bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Complexity One‐Pot Golden Gate Assembly
Authors: Sikkema Andrew P. , Tabatabaei S. Kasra , Lee Yan‐Jiun , Lund Sean , Lohman Gregory J. S. 
Published: September 2023

AbstractGolden Gate Assembly is a flexible method of DNA assembly and cloning that permits the joining of multiple fragments in a single reaction through predefined connections. The method depends on cutting DNA using a Type IIS restriction enzyme, which cuts outside its recognition site and therefore can generate overhangs of any sequence while separating the recognition site from the generated fragment. By choosing compatible fusion sites, Golden Gate permits the joining of multiple DNA fragments in a defined order in a single reaction. Conventionally, this method has been used to join five to eight fragments in a single assembly round, with yield and accuracy dropping off rapidly for more complex assemblies. Recently, we demonstrated the application of comprehensive measurements of ligation fidelity and bias data using data‐optimized assembly design (DAD) to enable a high degree of assembly accuracy for very complex assemblies with the simultaneous joining of as many as 52 fragments in one reaction. Here, we describe methods for applying DAD principles and online tools to evaluate the fidelity of existing fusion site sets and assembly standards, selecting new optimal sets, and adding fusion sites to existing assemblies. We further describe the application of DAD to divide known sequences at optimal points, including designing one‐pot assemblies of small genomes. Using the T7 bacteriophage genome as an example, we present a protocol that includes removal of native Type IIS sites (domestication) simultaneously with parts generation by PCR. Finally, we present recommended cycling protocols for assemblies of medium to high complexity (12‐36 fragments), methods for producing high‐quality parts, examples highlighting the importance of DNA purity and fragment stoichiometric balance for optimal assembly outcomes, and methods for assessing assembly success. © 2023 New England Biolabs, Inc. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Assessing the fidelity of an overhang set using the NEBridge Ligase Fidelity ViewerBasic Protocol 2: Generating a high‐fidelity overhang set using the NEBridge GetSet ToolAlternate Protocol 1: Expanding an existing overhang set using the NEBridge GetSet ToolBasic Protocol 3: Dividing a genomic sequence with optimal fusion sites using the NEBridge SplitSet ToolBasic Protocol 4: One‐pot Golden Gate Assembly of 12 fragments into a destination plasmidAlternate Protocol 2: One‐pot Golden Gate Assembly of 24+ fragments into a destination plasmidBasic Protocol 5: One‐pot Golden Gate Assembly of the T7 bacteriophage genome from 12+ partsSupport Protocol 1: Generation of high‐purity amplicons for assemblySupport Protocol 2: Cloning assembly parts into a holding vectorSupport Protocol 3: Quantifying DNA concentration using a Qubit 4 fluorometerSupport Protocol 4: Visualizing large assemblies via TapeStationSupport Protocol 5: Validating phage genome assemblies via ONT long‐read sequencing
Biaxial and Uniaxial Tensile Strains Effects on Electronic, Optical, and Thermoelectric Properties of ScBiTe3 Compound
Authors: Benyoussef Safae , Jabar Abderrahim , Bahmad Lahoucine 
Published: September 2023

AbstractUsing first‐principles density‐functional theory (DFT), this study thoroughly investigates the effects of biaxial and uniaxial tensile strains on the electronic, optical, and thermoelectric properties of the perovskite ScBiTe3. This latter compound is a semiconductor material, according to its electronic band structures, with an indirect bandgap value of 0.891 eV. Additionally, the bandgap of each structure exhibits a decreasing tendency under compressive strain and an increasing trend under tensile strain, and the bandgap changes from indirect to direct bandgap when the tensile strain is applied along the a and b directions. Due to their band properties, these materials have excellent absorption ability in the visible region, as evidenced by optical properties like dielectric functions, absorption coefficients, and electron loss functions. It is found that the highest value of the power factor (PF) is 4.1 × 1011 W−1K−2s−1 and the highest value of the figure of merit (ZT) is 0.84. Such values are obtained for the specific strain value of 10% strain along the “a” and “b” directions. This confirms that this material can be a potential candidate for thermoelectric device applications.
Recent Advancements in Continuous Crystallization of Proteins
Authors: Vikram M. V. , Yadav Manishkumar D. 
Published: September 2023

