bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction
Authors: Vachon Melody A. , Engel Katja , Beaver Rachel C. , Slater Greg F. , Binns W. Jeffrey , Neufeld Josh D. 
Published: November 2021

AbstractCharacterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.
Apoptosis-associated speck-like protein containing a CARD regulates the growth of pancreatic ductal adenocarcinoma
Authors: Koizumi Mitsuhito , Watanabe Takao , Masumoto Junya , Sunago Kotaro , Imamura Yoshiki , Kanemitsu Kozue , Kumagi Teru , Hiasa Yoichi 
Published: November 2021

AbstractApoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is a key adaptor protein of inflammasomes and a proapoptotic molecule; however, its roles in signal transduction in pancreatic ductal adenocarcinoma (PDAC) cells remain unknown. Here, we clarified the role and mechanisms of action of ASC in PDAC using clinical evidence and in vitro data. ASC expression in PDAC tissues was analyzed using public tumor datasets and immunohistochemistry results of patients who underwent surgery, and PDAC prognosis was investigated using the Kaplan–Meier Plotter. ASC expression in PDAC cells was downregulated using small-interfering RNA, and gene expression was assessed by RNA sequencing. Review of the Oncomine database and immunostaining of surgically removed tissues revealed elevated ASC expression in PDAC tumors relative to non-tumor tissue, indicating poor prognosis. We observed high ASC expression in multiple PDAC cells, with ASC silencing subsequently inhibiting PDAC cell growth and altering the expression of cell cycle-related genes. Specifically, ASC silencing reduced cyclin D1 levels and stopped the cell cycle at the G1 phase but did not modulate the expression of any apoptosis-related molecules. These results show that ASC inhibited tumor progression via cell cycle modulation in PDAC cells and could be a potential therapeutic target.
Impact of oxygen tension according to embryo stage of development: a prospective randomized study
Authors: Herbemont C. , Labrosse J. , Bennani-Smires B. , Cedrin-Durnerin I. , Peigne M. , Sermondade N. , Sarandi S. , Vivot A. , Vicaut E. , Talib Z. , Grynberg M. , Sifer C. 
Published: November 2021

AbstractHuman embryo culture under 2–8% O2 is recommended by ESHRE revised guidelines for good practices in IVF labs. Nevertheless, notably due to the higher costs of embryo culture under hypoxia, some laboratories perform embryo culture under atmospheric O2 tension (around 20%). Furthermore, recent meta-analyses concluded with low evidence to a superiority of hypoxia on IVF/ICSI outcomes. Interestingly, a study on mice embryos suggested that oxidative stress (OS) might only have an adverse impact on embryos at cleavage stage. Hence, we aimed to demonstrate for the first time in human embryos that OS has a negative impact only at cleavage stage and that sequential culture conditions (5% O2 from Day 0 to Day 2/3, then «conventional» conditions at 20% O2 until blastocyst stage) might be a valuable option for human embryo culture. 773 IVF/ICSI cycles were included in this randomized clinical trial from January 2016 to April 2018. At Day 0 (D0), patients were randomized using a 1:2 allocation ratio between group A (20% O2; n = 265) and group B (5% O2; n = 508). Extended culture (EC) was performed when ≥ 5 Day 2-good-quality-embryos were available (n = 88 in group A (20% O2)). In subgroup B, 195 EC cycles were randomized again at Day 2 (using 1:1 ratio) into groups B’ (5% O2 until Day 6 (n = 101)) or C (switch to 20% O2 from Day 2 to Day 6 (n = 94). Fertilization rate, cleavage-stage quality Day 2-top-quality-embryo (D2-TQE), blastocyst quality (Day 5-top-quality-blastocyst (D5-TQB) and implantation rate (IR) were compared between groups A and B (= cleavage-stage analysis), or A(20% O2), B’(5% O2) and C(5%-to-20% O2). Overall, characteristics were similar between groups A and B. Significantly higher rates of early-cleaved embryos, top-quality and good-quality embryos on Day 2 were obtained in group B compared to group A (P < 0.05). This association between oxygen tension and embryo quality at D2 was confirmed using an adjusted model (P < 0.05). Regarding blastocyst quality, culture under 20% O2 from Day 0 to Day 6 (group A) resulted in significantly lower Day 5-TQB number and rates (P < 0.05) compared to both groups B’ and C. Furthermore, blastocyst quality was statistically equivalent between groups B’ and C (P = 0.45). At Day 6, TQB numbers and rates were also significantly higher in groups B’ and C compared to group A (P < 0.05). These results were confirmed analyzing adjusted mean differences for number of Day 5 and Day 6 top quality embryos obtained in group A when compared to those respectively in groups B’ and C (P < 0.05). No difference in clinical outcomes following blastocyst transfers was observed. These results would encourage to systematically culture embryos under hypoxia at least during early development stages, since OS might be detrimental exclusively before embryonic genome activation.
Lipopolysaccharide-induced neuroinflammation disrupts functional connectivity and community structure in primary cortical microtissues
Authors: Atherton Elaina , Brown Sophie , Papiez Emily , Restrepo Maria I. , Borton David A. 
Published: November 2021

