bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-contamination of CRISPR guides and other unrelated nucleotide sequences among commercial oligonucleotides
Authors: Arakawa Hiroshi , Miura Hiromi , Quadros Rolen M , Ohtsuka Masato , Gurumurthy Channabasavaiah B 
Published: February 2024

Abstract
Custom oligonucleotides (oligos) are widely used reagents in biomedical research. Some common applications of oligos include polymerase chain reaction (PCR), sequencing, hybridization, microarray, and library construction. The reliability of oligos in such applications depends on their purity and specificity. Here, we report that commercially available oligos are frequently contaminated with nonspecific sequences (i.e. other unrelated oligonucleotides). Most of the oligos that we designed to amplify clustered regularly interspersed palindromic repeats (CRISPR) guide sequences contained nonspecific CRISPR guides. These contaminants were detected in research-grade oligos procured from eight commercial oligo-suppliers located in three different geographic regions of the world. Deep sequencing of some of the oligos revealed a variety of contaminants. Given the wide range of applications of oligos, the impact of oligo cross-contamination varies greatly depending on the field and the experimental method. Incorporating appropriate control experiments in research design can help ensure that the quality of oligo reagents meets the intended purpose. This can also minimize risk depending on the purposes for which the oligos are used.
Discontinuous phase diagram of amorphous carbons
Authors: Zhu YinBo , Fang ZhouYu , Zhang ZhongTing , Wu HengAn 
Published: February 2024

ABSTRACT
The short-range order and medium-range order of amorphous carbons demonstrated in experiments allow us to rethink whether there exist intrinsic properties hidden by atomic disordering. Here we presented six representative phases of amorphous carbons (0.1–3.4 g/cm3), namely, disordered graphene network (DGN), high-density amorphous carbon (HDAC), amorphous diaphite (a-DG), amorphous diamond (a-D), paracrystalline diamond (p-D), and nano-polycrystalline diamond (NPD), respectively, classified by their topological features and microstructural characterizations that are comparable with experiments. To achieve a comprehensive physical landscape for amorphous carbons, a phase diagram was plotted in the sp3/sp2 versus density plane, in which the counterintuitive discontinuity originates from the inherent difference in topological microstructures, further guiding us to discover a variety of phase transitions among different amorphous carbons. Intriguingly, the power law, log(sp3/sp2) ∝ ρn, hints at intrinsic topology and hidden order in amorphous carbons, providing an insightful perspective to reacquaint atomic disorder in non-crystalline carbons.
Bias distribution and regulation in photoelectrochemical overall water-splitting cells
Authors: Dang Kun , Liu Siqin , Wu Lei , Tang Daojian , Xue Jing , Wang Jiaming , Ji Hongwei , Chen Chuncheng , Zhang Yuchao , Zhao Jincai 
Published: February 2024

ABSTRACT
The water oxidation half-reaction at anodes is always considered the rate-limiting step of overall water splitting (OWS), but the actual bias distribution between photoanodes and cathodes of photoelectrochemical (PEC) OWS cells has not been investigated systematically. In this work, we find that, for PEC cells consisting of photoanodes (nickel-modified n-Si [Ni/n-Si] and α-Fe2O3) with low photovoltage (Vph &lt; 1 V), a large portion of applied bias is exerted on the Pt cathode for satisfying the hydrogen evolution thermodynamics, showing a thermodynamics-controlled characteristic. In contrast, for photoanodes (TiO2 and BiVO4) with Vph &gt; 1 V, the bias required for cathode activation can be significantly reduced, exhibiting a kinetics-controlled characteristic. Further investigations show that the bias distribution can be regulated by tuning the electrolyte pH and using alternative half-reaction couplings. Accordingly, a volcano plot is presented for the rational design of the overall reactions and unbiased PEC cells. Motivated by this, an unbiased PEC cell consisting of a simple Ni/n-Si photoanode and Pt cathode is assembled, delivering a photocurrent density of 5.3 ± 0.2 mA cm−2.
Micelle-directed self-assembly of single-crystal-like mesoporous stoichiometric oxides for high-performance lithium storage
Authors: Wan Yanhua , Wang Changyao , Zhang Xingmiao , Yin Yang , Liu Mengmeng , Ma Bing , Duan Linlin , Ma Yuzhu , Zhang Wei , Zheng Changlin , Chao Dongliang , Wang Fei , Xia Yongyao , Li Wei 
Published: February 2024

