bluuebunny/crossref_metadata_2025 huggingface dataset:
A case of a renal abscess caused by Salmonella bareilly in a previously healthy boy
Authors: Nakamura Tomomi , Ido Masaru , Ogawa Masahiro , Sasaki Naoya , Nakamura Haruna , Hasegawa Yoshihiro , Bonno Motoki , Tanaka Shigeki
Published: March 2022

Background

Renal abscesses are relatively uncommon in children, and usually due to Gram-negative rods or Staphylococcus aureus, whereas abscesses caused by Salmonella are very rare.

Case presentation

We present the case of a previously healthy 10-year-old boy who had a renal abscess due to Salmonella bareilly. He responded well to treatment with antibiotics, and computed tomography (CT)-guided drainage of the abscess. His blood, urine and abscess aspirate cultures were sterile, but a broad-range 16S rDNA polymerase chain reaction (PCR) assay of the aspirate followed by analysis of four Salmonella genes (fliC, fliD, sopE2, and spaO) identified S. bareilly as the causative agent.

Conclusion

To the best of our knowledge, this is the first report of renal abscess caused by S. bareilly.
Nomograms to predict the prognosis in malignant ovarian germ cell tumors: a large cohort study
Authors: Song Zixuan , Wang Yizi , Zhou Yangzi , Zhang Dandan
Published: March 2022

Background

Malignant ovarian germ cell tumors (MOGCTs) are rare gynecologic neoplasms. The use of nomograms that are based on various clinical indicators to predict the prognosis of MOGCTs are currently lacking.

Methods

Clinical and demographic information of patients with MOGCT recorded between 2004 and 2015 were obtained from the Surveillance, Epidemiology, and End Results database, and Cox regression analysis was performed to screen for important independent prognostic factors. Prognostic factors were used to construct predictive calculational charts for 1-year, 3-year, and 5-year overall survival (OS). The externally validated case cohort included a total of 121 MOGCT patients whose data were recorded from 2008 to 2019 from the database of the Shengjing Hospital of China Medical University.

Results

A total of 1401 patients with MOGCT were recruited for the study. A nomogram was used to forecast the 1-year, 3-year, and 5-year OS using data pertaining to age, International Federation of Gynecology and Obstetrics (FIGO) staging, histological subtype and grade, and surgical type. Nomograms have a more accurate predictive ability and clinical utility than FIGO staging alone. Internal and external validation also demonstrated satisfactory consistency between projected and actual OS.

Conclusions

A nomogram constructed using multiple clinical indicators provided a more accurate prognosis than FIGO staging alone. This nomogram may assist clinicians in identifying patients who are at increased risk, thus implementing individualized treatment regimens.
Impact of the COVID-19 pandemic on management of children and adolescents with Type 1 diabetes
Authors: Choudhary Abha , Adhikari Soumya , White Perrin C.
Published: March 2022

Background

The coronavirus disease-2019 (COVID-19) pandemic had widespread impacts on the lives of parents and children. We determined how the pandemic affected Type 1 diabetes patients at a large urban pediatric teaching hospital.

Methods

We compared patient characteristics, glycemic control, PHQ-9 depression screen, in person and virtual outpatient encounters, hospitalizations and continuous glucose monitor (CGM) utilization in approximately 1600 patients in 1 year periods preceding and following the local imposition of COVID-related restrictions on 3/15/2020 (“2019” and “2020” groups, respectively).

Results

In a generalized linear model, increasing age, non-commercial insurance, Black and Hispanic race/ethnicity, and non-utilization of CGMs were all associated with higher hemoglobin A1c (HbA1c), but there was no difference between the 2019 and 2020 groups. The time in range in CGM users was lower with non-commercial insurance and in Black and Hispanic patients; it improved slightly from 2019 to 2020. CGM utilization by patients with non-commercial insurance (93% of such patients were in government programs, 7% uninsured or “other”) increased markedly. In 2020, patients with commercial insurance (i.e., private-pay or provided by an employer) had fewer office visits, but insurance status did not influence utilization of the virtual visit platform. There was no change in hospitalization frequency from 2019 to 2020 in either commercially or non-commercially insured patients, but patients with non-commercial insurance were hospitalized at markedly higher frequencies in both years. PHQ-9 scores were unchanged.

Conclusions

Hospitalization frequency, glycemic control and depression screening were unchanged in our large urban pediatric teaching hospital during the COVID pandemic. Increased utilization of CGM and rapid adoption of telemedicine may have ameliorated the impact of the pandemic on disease management.
Evaluating family knowledge about sexual health in patients with severe mental illness: a qualitative study in Iran
Authors: Mirsepassi Zahra , Raisi Firoozeh , Shahvari Zahra , FirooziKhojastefar Reihaneh , Yahyavi Seyyed Taha
Published: March 2022

Introduction

Although paying more attention to sex education in patients with severe mental illness is recommended in the literature, the role of families has not been specifically clarified. 

