bluuebunny/crossref_metadata_2025_split huggingface dataset:
The challenges presented by haematopoietic stem cell transplantation in children with primary immunodeficiency
Authors: Gennery A R 
Published: May 2020

Abstract

Introduction or background
For many primary immunodeficiencies (PIDs), haematopoietic stem cell transplantation (HSCT) offers treatment to cure disease. However, patients with PID present a unique set of challenges when considering HSCT.

Sources of data
Review of recent literature.

Areas of agreement
The most significant recent impact on successful outcome is introduction of newborn screening programmes for diagnosis of severe combined immunodeficiency—wider adoption of screening in an increasing number of countries will see further improvements. Other PIDs have better outcomes when treated earlier, before development of co-morbidities—early referral for consideration of HSCT is important. Evolution of conditioning regimens is improving short- and long-term toxicities—targeted busulfan and low-toxicity myeloablative treosulfan regimens deliver good survival with reduced short-term toxicities.

Areas of controversy
The most radical development, still in clinical trials, is the use of mono-antibody-based conditioning, which eliminates the requirement for chemotherapy and is likely to become much more important in HSCT for non-malignant disease in the future.

Growing points
Multidisciplinary working for optimum care is essential.

Areas timely for developing research
International collaborations are important to learn about rare presentations and complications, and to formulate the most effective and safe treatment strategies.
Clinical Features and Genetic Risk of Demyelination Following Anti-TNF Treatment
Authors: Lin Simeng , Green Harry D , Hendy Peter , Heerasing Neel M , Chanchlani Neil , Hamilton Benjamin , Walker Gareth J , Heap Graham A , Hobart Jeremy , Martin Roswell J , Coles Alasdair J , Silverberg Mark S , Irving Peter M , Chung-Faye Guy , Silber Eli , Cummings J R Fraser , Lytvyak Ellina , Andersen Vibeke , Wood Andrew R , Tyrrell Jessica , Beaumont Robin N , Weedon Michael N , Kennedy Nicholas A , Spiers Alexander , Harrower Timothy , Goodhand James R , Ahmad Tariq 
Published: May 2020

Abstract

Background
Anti-TNF exposure has been linked to demyelination events. We sought to describe the clinical features of demyelination events following anti-TNF treatment and to test whether affected patients were genetically predisposed to multiple sclerosis [MS].

Methods
We conducted a case-control study to describe the clinical features of demyelination events following anti-TNF exposure. We compared genetic risk scores [GRS], calculated using carriage of 43 susceptibility loci for MS, in 48 cases with 1219 patients exposed to anti-TNF who did not develop demyelination.

Results
Overall, 39 [74%] cases were female. The median age [range] of patients at time of demyelination was 41.5 years [20.7–63.2]. The median duration of anti-TNF treatment was 21.3 months [0.5-99.4] and 19 [36%] patients were receiving concomitant immunomodulators. Most patients had central demyelination affecting the brain, spinal cord, or both. Complete recovery was reported in 12 [23%] patients after a median time of 6.8 months [0.1–28.7]. After 33.0 months of follow-up, partial recovery was observed in 29 [55%] patients, relapsing and remitting episodes in nine [17%], progressive symptoms in three [6%]: two [4%] patients were diagnosed with MS. There was no significant difference between MS GRS scores in cases (mean -3.5 × 10–4, standard deviation [SD] 0.0039) and controls [mean -1.1 × 10–3, SD 0.0042] [p = 0.23].

Conclusions
Patients who experienced demyelination events following anti-TNF exposure were more likely female, less frequently treated with an immunomodulator, and had a similar genetic risk to anti-TNF exposed controls who did not experience demyelination events. Large prospective studies with pre-treatment neuroimaging are required to identify genetic susceptibility loci.
Simplified determination of commissural orientation in bicuspid aortic valves
Authors: Froede Lennart , Schäfers Sebastian , Wagenpfeil Gudrun , Raddatz Alexander , Hoffmann Klaus , Schäfers Hans-Joachim 
Published: May 2020

Abstract

OBJECTIVES

In bicuspid aortic valves (BAV), commissural orientation (CO) varies between 180° and close to 120°. Postoperative CO has a strong effect on repair durability, and different repair approaches have been proposed according to CO; it is thus important for aortic repair. A precise, simple and reproducible determination by preoperative echocardiography would facilitate intraoperative decision-making. We compared 4 different methods of determination of CO in BAV.