AbstractThree-dimensional (3D) neural microtissues are a powerful in vitro paradigm for studying brain development and disease under controlled conditions, while maintaining many key attributes of the in vivo environment. Here, we used primary cortical microtissues to study the effects of neuroinflammation on neural microcircuits. We demonstrated the use of a genetically encoded calcium indicator combined with a novel live-imaging platform to record spontaneous calcium transients in microtissues from day 14–34 in vitro. We implemented graph theory analysis of calcium activity to characterize underlying functional connectivity and community structure of microcircuits, which are capable of capturing subtle changes in network dynamics during early disease states. We found that microtissues cultured for 34 days displayed functional remodeling of microcircuits and that community structure strengthened over time. Lipopolysaccharide, a neuroinflammatory agent, significantly increased functional connectivity and disrupted community structure 5–9 days after exposure. These microcircuit-level changes have broad implications for the role of neuroinflammation in functional dysregulation of neural networks.
Computer-assisted classification of contrarian claims about climate change
Authors: Coan Travis G. , Boussalis Constantine , Cook John , Nanko Mirjam O. 
Published: November 2021

AbstractA growing body of scholarship investigates the role of misinformation in shaping the debate on climate change. Our research builds on and extends this literature by (1) developing and validating a comprehensive taxonomy of climate contrarianism, (2) conducting the largest content analysis to date on contrarian claims, (3) developing a computational model to accurately classify specific claims, and (4) drawing on an extensive corpus from conservative think-tank (CTTs) websites and contrarian blogs to construct a detailed history of claims over the past 20 years. Our study finds that the claims utilized by CTTs and contrarian blogs have focused on attacking the integrity of climate science and scientists and, increasingly, has challenged climate policy and renewable energy. We further demonstrate the utility of our approach by exploring the influence of corporate and foundation funding on the production and dissemination of specific contrarian claims.
Hierarchical porous materials made by stereolithographic printing of photo-curable emulsions
Authors: Kleger Nicole , Minas Clara , Bosshard Patrick , Mattich Iacopo , Masania Kunal , Studart André R. 
Published: November 2021

AbstractPorous materials are relevant for a broad range of technologies from catalysis and filtration, to tissue engineering and lightweight structures. Controlling the porosity of these materials over multiple length scales often leads to enticing new functionalities and higher efficiency but has been limited by manufacturing challenges and the poor understanding of the properties of hierarchical structures. Here, we report an experimental platform for the design and manufacturing of hierarchical porous materials via the stereolithographic printing of stable photo-curable Pickering emulsions. In the printing process, the micron-sized droplets of the emulsified resins work as soft templates for the incorporation of microscale porosity within sequentially photo-polymerized layers. The light patterns used to polymerize each layer on the building stage further generate controlled pores with bespoke three-dimensional geometries at the millimetre scale. Using this combined fabrication approach, we create architectured lattices with mechanical properties tuneable over several orders of magnitude and large complex-shaped inorganic objects with unprecedented porous designs.
Development and internal validation of an algorithm to predict intraoperative risk of inadvertent hypothermia based on preoperative data
Authors: Wallisch C. , Zeiner S. , Scholten P. , Dibiasi C. , Kimberger O. 
Published: November 2021

AbstractIntraoperative hypothermia increases perioperative morbidity and identifying patients at risk preoperatively is challenging. The aim of this study was to develop and internally validate prediction models for intraoperative hypothermia occurring despite active warming and to implement the algorithm in an online risk estimation tool. The final dataset included 36,371 surgery cases between September 2013 and May 2019 at the Vienna General Hospital. The primary outcome was minimum temperature measured during surgery. Preoperative data, initial vital signs measured before induction of anesthesia, and known comorbidities recorded in the preanesthetic clinic (PAC) were available, and the final predictors were selected by forward selection and backward elimination. Three models with different levels of information were developed and their predictive performance for minimum temperature below 36 °C and 35.5 °C was assessed using discrimination and calibration. Moderate hypothermia (below 35.5 °C) was observed in 18.2% of cases. The algorithm to predict inadvertent intraoperative hypothermia performed well with concordance statistics of 0.71 (36 °C) and 0.70 (35.5 °C) for the model including data from the preanesthetic clinic. All models were well-calibrated for 36 °C and 35.5 °C. Finally, a web-based implementation of the algorithm was programmed to facilitate the calculation of the probabilistic prediction of a patient’s core temperature to fall below 35.5 °C during surgery. The results indicate that inadvertent intraoperative hypothermia still occurs frequently despite active warming. Additional thermoregulatory measures may be needed to increase the rate of perioperative normothermia. The developed prediction models can support clinical decision-makers in identifying the patients at risk for intraoperative hypothermia and help optimize allocation of additional thermoregulatory interventions.
Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
Authors: Nowak Albina , Murik Omer , Mann Tzvia , Zeevi David A. , Altarescu Gheona 
Published: November 2021

