bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation and Performance Evaluation of Quaternary Copolymer Sand Control Agent
Authors: Duan Ming , Wang Qihai , Chen Bin , Chen Huaxin , Li Xinliang , Fang Shenwen 
Published: January 2024

Summary
Sand production is a common problem in petroleum extraction, and the development of water-soluble polymer sand control agents is currently a research hotspot. However, this research does not provide details of the chemical structure and lacks discussions on adsorption and sand control mechanisms. Herein, a new water-soluble polymer sand control agent (PAADD) is reported on; it is a copolymer of 2-acrylamido-2-methylpropane sulfonic acid (AMPS), N-(3-dimethylaminopropyl) methacrylamide (DPM), a functional monomer (DAM) containing ketone groups and self-crosslinking properties, and acrylamide (AM). First, the synthesis conditions of PAADD are optimized, and then its sand control mechanism is explored. Experimental results reveal that PAADD can adsorb on the sand surface through electrostatic attraction and hydrogen bonding and change the surface properties of sand particles, which promotes the aggregation of sand particles and permits good sand control ability. In flow experiments, after the injection of PAADD solution (500 mg/L) into a sandpacked model with a permeability of 500 md, the critical sand production rate of the sandpacked model increased more than 100 times and the permeability damage rate (PDR) was 30–40%.
Design and Validation of Flim-timer for Measuring Protein Turnover in Cells Using Fluorescence Lifetime
Authors: Dikovskaya Dina , Bento-Pereira Claudia , Shiga Kanade , Corno Andrea , Higgins Maureen , Toth Rachel , Saurin Adrian , Dinkova-Kostova Albena 
Published: January 2024

Abstract

Measuring protein turnover in individual cells and subcellular compartments has been greatly assisted by fluorescence timers (FT) whose changing spectra, expressed as the ratio of fluorescence intensities, reflect their molecular age. However, FT quantification requires highly fluorescent samples, prohibiting their use for proteins with low or non-uniform expression. Here we developed a method that utilises fluorescence lifetime, a property largely independent of intensity, of a specifically designed FT (named FLIM-timer). The fluorescence lifetime of FLIM-timer reflected protein turnover in regions of high and low brightness with equally high precision. We demonstrate the versatility of this approach with several versions of FLIM-timer in two distinct experimental systems: 1) as a readout for efficacy of pharmacological inducers of Nrf2, the master regulator of redox homeostasis, and 2) as a tool to monitor cyclin B1 degradation during mitotic exit. Overall, the FLIM-timer methodology expands the applicability of FT for visualisation and quantification of protein turnover.
Comprehensive Analysis of Cuproptosis-related Genes Involved in Prognosis and Tumor Microenvironment Infiltration of Colorectal Cancer
Authors: Chen Weiyi , Hu Ke , Liu Yu , Li Xiaocheng , Peng Jing , Chen Lijun , Duan Shaoyi , Yang Qizhang 
Published: January 2024

Abstract
Colorectal cancer (CRC) is a common malignancy with high incidence and mortality rates. Cuproptosis, a novel form of copper-induced programmed cell death, contributes to tumor progression. Whether cuproptosis-related genes (CRGs) play a role in CRC remains unclear. Here, we systematically assessed CRG mutations in CRC. The expression of eight of the 10 CRGs was significantly different between CRC and normal tissues. CDKN2A and DLAT were identified as independent risk factors for predicting overall survival (OS) in CRC using univariate and multivariate Cox analyses, and a risk score model was constructed based on CDKN2A and DLAT. Patients with CRC were categorized into high- and low-risk groups based on their median risk scores, with those in the low-risk group having longer OS than those in the high-risk group. Receiver operating characteristic curve analysis indicated that the risk score model had good predictive accuracy for OS. Analysis of the TISCH and TISIDB database showed that CDKN2A and DLAT were associated with the TME, and the molecular subtypes and immune subtypes differed between CDKN2A and DLAT. Spearman’s analysis showed that CDKN2A and DLAT expressions were significantly associated with immune cell infiltration in CRC. Our research revealed CRGs’ prognostic value, particularly CDKN2A and DLAT, in CRC and demonstrated the relationship between CDKN2A/DLAT and immune infiltration in CRC, thereby contributing to the outcome evaluation of patients with CRC and identifying novel targets for CRC immunotherapy.
Accumulation of lncRNAs in cytoplasm upon DIS3 depletion leads to production of cryptic peptides detected in Multiple Myeloma.
Authors: Foretek Dominika , Gabriel Marc , Hatin Isabelle , Jarroux Julien , Pinskaya Marina , Pepermans Elise , Boonen Kurt , Topno Rachel , Slaninova Vera , Serna Marina , Llorca Oscar , Baggerman Geert , Bertrand Edouard , West Steven , Namy Olivier , Morillon Antonin 
Published: January 2024