METHODS
Preoperative transoesophageal echocardiograms of 62 patients with BAV were analysed. CO was measured using either the coaptation centre or the geometric centre of the root. The geometric centre of the root was determined through approximation using a circle or an ellipse, or the midpoint of a line between the centre of the non-fused and the fused sinuses.

RESULTS
The 3 different geometric methods led to almost identical results (interclass coefficient 0.98–0.99), with the line segment being the easiest to use. The use of the coaptation centre was associated with the underestimation of commissural angle of up to 30° compared to the geometric centre; the discrepancy was significant and most pronounced for asymmetric BAV (140–160°; P = 0.005).

CONCLUSIONS
CO can reproducibly be determined using a line segment between the centre of the non-fused and fused sinuses. The use of the coaptation centre can lead to misleading results, in particular in asymmetric BAVs.
Deploying Big Data to Crack the Genotype to Phenotype Code
Authors: Westerman Erica L , Bowman Sarah E J , Davidson Bradley , Davis Marcus C , Larson Eric R , Sanford Christopher P J 
Published: May 2020

SynopsisMechanistically connecting genotypes to phenotypes is a longstanding and central mission of biology. Deciphering these connections will unite questions and datasets across all scales from molecules to ecosystems. Although high-throughput sequencing has provided a rich platform on which to launch this effort, tools for deciphering mechanisms further along the genome to phenome pipeline remain limited. Machine learning approaches and other emerging computational tools hold the promise of augmenting human efforts to overcome these obstacles. This vision paper is the result of a Reintegrating Biology Workshop, bringing together the perspectives of integrative and comparative biologists to survey challenges and opportunities in cracking the genotype to phenotype code and thereby generating predictive frameworks across biological scales. Key recommendations include promoting the development of minimum “best practices” for the experimental design and collection of data; fostering sustained and long-term data repositories; promoting programs that recruit, train, and retain a diversity of talent; and providing funding to effectively support these highly cross-disciplinary efforts. We follow this discussion by highlighting a few specific transformative research opportunities that will be advanced by these efforts.
Clinical Validation of a SARS-CoV-2 Real-Time Reverse Transcription PCR Assay Targeting the Nucleocapsid Gene
Authors: SoRelle Jeffrey A , Frame Ithiel , Falcon Alejandra , Jacob Jerin , Wagenfuehr Jennifer , Mitui Midori , Park Jason Y , Filkins Laura 
Published: May 2020

Abstract

Background
Detection of SARS-CoV-2 viral RNA is important for the diagnosis and management of COVID-19.

Methods
We present a clinical validation of a reverse transcription PCR (RT-PCR) assay for the SARS-CoV-2 nucleocapsid (N1) gene. Off-board lysis on an automated nucleic acid extraction system was optimized with endemic coronaviruses (OC43 and NL63). Genomic RNA and SARS-CoV-2 RNA in a recombinant viral protein coat were used as control materials and compared for recovery from nucleic acid extraction.

Results
Nucleic acid extraction showed decreased recovery of endemic Coronavirus in vitro transcribed RNA (NL63) compared with attenuated virus (OC43). SARS-CoV-2 RNA had more reliable recovery from extraction through amplification than genomic RNA. Recovery of genomic RNA was improved by combining lysis buffer with clinical matrix before adding RNA. The RT-PCR assay demonstrated 100% in silico sensitivity and specificity. The accuracy across samples was 100% (75 of 75). Precision studies showed 100% intra-run, inter-run, and inter-technologist concordance. The limit of detection was 264 copies per milliliter (estimated 5 copies per reaction; 35.56 mean threshold cycle value).

Conclusions
This SARS-CoV-2 assay demonstrates appropriate characteristics for use under an Emergency Use Authorization. Endemic coronavirus controls were useful in optimizing the extraction procedure. In the absence of live or attenuated virus, recombinant virus in a protein coat is an appropriate control specimen type for assay validation during a pandemic.
Seasonal Occurrence and Abundance of Billbugs (Coleoptera: Curculionidae) in Georgia Sod Farms
Authors: Gireesh Midhula , Joseph Shimat V 
Published: May 2020

