bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equate groups: An innovative method to link multi-item instruments across studies
Authors: Eekhout Iris , Weber Ann M. , Buuren Stef 
Published: March 2022

Abstract
Background: Combining existing data sets for meta-analyses enables analyses across multiple contexts and conditions. However, the use of different measurement instruments in different studies hampers comparability. This paper proposes a novel method to link tools administered across multiple studies. Methods: The proposed methodology starts by forming equate groups, i.e., sets of items from different instruments with similar meanings. We fit the Rasch model to all data, with the additional restriction that items within the same equate group obtain identical difficulty estimates. The main modelling task is to divide equate groups into active (where the restriction holds) and passive (without the restriction) groups. We studied the method's performance in a simulation study and illustrated its practical application to early childhood development. Results: If we treat all equate groups as passive, the difficulty estimates of the identical items are unduly affected by differences in abilities between the study samples. On the other hand, when abilities are similar across samples, it is safer to set all equate groups to passive because any mis-specified equate groups can lead the restricted model to underperform. Our method deals with the common case between these two extremes where 1) we suspect a priori ability differences between samples, and 2) at least some of the items are equivalent across instruments. Conclusions: Our equating method presents a flexible alternative to the classic common-item nonequivalent-group design for existing data. We conclude that equate groups are an economical and exciting concept that enables insightful statistical analysis from seemingly disparate data sources.
Evaluation of the Gut Microbiome and Sex Hormones in Postmenopausal Women with Newly Diagnosed Hormone Receptor-Positive Breast Cancer Versus Healthy Women: A Prospective Case-Control Study
Authors: Kwa Maryann , Ruggles Kelly V , Novik Yelena , Franke Adrian A , Volkova Angelina , Flores Karina , Blaser Martin J , Speyer James , Oratz Ruth , Meyers Marleen , Jhaveri Komal , Fadel Ezeddin , Zamora Shelby , Heguy Adriana , Schluter Jonas , Adams Sylvia 
Published: March 2022

Abstract
Purpose
The functional composition and diversity of the gut microbiome (estrobolome) may affect breast cancer risk by modulation of systemic sex hormones. Gut bacteria with β-glucuronidase enzymatic activity may deconjugate estrogens, leading to increased estrogen reabsorption into the circulation thereby increasing breast cancer risk. We investigated the relationship between the gut bacterial microbiome and endogenous estrogens and related sex hormones in women with hormone receptor-positive breast cancer compared to healthy control women.
Methods
In this prospective case-control study, postmenopausal women (n = 46) with newly diagnosed stage I-III estrogen and/or progesterone receptor-positive breast cancer were compared with healthy postmenopausal female controls (n = 22). Bacterial composition of the gut microbiome was analyzed by 16S rRNA gene sequencing from fecal specimens. Plasma and urine sex hormones were quantified using high-performance liquid chromatography/mass spectrometry.
Results
We found evidence that some β-glucuronidase positive bacteria were enriched in the breast cancer patients compared to healthy controls, whereas abundances of some β-glucuronidase negative bacteria were reduced. There was also a wide distribution of prevalence of β-glucuronidase positive taxa in both the breast cancer subjects and healthy controls, as well as higher probability of breast cancer subjects having higher average β-glucuronidase levels. Significant differences were found in endogenous progesterone levels between the breast cancer patients and healthy controls.
Conclusion
This pilot study showed differences in the gut microbiome and endogenous progesterone levels among postmenopausal women with hormone receptor-positive breast cancer compared with healthy controls. These interesting findings may have implications for breast cancer risk and prevention and warrant further exploration.
Development of an efficient veterinary rabies vaccine production process in the avian suspension cell line AGE1.CR.pIX
Authors: Trabelsi Khaled , Zakour Meriem Ben , Jordan Ingo , Sandig Volker , rourou Samia , Kallel Hela 
Published: March 2022