Aim

This study aims to explore family knowledge about sexual health in patients with severe mental illness in Iran.

Methods

We conducted a total number of 21 interviews with 4 patients, 5 families, 7 psychiatrists, 1 general practitioner, 2 nurses, and 2 psychologists through purposive sampling. The text was analyzed using conventional qualitative content analysis.

Results

The family knowledge about patients’ sexual health is described in three subcategories: ‘informal sources for knowledge acquisition’, ‘common myths, and ‘inappropriate reaction to the patients’ needs”.

Conclusions

Family sex education should be integrated into a comprehensive rehabilitation program to promote sexual health in patients with severe mental illness. Family members should be aware of the necessity of accurate information about patients’ sexual concerns.
Relationship between sense of coherence and health-related behaviours in adolescents and young adults: a systematic review
Authors: da-Silva-Domingues Henrique , del-Pino-Casado Rafael , Palomino-Moral Pedro Ángel , López Martínez Catalina , Moreno-Cámara Sara , Frías-Osuna Antonio
Published: March 2022

Background

The sense of coherence is developed through the learning process and contributes to the positioning of individuals in the health-disease continuum, facilitating successful and adaptive personal outcomes. Health-related behaviours represent a health determinant of utmost importance for public health and the development of adolescent and youth health promotion policies, as they are related to the main risk factors and problems of morbidity and mortality in our society. Previous studies have analysed the relationship between sense of coherence and only some individual health outcomes such as oral health, the relationship of sense of coherence with smoking and alcohol consumption, concluding that salutogenic factors are related to quality of life and preventive behaviours. The aim of this systematic review was to describe the relationship of sense of coherence with different health-related behaviours investigated so far in the adolescent and youth population.

Methods

A systematic review was carried out in databases (PubMed, CINAHL, Scopus and PsycInfo) and in the bibliographies of the retrieved articles, without limitation of time or language. Associations between sense of coherence and health-related behaviours have been assessed.

Results

A total of 1214 investigations were reviewed and 21 of them were included in this systematic review. The relationship between sense of coherence and eight health-related behaviours were identified (alcohol use, physical activity, tobacco use, eating habits, rest periods, use of illegal substances, behaviours related to oral health and time spent in games on the computer).

Conclusions

Our results increase the available evidence and support the solid relationship of the sense of coherence with health behaviours both as a protective factor against risk behaviours and for its positive association with preventive and health promoting behaviours of adolescents, young adults and university students.
Mental health and workplace factors: comparison of the Ghanaian and Australian mining industry
Authors: Winifred Asare-Doku , Jane Rich Louise , Brian Kelly , Amponsah-Tawiah Kwesi , Carole James
Published: March 2022

Background

Mining is a global industry and contributes significantly to international economies. This study seeks to compare the patterns of psychological distress, job demand-control, and associated characteristics between two countries (Australia/Ghana) to increase understanding of cross-cultural factors relevant to mental health in this industry.

Method

A cross-sectional study design was used. Eight coal mines in Australia and five gold mines in Ghana. A total of 2622 mineworkers participated in this study. Kessler Psychological Distress Scale (K10), Job Content Questionnaire (JCQ), Alcohol Use Disorders Identification Test (AUDIT), the Berkman-Syme Social Network Index (SNI) and help-seeking questionnaire.

Results

Ghanaian mineworkers reported increased psychological distress compared to Australian mineworkers; Job demands outweighed control among Ghanaian mineworkers but was associated with lower risk of psychological distress compared to Australian mineworkers; Ghanaian mineworkers were significantly less likely to drink alcohol at risky levels but this was associated with higher psychological distress; Increased social network was associated with decreased psychological distress for both countries.

Conclusions

These findings identify cultural and geographical differences in the socio-demographics, workplace factors, psychological distress, and alcohol use in both countries. Cross-cultural occupational workplace factors and mental health issues are highlighted. Potential workplace interventions applicable in comparable settings are recommended.
Ubiquitylation is required for the incorporation of the Notch receptor into intraluminal vesicles to prevent prolonged and ligand-independent activation of the pathway
Authors: Schnute Björn , Shimizu Hideyuki , Lyga Marvin , Baron Martin , Klein Thomas
Published: March 2022

Background

Ubiquitylation of the ligands and the receptor plays an important part in the regulation of the activity of the evolutionary conserved Notch signalling pathway. However, its function for activation of Notch is not completely understood, despite the identification of several E3 ligases devoted to the receptor.

