bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heidelberg colorectal data set for surgical data science in the sensor operating room
Authors: Maier-Hein Lena , Wagner Martin , Ross Tobias , Reinke Annika , Bodenstedt Sebastian , Full Peter M. , Hempe Hellena , Mindroc-Filimon Diana , Scholz Patrick , Tran Thuy Nuong , Bruno Pierangela , Kisilenko Anna , Müller Benjamin , Davitashvili Tornike , Capek Manuela , Tizabi Minu D. , Eisenmann Matthias , Adler Tim J. , Gröhl Janek , Schellenberg Melanie , Seidlitz Silvia , Lai T. Y. Emmy , Pekdemir Bünyamin , Roethlingshoefer Veith , Both Fabian , Bittel Sebastian , Mengler Marc , Mündermann Lars , Apitz Martin , Kopp-Schneider Annette , Speidel Stefanie , Nickel Felix , Probst Pascal , Kenngott Hannes G. , Müller-Stich Beat P. 
Published: April 2021

AbstractImage-based tracking of medical instruments is an integral part of surgical data science applications. Previous research has addressed the tasks of detecting, segmenting and tracking medical instruments based on laparoscopic video data. However, the proposed methods still tend to fail when applied to challenging images and do not generalize well to data they have not been trained on. This paper introduces the Heidelberg Colorectal (HeiCo) data set - the first publicly available data set enabling comprehensive benchmarking of medical instrument detection and segmentation algorithms with a specific emphasis on method robustness and generalization capabilities. Our data set comprises 30 laparoscopic videos and corresponding sensor data from medical devices in the operating room for three different types of laparoscopic surgery. Annotations include surgical phase labels for all video frames as well as information on instrument presence and corresponding instance-wise segmentation masks for surgical instruments (if any) in more than 10,000 individual frames. The data has successfully been used to organize international competitions within the Endoscopic Vision Challenges 2017 and 2019.
Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer
Authors: Pateetin Prangwan , Hutvagner Gyorgy , Bajan Sarah , Padula Matthew P. , McGowan Eileen M. , Boonyaratanakornkit Viroj 
Published: April 2021

AbstractProgesterone receptor (PR) isoforms, PRA and PRB, act in a progesterone-independent and dependent manner to differentially modulate the biology of breast cancer cells. Here we show that the differences in PRA and PRB structure facilitate the binding of common and distinct protein interacting partners affecting the downstream signaling events of each PR-isoform. Tet-inducible HA-tagged PRA or HA-tagged PRB constructs were expressed in T47DC42 (PR/ER negative) breast cancer cells. Affinity purification coupled with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry technique was performed to comprehensively study PRA and PRB interacting partners in both unliganded and liganded conditions. To validate our findings, we applied both forward and reverse SILAC conditions to effectively minimize experimental errors. These datasets will be useful in investigating PRA- and PRB-specific molecular mechanisms and as a database for subsequent experiments to identify novel PRA and PRB interacting proteins that differentially mediated different biological functions in breast cancer.
Pro-inflammatory effects of DEHP in SGBS-derived adipocytes and THP-1 macrophages
Authors: Schaedlich Kristina , Beier Laura-Sophie , Kolbe Judith , Wabitsch Martin , Ernst Jana 
Published: April 2021

AbstractIn the member countries of the Organization for Economic Co-operation and Development (OECD), overweight and obesity affect the majority of the population. The use of environmental chemicals, such as the plasticizer DEHP, has largely increased simultaneously with this development. DEHP is an "obesogen" that interferes with normal adipocyte differentiation and energy homeostasis. Obesity in turn is accompanied by chronic low-grade adipose tissue inflammation, leading to metabolic disorders such as type II diabetes. The main actors in adipose tissue inflammation are adipocytes and macrophages. However, the impact of DEHP on adipose tissue inflammation and the crosstalk between adipocytes and macrophages are unknown and the subjects of the current study. The influence of DEHP on inflammation was investigated in human Simpson–Golabi–Behmel syndrome (SGBS)-derived adipocytes and human THP-1 macrophages. The proinflammatory markers IL8, MCP1, IL1β, TNFα and others were measured (qRT-PCR, ELISA) in SGBS-derived adipocytes treated with DEHP [day 0 (d0)–d4; 50 µg/ml] and THP-1 macrophages cultured with conditioned medium (CM) from DEHP-treated adipocytes (SGBS-CM) (from d4 and d8). DEHP exposure led to a proinflammatory state in SGBS-derived adipocytes (e.g., increased secretion of IL8 and MCP1). Surprisingly, exposure of THP-1 macrophages to SGBS-CM did not show DEHP-induced effects. However, we demonstrated that medium containing (pre)adipocyte-secreted factors had a significant impact on the expression and secretion of macrophage and inflammatory markers in THP-1 macrophages in general and led to the significantly increased accumulation of intracellular lipid droplets.
A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Authors: Davey Karen , Wong Daniel , Konopacki Filip , Kwa Eugene , Ly Tony , Fiegler Heike , Sibley Christopher R. 
Published: April 2021