Abstract
Background: Mass vaccination of dogs as important rabies reservoir is proposed to most effectively reduce and eliminate rabies also in humans. However, a minimum coverage of 70% needs to be achieved for control of the disease in zoonotic regions. In numerous developing countries, dog vaccination rate is still dangerously low because of economic constraints and due to a high turnover in dog populations. Improved vaccine production processes may help to alleviate cost and supply limitations. In this work, we studied and optimized the replication and vaccine potency of PV rabies virus strain in the muscovy-duck derived AGE1.CR and AGE1.CR.pIX suspension cell lines.Results: The BHK-21-adapted PV rabies virus strain replicated efficiently in the avian cell lines without requirement for prior passaging.CR.pIX was previously shown to augment heat shock responses and supported slightly higher infectious titers compared to the parental CR cell line. Both cell lines allowed replication of rabies virus also in absence of recombinant IGF, the only complex component of the chemically defined medium that was developed for the two cell lines. After scale-up from optimization experiments in shake flask to production in 7-l bioreactors peak virus titers of 2.4x108 FFU/ml were obtained. The potency of inactivated rabies virus harvest according to the NIH test was 3.5 IU/ml. Perfusion with the chemically defined medium during the virus replication phase improved the potency of the vaccine 2-fold, and increased the number of doses 9.6 fold.Conclusion: This study demonstrates that a rabies vaccine for animal vaccination can be produced efficiently in the AGE1.CR.pIX suspension cell line in a scalable process in chemically defined medium.
Clinicopathologic Features, Chronic Renal Damage and Short-Term Outcomes of Glomerular Diseases in a Middle East Tertiary Care Center
Authors: Abdulaziz Hoda M. M. , Sayed-Ahmed Nagy , Atwa Dina Abdallah Ibrahim , Nassar Mohammed K. 
Published: March 2022

Abstract
Background
Glomerular diseases (GDs) place a significant burden on patients and health-care systems, and they are a leading cause of end-stage renal disease (ESRD) globally. There is no national register for GDs in Egypt, and the outcomes of GDs are not extensively examined. As a result, studying GDs patterns and outcomes, as well as the association between chronic renal injury at presentation and GDs outcome, was of great interest.
Methods
Patients with biopsy-proven GDs, presenting to an Egyptian tertiary care center were enrolled and prospectively followed-up for 6 months, death or reaching ESRD. Chronic renal damage was assessed at diagnosis by the total renal chronicity.
Results
Sixty-six individuals with biopsy-confirmed GDs were enrolled in the study. The most common reasons for a renal biopsy were unexplained kidney function decrease (62%), followed by subnephrotic (23%) and nephrotic presentation (15%). The most common histological patterns were diffuse proliferative glomerulonephritis (GN), membranoproliferative GN (MPGN), and sclerosing GN. Primary and secondary GDs made up 30.3% and 69.7% of the cases, respectively. At the end of the 6-month follow-up, 28 patients had recovered their renal function, 19 had advanced to ESRD, and 7 had died. The most significant predictors of renal recovery were hemoglobin level and the total renal chronicity score.
Conclusion
In this tertiary care center Egyptian cohort, secondary GDs appear to be more frequent than primary GDs, diffuse proliferative GN was the most common histopathological pattern, and rapid renal recovery was not the rule in this short period. The renal chronicity score could accurately predict the renal outcome.
Trial Registration:
Approval for this study was granted by the Mansoura Faculty of Medicine Institutional Research Board (IRB) (approval no. MD/17.05.13).
Constitutive Chitosanase from Bacillus Thuringiensis B-387 and its Potential for Preparation of Antimicrobial Chitooligomers
Authors: Aktuganov Gleb , Safina Violetta , Galimzianova Nailya , Gilvanova Elena , Kuzmina Lyudmila , Melentiev Alexander , Baymiev Andrei , Lopatin Sergey 
Published: March 2022

Abstract
Ability of the insecticide strain B. thuringiensis var. dendrolimus B-387 to high constitutive production (3-12.5 U/mL) of extracellular chitosanase was found for first time. The enzyme was purified in 94-fold by ultrafiltration, affinity sorption and cation-exchanged chromatography and characterized biochemically. Molecular mass of the chitosanase determined using SDS-PAGE is 40 kDa. Temperature and pH-optima of the enzyme are 55◦C and pH 6.5, respectively; the chitosanase was stable under 50–60◦C and pH 4-10.5. Purified chitosanase most rapidly (Vmax~43 µM/mL×min, KM~0.22 mg/mL, kcat ~ 4.79×104 s− 1) hydrolyzed soluble chitosan of deacetylation degree (DD) 85% by endo-mode, and no degraded colloidal chitin, CM-cellulose and some other glucans. Main reaction products of the chitosan enzymolysis included chitobiose, chitotriose and chitotetraose. In addition to small chitooligosaccharides (CHOs), studied chitosanase generated also low-molecular weight chitosan (LMWC) with average Mw in range 14–46 kDa and recovery 14–35%, depending of enzyme / substrate ratio and incubation temperature. Chitosan (DD 85 and 50%) oligomers prepared using crude chitosanase from B. thuringiensis B-387 indicated higher antifungal and antibacterial activities in vitro in comparison with initial polysaccharides. The findings evidence the chitosanase B-387 promising for bioactive CHOs preparation.
AI-powered pan-species computational pathology: bridging clinic and wildlife care
Authors: AbdulJabbar Khalid , Castillo Simon , Hughes Katherine , Davidson Hannah , Boddy Amy , Abegglen Lisa , Murchison Elizabeth , Graham Trevor , Spiro Simon , Palmieri Chiara , Yuan Yinyin 
Published: March 2022

