelated symptoms (“You need a team”,conducive setting, role clarity and collaboration); (2) Streamlining information sharing and access (symptom data repository,common language for coordinated care); (3) Reshaping expectations (expectations for follow-up,managing symptom persistence).ConclusionsWe found that use of PROMs in routine hemodialysis care highlighted symptom interrelatedness and complexity and helped to streamline involvement of the interdisciplinary care team. Issues such as role flexibility and resource constraints may influence sustainability of routine PROM use in the outpatient hemodialysis setting.