Abstract
The billbug, Sphenophorus spp. (Coleoptera: Curculionidae), is an important pest complex in sod farms in Georgia. Larval feeding within stolons and on roots affects spring recovery of slow-growing zoysiagrass and poses a serious challenge to machine harvesting, as the damaged turfgrass rarely holds together. Little is known about major billbug species and their seasonal occurrence and abundance in Georgia sod farms, as most previous research was conducted in golf courses in the region. In 2018 and 2019, adult billbugs were sampled from five zoysiagrass sod field sites in central Georgia. Four linear pitfall traps were used per site from February to December each year, and the traps were checked at weekly intervals. The data show that &gt;98% of the sampled billbugs were the hunting billbug, Sphenophorus venatus vestitus Chittenden, whereas the nutgrass billbug, Sphenophorus cariosus Olivier; uneven billbug, Sphenophorus inaequalis Say; and vegetable weevil, Listroderes difficilis Germain were the minor species. Seasonal billbug capture was influenced by turfgrass phenology (e.g., early-growth-stage, late-growth-stage or fully grown turfgrass). The numbers of Sphenophorus spp. collected were significantly greater in the fully grown turfgrass than in the early- or late-growth-stage turfgrasses. Significantly greater densities of billbug were found in Zoysia matrella (L.) Merrill (‘Zeon’) and the Z. matrella × Zoysia pacifica (Goudswaard) M. Hotta & S. Kuroki hybrid (‘Emerald’) than in the Zoysia japonica (Steudel) cultivars ‘El Toro’ and ‘Zenith’. Similar numbers of male and female billbugs were collected from the sod field sites.
Characteristics of Hospitalized Pediatric Coronavirus Disease 2019 Cases in Chicago, Illinois, March–April 2020
Authors: Mannheim Jonathan , Gretsch Stephanie , Layden Jennifer E , Fricchione Marielle J 
Published: May 2020

Abstract

Background
To date, no report on coronavirus disease 2019 (COVID-19) pediatric patients in a large urban center with data on underlying comorbidities and coinfection for hospitalized cases has been published.

Methods
This was a case series of Chicago COVID-19 patients aged 0–17 years reported to the Chicago Department of Public Health (CDPH) from March 5 to April 8, 2020. Enhanced case investigation was performed. χ 2 and Wilcoxon 2-sample tests were used to compare characteristics among hospitalized and nonhospitalized cases.

Results
During March 5–April 8, 2020, 6369 laboratory-confirmed cases of COVID-19 were reported to CDPH; 64 (1.0%) were among children aged 0–17 years. Ten patients (16%) were hospitalized, and 7 (70%) required intensive care (median length of hospitalization, 4 days [range, 1–14 days]). Reported fever and dyspnea were significantly higher in hospitalized patients than in nonhospitalized patients (9/10 vs 28/54, P = .04 and 7/10 vs 10/54, P = .002, respectively). Hospitalized patients were significantly younger than nonhospitalized patients (median, 3.5 years vs 12 years; P = .03) and all either had an underlying comorbidity or coinfection. Among the 34 unique households with multiple laboratory-confirmed infections, the median number of laboratory-confirmed infections was 2 (range, 2–5), and 31 (91%) households had at least 1 COVID-19–infected adult. For 15 households with available data to assess transmission, 11 (73%) were adult-to-child, 2 (13%) child-to-child, and 2 (13%) child-to-adult.

Conclusions
Enhanced case investigation of hospitalized patients revealed that underlying comorbidities and coinfection might have contributed to severe disease. Given frequency of household transmission, healthcare providers should consider alternative dispositional planning for affected families of children living with comorbidities.
BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit
Authors: Yan Fang , Gao Yushuo , Pang Xiaoqin , Xu Xin , Zhu Ning , Chan Helen , Hu Guojian , Wu Mengbo , Yuan Yujin , Li Honghai , Zhong Silin , Hada Wuriyanghan , Deng Wei , Li Zhengguo 
Published: May 2020

