bluuebunny/crossref_metadata_2025_split huggingface dataset:
Separation of Large Circular DNA by Electrophoresis in Agarose Gels
Authors: Cole Kenneth D. , Tellez Carlos M. 
Published: July 2002

AbstractThe electrophoresis of circular DNA, ranging in size from 4.4 kilobase pairs (kbp) to 220 kbp, was studied in agarose gels. Bacterial artificial chromosome (BAC) DNA was used as a source of large supercoiled and open circular (relaxed) forms. The open circles above approximately 50 kbp were trapped at the sample wells of 1% agarose gels during electrophoresis at 3 V/cm. Field inversion gel electrophoresis (FIGE) was used to relieve the trapping of the open circles in the gels. Using FIGE (30 s forward pulse time), open circles with sizes of 115 and 220 kbp required reverse pulse times of 3 and 6 s, respectively, to free the circles from open‐ended gel fibers. A minimum in the gel velocity of the open circles was measured at approximately 20 kbp. Open circles below approximately 20 kbp migrated slower than the supercoiled forms, and above 20 kbp the order was reversed. These results indicate that when the size of the open circles exceeded the average pore size of a gel and it was forced to span multiple pores, the open circles gained a mobility advantage. Decreasing the ionic strength of the electrophoresis buffer significantly decreased the mobility of the smaller circles and slightly increased the mobility of the larger circles.
Polymorphisms at the DRD2 locus in early‐onset alcohol dependence in the Indian population
Authors: Shaikh Kauser J. , Naveen Daniel , Sherrin Tessi , Murthy Ashlesh , Thennarasu K. , Anand Anuranjan , Benegal Vivek , Jain Sanjeev 
Published: July 2002

AbstractThe susceptibility to alcohol dependence is probably of polygenic origin. Association studies have attempted to identify possible candidate genes that may contribute to the risk to developing dependence. Severe forms of the alcoholism phenotype have been associated with an increased frequency of the Taq A1 allele at the DRD2 locus. Ethnic stratification and non‐comparable phenotype may have contributed to the contradictory results in previous studies. We identified probands, using the Schedules of Assessment of Neuropsychiatry (SCAN) schedule, who had onset of alcohol dependence (ICD‐10) before 25 years of age. Family members were interviewed using the Family Interview for Genetic Studies (FIGS) schedule to identify patients who had two first‐degree relatives with alcohol dependence. Fifty subjects who fulfilled the criteria were selected for the study. These were compared to a normal population from a similar background. The allele frequencies did not differ between the two groups. The Taq1a polymorphism does not seem to be associated with alcoholism in this group of severely affected, young age of onset probands in the southern Indian population.
Using traveling salesman problem algorithms for evolutionary tree construction
Authors: Korostensky Chantal , Gonnet Gaston H. 
Published: July 2002

Abstract
Motivation: The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity.
Results: We present a new tree construction method that constructs a tree with minimum score for a given set of sequences, where the score is the amount of evolution measured in PAM distances. To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). The input for the TSP algorithm are the pairwise distances of the sequences and the output is a circular tour through the optimal, unknown tree plus the minimum score of the tree. The circular order and the score can be used to construct the topology of the optimal tree. Our method can be used for any scoring function that correlates to the amount of changes along the branches of an evolutionary tree, for instance it could also be used for parsimony scores, but it cannot be used for least squares fit of distances. A TSP solution reduces the space of all possible trees to \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(2^{n}\) \end{document}. Using this order, we can guarantee that we reconstruct a correct evolutionary tree if the absolute value of the error for each distance measurement is smaller than \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\frac{x}{2}\) \end{document}, where \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(x\) \end{document}is the length of the shortest edge in the tree. For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. Finally simulations and experiments with real data are shown.
Availability: The software may be used via our cbrg server at http://cbrg.inf.ethz.ch/MultAlign.
Contact: chantal.roth@nobilitas.com
Supplementary information: An html and postscript version of this paper is available at http://chantal.nobilitas.com/(Papers section).
* To whom correspondence should be addressed.
Working hours, side work, and depressive symptoms in physicians: A nationwide cross-sectional study in Japan
Authors: Okawara Makoto , Ishimaru Tomohiro , Yoshikawa Toru , Kido Michiko , Nakashima Yoshifumi , Nakayasu Anna , Kimori Kokuto , Imamura Satoshi , Matsumoto Kichiro 
Published: December 2022

Abstract

Objectives
Long working hours in Japan is a social concern. This is also true for the working hours of physicians, who often do side work in addition to working at their main hospital. New physician work regulations to be implemented in Japan require work-hour management, including side work. This study examined the association between physicians' overtime and side work hours and their health outcomes.

