bluuebunny/crossref_metadata_2025_split huggingface dataset:
735 An Unusual Case of Cervical Potts Disease in A Pediatric Patient
Authors: Pandya B , Shogan A 
Published: October 2021

Abstract
Pott’s disease is a form of extrapulmonary tuberculosis (TB) affecting the spine. Approximately 10% of individuals with extrapulmonary TB will have skeletal manifestations with the most common area affected being the spine, followed by the hip and knee. Within the spine, Pott’s disease has a predilection for affecting the thoraco-lumbar region, with the cervical spine being the least affected. Here, we report a case of cervical Pott’s disease in a 16-year-old child, with no risk factors for TB, presenting with neck pain and stiffness. Initial blood results were unremarkable, but a CT scan showed a C5 vertebral body fracture and mild canal stenosis. A sagittal MRI scan demonstrated canal stenosis and a pathologic compression fracture of the C5 vertebrae, a soft tissue mass extending into the epidural and prevertebral spaces and associated cervical cord compression. A trans-oral biopsy confirmed TB and a diagnosis of Pott’s disease. She underwent HALO placement and needed further fusion surgery. She was started on anti-tuberculous therapy and made a good recovery post-operatively.
1658 Duodenal Stricture Secondary to Chronic Pancreatitis; A Case Report
Authors: Heer B 
Published: October 2021

Abstract
The complications of chronic pancreatitis are well established; however, the incidence of duodenal strictures in the context of previous necrotising pancreas is uncommon.
I herein report the case of a 30-year Caucasian woman who presents with reduced oral intake, vomiting and profound cachexia. Medical history of note includes necrotising pancreatitis and umbilical hernia repair. Computed tomography scan revealed multiple cystic collections in the anterior pararenal space. Oesophagogastroduodenoscopy (OGD) revealed a duodenal stricture, which was histologically benign. Endoscopic insertion of a percutaneous jejunostomy (PEJ) unfortunately failed.
Upon counselling with the patient, the decision was made to perform a laparotomy with loop gastrojejunostomy and jejunostomy tube insertion. The patient was subsequently able to be fed, initially with the aid of dieticians, and trained for independent care at home.
This case highlights the uncommon complication of duodenal stricture in the context of chronic pancreatitis, and the importance of timely diagnosis and management.
1423 Quality and Efficacy of Multidisciplinary Team (MDT) Discussion Quality Assessment Tools and Checklists: A Systematic Review
Authors: Brown G , Young A , Rymell R 
Published: October 2021

Abstract

Aim
MDT discussion is the gold standard for cancer care in the UK. With the cancer incidence and complexity of treatments both increasing, demand for MDT discussion is growing. The need for efficiency, whilst maintaining high standards, is therefore clear. Paper-based MDT quality assessment tools and discussion checklists may represent a practical method of monitoring and improving MDT practice. This review aims to describe and appraise these tools, as well as consider their value to quality improvement.

Method
MEDLINE, Embase and PsycInfo were searched using pre-defined terms. PRISMA methodology was followed throughout. Studies were included if they described the development of a relevant tool/checklist, or if an element of the methodology further informed tool quality assessment. To investigate efficacy, studies using a tool as a method of quality improvement in MDT practice were also included. Study quality was appraised using the COSMIN risk of bias checklist or the Newcastle-Ottawa scale, depending on study type.

Results
The search returned 6888 results. 17 studies were included, and 6 different tools were identified. Overall, methodological quality in tool development was adequate to very good for assessed aspects of validity and reliability. Clinician feedback was positive. In one study, the introduction of a discussion checklist improved MDT ability to reach a decision from 82.2% to 92.7%. Improvement was also noted in the quality of information presented and the quality of teamwork.

Conclusions
Several tools for assessing and guiding MDT discussions are available. Although limited, current evidence indicates sufficient rigour in their development and their potential for quality improvement.
A welfare analysis of Norway’s export promotion programme for whitefish
Authors: Kinnucan Henry W , Das Abhipsita , Pettersen Ingrid Kristine 
Published: October 2021

Abstract
Norway recently increased the effective levy used to fund its export promotion programme for whitefish by 21 per cent. Study results suggest the intensified programme is welfare increasing. The net social gain, defined as the difference between the increase in economic surplus associated with the increased advertising and the decrease in economic surplus associated with the increased effective levy, is estimated at between $20 million and $136 million per year, for a best-bet estimate $60 million. The associated benefit–cost ratio (BCR), defined as the ratio of the aforementioned changes in economic surplus, is estimated at between 11 and 71, for a best-bet estimate of 32. The BCR is invariant to the supply elasticity. The invariance property is useful as it implies that the BCR can be estimated using strictly demand-side information; there is no need to estimate the supply side of the market. The current levy of 0.75 per cent appears to be well below the levy that would maximise producer welfare.
A Mixed-Effects Model of Associations Between Interleukin-6 and Hippocampal Volume
Authors: Harrell Erin R , Bui Chuong , Newman Sharlene D ,   Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: October 2021