Abstract
Some long noncoding (lnc)RNAs harbor the potential to produce functional micropeptides. Despite the increasing recognition of their significance, the regulatory dynamics of cytoplasmic lncRNA expression, decay, and translation remain poorly understood. Here, we investigate the role of ribonucleases in controlling cytoplasmic levels of lncRNAs. By transcriptomic analysis we identified DIS3 but not XRN1 as a major enzyme preventing accumulation of lncRNAs in cytoplasm. Single-molecule experiments illustrate an example of DIS3-sensitive transcript (DIST) accumulation in the nucleus preceding the one in the cytoplasm, suggesting a sequential series of events. Approximately 14.5% of the DISTs contain at least one actively translated open reading frame (ORF). This finding is highly relevant to Multiple Myeloma bone marrow cancer patients’ cases with mutations impairing the DIS3 enzymatic activity and revealing a subgroup of overexpressed translatable DISTs. Immunopeptidomic approach identified the association of DIST-derived peptides with the major histocompatibility complex class I (MHCI). Notably, the low expression of DISTs in healthy tissues emphasizes their potential as targets for cancer-specific immunotherapies. Our findings shed light on the intricate regulatory mechanisms governing cytoplasmic lncRNA dynamics and highlight their clinical relevance in the context of bone marrow cancers, providing a foundation for future investigations into novel therapeutic strategies.
An Open Source R Package for Detection of Adverse Events Under-Reporting in Clinical Trials - Implementation and Validation by the IMPALA (Inter coMPany quALity Analytics) Consortium
Authors: Koneswarakantha Björn , Adyanthaya Ronojit , Emerson Jennifer , Collin Frederik , Keller Annett , Mattheus Michaela , Spyroglou Ioannis , Donevska Sandra , Ménard Timothé 
Published: January 2024

Abstract

Accurate and timely reporting of adverse events (AE) in clinical trials is crucial to ensuring data integrity and patient safety. However, AE under-reporting remains a challenge, often highlighted in Good Clinical Practice (GCP) audits and inspections. Traditional detection methods, such as on-site investigator audits via manual source data verification (SDV), have limitations. Addressing this, the open-source R package {simaerep} was developed to facilitate rapid, comprehensive, and near-real-time detection of AE under-reporting at each clinical trial site. This package leverages patient-level AE and visit data for its analyses. To validate its efficacy, three member companies from the Inter-coMPany quALity Analytics (IMPALA) consortium independently assessed the package. Results showed that {simaerep} consistently and effectively identified AE under-reporting across all three companies, particularly when there were significant differences in AE rates between compliant and non-compliant sites. Furthermore, {simaerep}'s detection rates surpassed heuristic methods, and it identified 50% of all detectable sites as early as 25% into the designated study duration. The open-source package can be embedded into audits to enable fast, holistic and repeatable quality oversight of clinical trials.
Novel variants in the SOX11 gene: additional evidence for the involvement of SOX11 in hypogonadotropic hypogonadism
Authors: Vieira Tarsis , Schincariol-Manhe Beatriz , Campagnolo Érica , Spineli-Silva Samira , de Leeuw Nicole , Correia-Costa Gabriela , Pessoa André , de Souza Carolina , Stevens Cathy , Javaher Poupak , Scallet Helena , Mohr Julia , Biskup Saskia , Herkert Johanna , Pfundt Rolph , Mehta Lakshmi , Rekab Aisha , Elloumi Houda , Maciel-Guerra Andréa , Lopes Vera Lucia Gil da Silva , Santos Ana dos , Sanyoura May 
Published: January 2024