AbstractRecently, there have been many studies and reports on various continuous protein crystallization processes. Due to the increasing demand for pharmaceutical proteins such as insulin and monoclonal antibodies, it has become essential to optimize the current industrial processes to meet these demands. There are various comparisons to be made between current batch crystallization processes and continuous processes for proteins. This review paper aims to review the recent advancements in continuous protein crystallization processes, such as slug flow crystallizers, oscillatory baffled crystallizers, and mixed suspension mixed product removal (MSMPR) crystallizers.
LncRNA NEAT1 suppresses cellular senescence in hepatocellular carcinoma via KIF11‐dependent repression of CDKN2A
Authors: Chen Danlei , Wang Jinghao , Li Yang , Xu Chenglin , Fanzheng Meng , Zhang Pengfei , Liu Lianxin 
Published: September 2023

AbstractBackgroundHepatocellular carcinoma (HCC) is the third leading cause of cancer‐related deaths worldwide. Therapeutic options for advanced HCC are limited, which is due to a lack of full understanding of pathogenesis. Cellular senescence is a state of cell cycle arrest, which plays important roles in the pathogenesis of HCC. Mechanisms underlying hepatocellular senescence are not fully understood. LncRNA NEAT1 acts as an oncogene and contributes to the development of HCC. Whether NEAT1 modulates hepatocellular senescence in HCC is unknown.MethodsThe role of NEAT1 and KIF11 in cellular senescence and tumor growth in HCC was assessed both in vitro and in vivo. RNA pulldown, mass spectrometry, Chromatin immunoprecipitation (ChIP), luciferase reporter assays, RNA FISH and immunofluorescence (IF) staining were used to explore the detailed molecular mechanism of NEAT1 and KIF11 in cellular senescence of HCC.ResultsWe found that NEAT1 was upregulated in tumor tissues and hepatoma cells, which negatively correlated with a senescence biomarker CDKN2A encoding p16INK4a and p14ARF proteins. NEAT1 was reduced in senescent hepatoma cells induced by doxorubicin (DOXO) or serum starvation. Furthermore, NEAT1 deficiency caused senescence in cultured hepatoma cells, and protected against the progression of HCC in a mouse model. During senescence, NEAT1 translocated into cytosol and interacted with a motor protein KIF11, resulting in KIF11 protein degradation and subsequent increased expression of CDKN2A in cultured hepatoma cells. Furthermore, KIF11 knockdown caused senescence in cultured hepatoma cells. Genetic deletion of Kif11 in hepatocytes inhibited the development of HCC in a mouse model.ConclusionsConclusively, NEAT1 overexpression reduces senescence and promotes tumor progression in HCC tissues and hepatoma cells, whereas NEAT1 deficiency causes senescence and inhibits tumor progression in HCC. This is associated with KIF11‐dependent repression of CDKN2A. These findings lay the foundation to develop potential therapies for HCC by inhibiting NEAT1 and KIF11 or inducing senescence.
Development of “personality” in the domestic cat: A longitudinal study
Authors: Urrutia Andrea , Bánszegi Oxána , Szenczi Péter , Hudson Robyn 
Published: September 2023

AbstractAlthough individual differences in the behavior of animals, sometimes referred to as personality, have recently received considerable attention, the development of such differences remains understudied. We previously found consistent individual differences in behavior in four tests simulating everyday contexts in 74 preweaning age kittens from 16 litters of the domestic cat. To study the development of consistent among‐individual differences in four behavioral traits in cats, we followed a subset of these same individuals and repeated the same tests at 6 and 12 months of age. Some individual differences in behavior became increasingly repeatable with age due to a combination of decreased individual‐level variance (canalization) and increased among‐individual variance; these changes in variance and repeatability continued into adulthood (12 months). We did not observe behavioral syndromes at any age, in contrast to our previous reports in a different population of adult cats. The mechanisms that underlie increased repeatability with age and the possibility of personality structure differing between populations in this species remain to be studied.
Effects of door‐to‐tolvaptan time on short‐term clinical outcome in patients with acute heart failure
Authors: Nomura Ryohei , Morishita Tetsuji , Sato Yusuke , Aoyama Daisetu , Shimizu Tomohiro , Uzui Hiroyasu , Nakano Akira , Tada Hiroshi 
Published: September 2023