Abstract
Previous studies report hippocampal volume loss can help predict conversion from normative aging to mild cognitive impairment to dementia. Additionally, a growing literature indicates that stress-related allostatic load may increase disease vulnerability. The current study examined the relationship between stress-related cytokines (ie, interleukin-6 [IL-6]), cognition as measured by Mini-Mental State Examination (MMSE) scores, and hippocampal volume. Mixed models were employed to examine both within- (across time) and between-subject effects of IL-6 and hippocampal volume on MMSE score among 566 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). The within-subject analysis found left hippocampal volume significantly (p = .009) predicted MMSE score. Between-subject analysis found the effect of IL-6 on MMSE was moderated by right hippocampal volume (p = .001). These results replicate previous findings and also extend prior work demonstrating stress-related cytokines may play a role in Alzheimer’s disease progression.
Tres desafíos de legitimidad del Sistema Interamericano de Derechos HumanosThree legitimacy challenges to the Inter-American System of Human Rights
Authors: Bernal Carlos 
Published: October 2021

Abstract
This article analyses three core challenges that hinder the legitimacy of the Inter-American System of Human Rights. They relate to the Inter-American standards, the observance of due process, and the nature and proportionality of compensatory remedies. The analysis accounts for challenges, and outlines a proposal for overcoming them as well.
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
Authors: Jagoda Evelyn , Xue James R , Reilly Steven K , Dannemann Michael , Racimo Fernando , Huerta-Sanchez Emilia , Sankararaman Sriram , Kelso Janet , Pagani Luca , Sabeti Pardis C , Capellini Terence D 
Published: October 2021

Abstract
Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.
3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database
Authors: Quan Cheng , Ping Jie , Lu Hao , Zhou Gangqiao , Lu Yiming 
Published: October 2021

Abstract
The rapid development of single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) technologies presents both challenges and opportunities for the annotation of noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variant annotation, to expand its applications to structural variation (SV) and to implement variant annotation down to single-cell resolution. The updates of 3DSNP include (i) annotation of 108 317 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures, (ii) evaluation of the accessible chromatin peaks flanking the variants across 126 cell types/subtypes in 15 human fetal tissues and 54 cell types/subtypes in 25 human adult tissues by integrating scATAC-seq data and (iii) expansion of Hi-C data to 49 human cell types. In summary, this version is a significant and comprehensive improvement over the previous version. The 3DSNP v2.0 database is freely available at https://omic.tech/3dsnpv2/.
piRBase: integrating piRNA annotation in all aspects
Authors: Wang Jiajia , Shi Yirong , Zhou Honghong , Zhang Peng , Song Tingrui , Ying Zhiye , Yu Haopeng , Li Yanyan , Zhao Yi , Zeng Xiaoxi , He Shunmin , Chen Runsheng 
Published: October 2021

Abstract
Piwi-interacting RNAs are a type of small noncoding RNA that have various functions. piRBase is a manually curated resource focused on assisting piRNA functional analysis. piRBase release v3.0 is committed to providing more comprehensive piRNA related information. The latest release covers &gt;181 million unique piRNA sequences, including 440 datasets from 44 species. More disease-related piRNAs and piRNA targets have been collected and displayed. The regulatory relationships between piRNAs and targets have been visualized. In addition to the reuse and expansion of the content in the previous version, the latest version has additional new content, including gold standard piRNA sets, piRNA clusters, piRNA variants, splicing-junction piRNAs, and piRNA expression data. In addition, the entire web interface has been redesigned to provide a better experience for users. piRBase release v3.0 is free to access, browse, search, and download at http://bigdata.ibp.ac.cn/piRBase.
SPIRE—a software tool for bicontinuous phase recognition: application for plastid cubic membranes
Authors: Hain Tobias M , Bykowski Michał , Saba Matthias , Evans Myfanwy E , Schröder-Turk Gerd E , Kowalewska Łucja 
Published: October 2021