ABSTRACT
Due to their uncontrollable assembly and crystallization process, the synthesis of mesoporous metal oxide single crystals remains a formidable challenge. Herein, we report the synthesis of single-crystal-like mesoporous Li2TiSiO5 by using soft micelles as templates. The key lies in the atomic-scale self-assembly and step-crystallization processes, which ensure the formation of single-crystal-like mesoporous Li2TiSiO5 microparticles via an oriented attachment growth mechanism under the confinement of an in-situ formed carbon matrix. The mesoporous Li2TiSiO5 anode achieves a superior rate capability (148 mAh g−1 at 5.0 A g−1) and outstanding long-term cycling stability (138 mAh g−1 after 3000 cycles at 2.0 A g−1) for lithium storage as a result of the ultrafast Li+ diffusion caused by penetrating mesochannels and nanosized crystal frameworks (5–10 nm). In comparison, bulk Li2TiSiO5 exhibits poor rate capability and cycle performance due to micron-scale diffusion lengths. This method is very simple and reproducible, heralding a new way of designing and synthesizing mesoporous single crystals with controllable frameworks and chemical functionalities.
Structural reforms and income distribution: new evidence for OECD countries
Authors: Wiese Rasmus , Jalles João Tovar , de Haan Jakob 
Published: February 2024

Abstract
This article examines the impact of labour market and product market reforms on income inequality for 25 OECD countries between 1970 and 2020, using the local projections approach and an updated narrative-based dataset of the reform indicators. Our results suggest that both types of (endogenized) market-oriented reforms increase income inequality, but the effects are small. Consistent with this finding is that counter-reforms lead to less income inequality. Our results also indicate that the inequality-increasing effect of market-oriented reforms is mostly a result of more income going to the top of the income distribution.
Evolution of accretion disk structure of the black hole X-ray binary MAXI J1820+070 during the rebrightening phase
Authors: Yoshitake Tomohiro , Shidatsu Megumi , Ueda Yoshihiro , Nogami Daisaku , Murata Katsuhiro L , Higuchi Narikazu , Isogai Keisuke , Maehara Hiroyuki , Mineshige Shin , Negoro Hitoshi , Kawai Nobuyuki , Yatsu Yoichi , Sasada Mahito , Takahashi Ichiro , Niwano Masafumi , Saito Tomoki , Takayama Masaki , Oasa Yumiko , Takarada Takuya , Shigeyoshi Takumi ,   OISTER Collaboration
Published: February 2024

Abstract
To understand the evolution of global accretion disk structure in the “rebrightening” phase of MAXI J1820+070, we perform a comprehensive analysis of its near infrared/optical/UV to X-ray spectral energy distribution (SED) utilizing data obtained by OISTER, Las Cumbres Observatory (LCO), Swift, NICER, and NuSTAR in 2019. Optical spectra observed with Seimei telescope in 2019 and 2020 are also analyzed. On the basis of the optical and X-ray light curves and their flux ratios, we divide the whole phase into three periods, Periods I (flux rise), II (decay), and III (dim). In the first two periods, the source stayed in the low/hard state (LHS), where the X-ray (0.3–30 keV) and optical/UV SED can both be fitted with power-law models. We interpret that the X-ray emission arises from hot corona via Comptonization, whereas the optical/UV flux is dominated by synchrotron radiation from the jets, with a partial contribution from the irradiated disk. The optical/UV power-law component smoothly connects to a simultaneous radio flux, supporting its jet origin. Balmer line profiles in the optical spectra indicate that the inner radius of an irradiated disk slightly decreased from ∼2 × 105rg (Period I) to ∼1 × 105rg (Period II), where rg is the gravitational radius, implying a change of the hot corona geometry. In Period III, the SED can be reproduced by an advection-dominated accretion flow and jet emission. However, the double-peaked Hα emission line indicates that a cool disk remained at large radii.
La prise en charge des nourrissons de 90 jours ou moins, fiévreux mais dans un bon état général
Authors: Burstein Brett , Lirette Marie-Pier , Beck Carolyn , Chauvin-Kimoff Laurel , Chan Kevin 
Published: February 2024