AbstractAimsWe investigated the effects of door‐to‐tolvaptan (D2T) time on short‐term urine volume and in‐hospital clinical outcomes in patients with acute heart failure (AHF).Methods and resultsPatients with AHF, treated with tolvaptan at two hospitals, were enrolled in this retrospective observational study. The D2T time was defined as the time elapsed from the arrival of a patient at a participating hospital to the first administration of tolvaptan. The group with the D2T time within 6 h was defined as the ‘early group’. The primary outcome was 48‐h urine volume. The secondary outcomes were in‐hospital death, length of hospital stay, and worsening renal function (WRF) incidence. A restricted cubic spline model was used to evaluate the presence of a nonlinear association between the D2T time and 48‐h urine volume and the odds ratio of WRF incidence. Our study included a total of 138 patients with AHF who were started on tolvaptan after hospitalization. The median D2T time was 5.3 h (interquartile range: 3.0–31.9 h). Seventy‐four patients (53.6%) were classified to be in the early group. Baseline characteristics were similar in the two groups: mean age (85.4 ± 9.6 years vs. 84.5 ± 9.5 years; P = 0.59) and male sex (n = 22 [33.3%] vs. n = 29 [46%]; P = 0.16), except that patients in the early group had higher systolic blood pressure than those in the delayed group (138.2 ± 22.9 vs. 125.7 ± 21.7; P = 0.001). The initial tolvaptan dose in the delayed group was much lower than that in the early group (7.5 [7.5, 7.5] vs. 7.5 [5.6, 7.5] mg; P = 0.01). Total urine volume in 48 h did not differ in the early and delayed groups (4113 ± 1758 mL vs. 4201 ± 1893 mL; P = 0.80). The relationship between D2T time and total urine volume within 48 h increased slightly, with a peak at a D2T time of 15 h, and gradually decreased, thereafter. In‐hospital death and the length of hospital stay did not differ significantly between the two groups (n = 1, 1.3% vs. n = 4, 6.3%; P = 0.18, and 5.0 [12.0, 30.0] vs. 22.0 [14.5, 30.0] days; P = 0.17, respectively). Notably, the restricted cubic spline model for the odds ratio of WRF incidence increased as the D2T time was delayed (P for effect<0.01).ConclusionsThe shorter D2T time did not affect the short‐term urine volume and in‐hospital outcomes but reduced the risk of WRF incidence in patients with AHF.
Assessing the Biodegradability of Tire Tread Particles and Influencing Factors
Authors: Nielsen Ann Flemming , Polesel Fabio , Ahonen Tiia , Palmqvist Annemette , Baun Anders , Hartmann Nanna B. 
Published: September 2023

Abstract
Abrasion of tire tread, caused by friction between vehicle tires and road surfaces, causes release of tire wear particles (TWPs) into various environmental compartments. These TWPs contribute to chemical, microplastic, and particulate matter pollution. Their fate remains largely unknown, especially regarding the extent and form in which they persist in the environment. The present study investigated (1) the biodegradability of tread particles (TPs) in the form of ground tire tread, (2) how accelerated ultraviolet (UV) weathering affects their biodegradability, and (3) which TP constituents are likely contributors to TP biodegradability based on their individual biodegradability. A series of closed-bottle tests, with aerobic aqueous medium inoculated with activated sludge, were carried out for pristine TPs, UV-weathered TPs, and selected TP constituents; natural rubber (NR), isoprene rubber (IR), butadiene rubber (BR), and treated distillate aromatic extracts (TDAE). Biodegradation was monitored by manometric respirometry, quantifying biological oxygen consumption over 28 days. Pristine TP biodegradability was found to be 4.5%; UV-weathered TPs showed higher biodegradability of 6.7% and 8.0% with similar and increased inoculum concentrations, respectively. The observed TP biodegradation was mainly attributed to biodegradation of NR and TDAE, with individual biodegradability of 35.4% and 8.0%, respectively; IR and BR showed negligible biodegradability. These findings indicate that biodegradability of individual constituents is decreased by a factor of 2 to 5 when compounded into TPs. Through scanning electron microscopy analysis, biodegradation was found to cause surface erosion. Processes of TP biodegradation are expected to change throughout their lifetime as new constituents are incorporated from the road and others degrade and/or leach out. Tire emissions likely persist as particles with an increased fraction of synthetic rubbers and carbon black. Environ Toxicol Chem 2024;43:31–41. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Dose Addition Models Accurately Predict the Subacute Effects of a Mixture of Perfluorooctane Sulfonate and Perfluorooctanoic Acid on Japanese Quail (Coturnix japonica) Chick Mortality
Authors: Gray L. Earl , Conley Justin M. , Bursian Steven J. 
Published: September 2023