Abstract
Bicontinuous membranes in cell organelles epitomize nature’s ability to create complex functional nanostructures. Like their synthetic counterparts, these membranes are characterized by continuous membrane sheets draped onto topologically complex saddle-shaped surfaces with a periodic network-like structure. Their structure sizes, (around 50–500 nm), and fluid nature make transmission electron microscopy (TEM) the analysis method of choice to decipher their nanostructural features. Here we present a tool, Surface Projection Image Recognition Environment (SPIRE), to identify bicontinuous structures from TEM sections through interactive identification by comparison to mathematical “nodal surface” models. The prolamellar body (PLB) of plant etioplasts is a bicontinuous membrane structure with a key physiological role in chloroplast biogenesis. However, the determination of its spatial structural features has been held back by the lack of tools enabling the identification and quantitative analysis of symmetric membrane conformations. Using our SPIRE tool, we achieved a robust identification of the bicontinuous diamond surface as the dominant PLB geometry in angiosperm etioplasts in contrast to earlier long-standing assertions in the literature. Our data also provide insights into membrane storage capacities of PLBs with different volume proportions and hint at the limited role of a plastid ribosome localization directly inside the PLB grid for its proper functioning. This represents an important step in understanding their as yet elusive structure–function relationship.
Single-cell genomics in plants: current state, future directions, and hurdles to overcome
Authors: Cuperus Josh T 
Published: October 2021

Abstract
Single-cell genomics has the potential to revolutionize the study of plant development and tissue-specific responses to environmental stimuli by revealing heretofore unknown players and gene regulatory processes. Here, I focus on the current state of single-cell genomics in plants, emerging technologies and applications, in addition to outlining possible future directions for experiments. I describe approaches to enable cheaper and larger experiments and technologies to measure multiple types of molecules to better model and understand cell types and their different states and trajectories throughout development. Lastly, I discuss the inherent limitations of single-cell studies and the technological hurdles that need to be overcome to widely apply single-cell genomics in crops to generate the greatest possible knowledge gain.
qGL3/OsPPKL1 induces phosphorylation of 14-3-3 protein OsGF14b to inhibit OsBZR1 function in brassinosteroid signaling
Authors: Gao Xiuying , Zhang Jiaqi , Cai Guang , Du Huaying , Li Jianbo , Wang Ruqin , Wang Yuji , Yin Jing , Zhang Wencai , Zhang Hongsheng , Huang Ji 
Published: October 2021

AbstractBrassinosteroids (BRs) play essential roles in regulating plant growth and development, however, gaps still remain in our understanding of the BR signaling network. We previously cloned a grain length quantitative trait locus qGL3, encoding a rice (Oryza sativa L.) protein phosphatase with Kelch-like repeat domain (OsPPKL1), that negatively regulates grain length and BR signaling. To further explore the BR signaling network, we performed phosphoproteomic analysis to screen qGL3-regulated downstream components. We selected a 14-3-3 protein OsGF14b from the phosphoproteomic data for further analysis. qGL3 promoted the phosphorylation of OsGF14b and induced the interaction intensity between OsGF14b and OsBZR1. In addition, phosphorylation of OsGF14b played an important role in regulating nucleocytoplasmic shuttling of OsBZR1. The serine acids (Ser258Ser259) residues of OsGF14b play an essential role in BR-mediated responses and plant development. Genetic and molecular analyses indicated that OsGF14b functions as a negative regulator in BR signaling and represses the transcriptional activation activity of OsBZR1. Collectively, these results demonstrate that qGL3 induces the phosphorylation of OsGF14b, which modulates nucleocytoplasmic shuttling and transcriptional activation activity of OsBZR1, to eventually negatively regulate BR signaling and grain length in rice.
COVID-19 outcomes among pregnant and nonpregnant women at reproductive age in Egypt
Authors: BahaaEldin Hala , El Sood Hanaa Abu , Samy Sahar , Khader Yousef , AbdelFatah Mohamad , Hassany Mohamed , Afifi Salma , Eid Alaa 
Published: October 2021

Abstract

Background
To describe demographic, clinical and epidemiological characteristics of pregnant and nonpregnant women with confirmed COVID-19 at reproductive age and determine risk factors of COVID-19 severe outcomes during pregnancy.

Methods
A retrospective study for females aged 18–49 with confirmed COVID-19 by RT-PCR in Egypt, February–July 2020. Data were obtained from Egypt National Surveillance, bivariate and multivariate analysis for demographic and clinical characteristics and outcomes of COVID-19 between pregnant and nonpregnant women including ICU admission, need for ventilator and death was performed.

Results
A total of 23 095 females were identified, with mean (SD) age of 35.1 (8.1) year. Of those, 408 (1.8%) were pregnant, with mean (SD) age of 29.3 (8.1) years. Compared to nonpregnant, pregnant patients were more likely to be admitted to hospital (OR = 1.7 CI = 1.4–2.1), ICU (OR = 2.4, CI = 1.3–4.3), need ventilator (OR = 3.9, CI = 2.1–7.4) and have severe outcome (OR = 3.0, CI = 1.9–4.7). Factors associated with severe outcome included: pregnancy, age &gt; 30 years, underlying medical conditions, and living in rural areas.