AbstractSingle cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3′ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system's ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.
Low expression of the PPARγ-regulated gene thioredoxin-interacting protein accompanies human melanoma progression and promotes experimental lung metastases
Authors: Meylan Patrick , Pich Christine , Winkler Carine , Ginster Stefanie , Mury Lionel , Sgandurra Marie , Dreos René , Frederick Dennie Tompers , Hammond Marc , Boland Genevieve Marie , Michalik Liliane 
Published: April 2021

AbstractThe thioredoxin system plays key roles in regulating cancer cell malignancy. Here we identify the Thioredoxin-interacting protein (TXNIP) as a gene, which expression is regulated by PPARγ in melanoma cells. We show that high TXNIP expression levels associate with benign melanocytic lesions, with tumor regression in patients on MAP kinase targeted therapy, with decreased proliferation in patients’ melanoma biopsies, and with cell cycle arrest in human melanoma cell lines. In contrast, reduced TXNIP expression associates with advanced melanoma and with disease progression in patients. TXNIP depletion in human melanoma cells altered the expression of integrin beta-3 and the localization of the integrin alpha-v/beta-3 dimer at their surface. Moreover, TXNIP depletion affected human melanoma cell motility and improved their capacity to colonize mouse lungs in an in vivo assay. This study establishes TXNIP as a PPARγ-regulated gene in melanoma cells, thereby suggesting a link between these two proteins both involved in the regulation of cancer and of energy metabolism. It also reveals that the decrease in TXNIP expression, which is observed in advanced patient tumors, likely favors lung metastatic seeding of malignant cells.
Root NRT, NiR, AMT, GS, GOGAT and GDH expression levels reveal NO and ABA mediated drought tolerance in Brassica juncea L.
Authors: Sahay Seema , Robledo-Arratia Luis , Glowacka Katarzyna , Gupta Meetu 
Published: April 2021

AbstractLittle is known about the interactive effects of exogenous nitric oxide (NO) and abscisic acid (ABA) on nitrogen (N) metabolism and related changes at molecular and biochemical levels under drought stress. The present study highlights the independent and combined effect of NO and ABA (grouped as “nitrate agonists”) on expression profiles of representative key genes known to be involved in N-uptake and assimilation, together with proline metabolism, N–NO metabolism enzyme’s activity and nutrient content in polyethylene glycol (PEG) treated roots of Indian mustard (B. juncea cv.Varuna). Here we report that PEG mediated drought stress negatively inhibited growth performance, as manifested by reduced biomass (fresh and dry weight) production. Total N content and other nitrogenous compounds (NO3−, NO2−) were decreased; however, NH4+, NH4+/ NO3−ratio and total free amino acids content were increased. These results were positively correlated with the PEG induced changes in expression of genes and enzymes involved in N-uptake and assimilation. Also, PEG supply lowered the content of macro- and micro-nutrients but proline level and the activity of ∆1-pyrroline-5-carboxylate synthetase increased indicating increased oxidative stress. However, all these responses were reversed upon the exogenous application of nitrate agonists (PEG + NO, PEG + NO + ABA, and PEG + ABA) where NO containing nitrate agonist treatment i.e. PEG + NO was significantly more effective than PEG + ABA in alleviating drought stress. Further, increases in activities of L-arginine dependent NOS-like enzyme and S-nitrosoglutathione reductase were observed under nitrate agonist treatments. This indicates that the balanced endogenous change in NO and ABA levels together during synthesis and degradation of NO mitigated the oxidative stress in Indian mustard seedlings. Overall, our results reveal that NO independently or together with ABA may contribute to improved crop growth and productivity under drought stress.
Association of preoperative seizures with tumor metabolites quantified by magnetic resonance spectroscopy in gliomas
Authors: Nakae Shunsuke , Kumon Masanobu , Murayama Kazuhiro , Ohba Shigeo , Sasaki Hikaru , Inamasu Joji , Kuwahara Kiyonori , Yamada Seiji , Abe Masato , Hirose Yuichi 
Published: April 2021