Abstract
Biomonitoring data have consistently demonstrated that fish, wildlife, and humans are exposed to multiple per- and polyfluoroalkyl substances (PFAS) in drinking water and foods. Despite ubiquitous exposure to mixtures of PFAS, there is a lack of in vivo PFAS mixture research that addresses whether these chemicals act in a cumulative, dose-additive (DA) manner or whether they behave independently. For this reason, there is a critical need for mixtures studies designed to evaluate the cumulative toxicity and potential chemical interactions to support the assessment of human and ecological risks and also to define appropriate regulatory actions. Our primary objective was to evaluate the previously published Japanese quail chick mortality concentration–response data for perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), and the mixture of PFOS + PFOA and to use statistical modeling to determine whether the effects of the mixtures were accurately predicted by either DA or response addition modeling. In addition, we wanted to compare different DA models to determine whether one model produced more accurate predictions than the others. Our results support the hypothesis of cumulative effects on shared endpoints from PFOA and PFOS co-exposure and DA approaches for predictive estimates of cumulative effects. Given the limited number of in vivo studies that have been executed with enough individual PFAS and PFAS mixture concentration–response data to test the hypothesis of DA for PFAS mixtures, this re-analysis of the data is an important contribution to our understanding of how PFAS mixtures act. The analysis will provide support for regulatory agencies as they begin to implement PFAS cumulative hazard assessments in higher vertebrates. Environ Toxicol Chem 2024;43:97–104. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Naringenin prevents non‐alcoholic steatohepatitis by modulating the host metabolome and intestinal microbiome in MCD diet‐fed mice
Authors: Cao Peng , Yue Ming , Cheng Yuanlei , Sullivan Mitchell A. , Chen Wen , Yu Huifan , Li Fei , Wu Sanlan , Lv Yongning , Zhai Xuejia , Zhang Yu 
Published: September 2023

AbstractNon‐alcoholic steatohepatitis (NASH) is a severe inflammatory phase of the non‐alcoholic fatty liver disease (NAFLD) spectrum and can progress to advanced stages of NAFLD if left untreated. This study uses multi‐omics data to elucidate the underlying mechanism of naringenin's reported benefit in alleviating (NASH). Male mice were fed a NASH‐inducing (methionine‐choline‐deficient) MCD diet with or without naringenin supplementation for 6 weeks. Naringenin prevented NASH‐induced histopathological liver damage and reversed the abnormal levels of hepatic triglyceride (TG)/total cholesterol (TC), serum TG/TC, serum alanine aminotransferase/aspartate transaminase, and hepatic malondialdehyde and glutathione. Importantly, naringenin intervention significantly modulated the relative abundance of gut microbiota and the host metabolomic profile. We detected more than 700 metabolites in the serum and found that the gut genus levels of Anaeroplasma and the [Eubacterium] nodatum group were closely associated with xanthine, 2‐picoline, and securinine, respectively. Tuzzerella alterations showed the highest number of associations with host endogenous metabolites such as FAHFA (8:0/10:0), FFA (20:2), carnitine C8:1, tridecanedioic acid, securinine, acetylvaline, DL‐O‐tyrosine, and Phe‐Asn. This study indicates that the interplay between host serum metabolites and gut microbiota may contribute to the therapeutic effect of naringenin against NASH.
Market‐wide overconfidence and stock returns
Authors: Chen Qiang , Han Yu , Huang Ying 
Published: September 2023