AbstractMore than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
Cancer classification using machine learning and HRV analysis: preliminary evidence from a pilot study
Authors: Vigier Marta , Vigier Benjamin , Andritsch Elisabeth , Schwerdtfeger Andreas R. 
Published: November 2021

AbstractMost cancer patients exhibit autonomic dysfunction with attenuated heart rate variability (HRV) levels compared to healthy controls. This research aimed to create and evaluate a machine learning (ML) model enabling discrimination between cancer patients and healthy controls based on 5-min-ECG recordings. We selected 12 HRV features based on previous research and compared the results between cancer patients and healthy individuals using Wilcoxon sum-rank test. Recursive Feature Elimination (RFE) identified the top five features, averaged over 5 min and employed them as input to three different ML. Next, we created an ensemble model based on a stacking method that aggregated the predictions from all three base classifiers. All HRV features were significantly different between the two groups. SDNN, RMSSD, pNN50%, HRV triangular index, and SD1 were selected by RFE and used as an input to three different ML. All three base-classifiers performed above chance level, RF being the most efficient with a testing accuracy of 83%. The ensemble model showed a classification accuracy of 86% and an AUC of 0.95. The results obtained by ML algorithms suggest HRV parameters could be a reliable input for differentiating between cancer patients and healthy controls. Results should be interpreted in light of some limitations that call for replication studies with larger sample sizes.
Comparison of heads up three dimensional visualization system to conventional microscope in retinopathy of prematurity related tractional retinal detachment
Authors: AlZaid Abdulrahman , Alsakran Wael A. , Alsulaiman Sulaiman M. , Mura Marco 
Published: November 2021

AbstractTo report the outcomes, advantages and disadvantages of a heads-up three-dimensional (3D) visualization system compared to the conventional microscope in pediatric tractional retinal detachment (TRD) surgery secondary to advanced stage retinopathy of prematurity (ROP). Medical records of patients with ROP stage 4 or 5 who underwent surgery for tractional retinal detachment at King Khaled Eye Specialist Hospital between September 2017 and July 2019 were identified and reviewed. Eyes were divided into 2 groups, eyes that underwent surgery with a 3D heads-up platform (3D group) and eyes that underwent surgery with a conventional microscope (conventional group). Data were collected on neonatal history, visual acuity, intraoperative complications and success rates between groups.Eighteen eyes of 14 patients who underwent surgical repair of TRD related to ROP. Postoperative outcomes were compared between 10 eyes (7 patients) in the 3D group and 8 eyes (7 patients) in the conventional group There was no statistically significant difference in success rate between both groups (75% conventional group vs 70% 3D group). Partial or complete reattachment was achieved in 7 eyes in 3D group compared to 6 eyes in conventional group. Lower postmenstrual age at the time of the first surgery and presence of retinal breaks were associated with poorer surgical outcome. Heads up 3D visualization system is feasible in tractional retinal detachment related to ROP with similar success rate and no increased risk of complications when compared to conventional microscope. This system may be advantageous in advanced pediatric tractional retinal detachment surgeries.
Climate change affects the parasitism rate and impairs the regulation of genes related to oxidative stress and ionoregulation of Colossoma macropomum
Authors: da Costa Jaqueline Custodio , de Souza Samara Silva , Castro Jonatas da Silva , Amanajás Renan Diego , Val Adalberto Luis 
Published: November 2021