Methods
We conducted a cross-sectional study using data from a survey of working physicians conducted by the Japan Medical Association from 2021 to 2022. Questionnaires completed by 2906 full-time working physicians aged 24–69, excluding junior resident doctors, were analyzed. Depressive symptoms and the presence of thoughts of death or suicide using the Quick Inventory of Depressive Symptomatology - Japanese version was used to assess health outcomes. Logistic regression analysis was performed using overtime at the main place of employment and side work hours as exposure factors.

Results
Both depressive symptoms and thoughts of death or suicide increased in the group with longer overtime hours at the main place of work. A similar tendency was observed for side work but adjusting for overtime hours eliminated the association. In other words, total working hours had an impact on health, regardless of whether overtime work at the main place of employment or side work.

Conclusions
Despite the existence of multiple hurdles to managing working hours, including side work, the working environment for physicians needs to be improved to protect their health and quality of medical care.
Molecular Hydration Tunes the Cation–π Interaction Strength in Aqueous Solution
Authors: Park Sohee , Lee Yongjin , Jho Yongseok , Hwang Dong Soo 
Published: December 2022

AbstractCation–π interactions are considered to be among the most important strong noncovalent interactions in aqueous solutions and as regulators of various biological phenomena, including biological adhesion, signal transduction, and liquid–liquid phase separation (LLPS). Despite their significant roles, cation–π interactions in aqueous environments are not systematically and experimentally understood. Here, we directly experimentally examined cation–π interactions between cationic and aromatic moieties common to biological systems using a surface forces apparatus (SFA) augmented by computational methods. Specifically, we chose cationic and aromatic moieties with different levels of hydration and observed how the molecular hydration of these moieties affects the formation and strengths of cation–π bonds. To date, the charge densities of the interacting moieties are primarily considered to modulate the interaction strength; however, it is experimentally and computationally revealed that the hydration strengths (or hydrophobic properties) of the interacting moieties are more important for controlling in underwater interactions.
Comparative Study between the 3D‐Liver Spheroid Models Developed from HepG2 and Immortalized Hepatocyte‐Like Cells with Primary Hepatic Stellate Coculture for Drug Metabolism Analysis and Anticancer Drug Screening
Authors: Sae‐be Arunsajee , Wiwatpanit Teerawat , Varatthan Thaveechai , Namporn Thanaphon , Laungkulldej Sasiwat , Thiabma Ratthiya , Jaiboonma Atchara , Sa‐ngiamsuntorn Khanit , Elson Daniel , Porter Alexandra E. , Sathirakul Korbtham , Hongeng Suradej , Ruenraroengsak Pakatip 
Published: December 2022

AbstractLiver spheroids may be the best alternative models for evaluating efficacy and toxicity of the new anticancer candidates and diagnostics for hepatocellular carcinoma (HCC). Here, novel 3D‐liver spheroid models are constructed from human hepatoma cells (HepG2)/ immortalized human hepatocyte‐like cells (imHCs) with primary hepatic stellate cells (HSCs) coculture using the ultralow attachment technique. Spheroid morphology, HSC distribution, metabolic activity, protein expressions, and drug penetration are evaluated. All developed 3D spheroid models exhibit in spherical shape with narrow size distribution, diameter between 639–743 (HepG2‐10%HSC) and 519–631 (imHC‐10%HSC) µm. Both imHC mono and coculture models significantly express normal liver biomarkers at the higher level than HepG2 models. While 3D‐HepG2 models significantly exhibit HCC biomarkers at the higher level than imHC models. HepG2 and imHC spheroids express basal cytochrom P450 (CYP450) enzymes at different levels depending on cell types, culture period, and ratio of coculture. Their metabolic activities for dextromethorphan (CYP2D6) tolbutamide (CYP2C9) and midazolam (CYP3A4) are routinely evaluated. For midazolam metabolism, imHC models allow the detection of phase II metabolic enzymes (UGT2B4 and UGT2B7). The presence of HSC in HepG2‐HSC model increases biological barrier for doxorubicin (DOX) penetration, and escalates IC50 of DOX from 61.4 to 127.2 µg mL−1.
Cationic telluroviologen derivatives as type‐I photosensitizers for tumor photodynamic theranostics
Authors: Sun Qi , Su Qi , Gao Yujing , Zhou Kun , Song Weijie , Quan Penghe , Yang Xiaojian , Ge Zhishen , Zhang Yanmin , He Gang 
Published: December 2022

