bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature
Authors: Arnaboldi Valerio , Cho Jaehyoung , Sternberg Paul W 
Published: March 2021

Abstract
Finding relevant information from newly published scientific papers is becoming increasingly difficult due to the pace at which articles are published every year as well as the increasing amount of information per paper. Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information. In addition, scientific search engines such as PubMed and text-mining tools such as Textpresso allow researchers to easily search for specific biological aspects from newly published papers, facilitating knowledge transfer. However, digesting the information returned by these systems—often a large number of documents—still requires considerable effort. In this paper, we present Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines. Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment.
Database URL: https://wormicloud.textpressolab.com
Antibiotic prescribing and use of corticosteroids for the emergency department management of acute uncomplicated pharyngitis
Authors: Sheridan Conor , Grewal Keerat , Thompson Cameron , Borgundvaag Bjug , McLeod Shelley L 
Published: March 2021

Abstract

Background
Acute pharyngitis is common in the ambulatory setting. The Modified Centor score uses five criteria to predict Group A Streptococcus (GAS) infection and can be used to guide management.

Objective
The objective of this study was to describe the emergency department (ED) management (throat cultures, antibiotics and corticosteroids) of acute, uncomplicated pharyngitis by Centor score.

Methods
This was a retrospective chart review of adult (&gt;17 years) patients with an ED discharge diagnosis of acute pharyngitis from January 2016 to December 2018.

Results
Of 638 patients included, 286 (44.8%) had a Centor score of 0–1, 328 (51.4%) had a score of 2–3 and 24 (3.8%) had a score of ≥4. Of those with a Centor score of 0–1, 83 (29.0%) had a throat culture, 88 (30.8%) were prescribed antibiotics, 15 (5.2%) were positive for GAS and 74 (25.9%) received corticosteroids. Of those with a Centor score of 2–3, 156 (47.6%) had a throat culture, 220 (67.1%) were prescribed antibiotics, 44 (13.4%) were positive for GAS and 145 (44.2%) received corticosteroids. Of those with a Centor score ≥4, 14 (58.3%) had a throat culture, 18 (75.0%) were prescribed antibiotics, 7 (29.2%) were positive for GAS and 12 (50.0%) received corticosteroids.

Conclusions
A higher Centor score was associated with a higher risk of GAS infection, increased antibiotic prescribing and use of corticosteroids. Many patients with low Centor scores were prescribed antibiotics and had throat cultures. Further work is required to understand clinical decision-making for the management of acute pharyngitis.
Dynamic gene expression in salivary glands of the cat flea during Rickettsia felis infection
Authors: Danchenko Monika , Laukaitis Hanna J , Macaluso Kevin R 
Published: March 2021

ABSTRACT
The cat flea, Ctenocephalides felis, is an arthropod vector capable of transmitting several human pathogens including Rickettsia species. Earlier studies identified Rickettsia felis in the salivary glands of the cat flea and transmission of rickettsiae during arthropod feeding. The saliva of hematophagous insects contains multiple biomolecules with anticlotting, vasodilatory and immunomodulatory activities. Notably, the exact role of salivary factors in the molecular interaction between flea-borne rickettsiae and their insect host is still largely unknown. To determine if R. felis modulates gene expression in the cat flea salivary glands, cat fleas were infected with R. felis and transcription patterns of selected salivary gland-derived factors, including antimicrobial peptides and flea-specific antigens, were assessed. Salivary glands were microdissected from infected and control cat fleas at different time points after exposure and total RNA was extracted and subjected to reverse-transcriptase quantitative PCR for gene expression analysis. During the experimental 10-day feeding period, a dynamic change in gene expression of immunity-related transcripts and salivary antigens between the two experimental groups was detected. The data indicated that defensin-2 (Cf-726), glycine-rich antimicrobial peptide (Cf-83), salivary antigens (Cf-169 and Cf-65) and deorphanized peptide (Cf-75) are flea-derived factors responsive to rickettsial infection.
Stability analysis-based reformulation of wave equations for poro-elastic media saturated with two fluids
Authors: Xiong Fansheng , Liu Jiawei , Guo Zhenwei , Liu Jianxin 
Published: March 2021