AbstractTomato (Solanum lycopersicum) is a model plant for studying fruit development and ripening. In this study, we found that down-regulation of a tomato bell-like homeodomain 4 (SlBL4) resulted in a slightly darker-green fruit phenotype and increased accumulation of starch, fructose, and glucose. Analysis of chlorophyll content and TEM observations was consistent with these phenotypes, indicating that SlBL4 was involved in chlorophyll accumulation and chloroplast formation. Ripened fruit of SlBL4-RNAi plants had noticeably decreased firmness, larger intercellular spaces, and thinner cell walls than the wild-type. RNA-seq identified differentially expressed genes involved in chlorophyll metabolism, chloroplast development, cell wall metabolism, and carotenoid metabolism. ChIP-seq identified (G/A) GCCCA (A/T/C) and (C/A/T) (C/A/T) AAAAA (G/A/T) (G/A) motifs. SlBL4 directly inhibited the expression of protoporphyrinogen oxidase (SlPPO), magnesium chelatase H subunit (SlCHLD), pectinesterase (SlPE), protochlorophyllide reductase (SlPOR), chlorophyll a/b binding protein 3B (SlCAB-3B), and homeobox protein knotted 2 (TKN2). In contrast, it positively regulated the expression of squamosa promoter binding protein-like colorless non-ripening (LeSPL-CNR). Our results indicate that SlBL4 is involved in chlorophyll accumulation, chloroplast development, cell wall metabolism, and the accumulation of carotenoids during tomato fruit ripening, and provide new insights for the transcriptional regulation mechanism of BELL-mediated fruit growth and ripening.
TRIM24 promotes stemness and invasiveness of glioblastoma cells via activating Sox2 expression
Authors: Zhang Lu-hua , Yin Yi-heng , Chen Hong-zun , Feng Shi-yu , Liu Jia-lin , Chen Ling , Fu Wen-liang , Sun Guo-chen , Yu Xin-guang , Xu Dong-gang 
Published: May 2020

Abstract

Background
Glioblastoma stem cells (GSCs) are a subpopulation of glioblastoma (GBM) cells that are critical for tumor invasion and treatment resistance. However, little is known about the function and mechanism of tripartite motif-containing 24 (TRIM24) in GSCs.

Methods
Immunofluorescence, flow cytometry, and western blot analyses were used to evaluate TRIM24 and cluster of differentiation (CD)133 expression profiles in GBM surgical specimens and GSC tumorspheres. Different TRIM24 expression levels in patients’ tumors, as measured by both immunohistochemistry and western blot, were related to their corresponding MRI data. Wound healing, Matrigel invasion, and xenograft immunohistochemistry were conducted to determine GBM cell invasion.

Results
We identified that TRIM24 was coexpressed with CD133 and Nestin in GBM tissues and tumorsphere cells. Limiting dilution assays and xenotransplantation experiments illustrated that knockdown of TRIM24 expression reduced GSC self-renewal capacity and invasive growth. TRIM24 expression levels were positively associated with the volumes of peritumoral T2 weighted image abnormality. Rescue experiments indicated TRIM24 participation in GBM infiltrative dissemination. Chromatin immunoprecipitation, reporter gene assay, PCR, western blot, and immunohistochemistry demonstrated that TRIM24 activated the expression of the pluripotency transcription factor sex determining region Y–box 2 (Sox2) to regulate GBM stemness and invasion in vitro and in vivo. Finally, the close relationship between TRIM24 and Sox2 was validated by testing samples enrolled in our study and exploring external databases.

Conclusions
Our findings uncover essential roles of the TRIM24–Sox2 axis in GBM stemness and invasiveness, suggesting TRIM24 as a potential target for effective GBM management.
Trends in Posterior Cervical Fusion for Deformity in the United States from 2000 to 2017
Authors: Safaee Michael M , Dalle Ore Cecilia L , Corso Katherine A , Ruppenkamp Jill W , Lau Darryl , Ames Christopher P 
Published: May 2020

ABSTRACT

BACKGROUND
Posterior cervical decompression and fusion (PCF) is a common treatment for cervical spondylotic myelopathy. Treatment paradigms are shifting from simple decompression and fusion to correcting cervical deformities.

OBJECTIVE
To identify trends in PCF with an emphasis on cervical deformity and surgical complexity.

METHODS
Adults who underwent PCF from 2000 to 2017 were retrospectively identified in the Premier Healthcare Database (PHD) using International Classification of Disease Codes (ICD) 9 and 10. Patients were dichotomized into those with or without deformity diagnosis. PCF complexity was defined by adjunct surgical codes, including anterior cervical fusion, extension to thoracic levels, and osteotomy. Patient characteristics, including demographics, functional comorbidity index (FCI), and hospital characteristics, were extracted and annual procedures were projected to the US population.

RESULTS
A total of 68 415 discharges for PCF were identified. Compound annual growth rate (CAGR) of PCF from 2000 to 2017 for nondeformity cases was 9.7% and 16.5% for deformity. The demographics with the greatest growth were deformity patients aged 65 to 74 yr (15.1%). The CAGR of anterior cervical fusion and extension to thoracic levels was higher for deformity patients compared to nondeformity patients, 13.6% versus 3.9% and 20.4% versus 16.6%, respectively.