AbstractGlobal climate change represents a critical threat to the environment since it influences organismic interactions, such as the host-parasite systems, mainly in ectotherms including fishes. Rising temperature and CO2are predicted to affect this interaction other and critical physiological processes in fish. Herein, we investigated the effects of different periods of exposure to climate change scenarios and to two degrees of parasitism by monogeneans in the host-parasite interaction, as well as the antioxidant and ionoregulatory responses of tambaqui (Colossoma macropomum), an important species in South American fishing and aquaculture. We hypothesized that temperature and CO2changes in combination with parasite infection would interfere with the host’s physiological processes that are related to oxidative stress and ionoregulation. We experimentally exposedC. macropomumto low and high levels of parasitism in the current and extreme climate scenarios (4.5 °C and 900 ppm CO2above current levels) for periods of seven and thirty days and we use as analyzed factors; the exposure time, the climate scenario and parasitism level in a 2 × 2 × 2 factorial through a three-way ANOVA as being fish the experimental unit (n = 8). An analysis of gill enzymatic and gene expression profile was performed to assess physiological (SOD, GPx and Na+/K+-ATPase enzymes) and molecular (Nrf2, SOD1, HIF-1αandNKAα1a genes) responses. A clear difference in the parasitism levels of individuals exposed to the extreme climate scenario was observed with a rapid and aggressive increase that was higher after 7 days of exposure though showed a decrease after 30 days. The combination of exposure to the extreme climate change scenario and parasitism caused oxidative stress and osmoregulatory disturbance, which was observed through the analysis of gene expression (Nrf2, SOD1, HIF-1αandNKAα1a) and antioxidant and ionoregulatory enzymes (SOD, GPx and Na+/K+-ATPase) on the host, possibly linked to inflammatory processes caused by the high degree of parasitism. In the coming years, these conditions may result in losses of performance for this species, and as such will represent ecological damage and economical losses, and result in a possible vulnerability in relation to food security.
Loss of ZNF677 expression is a predictive biomarker for lymph node metastasis in Middle Eastern Colorectal Cancer
Authors: Siraj Abdul K. , Parvathareddy Sandeep Kumar , Siraj Nabil , Al-Obaisi Khadija , Aldughaither Saud M. , AlManea Hadeel M. , AlHussaini Hussah F. , Al-Dayel Fouad , Al-Kuraya Khawla S. 
Published: November 2021

AbstractZinc-finger proteins are transcription factors with a “finger-like” domain that are widely involved in many biological processes. The zinc-finger protein 677 (ZNF677) belongs to the zinc-finger protein family. Previous reports have highlighted the tumor suppressive role of ZNF677 in thyroid and lung cancer. However, its role in colorectal cancer (CRC) has not been explored. ZNF677 protein expression was analyzed by immunohistochemistry in a large cohort of 1158 CRC patients. ZNF677 loss of expression was more frequent in CRC tissues (45.3%, 525/1158), when compared to that of normal tissue (5.1%, 11/214) (p < 0.0001) and was associated with mucinous histology (p = 0.0311), advanced pathological stage (p < 0.0001) and lymph node (LN) metastasis (p = 0.0374). Further analysis showed ZNF677 loss to be significantly enriched in LN metastatic CRC compared to overall cohort (p = 0.0258). More importantly, multivariate logistic regression analysis showed that ZNF677 loss is an independent predictor of LN metastasis in CRC (Odds ratio = 1.41; 95% confidence interval 1.05–1.87; p = 0.0203).The gain- and loss-of-function studies in CRC cell lines demonstrated that loss of ZNF677 protein expression prominently increased cell proliferation, progression of epithelial-mesenchymal transition and conferred chemoresistance, whereas its overexpression reversed the effect. In conclusion, loss of ZNF677 protein expression is common in Middle Eastern CRC and contributes to the prediction of biological aggressiveness of CRC. Therefore, ZNF677 could not only serve as a marker in predicting clinical prognosis in patient with CRC but also as a potential biomarker for personalized targeted therapy.
Identification and field verification of an aggregation pheromone from the white-spotted flower chafer, Protaetia brevitarsis Lewis (Coleoptera: Scarabaeidae)
Authors: Zhang Xiaofang , Wang Liuyang , Liu Chunqin , Liu Yongqiang , Mei Xiangdong , Wang Zhongyue , Zhang Tao 
Published: November 2021

AbstractThe white-spotted flower chafer (WSFC), Protaetia brevitarsis Lewis, is native to East Asia. Although their larvae are considered a potential resource insect for degrading plant residues, producing protein fodder, and processing to traditional medicine, adult WSFCs inflict damage to dozens of fruit and economic crops. The control of the WSFC still relies heavily on pesticides and the inefficient manual extraction of adults. Here, we report the identification and evaluation of the aggregation pheromone of WSFCs. From the headspace volatiles emitted from WSFC adults, anisole, 4-methylanisole, 2-heptanone and 2-nonanone were identified as WSFC-specific components. However, only anisole and 4-methylanisole elicited positive dose–response relationship in electroantennography tests, and only 4-methylanisole significantly attracted WSFCs of both sexes in olfactometer bioassays and field experiments. These results concluded that 4-methylanisole is the aggregation pheromone of WSFCs. Furthermore, we developed polyethylene vials as long-term dispensers of 4-methylanisole to attract and kill WSFCs. The polyethylene vial lures could effectively attracted WSFCs for more than four weeks. Pheromone-based lures can be developed as an environmentally friendly protocol for monitoring and controlling WSFC adults.