AbstractThe hypoxia of the tumor microenvironment (TME) seriously restricts the photodynamic therapy (PDT) effect of conventional type‐II photosensitizers, which are highly dependent on O2. In this work, a new type‐I photosensitizer (TPE‐TeV‐PPh3) consisting of a tetraphenylethylene group (TPE) as a bioimaging moiety, triphenyl‐phosphine (PPh3) as a mitochondria‐targeting group, and telluroviologen (TeV2+) as a reactive oxygen species (O2•−, •OH) generating moiety is developed. The luminescence intensity of TPE‐TeV‐PPh3 increased significantly after specific oxidation by excess H2O2 in the TME without responding to normal tissues via the formation of Te═O bond, which can be used for monitoring abnormal H2O2, positioning, and imaging of tumors. TPE‐TeV‐PPh3 with highly reactive radicals generation and stronger hypoxia tolerance realizes efficient cancer cell killing under hypoxic conditions, achieving 88% tumor growth inhibition. Therefore, TPE‐TeV‐PPh3 with low phototoxicity in normal tissue achieves tumor imaging and effective PDT toward solid tumors in response to high concentrations of H2O2 in the TME, which provides a new strategy for the development of type‐I photosensitizers.
Measurement of physicochemical properties of green aqueous amino acid‐based ionic liquids and their correlation with temperature and concentration
Authors: Nashed Omar , Talib Nur Khairunnisa , Lal Bhajan , Ghanem Ouahid Ben , Mohshim Dzeti Farhah , Sabil Khalik M. , Shariff Azmi Mohd 
Published: December 2022

AbstractIonic liquids have attracted immense attention due to their unique properties and potential industrial applications. Green ionic liquids such as amino acid‐based ionic liquids (AAILs) are promising solvents due to their proven low toxicity. The properties of newly known substances are unavailable, especially when they are in aqueous solutions. This information is essential, and they must be understood before employing these materials in any application for technical, safety, and economical reasons. In this study, three types of AAILs were examined, namely; 1‐octyl‐3‐methylimidazolium glycine [OMIM][Gly], 1‐octyl‐3‐methylimidazolium alanine [OMIM][Ala], and 1‐octyl‐3‐methylimidazolium proline [OMIM][Pro]. The aqueous solutions were prepared at concentrations of 1, 10, 20, and 30 wt.%. The pH and electrical conductivity were measured at room temperature and atmospheric pressure. Moreover, volumetric properties such as density, molar volume, excess molar volume, and thermal expansion were also determined at atmospheric pressure over a temperature range of 298.15–338.15 K. An empirical correlation was also developed to correlate the volumetric parameters with temperature and concentration. The results showed that AAILs solutions are alkaline in nature. Moreover, they increase the electrical conductivity of water. Additionally, molar volume, excess molar volume, and isobaric thermal expansion increased as the temperature increased, whereas the density decreased with an increase in temperature. A discussion on the effect of anions was presented. The developed empirical correlation exhibited an accurate prediction of the volumetric properties with R2 > 0.9762.
Flexural behavior of pMWCNTs filled glass fiber/epoxy nanocomposites: Synthesis and interfacial failure
Authors: Mandal Samir , Sethi Sanghamitra , Biswas Krishanu 
Published: December 2022