Results

Here we analysed a variant of the Notch receptor where all lysines in its intracellular domain are replaced by arginines. Our analysis of this variant revealed that ubiquitylation of Notch is not essential for its endocytosis. We identified two functions for ubiquitylation of lysines in the Notch receptor. First, it is required for the degradation of free Notch intracellular domain (NICD) in the nucleus, which prevents a prolonged activation of the pathway. More importantly, it is also required for the incorporation of Notch into intraluminal vesicles of maturing endosomes to prevent ligand-independent activation of the pathway from late endosomal compartments.

Conclusions

The findings clarify the role of lysine-dependent ubiquitylation of the Notch receptor and indicate that Notch is endocytosed by several independent operating mechanisms.
Green Christmas: bryophytes as ornamentals in Croatian traditional nativity scenes
Authors: Bučar Marija , Šegota Vedran , Rimac Anja , Koletić Nikola , Marić Tihana , Alegro Antun
Published: March 2022

Background

The bryophytes are a plant group that is smaller than and not as well known as the vascular plants. They are less used and are almost completely neglected in ethnobotanical studies. Traditional nativity scenes depicting the birth of Christ are commonly decorated with both vascular plants and bryophytes. The aim of this study was to document the diversity of decorative bryophytes sold during the Advent season at farmers’ markets in Croatia (Southeastern Europe, Balkan Peninsula).

Methods

Twenty-eight farmers’ markets in the two largest Croatian cities (Zagreb in the continental part and Split in the Mediterranean part) were studied in the search for local vendors selling bryophytes during the pre-Christmas season. The bryophytes collected were identified and analysed with respect to families, growth type, life forms and threat status.

Results

Among 275 collected specimens, 43 moss and four liverwort species were identified. The mean number of species per vendor was 3.5. The most frequent species wereHypnum cupressiforme,Homalothecium sericeumandCtenidium molluscum. Mats, wefts and tufts were the most common life-forms, while pleurocarpous prevailed over acrocarpous mosses, as they are usually pinnately branched and form large carpets, suitable for decorations. The overall selection of bryophytes and the decorations made of them were more diverse and abundant in inland Croatia, where 49 vendors at 15 farmers’ markets sold goods containing 43 species. In Mediterranean Croatia, at six farmers’ markets only 29 vendors sold goods, which contained 18 species. A considerable number of species that are less attractive to harvesters were collected non-intentionally, entangled in carpets of other, more frequent species. Among them,Rhodobryum ontarienseandLoeskeobryum brevirostreare rare and insufficiently recorded in Croatia so far.

Conclusions

The present study provided a first perspective on the use of bryophytes in traditional nativity scenes in Croatia and Southeastern Europe, contributing to scarce ethnobotanical documentation of the decorative use of bryophytes in Christmas festivities in Europe and globally.
Brucein D augments the chemosensitivity of gemcitabine in pancreatic cancer via inhibiting the Nrf2 pathway
Authors: Zhang Juan , Xu Hong-Xi , Cho William Chi Shing , Cheuk Wah , Li Yang , Huang Qiong-Hui , Yang Wen , Xian Yan-Fang , Lin Zhi-Xiu
Published: March 2022

Background

Gemcitabine (GEM) is the first-line chemotherapeutic drug used to treat pancreatic ductal adenocarcinoma carcinoma (PDAC), but chemoresistance is often encountered clinically. Nrf2, an oxidative stress responsive transcription factor, is an important contributor to chemoresistance and poor prognosis of PDAC. Brucein D (BD), a naturally occurring quassinoid, has been reported to exert anti-tumor effect in several cancers including PDAC. In this study, we aimed to investigate the efficacy of BD and the role of Nrf2 axes on the chemosensitivity of GEM and elucidate the underlying molecular mechanisms.

Methods

Analyses of clinical samples of PDAC and GEPIA database were first conducted to identify the expression of Nrf2 in PDAC. We then established cell lines with stable deletion of Nrf2 through transfecting lentivirus into PDAC cells. Quantitative real-time PCR (qRT-PCR) and Western blotting were performed to determine the expression of Nrf2 in these cell lines. The effects of BD and Nrf2 axes on PDAC cell proliferation, colony-formation, tumor growth and chemosensitivity were determined both in vitro and in vivo. Orthotopic xenograft and genetically engineered KPC mouse models of PDAC were used to evaluate the anti-pancreatic cancer effects of BD and GEM.

Results

Nrf2 was highly expressed in PDAC in the clinical samples and GEPIA analysis. Gain- and lost-function study demonstrated that Nrf2 affected the chemosensitivity of GEM on PDAC cells both in vitro and in vivo. We further found that BD effectively inhibited PDAC cell proliferation and enhanced the chemosensitivity of GEM. Mechanistic studies revealed that BD sensitized GEM in PDAC cells through the ubiquitin–proteasome-dependent degradation of Nrf2, and downregulating the Nrf2 pathway. Silencing of Nrf2 plus BD treatment resulted in more potent inhibitory effects of GEM. In contrast, Nrf2 activation attenuated the chemosensitivity of GEM, indicating that the action of BD was Nrf2 dependent. Finally, the efficacy of BD alone and in combination with GEM on PDAC was validated on both orthotopic xenograft and genetically engineered KPC mouse models.