Abstract
Cancers occur across species. Understanding what is consistent and varies across species can provide new insights into cancer initiation and evolution, with significant implications for advancing human healthcare, animal welfare, and wildlife conservation. We built the pan-species cancer digital pathology atlas (PANCAD) and conducted the first pan-species study of computational comparative pathology using a supervised convolutional neural network algorithm trained on human samples. The artificial intelligence algorithm achieves high accuracy in measuring immune response through single-cell classification for two transmissible cancers (canine transmissible venereal tumour, 0.94; Tasmanian devil facial tumour disease, 0.88). Furthermore, in 18 other vertebrate species (mammalia=11, reptilia=4, aves=2, and amphibia=1), accuracy (0.57-0.94) was influenced by cell morphological similarity preserved across different taxonomic groups, tumour sites, and variations in the immune compartment. A new metric, named morphospace overlap, was developed to guide veterinary pathologists towards rational deployment of this technology on new samples. This study provides the foundation and guidelines for transferring artificial intelligence technologies to veterinary pathology based on a new understanding of morphological conservation, which could vastly accelerate new developments in veterinary medicine and comparative oncology.
Landscape-scale repercussions of global action for climate and biodiversity protection
Authors: von Jeetze Patrick , Weindl Isabelle , Johnson Justin , Borrelli Pasquale , Panagos Panos , Bacca Edna Molina , Karstens Kristine , Humpenöder Florian , Dietrich Jan , Minoli Sara , Müller Christoph , Lotze-Campen Hermann , Popp Alexander 
Published: March 2022

Abstract
Habitat loss and biotic homogenisation are undermining the stable supply of nature’s contributions to people (NCP) that underpin the long-term productivity and resilience in farmed landscapes. Growing demand for land-based products, and global ambitions for climate and area-based protection are likely to increase land competition, which could further drive intensification and landscape simplification. Yet, little is known about the repercussions of such global land-use transitions for key regulating NCP in farmed landscapes. By using an integrated, globally consistent modelling approach, we analyse how global land-use dynamics could drive fine-scale changes in landscape structure, pollination, and soil erosion across different land-use futures. Here we show that, if not addressed, increased land competition and concurrent landscape-scale changes could reinforce global negative trends for key regulating NCP. However, we also find that global efforts towards land carbon uptake and biodiversity conservation could be augmented to produce co-benefits in agricultural settings. Our results indicate that integrating at least 20 % (semi-)natural habitat into farmed landscapes would not cause trade-offs of carbon emissions or natural land conversion, despite shifts in spatial land-use patterns. Our findings underline the importance of considering landscape-scale repercussions while assessing changes in multiple material and regulating NCP across different land-use futures.
The clinical relevance of unfolded protein response signaling in breast cancer
Authors: Oshi Masanori , Roy Arya Mariam , Gandhi Shipra , Tokumaru Yoshihisa , Yan Li , Yamada Akimitsu , Endo Itaru , Takabe Kazuaki 
Published: March 2022