RÉsumÉ
On constate des pratiques très variées en matière d’évaluation et de prise en charge des jeunes nourrissons fiévreux. Bien que la plupart des jeunes nourrissons fiévreux mais dans un bon état général soient atteints d’une maladie virale, il est essentiel de détecter ceux qui sont à risque de présenter des infections bactériennes invasives, notamment une bactériémie et une méningite bactérienne. Le présent document de principes porte sur les nourrissons de 90 jours ou moins dont la température rectale est de 38,0 °C ou plus, mais qui semblent être dans un bon état général. Il est conseillé d’appliquer les récents critères de stratification du risque pour orienter la prise en charge, ainsi que d’intégrer la procalcitonine à l’évaluation diagnostique. Les décisions sur la prise en charge des nourrissons qui satisfont aux critères de faible risque devraient refléter la probabilité d’une maladie, tenir compte de l’équilibre entre les risques et les préjudices potentiels et faire participer les parents ou les proches aux décisions lorsque diverses options sont possibles. La prise en charge optimale peut également dépendre de considérations pragmatiques, telles que l’accès à des examens diagnostiques, à des unités d’observation, à des soins tertiaires et à un suivi. Des éléments particuliers, tels que la mesure de la température, le risque d’infection invasive à Herpes simplex et la fièvre postvaccinale, sont également abordés.
Management of well-appearing febrile young infants aged ≤90 days
Authors: Burstein Brett , Lirette Marie-Pier , Beck Carolyn , Chauvin-Kimoff Laurel , Chan Kevin 
Published: February 2024

Abstract
The evaluation and management of young infants presenting with fever remains an area of significant practice variation. While most well-appearing febrile young infants have a viral illness, identifying those at risk for invasive bacterial infections, specifically bacteremia and bacterial meningitis, is critical. This statement considers infants aged ≤90 days who present with a rectal temperature ≥38.0°C but appear well otherwise. Applying recent risk-stratification criteria to guide management and incorporating diagnostic testing with procalcitonin are advised. Management decisions for infants meeting low-risk criteria should reflect the probability of disease, consider the balance of risks and potential harm, and include parents/caregivers in shared decision-making when options exist. Optimal management may also be influenced by pragmatic considerations, such as access to diagnostic investigations, observation units, tertiary care, and follow-up. Special considerations such as temperature measurement, risk for invasive herpes simplex infection, and post-immunization fever are also discussed.
MYB transcription factors encoded by diversified tandem gene clusters cause varied Morella rubra fruit color
Authors: Xue Lei , Liu Xiaofen , Wang Wenli , Huang Dan , Ren Chuanhong , Huang Xiaorong , Yin Xueren , Lin-Wang Kui , Allan Andrew C , Chen Kunsong , Xu Changjie 
Published: February 2024

Abstract
Chinese bayberry (Morella rubra) is a fruit tree with a remarkable variation in fruit color, ranging from white to dark red as determined by anthocyanin content. In dark red “Biqi” (BQ), red “Dongkui” (DK), pink “Fenhong” (FH), and white “Shuijing” (SJ), we identified an anthocyanin-related MYB transcription factor-encoding gene cluster of four members, i.e. MrMYB1.1, MrMYB1.2, MrMYB1.3, and MrMYB2. Collinear analysis revealed that the MYB tandem cluster may have occurred in a highly conserved region of many eudicot genomes. Two alleles of MrMYB1.1 were observed; MrMYB1.1-1 (MrMYB1.1n) was a full-length allele and homozygous in “BQ”, MrMYB1.1-2 (MrMYB1.1d) was a nonfunctional allele with a single base deletion and homozygous in “SJ”, and MrMYB1.1n/MrMYB1.1d were heterozygous in “DK” and “FH”. In these four cultivars, expression of MrMYB1.1, MrMYB1.2, and MrMYB2 was enhanced during ripening. Both alleles were equally expressed in MrMYB1.1n/MrMYB1.1d heterozygous cultivars as revealed by a cleaved amplified polymorphic sequence marker. Expression of MrMYB1.3 was restricted to some dark red cultivars only. Functional characterization revealed that MrMYB1.1n and MrMYB1.3 can induce anthocyanin accumulation while MrMYB1.1d, MrMYB1.2, and MrMYB2 cannot. DNA–protein interaction assays indicated that MrMYB1.1n and MrMYB1.3 can directly bind to and activate the promoters of anthocyanin-related genes via interaction with a MYC-like basic helix-loop-helix protein MrbHLH1. We concluded that the specific genotype of MrMYB1.1 alleles, as well as the exclusive expression of MrMYB1.3 in some dark red cultivars, contributes to fruit color variation. The study provides insights into the mechanisms for regulation of plant anthocyanin accumulation by MYB tandem clusters.
Understanding Artificial Agency
Authors: Dung Leonard 
Published: February 2024