Abstract

Pathogenic SOX11 variants have been associated with intellectual developmental disorder with microcephaly, and with or without ocular malformations or hypogonadotropic hypogonadism (IDDMOH, OMIM # 615866). In this article, we report seven new patients with SOX11 variants, five of whom have features suggestive of hypogonadotropic hypogonadism (HH). The main clinical features included neurodevelopmental delay (7/7) and intellectual disability (5/7), autism/attention deficit hyperactivity disorder (5/7), microcephaly (4/7), short stature (4/7), hypotonia (4/7), and clinodactyly of the 5th fingers (5/7). HH was confirmed in two female patients with primary amenorrhea, nonvisualized/prepubertal size of the uterus, and nonvisualized ovaries. Two of the male patients presented with micropenis, two had cryptorchidism, and one had decreased testicular size. These findings are suggestive of HH and appear to be more common than previously described among individuals with pathogenic SOX11 variants. Therefore, SOX11 should be included in diagnostic gene panels for patients with hypogonadotropic hypogonadism.
Scalable Fabrication of High-Performance Flexible Transparent Conducting Electrodes via Blade-Coating and Photonic Curing for Optoelectronic Applications
Authors: Hsu Julia , Piper Robert , Bhandari Bishal , Bonner Justin , Davis Matthew , Valdez Marisol 
Published: January 2024

Abstract
Flexible transparent conducting electrodes (TCEs) are critical components for many optoelectronic applications. Currently, indium tin oxide (ITO) TCEs dominate the market, but it is difficult to achieve high-performance ITO on plastic substrates. Metal nanostructures are promising alternatives for flexible TCEs because of their high transparency, excellent electrical conductance, and compatibility with roll-to-roll manufacturing. In this work, we combine flexographically printed Ag metal bus lines with a blade-coated Ag nanowire layer that is overcoated with indium zinc oxide and photonically cured to create flexible hybrid TCEs on polyethylene terephthalate (PET) substrates. Photonic curing is a promising alternative to thermal annealing as it can rapidly elevate the temperature of specific layers within microseconds or milliseconds without significantly increasing the temperature of low thermal budget plastic substrates. We chose blade-coating and photonic curing to fabricate the hybrid TCEs because both processes can be scaled to large areas. Our hybrid TCE achieves an average transmittance of 81%, an average sheet resistance of 11 Ω/sq, and a surface roughness of 4.3 nm. To evaluate the hybrid TCE performance, we fabricated halide perovskite solar cells on them and compared the results to solar cells made on commercially available PET/TCE substrates. Finally, we scaled up the blade-coating and photonic curing process from 1 in x 3 in samples to 7 in x 8 in samples to demonstrate uniform fabrication of large-area hybrid TCEs.
Cadmium toxicity to and accumulation in a soil collembolan (Folsomia candida): major factors and prediction using a back-propagation neural network mode
Authors: Li Simin , Li Zhu , Ke Xin , Wisawapipat Worachart , Christie Peter , Wu Longhua 
Published: January 2024

Abstract
Accurate prediction of cadmium (Cd) ecotoxicity to and accumulation in soil biota is important in soil health. However, very limited information on Cd ecotoxicity on naturally contaminated soils. Herein, we investigated soil Cd ecotoxicity using Folsomia candida, a standard single-species test animal, in 28 naturally Cd-contaminated soils, and the back-propagation neural network (BPNN) model was used to predict Cd ecotoxicity to and accumulation in F. candida. Soil total Cd and pH were the primary soil properties affecting Cd toxicity. However, soil pH was the main factor when the total Cd concentration was ˂ 3 mg kg− 1. Interestingly, correlation analysis and the K-spiked test confirmed nutrient potassium (K) was essential for Cd accumulation, highlighting the significance of studying K in Cd accumulation. The BPNN model showed greater prediction accuracy of collembolan survival rate (R2 = 0.797), reproduction inhibitory rate (R2 = 0.827), body Cd concentration (R2 = 0.961), and Cd bioaccumulation factor (R2 = 0.964) than multiple linear regression models. Then the developed BPNN model was used to predict Cd ecological risks in 57 soils in southern China. Compared to multiple linear regression models, the BPNN models can better identify high-risk regions. This study highlights the potential of BPNN as a novel and rapid tool for the evaluation and monitoring of Cd ecotoxicity in naturally contaminated soils.
Electrochemical deuterated ammonia (ND3) production at A cm-2 current densities
Authors: Zhang Zishuai , Zhu Pan , Qin Jiangzhou , Li Jun , Zuo Kuichang 
Published: January 2024