AbstractIn this paper, a novel measurement of overconfidence over the market is developed based on the size of ambiguity (the confidence of investors in information). The proposed measure of market‐wide overconfidence is consistent with the predictions motivated by prior literature. It has a significant negative association with the next‐month market excess return. Associations between the overconfidence measure and riskier portfolio returns behave stronger and last longer, implying a risk‐taking proclivity of overconfident investors.
Dynamic connectedness between energy markets and the Brazilian cash market: An empirical analysis pre‐ and post‐COVID‐19
Authors: Palazzi Rafael Baptista , Assaf Ata , Klotzle Marcelo Cabus 
Published: September 2023

AbstractBrazil's significant commodity production is internationally recognized, yet the absence of a mature futures market exposes it to price risks and international shocks. This study explores the dynamic connectedness between commodity futures and the Brazilian cash markets, using a time‐varying parameter vector autoregressive model. We also assess COVID‐19's impact on this connectedness. We find a significant influence of oil prices on Brazilian ethanol prices, and particularly emphasize the Heating Oil spillover effect on ethanol in the post‐COVID‐19 era. We also note the ascension of Brazilian soybean spot markets' international significance since 2017, amplifying their role in global grain price discovery. Finally, by computing hedge ratios and effectiveness between commodity futures contracts and Brazilian spot prices, our study reveals soybean cash price as the most effective hedge. These insights deepen comprehension of connectedness within Brazilian commodity markets, thereby guiding investors and policymakers in strategic energy policy decisions.
Chromatic fusion: Generative multimodal neuroimaging data fusion provides multi‐informed insights into schizophrenia
Authors: Geenjaar Eloy P.T. , Lewis Noah L. , Fedorov Alex , Wu Lei , Ford Judith M. , Preda Adrian , Plis Sergey M. , Calhoun Vince D. 
Published: September 2023

AbstractThis work proposes a novel generative multimodal approach to jointly analyze multimodal data while linking the multimodal information to colors. We apply our proposed framework, which disentangles multimodal data into private and shared sets of features from pairs of structural (sMRI), functional (sFNC and ICA), and diffusion MRI data (FA maps). With our approach, we find that heterogeneity in schizophrenia is potentially a function of modality pairs. Results show (1) schizophrenia is highly multimodal and includes changes in specific networks, (2) non‐linear relationships with schizophrenia are observed when interpolating among shared latent dimensions, and (3) we observe a decrease in the modularity of functional connectivity and decreased visual‐sensorimotor connectivity for schizophrenia patients for the FA‐sFNC and sMRI‐sFNC modality pairs, respectively. Additionally, our results generally indicate decreased fractional corpus callosum anisotropy, and decreased spatial ICA map and voxel‐based morphometry strength in the superior frontal lobe as found in the FA‐sFNC, sMRI‐FA, and sMRI‐ICA modality pair clusters. In sum, we introduce a powerful new multimodal neuroimaging framework designed to provide a rich and intuitive understanding of the data which we hope challenges the reader to think differently about how modalities interact.
Analysis of quality standards for industrial collaborative robots based on user‐centered design framework
Authors: Heo In Seok , Putri Alivia K. H. , Kim Beom Su , Kwon Min Seong , Kim Sang Ho 
Published: September 2023

AbstractIndustrial collaborative robots have become increasingly important in recent years due to their ability to work safely and efficiently alongside humans. As a result, there is a growing need for evaluation standards to ensure the quality of collaborative robots. However, existing studies only consider system‐centered and technical aspects of collaborative robots, and there is a lack of research on user‐centered quality evaluation. In this study, we identified 21 user requirements based on a user‐centered design framework and confirmed the limitations of existing quality standards by reviewing the standard clauses for collaborative robots. It was found that user needs to be related to performance, safety, and even usability and enjoyment are already being expressed according to the user‐centered design framework, but the quality standards for these needs only present design principles or do not consider them at all. This study provides information on the quality attributes that need to be fulfilled to satisfy user requirements and suggests the need and direction for further research on the user‐centered evaluation of collaborative robots. Accordingly, the user's perception and experience of collaborative robots are expected to improve.