SUMMARY
The stability of partial differential equations determines the properties of their solutions. This study focuses on the stability analysis of the equations describing wave propagation in fluids-saturated porous media. We briefly introduce the stability analysis method for the wave propagation equations and discuss the adverse effects on the solutions. In this way, the first part of this paper is mainly devoted to the analysis of the Tuncay and Corapcioglu's (TC) model, which describes the dynamic behaviour of porous media saturated with two immiscible fluids. It is pointed out that the TC model allows spatially bounded but time-exponentially exploding solutions and may yield unstable numerical results. Based on the deduced unstable factors, we construct a stable equivalent fluid (SEF) model. We rigorously analyse the stability of the SEF model using the energy method. For predicting the influence of saturation on wave velocity, the robustness of this model is preserved due to its consistency with the original TC model. Furthermore, the numerical simulations of the wavefields show that the results of the TC model exponentially increase with time after the initial effective wave signal, which does not occur in the SEF model curves. This indicates the necessity of considering the stability from a mathematical point of view during the construction of physical model. It could be useful to merge the mathematical stability theory with the geophysical wave propagation modelling theory.
Design and analysis of waste heat recovery from residential air conditioning units for cooling and pure water production
Authors: Rady Mohamed , Albatati Faisal , Hegab Abdelkarim , Abuhabaya Abdullah , Attar Alaa 
Published: March 2021

Abstract:
The present article reports on the analysis of waste heat and condensate recovery from residential air conditioning (AC) units in different climatic regions in Saudi Arabia. Simulation results obtained using a transient dynamic model show that significant amounts of waste heat and water condensate are rejected to the environment in hot and humid climate regions. A multi-generation system for simultaneous cooling and pure water production using condensate and waste heat recovery is designed and implemented in TRNSYS environment. A refrigerant to water de-superheater is introduced after the compressor to extract energy from the high temperature superheated refrigerant gas for heating saline water that is used as a feed to drive an air gap membrane desalination unit. The production of pure water is analyzed for both batch and continuous cooling modes of the membrane desalination unit. The amount of pure water production shows the potential of proposed system to supply pure water requirements in hot and humid climates in Saudi Arabia. The monthly average coefficient of performance of multi-generation residential AC units with continuous cooling of desalination unit is shown to be improved by ~6.61%. The monthly average gained output ratio of membrane desalination unit is higher than 1.14.
Multiplex Real-Time PCR Method for Simultaneous Detection and Differentiation of Goat pox Virus, Sheeppox Virus, and Lumpy Skin Disease Virus
Authors: Wang Huiyu , Kong Yufang , Mei Lin , Lv Jizhou , Wu Shaoqiang , Lin Xiangmei , Han Xueqing 
Published: March 2021

Abstract

Background
The diseases caused by the Capripoxvirus species have very similar symptoms and are difficult to distinguish clinically. According to a recent report, Capripoxvirus are not strictly host specific.

Objective
This study aimed to identify the viruses from ovine (include sheep and goat) or bovine, which will assist in selecting the appropriate vaccine and correct measures to control diseases.

Method
Universal primers for all Capripoxvirus and specific probes for lumpy skin disease virus, sheeppox virus, and goatpox virus were designed and analyzed to identify the viruses from ovine (including sheep and goats) or bovine species. The parameters of the system, such as the annealing temperatures and the quantities of primers and probes used, were optimized. The sensitivity, speciﬁcity, and reproducibility were tested.

Results
Each probe showed a specific fluorescent signal, with no cross reaction with other pathogens that cause symptoms similar to those of the poxviruses. The LOD was 102 copies of the target genome DNA. The 557 local clinical samples and samples from Ethiopia were successfully detected and the results were consistent with a restriction fragment length polymorphism PCR analysis of the P32 and RPO30 genes and gene sequencing.

Conclusions
This optimized real-time PCR detection system has good diagnostic sensitivity and specificity and can be used for the rapid and effective differential diagnosis of these diseases in goats, sheep, and cattle.

Highlights
It is a rapid detection method to distinguish the viruses from ovine (include sheep and goat) or bovine.
Reinforcement of rectal anastomoses with a collagen-based haemostatic patch: a case series report
Authors: Kornfeld Dan 
Published: March 2021