Abstract
Deuterated ammonia (ND3) treatment contributes significantly to the reliability of semiconductors in manufacturing. Current ND3 production suffers from high energy consumption, CO2 emissions and capital expenditure. In this study, we present an electrochemical approach using iron (Fe) single-atom catalysts supported by nitrogen-doped carbon in an electrolyzer, operating at A cm-2 current densities for ND3 production. Through systematic optimization of catalyst composition, electrode/electrolyzer architectures, anodic reactions, and operating conditions, the system achieved a ND3 selectivity exceeding 80% at 200 mA cm-2 and 60% at 600 mA cm-2, with a maximal production rate of 1.73 mmol h-1 cm-2 and stability over 100 hours (assessed at 200 mA cm-2). The full cell voltage is 3.2 V when combined with an oxygen evolution reaction (OER) anode, and it decreases to 2.3 V when coupled with a hydrogen oxidation reaction (HOR) anode at 600 mA cm-2. Techno-economic analysis (TEA) results demonstrate a fivefold energy consumption reduction to 0.19 MJ molND3-1, threefold emission reduction to 16.13 g molND3-1, and threefold cost reduction to $6,000 from $27,000 kgND3-1, highlighting the potential for widespread commercialization and contributing to the more environmentally sustainable ND3 production.
Machine Learned Interatomic Potentials for Ternary Carbides trained on the AFLOW Database
Authors: Zurek Eva , Roberts Josiah , Rijal Biswas , Divilov Simon , Maria Jon-Paul , Fahrenholtz William , Wolfe Douglas , Brenner Donald , Curtarolo Stefano 
Published: January 2024

Abstract

Large density functional theory (DFT) databases are a treasure trove of energies, forces and stresses that can be used to train machine learned
interatomic potentials for atomistic modeling. Herein, we employ structural relaxations from the AFLOW database to train moment tensor
potentials (MTPs) for four carbide systems: HfTaC, HfZrC, MoWC and TaTiC. The resulting MTPs are used to relax ∼6300 random symmetric
structures, and subsequently improved via active learning to generate robust potentials (RP) that can be applied to a wide variety of structures,
and accurate potentials (AP) designed only for low-energy systems. This protocol is shown to yield convex hulls that are indistinguishable
from those predicted by AFLOW for the HfTaC, HfZrC and TaTiC systems, and in the case of the CMoW system to predict thermodynamically
stable structures that are not found within AFLOW, highlighting the potential of the employed protocol within crystal structure prediction.
Relaxation of over three hundred Mo1−xWxC stoichiometry crystals first with the RP then with the AP yields formation enthalpies that are in
excellent agreement with those obtained via DFT.
Assessing the Effects of Ghost Nets on Coral Health: An Examination of Coral Reefs on Androth Island, Lakshadweep
Authors: NM Sahab , PV Ahmed Amirsha , CN Abdul Raheem , A.T Damodhar , T Aboo hashim 
Published: January 2024

Abstract
In our study, we investigated the impact of derelict fishing gear on coral reefs in various locations on the Androth reef of the Lakshadweep. We found significant variations in coral health across the surveyed sites, with some areas showing a high percentage of live coral while others exhibiting a high percentage of dead coral. Ghost nets snagged on reefs at all depths had a significant negative impact on coral health, according to pairwise analyses. Pearson's correlation analysis of coral health and stress relationships confirmed a significant relationship between ghost nets and coral health (LC, DC, R, and AA) at all sampled depths. In our analysis, we examined coral mortality, tissue loss, and variations in zooxanthellae density among different coral species. The average sedimentation ranges recorded monthly were 49.75 ± 43.2 and 116 ± 41.05, respectively. The sedimentation rate in the Androth reefs of the Lakshadweep was approximately five times greater than in the other regions. During our survey, we observed abandoned fishing gear, including 6 mm fishing ghost nets (28%), 5 mm fishing ghost nets (11%), ropes (31%), buoys (19%), and lines (11%) across the study sites. The overall composition of live coral cover on averaged was 22.1%, while dead coral accounted for 24.3% and rubble constituted 53.6%. Furthermore, we removed more than 48 kg of ghost nets from the NIOT underwater pipe, and significant quantities of these nets were retrieved from sites SW3 and SW2 (12.5 kg each) during our efforts. This study highlights the critical importance of addressing ghost net entanglement and its detrimental effects on coral health, as well as the urgent need for conservation efforts in the surveyed reef ecosystems.
Investigating the Effects of Monarda Didyma L. Extract Supplementation on Biological Aging of Susceptible Population: Protocol of a Randomized, Placebo- Controlled, Double-blind Parallel Clinical Trial
Authors: Campisi Manuela , Cannella Luana , Baumann Julia , Pavanello Sofia 
Published: January 2024