Conclusions

BD was able to enhance the chemosensitivity of GEM in PDAC through inhibition of the Nrf2 pathway. Our experimental findings indicate that BD, a potent Nrf2 inhibitor, holds promise for further development into a novel adjuvant therapy for PDAC.
Effect of micro-algae Schizochytrium sp. supplementation in plant diet on reproduction of female rainbow trout (Oncorhynchus mykiss): maternal programming impact of progeny
Authors: Cardona Emilie , Segret Emilien , Cachelou Yoann , Vanderesse Thibaut , Larroquet Laurence , Hermann Alexandre , Surget Anne , Corraze Geneviève , Cachelou Frederic , Bobe Julien , Skiba-Cassy Sandrine
Published: March 2022

Background

The broodstock diet, and in particular the lipid and fatty acid composition of the diet, is known to play a key role in reproductive efficiency and survival of the progeny in fish. A major problem when replacing both fish meal and fish oil by plant sources is the lack of n-3 long chain polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). To address this problem, we studied the effect of the plant-based diet supplemented with Schizochytrium sp. microalgae, source of DHA, compared to a conventional commercial diet rich in fish meal and fish oil on reproductive performance and egg quality and the consequences on progeny, in female rainbow trout broodstock.

Results

The results demonstrated that DHA-rich microalgae supplementation in a plant-based diet allowed for the maintenance of reproductive performance and egg quality comparable to a conventional commercial feed rich in fish meal and fish oil and led to an increased significant fry survival after resorption. Moreover, when females were fed a plant-based diet supplemented with micro-algae, the 4-month-old progenies showed a significant higher growth when they were challenged with a similar diet as broodstock during 1 month. We provide evidence for metabolic programming in which the maternal dietary induced significant protracted effects on lipid metabolism of progeny.

Conclusions

The present study demonstrates that supplementation of a plant-based diet with DHA-rich microalgae can be an effective alternative to fish meal and fish oil in rainbow trout broodstock aquafeed.
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
Authors: Sim Choon K. , Kashaf Sara Saheb , Stacy Apollo , Proctor Diana M. , Almeida Alexandre , Bouladoux Nicolas , Chen Mark ,   NISC Comparative Sequencing Program, Finn Robert D. , Belkaid Yasmine , Conlan Sean , Segre Julia A.
Published: March 2022

Background

The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically present. When these bacteria are present at very low levels, they are often undetectable in hospital surveillance cultures, known as occult or subclinical colonization. Through the receipt of antibiotics, these subclinical pathogens can increase to sufficiently high levels to become detectable, in a process called outgrowth. However, little is known about the interaction between gut microbiota and Enterobacteriaceae during occult colonization and outgrowth.

Results

We developed a clinically relevant mouse model for studying occult colonization. Conventional wild-type mice without antibiotic pre-treatment were exposed to Klebsiella pneumoniae but rapidly tested negative for colonization. This occult colonization was found to perturb the microbiome as detected by both 16S rRNA amplicon and shotgun metagenomic sequencing. Outgrowth of occult K. pneumoniae was induced either by a four-antibiotic cocktail or by individual receipt of ampicillin, vancomycin, or azithromycin, which all reduced overall microbial diversity. Notably, vancomycin was shown to trigger K. pneumoniae outgrowth in only a subset of exposed animals (outgrowth-susceptible). To identify factors that underlie outgrowth susceptibility, we analyzed microbiome-encoded gene functions and were able to classify outgrowth-susceptible microbiomes using pathways associated with mRNA stability. Lastly, an evolutionary approach illuminated the importance of xylose metabolism in K. pneumoniae colonization, supporting xylose abundance as a second susceptibility indicator. We showed that our model is generalizable to other pathogens, including carbapenem-resistant Escherichia coli and Enterobacter cloacae.

Conclusions

Our modeling of occult colonization and outgrowth could help the development of strategies to mitigate the risk of subsequent infection and transmission in medical facilities and the wider community. This study suggests that microbiota mRNA and small-molecule metabolites may be used to predict outgrowth-susceptibility.
Microbiome function predicts amphibian chytridiomycosis disease dynamics
Authors: Bates Kieran A. , Sommer Ulf , Hopkins Kevin P. , Shelton Jennifer M. G. , Wierzbicki Claudia , Sergeant Christopher , Tapley Benjamin , Michaels Christopher J. , Schmeller Dirk S. , Loyau Adeline , Bosch Jaime , Viant Mark R. , Harrison Xavier A. , Garner Trenton W. J. , Fisher Matthew C.
Published: March 2022

Background

The fungal pathogen
Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.