Abstract
In this case series report of 10 colorectal cancer patients, a polyethylene glycol-coated collagen-based haemostatic patch was applied after rectal resection to reinforce rectal anastomoses and reduce anastomotic leakage. Patients underwent rectal resection and anastomoses were stapled in place. The patch—Hemopatch®—was applied to 75% of the anastomotic circumference. The surgeon judged the simplicity of application using a reinforcement of rectal anastomosis score. Mean age of patients was 68.1 (range 50–94) years. The patch was successfully applied in eight patients; in seven patients, patch application was straightforward or only slightly complex, according to the reinforcement of rectal anastomosis score. Seven of eight patients experienced no leakage or signs of stricture 6 weeks post-surgery. All patients underwent radical resection. It is possible to apply Hemopatch® during colorectal surgery. However, the patch application procedure needs to be standardized and efficacy needs to be evaluated by conducting larger clinical studies.
A traumatic ulnar artery aneurysm in an infant
Authors: Odajima Rika , Nishimoto Soh , Kawai Kenichiro , Ishise Hisako , Kakibuchi Masao 
Published: March 2021

ABSTRACT
Ulnar artery aneurysm is very rare in infancy. Only a few reports have been done. We report an 8-month-old baby with true ulnar artery aneurysm on her hypothenar eminence. She had no specific past medical history, but an episode of falling. We resected the pulsating mass compressing the ulnar nerve, utilizing a surgical microscope. Reconstruction of the vascular deficit was not performed. She presented no functional deficit of the hand and no evidence of growth disturbance so far. As hypothenar eminence is a susceptible part for repetitive strikes, and as vein is fragile to the pressure, bypassing arterial route with vein graft is not recommended unless there is no other option.
BIMG-05. TO BE OR NOT TO BE GLYCOLYTIC: DEUTERATED GLUCOSE-BASED ASSESSMENT OF THE WARBURG EFFECT ALLOWS NON-INVASIVE IMAGING OF TUMOR BURDEN AND TREATMENT RESPONSE IN MUTANT IDH GLIOMAS IN VIVO
Authors: Taglang Celine , Batsios Georgios , Tran Meryssa , Gillepsie Anne Marie , Luchman Hema Artee , Pieper Russell O , Ronen Sabrina M , Viswanath Pavithra 
Published: March 2021

Abstract
The Warburg effect, characterized by elevated glucose uptake and flux to lactate, is a metabolic hallmark of cancer. Recent studies have identified deuterium 2H-magnetic resonance spectroscopy (MRS) using 6,6’-2H-glucose as a novel method of imaging the Warburg effect in high-grade primary glioblastomas (GBMs). However, its utility for imaging low-grade gliomas has not been tested. The goal of this study was to determine whether 6,6’-2H-glucose can be used for imaging tumor burden and treatment response in mutant isocitrate dehydrogenase (IDHmut) low-grade gliomas in vivo. We examined mice bearing orthotopic tumors of the patient-derived BT257 astrocytoma model. 1H-MRS, providing a readout of steady-state metabolite levels, confirmed the presence of 2-hydroxyglutarate, the product of IDHmut, in BT257 tumor tissue but not normal brain. Previous studies comparing IDHmut gliomas with GBMs suggest that IDHmut gliomas undergo lactate dehydrogenase silencing, potentially leading to a non-glycolytic phenotype. Nevertheless, our results indicated that, compared to normal brain, glucose uptake and concomitant flux to lactate were significantly higher in BT257 tumor tissue. Importantly, 6,6’-2H-glucose metabolism to lactate was observed in BT257 tumor-bearing mice, but not tumor-free mice. Furthermore, imaging studies confirmed spatial localization of lactate production to the tumor vs. contralateral normal brain. We then examined the ability of 6,6’-2H-glucose to assess treatment response. Poly-(adenosine 5′-diphosphate-ribose) polymerase inhibitors (PARPi) inhibit IDHmut glioma growth and are in clinical trials for IDHmut glioma patients. Treatment with the PARPi niraparib reduced 6,6’-2H-glucose flux to lactate in BT257 tumor-bearing mice. Importantly, this reduction was observed at early time-points when no difference in tumor volume could be detected using anatomical imaging, pointing to the ability of 6,6’-2H-glucose to assess pseudoprogression. Collectively, our results suggest that IDHmut gliomas display a glycolytic phenotype amenable to non-invasive 2H-MRS-based imaging of tumor burden and treatment response.
BIMG-15. LACTATE AND GLUTATHIONE LEVELS DETECTED WITH PROTON MR SPECTROSCOPY ARE ASSOCIATED WITH POOR SURVIVAL IN IDH WILD TYPE TERTP MUTANT DIFFUSE GLIOMAS
Authors: Sacli-Bilmez Banu , Danyeli Ayça Ersen , Yakicier Cengiz , Pamir M Necmettin , Özduman Koray , Dincer Alp , Ozturk-Isik Esin 
Published: March 2021