AbstractGlass fiber reinforced polymer composite (GFRP) encounter many practical situations during its application, exposed to different temperature fluctuation. Absorption of moisture and the fluctuated thermal environment cause mechanical degradation of GFRP. The current plan is to explore the mechanical and chemical behavior of pristine multiwall carbon nanotubes(pMWCNTs)‐glass fiber strengthens epoxy composites during thermal shock (TS). The laminates were prepared by the hand‐lay‐up process followed by compression molding. The thermal shock was performed at the temperature for the required samples was 135°C for 24 h, followed by −135°C for 24 h. A flexural test has been carried out at 1 mm/min loading speed. 0.2 wt% pMWCNTs filled nanocomposite appeared to have the highest flexural strength and modulus compared to ambient samples. The thermomechanical behavior of nanocomposites has been accomplished by analyzing the dynamic mechanical thermal analysis graph (DMTA). Field emission scanning electron microscope (FESEM) analyzed the fracture surface of in‐situ mechanical failure samples to find out the primary failure modes for strengthening and weakening mechanisms. The glass transition temperature (Tg) of the nanocomposite observed decreased due to homogeneous dispersion of pMWCNTs, imparting some effect on crosslink density and reinforcement up to 0.2 wt%. This study reveals that the uniform distribution of pMWCNTs and thermal shock treatment enhances the matrix stiffness and improves the mechanical properties.
Degradation of wheat straw/polylactic acid composites with and without sodium alginate in natural soil and the effects on soil microorganisms
Authors: Chai Xicun , He Chunxia , Liu Yutao , Niyitanga Evode , Wang Luyang , Zhang Weixing 
Published: December 2022

AbstractIn order to improve the degradability of polylactic acid (PLA) composites and screen PLA degradation microorganisms. Sodium alginate was added into the wheat straw/PLA composites, and both composites (with/without sodium alginate) were buried in natural soil for 100 consecutive days subsequently. Weight loss and characterization of the PLA composites, carbon and nitrogen content in soil and microbial community composition were detected after degradation, with the result that the degradability of the PLA composites was greatly improved after the addition of sodium alginate. The weight loss of PLA composites with sodium alginate was 8.5%, which was 1.81 times that of PLA composites without sodium alginate. Sodium alginate and/or wheat straw in the PLA composites took the lead in the beginning course of the degradation. The added sodium alginate serves the purpose of making it easier to degrade the crystallization zone of the PLA composites. Bionectriaceae in the soil shoots up in the number after degradation, signifying its potential to be part of the microorganism family serving to degrade PLA composites. The results would help reveal the degradation mechanism of PLA composites and provide support for the screening of PLA composites degradation microorganisms.
Synthesis and properties of copolyarylates containing phenol red units
Authors: Wang Zhoufeng , Hu Junwei , Wang Bolin , Liu Yingying , Long Xiubo 
Published: December 2022

AbstractA series of novel copolyarylates(co‐PARs) containing phenol red units in the backbone were synthesized by interfacial polymerization at 10°C from bisphenol A (BPA), phenol red (PR) and diacid chloride monomers. The obtained copolyarylates (co‐PARs) are all amorphous, the inherent viscosity (ηinh) of 0.22–0.62 dl g−1, and the number‐ and weight‐average molecular weight are 10,200–46,200 and 38,600–203,600, respectively. Adding a small number of PR units to the molecular chains improved the processing fluidity of polyarylates, and the glass transition temperatures (Tg) decreased from 202.8 to 166.7°C. In addition, the co‐PARs have excellent thermal stability with the maximum thermal decomposition temperature of 532.4–545.2°C. The co‐PARs show the best mechanical properties (57.6 MPa) when the PR content is 15 mol%. The transmittances of the co‐PARs at 400 and 450 nm are 79.2%–97.9% and 87.0%–99.8%, respectively, and the cut‐off wavelength is between 320 and 328 nm. The designed and synthesized copolyarylates can be considered as a promising and easy‐to‐process high‐performance engineering plastic.
The Characteristics of Patients With COVID‐19–Associated Pediatric Vasculitis: An International, Multicenter Study
Authors: Batu Ezgi D. , Sener Seher , Ozomay Baykal Gulcan , Arslanoglu Aydin Elif , Özdel Semanur , Gagro Alenka , Esen Esra , Heshin‐Bekenstein Merav , Akpınar Tekgöz Nilüfer , Demirkan Fatma G. , Ozturk Kubra , Vougiouka Olga , Sonmez H. Emine , Maggio Maria Cristina , Kaya Akca Ummusen , Jelusic Marija , Pac Kısaarslan Aysenur , Acar Banu , Aktay Ayaz Nuray , Sözeri Betül , Özen Seza ,   the Pediatric Rheumatology European Society (PReS) Vasculitis Working Party
Published: December 2022