Abstract
Purpose
Protein homeostasis regulated by the Endoplasmic Reticulum (ER) is a recognized process involved in cancer progression. ER stress activates the Unfolded Protein Response (UPR) and has been implicated in a variety of cancers. Given the role of the UPR activation in carcinogenesis, we hypothesized that UPR activation could be associated with pathological progression, higher clinical stage, and worse survival in breast cancer.
Methods
A total of 4,416 breast cancer patients from multiple independent cohorts were analyzed. We defined the UPR pathway score by the degree of enrichment by Gene Set Variant Analysis and median was used to divide high vs low score groups in each cohort.
Results
High UPR breast cancer significantly enriched not only cell proliferation-related but also other pro-cancerous gene sets consistently in both METABIC and GSE96058 cohort. Majority of UPR pathway score high cells in the bulk tumor were tumor cells compared to other cells, including stromal, T-, B-, and myeloid-cells (p < 0.001). UPR score was significantly associated with advanced stage, high grade, and triple negative breast cancer (TNBC) (all p < 0.001). High UPR breast cancer was associated with worse patient survival in both cohorts (all p < 0.001). Among breast cancer subtype, ER-positive/HER2-negative breast cancer with high UPR was significantly associated with worse survival, but neither HER-positive nor TNBC. High UPR ER-positive/HER2-negative breast cancer was infiltrated with high level of Th1 and Th2 cells, M1 macrophage, and plasma cells. On the other hand, they were significantly infiltrated with high level of several types of stromal cells in tumor microenvironment (all p < 0.001). Finally, high UPR metastatic breast cancer was also associated with worse patient survival (p = 0.041).
Conclusion
UPR signaling is associated with cancer aggressiveness, and worse survival, especially ER-positive/HER2-negative breast cancer subtype.
Microbacterium caeni sp. nov., a novel species isolated from sludge in Yeosu, Korea
Authors: Jung You-Jung , Lee Sang-Hoon , Kim Na-Kyung , Yoon Hyeokjun , Jeong Garam , Lee Byoung-Hee , Park Hee-Deung , Hur Moonsuk 
Published: March 2022

Abstract
A gram-positive, white-pigmented, aerobic, rod-shaped bacterium, designated strain NIBRBAC000506063T, was isolated from a sludge sample from Yeosu, Korea. Optimal growth of strain NIBRBAC000506063T was observed at 25 °C and pH 8.0, in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NIBRBAC000506063T belongs to the genus Microbacterium and is closely related to Microbacterium invictum DC-200T (98.3 % sequence similarity). Next-generation sequencing (NGS) analysis indicated that the strain NIBRBAC000506063T genome was comprised of one circular chromosome (2,576,190 bp, G+C content: 69.14 mol%) and one plasmid (465,341 bp, G+C content: 68.45 mol%) with 4,046 coding sequences, 47 tRNAs, and 4 rRNAs. The major respiratory isoprenoid quinone was MK12, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids, and glycolipids. The major fatty acids of strain NIBRBAC000506063T were C16:0 iso and C15:0 anteiso, and the G+C content of the genomic DNA was 69.5 mol%. Based on the polyphasic taxonomic data obtained in this study, it is proposed that strain NIBRBAC000506063T represents a novel species of the genus Microbacterium. The type strain is NIBRBAC000506063T (=KCTC49453T =DSM111108T).
Screening of probable carcinogenic agonists of Aryl Hydrocarbon Receptor (AhR) from various pesticides using computational molecular biology approach
Authors: Singh Arshwinder , Singh Rhythumwinder , Kaur Prabhjot , Upadhyay Atul Kumar 
Published: March 2022

Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated cytosolic transcription factor. Once activated AhR stimulates the pathways that are directly or indirectly linked to inflammation and breast cancer. Exogenous agonists of AhR including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzopyrene are found to be carcinogenic in nature. Breast cancer being the most prevalent cancer, makes it an important aspect to look for new exogenous agonists of AhR with carcinogenic properties. In this study, an effort has been made to screen new agonist from pesticides, which may have role in breast cancer development. Primarily, the structure of AhR PAS domain was determined by using SWISS-MODEL server. Thereafter, probable carcinogenic molecules from pesticides were screened and molecular docking studies were performed to identify potential binders with good energetics. Detailed structural analysis have resulted in four molecules namely, Isopyrazam, Noviflumuron, Oxyfluorfen and Resmethrin, that showed higher negative binding energy, when compared to TCDD. Molecular Dynamics Simulation studies of AhR- Isopyrazam were further carried out to prove the stability of the complex which suggests that presence of these agonist in different pesticides may have major role to play to cause breast cancer. Avoiding or minimizing the use of these compounds in the pesticides may be a strategy to combat breast cancer in future.
Study Protocol. Evaluating the life-course health impact of a city-wide system approach to improve air quality in Bradford, UK: A quasi-experimental study with implementation and process evaluation
Authors: McEachan Rosemary R C , Rashid Rukhsana , Santorelli Gillian , Tate James , Thorpe Jamie , McQuaid James B , Wright John , Pickett Kate E , Pringle Kirsty , Bojke Laura , Jones Sally , Islam Shahid , Walker Simon , Yang Tiffany C , Bryant Maria 
Published: March 2022