Abstract
Background
Manipulations to decelerate biological aging and extend health span are major challenges for health given the social and healthcare costs of aging population. Excessive oxidative stress and inflammation are primary drivers in biological aging and age-related diseases. Didymin, a natural bioactive flavonoid and the major polyphenol of Monarda didyma L., has showed a crucial anti-inflammatory role. This clinical study aims to investigate the potential benefits of a 12-weeks supplementation of Monarda didyma L. extract on reducing / delaying the biological aging of a susceptible population of aging workers.
Methods
This is a randomized, placebo-controlled, double-blind, parallel design and monocentric clinical trial. Study population will comprise 80 participants, aged 45–65 years, randomly allocated to both Intervention group (supplementation of Monarda didyma L. extract) and placebo control group (placebo supplementation) for a 12-weeks period of treatment. All study participants, who will be enrolled at the Occupational Medicine Unit – Azienda Ospedale Università of Padova providing a written informed consent, will undergo clinical examination, an interview with structured questionnaires (demographic data, lifestyle, information quality of life and sleeping patterns) and collection of fasting blood for evaluation of indicators of biological aging as primary outcomes (DNA methylation age, telomere length, mitochondrial DNA copy number), as well as secondary outcomes including basic biochemistry and inflammation markers (emocrome, glycemia, insulin, total cholesterol, low and high density lipoproteins, triglycerides, creatinine, telomerase expression, C-reactive protein, interleukin6, aspartate transaminase, alanine transaminase, gamma-glutamyl transferase) and salivary sample for cortisol analysis. Clinical examination and sample collection, to assess primary and secondary outcomes, will be performed at enrollment and at the follow up after of this treatment. Tracking of additional parameters (heart rate, sleep, mobility) will be performed along the study period by using a wearable MiBand 7 watch and a daily diary to determine compliance and record effects on stress, well-being and health status.
Discussion
The success of this research could represent a turning point in the healthy aging research, leading to rejuvenation by means of a sustainable and safe intervention, accessible to everybody in order to extend health span.
Trial registration:
ClinicalTrials.gov PRS (NCT05399966), registration date: May 17, 2022.
In-Depth metallurgical, design, and mechanical analysis of Reciproc Blue and four replica-like endodontic systems
Authors: Campos Gustavo Oliveira , Silva Jessica Dornelas , Buono Vicente Tadeu Lopes , Santos Leandro Arruda , Peixoto Isabella Faria da Cunha , Viana Ana Cecília Diniz 
Published: January 2024

Abstract
Objectives
This work aimed to evaluate the metallurgical, geometrical, and mechanical properties of 5 reciprocating endodontic files with similar cross-sectional geometry.
Materials and Methods
Reciproc Blue, ProDesign R, V File, V + File, and Univy One files were used. The evaluation of diameters was performed through high-quality photographs and Image J software. Cross-sectional scanning electron microscopy was performed in order to measure the 3 mm from the tip cross-sectional area and other aspects related to the active blade and tip. Differential scanning calorimetry tests were employed to assess the transformation temperatures and X-ray diffraction was used to identify the atomic structures. Standardized bending torsion tests were performed to evaluate the mechanical responses of the files.
Results
Significant differences were observed in the cross-sectional areas of the instruments. R-phase was predominated in most instruments, except for the Univy One system, which exhibited a combination of martensite and R-phase. The ProDesign R system demonstrated superior flexibility, while the Reciprocal Blue and V File systems exhibited greater resistance to torsion.
Conclusions
The cross-sectional area emerged as a pivotal factor influencing the mechanical characteristics of the studied files. However, the Univy One system presented high flexibility and large angular deflection despite having the highest cross-sectional area value, which suggests that the metallurgical aspects of this instrument play a major role in its mechanical behavior.
Clinical relevance:
Mechanical properties of endodontic files, such as flexibility, are very important to prevent failures during clinical practice and keep the original shape of the root canal.
Predictive modeling of molds effective elimination by external inactivation sources
Authors: Demo Pavel , Přeučil Filip , Tichá Petra , Domonkos Mária 
Published: January 2024

Abstract
Presented paper deals with a novel application of the (nonlinear) logistic equation to model an elimination of microscopic filaments types of fungi-molds from affected materials via different external inactivation techniques. It is shown that if the inactivation rate of the external source is greater than the maximum natural growth rate of mycelium, the mold colony becomes destroyed after a finite time. Otherwise, the mycelium may survive the external attack only at a sufficiently large initial concentration of the inoculum. Theoretically determined growth curves are compared with the experimental data for Aspergillus brasiliensis mold inactivated by using both cold atmospheric plasma (CAP) and UV-germicidal lamp. Model presented in the article may be applied also to other classes of microorganisms (e.g. bacteria).