Abstract
Telomerase reverse transcriptase promoter (TERTp) mutations in the absence of IDH mutations (TERTp-only) are recently proposed as a characteristic of glioblastoma regardless of the morphological grade. This study aims to analyze metabolic profiles of TERTp-only gliomas using proton magnetic resonance spectroscopy (1H-MRS) and evaluate the effect of metabolite concentrations on progression-free survival (PFS) and overall survival (OS). The patient cohort consisted of 56 TERTp-only gliomas (35M/21F, mean age: 58±10.37 years, 44 glioblastomas (GBM), and 12 lower-grade gliomas with TERTp-mutation but no IDH-mutations). All patients underwent preoperative diagnostic 1H-MRS using a 3T MR scanner with a 32-channel head coil. 1H-MRS was obtained from a manually placed region of interest with no necrosis, edema, and hemorrhage, using a Point Resolved Spectroscopy (PRESS) sequence (TR/TE=2000/30 ms, 1024 points). LCModel spectral fitting program was used for quantification of MR spectroscopic peak concentrations of 17 metabolites. The patients were divided into two groups using median values of the metabolite intensities, and Kaplan-Meier survival analysis followed by a log-rank test was used to determine the effects of metabolite concentrations on OS and PFS. Median PFS and OS of TERTp-only gliomas were 11 and 17 months, respectively. TERTp-only LGG patients had longer OS and PFS than TERTp-only GBM patients (p=0.022 for OS and p=0.018 for PFS). Significantly shorter OS and PFS were identified in TERTp-only gliomas, who had higher GSH/tCr (p=0.011 for OS and p=0.004 for PFS) and higher Lac/tCr (p=0.014 for OS and p=0.012 for PFS). Lactate is a marker of necrosis and a sign of malignancy. On the other hand, both tCr and GSH were lower, which resulted in higher GSH/tCr, in TERTp-only GBM. The results of this study indicate that high Lac/tCr and GSH/tCr might be indicators of poor prognosis in TERTp-only gliomas. This study has been supported by TUBITAK 1003 grant 216S432.
BIMG-16. TRACKING TTFIELDS-INDUCED ALTERATIONS IN GLIOBLASTOMA METABOLISM WITH [18F]DASA-23, A NON-INVASIVE PROBE OF PYRUVATE KINASE M2 (PKM2)
Authors: Patel Chirag , Beinat Corinne , Xie Yuanyang , Chang Edwin , Gambhir Sanjiv 
Published: March 2021

Abstract
Despite the anti-proliferative and survival benefits from tumor treating fields (TTFields) in human glioblastoma (hGBM), little is known about the effects of this form of alternating electric fields therapy on the aberrant glycolysis of hGBM. [18F]FDG is the most common radiotracer in cancer metabolic imaging, but its utility in hGBM is impaired due to high glucose uptake in normal brain tissue. With TTFields, radiochemistry, Western blot, and immunofluorescence microscopy, we identified pyruvate kinase M2 (PKM2) as a biomarker of hGBM response to therapeutic TTFields. We used [18F]DASA-23, a novel radiotracer that measures PKM2 expression and which has been shown to be safe in humans, to detect a shift away from hGBM aberrant glycolysis in response to TTFields. Compared to unexposed hGBM, [18F]DASA-23 uptake was reduced in hGBM exposed to TTFields (53%, P&lt; 0.05) or temozolomide chemotherapy (33%, P &gt; 0.05) for 3 d. A 6-d TTFields exposure resulted in a 31% reduction (P = 0.043) in 60-min uptake of [18F]DASA-23. [18F]DASA-23 was retained after a 10 but not 30-min wash-out period. Compared to [18F]FDG, [18F]DASA-23 demonstrated a 4- to 9-fold greater uptake, implying an improved tumor-to-background ratio. Furthermore, compared to no-TTFields exposure, a 6-d TTFields exposure caused a 35% reduction in [18F]DASA-23 30-min uptake compared to only an 8% reduction in [18F]FDG 30-min uptake. Quantitative Western blot analysis and qualitative immunofluorescence for PKM2 confirmed the TTFields-induced reduction in PKM2 expression. This is the first study to demonstrate that TTFields impairs hGBM aberrant glycolytic metabolism through reduced PKM2 expression, which can be non-invasively detected by the [18F]DASA-23 radiotracer.
BIMG-18. ELEVATED CYSTATHIONINE IN MEDULLOBLASTOMA DEMONSTRATES TUMOR-SPECIFIC METHIONINE METABOLISM
Authors: Tikunov Andrey , Rosen Elias , Babcock Ben , Weir Seth , Parnham Stuart , Macdonald Jeffrey 
Published: March 2021