Abstract
Background
Air quality is a major public health threat linked to poor birth outcomes, respiratory and cardiovascular disease, and premature mortality. Deprived groups and children are disproportionately affected. Bradford will implement a Clean Air Zone (CAZ) as part of the Bradford Clean Air Plan (B-CAP) in 2022 to reduce pollution, providing a natural experiment. The aim of the current study is to evaluate the impact of the B-CAP on health outcomes and air quality, inequalities and explore value for money. An embedded process and implementation evaluation will also explore barriers and facilitators to implementation, impact on attitudes and behaviours, and any adverse consequences.
Methods
The study is split into 4 work packages (WP). WP1A: 20 interviews with decision makers, 20 interviews with key stakeholders; 10 public focus groups and documentary analysis of key reports will assess implementation barriers, acceptability and adverse or unanticipated consequences at 1 year post-implementation (defined as point at which charging CAZ goes ‘live’). WP1B: A population survey (n = 2000) will assess travel behaviour and attitudes at baseline and change at 1 year post-implementation). WP2: Routine air quality measurements will be supplemented with data from mobile pollution sensors in 12 schools collected by N = 240 pupil citizen scientists (4 within, 4 bordering and 4 distal to CAZ boundary). Pupils will carry sensors over four monitoring periods over a 12 month period (two pre, and two post-implementation). We will explore whether reductions in pollution vary by CAZ proximity. WP3A: We will conduct a quasi-experimental interrupted time series analysis using a longitudinal routine health dataset of > 530,000 Bradford residents comparing trends (3 years prior vs 3 years post) in respiratory health (assessed via emergency/GP attendances. WP3B: We will use the richly-characterised Born in Bradford cohort (13,500 children) to explore health inequalities in respiratory health using detailed socio-economic data. WP4: will entail a multi-sectoral health economic evaluation to determine value for money of the B-CAP.
Discussion
This will be first comprehensive quasi-experimental evaluation of a city-wide policy intervention to improve air quality. The findings will be of value for other areas implementing this type of approach.
Registration:
ISRCTN67530835 https://doi.org/10.1186/ISRCTN67530835
Clinical Study of α 2-MG, PCX, AFU, RBP-4 and CysC in type 2 Diabetes Mellitus and Diabetic Nephropathy
Authors: Li JingJing , Yan ZhaoLi 
Published: March 2022

Abstract
BackgroundDiabetic nephropathy (DN) is one of the most common chronic complications of diabetes mellitus (DM). The changes of α2-macroglobulin (α2-MG), podocalysin (PCX), α-L-fucosidase (AFU), retinol binding protein-4 (RBP-4), cystatin C(CysC) and clinical indicators in patients with or without DN.To explore their role and significance in type 2 diabetes (T2DM) and DN.MethodsA total of 203 T2DM patients admitted to hospital from December 2018 to December 2020 were collected and divided into DN group (115 cases) and NDN group (88 cases). Urine α2-MG, PCX and AFU levels, serum RBP-4 and CysC levels were determined, and other clinical indicators were collected.Results1.Comparison of general data between groups: the levels of CysC, RBP-4, α2-MG/UCr,PCX/UCr and AFU/UCr in DN group were higher than those in NDN group (P<0.05). 2. Comparison of ACR stage and renal function stage of CKD: ①ACR stage: CysC, RBP-4, α2-MG/UCr,PCX/UCr,AFU/UCr increased with the increase of ACR stage(P<0.05). ② Renal function stage of CKD: CysC, RBP-4,α2-MG/UCr, PCX/UCr, AFU/UCr increased with the increase of renal function stage of CKD(P<0.05). 3. Partial correlation analysis after adjusting gender and age: CysC, RBP-4,α2-MG/UCr,PCX/UCr, AFU/UCr were positively correlated with UACR, Scr, Urea, UTP/24h, NLR, but negatively correlated with eGFR(P<0.05). 2.ROC curve: (1) Analysis of single index on DN diagnosis: AUCROC of UACR, eGFR, CysC,RBP-4, α2-MG/UCr,PCX/UCr and AFU/UCr were 0.97, 0.77, 0.80, 0.76, 0.83, 0.86, 0.79, respectively. (2) Analysis of combined indicators for DN diagnosis:AUCROC of α2-MG/UCr+PCX/UCr,α2-MG/UCr+AFU/UCr,α2-MG/UCr+PCX/UCr+AFU/UCr,α2-MG/UCr+PCX/UCr+AFU/UCr were 0.88, 0.88, 0.86, 0.89.Conclusion: ﻿1.α2-MG, PCX and AFU are related to the occurrence and development of DN. 2. RBP-4, CysC, PCX, AFU and α2-MG have better diagnostic value,but UACR has the best diagnostic value. 3.PCX can reflect early renal damage.