Methods

Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.

Results

Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.

Conclusions

Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection.
MetaDecoder: a novel method for clustering metagenomic contigs
Authors: Liu Cong-Cong , Dong Shan-Shan , Chen Jia-Bin , Wang Chen , Ning Pan , Guo Yan , Yang Tie-Lin
Published: March 2022

Background

Clustering the metagenomic contigs into potential genomes is a key step to investigate the functional roles of microbial populations. Existing algorithms have achieved considerable success with simulated or real sequencing datasets. However, accurately classifying contigs from complex metagenomes is still a challenge.

Results

We introduced a novel clustering algorithm, MetaDecoder, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. MetaDecoder was built as a two-layer model with the first layer being a GPU-based modified Dirichlet process Gaussian mixture model (DPGMM), which controls the weight of each DPGMM cluster to avoid over-segmentation by dynamically dissolving contigs in small clusters and reassigning them to the remaining clusters. The second layer comprises a semi-supervised k-mer frequency probabilistic model and a modified Gaussian mixture model for modeling the coverage based on single copy marker genes. Benchmarks on simulated and real-world datasets demonstrated that MetaDecoder can be served as a promising approach for effectively clustering metagenomic contigs.

Conclusions

In conclusion, we developed the GPU-based MetaDecoder for effectively clustering metagenomic contigs and reconstructing microbial communities from microbial data. Applying MetaDecoder on both simulated and real-world datasets demonstrated that it could generate more complete clusters with lower contamination. Using MetaDecoder, we identified novel high-quality genomes and expanded the existing catalog of bacterial genomes.
Interplay of disability, caregiver impact, and out-of-pocket expenditures in Duchenne muscular dystrophy: a cohort study
Authors: Schwartz Carolyn E. , Stark Roland B. , Borowiec Katrina , Audhya Ivana F. , Gooch Katherine L.
Published: March 2022

Background

Providing caregiving support to people with Duchenne muscular dystrophy (DMD) is challenging, beginning in early childhood, and continuing through the progression of multidimensional disability. This study addressed the interplay between caregiver impact, out-of-pocket expenditures, and DMD disability. To examine these interconnections, we investigated the association between caregiver impact domains and out-of-pocket expenditures; and the presence of clusters in caregivers on the basis of DMD-related disability domains in the patients for whom they provided caregiving support.

Methods

This web-based study recruited 566 DMD caregivers (140 males, 426 females; mean age 41.6 years, SD 8.8, range 21–72), examining caregiver impact using the DMD Caregiver Impact Measure, PROMIS-derived parent-proxy (PPP) measures of their child’s disability, and items tapping out-of-pocket expenditures related to home and vehicle accommodations and assistive devices. T-tests compared caregiver impact scores by out-of-pocket expenditures incurred. Latent Profile Analyses (LPA) were conducted to generate impact profiles related to child’s disability as reported by caregiver proxies.

Results

Higher out-of-pocket expenditures were generally associated with worse impact on the subscales, but several expenditures (e.g., kitchen, bathroom, scooter) were associated with lower impact. LPA indicated that the four-group solution provided the best relative fit and yielded good profile separation (entropy = 0.91). Caregivers with lowest impact reported the highest mobility, cognitive, and upper extremity functioning of their DMD care recipients, whereas the highest caregiver impact was driven by their care recipient’s negative affect and fatigue. The upper-middle impact group showed great variability in proxy-disability domains, whereas the lower-middle group had similar levels of disability across domains. Profiles were represented across all child ages.

Conclusion

Out-of-pocket expenditures were often associated with worse caregiver impact, but some associated with milder impact (i.e., bathroom or kitchen modification, investing in a ceiling lift or medical scooter). While their son’s level of disability and age were related to impact on the DMD caregiver, the domains giving rise to highest caregiver impact were not the most visible aspects of disability, such as mobility, but rather negative affect and fatigue. Other contextual attributes are likely implicated, and will be addressed in the companion paper.
Preoperative hematological inflammatory markers associated with grade and survival in Meningiomas
Authors: de Oliveira Silva Camila Batista , Araújo Bruna , Ongaratti Bárbara Roberta , dos Santos Tainá Mafalda , Rech Carolina Garcia Soares Leães , Coutinho Lígia Barbosa , Ferreira Nelson Pires , da Costa Oliveira Miriam , Pereira-Lima Julia Fernanda Semmelmann
Published: March 2022