AbstractSeizures are common in patients with gliomas; however, the mechanisms of epileptogenesis in gliomas have not been fully understood. This study hypothesized that analyzing quantified metabolites using magnetic resonance spectroscopy (MRS) might provide novel insights to better understand the epileptogenesis in gliomas, and specific metabolites might be indicators of preoperative seizures in gliomas. We retrospectively investigated patient information (gender, age at diagnosis of tumor, their survival time) and tumor information (location, histology, genetic features, and metabolites according to MRS) in patients with gliomas. The data were correlated with the incidence of seizure and analyzed statistically. Of 146 adult supratentorial gliomas, isocitrate dehydrogenase (IDH) mutant tumors significantly indicated higher incidence of preoperative seizures than IDH wild-type gliomas. However, MRS study indicated that glutamate concentration in IDH wild-type gliomas was higher than that in IDH mutant gliomas. Glutamate was not associated with high frequency of preoperative seizures in patients with gliomas. Instead, increased total N-acetyl-l-aspartate (tNAA) was significantly associated with them. Moreover, multivariable analysis indicated that increased level of tNAA was an independent predictor of preoperative seizures. According to MRS analysis, tNAA, rather than glutamate, might be a useful to detect preoperative seizures in patient with supratentorial gliomas.
Novel Prosopis juliflora leaf ethanolic extract as natural antimicrobial agent against food spoiling microorganisms
Authors: Saleh Iman , Abu-Dieyeh Mohammed H. 
Published: April 2021

AbstractFresh produces spoilage is a worldwide concern that accompany the global increase in food demand. Adverse human health and environmental effects of commercial spoilage control agents are major public concern. In this study,Prosopis julifloraleaves and fruit extracts had their antimicrobial activities evaluated against the growth of selected bacteria and yeast, and against mycelial growth and conidial germination of selected mycotoxins-producing fungi.P. juliflorawater-soluble leaf ethanolic (PJ-WS-LE) extract with its novel extraction method showed the strongest antibacterial activity. Antimicrobial tests showed total inhibition ofBotrytis cinerea,Alternaria alternata,Bacillus subtilis,Staphylococcus aureusandCandida albicanswith MICs ranging between 0.125 and 1 mg/ml. Percent inhibition of mycelial growth (PIMG) of the extract was also determined against seven other fungal strains with highest value againstGeotrichum candidum(66.2%). Even the least affected fungal strain showed alterations in their hyphae and spores exposed to PJ-WS-LE extract when observed using scanning electron microscope (SEM), alterations include exfoliated flakes, pores, vacuolation and applanation. Small-scale fruit bioassays controlled experiment showed high efficacy of the extract in protecting inoculated cherry tomato samples fromB. cinereaandA. alternatainfections. In conclusion, PJ-WS-LE extract is a feasible, natural antifungal agent that can replace common anti-spoiling chemicals.
The ratio and difference of urine protein-to-creatinine ratio and albumin-to-creatinine ratio facilitate risk prediction of all-cause mortality
Authors: Chang David Ray , Yeh Hung-Chieh , Ting I-Wen , Lin Chen-Yuan , Huang Han-Chun , Chiang Hsiu-Yin , Chang Shih-Ni , Tsai Hsiu-Chen , Lo Yen-Chun , Hsiao Chiung-Tzu , Chu Pei-Lun , Kuo Chin-Chi 
Published: April 2021

AbstractThe role of the difference and ratio of albuminuria (urine albumin-to-creatinine ratio, uACR) and proteinuria (urine protein-to-creatinine ratio, uPCR) has not been systematically evaluated with all-cause mortality. We retrospectively analyzed 2904 patients with concurrently measured uACR and uPCR from the same urine specimen in a tertiary hospital in Taiwan. The urinary albumin-to-protein ratio (uAPR) was derived by dividing uACR by uPCR, whereas urinary non-albumin protein (uNAP) was calculated by subtracting uACR from uPCR. Conventional severity categories of uACR and uPCR were also used to establish a concordance matrix and develop a corresponding risk matrix. The median age at enrollment was 58.6 years (interquartile range 45.4–70.8). During the 12,391 person-years of follow-up, 657 deaths occurred. For each doubling increase in uPCR, uACR, and uNAP, the adjusted hazard ratios (aHRs) of all-cause mortality were 1.29 (95% confidence interval [CI] 1.24–1.35), 1.12 (1.09–1.16), and 1.41 (1.34–1.49), respectively. For each 10% increase in uAPR, it was 1.02 (95% CI 0.98–1.06). The linear dose–response association with all-cause mortality was only observed with uPCR and uNAP. The 3 × 3 risk matrices revealed that patients with severe proteinuria and normal albuminuria had the highest risk of all-cause mortality (aHR 5.25, 95% CI 1.88, 14.63). uNAP significantly improved the discriminative performance compared to that of uPCR (c statistics: 0.834 vs. 0.828, p-value = 0.032). Our study findings advocate for simultaneous measurements of uPCR and uACR in daily practice to derive uAPR and uNAP, which can provide a better mortality prognostic assessment.
Anticipating the impact of COVID19 and comorbidities on the South African healthcare system by agent-based simulations
Authors: Schlüter Jan Christian , Sörensen Leif , Bossert Andreas , Kersting Moritz , Staab Wieland , Wacker Benjamin 
Published: April 2021