ObjectiveCOVID‐19–associated pediatric vasculitis, other than Kawasaki disease (KD)–like vasculitis in multisystem inflammatory syndrome in children (MIS‐C), is very rare. This study sought to analyze the characteristics, treatment, and outcomes in patients with COVID‐19–associated pediatric vasculitis (excluding KD‐like vasculitis in MIS‐C).MethodsThe inclusion criteria were as follows: 1) age <18 years at vasculitis onset; 2) evidence of vasculitis; 3) evidence of SARS–CoV‐2 exposure; and 4) ≤3 months between SARS–CoV‐2 exposure and vasculitis onset. Patients with MIS‐C were excluded. The features of the subset of patients in our cohort who had COVID‐19–associated pediatric IgA vasculitis/Henoch Schönlein purpura (IgAV/HSP) were compared against a pre‐pandemic cohort of pediatric IgAV/HSP patients.ResultsForty‐one patients (median age 8.3 years; male to female ratio 1.3) were included from 14 centers and 6 countries. The most frequent vasculitis subtype was IgAV/HSP (n = 30). The median duration between SARS–CoV‐2 exposure and vasculitis onset was 13 days. Involvement of the skin (92.7%) and of the gastrointestinal system (61%) were the most common manifestations of vasculitis. Most patients (68.3%) received glucocorticoids, and 14.6% also received additional immunosuppressive drugs. Remission was achieved in all patients. All of the patients with IgAV/HSP in our cohort had skin manifestations, while 18 (60%) had gastrointestinal involvement and 13 (43.3%) had renal involvement. When we compared the features of this subset of 30 patients to those of a pre‐pandemic pediatric IgAV/HSP cohort (n = 159), the clinical characteristics of fever and renal involvement were more common in our COVID‐19–associated pediatric IgAV/HSP cohort (fever, 30% versus 5%, respectively [P < 0.001]; renal involvement, 43.3% versus 17.6%, respectively [P = 0.002]). Recovery without treatment and complete recovery were each less frequent among our COVID‐19‐associated pediatric IgAV/HSP patients compared to the pre‐pandemic pediatric IgAV/HSP cohort (recovery without treatment, 10% versus 39%, respectively [P = 0.002]; complete recovery, 86.7% versus 99.4%, respectively [P = 0.002]).ConclusionThis is the largest cohort of children with COVID‐19–associated vasculitis (excluding MIS‐C) studied to date. Our findings suggest that children with COVID‐19–associated IgAV/HSP experience a more severe disease course compared to pediatric IgAV/HSP patients before the pandemic.
Oxoiron(IV)‐dominated Heterogeneous Fenton‐like Mechanism of Fe‐Doped MoS2
Authors: Hu Shiyu , Guo Rujia , Gao Yiqian , Chen Feng 
Published: December 2022

AbstractOxoiron(IV) species are a critical intermediate in the Fe‐based Fenton‐like process at circumneutral pH, and its oxidative reactivity is closely related to the ligands. An optional inorganic host material, MoS2, is selected to construct a highly reactive sulfur ligand coordinated Fe species in this work. The Fe species doped in MoS2 is presented as the FeII centre and triggers the transformation of the 2H phase to the octahedral 1T phase MoS2. The role of the interaction between doped Fe and the MoS2 host lattice on the formation of oxoiron(IV) is studied. A significant Fenton‐like reactivity and a remarkable accumulation of oxoiron(IV) species were observed for Fe‐MoS2. The quenching experiment was implemented to disclose the predominant role of oxoiron(IV) species in the Fe‐MoS2/H2O2 Fenton‐like system. Furthermore, oxoiron(IV) species could transform into the ⋅O2− and 1O2, which further expedites the Fenton‐like reaction.
Ancient Darwinian replicators nested within eubacterial genomes
Authors: Bertels Frederic , Rainey Paul B. 
Published: December 2022

AbstractIntegrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on non‐jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.