Meningiomas represent the most frequently diagnosed intracranial tumors. Inflammatory cells present in the tumor can modulate both antitumor and protumor functions, and modify the therapeutic response. Hematological inflammatory parameters have provided prognostic information useful in the treatment and clinical evaluation of several tumors. The aim of this study was to evaluate preoperative hematological markers of patients with meningiomas and to relate them to clinical variables and recurrence-regrowth free survival. Eighty-nine patients without corticosteroid therapy were included. Blood test results and tumor characteristics were collected from medical records. Associations between clinical characteristics and the recurrence-regrowth free survival (RFS) were evaluated using Cox proportional hazard analysis and Kaplan-Meier curves. The receiver operating characteristic (ROC) curves were constructed. Of the 89 cases, 73 (82%) were grade I and 16 (18%) grade II. The mean age was 53 ± 13.9 years, with higher frequency in women. Anemia was observed in 23.6% and neutrophilia in 42% of the patients. In univariate analysis, anemia (p = 0.04), neutrophilia (p = 0.02) and neutrophil/lymphocyt ratio (NLR) (p = 0.02) were associated with an increased risk of recurrence-regrowth and shorter RFS. In multivariate analysis, anemia and NLR > 4.1 represented a higher risk of recurrence-regrowth (p = 0.003). The ROC curve analysis showed that only the lymphocyte/monocyte (L/M) > 2.5 was able to predict the tumor grade. The preoperative presence of anemia, neutrophilia, NLR > 4.1 and L/M > 2.5 were associated with a worse prognosis in meningiomas. The use of preoperative hematological inflammatory parameters as prognostic factors can be promissing for evaluation and follow-up of meningiomas.
Expanding the field: using digital to diversify learning in outdoor science
Authors: Stagg Bethan C. , Dillon Justin , Maddison Janine
Published: March 2022

This is an empirical study of teacher experiences with school learners (7–18 years) engaging in cross-curricular environmental science during the COVID-19 pandemic. The study focuses on #FieldworkLive, a programme of live-streamed outdoor science lessons produced by the Field Studies Council and Encounter Edu during the UK lockdown (April – May 2020). The experiences of approximately 377,000 teachers and students from 32 countries were captured using an online survey and direct staff consultation. This delivery method allowed us to reach untapped audiences and to provide learners with a virtual fieldwork experience during the constraints of lockdown. Teachers were highly positive about the technology-enhanced learning which provided them with novel perspectives and approaches for the classroom. We propose a model for the affordances provided by this delivery approach based on the Technological Pedagogical Content Knowledge framework. The Field Studies Council has developed a flexible package of multimedia resources for secondary schools as a route to enriching outdoor experience and learning despite the constraints imposed by the pandemic.
The significance of fibroblast growth factor-2 and kidney injury molecule-1 as biomarker of interstitial renal fibrosis in glomerulonephritis
Authors: Shaker Amr M. , Rakha Nahal K. , El-Shehaby Amal M. R. , Ramzy Tarek , Hamza Wael M. , Elkhatib Mohamed M.
Published: March 2022

Background

Renal tubulointerstitial fibrosis is a structural marker and prominent pathological characteristic of chronic progressive kidney disease, fibroblast growth factor-2 (FGF2) is a key fibrogenic cytokine that is likely to be involved in the pathogenesis of renal fibrosis, kidney injury molecule-1 (KIM-1) is one of the most promising, early biomarkers of renal disease, either acute or chronic, due to its translatability between preclinical and clinical trials. It is believed that this molecule participates in the process of both kidney injury and healing.

Methods

We prospectively enrolled a cohort study of eighty adult patients who had glomerular diseases (with glomerular filtration rate (GFR) > 30 ml/min/m2); serum level of FGF-2 and KIM-1 was measured at the same time of renal biopsy and was correlated with the degree of interstitial renal fibrosis.

Results

We found a significant positive correlation between FGF-2 and KIM-1 and the degree of interstitial renal fibrosis, albumin, and creatinine (P≤ 0.001), and a negative significant correlation with GFR and proteinuria. there is a positive significant correlation between serum KIM-1 and FGF-2 and hypertension with a significant P value (<0.001) that serum KIM-1 has sensitivity 90% and specificity of 95% and serum FGF-2 has sensitivity 95% and specificity 95% for detection of interstitial renal fibrosis.

Conclusions

Serum FGF-2 and KIM-1 seem to be a non-invasive novel biomarker of interstitial renal fibrosis in glomerulonephritis patients. It may become a useful biomarker without the need for the invasive maneuver of the renal biopsy. FGF-2 and KIM-1 are expected to be therapeutic targets for kidney injury.
The role of CGIAR Germplasm Health Units in averting endemic crop diseases: the example of rice blast in Bangladesh
Authors: Enriquez Yuji , Smale Melinda , Jamora Nelissa , Hossain Mohammod , Kumar Lava
Published: March 2022

Background

One of the less known benefits of the CGIAR is the facilitation of international agricultural research for crop improvement by providing a continuous supply of breeding materials for the development of disease resistant varieties. The Germplasm Health Units (GHUs) of the CGIAR are phytosanitary mechanisms put in place to help ensure safe (from pests and diseases) and efficient international transfer of germplasm among genebanks and breeding programs around the world. To date, there is no systematic documentation of the pathways and extent to which GHUs contribute to economic impact in recipient countries.