Conclusion
Pregnant women with COVID-19 are at higher risk of severe symptoms and outcome including ICU admission, requiring ventilator and death. To reduce risk of severe outcome, counseling about for seeking medical care and health education about COVID-19 preventive measures should be performed.
Shaping the Future of Social Work Practice in Healthcare: Addressing COVID-19 Needs through Integrated Primary Care
Authors: Dennelly Lauren , Sousa Cindy , Roberts Kate 
Published: October 2021

Abstract
COVID-19 has illustrated the urgency of promoting integrated healthcare as the model of the future, with social workers not only supporting the physical and mental health of providers and patients, but also leading efforts to transform systems, policies, and social work education. Primary care, where the role of social workers is continuing to grow, is a central location for integrating the treatment of medical, social, and behavioral problems. In these settings, social workers can take the lead to meet community needs, assist in public health efforts, and bolster the frontline medical workforce. The following article reflects upon what we as social workers have learned a year into the global pandemic and how we can apply this knowledge to shaping the future of social work in primary care. Authors consider how the multiple medical and psychosocial needs of patients affected by COVID-19 are addressed in primary care through three core functions of social work: providing behavioral healthcare, coordinating care, and undertaking population health-based interventions. Article ends with a discussion about how social work can respond to the urgent task of transforming health within the context of social work practice, policy, and education for the next generation of healthcare social workers.
A CRISPR/Cas9 method facilitates efficient oligo-mediated gene editing in Debaryomyces hansenii
Authors: Strucko Tomas , Andersen Niklas L , Mahler Mikkel R , Martínez José L , Mortensen Uffe H 
Published: October 2021

Abstract
Halophilic and osmotolerant yeast Debaryomyces hansenii has a high potential for cell factory applications due to its resistance to harsh environmental factors and compatibility with a wide substrate range. However, currently available genetic techniques do not allow the full potential of D. hansenii as a cell factory to be harnessed. Moreover, most of the currently available tools rely on the use of auxotrophic markers that are not suitable in wild-type prototrophic strains. In addition, the preferred non-homologous end-joining (NHEJ) DNA damage repair mechanism poses further challenges when precise gene targeting is required. In this study, we present a novel plasmid-based CRISPRCUG/Cas9 method for easy and efficient gene editing of the prototrophic strains of D. hansenii. Our toolset design is based on a dominant marker and facilitates quick assembly of the vectors expressing Cas9 and single or multiple single-guide RNAs (sgRNAs) that provide the possibility for multiplex gene engineering even in prototrophic strains. Moreover, we have constructed NHEJ-deficient D. hansenii that enable our CRISPRCUG/Cas9 tools to support the highly efficient introduction of point mutations and single/double gene deletions. Importantly, we also demonstrate that 90-nt single-stranded DNA oligonucleotides are sufficient for direct repair of DNA breaks induced by sgRNA-Cas9, resulting in precise edits reaching 100% efficiencies. In conclusion, tools developed in this study will greatly advance basic and applied research in D. hansenii. In addition, we envision that our tools can be rapidly adapted for gene editing of other non-conventional yeast species including the ones belonging to the CUG clade.
Dose–response genotoxicity of triclosan in mice: an estimate of acceptable daily intake based on organ toxicity
Authors: Cao Yiyi , Xi Jing , You Xinyue , Liu Weiying , Luan Yang 
Published: October 2021

Abstract
Triclosan (TCS) is widely used and it bioaccumulates in humans. We found that TCS induced DNA damage in TK6 cell in our previous work. Herein, we performed a pilot assay of the TK6 cell/TK gene (TK+/−) mutation assay without metabolic activation for 24 h and found that TCS significantly induced mutation frequency. We further investigated the dose–response toxicity and genotoxicity of TCS. We combined the newly developed Pig-a gene mutation assay with bone marrow micronucleus (MN) test in a 19-day short-term study. ICR mice were administered orally with TCS at six dose levels from 0 to1000 mg/kg/day. We quantitatively assessed the dose–response relationships for the Pig-a assay, MN test, and organ coefficient data for possible points of departure (PoDs) by estimating the benchmark dose using PROAST software. We did not observe elevated Pig-a mutant frequency or MN frequency in TCS-treated mice. But a dose-dependent and statistically significant increase in liver organ coefficient data was observed. The PoD and acceptable daily intake based on organ toxicity were further developed and no greater than 1.82 and 0.00182 mg/kg/day, respectively, indicating that the toxicity of TCS may has been underestimated in previous studies and greater attention should be paid to low-level TCS exposure.