CONCLUSION
Rates of PCF for deformity are increasing at a greater rate than nondeformity PCF. The most growth was seen among deformity patients aged 65 to 74 yr. Surgical complexity is also changing with increasing use of anterior cervical fusion and extension of PCF to include thoracic levels.
Performance evaluation of the aerogel RICH counter for the Belle II spectrometer using early beam collision data
Authors: Yonenaga M , Adachi I , Burmistrov L , Le Diberder F , Iijima T , Iwata S , Kakimoto S , Kakuno H , Karyan G , Kawai H , Kawasaki T , Kindo H , Kitamura H , Kobayashi M , Kohriki T , Konno T , Korpar S , Križan P , Kumita T , Kuze K , Lai Y , Mrvar M , Nazaryan G , Nishida S , Nishimura M , Ogawa K , Ogawa S , Pestotnik R , Seljak A , Shoji M , Sumiyoshi T , Tabata M , Tamechika S , Yusa Y , Šantelj L 
Published: May 2020

Abstract
The Aerogel Ring Imaging Cherenkov (ARICH) counter serves as a particle identification device in the forward end-cap region of the Belle II spectrometer. It is capable of identifying pions and kaons with momenta up to $4\&gt;$GeV$\&gt;$c$^{-1}$ by detecting Cherenkov photons emitted in the silica aerogel radiator. After the detector alignment and calibration of the probability density function, we evaluate the performance of the ARICH counter using early beam collision data. Event samples of $D^{\ast +} \to D^0 \pi^+ (D^0 \to K^-\pi^+)$ were used to determine the $\pi(K)$ efficiency and the $K(\pi)$ misidentification probability. We found that the ARICH counter is capable of separating kaons from pions with an identification efficiency of $93.5 \pm 0.6 \, \%$ at a pion misidentification probability of $10.9 \pm 0.9 \, \%$. This paper describes the identification method of the counter and the evaluation of the performance during its early operation.
Evaluating the Mobilization Effect of Online Political Network Structures: A Comparison between the Black Lives Matter Network and Ideal Type Network Configurations
Authors: Hsiao Yuan 
Published: May 2020

AbstractDo online networks encourage political participation? Much research has theorized on how digital networks transmit mobilizing content, fewer studies examine the structure of online networks, and even fewer test how the structure of online networks affects participation for political behaviors with differing costs. From a structural network perspective, I highlight the puzzle: If according to recent literature, digital networks are loose with many weak ties, how can such a network configuration facilitate high-cost political behavior that requires multiple social reinforcements? I map the following relationships among 655 Twitter users who follow the Black Lives Matter Sacramento chapter and compare the structure of the digital network to three commonly observed ideal type networks. The results show that the digital network is structurally distinct from the ideal types, as it is characterized by an extremely dense cluster but also with many loosely connected components, which I describe as a “cluster-connective network.” Results from computer experiments further show that paradoxically, this “cluster-connective” configuration benefits participation for high-cost behavior but hinders participation for low-cost behavior. The results illustrate how a structural network perspective helps scholars move from the question of whether digital networks facilitate participation to the conditions under which digital networks encourage participation.
A Sociological Survey of Japanese International Relations Journals and University Education: Still a Discipline ‘In Between’?
Authors: KOLMAŠ Michal , KOZISEK David 
Published: May 2020

AbstractThe Japanese discipline of international relations has been understood as a product of interaction with its Western other, formed and developed much like Japanese contested identity. But although much attention has been paid to how the discipline emerged and evolved, very little has been written about how the discipline looks now. To remedy that, we apply a sociology of knowledge perspective to find out whether the Japanese discipline of IR does still possess distinct qualities or whether there has been growing influence from its Euro-American counterpart. We proceed in two steps: (a) We analyze 175 articles from the Japanese language IR journals Kokusai seiji, Kokusai mondai, Kokusai anzen hoshō, Heiwa kenkyū, Ajia kenkyū, Revaiasan and Nenpō seijigaku, and dissect them according to topics, focus, author background and theories/methods used; (b) We conduct four case studies of IR education at Japanese universities to demonstrate how the discipline is taught, with a focus on lecturer background, experience and syllabus composition. Our findings suggest that although there remains a preoccupation with diplomatic history, loose methodology and either realist or atheoretical studies, there is a clear trend of convergence toward Euro-American standards, especially in university education.