Abstract
We investigated tumor-specific metabolism medulloblastoma using a non-biased MS-imaging screen and identified a pattern of methionine flux that may present a therapeutic opportunity. We studied brain tumors that form in mice genetically engineered to develop Sonic Hedgehog (SHH)-driven medulloblastoma. We subjected sagittal sections including brain and medulloblastoma to MS-imaging, generating concentration maps for hundreds of metabolites MW 100–400. We then confirmed results by analyzing tumor, brain and blood by LC-MS/MS, high-resolution NMR and 2D NMR-TOCSY, and used immunohistochemistry to determine the cellular localization of implicated enzymes. MS imaging, accomplished by matrix-assisted laser desorption electrospray ionization (MALDESI), detected cystathionine at an order of magnitude higher concentration in medulloblastomas compared to adjacent brain. No other metabolite showed such a strong, tumor-specific localization. LC-MS/MS and NMR methods confirmed cystathionine elevation. As cystathionine is the product of homocysteine and serine, catalyzed by cystathionine beta-synthase (CBS), we investigated CBS expression by IHC. Consistent with prior studies, we found that only astrocytes expressed CBS, both in the normal brain and within the tumors. ScRNA-seq confirmed Cbs only in astrocytes, and showed tumor cells express methionine-metabolizing enzymes Mat2a, Dnmt1, Ancy and Mtr. Together, these findings show that tumor cells generate and export homocysteine, which astrocytes convert to cystathionine. Tumor cystathionine generation responded to changes in methionine- cycle metabolites. In vivo, systemic administration of homocysteine increased tumor cystathionine which decreased in response to systemic folate, the methyl donor for homocysteine methyltransferase. Cystathionine itself was inert in tumors as tumor cells cultured in up to 8 mM cystathionine showed no change in cell cycle progression. Our studies show that medulloblastomas utilize methionine and generate homocysteine, but avoid folate-dependent homocysteine-methionine recycling by exporting homocysteine for detoxification by local astrocytes. This model suggests that treatments that impose methionine scarcity, folate scarcity or CBS inhibition may produce anti-tumor effects in medulloblastoma.
BIMG-21. DEUTERIUM METABOLIC IMAGING (DMI), A NEW, MRI-BASED TECHNIQUE FOR MAPPING BRAIN TUMOR METABOLISM IN VIVO
Authors: Corbin Zachary , Fulbright Robert , Rothman Douglas , de Graaf Robin , De Feyter Henk 
Published: March 2021

Abstract
Deuterium Metabolic Imaging (DMI) combines 3D deuterium (2H) magnetic resonance spectroscopic imaging (MRSI) with administration of a 2H-labeled substrate to map uptake and metabolism of the substrate. DMI has been implemented on a 4 Tesla clinical research MRI scanner, and on an 11.7 Tesla preclinical MRI scanner, and has been used with 2H-labeled glucose, acetate and choline. DMI data are presented as color maps of concentration of the 2H-labeled substrate and its metabolites, overlaid on anatomical MR images. In rat and mouse models of glioblastoma, DMI data acquired at 5 to 8 uL resolution following intravenous 2H-glucose infusion clearly showed the Warburg effect in the tumor lesions. The Warburg effect is indicated by the ratio of 2H-labeled lactate/glutamate+glutamine (Glx). High levels of 2H-labeled lactate and low levels of 2H-labeled Glx are the result of a high rate of glycolysis and low rate of oxidative glucose metabolism. Because DMI detects both glucose and its downstream metabolism, the technique does not suffer from low image contrast with normal brain, as is the case with FDG-PET that detects glucose uptake only. For clinical research studies patients orally consumed 0.75g/kg of 2H-glucose dissolved in water. The observations made in the animal models were confirmed in several patients with recurrent GBM, showing hotspots in the lac/Glx maps (8 mL resolution), coinciding with the area of the tumor lesion. In patients with meningioma, no Warburg effect was detected using DMI. Furthermore, DMI data acquired in a patient with GBM one week after finishing 30 days of radiation therapy, also showed no high levels of 2H-labeled lactate in the lesion. These data indicate that the presence of the Warburg effect could correlate with tumor grade and/or aggressiveness, and that DMI of glucose metabolism could potentially be a biomarker of therapy effect.