AbstractTuberculosis (TB) is the 10th leading cause of death worldwide, and since 2007 it has been the main cause of death from a single infectious agent, ranking above HIV/AIDS. The current COVID-19 is a pandemic which caused many deaths around the world. The danger is not only a coinfection as observed for TB and HIV for a long time, but that both TB and SARS-CoV-2 affect the respiratory organs and thus potentiate their effect or accelerate the critical course. A key public health priority during the emergence of a novel pathogen is the estimation of the clinical need to assure adequate medical treatment. This requires a correct adjustment to the critical case detection rate and the prediction of possible scenarios based on known patterns. The African continent faces constraining preconditions in regard to healthcare capacities and social welfare which may hinder required countermeasures. However, given the high TB prevalence rates, COVID-19 may show a particular severe course in respective African countries, e.g. South Africa. Using WHO’s TB and public infrastructure data, we conservatively estimate that the symptomatic critical case rate, which affects the healthcare system, is between 8 and 12% due to the interaction of COVID-19 and TB, for a TB population of 0.52% in South Africa. This TB prevalence leads to a significant increase in the peak load of critical cases of COVID-19 patients and potentially exceeds current healthcare capacities.
Optimized imaging methods for species-level identification of food-contaminating beetles
Authors: Bera Tanmay , Wu Leihong , Ding Hongjian , Semey Howard , Barnes Amy , Liu Zhichao , Vyas Himansu , Tong Weida , Xu Joshua 
Published: April 2021

AbstractIdentifying the exact species of pantry beetle responsible for food contamination, is imperative in assessing the risks associated with contamination scenarios. Each beetle species is known to have unique patterns on their hardened forewings (known as elytra) through which they can be identified. Currently, this is done through manual microanalysis of the insect or their fragments in contaminated food samples. We envision that the use of automated pattern analysis would expedite and scale up the identification process. However, such automation would require images to be captured in a consistent manner, thereby enabling the creation of large repositories of high-quality images. Presently, there is no standard imaging technique for capturing images of beetle elytra, which consequently means, there is no standard method of beetle species identification through elytral pattern analysis. This deficiency inspired us to optimize and standardize imaging methods, especially for food-contaminating beetles. For this endeavor, we chose multiple species of beetles belonging to different families or genera that have near-identical elytral patterns, and thus are difficult to identify correctly at the species level. Our optimized imaging method provides enhanced images such that the elytral patterns between individual species could easily be distinguished from each other, through visual observation. We believe such standardization is critical in developing automated species identification of pantry beetles and/or other insects. This eventually may lead to improved taxonomical classification, allowing for better management of food contamination and ecological conservation.
Cardiometabolic risks of SARS-CoV-2 hospitalization using Mendelian Randomization
Authors: Lorincz-Comi Noah , Zhu Xiaofeng 
Published: April 2021

AbstractMany cardiometabolic conditions have demonstrated associative evidence with COVID-19 hospitalization risk. However, the observational designs of the studies in which these associations are observed preclude causal inferences of hospitalization risk. Mendelian Randomization (MR) is an alternative risk estimation method more robust to these limitations that allows for causal inferences. We applied four MR methods (MRMix, IMRP, IVW, MREgger) to publicly available GWAS summary statistics from European (COVID-19 GWAS n = 2956) and multi-ethnic populations (COVID-19 GWAS n = 10,908) to better understand extant causal associations between Type II Diabetes (GWAS n = 659,316), BMI (n = 681,275), diastolic and systolic blood pressure, and pulse pressure (n = 757,601 for each) and COVID-19 hospitalization risk across populations. Although no significant causal effect evidence was observed, our data suggested a trend of increasing hospitalization risk for Type II diabetes (IMRP OR, 95% CI 1.67, 0.96–2.92) and pulse pressure (OR, 95% CI 1.27, 0.97–1.66) in the multi-ethnic sample. Type II diabetes and Pulse pressure demonstrates a potential causal association with COVID-19 hospitalization risk, the proper treatment of which may work to reduce the risk of a severe COVID-19 illness requiring hospitalization. However, GWAS of COVID-19 with large sample size is warranted to confirm the causality.
Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean
Authors: Kofsky Janice , Zhang Hengyou , Song Bao-Hua 
Published: April 2021

AbstractSoybean cyst nematode (SCN, Heterodera glycineIchinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it’s gene pool is indisputably more diverse thanG. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions ofG. sojaandG. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.