Abstract
Which artificial intelligence (AI) systems are agents? To answer this question, I propose a multidimensional account of agency. According to this account, a system's agency profile is jointly determined by its level of goal-directedness and autonomy as well as is abilities for directly impacting the surrounding world, long-term planning and acting for reasons. Rooted in extant theories of agency, this account enables fine-grained, nuanced comparative characterizations of artificial agency. I show that this account has multiple important virtues and is more informative than alternatives. More speculatively, it may help to illuminate two important emerging questions in AI ethics: 1. Can agency contribute to the moral status of non-human beings, and how? 2. When and why might AI systems exhibit power-seeking behaviour and does this pose an existential risk to humanity?
Optimal Allocation via Waitlists: Simplicity Through Information Design
Authors: Ashlagi Itai , Monachou Faidra , Nikzad Afshin 
Published: February 2024

Abstract
We study non-monetary markets where objects that arrive over time are allocated to unit-demand agents with private types, such as in the allocation of public housing or deceased-donor organs. An agent’s value for an object is supermodular in her type and the object quality, and her payoff is her value minus her waiting cost. The social planner’s objective is a weighted sum of allocative efficiency (i.e. the sum of values) and welfare (i.e. the sum of payoffs). We identify optimal mechanisms in the class of direct-revelation mechanisms. When the social planner can design the information disclosed to the agents about the objects, the optimal mechanism has a simple implementation: a first-come first-served waitlist with deferrals. In this implementation, the object qualities are partitioned into intervals; only the interval containing the object quality is disclosed to agents. When the planner places a higher weight on welfare, optimal disclosure policies become coarser.
The information required by people with inflammatory arthritis when taking Methotrexate: a mixed-methods systematic review
Authors: Logan Sarah J , Hider Samantha , Green Julie , Ryan Sarah J 
Published: February 2024

Abstract

Objectives
This mixed-methods systematic review aimed to identify and synthesize knowledge of the characteristics, content, and preferred format of information to support people with inflammatory arthritis (IA) to take MTX.

Methods
A literature search using MEDLINE, The Cochrane Library, EMBASE, CINAHL, PsychInfo, GreyEU, Web of Science and Open Dissertation was conducted to identify all studies published from 2000 to December 2022. Included studies detailed factors related to MTX information needs of people aged ≥18 years with IA published in English. The Joanna Briggs Institute Guidelines (JBI) for convergent integrated mixed-methods systematic reviews were followed using validated tools for data extraction and quality. The data was analysed using reflexive thematic analysis.

Results
Thirteen studies (seven quantitative, two mixed-methods and four qualitative) were included, involving 3425 adults, mainly female n = 2434 (71%), age 20–84 years. An overarching theme of a requirement for person-centred care was developed, with three interlinking themes: (1) accepting the need for treatment with MTX, (2) concerns about taking MTX, and (3) a need for tailored information and support. Limitations of the evidence included the use of heterogeneous outcome measures and instruments for measuring information needs.

Conclusion
People with IA have individual, multifaceted information and support needs about MTX that are often unresolved when a one-size-fits-all approach is used. The findings of this review can inform rheumatology training to support a person-centred approach to identifying and addressing the specific needs and concerns and development of consistent easy-to-understand accessible MTX information.
Fragmented QRS complex could predict all-cause mortality in patients with connective tissue disease–associated pulmonary arterial hypertension
Authors: Dai Jiayi , Liu Ting , Zhang Hang , Sun Xiaoxuan , Tang Yinghong , Qian Wei , Zhang Yue , Ye Huangshu , Shan Linwei , Li Lin , Du Mengdi , Li Dongyu , Zhu Yinsu , Ma Kefan , Liu Lin , Wang Qiang , Zhou Lei 
Published: February 2024

Abstract

Objectives
To investigate the prognostic impact and pathophysiological characteristics of fragmented QRS complex (fQRS) on patients with CTD-associated pulmonary arterial hypertension (CTD-PAH).