Methods

We conducted interviews with key experts and reviewed secondary literature and data to trace the pathways through which the GHU of the International Rice Research Institute (IRRI) contributes to the impact of breeding for rice blast. We applied an ex ante economic surplus framework to the case of rice blast in Bangladesh, considering productivity maintenance and time saving factors from GHU facilitation. Data were drawn from a national panel dataset of farm households (from 2013 to 2016 with about 4490 households) and field surveys of blast incidence and severity (from 2011 to 2012 in 10 agroecological zones). We augmented our model with Monte Carlo sampling to simulate distributions of parameters.

Results

Our model predicts that, in the most probable scenario (modal values), the IRRI GHU contributed about US$ 5.9 million of the total US$ 295 million net benefits over a 20-year time frame of continuous blast resistance breeding and deployment. In the most optimistic conditions (maximum), the IRRI GHU contributed as much as US$ 62 million of the US$ 1.46 billion benefits. The modal benefit–cost ratio of the GHU in this breeding program alone was estimated at 112. The results are sensitive to the rate of yield savings, which is contingent on yield levels, timing of deployment, effectiveness of resistance, and lifespan of resistance to blast.

Conclusions

The study reinforces the important, and often overlooked, role of the GHUs in the international agricultural research that aims to enhance genetic gains in crops through efficient and timely access to clean and healthy germplasm.
Genomic structural variation in tomato and its role in plant immunity
Authors: Jobson Emma , Roberts Robyn
Published: March 2022

It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.
Study on surface modification and fabrication of surface composites of magnesium alloys by friction stir processing: a review
Authors: Manroo Suhail Ahmed , Khan Noor Zaman , Ahmad Babar
Published: March 2022

Magnesium alloys and their composites are fast replacing aluminum alloys and other materials in the aerospace and automotive industries. Significant progress has been made in the fabrication of these composites to make them materials of choice for these industries. The choice of the fabrication process is crucial to realize the composites with properties that can compete with the materials currently in vogue. Conventional methods of fabrication of magnesium alloys and their composites are seriously limited as they lead to defects such as porosity and particle clustering. Friction stir processing (FSP) is turning out to be a promising fabrication technique to surmount these challenges. The process being a solid state technique is highly amenable to production of surface modified composites with very attractive mechanical and tribological properties. The main factor making FSP attractive is the relative ease of modification of the surface layers and the incorporation of reinforcement particles. The underlying plastic deformation in FSP ensures that the reinforcement particles are incorporated and distributed uniformly throughout the matrix. This paper attempts to review the current status of FSP as a technique of enabling the surface modification and fabrication of surface composites of magnesium alloys. The objective is to summarize the progress made towards the realization of surface-modified magnesium alloys, primarily in two systems, namely, Mg-AZ system and Mg/rare earth system. The operating conditions (and process parameters) and their subsequent effect on mechanical and tribological properties of the fabricated composites are summarized through the consideration of fabrication of three representative systems, viz., Mg-metal oxide (Mg-MO), Mg-metal carbide (Mg-MC), and Mg-carbon nano tube (Mg-CNT) systems.
Copy number variants in the context of evolving psychogenomic understanding
Authors: Roberts Kris
Published: March 2022

There are well-established links between recurring copy number variants (CNVs) (ubiquitous structural variations within chromosomes) and many psychiatric diagnoses. This article considers potential advances that enhanced understanding of CNVs might offer psychiatry – a scientifically rigorous footing for the discipline and personalised prescribing based on genetic data that would benefit patients from pre-diagnosis to treatment.
HealthTree Cure Hub: A Patient-Derived, Patient-Driven Clinical Cancer Information Platform Used to Overcome Hurdles and Accelerate Research in Multiple Myeloma
Authors: Sweeney Nathan W. , Ahlstrom Jennifer M. , Fonseca Rafael , Davies Faith E. , Thompson Michael A.
Published: March 2022

PURPOSE

The study of rare diseases, such as multiple myeloma (MM), often experiences unique research hurdles that can delay or prevent lifesaving discoveries. HealthTree Cure Hub is a first-in-class software program designed to overcome these potential research hurdles.

METHODS

We assessed whether HealthTree Cure Hub improved four commonly experienced research hurdles such as (1) small numbers of patient accrual to clinical trials and research studies, (2) shallow and isolated data sets, (3) high costs to answer research questions, and (4) lack of long-term follow-up patient data.