Methods
This was a multicentre retrospective study recruiting 141 patients with CTD-PAH diagnosed by right heart catheterization (114 cases in the discovery cohort and 27 cases in the validation cohort). fQRS and ST-T change were detected on conventional 12-lead ECG. Patients were followed up every 3 months to update their status and the primary endpoint was all-cause death. Clinical information and ECG characteristics were compared between survival and death groups and Kaplan–Meier curve was used for survival analysis.

Results
There were significant differences in age, gender, 6-min walk distance, N-terminal pro-brain natriuretic peptide, World Health Organization class, presence of fQRS, and presence of ST-T change in inferior leads between survival group and death group. Inferior fQRS and ST-T change were significantly associated with right ventricular dilatation and reduced right ventricular ejection fraction. Kaplan–Meier curve showed that all-cause mortality was higher in CTD-PAH with fQRS (P = 0.003) and inferior ST-T change (P = 0.012). Low- and intermediate-risk CTD-PAH with inferior ST-T change had higher all-cause mortality (P = 0.005). The prognostic value of fQRS and inferior ST-T change was validated in external validation cohort.

Conclusion
The presence of inferior fQRS and ST-T change could predict poor prognosis in CTD-PAH.

Clinical trial registration
NCT05980728, https://clinicaltrials.gov.
Where are we now in biologic drugs for myositis?
Authors: Neves Ana , Viveiros Luísa , Venturelli Veronica , Isenberg David A 
Published: February 2024

Abstract
Idiopathic inflammatory myopathies (IIMs) are a rare and heterogeneous group of chronic autoimmune disorders. Up to 40% of IIM patients have long-term sequelae and significant functional disability. Its management can be challenging and new therapies are badly needed. The small number of cases with diverse presentations and different diagnostic criteria significantly affect clinical trial results. Only IVIG has been internationally approved for IIM patients. Most clinical trials of new biologic therapies have failed to meet their primary endpoints in IIM, with only one biologic drug recommended for refractory IIM treatment (rituximab), although not approved. We review several new emerging biologic drugs, including B cell depletion therapies, abatacept, Janus kinase inhibitors, and aldesleukin. Encouragingly, some phase II randomized controlled trials have evaluated the efficacy and safety of new biologics in IIM, demonstrating an improvement in clinical and laboratory measures.
Seven-year follow-up atherosclerotic plaque progression in patients with antiphospholipid syndrome versus diabetes mellitus and healthy controls
Authors: Evangelatos Gerasimos , Tentolouris Nikolaos , Sfikakis Petros P , Tektonidou Maria G 
Published: February 2024

Abstract

Objectives
Patients with antiphospholipid syndrome (APS) carry a substantial burden of cardiovascular disease and subclinical atherosclerosis. We aimed to assess a 7-year follow-up atherosclerotic plaque progression in APS patients versus diabetes mellitus (DM) and healthy controls (HC).

Methods
Eighty-six patients with thrombotic APS, 86 with DM and 86 HC (all age- and sex-matched) who underwent a baseline ultrasound of carotid and femoral arteries were invited for a 7-year follow-up ultrasonography examination. We compared atherosclerosis progression among the three groups and examined determinants of plaque progression in APS patients.

Results
Sixty-four APS patients (75% females, 43.8% with primary APS), 58 patients with DM and 66 HC were included in the 7-year ultrasound re-evaluation. New plaque was detected in 51.6%, 36.2% and 25.8% of APS, DM and HC subjects, respectively. After adjusting for traditional cardiovascular risk factors (CVRFs) and baseline plaque presence, APS patients showed a 3-fold (OR = 3.07, P = 0.007) higher risk for atherosclerosis progression versus HC and 2-fold (OR = 2.25, P = 0.047) higher risk than DM patients. In multivariate analysis in the APS group, plaque progression was independently associated with systemic lupus erythematosus (SLE) co-existence (OR = 7.78, P = 0.005) and number of CVRFs (OR = 3.02, P = 0.002), after adjusting for disease-related parameters and CVRF-related medications. Sustained low-density lipoprotein target attainment reduced plaque progression risk (OR = 0.34, P = 0.021).

Conclusion
Half of APS patients develop new atherosclerotic plaques over a 7-year follow-up, having a three-times higher risk versus HC. Concomitant SLE and number of traditional CVRFs are associated with plaque progression, supporting the need for thorough CVRF assessment and control.