RESULTS

As of June 2021, HealthTree Cure Hub, with its unique portal features, has attracted 9,225 patients with MM and diverse demographic backgrounds. While completing an online health profile, patients shared comprehensive data, as well as provided consent to contribute data from electronic medical records. Portal use answered research questions using patient-driven real-world data. This also cultivated relationships with patients and established communication channels that enabled continual patient contact to allow for long-term follow-up.

CONCLUSION

These results suggest that a patient-driven data capture tool such as HealthTree Cure Hub will help alleviate common research hurdles, which, in turn, will accelerate MM research, develop new hypotheses, and ultimately improve survival.
Clopidogrel Bolus is Inferior to Sustained Clopidogrel Pretreatment in Patients Undergoing Carotid Artery Stent Placement
Authors: Qureshi Adnan I. , Huang Wei , Lobanova Iryna , Ishfaq M. Fawad , French Brandi R. , Siddiq Farhan , Gomez Camilo R.
Published: March 2022

BACKGROUND:

Clopidogrel bolus is an option used before carotid artery stent (CAS) placement when sustained clopidogrel pretreatment is not used.

OBJECTIVE:

To compare the effect of clopidogrel bolus (450 mg administered ≥4 hours) with sustained clopidogrel pretreatment (48 hours or greater) before CAS among patients recruited in the Carotid Revascularization Endarterectomy versus Stenting Trial.

METHODS:

We compared the rates of primary end point (either any stroke, myocardial infarction, or death during the periprocedural period or any ipsilateral stroke within 4 years) between patients who received clopidogrel bolus and those who received sustained clopidogrel pretreatment using Cox proportional hazards analysis after adjusting for age, sex, symptomatic status, and initial severity of stenosis (≥70% vs <70%) over 4 years.

RESULTS:

The rate of periprocedural stroke (7.3% vs 3.4%, P = .03) and primary end point (11.3% vs 5.9%, P = .02) was significantly higher among patients who received clopidogrel bolus. The risk of primary end point was significantly higher in patients who received clopidogrel bolus (hazards ratio 1.9, 95% CI 1.1–3.4, P = .02) after adjusting for potential confounders. The overall mean (±standard deviation) primary end point–free survival based on Kaplan–Meier analysis was 7.0 ± 0.2 years for patients who received clopidogrel bolus and 8.9 ± 0.1 years for those who received sustained clopidogrel pretreatment (log-rank test P = .011).

CONCLUSION:

Clopidogrel bolus was associated with higher rates of adverse outcomes compared with sustained clopidogrel pretreatment in patients who underwent CAS. Therefore, clopidogrel bolus may not be equivalent to sustained clopidogrel pretreatment.
ASSFN Position Statement on Deep Brain Stimulation for Medication-Refractory Epilepsy
Authors: Gummadavelli Abhijeet , Englot Dario J. , Schwalb Jason M. , Wu Chengyuan , Gonzalez-Martinez Jorge , Niemat Joseph , Gerrard Jason L.
Published: March 2022

Neuromodulation has taken a foothold in the landscape of surgical treatment for medically refractory epilepsies and offers additional surgical treatment options for patients who are not candidates for resective/ablative surgery. Approximately one third of patients with epilepsy suffer with medication-refractory epilepsy. A persistent underuse of epilepsy surgery exists. Neuromodulation treatments including deep brain stimulation (DBS) expand the surgical options for patients with epilepsy and provide options for patients who are not candidates for resective surgery. DBS of the bilateral anterior nucleus of the thalamus is an Food and Drug Administration-approved, safe, and efficacious treatment option for patients with refractory focal epilepsy. The purpose of this consensus position statement is to summarize evidence, provide recommendations, and identify indications and populations for future investigation in DBS for epilepsy. The recommendations of the American Society of Functional and Stereotactic Neurosurgeons are based on several randomized and blinded clinical trials with high-quality data to support the use of DBS to the anterior nucleus of the thalamus for the treatment of refractory focal-onset seizures.
[18F]FDG-PET/CT Demonstration of Young Adult Onset Stills Disease Mimicking Lymphoma
Authors: Nawwar Ayah Adel , Searle Julie , Hodby Katherine , Chavda Nikesh Dhiraj , Qamhia Naim , Lyburn Iain Douglas
Published: March 2022

Adult-onset Still’s disease (AOSD) is an inflammatory disease of unknown aetiology, with no specific diagnostic tests. A 17-year-old female presented with fevers, night sweats and weight loss. Markedly FDG avid lymphadenopathy, and diffuse marrow and splenic uptake were demonstrated on [18F]FDG-PET/CT, most suggestive of lymphoma. After extensive investigations, the working diagnosis of AOSD was made. Other conditions, such AOSD, in addition to lymphoproliferative disorders, should be considered in the differential diagnosis of widespread avid lymphadenopathy in a teenager/young adult